Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007788.1 Hibiscus syriacus cultivar Beakdansim tig00110074_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: 141916
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:3331 original size:18 final size:18
Alignment explanation
Indices: 3280--3331 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
3270 TTTTGAATTC
3280 TTTTCTTTTCTTTTCT-TCT
1 TTTTC-TTTCTTTT-TGTCT
3299 TTCTTC-TTCTTTTTGTCT
1 TT-TTCTTTCTTTTTGTCT
3317 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
3332 CACTCCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 2 0.07
20 3 0.10
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTTCTTTCTTTTTGTCT
Found at i:28707 original size:17 final size:17
Alignment explanation
Indices: 28666--28737 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
28656 ATTCATGCAT
28666 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
28683 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
28701 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
28718 CTAGTTCATTTATTAGA
1 CTAGTTCATTAATTAAA
28735 CTA
1 CTA
28738 ACTCTTAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
17 33 0.72
18 13 0.28
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:29350 original size:22 final size:21
Alignment explanation
Indices: 29324--29364 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
29314 GTGTGAAAAT
29324 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
29346 TGATGGTTTTGATGATGAA
1 TGATGGTCTTGATGATGAA
29365 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.34, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:31034 original size:18 final size:18
Alignment explanation
Indices: 31006--31040 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30996 CATTGATTCA
31006 TGAAAGGTGATG-ACTCT
1 TGAAAGGTGATGTACTCT
31023 TGAAATGGTGATGTACTC
1 TGAAA-GGTGATGTACTC
31041 ATAAGTCACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (18 bp):
TGAAAGGTGATGTACTCT
Found at i:33883 original size:22 final size:21
Alignment explanation
Indices: 33857--33897 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
33847 CTGCGAAAAT
33857 TGATGG-TCTTGATGGATGAAGA
1 TGATGGCT-TTGAT-GATGAAGA
33879 TGATGGCTTTGATGATGAA
1 TGATGGCTTTGATGATGAA
33898 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 11 0.61
23 1 0.06
ACGTcount: A:0.27, C:0.05, G:0.34, T:0.34
Consensus pattern (21 bp):
TGATGGCTTTGATGATGAAGA
Found at i:34795 original size:10 final size:11
Alignment explanation
Indices: 34772--34810 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
34762 GATGATGGTA
34772 TAGCTCCAATT
1 TAGCTCCAATT
34783 TAGCTCC-ATT
1 TAGCTCCAATT
*
34793 TAGCTCCAATG
1 TAGCTCCAATT
34804 TAGCTCC
1 TAGCTCC
34811 CAAGTGTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (11 bp):
TAGCTCCAATT
Found at i:36079 original size:91 final size:90
Alignment explanation
Indices: 35911--36092 Score: 267
Period size: 91 Copynumber: 2.0 Consensus size: 90
35901 CCTAGAACAC
*
35911 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATTGGATCATTTAGGCGCCAAGATGA
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATTGGATCATTTAGGCGCCAAGATGA
35976 AGAGTTCTCTCCCTATTC-AGCCAAG
66 AGAGTTCTCTCCCTATTCGA-CCAAG
** * * * *
36001 CCATGTGTTTTGCATGTGATCAGCCCCCATGTTCCTTGCATGTGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCAT-TGGATCATTTAGGCGCCAAGATG
*
36066 AAGGGTTCTCTCCCTATTCGACCAAG
65 AAGAGTTCTCTCCCTATTCGACCAAG
36092 C
1 C
36093 ATCAACTACC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 35 0.43
91 46 0.56
92 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (90 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATTGGATCATTTAGGCGCCAAGATGA
AGAGTTCTCTCCCTATTCGACCAAG
Found at i:36818 original size:14 final size:14
Alignment explanation
Indices: 36799--36825 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36789 AACGTGCAAC
36799 AATACAAAAAGAAA
1 AATACAAAAAGAAA
36813 AATACAAAAAGAA
1 AATACAAAAAGAA
36826 GTGCAACTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
AATACAAAAAGAAA
Found at i:39811 original size:10 final size:10
Alignment explanation
Indices: 39796--39843 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
39786 TATTTTTTTT
39796 CAAAAAAAAA
1 CAAAAAAAAA
39806 CAAAAAAAAA
1 CAAAAAAAAA
****
39816 GGGCAAAAAA
1 CAAAAAAAAA
39826 CAAAAAAAAA
1 CAAAAAAAAA
39836 GCAAAAAA
1 -CAAAAAA
39844 TCCAAAATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
10 22 0.76
11 7 0.24
ACGTcount: A:0.81, C:0.10, G:0.08, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:39850 original size:20 final size:19
Alignment explanation
Indices: 39800--39843 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
39790 TTTTTTCAAA
39800 AAAAAACAAAAAAAAAGGGC
1 AAAAAACAAAAAAAAA-GGC
39820 AAAAAACAAAAAAAAA-GC
1 AAAAAACAAAAAAAAAGGC
39838 AAAAAA
1 AAAAAA
39844 TCCAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.33
20 16 0.67
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (19 bp):
AAAAAACAAAAAAAAAGGC
Found at i:50343 original size:13 final size:11
Alignment explanation
Indices: 50323--50443 Score: 86
Period size: 11 Copynumber: 10.2 Consensus size: 11
50313 AATATAGGCG
50323 TGATATGGTGA
1 TGATATGGTGA
50334 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
50347 TGATATAGGCG-
1 TGATAT-GGTGA
50358 TGATAATGGTGA
1 TGAT-ATGGTGA
50370 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
50383 TGATATAGGCG-
1 TGATAT-GGTGA
50394 TGATAATGGTGA
1 TGAT-ATGGTGA
50406 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
50419 TGATATAGGCG-
1 TGATAT-GGTGA
50430 TGATAATGGTGA
1 TGAT-ATGGTGA
50442 TG
1 TG
50444 GACAGATTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
11 33 0.37
12 24 0.27
13 29 0.33
14 3 0.03
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:50368 original size:23 final size:24
Alignment explanation
Indices: 50329--50443 Score: 82
Period size: 23 Copynumber: 4.8 Consensus size: 24
50319 GGCGTGATAT
50329 GGTGATGGAATATGGTGATGATATAG
1 GGTGAT-G-ATATGGTGATGATATAG
*
50355 GCGTGAT-A-ATGGTGATGGA-ATAT
1 G-GTGATGATATGGTGAT-GATATAG
* *
50378 GGTGATGATATAGGCG-TGATA-AT
1 GGTGATGATAT-GGTGATGATATAG
50401 GGTGATGGACTATGGTGATGATATAG
1 GGTGAT-GA-TATGGTGATGATATAG
50427 GCGTGAT-A-ATGGTGATG
1 G-GTGATGATATGGTGATG
50444 GACAGATTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
22 5 0.07
23 32 0.43
24 12 0.16
25 12 0.16
26 3 0.04
27 10 0.14
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (24 bp):
GGTGATGATATGGTGATGATATAG
Found at i:50446 original size:36 final size:36
Alignment explanation
Indices: 50308--50445 Score: 251
Period size: 36 Copynumber: 3.9 Consensus size: 36
50298 ATTTATAAGT
*
50308 GTGATAATATAGGCGTGAT-ATGGTGATGGAATATG
1 GTGATGATATAGGCGTGATAATGGTGATGGAATATG
50343 GTGATGATATAGGCGTGATAATGGTGATGGAATATG
1 GTGATGATATAGGCGTGATAATGGTGATGGAATATG
*
50379 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
1 GTGATGATATAGGCGTGATAATGGTGATGGAATATG
50415 GTGATGATATAGGCGTGATAATGGTGATGGA
1 GTGATGATATAGGCGTGATAATGGTGATGGA
50446 CAGATTGTAT
Statistics
Matches: 100, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
35 18 0.18
36 82 0.82
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
GTGATGATATAGGCGTGATAATGGTGATGGAATATG
Found at i:54367 original size:13 final size:12
Alignment explanation
Indices: 54348--54469 Score: 64
Period size: 11 Copynumber: 10.2 Consensus size: 12
54338 ATATAGGCGT
54348 GATATGGTGATG
1 GATATGGTGATG
54360 GAATATGGTGAT-
1 G-ATATGGTGATG
*
54372 GATATAGGCG-T-
1 GATAT-GGTGATG
54383 GATAATGGTGATG
1 GAT-ATGGTGATG
54396 GAATATGGTGAT-
1 G-ATATGGTGATG
*
54408 GATATAGGCG-T-
1 GATAT-GGTGATG
*
54419 GATAATGGTGATA
1 GAT-ATGGTGATG
54432 GACTATGGTGAT-
1 GA-TATGGTGATG
*
54444 GATATAGGCG-T-
1 GATAT-GGTGATG
54455 GATAATGGTGATG
1 GAT-ATGGTGATG
54468 GA
1 GA
54470 CAGATTGTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
11 32 0.36
12 23 0.26
13 31 0.35
14 3 0.03
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:54392 original size:23 final size:24
Alignment explanation
Indices: 54353--54467 Score: 82
Period size: 23 Copynumber: 4.8 Consensus size: 24
54343 GGCGTGATAT
54353 GGTGATGGAATATGGTGATGATATAG
1 GGTGAT-G-ATATGGTGATGATATAG
*
54379 GCGTGAT-A-ATGGTGATGGA-ATAT
1 G-GTGATGATATGGTGAT-GATATAG
* *
54402 GGTGATGATATAGGCG-TGATA-AT
1 GGTGATGATAT-GGTGATGATATAG
54425 GGTGATAGACTATGGTGATGATATAG
1 GGTGAT-GA-TATGGTGATGATATAG
54451 GCGTGAT-A-ATGGTGATG
1 G-GTGATGATATGGTGATG
54468 GACAGATTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
22 5 0.07
23 32 0.43
24 12 0.16
25 12 0.16
26 3 0.04
27 10 0.14
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.30
Consensus pattern (24 bp):
GGTGATGATATGGTGATGATATAG
Found at i:54398 original size:36 final size:36
Alignment explanation
Indices: 54330--54469 Score: 246
Period size: 36 Copynumber: 3.9 Consensus size: 36
54320 ATTTATAAGT
*
54330 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
54365 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
54401 TGGTGATGATATAGGCGTGATAATGGTGATAGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
54437 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
54470 CAGATTGTAT
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 20 0.20
36 80 0.80
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:54853 original size:19 final size:20
Alignment explanation
Indices: 54806--54856 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
54796 GAAACCCCTT
**
54806 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
54826 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
54845 TGAAGATACATG
1 TGAAAATACATG
54857 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:58465 original size:24 final size:21
Alignment explanation
Indices: 58431--58473 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
58421 TCCACAAGAC
*
58431 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
58453 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
58474 ATGTGCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:60329 original size:91 final size:91
Alignment explanation
Indices: 60174--60356 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
60164 CCTAGAACAC
*
60174 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
60239 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * * *
60265 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
*
60330 AAGAGTTCTCTCCCTATTTGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
60356 C
1 C
60357 ATCAACTACC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:90412 original size:5 final size:5
Alignment explanation
Indices: 90398--90431 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
90388 GTGCTTCAAC
90398 TTTC- TTTCT TTTCT TTTCT TTTCT TTT-T TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
90432 CCTCTTTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.29
5 20 0.71
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:90437 original size:15 final size:15
Alignment explanation
Indices: 90398--90438 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
90388 GTGCTTCAAC
90398 TTTCTT-TCTTTTCT
1 TTTCTTCTCTTTTCT
*
90412 TTTCTTTTCTTTT-T
1 TTTCTTCTCTTTTCT
90426 TTTCTTCCTCTTT
1 TTTCTT-CTCTTT
90439 GAGTGCTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTCTCTTTTCT
Found at i:90475 original size:22 final size:25
Alignment explanation
Indices: 90426--90479 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 25
90416 TTTTCTTTTT
90426 TTTCTTCCTCTTTGAGTGCTTTCAA
1 TTTCTTCCTCTTTGAGTGCTTTCAA
*
90451 TTTCTT-CT-TTTGAGTGCTTTCAT
1 TTTCTTCCTCTTTGAGTGCTTTCAA
90474 TTTCTT
1 TTTCTT
90480 TGCTGGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 20 0.71
24 2 0.07
25 6 0.21
ACGTcount: A:0.09, C:0.20, G:0.11, T:0.59
Consensus pattern (25 bp):
TTTCTTCCTCTTTGAGTGCTTTCAA
Found at i:96906 original size:28 final size:26
Alignment explanation
Indices: 96853--96909 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
96843 TTCCTTGCTT
* *
96853 TTTCTTCTTTTGAGTGCTGGATTTTC
1 TTTCTTCTTTTGAGTGCTGCAATTTC
*
96879 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTT-GAGTGCTGCAATTTC
96907 TTT
1 TTT
96910 TTTTTTCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 7 0.27
28 15 0.58
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.60
Consensus pattern (26 bp):
TTTCTTCTTTTGAGTGCTGCAATTTC
Found at i:99528 original size:13 final size:13
Alignment explanation
Indices: 99506--99535 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
99496 ACTAAACACC
99506 TTTC-ACATACCT
1 TTTCAACATACCT
99518 TTTCAACATACCT
1 TTTCAACATACCT
99531 TTTCA
1 TTTCA
99536 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:105151 original size:24 final size:21
Alignment explanation
Indices: 105116--105158 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
105106 GGCTCATTCT
*
105116 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
105139 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
105159 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:116866 original size:13 final size:13
Alignment explanation
Indices: 116848--116874 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
116838 TGGCCAAAGA
116848 TGAAAAGGTATGT
1 TGAAAAGGTATGT
116861 TGAAAAGGTATGT
1 TGAAAAGGTATGT
116874 T
1 T
116875 AAAGGTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:121930 original size:19 final size:20
Alignment explanation
Indices: 121906--121948 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
121896 GTGCTACAAC
* *
121906 AAAAAAAC-AACAGGAAAGA
1 AAAAAAACAAAAAGAAAAGA
121925 AAAAAAACAAAAAGAAAAGA
1 AAAAAAACAAAAAGAAAAGA
121945 AAAA
1 AAAA
121949 GACTCCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAGAAAAGA
Found at i:122034 original size:24 final size:24
Alignment explanation
Indices: 121979--122027 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
121969 AGTGCAAAAG
* *
121979 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
*
122003 AAAGCAAAGAAAAAG-TGAAGCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
122026 AA
1 AA
122028 TTGCAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAGCAA
Found at i:123908 original size:686 final size:687
Alignment explanation
Indices: 122593--123974 Score: 2577
Period size: 686 Copynumber: 2.0 Consensus size: 687
122583 ACTCATTGGC
*
122593 GAAATGATGAGAATATTTCGTGAAGAGTTCGATGCTCTTCATGAAAAGATAGATCGGTGCCAGGA
1 GAAATGATGAGAATATTTCGTGAAGAGTTCGATGCTCTTCATGAAAAGATAGATCGGCGCCAGGA
122658 TCTATCACCAGGCCGTAATAATAGAGTTCCTAGAAGACAACAACCACCACCCCCTCCAGAAGAAG
66 TCTATCACCAGGCCGTAATAATAGAGTTCCTAGAAG--AACAACCACCACCCCCTCCAGAAGAAG
122723 AAGTTCAAGAAAATTTTGACGAGGGAGAACAAGTAGCATTCCAAGTCCCTAGACGTGCCATTGTT
129 AAGTTCAAGAAAATTTTGACGAGGGAGAACAAGTAGCATTCCAAGTCCCTAGACGTGCCATTGTT
122788 GATGATAATCTGAGTAATATCAAGATCAAAATTCCTCAATTTCAAGGAAAAACTGATCCTGAAGC
194 GATGATAATCTGAGTAATATCAAGATCAAAATTCCTCAATTTCAAGGAAAAACTGATCCTGAAGC
122853 TTATCTCGAATGGGAAAGCAAAGTGGAACATGTTTTTAGTTGCCACAACTATTCCAAAATGAAGA
259 TTATCTCGAATGGGAAAGCAAAGTGGAACATGTTTTTAGTTGCCACAACTATTCCAAAATGAAGA
122918 AAGTGAGATTGGCAGCCATGGAGTTCAAGACTATGCTTTAATATGGTGAGATCAACTTACTTTGA
324 AAGTGAGATTGGCAGCCATGGAGTTCAAGACTATGCTTTAATATGGTGAGATCAACTTACTTTGA
122983 ACCAAAGGAGGAATGGAGAACGACCGGTCTCAACTTGGCTTGAAATGAAAGGTATTATGCGGAAA
389 ACCAAAGGAGGAATGGAGAACGACCGGTCTCAACTTGGCTTGAAATGAAAGGTATTATGCGGAAA
123048 CGATTCATTCCTGTTCACTATCATCGTGACTTGTTTCAAAAGTTACAGAATCTAAAACAAGGCCA
454 CGATTCATTCCTGTTCACTATCATCGTGACTTGTTTCAAAAGTTACAGAATCTAAAACAAGGCCA
123113 TAGGAGTGTGGAGGACTATTATAAAGAGATGGAAGTGGCAATGATCCAAGTCAACATTGAGGAGG
519 TAGGAGTGTGGAGGACTATTATAAAGAGATGGAAGTGGCAATGATCCAAGTCAACATTGAGGAGG
*
123178 ATCTTGAAGCAACTATGGCGAGATTCCTTGCTGGACTTAATCCCGAAATTGCCAATACCTTGGAA
584 ATCTTGAAGCAACTATGGCGAGATTCCTTACTGGACTTAATCCCGAAATTGCCAATACCTTGGAA
* *
123243 TTGTATCATTATATCAAAATGGATGAGATGGTGCAAATG
649 TTGTATCATTACATCAAAATGGATAAGATGGTGCAAATG
* * *
123282 GAAATGATGAGAATGTTTCGTGAAGAGTTTGATGCTCTTTATGAAAAGATAGATCGGCGCCAGGA
1 GAAATGATGAGAATATTTCGTGAAGAGTTCGATGCTCTTCATGAAAAGATAGATCGGCGCCAGGA
*
123347 TCTATCACCAGTCCGTAATAATAGAGTTCCTAGAAG-ACAACCACCACCCCCTCCAGAAGAAGAA
66 TCTATCACCAGGCCGTAATAATAGAGTTCCTAGAAGAACAACCACCACCCCCTCCAGAAGAAGAA
*
123411 GTTCAAGAAAATTTTGACGAGGGAGAACAAGTAGGATTCCAAGTCCCTAGACGTGCCATTGTTGA
131 GTTCAAGAAAATTTTGACGAGGGAGAACAAGTAGCATTCCAAGTCCCTAGACGTGCCATTGTTGA
*
123476 TGATAATCTGAGTAATATCAAGATCAAAATTCCTCAATTTCAAGGAAAAACTTATCCTGAAGCTT
196 TGATAATCTGAGTAATATCAAGATCAAAATTCCTCAATTTCAAGGAAAAACTGATCCTGAAGCTT
* * *
123541 ATCTCTAATGGGAAAGCAAAGTGGAACATGTTTTTAGTTTCCACAACTATTCCGAAATGAAGAAA
261 ATCTCGAATGGGAAAGCAAAGTGGAACATGTTTTTAGTTGCCACAACTATTCCAAAATGAAGAAA
123606 GTGAGATTGGCAGCCATGGAGTTCAAGACTATGCTTTAATATGGTGAGATCAACTTACTTTGAAC
326 GTGAGATTGGCAGCCATGGAGTTCAAGACTATGCTTTAATATGGTGAGATCAACTTACTTTGAAC
123671 CAAAGGAGGAATGGAGAACGACCGGTCTCAACTTGGCTTGAAATGAAAGGTATTATGCGGAAACG
391 CAAAGGAGGAATGGAGAACGACCGGTCTCAACTTGGCTTGAAATGAAAGGTATTATGCGGAAACG
*
123736 ATTCATTCCTGTTCACTATCATCGTGACTTGTTTCAAAAGTTACAGAATCTGAAACAAGGCCATA
456 ATTCATTCCTGTTCACTATCATCGTGACTTGTTTCAAAAGTTACAGAATCTAAAACAAGGCCATA
*
123801 GGAGTGTGGAGGACTATTATAAAGAGATGGAAGTGGCAATGATCCGAGTCAACATTGAGGAGGAT
521 GGAGTGTGGAGGACTATTATAAAGAGATGGAAGTGGCAATGATCCAAGTCAACATTGAGGAGGAT
*
123866 CTTGAAGCAACTATGTCGAGATTCCTTACTGGACTTAATCCCGAAATTGCCAATACCTTGGAATT
586 CTTGAAGCAACTATGGCGAGATTCCTTACTGGACTTAATCCCGAAATTGCCAATACCTTGGAATT
*
123931 GTATCATTACATCGAAATGGATAAGATGGTGCAAATG
651 GTATCATTACATCAAAATGGATAAGATGGTGCAAATG
*
123968 GCAATGA
1 GAAATGA
123975 AAATTGAAAG
Statistics
Matches: 675, Mismatches: 18, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
686 579 0.86
689 96 0.14
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (687 bp):
GAAATGATGAGAATATTTCGTGAAGAGTTCGATGCTCTTCATGAAAAGATAGATCGGCGCCAGGA
TCTATCACCAGGCCGTAATAATAGAGTTCCTAGAAGAACAACCACCACCCCCTCCAGAAGAAGAA
GTTCAAGAAAATTTTGACGAGGGAGAACAAGTAGCATTCCAAGTCCCTAGACGTGCCATTGTTGA
TGATAATCTGAGTAATATCAAGATCAAAATTCCTCAATTTCAAGGAAAAACTGATCCTGAAGCTT
ATCTCGAATGGGAAAGCAAAGTGGAACATGTTTTTAGTTGCCACAACTATTCCAAAATGAAGAAA
GTGAGATTGGCAGCCATGGAGTTCAAGACTATGCTTTAATATGGTGAGATCAACTTACTTTGAAC
CAAAGGAGGAATGGAGAACGACCGGTCTCAACTTGGCTTGAAATGAAAGGTATTATGCGGAAACG
ATTCATTCCTGTTCACTATCATCGTGACTTGTTTCAAAAGTTACAGAATCTAAAACAAGGCCATA
GGAGTGTGGAGGACTATTATAAAGAGATGGAAGTGGCAATGATCCAAGTCAACATTGAGGAGGAT
CTTGAAGCAACTATGGCGAGATTCCTTACTGGACTTAATCCCGAAATTGCCAATACCTTGGAATT
GTATCATTACATCAAAATGGATAAGATGGTGCAAATG
Found at i:128418 original size:26 final size:26
Alignment explanation
Indices: 128389--128451 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
128379 GAGTGCAAAA
128389 AGAAAAGACA-AAAAGAAAAAAAATTC
1 AGAAAAGA-AGAAAAGAAAAAAAATTC
*
128415 AGAAAAGAAGAAAAGAAAAAAAGTTC
1 AGAAAAGAAGAAAAGAAAAAAAATTC
128441 A-AAAAG-AGAAA
1 AGAAAAGAAGAAA
128452 GCAAGCCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
24 5 0.14
25 6 0.17
26 24 0.69
ACGTcount: A:0.73, C:0.05, G:0.16, T:0.06
Consensus pattern (26 bp):
AGAAAAGAAGAAAAGAAAAAAAATTC
Found at i:138007 original size:72 final size:72
Alignment explanation
Indices: 137888--138036 Score: 237
Period size: 72 Copynumber: 2.1 Consensus size: 72
137878 ATGCAAGCTT
* *
137888 GAAGGTAGCTCAACGCACATCCAAGGCTGCTGATGTAAGGCACTGTACCTTGTCAATTGATTGTG
1 GAAGGTAGCTCAACGCACATCCAAGGCTACTGATGTAAGACACTGTACCTTGTCAATTGATTGTG
137953 GATCTAG
66 GATCTAG
* * *
137960 GAAGGTAGCTCAACTCA-TTCCGAGGCTACTGATGTAAGACACTTGTACCTTGTCAATTGATTGT
1 GAAGGTAGCTCAACGCACATCCAAGGCTACTGATGTAAGACAC-TGTACCTTGTCAATTGATTGT
138024 GGATCTAG
65 GGATCTAG
138032 GAAGG
1 GAAGG
138037 AAGCAAAACA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 21 0.30
72 50 0.70
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (72 bp):
GAAGGTAGCTCAACGCACATCCAAGGCTACTGATGTAAGACACTGTACCTTGTCAATTGATTGTG
GATCTAG
Found at i:140799 original size:16 final size:16
Alignment explanation
Indices: 140778--140809 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
140768 TAGTTAGCTC
140778 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
140794 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
140810 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Done.