Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005834.1 Hibiscus syriacus cultivar Beakdansim tig00013678_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: 71894
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:7144 original size:36 final size:38
Alignment explanation
Indices: 7097--7170 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
7087 TAAAGAATTC
7097 GAATGCTCTTTCT-AAAAAAAT-TCAAAGCAATTGACT
1 GAATGCTCTTTCTAAAAAAAATCTCAAAGCAATTGACT
7133 GAATGCTCTTTCTAAAAAAAATCTCAAAGCAATTGACT
1 GAATGCTCTTTCTAAAAAAAATCTCAAAGCAATTGACT
7171 AACATCAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 13 0.36
37 8 0.22
38 15 0.42
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (38 bp):
GAATGCTCTTTCTAAAAAAAATCTCAAAGCAATTGACT
Found at i:15275 original size:20 final size:20
Alignment explanation
Indices: 15250--15297 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
15240 ATTATTTGTA
15250 AACACCA-TTTTTCAACACC
1 AACACCATTTTTTCAACACC
15269 TAACACCCCATTTTTTCAACACC
1 -AACA--CCATTTTTTCAACACC
15292 AACACC
1 AACACC
15298 CATCATCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 6 0.24
22 7 0.28
23 12 0.48
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (20 bp):
AACACCATTTTTTCAACACC
Found at i:16060 original size:40 final size:41
Alignment explanation
Indices: 16011--16096 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 41
16001 ATATACGTGC
16011 ATATCCATTATAAATATA-TTATAATATTTAAATAATATAT
1 ATATCCATTATAAATATAGTTATAATATTTAAATAATATAT
16051 ATATCCATTATAAATATATGTTATAATATTTAAATAATATAT
1 ATATCCATTATAAATATA-GTTATAATATTTAAATAATATAT
16093 ATAT
1 ATAT
16097 ATATATAACA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 18 0.41
42 26 0.59
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (41 bp):
ATATCCATTATAAATATAGTTATAATATTTAAATAATATAT
Found at i:22460 original size:16 final size:16
Alignment explanation
Indices: 22436--22466 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22426 CACCCCCAAC
22436 GTCCCTGCTTCATACT
1 GTCCCTGCTTCATACT
*
22452 GTCCTTGCTTCATAC
1 GTCCCTGCTTCATAC
22467 ATAAGGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.35, G:0.13, T:0.39
Consensus pattern (16 bp):
GTCCCTGCTTCATACT
Found at i:24317 original size:2 final size:2
Alignment explanation
Indices: 24310--24348 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24300 GAGCTGATTG
24310 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
24349 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24353 original size:2 final size:2
Alignment explanation
Indices: 24348--24383 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24338 ATATATATAT
24348 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
24384 TGACCAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:32590 original size:2 final size:2
Alignment explanation
Indices: 32583--32609 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32573 TACCCATAGT
32583 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
32610 TGTACTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38183 original size:2 final size:2
Alignment explanation
Indices: 38176--38207 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38166 CAATCAACAA
38176 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
38208 TATCAAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44334 original size:21 final size:19
Alignment explanation
Indices: 44302--44340 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
44292 GCTAAGTTTG
*
44302 ATTTTTTTTTAAATATATA
1 ATTTTTTTTTAAAAATATA
44321 ATTTTTTTCATTAAAAATAT
1 ATTTTTTT--TTAAAAATAT
44341 TAACTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTTTTTTAAAAATATA
Found at i:45207 original size:19 final size:19
Alignment explanation
Indices: 45183--45299 Score: 117
Period size: 19 Copynumber: 5.7 Consensus size: 19
45173 CATATTCGCA
45183 TTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCG
*
45202 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
45223 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
45244 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
45265 TTGCGATTTATTCCAAGCTCG
1 TTGCGA--TAGTCCAAGTTCG
45286 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
45300 AATCGCAACG
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
19 32 0.40
21 32 0.40
23 17 0.21
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:45226 original size:21 final size:21
Alignment explanation
Indices: 45177--45299 Score: 114
Period size: 21 Copynumber: 6.0 Consensus size: 21
45167 GATTTACATA
*
45177 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
45198 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
45217 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
45240 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
45259 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
45282 --CTCGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
45300 AATCGCAACG
Statistics
Matches: 84, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
19 33 0.39
21 35 0.42
23 16 0.19
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:45246 original size:42 final size:42
Alignment explanation
Indices: 45192--45299 Score: 189
Period size: 42 Copynumber: 2.6 Consensus size: 42
45182 ATTGCGATAG
*
45192 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
*
45234 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
*
45276 TCCAAGCTCGTTGCGATAGTCCAA
1 TCCAAGTTCGTTGCGATAGTCCAA
45300 AATCGCAACG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.33
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
Found at i:45410 original size:12 final size:12
Alignment explanation
Indices: 45389--45427 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
45379 CGTATTACCA
*
45389 CGACCACGACCC
1 CGACCCCGACCC
45401 CGACCCCGACCC
1 CGACCCCGACCC
45413 CGA-CCCGA-CC
1 CGACCCCGACCC
45423 CGACC
1 CGACC
45428 AGAGACGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 5 0.20
11 6 0.24
12 14 0.56
ACGTcount: A:0.21, C:0.62, G:0.18, T:0.00
Consensus pattern (12 bp):
CGACCCCGACCC
Found at i:46108 original size:21 final size:21
Alignment explanation
Indices: 46084--46193 Score: 138
Period size: 21 Copynumber: 5.3 Consensus size: 21
46074 TGCGAATATG
46084 TTGCGATAGTCGAAGTTCGCA
1 TTGCGATAGTCGAAGTTCGCA
*
46105 TTGCGATAGTCG-ACTATCGCA
1 TTGCGATAGTCGAAGT-TCGCA
*
46126 TTGCGAT-TTAC-ATA-TTCGCA
1 TTGCGATAGT-CGA-AGTTCGCA
*
46146 TTGCGATAGTCCAAGTTCGCA
1 TTGCGATAGTCGAAGTTCGCA
46167 TTGCGATAGTCGAAGTTCGCA
1 TTGCGATAGTCGAAGTTCGCA
46188 TTGCGA
1 TTGCGA
46194 ATCTGGAAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
20 17 0.22
21 60 0.77
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTCGCA
Found at i:53686 original size:21 final size:21
Alignment explanation
Indices: 53675--53843 Score: 194
Period size: 21 Copynumber: 7.6 Consensus size: 21
53665 TGCGGCTGCG
* * *
53675 GCTGCTGTTGTTGTTGCTGCT
1 GCTGCTGCTGCTGTTGTTGCT
53696 GCTGCTGCTGCTGTTGTAGTTGCT
1 GCTGCTGCTGCTGTT---GTTGCT
*
53720 GTTGCTGCTGCTGTTGTTGCT
1 GCTGCTGCTGCTGTTGTTGCT
*
53741 GCTGCTGCTGTTGTTGTTGCT
1 GCTGCTGCTGCTGTTGTTGCT
*
53762 GCTGCTGCTGTTGTTGTTGCTGCT
1 GCTGCTGCTGCTGTTG-T--TGCT
53786 GCTGCTGCTGCTGTTGTTGCT
1 GCTGCTGCTGCTGTTGTTGCT
*
53807 GCTGCTGTTGCTGCTGTTGTTGTT
1 GCTGC---TGCTGCTGTTGTTGCT
53831 GCTGCTGCTGCTG
1 GCTGCTGCTGCTG
53844 CTGAGCATGC
Statistics
Matches: 131, Mismatches: 8, Indels: 18
0.83 0.05 0.11
Matches are distributed among these distances:
21 71 0.54
22 1 0.01
23 1 0.01
24 58 0.44
ACGTcount: A:0.01, C:0.21, G:0.34, T:0.45
Consensus pattern (21 bp):
GCTGCTGCTGCTGTTGTTGCT
Found at i:53690 original size:24 final size:24
Alignment explanation
Indices: 53661--53846 Score: 252
Period size: 24 Copynumber: 7.9 Consensus size: 24
53651 CATCCCTTCT
* *
53661 TTGTTGCGGCTGCGGCTGCTGTTG
1 TTGTTGCTGCTGCTGCTGCTGTTG
*
53685 TTGTTGCTGCTGCTGCTGCTGCTG
1 TTGTTGCTGCTGCTGCTGCTGTTG
* * * *
53709 TTGTAGTTGCTGTTGCTGCTGCTG
1 TTGTTGCTGCTGCTGCTGCTGTTG
53733 TTG-T--TGCTGCTGCTGCTGTTG
1 TTGTTGCTGCTGCTGCTGCTGTTG
*
53754 TTGTTGCTGCTGCTGCTGTTGTTG
1 TTGTTGCTGCTGCTGCTGCTGTTG
*
53778 TTGCTGCTGCTGCTGCTGCTGTTG
1 TTGTTGCTGCTGCTGCTGCTGTTG
* *
53802 TTGCTGCTGCTGTTGCTGCTGTTG
1 TTGTTGCTGCTGCTGCTGCTGTTG
53826 TTGTTGCTGCTGCTGCTGCTG
1 TTGTTGCTGCTGCTGCTGCTG
53847 AGCATGCCTC
Statistics
Matches: 144, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
21 18 0.12
22 1 0.01
24 125 0.87
ACGTcount: A:0.01, C:0.21, G:0.34, T:0.44
Consensus pattern (24 bp):
TTGTTGCTGCTGCTGCTGCTGTTG
Found at i:53695 original size:3 final size:3
Alignment explanation
Indices: 53669--53846 Score: 151
Period size: 3 Copynumber: 59.3 Consensus size: 3
53659 CTTTGTTGCG
* * * * * *
53669 GCT GCG GCT GCT GTT GTT GTT GCT GCT GCT GCT GCT GCT GTT G-T AGTT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT -GCT
* * * * * *
53717 GCT GTT GCT GCT GCT GTT GTT GCT GCT GCT GCT GTT GTT GTT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* * * * *
53765 GCT GCT GTT GTT GTT GCT GCT GCT GCT GCT GCT GTT GTT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* * * *
53813 GTT GCT GCT GTT GTT GTT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
53847 AGCATGCCTC
Statistics
Matches: 153, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
2 1 0.01
3 151 0.99
4 1 0.01
ACGTcount: A:0.01, C:0.21, G:0.34, T:0.44
Consensus pattern (3 bp):
GCT
Found at i:61096 original size:13 final size:13
Alignment explanation
Indices: 61078--61135 Score: 80
Period size: 13 Copynumber: 4.3 Consensus size: 13
61068 GTCACAACCC
61078 GACCCGACCCGTT
1 GACCCGACCCGTT
61091 GACCCGACCCGTT
1 GACCCGACCCGTT
*
61104 TACCCGACCCGTT
1 GACCCGACCCGTT
*
61117 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
61132 GACC
1 GACC
61136 AAAACTTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
13 28 0.70
15 12 0.30
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:62445 original size:18 final size:18
Alignment explanation
Indices: 62405--62445 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
62395 ATTGTTCGAA
*
62405 AAGATTGAAGTAAATGAT
1 AAGATTGAAGTAAATAAT
* *
62423 TAGATTGAATTAAATAAT
1 AAGATTGAAGTAAATAAT
62441 AAGAT
1 AAGAT
62446 CAGATGGAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (18 bp):
AAGATTGAAGTAAATAAT
Found at i:63612 original size:24 final size:23
Alignment explanation
Indices: 63585--63659 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 23
63575 AATTATTTTA
* *
63585 TCTGATTTTCGACTTGAATTCTGT
1 TCTGATTTT-GACCTGAATTATGT
**
63609 TCTGATACATGACCTGAATTATGT
1 TCTGAT-TTTGACCTGAATTATGT
** *
63633 TCTGATTTCTGATATGGATTATGT
1 TCTGATTT-TGACCTGAATTATGT
63657 TCT
1 TCT
63660 AATATCTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
24 39 0.98
25 1 0.03
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (23 bp):
TCTGATTTTGACCTGAATTATGT
Found at i:63637 original size:12 final size:12
Alignment explanation
Indices: 63622--63691 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
63612 GATACATGAC
*
63622 CTGAATTATGTT
1 CTGAATTCTGTT
* *
63634 CTGATTTCTGAT
1 CTGAATTCTGTT
* * *
63646 ATGGATTATGTT
1 CTGAATTCTGTT
63658 CT-AATATCTGTT
1 CTGAAT-TCTGTT
63670 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
63682 TTGATTTCTG
1 CTGAATTCTG
63692 ATATCTCCGT
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.88
13 3 0.07
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:63681 original size:24 final size:24
Alignment explanation
Indices: 63599--63693 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 24
63589 ATTTTCGACT
* *
63599 TGAATTCTGTTCTGATA-CATGACC
1 TGAATTATGTTCTGATATC-TGATC
* *
63623 TGAATTATGTTCTGATTTCTGATA
1 TGAATTATGTTCTGATATCTGATC
* * *
63647 TGGATTATGTTCTAATATCTGTTC
1 TGAATTATGTTCTGATATCTGATC
* * *
63671 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTATGTTCTGATATCTGAT
63694 ATCTCCGTTT
Statistics
Matches: 55, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
24 54 0.98
25 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGAATTATGTTCTGATATCTGATC
Found at i:65750 original size:13 final size:13
Alignment explanation
Indices: 65732--65756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65722 GGTCACAAAC
65732 CGACCCGACCCGT
1 CGACCCGACCCGT
65745 CGACCCGACCCG
1 CGACCCGACCCG
65757 ACCCGTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.56, G:0.24, T:0.04
Consensus pattern (13 bp):
CGACCCGACCCGT
Found at i:65754 original size:18 final size:18
Alignment explanation
Indices: 65731--65774 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
65721 TGGTCACAAA
65731 CCGACCCGACCCGTCGAC
1 CCGACCCGACCCGTCGAC
**
65749 CCGACCCGACCCGTTTAC
1 CCGACCCGACCCGTCGAC
65767 CCGACCCG
1 CCGACCCG
65775 TTTACCCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.55, G:0.20, T:0.09
Consensus pattern (18 bp):
CCGACCCGACCCGTCGAC
Found at i:65768 original size:13 final size:13
Alignment explanation
Indices: 65752--65789 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
65742 CGTCGACCCG
65752 ACCCGACCCGTTT
1 ACCCGACCCGTTT
65765 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
65778 ACCCGATCCGTT
1 ACCCGACCCGTT
65790 GACCGTTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.45, G:0.16, T:0.24
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:67123 original size:18 final size:18
Alignment explanation
Indices: 67083--67123 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
67073 ATTGTTCGAA
*
67083 AAGATTGAAGTAAATGAT
1 AAGATTGAAGTAAATAAT
* *
67101 TAGATTGAATTAAATAAT
1 AAGATTGAAGTAAATAAT
67119 AAGAT
1 AAGAT
67124 CAGATGGAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (18 bp):
AAGATTGAAGTAAATAAT
Found at i:68288 original size:24 final size:23
Alignment explanation
Indices: 68261--68316 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
68251 ACTTATTTTA
* *
68261 TCTGATTTTCGACTTGAATTCTGT
1 TCTGATTTT-GACCTGAATTATGT
**
68285 TCTGATACATGACCTGAATTATGT
1 TCTGAT-TTTGACCTGAATTATGT
68309 TCTGATTT
1 TCTGATTT
68317 AATATGGATT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46
Consensus pattern (23 bp):
TCTGATTTTGACCTGAATTATGT
Found at i:68343 original size:12 final size:12
Alignment explanation
Indices: 68324--68365 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
68314 TTTAATATGG
68324 ATTCTGTTCT-A
1 ATTCTGTTCTGA
68335 ATATCTGTTCTGA
1 AT-TCTGTTCTGA
*
68348 ATTCTGTTTTGA
1 ATTCTGTTCTGA
*
68360 TTTCTG
1 ATTCTG
68366 ATATCTCCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 2 0.07
12 22 0.81
13 3 0.11
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (12 bp):
ATTCTGTTCTGA
Found at i:70452 original size:13 final size:13
Alignment explanation
Indices: 70452--70476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
70442 CCGTTGACCC
70452 GACCCGACCCGTT
1 GACCCGACCCGTT
70465 GACCCGACCCGT
1 GACCCGACCCGT
70477 AACCGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:70452 original size:18 final size:18
Alignment explanation
Indices: 70429--70487 Score: 100
Period size: 18 Copynumber: 3.2 Consensus size: 18
70419 GTCACAACCC
70429 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
70447 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
70465 GACCCGACCCGTAACCGTT
1 GACCCGACCCG-ACCCGTT
70484 GACC
1 GACC
70488 GTTGACCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
18 29 0.74
19 10 0.26
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Done.