Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004558.1 Hibiscus syriacus cultivar Beakdansim tig00010130_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: 154116
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:8489 original size:12 final size:12
Alignment explanation
Indices: 8468--8497 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
8458 AATGATATGT
8468 GAAAAATAGAGA
1 GAAAAATAGAGA
*
8480 GAAAACTAGAGA
1 GAAAAATAGAGA
8492 GAAAAA
1 GAAAAA
8498 GAAGATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:8688 original size:13 final size:14
Alignment explanation
Indices: 8670--8698 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
8660 AAGATAAAAT
8670 AAAATAATATT-TA
1 AAAATAATATTCTA
8683 AAAATAATATTCTA
1 AAAATAATATTCTA
8697 AA
1 AA
8699 TCCTAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATAATATTCTA
Found at i:8701 original size:86 final size:85
Alignment explanation
Indices: 8584--8756 Score: 219
Period size: 86 Copynumber: 2.0 Consensus size: 85
8574 AATTACAAGC
* * * *
8584 TAAAGATAATTTTAAAATAATATCTTAAATCCTAATTAAAACATTTAAAA-TTATTTAAATTAAA
1 TAAAGATAATTTTAAAATAATATCTTAAATCCTAATTAAAACA-CTAAAACCTATTCAAACTAAA
8648 ATA-TCTAAAACAAAGATAAAA
65 ATACT-TAAAACAAAGATAAAA
* *
8669 TAAA-ATAATATTTAAAAATAATAT-TCTAAATCCTAATTGAAATACTAAAACCTATTCAAACTA
1 TAAAGATAAT-TTT-AAAATAATATCT-TAAATCCTAATTAAAACACTAAAACCTATTCAAACTA
8732 AAATACTTAAAACAAAGATAAAA
63 AAATACTTAAAACAAAGATAAAA
8755 TA
1 TA
8757 TAATGTTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
84 5 0.06
85 13 0.17
86 58 0.75
87 1 0.01
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (85 bp):
TAAAGATAATTTTAAAATAATATCTTAAATCCTAATTAAAACACTAAAACCTATTCAAACTAAAA
TACTTAAAACAAAGATAAAA
Found at i:10122 original size:18 final size:18
Alignment explanation
Indices: 10099--10145 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
10089 ATCTCTTTAA
10099 ATTATTTATTTAATTATT
1 ATTATTTATTTAATTATT
*
10117 ATTATTTATTTAATTCTT
1 ATTATTTATTTAATTATT
10135 ATCT-TTTATTT
1 AT-TATTTATTT
10146 TAAAAACAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTATTTATTTAATTATT
Found at i:10252 original size:26 final size:25
Alignment explanation
Indices: 10207--10256 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
10197 TAATTTCCCA
*
10207 TTTTTTTATTATTACTTATTTATTG
1 TTTTTTTATTATAACTTATTTATTG
10232 TTTTTTTAAATTATAAC-TATTTATT
1 TTTTTTT--ATTATAACTTATTTATT
10257 TTATTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 8 0.36
27 7 0.32
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (25 bp):
TTTTTTTATTATAACTTATTTATTG
Found at i:14942 original size:5 final size:5
Alignment explanation
Indices: 14929--14996 Score: 73
Period size: 5 Copynumber: 13.0 Consensus size: 5
14919 GAGGCAACCC
* * * *
14929 ATTTC ATTTT ATTTTT ATTTT ATTTT ATTTC ATTTT ATTTT CGTTTT ATTTC
1 ATTTT ATTTT A-TTTT ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT ATTTT
14981 ATTTT ATTTTT ATTTT
1 ATTTT A-TTTT ATTTT
14997 TAACAAACCT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 39 0.74
6 14 0.26
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:14958 original size:21 final size:21
Alignment explanation
Indices: 14941--14996 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
14931 TTCATTTTAT
14941 TTTTA-TTTTATTTTATTTCA
1 TTTTATTTTTATTTTATTTCA
**
14961 TTTTATTTTCGTTTTATTTCA
1 TTTTATTTTTATTTTATTTCA
14982 TTTTATTTTTATTTT
1 TTTTATTTTTATTTT
14997 TAACAAACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTATTTTTATTTTATTTCA
Found at i:14965 original size:26 final size:26
Alignment explanation
Indices: 14928--14998 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
14918 GGAGGCAACC
14928 CATTTCATTTTATTTTTATTTTATTT
1 CATTTCATTTTATTTTTATTTTATTT
* **
14954 TATTTCATTTTATTTTCGTTTTATTT
1 CATTTCATTTTATTTTTATTTTATTT
*
14980 CATTTTATTTTTATTTTTA
1 CATTTCA-TTTTATTTTTA
14999 ACAAACCTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 28 0.76
27 9 0.24
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.73
Consensus pattern (26 bp):
CATTTCATTTTATTTTTATTTTATTT
Found at i:17954 original size:18 final size:18
Alignment explanation
Indices: 17931--17973 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
17921 CTTTAGATGA
*
17931 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
17949 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
17967 TTTATTT
1 TTTATTT
17974 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:26398 original size:2 final size:2
Alignment explanation
Indices: 26391--26449 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
26381 AATGAAGTAA
26391 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
*
26433 AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT A
26450 AGAAGGATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:26600 original size:14 final size:14
Alignment explanation
Indices: 26583--26624 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
26573 ATAATACTTT
26583 TTAATATAAATATA
1 TTAATATAAATATA
* *
26597 TTAATATGAATAAAA
1 TTAATATAAAT-ATA
26612 TTAA-ATAAATATA
1 TTAATATAAATATA
26625 AAATGAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 2 0.09
14 15 0.65
15 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
TTAATATAAATATA
Found at i:26635 original size:25 final size:27
Alignment explanation
Indices: 26583--26645 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 27
26573 ATAATACTTT
26583 TTAATATAAATATATTAATATGAATAAAA
1 TTAA-ATAAATATA-TAATATGAATAAAA
26612 TTAAATAAATATA-AA-ATGAATAAAA
1 TTAAATAAATATATAATATGAATAAAA
*
26637 ATAGAATAA
1 TTA-AATAA
26646 TTTGAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 12 0.38
26 7 0.22
28 9 0.28
29 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (27 bp):
TTAAATAAATATATAATATGAATAAAA
Found at i:26664 original size:20 final size:20
Alignment explanation
Indices: 26614--26665 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
26604 GAATAAAATT
**
26614 AAATAAATATAAAATGAATAA
1 AAATAAA-ATAATTTGAATAA
*
26635 AAATAGAATAATTTGAATAA
1 AAATAAAATAATTTGAATAA
*
26655 AACTAAAATAA
1 AAATAAAATAA
26666 CTATATATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
AAATAAAATAATTTGAATAA
Found at i:26882 original size:26 final size:25
Alignment explanation
Indices: 26832--26891 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
26822 ATAAAATAAC
*
26832 TAAATTAAATATATAAAAATTAAAT
1 TAAATTAAATATATAAAAATCAAAT
*
26857 TAAATTACAATGTAATAAAAA-CAAAT
1 TAAATTA-AATAT-ATAAAAATCAAAT
*
26883 AAAATTAAA
1 TAAATTAAA
26892 ATTACATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 9 0.30
26 14 0.47
27 7 0.23
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (25 bp):
TAAATTAAATATATAAAAATCAAAT
Found at i:27691 original size:18 final size:17
Alignment explanation
Indices: 27668--27715 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
27658 ATGCTTTCTC
27668 TCTTGTTTCTCT-ATGATT
1 TCTTGTTTCT-TGATG-TT
*
27686 TCTTGTTGCTTGATGTT
1 TCTTGTTTCTTGATGTT
27703 TCTTGTTT-TTGAT
1 TCTTGTTTCTTGAT
27716 CAATGGCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 10 0.37
18 12 0.44
ACGTcount: A:0.08, C:0.12, G:0.17, T:0.62
Consensus pattern (17 bp):
TCTTGTTTCTTGATGTT
Found at i:28035 original size:76 final size:77
Alignment explanation
Indices: 27906--28117 Score: 293
Period size: 76 Copynumber: 2.8 Consensus size: 77
27896 CCGTTGTACA
* * * *
27906 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
**
27970 -CAAAACTGTTT
66 CCAAAACCATTT
* *
27981 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
28046 CCAAAACCATTT
66 CCAAAACCATTT
* * *
28058 AGGGGGGAATCGGTTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGGAATCGG-TTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
28118 TTTGGCTTTG
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
75 19 0.16
76 39 0.32
77 22 0.18
78 10 0.08
79 31 0.26
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.25
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
CCAAAACCATTT
Found at i:30744 original size:20 final size:21
Alignment explanation
Indices: 30690--30752 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
30680 GATTCCCCTG
30690 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
30714 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
30734 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
30753 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:36657 original size:76 final size:77
Alignment explanation
Indices: 36528--36739 Score: 275
Period size: 76 Copynumber: 2.8 Consensus size: 77
36518 CCGTTGTACA
* * * * *
36528 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTAGTAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTAGGAG
**
36592 -CAAAACTGTTT
66 CCAAAACCATTT
* * *
36603 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTAGGAG
36668 CCAAAACCATTT
66 CCAAAACCATTT
* * *
36680 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGGAATCGGTTCCTCCTAT--GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
36740 TTTGGCTTTG
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 19 0.16
76 37 0.31
77 32 0.27
79 31 0.26
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.25
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTAGGAG
CCAAAACCATTT
Found at i:37836 original size:3 final size:3
Alignment explanation
Indices: 37828--37907 Score: 108
Period size: 3 Copynumber: 27.0 Consensus size: 3
37818 GCCTGTAATT
* *
37828 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TTA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
37875 TAA TAA TAA TTG TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37908 AAATGAAATG
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:38214 original size:85 final size:85
Alignment explanation
Indices: 38109--38269 Score: 234
Period size: 85 Copynumber: 1.9 Consensus size: 85
38099 AAGATAATTC
* * *
38109 TTAAAATAACATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAATATACCTAAAAC
1 TTAAAATAACATCATAAATCCTAAGTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAAC
38173 AAAGATAAAATAAAATAATAT
65 AAAGATAAAATAAAATAATAT
* * * * *
38194 TTAAAATTATATCATAAATCCTAAGTGAAATACTAAAACCTATTTAAACTAAAATACTTAAAACA
1 TTAAAATAACATCATAAATCCTAAGTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAACA
38259 AAGATAAAATA
66 AAGATAAAATA
38270 TAATGTTTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
84 5 0.07
85 62 0.93
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (85 bp):
TTAAAATAACATCATAAATCCTAAGTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAACA
AAGATAAAATAAAATAATAT
Found at i:39421 original size:18 final size:18
Alignment explanation
Indices: 39389--39424 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39379 TGTTTCACGT
**
39389 AAAAAATATTTAAATTTA
1 AAAAAATATAAAAATTTA
39407 AAAAAATATAAAAATTTA
1 AAAAAATATAAAAATTTA
39425 TATATAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAATATAAAAATTTA
Found at i:39465 original size:72 final size:73
Alignment explanation
Indices: 39354--39498 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
39344 TATATATTCG
39354 ATATAATTTTAGTTTAATAGTATTTTGTTTCACGT-AAAAAATATTTAAATTTAAAAAAATATAA
1 ATATAATTTTAGTTTAATAGTATTTTGTTTCACGTAAAAAAATATTTAAATTTAAAAAAATATAA
39418 AAATTTAT
66 AAATTTAT
*
39426 ATATAATTTTAGTTTAATAGTATTTTGTTTCATGTAAAAAAATATTTAAATTTAAAAAAATATAA
1 ATATAATTTTAGTTTAATAGTATTTTGTTTCACGTAAAAAAATATTTAAATTTAAAAAAATATAA
39491 AAATTTAT
66 AAATTTAT
39499 TAAATATTTA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 34 0.48
73 37 0.52
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.45
Consensus pattern (73 bp):
ATATAATTTTAGTTTAATAGTATTTTGTTTCACGTAAAAAAATATTTAAATTTAAAAAAATATAA
AAATTTAT
Found at i:39494 original size:18 final size:18
Alignment explanation
Indices: 39460--39497 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39450 TTGTTTCATG
**
39460 TAAAAAAATATTTAAATT
1 TAAAAAAATATAAAAATT
39478 TAAAAAAATATAAAAATT
1 TAAAAAAATATAAAAATT
39496 TA
1 TA
39498 TTAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAAAATATAAAAATT
Found at i:41740 original size:14 final size:17
Alignment explanation
Indices: 41723--41778 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 17
41713 ATTTACTTAT
41723 ATAA-AATAAT-AAA-A
1 ATAATAATAATGAAATA
41737 ATAATAATAATGAAATA
1 ATAATAATAATGAAATA
* *
41754 ATAAT--TAAAGCAATA
1 ATAATAATAATGAAATA
41769 ATAATAATAA
1 ATAATAATAA
41779 AATAATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 4 0.11
15 19 0.54
16 3 0.09
17 9 0.26
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (17 bp):
ATAATAATAATGAAATA
Found at i:41742 original size:3 final size:3
Alignment explanation
Indices: 41723--41785 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
41713 ATTTACTTAT
* * **
41723 ATA A-A ATA ATA AAA ATA ATA ATA ATG A-A ATA ATA ATTA A-A GCA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
41766 ATA ATA ATA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
41786 TTTCAAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
2 6 0.12
3 39 0.81
4 3 0.06
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:41796 original size:26 final size:27
Alignment explanation
Indices: 41727--41785 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
41717 ACTTATATAA
*
41727 AATAA-TAAAAATAATAATAATGAAAT
1 AATAATTAAAAATAATAATAATAAAAT
41753 AATAATTAAAGCAATAATAATAATAAAAT
1 AATAATTAAA--AATAATAATAATAAAAT
41782 AATA
1 AATA
41786 TTTCAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 5 0.17
27 4 0.14
29 20 0.69
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (27 bp):
AATAATTAAAAATAATAATAATAAAAT
Found at i:41904 original size:2 final size:2
Alignment explanation
Indices: 41897--41938 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
41887 ATTTACCTAA
41897 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
41939 GCTGATAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43038 original size:3 final size:3
Alignment explanation
Indices: 43030--43075 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
43020 ATGATAAAAT
*
43030 TAA TAA TAAA TAA TAA TAT TAA T-A TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
43076 AAAAAAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:43056 original size:11 final size:11
Alignment explanation
Indices: 43030--43075 Score: 53
Period size: 10 Copynumber: 4.3 Consensus size: 11
43020 ATGATAAAAT
43030 TAATAATA-AA
1 TAATAATATAA
43040 TAATAATATTAA
1 TAATAATA-TAA
43052 T-ATAATAATAA
1 TAATAAT-ATAA
43063 TAATAA-ATAA
1 TAATAATATAA
43073 TAA
1 TAA
43076 AAAAAAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 15 0.47
11 9 0.28
12 8 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAATATAA
Found at i:43428 original size:113 final size:112
Alignment explanation
Indices: 43295--44315 Score: 1285
Period size: 113 Copynumber: 9.0 Consensus size: 112
43285 GTAACTTAGC
* ** *
43295 AAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCCGTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
43360 ATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCAA-TGATGAATTTAAGCA
43408 AAAGGTTGAACAAATTCTTCTCA-T-T--ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * * *
43469 ATGAACTCGAC-CTGGCAATGCTT-ATCCATTGAATGATGAATTTAAGCAA
66 ATGAACT-TTCTCTGGAAAAG-TTGATCCA-TCAATGATGAATTTAAGC-A
43518 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
43583 ATGAACTTTCTCTGGAAAATTTGATCCATCAAGTGATGAATTTAAGCA
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCAA-TGATGAATTTAAGCA
43631 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
43696 ATGAACTTTCTCTGGAAATA-CTGATCCATCGAATGATGAATTTAAGTAA
66 ATGAACTTTCTCTGGAAA-AGTTGATCCATC-AATGATGAATTTAAG-CA
*
43745 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
43810 ATGAACTTTCTCTGGAAAACTTGATCCATCAAGTGATAAATTTAAGCA
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCAA-TGATGAATTTAAGCA
*
43858 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCATCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
43923 ATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCGA
66 ATGAACTTTCTCTGGAAAAGTTGATCCATC-AATGATGAATTTAAGC-A
* * *
43972 AAA-GTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * * * * *
44036 ATGAACTCGAC-CTGGAAATGTTGATGATGATCTATCTATTTCTATGAT-AGAGTCATGCA
66 ATGAACT-TTCTCTGGAAA-----A-GTTGATC---C-A--TCAATGATGA-ATTTAAGCA
* * *
44095 AAAGGTTGAACAAATTATTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * * *
44160 ATGAACTTGAC-CTGGCAATGCTGATCCATCAAATGATGAATTCAAACA
66 ATGAACTT-TCTCTGGAAAAGTTGATCCATC-AATGATGAATTTAAGCA
* *
44208 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
44272 ATGAACTCT-TCTGGAAATGTTGATCCATTGAATGATGGATTTAA
66 ATGAACTTTCTCTGGAAAAGTTGATCCA-TCAATGATGAATTTAA
44316 ATCTTTGCTA
Statistics
Matches: 804, Mismatches: 66, Indels: 78
0.85 0.07 0.08
Matches are distributed among these distances:
109 67 0.08
110 30 0.04
111 29 0.04
112 37 0.05
113 354 0.44
114 184 0.23
115 1 0.00
118 6 0.01
119 6 0.01
122 1 0.00
123 6 0.01
124 81 0.10
125 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGTTGATCCATCAATGATGAATTTAAGCA
Found at i:43781 original size:227 final size:226
Alignment explanation
Indices: 43295--44299 Score: 1418
Period size: 227 Copynumber: 4.4 Consensus size: 226
43285 GTAACTTAGC
* * *
43295 AAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCCGTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
43360 ATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAATTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTC
* *
43425 TTCTCA-T-T--ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACCTGGAA
* * *
43486 ATGCTTATCCATTGAATGATGAATTTAAGCAA
195 ATGCTGATCCATCGAATGATGAATTCAAGCAA
*
43518 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
43583 ATGAACTTTCTCTGGAAAATTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAATTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTC
*
43648 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTAC-CTGGAA
* * *
43713 ATACTGATCCATCGAATGATGAATTTAAGTAA
195 ATGCTGATCCATCGAATGATGAATTCAAGCAA
* *
43745 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
43810 ATGAACTTTCTCTGGAAAACTTGATCCATCAAGTGATAAATTTAAGCAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAATTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTC
* *
43875 TTCTCATTATGAACTTCATCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTAC-CTGGAA
*
43940 ATGCTGATCCATCGAATGATGAATTCAAGCGA
195 ATGCTGATCCATCGAATGATGAATTCAAGCAA
* *
43972 AAA-GTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * * ** * * * *
44036 ATGAACTCGAC-CTGGAAATGTTGATGATGATCTATCTATTTCTATGATAGAGTCATGCAAAAGG
66 ATGAACT-TTCTCTGGAAA-----AT-TTGATCCATC-AAGT-GATG--A-ATTTAAGCAAAAGG
* * *
44100 TTGAACAAATTATTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
119 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
44165 CTTGACCTGGCAATGCTGATCCATCAAATGATGAATTCAAACAA
184 CTT-ACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAA
44209 AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
44272 ATGAACTCT-TCTGG-AAATGTTGATCCAT
66 ATGAACTTTCTCTGGAAAAT-TTGATCCAT
44300 TGAATGATGG
Statistics
Matches: 711, Mismatches: 52, Indels: 32
0.89 0.07 0.04
Matches are distributed among these distances:
223 130 0.18
224 1 0.00
225 1 0.00
226 72 0.10
227 299 0.42
229 10 0.01
231 1 0.00
232 8 0.01
233 2 0.00
234 4 0.01
235 4 0.01
236 32 0.05
237 146 0.21
238 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (226 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAATTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACCTGGAAA
TGCTGATCCATCGAATGATGAATTCAAGCAA
Found at i:43962 original size:340 final size:340
Alignment explanation
Indices: 43295--44315 Score: 1367
Period size: 340 Copynumber: 3.0 Consensus size: 340
43285 GTAACTTAGC
* * *
43295 AAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCCGTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
43360 ATGAACTTTCTCTAGAAA-AGTTGATCCATCAAGTGATGAATTTAAG-CAAAAGGTTGAACAAAT
66 ATGAACTTTCTCTGGAAATAGATGATCCATCAA-TGATGAATTTAAGTAAAAAGGTTGAACAAAT
*
43423 TCTTCTCA-T-T--ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACCTGG
*
43484 CAATGCTT-ATCCATTGAATGATGAATTTAAGCAAAAAGGTTGAACAAATTCTTCTCATTATGAA
194 CAATGCTTGATCCA-TCAATGATGAATTTAAGC-AAAAGGTTGAACAAATTCTTCTCATTATGAA
43548 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAT-TTGATCCAT
257 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAATGTTGATCCAT
43612 C-AAGTGATGAATTTAAGC-A
321 CGAA-TGATGAATTTAAGCGA
*
43631 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
43696 ATGAACTTTCTCTGGAAATA-CTGATCCATCGAATGATGAATTTAAGTAAAAAGGTTGAACAAAT
66 ATGAACTTTCTCTGGAAATAGATGATCCATC-AATGATGAATTTAAGTAAAAAGGTTGAACAAAT
* *
43760 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTTTCTCTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTAC-CTGG
** *
43825 -AAAACTTGATCCATCAAGTGATAAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
194 CAATGCTTGATCCATCAA-TGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
43889 TTCATCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCG
258 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCG
*
43954 AATGATGAATTCAAGCGA
323 AATGATGAATTTAAGCGA
* *
43972 AAA-GTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * * * ** *
44036 ATGAACTCGAC-CTGGAAATGTTGATGATGATCTATCTAT-TTCTATGATAGAGTCATGCAAAAG
66 ATGAACT-TTCTCTGGAAA---T-A-GATGATCCATCAATGATGAAT-TTA-AGT-A---AAAAG
* * *
44099 GTTGAACAAATTATTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
119 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * *
44164 ACTTGACCTGGCAATGC-TGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTC
184 ACTT-ACCTGGCAATGCTTGATCCATC-AATGATGAATTTAAGCAAAAGGTTGAACAAATTCTTC
*
44228 TCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TCTGGAAATG
247 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATG
* *
44291 TTGATCCATTGAATGATGGATTTAA
312 TTGATCCATCGAATGATGAATTTAA
44316 ATCTTTGCTA
Statistics
Matches: 609, Mismatches: 47, Indels: 46
0.87 0.07 0.07
Matches are distributed among these distances:
336 100 0.16
337 27 0.04
338 1 0.00
339 5 0.01
340 183 0.30
341 71 0.12
343 1 0.00
344 4 0.01
345 4 0.01
346 11 0.02
347 1 0.00
348 31 0.05
349 33 0.05
350 131 0.22
351 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (340 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATAGATGATCCATCAATGATGAATTTAAGTAAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACCTGGCA
ATGCTTGATCCATCAATGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCGAAT
GATGAATTTAAGCGA
Found at i:44741 original size:22 final size:22
Alignment explanation
Indices: 44716--44770 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
44706 GATAAAGCTT
*
44716 TCATCTTTGAAAAGAG-AATCTG
1 TCATCTTTGAAAAG-GTAATCTA
*
44738 TCATCTTTAAAAAGGTAATCTA
1 TCATCTTTGAAAAGGTAATCTA
44760 TCATCTTTGAA
1 TCATCTTTGAA
44771 GGGTGTAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGGTAATCTA
Found at i:47546 original size:114 final size:114
Alignment explanation
Indices: 47346--47565 Score: 343
Period size: 114 Copynumber: 1.9 Consensus size: 114
47336 GATCATGCAG
* * * * *
47346 TTCATCTTTCAATTCCAATGATTGGTTATGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGAGGTTCATACCAAACCAGATCAGAAAACTCAAAGA
*
47411 ACATTTCCAGAAGATGCTATTGGGTTTCCTTATTTCTACTATGAGCAAA
66 ACATTTCAAGAAGATGCTATTGGGTTTCCTTATTTCTACTATGAGCAAA
* *
47460 TTCATCTTTCAAATCTAATGATTGGTTTTGAGGTTCATACCAAACCAGATCAGAAAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGAGGTTCATACCAAACCAGATCAGAAAACTCAAAGA
*
47525 ACACTTT-AAGAAGATGCTATTGGGTTTTCTTATTTCTACTA
66 ACA-TTTCAAGAAGATGCTATTGGGTTTCCTTATTTCTACTA
47566 CGAGAACGTG
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 93 0.97
115 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTATGAGGTTCATACCAAACCAGATCAGAAAACTCAAAGA
ACATTTCAAGAAGATGCTATTGGGTTTCCTTATTTCTACTATGAGCAAA
Found at i:51795 original size:36 final size:36
Alignment explanation
Indices: 51718--51807 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
51708 GTAAATACGA
* *
51718 AAATGCATAA-ATGCAAAAATAAGAATGCAAACTGTG
1 AAATGCA-AAGATGCAAAAATAAGAATACAAAATGTG
* *
51754 TAATGCAAAGATGTAAAAAGTAAGAATACAAAATG-G
1 AAATGCAAAGATGCAAAAA-TAAGAATACAAAATGTG
* *
51790 AAATGCACAGATACAAAA
1 AAATGCAAAGATGCAAAA
51808 TGTAAATGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 2 0.05
36 29 0.66
37 13 0.30
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.18
Consensus pattern (36 bp):
AAATGCAAAGATGCAAAAATAAGAATACAAAATGTG
Found at i:54168 original size:21 final size:22
Alignment explanation
Indices: 54125--54184 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
54115 AAAATACTTG
54125 AAAATA-AAATAAAAATATTATA
1 AAAATATAAATAAAAATA-TATA
*
54147 AAAATATACATAAAAATA-ATA
1 AAAATATAAATAAAAATATATA
* *
54168 AATATATATATAAAAAT
1 AAAATATAAATAAAAAT
54185 TTTGAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.53
22 6 0.18
23 10 0.29
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATATAAATAAAAATATATA
Found at i:55014 original size:3 final size:3
Alignment explanation
Indices: 54999--55057 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
54989 TACTTATATA
* * **
54999 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
55043 AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT A
55058 TTGCAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:55066 original size:26 final size:28
Alignment explanation
Indices: 55007--55068 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
54997 TAAATAATAA
*
55007 AAATAATAATAATGAAATAATAATTAAAGC
1 AAATAATAATAATAAAATAATAATT--AGC
55037 -AATAATAATAATAAAATAAT-ATT-GC
1 AAATAATAATAATAAAATAATAATTAGC
55062 AAATAAT
1 AAATAAT
55069 GATTAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 6 0.20
28 3 0.10
29 19 0.63
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (28 bp):
AAATAATAATAATAAAATAATAATTAGC
Found at i:55290 original size:2 final size:2
Alignment explanation
Indices: 55283--55311 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55273 GATATTTACC
55283 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
55312 GCTGATAAGG
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:56625 original size:42 final size:42
Alignment explanation
Indices: 56558--56779 Score: 198
Period size: 42 Copynumber: 5.2 Consensus size: 42
56548 TTTGTGGAAA
** *
56558 AAAAACGCTGCAAAAGGTCATATCTATAGCGGCGTTTTTGTAAC
1 AAAAAC-C-GCAAAAGGTCGGATCTATAGCGGCATTTTTGTAAC
*
56602 AAAAACCGCAAAAGGTCGGATCTATAGCGTCATTTTT-TGAAC
1 AAAAACCGCAAAAGGTCGGATCTATAGCGGCATTTTTGT-AAC
** * * * * *
56644 AAACTCCGCAATAGGTTGAGATCTATAGCAGCATTTTCG-AAA
1 AAAAACCGCAAAAGGTCG-GATCTATAGCGGCATTTTTGTAAC
* ** *
56686 AAAACACCACAAAAGGTTAGATCTATTA-CGGCATTTTTGTAAT
1 AAAA-ACCGCAAAAGGTCGGATCTA-TAGCGGCATTTTTGTAAC
** *
56729 AAACGCCGCAAAAGGTCGGATCTATAGCGGCATTTTTGGAAC
1 AAAAACCGCAAAAGGTCGGATCTATAGCGGCATTTTTGTAAC
*
56771 AAACACCGC
1 AAAAACCGC
56780 TAATTACCGT
Statistics
Matches: 143, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
41 3 0.02
42 100 0.70
43 34 0.24
44 6 0.04
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (42 bp):
AAAAACCGCAAAAGGTCGGATCTATAGCGGCATTTTTGTAAC
Found at i:56699 original size:85 final size:84
Alignment explanation
Indices: 56560--56764 Score: 218
Period size: 85 Copynumber: 2.4 Consensus size: 84
56550 TGTGGAAAAA
* ** * * * * *
56560 AAACGCTGCAAAAGGTCATATCTATAGCGGCGTTTTTGTAACAAAAACCGCAAAAGGTCGGATCT
1 AAACGCCGCAAAAGGTCGGATCTATAGCGGCATTTTCGTAAAAAAAACCACAAAAGGTCAGATCT
*
56625 A-TAGCGTCATTTTT-TGAAC
66 ATTA-CGGCATTTTTGT-AAC
* * * * *
56644 AAACTCCGCAATAGGTTGAGATCTATAGCAGCATTTTCG-AAAAAAACACCACAAAAGGTTAGAT
1 AAACGCCGCAAAAGGTCG-GATCTATAGCGGCATTTTCGTAAAAAAA-ACCACAAAAGGTCAGAT
*
56708 CTATTACGGCATTTTTGTAAT
64 CTATTACGGCATTTTTGTAAC
56729 AAACGCCGCAAAAGGTCGGATCTATAGCGGCATTTT
1 AAACGCCGCAAAAGGTCGGATCTATAGCGGCATTTT
56765 TGGAACAAAC
Statistics
Matches: 98, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
84 36 0.37
85 59 0.60
86 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (84 bp):
AAACGCCGCAAAAGGTCGGATCTATAGCGGCATTTTCGTAAAAAAAACCACAAAAGGTCAGATCT
ATTACGGCATTTTTGTAAC
Found at i:62453 original size:15 final size:16
Alignment explanation
Indices: 62416--62452 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
62406 TAAACTAAAT
62416 GAAAAACCAACTTGAA
1 GAAAAACCAACTTGAA
62432 GAAAAACCAACTTGAA
1 GAAAAACCAACTTGAA
62448 GAAAA
1 GAAAA
62453 CTTACCTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.11
Consensus pattern (16 bp):
GAAAAACCAACTTGAA
Found at i:69851 original size:65 final size:63
Alignment explanation
Indices: 69734--69941 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 63
69724 TTTCAGAGTG
* * * **
69734 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCA-CAGT-CATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATT
69797 TC
62 TC
*
69799 ATGCATCGATGCACA-TACTATGCATCGATGCACTTAGAG-T-TTTATGAAAACATCGAATGCAT
1 ATGCATCGATGCACAGT-C-ATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCAT
*
69861 TTG
61 TTC
* *
69864 ATGCATCGATGCACCAGTCATGCATCGATGCAGTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCA-CAGTCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
69928 ATGCATCGATGCAC
1 ATGCATCGATGCAC
69942 TCTTAGTGAA
Statistics
Matches: 124, Mismatches: 9, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 48 0.39
65 62 0.50
66 6 0.05
67 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAGTCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
Found at i:75320 original size:44 final size:44
Alignment explanation
Indices: 75271--75367 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
75261 TTGTGCTTCA
* *
75271 TGCATCGATAC-ACTTAAAAGTGCATCGATGCATC-CCTTTGAATG
1 TGCATCGATACGACATAAAAGTGCACCGATGCA-CGCC-TTGAATG
* * *
75315 TGCATCGATACGCCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACGACATAAAAGTGCACCGATGCACGCCTTGAATG
75359 TGCATCGAT
1 TGCATCGAT
75368 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 28 0.61
45 18 0.39
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.26
Consensus pattern (44 bp):
TGCATCGATACGACATAAAAGTGCACCGATGCACGCCTTGAATG
Found at i:75356 original size:23 final size:23
Alignment explanation
Indices: 75290--75371 Score: 98
Period size: 23 Copynumber: 3.6 Consensus size: 23
75280 ACACTTAAAA
75290 GTGCATCGATGCATC-CCTTTGAAT
1 GTGCATCGATGCA-CGCC-TTGAAT
* *
75314 GTGCATCGAT--ACGCCATGAAG
1 GTGCATCGATGCACGCCTTGAAT
*
75335 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACGCCTTGAAT
75358 GTGCATCGATGCAC
1 GTGCATCGATGCAC
75372 AAGGCCATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 14 0.29
22 3 0.06
23 22 0.45
24 10 0.20
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (23 bp):
GTGCATCGATGCACGCCTTGAAT
Found at i:78065 original size:65 final size:63
Alignment explanation
Indices: 77948--78155 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 63
77938 TTTCAGAGTG
* * **
77948 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATT
78011 TC
62 TC
* *
78013 ATGCATCGATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCTTT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATT
*
78076 TG
62 TC
* * * *
78078 ATGCATCGATACACCAGCCATGCCTCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
78142 ATGCATCGATGCAC
1 ATGCATCGATGCAC
78156 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.39
65 64 0.53
66 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
Found at i:79553 original size:21 final size:21
Alignment explanation
Indices: 79513--79553 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
79503 TTTCTTAAAA
* * *
79513 TCATTTACTCAACATTTGAAC
1 TCATTTACACAAAATATGAAC
79534 TCATTTACACAAAATATGAA
1 TCATTTACACAAAATATGAA
79554 AACATTAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (21 bp):
TCATTTACACAAAATATGAAC
Found at i:80364 original size:35 final size:35
Alignment explanation
Indices: 80313--80391 Score: 140
Period size: 35 Copynumber: 2.3 Consensus size: 35
80303 AGTTTGATAT
* *
80313 AAGTATTGTAGAAACGAACTTTTAAAAACTTTTAA
1 AAGTGTTGTAGAAACGAACTTTTAAAAACGTTTAA
80348 AAGTGTTGTAGAAACGAACTTTTAAAAACGTTTAA
1 AAGTGTTGTAGAAACGAACTTTTAAAAACGTTTAA
80383 AAGTGTTGT
1 AAGTGTTGT
80392 GCAAAAAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (35 bp):
AAGTGTTGTAGAAACGAACTTTTAAAAACGTTTAA
Found at i:84357 original size:3 final size:3
Alignment explanation
Indices: 84349--84382 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
84339 ATTATTTATT
84349 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
84383 TAAATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:84822 original size:113 final size:113
Alignment explanation
Indices: 84705--84966 Score: 470
Period size: 113 Copynumber: 2.3 Consensus size: 113
84695 ATAGGGTCAT
* *
84705 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATTAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
* *
84770 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGGATTTGA
66 ATTATAAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGA
* *
84818 GCAAAAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
84883 ATTATAAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGA
66 ATTATAAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGA
84931 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTT
84967 TCTCTGGAAA
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 142 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
ATTATAAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGA
Found at i:84995 original size:73 final size:73
Alignment explanation
Indices: 84876--85039 Score: 310
Period size: 73 Copynumber: 2.2 Consensus size: 73
84866 TCAGATGAGT
* *
84876 TCTTCTCATTATAAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
1 TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
84941 GAACAAGC
66 GAACAAGC
84949 TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
1 TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
85014 GAACAAGC
66 GAACAAGC
85022 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
85040 CTTCTTCCTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 89 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (73 bp):
TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
GAACAAGC
Found at i:85088 original size:186 final size:184
Alignment explanation
Indices: 84763--85114 Score: 616
Period size: 186 Copynumber: 1.9 Consensus size: 184
84753 TCAAATTAGT
* *
84763 TCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGGATTTGAGCAAAAGATT
1 TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGATT
84828 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACT
66 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACT
84893 TTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
131 TTCTCTGGAAAAGTTGATCCAT--AGTGATGGATTTGAGCAAAAGGTTGAACAAGC
*
84949 TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
1 TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGATT
*
85014 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
66 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACT
* *
85079 CTT-TCTGGAAATGTTGATCCATTGTGATGGATTTGA
131 -TTCTCTGGAAAAGTTGATCCATAGTGATGGATTTGA
85115 ATCTTTGCTA
Statistics
Matches: 159, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
184 13 0.08
186 144 0.91
187 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (184 bp):
TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGATT
GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACT
TTCTCTGGAAAAGTTGATCCATAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
Found at i:86312 original size:18 final size:17
Alignment explanation
Indices: 86262--86312 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
86252 ATAAAAGAAT
*
86262 AAATTGAATTTCGAAAA
1 AAATTGAATTTAGAAAA
86279 TAAATTGAA--TA-AAAA
1 -AAATTGAATTTAGAAAA
*
86294 AAATTGAATTTAGAGAA
1 AAATTGAATTTAGAAAA
86311 AA
1 AA
86313 TAAACTTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 8 0.29
15 4 0.14
16 3 0.11
17 5 0.18
18 8 0.29
ACGTcount: A:0.59, C:0.02, G:0.12, T:0.27
Consensus pattern (17 bp):
AAATTGAATTTAGAAAA
Found at i:86680 original size:16 final size:17
Alignment explanation
Indices: 86659--86701 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
86649 TGACCCTCTC
86659 TTTTTTATTTTCTTCTT
1 TTTTTTATTTTCTTCTT
86676 TTTTTT-TCTTT-TTCTT
1 TTTTTTAT-TTTCTTCTT
86692 TTTTTTATTT
1 TTTTTTATTT
86702 CATTTGTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTATTTTCTTCTT
Found at i:86681 original size:19 final size:18
Alignment explanation
Indices: 86666--86702 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
86656 CTCTTTTTTA
86666 TTTTCTTCTTTTTTTTTCT
1 TTTTCTT-TTTTTTTTTCT
86685 TTTTCTTTTTTTTATTTC
1 TTTTCTTTTTTTT-TTTC
86703 ATTTGTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTCTTTTTTTTTTTCT
Found at i:86682 original size:13 final size:12
Alignment explanation
Indices: 86657--86695 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
86647 CTTGACCCTC
*
86657 TCTTTTTTATTT
1 TCTTTTTTTTTT
86669 TCTTCTTTTTTTT
1 TCTT-TTTTTTTT
86682 TCTTTTTCTTTTT
1 TCTTTTT-TTTTT
86695 T
1 T
86696 TTATTTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:90260 original size:9 final size:9
Alignment explanation
Indices: 90237--90267 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
90227 GAAAAATAAT
90237 GAATGTAAA
1 GAATGTAAA
90246 -AATGTAAA
1 GAATGTAAA
90254 GAATGTAAA
1 GAATGTAAA
90263 GAATG
1 GAATG
90268 ATTGCGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
GAATGTAAA
Found at i:94072 original size:15 final size:15
Alignment explanation
Indices: 94049--94080 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
94039 TGCAATGAAT
94049 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
94064 AATGCATGTATGCAA
1 AATGAATGTATGCAA
94079 AA
1 AA
94081 GGTATTGATC
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:96773 original size:3 final size:3
Alignment explanation
Indices: 96765--96805 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
96755 TATTTATTTT
*
96765 ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
96806 TAAATAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:97992 original size:5 final size:5
Alignment explanation
Indices: 97982--98360 Score: 667
Period size: 5 Copynumber: 78.4 Consensus size: 5
97972 TAAAACAATG
97982 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
98032 AT-AT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
98080 AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
98128 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-AAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
98177 ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
98225 ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
98272 ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
98321 ATAAT AT-AT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
98361 CTTAAATCCT
Statistics
Matches: 361, Mismatches: 0, Indels: 26
0.93 0.00 0.07
Matches are distributed among these distances:
3 4 0.01
4 40 0.11
5 317 0.88
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:98394 original size:9 final size:9
Alignment explanation
Indices: 98382--98408 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
98372 ATTAAAATAC
98382 TTTAAATTA
1 TTTAAATTA
98391 TTTAAATTA
1 TTTAAATTA
98400 TTTAAATTA
1 TTTAAATTA
98409 AAATATCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTAAATTA
Found at i:98938 original size:170 final size:170
Alignment explanation
Indices: 98653--98993 Score: 646
Period size: 170 Copynumber: 2.0 Consensus size: 170
98643 TGCAATTTTC
*
98653 AGAATCTAACATCCTGCACGGAAAATAAATCAAAACGAATAAATAAATTATAAAAAATAATAATT
1 AGAATCTAACATCCTGCACGGAAAATAAATCAAAACAAATAAATAAATTATAAAAAATAATAATT
*
98718 ATGAAATAATTTAAAAATAAAATAATAACTAAATAAATCACGGGCAACGGTGAAAAAGTATCCAA
66 ATGAAATAATTTAAAAATAAAATAATAACTAAATAAATCACGGACAACGGTGAAAAAGTATCCAA
98783 CACGTTTCGACAATGACTTTATGCACCACTAATTTACCTG
131 CACGTTTCGACAATGACTTTATGCACCACTAATTTACCTG
* *
98823 AGAATCTAACATTCTGCACGGAAAATAAATCAAAACAAATAAATAAGTTATAAAAAATAATAATT
1 AGAATCTAACATCCTGCACGGAAAATAAATCAAAACAAATAAATAAATTATAAAAAATAATAATT
98888 ATGAAATAATTTAAAAATAAAATAATAACTAAATAAATCACGGACAACGGTGAAAAAGTATCCAA
66 ATGAAATAATTTAAAAATAAAATAATAACTAAATAAATCACGGACAACGGTGAAAAAGTATCCAA
98953 CACGTTTCGACAATGACTTTATGCACCACTAATTTACCTG
131 CACGTTTCGACAATGACTTTATGCACCACTAATTTACCTG
98993 A
1 A
98994 TGAGTTCTTA
Statistics
Matches: 167, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 167 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (170 bp):
AGAATCTAACATCCTGCACGGAAAATAAATCAAAACAAATAAATAAATTATAAAAAATAATAATT
ATGAAATAATTTAAAAATAAAATAATAACTAAATAAATCACGGACAACGGTGAAAAAGTATCCAA
CACGTTTCGACAATGACTTTATGCACCACTAATTTACCTG
Found at i:109727 original size:14 final size:14
Alignment explanation
Indices: 109710--109739 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
109700 GCTTTACATT
*
109710 TTTCAATATTTTAA
1 TTTCAATACTTTAA
109724 TTTCAATACTTTAA
1 TTTCAATACTTTAA
109738 TT
1 TT
109740 ATTACATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTCAATACTTTAA
Found at i:110830 original size:28 final size:28
Alignment explanation
Indices: 110759--110824 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
110749 TAATCCTTTC
* *
110759 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATACTTATTA
110787 TTTTCATAATATTTATATATA-TTATT-
1 TTTTCATAATATTTATATATACTTATTA
110813 TTTT-ATTAATAT
1 TTTTCA-TAATAT
110825 CTTTATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 1 0.03
26 10 0.29
27 5 0.14
28 19 0.54
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTCATAATATTTATATATACTTATTA
Found at i:111336 original size:16 final size:16
Alignment explanation
Indices: 111315--111348 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
111305 ATTATTATTT
111315 TTCCCTCTCTGAATAA
1 TTCCCTCTCTGAATAA
111331 TTCCCTCTCTGAATAA
1 TTCCCTCTCTGAATAA
111347 TT
1 TT
111349 ACATGCGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.41
Consensus pattern (16 bp):
TTCCCTCTCTGAATAA
Found at i:112966 original size:14 final size:14
Alignment explanation
Indices: 112949--112996 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
112939 CATCCTTAGT
112949 TTTGCATTGTCGTA
1 TTTGCATTGTCGTA
*
112963 TTTGCATTTTC--A
1 TTTGCATTGTCGTA
*
112975 TTTGCATTGTTGTA
1 TTTGCATTGTCGTA
*
112989 TTTTCATT
1 TTTGCATT
112997 TGCATTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 10 0.36
14 18 0.64
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (14 bp):
TTTGCATTGTCGTA
Found at i:112989 original size:26 final size:26
Alignment explanation
Indices: 112949--113008 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
112939 CATCCTTAGT
*
112949 TTTGCATTGTCGTATTTGCATTTTCA
1 TTTGCATTGTCGTATTTGCATTTGCA
* *
112975 TTTGCATTGTTGTATTTTCATTTGCA
1 TTTGCATTGTCGTATTTGCATTTGCA
*
113001 TTTTCATT
1 TTTGCATT
113009 TGCATCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.58
Consensus pattern (26 bp):
TTTGCATTGTCGTATTTGCATTTGCA
Found at i:115983 original size:2 final size:2
Alignment explanation
Indices: 115971--116002 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
115961 ATCCTTTCAA
*
115971 AT AT AT GT 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
116003 CCCTTGTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116323 original size:27 final size:25
Alignment explanation
Indices: 116282--116339 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 25
116272 ATTCTCATTC
**
116282 AAAAAAAAGTGAAAAAAGTGAAAAAGA
1 AAAAAAAAGAAAAAAAAG-GAAAAA-A
116309 AAAAAAAAGAAAAAAAAGGAAAAAA
1 AAAAAAAAGAAAAAAAAGGAAAAAA
116334 AAAAAA
1 AAAAAA
116340 GAAAAATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 7 0.24
26 6 0.21
27 16 0.55
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (25 bp):
AAAAAAAAGAAAAAAAAGGAAAAAA
Found at i:116345 original size:10 final size:10
Alignment explanation
Indices: 116302--116345 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
116292 GAAAAAAGTG
116302 AAAAAGAAAA
1 AAAAAGAAAA
116312 AAAAAGAAAA
1 AAAAAGAAAA
*
116322 AAAAGGAAAA
1 AAAAAGAAAA
116332 AAAAA-AAAGA
1 AAAAAGAAA-A
116342 AAAA
1 AAAA
116346 TTGAGTCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 3 0.10
10 28 0.90
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:119469 original size:70 final size:71
Alignment explanation
Indices: 119298--119469 Score: 258
Period size: 75 Copynumber: 2.4 Consensus size: 71
119288 TTCACGTCAA
119298 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATAATGGCGCATTTTGAACG
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATAA----GCATTTTGAACG
*
119363 TCTGTATTAG
62 TCTATATTAG
119373 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATAA-CATTTTGAACGT-TC
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATAAGCATTTTGAACGTCT-
119436 ATATTAG
65 ATATTAG
* *
119443 TAAATGTTGGGGCATGCTGAAGGCCCA
1 CAAATGTTGGGGCATGCTGAAAGCCCA
119470 CATCATTATG
Statistics
Matches: 93, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
69 1 0.01
70 43 0.46
75 49 0.53
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (71 bp):
CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATAAGCATTTTGAACGTCTA
TATTAG
Found at i:120867 original size:22 final size:22
Alignment explanation
Indices: 120812--120886 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
120802 TCTACATTCC
120812 CCAAAGATGATAGATTCTCTCTT
1 CCAAAGATGATAGATTCTCT-TT
*
120835 --AAAAATGATAGATTCTCTTT
1 CCAAAGATGATAGATTCTCTTT
*
120855 CCAAAGATGATAGATTTTCTTT
1 CCAAAGATGATAGATTCTCTTT
*
120877 TCAAAGATGA
1 CCAAAGATGA
120887 AAGCTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.04
21 17 0.37
22 27 0.59
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
CCAAAGATGATAGATTCTCTTT
Found at i:121682 original size:36 final size:36
Alignment explanation
Indices: 121642--121835 Score: 138
Period size: 37 Copynumber: 5.3 Consensus size: 36
121632 GTTTTTCTTA
** *
121642 AAACAAAATGCATCTCGCTTGAGACAGTTTCACTCG
1 AAACAAAATTTATCTCGCTTGAGATAGTTTCACTCG
* * ** **
121678 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACAA-AATTTATCTCGCTTGAGATAGTTTCACTCG
* *
121715 AAACAAAATTTGTCTTGCTTGAGATAGTTTCACTCG
1 AAACAAAATTTATCTCGCTTGAGATAGTTTCACTCG
** * ** *
121751 AAACAACAATTTATCTTACTTGAGATTGTTTTTCT-T
1 AAACAA-AATTTATCTCGCTTGAGATAGTTTCACTCG
* ** * * *
121787 AATACAAGATTCGTCTCGCTTGAGACAATTTCACTAG
1 AA-ACAAAATTTATCTCGCTTGAGATAGTTTCACTCG
121824 AAACAGAAATTT
1 AAACA-AAATTT
121836 CCATCACTCG
Statistics
Matches: 117, Mismatches: 36, Indels: 9
0.72 0.22 0.06
Matches are distributed among these distances:
36 57 0.49
37 60 0.51
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (36 bp):
AAACAAAATTTATCTCGCTTGAGATAGTTTCACTCG
Found at i:121701 original size:37 final size:37
Alignment explanation
Indices: 121609--121781 Score: 152
Period size: 36 Copynumber: 4.7 Consensus size: 37
121599 GTTTTCAAAT
* * ** *
121609 AACAATTTATATCACTTGAGATTGTTTTTCTTAAAAC
1 AACAATTTATCTCACTTGAGATAGTTTCACTCAAAAC
** * * *
121646 AA-AATGCATCTCGCTTGAGACAGTTTCACTCGAAAC
1 AACAATTTATCTCACTTGAGATAGTTTCACTCAAAAC
* ** *
121682 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 AACAATTTATCTCACTTGAGATAGTTTCACTCAAAAC
* ** *
121719 AA-AATTTGTCTTGCTTGAGATAGTTTCACTCGAAAC
1 AACAATTTATCTCACTTGAGATAGTTTCACTCAAAAC
* *
121755 AACAATTTATCTTACTTGAGATTGTTT
1 AACAATTTATCTCACTTGAGATAGTTT
121782 TTCTTAATAC
Statistics
Matches: 104, Mismatches: 30, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
36 54 0.52
37 50 0.48
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (37 bp):
AACAATTTATCTCACTTGAGATAGTTTCACTCAAAAC
Found at i:121835 original size:73 final size:73
Alignment explanation
Indices: 121609--121828 Score: 341
Period size: 73 Copynumber: 3.0 Consensus size: 73
121599 GTTTTCAAAT
* * *
121609 AACAATTTATATCACTTGAGATTGTTTTTCTTAAAACAAAATGCATCTCGCTTGAGACAGTTTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
121674 CTCGAAAC
66 CTCGAAAC
* * *
121682 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTTGCTTGAGATAGTTTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
121747 CTCGAAAC
66 CTCGAAAC
* * * *
121755 AACAATTTATCTTACTTGAGATTGTTTTTCTTAATACAAGATTCGTCTCGCTTGAGACAATTTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
*
121820 CTAGAAAC
66 CTCGAAAC
121828 A
1 A
121829 GAAATTTCCA
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 133 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (73 bp):
AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
CTCGAAAC
Found at i:122209 original size:122 final size:123
Alignment explanation
Indices: 121850--122336 Score: 686
Period size: 122 Copynumber: 4.0 Consensus size: 123
121840 CACTCGATGG
* * * * *
121850 ATCAACATTTCCAGAGGAAGTTCGTAATGAGAAGAACTTATCTAAAGAGGAA-AGAGAAGTTCAT
1 ATCAACATTTCCAGAAG-TGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGA-AGAAGTTCAT
* * * *
121914 AATGAGAAGAACTTGTTCAACCTTTTGC-TCGATTCTATCCCAAAAGGAGATAGATCAAC
64 AATGAGAAGAACTTGTTCAACCTTTTGCATCGACTCTATCACAGAAGGAGATAGATCAGC
*
121973 ACCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGA-G--GAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * *
122035 TGAGAATAATTTATTCAACCTTTTG-ATCGACGCTATCACAGAAGGAGATAGATCAGC
66 TGAGAAGAACTTGTTCAACCTTTTGCATCGACTCTATCACAGAAGGAGATAGATCAGC
* *
122092 ATCAATATTTCCAGAAGTGTTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * *
122157 TGAGAAGAACTTGTTTAACCTTTTACAT-GACTCTATCATAGAAGGAGATAGATCAGT
66 TGAGAAGAACTTGTTCAACCTTTTGCATCGACTCTATCACAGAAGGAGATAGATCAGC
122214 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGGAA-AAGTTCATA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAA-GAAGAAGTTCATA
* *
122278 ATGAGAAGAACTTGTTCAACCTTTTGC-TTGACTCTATCACAGAAGGAGATATATCAGC
65 ATGAGAAGAACTTGTTCAACCTTTTGCATCGACTCTATCACAGAAGGAGATAGATCAGC
122336 A
1 A
122337 CATAATGAGA
Statistics
Matches: 324, Mismatches: 32, Indels: 17
0.87 0.09 0.05
Matches are distributed among these distances:
119 104 0.32
120 2 0.01
121 2 0.01
122 196 0.60
123 20 0.06
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (123 bp):
ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCATCGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:122389 original size:241 final size:241
Alignment explanation
Indices: 121894--122355 Score: 603
Period size: 241 Copynumber: 1.9 Consensus size: 241
121884 AACTTATCTA
* * *
121894 AAGAGGAA-AGAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCCAAA
1 AAGAGGAAGA-AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTCGACTCTATCACAAA
121958 AGGAGATAGATCAACACCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGA
65 AGGAGATAGATCAACACCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGA
* *
122023 AGAAGTTCATAATGAGAATAATTTATTCAACCTTTTGATCGACGCTATCACAGAAGGAGATAGAT
130 AGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGATCGACGCTATCACAGAAGGAGATAGAT
* **** ** * *
122088 CAGCATCAATATTTCCAGAAGTGTTCATAATGAGAAGAACTCATTTG
195 CAGCATCAATATATCCAGAAAAACTCATAATGAGAAGAACGAAGTTC
* * *
122135 AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTACAT-GACTCTATCATAGA
1 AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC-TCGACTCTATCACAAA
** *
122199 AGGAGATAGATCAGTATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGA
65 AGGAGATAGATCAACACCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGA
* * * *
122264 AGGAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATA
130 A-G--AAGTTCATAATGAGAAGAACTTATTCAACCTTTTGATCGACGCTATCACAGAAGGAGATA
* *
122329 TATCAGCA-C-ATA-AT-GAGAAAAACTCAT
192 GATCAGCATCAATATATCCAGAAAAACTCAT
122356 CTGAAGAGGA
Statistics
Matches: 194, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
240 8 0.04
241 118 0.61
242 6 0.03
243 1 0.01
244 61 0.31
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (241 bp):
AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTCGACTCTATCACAAAA
GGAGATAGATCAACACCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAA
GAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGATCGACGCTATCACAGAAGGAGATAGATC
AGCATCAATATATCCAGAAAAACTCATAATGAGAAGAACGAAGTTC
Found at i:122495 original size:139 final size:137
Alignment explanation
Indices: 122337--122678 Score: 447
Period size: 137 Copynumber: 2.5 Consensus size: 137
122327 TATATCAGCA
* *
122337 CATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCT
1 CATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
* * * *
122402 TAACTTGATTCATCACCTATGGAA-TTGAATGAAATAATAACCTCTCTTGAGGATCAATATTTTC
66 TAACTTAATTCATCACATAT-GAAGTTGAAT-AAAT-AGAACCTCTCTTGAGGATCAACATTTTC
122466 AG-AGAAAGTT
128 AGAAG-AAGTT
*
122476 CATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGCTCATAATGAGAAGAACTTGTTCAACCT
1 CATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
** * * * * *
122541 TGCCTTAATTCATCACATATGAAGTTGAATCAATGGCACCTCTTTTGAGGATCAGCATTTTCAGA
66 TAACTTAATTCATCACATATGAAGTTGAATAAATAGAACCTCTCTTGAGGATCAACATTTTCAGA
*
122606 AGGAGTT
131 AGAAGTT
* * * *
122613 CACAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAATCG-GAAGAACTTATTCAGCC
1 CATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT-GAGAAGAACTTGTTCAACC
122677 TT
65 TT
122679 TTACTCGACT
Statistics
Matches: 180, Mismatches: 20, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
137 87 0.48
138 9 0.05
139 84 0.47
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (137 bp):
CATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
TAACTTAATTCATCACATATGAAGTTGAATAAATAGAACCTCTCTTGAGGATCAACATTTTCAGA
AGAAGTT
Found at i:132211 original size:11 final size:10
Alignment explanation
Indices: 132189--132225 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
132179 AATTAAATTA
132189 TGTTTAAA-G
1 TGTTTAAATG
132198 TGTTTAAAATG
1 TGTTT-AAATG
132209 TGTTTAAAT-
1 TGTTTAAATG
132218 TGTTTAAA
1 TGTTTAAA
132226 ATATGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 13 0.50
10 7 0.27
11 6 0.23
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (10 bp):
TGTTTAAATG
Found at i:132212 original size:20 final size:20
Alignment explanation
Indices: 132189--132227 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
132179 AATTAAATTA
132189 TGTTTAAAGTGTTTAAAATG
1 TGTTTAAAGTGTTTAAAATG
*
132209 TGTTTAAATTGTTTAAAAT
1 TGTTTAAAGTGTTTAAAAT
132228 ATGAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
TGTTTAAAGTGTTTAAAATG
Found at i:134223 original size:22 final size:26
Alignment explanation
Indices: 134198--134250 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 26
134188 AAGTTTTGTG
134198 CTTAAAT-TCTATT-TTATTTT-AA-
1 CTTAAATCTCTATTGTTATTTTGAAC
*
134220 CTT-ACTCTCTATTGTTATTTTGAAC
1 CTTAAATCTCTATTGTTATTTTGAAC
134245 CTTAAA
1 CTTAAA
134251 GTTTGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 2 0.08
22 9 0.38
23 7 0.29
24 2 0.08
25 3 0.12
26 1 0.04
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (26 bp):
CTTAAATCTCTATTGTTATTTTGAAC
Found at i:134529 original size:2 final size:2
Alignment explanation
Indices: 134522--134547 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
134512 TTCTAAATTG
134522 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
134548 GAAATATTTT
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):
AT
Found at i:137953 original size:19 final size:19
Alignment explanation
Indices: 137913--137955 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
137903 GAGCCTTCTA
*
137913 GAACCAATCCAGTCAGATC
1 GAACCAATCCAGTCAGACC
*
137932 GAACCAATCCAGTCAGGCC
1 GAACCAATCCAGTCAGACC
137951 GAACC
1 GAACC
137956 GAGTCAAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.12
Consensus pattern (19 bp):
GAACCAATCCAGTCAGACC
Found at i:145045 original size:22 final size:22
Alignment explanation
Indices: 145019--145101 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
145009 TTAGTACAGA
145019 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* *
145041 GGGAA-CTGATTCCCCATTTGAAG
1 GGGAATC-GATACCCC-CTTGAAG
* * *
145064 GGGAACCGATTCCCCCTTGTAG
1 GGGAATCGATACCCCCTTGAAG
145086 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
145102 CTGGGGTTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.02
22 31 0.60
23 19 0.37
24 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:145065 original size:23 final size:23
Alignment explanation
Indices: 145035--145100 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
145025 CGATACCCCC
*
145035 TTGAAGGGGAACTGATTCCCCAT
1 TTGAAGGGGAACCGATTCCCCAT
*
145058 TTGAAGGGGAACCGATTCCCC-C
1 TTGAAGGGGAACCGATTCCCCAT
* * *
145080 TTGTAGGGGAATCGATACCCC
1 TTGAAGGGGAACCGATTCCCC
145101 CCTGGGGTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 18 0.47
23 20 0.53
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.23
Consensus pattern (23 bp):
TTGAAGGGGAACCGATTCCCCAT
Found at i:146659 original size:18 final size:19
Alignment explanation
Indices: 146633--146680 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
146623 AACGACTCCG
* *
146633 ACGATGAACCAGAAC-AGC
1 ACGAGGAACAAGAACGAGC
*
146651 ACGAGGAACAAGCACGAGC
1 ACGAGGAACAAGAACGAGC
146670 A-GAGGAACAAG
1 ACGAGGAACAAG
146681 CACAGCCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.46, C:0.23, G:0.29, T:0.02
Consensus pattern (19 bp):
ACGAGGAACAAGAACGAGC
Found at i:146681 original size:18 final size:17
Alignment explanation
Indices: 146646--146693 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 17
146636 ATGAACCAGA
146646 ACAGCACGAGGAACAAGC
1 ACAGCA-GAGGAACAAGC
146664 ACGAGCAGAGGAACAAGC
1 AC-AGCAGAGGAACAAGC
146682 ACAGCCAGAGGA
1 ACAG-CAGAGGA
146694 TCAAATGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.07
18 22 0.79
19 4 0.14
ACGTcount: A:0.44, C:0.25, G:0.31, T:0.00
Consensus pattern (17 bp):
ACAGCAGAGGAACAAGC
Found at i:150484 original size:19 final size:19
Alignment explanation
Indices: 150456--150495 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
150446 GACACCTCAG
150456 ATCGGATCGATTCACCCAC
1 ATCGGATCGATTCACCCAC
*
150475 ATCGGTTCGATTCACCCAC
1 ATCGGATCGATTCACCCAC
150494 AT
1 AT
150496 TGGTCTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (19 bp):
ATCGGATCGATTCACCCAC
Found at i:153487 original size:309 final size:306
Alignment explanation
Indices: 152923--153536 Score: 817
Period size: 309 Copynumber: 2.0 Consensus size: 306
152913 TAGCTCTTAC
*
152923 GAACAACCAAAATAAGCCAAGAGGGGGTGAATTTGCCTTTTAAGAATTTGTAGAAGCAACCGAAA
1 GAACAACCAAAATAAGCCAAGAGGGGGTGAATTGGCCTTTTAAGAATTTGTAGAAGCAACCGAAA
*
152988 AATAAAACATTTTGCACAACGATTTAGAGTGGTTTGACTTTCTAAACCAAAGTCTACAACATCCA
66 AATAAAACATTTTGCACAACGATTTAGAGTGGTTCGACTTTCTAAACCAAAGTCT--AACATCCA
* ** * * * * * * * *
153053 CTACTTTAGCATCATGGTATGGATTTATCAAATCCACTAGATTTTCTTACCTTTAAGGACAAGGT
129 CTACCTTAGCATCATACTAAGAATTTATAAAATCCACTAAATTGTCTTACCTTTAAAGAAAAGAT
* * *
153118 ATAACCTTACAAACACTTCAAGGTTATATCCCAAAACCTTGAATACACATTCCCCAAAGAGTAAG
194 ATAACCTTACAAACACTTCAAGGTTATATACCAAAACCTTGAATACACACTCCCCAAAGAGTAAA
* * *
153183 TACAAATTTAGCAAACAAAGTGAAAACCTCACAAGGCAAATATGTTTTAA
259 TACAAATTTAACAAACAAA-AGAAAACCTCAC-AGGAAAATATGTTTTAA
** * * *
153233 GAACAACTGAAATAAGCCAAGAGGGGGTGAATTGGCCTTTT-AGAAATTTGTGGGAGCAACC-AC
1 GAACAACCAAAATAAGCCAAGAGGGGGTGAATTGGCCTTTTAAG-AATTTGTAGAAGCAACCGAA
*
153296 AAATTAAA-ATTCTTGCACAACGATTTAGAGTGGTTCGACTTTCTAAACCAAAGTCT-ACATCCA
65 AAATAAAACATT-TTGCACAACGATTTAGAGTGGTTCGACTTTCTAAACCAAAGTCTAACATCCA
*
153359 CTACCTTAGCATCCATACTAAGAATTTCTAAAATCCACTAAATGTGT-TTACCTTTAAAGAAAAG
129 CTACCTTAGCAT-CATACTAAGAATTTATAAAATCCACTAAAT-TGTCTTACCTTTAAAGAAAAG
* * *
153423 ATGTAACCTTACAAACACTTCAAGGTT-TATACCAGAAAGCCTTGAATGCACACTCTCTCAAAGA
192 ATATAACCTTACAAACACTTCAAGGTTATATACCA-AAA-CCTTGAATACACACTC-CCCAAAGA
*
153487 GTAAATACAAATTTAACAAACAAAAGAAAATCTCACAGGAAAATATGTTT
254 GTAAATACAAATTTAACAAACAAAAGAAAACCTCACAGGAAAATATGTTT
153537 GCACAAATTA
Statistics
Matches: 267, Mismatches: 30, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
306 24 0.09
307 79 0.30
308 29 0.11
309 82 0.31
310 53 0.20
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (306 bp):
GAACAACCAAAATAAGCCAAGAGGGGGTGAATTGGCCTTTTAAGAATTTGTAGAAGCAACCGAAA
AATAAAACATTTTGCACAACGATTTAGAGTGGTTCGACTTTCTAAACCAAAGTCTAACATCCACT
ACCTTAGCATCATACTAAGAATTTATAAAATCCACTAAATTGTCTTACCTTTAAAGAAAAGATAT
AACCTTACAAACACTTCAAGGTTATATACCAAAACCTTGAATACACACTCCCCAAAGAGTAAATA
CAAATTTAACAAACAAAAGAAAACCTCACAGGAAAATATGTTTTAA
Found at i:153827 original size:12 final size:13
Alignment explanation
Indices: 153803--153835 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
153793 ATTTGGACTT
153803 TGAATTATTTTTGA
1 TGAATT-TTTTTGA
153817 T-AATTTTTTTGA
1 TGAATTTTTTTGA
153829 TGAATTT
1 TGAATTT
153836 GATTAAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 9 0.50
14 1 0.06
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (13 bp):
TGAATTTTTTTGA
Done.