Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002166.1 Hibiscus syriacus cultivar Beakdansim tig00004422_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: 90190
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:715 original size:21 final size:21
Alignment explanation
Indices: 677--716 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
667 TTCTCACATG
* *
677 AAGAAAAAAATTATACAAGGT
1 AAGAAAAAAACTAAACAAGGT
*
698 AAGAAAACAACTAAACAAG
1 AAGAAAAAAACTAAACAAG
717 ATGCTTTGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.10, G:0.12, T:0.12
Consensus pattern (21 bp):
AAGAAAAAAACTAAACAAGGT
Found at i:4134 original size:23 final size:23
Alignment explanation
Indices: 4106--4149 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4096 TAAAGCTTTT
4106 ATAAAACATGTAGTAATTTTATC
1 ATAAAACATGTAGTAATTTTATC
* *
4129 ATAAAATATGTGGTAATTTTA
1 ATAAAACATGTAGTAATTTTA
4150 AAGCATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (23 bp):
ATAAAACATGTAGTAATTTTATC
Found at i:4712 original size:23 final size:23
Alignment explanation
Indices: 4646--4705 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
4636 CCATCCGACT
*
4646 GAGCTATGCGAGGGCAGCCGAGC
1 GAGCTGTGCGAGGGCAGCCGAGC
4669 GAGCTGTGCGAGGGCAGCCGAGC
1 GAGCTGTGCGAGGGCAGCCGAGC
4692 GAGCTGTGCGAGGG
1 GAGCTGTGCGAGGG
4706 AATCCGATGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.23, G:0.48, T:0.10
Consensus pattern (23 bp):
GAGCTGTGCGAGGGCAGCCGAGC
Found at i:4718 original size:33 final size:33
Alignment explanation
Indices: 4681--4745 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
4671 GCTGTGCGAG
*
4681 GGCAGCCGAGCGAGCTGTGCGAGGGAATCCGAT
1 GGCAGCCGAGCGAGCTATGCGAGGGAATCCGAT
*
4714 GGCAGCCGAGCGAGCTATGCGAGGGCATCCGA
1 GGCAGCCGAGCGAGCTATGCGAGGGAATCCGA
4746 GCAAGCAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.42, T:0.11
Consensus pattern (33 bp):
GGCAGCCGAGCGAGCTATGCGAGGGAATCCGAT
Found at i:4808 original size:29 final size:29
Alignment explanation
Indices: 4762--4817 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
4752 AAGCAAGGGT
*
4762 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGAGCATGGCGACCTACA
4791 AGGTCGCCCGGAGAGCATGGCGACCTA
1 AGGTCGCCCGGAGAGCATGGCGACCTA
4818 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.36, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGAGCATGGCGACCTACA
Found at i:5497 original size:20 final size:20
Alignment explanation
Indices: 5469--5507 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5459 GTAATTATGT
*
5469 AAAAGTAAATTATTTTTATA
1 AAAAGTAAATTATATTTATA
*
5489 AAAATTAAATTATATTTAT
1 AAAAGTAAATTATATTTAT
5508 TTTATGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
AAAAGTAAATTATATTTATA
Found at i:13475 original size:29 final size:31
Alignment explanation
Indices: 13403--13476 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 31
13393 CAATTTAACG
13403 GTTCAGTGGTATAATTGAAACAAAAATCAAA
1 GTTCAGTGGTATAATTGAAACAAAAATCAAA
* * * *
13434 GTTCAATGCTATAATTG-AA-AAAATTGAAA
1 GTTCAGTGGTATAATTGAAACAAAAATCAAA
*
13463 GTTTAGTGGTATAA
1 GTTCAGTGGTATAA
13477 ACAATTCAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 19 0.53
30 2 0.06
31 15 0.42
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.31
Consensus pattern (31 bp):
GTTCAGTGGTATAATTGAAACAAAAATCAAA
Found at i:25092 original size:14 final size:14
Alignment explanation
Indices: 25073--25104 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25063 GATTGGATTA
*
25073 AATATAAACGAACG
1 AATATAAACAAACG
25087 AATATAAACAAACG
1 AATATAAACAAACG
25101 AATA
1 AATA
25105 ACCGAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.16
Consensus pattern (14 bp):
AATATAAACAAACG
Found at i:27465 original size:2 final size:2
Alignment explanation
Indices: 27458--27484 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27448 TCTACCACGA
27458 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 A
27485 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27489 original size:2 final size:2
Alignment explanation
Indices: 27484--27511 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27474 ATATATATAT
27484 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
27512 GCCTTGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27865 original size:12 final size:12
Alignment explanation
Indices: 27848--27872 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27838 ATTAAATTTG
27848 AAAAAAAAGAAA
1 AAAAAAAAGAAA
27860 AAAAAAAAGAAA
1 AAAAAAAAGAAA
27872 A
1 A
27873 CATGTGACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:38422 original size:16 final size:16
Alignment explanation
Indices: 38397--38430 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
38387 ATCTCCATCG
38397 TTGCTTTCTTGT-TGC
1 TTGCTTTCTTGTCTGC
38412 TTGCATTTCTTGTCTGC
1 TTGC-TTTCTTGTCTGC
38429 TT
1 TT
38431 CCCAAAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.03, C:0.21, G:0.18, T:0.59
Consensus pattern (16 bp):
TTGCTTTCTTGTCTGC
Found at i:48402 original size:21 final size:23
Alignment explanation
Indices: 48362--48404 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
48352 TTTCAATTTA
*
48362 AAATATAAAAATATTCAAAAATT
1 AAATATAAAAATACTCAAAAATT
48385 AAATA-AAAAATACT-AAAAAT
1 AAATATAAAAATACTCAAAAAT
48405 ACTAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (23 bp):
AAATATAAAAATACTCAAAAATT
Found at i:48565 original size:29 final size:30
Alignment explanation
Indices: 48532--48589 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
48522 ATTTAAATAT
48532 TATAAAGA-AAACAATTTAATAATTTTTTG
1 TATAAAGATAAACAATTTAATAATTTTTTG
* ** *
48561 TATAAATATATTCAATTTAATATTTTTTT
1 TATAAAGATAAACAATTTAATAATTTTTT
48590 AAAAATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (30 bp):
TATAAAGATAAACAATTTAATAATTTTTTG
Found at i:58175 original size:16 final size:16
Alignment explanation
Indices: 58156--58190 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
58146 AGTATCTTAA
58156 TTTCAAAAAAAAATAT
1 TTTCAAAAAAAAATAT
**
58172 TTTCAATGAAAAATAT
1 TTTCAAAAAAAAATAT
58188 TTT
1 TTT
58191 ATCAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (16 bp):
TTTCAAAAAAAAATAT
Found at i:58677 original size:28 final size:29
Alignment explanation
Indices: 58623--58679 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
58613 ATTTTTTATT
*
58623 ATATTTATAGTATTAAATATAGATTTTTA
1 ATATTTATAGAATTAAATATAGATTTTTA
*
58652 ATATTTATA-AATTATAATAT-TATTTTTA
1 ATATTTATAGAATTA-AATATAGATTTTTA
58680 TAAATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
ATATTTATAGAATTAAATATAGATTTTTA
Found at i:62205 original size:21 final size:21
Alignment explanation
Indices: 62131--62224 Score: 89
Period size: 21 Copynumber: 4.4 Consensus size: 21
62121 GGTTAAGATC
*
62131 TTTCGATGAAAAGACTTAACCT
1 TTTC-ATGAAAGGACTTAACCT
* * * **
62153 TTTGATTAAAAGACTTCTCCT
1 TTTCATGAAAGGACTTAACCT
* *
62174 TTTGATGAAAGGGCTTAACCT
1 TTTCATGAAAGGACTTAACCT
* *
62195 TTTCATGAAAGGATTTAATCT
1 TTTCATGAAAGGACTTAACCT
62216 TTTCATGAA
1 TTTCATGAA
62225 GAGAATTGTT
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
21 56 0.95
22 3 0.05
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
TTTCATGAAAGGACTTAACCT
Found at i:65670 original size:15 final size:15
Alignment explanation
Indices: 65629--65712 Score: 55
Period size: 15 Copynumber: 5.7 Consensus size: 15
65619 AAGTGTCGTT
* *
65629 TATTCACTTAGAACA
1 TATTCACATAGAAAA
*
65644 CATTCATC-TAGAAAA
1 TATTCA-CATAGAAAA
*
65659 TATTCACATAGAACA
1 TATTCACATAGAAAA
* * *
65674 TTTTCACGTAGAATA
1 TATTCACATAGAAAA
* *
65689 T-TTGACATATAAAA
1 TATTCACATAGAAAA
*
65703 TCTTCACATA
1 TATTCACATA
65713 CTAATAAAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
14 11 0.20
15 42 0.78
16 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (15 bp):
TATTCACATAGAAAA
Found at i:67801 original size:7 final size:7
Alignment explanation
Indices: 67789--67821 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
67779 TATCACCCAG
67789 CAAGCTC
1 CAAGCTC
67796 CAAGCTC
1 CAAGCTC
67803 CAAGCTC
1 CAAGCTC
67810 CAAGCTC
1 CAAGCTC
67817 CAAGC
1 CAAGC
67822 CAGTTACTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.42, G:0.15, T:0.12
Consensus pattern (7 bp):
CAAGCTC
Found at i:69490 original size:18 final size:18
Alignment explanation
Indices: 69436--69478 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
69426 CGAAGTTGGC
*
69436 GTCATAGCCGGGGGAGGT
1 GTCATAGCTGGGGGAGGT
*
69454 GTCATGGCTGGGGGAGGT
1 GTCATAGCTGGGGGAGGT
69472 GTCATAG
1 GTCATAG
69479 TGGTGGGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.49, T:0.21
Consensus pattern (18 bp):
GTCATAGCTGGGGGAGGT
Found at i:72230 original size:14 final size:14
Alignment explanation
Indices: 72211--72252 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
72201 CATTCAATAT
*
72211 TTTGTTTGTTTATG
1 TTTGTTCGTTTATG
*
72225 TTTGTTCATTTATG
1 TTTGTTCGTTTATG
*
72239 TTTATTCGTTTATG
1 TTTGTTCGTTTATG
72253 CTCGTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.05, G:0.17, T:0.67
Consensus pattern (14 bp):
TTTGTTCGTTTATG
Found at i:72362 original size:16 final size:17
Alignment explanation
Indices: 72321--72363 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
72311 AATTTTAACC
72321 TTAAACCCATTAATATT
1 TTAAACCCATTAATATT
72338 TTAAAACCCGATT-A-ATT
1 TT-AAACCC-ATTAATATT
72355 TTAAACCCA
1 TTAAACCCA
72364 AATAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 6 0.25
17 7 0.29
18 7 0.29
19 3 0.12
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (17 bp):
TTAAACCCATTAATATT
Found at i:73599 original size:39 final size:40
Alignment explanation
Indices: 73551--73626 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
73541 TGAAAGTGAA
*
73551 TAAAATTCAAT-AAAAAAAGAATGTAAAGCTAAAAAATAT
1 TAAAATTCAATAAAAAAAAGAATGTAAAGATAAAAAATAT
*
73590 TAAAATTCAATAAAAAAAATAATGTAAAGATAAAAAA
1 TAAAATTCAATAAAAAAAAGAATGTAAAGATAAAAAA
73627 ATATCACCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 11 0.32
40 23 0.68
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (40 bp):
TAAAATTCAATAAAAAAAAGAATGTAAAGATAAAAAATAT
Found at i:74333 original size:333 final size:334
Alignment explanation
Indices: 73696--75023 Score: 2254
Period size: 325 Copynumber: 4.0 Consensus size: 334
73686 ATATTAAATT
* *
73696 ATAATTTTATTAAAAATGAATAAATATTAATAACTGTTGTTAAAAAATAATAATTAATGAATAAT
1 ATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTT-AAAAATAATAATTAATGAATAAT
*
73761 AATTCATTTGATCCCTCAAATGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
65 AATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATATTTTTTATATTTTTAAACAAT
* *
73826 TAATTTTAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATACTTTTTAAATTATAAAATA
130 TAATTTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATAATTTTTAAATTATAAAATA
*
73891 TTTATCATCATCATCATCATTTTGTAAAATAAATAATAGTTATAAAACTTTTATAAAATTATTCA
195 TTTATCATCATCATCATCATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCA
* *
73956 TATTTTAAAATCCTTACCCTCAAAGTTTTCCTATACTAGATTATACATATTGTGTAATTTCATGC
260 TATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTCATGC
74021 AAAAATCAAA
325 AAAAATCAAA
*
74031 ATAATTTTATT-AAAATGAATAAACATTATTAATTGTTGTTAAAAAATAATAATTAATGAATAAT
1 ATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTT-AAAAATAATAATTAATGAATAAT
74095 AATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATATATTTTTATATTTTTAAACAA
65 AATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATAT-TTTTTATATTTTTAAACAA
*
74160 TTAATTTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATAATTTTTAAAATTATAATA
129 TTAATTTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATAATTTTT-AAATTATAAAA
*
74225 TA-TT-T-ATCATCATCATCATTTTGTAAAATAAATCCTAGTTATAAAACTTTTATAAAATTATT
193 TATTTATCATCATCATCATCATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATT
* * * *
74287 CATATTTTGAAATACTTACCTTCAAAGTTTTTCTATACTAGATTATATGTATTGTGTAATTTCAT
258 CATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTCAT
74352 GCAAAAATCAAA
323 GCAAAAATCAAA
74364 ATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATA
1 ATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATA
74429 ATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTT-A-A-----TATATTTTTAAACAATT
66 ATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATATTTTTTATATTTTTAAACAATT
*
74487 AATTTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAATATA
131 AATTTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATAA-TTTTTAAATTATAAAATA
*
74552 -TT-T-ATCATCATCATCATTTTGTAAAATAAATCCTAGTTATAAAACTTTTATAAAATTATTCA
195 TTTATCATCATCATCATCATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCA
* * *
74614 TATTTTGAAATACTTACCTTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCATGC
260 TATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTCATGC
74679 AAAAATCAAA
325 AAAAATCAAA
* *
74689 ATAATTTTATTAAAAATGAATAAACATTATTAAATGTTGTTAAAAATAATAATTAATGAATAATT
1 ATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATA
*
74754 ATTCATTTGATCCCTCAAATGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATT
66 ATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATATTTTTTATATTTTTAAACAATT
*
74819 AATTTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTAAATTATAAAATAT
131 AATTTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATAATTTTTAAATTATAAAATAT
*
74884 TTATCATCATCATCATCATTTTGTAAAATAAATACTAGTTAT-AAATTTTTATAAAATTATTCAT
196 TTATCATCATCATCATCATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCAT
* * *
74948 ATTTTAAAATACTTACCCTCATAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTTATACA
261 ATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTCATGCA
75013 AAAATCAAA
326 AAAATCAAA
75022 AT
1 AT
75024 TTATCGAGTT
Statistics
Matches: 949, Mismatches: 30, Indels: 30
0.94 0.03 0.03
Matches are distributed among these distances:
325 313 0.33
326 6 0.01
327 1 0.00
331 18 0.02
332 65 0.07
333 292 0.31
334 159 0.17
335 83 0.09
336 12 0.01
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (334 bp):
ATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATA
ATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATATTTTTTATATTTTTAAACAATT
AATTTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATAATTTTTAAATTATAAAATAT
TTATCATCATCATCATCATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCAT
ATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTCATGCA
AAAATCAAA
Found at i:74639 original size:658 final size:664
Alignment explanation
Indices: 73696--75023 Score: 2255
Period size: 658 Copynumber: 2.0 Consensus size: 664
73686 ATATTAAATT
*
73696 ATAATTTTATTAAAAATGAATAAATATTAATAACTGTTGTTAAAAAATAATAATTAATGAATAAT
1 ATAATTTTATTAAAAATGAATAAACATTAATAACTGTTGTTAAAAAATAATAATTAATGAATAAT
*
73761 AATTCATTTGATCCCTCAAATGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
66 AATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATA----TTATATTTTTAAACAAT
*
73826 TAATTTTAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATACTTTTTAAATTATAAAATA
127 TAATTTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATACTTTTTAAATTATAAAATA
73891 TTTATCATCATCATCATCATTTTGTAAAATAAATAATAGTTATAAAACTTTTATAAAATTATTCA
192 TTTATCATCATCATCATCATTTTGTAAAATAAATAATAGTTATAAAACTTTTATAAAATTATTCA
*
73956 TATTTTAAAATCCTTACCCTCAAAGTTTTCCTATACTAGATTATACATATTGTGTAATTTCATGC
257 TATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACATATTGTGTAATTTCATGC
*
74021 AAAAATCAAAATAATTTTATT-AAAATGAATAAACATTATTAATTGTTGTTAAAAAATAATAATT
322 AAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAAATGTTGTT-AAAAATAATAATT
74085 AATGAATAATAATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATATATTTTTATAT
386 AATGAATAATAATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATAT-TTTTTATAT
*
74150 TTTTAAACAATTAATTTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATAATTTTTAA
450 TTTTAAACAATTAATTTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTT-A
* *
74215 AATTATAATATA-TT-T-ATCATCATCATCATTTTGTAAAATAAATCCTAGTTATAAAACTTTTA
514 AATTATAAAATATTTATCATCATCATCATCATTTTGTAAAATAAATACTAGTTAT-AAACTTTTA
* * * *
74277 TAAAATTATTCATATTTTGAAATACTTACCTTCAAAGTTTTTCTATACTAGATTATATGTATTGT
578 TAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGT
*
74342 GTAATTTCATGCAAAAATCAAA
643 GTAATTTCATACAAAAATCAAA
*
74364 ATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTT-AAAAATAATAATTAATGAATAAT
1 ATAATTTTATTAAAAATGAATAAACATTAATAACTGTTGTTAAAAAATAATAATTAATGAATAAT
74428 AATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTT-A-A-TATATTTTTAAACAATTAAT
66 AATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATATTATATTTTTAAACAATTAAT
* *
74490 TTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAATATA-TT
131 TTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTAT-ACTTTTTAAATTATAAAATATTT
**
74554 -T-ATCATCATCATCATTTTGTAAAATAAATCCTAGTTATAAAACTTTTATAAAATTATTCATAT
195 ATCATCATCATCATCATTTTGTAAAATAAATAATAGTTATAAAACTTTTATAAAATTATTCATAT
* * **
74617 TTTGAAATACTTACCTTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCATGCAAA
260 TTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACATATTGTGTAATTTCATGCAAA
74682 AATCAAAATAATTTTATTAAAAATGAATAAACATTATTAAATGTTGTTAAAAATAATAATTAATG
325 AATCAAAATAATTTTATTAAAAATGAATAAACATTATTAAATGTTGTTAAAAATAATAATTAATG
* *
74747 AATAATTATTCATTTGATCCCTCAAATGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
390 AATAATAATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATATTTTTTATATTTTTA
74812 AACAATTAATTTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTAAATTAT
455 AACAATTAATTTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTAAATTAT
*
74877 AAAATATTTATCATCATCATCATCATTTTGTAAAATAAATACTAGTTATAAATTTTTATAAAATT
520 AAAATATTTATCATCATCATCATCATTTTGTAAAATAAATACTAGTTATAAACTTTTATAAAATT
*
74942 ATTCATATTTTAAAATACTTACCCTCATAGTTTTCCTATACTAGATTATACGTATTGTGTAATTT
585 ATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTT
*
75007 TATACAAAAATCAAA
650 CATACAAAAATCAAA
75022 AT
1 AT
75024 TTATCGAGTT
Statistics
Matches: 628, Mismatches: 27, Indels: 20
0.93 0.04 0.03
Matches are distributed among these distances:
656 12 0.02
657 73 0.12
658 295 0.47
659 65 0.10
660 62 0.10
661 18 0.03
665 1 0.00
666 1 0.00
667 62 0.10
668 39 0.06
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (664 bp):
ATAATTTTATTAAAAATGAATAAACATTAATAACTGTTGTTAAAAAATAATAATTAATGAATAAT
AATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATATTATATTTTTAAACAATTAAT
TTTAAAAGTCAATAAACTTTTCAAAAATATATGAAATTTATACTTTTTAAATTATAAAATATTTA
TCATCATCATCATCATTTTGTAAAATAAATAATAGTTATAAAACTTTTATAAAATTATTCATATT
TTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACATATTGTGTAATTTCATGCAAAA
ATCAAAATAATTTTATTAAAAATGAATAAACATTATTAAATGTTGTTAAAAATAATAATTAATGA
ATAATAATTCATTTGATCCCTCAAATGTAATTAAAAGCTTATTTTAATATTTTTTATATTTTTAA
ACAATTAATTTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTAAATTATA
AAATATTTATCATCATCATCATCATTTTGTAAAATAAATACTAGTTATAAACTTTTATAAAATTA
TTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTC
ATACAAAAATCAAA
Found at i:76598 original size:16 final size:16
Alignment explanation
Indices: 76577--76615 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
76567 TTGATCTCTA
76577 GTTATTTAT-GATGGAT
1 GTTATTTATAG-TGGAT
76593 GTTATTTATAGTGGAT
1 GTTATTTATAGTGGAT
76609 GTTATTT
1 GTTATTT
76616 CGGGTATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (16 bp):
GTTATTTATAGTGGAT
Found at i:76826 original size:26 final size:26
Alignment explanation
Indices: 76797--76850 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
76787 ACTTAGTGCA
*
76797 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACAACCTTATGTGTAT
76823 TATGGTGGGCACAACCTTATGTGTAT
1 TATGGTGGGCACAACCTTATGTGTAT
76849 TA
1 TA
76851 GCACTTCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TATGGTGGGCACAACCTTATGTGTAT
Found at i:81940 original size:42 final size:42
Alignment explanation
Indices: 81880--81987 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
81870 TATCACCCCC
* * *
81880 CCACCATCTCTAGGTTCATCTACACCATTTCCACCCCCAG-T
1 CCACCATCTGTAGATTCATCTACACCATTTCCACCACCAGAT
* * *
81921 GCCACCATATGTAGATTCATTTACACCATTTCCGCCACCAGCAT
1 -CCACCATCTGTAGATTCATCTACACCATTTCCACCACCAG-AT
*
81965 CCA-CATCTGTAGATTCGTCTACA
1 CCACCATCTGTAGATTCATCTACA
81988 GAAGAAAGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 51 0.93
43 3 0.05
44 1 0.02
ACGTcount: A:0.25, C:0.37, G:0.10, T:0.28
Consensus pattern (42 bp):
CCACCATCTGTAGATTCATCTACACCATTTCCACCACCAGAT
Found at i:82841 original size:15 final size:15
Alignment explanation
Indices: 82813--82863 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
82803 TTCTGTAAAA
*
82813 TGAATTACTAGAATT
1 TGAATTACTGGAATT
*
82828 TGAATGACTGGAATT
1 TGAATTACTGGAATT
*
82843 TGAATTACTGAAATT
1 TGAATTACTGGAATT
82858 TGAATT
1 TGAATT
82864 CTGAAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:82869 original size:14 final size:14
Alignment explanation
Indices: 82824--82869 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
82814 GAATTACTAG
* *
82824 AATTTGAATGACTGG
1 AATTTGAAT-TCTGA
82839 AATTTGAATTACTGA
1 AATTTGAATT-CTGA
82854 AATTTGAATTCTGA
1 AATTTGAATTCTGA
82868 AA
1 AA
82870 AATGAATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 6 0.21
15 22 0.79
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (14 bp):
AATTTGAATTCTGA
Found at i:83331 original size:27 final size:26
Alignment explanation
Indices: 83259--83336 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 26
83249 AAATATTATT
83259 AGATTATTATATTAATATTAAATATATAA
1 AGATTATTATATT--TA-TAAATATATAA
* *
83288 ATAATATTACTCA-TTATAAATATATAA
1 AGATTATTA-T-ATTTATAAATATATAA
83315 AGATTTATTATATTTATAAATA
1 AGA-TTATTATATTTATAAATA
83337 AAATATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 1 0.02
27 23 0.56
28 7 0.17
29 7 0.17
30 2 0.05
31 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (26 bp):
AGATTATTATATTTATAAATATATAA
Found at i:83375 original size:52 final size:51
Alignment explanation
Indices: 83244--83438 Score: 116
Period size: 52 Copynumber: 3.7 Consensus size: 51
83234 TTAAATATCT
* *
83244 TTATTAAATATTATTAGATTATTATATTAATATTAAATATATAA-ATAATA-TTACTCA
1 TTATTATATATAATT-GATTATTATATT--TA-TAAATA-A-AATATAATATTTA-T-A
* *
83301 TTATAAATATATAA-AGATTTATTATATTTATAAATAAAATATAATATCTTATA
1 TTAT-TATATATAATTGA-TTATTATATTTATAAATAAAATATAATAT-TTATA
* * *
83354 TTATTATATATAATTGATTATTTTA-CTATAATATTAAAAATATAAT-TTAATA
1 TTATTATATATAATTGATTATTATATTTATAA-A-T-AAAATATAATATTTATA
* * * *
83406 TTATTATAAAT-ATTAATAAATATATTT-TAAATA
1 TTATTATATATAATTGATTATTATATTTATAAATA
83439 TTTTAATAAT
Statistics
Matches: 113, Mismatches: 15, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 1 0.01
51 17 0.15
52 33 0.29
53 16 0.14
54 17 0.15
55 5 0.04
56 2 0.02
57 14 0.12
58 6 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (51 bp):
TTATTATATATAATTGATTATTATATTTATAAATAAAATATAATATTTATA
Found at i:83399 original size:32 final size:32
Alignment explanation
Indices: 83351--83429 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
83341 ATAATATCTT
* * *
83351 ATATTATTATATATAATTGATTATT-TTACTATA
1 ATATTAATAAATATAATTGAATATTATTA-TA-A
*
83384 ATATTAA-AAATATAATTTAATATTATTATAA
1 ATATTAATAAATATAATTGAATATTATTATAA
83415 ATATTAATAAATATA
1 ATATTAATAAATATA
83430 TTTTAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 8 0.20
32 23 0.57
33 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (32 bp):
ATATTAATAAATATAATTGAATATTATTATAA
Found at i:83416 original size:22 final size:21
Alignment explanation
Indices: 83384--83450 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
83374 TTTTACTATA
*
83384 ATATTAAAAATATAATTTAAT
1 ATATTATAAATATAATTTAAT
*
83405 ATTATTATAAATATTAA-TAAAT
1 A-TATTATAAATA-TAATTTAAT
*
83427 ATATTTTAAATAT--TTTAAT
1 ATATTATAAATATAATTTAAT
83446 A-ATTA
1 ATATTA
83451 ATATTTTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
18 3 0.08
19 5 0.13
20 1 0.03
21 11 0.29
22 15 0.39
23 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATTATAAATATAATTTAAT
Found at i:83453 original size:30 final size:30
Alignment explanation
Indices: 83382--83453 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 30
83372 TATTTTACTA
83382 TAAT-ATTAA-AAATATAATTTAATATTAT
1 TAATAATTAATAAATATAATTTAATATTAT
* *
83410 TATAAATATTAATAAATATATTTTAAATATT-T
1 TA-ATA-ATTAATAAATATAATTT-AATATTAT
83442 TAATAATTAATA
1 TAATAATTAATA
83454 TTTTGATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.06
29 1 0.03
30 7 0.19
31 7 0.19
32 13 0.36
33 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAATAATTAATAAATATAATTTAATATTAT
Found at i:83722 original size:41 final size:41
Alignment explanation
Indices: 83662--83743 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
83652 ACCAAATACT
* **
83662 GGAAAACATTTTCCGGAAAACGAATTATGTGAAACAAACAC
1 GGAAAACATTTTCCAGAAAACGAATTACATGAAACAAACAC
83703 GGAAAACATTTTCCAGAAAACGAATTACATGAAACAAACAC
1 GGAAAACATTTTCCAGAAAACGAATTACATGAAACAAACAC
83744 AGGATTTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (41 bp):
GGAAAACATTTTCCAGAAAACGAATTACATGAAACAAACAC
Done.