Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002375.1 Hibiscus syriacus cultivar Beakdansim tig00004853_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: 123093
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6331 original size:10 final size:10
Alignment explanation
Indices: 6318--6366 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
6308 TATATGTATA
6318 TTTTATAATT
1 TTTTATAATT
**
6328 TTTTATGTTT
1 TTTTATAATT
*
6338 TTTTACAA--
1 TTTTATAATT
6346 TTTTAT-ATT
1 TTTTATAATT
6355 TTTTATAATT
1 TTTTATAATT
6365 TT
1 TT
6367 AAAAATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
7 1 0.03
8 5 0.17
9 6 0.20
10 18 0.60
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTATAATT
Found at i:6356 original size:17 final size:17
Alignment explanation
Indices: 6336--6404 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
6326 TTTTTTATGT
6336 TTTTTTACAATTTTATA
1 TTTTTTACAATTTTATA
*
6353 TTTTTTATAATTTTAAAAATA
1 TTTTTTACAATTTT----ATA
*
6374 TTTTTTACAATTCTATA
1 TTTTTTACAATTTTATA
* *
6391 ATATTTA-AATTTTA
1 TTTTTTACAATTTTA
6405 AATAATTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
16 6 0.14
17 21 0.50
21 15 0.36
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTTACAATTTTATA
Found at i:6377 original size:20 final size:21
Alignment explanation
Indices: 6350--6444 Score: 78
Period size: 20 Copynumber: 4.8 Consensus size: 21
6340 TTACAATTTT
6350 ATATTTTTTATAATTTTAAAA
1 ATATTTTTTATAATTTTAAAA
* * *
6371 ATATTTTTTACAATTCT-ATA
1 ATATTTTTTATAATTTTAAAA
6391 ATA---TTTA-AATTTTAAATA
1 ATATTTTTTATAATTTTAAA-A
* * *
6409 AT-TCTTGTA-CATTTTAAAA
1 ATATTTTTTATAATTTTAAAA
6428 ATATTTTTTATAATTTT
1 ATATTTTTTATAATTTT
6445 TAAATAATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
16 5 0.09
17 5 0.09
18 3 0.05
19 3 0.05
20 21 0.37
21 20 0.35
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (21 bp):
ATATTTTTTATAATTTTAAAA
Found at i:6454 original size:21 final size:19
Alignment explanation
Indices: 6336--6454 Score: 70
Period size: 21 Copynumber: 6.2 Consensus size: 19
6326 TTTTTTATGT
6336 TTTTTTACAATTTT--AT-A
1 TTTTTTA-AATTTTAAATAA
*
6353 TTTTTTATAATTTTAAAAATA
1 TTTTTTA-AATTTTAAATA-A
*
6374 TTTTTTACAATTCT--ATAA
1 TTTTTTA-AATTTTAAATAA
*
6392 -TATTTAAATTTTAAATAA
1 TTTTTTAAATTTTAAATAA
* * *
6410 TTCTTGTACATTTTAAAAATA
1 TT-TTTTAAATTTTAAATA-A
6431 TTTTTTATAATTTTTAAATAA
1 TTTTTTA-AA-TTTTAAATAA
6452 TTT
1 TTT
6455 GTACAAGTTA
Statistics
Matches: 77, Mismatches: 14, Indels: 18
0.71 0.13 0.17
Matches are distributed among these distances:
16 5 0.06
17 18 0.23
18 5 0.06
19 4 0.05
20 16 0.21
21 21 0.27
22 8 0.10
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (19 bp):
TTTTTTAAATTTTAAATAA
Found at i:9327 original size:23 final size:21
Alignment explanation
Indices: 9278--9329 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
9268 ACATATTTAA
9278 ATAATCA-TTT-AAAATAAAT
1 ATAATCATTTTAAAAATAAAT
9297 A-AAT-ATTTTAAAAATATATAT
1 ATAATCATTTTAAAAATA-A-AT
9318 ATAATCATTTTA
1 ATAATCATTTTA
9330 CACGTGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 1 0.04
18 6 0.22
19 7 0.26
20 1 0.04
21 3 0.11
22 3 0.11
23 6 0.22
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAATCATTTTAAAAATAAAT
Found at i:19421 original size:97 final size:98
Alignment explanation
Indices: 19290--19469 Score: 283
Period size: 97 Copynumber: 1.8 Consensus size: 98
19280 TACTCTCCTG
* * *
19290 TCTCTAGCTCAATTTAGCAACATATGGATCTAATTTAGCCAGCCTTTCTAGATTGTGTTT-TTCT
1 TCTCTAGCACAATGTAGCAACATATGGATCTAATTTAGCCAGCCTTTCTAGATTGTCTTTGTTCT
19354 GTTTTCTCAAGGGTCTCTTTGTCCCTACTGTCA
66 GTTTTCTCAAGGGTCTCTTTGTCCCTACTGTCA
* * *
19387 TCTCTGGCACAATGTAGCAACATATTGA-CTTAATTTAGTCAGCCTTTCTAGATTGTCTTTGTTC
1 TCTCTAGCACAATGTAGCAACATATGGATC-TAATTTAGCCAGCCTTTCTAGATTGTCTTTGTTC
19451 TGTTTTCTCAAGGGTCTCT
65 TGTTTTCTCAAGGGTCTCT
19470 AACATTTAGG
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
96 1 0.01
97 52 0.69
98 22 0.29
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (98 bp):
TCTCTAGCACAATGTAGCAACATATGGATCTAATTTAGCCAGCCTTTCTAGATTGTCTTTGTTCT
GTTTTCTCAAGGGTCTCTTTGTCCCTACTGTCA
Found at i:20099 original size:16 final size:16
Alignment explanation
Indices: 20078--20108 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20068 AATTTGTTGC
20078 TTAGTTTTTTCTAACA
1 TTAGTTTTTTCTAACA
20094 TTAGTTTTTTCTAAC
1 TTAGTTTTTTCTAAC
20109 CTTTCGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (16 bp):
TTAGTTTTTTCTAACA
Found at i:29763 original size:18 final size:18
Alignment explanation
Indices: 29740--29774 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29730 AACTTCCCCA
29740 AGAAATCAACCTCCCCTG
1 AGAAATCAACCTCCCCTG
*
29758 AGAAATCAACCTTCCCT
1 AGAAATCAACCTCCCCT
29775 AATTACCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.37, G:0.09, T:0.20
Consensus pattern (18 bp):
AGAAATCAACCTCCCCTG
Found at i:30098 original size:14 final size:14
Alignment explanation
Indices: 30079--30106 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30069 TAGCAGAACC
30079 AAAGACTTGTACAT
1 AAAGACTTGTACAT
30093 AAAGACTTGTACAT
1 AAAGACTTGTACAT
30107 CCTGTTCAAT
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
AAAGACTTGTACAT
Found at i:44521 original size:156 final size:155
Alignment explanation
Indices: 44237--44539 Score: 366
Period size: 156 Copynumber: 1.9 Consensus size: 155
44227 GAATTCATAT
*
44237 TAAAGGTAAATAATAAATTTGCTAATAGGTAAATAACACTTCAAAAAAATGAGTACATGGTAATA
1 TAAAGGTAAATAATAAATTTGCTAATAGGTAAATAACACTCCAAAAAAATGAGTACA-GGTAATA
*
44302 TAGACTAAACCTAAACTAGTATATAAACTTTGATAAGAAAAAAAAAGTCAACAAATTGACCTATT
65 TAGAATAAACCTAAACTAGTATATAAACTTTGATAAGAAAAAAAAAGTCAACAAATTGACCTA-T
44367 ATATTTTGTTCAATCTAGGATTGCATGG
129 -TATTTTGTTCAATCTAGGATTGCATGG
* * *
44395 TAAAGGTAAATACTAAGTTTGCT-ATAGGTAAATAACACTCCAAAGAAATGCA-TACA-GTAATA
1 TAAAGGTAAATAATAAATTTGCTAATAGGTAAATAACACTCCAAAAAAATG-AGTACAGGTAATA
* * * * *** **
44457 TAGAGATAAACCTATATTAGTTTCTAAACTTTTG-TTTTAAAAAAAGGGT-AA-AAAGCTTGACC
65 TAGA-ATAAACCTAAACTAGTATATAAAC-TTTGATAAGAAAAAAAAAGTCAACAAA--TTGACC
44519 TATTATTTTGTTCAATCTAGG
126 TATTATTTTGTTCAATCTAGG
44540 GTTAAATATT
Statistics
Matches: 126, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
154 21 0.17
155 13 0.10
156 37 0.29
157 33 0.26
158 22 0.17
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (155 bp):
TAAAGGTAAATAATAAATTTGCTAATAGGTAAATAACACTCCAAAAAAATGAGTACAGGTAATAT
AGAATAAACCTAAACTAGTATATAAACTTTGATAAGAAAAAAAAAGTCAACAAATTGACCTATTA
TTTTGTTCAATCTAGGATTGCATGG
Found at i:49590 original size:19 final size:20
Alignment explanation
Indices: 49566--49616 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
49556 AATGACCAAT
49566 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
49585 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
49605 AAAATCGCAACG
1 AAAATCGCAACG
49617 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:49610 original size:20 final size:20
Alignment explanation
Indices: 49566--49843 Score: 148
Period size: 20 Copynumber: 13.6 Consensus size: 20
49556 AATGACCAAT
* *
49566 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
49585 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
49605 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
49625 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
49645 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
49666 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
49689 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
49709 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
49729 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
49749 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
49772 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
49792 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
49812 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
49832 AAAATCGCAACG
1 AAAATCGCAACG
49844 TTAAAAAGAA
Statistics
Matches: 204, Mismatches: 43, Indels: 23
0.76 0.16 0.09
Matches are distributed among these distances:
19 17 0.08
20 144 0.71
21 14 0.07
23 29 0.14
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:49778 original size:63 final size:63
Alignment explanation
Indices: 49711--49833 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 63
49701 CGATTGATTG
* * * * *
49711 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAGAA
49774 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAA
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAA
49834 AATCGCAACG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (63 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAGAA
Found at i:49780 original size:83 final size:83
Alignment explanation
Indices: 49670--49843 Score: 258
Period size: 83 Copynumber: 2.1 Consensus size: 83
49660 GCTTCCAAGT
* ** * * *
49670 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* * *
49735 GCAATGCGATTGAGAGAG
66 GCAACGCGATTGAGAAAA
49753 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
*
49818 GCAACGCGATTTAGAAAA
66 GCAACGCGATTGAGAAAA
49836 TCGCAACG
1 TCGCAACG
49844 TTAAAAAGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAACGCGATTGAGAAAA
Found at i:49853 original size:20 final size:20
Alignment explanation
Indices: 49830--49873 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
49820 AACGCGATTT
*
49830 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
49850 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
49870 AGAA
1 AGAA
49874 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:49962 original size:6 final size:6
Alignment explanation
Indices: 49951--49994 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
49941 GACACGTATT
49951 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
49995 CGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:50701 original size:6 final size:6
Alignment explanation
Indices: 50685--50854 Score: 333
Period size: 6 Copynumber: 28.5 Consensus size: 6
50675 TCTCGTCTCG
50685 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
50732 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
50780 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
50828 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
50855 AATACGTGTC
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.03
6 159 0.97
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:50965 original size:20 final size:20
Alignment explanation
Indices: 50942--51199 Score: 135
Period size: 20 Copynumber: 12.6 Consensus size: 20
50932 TTCTTTTGAC
50942 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
50962 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
50982 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
51002 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
51025 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
51045 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
51065 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
51088 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
51109 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
51127 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
51149 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
51169 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
51188 CGTTGCGATTTT
1 CGTTGCGATTTT
51200 ATTGGTCATT
Statistics
Matches: 187, Mismatches: 40, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.01
19 17 0.09
20 121 0.65
21 15 0.08
22 5 0.03
23 27 0.14
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:51025 original size:63 final size:63
Alignment explanation
Indices: 50952--51095 Score: 234
Period size: 63 Copynumber: 2.3 Consensus size: 63
50942 CGTTGCGATT
* * ** *
50952 TTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCATTGCGATTCTC
*
51015 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCATTGCGATTTTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCATTGCGATTCTC
51078 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
51096 ACTTGGAAGC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 75 1.00
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.35
Consensus pattern (63 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCATTGCGATTCTC
Found at i:51039 original size:43 final size:40
Alignment explanation
Indices: 50957--51072 Score: 142
Period size: 43 Copynumber: 2.8 Consensus size: 40
50947 CGATTTTCTA
* * *
50957 AATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTCTCTC
1 AATCGCATTGCGATTCTCTCAATCGCATTGCGACTCTCTC
* *
50997 AGTCGCATTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTC
1 AATCGCATTGCGATTCTC-TC--AATCGCATTGCGACTCTCTC
**
51040 AATCGCATTGCGATTCAATCAATCGCATTGCGA
1 AATCGCATTGCGATTCTCTCAATCGCATTGCGA
51073 TTTTCTTCTA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 28 0.44
41 2 0.03
42 2 0.03
43 32 0.50
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (40 bp):
AATCGCATTGCGATTCTCTCAATCGCATTGCGACTCTCTC
Found at i:51087 original size:43 final size:40
Alignment explanation
Indices: 50944--51095 Score: 133
Period size: 43 Copynumber: 3.6 Consensus size: 40
50934 CTTTTGACCG
* * ** *
50944 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCAATCAATCGCA
* * ** *
50984 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCATTGCGATTC-AATC--AATCGCA
* *
51027 TTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCAATCAATCGCA
*
51067 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TTC-TCTAAATCGCATTGCGA
51096 ACTTGGAAGC
Statistics
Matches: 90, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
40 37 0.41
41 2 0.02
42 4 0.04
43 47 0.52
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCAATCAATCGCA
Found at i:51189 original size:19 final size:20
Alignment explanation
Indices: 51149--51199 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
51139 TTCTTTTTAA
*
51149 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
51169 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
51188 CGTTGCGATTTT
1 CGTTGCGATTTT
51200 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:51749 original size:13 final size:13
Alignment explanation
Indices: 51728--51782 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
51718 AAGTTCGATA
*
51728 AATTCAAATACTT
1 AATTGAAATACTT
51741 AATTGAAATACTT
1 AATTGAAATACTT
* *
51754 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
51768 AATTGAAATACTT
1 AATTGAAATACTT
51781 AA
1 AA
51783 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:51864 original size:32 final size:33
Alignment explanation
Indices: 51768--51866 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
51758 AACTCAACAT
* * *
51768 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
51801 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
51834 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
51866 A
1 A
51867 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:51885 original size:21 final size:21
Alignment explanation
Indices: 51861--51900 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
51851 ACTTCAAGTT
51861 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
51882 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
51901 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:69051 original size:29 final size:31
Alignment explanation
Indices: 68991--69055 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
68981 GTTTTCAAAC
*
68991 AAAATATATTCAATTTTAAACTTTGTTCATT
1 AAAATATATTCAATTTTAAACTTTATTCATT
*
69022 AAAATAT-TT-AATTTTAAA-TATTATTTATT
1 AAAATATATTCAATTTTAAACT-TTATTCATT
69051 AAAAT
1 AAAAT
69056 TTAAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 21 0.68
30 2 0.06
31 7 0.23
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (31 bp):
AAAATATATTCAATTTTAAACTTTATTCATT
Found at i:73602 original size:2 final size:2
Alignment explanation
Indices: 73595--73619 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
73585 ACGTACATAC
73595 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
73620 AATTATCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:77360 original size:60 final size:62
Alignment explanation
Indices: 77296--77417 Score: 151
Period size: 61 Copynumber: 2.0 Consensus size: 62
77286 ATAGTTTAGG
* * * *
77296 GATGAAATTAAAATGTT-TAAAAGTTTAAGGA-ATAATTTAAAAT-AAGATTTATAATTTGGA
1 GATGAAATTAAAATATTCAAAAAATTTAAAGACA-AATTTAAAATGAAGATTTATAATTTGGA
* * *
77356 GATGAAATTGAAATATTCAAAAAATTTAAAGACAAATTTAAAATGAAGGTTTATAGTTTGGA
1 GATGAAATTAAAATATTCAAAAAATTTAAAGACAAATTTAAAATGAAGATTTATAATTTGGA
77418 AGCAATTAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 15 0.29
61 21 0.40
62 16 0.31
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (62 bp):
GATGAAATTAAAATATTCAAAAAATTTAAAGACAAATTTAAAATGAAGATTTATAATTTGGA
Found at i:83238 original size:22 final size:22
Alignment explanation
Indices: 83169--83239 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 22
83159 CTTATCTAAC
83169 TTTTAAA-AATTAAAATTTTTATA
1 TTTTAAATAATT--AATTTTTATA
* * *
83192 CTTTGATCATAATT-ATTTTAAATA
1 -TTTTA-AATAATTAATTTT-TATA
83216 TTTTAAATAATTAATTTTTATA
1 TTTTAAATAATTAATTTTTATA
83238 TT
1 TT
83240 CAAAATTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
22 11 0.30
23 14 0.38
24 7 0.19
25 1 0.03
26 4 0.11
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (22 bp):
TTTTAAATAATTAATTTTTATA
Found at i:84299 original size:36 final size:34
Alignment explanation
Indices: 84252--84362 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 34
84242 AAATCTTTCT
*
84252 GTTCGATTTGAATCGGAAGTGCCGATGTCTTCTTCC
1 GTTCGACTTGAATCGGAAGTG-CGATG-CTTCTTCC
* *
84288 GTTCGACTTGAATCGGAAGTGTCGATACCTCCTTCC
1 GTTCGACTTGAATCGGAAGTG-CGAT-GCTTCTTCC
* *
84324 GTTTGACTTGAATCGGAAGTGCGATGCTTTCTTTC
1 GTTCGACTTGAATCGGAAGTGCGATGC-TTCTTCC
84359 GTTC
1 GTTC
84363 TTCTTATTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
34 1 0.02
35 12 0.19
36 51 0.80
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (34 bp):
GTTCGACTTGAATCGGAAGTGCGATGCTTCTTCC
Found at i:92199 original size:21 final size:21
Alignment explanation
Indices: 92166--92219 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
92156 ATTTCCAGAT
*
92166 TCGCAACGCGAACTTCGACTA
1 TCGCAAAGCGAACTTCGACTA
* * *
92187 TCTCAATGCGAACTTGGACTA
1 TCGCAAAGCGAACTTCGACTA
92208 TCGCAAAGCGAA
1 TCGCAAAGCGAA
92220 TATATAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAAAGCGAACTTCGACTA
Found at i:92242 original size:6 final size:6
Alignment explanation
Indices: 92231--92264 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
92221 ATATAAATCG
*
92231 CGACCA CGACCA CGACAA CGACCA CGACC- CGACC
1 CGACCA CGACCA CGACCA CGACCA CGACCA CGACC
92265 CAAGACGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
CGACCA
Found at i:92922 original size:21 final size:21
Alignment explanation
Indices: 92898--92966 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
92888 TTTGGAATAA
*
92898 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * *
92919 ATCGCAATGCGATA-GTCAACT
1 ATCGCAACGCGA-ACTTCGACT
92940 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
92961 ATCGCA
1 ATCGCA
92967 TTACGATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:92987 original size:20 final size:20
Alignment explanation
Indices: 92962--93030 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
92952 ACTTCGACTA
*
92962 TCGCATTACGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
92982 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
*
93003 TCGCATTGCAATTTACATAT
1 TCGCATTGCGATTTACATAT
93023 TCGCATTG
1 TCGCATTG
93031 TGATAGTCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.05
20 22 0.55
21 14 0.35
22 2 0.05
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:93000 original size:41 final size:41
Alignment explanation
Indices: 92955--93038 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
92945 AACGCGAACT
*
92955 TCGACTATCGCATTACGATTTACATATTCGCATTGCGATAG
1 TCGACTATCGCATTACAATTTACATATTCGCATTGCGATAG
* *
92996 TCGACTATCGCATTGCAATTTACATATTCGCATTGTGATAG
1 TCGACTATCGCATTACAATTTACATATTCGCATTGCGATAG
93037 TC
1 TC
93039 CAAGTTCGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (41 bp):
TCGACTATCGCATTACAATTTACATATTCGCATTGCGATAG
Found at i:93008 original size:21 final size:21
Alignment explanation
Indices: 92915--93011 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
92905 CGCGAACTTG
*
92915 GACTATCGCAATGCGATAGTC
1 GACTATCGCATTGCGATAGTC
* ** *
92936 AACTATCGCAACGCGA-ACTTC
1 GACTATCGCATTGCGATA-GTC
*
92957 GACTATCGCATTACGAT--T-
1 GACTATCGCATTGCGATAGTC
*
92975 TACATATTCGCATTGCGATAGTC
1 GAC-TA-TCGCATTGCGATAGTC
92998 GACTATCGCATTGC
1 GACTATCGCATTGC
93012 AATTTACATA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 12 0.20
21 37 0.63
22 3 0.05
23 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
GACTATCGCATTGCGATAGTC
Found at i:93074 original size:21 final size:21
Alignment explanation
Indices: 93048--93208 Score: 204
Period size: 21 Copynumber: 7.7 Consensus size: 21
93038 CCAAGTTCGT
93048 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
* *
93069 AAGTTCGCGTTGCGATAGTCC
1 AAGTTCGCATTGCGATAGTCG
*
93090 AAGTTCGCATTGCAATAGTCG
1 AAGTTCGCATTGCGATAGTCG
* *
93111 -ACTATCGCATTGCGAT-TTAC-
1 AAGT-TCGCATTGCGATAGT-CG
*
93131 ATA-TTCGCATTGCGATAGTCC
1 A-AGTTCGCATTGCGATAGTCG
93152 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
93173 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
*
93194 AAGTTCGCGTTGCGA
1 AAGTTCGCATTGCGA
93209 ATCTGGAAAC
Statistics
Matches: 122, Mismatches: 11, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.14
21 104 0.85
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (21 bp):
AAGTTCGCATTGCGATAGTCG
Found at i:93150 original size:62 final size:62
Alignment explanation
Indices: 93072--93188 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
93062 ATAGTCGAAG
*
93072 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCAATAGTCG-ACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCAATAGTCGAACT-TCGCATTGCGATTTACATA
* *
93134 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCATTGCGAT
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCAATAGTCGAACTTCGCATTGCGAT
93189 AGTCGAAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
62 49 0.96
63 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCAATAGTCGAACTTCGCATTGCGATTTACATA
Found at i:94756 original size:16 final size:16
Alignment explanation
Indices: 94735--94765 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
94725 ATATCAGTGC
94735 ACATCACTAGTGGTGA
1 ACATCACTAGTGGTGA
94751 ACATCACTAGTGGTG
1 ACATCACTAGTGGTG
94766 CATATAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (16 bp):
ACATCACTAGTGGTGA
Found at i:100722 original size:27 final size:28
Alignment explanation
Indices: 100691--100757 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
100681 AGAGCAGATG
*
100691 ACACA-TTGGCAATTTCATCAGATTTTT
1 ACACACTTGACAATTTCATCAGATTTTT
**
100718 ACACAGCTTGATTATTTCATCAGATTTTT
1 ACACA-CTTGACAATTTCATCAGATTTTT
100747 ACACAGCTTGA
1 ACACA-CTTGA
100758 TTAAGAACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 5 0.14
29 30 0.86
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (28 bp):
ACACACTTGACAATTTCATCAGATTTTT
Found at i:100735 original size:29 final size:29
Alignment explanation
Indices: 100702--100760 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
100692 CACATTGGCA
100702 ATTTCATCAGATTTTTACACAGCTTGATT
1 ATTTCATCAGATTTTTACACAGCTTGATT
100731 ATTTCATCAGATTTTTACACAGCTTGATT
1 ATTTCATCAGATTTTTACACAGCTTGATT
100760 A
1 A
100761 AGAACACCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (29 bp):
ATTTCATCAGATTTTTACACAGCTTGATT
Found at i:110474 original size:17 final size:18
Alignment explanation
Indices: 110441--110474 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
110431 TCCAACAAAC
*
110441 TACATATAAAAATAATTT
1 TACATATAAAAACAATTT
110459 TACATAT-AAAACAATT
1 TACATATAAAAACAATT
110475 AAACACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (18 bp):
TACATATAAAAACAATTT
Found at i:110566 original size:24 final size:25
Alignment explanation
Indices: 110524--110570 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
110514 GTATATAACT
110524 TTATATATTATCAATAAATCAAATGA
1 TTATATATTATCAATAAAT-AAATGA
110550 TTATATATTAT-AA-AAATAAAT
1 TTATATATTATCAATAAATAAAT
110571 TTAATAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 4 0.19
25 2 0.10
26 11 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
TTATATATTATCAATAAATAAATGA
Found at i:111250 original size:25 final size:27
Alignment explanation
Indices: 111206--111264 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
111196 CAATAATAGT
* ** *
111206 AAAATATATATTAAATTATTTTTATAA
1 AAAATATATAATAAATTATTAATAGAA
111233 AAAATATA-AATAAA-TATTAATAGAA
1 AAAATATATAATAAATTATTAATAGAA
111258 AAAATAT
1 AAAATAT
111265 TTTTTCTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 15 0.54
26 5 0.18
27 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AAAATATATAATAAATTATTAATAGAA
Done.