Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008939.1 Hibiscus syriacus cultivar Beakdansim tig00112257_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: 68171
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2377 original size:13 final size:13
Alignment explanation
Indices: 2359--2385 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2349 GAATAAGAAG
2359 AATATATATATAT
1 AATATATATATAT
2372 AATATATATATAT
1 AATATATATATAT
2385 A
1 A
2386 CAGTTAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATATATATAT
Found at i:4459 original size:19 final size:19
Alignment explanation
Indices: 4439--4473 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4429 TAAAACTATT
4439 TTTTAT-TAT-ATTATTTA
1 TTTTATATATGATTATTTA
4456 TTTTATATATGATTATTT
1 TTTTATATATGATTATTT
4474 GAAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTATATATGATTATTTA
Found at i:8850 original size:9 final size:9
Alignment explanation
Indices: 8835--8885 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
8825 TTTTCATCCG
8835 ATTTTTTTT
1 ATTTTTTTT
*
8844 CTTTTTTTT
1 ATTTTTTTT
* *
8853 CTCTTTTTT
1 ATTTTTTTT
8862 ATTTTATTTT
1 ATTTT-TTTT
8872 ATTTTATTTT
1 ATTTT-TTTT
8882 ATTT
1 ATTT
8886 ATTATTTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
9 19 0.51
10 18 0.49
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:8866 original size:5 final size:5
Alignment explanation
Indices: 8858--8885 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
8848 TTTTTCTCTT
8858 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
8886 ATTATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:8965 original size:37 final size:36
Alignment explanation
Indices: 8923--9159 Score: 138
Period size: 39 Copynumber: 6.5 Consensus size: 36
8913 ATCAATATAG
8923 TATAATTTTTGAAAATATTTTTTGAAAAAATATAATA
1 TATAATTTTTGAAAATA-TTTTTGAAAAAATATAATA
* *
8960 TATAATTTTTAGAAAACGAATTTTGAAAAAATATATAATA
1 TATAATTTTT-GAAAA-TATTTTTG-AAAAA-ATATAATA
* *
9000 TATAGTTTTGGAAAATATTTTT---AAAATAT-ATA
1 TATAATTTTTGAAAATATTTTTGAAAAAATATAATA
* * *
9032 TAT-A--TAT-AATATAGTTTTTGAAAACATATATAT-
1 TATAATTTTTGAAAATA-TTTTTGAAAAAATATA-ATA
* *
9065 TATATAGTTTTGAAAA-CTTTTTGAAAACATGTATATAATA
1 TATA-ATTTTTGAAAATATTTTTGAAAA-A---ATATAATA
* * * *
9105 TATAGTTTTTAAAAACA-TTTTGAAAACATATATATAA
1 TATAATTTTTGAAAATATTTTTGAAAAAATATA-AT-A
*
9142 TATAGTTTTT-AAAATATT
1 TATAATTTTTGAAAATATT
9160 ATAATATATA
Statistics
Matches: 155, Mismatches: 21, Indels: 48
0.69 0.09 0.21
Matches are distributed among these distances:
28 5 0.03
29 6 0.04
32 12 0.08
33 7 0.05
34 5 0.03
35 6 0.04
36 17 0.11
37 24 0.15
38 18 0.12
39 30 0.19
40 25 0.16
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (36 bp):
TATAATTTTTGAAAATATTTTTGAAAAAATATAATA
Found at i:8984 original size:38 final size:36
Alignment explanation
Indices: 8923--9041 Score: 107
Period size: 38 Copynumber: 3.2 Consensus size: 36
8913 ATCAATATAG
*
8923 TATAATTTTT-GAAAATATTTTTTGAAAAAATATAATA
1 TATAATTTTTAGAAAA-A-ATTTTGAAAAAATATAATA
8960 TATAATTTTTAGAAAACGAATTTTGAAAAAATAT-ATAA
1 TATAATTTTTAGAAAA--AATTTTGAAAAAATATAAT-A
* * * * *
8998 TATATAGTTTTGGAAAATATTTTTAAAATATATATATA
1 TATA-ATTTTTAGAAAAAATTTTGAAAAAATATA-ATA
9036 TATAAT
1 TATAAT
9042 ATAGTTTTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
37 26 0.38
38 29 0.43
39 13 0.19
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.44
Consensus pattern (36 bp):
TATAATTTTTAGAAAAAATTTTGAAAAAATATAATA
Found at i:9061 original size:67 final size:64
Alignment explanation
Indices: 8980--9122 Score: 189
Period size: 67 Copynumber: 2.2 Consensus size: 64
8970 AGAAAACGAA
* * *
8980 TTTTGAAAAAATATATAATATATAGTTTTGGAAAA-TATTTTTAAAATATATATATATATAATAT
1 TTTTGAAAACATATATAATATATAGTTTT-GAAAACT-TTTTGAAAACATATATATA-AT-ATAT
9044 AGT
62 AGT
* *
9047 TTTTGAAAACATATATATTATATAGTTTTGAAAACTTTTTGAAAACATGTATATAATATATAGT
1 TTTTGAAAACATATATAATATATAGTTTTGAAAACTTTTTGAAAACATATATATAATATATAGT
*
9111 TTTTAAAAACAT
1 TTTTGAAAACAT
9123 TTTGAAAACA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
64 18 0.26
65 2 0.03
66 21 0.30
67 28 0.41
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (64 bp):
TTTTGAAAACATATATAATATATAGTTTTGAAAACTTTTTGAAAACATATATATAATATATAGT
Found at i:9068 original size:24 final size:24
Alignment explanation
Indices: 9033--9081 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
9023 AAATATATAT
9033 ATATATAATATAGT-TTTTGAAAAC
1 ATATATAATATA-TATTTTGAAAAC
*
9057 ATATATATTATATAGTTTTGAAAAC
1 ATATATAATATATA-TTTTGAAAAC
9082 TTTTTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 11 0.50
25 10 0.45
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (24 bp):
ATATATAATATATATTTTGAAAAC
Found at i:9071 original size:26 final size:25
Alignment explanation
Indices: 9031--9081 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
9021 TAAAATATAT
9031 ATATATATAATATAGTTTTTGAAAAC
1 ATATATATAATATAG-TTTTGAAAAC
*
9057 ATATATATTATATAGTTTTGAAAAC
1 ATATATATAATATAGTTTTGAAAAC
9082 TTTTTGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (25 bp):
ATATATATAATATAGTTTTGAAAAC
Found at i:9080 original size:105 final size:106
Alignment explanation
Indices: 8941--9145 Score: 258
Period size: 105 Copynumber: 1.9 Consensus size: 106
8931 TTGAAAATAT
*
8941 TTTTTGAAAAAATATAATATATAATTTTTAGAAAACGAATTTTGAAAA-A-ATATATAATATATA
1 TTTTTGAAAAAATATAATATATAAGTTTTAGAAAAC--ATTTTGAAAACATATATATAATATATA
* * * *
9004 GTTTTGGAAAATATTTTTAAAATATATATAT-ATATAATATAG
64 GTTTTGAAAAACATTTTGAAAACATATATATAATATAATATAG
* * *
9046 TTTTTGAAAACATAT-ATATTATATAGTTTT-GAAAACTTTTTGAAAACATGTATATAATATATA
1 TTTTTGAAAAAATATAATA-TATA-AGTTTTAGAAAACATTTTGAAAACATATATATAATATATA
*
9109 GTTTTTAAAAACATTTTGAAAACATATATATAATATA
64 GTTTTGAAAAACATTTTGAAAACATATATATAATATA
9146 GTTTTTAAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
103 9 0.10
104 4 0.05
105 63 0.73
106 10 0.12
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (106 bp):
TTTTTGAAAAAATATAATATATAAGTTTTAGAAAACATTTTGAAAACATATATATAATATATAGT
TTTGAAAAACATTTTGAAAACATATATATAATATAATATAG
Found at i:9155 original size:25 final size:22
Alignment explanation
Indices: 9122--9167 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
9112 TTTAAAAACA
9122 TTTTGAAAACATATATATAATATAG
1 TTTTG-AAA-ATAT-TATAATATAG
*
9147 TTTTTAAAATATTATAATATA
1 TTTTGAAAATATTATAATATA
9168 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
24 3 0.15
25 4 0.20
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTTGAAAATATTATAATATAG
Found at i:9170 original size:2 final size:2
Alignment explanation
Indices: 9155--9266 Score: 189
Period size: 2 Copynumber: 58.5 Consensus size: 2
9145 AGTTTTTAAA
9155 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9194 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9235 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9267 CAATTTTTAA
Statistics
Matches: 105, Mismatches: 0, Indels: 10
0.91 0.00 0.09
Matches are distributed among these distances:
1 5 0.05
2 100 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9300 original size:40 final size:39
Alignment explanation
Indices: 9251--9335 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
9241 ATATATATAT
* *
9251 ATATATATATAATATACAATTTTTAAAAAAT-ATTTTGAAA
1 ATATGTATATAATATA-AAGTTTT-AAAAATGATTTTGAAA
* *
9291 ATATGTATATAATATATAGTTTTGAAAATGATTTTGAAA
1 ATATGTATATAATATAAAGTTTTAAAAATGATTTTGAAA
9330 ATATGT
1 ATATGT
9336 TTTATAGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 5 0.12
39 20 0.50
40 15 0.38
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (39 bp):
ATATGTATATAATATAAAGTTTTAAAAATGATTTTGAAA
Found at i:9368 original size:35 final size:38
Alignment explanation
Indices: 9317--9409 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 38
9307 TAGTTTTGAA
* * *
9317 AATGATTTTGAAAATATGT-TT-TATAGTTTCAAAAAT
1 AATGTTTTTGAAAATATATATTGTATAGTTTCAAAAAC
* *
9353 AAT-TTTTTGAAAATATATATTGTATGGTTTTAAAAAC
1 AATGTTTTTGAAAATATATATTGTATAGTTTCAAAAAC
*
9390 AATGTTTTTGATAATATATA
1 AATGTTTTTGAAAATATATA
9410 ATATATAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
35 13 0.27
36 5 0.10
37 15 0.31
38 15 0.31
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (38 bp):
AATGTTTTTGAAAATATATATTGTATAGTTTCAAAAAC
Found at i:9457 original size:12 final size:12
Alignment explanation
Indices: 9442--9504 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 12
9432 TTTTTATTTT
*
9442 TTATTTTATATA
1 TTATATTATATA
9454 TTATATTATATTA
1 TTATATTATA-TA
*
9467 ATACTATT-TATTA
1 TTA-TATTATA-TA
9480 TT-TATTATATA
1 TTATATTATATA
*
9491 TT-TATTATTTA
1 TTATATTATATA
9502 TTA
1 TTA
9505 ATGTTTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 18 0.42
12 11 0.26
13 10 0.23
14 4 0.09
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATATTATATA
Found at i:9518 original size:18 final size:18
Alignment explanation
Indices: 9434--9504 Score: 81
Period size: 18 Copynumber: 3.8 Consensus size: 18
9424 AAATGATTTT
* *
9434 TTTATTTTTTATTTTATA
1 TTTATTATTTATTATATA
9452 TATTA-TATTATATTAATACTA
1 T-TTATTATT-TATT-ATA-TA
9473 TTTATTATTTATTATATA
1 TTTATTATTTATTATATA
9491 TTTATTATTTATTA
1 TTTATTATTTATTA
9505 ATGTTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 20 0.43
19 10 0.22
20 9 0.20
21 7 0.15
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATTATTTATTATATA
Found at i:10064 original size:22 final size:22
Alignment explanation
Indices: 10024--10065 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
10014 TCGAACACAT
*
10024 ATCAGAGAACACAACACAACAA
1 ATCAGAGAACACAAAACAACAA
10046 ATCAGAGAAC-CATAAACAAC
1 ATCAGAGAACACA-AAACAAC
10066 CAAACACGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.57, C:0.26, G:0.10, T:0.07
Consensus pattern (22 bp):
ATCAGAGAACACAAAACAACAA
Found at i:14059 original size:835 final size:835
Alignment explanation
Indices: 12450--14123 Score: 3303
Period size: 835 Copynumber: 2.0 Consensus size: 835
12440 CAGGGTATTC
12450 AACCGGTGTCAAAAGAAGGCAAAAGACGAATCAACCTGTCAGAAGTTGTTCGGGGTCTAGAAGAA
1 AACCGGTGTCAAAAGAAGGCAAAAGACGAATCAACCTGTCAGAAGTTGTTCGGGGTCTAGAAGAA
12515 TATACCTTTAAAATGTTTTTTGTCTCTTAAGAAATAACACTTTTGTCCCCAATAAGGATTATTTA
66 TATACCTTTAAAATGTTTTTTGTCTCTTAAGAAATAACACTTTTGTCCCCAATAAGGATTATTTA
12580 TAATAATAGACACATTTTTGGATCAATGCCTCAAACATTTCATGCATCATGCATTTAGACATATT
131 TAATAATAGACACATTTTTGGATCAATGCCTCAAACATTTCATGCATCATGCATTTAGACATATT
12645 TTGCATTTTTTTTCTTCATTACATTCACATTAACTAACAAGAGATGTCTCATAAAAAATAAACAA
196 TTGCATTTTTTTTCTTCATTACATTCACATTAACTAACAAGAGATGTCTCATAAAAAATAAACAA
12710 ACACTGGACATTCCACCTCAAGCGTTGGACACACCTCATCCACATAACACTCGAAAATGAAAGCT
261 ACACTGGACATTCCACCTCAAGCGTTGGACACACCTCATCCACATAACACTCGAAAATGAAAGCT
12775 AAGATTGCTCAACTTGAAGCGAACATACTAAGCTTACAGAAGAAACTGGAAGAAAAAATAAGTCA
326 AAGATTGCTCAACTTGAAGCGAACATACTAAGCTTACAGAAGAAACTGGAAGAAAAAATAAGTCA
*
12840 AAATCAAAATATACCTAGGATTCCATCACTAGAAACCAAGACATGTTGGTTGACAATATTATTTC
391 AAATCAAAAAATACCTAGGATTCCATCACTAGAAACCAAGACATGTTGGTTGACAATATTATTTC
12905 AAGGTTGTCCGGCCTGAATCAAATGAATGCTCTTGGGGAAGGGGCATCTGAGGGGGTGGATGTAC
456 AAGGTTGTCCGGCCTGAATCAAATGAATGCTCTTGGGGAAGGGGCATCTGAGGGGGTGGATGTAC
12970 CGCCTACTCCACAGTTGGTAATTTCACTTGGAATCTTACCAGGACTTCAAGGGGTTTCATCGGCC
521 CGCCTACTCCACAGTTGGTAATTTCACTTGGAATCTTACCAGGACTTCAAGGGGTTTCATCGGCC
13035 ACGAAAGCACATGCCTTTGTAACTAACCTTCAAAATAATTCAGATGGTTACCGCATTCCGAAATT
586 ACGAAAGCACATGCCTTTGTAACTAACCTTCAAAATAATTCAGATGGTTACCGCATTCCGAAATT
13100 TGACGAGGAAGTCAAAACAAAGATGATAGAAATGACCATTAAACAAGGAGGCAGGTCGAGTAGAA
651 TGACGAGGAAGTCAAAACAAAGATGATAGAAATGACCATTAAACAAGGAGGCAGGTCGAGTAGAA
*
13165 AACCTCCCTTGAAGAATAAAGAAGGAGAGATCATTAGCATTTTAAACGCTAGCAAAGGTGTTACA
716 AACCTCCCTTGAAGAATAAAGAAAGAGAGATCATTAGCATTTTAAACGCTAGCAAAGGTGTTACA
*
13230 ATCTTCAAATCAAAACTAATTGCAGTTGTACCATATTCTAGACAAGATTCGAGAG
781 ATCTTCAAATCAAAACTAATTACAGTTGTACCATATTCTAGACAAGATTCGAGAG
13285 AACCGGTGTCAAAAGAAGGCAAAAGACGAATCAACCTGTCAGAAGTTGTTCGGGGTCTAGAAGAA
1 AACCGGTGTCAAAAGAAGGCAAAAGACGAATCAACCTGTCAGAAGTTGTTCGGGGTCTAGAAGAA
13350 TATACCTTTAAAATGTTTTTTGTCTCTTAAGAAATAACACTTTTGTCCCCAATAAGGATTATTTA
66 TATACCTTTAAAATGTTTTTTGTCTCTTAAGAAATAACACTTTTGTCCCCAATAAGGATTATTTA
*
13415 TAATAATAGACACATTTTTGGATTAATGCCTCAAACATTTCATGCATCATGCATTTAGACATATT
131 TAATAATAGACACATTTTTGGATCAATGCCTCAAACATTTCATGCATCATGCATTTAGACATATT
13480 TTGCATTTTTTTTCTTCATTACATTCACATTAACTAACAAGAGATGTCTCATAAAAAATAAACAA
196 TTGCATTTTTTTTCTTCATTACATTCACATTAACTAACAAGAGATGTCTCATAAAAAATAAACAA
*
13545 ACACTGGACATTCCACCTCAAGCGTTGGACACACCTCATCCACATAACACTCGAAAATGGAAGCT
261 ACACTGGACATTCCACCTCAAGCGTTGGACACACCTCATCCACATAACACTCGAAAATGAAAGCT
13610 AAGATTGCTCAACTTGAAGCGAACATACTAAGCTTACAGAAGAAACTGGAAGAAAAAATAAGTCA
326 AAGATTGCTCAACTTGAAGCGAACATACTAAGCTTACAGAAGAAACTGGAAGAAAAAATAAGTCA
13675 AAATCAAAAAATACCTAGGATTCCATCACTAGAAACCAAGACATGTTGGTTGACAATATTATTTC
391 AAATCAAAAAATACCTAGGATTCCATCACTAGAAACCAAGACATGTTGGTTGACAATATTATTTC
13740 AAGGTTGTCCGGCCTGAATCAAATGAATGCTCTTGGGGAAGGGGCATCTGAGGGGGTGGATGTAC
456 AAGGTTGTCCGGCCTGAATCAAATGAATGCTCTTGGGGAAGGGGCATCTGAGGGGGTGGATGTAC
13805 CGCCTACTCCACAGTTGGTAATTTCACTTGGAATCTTACCAGGACTTCAAGGGGTTTCATCGGCC
521 CGCCTACTCCACAGTTGGTAATTTCACTTGGAATCTTACCAGGACTTCAAGGGGTTTCATCGGCC
13870 ACGAAAGCACATGCCTTTGTAACTAACCTTCAAAATAATTCAGATGGTTACCGCATTCCGAAATT
586 ACGAAAGCACATGCCTTTGTAACTAACCTTCAAAATAATTCAGATGGTTACCGCATTCCGAAATT
13935 TGACGAGGAAGTCAAAACAAAGATGATAGAAATGACCATTAAACAAGGAGGCAGGTCGAGTAGAA
651 TGACGAGGAAGTCAAAACAAAGATGATAGAAATGACCATTAAACAAGGAGGCAGGTCGAGTAGAA
14000 AACCTCCCTTGAAGAATAAAGAAAGAGAGATCATTAGCATTTTAAACGCTAGCAAAGGTGTTACA
716 AACCTCCCTTGAAGAATAAAGAAAGAGAGATCATTAGCATTTTAAACGCTAGCAAAGGTGTTACA
14065 ATCTTCAAATCAAAACTAATTACAGTTGTACCATATTCTAGACAAGATTCGAGAG
781 ATCTTCAAATCAAAACTAATTACAGTTGTACCATATTCTAGACAAGATTCGAGAG
14120 AACC
1 AACC
14124 AAGGAAAGAA
Statistics
Matches: 834, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
835 834 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (835 bp):
AACCGGTGTCAAAAGAAGGCAAAAGACGAATCAACCTGTCAGAAGTTGTTCGGGGTCTAGAAGAA
TATACCTTTAAAATGTTTTTTGTCTCTTAAGAAATAACACTTTTGTCCCCAATAAGGATTATTTA
TAATAATAGACACATTTTTGGATCAATGCCTCAAACATTTCATGCATCATGCATTTAGACATATT
TTGCATTTTTTTTCTTCATTACATTCACATTAACTAACAAGAGATGTCTCATAAAAAATAAACAA
ACACTGGACATTCCACCTCAAGCGTTGGACACACCTCATCCACATAACACTCGAAAATGAAAGCT
AAGATTGCTCAACTTGAAGCGAACATACTAAGCTTACAGAAGAAACTGGAAGAAAAAATAAGTCA
AAATCAAAAAATACCTAGGATTCCATCACTAGAAACCAAGACATGTTGGTTGACAATATTATTTC
AAGGTTGTCCGGCCTGAATCAAATGAATGCTCTTGGGGAAGGGGCATCTGAGGGGGTGGATGTAC
CGCCTACTCCACAGTTGGTAATTTCACTTGGAATCTTACCAGGACTTCAAGGGGTTTCATCGGCC
ACGAAAGCACATGCCTTTGTAACTAACCTTCAAAATAATTCAGATGGTTACCGCATTCCGAAATT
TGACGAGGAAGTCAAAACAAAGATGATAGAAATGACCATTAAACAAGGAGGCAGGTCGAGTAGAA
AACCTCCCTTGAAGAATAAAGAAAGAGAGATCATTAGCATTTTAAACGCTAGCAAAGGTGTTACA
ATCTTCAAATCAAAACTAATTACAGTTGTACCATATTCTAGACAAGATTCGAGAG
Found at i:15570 original size:99 final size:99
Alignment explanation
Indices: 15449--15650 Score: 314
Period size: 99 Copynumber: 2.0 Consensus size: 99
15439 TTATAATATT
* * *
15449 ATATATATACAATAAAGCTTGAGCTGTCCCTTTAGAGCAATTGGTTAAACACCCCGACTTTATGG
1 ATATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTAGTTAAACACCCCGACTTTATGG
*
15514 ATAAGATTCAGCTAGCTTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
* * * * *
15548 ATATCTATACAATAAAGCTTGAGTTGTCCCTCTAAAGTAATTAGTTAAACATCCCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTAGTTAAACACCCCGACTTTATGG
*
15613 ATAAGGTTCAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
15647 ATAT
1 ATAT
15651 TGAGCTATCC
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 93 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTAGTTAAACACCCCGACTTTATGG
ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
Found at i:17428 original size:83 final size:83
Alignment explanation
Indices: 17091--17810 Score: 743
Period size: 83 Copynumber: 8.5 Consensus size: 83
17081 TAAAGAAACT
* * * *
17091 ATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCT-TCCAGTAAAAAACCTTCGAGTTCGATTAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGATATCTGT-C---AACAAACCTTCGAGTTCGATTAC
17155 ATTCAGCTCAAGGACATATCAA
62 ATTCAGCTCAAGGACATATCAA
* * * * * ** *
17177 ATTTGCAGCATAACTCAAGGCGAGAA-AGACTATCTGCCAGTAAAAAATGTTTGAGCTT-GATTA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGA-TATCTGTC---AACAAACCTTCGAG-TTCGATTA
* * * *
17240 CATTAAGCTAAAGGGCATATTAA
61 CATTCAGCTCAAGGACATATCAA
* * * * * *
17263 ATATACATG-ATAGCTCAAGGTGAGAAGAGTTATATGTCAACCAAAACCTTCGAGTTCGATTATA
1 ATTTACA-GCATAGCTCAAGGCGAGAAGGGATATCTGTCAA-C-AAACCTTCGAGTTCGATTACA
17327 TTCAGCTCAAGGGA-ATATCAA
63 TTCAGCTCAA-GGACATATCAA
* * *
17348 ATTTACAGAATAGCTCAAGGCGAGAAGGGATATCTGTCAACAAACCTTCTAGTTTGATTACATTC
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGATATCTGTCAACAAACCTTCGAGTTCGATTACATTC
*
17413 AACTCAAGGACATATCAA
66 AGCTCAAGGACATATCAA
* * * ** * * *
17431 ATTTACATCATAACTCAAGGTGAGAAGGTTTATTTTTCAATAAAAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGATATCTGTC-A-ACAAACCTTCGAGTTCGATTACAT
*
17496 TCAGCTCAAGGGCATATCAA
64 TCAGCTCAAGGACATATCAA
* * *
17516 ATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAACCTTCGAGTTTGATTACATTC
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGATATCTGTCAACAAACCTTCGAGTTCGATTACATTC
17581 AGCTCAAGGACATATCAA
66 AGCTCAAGGACATATCAA
* * * * * *
17599 ATTTATAGCATAACTCAAGGCAAGAAGGGTTATTTGTCAATAAAAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGATATCTGTC-A-ACAAACCTTCGAGTTCGATTACAT
* *
17664 TTAGCTCAATGG-TATATCAA
64 TCAGCTCAA-GGACATATCAA
* * * *
17684 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTTAACAAACCTTCAAGTTTGATTACATTC
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGATATCTGTCAACAAACCTTCGAGTTCGATTACATTC
* *
17749 AGCTCAAGGGCATATTAA
66 AGCTCAAGGACATATCAA
*
17767 ATTTACAGCATAAG-TCAAGGCGAGAAGGGATGTCTGTCAACAAA
1 ATTTACAGCAT-AGCTCAAGGCGAGAAGGGATATCTGTCAACAAA
17811 AAAACTTTCG
Statistics
Matches: 530, Mismatches: 86, Indels: 39
0.81 0.13 0.06
Matches are distributed among these distances:
82 5 0.01
83 212 0.40
84 10 0.02
85 202 0.38
86 96 0.18
87 5 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (83 bp):
ATTTACAGCATAGCTCAAGGCGAGAAGGGATATCTGTCAACAAACCTTCGAGTTCGATTACATTC
AGCTCAAGGACATATCAA
Found at i:17795 original size:168 final size:168
Alignment explanation
Indices: 17091--17840 Score: 878
Period size: 168 Copynumber: 4.4 Consensus size: 168
17081 TAAAGAAACT
* * * *
17091 ATTTACAGCAT-AGCTCAAGGCAAGAAGGGCTATCTT-CCAGTAAAAAACCTTCGAGTTCGATTA
1 ATTTACAGCATAAG-TCAAGGCGAGAAGGGTTAT-TTGTCAAT-AAAAACCTTCGAGTTCGATTA
* * * * * * *
17154 TATTCAGCTCAAGGACATATCAAATTTGCAGCATAACTCAAGGCGAGAAAGACTATCTGCCAGTA
63 CATTCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTC---A
* ** * * * * * *
17219 AAAAATGTTTGAGCTTGATTACATTAAGCTAAAGGGCATATTAA
125 ACAAACCTTCGAGTTTGATTACATTCAGCTCAAGGACATATCAA
* * * * ** *
17263 ATATACATG-AT-AGCTCAAGGTGAGAAGAGTTATATGTCAACCAAAACCTTCGAGTTCGATTAT
1 ATTTACA-GCATAAG-TCAAGGCGAGAAGGGTTATTTGTCAATAAAAACCTTCGAGTTCGATTAC
* * *
17326 ATTCAGCTCAAGGGAATATCAAATTTACAGAATAGCTCAAGGCGAGAAGGGATATCTGTCAACAA
64 ATTCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAA
* *
17391 ACCTTCTAGTTTGATTACATTCAACTCAAGGACATATCAA
129 ACCTTCGAGTTTGATTACATTCAGCTCAAGGACATATCAA
* * * * *
17431 ATTTACATCATAACTCAAGGTGAGAAGGTTTATTTTTCAATAAAAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAAGTCAAGGCGAGAAGGGTTATTTGTCAATAAAAACCTTCGAGTTCGATTACAT
*
17496 TCAGCTCAAGGGCATATCAAATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAC
66 TCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAC
17561 CTTCGAGTTTGATTACATTCAGCTCAAGGACATATCAA
131 CTTCGAGTTTGATTACATTCAGCTCAAGGACATATCAA
* * *
17599 ATTTATAGCATAACTCAAGGCAAGAAGGGTTATTTGTCAATAAAAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAAGTCAAGGCGAGAAGGGTTATTTGTCAATAAAAACCTTCGAGTTCGATTACAT
* * * *
17664 TTAGCTCAATGGTATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTTAACAAAC
66 TCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAC
* * *
17729 CTTCAAGTTTGATTACATTCAGCTCAAGGGCATATTAA
131 CTTCGAGTTTGATTACATTCAGCTCAAGGACATATCAA
* * * * * ** *
17767 ATTTACAGCATAAGTCAAGGCGAGAAGGGATGTCTGTCAACAAAAAAACTTTCGAGTTTAATTCC
1 ATTTACAGCATAAGTCAAGGCGAGAAGGGTTATTTGTC-A-ATAAAAACCTTCGAGTTCGATTAC
17832 ATTCAGCTC
64 ATTCAGCTC
17841 GATGACAAAT
Statistics
Matches: 500, Mismatches: 72, Indels: 14
0.85 0.12 0.02
Matches are distributed among these distances:
168 369 0.74
169 2 0.00
170 27 0.05
171 73 0.15
172 28 0.06
173 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (168 bp):
ATTTACAGCATAAGTCAAGGCGAGAAGGGTTATTTGTCAATAAAAACCTTCGAGTTCGATTACAT
TCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAC
CTTCGAGTTTGATTACATTCAGCTCAAGGACATATCAA
Found at i:18155 original size:260 final size:260
Alignment explanation
Indices: 17693--18183 Score: 575
Period size: 260 Copynumber: 1.9 Consensus size: 260
17683 AATTTACAGC
* * *
17693 ATAGCTCAAGGCGAGAAGGGCTATCTGTTAACAAACCTTCAAGTTTGATTACATTCAGCTCAAGG
1 ATAGCTCAAGGAGAGAAGGGCTATCTGTCAACAAACCTTCAAGTTCGATTACATTCAGCTCAAGG
** * *
17758 GCATATTAAATTTACAGCATAAGTCAAGGCGAGAAGGGATGTCTGTCAACAAAAAAACTTTCGAG
66 GCATAACAAACTTACAGCATAAGTCAAGGCGAGAAGGGATATCTGTCAACAAAAAAACTTTCGAG
* * * * * *
17823 TTTAATTCCATTCAGCTCGATGACAAATCGACCACATGGAAGCAGCGAGAATCTACTTTTTGGTT
131 TTCAATTCCATTCAGCTCGATGACAAATCAACCACATGGAAGCAGCGAGAAACTACTTTTCGATC
17888 AAAGTTTAAACCAAGGTCTTTAAGTCAAGAAGAAGATCTGAGGCAATCTCTCAATCTAGTACAAT
196 AAAGTTTAAACCAAGGTCTTTAAGTCAAGAAGAAGATCTGAGGCAATCTCTCAATCTAGTACAAT
* * * *
17953 ATAGCTCAAGGAGAGAATGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTTAGCTCAT
1 ATAGCTCAAGGAGAGAAGGGCTATCTGTCAAC--AAACCTTCAAGTTCGATTACATTCAGCTCA-
*** *
18018 A-GGCATAACAAACTTACAGCAT-AGCTCAAGGCGAGAA-GGACTATCTGTC-A-ATGGAGACTT
63 AGGGCATAACAAACTTACAGCATAAG-TCAAGGCGAGAAGGGA-TATCTGTCAACAAAAAAACTT
* *** * * *
18078 TCGAGTTCAATTCCATTCAGCTTGA-GAGTGTATCAACCGCAT-TATAGTAGCGA-ATAACTACT
126 TCGAGTTCAATTCCATTCAGCTCGATGA-CAAATCAACCACATGGA-AGCAGCGAGA-AACTACT
* * *
18140 TTTCGATCGAAGTTTAAACCGATGTCTTTAAGTCAAGAAGAAGA
188 TTTCGATCAAAGTTTAAACCAAGGTCTTTAAGTCAAGAAGAAGA
18184 CATGGGTTAG
Statistics
Matches: 192, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
259 4 0.02
260 118 0.61
261 6 0.03
262 63 0.33
263 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (260 bp):
ATAGCTCAAGGAGAGAAGGGCTATCTGTCAACAAACCTTCAAGTTCGATTACATTCAGCTCAAGG
GCATAACAAACTTACAGCATAAGTCAAGGCGAGAAGGGATATCTGTCAACAAAAAAACTTTCGAG
TTCAATTCCATTCAGCTCGATGACAAATCAACCACATGGAAGCAGCGAGAAACTACTTTTCGATC
AAAGTTTAAACCAAGGTCTTTAAGTCAAGAAGAAGATCTGAGGCAATCTCTCAATCTAGTACAAT
Found at i:18521 original size:48 final size:48
Alignment explanation
Indices: 18468--18569 Score: 186
Period size: 48 Copynumber: 2.1 Consensus size: 48
18458 TCAATTTAAC
*
18468 AGGGAGTTACTCCTAATTGCAATATCATAGTCAATTTTCAACTCCACA
1 AGGGAGTTACTCCTAATTGCAATATCAGAGTCAATTTTCAACTCCACA
*
18516 AGGGAGTTACTCTTAATTGCAATATCAGAGTCAATTTTCAACTCCACA
1 AGGGAGTTACTCCTAATTGCAATATCAGAGTCAATTTTCAACTCCACA
18564 AGGGAG
1 AGGGAG
18570 GATATTAGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (48 bp):
AGGGAGTTACTCCTAATTGCAATATCAGAGTCAATTTTCAACTCCACA
Found at i:18737 original size:15 final size:16
Alignment explanation
Indices: 18703--18737 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
18693 TTTTTCTCTC
18703 TTTTTATTTTATTTTA
1 TTTTTATTTTATTTTA
18719 TTTTTA-TTTA-TTTA
1 TTTTTATTTTATTTTA
18733 TTTTT
1 TTTTT
18738 GTATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 4 0.21
16 6 0.32
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTATTTTATTTTA
Found at i:18881 original size:34 final size:34
Alignment explanation
Indices: 18842--19033 Score: 158
Period size: 36 Copynumber: 5.4 Consensus size: 34
18832 ATATATATAT
18842 ATATATATCATATAGTTTTGAAAATTATTTTTGAA
1 ATATATATCATATAGTTTTGAAAA-TATTTTTGAA
* *
18877 TATATATATTATATAGTTTTGAAAACA-TTTTGAAA
1 -ATATATATCATATAGTTTTGAAAATATTTTTG-AA
* * **
18912 ATATATATCATATAGTTTTTAAAACTGTTTTCAAAA
1 ATATATATCATATAGTTTTGAAAA-TATTTT-TGAA
* *
18948 ATATATATTATATAGTTTTGAAAACA-TTTTGAAAAA
1 ATATATATCATATAGTTTTGAAAATATTTTTG---AA
* *
18984 ATATATATAATATATACTTTTGGAAAATATTTTT-AA
1 ATATATAT--CATATAGTTTT-GAAAATATTTTTGAA
19020 TATATATAT-ATATA
1 -ATATATATCATATA
19034 TATATATATA
Statistics
Matches: 128, Mismatches: 16, Indels: 26
0.75 0.09 0.15
Matches are distributed among these distances:
34 35 0.27
35 3 0.02
36 62 0.48
37 8 0.06
38 10 0.08
39 6 0.05
40 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (34 bp):
ATATATATCATATAGTTTTGAAAATATTTTTGAA
Found at i:18882 original size:38 final size:35
Alignment explanation
Indices: 18838--19354 Score: 282
Period size: 39 Copynumber: 13.8 Consensus size: 35
18828 ATATATATAT
*
18838 ATATATATATATCATATAGTTTTGAAAATTATTTTTGA
1 ATATATATATAT-ATATAGTTTTGAAAA-CA-TTTTGA
18876 ATATATATAT-TATATAGTTTTGAAAACATTTTGA
1 ATATATATATATATATAGTTTTGAAAACATTTTGA
* * *
18910 A-A-ATATATATCATATAGTTTTTAAAACTGTTTTCA
1 ATATATATATAT-ATATAGTTTTGAAAAC-ATTTTGA
*
18945 A-AAATATATATTATATAGTTTTGAAAACATTTTGAAA
1 ATATATATATA-TATATAGTTTTGAAAACATTTTG--A
* * * *
18982 AAATATATATAATATATACTTTTGGAAAATATTTTTA
1 ATATATATAT-ATATATAGTTTT-GAAAACATTTTGA
*
19019 ATATATATATATATATA-TATATAT-ATAATATAGTTTTTGA
1 ATATATATATATATATAGT-T-T-TGA-AA-ACA--TTTTGA
* * * *
19059 AAATATATATATTATATAATTTTGGAGACATTTTTGAAA
1 ATATATATATA-TATATAGTTTTGAAAACA-TTTTG--A
* *
19098 ACATATATATGTTATATAGTTTTGAAAACATTTTGAAA
1 ATATATATAT-ATATATAGTTTTGAAAACATTTTG--A
* *
19136 ACATATATATAATATATAGTTTTTAAAAACATTTTGAAA
1 ATATATATAT-ATATATAG-TTTTGAAAACATTTTG--A
* *
19175 ACATATATATAATATATAGTTTTTAAAAACATTTTGAAA
1 ATATATATAT-ATATATAG-TTTTGAAAACATTTTG--A
* * * *
19214 ATATATATATAATATATAATTTTTAAAAAAATATTTTAAAA
1 ATATATATAT-ATATAT-AGTTTT--GAAAACATTTT--GA
* *
19255 ATATGTATATAATATATAGTTTTGAAAATGATTTTGA
1 ATATATATAT-ATATATAGTTTTGAAAA-CATTTTGA
* *
19292 A-A-ATATGT-TATATAGTTTT-AAAATTAATTTTTTGA
1 ATATATATATATATATAGTTTTGAAAA--CA--TTTTGA
* * *
19327 AAATATATAT-TGTATGGTTTTGAAAACA
1 ATATATATATATATATAGTTTTGAAAACA
19355 ATGTTTTTGA
Statistics
Matches: 402, Mismatches: 41, Indels: 74
0.78 0.08 0.14
Matches are distributed among these distances:
32 10 0.02
33 15 0.04
34 22 0.05
35 24 0.06
36 49 0.12
37 39 0.10
38 66 0.16
39 120 0.30
40 22 0.05
41 34 0.08
42 1 0.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (35 bp):
ATATATATATATATATAGTTTTGAAAACATTTTGA
Found at i:19027 original size:39 final size:38
Alignment explanation
Indices: 18836--19297 Score: 398
Period size: 39 Copynumber: 12.1 Consensus size: 38
18826 AAATATATAT
18836 ATATATATATATATCATATAGTTTTGAAAATTATTTTTG--A
1 ATATATATATA-AT-ATATAGTTTTGAAAA-TA-TTTTGAAA
*
18876 ATATATATAT--TATATAGTTTTGAAAACATTTTG-AA
1 ATATATATATAATATATAGTTTTGAAAATATTTTGAAA
* * * *
18911 A-ATATATAT--CATATAGTTTTTAAAACTGTTTTCAAA
1 ATATATATATAATATATAGTTTTGAAAA-TATTTTGAAA
*
18947 A-ATATATAT--TATATAGTTTTGAAAACATTTTGAAA
1 ATATATATATAATATATAGTTTTGAAAATATTTTGAAA
* * * *
18982 AAATATATATAATATATACTTTTGGAAAATATTTTTAAT
1 ATATATATATAATATATAGTTTT-GAAAATATTTTGAAA
* *
19021 ATATATATATATATATATA-TATAT-AATATAGTTTTTGAAA
1 ATATATATATA-ATATATAGT-TTTGAAAATA--TTTTGAAA
* *
19061 ATATATATAT--TATATAATTTTGGAGACAT-TTTTGAAA
1 ATATATATATAATATATAGTTTT-GA-AAATATTTTGAAA
* ** *
19098 ACATATATATGTTATATAGTTTTGAAAACATTTTGAAA
1 ATATATATATAATATATAGTTTTGAAAATATTTTGAAA
* * *
19136 ACATATATATAATATATAGTTTTTAAAAACATTTTGAAA
1 ATATATATATAATATATAG-TTTTGAAAATATTTTGAAA
* * *
19175 ACATATATATAATATATAGTTTTTAAAAACATTTTGAAA
1 ATATATATATAATATATAG-TTTTGAAAATATTTTGAAA
* * *
19214 ATATATATATAATATATAATTTTTAAAAAAATATTTTAAAA
1 ATATATATATAATATAT-AGTTTT--GAAAATATTTTGAAA
*
19255 ATATGTATATAATATATAGTTTTGAAAATGATTTTGAAA
1 ATATATATATAATATATAGTTTTGAAAAT-ATTTTGAAA
19294 ATAT
1 ATAT
19298 GTTATATAGT
Statistics
Matches: 362, Mismatches: 37, Indels: 47
0.81 0.08 0.11
Matches are distributed among these distances:
34 27 0.07
35 15 0.04
36 48 0.13
37 28 0.08
38 48 0.13
39 123 0.34
40 44 0.12
41 29 0.08
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (38 bp):
ATATATATATAATATATAGTTTTGAAAATATTTTGAAA
Found at i:19070 original size:2 final size:2
Alignment explanation
Indices: 19019--19050 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
19009 AATATTTTTA
19019 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19051 GTTTTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19104 original size:77 final size:74
Alignment explanation
Indices: 18876--19297 Score: 314
Period size: 77 Copynumber: 5.5 Consensus size: 74
18866 TTATTTTTGA
* **
18876 ATATATATAT-TATATAGTTTTGAAAACATTTTGAAAATATATATCATATAGT--TTTTAAAAC-
1 ATATATATATATATATAGTTTT-AAAACATTTTGAAAATATATATAATATA-TAATTTTGGAACA
*
18937 TGTTTT-CAAA-
64 T-TTTTGAAAAC
* *
18947 A-ATATATAT-TATATAGTTTTGAAAACATTTTGAAAAAATATATATAATATATACTTTTGGAAA
1 ATATATATATATATATAGTTTT-AAAACATTTTG--AAAATATATATAATATATAATTTTGGAAC
* * *
19010 ATATTTTTAATAT
63 AT-TTTTGAAAAC
* ** *
19023 ATATATATATATATATA-TATATAATATAGTTTTTGAAAATATATATATTATATAATTTTGGAGA
1 ATATATATATATATATAGT-TTTAA-A-ACATTTTGAAAATATATATAATATATAATTTTGGA-A
19087 CATTTTTGAAAAC
62 CATTTTTGAAAAC
* * **
19100 ATATATATGT-TATATAGTTTTGAAAACATTTTGAAAACATATATATAATATATAGTTTTTAAAA
1 ATATATATATATATATAGTTTT-AAAACATTTTG-AAA-ATATATATAATATATA-ATTTT-GGA
19164 ACA-TTTTGAAAAC
61 ACATTTTTGAAAAC
**
19177 ATATATATA-ATATATAGTTTTTAAAAACATTTTGAAAATATATATATAATATATAATTTTTAAA
1 ATATATATATATATATAG-TTTT-AAAACATTTTG-AAA-ATATATATAATATATAA-TTTT-GG
*
19241 AAAATATTTT-AAAA-
60 AACAT-TTTTGAAAAC
* *
19255 ATATGTATATAATATATAGTTTTGAAAATGATTTTGAAAATAT
1 ATATATATAT-ATATATAGTTTT-AAAA-CATTTTGAAAATAT
19298 GTTATATAGT
Statistics
Matches: 292, Mismatches: 32, Indels: 47
0.79 0.09 0.13
Matches are distributed among these distances:
70 31 0.11
71 2 0.01
72 16 0.05
73 6 0.02
74 5 0.02
75 8 0.03
76 13 0.04
77 95 0.33
78 76 0.26
79 22 0.08
80 18 0.06
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (74 bp):
ATATATATATATATATAGTTTTAAAACATTTTGAAAATATATATAATATATAATTTTGGAACATT
TTTGAAAAC
Found at i:19322 original size:33 final size:34
Alignment explanation
Indices: 19267--19370 Score: 95
Period size: 37 Copynumber: 2.9 Consensus size: 34
19257 ATGTATATAA
*
19267 TATATAGTTTTGAAAATGA-TTTTGAAAATATGT
1 TATATAGTTTTGAAAATAATTTTTGAAAATATGT
*
19300 TATATAGTTTT-AAAATTAATTTTTTGAAAATATATAT
1 TATATAGTTTTGAAAA-TAA-TTTTTG-AAA-ATATGT
* * *
19337 TGTATGGTTTTGAAAACAATGTTTTTGAAAATAT
1 TATATAGTTTTGAAAATAA--TTTTTGAAAATAT
19371 ATAATATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
32 4 0.07
33 13 0.22
35 5 0.09
36 7 0.12
37 19 0.33
38 10 0.17
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.47
Consensus pattern (34 bp):
TATATAGTTTTGAAAATAATTTTTGAAAATATGT
Found at i:19897 original size:14 final size:14
Alignment explanation
Indices: 19878--19905 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19868 ACCACAGAAC
19878 GATCATCGAACACA
1 GATCATCGAACACA
19892 GATCATCGAACACA
1 GATCATCGAACACA
19906 ACACAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (14 bp):
GATCATCGAACACA
Found at i:20576 original size:3 final size:3
Alignment explanation
Indices: 20568--20595 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
20558 TTCATATTTC
20568 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
20596 CTCATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:20696 original size:8 final size:9
Alignment explanation
Indices: 20681--20712 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
20671 TAAAATTTAA
20681 ATTTTTTTT
1 ATTTTTTTT
20690 ATTTTTTTT
1 ATTTTTTTT
20699 ATTTTTTTT
1 ATTTTTTTT
20708 ATTTT
1 ATTTT
20713 AATATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:20814 original size:59 final size:56
Alignment explanation
Indices: 20686--20816 Score: 137
Period size: 59 Copynumber: 2.3 Consensus size: 56
20676 TTTAAATTTT
*
20686 TTTTAT-TTTTTTTATTTTTTTTATTTTAATATTTTCTTAATTGTATTTCATTTCA
1 TTTTATATTTTTTTATTTTTTTTATTTTAATATTTTCTTAACTGTATTTCATTTCA
*
20741 TTTTATATTATTTTTATTTCTTTTCTCTTTTAATATTGTTGCATTTAACT-T-TTTCATTT-A
1 TTTTATATT-TTTTTATTT-TTTT-TATTTTAATATT-TT-C--TTAACTGTATTTCATTTCA
20801 TTTTA-ACTTTTTTTAT
1 TTTTATA-TTTTTTTAT
20817 GATTTAATAT
Statistics
Matches: 65, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
55 6 0.09
56 2 0.03
57 9 0.14
58 4 0.06
59 19 0.29
60 10 0.15
61 9 0.14
62 1 0.02
63 5 0.08
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.70
Consensus pattern (56 bp):
TTTTATATTTTTTTATTTTTTTTATTTTAATATTTTCTTAACTGTATTTCATTTCA
Found at i:21279 original size:2 final size:2
Alignment explanation
Indices: 21274--21316 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
21264 TTAAAATAAT
21274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21316 T
1 T
21317 TGTTGTCCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21489 original size:25 final size:25
Alignment explanation
Indices: 21455--21511 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
21445 ACCCCTGTTG
21455 GTTTTATATTATTTTCTTAATTTCA
1 GTTTTATATTATTTTCTTAATTTCA
21480 GTTTTATATTATTTTCTTAATTTCA
1 GTTTTATATTATTTTCTTAATTTCA
*
21505 GTATTAT
1 GTTTTAT
21512 TGTTAGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (25 bp):
GTTTTATATTATTTTCTTAATTTCA
Found at i:27394 original size:31 final size:31
Alignment explanation
Indices: 27359--27449 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 31
27349 GAAGGAACTA
* *
27359 TCCATATGTTTCGAAGAACATAGGTAACCTG
1 TCCATATGTCTCGAAGAACATAGGTAACCAG
* *
27390 TCCATATGTCCCGAACG-ACATAGGTAAACAG
1 TCCATATGTCTCGAA-GAACATAGGTAACCAG
*
27421 TTCATATGTCTCGAA-AGACATAGGTAACC
1 TCCATATGTCTCGAAGA-ACATAGGTAACC
27450 CTCGACTCTT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
31 49 0.98
32 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (31 bp):
TCCATATGTCTCGAAGAACATAGGTAACCAG
Found at i:32343 original size:31 final size:31
Alignment explanation
Indices: 32308--32381 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
32298 GCTCCTAAGA
*
32308 ACATAGGTAACCTGTCCATATATCCCGAAAG
1 ACATAGGTAACCTGTCCATATATCCCAAAAG
** * * *
32339 ACATAGGTAAATTGTTCATATGTCTCAAAAG
1 ACATAGGTAACCTGTCCATATATCCCAAAAG
32370 ACATAGGTAACC
1 ACATAGGTAACC
32382 CTCGACTCTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (31 bp):
ACATAGGTAACCTGTCCATATATCCCAAAAG
Found at i:32640 original size:2 final size:2
Alignment explanation
Indices: 32633--32669 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
32623 CTCTATTGTC
*
32633 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
32670 CACATAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:34599 original size:24 final size:24
Alignment explanation
Indices: 34567--34745 Score: 71
Period size: 24 Copynumber: 7.2 Consensus size: 24
34557 TGATATGATT
34567 TAATAATAATTACTAATGATTTAA
1 TAATAATAATTACTAATGATTTAA
* *
34591 TAATAATAATT--TAATGAATTGA
1 TAATAATAATTACTAATGATTTAA
* * * * *
34613 TACTAATGATTTAATAAT-AATTAC
1 TAATAAT-AATTACTAATGATTTAA
* * *
34637 TAATAATGATTTAATAATGATTACTAC
1 TAATAAT-AATTACTAATGATT--TAA
* *
34664 TGATAATGAAATTA-TAAT-ATTTAC
1 TAATAAT--AATTACTAATGATTTAA
* * *
34688 TAATAATGATTTCATAATGATTACAAA
1 TAATAATAATTAC-TAATGATT--TAA
*
34715 TTATAATAATTACTAATAATGATTTAA
1 TAATAATAATTAC---TAATGATTTAA
34742 TAAT
1 TAAT
34746 GATTACTAAT
Statistics
Matches: 120, Mismatches: 21, Indels: 25
0.72 0.13 0.15
Matches are distributed among these distances:
22 18 0.15
23 3 0.03
24 45 0.38
25 9 0.08
26 3 0.03
27 29 0.24
28 4 0.03
29 9 0.08
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.41
Consensus pattern (24 bp):
TAATAATAATTACTAATGATTTAA
Found at i:34688 original size:151 final size:152
Alignment explanation
Indices: 34526--34811 Score: 343
Period size: 151 Copynumber: 1.9 Consensus size: 152
34516 TATTGATTTA
* * * * * *
34526 ATAATAATTACTAGTAATGATTTAATCAGTG-TGATATGATT-TAATAATAATTACTAATGATTT
1 ATAATAATTACTAATAATGATTTAAT-AATGATGACA-AATTATAATAATAACTAATAATGATTT
34589 AATAAT-A-A-TAATTTAATGAATTGATACTAATGA-TT-TAATAATAATTACTAATAATGATTT
64 AATAATGATACTAATTTAAT-AA-T-AT-CTAATGATTTATAATAATAATTACTAATAATGATTT
34649 AATAATGATTACTACTGATAATGAAATT
125 AATAATGATTACTACTGATAATGAAATT
* * * *
34677 ATAATATTTACTAATAATGATTTCATAATGATTACAAATTATAATAATTACTAATAATGATTTAA
1 ATAATAATTACTAATAATGATTTAATAATGATGACAAATTATAATAATAACTAATAATGATTTAA
* *
34742 TAATGATTACTAATTTAATAATATTTAATGATTTGATAATAATGATTACTAATAATGATTTAATA
66 TAATGA-TACTAATTTAATAATATCTAATGATTT-ATAATAATAATTACTAATAATGATTTAATA
34807 ATGAT
129 ATGAT
34812 AATAATGATT
Statistics
Matches: 114, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
150 6 0.05
151 57 0.50
152 5 0.04
153 1 0.01
154 36 0.32
155 9 0.08
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (152 bp):
ATAATAATTACTAATAATGATTTAATAATGATGACAAATTATAATAATAACTAATAATGATTTAA
TAATGATACTAATTTAATAATATCTAATGATTTATAATAATAATTACTAATAATGATTTAATAAT
GATTACTACTGATAATGAAATT
Found at i:34692 original size:40 final size:40
Alignment explanation
Indices: 34648--34763 Score: 130
Period size: 40 Copynumber: 2.9 Consensus size: 40
34638 AATAATGATT
* * *
34648 TAATAATGATTAC-TACTGATAATGAAATTATAATATTTAC
1 TAATAATGATTACATAATGATAA-CAAATTATAATAATTAC
* *
34688 TAATAATGATTTCATAATGATTACAAATTATAATAATTAC
1 TAATAATGATTACATAATGATAACAAATTATAATAATTAC
* *
34728 TAATAATGATTTA-ATAATGATTACTAATT-TAATAAT
1 TAATAATGA-TTACATAATGATAACAAATTATAATAAT
34764 ATTTAATGAT
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
39 7 0.10
40 51 0.76
41 9 0.13
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (40 bp):
TAATAATGATTACATAATGATAACAAATTATAATAATTAC
Found at i:34743 original size:21 final size:21
Alignment explanation
Indices: 34688--34827 Score: 59
Period size: 20 Copynumber: 6.8 Consensus size: 21
34678 TAATATTTAC
*
34688 TAATAATGATTTCATAA-TGA
1 TAATAATGATTTAATAATTGA
* *
34708 TTACAA--ATTATAATAATT-A
1 TAATAATGATT-TAATAATTGA
34727 CTAATAATGATTTAATAA-TGA
1 -TAATAATGATTTAATAATTGA
* *
34748 T--TACTAATTTAATAA-T-A
1 TAATAATGATTTAATAATTGA
* *
34765 T-TTAATGATTTGATAATAATGATTA
1 TAATAATGA-TT--TAATAAT--TGA
34790 CTAATAATGATTTAATAA-TGA
1 -TAATAATGATTTAATAATTGA
*
34811 TAATAATGATTTGATAA
1 TAATAATGATTTAATAA
34828 CATTTTTTAT
Statistics
Matches: 92, Mismatches: 12, Indels: 32
0.68 0.09 0.24
Matches are distributed among these distances:
17 2 0.02
18 20 0.22
19 8 0.09
20 27 0.29
21 15 0.16
22 3 0.03
24 7 0.08
25 1 0.01
26 3 0.03
27 6 0.07
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (21 bp):
TAATAATGATTTAATAATTGA
Found at i:34757 original size:18 final size:18
Alignment explanation
Indices: 34736--34794 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
34726 ACTAATAATG
34736 ATTTAATAATGATTACTA
1 ATTTAATAATGATTACTA
*
34754 ATTTAATAAT-ATTTAATGA
1 ATTTAATAATGA-TTACT-A
*
34773 TTTGATAATAATGATTACTA
1 ATT--TAATAATGATTACTA
34793 AT
1 AT
34795 AATGATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 1 0.03
18 14 0.44
19 3 0.09
20 2 0.06
21 11 0.34
22 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (18 bp):
ATTTAATAATGATTACTA
Found at i:34782 original size:39 final size:40
Alignment explanation
Indices: 34673--34794 Score: 153
Period size: 40 Copynumber: 3.1 Consensus size: 40
34663 CTGATAATGA
* * *
34673 AATTATAATATTTACTAATAATGATTTCATAATGATTACA
1 AATTATAATAATTACTAATAATGATTTAATAATGATTACT
34713 AATTATAATAATTACTAATAATGATTTAATAATGATTACT
1 AATTATAATAATTACTAATAATGATTTAATAATGATTACT
*
34753 AATT-TAATAA-TA-T-TTAATGATTTGATAATAATGATTACT
1 AATTATAATAATTACTAATAATGA-TT--TAATAATGATTACT
34792 AAT
1 AAT
34795 AATGATTTAA
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
36 6 0.08
37 3 0.04
38 2 0.03
39 23 0.31
40 41 0.55
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (40 bp):
AATTATAATAATTACTAATAATGATTTAATAATGATTACT
Found at i:34827 original size:14 final size:13
Alignment explanation
Indices: 34767--34811 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
34757 TAATAATATT
34767 TAATGATTTGATAA
1 TAATGATTT-ATAA
34781 TAATGA-TTACTAA
1 TAATGATTTA-TAA
34794 TAATGA-TT-TAA
1 TAATGATTTATAA
34805 TAATGAT
1 TAATGAT
34812 AATAATGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 13 0.45
14 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.42
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:35156 original size:24 final size:24
Alignment explanation
Indices: 35128--35189 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
35118 ATACCATAAT
35128 GTAGTATCGATACTACTCTATATA
1 GTAGTATCGATACTACTCTATATA
*
35152 GTAGTATCGATACTCCTCTATATA
1 GTAGTATCGATACTACTCTATATA
** *
35176 ACAGTATTGATACT
1 GTAGTATCGATACT
35190 CATTTGACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (24 bp):
GTAGTATCGATACTACTCTATATA
Found at i:35374 original size:11 final size:11
Alignment explanation
Indices: 35335--35505 Score: 85
Period size: 11 Copynumber: 13.8 Consensus size: 11
35325 ACGACTCTAT
35335 TGATTTAATTAA
1 TGATTTAA-TAA
35347 TGATTTGATACTAA
1 TGATTT-A-A-TAA
35361 TGATTTAATAA
1 TGATTTAATAA
35372 TGATTACTAATAA
1 TGATT--TAATAA
35385 TGATTTAATAA
1 TGATTTAATAA
35396 TGATTATTAATTTAAA
1 TGA-T-TTAA--T-AA
*
35412 T-ATTT-TTAA
1 TGATTTAATAA
35421 TGATTTCATACTAA
1 TGATTT-A-A-TAA
*
35435 TGATTTAGTAA
1 TGATTTAATAA
35446 TGATTACTAATAA
1 TGATT--TAATAA
35459 TGAAATTATAATAA
1 TG--ATT-TAATAA
* * *
35473 TTACTACTAATGA
1 TGA-T-TTAATAA
*
35486 TGTTTTAATAA
1 TGATTTAATAA
35497 TGATTTAAT
1 TGATTTAAT
35506 GATTAAATAT
Statistics
Matches: 125, Mismatches: 14, Indels: 41
0.69 0.08 0.23
Matches are distributed among these distances:
9 3 0.02
10 5 0.04
11 38 0.30
12 10 0.08
13 34 0.27
14 27 0.22
15 5 0.04
16 3 0.02
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (11 bp):
TGATTTAATAA
Found at i:35390 original size:24 final size:24
Alignment explanation
Indices: 35335--35501 Score: 133
Period size: 24 Copynumber: 6.7 Consensus size: 24
35325 ACGACTCTAT
*
35335 TGATTTAATTAATGATTTGA-TACTAA
1 TGATTTAA-TAATGA-TT-ACTAATAA
35361 TGATTTAATAATGATTACTAATAA
1 TGATTTAATAATGATTACTAATAA
*
35385 TGATTTAATAATGATTATTAATTTAAA
1 TGATTTAATAATGATTACTAA--T-AA
* * *
35412 T-ATTT-TTAATGATTTCATACTAA
1 TGATTTAATAATGATTAC-TAATAA
*
35435 TGATTTAGTAATGATTACTAATAA
1 TGATTTAATAATGATTACTAATAA
* * *
35459 TGAAATTATAATAATTACTACTAATGA
1 TG--ATT-TAATAATGATTACTAATAA
*
35486 TGTTTTAATAATGATT
1 TGATTTAATAATGATT
35502 TAATGATTAA
Statistics
Matches: 115, Mismatches: 16, Indels: 22
0.75 0.10 0.14
Matches are distributed among these distances:
23 4 0.03
24 48 0.42
25 25 0.22
26 18 0.16
27 20 0.17
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (24 bp):
TGATTTAATAATGATTACTAATAA
Found at i:35520 original size:8 final size:8
Alignment explanation
Indices: 35508--35702 Score: 63
Period size: 8 Copynumber: 28.0 Consensus size: 8
35498 GATTTAATGA
35508 TTAAATAT
1 TTAAATAT
35516 TTAAAT-T
1 TTAAATAT
35523 TT--AT-T
1 TTAAATAT
35528 TT-AATAT
1 TTAAATAT
*
35535 TTTAATAT
1 TTAAATAT
35543 TTAAAT-T
1 TTAAATAT
35550 TT--AT-T
1 TTAAATAT
35555 TT-AATAT
1 TTAAATAT
*
35562 TTAATTAT
1 TTAAATAT
*
35570 TGAAAT-T
1 TTAAATAT
35577 TT--AT-T
1 TTAAATAT
*
35582 TTAATTAT
1 TTAAATAT
*
35590 TGAAAT-T
1 TTAAATAT
35597 TT--AT-T
1 TTAAATAT
35602 TT-AATAT
1 TTAAATAT
35609 TTAAATAT
1 TTAAATAT
35617 TT-AA-A-
1 TTAAATAT
*
35622 TTAAATCT
1 TTAAATAT
* *
35630 TTAATCTTT
1 TTAA-ATAT
*
35639 TTAAATTT
1 TTAAATAT
*
35647 TTAAATTT
1 TTAAATAT
*
35655 TTTAATAT
1 TTAAATAT
35663 TT-AA-A-
1 TTAAATAT
*
35668 TTAAATCT
1 TTAAATAT
35676 TT-AAT-T
1 TTAAATAT
35682 TT---TAT
1 TTAAATAT
35687 TTAAATAT
1 TTAAATAT
35695 TTAAATAT
1 TTAAATAT
35703 AAATTTCATT
Statistics
Matches: 148, Mismatches: 16, Indels: 46
0.70 0.08 0.22
Matches are distributed among these distances:
4 1 0.01
5 27 0.18
6 15 0.10
7 27 0.18
8 72 0.49
9 6 0.04
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (8 bp):
TTAAATAT
Found at i:35538 original size:20 final size:20
Alignment explanation
Indices: 35511--35619 Score: 71
Period size: 20 Copynumber: 5.8 Consensus size: 20
35501 TTAATGATTA
35511 AATA-TTTAAATTTTATTTT
1 AATATTTTAAATTTTATTTT
35530 AATATTTT-AA---TA-TTT
1 AATATTTTAAATTTTATTTT
35545 AA-ATTTT--ATTTTAATATTT
1 AATATTTTAAATTTT-AT-TTT
*
35564 AAT-TATTGAAATTTTATTTT
1 AATAT-TTTAAATTTTATTTT
*
35584 AAT-TATTGAAATTTTATTTT
1 AATAT-TTTAAATTTTATTTT
35604 AATA-TTTAAATATTTA
1 AATATTTTAAAT-TTTA
35620 AATTAAATCT
Statistics
Matches: 75, Mismatches: 2, Indels: 25
0.74 0.02 0.25
Matches are distributed among these distances:
13 1 0.01
14 5 0.07
15 5 0.07
16 3 0.04
17 1 0.01
19 18 0.24
20 35 0.47
21 2 0.03
22 5 0.07
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AATATTTTAAATTTTATTTT
Found at i:35541 original size:27 final size:27
Alignment explanation
Indices: 35511--35700 Score: 142
Period size: 27 Copynumber: 7.4 Consensus size: 27
35501 TTAATGATTA
35511 AATATTTAAATTTTATTTTAATATTTT
1 AATATTTAAATTTTATTTTAATATTTT
35538 AATATTTAAATTTTATTTTAATA-TTT
1 AATATTTAAATTTTATTTTAATATTTT
*
35564 AATTATTGAAATTTTATTTT-A-A---T
1 AA-TATTTAAATTTTATTTTAATATTTT
* *
35587 --TATTGAAATTTTATTTTAATATTTA
1 AATATTTAAATTTTATTTTAATATTTT
** *
35612 AATATTTAAATTAAATCTTTAATCTTTTT
1 AATATTTAAATTTTAT-TTTAAT-ATTTT
*
35641 AAATTTTTAAA--TT-TTTTAATA-TTT
1 -AATATTTAAATTTTATTTTAATATTTT
*
35665 AA-A-TTAAATCTTTAATTTT--TATTTA
1 AATATTTAAAT-TTT-ATTTTAATATTTT
35690 AATATTTAAAT
1 AATATTTAAAT
35701 ATAAATTTCA
Statistics
Matches: 131, Mismatches: 13, Indels: 38
0.72 0.07 0.21
Matches are distributed among these distances:
20 17 0.13
21 6 0.05
22 1 0.01
23 3 0.02
24 7 0.05
25 5 0.04
26 17 0.13
27 57 0.44
28 6 0.05
29 3 0.02
30 9 0.07
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (27 bp):
AATATTTAAATTTTATTTTAATATTTT
Found at i:35609 original size:47 final size:46
Alignment explanation
Indices: 35532--35623 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 46
35522 TTTATTTTAA
* *
35532 TATTTTAATATTTAAATTTTATTTTAATATTTAATTATTGAAATTT
1 TATTTTAATATTGAAATTTTATTTTAATATTTAAATATTGAAATTT
*
35578 TATTTTAATTATTGAAATTTTATTTTAATATTTAAATATTTAAATT
1 TATTTTAA-TATTGAAATTTTATTTTAATATTTAAATATTGAAATT
35624 AAATCTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 8 0.19
47 34 0.81
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (46 bp):
TATTTTAATATTGAAATTTTATTTTAATATTTAAATATTGAAATTT
Found at i:35644 original size:17 final size:17
Alignment explanation
Indices: 35622--35669 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
35612 AATATTTAAA
35622 TTAAATCTTT-AATCTTT
1 TTAAATCTTTAAAT-TTT
*
35639 TTAAATTTTTAAATTTT
1 TTAAATCTTTAAATTTT
*
35656 TT-AATATTTAAATT
1 TTAAATCTTTAAATT
35670 AAATCTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 14 0.50
18 3 0.11
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAAATCTTTAAATTTT
Found at i:42065 original size:21 final size:21
Alignment explanation
Indices: 42039--42078 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42029 CCCCCTTTGA
*
42039 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
42060 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
42079 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:47425 original size:19 final size:19
Alignment explanation
Indices: 47401--47440 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
47391 CGAATAATTT
* *
47401 AATCGAATATATAATTTTA
1 AATCGAATATAAAATCTTA
*
47420 AATCGAGTATAAAATCTTA
1 AATCGAATATAAAATCTTA
47439 AA
1 AA
47441 ATTCATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (19 bp):
AATCGAATATAAAATCTTA
Found at i:47557 original size:13 final size:13
Alignment explanation
Indices: 47541--47575 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
47531 TAAGATTTTC
47541 TTTTTGAAAATCA
1 TTTTTGAAAATCA
47554 TTTTTG-AAATCA
1 TTTTTGAAAATCA
47566 TTTTTGAAAA
1 TTTTTGAAAA
47576 ATTACTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:52645 original size:20 final size:20
Alignment explanation
Indices: 52616--52658 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
52606 ATTCCACCAC
52616 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
52636 ATGCATCTATATGGTTCTAA
1 ATGCAACTATATGCTCCTAA
52656 ATG
1 ATG
52659 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:57599 original size:20 final size:20
Alignment explanation
Indices: 57570--57612 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
57560 ATTCCACCAC
57570 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* *
57590 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGCTCCTAA
57610 ATG
1 ATG
57613 GGCTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:62105 original size:21 final size:21
Alignment explanation
Indices: 62080--62136 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
62070 GGGAACGTAG
62080 GGGTATCGGTACACCTTCAAA
1 GGGTATCGGTACACCTTCAAA
*
62101 GGGTATCGATACACCTTCAAA
1 GGGTATCGGTACACCTTCAAA
62122 GGGTATCGGTACACC
1 GGGTATCGGTACACC
62137 CAGTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
GGGTATCGGTACACCTTCAAA
Found at i:66295 original size:20 final size:19
Alignment explanation
Indices: 66265--66305 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
66255 TTTTATCACA
*
66265 CTAAATTCTCTCAAATTCT
1 CTAAATTCTCTCAAATACT
66284 CTAAATTTCTCTCAAATACT
1 CTAAA-TTCTCTCAAATACT
66304 CT
1 CT
66306 CTTTTTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (19 bp):
CTAAATTCTCTCAAATACT
Found at i:66307 original size:12 final size:10
Alignment explanation
Indices: 66267--66306 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
66257 TTATCACACT
66267 AAATTCTCTC
1 AAATTCTCTC
66277 AAATTCTCT-
1 AAATTCTCTC
66286 AAATTTCTCTC
1 AAA-TTCTCTC
*
66297 AAATACTCTC
1 AAATTCTCTC
66307 TTTTTAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:66658 original size:101 final size:106
Alignment explanation
Indices: 66426--66665 Score: 355
Period size: 101 Copynumber: 2.3 Consensus size: 106
66416 TGGAAATCAT
*
66426 ATATCTCTACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTT-AA-TA-TAGT-A
*
66491 TATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
62 TATTAGTTGATATATTTAATGCATGATTATTAGATTAAGAATTAA
* * * *
66536 ATATCTCGATATTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTT-A-A-A-T-TATT
1 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAATATAGTATATT
66596 AGTTGATATATTTAATGCATGATTATTAGATTAAGAATTAA
66 AGTTGATATATTTAATGCATGATTATTAGATTAAGAATTAA
66637 ATATCTCGACACTTTGTTGATACGGTAAC
1 ATATCTCGACACTTTGTTGATACGGTAAC
66666 TCCAAAAACC
Statistics
Matches: 120, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
101 69 0.57
103 1 0.01
104 1 0.01
106 1 0.01
108 1 0.01
110 47 0.39
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (106 bp):
ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAATATAGTATATT
AGTTGATATATTTAATGCATGATTATTAGATTAAGAATTAA
Done.