Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003096.1 Hibiscus syriacus cultivar Beakdansim tig00006460_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: 56211
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:8479 original size:20 final size:20
Alignment explanation
Indices: 8454--8533 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
8444 TTTTAATGCA
* *
8454 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCTT
*
8474 GAGGGAACCGAT-CCCCTTT
1 GAGGGAACCGATACCCCCTT
*
8493 GAAGGGGAACCGATTCCCCCTT
1 G-A-GGGAACCGATACCCCCTT
* *
8515 AAGGGAATCGATACCCCCT
1 GAGGGAACCGATACCCCCT
8534 GGGTTCTGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 6 0.12
20 27 0.54
21 11 0.22
22 6 0.12
ACGTcount: A:0.26, C:0.31, G:0.25, T:0.17
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCTT
Found at i:11241 original size:20 final size:20
Alignment explanation
Indices: 11216--11270 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
11206 TTTACACTTA
11216 GGGAACCGATTCCCCTTAAG
1 GGGAACCGATTCCCCTTAAG
11236 GGGAACCGATTCCCCTTAAG
1 GGGAACCGATTCCCCTTAAG
*
11256 GGGTACCGATTCCCC
1 GGGAACCGATTCCCC
11271 CCACGCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.20
Consensus pattern (20 bp):
GGGAACCGATTCCCCTTAAG
Found at i:12712 original size:84 final size:85
Alignment explanation
Indices: 12612--13719 Score: 955
Period size: 84 Copynumber: 13.2 Consensus size: 85
12602 GGCCTTTTTT
* * * * *
12612 CCTTGAGCTATGCTGTAAAATGACGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-ATTGG
1 CCTTGAGTTATGCTGTAAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * **
12676 CTGAAAGATAACCCTTTTCG
66 TTGGAAGATAACCCTTCTAA
* * * * ** * * * *
12696 CCTTGATTTATGCTGTAAATTGGATATGTCTTTGAGCTGAATGGAATCAAACTCGAAGGTCTTTT
1 CCTTGAGTTATGCTGTAAAAT-GATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
* * *
12761 GTTGGCAGATAA-ACTTCTAG
65 GTTGGAAGATAACCCTTCTAA
*
12781 CCTTGAGTTATGCTG-CAAATGA-GATGCCTTTGAGCT-AGGCGTAGTCGAACTCGAAGGTCTTT
1 CCTTGAGTTATGCTGTAAAATGATG-TGCCTTTGAGCTGA-GCGTAGTCGAACTCGAAGGTCTTT
* * *
12843 TGTTGGCAA-ATAGCCCTTCTTA
64 GGTTGG-AAGATAACCCTTCTAA
* *
12865 CCTTGAGCTATG-T-TACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
1 CCTTGAGTTATGCTGTA-AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
*
12928 GTTGGCAGATAACCCTTCTAA
65 GTTGGAAGATAACCCTTCTAA
* * * * * *
12949 CCTTGAGTTATGGTGT-AAATGATATGCTTTTAAGCTGAGCGTAGTTGAACTCGAAGGTCTTTTG
1 CCTTGAGTTATGCTGTAAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* **
13013 TTGGCAA-ATAGCCCTTCTTG
66 TTGG-AAGATAACCCTTCTAA
* * * * * * *
13033 CCTTGAGCTATGTTG-CAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
1 CCTTGAGTTATGCTGTAAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* *
13097 TTGGCAGATAACCCTTCTAG
66 TTGGAAGATAACCCTTCTAA
* * ** * *
13117 CCTTGAGTTATACTG-CAAATGATGTGCCTCAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTG
1 CCTTGAGTTATGCTGTAAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* **
13181 TTGGCAA-ATAACCTTTCTTT
66 TTGG-AAGATAACCCTTCTAA
* * * * * * * * **
13201 CCTTGAGGTATGTTG-CAAATGATGTGCCTTGGAGTTTAGCGTAGTCGTACTCAAAGGTCTTTTA
1 CCTTGAGTTATGCTGTAAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* **
13265 TTGGCAGATAACCCTTCTTT
66 TTGGAAGATAACCCTTCTAA
** * * * * * *
13285 CCTTGACCTATGTTG-CAAATGATGTGCCTTGGAGTTGAGCTTAGTCGAACTCGAAGGTCTTTTG
1 CCTTGAGTTATGCTGTAAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * **
13349 TTCGCAGATAACCCTTCTTG
66 TTGGAAGATAACCCTTCTAA
* ** *
13369 CCTTGAGTTATGCTG-CAAATGATGTGCCTTACAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGG
1 CCTTGAGTTATGCTGTAAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
*
13433 TTGGTAGATAACCCTTCTAA
66 TTGGAAGATAACCCTTCTAA
* *
13453 CCTTGAGTTATGCTGT-AAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
1 CCTTGAGTTATGCTGTAAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTG
* * * **
13517 G-TGGCAGATAGCACTTCTTG
65 GTTGGAAGATAACCCTTCTAA
* * * * * * *
13537 CCTTGAGCTATGCTG-CAAATGATATGCCTTTGAGCTAAGCATAGTCGAACTCAAAGGTCTTTTG
1 CCTTGAGTTATGCTGTAAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
**
13601 TTGGCAA-ATAACCCTTCTTG
66 TTGG-AAGATAACCCTTCTAA
* * * * * *
13621 CCTTGAGCTATGTTG-CAAATGATGTGCC-TTGTAGCTGAGCGTAGTCAAACACGAAGGTCTTTT
1 CCTTGAGTTATGCTGTAAAATGATGTGCCTTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
* *
13684 GTTGGCAGATAACCCTTCTAG
65 GTTGGAAGATAACCCTTCTAA
* *
13705 CATTAAGTTATGCTG
1 CCTTGAGTTATGCTG
13720 CCAATAGTTT
Statistics
Matches: 857, Mismatches: 142, Indels: 50
0.82 0.14 0.05
Matches are distributed among these distances:
82 1 0.00
83 53 0.06
84 729 0.85
85 62 0.07
86 12 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (85 bp):
CCTTGAGTTATGCTGTAAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
TTGGAAGATAACCCTTCTAA
Found at i:12831 original size:168 final size:168
Alignment explanation
Indices: 12612--13720 Score: 1287
Period size: 168 Copynumber: 6.6 Consensus size: 168
12602 GGCCTTTTTT
* * * * * * *
12612 CCTTGAGCTATGCTGTAAAATGACGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-ATTGG
1 CCTTGAGTTATGCTG-CAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* * ** * * * * **
12676 CT-GAAAGATAACCCTT-TTCGCCTTGATTTATGCTGTAAATTGGATATGTCTTTGAGCTGAATG
65 TTGGCAA-ATAACCCTTCTT-GCCTTGAGCTATGCTGCAAA-T-GATGTGCCTTGGAGCTGAGCG
* * * * *
12739 GAATCAAACTCGAAGGTCTTTTGTTGGCAGATAA-ACTTCTAG
126 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
12781 CCTTGAGTTATGCTGCAAATGA-GATGCCTTTGAGCT-AGGCGTAGTCGAACTCGAAGGTCTTTT
1 CCTTGAGTTATGCTGCAAATGATG-TGCCTTTGAGCTGA-GCGTAGTCGAACTCGAAGGTCTTTT
* * * *
12844 GTTGGCAAATAGCCCTTCTTACCTTGAGCTATGTTACAAATGATGTGCCTTGGAGCTGAGCGTAG
64 GTTGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * *
12909 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAA
129 TCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* * * * * *
12949 CCTTGAGTTATGGTGTAAATGATATGCTTTTAAGCTGAGCGTAGTTGAACTCGAAGGTCTTTTGT
1 CCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * *
13014 TGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTACCTTGGAGCTGAGCGTAGTC
66 TGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
13079 GAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
131 GAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* ** *
13117 CCTTGAGTTATACTGCAAATGATGTGCCTCAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGT
1 CCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * * * * *
13182 TGGCAAATAACCTTTCTTTCCTTGAGGTATGTTGCAAATGATGTGCCTTGGAGTTTAGCGTAGTC
66 TGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * **
13247 GTACTCAAAGGTCTTTTATTGGCAGATAACCCTTCTTT
131 GAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
** * * * *
13285 CCTTGACCTATGTTGCAAATGATGTGCCTTGGAGTTGAGCTTAGTCGAACTCGAAGGTCTTTTGT
1 CCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * * **
13350 TCGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTACAGCTGAGCGTAGTC
66 TGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * * * *
13415 AAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTAA
131 GAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* * * *
13453 CCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
1 CCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * * * * * *
13518 TGGCAGATAGCACTTCTTGCCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTAAGCATAGTC
66 TGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* *
13583 GAACTCAAAGGTCTTTTGTTGGCAAATAACCCTTCTTG
131 GAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* * * *
13621 CCTTGAGCTATGTTGCAAATGATGTGCC-TTGTAGCTGAGCGTAGTCAAACACGAAGGTCTTTTG
1 CCTTGAGTTATGCTGCAAATGATGTGCCTTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* * * * *
13685 TTGGCAGATAACCCTTCTAGCATTAAGTTATGCTGC
65 TTGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGC
13721 CAATAGTTTC
Statistics
Matches: 807, Mismatches: 124, Indels: 19
0.85 0.13 0.02
Matches are distributed among these distances:
167 50 0.06
168 711 0.88
169 41 0.05
170 5 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (168 bp):
CCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
TGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
Found at i:13052 original size:252 final size:253
Alignment explanation
Indices: 12587--13719 Score: 1332
Period size: 252 Copynumber: 4.5 Consensus size: 253
12577 AACTCGATAA
* ** * * * * * *
12587 TTTTGTTGGCATATAGGCCTTTTTTCCTTGAGCTATGCTGTAAAATGACGTGCCTTTGAGCTGAG
1 TTTTGTTGGCAAATAACCCTTCTTACCTTGAGCTATGTTG-CAAATGATGTGCCTTAGAGCTGAG
* * * * * ** * ** *
12652 TGTAATCGAACTCGAAGGT-ATTGGCTGAAAGATAACCCTTTTCGCCTTGATTTATGCTGTAAAT
65 CGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAACCTTGAGTTATGCTGTAAA-
* ** * * * * *
12716 TGGATATGTCTTTGAGCTGAATGGAATCAAACTCGAAGGTCTTTTGTTGGCAGATA-AACTTCTA
129 T-GATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAGCACTTCTT
* * *
12780 GCCTTGAGTTATGCTGCAAATGA-GATGCCTTTGAGCTAG-GCGTAGTCGAACTCGAAGGTC
193 GCCTTGAGCTATGCTGCAAATGATG-TGCCTTGGAGCTAGAGCGTAGTCGAACTCAAAGGTC
* * *
12840 TTTTGTTGGCAAATAGCCCTTCTTACCTTGAGCTATGTTACAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAAATAACCCTTCTTACCTTGAGCTATGTTGCAAATGATGTGCCTTAGAGCTGAGC
* *
12905 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAACCTTGAGTTATGGTGTAAATG
66 GTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAACCTTGAGTTATGCTGTAAATG
** * * *
12970 ATATG-CTTTTAAGCTGAGCGTAGTTGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGC
131 ATATGTC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAGCACTTCTTGC
* *
13034 CTTGAGCTATGTTGCAAATGATGTACCTTGGAGCT-GAGCGTAGTCGAACTCAAAGGTC
195 CTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTAGAGCGTAGTCGAACTCAAAGGTC
* * ** *
13092 TTTTGTTGGCAGATAACCCTTC-TAGCCTTGAGTTATACTGCAAATGATGTGCCTCAGAGCTGAG
1 TTTTGTTGGCAAATAACCCTTCTTA-CCTTGAGCTATGTTGCAAATGATGTGCCTTAGAGCTGAG
* * * ** * * *
13156 CGTAGTCAAACTCGAAGGTCTTTTGTTGGCAAATAACCTTTCTTTCCTTGAGGTATGTTGCAAAT
65 CGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAACCTTGAGTTATGCTGTAAAT
* * * * * * * * * *
13221 GATGTGCCTTGGAGTTTAGCGTAGTCGTACTCAAAGGTCTTTTATTGGCAGATAACCCTTCTTTC
130 GATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAGCACTTCTTGC
* * * * *
13286 CTTGACCTATGTTGCAAATGATGTGCCTTGGAG-TTGAGCTTAGTCGAACTCGAAGGTC
195 CTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTAGAGCGTAGTCGAACTCAAAGGTC
* * * * * *
13344 TTTTGTTCGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTACAGCTGAGC
1 TTTTGTTGGCAAATAACCCTTCTTACCTTGAGCTATGTTGCAAATGATGTGCCTTAGAGCTGAGC
*
13409 GTAGTCAAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTAACCTTGAGTTATGCTGTAAATG
66 GTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAACCTTGAGTTATGCTGTAAATG
* *
13474 ATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATAGCACTTCTTGCC
131 ATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAGCACTTCTTGCC
* * *
13539 TTGAGCTATGCTGCAAATGATATGCCTTTGAGCTA-AGCATAGTCGAACTCAAAGGTC
196 TTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTAGAGCGTAGTCGAACTCAAAGGTC
*
13596 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTT-GTAGCTGAG
1 TTTTGTTGGCAAATAACCCTTCTTACCTTGAGCTATGTTGCAAATGATGTGCCTTAG-AGCTGAG
* * * * *
13660 CGTAGTCAAACACGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCATTAAGTTATGCTG
65 CGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAACCTTGAGTTATGCTG
13720 CCAATAGTTT
Statistics
Matches: 758, Mismatches: 111, Indels: 23
0.85 0.12 0.03
Matches are distributed among these distances:
250 1 0.00
251 48 0.06
252 636 0.84
253 73 0.10
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (253 bp):
TTTTGTTGGCAAATAACCCTTCTTACCTTGAGCTATGTTGCAAATGATGTGCCTTAGAGCTGAGC
GTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAACCTTGAGTTATGCTGTAAATG
ATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAGCACTTCTTGCC
TTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTAGAGCGTAGTCGAACTCAAAGGTC
Found at i:15044 original size:95 final size:95
Alignment explanation
Indices: 14843--15098 Score: 352
Period size: 95 Copynumber: 2.7 Consensus size: 95
14833 GGCTAGCTTA
* * * *
14843 ATCCATAAAGCCAGGGCGTTTAACCAATTTCTCTAGAGGGACAACTTAATATCATTGTA-TATAT
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTAT
*
14907 ATTATAATCACCTTTATCAGGCTAGTTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* *
14941 ATCCATAAAGCCAAGGCGTTTAACCAATTGCTCTAAAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* *
15006 TAATCACCTTTATTAGGCTAGCTGAATCTT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
* * * *
15036 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATAT
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT
15099 ATATGATATT
Statistics
Matches: 142, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
94 2 0.01
95 94 0.66
96 2 0.01
97 2 0.01
98 42 0.30
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:16917 original size:12 final size:12
Alignment explanation
Indices: 16900--16924 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16890 GTATCTATGC
16900 ACTGCTACAGTA
1 ACTGCTACAGTA
16912 ACTGCTACAGTA
1 ACTGCTACAGTA
16924 A
1 A
16925 TTTCCGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTGCTACAGTA
Found at i:17374 original size:46 final size:45
Alignment explanation
Indices: 17314--17490 Score: 250
Period size: 46 Copynumber: 3.9 Consensus size: 45
17304 GATAAAATCT
* * *
17314 CTTACCATTTATCCCAAAAGCACGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
17359 TTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
17405 CTTACCATTTAATCCCATAAGCTCGTAATCTTATTTTACCAATATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
** *
17451 CTTGTCA-TTATTCCATAAGCTCGTAAGCTTATTTT-CCAAT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAT
17491 TTATCATTTA
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
43 5 0.04
44 24 0.20
45 11 0.09
46 81 0.67
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:17644 original size:40 final size:40
Alignment explanation
Indices: 17565--17645 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
17555 ATAGGAGTCA
* * * *
17565 AATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
* *
17605 AATAATGCACCGTAGTGCTGAGGTCGGGATTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
17645 A
1 A
17646 GTACACCGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
Found at i:29553 original size:13 final size:13
Alignment explanation
Indices: 29537--29564 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29527 AAGTCCTTTA
29537 ATTTTTTATTTTT
1 ATTTTTTATTTTT
29550 ATTTTTTATTTTT
1 ATTTTTTATTTTT
29563 AT
1 AT
29565 AAATGAGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:29716 original size:42 final size:43
Alignment explanation
Indices: 29560--29945 Score: 375
Period size: 44 Copynumber: 9.0 Consensus size: 43
29550 ATTTTTTATT
* *
29560 TTTATAAATGAGG-TCTCTAATTTTTGT-AAT-TCAACTTTTTTATC
1 TTTATAATTGAGGCTC-CTAATTTTT-TCAATCTC-AC-TTTTTACC
* * **
29604 TTTATAATTGAGG-TCCTTAATTTTTTCAATCTTATTTTATTATA
1 TTTATAATTGAGGCTCC-TAATTTTTTCAATCTCACTTT-TTACC
* *
29648 TTTATAATTGATGAC-CCTAAGTTTTTCAATCAT-ACTTTTTACC
1 TTTATAATTGA-GGCTCCTAATTTTTTCAATC-TCACTTTTTACC
*
29691 TTTATAATTGA-GCTCCTAATTTTTTCAATCTCACTTTCTACC
1 TTTATAATTGAGGCTCCTAATTTTTTCAATCTCACTTTTTACC
* *
29733 TTTATAATTGAGGCCCCTAATTGTTT-AATCTCACTTTTTACC
1 TTTATAATTGAGGCTCCTAATTTTTTCAATCTCACTTTTTACC
* *
29775 TTTATAATTGAGGCCCCTAATTTTTTTCAATCTCATTTTTTA-C
1 TTTATAATTGAGGCTCCTAA-TTTTTTCAATCTCACTTTTTACC
* * * *
29818 TTATATAATTTAGGCCCCAAATTTTTTCAATCTCACTTTTTAAC
1 TT-TATAATTGAGGCTCCTAATTTTTTCAATCTCACTTTTTACC
* *
29862 TTTAATAATTGAGGC-CTTAATTTTTTTAATCTCACTTTTTACC
1 TTT-ATAATTGAGGCTCCTAATTTTTTCAATCTCACTTTTTACC
* *
29905 TTTATAATTGA-GATCCCTAA-TTTTTCATTCAT-ACTTTTTAC
1 TTTATAATTGAGGCT-CCTAATTTTTTCAATC-TCACTTTTTAC
29946 TTTCATAGTT
Statistics
Matches: 295, Mismatches: 29, Indels: 38
0.81 0.08 0.10
Matches are distributed among these distances:
41 3 0.01
42 95 0.32
43 92 0.31
44 100 0.34
45 5 0.02
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (43 bp):
TTTATAATTGAGGCTCCTAATTTTTTCAATCTCACTTTTTACC
Found at i:29886 original size:86 final size:86
Alignment explanation
Indices: 29560--29945 Score: 403
Period size: 86 Copynumber: 4.5 Consensus size: 86
29550 ATTTTTTATT
* * * * * *
29560 TTTATAAATGAGGTCTCTAATTTTTGT-AAT-TCAACTTTTTTATCTTTATAATTGAGGTCCTTA
1 TTTATAATTGAGGCCCCTAATTTTT-TCAATCTC-AC-TTTTTACCTTTATAATTGAGGCCCCTA
* * **
29623 ATTTTTTCAATCTTATTTTATTATA
63 ATTTTTTCAATCTCACTTT-TTACC
* * * *
29648 TTTATAATTGATGACCCTAAGTTTTTCAATCAT-ACTTTTTACCTTTATAATTGA-GCTCCTAAT
1 TTTATAATTGAGGCCCCTAATTTTTTCAATC-TCACTTTTTACCTTTATAATTGAGGCCCCTAAT
*
29711 TTTTTCAATCTCACTTTCTACC
65 TTTTTCAATCTCACTTTTTACC
*
29733 TTTATAATTGAGGCCCCTAATTGTTT-AATCTCACTTTTTACCTTTATAATTGAGGCCCCTAATT
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGCCCCTAA-T
*
29797 TTTTTCAATCTCATTTTTTA-C
65 TTTTTCAATCTCACTTTTTACC
* * * *
29818 TTATATAATTTAGGCCCCAAATTTTTTCAATCTCACTTTTTAACTTTAATAATTGAGG-CCTTAA
1 TT-TATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTTTACCTTT-ATAATTGAGGCCCCTAA
*
29882 TTTTTTTAATCTCACTTTTTACC
64 TTTTTTCAATCTCACTTTTTACC
** *
29905 TTTATAATTGAGATCCCTAA-TTTTTCATTCAT-ACTTTTTAC
1 TTTATAATTGAGGCCCCTAATTTTTTCAATC-TCACTTTTTAC
29946 TTTCATAGTT
Statistics
Matches: 253, Mismatches: 34, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
83 1 0.00
84 25 0.10
85 51 0.20
86 95 0.38
87 45 0.18
88 35 0.14
90 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (86 bp):
TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGCCCCTAATT
TTTTCAATCTCACTTTTTACC
Found at i:29926 original size:43 final size:43
Alignment explanation
Indices: 29560--29968 Score: 406
Period size: 42 Copynumber: 9.5 Consensus size: 43
29550 ATTTTTTATT
* * *
29560 TTTATAAATGAGGTCTCTAATTTTTGT-AAT-TCAACTTTTTTATC
1 TTTATAATTGAGGTCCCTAATTTTT-TCAATCTC-AC-TTTTTACC
* * * **
29604 TTTATAATTGAGGTCCTTAATTTTTTCAATCTTATTTTATTATA
1 TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTT-TTACC
* * *
29648 TTTATAATTGATGACCCTAAGTTTTTCAATCAT-ACTTTTTACC
1 TTTATAATTGAGGTCCCTAATTTTTTCAATC-TCACTTTTTACC
* *
29691 TTTATAATTGAGCT-CCTAATTTTTTCAATCTCACTTTCTACC
1 TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
* *
29733 TTTATAATTGAGGCCCCTAATTGTTT-AATCTCACTTTTTACC
1 TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
* *
29775 TTTATAATTGAGGCCCCTAATTTTTTTCAATCTCATTTTTTA-C
1 TTTATAATTGAGGTCCCTAA-TTTTTTCAATCTCACTTTTTACC
* * * *
29818 TTATATAATTTAGGCCCCAAATTTTTTCAATCTCACTTTTTAAC
1 TT-TATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
* *
29862 TTTAATAATTGAGG-CCTTAATTTTTTTAATCTCACTTTTTACC
1 TTT-ATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
* *
29905 TTTATAATTGAGATCCCTAA-TTTTTCATTCAT-ACTTTTTA-C
1 TTTATAATTGAGGTCCCTAATTTTTTCAATC-TCACTTTTTACC
* * *
29946 TTTCATAGTTTAAGTCCCTAATT
1 TTT-ATAATTGAGGTCCCTAATT
29969 AATTATTTTT
Statistics
Matches: 310, Mismatches: 40, Indels: 31
0.81 0.10 0.08
Matches are distributed among these distances:
41 5 0.02
42 109 0.35
43 92 0.30
44 102 0.33
45 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (43 bp):
TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
Found at i:32512 original size:3 final size:3
Alignment explanation
Indices: 32506--32548 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
32496 AAATTATTAA
32506 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
32549 AGTGTGTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:38133 original size:15 final size:15
Alignment explanation
Indices: 38113--38142 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38103 TTCGAATATA
38113 GAATGAATTAAGGAT
1 GAATGAATTAAGGAT
38128 GAATGAATTAAGGAT
1 GAATGAATTAAGGAT
38143 TCTTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (15 bp):
GAATGAATTAAGGAT
Found at i:40133 original size:10 final size:10
Alignment explanation
Indices: 40122--40178 Score: 71
Period size: 10 Copynumber: 5.5 Consensus size: 10
40112 ACAAACAAAC
40122 AAAAGTAAACA
1 AAAAGTAAA-A
40133 AAAAG-AAAA
1 AAAAGTAAAA
40142 AAAAGTAAAA
1 AAAAGTAAAA
*
40152 AAAAGAAGAAGA
1 AAAAGTA-AA-A
40164 AAAAGTAAAA
1 AAAAGTAAAA
40174 AAAAG
1 AAAAG
40179 CAAAGATCAG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 6 0.15
10 19 0.46
11 9 0.22
12 7 0.17
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAAGTAAAA
Found at i:40166 original size:22 final size:19
Alignment explanation
Indices: 40108--40178 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 19
40098 ATTTTGTAAA
* *
40108 AAAAACAAACAAACAAAAGT
1 AAAAA-AAAGAAAAAAAAGT
40128 AAACAAAAAGAAAAAAAAGT
1 AAA-AAAAAGAAAAAAAAGT
40148 AAAAAAAAGAAGAAGAAAAAGT
1 AAAAAAAAG-A-AA-AAAAAGT
40170 AAAAAAAAG
1 AAAAAAAAG
40179 CAAAGATCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.13
20 19 0.42
21 4 0.09
22 16 0.36
ACGTcount: A:0.79, C:0.06, G:0.11, T:0.04
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAAGT
Found at i:42539 original size:76 final size:76
Alignment explanation
Indices: 42431--42609 Score: 217
Period size: 76 Copynumber: 2.4 Consensus size: 76
42421 GAAGATTTTA
* * **
42431 TCTCGCTTGAGAC-AGTTTCCCTTGAAATAA-ATTTTG--TCTTC-CTTGAGATGGTTTTTCTTA
1 TCTCGCTTGAGACAACTTTCCCTTGAAACAAGAAATTGAATC-TCACTTGAGATGGTTTTTCTTA
42491 AAACCAAATTCG
65 AAACCAAATTCG
42503 TCTCGCTTGAGACAACTTTCCCTTGAAACAAGAAATTGAATCTCACTTGAGATGGTTTTTCTTAA
1 TCTCGCTTGAGACAACTTTCCCTTGAAACAAGAAATTGAATCTCACTTGAGATGGTTTTTCTTAA
** *
42568 AACTTACTTCG
66 AACCAAATTCG
* *
42579 TCTTGCTTGAGATAACTTT-CCTTCGAAACAA
1 TCTCGCTTGAGACAACTTTCCCTT-GAAACAA
42610 AATTTATCTC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
72 13 0.14
73 15 0.16
74 4 0.04
75 6 0.07
76 54 0.59
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (76 bp):
TCTCGCTTGAGACAACTTTCCCTTGAAACAAGAAATTGAATCTCACTTGAGATGGTTTTTCTTAA
AACCAAATTCG
Found at i:43132 original size:136 final size:136
Alignment explanation
Indices: 42885--43506 Score: 769
Period size: 136 Copynumber: 4.6 Consensus size: 136
42875 AGATAAACAT
* * *
42885 ATCAACATTTCCAGT-ACAAAGTTCATAATGAGAATAACTCATCCA-ACAGAGGGAGAAGAAGTT
1 ATCAACATTTCCATTGA-AGAGTTCATAATGAGAAGAACTCAT-CAGACAGAGGGAGAAGAAGTT
* ***
42948 CATAATGAGAAGAGCTTGTTTGACCTATCACTCGATTCACAATATTTCGAATCAGTGACACCTCA
64 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCA
*
43013 CTTGATGG
129 CTTGAGGG
* * * * *
43021 ATTAACATTTCCAATTG-AGAGTTCATAATGAGAAAAACTCATCAGATAGAGGGACAAGAAGTTT
1 ATCAACATTTCC-ATTGAAGAGTTCATAATGAGAAGAACTCATCAGACAGAGGGAGAAGAAGTTC
* ***
43085 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGATACCTTGT
65 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCAC
43150 TTGAGGG
130 TTGAGGG
* * * *
43157 ATCAATATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAATTCA
1 ATCAACATTTCCATTGAAGAGTTCATAATGAGAAGAACTCATCAGACAGAGGGAGAAGAAGTTCA
* *
43222 TAATGAGAAGAGCTTGTTCGACCTATCACTTGATTCACGGCATTTCGAATCAGTGACGCCTCACT
66 TAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACT
43287 TGAGGG
131 TGAGGG
** * * * * * * *
43293 ATTGATATTTCCA-TGGAGAGTTCATAATGAGAATAACTTATCCGAAAGAGGAAGAAGAAGTTCA
1 ATCAACATTTCCATTGAAGAGTTCATAATGAGAAGAACTCATCAGACAGAGGGAGAAGAAGTTCA
* * * ** *
43357 TAATGAGAAGAGATTGTTTGACCTATCACTCGATTCACGGTATTTCGAATCAGTGATGCCTCGCT
66 TAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACT
43422 TGAGGG
131 TGAGGG
* *
43428 ATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATC-GTA-A-A-GGAG-A-AAGTTC
1 ATCAACATTTCCATTGAAGAGTTCATAATGAGAAGAACTCATCAG-ACAGAGGGAGAAGAAGTTC
*
43487 ATAATGAGAAGAACTTGTTC
65 ATAATGAGAAGAGCTTGTTC
43507 CTTTCAAATT
Statistics
Matches: 425, Mismatches: 55, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
131 23 0.05
132 1 0.00
133 3 0.01
134 1 0.00
135 127 0.30
136 268 0.63
137 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (136 bp):
ATCAACATTTCCATTGAAGAGTTCATAATGAGAAGAACTCATCAGACAGAGGGAGAAGAAGTTCA
TAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACT
TGAGGG
Found at i:43459 original size:271 final size:271
Alignment explanation
Indices: 42885--43506 Score: 871
Period size: 271 Copynumber: 2.3 Consensus size: 271
42875 AGATAAACAT
* * * *
42885 ATCAACATTTCCAGT-ACAAAGTTCATAATGAGAATAACTCATCCAACAGAGGGAGAAGAAGTTC
1 ATCAACATTTCCAATGA-AGAGTTCATAATGAGAAGAACTCAT-CGACAGAGGGAGAAGAAGTTC
* *
42949 ATAATGAGAAGAGCTTGTTTGACCTATCACTCGATTCACAATATTTCGAATCAGTGACACCTCAC
64 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCAC
* * * *
43014 TTGATGGATTAACATTTCCAATTGAGAGTTCATAATGAGAAAAACTCATCAGATAGAGGGACAAG
129 TTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCAGAAAGAGGAACAAG
* *
43079 AAGTTTATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGATA
194 AAGTTCATAATGAGAAGAGATTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGATA
* *
43144 CCTTGTTTGAGGG
259 CCTCGCTTGAGGG
* * *
43157 ATCAATATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAATTCA
1 ATCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATC-GACAGAGGGAGAAGAAGTTCA
* ** *
43222 TAATGAGAAGAGCTTGTTCGACCTATCACTTGATTCACGGCATTTCGAATCAGTGACGCCTCACT
65 TAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCACT
* * * * * *
43287 TGAGGGATTGATATTTCC-ATGGAGAGTTCATAATGAGAATAACTTATCCGAAAGAGGAAGAAGA
130 TGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCAGAAAGAGGAACAAGA
* * *
43351 AGTTCATAATGAGAAGAGATTGTTTGACCTATCACTCGATTCACGGTATTTCGAATCAGTGATGC
195 AGTTCATAATGAGAAGAGATTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGATAC
43416 CTCGCTTGAGGG
260 CTCGCTTGAGGG
*
43428 ATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCGTA-A-A-GGAG-A-AAGTTCA
1 ATCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCG-ACAGAGGGAGAAGAAGTTCA
*
43488 TAATGAGAAGAACTTGTTC
65 TAATGAGAAGAGCTTGTTC
43507 CTTTCAAATT
Statistics
Matches: 314, Mismatches: 33, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
266 24 0.08
267 1 0.00
268 4 0.01
269 1 0.00
270 2 0.01
271 151 0.48
272 130 0.41
273 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (271 bp):
ATCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCGACAGAGGGAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCACTT
GAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCAGAAAGAGGAACAAGAA
GTTCATAATGAGAAGAGATTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGATACC
TCGCTTGAGGG
Found at i:48286 original size:21 final size:21
Alignment explanation
Indices: 48260--48299 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48250 CCCCCTTTGA
*
48260 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
48281 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
48300 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:54163 original size:43 final size:42
Alignment explanation
Indices: 54107--54233 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 42
54097 TTTTAGTTAA
*
54107 GTCCTTTAATTTTTTAAATTTTATTTTTTATTTTTATAAATGAG
1 GTCC-TTAATTTTTT-AATTTTATTTTTTATATTTATAAATGAG
** *
54151 GT-CTCTAATTTTTGTAATTCAACTTTTTTATATTTATAATTGAG
1 GTCCT-TAATTTTT-TAATTTTA-TTTTTTATATTTATAAATGAG
*
54195 GTCCTTAATTTTTTCAATCTTATTTTATTATATTTATAA
1 GTCCTTAATTTTTT-AATTTTATTTT-TTATATTTATAA
54234 TTGATGACCC
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
42 1 0.01
43 19 0.27
44 48 0.69
45 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (42 bp):
GTCCTTAATTTTTTAATTTTATTTTTTATATTTATAAATGAG
Found at i:54226 original size:44 final size:43
Alignment explanation
Indices: 54139--54546 Score: 372
Period size: 42 Copynumber: 9.5 Consensus size: 43
54129 ATTTTTTATT
* * **
54139 TTTATAAATGAGGTCTCTAATTTTTGT-AAT-TCAACTTTTTTATA
1 TTTATAATTGAGGTCCCTAATTTTT-TCAATCTC-AC-TTTTTACC
* * * **
54183 TTTATAATTGAGGTCCTTAATTTTTTCAATCTTATTTTATTATA
1 TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTT-TTACC
* * *
54227 TTTATAATTGATGACCCTAAGTTTTTCAATCAT-ACTTTTTACC
1 TTTATAATTGAGGTCCCTAATTTTTTCAATC-TCACTTTTTACC
* *
54270 TTTATAATTGAGCT-CCTAATTTTTTCAATCTCACTTTCTACC
1 TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
* *
54312 TTTATAATTGAGGCCCCTAATTGTTT-AATCTCACTTTTTACC
1 TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
* * *
54354 TTTATAATTGAGGCCCCTATTTTTTTTCAATCTCATTTTTTA-C
1 TTTATAATTGAGGTCCCTA-ATTTTTTCAATCTCACTTTTTACC
* * *
54397 TTATATAATTTA-GTCCCCAAATTTTTTCAATCTCACTTTTTAAC
1 TT-TATAATTGAGGT-CCCTAATTTTTTCAATCTCACTTTTTACC
* *
54441 TTTAATAATTGAGG-CCTTAATTTTTTTAATCTCAC-TTTTACC
1 TTT-ATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
* *
54483 TTTATAATTGAGATCCCTAA-TTTTTCATTCAT-ACTTTTTA-C
1 TTTATAATTGAGGTCCCTAATTTTTTCAATC-TCACTTTTTACC
* * *
54524 TTTCATAGTTTAAGTCCCTAATT
1 TTT-ATAATTGAGGTCCCTAATT
54547 ATTATTTTTC
Statistics
Matches: 304, Mismatches: 42, Indels: 37
0.79 0.11 0.10
Matches are distributed among these distances:
41 24 0.08
42 103 0.34
43 77 0.25
44 97 0.32
45 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (43 bp):
TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
Found at i:54295 original size:42 final size:42
Alignment explanation
Indices: 54139--54523 Score: 322
Period size: 44 Copynumber: 9.0 Consensus size: 42
54129 ATTTTTTATT
* * **
54139 TTTATAAATGAGGTCTCTAATTTTTGT-AAT-TCAACTTTTTTATA
1 TTTATAATTGAGCTC-CTAATTTTT-TCAATCTC-AC-TTTTTACC
* * * **
54183 TTTATAATTGAGGTCCTTAATTTTTTCAATCTTATTTTATTATA
1 TTTATAATTGAGCTCC-TAATTTTTTCAATCTCACTTT-TTACC
*
54227 TTTATAATTGATGAC-CCTAAGTTTTTCAATCAT-ACTTTTTACC
1 TTTATAATTGA-G-CTCCTAATTTTTTCAATC-TCACTTTTTACC
*
54270 TTTATAATTGAGCTCCTAATTTTTTCAATCTCACTTTCTACC
1 TTTATAATTGAGCTCCTAATTTTTTCAATCTCACTTTTTACC
* *
54312 TTTATAATTGAGGCCCCTAATTGTTT-AATCTCACTTTTTACC
1 TTTATAATTGA-GCTCCTAATTTTTTCAATCTCACTTTTTACC
* * *
54354 TTTATAATTGAGGCCCCTATTTTTTTTCAATCTCATTTTTTA-C
1 TTTATAATTGA-GCTCCTA-ATTTTTTCAATCTCACTTTTTACC
* * * *
54397 TTATATAATTTAGTCCCCAAATTTTTTCAATCTCACTTTTTAAC
1 TT-TATAATTGAG-CTCCTAATTTTTTCAATCTCACTTTTTACC
* *
54441 TTTAATAATTGAGGC-CTTAATTTTTTTAATCTCAC-TTTTACC
1 TTT-ATAATTGA-GCTCCTAATTTTTTCAATCTCACTTTTTACC
* *
54483 TTTATAATTGAGATCCCTAA-TTTTTCATTCAT-ACTTTTTAC
1 TTTATAATTGAGCT-CCTAATTTTTTCAATC-TCACTTTTTAC
54524 TTTCATAGTT
Statistics
Matches: 291, Mismatches: 29, Indels: 44
0.80 0.08 0.12
Matches are distributed among these distances:
40 1 0.00
41 20 0.07
42 90 0.31
43 78 0.27
44 96 0.33
45 6 0.02
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.50
Consensus pattern (42 bp):
TTTATAATTGAGCTCCTAATTTTTTCAATCTCACTTTTTACC
Found at i:54431 original size:129 final size:126
Alignment explanation
Indices: 54183--54523 Score: 395
Period size: 129 Copynumber: 2.7 Consensus size: 126
54173 CTTTTTTATA
* * ** *
54183 TTTATAATTGAGGTCCTTAATTTTTTCAATCTTATTTTATTATATTTATAATTGATGACCCTAAG
1 TTTATAATTGAGG-CCTTAATTTTTT-AATCTCACTTT-TTACCTTTATAATTGAGGACCCTAAG
* * *
54248 TTTTTCAATCATACTTTTTACCTTTATAATTGAGCTCCTAATTTTTTCAATCTCACTTTCTACC
63 TTTTTCAATCATACTTTTTACCTTTATAATTGAGCCCCAAATTTTTTCAATCTCACTTTCTAAC
* * * **
54312 TTTATAATTGAGGCCCCTAATTGTTTAATCTCACTTTTTACCTTTATAATTGAGGCCCCTATTTT
1 TTTATAATTGAGG-CCTTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAGGACCCTA-AGT
* * *
54377 TTTTCAATC-TCATTTTTTA-CTTATATAATTTAGTCCCCAAATTTTTTCAATCTCACTTTTTAA
64 TTTTCAATCAT-ACTTTTTACCTT-TATAATTGAG-CCCCAAATTTTTTCAATCTCACTTTCTAA
54440 C
126 C
54441 TTTAATAATTGAGGCCTTAATTTTTTTAATCTCAC-TTTTACCTTTATAATTGA-GATCCCTAA-
1 TTT-ATAATTGAGGCCTTAA-TTTTTTAATCTCACTTTTTACCTTTATAATTGAGGA-CCCTAAG
*
54503 TTTTTCATTCATACTTTTTAC
63 TTTTTCAATCATACTTTTTAC
54524 TTTCATAGTT
Statistics
Matches: 180, Mismatches: 23, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
127 40 0.22
128 37 0.21
129 80 0.44
130 23 0.13
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (126 bp):
TTTATAATTGAGGCCTTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAGGACCCTAAGTTT
TTCAATCATACTTTTTACCTTTATAATTGAGCCCCAAATTTTTTCAATCTCACTTTCTAAC
Found at i:54521 original size:171 final size:170
Alignment explanation
Indices: 54139--54523 Score: 426
Period size: 171 Copynumber: 2.2 Consensus size: 170
54129 ATTTTTTATT
* * * * *
54139 TTTATAAATGAGGTCTCTAATTTTTGTAATTCA-ACTTTTTTATATTTATAATTGAGGTCCTTAA
1 TTTATAATTGAGGTCCCTAA-TTTT-T-ATTCATAC-TTTTTACATTTATAATTGAGGCCCCTAA
* * *
54203 TTTTTTCAATCTTATTTTATTATATTTATAATTGATGACCCTAAGTTTTTCAATCATACTTTTTA
62 TTTTTTCAATCTCATTTTATTATATATATAATTGATGACCCAAAGTTTTTCAATCATACTTTTTA
*
54268 CCTTTATAATTGAGCTCCTAATTTTTTCAATCTCACTTTCTACC
127 ACTTTATAATTGAGCTCCTAATTTTTTCAATCTCACTTTCTACC
* * * *
54312 TTTATAATTGAGGCCCCTAATTGTTTAATC-TCACTTTTTACCTTTATAATTGAGGCCCCTATTT
1 TTTATAATTGAGGTCCCTAATT-TTTATTCAT-ACTTTTTACATTTATAATTGAGGCCCCTA-AT
* * *
54376 TTTTTCAATCTCATTTT-TTACT-TATATAATTTA-GTCCCCAAATTTTTTCAATC-TCACTTTT
63 TTTTTCAATCTCATTTTATTA-TATATATAATTGATG-ACCCAAAGTTTTTCAATCAT-ACTTTT
* *
54437 TAACTTTAATAATTGAGGC-CTTAATTTTTTTAATCTCACTTT-TACC
125 TAACTTT-ATAATTGA-GCTCCTAATTTTTTCAATCTCACTTTCTACC
*
54483 TTTATAATTGAGATCCCTAATTTTTCATTCATACTTTTTAC
1 TTTATAATTGAGGTCCCTAATTTTT-ATTCATACTTTTTAC
54524 TTTCATAGTT
Statistics
Matches: 180, Mismatches: 21, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
170 5 0.03
171 101 0.56
172 53 0.29
173 21 0.12
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.50
Consensus pattern (170 bp):
TTTATAATTGAGGTCCCTAATTTTTATTCATACTTTTTACATTTATAATTGAGGCCCCTAATTTT
TTCAATCTCATTTTATTATATATATAATTGATGACCCAAAGTTTTTCAATCATACTTTTTAACTT
TATAATTGAGCTCCTAATTTTTTCAATCTCACTTTCTACC
Done.