Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003843.1 Hibiscus syriacus cultivar Beakdansim tig00008235_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: 187331
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:6309 original size:16 final size:17
Alignment explanation
Indices: 6290--6326 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
6280 TTTATTATTA
6290 ATTATTATTATTG-TTT
1 ATTATTATTATTGTTTT
*
6306 ATTATTGTTATTGTTTT
1 ATTATTATTATTGTTTT
6323 ATTA
1 ATTA
6327 ATAATATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (17 bp):
ATTATTATTATTGTTTT
Found at i:9544 original size:16 final size:17
Alignment explanation
Indices: 9523--9556 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
9513 TTTATTCACA
9523 TGAATAGTG-AATTTTG
1 TGAATAGTGAAATTTTG
9539 TGAATAGTGAAATTTTG
1 TGAATAGTGAAATTTTG
9556 T
1 T
9557 CGGCGATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (17 bp):
TGAATAGTGAAATTTTG
Found at i:13640 original size:7 final size:7
Alignment explanation
Indices: 13628--13652 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13618 AAGTCAAATT
13628 TGGAGGC
1 TGGAGGC
13635 TGGAGGC
1 TGGAGGC
13642 TGGAGGC
1 TGGAGGC
13649 TGGA
1 TGGA
13653 AATCAAAGCT
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:0.16, C:0.12, G:0.56, T:0.16
Consensus pattern (7 bp):
TGGAGGC
Found at i:15747 original size:33 final size:34
Alignment explanation
Indices: 15688--15783 Score: 135
Period size: 33 Copynumber: 2.9 Consensus size: 34
15678 ACCATGTGCA
**
15688 AAGTTGGCCACCTTCCAAAGATGAAATTTTC-AAT
1 AAGTTGGCCACCAACC-AAGATGAAATTTTCAAAT
15722 AAGTTGGCCACCAACCAAGATGAAA-TTTCAAAT
1 AAGTTGGCCACCAACCAAGATGAAATTTTCAAAT
*
15755 AAGTTGGCCGCCAACCAAGATG-AATTTTC
1 AAGTTGGCCACCAACCAAGATGAAATTTTC
15784 CAACTTGTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
32 6 0.11
33 37 0.65
34 14 0.25
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAGATGAAATTTTCAAAT
Found at i:20450 original size:15 final size:14
Alignment explanation
Indices: 20430--20465 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
20420 TTTAGCAGAC
*
20430 TTTATTTCATTTTAA
1 TTTATTTCATTCT-A
20445 TTTATTTCATTCTA
1 TTTATTTCATTCTA
20459 TTTATTT
1 TTTATTT
20466 TATCTGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATTTCATTCTA
Found at i:35142 original size:20 final size:20
Alignment explanation
Indices: 35109--35147 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35099 TAGTTTTATA
*
35109 AAGTTTTCTCTTTTCTATTC
1 AAGTTTTCACTTTTCTATTC
* *
35129 AAGTTTTCAGTTTTTTATT
1 AAGTTTTCACTTTTCTATT
35148 TTAAGTTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.08, T:0.62
Consensus pattern (20 bp):
AAGTTTTCACTTTTCTATTC
Found at i:39210 original size:46 final size:46
Alignment explanation
Indices: 39160--39351 Score: 269
Period size: 46 Copynumber: 4.2 Consensus size: 46
39150 TATGGTCTCT
* * *
39160 TTTCATGCATTAATACATCCTTTCATGCATTTTAATCATGCCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATCATGGCATCC
* * *
39206 TTTCATCCCTTAATGCATCCTTTCACGCATTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATCATGGCATCC
* * *
39252 TTTCATGCCTTGATGCATCCTTTCATGCATTTTAGTTC-TGACATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTA-ATCATGGCATCC
* *
39298 TTTCATGCCTTAATGCATCCTTTCATGCAATTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATCATGGCATCC
39344 TTTCATGC
1 TTTCATGC
39352 AATTTAATTA
Statistics
Matches: 127, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
45 1 0.01
46 125 0.98
47 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATCATGGCATCC
Found at i:39211 original size:26 final size:25
Alignment explanation
Indices: 39175--39745 Score: 255
Period size: 26 Copynumber: 24.5 Consensus size: 25
39165 TGCATTAATA
*
39175 CATCCTTTCATGCATTTTAATCATG
1 CATCCTTTCATGCATTTTAATTATG
**
39200 CCATCCTTTCAT-C-CCTT-A--ATG
1 -CATCCTTTCATGCATTTTAATTATG
*
39221 CATCCTTTCACGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTAT-G
* *
39247 CATCCTTTCATGC---CT--TGATG
1 CATCCTTTCATGCATTTTAATTATG
* *
39267 CATCCTTTCATGCATTTTAGTTCTG
1 CATCCTTTCATGCATTTTAATTATG
*
39292 ACATCCTTTCATGC--CTT-A--ATG
1 -CATCCTTTCATGCATTTTAATTATG
*
39313 CATCCTTTCATGCAATTTAATTATGG
1 CATCCTTTCATGCATTTTAATTAT-G
*
39339 CATCCTTTCATGCAATTTAATTATGG
1 CATCCTTTCATGCATTTTAATTAT-G
*
39365 CATCCTTTCATG-A-CTT-A--ATG
1 CATCCTTTCATGCATTTTAATTATG
* * *
39385 CATCCATTCATGCATTTTAGTTACG
1 CATCCTTTCATGCATTTTAATTATG
* *
39410 ACATCCTTTTATGC--CTTAA-T-T-
1 -CATCCTTTCATGCATTTTAATTATG
*
39431 CATCCTTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGCATTTTAATTAT-G
* *
39457 CAACCTTTCATGC--CTTAA-TA--
1 CATCCTTTCATGCATTTTAATTATG
* *
39477 CATCATTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGCATTTTAATTAT-G
* *
39503 AATCCTTTCATGC--CTT-A--ATG
1 CATCCTTTCATGCATTTTAATTATG
*
39523 CAT-ATGTTCATGCATTTTAATTATGG
1 CATCCT-TTCATGCATTTTAATTAT-G
**
39549 CATCCTTTCAT--ACCTT-A--ATG
1 CATCCTTTCATGCATTTTAATTATG
* *
39569 CATCATTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGCATTTTAATTAT-G
* *
39595 CATCCTTTAATGC--CTT-A--ATG
1 CATCCTTTCATGCATTTTAATTATG
* *
39615 CATCCGTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGCATTTTAATTAT-G
* *
39641 CATCATTTCATGC--CTT-A--ATG
1 CATCCTTTCATGCATTTTAATTATG
* *
39661 CATCCGTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGCATTTTAATTAT-G
* *
39687 CATCCTTTCTTGC--CTT-A--ATG
1 CATCCTTTCATGCATTTTAATTATG
* *
39707 CATTCATTCATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTAT-G
39733 CATCCTTTCATGC
1 CATCCTTTCATGC
39746 CATAATGCAT
Statistics
Matches: 402, Mismatches: 75, Indels: 136
0.66 0.12 0.22
Matches are distributed among these distances:
19 1 0.00
20 128 0.32
21 22 0.05
22 23 0.06
23 15 0.04
24 24 0.06
25 21 0.05
26 167 0.42
27 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (25 bp):
CATCCTTTCATGCATTTTAATTATG
Found at i:39309 original size:92 final size:92
Alignment explanation
Indices: 39160--39352 Score: 298
Period size: 92 Copynumber: 2.1 Consensus size: 92
39150 TATGGTCTCT
*
39160 TTTCATGCATTAATACATCCTTTCATGCATTTTAATCATGCCATCCTTTCATCCCTTAATGCATC
1 TTTCATGCATTAATACATCCTTTCATGCATTTTAATCATGACATCCTTTCATCCCTTAATGCATC
*
39225 CTTTCACGCATTTTAATTATGGCATCC
66 CTTTCACGCAATTTAATTATGGCATCC
* * * * *
39252 TTTCATGCCTTGATGCATCCTTTCATGCATTTTAGTTC-TGACATCCTTTCATGCCTTAATGCAT
1 TTTCATGCATTAATACATCCTTTCATGCATTTTA-ATCATGACATCCTTTCATCCCTTAATGCAT
*
39316 CCTTTCATGCAATTTAATTATGGCATCC
65 CCTTTCACGCAATTTAATTATGGCATCC
39344 TTTCATGCA
1 TTTCATGCA
39353 ATTTAATTAT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 89 0.98
93 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (92 bp):
TTTCATGCATTAATACATCCTTTCATGCATTTTAATCATGACATCCTTTCATCCCTTAATGCATC
CTTTCACGCAATTTAATTATGGCATCC
Found at i:39388 original size:46 final size:46
Alignment explanation
Indices: 39338--39778 Score: 632
Period size: 46 Copynumber: 9.6 Consensus size: 46
39328 TTTAATTATG
* * *
39338 GCATCCTTTCATGCAATTTAATTATGGCATCCTTTCATGACTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* * * *
39384 GCATCCATTCATGCATTTTAGTTACGACATCCTTTTATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
39430 TCATCCTTTCATGCATTTTAGTTATGGCAACCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* * *
39476 ACATCATTTCATGCATTTTAGTTATGGAATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* * *
39522 GCAT-ATGTTCATGCATTTTAATTATGGCATCCTTTCATACCTTAAT
1 GCATCCT-TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
39568 GCATCATTTCATGCATTTTAGTTATGGCATCCTTTAATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
39614 GCATCCGTTCATGCATTTTAGTTATGGCATCATTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* *
39660 GCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCTTGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* * * *
39706 GCATTCATTCATGCATTTTAATTATGGCATCCTTTCATGCCATAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
*
39752 GCATCCTTTCATTCATTTTAGTTATGG
1 GCATCCTTTCATGCATTTTAGTTATGG
39779 ATTCTGTTTA
Statistics
Matches: 354, Mismatches: 39, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
45 2 0.01
46 350 0.99
47 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
Found at i:39389 original size:164 final size:164
Alignment explanation
Indices: 39175--39515 Score: 493
Period size: 164 Copynumber: 2.1 Consensus size: 164
39165 TGCATTAATA
* * *
39175 CATCCTTTCATGCATTTTAATCATGCCATCCTTTCATCCCTTAATGCATCCTTTCACGCATTTTA
1 CATCCTTTCATGCAATTTAATCATGCCATCCTTTCATCACTTAATGCATCCATTCACGCATTTTA
* * * * *
39240 ATTATGGCATCCTTTCATGCCTTGATGCATCCTTTCATGCATTTTAGTTCTGACATCCTTTCATG
66 ATTACGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGACAACCTTTCATG
* *
39305 CCTTAATGCATCCTTTCATGCAATTTAATTATGG
131 CCTTAATACATCATTTCATGCAATTTAATTATGG
* * * *
39339 CATCCTTTCATGCAATTTAATTATGGCATCCTTTCATGACTTAATGCATCCATTCATGCATTTTA
1 CATCCTTTCATGCAATTTAATCATGCCATCCTTTCATCACTTAATGCATCCATTCACGCATTTTA
* * * *
39404 GTTACGACATCCTTTTATGCCTTAATTCATCCTTTCATGCATTTTAGTTATGGCAACCTTTCATG
66 ATTACGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGACAACCTTTCATG
* *
39469 CCTTAATACATCATTTCATGCATTTTAGTTATGG
131 CCTTAATACATCATTTCATGCAATTTAATTATGG
*
39503 AATCCTTTCATGC
1 CATCCTTTCATGC
39516 CTTAATGCAT
Statistics
Matches: 156, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
164 156 1.00
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (164 bp):
CATCCTTTCATGCAATTTAATCATGCCATCCTTTCATCACTTAATGCATCCATTCACGCATTTTA
ATTACGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGACAACCTTTCATG
CCTTAATACATCATTTCATGCAATTTAATTATGG
Found at i:39522 original size:210 final size:210
Alignment explanation
Indices: 39160--39559 Score: 590
Period size: 210 Copynumber: 1.9 Consensus size: 210
39150 TATGGTCTCT
* * *
39160 TTTCATGCATTAATACATCCTTTCATGCATTTTAATCATGCCATCCTTTCATCCCTTAATGCATC
1 TTTCATGCATTAATACATCCATTCATGCATTTTAATCACGACATCCTTTCATCCCTTAATGCATC
* * * * *
39225 CTTTCACGCATTTTAATTATGGCATCCTTTCATGCCTTGATGCATCCTTTCATGCATTTTAGTTC
66 CTTTCACGCATTTTAATTATGGCAACCTTTCATGCCTTAATACATCATTTCATGCATTTTAGTTA
*
39290 TGACATCCTTTCATGCCTTAATGCATCCT-TTCATGCAATTTAATTATGGCATCCTTTCATGCAA
131 TGACATCCTTTCATGCCTTAATGCAT-ATGTTCATGCAATTTAATTATGGCATCCTTTCATGCAA
39354 TTTAATTATGGCATCC
195 TTTAATTATGGCATCC
* * * * * *
39370 TTTCATG-ACTTAATGCATCCATTCATGCATTTTAGTTACGACATCCTTTTATGCCTTAATTCAT
1 TTTCATGCA-TTAATACATCCATTCATGCATTTTAATCACGACATCCTTTCATCCCTTAATGCAT
* *
39434 CCTTTCATGCATTTTAGTTATGGCAACCTTTCATGCCTTAATACATCATTTCATGCATTTTAGTT
65 CCTTTCACGCATTTTAATTATGGCAACCTTTCATGCCTTAATACATCATTTCATGCATTTTAGTT
*
39499 ATGGA-ATCCTTTCATGCCTTAATGCATATGTTCATGCATTTTAATTATGGCATCCTTTCAT
130 AT-GACATCCTTTCATGCCTTAATGCATATGTTCATGCAATTTAATTATGGCATCCTTTCAT
39560 ACCTTAATGC
Statistics
Matches: 169, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
209 2 0.01
210 165 0.98
211 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.43
Consensus pattern (210 bp):
TTTCATGCATTAATACATCCATTCATGCATTTTAATCACGACATCCTTTCATCCCTTAATGCATC
CTTTCACGCATTTTAATTATGGCAACCTTTCATGCCTTAATACATCATTTCATGCATTTTAGTTA
TGACATCCTTTCATGCCTTAATGCATATGTTCATGCAATTTAATTATGGCATCCTTTCATGCAAT
TTAATTATGGCATCC
Found at i:39627 original size:20 final size:20
Alignment explanation
Indices: 39594--39673 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 20
39584 TTTAGTTATG
* *
39594 GCATCCTTTAATGCCTTAAT
1 GCATCCGTTCATGCCTTAAT
*
39614 GCATCCGTTCATGCATTTTAGTTAT
1 GCATCCGTTCATGC--CTTA---AT
**
39639 GGCATCATTTCATGCCTTAAT
1 -GCATCCGTTCATGCCTTAAT
39660 GCATCCGTTCATGC
1 GCATCCGTTCATGC
39674 ATTTTAGTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
20 24 0.52
21 2 0.04
22 3 0.07
24 3 0.07
25 2 0.04
26 12 0.26
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (20 bp):
GCATCCGTTCATGCCTTAAT
Found at i:46612 original size:46 final size:46
Alignment explanation
Indices: 46553--47144 Score: 758
Period size: 46 Copynumber: 12.9 Consensus size: 46
46543 TATGGTATAT
* * *
46553 TTTCATGCATTAATACATCCGTTCATGCATTTTAATCATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* * * *
46599 TTTCATTCCTTAATGTATCC-TCTCATGTATTTTAATTATGGAATCC
1 TTTCATGCCTTAATGCATCCGT-TCATGCATTTTAATTATGGCATCC
* * ** * * *
46645 TTTAATGCCTTAATGCTTCTTTTCATGCATTTTAGTTATGCCGTCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
*
46691 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* * *
46737 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGTCATCT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* * * * *
46783 TTTCATGCCTTAATTCATTCTTTCATGCATTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
*
46829 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* * * *
46875 TTTCATGCCTTAATGCATCCTTTCATTCATTTTAGTTATGGTATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
*
46921 TTTCATGCCTTAATGCATCC-TTACATGCATTTTAATTATGGAATCC
1 TTTCATGCCTTAATGCATCCGTT-CATGCATTTTAATTATGGCATCC
* * * ** * *
46967 TTTCATGCCTGATTGAATATGTTCATGCA-TTTAGTTATAGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* *
47012 TTTCATGCCTTAATGCATCCGTTCATACATTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
*
47058 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTTTGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* ** *
47104 TTTCATGCATTAATGCATCTTTTCATGCATTTTAGTTATGG
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGG
47145 ATTCAGTTTA
Statistics
Matches: 472, Mismatches: 69, Indels: 10
0.86 0.13 0.02
Matches are distributed among these distances:
45 39 0.08
46 430 0.91
47 3 0.01
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
Found at i:46694 original size:26 final size:24
Alignment explanation
Indices: 46665--47143 Score: 214
Period size: 20 Copynumber: 20.8 Consensus size: 24
46655 TAATGCTTCT
*
46665 TTTCATGCATTTTAGTTATGCCGTCC
1 TTTCATGCATTTTA-TTATG-CATCC
*
46691 TTTCATGC--CTTA--ATGCATCC
1 TTTCATGCATTTTATTATGCATCC
46711 TTTCATGCATTTTAATTATGGCATCC
1 TTTCATGCATTTT-ATTAT-GCATCC
*
46737 TTTCATGC--CTTA--ATGCATCC
1 TTTCATGCATTTTATTATGCATCC
* *
46757 GTTCATGCATTTTAGTTATGTCATCT
1 TTTCATGCATTTTA-TTATG-CATCC
* * *
46783 TTTCATGC--CTTA--ATTCATTC
1 TTTCATGCATTTTATTATGCATCC
46803 TTTCATGCATTTTAGTTATGACATCC
1 TTTCATGCATTTTA-TTATG-CATCC
*
46829 TTTCATGC--CTTA--ATGCATCC
1 TTTCATGCATTTTATTATGCATCC
* *
46849 GTTCATGCATTTTAATTATGGCATCT
1 TTTCATGCATTTT-ATTAT-GCATCC
*
46875 TTTCATGC--CTTA--ATGCATCC
1 TTTCATGCATTTTATTATGCATCC
* *
46895 TTTCATTCATTTTAGTTATGGTATCC
1 TTTCATGCATTTTA-TTAT-GCATCC
*
46921 TTTCATGC--CTTA--ATGCATCC
1 TTTCATGCATTTTATTATGCATCC
* *
46941 TTACATGCATTTTAATTATGGAATCC
1 TTTCATGCATTTT-ATTAT-GCATCC
* * * *
46967 TTTCATGC--CTGA-T-TGAAT-A
1 TTTCATGCATTTTATTATGCATCC
46986 TGTTCATGCA-TTTAGTTATAGCATCC
1 T-TTCATGCATTTTA-TTAT-GCATCC
*
47012 TTTCATGC--CTTA--ATGCATCC
1 TTTCATGCATTTTATTATGCATCC
* *
47032 GTTCATACATTTTAGTTATGGCATCC
1 TTTCATGCATTTTA-TTAT-GCATCC
*
47058 TTTCATGC--CTTA--ATGCATCC
1 TTTCATGCATTTTATTATGCATCC
* *
47078 GTTCATGCATTTTAATTTTGGCATCC
1 TTTCATGCATTTT-ATTAT-GCATCC
*
47104 TTTCATGCA--TTA--ATGCATCT
1 TTTCATGCATTTTATTATGCATCC
47124 TTTCATGCATTTTAGTTATG
1 TTTCATGCATTTTA-TTATG
47144 GATTCAGTTT
Statistics
Matches: 341, Mismatches: 52, Indels: 121
0.66 0.10 0.24
Matches are distributed among these distances:
19 1 0.00
20 122 0.36
21 22 0.06
22 24 0.07
23 9 0.03
24 26 0.08
25 29 0.09
26 108 0.32
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.45
Consensus pattern (24 bp):
TTTCATGCATTTTATTATGCATCC
Found at i:56454 original size:2 final size:2
Alignment explanation
Indices: 56447--56499 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
56437 TCCACTCTTT
56447 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
56489 TA TA TA TA TA T
1 TA TA TA TA TA T
56500 TCTTACCTCG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57598 original size:15 final size:15
Alignment explanation
Indices: 57578--57609 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
57568 CTTTAAATTC
57578 AAGACAATTTCTTTA
1 AAGACAATTTCTTTA
57593 AAGACAATTTCTTTA
1 AAGACAATTTCTTTA
57608 AA
1 AA
57610 TATATTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (15 bp):
AAGACAATTTCTTTA
Found at i:63333 original size:34 final size:34
Alignment explanation
Indices: 63290--63392 Score: 206
Period size: 34 Copynumber: 3.0 Consensus size: 34
63280 AAAAAGAAAT
63290 TTTTGAGTGCTCGTGTGAAATTGACTATAACAGG
1 TTTTGAGTGCTCGTGTGAAATTGACTATAACAGG
63324 TTTTGAGTGCTCGTGTGAAATTGACTATAACAGG
1 TTTTGAGTGCTCGTGTGAAATTGACTATAACAGG
63358 TTTTGAGTGCTCGTGTGAAATTGACTATAACAGG
1 TTTTGAGTGCTCGTGTGAAATTGACTATAACAGG
63392 T
1 T
63393 GTTCCTTAAC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (34 bp):
TTTTGAGTGCTCGTGTGAAATTGACTATAACAGG
Found at i:66149 original size:12 final size:12
Alignment explanation
Indices: 66132--66157 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
66122 TATTTTATTA
66132 CCTTTGATGAAG
1 CCTTTGATGAAG
66144 CCTTTGATGAAG
1 CCTTTGATGAAG
66156 CC
1 CC
66158 AGATGTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (12 bp):
CCTTTGATGAAG
Found at i:69252 original size:23 final size:24
Alignment explanation
Indices: 69225--69283 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
69215 AAGTTGTTTT
69225 TAAAATAAAAAATAA-AAAATAAA
1 TAAAATAAAAAATAATAAAATAAA
* *
69248 TAAAA-GAAAAATAATTAAATAAA
1 TAAAATAAAAAATAATAAAATAAA
* *
69271 CAAATTAAAAAAT
1 TAAAATAAAAAAT
69284 TGAGATAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 8 0.28
23 15 0.52
24 6 0.21
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (24 bp):
TAAAATAAAAAATAATAAAATAAA
Found at i:69259 original size:15 final size:15
Alignment explanation
Indices: 69226--69275 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
69216 AGTTGTTTTT
69226 AAAATAAA-AAATAA
1 AAAATAAATAAATAA
69240 AAAATAAATAAA-AGA
1 AAAATAAATAAATA-A
*
69255 AAAATAATTAAATAA
1 AAAATAAATAAATAA
69270 ACAAAT
1 A-AAAT
69276 TAAAAAATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 9 0.29
15 17 0.55
16 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (15 bp):
AAAATAAATAAATAA
Found at i:69951 original size:19 final size:19
Alignment explanation
Indices: 69895--69957 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
69885 CTATTTAAAC
**
69895 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
69915 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
69935 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
69954 TAAA
1 TAAA
69958 CTAAAATGCC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:77679 original size:19 final size:19
Alignment explanation
Indices: 77651--77761 Score: 59
Period size: 19 Copynumber: 5.8 Consensus size: 19
77641 ATATAATATT
*
77651 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* *
77670 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAAATA
* *
77689 --AAATACCTAA-AACAAAGA
1 CTAAA-ACCTAATTA-AAATA
** **
77707 -TAAAATATAAAAAAAATA
1 CTAAAACCTAATTAAAATA
*
77725 TCCTAAAACTTAATTAAAATA
1 --CTAAAACCTAATTAAAATA
*
77746 CTAAAACCTATTTAAA
1 CTAAAACCTAATTAAA
77762 CTAAAATAGA
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
17 4 0.06
18 16 0.23
19 35 0.51
21 14 0.20
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.27
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:77714 original size:65 final size:65
Alignment explanation
Indices: 77587--77714 Score: 179
Period size: 65 Copynumber: 2.0 Consensus size: 65
77577 TAAAACATCT
* *
77587 TAAATCATAATTAAAACACTTAAAACTATTTAAACTAAATTACCTAAAAAAATAATATAATATTC
1 TAAATCATAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAAAAATAATAAAATATTC
* * *
77652 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAA-GATAAAATAT
1 TAAATCATAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAA-AAATAATAAAATAT
77715 AAAAAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
64 5 0.09
65 48 0.86
66 3 0.05
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (65 bp):
TAAATCATAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAAAAATAATAAAATATTC
Found at i:89744 original size:19 final size:19
Alignment explanation
Indices: 89720--89760 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
89710 AAGCCAAACT
* *
89720 GAGCCATTTGAGTTGAACC
1 GAGCCACTTGAGTCGAACC
89739 GAGCCACTTGAGTCGAACC
1 GAGCCACTTGAGTCGAACC
89758 GAG
1 GAG
89761 TGATGCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (19 bp):
GAGCCACTTGAGTCGAACC
Found at i:90565 original size:27 final size:27
Alignment explanation
Indices: 90535--90633 Score: 117
Period size: 27 Copynumber: 3.7 Consensus size: 27
90525 TTGAATTGAA
* *
90535 CAAAATGACTAAAATACCCCTAAACTC
1 CAAAATGACCAAAATACCCTTAAACTC
* * *
90562 CAAAATGACCAAATTATCCTTAAACAC
1 CAAAATGACCAAAATACCCTTAAACTC
* * * *
90589 CAAAATGACCAAATTATCTTTGAACTC
1 CAAAATGACCAAAATACCCTTAAACTC
90616 CAAAATGACCAAAATACC
1 CAAAATGACCAAAATACC
90634 TAAAGCTTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.21
Consensus pattern (27 bp):
CAAAATGACCAAAATACCCTTAAACTC
Found at i:93584 original size:106 final size:104
Alignment explanation
Indices: 93459--93760 Score: 362
Period size: 106 Copynumber: 2.8 Consensus size: 104
93449 AAAATTAGTT
* * *
93459 GTTAATAGAGTCTGTACCATAATAATG-CGAGTCGTACCACGGATCGGGTCACAGCAAGTTC-AT
1 GTTAATAGAGTCTGGACCATAATAATGTGGA-TCGTACC-CGGATCGGGTCACA-CAAGGTCGA-
* *
93522 ATATTAATTCAAACAAATTAATAAAAAGAATTAACAATTAGGA
62 ATAATAATTCAAACAAATTAATAAAAAGAATTAACAATTAGAA
** *
93565 GTTAATAGAGT-TCGGACCATAATAATGTGGATCGTAGCCTTGATCGGGTCACCATAAGGTCGAA
1 GTTAATAGAGTCT-GGACCATAATAATGTGGATCGTA-CCCGGATCGGGTCA-CACAAGGTCGAA
93629 TAATAATTCAAACAAATTAATAAAAAGAATTAACAATTAGAA
63 TAATAATTCAAACAAATTAATAAAAAGAATTAACAATTAGAA
* * *
93671 GTTAATAGAATCTGGACAATAATAATGTGGATCATACCTCGGATCGGGTCACCACAAGGTCGAAT
1 GTTAATAGAGTCTGGACCATAATAATGTGGATCGTACC-CGGATCGGGTCA-CACAAGGTCGAAT
*
93736 CAA-ACA-TCAAATAAATTAATAAAAA
64 -AATA-ATTCAAACAAATTAATAAAAA
93761 AGCGGCTAAA
Statistics
Matches: 172, Mismatches: 15, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
105 3 0.02
106 158 0.92
107 11 0.06
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (104 bp):
GTTAATAGAGTCTGGACCATAATAATGTGGATCGTACCCGGATCGGGTCACACAAGGTCGAATAA
TAATTCAAACAAATTAATAAAAAGAATTAACAATTAGAA
Found at i:97080 original size:23 final size:23
Alignment explanation
Indices: 97054--97121 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
97044 GGTTAGGGTA
* *
97054 GGCTTTGGGTCGGGTTCAGTTTG
1 GGCTTCGGGTCGGGTTCTGTTTG
* * *
97077 GGCTTCGTGTTGGGTTCTTTTTG
1 GGCTTCGGGTCGGGTTCTGTTTG
*
97100 GGCTCCGGGTCGGGTTCTGTTT
1 GGCTTCGGGTCGGGTTCTGTTT
97122 ATGGTTTTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.01, C:0.16, G:0.40, T:0.43
Consensus pattern (23 bp):
GGCTTCGGGTCGGGTTCTGTTTG
Found at i:105440 original size:29 final size:29
Alignment explanation
Indices: 105359--105440 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
105349 GCACCCATTT
* *
105359 CGAATTAATTACCAAAATAGCACAAAAAC
1 CGAATTATTTACCAAAATAGCACCAAAAC
* *
105388 CAAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAAAATAGCACCAAAAC
*
105417 TGAATTATTTACCAAAATAGCACC
1 CGAATTATTTACCAAAATAGCACC
105441 GGTCAATGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.22
Consensus pattern (29 bp):
CGAATTATTTACCAAAATAGCACCAAAAC
Found at i:105465 original size:12 final size:13
Alignment explanation
Indices: 105448--105476 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
105438 ACCGGTCAAT
105448 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
105460 GGTCAACGGGTCG
1 GGTCAACGGGTCG
105473 GGTC
1 GGTC
105477 GTGACCGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:112871 original size:29 final size:28
Alignment explanation
Indices: 112839--112912 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 28
112829 TTCGATTTAA
*
112839 TTACATGAATAGCACCAAAACTGAATTAT
1 TTACA-GAATAGCACCAAAACTGAAATAT
112868 TTACCAGAATAGCACCAAAACTGAAATAT
1 TTA-CAGAATAGCACCAAAACTGAAATAT
*
112897 TTACCAAAATAGCACC
1 TTA-CAGAATAGCACC
112913 GGTCAACGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 40 0.95
30 2 0.05
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (28 bp):
TTACAGAATAGCACCAAAACTGAAATAT
Found at i:113625 original size:28 final size:28
Alignment explanation
Indices: 113594--113661 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
113584 CATTTTACAC
*
113594 AAATAACACCTTTTTAAA-ATAATTACCA
1 AAATAACACCATTTTAAATA-AATTACCA
* *
113622 AAATAATACCCATTTTGAATAAATTACCA
1 AAATAACA-CCATTTTAAATAAATTACCA
*
113651 GAATAACACCA
1 AAATAACACCA
113662 AAACTGAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 10 0.30
29 22 0.67
30 1 0.03
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.28
Consensus pattern (28 bp):
AAATAACACCATTTTAAATAAATTACCA
Found at i:113669 original size:29 final size:29
Alignment explanation
Indices: 113645--113747 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
113635 TTTGAATAAA
*
113645 TTACCAGAATAACACCAAAACTGAATTAT
1 TTACCAGAATAGCACCAAAACTGAATTAT
* *
113674 TTACCAAAATAGCATCAAAACTGAATTAT
1 TTACCAGAATAGCACCAAAACTGAATTAT
* * *
113703 TTACCAGAATAGCACTAAAACTGGATTTT
1 TTACCAGAATAGCACCAAAACTGAATTAT
*
113732 TTACCAAAATAGCACC
1 TTACCAGAATAGCACC
113748 GGCCAACAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26
Consensus pattern (29 bp):
TTACCAGAATAGCACCAAAACTGAATTAT
Found at i:113794 original size:12 final size:13
Alignment explanation
Indices: 113764--113797 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
113754 CAGTCAACCG
*
113764 GGTCGGGTAAACA
1 GGTCGGGTCAACA
113777 GGTCGGGTCAAC-
1 GGTCGGGTCAACA
113789 GGTCGGGTC
1 GGTCGGGTC
113798 GGGTCAACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.18, C:0.21, G:0.44, T:0.18
Consensus pattern (13 bp):
GGTCGGGTCAACA
Found at i:113799 original size:17 final size:18
Alignment explanation
Indices: 113777--113816 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
113767 CGGGTAAACA
113777 GGTCGGGTCAAC-GGTCG
1 GGTCGGGTCAACAGGTCG
113794 GGTCGGGTCAACAGGTCG
1 GGTCGGGTCAACAGGTCG
113812 GGTCG
1 GGTCG
113817 TGAACGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.17
Consensus pattern (18 bp):
GGTCGGGTCAACAGGTCG
Found at i:115226 original size:10 final size:10
Alignment explanation
Indices: 115211--115236 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
115201 CGCTACTAGT
115211 GAACCGGTCA
1 GAACCGGTCA
115221 GAACCGGTCA
1 GAACCGGTCA
115231 GAACCG
1 GAACCG
115237 TTGAACCGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.31, T:0.08
Consensus pattern (10 bp):
GAACCGGTCA
Found at i:117520 original size:10 final size:10
Alignment explanation
Indices: 117505--117529 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
117495 AGGACGAGTA
117505 CATACCATTC
1 CATACCATTC
117515 CATACCATTC
1 CATACCATTC
117525 CATAC
1 CATAC
117530 ATCAAGCAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (10 bp):
CATACCATTC
Found at i:136363 original size:21 final size:22
Alignment explanation
Indices: 136325--136365 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
136315 AATATAGTAA
136325 ATTTCATAGATTAAGTCATTTG
1 ATTTCATAGATTAAGTCATTTG
* *
136347 ATTT-ATAGTTTATGTCATT
1 ATTTCATAGATTAAGTCATT
136366 GATCGCTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.51
Consensus pattern (22 bp):
ATTTCATAGATTAAGTCATTTG
Found at i:136827 original size:28 final size:25
Alignment explanation
Indices: 136763--136813 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
136753 GGGGAAGTTT
*
136763 TCATTGACTTTGATTATTTTTGTTG
1 TCATCGACTTTGATTATTTTTGTTG
136788 TCATCGACTTTGATTATTTTTGTTG
1 TCATCGACTTTGATTATTTTTGTTG
136813 T
1 T
136814 TATCATCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.59
Consensus pattern (25 bp):
TCATCGACTTTGATTATTTTTGTTG
Found at i:137175 original size:3 final size:3
Alignment explanation
Indices: 137169--137207 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
137159 AATAATAATA
*
137169 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
137208 GCCATTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:138310 original size:53 final size:53
Alignment explanation
Indices: 138252--138357 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
138242 GATTCTAGAG
*
138252 TATGGAGGTTCAGCCCTGATCCAGCTGGTAAATCCTTATGGACCTGAGGATAC
1 TATGGAGGTTCAGCCCTGATCCAGCTGGTAAATCCTTACGGACCTGAGGATAC
*
138305 TATGGAGGTTCAGCCCTGATCGAGCTGGTAAATCCTTACGGACCTGAGGATAC
1 TATGGAGGTTCAGCCCTGATCCAGCTGGTAAATCCTTACGGACCTGAGGATAC
138358 CCTTGGGTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (53 bp):
TATGGAGGTTCAGCCCTGATCCAGCTGGTAAATCCTTACGGACCTGAGGATAC
Found at i:141082 original size:20 final size:19
Alignment explanation
Indices: 141058--141101 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
141048 AGTTTTCTCT
*
141058 TTTTTTTTTTTCAAGTTTTCA
1 TTTTTTATTTT-AAGTTTT-A
141079 TTTTTTATTTTAAGTTTTA
1 TTTTTTATTTTAAGTTTTA
141098 TTTT
1 TTTT
141102 CAAATATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 7 0.32
21 10 0.45
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.75
Consensus pattern (19 bp):
TTTTTTATTTTAAGTTTTA
Found at i:141084 original size:19 final size:19
Alignment explanation
Indices: 141059--141101 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
141049 GTTTTCTCTT
*
141059 TTTTTTTTTTCAAGTTTTCA
1 TTTTTTATTTCAAGTTTT-A
*
141079 TTTTTTATTTTAAGTTTTA
1 TTTTTTATTTCAAGTTTTA
141098 TTTT
1 TTTT
141102 CAAATATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTTATTTCAAGTTTTA
Found at i:142929 original size:21 final size:21
Alignment explanation
Indices: 142899--142951 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
142889 GTTAGCAATT
* *
142899 TCACAAGAAAAGCTGGTTACA
1 TCACAGGAAAAGCTAGTTACA
* **
142920 TCTCAGGAAAAGCTAGTTGTA
1 TCACAGGAAAAGCTAGTTACA
142941 TCACAGGAAAA
1 TCACAGGAAAA
142952 ATTCCAAAGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCACAGGAAAAGCTAGTTACA
Found at i:144552 original size:11 final size:11
Alignment explanation
Indices: 144533--144568 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
144523 AGGCAACCCA
144533 TTTCGTTTTAT
1 TTTCGTTTTAT
* *
144544 TTTCATTTTAA
1 TTTCGTTTTAT
144555 TTTCGTTTTAT
1 TTTCGTTTTAT
144566 TTT
1 TTT
144569 TAGAAAAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.14, C:0.08, G:0.06, T:0.72
Consensus pattern (11 bp):
TTTCGTTTTAT
Found at i:148660 original size:14 final size:14
Alignment explanation
Indices: 148625--148678 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
148615 GGCCCAGTCA
*
148625 CCGAGTCAACTCGAT
1 CCGAGTCAAC-CCAT
* *
148640 CCAAGTCTACCCAT
1 CCGAGTCAACCCAT
*
148654 CCGAGTCAACCCGT
1 CCGAGTCAACCCAT
148668 CCGAGTCAACC
1 CCGAGTCAACC
148679 GTGTTGACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 25 0.76
15 8 0.24
ACGTcount: A:0.26, C:0.41, G:0.17, T:0.17
Consensus pattern (14 bp):
CCGAGTCAACCCAT
Found at i:148697 original size:14 final size:14
Alignment explanation
Indices: 148680--148707 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
148670 GAGTCAACCG
148680 TGTTGACTTTGACC
1 TGTTGACTTTGACC
148694 TGTTGACTTTGACC
1 TGTTGACTTTGACC
148708 ATTGACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
TGTTGACTTTGACC
Found at i:153491 original size:29 final size:29
Alignment explanation
Indices: 153444--153512 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
153434 AACAACCATT
* * *
153444 TTACGAAAATAGCATCATTTTTAAAACAA
1 TTACCAAAATAGCACCATTTTCAAAACAA
* *
153473 TTACCAAAATATCACCATTTTCAAAATAA
1 TTACCAAAATAGCACCATTTTCAAAACAA
*
153502 TTACTAAAATA
1 TTACCAAAATA
153513 ACAATTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (29 bp):
TTACCAAAATAGCACCATTTTCAAAACAA
Found at i:153619 original size:29 final size:29
Alignment explanation
Indices: 153553--153620 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
153543 TAATTATGAA
*
153553 AATAACACCTTTTTCAAAATAATTACCAG
1 AATAACACCCTTTTCAAAATAATTACCAG
** * *
153582 AATGGCACCCTTTTCTAAATAATTACCAT
1 AATAACACCCTTTTCAAAATAATTACCAG
153611 AATAACACCC
1 AATAACACCC
153621 GATCAACGGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.29
Consensus pattern (29 bp):
AATAACACCCTTTTCAAAATAATTACCAG
Found at i:157364 original size:21 final size:21
Alignment explanation
Indices: 157338--157384 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
157328 GCATTTTTCA
*
157338 GAAAAATGATAGATCCCTTTG
1 GAAAAATGATACATCCCTTTG
* *
157359 GAAAAATGATCCATCCCTTTT
1 GAAAAATGATACATCCCTTTG
157380 GAAAA
1 GAAAA
157385 GGATTGATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
GAAAAATGATACATCCCTTTG
Found at i:163070 original size:2 final size:2
Alignment explanation
Indices: 163063--163088 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
163053 AAAGGTCACC
163063 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
163089 CAAATACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:170981 original size:71 final size:75
Alignment explanation
Indices: 170899--171088 Score: 255
Period size: 76 Copynumber: 2.6 Consensus size: 75
170889 TAAAACATCT
* * * *
170899 TAAATACTAATTAAAATACTTAAAA-CTATTTAAACCAAAATACCT-AA-AAA-ATAATAT-TTA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAA
*
170959 AAATAATATTA
65 AAATAATATCA
170970 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT-AAACAAAGATAAAATATAA
*
171035 AAATAATATCC
65 AAATAATATCA
* *
171046 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
171089 AAATATAAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
70 5 0.05
71 37 0.35
73 2 0.02
74 3 0.03
75 6 0.06
76 52 0.50
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (75 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAAA
AATAATATCA
Found at i:171112 original size:76 final size:74
Alignment explanation
Indices: 170905--171124 Score: 254
Period size: 76 Copynumber: 3.0 Consensus size: 74
170895 ATCTTAAATA
* *
170905 CTAATTAAAATACTTAAAA-CTATTTAAACCAAAATAC--CTAAAAA-ATAATATTTAAAATAAT
1 CTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAATAAAAATATAATATTTAAAATAAT
** *
170966 ATTATAAATC
65 ATCCTAAAAC
* *
170976 CTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAA-ACAAAGATAAAATA-TAAAAAT
1 CTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAATA-AAA-ATATAATATTTAAAAT
171039 AATATCCTAAAAC
62 AATATCCTAAAAC
* * *
171052 TTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAATATAAAATATAATGTTTAAAATATT
1 CTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAATA-AAAATATAATATTTAAAATAAT
171117 ATCCTAAA
65 ATCCTAAA
171125 CTTGAGTTTA
Statistics
Matches: 126, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
70 5 0.04
71 29 0.23
72 1 0.01
74 10 0.08
75 24 0.19
76 52 0.41
77 5 0.04
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (74 bp):
CTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAATAAAAATATAATATTTAAAATAATA
TCCTAAAAC
Found at i:172752 original size:5 final size:5
Alignment explanation
Indices: 172742--172829 Score: 52
Period size: 5 Copynumber: 17.0 Consensus size: 5
172732 AAAAAATAAT
* * ***
172742 TAAAA TAAAA T-AAA TAGAA TGAAAA TAAAG TTTTA TAAAAA TAAAA TAAAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA T-AAAA TAAAA T-AAAA
* * * *
172794 TAAAA TGAAA TAGAAC GAAAA TAAAA TGAAA TAAAA
1 TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA
172830 AAATAGAACG
Statistics
Matches: 60, Mismatches: 18, Indels: 10
0.68 0.20 0.11
Matches are distributed among these distances:
4 4 0.07
5 42 0.70
6 14 0.23
ACGTcount: A:0.69, C:0.01, G:0.08, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:172766 original size:15 final size:14
Alignment explanation
Indices: 172734--172834 Score: 51
Period size: 16 Copynumber: 6.7 Consensus size: 14
172724 TCCAGAGAAA
*
172734 AAAATAATTAAAAT
1 AAAATAAATAAAAT
*
172748 AAAATAAATAGAAT
1 AAAATAAATAAAAT
***
172762 GAAAATAAAGTTTTAT
1 -AAAATAAA-TAAAAT
172778 AAAAATAAAATAAAAAT
1 -AAAAT-AAAT-AAAAT
**
172795 AAAATGAAATAGAACG
1 AAAAT-AAATA-AAAT
*
172811 AAAATAAAATGAAAT
1 AAAAT-AAATAAAAT
172826 AAAA-AAATA
1 AAAATAAATA
172835 GAACGAAATG
Statistics
Matches: 65, Mismatches: 17, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
13 4 0.06
14 12 0.18
15 15 0.23
16 29 0.45
17 5 0.08
ACGTcount: A:0.70, C:0.01, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:172804 original size:21 final size:21
Alignment explanation
Indices: 172780--172829 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
172770 AGTTTTATAA
*
172780 AAATAAAATAAAAATAAAATG
1 AAATAAAACAAAAATAAAATG
* *
172801 AAATAGAACGAAAATAAAATG
1 AAATAAAACAAAAATAAAATG
172822 AAATAAAA
1 AAATAAAA
172830 AAATAGAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (21 bp):
AAATAAAACAAAAATAAAATG
Found at i:179037 original size:19 final size:19
Alignment explanation
Indices: 179009--179121 Score: 63
Period size: 19 Copynumber: 6.0 Consensus size: 19
178999 AAATAATATT
*
179009 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* *
179028 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAAATA
* *
179047 --AAATACCTAA-AACAAAGA
1 CTAAA-ACCTAATTA-AAATA
** * * *
179065 -TAAAATATAAAATAATATT
1 CTAAAACCT-AATTAAAATA
*
179084 CTAAAACTTAATTAAAATA
1 CTAAAACCTAATTAAAATA
*
179103 CTAAAACCTATTTAAAATA
1 CTAAAACCTAATTAAAATA
179122 AAATAAAAAG
Statistics
Matches: 68, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
17 4 0.06
18 10 0.15
19 47 0.69
20 7 0.10
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:179039 original size:71 final size:74
Alignment explanation
Indices: 178945--179126 Score: 264
Period size: 75 Copynumber: 2.5 Consensus size: 74
178935 ATCTTTAATT
* * *
178945 CTAATTAAAACACGTAAAA-CTATTTAAACTAAAATACCT-AA-AAA-ATAATATTTAAAATAAT
1 CTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAAAATAAT
*
179006 ATTCTAAATC
65 ATTCTAAAAC
179016 CTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAATAAT
1 CTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT-AAACAAAGATAAAATATAAAATAAT
179081 ATTCTAAAAC
65 ATTCTAAAAC
* *
179091 TTAATTAAAATACTAAAACCTATTTAAAATAAAATA
1 CTAATTAAAATACTAAAACCTATTTAAACTAAAATA
179127 AAAAGATAAA
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
70 5 0.05
71 32 0.32
73 2 0.02
74 3 0.03
75 58 0.58
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (74 bp):
CTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAAAATAATA
TTCTAAAAC
Found at i:179152 original size:75 final size:74
Alignment explanation
Indices: 178945--179163 Score: 218
Period size: 75 Copynumber: 3.0 Consensus size: 74
178935 ATCTTTAATT
* * **
178945 CTAATTAAAACACGTAAAA-CTATTTAAACTAAAATAC-CTA-A-AAAATA-ATATTTAAAATAA
1 CTAATTAAAATAC-TAAAACCTATTTAAAATAAAATACAAAACATAAAATATA-ATTTAAAATAA
*
179005 TATTCTAAATC
64 TATTCTAAAAC
* * * *
179016 CTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACA-AAGATAAAATATAAAATAA
1 CTAATTAAAATACTAAAACCTATTTAAAATAAAATA-C-AAAACATAAAATATAATTTAAAATAA
179080 TATTCTAAAAC
64 TATTCTAAAAC
* * *
179091 TTAATTAAAATACTAAAACCTATTTAAAATAAAATA-AAAAGATAAAATATAATGTTCAAAATAT
1 CTAATTAAAATACTAAAACCTATTTAAAATAAAATACAAAACATAAAATATAAT-TT-AAAATAA
*
179155 TATCCTAAA
64 TATTCTAAA
179164 CTTGGGTTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
70 5 0.04
71 29 0.23
72 6 0.05
73 8 0.06
74 2 0.02
75 74 0.59
76 1 0.01
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (74 bp):
CTAATTAAAATACTAAAACCTATTTAAAATAAAATACAAAACATAAAATATAATTTAAAATAATA
TTCTAAAAC
Found at i:179493 original size:23 final size:23
Alignment explanation
Indices: 179418--179493 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
179408 TAAATCGTAT
179418 TTAATAGA-AAACTAGAATCCTACA
1 TTAATA-ACAAACTAGAATCCTA-A
* *
179442 -TAATAGCAAATTAGAATCCTAA
1 TTAATAACAAACTAGAATCCTAA
179464 TTAATAACAAACTAGAATCCTAA
1 TTAATAACAAACTAGAATCCTAA
179487 TTAATAA
1 TTAATAA
179494 AATAATAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 1 0.02
23 45 0.98
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (23 bp):
TTAATAACAAACTAGAATCCTAA
Found at i:183302 original size:21 final size:22
Alignment explanation
Indices: 183264--183304 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
183254 AATATAGTAA
183264 ATTTCATAGATTAAGTCATTTG
1 ATTTCATAGATTAAGTCATTTG
* *
183286 ATTT-ATAGTTTATGTCATT
1 ATTTCATAGATTAAGTCATT
183305 GATCGCTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.51
Consensus pattern (22 bp):
ATTTCATAGATTAAGTCATTTG
Done.