Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168282.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_51, 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: 160351
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 1000 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:88785 original size:14 final size:15
Alignment explanation
Indices: 88766--88807 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
88756 CCGAGCCGAG
88766 CCGAGCCGTTCTTC-
1 CCGAGCCGTTCTTCT
88780 CCGAGCCG--CTTCT
1 CCGAGCCGTTCTTCT
88793 CCGAGCCGTT-TTCT
1 CCGAGCCGTTCTTCT
88807 C
1 C
88808 TTCCTTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.16
13 8 0.32
14 13 0.52
ACGTcount: A:0.07, C:0.43, G:0.21, T:0.29
Consensus pattern (15 bp):
CCGAGCCGTTCTTCT
Found at i:88798 original size:13 final size:14
Alignment explanation
Indices: 88766--88802 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
88756 CCGAGCCGAG
88766 CCGAGCCGTTCTTC
1 CCGAGCCGTTCTTC
88780 CCGAGCCG--CTTC
1 CCGAGCCGTTCTTC
88792 TCCGAGCCGTT
1 -CCGAGCCGTT
88803 TTCTCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.08, C:0.43, G:0.24, T:0.24
Consensus pattern (14 bp):
CCGAGCCGTTCTTC
Found at i:88860 original size:1 final size:1
Alignment explanation
Indices: 88854--88886 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
88844 CCGCTCCAGG
88854 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
88887 GACTTTGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:89362 original size:152 final size:152
Alignment explanation
Indices: 88913--89349 Score: 788
Period size: 152 Copynumber: 2.9 Consensus size: 152
88903 TTGATTTTTT
* * *
88913 TTTTCTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
*
88978 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGATTCAATTGAGAATAA
89043 TTTCCAATAATTAATTGGATGA
131 TTTCCAATAATTAATTGGATGA
89065 TTTTGTATTTTT-TTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTG
1 TTTTGT-TTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTG
89129 CATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTT-AATTGAGAAT
65 CATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGA-TTCAATTGAGAAT
89193 AATTTCCAATAATTAATTGGATGA
129 AATTTCCAATAATTAATTGGATGA
*
89217 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
*
89282 ATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGATTCAATTGAGAATAA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGATTCAATTGAGAATAA
89347 TTT
131 TTT
89350 TCAACAACTA
Statistics
Matches: 275, Mismatches: 6, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
151 7 0.03
152 262 0.95
153 6 0.02
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (152 bp):
TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGATTCAATTGAGAATAA
TTTCCAATAATTAATTGGATGA
Found at i:92614 original size:1 final size:1
Alignment explanation
Indices: 92610--92639 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
92600 GTAATTTTTG
92610 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
92640 CACCACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:93027 original size:7 final size:7
Alignment explanation
Indices: 93017--93079 Score: 81
Period size: 7 Copynumber: 8.9 Consensus size: 7
93007 AATGATGAAA
93017 AAAAAAG
1 AAAAAAG
*
93024 AAAAAAA
1 AAAAAAG
93031 AAAAAAG
1 AAAAAAG
93038 AAAAAAG
1 AAAAAAG
*
93045 AAAAAAA
1 AAAAAAG
93052 AAAAAAG
1 AAAAAAG
93059 AAAAAATG
1 AAAAAA-G
* *
93067 AGAAAAT
1 AAAAAAG
93074 AAAAAA
1 AAAAAA
93080 AGAGATTCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
7 42 0.88
8 6 0.12
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:93041 original size:21 final size:21
Alignment explanation
Indices: 93017--93082 Score: 105
Period size: 21 Copynumber: 3.0 Consensus size: 21
93007 AATGATGAAA
93017 AAAAAAGAAAAAAAAAAAAAG
1 AAAAAAGAAAAAAAAAAAAAG
93038 AAAAAAGAAAAAAAAAAAAAG
1 AAAAAAGAAAAAAAAAAAAAG
*
93059 AAAAAATGAGAAAATAAAAAAAG
1 AAAAAA-GA-AAAAAAAAAAAAG
93082 A
1 A
93083 GATTCAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
21 27 0.64
22 2 0.05
23 13 0.31
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAAAAAAG
Found at i:93080 original size:1 final size:1
Alignment explanation
Indices: 93014--93064 Score: 66
Period size: 1 Copynumber: 51.0 Consensus size: 1
93004 AAAAATGATG
* * * *
93014 AAAAAAAAAGAAAAAAAAAAAAAGAAAAAAGAAAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
93065 TGAGAAAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:93084 original size:15 final size:15
Alignment explanation
Indices: 93016--93082 Score: 93
Period size: 14 Copynumber: 4.6 Consensus size: 15
93006 AAATGATGAA
93016 AAAAAAAGAAAAAA-
1 AAAAAAAGAAAAAAG
93030 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
93045 AAAAAAA-AAAAAAG
1 AAAAAAAGAAAAAAG
* * *
93059 AAAAAATGAGAAAAT
1 AAAAAAAGAAAAAAG
93074 AAAAAAAGA
1 AAAAAAAGA
93083 GATTCAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
14 27 0.57
15 20 0.43
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:94356 original size:41 final size:39
Alignment explanation
Indices: 94240--94804 Score: 730
Period size: 41 Copynumber: 13.9 Consensus size: 39
94230 ATTTAGGAGT
94240 ATTTA-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAGAGGAGCA
94279 ATTTACTTTTCAAAGTCGTT-CCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCA
*
94317 ATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-T-CGTTGCCTCTGTTTAGAGGAGCA
* *
94358 ATTTATTTTTCAAAGTCGTGGTACCT-TGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
94398 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAGAGGAGCA
94438 ATTTACTTTTTCAAAGTTCCGTTGGTTACCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTTCAAAG-T-CGTT-G---CCTCTGTTTAGAGGAGCA
94484 ATTTA-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAGAGGAGCA
*
94523 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
94564 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAGAGGAGCA
*
94604 ATTTAC-TTTCAAAGTCGTGGTGCCTCTGTTGAG-GGAGCA
1 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
*
94643 ATTTACTTTTTAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
* *
94684 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
*
94725 ATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-T-CGTTGCCTCTG-TTTAGAGGAGCA
*
94767 ATTTAC-TTTCAAAAGTCGTTGAGTCTCTGTTTAGAGGA
1 ATTTACTTTTC-AAAGTCGTT--GCCTCTGTTTAGAGGA
94805 ACTTCGGCAA
Statistics
Matches: 481, Mismatches: 17, Indels: 54
0.87 0.03 0.10
Matches are distributed among these distances:
38 36 0.07
39 65 0.14
40 137 0.28
41 165 0.34
42 36 0.07
43 8 0.02
44 11 0.02
46 23 0.05
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.39
Consensus pattern (39 bp):
ATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:94614 original size:80 final size:81
Alignment explanation
Indices: 94240--94804 Score: 866
Period size: 81 Copynumber: 7.0 Consensus size: 81
94230 ATTTAGGAGT
94240 ATTTA-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--T-CC
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACC
94301 TCTGTTTAGAGGAGCA
66 TCTGTTTAGAGGAGCA
* *
94317 ATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTAC
1 ATTTACTTTTCAAAGTT-CGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTAC
94382 CT-TGTTTAGAGGAGCA
65 CTCTGTTTAGAGGAGCA
94398 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGTTCCGTTGG
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTAC-TTTTCAAAG-T-CG-TGG
94463 TTACCTCTGTTTAGAGGAGCA
62 -TACCTCTGTTTAGAGGAGCA
94484 ATTTA-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACC
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACC
94548 TCTGTTTAGAGGAGCA
66 TCTGTTTAGAGGAGCA
*
94564 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCAAAGTCGTGGTGCC
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACC
*
94628 TCTGTTGAG-GGAGCA
66 TCTGTTTAGAGGAGCA
*
94643 ATTTACTTTTTAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTA
1 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTA
*
94707 CCTCTGTTGAGAGGAGCA
64 CCTCTGTTTAGAGGAGCA
*
94725 ATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTTAGAGGAGCAATTTAC-TTTCAAAAGTCGTTGA
1 ATTTACTTTTCAAAGTT-CGTTGCCTCTG-TTTAGAGGAGCAATTTACTTTTC-AAAGTCG-TG-
94789 GT--CTCTGTTTAGAGGA
61 GTACCTCTGTTTAGAGGA
94805 ACTTCGGCAA
Statistics
Matches: 456, Mismatches: 10, Indels: 38
0.90 0.02 0.08
Matches are distributed among these distances:
77 5 0.01
78 15 0.03
79 61 0.13
80 104 0.23
81 109 0.24
82 37 0.08
83 42 0.09
84 17 0.04
85 47 0.10
86 19 0.04
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.39
Consensus pattern (81 bp):
ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACC
TCTGTTTAGAGGAGCA
Found at i:94831 original size:9 final size:9
Alignment explanation
Indices: 94813--94882 Score: 80
Period size: 8 Copynumber: 8.3 Consensus size: 9
94803 GAACTTCGGC
94813 AAAAAA-AA
1 AAAAAACAA
94821 AAAAAACAA
1 AAAAAACAA
94830 AAAAAAC-A
1 AAAAAACAA
94838 AAAAAAC--
1 AAAAAACAA
94845 -AAAAACAA
1 AAAAAACAA
*
94853 AAAAATCAA
1 AAAAAACAA
94862 AAAAAA-AA
1 AAAAAACAA
94870 AAAAAATCAA
1 AAAAAA-CAA
94880 AAA
1 AAA
94883 TAAAAATGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
6 6 0.11
8 22 0.41
9 21 0.39
10 5 0.09
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.03
Consensus pattern (9 bp):
AAAAAACAA
Found at i:94843 original size:23 final size:23
Alignment explanation
Indices: 94814--94872 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
94804 AACTTCGGCA
94814 AAAAAAAAAAAAACAAAAAAAAC
1 AAAAAAAAAAAAACAAAAAAAAC
* *
94837 AAAAAAACAAAAACAAAAAAATC
1 AAAAAAAAAAAAACAAAAAAAAC
94860 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
94873 AAATCAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.90, C:0.08, G:0.00, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAAAAACAAAAAAAAC
Found at i:94848 original size:32 final size:33
Alignment explanation
Indices: 94812--94888 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 33
94802 GGAACTTCGG
*
94812 CAAAAAAAAAAAAAACAAAAAAAACAAAAAAA-
1 CAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAT
* *
94844 CAAAAACAAAAAAATCAAAAAAAAAAAAAAAAT
1 CAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAT
*
94877 CAAAAATAAAAA
1 CAAAAAAAAAAA
94889 TGTTGAGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 29 0.73
33 11 0.28
ACGTcount: A:0.87, C:0.09, G:0.00, T:0.04
Consensus pattern (33 bp):
CAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAT
Found at i:94888 original size:1 final size:1
Alignment explanation
Indices: 94813--94875 Score: 72
Period size: 1 Copynumber: 63.0 Consensus size: 1
94803 GAACTTCGGC
* * * * **
94813 AAAAAAAAAAAAAACAAAAAAAACAAAAAAACAAAAACAAAAAAATCAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
94876 TCAAAAATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.90, C:0.08, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:95168 original size:10 final size:10
Alignment explanation
Indices: 95140--95185 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
95130 ATATGTATAT
95140 TTATTTA-TA
1 TTATTTATTA
*
95149 GTTATATATTTA
1 -TTATTTA-TTA
95161 TTA-TTATTA
1 TTATTTATTA
95170 TTATTTATTA
1 TTATTTATTA
95180 TTATTT
1 TTATTT
95186 TTGTAAGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 6 0.19
10 20 0.65
11 3 0.10
12 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATTTATTA
Found at i:95789 original size:20 final size:20
Alignment explanation
Indices: 95766--95809 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
95756 TGCCCAGTTT
*
95766 CCGGCGAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
95786 CCGGCAAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
95806 CCGG
1 CCGG
95810 TGAATTTCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.32, G:0.25, T:0.05
Consensus pattern (20 bp):
CCGGCAAAGAATCCCAGAAA
Found at i:111253 original size:13 final size:13
Alignment explanation
Indices: 111237--111275 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
111227 TTCATCAATT
111237 TAAATTTTTAATA
1 TAAATTTTTAATA
*
111250 TAAATTTTT-ATT
1 TAAATTTTTAATA
111262 TAATATTTTTAATA
1 TAA-ATTTTTAATA
111276 AAAAAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 15 0.68
14 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATTTTTAATA
Found at i:111875 original size:27 final size:27
Alignment explanation
Indices: 111823--111873 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
111813 TGATATAAAA
* * *
111823 TAATTTTATGAATTTTCAATTATTTAT
1 TAATTTTATAAATATTAAATTATTTAT
111850 TAATTTTATAAATATTAAA-TATTT
1 TAATTTTATAAATATTAAATTATTT
111874 TAAAATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
TAATTTTATAAATATTAAATTATTTAT
Found at i:121186 original size:15 final size:14
Alignment explanation
Indices: 121168--121224 Score: 62
Period size: 15 Copynumber: 4.0 Consensus size: 14
121158 TGTATTTAAG
121168 TTTTTTTTATTTTC
1 TTTTTTTTATTTTC
*
121182 -TTTTTTTATTTTGA
1 TTTTTTTTATTTT-C
*
121196 TTTTTTTGATTTATC
1 TTTTTTTTATTT-TC
*
121211 TATTTTTTATTTTC
1 TTTTTTTTATTTTC
121225 ATTTAATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 12 0.34
14 2 0.06
15 20 0.57
16 1 0.03
ACGTcount: A:0.12, C:0.05, G:0.04, T:0.79
Consensus pattern (14 bp):
TTTTTTTTATTTTC
Found at i:121217 original size:30 final size:28
Alignment explanation
Indices: 121168--121228 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 28
121158 TGTATTTAAG
* *
121168 TTTTTTTTATTTTCTTTTTTTATTTTGA
1 TTTTTTTGATTTTCTTTTTTTATTTTCA
121196 TTTTTTTGATTTATCTATTTTTTATTTTCA
1 TTTTTTTGATTT-TCT-TTTTTTATTTTCA
121226 TTT
1 TTT
121229 AATTATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 11 0.38
29 3 0.10
30 15 0.52
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (28 bp):
TTTTTTTGATTTTCTTTTTTTATTTTCA
Found at i:121707 original size:16 final size:16
Alignment explanation
Indices: 121678--121731 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
121668 TAAATACTAA
121678 TAAATAAATAAAAATAT
1 TAAA-AAATAAAAATAT
*
121695 TGATAAAATAAAAATAT
1 T-AAAAAATAAAAATAT
121712 TAAAAAATAAAAATAAT
1 TAAAAAATAAAAAT-AT
121729 TAA
1 TAA
121732 TTAAGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 12 0.36
17 19 0.58
18 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
TAAAAAATAAAAATAT
Found at i:123393 original size:19 final size:19
Alignment explanation
Indices: 123371--123407 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
123361 ACTTGTAATC
*
123371 TTTTTAATATTAAACTATA
1 TTTTTAATACTAAACTATA
*
123390 TTTTTCATACTAAACTAT
1 TTTTTAATACTAAACTAT
123408 TATATATAAA
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:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTAATACTAAACTATA
Found at i:123560 original size:20 final size:20
Alignment explanation
Indices: 123535--123572 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
123525 TAAATAATAA
*
123535 AAAATAATTATTTTAAAAAT
1 AAAATAATAATTTTAAAAAT
123555 AAAATAATAATTTTAAAA
1 AAAATAATAATTTTAAAA
123573 TAATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATAATAATTTTAAAAAT
Found at i:123574 original size:19 final size:19
Alignment explanation
Indices: 123535--123588 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
123525 TAAATAATAA
*
123535 AAAATAATTATTTTAAAAAT
1 AAAATAATAATTTT-AAAAT
123555 AAAATAATAATTTTAAAAT
1 AAAATAATAATTTTAAAAT
* *
123574 -AATTAAAAATTTTAA
1 AAAATAATAATTTTAA
123589 TATATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 13 0.42
19 5 0.16
20 13 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAATAATTTTAAAAT
Found at i:125099 original size:2 final size:2
Alignment explanation
Indices: 125092--125121 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
125082 GTTTTAATTA
*
125092 AT AT AT AT AC 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
125122 TTGTATGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:127567 original size:22 final size:20
Alignment explanation
Indices: 127541--127582 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
127531 ATGAAATAAT
127541 ATTTTAATTTAATATAATAAAA
1 ATTTTAATTT--TATAATAAAA
*
127563 ATTTTTATTTTATAATAAAA
1 ATTTTAATTTTATAATAAAA
127583 TTATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTAATTTTATAATAAAA
Found at i:127638 original size:17 final size:17
Alignment explanation
Indices: 127618--127657 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
127608 TATTATGAAC
*
127618 TAAAAATTATTATTTTA
1 TAAAAATTATTATTATA
**
127635 TAAATTTTATTATTATA
1 TAAAAATTATTATTATA
127652 TAAAAA
1 TAAAAA
127658 ATTAATTAAC
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAAAATTATTATTATA
Found at i:127842 original size:19 final size:20
Alignment explanation
Indices: 127820--127862 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
127810 TTTTACATAA
*
127820 AAATAATTTATTGATTTT-T
1 AAATAATTTATTAATTTTAT
*
127839 AAATTATTTATTAATTTTAT
1 AAATAATTTATTAATTTTAT
127859 AAAT
1 AAAT
127863 GTTAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AAATAATTTATTAATTTTAT
Found at i:128511 original size:18 final size:18
Alignment explanation
Indices: 128488--128523 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
128478 TATATGATAG
*
128488 ATTTTTAAAAATTTATTA
1 ATTTTTAAAAATATATTA
*
128506 ATTTTTATAAATATATTA
1 ATTTTTAAAAATATATTA
128524 TTATAAAATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTAAAAATATATTA
Found at i:129586 original size:21 final size:19
Alignment explanation
Indices: 129562--129600 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
129552 TAAAATCAAT
129562 AATTTGATTATAAATTTTTAG
1 AATTT-ATT-TAAATTTTTAG
*
129583 AATTTATTTATATTTTTA
1 AATTTATTTAAATTTTTA
129601 AAATCGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
AATTTATTTAAATTTTTAG
Found at i:130862 original size:17 final size:17
Alignment explanation
Indices: 130842--130885 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
130832 TATTATGAAT
*
130842 TAAAAATTATTATTTTA
1 TAAAAATTATTATTATA
**
130859 TAAATTTTATTATTATA
1 TAAAAATTATTATTATA
130876 TAAATAATTA
1 TAAA-AATTA
130886 ACAACTAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAAAATTATTATTATA
Found at i:131068 original size:20 final size:20
Alignment explanation
Indices: 131040--131086 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
131030 ATTTGACATA
*
131040 AAATAATTTATGAATTTTTT
1 AAATAATTTATGAATTTTAT
* *
131060 AAATTATTTATTAATTTTAT
1 AAATAATTTATGAATTTTAT
131080 AAA-AATT
1 AAATAATT
131087 AAATAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATAATTTATGAATTTTAT
Found at i:134001 original size:13 final size:12
Alignment explanation
Indices: 133965--134016 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
133955 GGTAAGCCCA
133965 ATTTTATTTTAT
1 ATTTTATTTTAT
*
133977 ATTTT-TGTTAT
1 ATTTTATTTTAT
133988 -TTTTATTTTAT
1 ATTTTATTTTAT
*
133999 ATTTTATGTATAT
1 ATTTTAT-TTTAT
134012 ATTTT
1 ATTTT
134017 CCTTTATATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 4 0.12
11 10 0.29
12 11 0.32
13 9 0.26
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (12 bp):
ATTTTATTTTAT
Found at i:134022 original size:25 final size:25
Alignment explanation
Indices: 133965--134039 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 25
133955 GGTAAGCCCA
*
133965 ATTTTATTTTATATTTT-TGT-TAT
1 ATTTTACTTTATATTTTATGTATAT
*
133988 -TTTTATTTTATATTTTATGTATAT
1 ATTTTACTTTATATTTTATGTATAT
* ** *
134012 ATTTTCCTTTATATCCTATGTATTT
1 ATTTTACTTTATATTTTATGTATAT
134037 ATT
1 ATT
134040 ATTTATTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 16 0.36
23 3 0.07
24 3 0.07
25 22 0.50
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (25 bp):
ATTTTACTTTATATTTTATGTATAT
Found at i:134135 original size:24 final size:24
Alignment explanation
Indices: 134108--134208 Score: 93
Period size: 24 Copynumber: 4.2 Consensus size: 24
134098 ATTTTTTATT
*
134108 TTATATGTATT-TTTATTTATCTAA
1 TTATAT-TATTATTTATTTATCTTA
*
134132 TTATA-TATTTATTTATCTGT-TATTA
1 TTATATTA-TTATTTAT-T-TATCTTA
134157 TTATTATTATT-TTTATTTATCTTA
1 TTA-TATTATTATTTATTTATCTTA
* *
134181 TAATATTATTATTGATTTATCTTA
1 TTATATTATTATTTATTTATCTTA
134205 TTAT
1 TTAT
134209 TATTTTTCTA
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
22 2 0.03
23 10 0.16
24 32 0.51
25 12 0.19
26 5 0.08
27 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (24 bp):
TTATATTATTATTTATTTATCTTA
Found at i:134177 original size:29 final size:29
Alignment explanation
Indices: 134131--134198 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
134121 TATTTATCTA
* *
134131 ATTA-TATATTTATTTATCTGT-TATTATT
1 ATTATTATTTTTATTTATCT-TATAATATT
134159 ATTATTATTTTTATTTATCTTATAATATT
1 ATTATTATTTTTATTTATCTTATAATATT
134188 ATTATTGATTT
1 ATTATT-ATTT
134199 ATCTTATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 5 0.14
29 26 0.74
30 4 0.11
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (29 bp):
ATTATTATTTTTATTTATCTTATAATATT
Found at i:134205 original size:16 final size:15
Alignment explanation
Indices: 134115--134228 Score: 60
Period size: 15 Copynumber: 7.7 Consensus size: 15
134105 ATTTTATATG
*
134115 TATTTTTATTTATCT
1 TATTATTATTTATCT
*
134130 AATTATATATTTAT-T
1 TATTAT-TATTTATCT
* *
134145 TATCTGTTA-TTATTAT
1 TAT-TATTATTTA-TCT
134161 TATTATT-TTTAT-T
1 TATTATTATTTATCT
* * *
134174 TA-TCTTA-TAATAT
1 TATTATTATTTATCT
134187 TATTATTGATTTATCT
1 TATTATT-ATTTATCT
*
134203 TATTATTATTTTTCT
1 TATTATTATTTATCT
*
134218 AATTATCTATT
1 TATTAT-TATT
134229 AATTTTTTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
12 6 0.08
13 6 0.08
14 7 0.09
15 29 0.38
16 28 0.37
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTATTATTTATCT
Found at i:135160 original size:17 final size:16
Alignment explanation
Indices: 135127--135232 Score: 81
Period size: 16 Copynumber: 6.5 Consensus size: 16
135117 TTAGATTAGG
* *
135127 TTTATTTAATATTATT
1 TTTATTTTATTTTATT
135143 TTTATCTTTATTTTATT
1 TTTAT-TTTATTTTATT
* *
135160 TTTATTTTTTTTTACT
1 TTTATTTTATTTTATT
** *
135176 TTTCCTTT-TTTTATA
1 TTTATTTTATTTTATT
*
135191 TTTA-TTTATTTTCACT
1 TTTATTTTATTTT-ATT
*
135207 TTTATTTTGTTTTATT
1 TTTATTTTATTTTATT
135223 ATTCTATTTT
1 -TT-TATTTT
135233 CTTTAAATAA
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
14 3 0.04
15 12 0.17
16 27 0.38
17 23 0.32
18 6 0.08
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.75
Consensus pattern (16 bp):
TTTATTTTATTTTATT
Found at i:135178 original size:6 final size:5
Alignment explanation
Indices: 135127--135222 Score: 61
Period size: 5 Copynumber: 18.2 Consensus size: 5
135117 TTAGATTAGG
* * *
135127 TTTAT TTAAT ATTATT TTTAT CTTTAT TTTATT TTTAT TTTTT TTTACT
1 TTTAT TTTAT TTTA-T TTTAT -TTTAT TTTA-T TTTAT TTTAT TTTA-T
** *
135176 TTTCC TTT-T TTTAT ATTTA- TTTAT TTTCACT TTTAT TTTGT TTTAT
1 TTTAT TTTAT TTTAT -TTTAT TTTAT TTT-A-T TTTAT TTTAT TTTAT
135222 T
1 T
135223 ATTCTATTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
4 7 0.10
5 36 0.51
6 24 0.34
7 4 0.06
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:135186 original size:25 final size:25
Alignment explanation
Indices: 135158--135209 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
135148 CTTTATTTTA
* *
135158 TTTTTATTTTTTTTTACTTTTC-CTT
1 TTTTTATATTTATTTA-TTTTCACTT
135183 TTTTTATATTTATTTATTTTCACTT
1 TTTTTATATTTATTTATTTTCACTT
135208 TT
1 TT
135210 ATTTTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTATATTTATTTATTTTCACTT
Found at i:135195 original size:31 final size:32
Alignment explanation
Indices: 135142--135232 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 32
135132 TTAATATTAT
* *
135142 TTTTATCTTTATTTTATTTTTATTTTTTTTTAC
1 TTTTA-CTTTATTTTATATTTATTTTTTTTCAC
* *
135175 TTTTCCTTT-TTTTATATTTATTTATTTTCAC
1 TTTTACTTTATTTTATATTTATTTTTTTTCAC
* *
135206 TTTTATTTTGTTTTATTATTCTATTTT
1 TTTTACTTTATTTTA-TATT-TATTTT
135233 CTTTAAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
31 26 0.54
32 9 0.19
33 8 0.17
34 5 0.10
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (32 bp):
TTTTACTTTATTTTATATTTATTTTTTTTCAC
Found at i:135330 original size:59 final size:57
Alignment explanation
Indices: 135255--135645 Score: 419
Period size: 59 Copynumber: 6.6 Consensus size: 57
135245 ATAAAAATAT
135255 ATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAA
1 ATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAA
** * * *
135312 AGGGGTTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCTAAAAA
1 A--TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTT-C-AAAAA
* * * **
135374 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTTTAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-ATTTCAAAAA
* ** * **
135432 AGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAATTTTTGAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAA-TTTCAAAAA
*
135491 ATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTTCAAAAAA
1 ATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTT-AAAAATAAAATTTC-AAAAA
* * * **
135550 ATAATTTTTTGATGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAGCTTCAAAAGA
1 AT-A-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAA-A
135610 ATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCC
1 ATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCC
135646 CTACACAAAA
Statistics
Matches: 282, Mismatches: 35, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
57 2 0.01
58 77 0.27
59 98 0.35
60 66 0.23
61 32 0.11
62 7 0.02
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (57 bp):
ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAA
Found at i:135644 original size:119 final size:114
Alignment explanation
Indices: 135255--135645 Score: 521
Period size: 119 Copynumber: 3.3 Consensus size: 114
135245 ATAAAAATAT
* *
135255 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAGGGGTTT
1 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA--GATTT
* *
135320 TTGAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCTAAAAA
64 TTGAAGAAAAGTTGAAAGTATCAATTTTCC-TCAAAATTAAAGTTT-C-AAAAA
* * **
135374 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTTTAAAAAGATTTT
1 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTTCAAAAAAGATTTT
* * * **
135439 TGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAATTTTTGAAAA
65 TGAAGAAAAGTTGAAAGTATCAATTTTCCTCAAAATT--AAAGTTTCAAAAA
*
135491 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTTCAAAAAAATAATT
1 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTT-AAAAATAAATTTTC-AAAAAA-GA-T
* *
135556 TTTTGATGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAGCTTCAAAAGA
62 TTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAGTTTCAAAA-A
135610 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCC
1 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCC
135646 CTACACAAAA
Statistics
Matches: 240, Mismatches: 24, Indels: 16
0.86 0.09 0.06
Matches are distributed among these distances:
117 49 0.20
118 55 0.23
119 89 0.37
120 47 0.20
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (114 bp):
ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGATTTTT
GAAGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAGTTTCAAAAA
Found at i:140986 original size:41 final size:41
Alignment explanation
Indices: 140843--141227 Score: 476
Period size: 41 Copynumber: 9.2 Consensus size: 41
140833 GATTGTCAAT
*
140843 GAGCAATTTATTTTCCAAAGTTTCGT--TGCCTCTGTTTAGAG
1 GAGCAATTTACTTTCCAAAG--TCGTGGTGCCTCTGTTTAGAG
140884 GAGCAATTTACTTTCTCAAAGTTTCGT--TGCCTCTGTTTAGAGG
1 GAGCAATTTACTTTC-CAAAG--TCGTGGTGCCTCTGTTTAGA-G
* *
140927 CAGAGCAGTTTACTTTCCAAAGTCGTAGTGCCTCTGTTTAGAG
1 --GAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
*
140970 GAGCAATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
* * *
141011 GAGCAATTTATTTTCCCAAAGTCGTGGTGCCTTTGTTTAAAG
1 GAGCAATTTACTTT-CCAAAGTCGTGGTGCCTCTGTTTAGAG
* *
141053 GAGCAATTTATTTTCCAAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
141094 GAGCAATTTACTTTCCCAAAGTTACGT--TGCCTCTGTTTAGAG
1 GAGCAATTTACTTT-CCAAAG-T-CGTGGTGCCTCTGTTTAGAG
*
141136 GAGCAATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
* * * * *
141177 GAGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
1 GAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
*
141218 GAGCCATTTA
1 GAGCAATTTA
141228 TGTTTTTCAA
Statistics
Matches: 310, Mismatches: 22, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
39 2 0.01
40 1 0.00
41 167 0.54
42 102 0.33
43 3 0.01
44 21 0.07
45 14 0.05
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (41 bp):
GAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
Found at i:141058 original size:83 final size:81
Alignment explanation
Indices: 140843--141227 Score: 497
Period size: 83 Copynumber: 4.6 Consensus size: 81
140833 GATTGTCAAT
140843 GAGCAATTTATTTTCCAAAGTTTCGT-TGCCTCTGTTTAGAGGAGCAATTTACTTTCTCAAAGT-
1 GAGCAATTTATTTTCCAAAG--TCGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTC-CAAAGTC
* *
140906 TTCGTTGCCTCTGTTTAGAGG
63 AT-GGTGCCTCTGTTTAGA-G
* *
140927 CAGAGCAGTTTACTTTCCAAAGTCGTAGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
1 --GAGCAATTTATTTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
140992 ATGGTGCCTCTGTTTAGAG
63 ATGGTGCCTCTGTTTAGAG
* * * **
141011 GAGCAATTTATTTTCCCAAAGTCGTGGTGCCTTTGTTTAAAGGAGCAATTTATTTTCCAAAGTTG
1 GAGCAATTTATTTT-CCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCA
141076 TGGTGCCTCTGTTTAGAG
64 TGGTGCCTCTGTTTAGAG
*
141094 GAGCAATTTACTTTCCCAAAGTTACGT-TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
1 GAGCAATTTA-TTTTCCAAAG-T-CGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
141158 ATGGTGCCTCTGTTTAGAG
63 ATGGTGCCTCTGTTTAGAG
* * * *
141177 GAGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTA
1 GAGCAATTTATTTTCCAAAGTCG-TGTGCCTCTGTTTAGAGGAGCAATTTA
141228 TGTTTTTCAA
Statistics
Matches: 267, Mismatches: 23, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
80 2 0.01
81 2 0.01
82 42 0.16
83 139 0.52
84 9 0.03
85 24 0.09
86 49 0.18
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (81 bp):
GAGCAATTTATTTTCCAAAGTCGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCATG
GTGCCTCTGTTTAGAG
Found at i:141282 original size:1 final size:1
Alignment explanation
Indices: 141272--141359 Score: 59
Period size: 1 Copynumber: 88.0 Consensus size: 1
141262 AGCTTTGGTC
* * * * * * * * * *
141272 AAAAACAAAAAAACAAACAAAAACAAAAAAAACAAAAAAATAAAAAAAACAAACAAAAAACAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
141337 AAAAAACAAACAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
141360 TGAAAATGTT
Statistics
Matches: 61, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.85, C:0.14, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:141310 original size:11 final size:11
Alignment explanation
Indices: 141272--141359 Score: 92
Period size: 11 Copynumber: 8.1 Consensus size: 11
141262 AGCTTTGGTC
141272 AAAAACAAAAA
1 AAAAACAAAAA
141283 AACAAACAAAAA
1 AA-AAACAAAAA
*
141295 CAAAAA-AAACA
1 -AAAAACAAAAA
*
141306 AAAAA-ATAAA
1 AAAAACAAAAA
*
141316 AAAAACAAACA
1 AAAAACAAAAA
*
141327 AAAAACAAACA
1 AAAAACAAAAA
*
141338 AAAAAC-AAAC
1 AAAAACAAAAA
141348 AAAAACAAAAA
1 AAAAACAAAAA
141359 A
1 A
141360 TGAAAATGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
10 21 0.32
11 30 0.46
12 12 0.18
13 2 0.03
ACGTcount: A:0.85, C:0.14, G:0.00, T:0.01
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:141316 original size:22 final size:21
Alignment explanation
Indices: 141272--141359 Score: 108
Period size: 21 Copynumber: 4.1 Consensus size: 21
141262 AGCTTTGGTC
*
141272 AAAAACAAAAAAACAAACAAAA
1 AAAAACAAACAAA-AAACAAAA
*
141294 ACAAAAAAAACAAAAAA-ATAAA
1 A-AAAACAAACAAAAAACA-AAA
141316 AAAAACAAACAAAAAACAAACA
1 AAAAACAAACAAAAAACAAA-A
141338 AAAAACAAAC-AAAAACAAAA
1 AAAAACAAACAAAAAACAAAA
141358 AA
1 AA
141360 TGAAAATGTT
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.05
21 26 0.44
22 20 0.34
23 10 0.17
ACGTcount: A:0.85, C:0.14, G:0.00, T:0.01
Consensus pattern (21 bp):
AAAAACAAACAAAAAACAAAA
Found at i:141337 original size:32 final size:31
Alignment explanation
Indices: 141271--141358 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 31
141261 GAGCTTTGGT
141271 CAAAAACAAAAAAACAAACAAAAACAAAAAAAA
1 CAAAAA-AAAAAAA-AAACAAAAACAAAAAAAA
*
141304 CAAAAAAATAAAAAAAACAAACAA-AAAACAAA
1 CAAAAAAA-AAAAAAAACAAA-AACAAAAAAAA
*
141336 CAAAAAACAAACAAAAACAAAAA
1 CAAAAAA-AAAAAAAAACAAAAA
141359 ATGAAAATGT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
31 2 0.04
32 34 0.68
33 14 0.28
ACGTcount: A:0.84, C:0.15, G:0.00, T:0.01
Consensus pattern (31 bp):
CAAAAAAAAAAAAAAACAAAAACAAAAAAAA
Found at i:141542 original size:13 final size:13
Alignment explanation
Indices: 141507--141652 Score: 56
Period size: 13 Copynumber: 11.0 Consensus size: 13
141497 GTAAGCCTAA
141507 TTTTATTTTATA-
1 TTTTATTTTATAT
*
141519 -TTT-TTGT-TAT
1 TTTTATTTTATAT
141529 TTTTATTTTATA-
1 TTTTATTTTATAT
*
141541 TTTTA-TGTATAT
1 TTTTATTTTATAT
**
141553 ATTTTCCTTTATAT
1 -TTTTATTTTATAT
*
141567 CCTATGTA-TTTATTATT
1 --T-TTTATTTTA-TA-T
141584 TATTTATTATTACTAT
1 T-TTTATT-TTA-TAT
* *
141600 TTATTAATATATAT
1 TT-TTATTTTATAT
*
141614 TTTTATTTTATTT
1 TTTTATTTTATAT
*
141627 TTTTCCTTTTAT-T
1 TTTT-ATTTTATAT
141640 TTTTATTTTATAT
1 TTTTATTTTATAT
141653 GTATTTTTAT
Statistics
Matches: 101, Mismatches: 17, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
9 2 0.02
10 3 0.03
11 11 0.11
12 14 0.14
13 24 0.24
14 17 0.17
15 13 0.13
16 11 0.11
17 6 0.06
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTATTTTATAT
Found at i:141563 original size:25 final size:25
Alignment explanation
Indices: 141506--141580 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 25
141496 GGTAAGCCTA
*
141506 ATTTTATTTTATATTTT-TGT-TAT
1 ATTTTACTTTATATTTTATGTATAT
*
141529 -TTTTATTTTATATTTTATGTATAT
1 ATTTTACTTTATATTTTATGTATAT
* ** *
141553 ATTTTCCTTTATATCCTATGTATTT
1 ATTTTACTTTATATTTTATGTATAT
141578 ATT
1 ATT
141581 ATTTATTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 16 0.36
23 3 0.07
24 3 0.07
25 22 0.50
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (25 bp):
ATTTTACTTTATATTTTATGTATAT
Found at i:141595 original size:14 final size:14
Alignment explanation
Indices: 141576--141751 Score: 79
Period size: 14 Copynumber: 12.6 Consensus size: 14
141566 TCCTATGTAT
141576 TTATTATTTATTTA
1 TTATTATTTATTTA
*
141590 TTATTA-CTATTTA
1 TTATTATTTATTTA
141603 TTAATATATATT-TTTA
1 TT-AT-TAT-TTATTTA
* *
141619 TT-TTATTTTTTTCC
1 TTATTATTTATTT-A
141633 TT-TTATTT-TTTA
1 TTATTATTTATTTA
*
141645 TT-TTA--TATGTA
1 TTATTATTTATTTA
* *
141656 TTTTTATTTATCTAA
1 TTATTATTTAT-TTA
141671 TTATATATTTATTTA
1 TTAT-TATTTATTTA
*
141686 TCTGTTA-TTA-TTA
1 T-TATTATTTATTTA
141699 TTATTATTTTATTTA
1 TTATTA-TTTATTTA
* *
141714 -TCTTA-TAATATTA
1 TTATTATTTAT-TTA
*
141727 TTTTTGATTTATCTTA
1 TTATT-ATTTAT-TTA
141743 TTATTATTT
1 TTATTATTT
141752 TTCTAATTAT
Statistics
Matches: 125, Mismatches: 17, Indels: 39
0.69 0.09 0.22
Matches are distributed among these distances:
10 1 0.01
11 5 0.04
12 17 0.14
13 24 0.19
14 33 0.26
15 19 0.15
16 25 0.20
17 1 0.01
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (14 bp):
TTATTATTTATTTA
Found at i:141710 original size:28 final size:26
Alignment explanation
Indices: 141575--141750 Score: 97
Period size: 25 Copynumber: 6.8 Consensus size: 26
141565 ATCCTATGTA
*
141575 TTTA-TTAT-TTATTTATTATTACTA-
1 TTTATTTATCTTA-TTATTATTATTAT
* * *
141599 TTTATTAATATATATTTTTATT-TTAT
1 TTTATTTATCT-TATTATTATTATTAT
*
141625 TTT-TTT-CCTT-TTATT-TT-TTAT
1 TTTATTTATCTTATTATTATTATTAT
*
141646 TTTATATGTATTTTTATTTATCTAATTA-TAT
1 TTTAT-T-TA-TCTTA-TTAT-T-ATTATTAT
141677 ATTTATTTATCTGTTATTATTATTATTAT
1 -TTTATTTATC--TTATTATTATTATTAT
*
141706 TTTATTTATCTTA-TAATATTATT-T
1 TTTATTTATCTTATTATTATTATTAT
*
141730 TTGATTTATCTTATTATTATT
1 TTTATTTATCTTATTATTATT
141751 TTTCTAATTA
Statistics
Matches: 119, Mismatches: 13, Indels: 39
0.70 0.08 0.23
Matches are distributed among these distances:
21 9 0.08
22 5 0.04
23 2 0.02
24 19 0.16
25 22 0.18
26 16 0.13
27 2 0.02
28 18 0.15
29 6 0.05
30 6 0.05
31 9 0.08
32 5 0.04
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTATTTATCTTATTATTATTATTAT
Found at i:141753 original size:22 final size:22
Alignment explanation
Indices: 141656--141777 Score: 106
Period size: 24 Copynumber: 5.3 Consensus size: 22
141646 TTTATATGTA
*
141656 TTTTTATTTATCTAATTATATAT
1 TTTTTATTTATCTTATTAT-TAT
*
141679 TTATTTATCTGT-TATTATTATTAT
1 TT-TTTAT-T-TATCTTATTATTAT
141703 TATTTTATTTATCTTATAATATTAT
1 T-TTTTATTTATCTTAT--TATTAT
*
141728 TTTTGATTTATCTTATTATTAT
1 TTTTTATTTATCTTATTATTAT
* *
141750 TTTTCTAATTATC-TATTAAT-T
1 TTTT-TATTTATCTTATTATTAT
141771 TTTTTAT
1 TTTTTAT
141778 CTGATTTTTA
Statistics
Matches: 83, Mismatches: 8, Indels: 19
0.75 0.07 0.17
Matches are distributed among these distances:
20 2 0.02
21 5 0.06
22 17 0.20
23 14 0.17
24 28 0.34
25 16 0.19
26 1 0.01
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTTTATTTATCTTATTATTAT
Found at i:142288 original size:19 final size:20
Alignment explanation
Indices: 142264--142306 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
142254 GAACTACCGA
*
142264 TGAAAAA-CCCAGATTCCGG
1 TGAAAAATCCCAGAATCCGG
*
142283 TGAAAAATCTCAGAATCCGG
1 TGAAAAATCCCAGAATCCGG
142303 TGAA
1 TGAA
142307 TATTCAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
TGAAAAATCCCAGAATCCGG
Found at i:142713 original size:17 final size:15
Alignment explanation
Indices: 142691--142790 Score: 67
Period size: 16 Copynumber: 6.2 Consensus size: 15
142681 TTATTTAATA
142691 TTATTTTTATCTTTATT
1 TTATTTTTAT-TTT-TT
142708 TTATTTTTATTTTTT
1 TTATTTTTATTTTTT
* *
142723 TTACTCATCT-TTTTTT
1 TTA-T-TTTTATTTTTT
*
142739 TTCTTTTTATTTATTT
1 TTATTTTTATTT-TTT
* *
142755 TCACTTTTATTTTGTT
1 TTATTTTTATTTT-TT
*
142771 TTATTATTCTATTTTCT
1 TTATT-TT-TATTTTTT
142788 TTA
1 TTA
142791 AATGAAAATT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
14 2 0.03
15 10 0.15
16 29 0.45
17 18 0.28
18 6 0.09
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.75
Consensus pattern (15 bp):
TTATTTTTATTTTTT
Found at i:142725 original size:26 final size:25
Alignment explanation
Indices: 142680--142785 Score: 71
Period size: 26 Copynumber: 4.3 Consensus size: 25
142670 TTAGATTAGG
* *
142680 TTTATTTAATATTATTTTTATCTTTAT
1 TTTATTT-TTATTTTTTTTA-CTTTAT
*
142707 TTTATTTTTATTTTTTTTAC-TCAT
1 TTTATTTTTATTTTTTTTACTTTAT
* *
142731 CTT-TTTTT-TTCTTTTTA-TTTAT
1 TTTATTTTTATTTTTTTTACTTTAT
*
142753 TTTCACTTTTATTTTGTTTTA--TTAT
1 TTT-ATTTTTATTTT-TTTTACTTTAT
*
142778 TCTATTTT
1 TTTATTTT
142786 CTTTAAATGA
Statistics
Matches: 63, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
22 13 0.21
23 5 0.08
24 13 0.21
25 10 0.16
26 15 0.24
27 7 0.11
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.75
Consensus pattern (25 bp):
TTTATTTTTATTTTTTTTACTTTAT
Found at i:142762 original size:22 final size:23
Alignment explanation
Indices: 142737--142789 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
142727 TCATCTTTTT
142737 TTTTCTTTT-TATTTATT-TTC-A
1 TTTTCTTTTGT-TTTATTATTCTA
*
142758 CTTTTATTTTGTTTTATTATTCTA
1 -TTTTCTTTTGTTTTATTATTCTA
142782 TTTTCTTT
1 TTTTCTTT
142790 AAATGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 14 0.54
23 11 0.42
24 1 0.04
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTCTTTTGTTTTATTATTCTA
Found at i:143006 original size:59 final size:56
Alignment explanation
Indices: 142803--143135 Score: 333
Period size: 58 Copynumber: 5.7 Consensus size: 56
142793 TGAAAATTAA
* **
142803 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAAAATTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAATTTTC
** * *
142859 AAAAAAGGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTT
1 AAAAAA--TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAA-AAA-TTTTC
** * * * *
142919 AAAAAGGATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAAATTTTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT-TAAA--AAAAATTTTC
* *
142978 GAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAA-AAATTTTC
* * * ** **
143036 AAAAAAATAAATTTTTGAGAAAAAGTTGAAACTATCAATTTTCCTCGAAATTAAAGCTTC
1 -AAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT-TAAAAAAAATTTTC
*
143096 AAAAGAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAA-AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
143136 TCCTGCACAA
Statistics
Matches: 232, Mismatches: 31, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
56 6 0.03
57 2 0.01
58 108 0.47
59 60 0.26
60 19 0.08
61 37 0.16
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.35
Consensus pattern (56 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAATTTTC
Found at i:143181 original size:6 final size:6
Alignment explanation
Indices: 143167--143200 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
143157 CTTTTCTTTC
*
143167 TTTTTA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
143201 TCTTTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.74
Consensus pattern (6 bp):
TTTTGA
Found at i:146838 original size:358 final size:359
Alignment explanation
Indices: 146396--147992 Score: 2075
Period size: 357 Copynumber: 4.5 Consensus size: 359
146386 AAGGTGGTTT
*
146396 ATAATAAAAGACGCCTTTAATAATCCGAAAAAAATTTTTTTAGGGAAATTATTAAAGGCGTTGTT
1 ATAATAAAAGATGCCTTTAATAATCCG-AAAAAATTTTTTTAGGGAAATTATTAAAGGCGTTGTT
* * ** *
146461 ATT-TG-AAATCGCATTCAGTAATTATATACAAACTGTGATAAAAATTATTAAAGGCGTCTATCT
65 -TTCTGCAAACCGCCTTCAGTAATTATATACAAACTGTGATAGGAATTATTAAAGGCATCTATCT
* * * *
146524 TAAATATACGCCTTCAATAATAGTGTTACAATTTGTGTGGTGGTATATAGAAGGTATTTTACAGT
129 TAAATATACGCCTTCAATAATAGTGTTACAATTTGTGTGGCGGTATATAGAAAGCATTTTACAAT
* *
146589 AGAAGACACCTTTAATAATT-CTCAAAATATTTAGTGAGAAAATTTTGAAGGCGTCTATTATTAA
194 AAAAGACACCTTTAATAATTCCT-AAAATATTTAGTGAGAAAATTTTAAAGGCGTCTATTATTAA
* *
146653 CAAATGCTTTCAGTAATGGATTACTAAGTTTAAACGTATATTGAAAGTG-C-TTCTTCTAATAAA
258 CAAATGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAAGTGCCATT-TTCTAATAAA
** *
146716 TGCCTTCCATTACCATCGTGGTATATTGAAGGCATGTC
322 CACCTTCCATTACCATCGTGGTATATTGAAGGCGTGTC
** * * *
146754 ATAATAAAAGACACCTTTAATAATCCGAGAAAATTTTTGTAGGGAAATTATTAAAGGCATTGTTT
1 ATAATAAAAGATGCCTTTAATAATCCGAAAAAATTTTTTTAGGGAAATTATTAAAGGCGTTGTTT
*
146819 TCTGCAAACCGCCTTCAGTAATTA-ACTACAAACTGTGATAGGAATTATTAAAGGCATCTTTCTT
66 TCTGCAAACCGCCTTCAGTAATTATA-TACAAACTGTGATAGGAATTATTAAAGGCATCTATCTT
** * * *
146883 GGATATACGCCTTCAATAACAGTGTTAGAATTTGTGTGGCGGTATATAGAAAGCATTTTACAGTA
130 AAATATACGCCTTCAATAATAGTGTTACAATTTGTGTGGCGGTATATAGAAAGCATTTTACAATA
* *
146948 GAAGACACCTTTAATAATTCCTAAAATATTTAGTG-GAAAAATTTTAAAGGCGTCTGTTATTAAC
195 AAAGACACCTTTAATAATTCCTAAAATATTTAGTGAG-AAAATTTTAAAGGCGTCTATTATTAAC
* *
147012 AAATGCCTACAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGTGCC-TTTTCTAATAAACA
259 AAATGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAAGTGCCATTTTCTAATAAACA
* * * *
147076 CCTTCCATTACCATCGTGATATATTGAAGGTGTTTT
324 CCTTCCATTACCATCGTGGTATATTGAAGGCGTGTC
* * * * * *
147112 ATAATAAAAGATGCCTTTAATAATCTGAAAAAAGTTTTTTAAGAAAATTATTGAAGGTGTTGTTT
1 ATAATAAAAGATGCCTTTAATAATCCGAAAAAATTTTTTTAGGGAAATTATTAAAGGCGTTGTTT
* * * * *
147177 GC--CAAAACTGCCTTCAGTAATTATATATAAACTGTGATAAGAATTGTTAAAGGCATCTATCTT
66 TCTGC-AAACCGCCTTCAGTAATTATATACAAACTGTGATAGGAATTATTAAAGGCATCTATCTT
*
147240 AAATATACGCCTTCAATAATAGTGTTACAATTTGTGTGGCGATATATAG-AAGACATTTTACAAT
130 AAATATACGCCTTCAATAATAGTGTTACAATTTGTGTGGCGGTATATAGAAAG-CATTTTACAAT
** * * * *
147304 AAAAGATGCCTTTAATAATT-CTCAAACTATTTAGTGAGAAAATTTTAAAGGTGTTTGTTATTAA
194 AAAAGACACCTTTAATAATTCCT-AAAATATTTAGTGAGAAAATTTTAAAGGCGTCTATTATTAA
147368 CAAATGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTG-AAG-GCACATTTTCTAATAAA
258 CAAATGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAAGTGC-CATTTTCTAATAAA
* * * * * *
147431 CGCCTTCCATTAACATCATGGTATATTGAAGACGTTTT
322 CACCTTCCATTACCATCGTGGTATATTGAAGGCGTGTC
* * * **
147469 ATAATAAAAAATGCCTTTAATAATTCAAAAAAATTTTTTTAGGGAAATTATTAAAGATGTTGTTT
1 ATAATAAAAGATGCCTTTAATAATCCGAAAAAATTTTTTTAGGGAAATTATTAAAGGCGTTGTTT
* * *
147534 TCT-AAAATCGCCTTCAGTAATTGTATACAAACTGTGATAGGAATTATTAAAGGCATCTATCTTA
66 TCTGCAAACCGCCTTCAGTAATTATATACAAACTGTGATAGGAATTATTAAAGGCATCTATCTTA
* * * * *
147598 AATATACGCCTTCAATAATGGTATTAAAATTTGTGTGACGGTATATAGAAAGTATTTTACAATAA
131 AATATACGCCTTCAATAATAGTGTTACAATTTGTGTGGCGGTATATAGAAAGCATTTTACAATAA
* ** * * *
147663 AAAATGCTTTTAATAATTCCTAAAATATTTAGTGGGAAAATTTTGAAGGCGTCTATTATTAACAA
196 AAGACACCTTTAATAATTCCTAAAATATTTAGTGAGAAAATTTTAAAGGCGTCTATTATTAACAA
*
147728 ATGCCTTTAGTAAT-GATTACTAAGTTTAAAGGTATATT-AAAG-GCACATTTTCTAATAAACAC
261 ATGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAAGTGC-CATTTTCTAATAAACAC
* *
147790 CTTTCATTACCATCGTGGTATATTGAAGGTGTGTC
325 CTTCCATTACCATCGTGGTATATTGAAGGCGTGTC
* *
147825 ATAATAAAAGATGCCTTTAATAATCCGAGAAAATTTTTTTAGAGAAATTATTGAAA-GCGTTGTT
1 ATAATAAAAGATGCCTTTAATAATCCGAAAAAATTTTTTTAGGGAAATTATT-AAAGGCGTTGTT
* ** *
147889 TTCTGC-AACTGCCTTCAGTAATTA-ACTACAAACTGTGATAGGAATTATTAAAGGTGTCTTTCT
65 TTCTGCAAACCGCCTTCAGTAATTATA-TACAAACTGTGATAGGAATTATTAAAGGCATCTATCT
** * * * * *
147952 TGGATAAATGCTTTCAATAATAGTGTTAGAATTTATGTGGC
129 TAAATATACGCCTTCAATAATAGTGTTACAATTTGTGTGGC
147993 AATATTTTCA
Statistics
Matches: 1088, Mismatches: 131, Indels: 42
0.86 0.10 0.03
Matches are distributed among these distances:
355 3 0.00
356 222 0.20
357 519 0.48
358 339 0.31
359 5 0.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (359 bp):
ATAATAAAAGATGCCTTTAATAATCCGAAAAAATTTTTTTAGGGAAATTATTAAAGGCGTTGTTT
TCTGCAAACCGCCTTCAGTAATTATATACAAACTGTGATAGGAATTATTAAAGGCATCTATCTTA
AATATACGCCTTCAATAATAGTGTTACAATTTGTGTGGCGGTATATAGAAAGCATTTTACAATAA
AAGACACCTTTAATAATTCCTAAAATATTTAGTGAGAAAATTTTAAAGGCGTCTATTATTAACAA
ATGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAAGTGCCATTTTCTAATAAACACC
TTCCATTACCATCGTGGTATATTGAAGGCGTGTC
Found at i:156533 original size:17 final size:16
Alignment explanation
Indices: 156511--156553 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
156501 AATAGTTTTG
156511 TAAATTTAATATAAAA
1 TAAATTTAATATAAAA
* *
156527 TACAATTTATTATACAA
1 TA-AATTTAATATAAAA
156544 TAAA-TTAATA
1 TAAATTTAATA
156554 AATAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 4 0.17
17 14 0.61
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATTTAATATAAAA
Found at i:158646 original size:25 final size:24
Alignment explanation
Indices: 158601--158653 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
158591 TTTTTTTTAA
*
158601 TTTTGATTTTTTTGATTTTATCTAT
1 TTTTGATTTTTTTGATATTAT-TAT
*
158626 TTTTGATTTTTATTTA-ATTATTAT
1 TTTTGATTTTT-TTGATATTATTAT
158650 TTTT
1 TTTT
158654 TAAATTATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 15 0.60
26 3 0.12
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.74
Consensus pattern (24 bp):
TTTTGATTTTTTTGATATTATTAT
Found at i:159114 original size:17 final size:17
Alignment explanation
Indices: 159092--159144 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
159082 AGGTTAATTT
159092 AAATAATAAAAAAATAA
1 AAATAATAAAAAAATAA
* * *
159109 AAATAATGATAAAATAG
1 AAATAATAAAAAAATAA
*
159126 AAATAA-AAAAAAACAA
1 AAATAATAAAAAAATAA
159142 AAA
1 AAA
159145 ATATTAATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (17 bp):
AAATAATAAAAAAATAA
Done.