Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001589.1 Hibiscus syriacus cultivar Beakdansim tig00003169_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: 118586
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1508 original size:24 final size:24
Alignment explanation
Indices: 1469--1554 Score: 109
Period size: 24 Copynumber: 3.6 Consensus size: 24
1459 CCCTAAATAA
* * *
1469 AACATAATTCACATCAGATATCAG
1 AACATAATCCAGATCAGAAATCAG
1493 AACATAATCCAGATCAGAAATCAG
1 AACATAATCCAGATCAGAAATCAG
* *
1517 AACAGAATTCAGATCAGAAATCAG
1 AACATAATCCAGATCAGAAATCAG
* *
1541 AACAAAAACCAGAT
1 AACATAATCCAGAT
1555 AAAAATATTC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.17
Consensus pattern (24 bp):
AACATAATCCAGATCAGAAATCAG
Found at i:1517 original size:12 final size:12
Alignment explanation
Indices: 1502--1541 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1492 GAACATAATC
1502 CAGATCAGAAAT
1 CAGATCAGAAAT
* *
1514 CAGAACAGAATT
1 CAGATCAGAAAT
1526 CAGATCAGAAAT
1 CAGATCAGAAAT
1538 CAGA
1 CAGA
1542 ACAAAAACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.15
Consensus pattern (12 bp):
CAGATCAGAAAT
Found at i:3847 original size:14 final size:14
Alignment explanation
Indices: 3814--3871 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
3804 TCAAAATCAA
* *
3814 CGAGTTAACCCAGT
1 CGAGTTGACTCAGT
3828 -GAGTTGACTCAGT
1 CGAGTTGACTCAGT
*
3841 CGAGTTGTCTCAGT
1 CGAGTTGACTCAGT
*
3855 ACGGGTTGACTCAGT
1 -CGAGTTGACTCAGT
3870 CG
1 CG
3872 GGTCAGGCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 11 0.30
14 14 0.38
15 12 0.32
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (14 bp):
CGAGTTGACTCAGT
Found at i:8345 original size:21 final size:23
Alignment explanation
Indices: 8313--8354 Score: 54
Period size: 21 Copynumber: 1.9 Consensus size: 23
8303 GGAGCATATA
8313 GGTATCCGTACT-CCT-TATAGG
1 GGTATCCGTACTACCTATATAGG
8334 GGTAT-CGATACTACCTATATA
1 GGTATCCG-TACTACCTATATA
8355 AAATTCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.11
21 9 0.50
22 3 0.17
23 4 0.22
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (23 bp):
GGTATCCGTACTACCTATATAGG
Found at i:14743 original size:17 final size:17
Alignment explanation
Indices: 14721--14753 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
14711 CAATCATAAT
14721 AAAACA-AAACAGTAAAA
1 AAAACATAAACA-TAAAA
14738 AAAACATAAACATAAA
1 AAAACATAAACATAAA
14754 TTAAAGGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.76, C:0.12, G:0.03, T:0.09
Consensus pattern (17 bp):
AAAACATAAACATAAAA
Found at i:21050 original size:3 final size:3
Alignment explanation
Indices: 21044--21081 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
21034 AAATAGACAT
21044 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
21082 TCGGGCCTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:21730 original size:133 final size:133
Alignment explanation
Indices: 21279--21744 Score: 571
Period size: 134 Copynumber: 3.5 Consensus size: 133
21269 ATTCCATTTT
* * * * *
21279 TCTTCAGGAAGACCAAATCTGAGAGAAGAAGAATTTGTTTCACTACTCTTTAGGGGAGATCAGAC
1 TCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTAATCTTTAGGGGAGATCAGAC
* * * * *
21344 TCGATAATATTTTGATCCACTTCACTGCTCTTAAGGGAAGATTGAATCAGAAA-TGATTTGCTTT
66 TCGAGAA-CTTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCA-AAATTGATTTGCTTC
*
21408 GCTGG
129 GCTGC
* *
21413 TCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCATTAAACTTTAGGGGAGATCAGAC
1 TCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTAATCTTTAGGGGAGATCAGAC
* * * * * * * *
21478 TCAAGATACTTTTGATTCACTAT-GCTGCTCATCAGGAAAGATTAAATCGAATTTGATTTGCTCC
66 TCGAGA-ACTTTTGATTCACT-TCACTGCTCTTCAGGGAAGATTGAATCAAAATTGATTTGCTTC
21542 GCTGC
129 GCTGC
* * * *
21547 TCTTCAAGAATACCAAATCTGAAAGAAGAAAAATCTGCTCCACTACTCTTTAGGGGAGATCAGAC
1 TCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTAATCTTTAGGGGAGATCAGAC
** *
21612 TCGAGACACTTTTGATTCACTTCACCACTCTTCAGGGAAGATTGAAT-AAAATTGATTTGCTTCA
66 TCGAGA-ACTTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAAAATTGATTTGCTTCG
21676 CTGC
130 CTGC
* * *
21680 TCTTCAGGAAGA-GAAACTCTGAAAGTAGAAGAATCTGCTCCACTAATCTTTAGGGGATATCAGA
1 TCTTCAGGAAGACCAAA-TCTGAAAGAAGAAGAATCTGCTCCACTAATCTTTAGGGGAGATCAGA
21744 C
65 C
21745 CTTTCAAAGA
Statistics
Matches: 281, Mismatches: 46, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
132 3 0.01
133 74 0.26
134 202 0.72
135 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (133 bp):
TCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTAATCTTTAGGGGAGATCAGAC
TCGAGAACTTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAAAATTGATTTGCTTCGC
TGC
Found at i:22538 original size:45 final size:45
Alignment explanation
Indices: 22442--22745 Score: 222
Period size: 45 Copynumber: 6.8 Consensus size: 45
22432 AAAATGACAT
* *
22442 CACTAAAATG-TTGACTTTTCTTCCCGAGAAAGTCAAGGAA-GACAA
1 CACTAAAA-GATTGACTTTTCTTCACGAGAAAGTCAA-GAAGGAAAA
* * * * * *
22487 CGCTAAAAGATTGAGTTTTCTACACGAGAAAGACAAGTAGGATAA
1 CACTAAAAGATTGACTTTTCTTCACGAGAAAGTCAAGAAGGAAAA
** * * *
22532 CACTAAACTATCGACTTCTCTTCACAAGAAAGTCAAGAAGGAAAA
1 CACTAAAAGATTGACTTTTCTTCACGAGAAAGTCAAGAAGGAAAA
* *** * * * *
22577 CACTAAAATATTGACCCCTCTTCACAAGAAAGTCAAGAAATG-CAT
1 CACTAAAAGATTGACTTTTCTTCACGAGAAAGTCAAG-AAGGAAAA
*** * *
22622 CACTAAAAGATTGACTCCACTTCACGAGTAAGTCAAGAA-TAAAA
1 CACTAAAAGATTGACTTTTCTTCACGAGAAAGTCAAGAAGGAAAA
* * * * * *
22666 AACTGAAAGATTGACTTCTATTCACGAGAAAGTC-AGGAGTAACAA
1 CACTAAAAGATTGACTTTTCTTCACGAGAAAGTCAAGAAGGAA-AA
* * *
22711 TACTAAAAGATTAACTTCTCTTCACGAGAAAGTCA
1 CACTAAAAGATTGACTTTTCTTCACGAGAAAGTCA
22746 GGAATAACAA
Statistics
Matches: 208, Mismatches: 44, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
43 3 0.01
44 37 0.18
45 165 0.79
46 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (45 bp):
CACTAAAAGATTGACTTTTCTTCACGAGAAAGTCAAGAAGGAAAA
Found at i:22626 original size:90 final size:89
Alignment explanation
Indices: 22532--22700 Score: 194
Period size: 89 Copynumber: 1.9 Consensus size: 89
22522 AGTAGGATAA
** * * * * *
22532 CACTAAACTATCGACTTCTCTTCACAAGAAAGTCAAGAAGGAAAACACTAAAATATTGACCCCTC
1 CACTAAAAGATCGACTCCACTTCACAAGAAAGTCAAGAA-GAAAAAACTAAAAGATTGACCCCTA
22597 TTCACAAGAAAGTCAAGAAATGCAT
65 TTCACAAGAAAGTCAAGAAATGCAT
* * * * * **
22622 CACTAAAAGATTGACTCCACTTCACGAGTAAGTCAAGAATAAAAAACTGAAAGATTGACTTCTAT
1 CACTAAAAGATCGACTCCACTTCACAAGAAAGTCAAGAAGAAAAAACTAAAAGATTGACCCCTAT
*
22687 TCACGAGAAAGTCA
66 TCACAAGAAAGTCA
22701 GGAGTAACAA
Statistics
Matches: 64, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
89 32 0.50
90 32 0.50
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (89 bp):
CACTAAAAGATCGACTCCACTTCACAAGAAAGTCAAGAAGAAAAAACTAAAAGATTGACCCCTAT
TCACAAGAAAGTCAAGAAATGCAT
Found at i:22767 original size:38 final size:38
Alignment explanation
Indices: 22716--23321 Score: 752
Period size: 38 Copynumber: 15.8 Consensus size: 38
22706 AACAATACTA
* * *
22716 AAAGATTAACTTCTCTTCACGAGAAAGTCAGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
22754 AAAGATTGACTTCTCTCCACGAGAAATTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
22792 AAAGATCGACTTCTCTTCATGAGGAAGTCAAGAATAA-
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
22829 AAACGATTCACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAA-GATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** *
22868 AAAGATTGA-TTCTTATTCTTGAGGAAATCAAGAATAAC
1 AAAGATTGACTTC-TCTTCACGAGGAAGTCAAGAATAAC
* * *
22906 ATTAAAAGATTGAATCCTCTTCGCGAGGAAGTC-AGTAATAAC
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAG-AATAAC
* *
22948 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
22986 AAAAATTGACTTCTCTTCACGAGGAAGACAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * *
23024 AAAGATCGACTTCTCTTTATGAGTAAGTGAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
23062 AAAGATTGAATTCTTTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
23100 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAGTAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
23138 AAATATTGACTTCTCTTCACGAGGAAGTC-AGTAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG-AATAAC
*
23176 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
23214 AAAGATTGACATCTCTTCATGAGGAAGTCGAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
23252 AAGGATTGACTTCTCTTCATGAGGAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
23290 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG
23322 TTGAAGCTTC
Statistics
Matches: 487, Mismatches: 69, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
37 8 0.02
38 441 0.91
39 7 0.01
41 2 0.00
42 27 0.06
43 2 0.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:25285 original size:7 final size:7
Alignment explanation
Indices: 25238--25327 Score: 78
Period size: 7 Copynumber: 12.6 Consensus size: 7
25228 ATACTTGATT
25238 TTTTCTC
1 TTTTCTC
*
25245 TTTTTTC
1 TTTTCTC
25252 TGTTTCCTC
1 T-TTT-CTC
25261 TTTTCT-
1 TTTTCTC
25267 TTTTCTC
1 TTTTCTC
25274 TTTTTCTC
1 -TTTTCTC
25282 TTTT-TC
1 TTTTCTC
*
25288 TTATTTCTT
1 -T-TTTCTC
* *
25297 TTTTATA
1 TTTTCTC
25304 TTTTCTC
1 TTTTCTC
25311 TTTTCTC
1 TTTTCTC
25318 TTTTCT-
1 TTTTCTC
25324 TTTT
1 TTTT
25328 TTCCCTTCTT
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
6 12 0.17
7 36 0.52
8 17 0.25
9 4 0.06
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (7 bp):
TTTTCTC
Found at i:25294 original size:29 final size:29
Alignment explanation
Indices: 25237--25327 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
25227 AATACTTGAT
*
25237 TTTTTCTCTTTTT-TCTGTTTCCTCTTTTC
1 TTTTTCTCTTTTTCTCT-TTTTCTCTTTTC
25266 TTTTTCTCTTTTTCTCTTTTTCT-TATTTC
1 TTTTTCTCTTTTTCTCTTTTTCTCT-TTTC
*
25295 TTTTT-TATATTTTCTC-TTTTCTCTTTTC
1 TTTTTCTCT-TTTTCTCTTTTTCTCTTTTC
25323 TTTTT
1 TTTTT
25328 TTCCCTTCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
28 18 0.32
29 35 0.62
30 3 0.05
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (29 bp):
TTTTTCTCTTTTTCTCTTTTTCTCTTTTC
Found at i:31589 original size:2 final size:2
Alignment explanation
Indices: 31582--31641 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
31572 TTTCCTAAAT
31582 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
31624 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
31642 GATTGTAGAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34190 original size:8 final size:8
Alignment explanation
Indices: 34177--34202 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
34167 AGAAATCAAC
34177 AAAAAAGA
1 AAAAAAGA
34185 AAAAAAGA
1 AAAAAAGA
34193 AAAAAAGA
1 AAAAAAGA
34201 AA
1 AA
34203 GTAGATATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:34640 original size:16 final size:16
Alignment explanation
Indices: 34602--34640 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
34592 GTTCATCAAC
*
34602 TTGCAGCTAGAAACCT
1 TTGCAGTTAGAAACCT
34618 TTGCAGTTAGAAACCT
1 TTGCAGTTAGAAACCT
34634 TTGCAGT
1 TTGCAGT
34641 GTACCATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (16 bp):
TTGCAGTTAGAAACCT
Found at i:42238 original size:42 final size:42
Alignment explanation
Indices: 42126--42238 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
42116 TCTTACTTAG
* * *
42126 TAAGTCCTTCAGGCCATC-AGTAAGTCTTTTGAGCATGATGAT
1 TAAGTCCTTCAGGCCATCTA-TAAGCCTTTCGAGCAAGATGAT
* * * *
42168 TAAATCCTTCGGGACATCTGTAAGCCTTTCGAGCAAGATGA-
1 TAAGTCCTTCAGGCCATCTATAAGCCTTTCGAGCAAGATGAT
*
42209 TAAGTCCTTCAGTCCATCTATAAGACCTTT
1 TAAGTCCTTCAGGCCATCTATAAG-CCTTT
42239 GGGCAGAATA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
41 19 0.33
42 38 0.67
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (42 bp):
TAAGTCCTTCAGGCCATCTATAAGCCTTTCGAGCAAGATGAT
Found at i:42403 original size:229 final size:227
Alignment explanation
Indices: 41910--43001 Score: 1263
Period size: 229 Copynumber: 4.7 Consensus size: 227
41900 GTCCATCAAC
* * * * *
41910 AAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTCGTTCGAGTAAAATGATAA
1 AAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
* * *
41975 GTCCTTCGGGCCATCTATAAGACCTTTGGGCTAGATGCTTTCACACGAATTTGAAAAATGAGAAA
66 GTCCTTCGGTCCATCTATAAGACCTTCGGGC-AGAT-CTTTCACATGAATTTGAAAAATGAGAAA
* * * **
42040 ACAATTTTCAAAGTTTCTCATTTAATGATTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAGTGA
129 GCGATTTTCAAAGTTTCTCATTTAATGTTTTCAG-AAATG-------TGAAAAGTAAGAAAACGA
*
42105 TTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGT
186 TTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGT
* *
42147 AAGTCTTTTGAGCATGATGATTAAATCCTTCGGGACATCTGTAAGCCTTTCGAGCAAGATGATAA
1 AAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
* * *
42212 GTCCTTCAGTCCATCTATAAGACCTTTGGGCAGAATATTTACACATGAATTTGAAAAAATGAGAA
66 GTCCTTCGGTCCATCTATAAGACCTTCGGGCAG-ATCTTT-CACATGAATTTG-AAAAATGAGAA
* **
42277 AGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGTAA-GTGAAAAGTAAGAAAATTATTTCCAA
128 AGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAATGTGAAAAGTAAGAAAACGATTTCCAA
*
42341 AGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAGT
193 AGTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGT
* * * * * *
42376 AAGTCGTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTCAGGCTTTCGAGCCAGGTGATAA
1 AAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
* * * * * * *
42441 GTCCTTCGGGT-TATCCATAAGACCTGCAGGTAGGATGTTTTCACGTGAAATTTGAAAAATGAGA
66 GTCCTTC-GGTCCATCTATAAGACCTTCGGGCA-GAT-CTTTCACATG-AATTTGAAAAATGAGA
** * * * * *
42505 AAGTTATTTCCAAAGTTTCTTATTTAATGCATTTTAAAAATGAAATTTTTTAAAAGTAAGAAAAC
127 AAGCGATTTTCAAAGTTTCTCATTTAATG--TTTT---CA-GAAA--TGTGAAAAGTAAGAAAAC
* *
42570 GATTTCCAAAGTTTCTTACTTAGTAATTTCCTTTGGGCCATCAGT
184 GATTTCCAAAGTTTCTTACTTAGTAA-GTCCTTCGGGCCATCAGT
* * * * *
42615 AAGTCTATCGAGCATGATGATTAAATCCTTCGGGTCATCTTTAAGCCTTTCTAGTAAGAGGATAA
1 AAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
* * * * * *
42680 GTCCTTTGGGCCATCTATAAGACCTTCGGGAATGATGTTTTCACATTAATTTGAAAAATAAGAAA
66 GTCCTTCGGTCCATCTATAAGACCTTCGGGCA-GAT-CTTTCACATGAATTTGAAAAATGAGAAA
*
42745 GTGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAA-GTGAAAAGTAAGAAAACGATTTCCAAA
129 GCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAATGTGAAAAGTAAGAAAACGATTTCCAAA
* *
42809 TTTTCTTACTTAGTAAGTCCTTCGGGTCATCAGT
194 GTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGT
* * * *
42843 AAGCCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGGCTTTCGAGCAAGATGATAA
1 AAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
* * *
42908 GTTCTTCGGTCCATCTATAAGACCTTCGGGCAAGATGCTTTCATATGGTATTTGTAAGAAAATGA
66 GTCCTTCGGTCCATCTATAAGACCTTCGGGC-AGAT-CTTTCACAT-GAATTTG--A-AAAATGA
42973 GAAAGCGATTTTCAAAGTTTCTCATTTAA
125 GAAAGCGATTTTCAAAGTTTCTCATTTAA
43002 AATATTTAAA
Statistics
Matches: 734, Mismatches: 98, Indels: 51
0.83 0.11 0.06
Matches are distributed among these distances:
228 109 0.15
229 223 0.30
230 12 0.02
231 5 0.01
232 38 0.05
233 1 0.00
234 1 0.00
235 3 0.00
236 10 0.01
237 102 0.14
238 125 0.17
239 105 0.14
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (227 bp):
AAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
GTCCTTCGGTCCATCTATAAGACCTTCGGGCAGATCTTTCACATGAATTTGAAAAATGAGAAAGC
GATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAATGTGAAAAGTAAGAAAACGATTTCCAAAGT
TTCTTACTTAGTAAGTCCTTCGGGCCATCAGT
Found at i:42761 original size:467 final size:465
Alignment explanation
Indices: 41910--43001 Score: 1445
Period size: 467 Copynumber: 2.3 Consensus size: 465
41900 GTCCATCAAC
* * * * *
41910 AAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGTAAGTCGTTCGAGTAAAATGATAA
1 AAGTCTTTCGAGCATGATGATTAAATCCTTC-GGTCATCTGTCAGGCTTTCGAGCAAGATGATAA
* ***
41975 GTCCTTCGGGCCATCTATAAGACCTTTGGGCTAGATGCTTTCACACGAATTTGAAAAATGAGAAA
65 GTCCTTCGGGCCATCCATAAGACCTGCAGGCTAGATGCTTTCACACGAATTTGAAAAATGAGAAA
* **
42040 ACAATTTTCAAAGTTTCTCATTTAATGATTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAGTGA
130 ACAATTTCCAAAGTTTCTCATTTAATGATTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAACGA
* *
42105 TTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTTGAGCATGATGATTA
195 TTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAAGTCTATCGAGCATGATGATTA
* *
42170 AATCCTTCGGGACATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCAGTCCATCTATAAGAC
260 AATCCTTCGGGACATCTGTAAGCCTTTCGAGCAAGAGGATAAGTCCTTCAGGCCATCTATAAGAC
* * *
42235 CTTTGGGCAGAATATTTACACATGAATTTGAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATT
325 CTTCGGGAAGAATATTTACACATGAATTTGAAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATT
* ** *
42300 TAATGTTTTCAGTAAGTGAAAAGTAAGAAAATTATTTCCAAAGTTTCTTACTTAGTAAGTCCTTT
390 TAATGTTTTCAGAAAGTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTC
42365 GGGCCATCAGT
455 GGGCCATCAGT
* * *
42376 AAGTCGTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTCAGGCTTTCGAGCCAGGTGATAA
1 AAGTCTTTCGAGCATGATGATTAAATCCTTCGG-TCATCTGTCAGGCTTTCGAGCAAGATGATAA
** * **
42441 GTCCTTCGGGTTATCCATAAGACCTGCAGG-TAGGATGTTTTCACGTGAAATTTGAAAAATGAGA
65 GTCCTTCGGGCCATCCATAAGACCTGCAGGCTA-GATGCTTTCACACG-AATTTGAAAAATGAGA
*** * * * *
42505 AAGTTATTTCCAAAGTTTCTTATTTAATGCATTTTA-AAAATGAAATTTTTTAAAAGTAAGAAAA
128 AAACAATTTCCAAAGTTTCTCATTTAATG-ATTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAA
* **
42569 CGATTTCCAAAGTTTCTTACTTAGTAATTTCCTTTGGGCCATCAGTAAGTCTATCGAGCATGATG
192 CGATTTCCAAAGTTTCTTACTTAGTAA-GTCCTTCAGGCCATCAGTAAGTCTATCGAGCATGATG
* * * * **
42634 ATTAAATCCTTCGGGTCATCTTTAAGCCTTTCTAGTAAGAGGATAAGTCCTTTGGGCCATCTATA
256 ATTAAATCCTTCGGGACATCTGTAAGCCTTTCGAGCAAGAGGATAAGTCCTTCAGGCCATCTATA
* * * *
42699 AGACCTTCGGGAATG-ATGTTTTCACATTAATTTG-AAAAATAAGAAAGTGATTTTCAAAGTTTC
321 AGACCTTCGGGAA-GAATATTTACACATGAATTTGAAAAAATAAGAAAGCGATTTTCAAAGTTTC
*
42762 TCATTTAATGTTTTCAGAAAGTGAAAAGTAAGAAAACGATTTCCAAATTTTCTTACTTAGTAAGT
385 TCATTTAATGTTTTCAGAAAGTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGT
*
42827 CCTTCGGGTCATCAGT
450 CCTTCGGGCCATCAGT
* *
42843 AAGCCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGGCTTTCGAGCAAGATGATAA
1 AAGTCTTTCGAGCATGATGATTAAATCCTTC-GGTCATCTGTCAGGCTTTCGAGCAAGATGATAA
* * * * * * * * *
42908 GTTCTTCGGTCCATCTATAAGACCTTCGGGCAAGATGCTTTCATATGGTATTTGTAAGAAAATGA
65 GTCCTTCGGGCCATCCATAAGACCTGCAGGCTAGATGCTTTCACA-CGAATTTG--A-AAAATGA
* * *
42973 GAAAGCGATTTTCAAAGTTTCTCATTTAA
126 GAAAACAATTTCCAAAGTTTCTCATTTAA
43002 AATATTTAAA
Statistics
Matches: 539, Mismatches: 75, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
465 4 0.01
466 89 0.17
467 287 0.53
468 125 0.23
469 2 0.00
470 32 0.06
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (465 bp):
AAGTCTTTCGAGCATGATGATTAAATCCTTCGGTCATCTGTCAGGCTTTCGAGCAAGATGATAAG
TCCTTCGGGCCATCCATAAGACCTGCAGGCTAGATGCTTTCACACGAATTTGAAAAATGAGAAAA
CAATTTCCAAAGTTTCTCATTTAATGATTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAACGAT
TTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAAGTCTATCGAGCATGATGATTAA
ATCCTTCGGGACATCTGTAAGCCTTTCGAGCAAGAGGATAAGTCCTTCAGGCCATCTATAAGACC
TTCGGGAAGAATATTTACACATGAATTTGAAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTT
AATGTTTTCAGAAAGTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCG
GGCCATCAGT
Found at i:42893 original size:42 final size:42
Alignment explanation
Indices: 42826--42905 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
42816 ACTTAGTAAG
*
42826 TCCTTCGGGTCATCAGTAAGCCTTTCAAGCATGATGATTAAA
1 TCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGATTAAA
* * * *
42868 TCCTTCGGGTCATCTGTCAGGCTTTCGAGCAAGATGAT
1 TCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGAT
42906 AAGTTCTTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (42 bp):
TCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGATTAAA
Found at i:53496 original size:24 final size:24
Alignment explanation
Indices: 53465--53564 Score: 119
Period size: 24 Copynumber: 4.2 Consensus size: 24
53455 TGTTCGGTAA
*
53465 TATGTTCGTTTAAGTTCGTTCATT
1 TATGTTCGTTTATGTTCGTTCATT
* *
53489 TATGTTCGTTTGTGTTCATTCATT
1 TATGTTCGTTTATGTTCGTTCATT
* *
53513 TATGTTCGTTTATGTTCGATCGTT
1 TATGTTCGTTTATGTTCGTTCATT
* ** *
53537 TATGTTCATTTATGAGCATTCATT
1 TATGTTCGTTTATGTTCGTTCATT
53561 TATG
1 TATG
53565 CTTAGACCAA
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (24 bp):
TATGTTCGTTTATGTTCGTTCATT
Found at i:53530 original size:48 final size:48
Alignment explanation
Indices: 53465--53564 Score: 137
Period size: 48 Copynumber: 2.1 Consensus size: 48
53455 TGTTCGGTAA
* * * **
53465 TATGTTCGTTTAAGTTCGTTCATTTATGTTCGTTTGTGTTCATTCATT
1 TATGTTCGTTTAAGTTCGATCATTTATGTTCATTTATGAGCATTCATT
* *
53513 TATGTTCGTTTATGTTCGATCGTTTATGTTCATTTATGAGCATTCATT
1 TATGTTCGTTTAAGTTCGATCATTTATGTTCATTTATGAGCATTCATT
53561 TATG
1 TATG
53565 CTTAGACCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (48 bp):
TATGTTCGTTTAAGTTCGATCATTTATGTTCATTTATGAGCATTCATT
Found at i:53788 original size:10 final size:10
Alignment explanation
Indices: 53733--53771 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
53723 AAAATCTATT
53733 TTCATTTATG
1 TTCATTTATG
* *
53743 TTCCTTTACG
1 TTCATTTATG
*
53753 TTCGTTTATG
1 TTCATTTATG
53763 TTCATTTAT
1 TTCATTTAT
53772 TGTGTTCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:54045 original size:110 final size:110
Alignment explanation
Indices: 53852--54087 Score: 454
Period size: 110 Copynumber: 2.1 Consensus size: 110
53842 CGTTTATCAT
*
53852 TTAAATGAACGAACATAAATGAACACGAACAAGCTACATTCCTTAACGAACGAGCACGAACAAGA
1 TTAAACGAACGAACATAAATGAACACGAACAAGCTACATTCCTTAACGAACGAGCACGAACAAGA
53917 ATTTTTTTCGTTTATGTTCGTATTCGTTCATTTGTTCGGTTAATG
66 ATTTTTTTCGTTTATGTTCGTATTCGTTCATTTGTTCGGTTAATG
*
53962 TTAAACGAACAAACATAAATGAACACGAACAAGCTACATTCCTTAACGAACGAGCACGAACAAGA
1 TTAAACGAACGAACATAAATGAACACGAACAAGCTACATTCCTTAACGAACGAGCACGAACAAGA
54027 ATTTTTTTCGTTTATGTTCGTATTCGTTCATTTGTTCGGTTAATG
66 ATTTTTTTCGTTTATGTTCGTATTCGTTCATTTGTTCGGTTAATG
54072 TTAAACGAACGAACAT
1 TTAAACGAACGAACAT
54088 GAACATACCT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 123 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (110 bp):
TTAAACGAACGAACATAAATGAACACGAACAAGCTACATTCCTTAACGAACGAGCACGAACAAGA
ATTTTTTTCGTTTATGTTCGTATTCGTTCATTTGTTCGGTTAATG
Found at i:55874 original size:18 final size:18
Alignment explanation
Indices: 55851--55886 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55841 TTTCAGTGAA
* *
55851 ATATGTATATATATATAT
1 ATATGTAAACATATATAT
55869 ATATGTAAACATATATAT
1 ATATGTAAACATATATAT
55887 TTATCAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATGTAAACATATATAT
Found at i:56628 original size:29 final size:29
Alignment explanation
Indices: 56571--56792 Score: 205
Period size: 29 Copynumber: 7.6 Consensus size: 29
56561 ACACCCTAAC
* *
56571 AAAAATTAATTACAAAACTAACATC-TTTTT
1 AAAAA-TAATTACAAAAATAGCA-CATTTTT
* * * * *
56601 AGAAATATTTACGAAATTAGCACATTTTA
1 AAAAATAATTACAAAAATAGCACATTTTT
* *
56630 AAAAATAATTACAAAAGTAGTACATTTTT
1 AAAAATAATTACAAAAATAGCACATTTTT
* * *
56659 AAAAATAATTATAAAAATAACACCTTTTT
1 AAAAATAATTACAAAAATAGCACATTTTT
* ** **
56688 AAAAATATTTACAAAAATATTACCGTTTT
1 AAAAATAATTACAAAAATAGCACATTTTT
* *
56717 AAAAATAATTACGAAAATAGCACATATTT
1 AAAAATAATTACAAAAATAGCACATTTTT
* * *
56746 AAAAATATTTACAAAAATATCA-TTGTTTT
1 AAAAATAATTACAAAAATAGCACAT-TTTT
56775 AAAAATAATTACAAAAAT
1 AAAAATAATTACAAAAAT
56793 GTCACCGGGT
Statistics
Matches: 155, Mismatches: 35, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
28 2 0.01
29 149 0.96
30 4 0.03
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATAATTACAAAAATAGCACATTTTT
Found at i:56697 original size:87 final size:86
Alignment explanation
Indices: 56571--56792 Score: 250
Period size: 87 Copynumber: 2.5 Consensus size: 86
56561 ACACCCTAAC
* * * *
56571 AAAAATTAATTACAAAACTAACATCTTTTTAGAAATATTTACGAAATTAGCA-CATTTTAAAAAA
1 AAAAA-TAATTACAAAAATAACA-CTTTTTAAAAATATTTACAAAAATAGCACCATTTT-AAAAA
* *
56635 TAATTAC-AAAAGTAGTACATTTTT
63 TAATTACGAAAA-TAGCACATATTT
* ** *
56659 AAAAATAATTATAAAAATAACACCTTTTTAAAAATATTTACAAAAATATTACCGTTTTAAAAATA
1 AAAAATAATTACAAAAATAACA-CTTTTTAAAAATATTTACAAAAATAGCACCATTTTAAAAATA
56724 ATTACGAAAATAGCACATATTT
65 ATTACGAAAATAGCACATATTT
* * * *
56746 AAAAATATTTACAAAAATATCATTGTTTTAAAAATAATTACAAAAAT
1 AAAAATAATTACAAAAATAACACT-TTTTAAAAATATTTACAAAAAT
56793 GTCACCGGGT
Statistics
Matches: 115, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
86 1 0.01
87 100 0.87
88 14 0.12
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.34
Consensus pattern (86 bp):
AAAAATAATTACAAAAATAACACTTTTTAAAAATATTTACAAAAATAGCACCATTTTAAAAATAA
TTACGAAAATAGCACATATTT
Found at i:63781 original size:29 final size:29
Alignment explanation
Indices: 63749--63941 Score: 251
Period size: 29 Copynumber: 6.7 Consensus size: 29
63739 CACCCTAGAA
* *
63749 AAAAATAATTACAAAACTAACACCTTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTT
* * *
63778 AAAAATATTTACGAAAATAGTACCTTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTT
63807 AAAAATAATTACAAAAATAGCACCTTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTT
* * * *
63836 AAAAATATTTATAAAAATATCACCGTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTT
*
63865 AAAAATAATTACAAAAATAGCACATTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTT
* * * *
63894 AAAAATATTTACAAAAATATCCCCGTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTT
*
63923 AAAAATAATTACGAAAATA
1 AAAAATAATTACAAAAATA
63942 TCATCGGGTC
Statistics
Matches: 140, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 140 1.00
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATAATTACAAAAATAGCACCTTTTT
Found at i:63831 original size:58 final size:58
Alignment explanation
Indices: 63749--63941 Score: 298
Period size: 58 Copynumber: 3.3 Consensus size: 58
63739 CACCCTAGAA
* * * *
63749 AAAAATAATTACAAAACTAACACCTTTTTAAAAATATTTACGAAAATAGT-ACCTTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTTAAAAATATTTACAAAAATA-TCACCGTTTT
*
63807 AAAAATAATTACAAAAATAGCACCTTTTTAAAAATATTTATAAAAATATCACCGTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTTAAAAATATTTACAAAAATATCACCGTTTT
* *
63865 AAAAATAATTACAAAAATAGCACATTTTTAAAAATATTTACAAAAATATCCCCGTTTT
1 AAAAATAATTACAAAAATAGCACCTTTTTAAAAATATTTACAAAAATATCACCGTTTT
*
63923 AAAAATAATTACGAAAATA
1 AAAAATAATTACAAAAATA
63942 TCATCGGGTC
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
57 1 0.01
58 124 0.99
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (58 bp):
AAAAATAATTACAAAAATAGCACCTTTTTAAAAATATTTACAAAAATATCACCGTTTT
Found at i:63971 original size:18 final size:18
Alignment explanation
Indices: 63948--63982 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
63938 AATATCATCG
63948 GGTCAGGTCGGGTCAACA
1 GGTCAGGTCGGGTCAACA
63966 GGTCAGGTCGGGTCAAC
1 GGTCAGGTCGGGTCAAC
63983 CCGGTTCGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.40, T:0.17
Consensus pattern (18 bp):
GGTCAGGTCGGGTCAACA
Found at i:67114 original size:18 final size:18
Alignment explanation
Indices: 67082--67120 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
67072 GCATTTACAT
**
67082 TTTACTTTCTGCATTGCA
1 TTTACTTTCCACATTGCA
*
67100 TTTACTTTCCACATTGTA
1 TTTACTTTCCACATTGCA
67118 TTT
1 TTT
67121 TATTCATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.54
Consensus pattern (18 bp):
TTTACTTTCCACATTGCA
Found at i:68029 original size:13 final size:13
Alignment explanation
Indices: 68011--68040 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
68001 AGGATTTATT
68011 GGTGAATTAGTAA
1 GGTGAATTAGTAA
68024 GGTGAATTAGTAA
1 GGTGAATTAGTAA
68037 GGTG
1 GGTG
68041 TGTTTTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (13 bp):
GGTGAATTAGTAA
Found at i:69279 original size:53 final size:53
Alignment explanation
Indices: 69147--69308 Score: 204
Period size: 52 Copynumber: 3.1 Consensus size: 53
69137 CAGTGTGTAC
* * * * **
69147 TTTCGGTACTATGTGTGCATCCATGTTATTCATAATAAGTTTGTG-ATTAGAA
1 TTTCGGCACTATGTGTACATCCATGGTATTCATAATGAGTTTGTGAATTACCA
* *
69199 TTTCGGCACTATGTGTGCATCCATGGTATTCATAATGAGTTAGTGAATTACCA
1 TTTCGGCACTATGTGTACATCCATGGTATTCATAATGAGTTTGTGAATTACCA
* *
69252 TTTTGGCACTATGTGTACA-CCTGTGGTATTC-TAATGAGTTTGTGAATTACCA
1 TTTCGGCACTATGTGTACATCC-ATGGTATTCATAATGAGTTTGTGAATTACCA
69304 TTTCG
1 TTTCG
69309 TTACCTTAGT
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
52 67 0.69
53 30 0.31
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (53 bp):
TTTCGGCACTATGTGTACATCCATGGTATTCATAATGAGTTTGTGAATTACCA
Found at i:74711 original size:20 final size:20
Alignment explanation
Indices: 74666--74715 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
74656 GTACTGATAA
*
74666 TATCGATACTGGTTGAAGAAG
1 TATCGATACTGATTGAAG-AG
74687 TATCGATACTGATATGAAG-G
1 TATCGATACTGAT-TGAAGAG
74707 TATCGATAC
1 TATCGATAC
74716 CAAAAGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:74742 original size:20 final size:20
Alignment explanation
Indices: 74686--74744 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
74676 GGTTGAAGAA
*
74686 GTATCGATACTGATATG-AAG
1 GTATCGATACTG-TAAGTAAG
*** *
74706 GTATCGATACCAAAAGTAAT
1 GTATCGATACTGTAAGTAAG
74726 GTATCGATACTGTAAGTAA
1 GTATCGATACTGTAAGTAA
74745 AGATGAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (20 bp):
GTATCGATACTGTAAGTAAG
Found at i:75466 original size:54 final size:53
Alignment explanation
Indices: 75402--75505 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 53
75392 GTACTATCGA
*
75402 CACTATGTGTGCATCCATGGTATTAAATAATGAGTTTGTGAATAACCATTTTGG
1 CACTATGTGTGCATCCATGGTATT-AATAATGAGTTTATGAATAACCATTTTGG
* *
75456 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTATGAATTACCATTT
1 CACTATGTGTGCATCCATGGTATTAATAATGAGTTTATGAATAACCATTT
75506 CGTTACCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 23 0.49
54 24 0.51
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (53 bp):
CACTATGTGTGCATCCATGGTATTAATAATGAGTTTATGAATAACCATTTTGG
Found at i:81315 original size:2 final size:2
Alignment explanation
Indices: 81265--81302 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
81255 CTTATTTATT
81265 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
81303 CATGTGCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:95610 original size:16 final size:17
Alignment explanation
Indices: 95583--95620 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
95573 ACGTCGCTTC
*
95583 TTCCACTTTTTCTCTTT
1 TTCCACTTTTTCCCTTT
95600 TTCCA-TTTTTCCCTTT
1 TTCCACTTTTTCCCTTT
*
95616 CTCCA
1 TTCCA
95621 AAACGACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.08, C:0.34, G:0.00, T:0.58
Consensus pattern (17 bp):
TTCCACTTTTTCCCTTT
Found at i:96334 original size:16 final size:16
Alignment explanation
Indices: 96313--96351 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
96303 ATGATGGTAT
*
96313 ACTGCAAAGTTTTCTA
1 ACTGCAAAGGTTTCTA
96329 ACTGCAAAGGTTTCTA
1 ACTGCAAAGGTTTCTA
*
96345 GCTGCAA
1 ACTGCAA
96352 GTTGATGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (16 bp):
ACTGCAAAGGTTTCTA
Found at i:99416 original size:13 final size:13
Alignment explanation
Indices: 99395--99433 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
99385 AATGACGCGC
* *
99395 AATGAGCGTTATA
1 AATGCGCGTCATA
99408 AATGCGCGTCATA
1 AATGCGCGTCATA
*
99421 AATGCGTGTCATA
1 AATGCGCGTCATA
99434 GATTTATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:101886 original size:2 final size:2
Alignment explanation
Indices: 101879--101906 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
101869 CGTGTATAAC
101879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
101907 TAAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105224 original size:43 final size:43
Alignment explanation
Indices: 105176--105272 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
105166 TCCAGACACG
* * *
105176 CCGCTACATGTCAAATCTATTGCAGCATTTTTTACT-CTAAACA
1 CCGCTACATATCAAATATATTGCAGCATGTTTTACTAC-AAACA
* * * *
105219 CCGCTATATATCAAATATATTGCGGCGTGTTTTACTACAAACG
1 CCGCTACATATCAAATATATTGCAGCATGTTTTACTACAAACA
105262 CCGCTACATAT
1 CCGCTACATAT
105273 TTATTCTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
43 44 0.98
44 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (43 bp):
CCGCTACATATCAAATATATTGCAGCATGTTTTACTACAAACA
Found at i:106087 original size:2 final size:2
Alignment explanation
Indices: 106080--106122 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
106070 AAATATAAAC
106080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
106122 A
1 A
106123 ATAGTGGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:107330 original size:53 final size:53
Alignment explanation
Indices: 107256--107380 Score: 216
Period size: 53 Copynumber: 2.4 Consensus size: 53
107246 CTTGACACTA
107256 TAAGAGC-TTCGAGAGATTGCCTGGTCCCTAGGCGAAACATTTCTAGACCTTG
1 TAAGAGCTTTCGAGAGATTGCCTGGTCCCTAGGCGAAACATTTCTAGACCTTG
* * *
107308 TAAGAGCTTTCGAGAGATTGCCTGGTGCTTAGGTGAAACATTTCTAGACCTTG
1 TAAGAGCTTTCGAGAGATTGCCTGGTCCCTAGGCGAAACATTTCTAGACCTTG
107361 TAAGAGCTTTCGAGAGATTG
1 TAAGAGCTTTCGAGAGATTG
107381 GCGTTTTTCT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 7 0.10
53 62 0.90
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (53 bp):
TAAGAGCTTTCGAGAGATTGCCTGGTCCCTAGGCGAAACATTTCTAGACCTTG
Found at i:111352 original size:103 final size:101
Alignment explanation
Indices: 111174--111378 Score: 293
Period size: 103 Copynumber: 2.0 Consensus size: 101
111164 TCACGGGATG
* * * *
111174 ACTCTACCTGACTAGCTCAGGGTGGACGGTATGCTCCCTTTCACTTAGAGTGTAGGATGGTAGTG
1 ACTCTACCTGACTAGCACAGGGTGGAAGGTATGATCCCTTTCACTTAGAATGTAGGATGGTAGTG
* ** * *
111239 TGATGAGCTGATTGTCCTTAATGTGTGCTTTAAAAAA
66 TGATGAGCTGACTCCCCTTAAAGTATGC-TTAAAAAA
* *
111276 ACTCTACCTGACTAGCACGGAGGTGGAAGGTATGATCCCTTTCACTTAGAATGTGGGATGGTAGT
1 ACTCTACCTGACTAGCACAG-GGTGGAAGGTATGATCCCTTTCACTTAGAATGTAGGATGGTAGT
111341 GTGATGAGCTGACTCCCCTTAAAGTATGCTTAAAAAA
65 GTGATGAGCTGACTCCCCTTAAAGTATGCTTAAAAAA
111378 A
1 A
111379 GTTGAAGTTA
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
102 27 0.30
103 64 0.70
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (101 bp):
ACTCTACCTGACTAGCACAGGGTGGAAGGTATGATCCCTTTCACTTAGAATGTAGGATGGTAGTG
TGATGAGCTGACTCCCCTTAAAGTATGCTTAAAAAA
Found at i:113073 original size:323 final size:323
Alignment explanation
Indices: 112485--113121 Score: 1229
Period size: 323 Copynumber: 2.0 Consensus size: 323
112475 ATGAATATTA
112485 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
1 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
*
112550 TTTTACCGTTAATGAATGATTAAGTATGTTTTTGTTAAGTGTTGTTTTGTTCACTGTTTTAACCT
66 TTTTACCGTTAATGAATGATTAAGTATGTTTTTGTTAAGTGTTGTTTAGTTCACTGTTTTAACCT
112615 TTTGCCTTGACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
131 TTTGCCTTGACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
* * *
112680 TTTATGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCGAGAGATTTAAGA
196 TGTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCAAGAGATTTAAGA
112745 TAGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCTGTCTTAGAG
261 TAGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCTGTCTTAGAG
112808 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
1 TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
112873 TTTTACCGTTAATGAATGATTAAGTATGTTTTTGTTAAGTGTTGTTTAGTTCACTGTTTTAACCT
66 TTTTACCGTTAATGAATGATTAAGTATGTTTTTGTTAAGTGTTGTTTAGTTCACTGTTTTAACCT
112938 TTTGCCTTGACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
131 TTTGCCTTGACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
*
113003 TGTAAGAGCTTTTGAGAGATTTTCATTTTTCTAGAAATTGATTCTTAGATTCAAGAGATTTAAGA
196 TGTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCAAGAGATTTAAGA
113068 TAGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCT
261 TAGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCT
113122 ACCTTAAAGA
Statistics
Matches: 309, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
323 309 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (323 bp):
TTGGGATGATGTTAAACTCACCAAATTGTTTTATTTGGTGTTGGGAATGCTTGGATGATATTTTA
TTTTACCGTTAATGAATGATTAAGTATGTTTTTGTTAAGTGTTGTTTAGTTCACTGTTTTAACCT
TTTGCCTTGACACTATAAGAGCTTCGAGAGATTGCATGGTGCCTAGGCGAAACATTTCTTGACCT
TGTAAGAGCTTTTGAGAGATTGTCATTTTTCTAGAAATTGATTCTTAGATTCAAGAGATTTAAGA
TAGATCTACATGAGCAATGGAATAGATCCGAGATGGTGATGTTCTAACCTGCCTGTCTTAGAG
Found at i:116099 original size:5 final size:5
Alignment explanation
Indices: 116089--116113 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
116079 AAAGGATCCC
116089 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
116114 CGAACTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:116560 original size:18 final size:19
Alignment explanation
Indices: 116529--116569 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
116519 TTTCAGAATC
116529 TTTTAATTCTAAAAATTAT
1 TTTTAATTCTAAAAATTAT
*
116548 TTTTTATTC-AAAAATTAT
1 TTTTAATTCTAAAAATTAT
116566 TTTT
1 TTTT
116570 GAAAAAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAATTCTAAAAATTAT
Done.