Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011332.1 Kokia drynarioides strain JFW-HI SEQ_126312, 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: 123941
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:10188 original size:24 final size:24
Alignment explanation
Indices: 10138--10191 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
10128 CCAAACAACC
*
10138 AAAACAGCAACAAAAATAATAGAA
1 AAAACAGCAACAAAAATAACAGAA
*
10162 AAAATAGCAACAAAAATAACA-ATA
1 AAAACAGCAACAAAAATAACAGA-A
10186 AAAACA
1 AAAACA
10192 ACACCAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.72, C:0.13, G:0.06, T:0.09
Consensus pattern (24 bp):
AAAACAGCAACAAAAATAACAGAA
Found at i:10200 original size:21 final size:19
Alignment explanation
Indices: 10179--10265 Score: 59
Period size: 19 Copynumber: 4.3 Consensus size: 19
10169 CAACAAAAAT
10179 AACAATAAAAACAACACCAA
1 AACAATAAAAA-AACACCAA
**
10199 TAGTAA-AAAAAATAGCACCAA
1 -AACAATAAAAAA-A-CACCAA
*
10220 AACAGTAAAAAAACACCAA
1 AACAATAAAAAAACACCAA
**
10239 AACAGCAAAAAATAGCAACCAA
1 AACAATAAAAAA-A-C-ACCAA
10261 AACAA
1 AACAA
10266 CAATATAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
19 18 0.34
20 10 0.19
21 16 0.30
22 9 0.17
ACGTcount: A:0.67, C:0.21, G:0.06, T:0.07
Consensus pattern (19 bp):
AACAATAAAAAAACACCAA
Found at i:10236 original size:19 final size:21
Alignment explanation
Indices: 10205--10264 Score: 88
Period size: 19 Copynumber: 2.9 Consensus size: 21
10195 CCAATAGTAA
*
10205 AAAAAATAGCACCAAAACAGT
1 AAAAAATAGCACCAAAACAGC
10226 AAAAAA-A-CACCAAAACAGC
1 AAAAAATAGCACCAAAACAGC
10245 AAAAAATAGCAACCAAAACA
1 AAAAAATAGC-ACCAAAACA
10265 ACAATATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
19 17 0.49
20 2 0.06
21 7 0.20
22 9 0.26
ACGTcount: A:0.67, C:0.22, G:0.07, T:0.05
Consensus pattern (21 bp):
AAAAAATAGCACCAAAACAGC
Found at i:12326 original size:21 final size:20
Alignment explanation
Indices: 12302--12375 Score: 53
Period size: 21 Copynumber: 3.7 Consensus size: 20
12292 AGGCGTTGCT
12302 GTTGAAGGAGGTGGTGCTGAA
1 GTTGAAGGAGGTGGTGC-GAA
* * * **
12323 GTTGTAGGTGGAGG-G-GTT
1 GTTGAAGGAGGTGGTGCGAA
12341 GTTGAAGGAGGTGGTGCGGAA
1 GTTGAAGGAGGTGGTGC-GAA
* *
12362 GTTGTAGGTGGTGG
1 GTTGAAGGAGGTGG
12376 AGTGGTGGTG
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
18 12 0.32
19 1 0.03
20 1 0.03
21 24 0.63
ACGTcount: A:0.18, C:0.03, G:0.53, T:0.27
Consensus pattern (20 bp):
GTTGAAGGAGGTGGTGCGAA
Found at i:24284 original size:27 final size:26
Alignment explanation
Indices: 24246--24296 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
24236 ACTATACTAA
24246 TTTTCTCAAATTGGTACCTAAACTTT
1 TTTTCTCAAATTGGTACCTAAACTTT
*
24272 TTTTGTCATAATTGGTACCTAAACT
1 TTTTCTCA-AATTGGTACCTAAACT
24297 ATTAAATCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (26 bp):
TTTTCTCAAATTGGTACCTAAACTTT
Found at i:27655 original size:4 final size:4
Alignment explanation
Indices: 27648--27675 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
27638 CATATATATA
27648 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
27676 GTGTCAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:29273 original size:10 final size:10
Alignment explanation
Indices: 29260--29295 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
29250 ATTTTTAAAA
29260 AATATTTTTT
1 AATATTTTTT
*
29270 AATATTTTTA
1 AATATTTTTT
*
29280 AATATTTTAT
1 AATATTTTTT
29290 AATATT
1 AATATT
29296 AAAATATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
AATATTTTTT
Found at i:29300 original size:18 final size:19
Alignment explanation
Indices: 29258--29302 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
29248 ATATTTTTAA
*
29258 AAAATATTTTTTAATATTTT
1 AAAATATTTTATAATA-TTT
*
29278 TAAATATTTTATAATA-TT
1 AAAATATTTTATAATATTT
29296 AAAATAT
1 AAAATAT
29303 AATTTATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 8 0.36
20 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAAATATTTTATAATATTT
Found at i:31094 original size:18 final size:18
Alignment explanation
Indices: 31071--31107 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31061 ATTTCAAAAC
31071 TGTCAAATATATTTTAAT
1 TGTCAAATATATTTTAAT
*
31089 TGTCAAGTATATTTTAAT
1 TGTCAAATATATTTTAAT
31107 T
1 T
31108 TTTTAAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (18 bp):
TGTCAAATATATTTTAAT
Found at i:31208 original size:18 final size:18
Alignment explanation
Indices: 31187--31227 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
31177 ATATTAATTA
31187 AAATAAAAATATACATTT
1 AAATAAAAATATACATTT
* * *
31205 AAATTAAATTATATATTT
1 AAATAAAAATATACATTT
31223 AAATA
1 AAATA
31228 TTATATAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATAAAAATATACATTT
Found at i:34907 original size:14 final size:14
Alignment explanation
Indices: 34884--34917 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
34874 TGCCACTTTG
*
34884 CTATTATATTGTTA
1 CTATTTTATTGTTA
34898 CTATTTTATTGTTA
1 CTATTTTATTGTTA
*
34912 TTATTT
1 CTATTT
34918 ATATATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (14 bp):
CTATTTTATTGTTA
Found at i:35715 original size:37 final size:36
Alignment explanation
Indices: 35665--35739 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 36
35655 TATACTTGTT
*
35665 TTAAAAAAAAAAAAAACATATAA-ATTTCAATTAATGA
1 TTAAAAAAAAAAAAAA-AT-TAATAATTCAATTAATGA
**
35702 TTAAAAATTAAAAAAAATTAATTAATTCAATTAATGA
1 TTAAAAAAAAAAAAAAATTAA-TAATTCAATTAATGA
35739 T
1 T
35740 AATTCGAGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 3 0.09
36 2 0.06
37 28 0.85
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (36 bp):
TTAAAAAAAAAAAAAAATTAATAATTCAATTAATGA
Found at i:44164 original size:208 final size:208
Alignment explanation
Indices: 43805--45010 Score: 1630
Period size: 208 Copynumber: 5.8 Consensus size: 208
43795 TGGACGAATG
* * * * * *
43805 AGTCTCATTTGTATTGAGTTTCGCTTCATTGGTTTGGTCTGCTTCTCTATATCTCATCAGGAATA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
* * *
43870 TGACCGCCTCATTGTTTCAATCCACTTCTCTATATCTCATTAGGAAGACAGATTTGGCTCACTTC
66 TGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTTCACTTC
* * * *
43935 TCTGCATCTCGTCAGGAAGATGACCGTTTTATTGCTTTGACCCACTTCTCTGCATCTCGTCAGGA
131 TCTGCATCTCGTCAAGAAGATGACCGATTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGA
44000 AGATGGGGTTTGA
196 AGATGGGGTTTGA
* *
44013 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTTGTCTATTTCTCTGTATCTCATCAGGAAGA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
* * * *
44078 TGACCGCCTCATTGTTTCAATCCACTTCTCTATATCTCATCAAGAAAAC-GAATTTGGTCCACTT
66 TGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAG-ATTTGGTTCACTT
* * * * * * * * * *
44142 ATCTGTATCTCATTAAGAAGATGACCGCTTTATTGCTTTGACCCATTTTTTTGTATCTCATTAAG
130 CTCTGCATCTCGTCAAGAAGATGACCGATTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGG
*
44207 AAGATGAGGTTTGA
195 AAGATGGGGTTTGA
* * * *
44221 AGTCTCGTTCGTATTGAGCTTCGCTTTATTGATTTGGTCTACTTCTCTATATTTCATCAGGAAGA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
* *
44286 TGACCGCCTCATTGTTTTAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGATTCACTTC
66 TGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTTCACTTC
* * * * * *
44351 TTTGTATCTCATCAAGAAGATGACCGCTTTATTACTTTGACCCACTTCTCTGTATCTAATCAGGA
131 TCTGCATCTCGTCAAGAAGATGACCGATTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGA
44416 AGATGGGGTTTGA
196 AGATGGGGTTTGA
* *
44429 AGTCTCATTCGTATTGAGCTTCGTTTCATTGATTTGGTCTACTTCTCTGTATCTCATAAGGAAGA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
* * * * *
44494 TGACTGTCTCATTGTTTTAATCCACTTCTTTGTATCTCATCAGGAAGACAGATTTGGTTTCAGTT
66 TGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGG-TTCACTT
* * *
44559 CTCTGCATCTCGTTAAGAAGATGACC-ACTTATTGGTTTGACCCACTTCTCTGTATCTCATCAGG
130 CTCTGCATCTCGTCAAGAAGATGACCGATTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGG
44623 AAGATGGGGTTTGA
195 AAGATGGGGTTTGA
* * *
44637 AGTCTCATTAGTATTGAGCTTCGCTTCATTGATTTGGTCCACTTATCTGTATCTCATCAGGAAGA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
* * *
44702 TGACTGCTTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTTTACTTC
66 TGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTTCACTTC
* * * * * * *
44767 TTTGCATCTCGTGAAGAAGATGACC-ACTTATTGGTTCGACCCACTTCTCTATATCTTATCAGGA
131 TCTGCATCTCGTCAAGAAGATGACCGATTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGA
44831 AGATGGGGTTTGA
196 AGATGGGGTTTGA
* * * ** * * *
44844 ATTTTCAATCACATTGAGCTGCGCTTCAATGATTTGGTCTACTTCTTTGTATCTCATCAGGAAGA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
* * **
44909 TGACTGCCTCATTGATTT-AATCCACTTCTCTGTATCTCATCAGAAAGATGGATTTGGTTCACTT
66 TGACCGCCTCATTG-TTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTTCACTT
* *
44973 CTCTGCATCTGGTCAGGAAGATGACC-ATTTTATTGCTT
130 CTCTGCATCTCGTCAAGAAGATGACCGA-TTTATTGCTT
45011 CGGATGATTG
Statistics
Matches: 885, Mismatches: 108, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
207 211 0.24
208 645 0.73
209 29 0.03
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (208 bp):
AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
TGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTTCACTTC
TCTGCATCTCGTCAAGAAGATGACCGATTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGA
AGATGGGGTTTGA
Found at i:45076 original size:39 final size:39
Alignment explanation
Indices: 45033--45251 Score: 251
Period size: 39 Copynumber: 5.6 Consensus size: 39
45023 ATTTGCCTCT
45033 TGATCGGGGTAAGAGATTGGATGACTGTAATCTGCCCCA
1 TGATCGGGGTAAGAGATTGGATGACTGTAATCTGCCCCA
* * * ** * * *
45072 TGATCGGGATAAAAGATCCGG-TGGTTGCAATCTACACCA
1 TGATCGGGGTAAGAGAT-TGGATGACTGTAATCTGCCCCA
*
45111 TGATCGGGGTAAGAGATTGGATGACTATAATCTGCCCCA
1 TGATCGGGGTAAGAGATTGGATGACTGTAATCTGCCCCA
* * * *
45150 TGATCGGAGTAAGAGATTGGATAACTGCAATCTGCACCA
1 TGATCGGGGTAAGAGATTGGATGACTGTAATCTGCCCCA
* * * * * *
45189 TGATCGGGGTAAAAGATCGGGTGGCAGTAATCTGCCTCA
1 TGATCGGGGTAAGAGATTGGATGACTGTAATCTGCCCCA
45228 TGATCGGGGTAAGAGATTGGATGA
1 TGATCGGGGTAAGAGATTGGATGA
45252 TGATGTAACT
Statistics
Matches: 142, Mismatches: 36, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
38 2 0.01
39 138 0.97
40 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (39 bp):
TGATCGGGGTAAGAGATTGGATGACTGTAATCTGCCCCA
Found at i:45221 original size:117 final size:117
Alignment explanation
Indices: 45033--45251 Score: 332
Period size: 117 Copynumber: 1.9 Consensus size: 117
45023 ATTTGCCTCT
* * * * **
45033 TGATCGGGGTAAGAGATTGGATGACTGTAATCTGCCCCATGATCGGGATAAAAGATCCGGTGGTT
1 TGATCGGAGTAAGAGATTGGATAACTGCAATCTGCACCATGATCGGGATAAAAGATCCGGTGGCA
45098 GCAATCTACAC-CATGATCGGGGTAAGAGATTGGATGACTATAATCTGCCCCA
66 GCAATCTAC-CTCATGATCGGGGTAAGAGATTGGATGACTATAATCTGCCCCA
* *
45150 TGATCGGAGTAAGAGATTGGATAACTGCAATCTGCACCATGATCGGGGTAAAAGATCGGGTGGCA
1 TGATCGGAGTAAGAGATTGGATAACTGCAATCTGCACCATGATCGGGATAAAAGATCCGGTGGCA
* *
45215 GTAATCTGCCTCATGATCGGGGTAAGAGATTGGATGA
66 GCAATCTACCTCATGATCGGGGTAAGAGATTGGATGA
45252 TGATGTAACT
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
116 1 0.01
117 90 0.99
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (117 bp):
TGATCGGAGTAAGAGATTGGATAACTGCAATCTGCACCATGATCGGGATAAAAGATCCGGTGGCA
GCAATCTACCTCATGATCGGGGTAAGAGATTGGATGACTATAATCTGCCCCA
Found at i:46688 original size:23 final size:26
Alignment explanation
Indices: 46658--46709 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
46648 ACCTCTCCTT
46658 TTCTTTTT-TT-ATT-TTTATTTTTC
1 TTCTTTTTCTTCATTATTTATTTTTC
*
46681 TTCTTTTTCTTCTTTATTTATTTTTC
1 TTCTTTTTCTTCATTATTTATTTTTC
46707 TTC
1 TTC
46710 ATCGAATCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 8 0.32
24 2 0.08
25 2 0.08
26 13 0.52
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (26 bp):
TTCTTTTTCTTCATTATTTATTTTTC
Found at i:52247 original size:30 final size:30
Alignment explanation
Indices: 52211--52365 Score: 120
Period size: 30 Copynumber: 5.2 Consensus size: 30
52201 CAATATTGTC
* *
52211 AAAGTTTGAGGCTCAAAATATAGTTTTAGA
1 AAAGTTTAAGGCTCAAAATATAATTTTAGA
* *
52241 AAAGTTTAAGGGTCAAAATGTAATTTTAGA
1 AAAGTTTAAGGCTCAAAATATAATTTTAGA
* * * * *
52271 TAAGTTTAGGGGTTAAAATGCA-AATTTGA-A
1 AAAGTTTAAGGCTCAAAAT--ATAATTTTAGA
* *
52301 AAAGTTTAAGGGTTAAAATATAATTTT-GTA
1 AAAGTTTAAGGCTCAAAATATAATTTTAG-A
* * * *
52331 AGAGTTTAGGGGTCAAAATGTAATTTTA-A
1 AAAGTTTAAGGCTCAAAATATAATTTTAGA
52360 AAAGTT
1 AAAGTT
52366 CGAGGACCTC
Statistics
Matches: 102, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
28 1 0.01
29 11 0.11
30 84 0.82
31 6 0.06
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (30 bp):
AAAGTTTAAGGCTCAAAATATAATTTTAGA
Found at i:52289 original size:60 final size:59
Alignment explanation
Indices: 52223--52365 Score: 166
Period size: 60 Copynumber: 2.4 Consensus size: 59
52213 AGTTTGAGGC
* *
52223 TCAAAATATAGTTTTAGAAAAGTTTAAGGGTCAAAATGTAATTTTAG-ATA-AGTTTAGGGG
1 TCAAAATATAATTTTA-AAAAGTTTAAGGGTCAAAATATAATTTT-GTA-AGAGTTTAGGGG
* * *
52283 TTAAAATGCA-AATTTGAAAAAGTTTAAGGGTTAAAATATAATTTTGTAAGAGTTTAGGGG
1 TCAAAAT--ATAATTTTAAAAAGTTTAAGGGTCAAAATATAATTTTGTAAGAGTTTAGGGG
*
52343 TCAAAATGTAATTTTAAAAAGTT
1 TCAAAATATAATTTTAAAAAGTT
52366 CGAGGACCTC
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
59 15 0.21
60 49 0.70
61 5 0.07
62 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.36
Consensus pattern (59 bp):
TCAAAATATAATTTTAAAAAGTTTAAGGGTCAAAATATAATTTTGTAAGAGTTTAGGGG
Found at i:57363 original size:6 final size:6
Alignment explanation
Indices: 57354--57379 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
57344 ATTCCAATCA
57354 CACTTT CACTTT CACTTT CACTTT CA
1 CACTTT CACTTT CACTTT CACTTT CA
57380 ATTTTGAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (6 bp):
CACTTT
Found at i:74847 original size:18 final size:19
Alignment explanation
Indices: 74821--74870 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
74811 TATTACTAGC
*
74821 GGTTTATCCACAAC-GAGT
1 GGTTCATCCACAACAGAGT
74839 GGTTCATCCACAACAATGAGT
1 GGTTCATCCACAAC-A-GAGT
74860 GGTTCATCCAC
1 GGTTCATCCAC
74871 GACGTGGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 13 0.46
21 15 0.54
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (19 bp):
GGTTCATCCACAACAGAGT
Found at i:74859 original size:21 final size:21
Alignment explanation
Indices: 74830--74870 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
74820 CGGTTTATCC
74830 ACAACGAGTGGTTCATCCACA
1 ACAACGAGTGGTTCATCCACA
*
74851 ACAATGAGTGGTTCATCCAC
1 ACAACGAGTGGTTCATCCAC
74871 GACGTGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (21 bp):
ACAACGAGTGGTTCATCCACA
Found at i:76898 original size:9 final size:9
Alignment explanation
Indices: 76884--76909 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
76874 GTTGTACATA
76884 AAAAAAAAG
1 AAAAAAAAG
76893 AAAAAAAAG
1 AAAAAAAAG
76902 AAAAAAAA
1 AAAAAAAA
76910 AAGAGAGGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:79155 original size:7 final size:7
Alignment explanation
Indices: 79143--79167 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
79133 TTTTAAAAAT
79143 AAATTTA
1 AAATTTA
79150 AAATTTA
1 AAATTTA
79157 AAATTTA
1 AAATTTA
79164 AAAT
1 AAAT
79168 ATATCATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:81848 original size:34 final size:34
Alignment explanation
Indices: 81805--81902 Score: 103
Period size: 33 Copynumber: 2.9 Consensus size: 34
81795 AAGCAAGTTT
*
81805 ATTGCTATTGTAATGATCTGTTATAAGCATGATA
1 ATTGCTATTGTATTGATCTGTTATAAGCATGATA
* * *
81839 ATTGTTATTGTGTTGAT-T-TTCAATAAGCAT-ATT
1 ATTGCTATTGTATTGATCTGTT--ATAAGCATGATA
* *
81872 ATTGCTACTGTATTGATCTGTTGTAAGCATG
1 ATTGCTATTGTATTGATCTGTTATAAGCATG
81903 TCATGTTGCA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
32 2 0.04
33 24 0.47
34 23 0.45
35 2 0.04
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45
Consensus pattern (34 bp):
ATTGCTATTGTATTGATCTGTTATAAGCATGATA
Found at i:81899 original size:33 final size:34
Alignment explanation
Indices: 81794--81902 Score: 107
Period size: 34 Copynumber: 3.2 Consensus size: 34
81784 AACCAAATGT
* * *
81794 TAAGCAAGTTTATTGCTATTGTAATGATCTGTTA
1 TAAGCATGATTATTGCTATTGTATTGATCTGTTA
* * *
81828 TAAGCATGATAATTGTTATTGTGTTGAT-T-TTCAA
1 TAAGCATGATTATTGCTATTGTATTGATCTGTT--A
* *
81862 TAAGCAT-ATTATTGCTACTGTATTGATCTGTTG
1 TAAGCATGATTATTGCTATTGTATTGATCTGTTA
81895 TAAGCATG
1 TAAGCATG
81903 TCATGTTGCA
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
32 2 0.03
33 24 0.41
34 31 0.53
35 2 0.03
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.44
Consensus pattern (34 bp):
TAAGCATGATTATTGCTATTGTATTGATCTGTTA
Found at i:84381 original size:37 final size:37
Alignment explanation
Indices: 84336--84426 Score: 137
Period size: 37 Copynumber: 2.5 Consensus size: 37
84326 GTTTGTATAA
* * *
84336 TATTCAGGCTATGTGCCTTGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTG
*
84373 TTTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTG
*
84410 TATTCAAGCTATGTGCC
1 TATTCAGGCTATGTGCC
84427 GGTGTTTTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTG
Found at i:84387 original size:21 final size:21
Alignment explanation
Indices: 84357--84447 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
84347 TGTGCCTTGT
*
84357 AGGCTTTGTGCCGGTGTTTTC
1 AGGCTATGTGCCGGTGTTTTC
84378 AGGCTATGTGCC--TAG---T-
1 AGGCTATGTGCCGGT-GTTTTC
* *
84394 AGGCT-TCGTGCCAGTGTATTC
1 AGGCTAT-GTGCCGGTGTTTTC
*
84415 AAGCTATGTGCCGGTGTTTTC
1 AGGCTATGTGCCGGTGTTTTC
84436 AGGCTATGTGCC
1 AGGCTATGTGCC
84448 TAGTAAGCTT
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
15 1 0.02
16 10 0.18
17 2 0.04
18 1 0.02
19 1 0.02
20 2 0.04
21 38 0.68
22 1 0.02
ACGTcount: A:0.13, C:0.21, G:0.31, T:0.35
Consensus pattern (21 bp):
AGGCTATGTGCCGGTGTTTTC
Found at i:84430 original size:58 final size:58
Alignment explanation
Indices: 84363--84484 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 58
84353 TTGTAGGCTT
* *
84363 TGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTGTATTCAAGCTA
1 TGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAAGCTTCGTGCCAGTGTAGTCAAGCTA
* * * *
84421 TGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAAGCTTCGTGTCGGTGTGGTCAGGCTA
1 TGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAAGCTTCGTGCCAGTGTAGTCAAGCTA
84479 TGTGCC
1 TGTGCC
84485 TAGTAGGCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.13, C:0.20, G:0.32, T:0.34
Consensus pattern (58 bp):
TGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAAGCTTCGTGCCAGTGTAGTCAAGCTA
Found at i:84525 original size:74 final size:74
Alignment explanation
Indices: 84421--84574 Score: 209
Period size: 74 Copynumber: 2.1 Consensus size: 74
84411 ATTCAAGCTA
* * * * *
84421 TGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAAGCTTCGTGTCGGTGTGGTCAGGCTATGTGCCT
1 TGTGCCGGTGTTTGCAGGCTATATGCCTAGTAAGCTTCGTGCCGGTGTAGTCAGGCTACGTGCCT
*
84486 AGTAGGCTT
66 AGCAGGCTT
* * * * *
84495 TGTGCTGGTGTTTGCAGGCTATATGTCTAGTAGGCTTCGTGCCGGTGTATTCGGGCTACGTGCCT
1 TGTGCCGGTGTTTGCAGGCTATATGCCTAGTAAGCTTCGTGCCGGTGTAGTCAGGCTACGTGCCT
84560 AGCAGGCTT
66 AGCAGGCTT
84569 TGTGCC
1 TGTGCC
84575 AATGATCCAA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.12, C:0.20, G:0.34, T:0.34
Consensus pattern (74 bp):
TGTGCCGGTGTTTGCAGGCTATATGCCTAGTAAGCTTCGTGCCGGTGTAGTCAGGCTACGTGCCT
AGCAGGCTT
Found at i:84567 original size:37 final size:36
Alignment explanation
Indices: 84422--84574 Score: 171
Period size: 37 Copynumber: 4.1 Consensus size: 36
84412 TTCAAGCTAT
*
84422 GTGCCGGTGTTTTCAGGCTATGTGCCTAGTAAGCTTC
1 GTGCCGGTG-TTTCAGGCTATGTGCCTAGTAGGCTTC
* * *
84459 GTGTCGGTGTGGTCAGGCTATGTGCCTAGTAGGCTTT
1 GTGCCGGTGT-TTCAGGCTATGTGCCTAGTAGGCTTC
* * *
84496 GTGCTGGTGTTTGCAGGCTATATGTCTAGTAGGCTTC
1 GTGCCGGTGTTT-CAGGCTATGTGCCTAGTAGGCTTC
* * * *
84533 GTGCCGGTGTATTCGGGCTACGTGCCTAGCAGGCTTT
1 GTGCCGGTGT-TTCAGGCTATGTGCCTAGTAGGCTTC
84570 GTGCC
1 GTGCC
84575 AATGATCCAA
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
36 2 0.02
37 92 0.96
38 2 0.02
ACGTcount: A:0.12, C:0.20, G:0.34, T:0.34
Consensus pattern (36 bp):
GTGCCGGTGTTTCAGGCTATGTGCCTAGTAGGCTTC
Found at i:95952 original size:111 final size:110
Alignment explanation
Indices: 95763--96015 Score: 303
Period size: 111 Copynumber: 2.3 Consensus size: 110
95753 TTTGTATAAT
*
95763 ATTCAGGCTATG-GCCTAGTAGGCTTCGTGCCGGTATTTTCAAGCAATGTGCCTAGTAGGCTTTG
1 ATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTATTTTCAAGCAATGTGCCTAGTAGGCTTTG
** * * * **
95827 TGTCGGCATTTTCAGGCTATGTGCCTTGTAGGCTTTGTGTTAGTG
66 TACCGGCATATTCAGGCTATGTGCCTAGTAGGCTTTATGCAAGTG
* * * *
95872 AATTCAGGCTATGTGCCTAGTAGGCTTTGTGTCAGTGTTTTCAAGCTATGTGCCTAGTAGGCTTC
1 -ATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTATTTTCAAGCAATGTGCCTAGTAGGCTT-
***
95937 T-TACCGTTGTATTCAGGCTATGTGCCTAGTAGGCTTTATGCAAGTG
64 TGTACCGGCATATTCAGGCTATGTGCCTAGTAGGCTTTATGCAAGTG
* * *
95983 TTTGTAGGCTATATGCCTAGTAGGCTTCGTGCC
1 ATT-CAGGCTATGTGCCTAGTAGGCTTCGTGCC
96016 GGTGTAATCC
Statistics
Matches: 120, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
110 14 0.12
111 105 0.88
112 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.37
Consensus pattern (110 bp):
ATTCAGGCTATGTGCCTAGTAGGCTTCGTGCCAGTATTTTCAAGCAATGTGCCTAGTAGGCTTTG
TACCGGCATATTCAGGCTATGTGCCTAGTAGGCTTTATGCAAGTG
Found at i:95992 original size:37 final size:35
Alignment explanation
Indices: 95764--96050 Score: 211
Period size: 37 Copynumber: 7.8 Consensus size: 35
95754 TTGTATAATA
* * *
95764 TTCAGGCTATG-GCCTAGTAGGCTTCGTGCCGGTATT
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTG-CAGT-GT
* * *
95800 TTCAAGCAATGTGCCTAGTAGGCTTTGTGTCGGCAT-T
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTG-CAG--TGT
* * *
95837 TTCAGGCTATGTGCCTTGTAGGCTTTGTGTTAGTGAA
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTG-CAGTG-T
95874 TTCAGGCTATGTGCCTAGTAGGCTTTGTGTCAGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTG-CAGTG-T
* * *
95911 TTCAAGCTATGTGCCTAGTAGGCTTCT-TACCGTTGT
1 TTCAGGCTATGTGCCTAGTAGGCTT-TGTGCAG-TGT
*
95947 ATTCAGGCTATGTGCCTAGTAGGCTTTATGCAAGTGT
1 -TTCAGGCTATGTGCCTAGTAGGCTTTGTGC-AGTGT
* * * *
95984 TTGTAGGCTATATGCCTAGTAGGCTTCGTGCCGGTGT
1 TT-CAGGCTATGTGCCTAGTAGGCTTTGTG-CAGTGT
* * * * *
96021 AATCCGGTTATGTGCCTTGCAGGCTTTGTG
1 -TTCAGGCTATGTGCCTAGTAGGCTTTGTG
96051 TCGATGATCC
Statistics
Matches: 205, Mismatches: 33, Indels: 25
0.78 0.13 0.10
Matches are distributed among these distances:
35 1 0.00
36 15 0.07
37 184 0.90
38 4 0.02
39 1 0.00
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (35 bp):
TTCAGGCTATGTGCCTAGTAGGCTTTGTGCAGTGT
Found at i:96033 original size:111 final size:111
Alignment explanation
Indices: 95763--96046 Score: 259
Period size: 111 Copynumber: 2.6 Consensus size: 111
95753 TTTGTATAAT
* * * ** * *
95763 ATTCAGGCTAT-GGCCTAGTAGGCTTCGTGCCGGTATTTTCAAGCAATGTGCCTAGTAGGCTT-T
1 ATTCAGGCTATATGCCTAGTAGGCTTCGTGCCAGTGTAATCAAGCTATGTGCCTAGCAGGCTTCT
** *** * * * **
95826 GTGTCGGCATTTTCAGGCTATGTGCCTTGTAGGCTTTGTGTTAGTGA
66 -TACCGTTGTATTCAGGCTATGTGCCTAGTAGGCTTTATGCAAGTGA
* * * ** *
95873 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGTCAGTGTTTTCAAGCTATGTGCCTAGTAGGCTTCT
1 ATTCAGGCTATATGCCTAGTAGGCTTCGTGCCAGTGTAATCAAGCTATGTGCCTAGCAGGCTTCT
95938 TACCGTTGTATTCAGGCTATGTGCCTAGTAGGCTTTATGCAAGTG-
66 TACCGTTGTATTCAGGCTATGTGCCTAGTAGGCTTTATGCAAGTGA
* * * ** * *
95983 TTTGTAGGCTATATGCCTAGTAGGCTTCGTGCCGGTGTAATCCGGTTATGTGCCTTGCAGGCTT
1 ATT-CAGGCTATATGCCTAGTAGGCTTCGTGCCAGTGTAATCAAGCTATGTGCCTAGCAGGCTT
96047 TGTGTCGATG
Statistics
Matches: 142, Mismatches: 29, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
110 13 0.09
111 128 0.90
112 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.37
Consensus pattern (111 bp):
ATTCAGGCTATATGCCTAGTAGGCTTCGTGCCAGTGTAATCAAGCTATGTGCCTAGCAGGCTTCT
TACCGTTGTATTCAGGCTATGTGCCTAGTAGGCTTTATGCAAGTGA
Found at i:96848 original size:71 final size:71
Alignment explanation
Indices: 96768--96925 Score: 273
Period size: 71 Copynumber: 2.2 Consensus size: 71
96758 CTCTCTTTTA
*
96768 GTTTT-GGTATCGGTAGTTAGAAGAGAGGTACCGATAGAAGTCTACAGACTAAGTAGTTCTACTT
1 GTTTTAGGTATCGGTAGTTAGAAGAGAGGTACCGATAAAAGTCTACAGACTAAGTAGTTCTACTT
96832 ACTGTG
66 ACTGTG
* * *
96838 GTTTTAGGTATCGATAGTTAGAAGAGAGGTACCGATAAAAGTCTATAGACTAAGTTGTTCTACTT
1 GTTTTAGGTATCGGTAGTTAGAAGAGAGGTACCGATAAAAGTCTACAGACTAAGTAGTTCTACTT
96903 ACTGTG
66 ACTGTG
96909 GTTTTAGGTATCGGTAG
1 GTTTTAGGTATCGGTAG
96926 AAGTTATTTG
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 5 0.06
71 77 0.94
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (71 bp):
GTTTTAGGTATCGGTAGTTAGAAGAGAGGTACCGATAAAAGTCTACAGACTAAGTAGTTCTACTT
ACTGTG
Found at i:97410 original size:34 final size:34
Alignment explanation
Indices: 97372--97441 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
97362 GTTAAAGGCG
* *
97372 TATTAAATGCTACTATATTGATA-TGTTATGAGCA
1 TATTAAATGCTACCAT-TTGAAATTGTTATGAGCA
*
97406 TATTAATTGCTACCATTTGAAATTGTTATGAGCA
1 TATTAAATGCTACCATTTGAAATTGTTATGAGCA
97440 TA
1 TA
97442 CCATAATGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 5 0.16
34 27 0.84
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (34 bp):
TATTAAATGCTACCATTTGAAATTGTTATGAGCA
Found at i:98840 original size:45 final size:45
Alignment explanation
Indices: 98776--98898 Score: 174
Period size: 45 Copynumber: 2.7 Consensus size: 45
98766 GTGTGAGCAG
* * *
98776 TTTATCTGCAACATTGAGTGGTTCATCCACACGGTATTAACAACT
1 TTTATCTGCAACAATGAGTGGTTTATCCACACCGTATTAACAACT
* * *
98821 TTTATCTACAACAATGAGTGGTTTATCCTCACCGTATTAGCAACT
1 TTTATCTGCAACAATGAGTGGTTTATCCACACCGTATTAACAACT
* *
98866 TTTATTTGCAACAATGAGTGATTTATCCACACC
1 TTTATCTGCAACAATGAGTGGTTTATCCACACC
98899 ATACTCGCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (45 bp):
TTTATCTGCAACAATGAGTGGTTTATCCACACCGTATTAACAACT
Found at i:98909 original size:45 final size:45
Alignment explanation
Indices: 98776--98912 Score: 139
Period size: 45 Copynumber: 3.0 Consensus size: 45
98766 GTGTGAGCAG
* * * * ** * *
98776 TTTATCTGCAACATTGAGTGGTTCATCCACACGGTATTAACAACT
1 TTTATCTACAACAATGAGTGATTTATCCACACCATACTAGCAACT
* * * *
98821 TTTATCTACAACAATGAGTGGTTTATCCTCACCGTATTAGCAACT
1 TTTATCTACAACAATGAGTGATTTATCCACACCATACTAGCAACT
* * *
98866 TTTATTTGCAACAATGAGTGATTTATCCACACCATACTCGCAACT
1 TTTATCTACAACAATGAGTGATTTATCCACACCATACTAGCAACT
98911 TT
1 TT
98913 AATATGCGAA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (45 bp):
TTTATCTACAACAATGAGTGATTTATCCACACCATACTAGCAACT
Found at i:99514 original size:23 final size:23
Alignment explanation
Indices: 99487--99543 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
99477 TAACGTGGCA
99487 TCCAGTCAGCAGCTTCTAGAAGG
1 TCCAGTCAGCAGCTTCTAGAAGG
*
99510 TCCAGTCAACAGCTTCTAGAAGG
1 TCCAGTCAGCAGCTTCTAGAAGG
*
99533 TCTAGTCAGCA
1 TCCAGTCAGCA
99544 ATGATGGACG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
TCCAGTCAGCAGCTTCTAGAAGG
Found at i:106016 original size:18 final size:17
Alignment explanation
Indices: 105967--106030 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 17
105957 CCATTGTTTT
105967 ATTATTTAATTTTATACTTC
1 ATTATTT-ATTTTAT--TTC
*
105987 ATTA-TTAATTTATTTC
1 ATTATTTATTTTATTTC
106003 AATTATTTATTTTATTTC
1 -ATTATTTATTTTATTTC
106021 --TATTTATTTT
1 ATTATTTATTTT
106031 TGGTATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 10 0.25
16 3 0.08
17 4 0.10
18 17 0.43
19 2 0.05
20 4 0.10
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTTATTTTATTTC
Found at i:106549 original size:124 final size:124
Alignment explanation
Indices: 106329--106576 Score: 469
Period size: 124 Copynumber: 2.0 Consensus size: 124
106319 CCCGATGCTT
*
106329 CTCCCTCATTCTTTATGCACTCGACAGCACCAAACCAATCGGACGAGGTAAACTCTGAACTCGTT
1 CTCCCTCATTCTTTATGCACTCGACAGCACCAAACCAATCGGACGAGGTAAACTCTAAACTCGTT
*
106394 AATATTCAACCTTTATTAATATACCTCCCCATTTTTGGATATACAGAGGATTTCAAGCA
66 AATATTCAACCTTTATTAATATACCACCCCATTTTTGGATATACAGAGGATTTCAAGCA
*
106453 CTCCCTCATTCTTTATGCACTCGACAGCACCAAACCAATCGGACGAGGTAAAGTCTAAACTCGTT
1 CTCCCTCATTCTTTATGCACTCGACAGCACCAAACCAATCGGACGAGGTAAACTCTAAACTCGTT
106518 AATATTCAACCTTTATTAATATACCACCCCATTTTTGGATATACAGAGGATTTCAAGCA
66 AATATTCAACCTTTATTAATATACCACCCCATTTTTGGATATACAGAGGATTTCAAGCA
106577 TGATTTTCCA
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 121 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.29
Consensus pattern (124 bp):
CTCCCTCATTCTTTATGCACTCGACAGCACCAAACCAATCGGACGAGGTAAACTCTAAACTCGTT
AATATTCAACCTTTATTAATATACCACCCCATTTTTGGATATACAGAGGATTTCAAGCA
Found at i:112024 original size:25 final size:23
Alignment explanation
Indices: 111996--112041 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
111986 AACAATACAG
*
111996 ATCTTACTCCCATCTGCTACACACC
1 ATCTT-CTCCCATC-CCTACACACC
*
112021 ATCTTCTTCCATCCCTACACA
1 ATCTTCTCCCATCCCTACACA
112042 ACAATTAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 7 0.37
25 5 0.26
ACGTcount: A:0.24, C:0.43, G:0.02, T:0.30
Consensus pattern (23 bp):
ATCTTCTCCCATCCCTACACACC
Found at i:118289 original size:29 final size:29
Alignment explanation
Indices: 118241--118353 Score: 136
Period size: 29 Copynumber: 3.9 Consensus size: 29
118231 ATAATATAGG
*
118241 TACAATTACAGATGCAGACATGATACAAA
1 TACAGTTACAGATGCAGACATGATACAAA
* * **
118270 TATAGTTACAGATGCGGACATGATACAGT
1 TACAGTTACAGATGCAGACATGATACAAA
* * * *
118299 TACAGTTATAGATGAAGACATAATACATA
1 TACAGTTACAGATGCAGACATGATACAAA
*
118328 TACAATTACAGATGCAGACATGATAC
1 TACAGTTACAGATGCAGACATGATAC
118354 CCCCATACGC
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (29 bp):
TACAGTTACAGATGCAGACATGATACAAA
Found at i:118319 original size:58 final size:58
Alignment explanation
Indices: 118241--118353 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
118231 ATAATATAGG
* * * * *
118241 TACAATTACAGATGCAGACATGATACAAATATAGTTACAGATGCGGACATGATACAGT
1 TACAATTACAGATGAAGACATAATACAAATACAATTACAGATGCAGACATGATACAGT
* * *
118299 TACAGTTATAGATGAAGACATAATACATATACAATTACAGATGCAGACATGATAC
1 TACAATTACAGATGAAGACATAATACAAATACAATTACAGATGCAGACATGATAC
118354 CCCCATACGC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (58 bp):
TACAATTACAGATGAAGACATAATACAAATACAATTACAGATGCAGACATGATACAGT
Found at i:122664 original size:16 final size:16
Alignment explanation
Indices: 122643--122673 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
122633 GCTAGGCAAT
122643 AGCACACAAAGTGCTG
1 AGCACACAAAGTGCTG
122659 AGCACACAAAGTGCT
1 AGCACACAAAGTGCT
122674 AATCAAAGAG
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:0.39, C:0.26, G:0.23, T:0.13
Consensus pattern (16 bp):
AGCACACAAAGTGCTG
Found at i:122719 original size:25 final size:23
Alignment explanation
Indices: 122658--122764 Score: 128
Period size: 23 Copynumber: 4.6 Consensus size: 23
122648 ACAAAGTGCT
* *
122658 GAGCACACAAAGTGCTAATCAAA
1 GAGCACACATAGTGCTAATCAGA
*
122681 GAGCACGCGA-AGTGCTAATAACAGA
1 GAGCACAC-ATAGTGCTAAT--CAGA
122706 GAGCACACATAGTGCTAATCAGA
1 GAGCACACATAGTGCTAATCAGA
*
122729 GAGCACACACAGTGCTAATCAGA
1 GAGCACACATAGTGCTAATCAGA
*
122752 GAGCGCAC-TAGTG
1 GAGCACACATAGTG
122765 TTCTTTAATG
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.05
23 49 0.66
24 2 0.03
25 19 0.26
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.14
Consensus pattern (23 bp):
GAGCACACATAGTGCTAATCAGA
Found at i:122732 original size:48 final size:46
Alignment explanation
Indices: 122658--122764 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 46
122648 ACAAAGTGCT
* *
122658 GAGCACACAAAGTGCTAATCAAAGAGCACGCGA-AGTGCTAATAACAGA
1 GAGCACACATAGTGCTAATCAAAGAGCACAC-ACAGTGCTAAT--CAGA
*
122706 GAGCACACATAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGA
1 GAGCACACATAGTGCTAATCAAAGAGCACACACAGTGCTAATCAGA
*
122752 GAGCGCAC-TAGTG
1 GAGCACACATAGTG
122765 TTCTTTAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
45 5 0.09
46 11 0.20
47 1 0.02
48 37 0.69
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.14
Consensus pattern (46 bp):
GAGCACACATAGTGCTAATCAAAGAGCACACACAGTGCTAATCAGA
Found at i:122856 original size:24 final size:26
Alignment explanation
Indices: 122818--122865 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
122808 TCTACATGGG
122818 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
122844 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
122866 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.