Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009576.1 Hibiscus syriacus cultivar Beakdansim tig00116944_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: 1684752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:3845 original size:17 final size:16
Alignment explanation
Indices: 3814--3843 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3804 TCATCGTATG
3814 TTTTTTTTCATTATAA
1 TTTTTTTTCATTATAA
3830 TTTTTTTTC-TTATA
1 TTTTTTTTCATTATA
3844 TAGTCCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTTCATTATAA
Found at i:7024 original size:72 final size:72
Alignment explanation
Indices: 6898--7044 Score: 258
Period size: 72 Copynumber: 2.0 Consensus size: 72
6888 TGATAAAATC
6898 TGATCCCAAAACTGTTTTAGTTGCAATTTGTGGATCGAGTATTCATTTACATTATGTCGTCGAGT
1 TGATCCCAAAACTGTTTTAGTTGCAATTTGTGGATCGAGTATTCATTTACATTATGTCGTCGAGT
6963 CAATGCT
66 CAATGCT
* * * *
6970 TGATCCCAAAGCTGTTTTAGTTGTAATTTGTGGATCGAGTATTCGTTTATATTATGTCGTCGAGT
1 TGATCCCAAAACTGTTTTAGTTGCAATTTGTGGATCGAGTATTCATTTACATTATGTCGTCGAGT
7035 CAATGCT
66 CAATGCT
7042 TGA
1 TGA
7045 AATATTAGGT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (72 bp):
TGATCCCAAAACTGTTTTAGTTGCAATTTGTGGATCGAGTATTCATTTACATTATGTCGTCGAGT
CAATGCT
Found at i:7051 original size:28 final size:28
Alignment explanation
Indices: 7018--7074 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
7008 GTATTCGTTT
* * *
7018 ATATTATGTCGTCGAGTCAATGCTTGAA
1 ATATTAGGTCATCGAGCCAATGCTTGAA
*
7046 ATATTAGGTCATTGAGCCAATGCTTGAA
1 ATATTAGGTCATCGAGCCAATGCTTGAA
7074 A
1 A
7075 GTAACGACGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (28 bp):
ATATTAGGTCATCGAGCCAATGCTTGAA
Found at i:11129 original size:14 final size:14
Alignment explanation
Indices: 11110--11138 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11100 AATTAAAATA
11110 AAATTGTAAAATTT
1 AAATTGTAAAATTT
11124 AAATTGTAAAATTT
1 AAATTGTAAAATTT
11138 A
1 A
11139 TATTACCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AAATTGTAAAATTT
Found at i:12105 original size:17 final size:17
Alignment explanation
Indices: 12083--12115 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12073 GTAATTATAT
*
12083 TTATATATATAGTTACA
1 TTATATATATAATTACA
12100 TTATATATATAATTAC
1 TTATATATATAATTAC
12116 TCTGTTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
TTATATATATAATTACA
Found at i:14991 original size:7 final size:7
Alignment explanation
Indices: 14974--15017 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
14964 TTTAAAATCA
14974 TTAAA-T
1 TTAAAGT
*
14980 TTAAATT
1 TTAAAGT
*
14987 TTAAACT
1 TTAAAGT
*
14994 TTAGAGT
1 TTAAAGT
15001 TTAAAGT
1 TTAAAGT
15008 TTAAAGT
1 TTAAAGT
15015 TTA
1 TTA
15018 TAATTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (7 bp):
TTAAAGT
Found at i:14996 original size:14 final size:13
Alignment explanation
Indices: 14974--15022 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
14964 TTTAAAATCA
*
14974 TTAAATTTAAATT
1 TTAAATTTAAAGT
*
14987 TTAAACTTTAGAGT
1 TTAAA-TTTAAAGT
15001 TTAAAGTTTAAAGT
1 TTAAA-TTTAAAGT
15015 TTATAATT
1 TTA-AATT
15023 AAAATAGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 5 0.17
14 23 0.77
15 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (13 bp):
TTAAATTTAAAGT
Found at i:15135 original size:15 final size:16
Alignment explanation
Indices: 15108--15139 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
15098 TTGGGAAAGT
15108 TATAAATATATTTTTA
1 TATAAATATATTTTTA
15124 TATAAA-ATATTTTTA
1 TATAAATATATTTTTA
15139 T
1 T
15140 TTATCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATAAATATATTTTTA
Found at i:15318 original size:25 final size:24
Alignment explanation
Indices: 15269--15318 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
15259 AAACCATTTT
*
15269 AACTTTTTTAAATAAATTATTTAA
1 AACTTTTTTAAATAAATTATATAA
*
15293 AACTTATTTTTAATATAA-TATATAA
1 AACTT-TTTTAAATA-AATTATATAA
15318 A
1 A
15319 TTATTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 5 0.23
25 15 0.68
26 2 0.09
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
AACTTTTTTAAATAAATTATATAA
Found at i:15508 original size:50 final size:51
Alignment explanation
Indices: 15445--15544 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 51
15435 GGAAAGCACG
* * *
15445 CCCCTTGCACCGCGCTATATGCTGATTTGGCGCCACGTGGATATAGCGCGT
1 CCCCTTGCACCGCGATATACGCTGATCTGGCGCCACGTGGATATAGCGCGT
* * *
15496 CCCC-TGCCCCGCGATATACGGTGATCTGGCGCCACGTGGGTATAGCGCG
1 CCCCTTGCACCGCGATATACGCTGATCTGGCGCCACGTGGATATAGCGCG
15545 CCCTCTGATC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 39 0.91
51 4 0.09
ACGTcount: A:0.15, C:0.33, G:0.30, T:0.22
Consensus pattern (51 bp):
CCCCTTGCACCGCGATATACGCTGATCTGGCGCCACGTGGATATAGCGCGT
Found at i:15558 original size:50 final size:50
Alignment explanation
Indices: 15467--15565 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
15457 CGCTATATGC
* *
15467 TGATTTGGCGCCACGTGGATATAGCGCGTCCCCTGCCCCGCGATATACGG
1 TGATCTGGCGCCACGTGGATATAGCGCGTCCCCTGACCCGCGATATACGG
* * *
15517 TGATCTGGCGCCACGTGGGTATAGCGCG-CCCTCTGATCCGCGTTATACG
1 TGATCTGGCGCCACGTGGATATAGCGCGTCCC-CTGACCCGCGATATACG
15566 CCACGTAGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 3 0.07
50 40 0.93
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.23
Consensus pattern (50 bp):
TGATCTGGCGCCACGTGGATATAGCGCGTCCCCTGACCCGCGATATACGG
Found at i:19215 original size:35 final size:34
Alignment explanation
Indices: 19130--19216 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
19120 ATTTGATATT
*
19130 TAAATACAACAAACTTACAATAATAATTAAATGG
1 TAAATACAACAAAATTACAATAATAATTAAATGG
* *
19164 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA-T-A-ATTAAATGG
19202 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
19217 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 2 0.04
37 4 0.09
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAATAATTAAATGG
Found at i:19455 original size:12 final size:12
Alignment explanation
Indices: 19428--19484 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
19418 ACTCCTCGCT
* *
19428 GTCATCATCATA
1 GTCATCATCGTC
19440 GTCATCATCGTC
1 GTCATCATCGTC
*
19452 GTCA-C--CATC
1 GTCATCATCGTC
*
19461 GTCATCGTCGTC
1 GTCATCATCGTC
19473 GTCATCATCGTC
1 GTCATCATCGTC
19485 ATTGTCCTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
9 7 0.19
10 1 0.03
11 1 0.03
12 28 0.76
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.32
Consensus pattern (12 bp):
GTCATCATCGTC
Found at i:19466 original size:21 final size:21
Alignment explanation
Indices: 19440--19486 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
19430 CATCATCATA
19440 GTCATCATCGTCGTCACCATC
1 GTCATCATCGTCGTCACCATC
* *
19461 GTCATCGTCGTCGTCATCATC
1 GTCATCATCGTCGTCACCATC
19482 GTCAT
1 GTCAT
19487 TGTCCTGAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.32
Consensus pattern (21 bp):
GTCATCATCGTCGTCACCATC
Found at i:21567 original size:111 final size:111
Alignment explanation
Indices: 21369--21590 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
21359 ATTACAAAAA
* *
21369 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
21434 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
21480 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
21545 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
21591 ATGATTTCCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:21732 original size:10 final size:10
Alignment explanation
Indices: 21713--21753 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
21703 ACCTTAAAAA
*
21713 GAGAGTATTT
1 GAGAGAATTT
21723 GAGAGAATTT
1 GAGAGAATTT
*
21733 TAGAGAATTT
1 GAGAGAATTT
21743 GAGAGAATTT
1 GAGAGAATTT
21753 G
1 G
21754 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:21930 original size:50 final size:51
Alignment explanation
Indices: 21875--22000 Score: 152
Period size: 50 Copynumber: 2.5 Consensus size: 51
21865 AGATATCCAG
* ** * *
21875 ATATAGCGCGGAT-CAGGGGGCACGCTATATTCACGTGGCG-CAAGATCACC
1 ATATAGCGCGGATGCAGGGGGCGCGCTATACCCACGTGACGCCAA-ATCAAC
* *
21925 GTATAGAGCGG-TGCAGGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
1 ATATAGCGCGGATGCAGGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
21975 ATATAGCGC-GATGCAGGGGGCGCGCT
1 ATATAGCGCGGATGCAGGGGGCGCGCT
22001 TTTCTGCTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 2 0.03
50 59 0.92
51 3 0.05
ACGTcount: A:0.25, C:0.26, G:0.33, T:0.16
Consensus pattern (51 bp):
ATATAGCGCGGATGCAGGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
Found at i:22876 original size:29 final size:29
Alignment explanation
Indices: 22843--22909 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
22833 TTGGAACGTA
* *
22843 TTAATAGTCAATAGATCATTTTATAACTT
1 TTAATAATCAATAAATCATTTTATAACTT
* * *
22872 TTAATAATTAATAAATTATTTTATAATTT
1 TTAATAATCAATAAATCATTTTATAACTT
22901 TTAATAATC
1 TTAATAATC
22910 GAAATACTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (29 bp):
TTAATAATCAATAAATCATTTTATAACTT
Found at i:25251 original size:21 final size:21
Alignment explanation
Indices: 25227--25266 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25217 ACAATGAAGT
25227 TTATGCCTCTTTAAAAAGACA
1 TTATGCCTCTTTAAAAAGACA
* * *
25248 TTATTCCTTTTTAACAAGA
1 TTATGCCTCTTTAAAAAGA
25267 TGGTTGTACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (21 bp):
TTATGCCTCTTTAAAAAGACA
Found at i:37987 original size:2 final size:2
Alignment explanation
Indices: 37980--38004 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37970 TTAATCTACA
37980 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
38005 ATTTACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38094 original size:13 final size:13
Alignment explanation
Indices: 38076--38117 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
38066 AATGACGCTC
38076 AATGCGCGTCATA
1 AATGCGCGTCATA
*
38089 AATGCGTGTCATA
1 AATGCGCGTCATA
* *
38102 AATGTGCGCCATA
1 AATGCGCGTCATA
38115 AAT
1 AAT
38118 TTATGACACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:38135 original size:26 final size:26
Alignment explanation
Indices: 38106--38162 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
38096 GTCATAAATG
38106 TGCGCCATAAATTTATGACACACAAT
1 TGCGCCATAAATTTATGACACACAAT
*
38132 TGCGCCATAGATTTATGACACACAAT
1 TGCGCCATAAATTTATGACACACAAT
38158 TGCGC
1 TGCGC
38163 GTCATCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (26 bp):
TGCGCCATAAATTTATGACACACAAT
Found at i:42303 original size:49 final size:49
Alignment explanation
Indices: 42232--42325 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 49
42222 AATAATATAT
*
42232 TATTATTACTATATCTATTTGACATAAAAACATATATAAAATTATAATA
1 TATTATTACTATATCTAATTGACATAAAAACATATATAAAATTATAATA
42281 TATTATTACTATATCTAATTGACATAAAAACATATATAAAATTAT
1 TATTATTACTATATCTAATTGACATAAAAACATATATAAAATTAT
42326 CTCTAAAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (49 bp):
TATTATTACTATATCTAATTGACATAAAAACATATATAAAATTATAATA
Found at i:42565 original size:16 final size:16
Alignment explanation
Indices: 42544--42574 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42534 ATTCAAGTAT
42544 ATTTATATATATAATG
1 ATTTATATATATAATG
42560 ATTTATATATATAAT
1 ATTTATATATATAAT
42575 TACCCCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
ATTTATATATATAATG
Found at i:44667 original size:4 final size:4
Alignment explanation
Indices: 44658--44683 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
44648 TTCAAACATA
44658 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
44684 CAAGTTAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:46310 original size:39 final size:39
Alignment explanation
Indices: 46251--46347 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 39
46241 AGGGGGAACA
* *
46251 AATTCTTCTCATTATAAACTTCTTCTCATTCTTTGGA-T
1 AATTCTTCTCATTATGAACTTCTTCTCATTCTTTGGACG
*
46289 AAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTTGGACG
1 AA-TTCTTCTCATTATGAACTTCTTCTCATTCTTTGGACG
46329 AATTCTTCTCATTATGAAC
1 AATTCTTCTCATTATGAAC
46348 CATTCCATTG
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
38 2 0.04
39 50 0.93
40 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (39 bp):
AATTCTTCTCATTATGAACTTCTTCTCATTCTTTGGACG
Found at i:46314 original size:17 final size:17
Alignment explanation
Indices: 46253--46316 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
46243 GGGGAACAAA
*
46253 TTCTTCTCATTATAAAC
1 TTCTTCTCATTATGAAC
* *
46270 TTCTTCTCATTCTTTGGATAAG
1 TTCTTCTCA-T-TAT-G--AAC
46292 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
46309 TTCTTCTC
1 TTCTTCTC
46317 CTTCTTTGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
17 19 0.51
18 1 0.03
19 3 0.08
20 2 0.05
21 1 0.03
22 11 0.30
ACGTcount: A:0.20, C:0.23, G:0.06, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:46535 original size:21 final size:21
Alignment explanation
Indices: 46511--46569 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
46501 AAAATAAACA
*
46511 ATTTCTTCTCATTATGAACTT
1 ATTTCTTCTCATTATGAACTG
*
46532 ATTT-TTCCTCATCA-G-A-TG
1 ATTTCTT-CTCATTATGAACTG
*
46550 AGTTCTTCTCATTATGAACT
1 ATTTCTTCTCATTATGAACT
46570 CTTTCATTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
18 10 0.34
19 4 0.14
20 4 0.14
21 11 0.38
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.47
Consensus pattern (21 bp):
ATTTCTTCTCATTATGAACTG
Found at i:47211 original size:101 final size:100
Alignment explanation
Indices: 47013--47228 Score: 247
Period size: 101 Copynumber: 2.1 Consensus size: 100
47003 TCTATTTCAG
* * * * *
47013 GTGAGATAAAATTTTGTTTCGAGTGAATAATTACAAAATTTGTGTTTCAAAGGAAAATGTCTCAA
1 GTGAGAT-AAATCTTGTTTCAAGTAAACAATTACAAAACTTGTGTTTCAAAGGAAAATGTCTCAA
* ** * *
47078 ACGAGACGACATTTCTTTTAAGAAAAACAATCTTAA
65 ACGAGACGAAATTGATTTCAAGAAAAACAATCTCAA
*
47114 GTGAGATAAATCTTGTTTCAAGTAAAGCAATTCCAAAACTTGTGCTTT-AAAGGAAAATGTCTCA
1 GTGAGATAAATCTTGTTTCAAGTAAA-CAATTACAAAACTTGTG-TTTCAAAGGAAAATGTCTCA
** * *
47178 AGTGAGAGGAAATTGATTTCAAGGAAAGA-AATCTCAA
64 AACGAGACGAAATTGATTTCAA-GAAAAACAATCTCAA
47215 GTGAGATAAATCTT
1 GTGAGATAAATCTT
47229 ATCGTATTAA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
100 16 0.16
101 73 0.75
102 8 0.08
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (100 bp):
GTGAGATAAATCTTGTTTCAAGTAAACAATTACAAAACTTGTGTTTCAAAGGAAAATGTCTCAAA
CGAGACGAAATTGATTTCAAGAAAAACAATCTCAA
Found at i:49206 original size:6 final size:6
Alignment explanation
Indices: 49195--49327 Score: 90
Period size: 6 Copynumber: 22.7 Consensus size: 6
49185 TTGCATATCA
49195 TTTTCT TTTTC- --TTCT TTTTCT TTTTCT TTTT-T TTTT-T TTTTCTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC--T
* *
49240 TTTTCCT TTATT-T TTTCCT TTAT-T TTTTC- TTTTCTT TTTTCT TTTT-T
1 TTTT-CT TT-TTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT
*
49287 TCTTTTT TTTTC- TTTT-T TTTTCAT TTCTTCT TTTTCT TTTT
1 T-TTTCT TTTTCT TTTTCT TTTTC-T TT-TTCT TTTTCT TTTT
49328 TCTTATGGTG
Statistics
Matches: 104, Mismatches: 5, Indels: 36
0.72 0.03 0.25
Matches are distributed among these distances:
3 3 0.03
5 30 0.29
6 44 0.42
7 16 0.15
8 10 0.10
9 1 0.01
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:49213 original size:15 final size:15
Alignment explanation
Indices: 49195--49327 Score: 91
Period size: 16 Copynumber: 8.7 Consensus size: 15
49185 TTGCATATCA
49195 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCT
*
49210 TTTTCTTTTTCTTTTT
1 TTTTCTTTTTC-TTCT
*
49226 TTTTTTTTTTCTT-T
1 TTTTCTTTTTCTTCT
*
49240 TTTTCCTTTATTTTTTCCT
1 TTTT-C-TT-TTTCTT-CT
*
49259 TTATT-TTTTCTTTTCTT
1 TT-TTCTTTT-TCTTC-T
49276 TTTTCTTTTT-TTC-
1 TTTTCTTTTTCTTCT
49289 TTTT-TTTTTCTT-T
1 TTTTCTTTTTCTTCT
49302 TTTT-TTCATTTCTTCT
1 TTTTCTT--TTTCTTCT
49318 TTTTCTTTTT
1 TTTTCTTTTT
49328 TCTTATGGTG
Statistics
Matches: 98, Mismatches: 4, Indels: 32
0.73 0.03 0.24
Matches are distributed among these distances:
12 5 0.05
13 12 0.12
14 5 0.05
15 25 0.26
16 26 0.27
17 20 0.20
19 3 0.03
20 2 0.02
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:49227 original size:24 final size:23
Alignment explanation
Indices: 49200--49327 Score: 104
Period size: 23 Copynumber: 5.3 Consensus size: 23
49190 TATCATTTTC
*
49200 TTTTTCTTCTTTTTCTTTTTCTT
1 TTTTTTTTCTTTTTCTTTTTCTT
49223 TTTTTTTT-TTTTTCTTTTTTTCCTT
1 TTTTTTTTCTTTTTC--TTTTT-CTT
* *
49248 TATTTTTTCCTTTAT-TTTTTCTT
1 T-TTTTTTTCTTTTTCTTTTTCTT
49271 TTCTTTTTTCTTTTT-TTCTTT-TT
1 TT-TTTTTTCTTTTTCTT-TTTCTT
49294 TTTTCTTTT-TTTTTCATTTCTTCTT
1 TTTT-TTTTCTTTTTC-TTT-TTCTT
49319 TTTCTTTTT
1 TTT-TTTTT
49328 TCTTATGGTG
Statistics
Matches: 87, Mismatches: 5, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
22 14 0.16
23 32 0.37
24 17 0.20
25 13 0.15
26 7 0.08
27 4 0.05
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTTTTCTTTTTCTTTTTCTT
Found at i:49327 original size:1 final size:1
Alignment explanation
Indices: 49195--49307 Score: 73
Period size: 1 Copynumber: 113.0 Consensus size: 1
49185 TTGCATATCA
* * * * * * ** * **
49195 TTTTCTTTTTCTTCTTTTTCTTTTTCTTTTTTTTTTTTTTTCTTTTTTTCCTTTATTTTTTCCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * *
49260 TATTTTTTCTTTTCTTTTTTCTTTTTTTCTTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
49308 CATTTCTTCT
Statistics
Matches: 82, Mismatches: 30, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 82 1.00
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:50938 original size:76 final size:76
Alignment explanation
Indices: 50730--50936 Score: 283
Period size: 75 Copynumber: 2.7 Consensus size: 76
50720 CAAAGCCAAA
* * * **
50730 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGT
50795 TTTGGCCCCGAG
65 TTTGGCCCCGAG
* * *
50807 ATTTCCAGAATGCTTGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
50872 TT-GCTCCGAG
66 TTGGCCCCGAG
* * *
50882 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCC
50937 CCCTTGTACA
Statistics
Matches: 115, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
74 17 0.15
75 39 0.34
76 37 0.32
77 22 0.19
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TTGGCCCCGAG
Found at i:55142 original size:23 final size:26
Alignment explanation
Indices: 55099--55148 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
55089 ATTATGAGAA
*
55099 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
55125 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
55148 A
1 A
55149 TCAGAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:56372 original size:17 final size:17
Alignment explanation
Indices: 56347--56380 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
56337 TATTTCGAAA
56347 AAAAATAAAATACAAAT
1 AAAAATAAAATACAAAT
*
56364 AAAAGTAAAATACAAAT
1 AAAAATAAAATACAAAT
56381 CTGAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATAAAATACAAAT
Found at i:57459 original size:112 final size:112
Alignment explanation
Indices: 57271--57904 Score: 867
Period size: 112 Copynumber: 5.6 Consensus size: 112
57261 AGCATCAAAC
** * * *
57271 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTACTACTTCATATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT-CTTCAGATAAGTTCTTCTCATT
57336 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCA
65 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCA
* *
57384 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
* *
57449 TGAACTTTCTCTAGAAATGTTAATCCATCAAGTGATGAATTC-GAGCA
66 TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAG-GCA
* *
57496 AAAGGTTAAACAATGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAA-ATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
** * *
57561 ATGAACTTTCTCTGGAAAAAATAATTCATCAAGTGATGAATTCAGGGA
65 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCA
* *
57609 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
* ** * ** * * * ** * *
57674 TGAACTCTAACTGGCACTGCTGATCCACCGGGTGATGAATTTAAGCA
66 TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCA
* *
57721 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
* * *
57786 TGAACTTTCTCTGGAAAAGTTAATCCATCAAATGATGGATT-TGAGCA
66 TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAG-GCA
* *
57833 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
*
57898 ATAAACT
65 ATGAACT
57905 CGACCTGGAA
Statistics
Matches: 455, Mismatches: 61, Indels: 10
0.87 0.12 0.02
Matches are distributed among these distances:
111 1 0.00
112 287 0.63
113 166 0.36
114 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (112 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCA
Found at i:57564 original size:225 final size:224
Alignment explanation
Indices: 57271--57905 Score: 966
Period size: 225 Copynumber: 2.8 Consensus size: 224
57261 AGCATCAAAC
* * * *
57271 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTACTACTTCATATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT-CTTCAGATAAGTTCTTCTCATT
*
57336 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTAAACAAATTC
65 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTC
* * **
57401 TTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTAGAAA
130 TTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTAGAAA
* * *
57466 TGTTAATCCATCAAGTGATGAATTCGAGCA
195 TGCTAATCCACCAAGTGATGAATTCAAGCA
*
57496 AAAGGTTAAACAATGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAA-GTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
** * *
57561 ATGAACTTTCTCTGGAAAAAATAATTCATCAAGTGATGAATTCAGGGAAAAGGTTGAACAAATTC
65 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTC
* * *
57626 TTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCAC
130 TTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTAGAAA
* ** *
57691 TGCTGATCCACCGGGTGATGAATTTAAGCA
195 TGCTAATCCACCAAGTGATGAATTCAAGCA
*
57721 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
* * *
57786 TGAACTTTCTCTGGAAAAGTTAATCCATCAAATGATGGATT-TGAGCAAAAGGTTGAACAAATTC
66 TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAG-GCAAAAGGTTGAACAAATTC
*
57850 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTC
130 TTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTC
57906 GACCTGGAAT
Statistics
Matches: 373, Mismatches: 34, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
223 1 0.00
224 131 0.35
225 214 0.57
226 27 0.07
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (224 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCT
TCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTAGAAAT
GCTAATCCACCAAGTGATGAATTCAAGCA
Found at i:57741 original size:337 final size:338
Alignment explanation
Indices: 57271--57904 Score: 957
Period size: 337 Copynumber: 1.9 Consensus size: 338
57261 AGCATCAAAC
* *
57271 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTACTACTTCATATGAGTTCTTCTCATT
1 AAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTACTACTTCAGATGAGTTCTTCTCATT
* ** * * * *
57336 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTAAACAAATTC
66 ATGAACTCTAACTGGAAAAGCTAATCCACCAAGTGATGAATTCAAGCAAAAAGTTAAACAAATTC
*
57401 TTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTAGAAA
131 TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTAGAAA
* * *
57466 TGTTAATCCATCAAGTGATGAATTCGAGCAAAAGGTTAAACAATGTTCTTCTCATTATGAACTTC
196 AGTTAATCCATCAAATGATGAATTCGAGCAAAAGGTTAAACAA-ATTCTTCTCATTATGAACTTC
*
57531 TTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAATAATTCATCAAGT
260 TTCTTCCTTCTTCAGATAAGTTCTTCTCATTATAAACTTTCTCTGGAAAAAATAATTCATCAAGT
57595 GATGAATTCAGGGA
325 GATGAATTCAGGGA
* * *
57609 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCT-CTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTACTACTTCAGATGAGTTCTTCTCATT
* ** * ** * * *
57673 ATGAACTCTAACTGGCACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAAGTTGAACAAGTTC
66 ATGAACTCTAACTGGAAAAGCTAATCCACCAAGTGATGAATTCAAGCAAAAAGTTAAACAAATTC
*
57738 TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
131 TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTAGAAA
* * * *
57803 AGTTAATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCT
196 AGTTAATCCATCAAATGATGAATTCGAGCAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCT
*
57868 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACT
261 TCTTCCTTCTTCAGATAAGTTCTTCTCATTATAAACT
57905 CGACCTGGAA
Statistics
Matches: 263, Mismatches: 32, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
336 26 0.10
337 199 0.76
338 38 0.14
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (338 bp):
AAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTACTACTTCAGATGAGTTCTTCTCATT
ATGAACTCTAACTGGAAAAGCTAATCCACCAAGTGATGAATTCAAGCAAAAAGTTAAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTAGAAA
AGTTAATCCATCAAATGATGAATTCGAGCAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCT
TCTTCCTTCTTCAGATAAGTTCTTCTCATTATAAACTTTCTCTGGAAAAAATAATTCATCAAGTG
ATGAATTCAGGGA
Found at i:58364 original size:22 final size:22
Alignment explanation
Indices: 58339--58393 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
58329 GATAAAGCTT
*
58339 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
58361 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
58383 TCATCTTTGAA
1 TCATCTTTGAA
58394 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:61099 original size:84 final size:84
Alignment explanation
Indices: 61000--61225 Score: 359
Period size: 84 Copynumber: 2.7 Consensus size: 84
60990 TGGTTCCTAC
* *
61000 CAAACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTGAACACATTAT-TCTTCCA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATATCTTCCA
61064 AATTCAATGATTAGTTCTGT
66 AATTCAATGATT-GTTCTGT
* *
61084 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATT-TATCTTCTA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATATCTTCCA
61147 AATTCAATGATTGTTCTGT
66 AATTCAATGATTGTTCTGT
* *
61166 CCAACCAGATCAGATAACTCAAAGAACACTTCCCAAAAGATGCTATTGAGCACATTATAT
1 CAAACCAGATCAGATAACTCAAAGAACACTT-CCAGAAGATGCTATTGAGCACATTATAT
61226 TTGTTCCAGT
Statistics
Matches: 131, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
82 38 0.29
83 38 0.29
84 52 0.40
85 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.28
Consensus pattern (84 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATATCTTCCA
AATTCAATGATTGTTCTGT
Found at i:70131 original size:17 final size:17
Alignment explanation
Indices: 70106--70139 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
70096 TATTTCGAAA
70106 AAAAATAAAATACAAAT
1 AAAAATAAAATACAAAT
*
70123 AAAAGTAAAATACAAAT
1 AAAAATAAAATACAAAT
70140 CTGAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATAAAATACAAAT
Found at i:72499 original size:19 final size:20
Alignment explanation
Indices: 72475--72536 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 20
72465 TTTTGGTGCA
*
72475 GAGGGAATCGA-TCCCCCCT
1 GAGGGAACCGATTCCCCCCT
72494 GAGGGAACCGATTCCCCCCTTT
1 GAGGGAACCGATTCCCCCC--T
72516 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
72537 CACAGGGGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 10 0.27
20 7 0.19
22 2 0.05
23 1 0.03
24 17 0.46
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCCT
Found at i:72543 original size:22 final size:22
Alignment explanation
Indices: 72496--72557 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
72486 TCCCCCCTGA
*
72496 GGGAACCGATTCCCCCCTTTGAAG
1 GGGAACCGATTCCCCCC--TCAAG
72520 GGGAACCGATTCCCCCC-CACAG
1 GGGAACCGATTCCCCCCTCA-AG
* *
72542 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
72558 TGGGGTTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 16 0.47
24 17 0.50
ACGTcount: A:0.23, C:0.39, G:0.24, T:0.15
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTCAAG
Found at i:74502 original size:15 final size:15
Alignment explanation
Indices: 74482--74521 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
74472 CATTTTTGAT
*
74482 ATTTTGGATTGTTTG
1 ATTTTGGATTGTTGG
74497 ATTTTGGATTGTTGG
1 ATTTTGGATTGTTGG
74512 ATTTTGGATT
1 ATTTTGGATT
74522 TATGATAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.28, T:0.57
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:74518 original size:7 final size:7
Alignment explanation
Indices: 74482--74522 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
74472 CATTTTTGAT
74482 ATTTTGG
1 ATTTTGG
*
74489 ATTGTTTG
1 ATT-TTGG
74497 ATTTTGG
1 ATTTTGG
74504 ATTGTTGG
1 ATT-TTGG
74512 ATTTTGG
1 ATTTTGG
74519 ATTT
1 ATTT
74523 ATGATAGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 17 0.57
8 13 0.43
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.59
Consensus pattern (7 bp):
ATTTTGG
Found at i:75258 original size:76 final size:77
Alignment explanation
Indices: 75099--75306 Score: 278
Period size: 76 Copynumber: 2.7 Consensus size: 77
75089 CAAAGCCAAA
* * * **
75099 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
75163 TTTTGGCCCCGAC
65 TTTTGGCCCCGAC
*
75176 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
75241 TTT-GCTCCGAG
66 TTTGGCCCCGAC
* * * *
75252 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
75307 TTGTACAACG
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 17 0.15
76 61 0.52
77 39 0.33
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAC
Found at i:76382 original size:21 final size:22
Alignment explanation
Indices: 76357--76400 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
76347 TGGATGGAAT
76357 AATAAAA-AATGTTAAA-AATGA
1 AATAAAATAATG-TAAAGAATGA
76378 AATAAAATAATGTAAAGAATGA
1 AATAAAATAATGTAAAGAATGA
76400 A
1 A
76401 TGGAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (22 bp):
AATAAAATAATGTAAAGAATGA
Found at i:77903 original size:6 final size:6
Alignment explanation
Indices: 77896--77930 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
77886 TAAACAAAAT
*
77896 GCAAAT GCAAAC GCAAAC GCAAAC GCAAAC GCAAA
1 GCAAAC GCAAAC GCAAAC GCAAAC GCAAAC GCAAA
77931 GATGCAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.29, G:0.17, T:0.03
Consensus pattern (6 bp):
GCAAAC
Found at i:80916 original size:42 final size:44
Alignment explanation
Indices: 80868--80958 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 44
80858 GACTAAATAG
80868 AATAAATAGAAAA-TAAAGCGCA-ATAA-TTAAA-G-ACTAAAATTA
1 AATAAATA-AAAAGTAAAGCGCAGA-AATTTAAATGCA-TAAAATTA
*
80910 AATAAATAAAAAGTAAAGGGCAGAAATTTAAATGCATAAAATTA
1 AATAAATAAAAAGTAAAGCGCAGAAATTTAAATGCATAAAATTA
80954 AATAA
1 AATAA
80959 CAAAAATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
41 4 0.09
42 18 0.42
43 6 0.14
44 14 0.33
45 1 0.02
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (44 bp):
AATAAATAAAAAGTAAAGCGCAGAAATTTAAATGCATAAAATTA
Found at i:81208 original size:4 final size:4
Alignment explanation
Indices: 81199--81227 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
81189 TAATAGCAAT
81199 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
81228 GTATAACAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:86551 original size:11 final size:11
Alignment explanation
Indices: 86535--86576 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
86525 TAATAATATT
86535 TTAAATTAATC
1 TTAAATTAATC
86546 TTAAATTAA-C
1 TTAAATTAATC
* *
86556 TTAAAAATCATC
1 TT-AAATTAATC
86568 TTAAATTAA
1 TTAAATTAA
86577 AGCATAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 3 0.12
11 19 0.76
12 3 0.12
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAATTAATC
Found at i:86551 original size:33 final size:33
Alignment explanation
Indices: 86513--86576 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
86503 TTGTAATTAT
* *
86513 TTAAATTAAACATAATAAT-ATTTTAAATTAATC
1 TTAAATT-AACATAAAAATCATCTTAAATTAATC
*
86546 TTAAATTAACTTAAAAATCATCTTAAATTAA
1 TTAAATTAACATAAAAATCATCTTAAATTAA
86577 AGCATAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.41
Consensus pattern (33 bp):
TTAAATTAACATAAAAATCATCTTAAATTAATC
Found at i:88804 original size:4 final size:4
Alignment explanation
Indices: 88790--88822 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
88780 ATGAAATCTG
*
88790 TTTA ATTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
88823 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:90229 original size:12 final size:12
Alignment explanation
Indices: 90212--90240 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
90202 ATAATTGTAC
90212 GAGTACGAACAT
1 GAGTACGAACAT
90224 GAGTACGAACAT
1 GAGTACGAACAT
90236 GAGTA
1 GAGTA
90241 GGGTTGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.28, T:0.17
Consensus pattern (12 bp):
GAGTACGAACAT
Found at i:90324 original size:14 final size:14
Alignment explanation
Indices: 90305--90334 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
90295 TTAATAAATG
90305 TATATTTAAATAAT
1 TATATTTAAATAAT
90319 TATATTTAAATAAT
1 TATATTTAAATAAT
90333 TA
1 TA
90335 AAAACTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATTTAAATAAT
Found at i:93522 original size:21 final size:21
Alignment explanation
Indices: 93498--93567 Score: 97
Period size: 21 Copynumber: 3.3 Consensus size: 21
93488 GCCATCTCCG
93498 CAGGGTTATATTCCTAGCCCT
1 CAGGGTTATATTCCTAGCCCT
93519 CAGGGTTATATTCCTAGCCCT
1 CAGGGTTATATTCCTAGCCCT
* * *
93540 CCA-GGTTACATGCCTAGCCCG
1 -CAGGGTTATATTCCTAGCCCT
93561 CAGGGTT
1 CAGGGTT
93568 TTATGACACC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.29
Consensus pattern (21 bp):
CAGGGTTATATTCCTAGCCCT
Found at i:94120 original size:34 final size:34
Alignment explanation
Indices: 94077--94149 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
94067 TTAAATGTTT
*
94077 TTAATATACAAATTATAGTATTCAAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
* * *
94111 TTAAAATACAAATTATGGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
94145 TTAAA
1 TTAAA
94150 TTCAACTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCAAAATTTAAAA
Found at i:94445 original size:63 final size:63
Alignment explanation
Indices: 94342--94466 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 63
94332 CAATGTCACG
* * *
94342 ACCAACTTATCACTTCACATTTATTCAATTTATCCGTAACATTTTATCCAATATATTCAAACA
1 ACCAACTTATCACTTAACATTTATTCAATTTATCCATAACAGTTTATCCAATATATTCAAACA
* *
94405 ACCAA-TTGATCACTTAACATTTATTCAATTTATTCATAACAGTTTATCCAATTTATTCAAAC
1 ACCAACTT-ATCACTTAACATTTATTCAATTTATCCATAACAGTTTATCCAATATATTCAAAC
94467 TTCACATAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 2 0.04
63 54 0.96
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (63 bp):
ACCAACTTATCACTTAACATTTATTCAATTTATCCATAACAGTTTATCCAATATATTCAAACA
Found at i:94450 original size:23 final size:22
Alignment explanation
Indices: 94358--94463 Score: 80
Period size: 23 Copynumber: 4.9 Consensus size: 22
94348 TTATCACTTC
* * *
94358 ACATTTATTCAATTTATCCGTA
1 ACATTTATCCAATTTATTCATA
*
94380 ACATTTTATCCAATATATTCA-A
1 ACA-TTTATCCAATTTATTCATA
*
94402 ACA---A-CCAATTGA-TCACTTA
1 ACATTTATCCAATTTATTCA--TA
*
94421 ACATTTATTCAATTTATTCATA
1 ACATTTATCCAATTTATTCATA
94443 ACAGTTTATCCAATTTATTCA
1 ACA-TTTATCCAATTTATTCA
94464 AACTTCACAT
Statistics
Matches: 65, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
16 3 0.05
17 6 0.09
18 1 0.02
19 4 0.06
22 13 0.20
23 35 0.54
24 3 0.05
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.42
Consensus pattern (22 bp):
ACATTTATCCAATTTATTCATA
Found at i:94940 original size:138 final size:138
Alignment explanation
Indices: 94598--95381 Score: 1232
Period size: 138 Copynumber: 5.7 Consensus size: 138
94588 CCATCCATCT
* * *
94598 ATAGTTCCCCGGGGGATATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGACAATGATAACATATTCTCTGACAAAATAAT
* * *
94663 CGAAGGCGC-CCCCCAGGAATGAGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
66 CGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
94727 TGACATGA
131 TGACATGA
* * * *
94735 ATAGTT-CCCGGGGGACATGAGTTAGATAATAAGGA-AATGATAATATATTATCTGACAAAATAA
1 ATAGTTCCCCGGGGGACATGAGTGACATAAT-AGGACAATGATAACATATTCTCTGACAAAATAA
94798 TCGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTA
65 TCGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTA
*
94863 CTGGCATGA
130 CTGACATGA
*
94872 ATAGTTCCCTGGGGGACATGAGTGACATAATAGGACAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGACAATGATAACATATTCTCTGACAAAATAAT
*
94937 CGAAGGCGCGCCCCCAGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
66 CGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
95002 TGACATGA
131 TGACATGA
* *
95010 ATAGTTCCCCGGGGGACATGAGTGACATAATATGAGAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGACAATGATAACATATTCTCTGACAAAATAAT
* * *
95075 CGAAGGCGCGCCCCCGGGAACGAGCTTTCACCCCTTTTCCAAGTCCCCTCAGAAATAATAGGTAC
66 CGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
*
95140 TGACATTA
131 TGACATGA
* * *
95148 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGATAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGACAATGATAACATATTCTCTGACAAAATAAT
* * * *
95213 CGAAGGCGCGACCCCGGGAATGCGCTTTCACCACTTTGCCAAGTCCCCTTAGAAATAATAAGTAC
66 CGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
95278 TGACATGA
131 TGACATGA
* ** * *
95286 ATAGTTCCTCAAGGGACATGAGTAACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGACAATGATAACATATTCTCTGACAAAATAAT
* * *
95351 CAAAGGTGCGCCCCCGGGAACGCGCCTTCAC
66 CGAAGGCGCGCCCCCGGGAACGCGCTTTCAC
95382 ATGAATAGTA
Statistics
Matches: 593, Mismatches: 50, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
136 56 0.09
137 78 0.13
138 459 0.77
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (138 bp):
ATAGTTCCCCGGGGGACATGAGTGACATAATAGGACAATGATAACATATTCTCTGACAAAATAAT
CGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
TGACATGA
Found at i:100837 original size:15 final size:14
Alignment explanation
Indices: 100807--100833 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
100797 AATGTAAAGC
100807 AAAAATAGAAAATA
1 AAAAATAGAAAATA
100821 AAAAATAGAAAAT
1 AAAAATAGAAAAT
100834 TAAATTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAATAGAAAATA
Found at i:100873 original size:14 final size:14
Alignment explanation
Indices: 100829--100881 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
100819 TAAAAAATAG
*
100829 AAAATTAAATTAAT
1 AAAATTAAATAAAT
* ** *
100843 GAAATTAAAGGACT
1 AAAATTAAATAAAT
100857 AAAATTAAATAAAT
1 AAAATTAAATAAAT
100871 AAAATATAAAT
1 AAAAT-TAAAT
100882 GACATACATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
14 25 0.83
15 5 0.17
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (14 bp):
AAAATTAAATAAAT
Found at i:101457 original size:18 final size:16
Alignment explanation
Indices: 101425--101455 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
101415 TGAAACTCGA
101425 CTCGAACTCAAAAAAG
1 CTCGAACTCAAAAAAG
101441 CTCGAACTCAAAAAA
1 CTCGAACTCAAAAAA
101456 AATTCAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.13
Consensus pattern (16 bp):
CTCGAACTCAAAAAAG
Found at i:101505 original size:24 final size:24
Alignment explanation
Indices: 101473--101537 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
101463 GAGCCCGATT
*
101473 GAGAATCGAGCTCGATTGAAGCTC
1 GAGACTCGAGCTCGATTGAAGCTC
101497 GAGACTCGAGCTCGATTGAAGCTC
1 GAGACTCGAGCTCGATTGAAGCTC
* *
101521 GAGACTCAAACTCGATT
1 GAGACTCGAGCTCGATT
101538 TTGAGCTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (24 bp):
GAGACTCGAGCTCGATTGAAGCTC
Found at i:103106 original size:7 final size:7
Alignment explanation
Indices: 103094--103207 Score: 66
Period size: 7 Copynumber: 16.3 Consensus size: 7
103084 CATAATTGGA
103094 TTTAGGG
1 TTTAGGG
103101 TTTAGGG
1 TTTAGGG
* *
103108 TTTAAGA
1 TTTAGGG
*
103115 TTTAGAG
1 TTTAGGG
*
103122 TTTAGGA
1 TTTAGGG
*
103129 TTTAAGG
1 TTTAGGG
*
103136 TTTATGG
1 TTTAGGG
*
103143 TTTATGG
1 TTTAGGG
* *
103150 TTTTGAG
1 TTTAGGG
*
103157 TTAAGGG
1 TTTAGGG
**
103164 TTTAAAG
1 TTTAGGG
*
103171 TTTATGG
1 TTTAGGG
* *
103178 TCTAGGA
1 TTTAGGG
*
103185 TTTAGGA
1 TTTAGGG
*
103192 TTTAGGA
1 TTTAGGG
*
103199 TTTAAGG
1 TTTAGGG
103206 TT
1 TT
103208 AATTACAAAT
Statistics
Matches: 80, Mismatches: 27, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 80 1.00
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:103117 original size:21 final size:21
Alignment explanation
Indices: 103092--103152 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
103082 CACATAATTG
103092 GATTTAGGGTTTAGGGTTTAA
1 GATTTAGGGTTTAGGGTTTAA
* *
103113 GATTTAGAGTTTAGGATTTAA
1 GATTTAGGGTTTAGGGTTTAA
* * *
103134 GGTTTATGGTTTATGGTTT
1 GATTTAGGGTTTAGGGTTT
103153 TGAGTTAAGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.48
Consensus pattern (21 bp):
GATTTAGGGTTTAGGGTTTAA
Found at i:103130 original size:35 final size:35
Alignment explanation
Indices: 103091--103207 Score: 128
Period size: 35 Copynumber: 3.3 Consensus size: 35
103081 TCACATAATT
* *
103091 GGATTTAGGGTTTAGGGTTTAAGATTTAGAGTTTA
1 GGATTTAAGGTTTATGGTTTAAGATTTAGAGTTTA
* * * *
103126 GGATTTAAGGTTTATGGTTTATGGTTTTGAGTTAA
1 GGATTTAAGGTTTATGGTTTAAGATTTAGAGTTTA
* * * *
103161 GGGTTTAAAGTTTATGGTCTAGGATTTAG-GATTTA
1 GGATTTAAGGTTTATGGTTTAAGATTTAGAG-TTTA
103196 GGATTTAAGGTT
1 GGATTTAAGGTT
103208 AATTACAAAT
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
34 1 0.02
35 65 0.98
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.44
Consensus pattern (35 bp):
GGATTTAAGGTTTATGGTTTAAGATTTAGAGTTTA
Found at i:103345 original size:21 final size:22
Alignment explanation
Indices: 103278--103339 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 22
103268 ATCGTGATAT
* *
103278 TAAATATTTGTCATTAGAAATATAT
1 TAAATATTTTTCATTAG--ATA-AA
103303 TAAATATTTTTCATTAGATAAA
1 TAAATATTTTTCATTAGATAAA
*
103325 TAAAT-TTTTTTATTA
1 TAAATATTTTTCATTA
103340 ATTAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.26
22 6 0.18
23 3 0.09
25 16 0.47
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (22 bp):
TAAATATTTTTCATTAGATAAA
Found at i:103641 original size:11 final size:11
Alignment explanation
Indices: 103625--103688 Score: 62
Period size: 11 Copynumber: 6.0 Consensus size: 11
103615 GTATTATAGA
103625 ATTTTTAATAT
1 ATTTTTAATAT
103636 ATTTTTAA-A-
1 ATTTTTAATAT
103645 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
103656 ACCATTAATGT
1 ATTTTTAATAT
103667 ATTTTTAATAT
1 ATTTTTAATAT
103678 ATTTTTAATAT
1 ATTTTTAATAT
103689 TGTAATTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 29 0.69
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:105020 original size:20 final size:20
Alignment explanation
Indices: 104997--105052 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 20
104987 TTGAACAAAC
*
104997 TCTTCTTATTATGAACTTTT
1 TCTTCTTATTATGAACTTGT
* * * *
105017 TCTTCCTCTT-TGGACGTGT
1 TCTTCTTATTATGAACTTGT
*
105036 TCTTCTCATTATGAACT
1 TCTTCTTATTATGAACT
105053 CTTCCACTGA
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.16, C:0.21, G:0.11, T:0.52
Consensus pattern (20 bp):
TCTTCTTATTATGAACTTGT
Found at i:105123 original size:118 final size:118
Alignment explanation
Indices: 104846--105895 Score: 557
Period size: 123 Copynumber: 8.7 Consensus size: 118
104836 TCTCTTCCTT
* * * **
104846 TGTGATAGAAT-TAATCAAAAGGTCGAACAAGTTCTT-TTCATTATGAACTTCTTCTTTTTCTTC
1 TGTGATGGAATCTAA-CAAAAGGTTGAACAAGCTCTTCTT-ATTATGAACTTCTTCTTCCTCTTC
* *
104909 GGATGAGTTCTTATCATTATGAACTCTTCTACTGGGAATGATGATCCATCTATTTC
64 GGATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAATGATGATCCATCTA-TTC
** * * * * *
104965 TACGATTGAATATAACAAAAGGTTGAACAAACTCTTCTTATTATGAACTTTTTCTTCCTCTTTGG
1 TGTGATGGAATCTAACAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGG
* * * **
105030 ACGTGTTCTTCTCATTATGAACTCTTCCACT-GAAATGACAATCCATCTCATTC
66 ATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAATGATGATCCATCT-ATTC
* * *
105083 TGTGATGGAATCTAGCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTGTTCTTCCTCTTTGG
1 TGTGATGGAATCTAACAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGG
* * * *
105148 ATAAGTTCTTCTTATTATGAACTC-TCTACTGGAAATGTTGATCCATCGA---
66 ATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAATGATGATCCATCTATTC
* * ** * *
105197 -GTGATGGAATCTATCAAAAGGTTGAACAAGTTCTTCAAATTATAAACTTCTTCTTCCTCTTCAG
1 TGTGATGGAATCTAACAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGG
* * * * *
105261 ATGAGTTCTTCTTATTACGAACTC--CTTCTGGAAATGTTGATGTTGCTCTATCTCCTTC
66 ATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAA---TGATGAT-C-C-ATCT-ATTC
* * * * * ** * *
105319 TGTGAT--AAGTCGAGCAAAAGGTTGAATAAGTTCTCCAGATTATGAACTTCTTCTTCATCTTCA
1 TGTGATGGAA-TCTAACAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCG
* * * * *
105382 GATGAGTTCTTCTTATTACGAA--CTTCTTCTGGAAATGTTGATGTTGCTCTATCTCCTTC
65 GATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAA---TGATGAT-C-C-ATCT-ATTC
* * * * * * * *
105441 TGCGATAGAGT-TGAGCAAAAGGTTGAATAAGTTCTT-TAGATTATGAACTTATTCTTCCTCTTC
1 TGTGATGGAATCT-AACAAAAGGTTGAACAAGCTCTTCT-TATTATGAACTTCTTCTTCCTCTTC
** * * * *
105504 ATATGAGTTCTTCTTATTATGAACTC--CTTCTGAAAATGTTGATGATGCTCTATCTCCTTC
64 GGATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAA---TGATGAT-C-C-ATCT-ATTC
* * * * * ** *
105564 TGCGATAGAGTC-AAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCA
1 TGTGATGGAATCTAA-CAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCG
* * * * *
105628 GATGAGTTATTCTTATTATGAAATC--CTTCTGGAAATGTTGATGCTGC-TCTATCTCC
65 GATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAATGATGAT-C--CATCTAT-T-C
* * * * * * * **
105684 TTCTACGATAGAGT-TGAGCAAAAGGTTGAATAAGTTTTTCAGATTATGAACTTCTTCTTCCTCT
1 -TGT--GATGGAATCT-AACAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCT
* * * * * * *
105748 TCAGATGAGTTCTTTTTATTACGAACTC--CTTCTGGAAATTTTGATGCTGCTCTTTCTCATTC
62 TCGGATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAA---TGATGAT-C-C-ATCT-ATTC
** * * * * * * ** * *
105810 TACGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAG
1 TGTGATGGAATCTAACAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGG
*
105875 ATGAGTTCTTCTTATTATGAA
66 ATGAGTTCTTCTCATTATGAA
105896 TTCCTTTTGG
Statistics
Matches: 795, Mismatches: 94, Indels: 80
0.82 0.10 0.08
Matches are distributed among these distances:
112 9 0.01
113 78 0.10
115 5 0.01
116 1 0.00
117 7 0.01
118 112 0.14
119 80 0.10
120 15 0.02
121 4 0.01
122 109 0.14
123 356 0.45
124 2 0.00
125 3 0.00
126 8 0.01
127 4 0.01
128 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (118 bp):
TGTGATGGAATCTAACAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGG
ATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAATGATGATCCATCTATTC
Found at i:105251 original size:113 final size:115
Alignment explanation
Indices: 104846--105301 Score: 449
Period size: 118 Copynumber: 3.9 Consensus size: 115
104836 TCTCTTCCTT
* * * **
104846 TGTGATAGAAT-TAATCAAAAGGTCGAACAAGTTCTT-TTCATTATGAACTTCTTCTTTTTCTTC
1 TGTGATGGAATCT-ATCAAAAGGTTGAACAAGCTCTTCTT-ATTATGAACTTCTTCTTCCTCTTC
* * *
104909 GGATGAGTTCTTATCATTATGAACTCTTCTACTGGGAATGATGATCCATCTA
64 GGATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAATGATGATCCATCCA
* * * * * *
104961 TTTCTACGATTGAATATAACAAAAGGTTGAACAAACTCTTCTTATTATGAACTTTTTCTTCCTCT
1 --TGT--GATGGAATCTATCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCT
* * * * **
105026 TTGGACGTGTTCTTCTCATTATGAACTCTTCCACT-GAAATGACAATCCATCTCA
62 TCGGATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAATGATGATCCATC-CA
* *
105080 TTCTGTGATGGAATCTAGCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTGTTCTTCCTCTT
1 ---TGTGATGGAATCTATCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTT
* * * * *
105145 TGGATAAGTTCTTCTTATTATGAACTC-TCTACTGGAAATGTTGATCCATCGA
63 CGGATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAATGATGATCCATCCA
* ** * *
105197 -GTGATGGAATCTATCAAAAGGTTGAACAAGTTCTTCAAATTATAAACTTCTTCTTCCTCTTCAG
1 TGTGATGGAATCTATCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGG
* * * *
105261 ATGAGTTCTTCTTATTACGAACTC--CTTCTGGAAATGTTGAT
66 ATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAATGATGAT
105302 GTTGCTCTAT
Statistics
Matches: 287, Mismatches: 45, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
112 16 0.06
113 78 0.27
117 8 0.03
118 103 0.36
119 76 0.26
120 6 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (115 bp):
TGTGATGGAATCTATCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGG
ATGAGTTCTTCTCATTATGAACTCTTCTACTGGAAATGATGATCCATCCA
Found at i:106163 original size:123 final size:123
Alignment explanation
Indices: 105211--106157 Score: 1455
Period size: 123 Copynumber: 7.7 Consensus size: 123
105201 TGGAATCTAT
* * *
105211 CAAAAGGTTGAACAAGTTCTTCAAATTATAAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
1 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
* *
105276 TACGAACTCCTTCTGGAAATGTTGATGTTGCTCTATCTCCTTCTGTGATA-AGTCGAG
66 TACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAG
* *
105333 CAAAAGGTTGAATAAGTTCTCCAGATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTTAT
1 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
* * *
105398 TACGAACTTCTTCTGGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTTGAG
66 TACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAG
* * *
105456 CAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTATTCTTCCTCTTCATATGAGTTCTTCTTAT
1 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
* * * *
105521 TATGAACTCCTTCTGAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCAAG
66 TACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAG
*
105579 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTTAT
1 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
* * * *
105644 TATGAAATCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTACGATAGAGTTGAG
66 TACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAG
* *
105702 CAAAAGGTTGAATAAGTTTTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTTTTAT
1 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
* * * *
105767 TACGAACTCCTTCTGGAAATTTTGATGCTGCTCTTTCTCATTCTACGATAGAGTCGAG
66 TACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAG
*
105825 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTTAT
1 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
* * * * * * *
105890 TATGAATTCCTTTTGGAAATGTTGATGCTGTTATATTTCATTCTGCGATAGAGTCGAG
66 TACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAG
** *
105948 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTAATCTTCCTCTTCATATGAGTTCTTCTTAT
1 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
** * * *
106013 TATTAACTCCTTCTAGAAATGTTGATCCTGCTCTATCTCCTTCTACGATAGAGTCGAG
66 TACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAG
* * *
106071 CAAAAGGTTAAATAAGTTCTTCAGATTATGAAATTCTTATTCCTCTTCAGATGAGTTCTTCTTAT
1 CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
*
106136 TACGAACTTCTTCTGGAAATGT
66 TACGAACTCCTTCTGGAAATGT
106158 CGATCCCTCG
Statistics
Matches: 751, Mismatches: 73, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
122 108 0.14
123 643 0.86
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (123 bp):
CAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
TACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAG
Found at i:108993 original size:3 final size:3
Alignment explanation
Indices: 108980--109028 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
108970 TTGATTCAAT
108980 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TT- TTC TT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
109024 TTC TT
1 TTC TT
109029 TTTTTTCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 8 0.19
3 35 0.81
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:109024 original size:7 final size:7
Alignment explanation
Indices: 108979--109104 Score: 91
Period size: 7 Copynumber: 17.4 Consensus size: 7
108969 CTTGATTCAA
108979 TTTCTTT
1 TTTCTTT
108986 TCTTCTTCT
1 T-TTCTT-T
108995 TCTTCTTCT
1 T-TTCTT-T
109004 TCTTC-TT
1 T-TTCTTT
*
109011 CTTCTTT
1 TTTCTTT
109018 TTTCTTT
1 TTTCTTT
109025 TCTT-TTT
1 T-TTCTTT
109032 TTTCTTT
1 TTTCTTT
109039 TTTCTTT
1 TTTCTTT
*
109046 ATTCTTT
1 TTTCTTT
*
109053 ATTCTTT
1 TTTCTTT
*
109060 ATTCTTT
1 TTTCTTT
*
109067 ATTCTTT
1 TTTCTTT
109074 TCTT-TTCT
1 T-TTCTT-T
109082 TTT-TTT
1 TTTCTTT
109088 CTTT-TTT
1 -TTTCTTT
109095 TTTCTTT
1 TTTCTTT
109102 TTT
1 TTT
109105 TCTAATAGAT
Statistics
Matches: 106, Mismatches: 4, Indels: 18
0.83 0.03 0.14
Matches are distributed among these distances:
6 9 0.08
7 70 0.66
8 12 0.11
9 15 0.14
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTCTTT
Found at i:109590 original size:6 final size:7
Alignment explanation
Indices: 109571--109600 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
109561 AATCAATCCC
109571 TCTTTTT
1 TCTTTTT
109578 TCTTTTT
1 TCTTTTT
109585 TCTTTTT
1 TCTTTTT
109592 TCTATTTT
1 TCT-TTTT
109600 T
1 T
109601 TTCTTCTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (7 bp):
TCTTTTT
Found at i:113928 original size:14 final size:14
Alignment explanation
Indices: 113911--113946 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
113901 AAGCAAAAAA
*
113911 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
113925 AAATTAAAGGACTG
1 AAATTAAAGGAATG
113939 AAATTAAA
1 AAATTAAA
113947 TAAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:116952 original size:42 final size:42
Alignment explanation
Indices: 116876--117136 Score: 427
Period size: 42 Copynumber: 6.3 Consensus size: 42
116866 CATATTCGCA
*
116876 TTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * * *
116916 TTACGATAGTCGAAGTTCGCATTGCCATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
116958 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
117000 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
117042 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
117084 TTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
117126 TTGCGATAGTC
1 TTGCGATAGTC
117137 CAAAATCGCA
Statistics
Matches: 205, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 23 0.11
41 2 0.01
42 180 0.88
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:117764 original size:40 final size:40
Alignment explanation
Indices: 117681--117813 Score: 221
Period size: 40 Copynumber: 3.3 Consensus size: 40
117671 TGCGATTTTG
117681 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
* * *
117723 GACTATTGCACCGAATTTGGAAAATAGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
117763 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
117803 GACTATCGCAA
1 GACTATCGCAA
117814 TGCGAATATG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
40 66 0.78
41 1 0.01
42 18 0.21
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (40 bp):
GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
Found at i:117773 original size:21 final size:21
Alignment explanation
Indices: 117706--117819 Score: 101
Period size: 21 Copynumber: 5.6 Consensus size: 21
117696 TTTGGAATAA
117706 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * * **
117727 ATTGC-AC-CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
117746 ATAGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
117767 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
117786 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
117807 ATCGCAATGCGAA
1 ATCGCAACGCGAA
117820 TATGTAAATC
Statistics
Matches: 69, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
19 27 0.39
20 4 0.06
21 38 0.55
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:117857 original size:21 final size:21
Alignment explanation
Indices: 117828--117876 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
117818 AATATGTAAA
*
117828 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
* *
117849 TCGCGTTGCTATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
117870 TCGCGTT
1 TCGCGTT
117877 ACGAGTCTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:121990 original size:8 final size:8
Alignment explanation
Indices: 121979--122037 Score: 54
Period size: 8 Copynumber: 7.9 Consensus size: 8
121969 GATGGGTGTT
121979 GGGATTTA
1 GGGATTTA
121987 GGGATTT-
1 GGGATTTA
121994 GGG-TTTA
1 GGGATTTA
* *
122001 GGTATTTT
1 GGGATTTA
*
122009 GAGATTTA
1 GGGATTTA
122017 GGGATTT-
1 GGGATTTA
122024 GGG-TTTA
1 GGGATTTA
*
122031 GGTATTT
1 GGGATTT
122038 TGAGGCTTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
6 6 0.15
7 10 0.25
8 24 0.60
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.46
Consensus pattern (8 bp):
GGGATTTA
Found at i:122002 original size:14 final size:14
Alignment explanation
Indices: 121977--122037 Score: 68
Period size: 14 Copynumber: 4.1 Consensus size: 14
121967 TAGATGGGTG
121977 TTGGGATTTAGGGAT
1 TTGGG-TTTAGGGAT
*
121992 TTGGGTTTAGGTATT
1 TTGGGTTTAGGGA-T
*
122007 TTGAGATTTAGGGAT
1 TTG-GGTTTAGGGAT
*
122022 TTGGGTTTAGGTAT
1 TTGGGTTTAGGGAT
122036 TT
1 TT
122038 TGAGGCTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 18 0.46
15 13 0.33
16 8 0.21
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (14 bp):
TTGGGTTTAGGGAT
Found at i:122015 original size:30 final size:30
Alignment explanation
Indices: 121981--122041 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
121971 TGGGTGTTGG
121981 GATTTAGGGATTTGGGTTTAGGTATTTTGA
1 GATTTAGGGATTTGGGTTTAGGTATTTTGA
122011 GATTTAGGGATTTGGGTTTAGGTATTTTGA
1 GATTTAGGGATTTGGGTTTAGGTATTTTGA
122041 G
1 G
122042 GCTTTGAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (30 bp):
GATTTAGGGATTTGGGTTTAGGTATTTTGA
Found at i:128350 original size:22 final size:20
Alignment explanation
Indices: 128309--128348 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
128299 ATAATGCTTC
128309 TGGGATATATGTTTGAGAGA
1 TGGGATATATGTTTGAGAGA
128329 TGGGATATATGTTTGAGAGA
1 TGGGATATATGTTTGAGAGA
128349 GAGATCTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (20 bp):
TGGGATATATGTTTGAGAGA
Found at i:146028 original size:21 final size:21
Alignment explanation
Indices: 146011--146054 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
146001 ATAAATTAGC
*
146011 AAATTTTGTCAAATAATTCCT
1 AAATTTTATCAAATAATTCCT
*
146032 AAATTTTATCAAATTAGTTCCT
1 AAATTTTATCAAA-TAATTCCT
146054 A
1 A
146055 GACTTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.43
Consensus pattern (21 bp):
AAATTTTATCAAATAATTCCT
Found at i:153620 original size:23 final size:24
Alignment explanation
Indices: 153588--153633 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
153578 ATTATAAATA
153588 ATATATATGTAAAATGTTTCGATT
1 ATATATATGTAAAATGTTTCGATT
153612 ATAT-TATGTAAAATGTTTCGAT
1 ATATATATGTAAAATGTTTCGAT
153634 AATGTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (24 bp):
ATATATATGTAAAATGTTTCGATT
Found at i:153640 original size:18 final size:20
Alignment explanation
Indices: 153589--153642 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 20
153579 TTATAAATAA
153589 TATATATGTAAAATGTTTCG
1 TATATATGTAAAATGTTTCG
153609 ATTATATTATGTAAAATGTTTCG
1 --TATA-TATGTAAAATGTTTCG
153632 -ATA-ATGTAAAA
1 TATATATGTAAAA
153643 ATTATAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.26
20 3 0.10
22 4 0.13
23 16 0.52
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.43
Consensus pattern (20 bp):
TATATATGTAAAATGTTTCG
Found at i:153685 original size:13 final size:13
Alignment explanation
Indices: 153656--153690 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
153646 ATAACTAATA
*
153656 ATATTAAAT-ATT
1 ATATTAAATAAAT
153668 ATATTAAATAAAT
1 ATATTAAATAAAT
153681 ATATTAAATA
1 ATATTAAATA
153691 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:153929 original size:33 final size:34
Alignment explanation
Indices: 153868--153966 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 34
153858 AAATTTAATG
*
153868 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
153902 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
153935 TTAAATTTCGAATAATA-AATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
153967 AACATTTATC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
33 39 0.71
34 16 0.29
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:154509 original size:21 final size:21
Alignment explanation
Indices: 154485--154545 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
154475 ATAAAACCCT
154485 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGCATGTAACCTG
154506 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGCATGTAACCTG
*
154527 GCGGGCTAGGAATGTAACC
1 GCGGGCTAGGCATGTAACC
154546 CTGCGGCTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.18
Consensus pattern (21 bp):
GCGGGCTAGGCATGTAACCTG
Found at i:154551 original size:21 final size:21
Alignment explanation
Indices: 154479--154570 Score: 111
Period size: 21 Copynumber: 4.5 Consensus size: 21
154469 TATGGTATAA
*
154479 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
154500 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
154521 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
154542 AACCCTGC-GGCT-CGAATGT
1 AACCCTGCGGGCTAGGAATGT
154561 AACCCTGCGG
1 AACCCTGCGG
154571 AGATGGCATA
Statistics
Matches: 66, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.21
20 8 0.12
21 41 0.62
22 3 0.05
ACGTcount: A:0.21, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:156360 original size:33 final size:30
Alignment explanation
Indices: 156321--156392 Score: 99
Period size: 33 Copynumber: 2.3 Consensus size: 30
156311 TAATCTAAAT
*
156321 AAATAATAATTATATAAATATTATTTAATAATA
1 AAATAATAATTACATAAATA-TA-TTAAT-ATA
*
156354 AAATAATATTTACATAAATATATTAATATA
1 AAATAATAATTACATAAATATATTAATATA
156384 AAATAATAA
1 AAATAATAA
156393 CTAAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.31
31 5 0.14
32 2 0.06
33 18 0.50
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (30 bp):
AAATAATAATTACATAAATATATTAATATA
Found at i:156401 original size:15 final size:16
Alignment explanation
Indices: 156383--156415 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
156373 ATATTAATAT
156383 AAAATAATAAC-TAAA
1 AAAATAATAACATAAA
*
156398 AAAATACTAACATAAA
1 AAAATAATAACATAAA
156414 AA
1 AA
156416 TAAATTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAATAACATAAA
Found at i:157338 original size:20 final size:21
Alignment explanation
Indices: 157313--157366 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
157303 GACCAACAAA
157313 TTCGCAACGCGAA-CTCCAAT
1 TTCGCAACGCGAATCTCCAAT
* *
157333 TTCGCAAC-CCAATTTCCAAT
1 TTCGCAACGCGAATCTCCAAT
157353 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
157367 ATGTAAATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.24
Consensus pattern (21 bp):
TTCGCAACGCGAATCTCCAAT
Found at i:157999 original size:20 final size:20
Alignment explanation
Indices: 157948--158000 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
157938 ATCGCAACGC
*
157948 AATTTTAGTTTCACGTTGCG
1 AATTTAAGTTTCACGTTGCG
* * * *
157968 ATTTTCATTTTCGCGTTGCG
1 AATTTAAGTTTCACGTTGCG
157988 AATTTAAGTTTCA
1 AATTTAAGTTTCA
158001 GAAACTACTC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (20 bp):
AATTTAAGTTTCACGTTGCG
Found at i:159977 original size:4 final size:4
Alignment explanation
Indices: 159968--160010 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
159958 TTTTTTCGGC
* * * *
159968 TTTA TTTA TTTA TTTA TTTA CTAA TTTA TGTA TTAA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
160011 TCAGCGGCCC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:159985 original size:12 final size:12
Alignment explanation
Indices: 159968--160010 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
159958 TTTTTTCGGC
*
159968 TTTATTTATTTA
1 TTTATTTATTAA
*
159980 TTTATTTACTAA
1 TTTATTTATTAA
*
159992 TTTATGTATTAA
1 TTTATTTATTAA
160004 TTTATTT
1 TTTATTT
160011 TCAGCGGCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTATTTATTAA
Found at i:160202 original size:43 final size:42
Alignment explanation
Indices: 160150--160270 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
160140 GCCCAATGCA
* * * *
160150 CCTATCATCATTCAAGAGGCGCCTCCTAGCGTTTAAGAGGCCC
1 CCTATCATCATTCAAGAGGCGCCTCCCACCGTTCAAGA-GACC
* * *
160193 CCTCTCATCA-TCGAAGAAGCTCCTCCCACCGTTCAAGAGACC
1 CCTATCATCATTC-AAGAGGCGCCTCCCACCGTTCAAGAGACC
* *
160235 CCTATCATCGTTCAAGAGGTC-CCGCCCACCGTTCAA
1 CCTATCATCATTCAAGAGG-CGCCTCCCACCGTTCAA
160271 CAGCCCGATT
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
42 32 0.50
43 32 0.50
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.21
Consensus pattern (42 bp):
CCTATCATCATTCAAGAGGCGCCTCCCACCGTTCAAGAGACC
Found at i:161676 original size:69 final size:67
Alignment explanation
Indices: 161601--161776 Score: 245
Period size: 66 Copynumber: 2.6 Consensus size: 67
161591 TGGGGTACAC
161601 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAA-TTGATGAGGAAATA
1 TTTTTTTGCTTGTTTAATTGAATTTGT--A---AAAGTTGATTTGTTTAATTTGATGAGGAAATA
161664 AGAATTA
61 AGAATTA
* * *
161671 -TTTTTTGCTTGTTTAATTG-ATTTGTAAAAGTTTATTTGTTTAATTTGATGTGTAAATAAGAAT
1 TTTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAAT
161734 TA
66 TA
161736 TTTTTTTGCTTGTTTAATT-AATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTT
161777 GTTTTAAATT
Statistics
Matches: 98, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
64 16 0.16
65 19 0.19
66 38 0.39
67 1 0.01
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.53
Consensus pattern (67 bp):
TTTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAAT
TA
Found at i:161901 original size:13 final size:13
Alignment explanation
Indices: 161866--161903 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
161856 GATAGTCAAA
161866 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
*
161879 TTCTG-TTTGCGAT
1 TTC-GCGTTGCGAT
161892 TTCGCGTTGCGA
1 TTCGCGTTGCGA
161904 ATTTGACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.05
13 19 0.90
14 1 0.05
ACGTcount: A:0.08, C:0.21, G:0.29, T:0.42
Consensus pattern (13 bp):
TTCGCGTTGCGAT
Found at i:165490 original size:21 final size:19
Alignment explanation
Indices: 165419--165474 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
165409 ACTAAAACTT
*
165419 GTTGCGAAATT-AAATTCA
1 GTTGCGAATTTGAAATTCA
165437 TGTTGCGAATTTGAAATTCA
1 -GTTGCGAATTTGAAATTCA
165457 GTTGCGAATTTGAAATTC
1 GTTGCGAATTTGAAATTC
165475 CGCGTTGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 28 0.80
20 7 0.20
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:165519 original size:40 final size:41
Alignment explanation
Indices: 165457--165592 Score: 154
Period size: 40 Copynumber: 3.4 Consensus size: 41
165447 TTGAAATTCA
* * *
165457 GTTGCGAATTTGA-AATTCCGCGTTGCAAATTTGACTTTTGT
1 GTTGCGAATTTGACTATT-CGCGTTGCGAATTTGACTTCTGT
* *
165498 ATTGTGAATTTGACTA-TCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTCTGT
* *
165538 GTTGCG-ATTT-ACAAATTCGCGTTGCGAATTTGACTTGTGT
1 GTTGCGAATTTGAC-TATTCGCGTTGCGAATTTGACTTCTGT
*
165578 GTTACGAATTTGACT
1 GTTGCGAATTTGACT
165593 TCTGTGTTGC
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
38 2 0.03
39 5 0.06
40 53 0.67
41 16 0.20
42 3 0.04
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (41 bp):
GTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTCTGT
Found at i:165526 original size:20 final size:20
Alignment explanation
Indices: 165457--165572 Score: 78
Period size: 20 Copynumber: 5.8 Consensus size: 20
165447 TTGAAATTCA
*
165457 GTTGCGAATTTGA-AATTCCGC
1 GTTGCGAATTTGACTA-T-CGC
* * * *
165478 GTTGCAAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
* *
165498 ATTGTGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
165518 GTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GC
*
165538 GTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
165558 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
165573 TGTGTGTTAC
Statistics
Matches: 71, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
18 2 0.03
19 6 0.08
20 42 0.59
21 19 0.27
22 2 0.03
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:165567 original size:60 final size:60
Alignment explanation
Indices: 165503--165621 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
165493 TTTGTATTGT
*
165503 GAATTTGACTAT-CGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGC
1 GAATTTGACT-TGCGCGTTACGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGC
* * * *
165563 GAATTTGACTTGTGTGTTACGAATTTGACTTCTGTGTTGCGATTTATAGATTCGCGTTG
1 GAATTTGACTTGCGCGTTACGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTG
165622 AGAAATTAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 1 0.02
60 52 0.98
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.41
Consensus pattern (60 bp):
GAATTTGACTTGCGCGTTACGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGC
Found at i:165587 original size:20 final size:20
Alignment explanation
Indices: 165484--165600 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 20
165474 CCGCGTTGCA
* * **
165484 AATTTGACTTTTGTATTGTG
1 AATTTGACTTCTGTGTTACG
* *
165504 AATTTGACTATC-GCGTTGCG
1 AATTTGACT-TCTGTGTTACG
*
165524 AATTTGACTTCTGTGTTGCG
1 AATTTGACTTCTGTGTTACG
* *
165544 -ATTT-ACAAATTC-GCGTTGCG
1 AATTTGAC---TTCTGTGTTACG
*
165564 AATTTGACTTGTGTGTTACG
1 AATTTGACTTCTGTGTTACG
165584 AATTTGACTTCTGTGTT
1 AATTTGACTTCTGTGTT
165601 GCGATTTATA
Statistics
Matches: 79, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
18 2 0.03
19 8 0.10
20 59 0.75
21 8 0.10
22 2 0.03
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (20 bp):
AATTTGACTTCTGTGTTACG
Found at i:167476 original size:21 final size:21
Alignment explanation
Indices: 167445--167502 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
167435 AACCTCATCA
*
167445 TTAATCACTGTAAATTATTACG
1 TTAAT-ACTGTAAATTACTACG
167467 TTAATACTGTAAATTACTACG
1 TTAATACTGTAAATTACTACG
* * *
167488 TCAACACTTTAAATT
1 TTAATACTGTAAATT
167503 GTCACATTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.40
Consensus pattern (21 bp):
TTAATACTGTAAATTACTACG
Found at i:171455 original size:18 final size:17
Alignment explanation
Indices: 171434--171477 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
171424 AATATTTAAG
171434 TAAAA-ATTAAGAAATAAT
1 TAAAATATTAA-AAAT-AT
*
171452 TAAAATTTTAAAAATAT
1 TAAAATATTAAAAATAT
171469 TAAAATATT
1 TAAAATATT
171478 CATAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 10 0.43
18 9 0.39
19 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TAAAATATTAAAAATAT
Found at i:171470 original size:17 final size:19
Alignment explanation
Indices: 171440--171474 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
171430 TAAGTAAAAA
171440 TTAAGAAATAATTAAAATT
1 TTAAGAAATAATTAAAATT
171459 TTAA-AAAT-ATTAAAAT
1 TTAAGAAATAATTAAAAT
171475 ATTCATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
TTAAGAAATAATTAAAATT
Found at i:190919 original size:2 final size:2
Alignment explanation
Indices: 190912--190940 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
190902 TTCAAAATGA
190912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
190941 GACTCAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:192057 original size:60 final size:61
Alignment explanation
Indices: 191984--192105 Score: 160
Period size: 60 Copynumber: 2.0 Consensus size: 61
191974 TTTAAATTGG
* * *
191984 TCCCTAAACTATGACTAT-CATTCTAAATT-ATACCTCAAACTTTTT-AACATTTCAATTTCA
1 TCCCCAAACTATGACT-TCCATTCTAAATTGAT-CCCCAAACTTTTTGAACATTCCAATTTCA
* *
192044 TCCCCAAACTATGACTTCCATTCTAAATTGGTCCCCAAGCTTTTTGAACATTCCAATTTCA
1 TCCCCAAACTATGACTTCCATTCTAAATTGATCCCCAAACTTTTTGAACATTCCAATTTCA
192105 T
1 T
192106 TTCAAACTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
59 1 0.02
60 37 0.69
61 16 0.30
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (61 bp):
TCCCCAAACTATGACTTCCATTCTAAATTGATCCCCAAACTTTTTGAACATTCCAATTTCA
Found at i:199741 original size:104 final size:105
Alignment explanation
Indices: 199599--199972 Score: 597
Period size: 105 Copynumber: 3.6 Consensus size: 105
199589 TTTGTCGGAT
*
199599 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCATTCTGGGGTGAATTTGAAA
* * * *
199664 GGAACATGTTCTTCTAATTACGAA-ATTCTCCTTTAGGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* * * * *
199703 GAGTTCTTCTCATTATGAACTTTTTTGGAAATGCTGATTCACCTCATTCTAGGTTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCATTCTGGGGTGAATTTGAAA
*
199768 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTATGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* *
199808 GAGTTATTCTCATTATGAACTCTTCTGGAAATATTGATTCACCTCATTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCATTCTGGGGTGAATTTGAAA
* *
199873 GGAACAAGCTCTTCTCATTACGAACCTTCCCCTTTAAGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
*
199913 GAGTTCTTCTCATTATAAACTCTTCTGGAAATGTTGATTCACCTCATTCTGGGGTGAATT
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCATTCTGGGGTGAATT
199973 ATAGTTGTTG
Statistics
Matches: 246, Mismatches: 23, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
104 81 0.33
105 165 0.67
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCATTCTGGGGTGAATTTGAAA
GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
Found at i:200903 original size:7 final size:7
Alignment explanation
Indices: 200891--200937 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
200881 TCTCGAACCC
200891 TCTTTTT
1 TCTTTTT
200898 TC--TTT
1 TCTTTTT
*
200903 TCATTTT
1 TCTTTTT
*
200910 T-TTATT
1 TCTTTTT
200916 TCTTTTT
1 TCTTTTT
200923 TCTTTTT
1 TCTTTTT
200930 TCTTTTT
1 TCTTTTT
200937 T
1 T
200938 TTCCTTTTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
5 5 0.15
6 4 0.12
7 25 0.74
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (7 bp):
TCTTTTT
Found at i:200935 original size:25 final size:24
Alignment explanation
Indices: 200891--200964 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
200881 TCTCGAACCC
*
200891 TCTTTTTTCTTTTCATT-TTTTTATT
1 TCTTTTTTCTTTT--TTCTTTTTTTT
200916 TCTTTTTTCTTTTTTCTTTTTTTT
1 TCTTTTTTCTTTTTTCTTTTTTTT
* *
200940 CCTTTTCCTT-TTTTTTCATTTTTTT
1 TCTTTT--TTCTTTTTTCTTTTTTTT
200965 CATTCATTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
23 2 0.05
24 12 0.28
25 27 0.63
26 2 0.05
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (24 bp):
TCTTTTTTCTTTTTTCTTTTTTTT
Found at i:213152 original size:21 final size:23
Alignment explanation
Indices: 213114--213167 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
213104 CGTTGAATAT
*
213114 GGGGGAATC-AGTATCCCCTTGG
1 GGGGGAATCGAGTACCCCCTTGG
213136 GGGGGAATCGA-TACCCCCTTGG
1 GGGGGAATCGAGTACCCCCTTGG
213158 GGGGGAATCG
1 GGGGGAATCG
213168 GTTCCCTCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.19, C:0.22, G:0.41, T:0.19
Consensus pattern (23 bp):
GGGGGAATCGAGTACCCCCTTGG
Found at i:215327 original size:22 final size:22
Alignment explanation
Indices: 215247--215327 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
215237 AGAACCCATG
*
215247 GGGGGTATCGATT-CCC-TCAA
1 GGGGGAATCGATTCCCCTTCAA
* *
215267 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCCCTTC-AA
215291 GGGGGAATC-AGTTCCCCTTCAA
1 GGGGGAATCGA-TTCCCCTTCAA
*
215313 GGGGGTATCGATTCC
1 GGGGGAATCGATTCC
215328 ATCTGCACTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 2 0.04
21 9 0.18
22 16 0.33
23 18 0.37
24 4 0.08
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:220770 original size:22 final size:22
Alignment explanation
Indices: 220744--220825 Score: 146
Period size: 22 Copynumber: 3.7 Consensus size: 22
220734 AAACCATTCA
*
220744 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTTCCCCCTTGG
220766 GGGGGAATCGGTTCCCCCTTGG
1 GGGGGAATCGGTTCCCCCTTGG
*
220788 GGGGGAATTGGTTCCCCCTTGG
1 GGGGGAATCGGTTCCCCCTTGG
220810 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
220826 TCTGAGCAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.11, C:0.26, G:0.41, T:0.22
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCCTTGG
Found at i:233479 original size:15 final size:15
Alignment explanation
Indices: 233459--233513 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
233449 TTTACCGGAT
233459 AAAAAACCGGTTTGA
1 AAAAAACCGGTTTGA
233474 AAAAAACCGGTTTGA
1 AAAAAACCGGTTTGA
233489 AAAAAACCGG-TT--
1 AAAAAACCGGTTTGA
233501 AAAAAACCGGTTT
1 AAAAAACCGGTTT
233514 TTATCCGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.26
13 2 0.05
14 2 0.05
15 25 0.64
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (15 bp):
AAAAAACCGGTTTGA
Found at i:233504 original size:27 final size:29
Alignment explanation
Indices: 233459--233513 Score: 87
Period size: 27 Copynumber: 1.9 Consensus size: 29
233449 TTTACCGGAT
233459 AAAAAACCGGTTTGAAAAAAACCGGTTTGA
1 AAAAAACCGGTTT-AAAAAAACCGGTTTGA
233489 AAAAAACCGG-TT-AAAAAACCGGTTT
1 AAAAAACCGGTTTAAAAAAACCGGTTT
233514 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 13 0.52
29 2 0.08
30 10 0.40
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (29 bp):
AAAAAACCGGTTTAAAAAAACCGGTTTGA
Done.