Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007078.1 Hibiscus syriacus cultivar Beakdansim tig00018474_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: 224527
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:8041 original size:31 final size:30
Alignment explanation
Indices: 8005--8062 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
7995 AACTTAAAAA
*
8005 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAA-ACTGAAATTTAAATAATTTT
*
8036 AGTTTTATAAACTGAAATTTAAATAAT
1 AGTTTTACAAACTGAAATTTAAATAAT
8063 CCATACAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (30 bp):
AGTTTTACAAACTGAAATTTAAATAATTTT
Found at i:8111 original size:22 final size:22
Alignment explanation
Indices: 8086--8492 Score: 554
Period size: 22 Copynumber: 18.5 Consensus size: 22
8076 ATAATAAATT
*
8086 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
**
8108 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
8130 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
8152 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
8174 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
8196 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* ***
8218 TTTTAAAATATATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
8240 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
* ***
8262 TTTTAAAAT-ATTTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
8283 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
8305 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
8327 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
8349 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
8371 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
8393 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATCCATA
*
8415 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
8437 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
8459 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
8481 TTTTAAAATAAA
1 TTTTAAAATAAA
8493 ATTTTAAAAT
Statistics
Matches: 338, Mismatches: 38, Indels: 18
0.86 0.10 0.05
Matches are distributed among these distances:
21 32 0.09
22 290 0.86
23 16 0.05
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:9720 original size:2 final size:2
Alignment explanation
Indices: 9713--9746 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9703 ACTACAGAGT
9713 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
9747 ATTTTTCTAA
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):
TA
Found at i:11536 original size:23 final size:24
Alignment explanation
Indices: 11492--11537 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11482 AGAAACATGC
11492 CACAAGAACAAAGAAAAAGTGTGA
1 CACAAGAACAAAGAAAAAGTGTGA
* *
11516 CACAATAACATAG-AAAAGTGTG
1 CACAAGAACAAAGAAAAAGTGTG
11538 TCTAATGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.54, C:0.13, G:0.20, T:0.13
Consensus pattern (24 bp):
CACAAGAACAAAGAAAAAGTGTGA
Found at i:12174 original size:43 final size:43
Alignment explanation
Indices: 12112--12209 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
12102 TTTCATTAAA
** *
12112 TAATTAATAATTTACTAATAGATAATAAAAATGA-TAAATTAT
1 TAATTAATAATTTTTTAATAAATAATAAAAATGACTAAATTAT
* * *
12154 TAATCTATTAATTTTTTAATAAATAATTAAAATTACTAAATTAT
1 TAAT-TAATAATTTTTTAATAAATAATAAAAATGACTAAATTAT
12198 TAATTAATAATT
1 TAATTAATAATT
12210 ATTGTTCTAC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
42 4 0.09
43 31 0.66
44 12 0.26
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (43 bp):
TAATTAATAATTTTTTAATAAATAATAAAAATGACTAAATTAT
Found at i:12187 original size:36 final size:36
Alignment explanation
Indices: 12134--12202 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
12124 TACTAATAGA
*
12134 TAATAAAAATGATAAATTA-TTAATCTATTAATTTTT
1 TAATAAAAATGATAAATTACTAAAT-TATTAATTTTT
*
12170 TAATAAATAATTA-AAATTACTAAATTATTAATT
1 TAATAAA-AATGATAAATTACTAAATTATTAATT
12203 AATAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 21 0.72
37 8 0.28
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (36 bp):
TAATAAAAATGATAAATTACTAAATTATTAATTTTT
Found at i:12554 original size:26 final size:29
Alignment explanation
Indices: 12487--12555 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 29
12477 TTTTAATGAG
12487 CTTAACGAGCAACGAGTCGAGCAACAATTTTT
1 CTTAACGAGC-ACGAGTCGAGCAACAA--TTT
* *
12519 CTTCATGAGCACGAGTCGAGCAA-AA-TT
1 CTTAACGAGCACGAGTCGAGCAACAATTT
12546 -TTAACGAGCA
1 CTTAACGAGCA
12556 TTCGCTATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 8 0.24
27 2 0.06
30 2 0.06
31 13 0.39
32 8 0.24
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (29 bp):
CTTAACGAGCACGAGTCGAGCAACAATTT
Found at i:14679 original size:15 final size:15
Alignment explanation
Indices: 14661--14742 Score: 52
Period size: 15 Copynumber: 5.7 Consensus size: 15
14651 AAATTTAGAA
14661 ATTATTATTAAATAT
1 ATTATTATTAAATAT
14676 ATTATT-TT-AATAGT
1 ATTATTATTAAATA-T
* *
14690 -TTGA--AATATAATAA
1 ATT-ATTATTA-AATAT
*
14704 ATAATTA-TAAATAT
1 ATTATTATTAAATAT
*
14718 ATTATTATAAAATAT
1 ATTATTATTAAATAT
14733 ATTATT-TTAA
1 ATTATTATTAA
14743 TTAGTTTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 19
0.66 0.09 0.25
Matches are distributed among these distances:
13 7 0.14
14 18 0.35
15 25 0.49
16 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTATTATTAAATAT
Found at i:14724 original size:14 final size:15
Alignment explanation
Indices: 14707--14738 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
14697 ATAATAAATA
14707 ATTAT-AAATATATT
1 ATTATAAAATATATT
14721 ATTATAAAATATATT
1 ATTATAAAATATATT
14736 ATT
1 ATT
14739 TTAATTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:15430 original size:14 final size:14
Alignment explanation
Indices: 15401--15484 Score: 113
Period size: 14 Copynumber: 6.1 Consensus size: 14
15391 CGTTCGTGAA
15401 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
15417 CGTTCATTTATG-T
1 CGTTCATTTATGTT
15430 --TT-ATTTATGTT
1 CGTTCATTTATGTT
15441 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
15455 CGTTCATTTATATT
1 CGTTCATTTATGTT
15469 CGTTCATTTATGTT
1 CGTTCATTTATGTT
15483 CG
1 CG
15485 AATAGAGGGC
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
10 7 0.11
11 3 0.05
13 3 0.05
14 41 0.66
15 3 0.05
16 5 0.08
ACGTcount: A:0.17, C:0.13, G:0.14, T:0.56
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:15884 original size:16 final size:16
Alignment explanation
Indices: 15859--15899 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
15849 AAAATATTTT
*
15859 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
15875 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
15891 T-TT-ATTTAT
1 TGTTCATTTAT
15900 TAAATTAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.25
15 2 0.08
16 16 0.67
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:26343 original size:22 final size:24
Alignment explanation
Indices: 26313--26371 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
26303 AAAAAGTTGA
26313 ATTTTAATATTAAA-T-TATAAAT
1 ATTTTAATATTAAATTATATAAAT
* **
26335 ATTTGAATAAAAAATTATATAAAT
1 ATTTTAATATTAAATTATATAAAT
26359 ATTTTAATCATTA
1 ATTTTAAT-ATTA
26372 TACTATCTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 11 0.39
23 1 0.04
24 14 0.50
25 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
ATTTTAATATTAAATTATATAAAT
Found at i:27854 original size:24 final size:23
Alignment explanation
Indices: 27797--27854 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
27787 TTAAAAATAT
27797 TTTTG-AAA-AATTAGGCCTTTA
1 TTTTGAAAATAATTAGGCCTTTA
27818 -TTTGAATAGATAATTAGGCCTATTA
1 TTTTGAA-A-ATAATTAGGCCT-TTA
27843 TTTTGAAAATAA
1 TTTTGAAAATAA
27855 GGGTAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
20 4 0.13
21 1 0.03
22 1 0.03
23 1 0.03
24 14 0.45
25 4 0.13
26 6 0.19
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (23 bp):
TTTTGAAAATAATTAGGCCTTTA
Found at i:39920 original size:120 final size:123
Alignment explanation
Indices: 39711--39944 Score: 341
Period size: 120 Copynumber: 1.9 Consensus size: 123
39701 TGTAAAACTT
39711 AAAATTAAAAATGAGTTTAATATTTTTTATTTAAATTATTTTATATAATTACTTTAAAATAATAA
1 AAAATTAAAAATGAGTTTAATATTTTTTATTTAAATTATTTTATATAATTACTTTAAAATAATAA
* * * *
39776 TATATAAAATATAATAAAATTAAAATTATATTTAAAATTATTTAGAGAATTCAAAATAC
66 TATATAAAATATAATAAAAATAAAA-TAAAATAAAAATTATTTAGAGAATTCAAAATAC
* ** *
39835 AAAA-TAAAAATGAGTTTAATA-TTTTTATTTAAATTA-TTT-TCTAATTTTTTTGAAATAATAA
1 AAAATTAAAAATGAGTTTAATATTTTTTATTTAAATTATTTTATATAATTACTTTAAAATAATAA
* *
39896 TATATAAATTATATTAAAAATAAAATAAAATAAAAATTATTTAGAGAAT
66 TATATAAAATATAATAAAAATAAAATAAAATAAAAATTATTTAGAGAAT
39945 ATAAATAATT
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
119 21 0.21
120 40 0.40
121 3 0.03
122 15 0.15
123 17 0.17
124 4 0.04
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (123 bp):
AAAATTAAAAATGAGTTTAATATTTTTTATTTAAATTATTTTATATAATTACTTTAAAATAATAA
TATATAAAATATAATAAAAATAAAATAAAATAAAAATTATTTAGAGAATTCAAAATAC
Found at i:39932 original size:28 final size:29
Alignment explanation
Indices: 39891--39952 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
39881 TTTTTGAAAT
* *
39891 AATAATATATAAATTATATTA-AAAATA-A
1 AATAAAATAAAAATTAT-TTAGAAAATATA
*
39919 AATAAAATAAAAATTATTTAGAGAATATA
1 AATAAAATAAAAATTATTTAGAAAATATA
39948 AATAA
1 AATAA
39953 TTAAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.10
28 20 0.69
29 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (29 bp):
AATAAAATAAAAATTATTTAGAAAATATA
Found at i:39970 original size:14 final size:13
Alignment explanation
Indices: 39942--39980 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
39932 TTATTTAGAG
39942 AATATAAATAATTA
1 AATA-AAATAATTA
39956 AATAAAATAATTTA
1 AATAAAATAA-TTA
39970 AATTAAAATAA
1 AA-TAAAATAA
39981 AAATATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAAAATAATTA
Found at i:39992 original size:20 final size:19
Alignment explanation
Indices: 39951--39992 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
39941 GAATATAAAT
*
39951 AATTAAATAAAATAATTTA
1 AATTAAATAAAATAATTAA
39970 AATTAAAATAAAA-ATATTAA
1 AATT-AAATAAAATA-ATTAA
39990 AAT
1 AAT
39993 CATATTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTAAATAAAATAATTAA
Found at i:40905 original size:21 final size:19
Alignment explanation
Indices: 40851--40907 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 19
40841 TGTCTAAAGT
40851 ATATTTTATT-ATATTTTTA
1 ATATTTTATTAAT-TTTTTA
40870 ATATTTTGTATTTAATTTATTTA
1 ATA-TTT-TA-TTAATTT-TTTA
40893 ATATTTTACTTAATT
1 ATATTTTA-TTAATT
40908 AATTGTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 10 0.31
22 7 0.22
23 9 0.28
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
ATATTTTATTAATTTTTTA
Found at i:43104 original size:13 final size:13
Alignment explanation
Indices: 43063--43106 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
43053 TATTTAGTAC
*
43063 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
43076 TGTTTATTGGACT
1 TTTTTATTGTAAT
43089 TTTTTATTGTAAT
1 TTTTTATTGTAAT
43102 TTTTT
1 TTTTT
43107 TATTTATCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:51620 original size:19 final size:19
Alignment explanation
Indices: 51596--51642 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
51586 CTATCTAAAA
51596 AGTTAAAAATTAAAGAATG
1 AGTTAAAAATTAAAGAATG
51615 AGTTAAAAATTAAAGAATG
1 AGTTAAAAATTAAAGAATG
51634 AGTTAAAAA
1 AGTTAAAAA
51643 GTACAGTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.26
Consensus pattern (19 bp):
AGTTAAAAATTAAAGAATG
Found at i:54729 original size:32 final size:32
Alignment explanation
Indices: 54688--54751 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
54678 ACGGTTTGAG
54688 TAGCTTCGAGTTCTTGTATAAGTAAAAAATCT
1 TAGCTTCGAGTTCTTGTATAAGTAAAAAATCT
* *
54720 TAGCTTCGAGTTCTTGTATATGTAAAATATCT
1 TAGCTTCGAGTTCTTGTATAAGTAAAAAATCT
54752 GTGAGAGGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (32 bp):
TAGCTTCGAGTTCTTGTATAAGTAAAAAATCT
Found at i:57432 original size:18 final size:18
Alignment explanation
Indices: 57409--57458 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
57399 TACTACAAAG
57409 GCATTAAAAAGAAGAAAT
1 GCATTAAAAAGAAGAAAT
57427 GCATTAAAAAGAAGAAAT
1 GCATTAAAAAGAAGAAAT
*
57445 ACATTAAAAA-AAGA
1 GCATTAAAAAGAAGA
57459 CAGAGATGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 4 0.13
18 27 0.87
ACGTcount: A:0.64, C:0.06, G:0.14, T:0.16
Consensus pattern (18 bp):
GCATTAAAAAGAAGAAAT
Found at i:61112 original size:32 final size:34
Alignment explanation
Indices: 61061--61130 Score: 99
Period size: 32 Copynumber: 2.1 Consensus size: 34
61051 ATCAGACTCG
* * *
61061 AAATCTAACCGATTTGATATTGATCC-AACCTAA
1 AAATCTAACCAATTCGATATTGATCCGAACCGAA
61094 AAATC-AACCAATTCGATATTGATCCGAACCGAA
1 AAATCTAACCAATTCGATATTGATCCGAACCGAA
61127 AAAT
1 AAAT
61131 AACTCATCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 18 0.55
33 15 0.45
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (34 bp):
AAATCTAACCAATTCGATATTGATCCGAACCGAA
Found at i:64459 original size:30 final size:31
Alignment explanation
Indices: 64401--64467 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
64391 TTCAAGTTCG
* * *
64401 AACATCAAATATATTAAGAATATTAACATTT
1 AACATCAAATATACTAAGAATATAAACATAT
* *
64432 AACATCAAATA-ACTAAGAGTGTAAACATAT
1 AACATCAAATATACTAAGAATATAAACATAT
64462 -ACATCA
1 AACATCA
64468 TCTCTACTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 6 0.19
30 14 0.45
31 11 0.35
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.28
Consensus pattern (31 bp):
AACATCAAATATACTAAGAATATAAACATAT
Found at i:66256 original size:39 final size:39
Alignment explanation
Indices: 66181--66300 Score: 120
Period size: 39 Copynumber: 3.1 Consensus size: 39
66171 TTTATAAAAT
66181 AATTTAGAATGTTAATGTGAAAAAAATTTAAGAAATTAAA
1 AATTTAGAATGTT-ATGTGAAAAAAATTTAAGAAATTAAA
** * **
66221 AATTTAGAATGTTATG-GTAGCAAAATTTAATAAATTAGG
1 AATTTAGAATGTTATGTG-AAAAAAATTTAAGAAATTAAA
* * *
66260 AATTTAGAATGTTAGAGTG-AAATAATTTAA-AAATTATA
1 AATTTAGAATGTTA-TGTGAAAAAAATTTAAGAAATTAAA
66298 AAT
1 AAT
66301 AAACATCTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
38 10 0.15
39 41 0.62
40 14 0.21
41 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.14, T:0.35
Consensus pattern (39 bp):
AATTTAGAATGTTATGTGAAAAAAATTTAAGAAATTAAA
Found at i:71643 original size:29 final size:29
Alignment explanation
Indices: 71596--71678 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
71586 CTCACCTAAC
71596 TAAATTGATGTAAGTAATGACATCATTAAT
1 TAAA-TGATGTAAGTAATGACATCATTAAT
* *
71626 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGTAATGACATCATTAAT
71655 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGTAATGACATCA
71679 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGTAATGACATCATTAAT
Found at i:76413 original size:29 final size:29
Alignment explanation
Indices: 76366--76448 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
76356 CTCACCTAAC
*
76366 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGTAATGACATCATTAAT
**
76396 TAAATGATGTAAGTAATGACATTTTTAAT
1 TAAATGATGTAAGTAATGACATCATTAAT
76425 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGTAATGACATCA
76449 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.35
Consensus pattern (29 bp):
TAAATGATGTAAGTAATGACATCATTAAT
Found at i:79566 original size:6 final size:6
Alignment explanation
Indices: 79555--79622 Score: 127
Period size: 6 Copynumber: 11.2 Consensus size: 6
79545 AATTTAGTGC
79555 GGGAAT GGGAAT GGGAAT GGGAAT GGGAAT GGGAAT GGGAAT GGGAAT
1 GGGAAT GGGAAT GGGAAT GGGAAT GGGAAT GGGAAT GGGAAT GGGAAT
79603 GGGAAT GGGAAT GGGGAAT G
1 GGGAAT GGGAAT -GGGAAT G
79623 ATCTTCTTCT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
6 55 0.90
7 6 0.10
ACGTcount: A:0.32, C:0.00, G:0.51, T:0.16
Consensus pattern (6 bp):
GGGAAT
Found at i:82244 original size:33 final size:32
Alignment explanation
Indices: 82200--82266 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
82190 TATGATGTGA
*
82200 GTTTTTATGAAATCAAACTT-ATTGATATTTAGG
1 GTTTTTATGAAAT-AAA-TTCATTGAGATTTAGG
* *
82233 GTTTTTGTGAAATAAATTCATTGAGATTTGGG
1 GTTTTTATGAAATAAATTCATTGAGATTTAGG
82265 GT
1 GT
82267 GGCTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 2 0.07
32 16 0.53
33 12 0.40
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (32 bp):
GTTTTTATGAAATAAATTCATTGAGATTTAGG
Found at i:83436 original size:288 final size:287
Alignment explanation
Indices: 82900--83450 Score: 723
Period size: 288 Copynumber: 1.9 Consensus size: 287
82890 AAATAATATT
* *
82900 TTATAATCAAAGGATCATTTTTTAACTTTTAATAGTCAAATAACTTAATAAAGCAATACCCTATA
1 TTATAATCAAAGGATCATTTTGTAACTTTTAATAGTCAAATAACCTAATAAAGCAATACCCTATA
* * * *
82965 GTTAGGGGACCATTTGTGTACTTTACCCTCTATTTTAATAGTGGATTAGATATTCACTGATTTTC
66 GTTAGGAGACCATTTGTGTACTTTACCCTCTATTTTAAGAGTGAATTAGACATTCACTGATTTTC
* ** * * **
83030 ATCTCTTAAATGACTATTATATCTTAGTCATCATGTTGACGTCAAACTTAAACAATTGTCAATTT
131 ATCTCTCAAATGACTATTATATCACAATCATCATATTGACGTCAAACTTAAACAACCGTCAATTT
* * *
83095 TTTAATAGAAAAGTACGAGTTTAGAACATGATGAATAATCATATGAGCATTTTGTAACTTTTAAT
196 TCTAACAGAAAAGTACGAGTTTAGAACATGATGAATAATCAGATGAGCATTTTGTAACTTTTAAT
83160 AGTCGGTGGATTAAACAAAACAACACG
261 AGTCGGTGGATTAAACAAAACAACACG
* * * * *
83187 TTATAGTCAAAAGGGTCATTTTGTAACTTTTAATAGTGAAATAACCTAATAAAGCAGTATCCTAT
1 TTATAATC-AAAGGATCATTTTGTAACTTTTAATAGTCAAATAACCTAATAAAGCAATACCCTAT
** * **
83252 AGTTATTATACCATTTGTGTACTTTACCCTCTATTTTAAGAGTGAATTAGACATTCTTTGATTTT
65 AGTTAGGAGACCATTTGTGTACTTTACCCTCTATTTTAAGAGTGAATTAGACATTCACTGATTTT
* * *
83317 CATCTCTCAAATGACTATCT-TATCACAATCGTCATATTGACGTTC-AGCTTAAACAACCGTCGA
130 CATCTCTCAAATGACTAT-TATATCACAATCATCATATTGACG-TCAAACTTAAACAACCGTCAA
* * * * *
83380 TTTTCTAACGGAAAA-TGACGAGTTGTA-AGCATGATGAATAATCAGGTGATCATTTTGTAATTT
193 TTTTCTAACAGAAAAGT-ACGAGTT-TAGAACATGATGAATAATCAGATGAGCATTTTGTAACTT
83443 TTAATAGT
256 TTAATAGT
83451 TAAGGGAACA
Statistics
Matches: 225, Mismatches: 34, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
287 8 0.04
288 212 0.94
289 5 0.02
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (287 bp):
TTATAATCAAAGGATCATTTTGTAACTTTTAATAGTCAAATAACCTAATAAAGCAATACCCTATA
GTTAGGAGACCATTTGTGTACTTTACCCTCTATTTTAAGAGTGAATTAGACATTCACTGATTTTC
ATCTCTCAAATGACTATTATATCACAATCATCATATTGACGTCAAACTTAAACAACCGTCAATTT
TCTAACAGAAAAGTACGAGTTTAGAACATGATGAATAATCAGATGAGCATTTTGTAACTTTTAAT
AGTCGGTGGATTAAACAAAACAACACG
Found at i:89245 original size:17 final size:17
Alignment explanation
Indices: 89223--89260 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
89213 CTTTGAAAAA
*
89223 TTTAAAT-TTTTATATAT
1 TTTAAATATTTT-TAAAT
89240 TTTAAATATTTTTAAAT
1 TTTAAATATTTTTAAAT
89257 TTTA
1 TTTA
89261 TAAGTTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTAAATATTTTTAAAT
Found at i:89410 original size:24 final size:24
Alignment explanation
Indices: 89378--89425 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
89368 TAAAAGAGAA
89378 TGTTATTCTCCAAGACTCAAATTC
1 TGTTATTCTCCAAGACTCAAATTC
89402 TGTTATTCTCCAAGACTCAAATTC
1 TGTTATTCTCCAAGACTCAAATTC
89426 AAATAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (24 bp):
TGTTATTCTCCAAGACTCAAATTC
Found at i:92319 original size:2 final size:2
Alignment explanation
Indices: 92269--92300 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
92259 ATCTACCAAC
92269 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
92301 TAGTACATAT
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:94769 original size:16 final size:18
Alignment explanation
Indices: 94727--94770 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 18
94717 ACCTATACGA
94727 TTAAATATTTAATAAATTT
1 TTAAATATTTAATAAA-TT
94746 TTAAAT-TTT--TAAA-T
1 TTAAATATTTAATAAATT
94760 TTAAATATTTA
1 TTAAATATTTA
94771 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 7 0.30
15 3 0.13
16 4 0.17
18 3 0.13
19 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATATTTAATAAATT
Found at i:94770 original size:22 final size:23
Alignment explanation
Indices: 94739--94792 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
94729 AAATATTTAA
*
94739 TAAATTTTTAAATTTTT-AAATT
1 TAAATATTTAAATTTTTAAAATT
*
94761 TAAATATTT-ATTTTTTAAAATT
1 TAAATATTTAAATTTTTAAAATT
94783 TAAATATTTA
1 TAAATATTTA
94793 TTTTTACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TAAATATTTAAATTTTTAAAATT
Found at i:94777 original size:21 final size:22
Alignment explanation
Indices: 94751--94797 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
94741 AATTTTTAAA
94751 TTTTT-AAATTTAAATATTTAT
1 TTTTTAAAATTTAAATATTTAT
94772 TTTTTAAAATTTAAATATTTAT
1 TTTTTAAAATTTAAATATTTAT
94794 TTTT
1 TTTT
94798 ACATGAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTTAAAATTTAAATATTTAT
Found at i:95459 original size:46 final size:46
Alignment explanation
Indices: 95376--95483 Score: 139
Period size: 46 Copynumber: 2.4 Consensus size: 46
95366 AAGTTTTATT
* * * *
95376 TAAAACATTA-TTTGTTCTATCGGAATATTAATATTGGACGCTATC
1 TAAAACATTATTTTTTTCTACCGAAATATTAATATTGGACGCTACC
* *
95421 T-AAACATTATTTTTTTCTACCGAAAATGTTAATATTGGATGCTACC
1 TAAAACATTATTTTTTTCTACCG-AAATATTAATATTGGACGCTACC
95467 TAAAACATTATTTTTTT
1 TAAAACATTATTTTTTT
95484 ATTGGATATT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
44 8 0.15
45 11 0.20
46 20 0.37
47 15 0.28
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (46 bp):
TAAAACATTATTTTTTTCTACCGAAATATTAATATTGGACGCTACC
Found at i:96438 original size:23 final size:22
Alignment explanation
Indices: 96390--96439 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
96380 AAACAACCGG
*
96390 AAAACATGTCAAAAGACACAAG
1 AAAACATGTCAAAAGACACAAA
96412 AAAACATGTCATAAAGACA-AATA
1 AAAACATGTCA-AAAGACACAA-A
96435 AAAAC
1 AAAAC
96440 GTGTTATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.62, C:0.16, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAACATGTCAAAAGACACAAA
Found at i:97237 original size:15 final size:16
Alignment explanation
Indices: 97217--97251 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
97207 TAAATAAACC
97217 AATAAATAAATTT-TA
1 AATAAATAAATTTATA
*
97232 AATAAATGAATTTATA
1 AATAAATAAATTTATA
97248 AATA
1 AATA
97252 TAAATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AATAAATAAATTTATA
Found at i:97760 original size:37 final size:37
Alignment explanation
Indices: 97648--97925 Score: 209
Period size: 37 Copynumber: 7.6 Consensus size: 37
97638 TGTAAATGGT
* * *
97648 TTTTATAAAATATATTTGAAAACATTTATATATTATATAG
1 TTTT-TAAAACATTTTTGAAAACA--AATATATTATATAG
* * * *
97688 TTTTTTAAAACGTTTGTGAAAATAAATATAATATATAG
1 -TTTTTAAAACATTTTTGAAAACAAATATATTATATAG
* * **
97726 CTTTTAAAACATTTTTCAAAACATGTATATTATATAG
1 TTTTTAAAACATTTTTGAAAACAAATATATTATATAG
*
97763 -TTTAAAAACA-TTTTG-----AAA-A-A-TATATAG
1 TTTTTAAAACATTTTTGAAAACAAATATATTATATAG
* *
97790 TTTTTAAAACA-TTTTGAAAACATTTATATATTATATAAT
1 TTTTTAAAACATTTTTGAAAACA--AATATATTATAT-AG
* * * *
97829 TTTTTAAAACGTTTTTAAAAATAAAATATAATATATAG
1 TTTTTAAAACATTTTTGAAAA-CAAATATATTATATAG
* * *
97867 TTTTTAAAATATTTTTGAAAATACATATATTATATAG
1 TTTTTAAAACATTTTTGAAAACAAATATATTATATAG
*
97904 TTTTTAAAACATTTTAGAAAAC
1 TTTTTAAAACATTTTTGAAAAC
97926 TATATAATTT
Statistics
Matches: 186, Mismatches: 37, Indels: 32
0.73 0.15 0.13
Matches are distributed among these distances:
27 7 0.04
28 15 0.08
29 1 0.01
30 1 0.01
33 1 0.01
35 5 0.03
36 10 0.05
37 62 0.33
38 36 0.19
39 21 0.11
40 22 0.12
41 5 0.03
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTTTAAAACATTTTTGAAAACAAATATATTATATAG
Found at i:97789 original size:27 final size:28
Alignment explanation
Indices: 97756--97809 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
97746 ACATGTATAT
97756 TATATAG-TTTAAAAACATTTTGAAAAA
1 TATATAGTTTTAAAAACATTTTGAAAAA
*
97783 TATATAGTTTTTAAAACATTTTGAAAA
1 TATATAGTTTTAAAAACATTTTGAAAA
97810 CATTTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (28 bp):
TATATAGTTTTAAAAACATTTTGAAAAA
Found at i:97833 original size:39 final size:38
Alignment explanation
Indices: 97782--97924 Score: 141
Period size: 39 Copynumber: 3.7 Consensus size: 38
97772 ATTTTGAAAA
*
97782 ATATATAGTTTTTAAAACATTTTGAAAACATTTATATATT
1 ATATA-AGTTTTTAAAACATTTTGAAAA-ATTAATATATT
* * * * *
97822 ATATAATTTTTTAAAACGTTTTTAAAAA-TAAAATATA
1 ATATAAGTTTTTAAAACATTTTGAAAAATTAATATATT
*
97859 ATATATAGTTTTTAAAATATTTTTG-AAAA-TACATATATT
1 ATATA-AGTTTTTAAAACA-TTTTGAAAAATTA-ATATATT
97898 ATAT-AGTTTTTAAAACATTTTAGAAAA
1 ATATAAGTTTTTAAAACATTTT-GAAAA
97925 CTATATAATT
Statistics
Matches: 85, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
36 4 0.05
37 24 0.28
38 20 0.24
39 32 0.38
40 5 0.06
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (38 bp):
ATATAAGTTTTTAAAACATTTTGAAAAATTAATATATT
Found at i:97984 original size:141 final size:138
Alignment explanation
Indices: 97662--97991 Score: 380
Period size: 140 Copynumber: 2.3 Consensus size: 138
97652 ATAAAATATA
* * *
97662 TTTGAAAACATTTATATATTATATAGTTTTTTAAAACGTTTGTGAAAAT-AAATATAATATATAG
1 TTTGAAAACA-TTATATAATATATA-ATTTTTAAAACGTTT-TAAAAATAAAATATAATATATAG
** *
97726 CTTTTAAAACATTTTTCAAAACATGTATATTATATAGTTTAAAAACATTTTGAAAAATATATAGT
63 CTTTTAAAACATTTTTCAAAACACATATATTATATAGTTTAAAAACATTTTGAAAAATATATAAT
*
97791 TTTTAAAACAT
128 TTTGAAAACAT
*
97802 TTTGAAAACATTTATATATTATATAATTTTTTAAAACGTTTTTAAAAATAAAATATAATATATAG
1 TTTGAAAACA-TTATATAATATATAA-TTTTTAAAACG-TTTTAAAAATAAAATATAATATATAG
* * * * * *
97867 TTTTTAAAATATTTTTGAAAATACATATATTATATAGTTTTTAAAACATTTTAGAAAACTATATA
63 CTTTTAAAACATTTTTCAAAACACATATATTATATAG-TTTAAAAACATTTT-GAAAAATATATA
*
97932 ATTTTGAAAATATTT
126 ATTTTGAAAACA--T
* *
97947 TTTTAAAA-A-TATATAATATATAA-TTTTAAAATGGTTTTAAAAATA
1 TTTGAAAACATTATATAATATATAATTTTTAAAA-CGTTTTAAAAATA
97992 TATATTATAT
Statistics
Matches: 166, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
140 61 0.37
141 50 0.30
142 26 0.16
143 20 0.12
144 1 0.01
145 8 0.05
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (138 bp):
TTTGAAAACATTATATAATATATAATTTTTAAAACGTTTTAAAAATAAAATATAATATATAGCTT
TTAAAACATTTTTCAAAACACATATATTATATAGTTTAAAAACATTTTGAAAAATATATAATTTT
GAAAACAT
Found at i:97985 original size:66 final size:64
Alignment explanation
Indices: 97858--97995 Score: 154
Period size: 66 Copynumber: 2.1 Consensus size: 64
97848 AATAAAATAT
* * * *
97858 AATATATAGTTTTTAAAATATTTTTGAAAATACATATATTATATAGTTTTTAAAACATTTTAGAA
1 AATATATAATTTTGAAAATATTTTTGAAAATACATATAATATATAGATTTTAAAACATTTTA-AA
* * **
97923 AACTATATAATTTTGAAAATATTTTTTTAAAA-ATATATAATATATA-ATTTTAAAATGGTTTTA
1 AA-TATATAATTTTGAAAATA-TTTTTGAAAATACATATAATATATAGATTTTAAAA-CATTTTA
97986 AA
63 AA
97988 AATATATA
1 AATATATA
97996 TTATATAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
64 6 0.10
65 14 0.23
66 33 0.53
67 9 0.15
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (64 bp):
AATATATAATTTTGAAAATATTTTTGAAAATACATATAATATATAGATTTTAAAACATTTTAAA
Found at i:97995 original size:36 final size:37
Alignment explanation
Indices: 97926--98008 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 37
97916 TTTAGAAAAC
** *
97926 TATATAATTTTGAAAATATTTTTTTAAAAATATATAA
1 TATATAATTTTGAAAATAGGTTTTAAAAAATATATAA
*
97963 TATATAATTTT-AAAAT-GGTTTT-AAAAATATATAT
1 TATATAATTTTGAAAATAGGTTTTAAAAAATATATAA
97997 TATATAGATTTT
1 TATATA-ATTTT
98009 TAGAAAATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 17 0.40
35 9 0.21
36 5 0.12
37 11 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (37 bp):
TATATAATTTTGAAAATAGGTTTTAAAAAATATATAA
Found at i:98670 original size:16 final size:16
Alignment explanation
Indices: 98649--98681 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
98639 GCAAATACAG
98649 AAACAAA-ACCCAAAAA
1 AAACAAATA-CCAAAAA
98665 AAACAAATACCAAAAA
1 AAACAAATACCAAAAA
98681 A
1 A
98682 CACCGAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.76, C:0.21, G:0.00, T:0.03
Consensus pattern (16 bp):
AAACAAATACCAAAAA
Found at i:101182 original size:19 final size:19
Alignment explanation
Indices: 101158--101199 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
101148 AGACATTTTA
101158 CATTTTGTTATTTTCTTTG
1 CATTTTGTTATTTTCTTTG
101177 CATTTTGTTATTTTCTTTG
1 CATTTTGTTATTTTCTTTG
101196 CATT
1 CATT
101200 CACATTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.67
Consensus pattern (19 bp):
CATTTTGTTATTTTCTTTG
Found at i:105029 original size:165 final size:163
Alignment explanation
Indices: 104687--105655 Score: 1101
Period size: 165 Copynumber: 5.9 Consensus size: 163
104677 TAAACAAACT
* *
104687 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCA
* * * *
104752 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TGACC-AAAGACC
* * * *
104817 TTTGAGTTTGACTACGCTCAGCTTCGAGGGCACATC
129 TTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATC
* *** *
104853 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGACTACA
* * *
104918 CTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATC-TG-CCAAAGA
62 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTGACCAAAGA
** * * * *
104980 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
127 CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATC
* * * * * *** *
105018 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCGAGTTCGACTACA
* *
105083 CTCAGCTTCGAGGGCACATCATTTGCA-CATTACTTAAGTCGAGAAGGGTTATCTTCCAACCAAA
62 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTT--GACCAAA
*
105147 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
125 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* *
105186 ATTTGTAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCA
* * * * *
105251 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TGACC-AAAGACC
* *
105316 TTTGAGTTCGACTACGCTCAGCT-CAACGACACATC
129 TTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
* *
105351 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCA
105416 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC-TGCCAACCAAAGAC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTG---ACCAAAGAC
* *
105480 CTTCGAGTTCGACTACACTCAGCTCCAAGGCATATC
128 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * * ***
105516 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTCGACTACA
* * * * *
105581 CTCAGC-TCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATC-TG-CTAAAGA
62 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTGACCAAAGA
*
105643 CCTTCAAGTTCGA
127 CCTTCGAGTTCGA
105656 TTATATTCAA
Statistics
Matches: 698, Mismatches: 81, Indels: 50
0.84 0.10 0.06
Matches are distributed among these distances:
163 2 0.00
164 71 0.10
165 354 0.51
166 65 0.09
167 4 0.01
168 85 0.12
169 91 0.13
170 26 0.04
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (163 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCA
GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTGACCAAAGACCTT
CGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:105265 original size:249 final size:249
Alignment explanation
Indices: 104687--105634 Score: 1424
Period size: 249 Copynumber: 3.8 Consensus size: 249
104677 TAAACAAACT
*
104687 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
104752 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
* * * *
104817 TTTGAGTTTGACTACGCTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
131 TTTGAGTTCGACTACGCTCAGC-TCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGG
*
104882 TTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
195 TTATCTTCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* *
104937 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
105002 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
* *
105067 TTTGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTGCA-CATTA-CTTAAGTCGAGAAGG
131 TTTGAGTTCGACTACGCTCAGC-TCAACGGCACATCATTTGCAGCA-TAGCTTAAGTCGAGAAGG
105130 GTTATCTTCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
194 GTTATCTTCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
105186 ATTTGTAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
105251 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
* *
105316 TTTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
131 TTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGT
* *** * * * *
105381 TATC-T---GCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
196 TATCTTCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATC
* ** *
105432 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACA
* * * * * * * * ** *
105497 CTCAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAA
62 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAA
*
105561 GACCTTTGAGTTCGACTACACTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
127 GACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
*
105626 GGGATATCT
192 GGGTTATCT
105635 GCTAAAGACC
Statistics
Matches: 650, Mismatches: 39, Indels: 18
0.92 0.06 0.03
Matches are distributed among these distances:
245 26 0.04
246 45 0.07
248 20 0.03
249 358 0.55
250 201 0.31
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (249 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
TTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGT
TATCTTCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:105587 original size:414 final size:414
Alignment explanation
Indices: 104700--105658 Score: 1315
Period size: 414 Copynumber: 2.3 Consensus size: 414
104690 TGCAGCATAG
* *** * * *
104700 CTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
1 CTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACACTCAGC-TCCAAG
* * * * * * *
104761 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTT
65 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGATATC--TG-CC-AAAGACCTTCGAGTTC
* * * * * *
104826 GACTACGCTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC
126 GATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAAGGTTATCTGCC
*
104891 AACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
191 AACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAG
*
104956 TCGAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
256 TCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
* ** * *
105021 TACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTC
321 TACAGCATAACTCAAGGCGAGAAGGGTTATCTGCAACCAAAAGACCTTCGAGTTCGACTACACTC
* * **
105086 AGCTTCGAGGGCACATCATTTGCACATTA
386 AGCTTCCAAGGCACATCATTTGCACACAA
* * *
105115 CTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1 CTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGG
* * **
105180 CACATCATTTGTAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
66 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGATATCTGCCAAAGACCTTCGAGTTCGATTA
* **
105245 CACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTG-TGACCA
131 CACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAAGGTTATCTGCCAACC-
105309 AAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGACACATCATTTGCAGCATAGCTTAAGTCG
195 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GACACATCATTTGCAGCATAGCTTAAGTCG
*
105373 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
259 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
* *
105438 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACACTCAG
324 AGCATAACTCAAGGCGAGAAGGGTTATCTG-CAACCAAAAGACCTTCGAGTTCGACTACACTCAG
*
105502 C-TCCAAGGCATATCATTTGCAGCACAA
388 CTTCCAAGGCACATCATTTGCA-CACAA
* *
105529 CTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACACTCAGCT-CAACG
1 CTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCCAA-G
* * *
105593 GCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCTAAAGACCTTCAAGTTCGATT
65 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGATATCTGCCAAAGACCTTCGAGTTCGATT
105658 A
130 A
105659 TATTCAACTT
Statistics
Matches: 480, Mismatches: 55, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
413 26 0.05
414 361 0.75
415 26 0.05
416 3 0.01
418 40 0.08
419 24 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (414 bp):
CTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGG
CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGATATCTGCCAAAGACCTTCGAGTTCGATTA
CACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAAGGTTATCTGCCAACCA
AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAG
CATAACTCAAGGCGAGAAGGGTTATCTGCAACCAAAAGACCTTCGAGTTCGACTACACTCAGCTT
CCAAGGCACATCATTTGCACACAA
Found at i:106405 original size:37 final size:37
Alignment explanation
Indices: 106334--106597 Score: 304
Period size: 37 Copynumber: 7.1 Consensus size: 37
106324 TGAAAACATT
* *
106334 TATATATTATATAGTTTTTTAAAACGTTTGTGAAAATA
1 TATATATTATATAG-TTTTTAAAACATTTTTGAAAATA
* * *
106372 AATATAATATATAGTTTTTAAAACATTTTTGAAAACA
1 TATATATTATATAGTTTTTAAAACATTTTTGAAAATA
* *
106409 TGTATATTATATAG-TTTAAAAACA-TTTTGAAAATA
1 TATATATTATATAGTTTTTAAAACATTTTTGAAAATA
*
106444 TATA-A-TATATAGTTTTTAAAACA-TTTTGAAAACATT
1 TATATATTATATAGTTTTTAAAACATTTTTG-AAA-ATA
* * *
106480 TATATATTATATAATTTTTTAAAACGTTTTTAAAAATAA
1 TATATATTATAT-AGTTTTTAAAACATTTTTGAAAAT-A
* * *
106519 AATATAATATATAGTTTTTAAAATATTTTTGAAAATA
1 TATATATTATATAGTTTTTAAAACATTTTTGAAAATA
*
106556 TATATATTATATAGTTTTTAAAACATTTTAGAAAACTA
1 TATATATTATATAGTTTTTAAAACATTTTTGAAAA-TA
106594 TATA
1 TATA
106598 ATTTTGAAAA
Statistics
Matches: 190, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
33 7 0.04
34 15 0.08
35 16 0.08
36 15 0.08
37 64 0.34
38 45 0.24
39 24 0.13
40 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (37 bp):
TATATATTATATAGTTTTTAAAACATTTTTGAAAATA
Found at i:106562 original size:147 final size:151
Alignment explanation
Indices: 106308--106599 Score: 468
Period size: 147 Copynumber: 2.0 Consensus size: 151
106298 TGCAAATGGA
* * *
106308 TTTTATAAAATATATTTGAAAACATTTATATATTATATAGTTTTTTAAAACGTTTGTGAAAATAA
1 TTTTATAAAACATATTTGAAAACATTTATATATTATATAATTTTTTAAAACGTTTGTAAAAATAA
*
106373 ATATAATATATAGTTTTTAAAACATTTTTGAAAACATGTATATTATATAG-TTTAAAAACATTTT
66 ATATAATATATAGTTTTTAAAACATTTTTGAAAACATATATATTATATAGTTTTAAAAACATTTT
106437 -GAAAA-TATATAATATATAG
131 AGAAAACTATATAATATATAG
*
106456 TTTT-TAAAACAT-TTTGAAAACATTTATATATTATATAATTTTTTAAAACGTTTTTAAAAATAA
1 TTTTATAAAACATATTTGAAAACATTTATATATTATATAATTTTTTAAAACGTTTGTAAAAAT-A
* * *
106519 AATATAATATATAGTTTTTAAAATATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTT
65 AATATAATATATAGTTTTTAAAACATTTTTGAAAACATATATATTATATAGTTTTAAAAACATTT
106584 TAGAAAACTATATAAT
130 TAGAAAACTATATAAT
106600 TTTGAAAATA
Statistics
Matches: 132, Mismatches: 8, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
146 46 0.35
147 56 0.42
148 17 0.13
149 5 0.04
150 8 0.06
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (151 bp):
TTTTATAAAACATATTTGAAAACATTTATATATTATATAATTTTTTAAAACGTTTGTAAAAATAA
ATATAATATATAGTTTTTAAAACATTTTTGAAAACATATATATTATATAGTTTTAAAAACATTTT
AGAAAACTATATAATATATAG
Found at i:112432 original size:3 final size:3
Alignment explanation
Indices: 112424--112450 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
112414 TAAGTTCTCA
112424 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
112451 CCTCCCTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:119081 original size:26 final size:28
Alignment explanation
Indices: 119051--119112 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
119041 GAAAATTTTA
119051 AGCTC-GC-GAGTTTTCGAGTCGAGTCG
1 AGCTCTGCAGAGTTTTCGAGTCGAGTCG
*
119077 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-C--TGCAGAGTTTTCGAGTCGAGTCG
119108 AGCTC
1 AGCTC
119113 AGCAATACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 2 0.07
31 23 0.77
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCTCTGCAGAGTTTTCGAGTCGAGTCG
Found at i:119755 original size:23 final size:23
Alignment explanation
Indices: 119729--119774 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
119719 AGTAGTTATC
119729 AAGTCTTTCATTAAGTTTTCTTT
1 AAGTCTTTCATTAAGTTTTCTTT
* * **
119752 AAGTTTTTCTTTTGGTTTTCTTT
1 AAGTCTTTCATTAAGTTTTCTTT
119775 CAATTATGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.63
Consensus pattern (23 bp):
AAGTCTTTCATTAAGTTTTCTTT
Found at i:120853 original size:24 final size:24
Alignment explanation
Indices: 120826--120871 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
120816 ACTTTTCCGG
120826 GAAATCACTTTTGTTCAAAATCGA
1 GAAATCACTTTTGTTCAAAATCGA
120850 GAAATCACTTTTGTTCAAAATC
1 GAAATCACTTTTGTTCAAAATC
120872 AAAGTCAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (24 bp):
GAAATCACTTTTGTTCAAAATCGA
Found at i:120926 original size:18 final size:18
Alignment explanation
Indices: 120868--120937 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
120858 TTTTGTTCAA
120868 AATCAAAGTCAAC--TTT
1 AATCAAAGTCAACGATTT
* * *
120884 AGTCAAAGTTAATAGATTT
1 AATCAAAGTCAA-CGATTT
**
120903 GGTCAAAGTCAACGATTT
1 AATCAAAGTCAACGATTT
*
120921 AATCAAAGTTAACGATT
1 AATCAAAGTCAACGATT
120938 CAGAGCTGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
16 10 0.24
18 19 0.45
19 13 0.31
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (18 bp):
AATCAAAGTCAACGATTT
Found at i:124745 original size:36 final size:35
Alignment explanation
Indices: 124705--124778 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 35
124695 TGATTTTATT
124705 TTTTTAATATTTTAATTC-TCAATACTTTAATTTTGA
1 TTTTTAATATTTTAA-TCAT-AATACTTTAATTTTGA
124741 TTTTTAATATTTTAATCAATAATACTTTAATTTTGA
1 TTTTTAATATTTTAATC-ATAATACTTTAATTTTGA
124777 TT
1 TT
124779 AAAAAAGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 2 0.06
36 33 0.92
37 1 0.03
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (35 bp):
TTTTTAATATTTTAATCATAATACTTTAATTTTGA
Found at i:125119 original size:2 final size:2
Alignment explanation
Indices: 125112--125150 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
125102 CTAAAATAAC
125112 TA 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 TA T
125151 TGAGGGTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:125867 original size:29 final size:30
Alignment explanation
Indices: 125826--125882 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
125816 TACATTTCCG
*
125826 TCCATCTAAAATTTTATAAATTCAAATTCA
1 TCCATCTAAAATTTTAAAAATTCAAATTCA
125856 TCCA-CTAAAATTTTAAAAATTCAAATT
1 TCCATCTAAAATTTTAAAAATTCAAATT
125883 TAATCCCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.39
Consensus pattern (30 bp):
TCCATCTAAAATTTTAAAAATTCAAATTCA
Found at i:126159 original size:2 final size:2
Alignment explanation
Indices: 126152--126260 Score: 218
Period size: 2 Copynumber: 54.5 Consensus size: 2
126142 TATTATATTC
126152 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
126194 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
126236 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 A
126261 GGGTTAGGAT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 107 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:126725 original size:303 final size:304
Alignment explanation
Indices: 126242--127157 Score: 1559
Period size: 303 Copynumber: 3.0 Consensus size: 304
126232 ATATATATAT
* * *
126242 ATATATATATATATATATAGGGTTAGGATCCAATTACATCTAGTGTAAAATTAAGAGTTTTACAT
1 ATATATATATATATATATAGGGTTAGGTTCCAGTTACACCTAGTGTAAAATTAAGAGTTTTACAT
*
126307 TTTTTATGACTGTTGAACAAGGGAAGTCAAAGGACGAGATTAACTTTTTGCTTTTTATCTTTTCA
66 TTTTTATGACTGTTGAACGAGGGAAGTCAAAGGACGAGATTAACTTTTTGCTTTTTATCTTTTCA
126372 TTTCCTATCGTTAATCTTAACATTAGATATTCATCATCCAACAGTCCTTAAAAAATGTAAAGCTC
131 TTTCCTATCGTTAATCTTAACATTAGATATTCATCATCCAACAGTCCTTAAAAAATGTAAAGCTC
* *
126437 TTAATTTTATACCAAGTGTAAGTGAATCATACCTCTCTCTCTATATATAATTCAGATACGATTAG
196 TTAATTTTATACCAAGTGTAAGTGAATCATACCTCTCTATATATATATAATTCAGATACGATTAG
126502 ATAAATAATGTACACTTGTAAGGTCCTTGAAGATTTGTATAGTC
261 ATAAATAATGTACACTTGTAAGGTCCTTGAAGATTTGTATAGTC
*
126546 -TATATATATATATATATAGGGTTAGGTTCCAGTTACACCTAGTGTAAAATTAAGAGTTTTATAT
1 ATATATATATATATATATAGGGTTAGGTTCCAGTTACACCTAGTGTAAAATTAAGAGTTTTACAT
*
126610 TTTTTATGACTGTTGAACGAGGGAAGTCAAAAGACGAGATTAACTTTTTGCTTTTTATCTTTTCA
66 TTTTTATGACTGTTGAACGAGGGAAGTCAAAGGACGAGATTAACTTTTTGCTTTTTATCTTTTCA
*
126675 TTTCCTATCGTTAATCTTAACATTAGATATTCATCATCCAACAATCCTTAAAAAATGTAAAGCTC
131 TTTCCTATCGTTAATCTTAACATTAGATATTCATCATCCAACAGTCCTTAAAAAATGTAAAGCTC
126740 TTAATTTTATACCAAGTGTAAGTGAATCATA-C-CTCTATATATATATAATTCAGATACGATTAG
196 TTAATTTTATACCAAGTGTAAGTGAATCATACCTCTCTATATATATATAATTCAGATACGATTAG
126803 ATAAATAATGTACACTTGTAAGGTCCTTGAAGATTTGTATAGTC
261 ATAAATAATGTACACTTGTAAGGTCCTTGAAGATTTGTATAGTC
* * * *
126847 TATATATATATATATATATAGGGTTAGGTTTCAGTTACACTTAATATAAAATTAAGAGTTTTACA
1 -ATATATATATATATATATAGGGTTAGGTTCCAGTTACACCTAGTGTAAAATTAAGAGTTTTACA
* *
126912 TTTTTTATGACGGTTGAACGAGGGAAGTCAAAGGACGAGATTAACTTTTTGTTTTTTATCTTTTC
65 TTTTTTATGACTGTTGAACGAGGGAAGTCAAAGGACGAGATTAACTTTTTGCTTTTTATCTTTTC
* * * *
126977 ATTTCCTATCGTTAATCTTAACATTTGATATTCGTCATCCAACGGTCCTTCAAAAATGTAAAGCT
130 ATTTCCTATCGTTAATCTTAACATTAGATATTCATCATCCAACAGTCCTTAAAAAATGTAAAGCT
* *
127042 CTTAATTTTATACCAAGTGTAAGTGAATCATACCCCTATATATATATATATATATAATTCAGATA
195 CTTAATTTTATACCAAGTGTAAGTGAATCATA--CC----TCTCTATATATATATAATTCAGATA
127107 CGATTAGATAAATAATGTACACTTGTAAGGTCCTTGAAGATTTGTATAGTC
254 CGATTAGATAAATAATGTACACTTGTAAGGTCCTTGAAGATTTGTATAGTC
127158 CATGAAGAAT
Statistics
Matches: 578, Mismatches: 24, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
301 73 0.13
302 1 0.00
303 430 0.74
306 1 0.00
311 73 0.13
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (304 bp):
ATATATATATATATATATAGGGTTAGGTTCCAGTTACACCTAGTGTAAAATTAAGAGTTTTACAT
TTTTTATGACTGTTGAACGAGGGAAGTCAAAGGACGAGATTAACTTTTTGCTTTTTATCTTTTCA
TTTCCTATCGTTAATCTTAACATTAGATATTCATCATCCAACAGTCCTTAAAAAATGTAAAGCTC
TTAATTTTATACCAAGTGTAAGTGAATCATACCTCTCTATATATATATAATTCAGATACGATTAG
ATAAATAATGTACACTTGTAAGGTCCTTGAAGATTTGTATAGTC
Found at i:129391 original size:15 final size:15
Alignment explanation
Indices: 129371--129399 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
129361 TTTAGTGGGC
129371 GGGCGGATGTGGGGT
1 GGGCGGATGTGGGGT
129386 GGGCGGATGTGGGG
1 GGGCGGATGTGGGG
129400 AAAGTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.69, T:0.17
Consensus pattern (15 bp):
GGGCGGATGTGGGGT
Found at i:131492 original size:5 final size:5
Alignment explanation
Indices: 131482--131510 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
131472 TGAGAGAATA
131482 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
131511 ACCCTAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:135794 original size:23 final size:24
Alignment explanation
Indices: 135753--135818 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
135743 GTTTACGTTC
* * *
135753 GTTCGTTTATGTTCTTTTAACTTT
1 GTTCATTTGTGTTCGTTTAACTTT
* **
135777 GTTTA-TTGTGTTCGTTTATGTTT
1 GTTCATTTGTGTTCGTTTAACTTT
135800 GTTCATTTGTGTTCGTTTA
1 GTTCATTTGTGTTCGTTTA
135819 TCATTTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.62
Consensus pattern (24 bp):
GTTCATTTGTGTTCGTTTAACTTT
Found at i:135814 original size:24 final size:23
Alignment explanation
Indices: 135774--135819 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
135764 TTCTTTTAAC
*
135774 TTTGTTTATTGTGTTCGTTTATG
1 TTTGTTCATTGTGTTCGTTTATG
135797 TTTGTTCATTTGTGTTCGTTTAT
1 TTTGTTCA-TTGTGTTCGTTTAT
135820 CATTTAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.09, C:0.07, G:0.20, T:0.65
Consensus pattern (23 bp):
TTTGTTCATTGTGTTCGTTTATG
Found at i:135848 original size:17 final size:17
Alignment explanation
Indices: 135826--135861 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
135816 TTATCATTTA
*
135826 AATGAACGAACACGAAC
1 AATGAACGAACACAAAC
135843 AATGAACGAACACAAAC
1 AATGAACGAACACAAAC
135860 AA
1 AA
135862 GCTACATTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (17 bp):
AATGAACGAACACAAAC
Found at i:137082 original size:6 final size:6
Alignment explanation
Indices: 137071--137099 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
137061 TTTATTTTAA
137071 ACGGGG ACGGGG ACGGGG ACGGGG ACGGG
1 ACGGGG ACGGGG ACGGGG ACGGGG ACGGG
137100 TTTGGTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.66, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:137138 original size:12 final size:12
Alignment explanation
Indices: 137110--137146 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
137100 TTTGGTAATC
137110 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
137123 CCCGCCCCGATA
1 CCCGCCCCGATA
*
137135 CCCGACCCGATA
1 CCCGCCCCGATA
137147 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:137199 original size:32 final size:32
Alignment explanation
Indices: 137147--137243 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 32
137137 CGACCCGATA
*
137147 AATATTAA-AAATAATT-ATTTATATATATATAT
1 AATATTAATAAAT--TTAATTTAAATATATATAT
* *
137179 AATATTAATAAATTTAATTTAAATA-AAAAAT
1 AATATTAATAAATTTAATTTAAATATATATAT
* *
137210 ATATATTTATATATTTAATTTAAATATATATAT
1 A-ATATTAATAAATTTAATTTAAATATATATAT
137243 A
1 A
137244 TATACCCGGC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
31 7 0.13
32 38 0.70
33 9 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
AATATTAATAAATTTAATTTAAATATATATAT
Found at i:139049 original size:14 final size:15
Alignment explanation
Indices: 139030--139059 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
139020 TTTTTCCTTG
139030 GTTTAGTTAT-TTAT
1 GTTTAGTTATCTTAT
139044 GTTTAGTTATCTTAT
1 GTTTAGTTATCTTAT
139059 G
1 G
139060 CTCATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (15 bp):
GTTTAGTTATCTTAT
Found at i:144276 original size:18 final size:18
Alignment explanation
Indices: 144253--144312 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
144243 ACCGGTCACA
144253 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
144271 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
144289 A-CCGACCCGTTAACCGTTG
1 ACCCGACCCG--ACCCGTTG
144308 ACCCG
1 ACCCG
144313 TTGACCGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 8 0.22
18 18 0.50
19 7 0.19
20 3 0.08
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:144312 original size:15 final size:15
Alignment explanation
Indices: 144292--144325 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
144282 CCCGTTTACC
144292 GACCCGTTAACCGTT
1 GACCCGTTAACCGTT
*
144307 GACCCGTTGACCGTT
1 GACCCGTTAACCGTT
144322 GACC
1 GACC
144326 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCGTTAACCGTT
Found at i:146883 original size:24 final size:24
Alignment explanation
Indices: 146787--146895 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
146777 GAATATTTTA
* *
146787 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
146811 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
146835 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
146859 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
146883 TTTGATTTCTGAT
1 TCTGATATCTGAT
146896 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:149051 original size:12 final size:13
Alignment explanation
Indices: 149018--149074 Score: 98
Period size: 13 Copynumber: 4.5 Consensus size: 13
149008 GTCACAACCC
149018 GACCCGACCCGTT
1 GACCCGACCCGTT
149031 GACCCGACCCGTT
1 GACCCGACCCGTT
*
149044 TA-CCGACCCGTT
1 GACCCGACCCGTT
149056 GACCCGACCCGTT
1 GACCCGACCCGTT
149069 GACCCG
1 GACCCG
149075 TTGACTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.27
13 30 0.73
ACGTcount: A:0.16, C:0.46, G:0.23, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:149051 original size:25 final size:25
Alignment explanation
Indices: 149021--149068 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
149011 ACAACCCGAC
149021 CCGACCCGTTGACCCGACCCGTTTA
1 CCGACCCGTTGACCCGACCCGTTTA
149046 CCGACCCGTTGACCCGACCCGTT
1 CCGACCCGTTGACCCGACCCGTT
149069 GACCCGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.15, C:0.46, G:0.21, T:0.19
Consensus pattern (25 bp):
CCGACCCGTTGACCCGACCCGTTTA
Found at i:151646 original size:24 final size:24
Alignment explanation
Indices: 151550--151658 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
151540 GAATATTTTA
* *
151550 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
151574 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
151598 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
151622 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
151646 TTTGATTTCTGAT
1 TCTGATATCTGAT
151659 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:153811 original size:18 final size:18
Alignment explanation
Indices: 153788--153863 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
153778 ACCGGTCACA
153788 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
153806 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
153823 ----TA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
153836 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
153854 ACCCGACCCG
1 ACCCGACCCG
153864 TTGACCGTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
12 10 0.20
13 1 0.02
17 1 0.02
18 38 0.76
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:153830 original size:12 final size:13
Alignment explanation
Indices: 153810--153869 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
153800 CCGTTGACCC
153810 GACCCGACCCGTT
1 GACCCGACCCGTT
*
153823 TA-CCGACCCGTT
1 GACCCGACCCGTT
153835 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
153853 GACCCGACCCGTT
1 GACCCGACCCGTT
153866 GACC
1 GACC
153870 GTTGACCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
12 10 0.26
13 17 0.44
17 1 0.03
18 11 0.28
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:153831 original size:30 final size:31
Alignment explanation
Indices: 153792--153869 Score: 140
Period size: 30 Copynumber: 2.5 Consensus size: 31
153782 GTCACAACCC
153792 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
153823 TA-CCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
153853 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
153870 GTTGACCGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 29 0.66
31 15 0.34
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:156432 original size:24 final size:24
Alignment explanation
Indices: 156336--156444 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
156326 GAATATTTTA
* * *
156336 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTATGT
* * *
156360 TTTGACATCTGATCTGAAATATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
156384 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
156408 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
156432 TTTGATTTCTGAT
1 TCTGATATCTGAT
156445 ATCTCCGTTT
Statistics
Matches: 64, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:161286 original size:35 final size:36
Alignment explanation
Indices: 161220--161287 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
161210 GCAACAAGTA
*
161220 GAGCAACAAATTTTATTAATGAGCACGAGTCGAATC
1 GAGCAACAAATTTTATTAACGAGCACGAGTCGAATC
161256 GAGCAACAAATTTT-TTAACGAGCACGAGTCGA
1 GAGCAACAAATTTTATTAACGAGCACGAGTCGA
161288 GCACTGCCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 17 0.55
36 14 0.45
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (36 bp):
GAGCAACAAATTTTATTAACGAGCACGAGTCGAATC
Found at i:166249 original size:19 final size:19
Alignment explanation
Indices: 166217--166253 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
166207 ATAACTAACA
* *
166217 AAATCTCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
166236 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
166254 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:166502 original size:22 final size:22
Alignment explanation
Indices: 166477--166527 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
166467 CTACGGCGAC
166477 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
166499 ATCCGTCCCTATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
166521 ATCCGTC
1 ATCCGTC
166528 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:166532 original size:20 final size:21
Alignment explanation
Indices: 166477--166534 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
166467 CTACGGCGAC
*
166477 ATCCGTCCCCATCTCCGACGAA
1 ATCCGT-CCTATCTCCGACGAA
*
166499 ATCCGTCCCTATCTCCGGCGAA
1 ATCCGT-CCTATCTCCGACGAA
166521 ATCCGT-CTATCTCC
1 ATCCGTCCTATCTCC
166535 ATCTCTCAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.24
22 26 0.76
ACGTcount: A:0.19, C:0.43, G:0.14, T:0.24
Consensus pattern (21 bp):
ATCCGTCCTATCTCCGACGAA
Found at i:166989 original size:20 final size:20
Alignment explanation
Indices: 166920--166989 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 20
166910 TCGCAACGCA
166920 ATTTT-AGTTTCGCGTTGCG
1 ATTTTCAGTTTCGCGTTGCG
166939 ATTTTCA-TTTCGCGTTGCG
1 ATTTTCAGTTTCGCGTTGCG
** * *
166958 ATAGTCATTTTCGTGTTGCG
1 ATTTTCAGTTTCGCGTTGCG
*
166978 ATTTTAAGTTTC
1 ATTTTCAGTTTC
166990 AGAAAATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 22 0.52
20 20 0.48
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.49
Consensus pattern (20 bp):
ATTTTCAGTTTCGCGTTGCG
Found at i:167929 original size:21 final size:22
Alignment explanation
Indices: 167905--167947 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
167895 AATTTCTATA
167905 TAATGTATCTAA-AATTA-TAAT
1 TAAT-TATCTAACAATTACTAAT
*
167926 TAATTATTTAACAATTACTAAT
1 TAATTATCTAACAATTACTAAT
167948 GTTTGTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (22 bp):
TAATTATCTAACAATTACTAAT
Found at i:168924 original size:20 final size:20
Alignment explanation
Indices: 168901--168949 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
168891 GAAACTTAAA
168901 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
168921 ATCGCAACGCGTAAATGACT
1 ATCGCAACGCGAAAATGACT
168941 ATCGCAACG
1 ATCGCAACG
168950 AGATAATCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:169005 original size:19 final size:19
Alignment explanation
Indices: 168956--169006 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
168946 AACGAGATAA
* *
168956 TCGCAATGCGAATTTAGTT
1 TCGCATTGCGATTTTAGTT
* *
168975 TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATTTTAGTT
168994 TCGCATTGCGATT
1 TCGCATTGCGATT
169007 ATCCCGTTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (19 bp):
TCGCATTGCGATTTTAGTT
Found at i:169050 original size:20 final size:20
Alignment explanation
Indices: 169027--169069 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
169017 GATAGTCAAA
169027 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
*
169047 TTCGTGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
169067 TTC
1 TTC
169070 AAAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTAAGT
Found at i:169813 original size:20 final size:20
Alignment explanation
Indices: 169788--169825 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
169778 GGATCATGAC
169788 ATTTCAATATG-CATATATTT
1 ATTTC-ATATGACATATATTT
169808 ATTTCATATGACATATAT
1 ATTTCATATGACATATAT
169826 AATCAGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (20 bp):
ATTTCATATGACATATATTT
Found at i:170107 original size:38 final size:38
Alignment explanation
Indices: 170013--170107 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
170003 TTCAGTATTC
* * * *
170013 GTCCCGTAGGACCTAGCATCCCGAAAGATGTAATTTGT
1 GTCCCGAAGGACCTGGCATCCCGAAAGATGTAATCTAT
* *
170051 GTCCCGAAGGACTTGGCATCCCGAAGGATGTAATCTAT
1 GTCCCGAAGGACCTGGCATCCCGAAAGATGTAATCTAT
*
170089 GTCCCGAAGGACCGGGCAT
1 GTCCCGAAGGACCTGGCAT
170108 ATGTCTTATA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.22
Consensus pattern (38 bp):
GTCCCGAAGGACCTGGCATCCCGAAAGATGTAATCTAT
Found at i:171840 original size:21 final size:21
Alignment explanation
Indices: 171749--171867 Score: 89
Period size: 21 Copynumber: 5.7 Consensus size: 21
171739 GACTCACCTG
171749 TCATCGTTCAAGAGG-CC-TC
1 TCATCGTTCAAGAGGCCCATC
* *
171768 TCATATCGTTCAAGAGGCCCCTA
1 TC--ATCGTTCAAGAGGCCCATC
** * *
171791 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCATC
* *
171812 TCACCGTTCAAGAGGCCCATG
1 TCATCGTTCAAGAGGCCCATC
* *
171833 TCATCGTTGAAGAGGTCCATC
1 TCATCGTTCAAGAGGCCCATC
* * *
171854 CCACCATTCAAGAG
1 TCATCGTTCAAGAG
171868 CCCGATTCAT
Statistics
Matches: 77, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
19 2 0.03
21 70 0.91
22 2 0.03
23 3 0.04
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCATC
Found at i:171846 original size:42 final size:42
Alignment explanation
Indices: 171747--171847 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
171737 CTGACTCACC
* * *
171747 TGTCATCGTTCAAGAGGCCTCTCATATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGCCCCTCATACCGTTCAAGAGGCCCA
* ** *
171789 TATCATCCCTCAAGAGTCCCCTC-TCACCGTTCAAGAGGCCCA
1 TGTCATCGTTCAAGAGGCCCCTCAT-ACCGTTCAAGAGGCCCA
*
171831 TGTCATCGTTGAAGAGG
1 TGTCATCGTTCAAGAGG
171848 TCCATCCCAC
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 1 0.02
42 45 0.98
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.25
Consensus pattern (42 bp):
TGTCATCGTTCAAGAGGCCCCTCATACCGTTCAAGAGGCCCA
Found at i:173213 original size:27 final size:26
Alignment explanation
Indices: 173162--173213 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
173152 TACACTTTTT
* **
173162 TTGATTGTTTAATTGATTATTAAAAG
1 TTGATTGTTTAATTGATGAGGAAAAG
173188 TTGATTTGTTTAATTGATGAGGAAAA
1 TTGA-TTGTTTAATTGATGAGGAAAA
173214 TAAGAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (26 bp):
TTGATTGTTTAATTGATGAGGAAAAG
Found at i:173434 original size:20 final size:20
Alignment explanation
Indices: 173387--173446 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
173377 AGGTACACTT
* * *
173387 TCGCAACGCTAAACTCAAAA
1 TCGCAATGCCAAAGTCAAAA
173407 TCGCAATGCCAAAGTCAAAA
1 TCGCAATGCCAAAGTCAAAA
* * *
173427 TCGTAATGCGAAAGGCAAAA
1 TCGCAATGCCAAAGTCAAAA
173447 GCACAACGCG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAATGCCAAAGTCAAAA
Found at i:173496 original size:20 final size:20
Alignment explanation
Indices: 173463--173565 Score: 134
Period size: 20 Copynumber: 5.2 Consensus size: 20
173453 CGCGAAAGTC
*
173463 AATTCGCGTTGCGATAATCT
1 AATTCGCGTTGCGATAATCA
* * *
173483 AATACGCTTTGCGATAGTCA
1 AATTCGCGTTGCGATAATCA
*
173503 AATTCCCGTTGCGATAATCA
1 AATTCGCGTTGCGATAATCA
* *
173523 AATTCACGTTGCGATAGTCA
1 AATTCGCGTTGCGATAATCA
*
173543 AATTCGCGTTGCGATATTCA
1 AATTCGCGTTGCGATAATCA
173563 AAT
1 AAT
173566 GAATGTGTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (20 bp):
AATTCGCGTTGCGATAATCA
Found at i:173514 original size:40 final size:40
Alignment explanation
Indices: 173454--173565 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
173444 AAAGCACAAC
* * * *
173454 GCGAAAGTC-AATTCGCGTTGCGATAATCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTTGCGATAATCAAATACACGTT
* *
173493 GCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTTGCGATAATCAAATACACGTT
*
173533 GCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 GCGATAGTCAAATTCGCGTTGCGATAATCAAAT
173566 GAATGTGTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 8 0.12
40 56 0.88
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (40 bp):
GCGATAGTCAAATTCGCGTTGCGATAATCAAATACACGTT
Found at i:176048 original size:24 final size:24
Alignment explanation
Indices: 176014--176067 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
176004 CTGAAACATC
*
176014 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACAAAG
* *
176038 ATCAAAGTCCGGGTATTGACAAAG
1 ATCAAAATCCGAGTATTGACAAAG
176062 ATCAAA
1 ATCAAA
176068 TTTCCAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACAAAG
Found at i:176913 original size:20 final size:20
Alignment explanation
Indices: 176888--176970 Score: 59
Period size: 20 Copynumber: 4.3 Consensus size: 20
176878 GAAATTCAGT
176888 GTTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAAAATCGC
* * *
176908 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAAAATCGC
*
176928 ATTGCG--AG--AAAATCGC
1 GTTGCGATAGTCAAAATCGC
** *
176944 AATGCGATAGTCAAAATCGT
1 GTTGCGATAGTCAAAATCGC
176964 GTTGCGA
1 GTTGCGA
176971 ATCTGGAAAC
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
16 11 0.24
18 2 0.04
19 1 0.02
20 32 0.70
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (20 bp):
GTTGCGATAGTCAAAATCGC
Found at i:178322 original size:50 final size:51
Alignment explanation
Indices: 178226--178323 Score: 121
Period size: 50 Copynumber: 1.9 Consensus size: 51
178216 TGATGAGTTT
* * *
178226 TAAAAAATAATTTTTTATTTAAATTTATCACGTCGATATGATAAGTTTGAA
1 TAAAAAATAATTTTTTATTTAAATTTATCACATCGATATAAAAAGTTTGAA
*
178277 TAAAATATAA-TTTTTA-TTAAATTTTATCACATC-ATGATAAAAAGTTT
1 TAAAAAATAATTTTTTATTTAAA-TTTATCACATCGAT-ATAAAAAGTTT
178324 AAACAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 7 0.17
50 25 0.61
51 9 0.22
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (51 bp):
TAAAAAATAATTTTTTATTTAAATTTATCACATCGATATAAAAAGTTTGAA
Found at i:181865 original size:21 final size:21
Alignment explanation
Indices: 181839--181933 Score: 111
Period size: 21 Copynumber: 4.5 Consensus size: 21
181829 AGGGTGTCAA
181839 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTAC
*
181860 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
***
181881 AGTGCATCCATGCACCTGAAC
1 AGTGCATCCATGCACCCCTAC
* * *
181902 TAGTGCATCGATGCA-CCTTGC
1 -AGTGCATCCATGCACCCCTAC
181923 AGTGCATCCAT
1 AGTGCATCCAT
181934 ACACTCCATT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
20 10 0.16
21 39 0.63
22 13 0.21
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:181924 original size:42 final size:42
Alignment explanation
Indices: 181839--181933 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
181829 AGGGTGTCAA
*
181839 AGTGCATCCATGCACCCCTACAGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCAACAGTGCATCCATGCACCCCTGC
** * *
181881 AGTGCATCCATGCACCTGAACTAGTGCATCGATGCA-CCTTGC
1 AGTGCATCCATGCACCCCAAC-AGTGCATCCATGCACCCCTGC
181923 AGTGCATCCAT
1 AGTGCATCCAT
181934 ACACTCCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 34 0.72
43 13 0.28
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (42 bp):
AGTGCATCCATGCACCCCAACAGTGCATCCATGCACCCCTGC
Found at i:181928 original size:20 final size:19
Alignment explanation
Indices: 181839--182029 Score: 106
Period size: 20 Copynumber: 9.7 Consensus size: 19
181829 AGGGTGTCAA
*
181839 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCA--CCTGC
181860 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA--CCTGC
181881 AGTGCATCCATGCACCTGAAC
1 AGTGCATCCATGCACCTG--C
*
181902 TAGTGCATCGATGCACCTTGC
1 -AGTGCATCCATGCACC-TGC
* *
181923 AGTGCATCCATACA-CTCC
1 AGTGCATCCATGCACCTGC
* * *
181941 A-T--TTCGAATGCA-CT-T
1 AGTGCATC-CATGCACCTGC
* *
181956 AGTGCATCGATGCATCATGC
1 AGTGCATCCATGCA-CCTGC
* *
181976 TGTGCATCGATGCATCCTGC
1 AGTGCATCCATGCA-CCTGC
* *
181996 TGTGCATCGATGCATCCTGC
1 AGTGCATCCATGCA-CCTGC
*
182016 TGTGCATCCATGCA
1 AGTGCATCCATGCA
182030 TGAAGGCTGC
Statistics
Matches: 143, Mismatches: 16, Indels: 23
0.79 0.09 0.13
Matches are distributed among these distances:
15 3 0.02
16 7 0.05
17 6 0.04
18 5 0.03
19 6 0.04
20 63 0.44
21 36 0.25
22 15 0.10
23 2 0.01
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (19 bp):
AGTGCATCCATGCACCTGC
Found at i:182030 original size:20 final size:20
Alignment explanation
Indices: 181957--182030 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
181947 AATGCACTTA
*
181957 GTGCATCGATGCATCATGCT
1 GTGCATCGATGCATCCTGCT
181977 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
181997 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
182017 GTGCATCCATGCAT
1 GTGCATCGATGCAT
182031 GAAGGCTGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.18, C:0.28, G:0.24, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:182425 original size:34 final size:32
Alignment explanation
Indices: 182386--182455 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
182376 TTTTGTAAAG
* *
182386 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
182420 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
182452 GGGA
1 GGGA
182456 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:185738 original size:6 final size:6
Alignment explanation
Indices: 185721--185764 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
185711 TAATATATAT
* * * *
185721 TAATAA TAATTA TTATTA TAATTA TAATAA TAATTA TTATTA TA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TA
185765 TAAATAACAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:185743 original size:12 final size:12
Alignment explanation
Indices: 185726--185764 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
185716 TATATTAATA
185726 ATAATTATTATT
1 ATAATTATTATT
* *
185738 ATAATTATAATA
1 ATAATTATTATT
185750 ATAATTATTATT
1 ATAATTATTATT
185762 ATA
1 ATA
185765 TAAATAACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATAATTATTATT
Found at i:185747 original size:21 final size:23
Alignment explanation
Indices: 185714--185771 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 23
185704 TATTAAATAA
*
185714 TATATATTAATAATAATTATTAT
1 TATATATTAATAATAATAATTAT
185737 TATA-ATT-ATAATAATAATTAT
1 TATATATTAATAATAATAATTAT
*
185758 TATTATATAAATAA
1 TA-TATATTAATAA
185772 CATTAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 15 0.50
22 5 0.17
23 6 0.20
24 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATTAATAATAATAATTAT
Found at i:186186 original size:87 final size:85
Alignment explanation
Indices: 186036--186210 Score: 201
Period size: 87 Copynumber: 2.0 Consensus size: 85
186026 GAACTTTCTT
* * * *
186036 TTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTATAAAGGTTGATCCATTAAGTGATGAAT
1 TTCTTCAAATGAGTTCTTCTCATTATGAAC-TTCTCTATAAAGGCTGATCCATCAAATAATGAA-
*
186101 TTGAA-CAAAAGGGTTAAACAAG
64 TTCAAGC-AAAGGGTTAAACAAG
* * ***
186123 TTCTTCAGATGAGTTCTTCTCATTATGAAC-TCTCTTTGGCGTTGCTGATCCATCAAATAATGAA
1 TTCTTCAAATGAGTTCTTCTCATTATGAACTTCTCTATAAAG--GCTGATCCATCAAATAATGAA
186187 TTCAAGCAAAGGGTTAAACAAG
64 TTCAAGCAAAGGGTTAAACAAG
186209 TT
1 TT
186211 TTTCTCATTA
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
85 7 0.09
86 21 0.28
87 47 0.63
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (85 bp):
TTCTTCAAATGAGTTCTTCTCATTATGAACTTCTCTATAAAGGCTGATCCATCAAATAATGAATT
CAAGCAAAGGGTTAAACAAG
Found at i:186329 original size:113 final size:113
Alignment explanation
Indices: 186123--186642 Score: 700
Period size: 113 Copynumber: 4.6 Consensus size: 113
186113 GTTAAACAAG
*** **** * * *
186123 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTTTGGCGTTGCTGATCCATCAAATAATGAAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGAT
* * * * * *
186188 -TCAAGCAAAGGGTTAAACAAGTTTTTCTCATTATGAACTTCTCCTTCC
66 CT-GAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * *
186236 TTCTTCAGATGAGTTCTTCTTATTATGAACTTTAACTGGAAAAGCTGATACATCAAGTGATGGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGAT
186301 CTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
66 CTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
*
186349 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGAT
* **
186414 CTGAGTAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC
66 CTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
*
186462 TTCTTCAAGTAATGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTGATCCATCAAGTGATG
1 TTCTTC-AG--ATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATG
* * *
186527 GATTTGAGCATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC
63 GATCTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * * ** *
186578 TCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAGCTGATCCATCAAGTGATGGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGAT
186643 TTAAATCTTT
Statistics
Matches: 363, Mismatches: 40, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
113 256 0.71
114 3 0.01
115 2 0.01
116 102 0.28
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.36
Consensus pattern (113 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGAT
CTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
Found at i:186561 original size:229 final size:226
Alignment explanation
Indices: 186123--186643 Score: 738
Period size: 229 Copynumber: 2.3 Consensus size: 226
186113 GTTAAACAAG
* **** * * *
186123 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTTTGGCGTTGCTGATCCATCAAATAATGAAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGCTGATCCATCAAGTGATGGAT
* * *
186188 TCAAGCAAAGGGTTAAACAAGTTTTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCT
66 TCAAGCAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCT
* *
186253 TCTTATTATGAACTTTAACTGGAAAAGCTGATACATCAAGTGATGGATCTGAGCAAAAGGTTGAA
131 TCTCATTATGAACTCTAACTGGAAAAGCTGATACATCAAGTGATGGATCTGAGCAAAAGGTTGAA
186318 CAAATTCTTCTCATTATGAACTTCTTCTTCC
196 CAAATTCTTCTCATTATGAACTTCTTCTTCC
***
186349 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGA-
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGCTGATCCATCAAGTGATGGAT
* * * *
186413 TCTGAGTAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAGTAATGAG
66 TC-AAGCAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTCCTTCCTTCTTC-AG--ATGAG
* * * *
186478 TTCTTCTCATTATGAACTCTACCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCATAAGGT
127 TTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATACATCAAGTGATGGATCTGAGCAAAAGGT
*
186543 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCC
192 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * * *
186578 TCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAGCTGATCCATCAAGTGATGGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGCTGATCCATCAAGTGATGGAT
186643 T
66 T
186644 TAAATCTTTG
Statistics
Matches: 258, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
225 2 0.01
226 98 0.38
227 2 0.01
229 155 0.60
230 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.36
Consensus pattern (226 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGCTGATCCATCAAGTGATGGAT
TCAAGCAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCTAACTGGAAAAGCTGATACATCAAGTGATGGATCTGAGCAAAAGGTTGAA
CAAATTCTTCTCATTATGAACTTCTTCTTCC
Found at i:187504 original size:83 final size:83
Alignment explanation
Indices: 187362--187829 Score: 857
Period size: 83 Copynumber: 5.6 Consensus size: 83
187352 GGTTCCTACT
*
187362 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-ACTCTTCCAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCA-TCTTCCAAT
187426 TTCAATGATTGGTTTTACC
65 TTCAATGATTGGTTTTACC
187445 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
* **
187510 TCAATGATTGGTTCTGTC
66 TCAATGATTGGTTTTACC
* *
187528 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
187593 TCAATGATTGGTTTTACC
66 TCAATGATTGGTTTTACC
187611 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
187676 TCAATGATTGGTTTTACC
66 TCAATGATTGGTTTTACC
187694 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
187759 TCAATGATTGGTTTTACC
66 TCAATGATTGGTTTTACC
*
187777 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
187830 GCATTTGTTC
Statistics
Matches: 372, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
83 371 1.00
84 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATT
TCAATGATTGGTTTTACC
Found at i:189202 original size:10 final size:10
Alignment explanation
Indices: 189189--189238 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
189179 CTTGACCGTC
189189 CTTTTTTCTT
1 CTTTTTTCTT
189199 CTTTTTTC-T
1 CTTTTTTCTT
*
189208 CTTTTTTTTT
1 CTTTTTTCTT
189218 C-TTTTT-TT
1 CTTTTTTCTT
189226 CTTTTTTTCTT
1 C-TTTTTTCTT
189237 CT
1 CT
189239 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
8 3 0.09
9 13 0.37
10 16 0.46
11 3 0.09
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:189211 original size:19 final size:18
Alignment explanation
Indices: 189189--189238 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
189179 CTTGACCGTC
189189 CTTTTTTCTTCTTTTTTCT
1 CTTTTTTCTTCTTTTTT-T
*
189208 CTTTTTTTTTCTTTTTTT
1 CTTTTTTCTTCTTTTTTT
189226 CTTTTTTTCTTCT
1 C-TTTTTTCTTCT
189239 CTTCAAGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
CTTTTTTCTTCTTTTTTT
Found at i:189236 original size:8 final size:8
Alignment explanation
Indices: 189191--189236 Score: 56
Period size: 8 Copynumber: 5.2 Consensus size: 8
189181 TGACCGTCCT
189191 TTTTTCTTC
1 TTTTT-TTC
189200 TTTTTTCTC
1 TTTTTT-TC
189209 TTTTTTTTTC
1 --TTTTTTTC
189219 TTTTTTTC
1 TTTTTTTC
189227 TTTTTTTC
1 TTTTTTTC
189235 TT
1 TT
189237 CTCTTCAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 19 0.56
9 7 0.21
10 2 0.06
11 6 0.18
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTC
Found at i:196587 original size:15 final size:15
Alignment explanation
Indices: 196564--196595 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
196554 TGAAATGAAT
196564 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
196579 AATGCATGTATGCAA
1 AATGAATGTATGCAA
196594 AA
1 AA
196596 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:202027 original size:3 final size:3
Alignment explanation
Indices: 202013--202061 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
202003 TGTAATATTA
* *
202013 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT TAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
202059 AAT
1 AAT
202062 TATTATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:202066 original size:9 final size:9
Alignment explanation
Indices: 202005--202068 Score: 78
Period size: 9 Copynumber: 7.2 Consensus size: 9
201995 TTGGGTTTTG
202005 TAAT-ATTA
1 TAATAATTA
202013 -AATAATATA
1 TAATAAT-TA
*
202022 TAATAATAA
1 TAATAATTA
*
202031 TAATAATAA
1 TAATAATTA
202040 TAATAATTA
1 TAATAATTA
202049 TAATAATTA
1 TAATAATTA
*
202058 TAATTATTA
1 TAATAATTA
202067 TA
1 TA
202069 TAAATAACAT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
7 3 0.06
8 2 0.04
9 39 0.78
10 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATAATTA
Found at i:209507 original size:22 final size:22
Alignment explanation
Indices: 209482--209523 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
209472 CGCGTTGAAT
209482 GTTGAACGGTTCAACATTCAGC
1 GTTGAACGGTTCAACATTCAGC
* *
209504 GTTGAATGGTTTAACATTCA
1 GTTGAACGGTTCAACATTCA
209524 AAGCTGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (22 bp):
GTTGAACGGTTCAACATTCAGC
Done.