Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001020.1 Hibiscus syriacus cultivar Beakdansim tig00002033_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: 73846
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:249 original size:16 final size:17
Alignment explanation
Indices: 230--267 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
220 TTTTAATAAA
*
230 TTTTGATATTA-ATTTG
1 TTTTAATATTAGATTTG
246 TTTTAATATTAGTATTTG
1 TTTTAATATTAG-ATTTG
264 TTTT
1 TTTT
268 TATCAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (17 bp):
TTTTAATATTAGATTTG
Found at i:1025 original size:35 final size:35
Alignment explanation
Indices: 960--1027 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
950 TTGGAAACTT
**
960 AGATGTCAGATTTCGGTTTCTCTCTGTTTTAGTTG
1 AGATGTCAGATTTCGGTTTCTCTCCATTTTAGTTG
* *
995 AGATGTCGGATATT-GGTTTCTTTCCATTTTAGT
1 AGATGTCAGAT-TTCGGTTTCTCTCCATTTTAGT
1028 CTTTCTTGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 26 0.93
36 2 0.07
ACGTcount: A:0.16, C:0.13, G:0.22, T:0.49
Consensus pattern (35 bp):
AGATGTCAGATTTCGGTTTCTCTCCATTTTAGTTG
Found at i:5836 original size:16 final size:16
Alignment explanation
Indices: 5815--5862 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
5805 TATTTTATTA
5815 TATTATATTTATTTTT
1 TATTATATTTATTTTT
5831 TATTAT-TATTATATTTT
1 TATTATAT-TTAT-TTTT
*
5848 TATTTTA-TTATTTTT
1 TATTATATTTATTTTT
5863 ACAGGTCCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 5 0.18
16 14 0.50
17 9 0.32
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TATTATATTTATTTTT
Found at i:5843 original size:22 final size:22
Alignment explanation
Indices: 5805--5859 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
5795 GTCTACAAAA
5805 TATTTTATTA-TATTATATTTAT
1 TATTTTATTATTATTATATTT-T
5827 T-TTTTATTATTATTATATTTT
1 TATTTTATTATTATTATATTTT
5848 TATTTTATTATT
1 TATTTTATTATT
5860 TTTACAGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TATTTTATTATTATTATATTTT
Found at i:5850 original size:14 final size:14
Alignment explanation
Indices: 5805--5863 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
5795 GTCTACAAAA
*
5805 TATTTTATTA-TAT
1 TATTTTATTATTTT
*
5818 TATATTTATTTTTTAT
1 TAT-TTTATTATTT-T
5834 TATTATTA-TATTTT
1 TATT-TTATTATTTT
5848 TATTTTATTATTTT
1 TATTTTATTATTTT
5862 TA
1 TA
5864 CAGGTCCGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 6 0.16
14 19 0.50
15 6 0.16
16 7 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTATTATTTT
Found at i:5859 original size:19 final size:19
Alignment explanation
Indices: 5807--5859 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
5797 CTACAAAATA
* *
5807 TTTTATTATATTATATTTAT
1 TTTTATTTTATTAT-TATAT
*
5827 TTTT-TATTATTATTATAT
1 TTTTATTTTATTATTATAT
5845 TTTTATTTTATTATT
1 TTTTATTTTATTATT
5860 TTTACAGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 8 0.29
19 16 0.57
20 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATTTTATTATTATAT
Found at i:5944 original size:30 final size:32
Alignment explanation
Indices: 5908--5977 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 32
5898 TTCAGAAAAT
*
5908 AAACCAACAT-TTTTA-TCTATTGAAACACTA
1 AAACCAACATATTTGAGTCTATTGAAACACTA
* *
5938 ACACCAACGTATTTGAGTTCTATTGAAACACTA
1 AAACCAACATATTTGAG-TCTATTGAAACACTA
5971 AAACCAA
1 AAACCAA
5978 AGCATTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 8 0.24
31 4 0.12
33 21 0.64
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (32 bp):
AAACCAACATATTTGAGTCTATTGAAACACTA
Found at i:6336 original size:17 final size:17
Alignment explanation
Indices: 6274--6336 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
6264 ATTTCATTTA
*
6274 TTTATTTATTTTATATT
1 TTTATTTTTTTTATATT
**
6291 TTTATTTTCTCCTA-ATT
1 TTTATTTT-TTTTATATT
* *
6308 TTAATTTTTTTTATTTT
1 TTTATTTTTTTTATATT
6325 TTTATTTTTTTT
1 TTTATTTTTTTT
6337 GTTATATATA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
16 3 0.08
17 30 0.83
18 3 0.08
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTTTTTATATT
Found at i:6385 original size:43 final size:41
Alignment explanation
Indices: 6303--6393 Score: 94
Period size: 43 Copynumber: 2.2 Consensus size: 41
6293 TATTTTCTCC
* * ** * *
6303 TAATTTTAATTTTTTTTATTTTTTTATTTTTTTTGTTATAT
1 TAATATTATTTTTTTTTATTTTTTTATTAATATTATTATAT
6344 ATATATATTATTTTTTTTTCA-TTTTTTATTAATATTATTATAT
1 -TA-ATATTATTTTTTTTT-ATTTTTTTATTAATATTATTATAT
6387 TAATATT
1 TAATATT
6394 TTTATTATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
41 5 0.12
42 4 0.10
43 31 0.76
44 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (41 bp):
TAATATTATTTTTTTTTATTTTTTTATTAATATTATTATAT
Found at i:6386 original size:35 final size:33
Alignment explanation
Indices: 6318--6399 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 33
6308 TTAATTTTTT
*
6318 TTATTTTTTTATTTTTTTTGTTATATATATATA
1 TTATTTTTTTATTTTTTTTATTATATATATATA
6351 TTATTTTTTT-TTCATTTTTTATTA-ATATTATTATA
1 TTATTTTTTTATT--TTTTTTATTATATA-TA-TATA
*
6386 TTAATATTTTTATT
1 TT-ATTTTTTTATT
6400 ATTCTTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
32 2 0.05
33 13 0.32
34 11 0.27
35 6 0.15
36 7 0.17
37 2 0.05
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (33 bp):
TTATTTTTTTATTTTTTTTATTATATATATATA
Found at i:19377 original size:141 final size:140
Alignment explanation
Indices: 19118--19525 Score: 512
Period size: 141 Copynumber: 2.9 Consensus size: 140
19108 GAATCTCAAG
** * *
19118 ATATAAAATCTGATACTACAAACGAAGTGGTTTCATCTGATGTGGATGGGGGTAATAGGATGACT
1 ATATAAAAAATGATACTACAAA-GGAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACT
* * *
19183 TCAGAATTGAGAAGCATGCCTGCTGGGACTGATGATTTGGGTACAGAGAAACAGGAATCTGGTTA
65 TCAGACTTGAGAAGCATGCCTGTTGGGACTGATGATTTGAGTACAGAGAAACAGGAATCTGGTTA
19248 TGATTCACAAT
130 TGATTCACAAT
* * * * *
19259 ATATAAAAGATGATACTACAAATGGAGTTGTTTCATCTGATATTGATGGGGGTGATAAGATGACT
1 ATATAAAAAATGATACTACAAA-GGAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACT
* ** * * *
19324 TCAGACTTGAGAAGCATGCCTGTTTGGACTGATGATTTGAGTGTAGAGGAACAGCAATCTGGTTT
65 TCAGACTTGAGAAGCATGCCTGTTGGGACTGATGATTTGAGTACAGAGAAACAGGAATCTGGTTA
*
19389 TGATTCAGAAT
130 TGATTCACAAT
* * * * * *
19400 ATTTAAAAAATTATACTACAAAAGAGGTGGTTTCCTCTGATGTTGGTGGGGATAATAGGATGACT
1 ATATAAAAAATGATACTACAAAGGA-GTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACT
* * * *
19465 TCAGACTCT-AGAATCATGCCTGTTGGGTCTGATAATTTGAGTACAGATAAACAGGAATCTG
65 TCAGACT-TGAGAAGCATGCCTGTTGGGACTGATGATTTGAGTACAGAGAAACAGGAATCTG
19526 AAGGATGCTC
Statistics
Matches: 226, Mismatches: 39, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
140 2 0.01
141 223 0.99
142 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (140 bp):
ATATAAAAAATGATACTACAAAGGAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACTT
CAGACTTGAGAAGCATGCCTGTTGGGACTGATGATTTGAGTACAGAGAAACAGGAATCTGGTTAT
GATTCACAAT
Found at i:19719 original size:174 final size:174
Alignment explanation
Indices: 19405--19895 Score: 714
Period size: 174 Copynumber: 2.8 Consensus size: 174
19395 AGAATATTTA
* * * * * *
19405 AAAAATTATACTACAAAAGAGGTGGTTTCCTCTGATGTTGGTGGGGATAATAGGATGACTTCAGA
1 AAAAATGAAACTACAAACGAAGTGGTTTCATCTGATGTTGATGGGGATAATAGGATGACTTCAGA
* * * * *
19470 CTCTAGAATCATGCCTGTTGGGTCTGAT-AATTTGAGTACAGATAAACAGGAATCTGAAGGATGC
66 CTCCAGAACCATGCCTGTTGGGACTGATGACTTT-AGTACAGAGAAACAGGAATCTGAAGGATGC
* * *
19534 TCTGGCTATGATTCACGTTTGCAGACTAAGGAACCTCAAGATATG
130 TCTGACTATGATTCACGCTTGCAGACTAAGGAACCTCAAGATACG
* * *
19579 AAAAATGAAACTGCTAACGAAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACTTCAGA
1 AAAAATGAAACTACAAACGAAGTGGTTTCATCTGATGTTGATGGGGATAATAGGATGACTTCAGA
19644 CTCCAGAACCATGCCTGTTGGGACTGATGACTTTAGTACAGAGAAACAGGAATCTGAAGGATGCT
66 CTCCAGAACCATGCCTGTTGGGACTGATGACTTTAGTACAGAGAAACAGGAATCTGAAGGATGCT
*
19709 CTGACTATGATTCACGCTTGCAGACTAAGGAACCTCAGGATACG
131 CTGACTATGATTCACGCTTGCAGACTAAGGAACCTCAAGATACG
* * * *
19753 AAAAATGACATTACAAATGAAGTGGTTTCATCTGATGTTGATGGCGATAATAGGATGACTTCAGA
1 AAAAATGAAACTACAAACGAAGTGGTTTCATCTGATGTTGATGGGGATAATAGGATGACTTCAGA
** * *
19818 CTTGAGAACCATTCCTGTTGGGACTGATGACTTTAGTACAGAGAAACATGAATCTGAAGGATGCT
66 CTCCAGAACCATGCCTGTTGGGACTGATGACTTTAGTACAGAGAAACAGGAATCTGAAGGATGCT
**
19883 CTGTTTATGATTC
131 CTGACTATGATTC
19896 TCAATTTGAG
Statistics
Matches: 285, Mismatches: 31, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
174 281 0.99
175 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (174 bp):
AAAAATGAAACTACAAACGAAGTGGTTTCATCTGATGTTGATGGGGATAATAGGATGACTTCAGA
CTCCAGAACCATGCCTGTTGGGACTGATGACTTTAGTACAGAGAAACAGGAATCTGAAGGATGCT
CTGACTATGATTCACGCTTGCAGACTAAGGAACCTCAAGATACG
Found at i:23093 original size:20 final size:20
Alignment explanation
Indices: 23070--23111 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
23060 TTTTCTTCGC
*
23070 CTTACCTTCTTTTTCTCTCT
1 CTTACCTTCTTCTTCTCTCT
**
23090 CTTATTTTCTTCTTCTCTCT
1 CTTACCTTCTTCTTCTCTCT
23110 CT
1 CT
23112 CTACTCTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (20 bp):
CTTACCTTCTTCTTCTCTCT
Found at i:25545 original size:174 final size:174
Alignment explanation
Indices: 25288--26455 Score: 1166
Period size: 174 Copynumber: 6.7 Consensus size: 174
25278 ACTTTGAACG
* *
25288 AAGTGGTTTCATCCT-ATGTCGATGGGGGTAATAAGATGACTTCAGACTTGAGAACCATGCCTGT
1 AAGTGGTTTCAT-CTGATGTTGATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGT
* ** * * *
25352 TGAGACTGATGACTTGAGTGTAGAGAAACTGGAATCTGAAGGATGCTTTCGTTATGATTCACACT
65 TGGGACTGATGACTTGAGTACAGAGAAACAGGAATCTGAAGGATGCTCTGGTTATGATTCACACT
* * * * *
25417 TGCAGATTAAGGAATCTCTAGATATAAAAGATGATACTATAGATA
130 TGCAGACTAAGGAACCTCAAGATATAAAACATGATACTACAGATA
* * * * * * * *
25462 AAGTGGTTCCATCTGATGTTGATGGAGATAATATGACGGCTTCAGACTTGCGAACCTTGCCTGTT
1 AAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGTT
* * * * * * * *
25527 GGGACCGATGATTTGAGTGA-ACAGAAGCATGAGTGTGAAGGATGCTCTGGTTATGATTCCCACT
66 GGGACTGATGACTTGAGT-ACAGAGAAACAGGAATCTGAAGGATGCTCTGGTTATGATTCACACT
* * * * *
25591 TGCAGACTAAGGAACCTCAAGATATAAAAAATGTTGCTACAAATG
130 TGCAGACTAAGGAACCTCAAGATATAAAACATGATACTACAGATA
* * * * * *
25636 AAGTGATTTCTTATGATGTTGGTGGGGTTAATATGATGACTTCAGACTTGAGAACCATGCCTGTT
1 AAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGTT
* * ** * * * *
25701 GGTAGTGATGACTCAAGTACAGAGAAACAGGAATGTGAAGGATGCCCTGATTATGATTTACACTT
66 GGGACTGATGACTTGAGTACAGAGAAACAGGAATCTGAAGGATGCTCTGGTTATGATTCACACTT
* * * *
25766 GCAGACTGAGGAACCTCAAGATATAAAAGATGATACTACAAACA
131 GCAGACTAAGGAACCTCAAGATATAAAACATGATACTACAGATA
* * **
25810 AAGTAGTTTCATCTGATGTTAATGGGGGTAATAGGATGACTTCAGACGAGAGAACCATGCCTGTT
1 AAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGTT
* * * * *
25875 GGAACTGATGACTTGAGTACAGAGAAACTGGAATCTGAAGCATGCTCTGGTTATGATGCACATTT
66 GGGACTGATGACTTGAGTACAGAGAAACAGGAATCTGAAGGATGCTCTGGTTATGATTCACACTT
** * * * * *
25940 GCAGAC-AAGTGAACCTCAAGATACGATACTTGATGCTA-TGAAA
131 GCAGACTAAG-GAACCTCAAGATATAAAACATGATACTACAGATA
* * * * *** *
25983 GAAGAGGTTTCATCTGATGTTGATGAGGGTAATAGGTTGACTTCAGACATGAGAATGGTGACTGT
1 -AAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGT
* * * * * * *
26048 TGGGACTGATGATTTGGGTATAGAGAAACAGGAATCCGAAGAATGCTCTGGCTATGACTCACACT
65 TGGGACTGATGACTTGAGTACAGAGAAACAGGAATCTGAAGGATGCTCTGGTTATGATTCACACT
* * * * * * *
26113 TGCTGACTAATGAACCTCAACATACAAAACATGATGCTA-TGAAA
130 TGCAGACTAAGGAACCTCAAGATATAAAACATGATACTACAGATA
* * * ** *
26157 GAAGTGGTTTCACCTTATGTTGATGGGGGTAATAGGTTGACTTCAGACTCAAGAACCATGCTTGT
1 -AAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGT
* * * * * * *
26222 TGGGATTGATGATTTGAGTACAGAGAAACAGGGATCTGAAGGATGTTATGGTTATGACTCACATT
65 TGGGACTGATGACTTGAGTACAGAGAAACAGGAATCTGAAGGATGCTCTGGTTATGATTCACACT
* * * * *
26287 TGCAGACTAAGGAATCTCAAGTTATAGAACATGACACTACA-ATTG
130 TGCAGACTAAGGAACCTCAAGATATAAAACATGATACTACAGA-TA
* * *
26332 CAGTGGTTTCATCTGATG-T--TGGGGGTAATAGGACGACTTCAGACTTGAGAACCATTCCTGTT
1 AAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGTT
* * * * * *
26394 GGGCCTGATGACTCGAGTACAGAGAAACCGGGATCTGAAGGATGTTCTGGTTATTATTCACA
66 GGGACTGATGACTTGAGTACAGAGAAACAGGAATCTGAAGGATGCTCTGGTTATGATTCACA
26456 ATTTAAGGAT
Statistics
Matches: 813, Mismatches: 173, Indels: 19
0.81 0.17 0.02
Matches are distributed among these distances:
171 91 0.11
173 8 0.01
174 712 0.88
175 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (174 bp):
AAGTGGTTTCATCTGATGTTGATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGTT
GGGACTGATGACTTGAGTACAGAGAAACAGGAATCTGAAGGATGCTCTGGTTATGATTCACACTT
GCAGACTAAGGAACCTCAAGATATAAAACATGATACTACAGATA
Found at i:26244 original size:522 final size:521
Alignment explanation
Indices: 25242--26447 Score: 1325
Period size: 522 Copynumber: 2.3 Consensus size: 521
25232 AAGCGAAGAG
* ***
25242 TTGCAGACTACA-AAACCTCAAGATATAAAAAATGACACTTTGAACGAAGTGGTTTCATCCT-AT
1 TTGCAGACTA-AGGAACCTCAAGATATAAAAAATGACACTACAAACGAAGTGGTTTCAT-CTGAT
* *
25305 GTCGATGGGGGTAATAAGATGACTTCAGACTTGAGAACCATGCCTGTT-GAGACTGATGACTTGA
64 GT-TATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGTTGGA-ACTGATGACTTGA
** * * * * *
25369 GTGTAGAGAAACTGGAATCTGAAGGATGCTTTCGTTATGATTCACACTTGCAGATTAAGGAATCT
127 GTACAGAGAAACTGGAATCTGAAGGATGCTCTGGTTATGATGCACACTTGCAGATCAAGGAACCT
* * * * * *
25434 CTAGATATAAAAGATGATACTATAGATAAAGTGGTTCCATCTGATGTTGATGGAGATAATATGAC
192 CAAGATACAAAACATGATACTATAGAAAAAGAGGTTCCATCTGATGTTGATGGAGATAATAGGAC
* * * * * * * * **
25499 GGCTTCAGACTTGCGAACCTTGCCTGTTGGGACCGATGATTTGAGTGAACAGAAGCATGAGTGTG
257 GACTTCAGACATGAGAACCGTGACTGTTGGGACCGATGATTTGAGTGAACAGAAACAGGAATCCG
* * * * * * *
25564 AAGGATGCTCTGGTTATGATTCCCACTTGCAGACTAAGGAACCTCAAGATATAAAAAATGTTGCT
322 AAGAATGCTCTGGCTATGACTCACACTTGCAGACTAAGGAACCTCAACATACAAAAAATGATGCT
** * * * **
25629 ACAAATGAAGTGATTTCTTATGATGTTGGTGGGGTTAATATGATGACTTCAGACTTGAGAACCAT
387 ACAAATGAAGTGATTTCACATGATGTTGATGGGGGTAATAGGATGACTTCAGACTCAAGAACCAT
* * * *
25694 GCCTGTTGGTAGTGATGACTCAAGTACAGAGAAACAGGAATGTGAAGGATGCCCTGATTATGATT
452 GCCTGTTGGGAGTGATGACTCAAGTACAGAGAAACAGGAATCTGAAGGATGCCATGATTATGACT
*
25759 TACAC
517 CACAC
* * * * *
25764 TTGCAGACTGAGGAACCTCAAGATATAAAAGATGATACTACAAACAAAGTAGTTTCATCTGATGT
1 TTGCAGACTAAGGAACCTCAAGATATAAAAAATGACACTACAAACGAAGTGGTTTCATCTGATGT
**
25829 TAATGGGGGTAATAGGATGACTTCAGACGAGAGAACCATGCCTGTTGGAACTGATGACTTGAGTA
66 T-ATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGTTGGAACTGATGACTTGAGTA
* *
25894 CAGAGAAACTGGAATCTGAAGCATGCTCTGGTTATGATGCACATTTGCAGA-CAAGTGAACCTCA
130 CAGAGAAACTGGAATCTGAAGGATGCTCTGGTTATGATGCACACTTGCAGATCAAG-GAACCTCA
* * * * * * **
25958 AGATACGATACTTGATGCTAT-GAAAGAAGAGGTTTCATCTGATGTTGAT-GAGGGTAATAGGTT
194 AGATACAAAACATGATACTATAGAAA-AAGAGGTTCCATCTGATGTTGATGGA-GATAATAGGAC
** * * *
26021 GACTTCAGACATGAGAATGGTGACTGTTGGGACTGATGATTTGGGT-ATAGAGAAACAGGAATCC
257 GACTTCAGACATGAGAACCGTGACTGTTGGGACCGATGATTTGAGTGA-ACAGAAACAGGAATCC
* * *
26085 GAAGAATGCTCTGGCTATGACTCACACTTGCTGACTAATGAACCTCAACATACAAAACATGATGC
321 GAAGAATGCTCTGGCTATGACTCACACTTGCAGACTAAGGAACCTCAACATACAAAAAATGATGC
* * * * *
26150 TATGAAA-GAAGTGGTTTCACCTTATGTTGATGGGGGTAATAGGTTGACTTCAGACTCAAGAACC
386 TA-CAAATGAAGTGATTTCACATGATGTTGATGGGGGTAATAGGATGACTTCAGACTCAAGAACC
* * * ** * ** *
26214 ATGCTTGTTGGGATTGATGATTTGAGTACAGAGAAACAGGGATCTGAAGGATGTTATGGTTATGA
450 ATGCCTGTTGGGAGTGATGACTCAAGTACAGAGAAACAGGAATCTGAAGGATGCCATGATTATGA
*
26279 CTCACAT
515 CTCACAC
* * * * ** *
26286 TTGCAGACTAAGGAATCTCAAGTTATAGAACATGACACTACAATTGCAGTGGTTTCATCTGATG-
1 TTGCAGACTAAGGAACCTCAAGATATAAAAAATGACACTACAAACGAAGTGGTTTCATCTGATGT
* * ** *
26350 T-TGGGGGTAATAGGACGACTTCAGACTTGAGAACCATTCCTGTTGGGCCTGATGACTCGAGTAC
66 TATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGTTGGAACTGATGACTTGAGTAC
* * *
26414 AGAGAAACCGGGATCTGAAGGATGTTCTGGTTAT
131 AGAGAAACTGGAATCTGAAGGATGCTCTGGTTAT
26448 TATTCACAAT
Statistics
Matches: 565, Mismatches: 110, Indels: 21
0.81 0.16 0.03
Matches are distributed among these distances:
519 86 0.15
521 13 0.02
522 461 0.82
523 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (521 bp):
TTGCAGACTAAGGAACCTCAAGATATAAAAAATGACACTACAAACGAAGTGGTTTCATCTGATGT
TATGGGGGTAATAGGATGACTTCAGACTTGAGAACCATGCCTGTTGGAACTGATGACTTGAGTAC
AGAGAAACTGGAATCTGAAGGATGCTCTGGTTATGATGCACACTTGCAGATCAAGGAACCTCAAG
ATACAAAACATGATACTATAGAAAAAGAGGTTCCATCTGATGTTGATGGAGATAATAGGACGACT
TCAGACATGAGAACCGTGACTGTTGGGACCGATGATTTGAGTGAACAGAAACAGGAATCCGAAGA
ATGCTCTGGCTATGACTCACACTTGCAGACTAAGGAACCTCAACATACAAAAAATGATGCTACAA
ATGAAGTGATTTCACATGATGTTGATGGGGGTAATAGGATGACTTCAGACTCAAGAACCATGCCT
GTTGGGAGTGATGACTCAAGTACAGAGAAACAGGAATCTGAAGGATGCCATGATTATGACTCACA
C
Found at i:37504 original size:21 final size:20
Alignment explanation
Indices: 37418--37575 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
37408 AAATGACCAA
**
37418 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
37437 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
37457 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
37477 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
37498 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
37519 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
37539 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
37560 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
37576 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:37604 original size:20 final size:20
Alignment explanation
Indices: 37542--37735 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
37532 CGATTTTCCA
* ** *
37542 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
37562 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
37582 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
37602 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
37622 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
37642 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
37662 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
37682 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
37702 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
37723 AAATCGCAACGCG
1 AAATCGCAACGCG
37736 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:37626 original size:60 final size:60
Alignment explanation
Indices: 37542--37735 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
37532 CGATTTTCCA
* ** * *
37542 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
37602 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
37662 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
37723 AAATCGCAACGCG
1 AAATCGCAACGCG
37736 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:38158 original size:33 final size:33
Alignment explanation
Indices: 38119--38189 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
38109 TTCACTTAGA
*
38119 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
38152 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
38185 TTTCA
1 TTTCA
38190 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:38326 original size:41 final size:38
Alignment explanation
Indices: 38262--38378 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
38252 TTCAATTTGC
* *
38262 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
38300 AGAATGACTGTCGCAACGAGAGAAATGACAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
38341 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
38374 AGAAT
1 AGAAT
38379 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:38342 original size:21 final size:21
Alignment explanation
Indices: 38269--38344 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
38259 TGCAGAAGAG
* *
38269 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
38290 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGACAA
38310 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
38331 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
38345 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:38348 original size:14 final size:14
Alignment explanation
Indices: 38329--38385 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
38319 GAGAAATGAC
38329 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
38343 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
38362 AATCGCAACGAGAG
1 AATCGCAACGAGAG
38376 AATCGCAACG
1 AATCGCAACG
38386 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:38366 original size:33 final size:33
Alignment explanation
Indices: 38321--38401 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
38311 CGCAACGAGA
*
38321 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
38354 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
38387 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
38402 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:38419 original size:19 final size:19
Alignment explanation
Indices: 38397--38480 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
38387 GAAACCAAAA
*
38397 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
38416 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
38430 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
38449 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
38468 TCGCGTTGCGATT
1 TCGCGTTGCGATT
38481 CTCTCGTTGC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 41 0.72
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:38480 original size:52 final size:52
Alignment explanation
Indices: 38397--38502 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
38387 GAAACCAAAA
38397 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
38449 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
38501 TC
1 TC
38503 AACCAAAAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:40355 original size:93 final size:93
Alignment explanation
Indices: 40196--40583 Score: 767
Period size: 93 Copynumber: 4.2 Consensus size: 93
40186 TAGATTGCTT
*
40196 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
40261 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
40289 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
40354 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
40382 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
40447 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
40475 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
40540 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
40568 AGTAAATTTGTTCGGT
1 AGTAAATTTGTTCGGT
40584 CGAAATAGTA
Statistics
Matches: 294, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 294 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:41713 original size:14 final size:14
Alignment explanation
Indices: 41694--41729 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
41684 ATTGTTTAAT
41694 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
41708 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
41722 TGATTTGT
1 TGATTTGT
41730 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:41852 original size:19 final size:19
Alignment explanation
Indices: 41836--41942 Score: 152
Period size: 19 Copynumber: 5.8 Consensus size: 19
41826 AAAAATGACT
41836 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
41855 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
41874 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
41888 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
41907 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
41927 ATCGCAATGCGGAAAT
1 ATCGCAATGC-GAAAT
41943 CGCAATGCGT
Statistics
Matches: 80, Mismatches: 2, Indels: 11
0.86 0.02 0.12
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.49
20 25 0.31
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:41944 original size:14 final size:14
Alignment explanation
Indices: 41925--41951 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41915 GCGGAAATGA
41925 AAATCGCAATGCGG
1 AAATCGCAATGCGG
41939 AAATCGCAATGCG
1 AAATCGCAATGCG
41952 TTTATAATTT
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:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
AAATCGCAATGCGG
Found at i:41965 original size:53 final size:53
Alignment explanation
Indices: 41836--41951 Score: 193
Period size: 52 Copynumber: 2.2 Consensus size: 53
41826 AAAAATGACT
41836 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
41888 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG-GA-A
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CGAGAGA
41941 ATCGCAATGCG
1 ATCGCAATGCG
41952 TTTATAATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
52 29 0.48
53 28 0.46
54 2 0.03
55 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:41995 original size:33 final size:33
Alignment explanation
Indices: 41958--42110 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
41948 TGCGTTTATA
41958 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
41991 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
42031 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
42062 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
42095 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
42111 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.54
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:42004 original size:19 final size:19
Alignment explanation
Indices: 41980--42195 Score: 247
Period size: 19 Copynumber: 12.4 Consensus size: 19
41970 GATTCTCTCG
41980 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41999 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
42018 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
42032 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42051 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
42070 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
42084 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42103 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
42122 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
42136 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
42155 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
42169 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42188 TTGCGATT
1 TTGCGATT
42196 CTCTCGTTGC
Statistics
Matches: 167, Mismatches: 10, Indels: 40
0.77 0.05 0.18
Matches are distributed among these distances:
14 29 0.17
16 22 0.13
17 23 0.14
19 93 0.56
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:42195 original size:52 final size:52
Alignment explanation
Indices: 41958--42167 Score: 411
Period size: 52 Copynumber: 4.0 Consensus size: 52
41948 TGCGTTTATA
41958 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
42010 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
42062 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
42114 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
42166 AT
1 AT
42168 GTTGGGATTT
Statistics
Matches: 157, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 157 1.00
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:42217 original size:33 final size:33
Alignment explanation
Indices: 41999--42209 Score: 232
Period size: 33 Copynumber: 6.2 Consensus size: 33
41989 TCATTTCGCA
41999 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
42032 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
42068 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
42103 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
42136 TTGCGATTTTAATTTCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
*
42169 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
42202 TTGCGATT
1 TTGCGATT
42210 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 18, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 100 0.68
34 1 0.01
35 5 0.03
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:44703 original size:24 final size:24
Alignment explanation
Indices: 44669--44715 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44659 CTGAAACATC
44669 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
44693 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
44716 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:45426 original size:20 final size:20
Alignment explanation
Indices: 45416--45584 Score: 198
Period size: 20 Copynumber: 8.4 Consensus size: 20
45406 TACAGATTCT
*
45416 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
* * *
45436 CGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGATACG
** *
45456 CGTTGCGATTTTTGGATTA-T
1 CGTTGCGATTTACGGA-TACG
45476 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
45496 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
45516 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
*
45536 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
45556 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
45576 CGTTGCGAT
1 CGTTGCGAT
45585 GGTCTACAGT
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.02
20 123 0.97
21 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:45458 original size:40 final size:39
Alignment explanation
Indices: 45403--45607 Score: 207
Period size: 40 Copynumber: 5.1 Consensus size: 39
45393 CAGTGTTGTA
* *
45403 ATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCG
1 ATTTACAGATACGCGTTGCGATTTACGGA-TATCGTTGCG
* * **
45443 ATTTACAGATTCTCGTTGCGATTTTTGGATTATCGTTGCG
1 ATTTACAGATACGCGTTGCGATTTACGGA-TATCGTTGCG
* *
45483 ATTTACGGATACGCGTTGCGATATACGGATA-CGCATTGCG
1 ATTTACAGATACGCGTTGCGATTTACGGATATCG--TTGCG
** *
45523 ATTTACCCATACGCGTTGCGATTTACGGATACACGTTGCG
1 ATTTACAGATACGCGTTGCGATTTACGGATA-TCGTTGCG
* *
45563 ATTTACGGATACGCGTTGCGATGGTCTACAG-TATCGTTGCG
1 ATTTACAGATACGCGTTGCGAT--T-TACGGATATCGTTGCG
45604 ATTT
1 ATTT
45608 TCCCAATTCG
Statistics
Matches: 143, Mismatches: 15, Indels: 13
0.84 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 119 0.83
41 11 0.08
42 5 0.03
43 4 0.03
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (39 bp):
ATTTACAGATACGCGTTGCGATTTACGGATATCGTTGCG
Found at i:52324 original size:22 final size:20
Alignment explanation
Indices: 52296--52341 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 20
52286 ATTAAATCCC
52296 TATTTTTATTAAATAAAAATAT
1 TATTTTT-TT-AATAAAAATAT
52318 TA-TTTTTTAATAAAAATAT
1 TATTTTTTTAATAAAAATAT
52337 TATTT
1 TATTT
52342 CGGGTATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.57
20 4 0.17
21 4 0.17
22 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTTTTTAATAAAAATAT
Found at i:56365 original size:18 final size:19
Alignment explanation
Indices: 56342--56379 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
56332 TATAAACATA
*
56342 TCACATCAATAT-TTTAAT
1 TCACATAAATATGTTTAAT
*
56360 TCACATAAATTTGTTTAAT
1 TCACATAAATATGTTTAAT
56379 T
1 T
56380 AGTGAGAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (19 bp):
TCACATAAATATGTTTAAT
Found at i:58980 original size:2 final size:2
Alignment explanation
Indices: 58973--59027 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
58963 TTGCCTCATG
58973 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
59015 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
59028 TGTATTTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59161 original size:23 final size:23
Alignment explanation
Indices: 59135--59218 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
59125 CTCGTATAAA
59135 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
59158 TGCACCAAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
59181 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
59204 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
59219 TATAATAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:63235 original size:15 final size:13
Alignment explanation
Indices: 63200--63237 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
63190 TAATTTGATG
63200 ATAATGAT-ATAA
1 ATAATGATAATAA
63212 ATAATGATAATAA
1 ATAATGATAATAA
63225 TATATATGATAAT
1 -ATA-ATGATAAT
63238 GCTAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 3 0.13
15 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (13 bp):
ATAATGATAATAA
Done.