Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000627.1 Hibiscus syriacus cultivar Beakdansim tig00001216_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: 50480
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1117 original size:4 final size:4
Alignment explanation
Indices: 1108--1160 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
1098 TAAAATAGTA
* *
1108 AAAT AAAT AAAT AAAT AAAGT AAAA AAAC AACAT AAAT AAA- AAATT AAAT
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AA-AT AAAT AAAT AAA-T AAAT
1158 AAA
1 AAA
1161 CATAAGTACA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
3 3 0.07
4 29 0.69
5 10 0.24
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:1294 original size:21 final size:22
Alignment explanation
Indices: 1270--1310 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1260 ATGCAAAATT
1270 GAAATT-ATAGT-AGCTAAATCA
1 GAAATTAATAGTGA-CTAAATCA
1291 GAAATTAATAGTGACTAAAT
1 GAAATTAATAGTGACTAAAT
1311 TAAAATAAAA
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:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (22 bp):
GAAATTAATAGTGACTAAATCA
Found at i:1316 original size:21 final size:20
Alignment explanation
Indices: 1265--1316 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
1255 CTAAAATGCA
*
1265 AAATTGAAATTATAGTAGCT
1 AAATTAAAATTATAGTAGCT
*
1285 AAATCAGAAATTAATAGT-GACT
1 AAATTA-AAATT-ATAGTAG-CT
1307 AAATTAAAAT
1 AAATTAAAAT
1317 AAAACAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.15
21 10 0.38
22 12 0.46
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.31
Consensus pattern (20 bp):
AAATTAAAATTATAGTAGCT
Found at i:1526 original size:106 final size:107
Alignment explanation
Indices: 1414--1616 Score: 284
Period size: 106 Copynumber: 1.9 Consensus size: 107
1404 TGGAATGAGA
* * *
1414 TTTACCAAAAAATATAAAGCATGCATGTAAATGAGAAAATTATGAAAACAGTCCCTAAT-GACTA
1 TTTACCAAAAAATACAAAGCATGCATATAAATGAGAAAATTAT-AAAACAGTCCCTAATAGACCA
1478 TTTTGCAAAAACACAGCAAA-TTTGGGGGACATGGACTGATAT
65 TTTTGCAAAAACACAGCAAAGTTTGGGGGACATGGACTGATAT
* * *
1520 TTTACCAAAAATTACAAAGCATTCATATAAATGGGAAAATTATAAAACAGTCCCTAATAGCGACC
1 TTTACCAAAAAATACAAAGCATGCATATAAATGAGAAAATTATAAAACAGTCCCTAATA--GACC
* * *
1585 ATTTTGTAAAAATACAGGAAAGTTTGGGGGAC
64 ATTTTGCAAAAACACAGCAAAGTTTGGGGGAC
1617 TTAAAATGTG
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
105 15 0.18
106 38 0.45
108 21 0.25
109 10 0.12
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (107 bp):
TTTACCAAAAAATACAAAGCATGCATATAAATGAGAAAATTATAAAACAGTCCCTAATAGACCAT
TTTGCAAAAACACAGCAAAGTTTGGGGGACATGGACTGATAT
Found at i:2316 original size:26 final size:26
Alignment explanation
Indices: 2286--2346 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
2276 TCGTGGCTCT
*
2286 CCTCTGGTTGGTGAAAATATCGACAA
1 CCTCTGGTTGGTGAAAAGATCGACAA
* *
2312 CCTCTGGTTGGTGCAAAGATCGACAG
1 CCTCTGGTTGGTGAAAAGATCGACAA
*
2338 TCTCTGGTT
1 CCTCTGGTT
2347 AGGGGAATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (26 bp):
CCTCTGGTTGGTGAAAAGATCGACAA
Found at i:6717 original size:20 final size:20
Alignment explanation
Indices: 6679--6717 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6669 ACGTGTTTAG
*
6679 TTTACTTATAATTGTATATC
1 TTTACTTATAATTGGATATC
6699 TTTA-TTATAATTTGGATAT
1 TTTACTTATAA-TTGGATAT
6718 TGGTGGGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (20 bp):
TTTACTTATAATTGGATATC
Found at i:13091 original size:26 final size:26
Alignment explanation
Indices: 13037--13092 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
13027 GTTGAGTGAA
* * * *
13037 AAAAAATTCAATGTATAGAATTTAGT
1 AAAAAATTAAATGTAGAGAATTCAAT
*
13063 AAAAAATTAAATGTAGAGAGTTCAAT
1 AAAAAATTAAATGTAGAGAATTCAAT
13089 AAAA
1 AAAA
13093 TTTTTGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (26 bp):
AAAAAATTAAATGTAGAGAATTCAAT
Found at i:15261 original size:29 final size:29
Alignment explanation
Indices: 15217--15328 Score: 188
Period size: 29 Copynumber: 3.9 Consensus size: 29
15207 TACCGGGGGT
*
15217 AGGTCGCCATGTACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
**
15246 AGGTCGCCATGCACGCTTGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
15275 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
15304 AGGTCGCCATGCACGCCCTGCGACC
1 AGGTCGCCATGCACGCCCGGCGACC
15329 TACCCCACGA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.20, C:0.42, G:0.28, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:15357 original size:10 final size:10
Alignment explanation
Indices: 15342--15434 Score: 68
Period size: 10 Copynumber: 9.3 Consensus size: 10
15332 CCCACGACCT
15342 CCATGCACGC
1 CCATGCACGC
15352 CCATGCACGC
1 CCATGCACGC
15362 CCATGCACGC
1 CCATGCACGC
*
15372 CCA-ACGAC-C
1 CCATGC-ACGC
*
15381 TCCATGCATGC
1 -CCATGCACGC
* *
15392 CCAGGCACGT
1 CCATGCACGC
*
15402 CCA-ACGAC-C
1 CCATGC-ACGC
*
15411 TCCATGCACGG
1 -CCATGCACGC
15422 CCATGCACGC
1 CCATGCACGC
15432 CCA
1 CCA
15435 ACGACCTCCA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
9 3 0.05
10 58 0.91
11 3 0.05
ACGTcount: A:0.23, C:0.47, G:0.19, T:0.11
Consensus pattern (10 bp):
CCATGCACGC
Found at i:15386 original size:30 final size:30
Alignment explanation
Indices: 15352--15454 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
15342 CCATGCACGC
15352 CCATGCACGCCCATGCACGCCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
* * *
15382 CCATGCATGCCCAGGCACGTCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
*
15412 CCATGCACGGCCATGCACGCCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
15442 CCATGCACGCCCA
1 CCATGCACGCCCA
15455 GCTCGCCAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.23, C:0.48, G:0.18, T:0.11
Consensus pattern (30 bp):
CCATGCACGCCCATGCACGCCCAACGACCT
Found at i:16094 original size:21 final size:21
Alignment explanation
Indices: 16069--16112 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16059 AATTTAGTTA
16069 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
16090 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
16111 AT
1 AT
16113 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:16126 original size:28 final size:28
Alignment explanation
Indices: 16089--16142 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
16079 TAGTATAAAT
*
16089 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
16117 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
16143 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:19271 original size:11 final size:11
Alignment explanation
Indices: 19255--19402 Score: 52
Period size: 11 Copynumber: 12.6 Consensus size: 11
19245 AATGATTTGA
19255 TAGTAATGATT
1 TAGTAATGATT
19266 TAGTAATGATT
1 TAGTAATGATT
* *
19277 AGTAATAATGAAAT
1 --TAGTAATG-ATT
* * *
19291 TA-TTATTAAT
1 TAGTAATGATT
19301 TATGT-ATGATT
1 TA-GTAATGATT
19312 TGATAGTAATGATT
1 T-A--GTAATGATT
19326 TAGTAATGATT
1 TAGTAATGATT
* *
19337 AGTAATAATGAAAT
1 --TAGTAATG-ATT
* * *
19351 TATTATTAATT
1 TAGTAATGATT
*
19362 T-TTAATGATTT
1 TAGTAATGA-TT
19373 GATAGTAATGATT
1 --TAGTAATGATT
19386 TAGTAATGA-T
1 TAGTAATGATT
19396 TAGTAAT
1 TAGTAAT
19403 AATGAAATTA
Statistics
Matches: 106, Mismatches: 16, Indels: 31
0.69 0.10 0.20
Matches are distributed among these distances:
10 18 0.17
11 42 0.40
12 9 0.08
13 20 0.19
14 17 0.16
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:19273 original size:60 final size:60
Alignment explanation
Indices: 19202--19684 Score: 762
Period size: 60 Copynumber: 8.2 Consensus size: 60
19192 GTATTTATAA
* *
19202 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
19262 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
*
19322 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
19382 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
*
19442 GACTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
19502 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
*
19562 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-T-T-T-A-ATGAT--T--T
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
* * *
19613 GA--TAGTAATGATTAGTAATAAT-AATTTATTATTAA-TATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
19670 GATTTAGTAATGATT
1 GATTTAGTAATGATT
19685 TGATAGTAAT
Statistics
Matches: 399, Mismatches: 9, Indels: 31
0.91 0.02 0.07
Matches are distributed among these distances:
47 1 0.00
48 13 0.03
49 21 0.05
51 4 0.01
52 1 0.00
53 5 0.01
55 5 0.01
56 1 0.00
57 4 0.01
58 1 0.00
59 14 0.04
60 325 0.81
61 4 0.01
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
Found at i:19339 original size:21 final size:20
Alignment explanation
Indices: 19315--19403 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 20
19305 TATGATTTGA
19315 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
19336 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * * *
19354 TATTAATTTTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
19375 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
19396 TAGTAATA
1 TAGTAATA
19404 ATGAAATTAT
Statistics
Matches: 48, Mismatches: 14, Indels: 13
0.64 0.19 0.17
Matches are distributed among these distances:
18 12 0.25
19 2 0.04
20 5 0.10
21 22 0.46
22 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:19451 original size:11 final size:10
Alignment explanation
Indices: 19435--19582 Score: 51
Period size: 10 Copynumber: 14.7 Consensus size: 10
19425 TATGATTTGA
19435 TAGTAATGACT
1 TAGTAATGA-T
19446 TAGTAATGAT
1 TAGTAATGAT
*
19456 TAGTAAT-AA
1 TAGTAATGAT
* *
19465 T-GAAATTAT
1 TAGTAATGAT
* *
19474 TATTAATTAT
1 TAGTAATGAT
*
19484 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
19495 TAGTAATGATT
1 TAGTAATGA-T
19506 TAGTAATGAT
1 TAGTAATGAT
*
19516 TAGTAAT-AA
1 TAGTAATGAT
* *
19525 T-GAAATTAT
1 TAGTAATGAT
* *
19534 TATTAATTAT
1 TAGTAATGAT
*
19544 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
19555 TAGTAATGATT
1 TAGTAATGA-T
19566 TAGTAATGAT
1 TAGTAATGAT
19576 TAGTAAT
1 TAGTAAT
19583 AATGAAATTA
Statistics
Matches: 105, Mismatches: 16, Indels: 33
0.68 0.10 0.21
Matches are distributed among these distances:
8 8 0.08
9 14 0.13
10 44 0.42
11 35 0.33
12 4 0.04
ACGTcount: A:0.40, C:0.01, G:0.16, T:0.44
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:19655 original size:21 final size:22
Alignment explanation
Indices: 19631--19700 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 22
19621 TGATTAGTAA
19631 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
19652 TAATGATTTGATATTAATGATTT
1 TAATAATTTGATATTAATGA-TT
* *
19675 AGTAATGATTTGATAGTAATGATT
1 --TAATAATTTGATATTAATGATT
19699 TA
1 TA
19701 CGACTTGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 15 0.36
22 4 0.10
23 2 0.05
24 2 0.05
25 19 0.45
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:19658 original size:48 final size:49
Alignment explanation
Indices: 19566--19680 Score: 187
Period size: 48 Copynumber: 2.3 Consensus size: 49
19556 AGTAATGATT
*
19566 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
19615 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
19663 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
19681 GATTTGATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 34 0.55
49 28 0.45
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:19668 original size:14 final size:14
Alignment explanation
Indices: 19652--19699 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
19642 TATTAATATT
*
19652 TAATGATTTGATAT
1 TAATGATTTGATAG
19666 TAATGA-TT--TAG
1 TAATGATTTGATAG
19677 TAATGATTTGATAG
1 TAATGATTTGATAG
19691 TAATGATTT
1 TAATGATTT
19700 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:19784 original size:7 final size:7
Alignment explanation
Indices: 19772--19798 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
19762 ATTTTTGGTT
19772 CAATGAA
1 CAATGAA
19779 CAATGAA
1 CAATGAA
19786 CAATGAA
1 CAATGAA
19793 CAATGA
1 CAATGA
19799 TTTAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CAATGAA
Found at i:19926 original size:14 final size:13
Alignment explanation
Indices: 19907--19971 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
19897 TTTAAATATT
19907 TAATGATTTGATAC
1 TAATGATTT-ATAC
19921 TAATGA-TT-TAC
1 TAATGATTTATAC
*
19932 TAAT--TAT-TAC
1 TAATGATTTATAC
19942 TAATGATTTAATAC
1 TAATGATTT-ATAC
*
19956 TAATTATTTGATAC
1 TAATGATTT-ATAC
19970 TA
1 TA
19972 GTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.19
11 7 0.17
12 2 0.05
13 2 0.05
14 23 0.55
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATGATTTATAC
Found at i:19943 original size:10 final size:11
Alignment explanation
Indices: 19918--19951 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
19908 AATGATTTGA
19918 TACTAATGATT
1 TACTAATGATT
*
19929 TACTAATTA-T
1 TACTAATGATT
19939 TACTAATGATT
1 TACTAATGATT
19950 TA
1 TA
19952 ATACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:19961 original size:21 final size:21
Alignment explanation
Indices: 19918--19961 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
19908 AATGATTTGA
* *
19918 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
19939 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
19960 TA
1 TA
19962 TTTGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:19978 original size:17 final size:17
Alignment explanation
Indices: 19956--19988 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19946 GATTTAATAC
19956 TAATTATTTGATACTAG
1 TAATTATTTGATACTAG
19973 TAATTATTTGATACTA
1 TAATTATTTGATACTA
19989 AACATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
TAATTATTTGATACTAG
Found at i:22158 original size:15 final size:14
Alignment explanation
Indices: 22135--22165 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
22125 TACAACACTA
22135 AACTTTAATATAAT
1 AACTTTAATATAAT
22149 AACTTATAATATAAT
1 AACTT-TAATATAAT
22164 AA
1 AA
22166 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:22173 original size:16 final size:16
Alignment explanation
Indices: 22140--22186 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
22130 CACTAAACTT
*
22140 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
22155 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
22171 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
22187 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:22296 original size:32 final size:34
Alignment explanation
Indices: 22221--22302 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
22211 CCAAACCCTT
* *
22221 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
22254 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
22287 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
22303 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:22308 original size:12 final size:12
Alignment explanation
Indices: 22283--22335 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
22273 TTTTTCATTA
*
22283 TAATATACT-AC
1 TAATAAACTAAC
*
22294 TAATAAACTTAC
1 TAATAAACTAAC
22306 TAACTAAAACTAAC
1 TAA-T-AAACTAAC
22320 TAATAAACTAAC
1 TAATAAACTAAC
22332 TAAT
1 TAAT
22336 TTTTTATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 8 0.22
12 17 0.46
13 2 0.05
14 10 0.27
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (12 bp):
TAATAAACTAAC
Found at i:22452 original size:45 final size:48
Alignment explanation
Indices: 22362--22452 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 48
22352 CAACAAACAA
22362 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
*
22410 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT
22453 AACTATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
44 12 0.29
45 11 0.27
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
Found at i:22521 original size:41 final size:40
Alignment explanation
Indices: 22433--22521 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
22423 TTAACAAAAC
* *
22433 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
22474 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
22515 AAACTAA
1 AAACTAA
22522 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:22586 original size:16 final size:18
Alignment explanation
Indices: 22557--22595 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
22547 ACTAATTAAC
*
22557 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
22575 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
22591 ATTTA
1 ATTTA
22596 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:22878 original size:50 final size:48
Alignment explanation
Indices: 22807--22913 Score: 173
Period size: 49 Copynumber: 2.2 Consensus size: 48
22797 TAGGATCACA
*
22807 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTAT-T
22856 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
22904 TGGC-TGCATG
1 TGGCATGCATG
22914 TGCATGCATG
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
47 6 0.11
48 5 0.09
49 32 0.57
50 13 0.23
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (48 bp):
TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
Found at i:23016 original size:29 final size:29
Alignment explanation
Indices: 22934--23010 Score: 154
Period size: 29 Copynumber: 2.7 Consensus size: 29
22924 GTCTGCAGGG
22934 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
22963 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
22992 GGCGACCTACAAGGTCGCC
1 GGCGACCTACAAGGTCGCC
23011 CAGACTGCGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.23, C:0.32, G:0.31, T:0.13
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:23090 original size:52 final size:52
Alignment explanation
Indices: 23034--23150 Score: 155
Period size: 52 Copynumber: 2.2 Consensus size: 52
23024 CTCTATTGGC
* * * *
23034 TGGCTTGCATGGCGACCTCTCCGTTGG-CTGGCTCGTCTGCATGGTGAGTATA
1 TGGCTTGTATGGC-ACCTCTCCATGGGTATGGCTCGTCTGCATGGTGAGTATA
* * *
23086 TGGCTTGTATGGCTCGTCTGCATGGGTATGGCTCGTCTGCATGGTGAGTATA
1 TGGCTTGTATGGCACCTCTCCATGGGTATGGCTCGTCTGCATGGTGAGTATA
23138 TGGCTTGTATGGC
1 TGGCTTGTATGGC
23151 TCGTATGTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 8 0.14
52 49 0.86
ACGTcount: A:0.12, C:0.21, G:0.34, T:0.33
Consensus pattern (52 bp):
TGGCTTGTATGGCACCTCTCCATGGGTATGGCTCGTCTGCATGGTGAGTATA
Found at i:23142 original size:24 final size:19
Alignment explanation
Indices: 23092--23129 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
23082 TATATGGCTT
23092 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
23111 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
23130 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (19 bp):
GTATGGCTCGTCTGCATGG
Found at i:32879 original size:18 final size:17
Alignment explanation
Indices: 32833--32880 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
32823 CATTAATATT
*
32833 AATATTTTAATATTTCA
1 AATATTTTAATATTTAA
*
32850 AATATATATAATAGTTTAA
1 AATAT-TTTAATA-TTTAA
32869 AATATTTTAATA
1 AATATTTTAATA
32881 ACGAACACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 5 0.19
18 12 0.46
19 9 0.35
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
AATATTTTAATATTTAA
Found at i:41807 original size:15 final size:16
Alignment explanation
Indices: 41789--41830 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
41779 AATATAAATA
41789 AATTTAAAATAATTT-
1 AATTTAAAATAATTTG
* *
41804 AATTTAACATATTTTG
1 AATTTAAAATAATTTG
*
41820 AATTTATAATA
1 AATTTAAAATA
41831 TATATCTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
AATTTAAAATAATTTG
Found at i:46001 original size:21 final size:21
Alignment explanation
Indices: 45968--46007 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
45958 AATTGCCCAG
45968 TACATAGGATATCGATACTCC
1 TACATAGGATATCGATACTCC
45989 TACA-AGGAGTATCGATACT
1 TACATAGGA-TATCGATACT
46008 ACCTTTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
TACATAGGATATCGATACTCC
Found at i:46026 original size:27 final size:27
Alignment explanation
Indices: 45996--46050 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
45986 TCCTACAAGG
45996 AGTATCGATACTACCTTTGTTATTTTT
1 AGTATCGATACTACCTTTGTTATTTTT
46023 AGTATCGATACTACCTTTGTTATTTTT
1 AGTATCGATACTACCTTTGTTATTTTT
46050 A
1 A
46051 TATAAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.51
Consensus pattern (27 bp):
AGTATCGATACTACCTTTGTTATTTTT
Found at i:48303 original size:23 final size:23
Alignment explanation
Indices: 48255--48339 Score: 100
Period size: 24 Copynumber: 3.7 Consensus size: 23
48245 TACGCAGTCA
*
48255 TTCGGGACAAATCTATGT-GTCC
1 TTCGGGACAAATCTACGTGGTCC
* *
48277 TTCGGGATAATTCTACGTGGTCC
1 TTCGGGACAAATCTACGTGGTCC
* * *
48300 TTCGGGACAAATTCTGCGCGATCC
1 TTCGGGACAAA-TCTACGTGGTCC
48324 TTCGGGACAAATCTAC
1 TTCGGGACAAATCTAC
48340 ATAGCACTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 15 0.29
23 17 0.33
24 20 0.38
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (23 bp):
TTCGGGACAAATCTACGTGGTCC
Done.