Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003240.1 Hibiscus syriacus cultivar Beakdansim tig00006813_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: 70979
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2614 original size:3 final size:3
Alignment explanation
Indices: 2606--2634 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2596 TTAAAAGTAA
2606 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2635 ATATATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4428 original size:16 final size:17
Alignment explanation
Indices: 4402--4442 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
4392 AATATTGAGA
4402 ATTTA-AATATTTTA-T
1 ATTTATAATATTTTACT
*
4417 ATTTTTAATATTTTACT
1 ATTTATAATATTTTACT
4434 ATTTATAAT
1 ATTTATAAT
4443 TTTATGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 4 0.18
16 9 0.41
17 9 0.41
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATAATATTTTACT
Found at i:4490 original size:16 final size:17
Alignment explanation
Indices: 4455--4491 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4445 TATGGAATGA
4455 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
4472 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
4488 AAAA
1 AAAA
4492 TGATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:4529 original size:16 final size:17
Alignment explanation
Indices: 4510--4541 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4500 TACTACCATA
4510 ATATTAT-TTTTATATT
1 ATATTATATTTTATATT
4526 ATATTATATTTTATAT
1 ATATTATATTTTATAT
4542 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:6584 original size:21 final size:20
Alignment explanation
Indices: 6525--6587 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
6515 CTTTTGTAAT
*
6525 TTTTTCAATTGTATTTTTAAA
1 TTTTT-AATTTTATTTTTAAA
* * *
6546 TTTTTTA-TTGATAATTTAAA
1 TTTTTAATTTTAT-TTTTAAA
6566 TTTTTAAATTTTATTTTTAAA
1 TTTTT-AATTTTATTTTTAAA
6587 T
1 T
6588 AAGTTGTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 13 0.41
22 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTTAATTTTATTTTTAAA
Found at i:9722 original size:24 final size:24
Alignment explanation
Indices: 9693--9741 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
9683 TTTATCCTTT
9693 TTCTCATTTTAGTTATTGACAATG
1 TTCTCATTTTAGTTATTGACAATG
*
9717 TTCTCATTTTAGTTATTGATAATG
1 TTCTCATTTTAGTTATTGACAATG
9741 T
1 T
9742 AGGTAACGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.53
Consensus pattern (24 bp):
TTCTCATTTTAGTTATTGACAATG
Found at i:11378 original size:6 final size:6
Alignment explanation
Indices: 11369--11408 Score: 71
Period size: 6 Copynumber: 6.5 Consensus size: 6
11359 AATTCCAATT
11369 GATGTA GATGTA GATGTA GATGTA GATGTA GATGTTA GAT
1 GATGTA GATGTA GATGTA GATGTA GATGTA GATG-TA GAT
11409 TTAATCCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (6 bp):
GATGTA
Found at i:32377 original size:2 final size:2
Alignment explanation
Indices: 32370--32402 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32360 CAAAGAATTC
32370 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 A
32403 ACACAAACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36388 original size:30 final size:30
Alignment explanation
Indices: 36352--36413 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
36342 ACAGTTCGAG
*
36352 TAGTTTTGGTAATGTGTGCTACATTGAACT
1 TAGTTTTGGCAATGTGTGCTACATTGAACT
*
36382 TAGTTTTGGCAATGTGTGCTACATTGGACT
1 TAGTTTTGGCAATGTGTGCTACATTGAACT
36412 TA
1 TA
36414 CATCTAGAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (30 bp):
TAGTTTTGGCAATGTGTGCTACATTGAACT
Found at i:36909 original size:261 final size:264
Alignment explanation
Indices: 36441--36966 Score: 1004
Period size: 261 Copynumber: 2.0 Consensus size: 264
36431 TGTTAAAACA
*
36441 GCTTTTCTTCATGAAAATCTTGAAGAAAAAAATTATATACTCCAGTCTGAAGGTTTTGAAGAAAA
1 GCTTTTCTTCATGAAAAACTTGAAGAAAAAAATTATATACTCCAGTCTGAAGGTTTTGAAGAAAA
36506 AGAAAAGAAGAACTTGATTTGCAGGTTGAACAAATCTCTATACGGTCTAAAGCAGGCACTGATAT
66 AGAAAAGAAGAACTTGATTTGCAGGTTGAACAAATCTCTATACGGTCTAAAGCAGGCACTGATAT
*
36571 GTTGGTATAAGAGATTTGATTCTTTCATTATGTGCCTTGGATATCACAGACTTAATGCAGACCCT
131 GTTGG-ATAAGAGATTTGATTCTTTCATTATGTGCCTTGGATATAACAGACTTAATGCAGACCCT
36636 TGTGCTTATTTCAAGAGGTCTGGTGATAACGATTTTGTTATATTGCTGTTGTATGTGGATGACAT
195 TGTGCTTATTTCAAGAGGTCTGGTGATAACGATTTTGTTATATTGCTGTTGTATGTGGATGACAT
36701 GTTAG
260 GTTAG
36706 GCTTTTCTTCATGAAAAACTTGAAGAAAAAAATTATATACTCCAGTCTGAAGGTTTTGAAGAAAA
1 GCTTTTCTTCATGAAAAACTTGAAGAAAAAAATTATATACTCCAGTCTGAAGGTTTTGAAGAAAA
36771 AG-AAAGAAGAACTTGATTTGCAGGTTGAACAAATCTCTATACGGTCTAAAGCAGGCACTGAT-T
66 AGAAAAGAAGAACTTGATTTGCAGGTTGAACAAATCTCTATACGGTCTAAAGCAGGCACTGATAT
36834 GTTGG-TAAGAGATTTGATTCTTTCATTATGTGCCTTGGATATAACAGACTTAATGCAGACCCTT
131 GTTGGATAAGAGATTTGATTCTTTCATTATGTGCCTTGGATATAACAGACTTAATGCAGACCCTT
36898 GTGCTTATTTCAAGAGGTCTGGTGATAACGATTTTGTTATATTGCTGTTGTATGTGGATGACATG
196 GTGCTTATTTCAAGAGGTCTGGTGATAACGATTTTGTTATATTGCTGTTGTATGTGGATGACATG
36963 TTAG
261 TTAG
36967 TTGCAAGACC
Statistics
Matches: 259, Mismatches: 2, Indels: 4
0.98 0.01 0.02
Matches are distributed among these distances:
261 127 0.49
263 6 0.02
264 60 0.23
265 66 0.25
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (264 bp):
GCTTTTCTTCATGAAAAACTTGAAGAAAAAAATTATATACTCCAGTCTGAAGGTTTTGAAGAAAA
AGAAAAGAAGAACTTGATTTGCAGGTTGAACAAATCTCTATACGGTCTAAAGCAGGCACTGATAT
GTTGGATAAGAGATTTGATTCTTTCATTATGTGCCTTGGATATAACAGACTTAATGCAGACCCTT
GTGCTTATTTCAAGAGGTCTGGTGATAACGATTTTGTTATATTGCTGTTGTATGTGGATGACATG
TTAG
Found at i:40039 original size:18 final size:19
Alignment explanation
Indices: 40004--40048 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
39994 TATGATTTCA
*
40004 AAAATAAAAATTAGACTTT
1 AAAATAAAAATTAAACTTT
40023 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTTT
*
40041 ATAATAAA
1 AAAATAAA
40049 TATCAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAAAATTAAACTTT
Found at i:48051 original size:2 final size:2
Alignment explanation
Indices: 48044--48081 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
48034 TCAAATAAGA
* *
48044 AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
48082 GGAATTGCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48523 original size:3 final size:3
Alignment explanation
Indices: 48515--48551 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
48505 ATAATTGGAT
*
48515 ATA ATA ATA ATA ATA ATA GTA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
48552 TGACCTCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:48531 original size:22 final size:22
Alignment explanation
Indices: 48504--48551 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
48494 AGATTTCAAA
*
48504 AATAATTGG-ATATAATAATAAT
1 AATAATAGGAATA-AATAATAAT
*
48526 AATAATAGTAATAAATAATAAT
1 AATAATAGGAATAAATAATAAT
48548 AATA
1 AATA
48552 TGACCTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (22 bp):
AATAATAGGAATAAATAATAAT
Found at i:60816 original size:38 final size:38
Alignment explanation
Indices: 60764--60859 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
60754 GTATAAACTA
* * *
60764 TGTCCCGAAGGACCTATCATCCCAAAGGATGTCATCTG
1 TGTCCCGAAAGACCTATCATCCCAAAGGATGTAATATG
* * *
60802 TGTCCCGAATGACCTATCATCTCGAAGGATGTAATATG
1 TGTCCCGAAAGACCTATCATCCCAAAGGATGTAATATG
60840 TGTCCCGAAAGACCTATCAT
1 TGTCCCGAAAGACCTATCAT
60860 ATGTCTCGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (38 bp):
TGTCCCGAAAGACCTATCATCCCAAAGGATGTAATATG
Found at i:66689 original size:13 final size:13
Alignment explanation
Indices: 66671--66700 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
66661 CTTAGTTGCG
66671 AAAATTAAAATTT
1 AAAATTAAAATTT
*
66684 AAAATTGAAATTT
1 AAAATTAAAATTT
66697 AAAA
1 AAAA
66701 ATTCGGTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:66868 original size:5 final size:5
Alignment explanation
Indices: 66854--66895 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
66844 TATACCAAAG
* *
66854 AAATA AAATA CAATA AAATTA AAATT AAATA AAA-A AAATA AA
1 AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAATA AA
66896 GAAGTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 4 0.13
5 22 0.71
6 5 0.16
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:66979 original size:23 final size:23
Alignment explanation
Indices: 66953--67005 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
66943 CATATGAGGT
*
66953 AAAAAAAAT-ACTAATAATAATTA
1 AAAAAAAATGA-TAATAATAAATA
*
66976 AAAAAACATGATAATAATAAATA
1 AAAAAAAATGATAATAATAAATA
*
66999 AATAAAA
1 AAAAAAA
67006 TAAAATAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAAAAAATGATAATAATAAATA
Found at i:66980 original size:20 final size:20
Alignment explanation
Indices: 66955--67013 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
66945 TATGAGGTAA
66955 AAAAAATAC-TAATAATAATT
1 AAAAAATACATAATAATAA-T
*
66975 AAAAAA-ACATGATAATAAT
1 AAAAAATACATAATAATAAT
66994 AAATAAATA-A-AATAA-AAT
1 AAA-AAATACATAATAATAAT
67012 AA
1 AA
67014 GAATTTAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.15
19 10 0.29
20 18 0.53
21 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAAATACATAATAATAAT
Found at i:68301 original size:36 final size:36
Alignment explanation
Indices: 68220--68402 Score: 164
Period size: 36 Copynumber: 5.1 Consensus size: 36
68210 ATTATGTTTC
* *
68220 CAAAATATTTTAAAAA-T-TATATAATATAT-TTTT
1 CAAAATGTTTTAAAAACTATATATTATATATATTTT
* * *
68253 AAAAATGTTTTAAAAACTATATGTTATATTTATTTT
1 CAAAATGTTTTAAAAACTATATATTATATATATTTT
* * *
68289 CAAAATGTTTTAAAAATTATATAATATAAATATTTT
1 CAAAATGTTTTAAAAACTATATATTATATATATTTT
*
68325 CAAACATGTTTTCAAAACTATATA-TATATATA-TTT
1 CAAA-ATGTTTTAAAAACTATATATTATATATATTTT
* * *
68360 AAAAATGGTTTCAAAAA-TCATATAATATACT-TATTTT
1 CAAAAT-GTTTTAAAAACT-ATATATTATA-TATATTTT
68397 CGAAAA
1 C-AAAA
68403 CTGATTTCTG
Statistics
Matches: 122, Mismatches: 18, Indels: 15
0.79 0.12 0.10
Matches are distributed among these distances:
33 14 0.11
34 4 0.03
35 28 0.23
36 51 0.42
37 21 0.17
38 4 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
CAAAATGTTTTAAAAACTATATATTATATATATTTT
Found at i:68386 original size:72 final size:73
Alignment explanation
Indices: 68238--68402 Score: 199
Period size: 72 Copynumber: 2.3 Consensus size: 73
68228 TTTAAAAATT
* * * * *
68238 ATATAATATATTTTTAAAAATGTTTTAAAAACTATATGTTATATTTATTTTCAAAATGTTTTAAA
1 ATATAA-ATATTTTCAAAAATGTTTTAAAAACTATATGATATATATATTTTAAAAATGTTTCAAA
*
68303 AATTATATA
65 AATCATATA
* *
68312 ATATAAATATTTTCAAACATGTTTTCAAAACTATAT-ATATATATA-TTTAAAAATGGTTTCAAA
1 ATATAAATATTTTCAAAAATGTTTTAAAAACTATATGATATATATATTTTAAAAAT-GTTTCAAA
68375 AATCATATA
65 AATCATATA
** *
68384 ATATACTTATTTTCGAAAA
1 ATATAAATATTTTCAAAAA
68403 CTGATTTCTG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
71 8 0.10
72 37 0.47
73 27 0.35
74 6 0.08
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (73 bp):
ATATAAATATTTTCAAAAATGTTTTAAAAACTATATGATATATATATTTTAAAAATGTTTCAAAA
ATCATATA
Found at i:68471 original size:2 final size:2
Alignment explanation
Indices: 68453--68499 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
68443 TTTCAAAGAT
** * *
68453 TA TA T- TA TA TA CG TA TA TA CA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
68494 TA TA TA
1 TA TA TA
68500 AAAGCAAACA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:69176 original size:84 final size:83
Alignment explanation
Indices: 68992--70457 Score: 1369
Period size: 84 Copynumber: 17.8 Consensus size: 83
68982 AACAGTAGTG
* * * **
68992 AATGATGTGTCATGGAGCTGA-TCGTAGTCGAACTCGAATGTC-TTTGTAACAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGT-GTAGTCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
* * * *
69055 CGCCTTGAGTTATACTGTA
65 CGACTTAAGTTATGCTGCA
* * *
69074 AATGATGTGTCGTT-GAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGACAACCCTTC
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTC
* * *
69138 TAGACTTAAGTTGTGTTGCA
64 TCGACTTAAGTTATGCTGCA
* * *
69158 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTCT
* *
69223 CGACTTAAGTTGTGTTGCA
65 CGACTTAAGTTATGCTGCA
* * * *
69242 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGATGGCAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTG-TTGCAGATAACCCTTCT
*
69307 CGACTTAAGTTATGCTACA
65 CGACTTAAGTTATGCTGCA
*** * * *
69326 AATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCG-GGGTC-TTTG--GCAGATAGCCCTTCT
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
*
69387 CGACTTAAGCTATGCTGCA
65 CGACTTAAGTTATGCTGCA
* * ** *
69406 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTCCT
1 AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTT-GTTGCAGATAACCCTTCT
* * * *
69471 AGCCTTGAGTTATGCTGTA
65 CGACTTAAGTTATGCTGCA
* * ** *
69490 AATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTG--GCAGATAGCCCTTCT
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
**
69552 CGACTTAAACTATGCTGCA
65 CGACTTAAGTTATGCTGCA
* * * *
69571 AATGATGTGCCTTGGAGCTGAGCGCAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTTT
1 AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTCT
69636 CGACTTAAGTTATGCTGCA
65 CGACTTAAGTTATGCTGCA
* * * * * * *
69655 AATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG-GGGTC-TTTG--GCAGATAGCCCTTAT
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
*
69716 CGACTTAAGCTATGCTGCA
65 CGACTTAAGTTATGCTGCA
** * * * **
69735 AATGATGTGCCTTTTATGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTC
1 AATGATGTGCCTTGGA-GCTGAGTGTAGTCGAACTCGAAGGTCTTTT-GTTGCAGATAACCCTTC
* * * *
69800 TAGCCTTGAGTTATGCTGTA
64 TCGACTTAAGTTATGCTGCA
* * * * ** *
69820 AATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTC-TTTG--GCAGATAGCCCTTCT
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
* * *
69882 CGAGTTAAGCTATGCTGCG
65 CGACTTAAGTTATGCTGCA
* *
69901 AATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTC
1 AATGATGTGCC-TTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTC
* * *
69965 TAGACTTAAGTTGTGTTGCA
64 TCGACTTAAGTTATGCTGCA
* * *
69985 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTT-GCAGATAACCCTTCT
70050 CGACTTAAGTTATGCTGC-
65 CGACTTAAGTTATGCTGCA
* * * ** *
70068 AATGATGTGCCCGTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTG--GCAGATAGCCCTTC
1 AATGATGTG-CC-TTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTC
*
70130 TCGACTTAAGCTATGCTGCA
64 TCGACTTAAGTTATGCTGCA
* ** *
70150 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC-AAGGTCTTTTGGTCACAGATAACCCTCCT
1 AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTT-GTTGCAGATAACCCTTCT
* * * *
70214 AGCCTTGAGTTATGCTGTA
65 CGACTTAAGTTATGCTGCA
* * * ** *
70233 AATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTG--GCAGATAGCCCTTCT
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCT
* *
70295 CGACTTAAGCTATGCTGTA
65 CGACTTAAGTTATGCTGCA
* * * * *
70314 AATGATGTGCCTTTGAGC-GAGTGTAATCGAACTCGAAGGTCTTTTGGTGACATATAACTCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTG-CAGATAACCCTTCT
* * **
70378 AGCCTTGGGTTATGCT--A
65 CGACTTAAGTTATGCTGCA
* * * *
70395 AATGATGTGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTC-TTTG--GCAGATAGCCCTTC
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCGAA-GGTCTTTTGTTGCAGATAACCCTTC
70456 TC
64 TC
70458 ACCTTGAGCT
Statistics
Matches: 1137, Mismatches: 200, Indels: 97
0.79 0.14 0.07
Matches are distributed among these distances:
79 61 0.05
80 184 0.16
81 164 0.14
82 60 0.05
83 107 0.09
84 401 0.35
85 156 0.14
86 4 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (83 bp):
AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGCAGATAACCCTTCTC
GACTTAAGTTATGCTGCA
Found at i:70358 original size:164 final size:163
Alignment explanation
Indices: 68992--70457 Score: 1435
Period size: 165 Copynumber: 8.9 Consensus size: 163
68982 AACAGTAGTG
* * * *
68992 AATGATGTGTCATGGAGCTGA-TCGTAGTCGAACTCGAATGTCTTT-GTAACAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGT-GTAATCGAACTCGAAGGTCTTTGGT--CAGATAACCCTTCT
* * * * * * *
69055 CGCCTTGAGTTATACTGTAAATGATGTGTCGTTG-AGCTGAGTGTAGTCGAACTCAAAGGTCTTT
63 CGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
* * * *
69119 TGTTAGCAGACAACCCTTCTAGACTTAAGTTGTGTTGCA
128 TG---GCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
* * *
69158 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGG-T--CAGATAACCCTTCT
* * * * *
69223 CGACTTAAGTTGTGTTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
63 CGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
*
69287 GGATGGCAGATAACCCTTCTCGACTTAAGTTATGCTACA
128 ---TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
*** * *
69326 AATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCG-GGGTCTTTGG-CAGATAGCCCTTCTCG
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCG
* *
69389 ACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
65 ACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
* * * * *
69453 GTCACAGATAACCCTCCTAGCCTTGAGTTATGCTGTA
130 G---CAGATAACCCTTCTCGACTTAAGTTATGCTGCA
* ** *
69490 AATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG-CAGATAGCCCTTCTCG
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCG
** * *
69554 ACTTAAACTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGCAGTCGAACTCAAAGGTCTTTTG
65 ACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCAAAGGTC--TT-
*
69618 TTGGCAGATAACCCTTTTCGACTTAAGTTATGCTGCA
127 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
* * * * * *
69655 AATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG-GGGTCTTTGG-CAGATAGCCCTTATCG
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCG
* * * * *
69718 ACTTAAGCTATGCTGCAAATGATGTGCCTTTTATGCTGAGCGTAATCGAACTCAAAGGTCTTTTG
65 ACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
* * * *
69783 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
130 G---CAGATAACCCTTCTCGACTTAAGTTATGCTGCA
* * * ** *
69820 AATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGG-CAGATAGCCCTTCTCG
1 AATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCG
* * * *
69884 AGTTAAGCTATGCTGCGAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
65 ACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCAAAGGTC--TT-
* * *
69948 TTGGCAGATAACCCTTCTAGACTTAAGTTGTGTTGCA
127 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
* * *
69985 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGG-T--CAGATAACCCTTCT
* * * ***
70050 CGACTTAAGTTATGCTGC-AATGATGTGCCCGTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-T
63 CGACTTAAGTTATGCTGCAAATGATGTGCCC-TTGAAGCTGAGCGTAGTCGAACTCAAAGGTCTT
* *
70113 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
127 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
* * *
70150 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC-AAGGTCTTTTGGTCACAGATAACCCTCCT
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCT
* * * * * * * ***
70214 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TT
63 CGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
* * *
70278 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTA
128 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
* * *
70314 AATGATGTGCCTTTGAGC-GAGTGTAATCGAACTCGAAGGTCTTTTGGTGACATATAACTCTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCT
* * ** * * * *
70378 AGCCTTGGGTTATGCT--AAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC-TT
63 CGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
*
70440 TGGCAGATAGCCCTTCTC
128 TGGCAGATAACCCTTCTC
70458 ACCTTGAGCT
Statistics
Matches: 1144, Mismatches: 124, Indels: 68
0.86 0.09 0.05
Matches are distributed among these distances:
161 3 0.00
162 64 0.06
163 16 0.01
164 374 0.33
165 379 0.33
166 93 0.08
167 20 0.02
168 149 0.13
169 44 0.04
171 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (163 bp):
AATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCGA
CTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
CAGATAACCCTTCTCGACTTAAGTTATGCTGCA
Done.