Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014574.1 Kokia drynarioides strain JFW-HI SEQ_129613, 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: 41005
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:3665 original size:17 final size:17
Alignment explanation
Indices: 3632--3665 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3622 GGGTGCTATA
*
3632 TTTTTACTATTTTGGTT
1 TTTTTACTATTTAGGTT
*
3649 TTTTTACTGTTTAGGTT
1 TTTTTACTATTTAGGTT
3666 GCTGTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.15, T:0.68
Consensus pattern (17 bp):
TTTTTACTATTTAGGTT
Found at i:3691 original size:21 final size:22
Alignment explanation
Indices: 3667--3708 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3657 GTTTAGGTTG
*
3667 CTGTTTTGATGTTGTT-TTTTA
1 CTGTTTTGATGCTGTTATTTTA
3688 CTGTTTTGATGCTGTTATTTT
1 CTGTTTTGATGCTGTTATTTT
3709 TGTTACTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.10, C:0.07, G:0.19, T:0.64
Consensus pattern (22 bp):
CTGTTTTGATGCTGTTATTTTA
Found at i:3734 original size:12 final size:11
Alignment explanation
Indices: 3718--3804 Score: 52
Period size: 12 Copynumber: 7.7 Consensus size: 11
3708 TTGTTACTAT
3718 TTTTGCTGTTA
1 TTTTGCTGTTA
* *
3729 TATTTGTTGTTG
1 T-TTTGCTGTTA
3741 TTTTGCTGTTA
1 TTTTGCTGTTA
* *
3752 TTTTTGTTGTTG
1 -TTTTGCTGTTA
3764 TTTT--TGTTA
1 TTTTGCTGTTA
** *
3773 TTTTTATTGTTG
1 -TTTTGCTGTTA
*
3785 TTTTGCTATTA
1 TTTTGCTGTTA
3796 TTTTTGCTG
1 -TTTTGCTG
3805 CTGTTTCGGT
Statistics
Matches: 57, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 20 0.35
12 29 0.51
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (11 bp):
TTTTGCTGTTA
Found at i:3748 original size:23 final size:23
Alignment explanation
Indices: 3697--3810 Score: 135
Period size: 23 Copynumber: 5.0 Consensus size: 23
3687 ACTGTTTTGA
*
3697 TGCTGTTATTTTTGTTACTAT-TTT
1 TGCTGTTATTTTTGTT-GT-TGTTT
*
3721 TGCTGTTATATTTGTTGTTGTTT
1 TGCTGTTATTTTTGTTGTTGTTT
3744 TGCTGTTATTTTTGTTGTTGTTT
1 TGCTGTTATTTTTGTTGTTGTTT
*
3767 T--TGTTATTTTTATTGTTGTTT
1 TGCTGTTATTTTTGTTGTTGTTT
* * *
3788 TGCTATTATTTTTGCTGCTGTTT
1 TGCTGTTATTTTTGTTGTTGTTT
3811 CGGTTGTTTG
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
21 20 0.25
22 1 0.01
23 43 0.54
24 15 0.19
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.68
Consensus pattern (23 bp):
TGCTGTTATTTTTGTTGTTGTTT
Found at i:3787 original size:44 final size:45
Alignment explanation
Indices: 3697--3810 Score: 133
Period size: 44 Copynumber: 2.5 Consensus size: 45
3687 ACTGTTTTGA
* *
3697 TGCTGTTATTTTTGTTACTAT-TTTTGCTGTTATATTTGTTGTTGTTT
1 TGCTGTTATTTTTGTT-GT-TGTTTT-CTGTTATATTTATTGTTGTTT
*
3744 TGCTGTTATTTTTGTTGTTGTTTT-TGTTATTTTTATTGTTGTTT
1 TGCTGTTATTTTTGTTGTTGTTTTCTGTTATATTTATTGTTGTTT
* * *
3788 TGCTATTATTTTTGCTGCTGTTT
1 TGCTGTTATTTTTGTTGTTGTTT
3811 CGGTTGTTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 38 0.63
45 1 0.02
46 5 0.08
47 16 0.27
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.68
Consensus pattern (45 bp):
TGCTGTTATTTTTGTTGTTGTTTTCTGTTATATTTATTGTTGTTT
Found at i:5940 original size:15 final size:15
Alignment explanation
Indices: 5920--5950 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5910 ATGAAACGAC
*
5920 AAAGCAACCTATCAA
1 AAAGCAACCCATCAA
5935 AAAGCAACCCATCAA
1 AAAGCAACCCATCAA
5950 A
1 A
5951 GGAAGGAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.29, G:0.06, T:0.10
Consensus pattern (15 bp):
AAAGCAACCCATCAA
Found at i:6189 original size:27 final size:27
Alignment explanation
Indices: 6138--6201 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
6128 TTTTTTACTT
6138 TAAACTCAAAACTTTGAACCTCAAACCC
1 TAAACTC-AAACTTTGAACCTCAAACCC
*
6166 TAAACTCAAATTTTGAA-CTCCAAACCC
1 TAAACTCAAACTTTGAACCT-CAAACCC
* *
6193 AAAATTCAA
1 TAAACTCAA
6202 GATTCAAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 2 0.06
27 23 0.72
28 7 0.22
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.23
Consensus pattern (27 bp):
TAAACTCAAACTTTGAACCTCAAACCC
Found at i:10264 original size:24 final size:24
Alignment explanation
Indices: 10237--10314 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 24
10227 CTTAGTTATC
10237 AATTTATTTACTATATGTTAATTA
1 AATTTATTTACTATATGTTAATTA
* * *
10261 AATTT-TTAAC-ATATGTATAGTTTTC
1 AATTTATTTACTATATGT-TA--ATTA
10286 AATTTATTTACTATATGTTAATTA
1 AATTTATTTACTATATGTTAATTA
10310 AATTT
1 AATTT
10315 TTAACATATG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
22 6 0.14
23 6 0.14
24 12 0.28
25 7 0.16
26 6 0.14
27 6 0.14
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (24 bp):
AATTTATTTACTATATGTTAATTA
Found at i:10268 original size:22 final size:22
Alignment explanation
Indices: 10249--10325 Score: 82
Period size: 22 Copynumber: 3.3 Consensus size: 22
10239 TTTATTTACT
10249 ATATGTTAATTAAATTTTTAAC
1 ATATGTTAATTAAATTTTTAAC
* * *
10271 ATATGTATAGTTTTCAATTTATTTAC
1 ATATGT-TA--ATTAAATTT-TTAAC
10297 TATATGTTAATTAAATTTTTAAC
1 -ATATGTTAATTAAATTTTTAAC
10320 ATATGT
1 ATATGT
10326 ATACTTATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
22 12 0.27
23 6 0.14
24 7 0.16
25 7 0.16
26 6 0.14
27 6 0.14
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.52
Consensus pattern (22 bp):
ATATGTTAATTAAATTTTTAAC
Found at i:10288 original size:49 final size:49
Alignment explanation
Indices: 10229--10335 Score: 196
Period size: 49 Copynumber: 2.2 Consensus size: 49
10219 TTTGTCAGCT
10229 TAGTTATCAATTTATTTACTATATGTTAATTAAATTTTTAACATATGTA
1 TAGTTATCAATTTATTTACTATATGTTAATTAAATTTTTAACATATGTA
*
10278 TAGTTTTCAATTTATTTACTATATGTTAATTAAATTTTTAACATATGTA
1 TAGTTATCAATTTATTTACTATATGTTAATTAAATTTTTAACATATGTA
*
10327 TACTTATCA
1 TAGTTATCA
10336 CAAGAACAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (49 bp):
TAGTTATCAATTTATTTACTATATGTTAATTAAATTTTTAACATATGTA
Found at i:10301 original size:27 final size:26
Alignment explanation
Indices: 10228--10305 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
10218 TTTTGTCAGC
*
10228 TTAGTTATCAATTTATTTACTATATG
1 TTAGTTTTCAATTTATTTACTATATG
* * *
10254 TTA--ATTAAATTT-TTAAC-ATATG
1 TTAGTTTTCAATTTATTTACTATATG
10276 TATAGTTTTCAATTTATTTACTATATG
1 T-TAGTTTTCAATTTATTTACTATATG
10303 TTA
1 TTA
10306 ATTAAATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
22 6 0.15
23 6 0.15
24 6 0.15
25 7 0.17
26 9 0.22
27 6 0.15
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.54
Consensus pattern (26 bp):
TTAGTTTTCAATTTATTTACTATATG
Found at i:13607 original size:38 final size:38
Alignment explanation
Indices: 13564--13645 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 38
13554 AAAGAACTAT
* *
13564 AAAAATTATAAAAAAAATAGAGATTGTAAAATATTGTA
1 AAAAATTATAAAAAAAATAGAAATTGTAAAAGATTGTA
* ** *
13602 GAAAATTATAAAATTATTAGAAATTGTAAAAGATTGTA
1 AAAAATTATAAAAAAAATAGAAATTGTAAAAGATTGTA
13640 AAAAAT
1 AAAAAT
13646 ATTAAATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (38 bp):
AAAAATTATAAAAAAAATAGAAATTGTAAAAGATTGTA
Found at i:13658 original size:27 final size:27
Alignment explanation
Indices: 13622--13675 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
13612 AAATTATTAG
* *
13622 AAATTGTAAAAGATTGTAAAAAATATT
1 AAATTGTAAAAAATAGTAAAAAATATT
* *
13649 AAATTTTAAAAAATAGTAAAAATTATT
1 AAATTGTAAAAAATAGTAAAAAATATT
13676 GTATCTTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (27 bp):
AAATTGTAAAAAATAGTAAAAAATATT
Found at i:13668 original size:37 final size:38
Alignment explanation
Indices: 13589--13669 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 38
13579 AATAGAGATT
* * * *
13589 GTAAAATATTGTAGAAAATTATAAAATTATTAGAAATT
1 GTAAAAGATTGTAGAAAAATATAAAATTATTAAAAATA
*
13627 GTAAAAGATTGTA-AAAAATATTAAATT-TTAAAAAATA
1 GTAAAAGATTGTAGAAAAATATAAAATTATT-AAAAATA
13664 GTAAAA
1 GTAAAA
13670 ATTATTGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 2 0.05
37 23 0.62
38 12 0.32
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (38 bp):
GTAAAAGATTGTAGAAAAATATAAAATTATTAAAAATA
Found at i:14107 original size:9 final size:9
Alignment explanation
Indices: 14079--14113 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
14069 ACATACGATT
14079 TTATAAAAA
1 TTATAAAAA
*
14088 TGTATACAAA
1 T-TATAAAAA
14098 TTATAAAAA
1 TTATAAAAA
14107 TTATAAA
1 TTATAAA
14114 TAAATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:14155 original size:19 final size:18
Alignment explanation
Indices: 14131--14180 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
14121 ATACCCATTT
*
14131 TTTATTTTTTAACATGAAA
1 TTTATTTTTTAAAAT-AAA
*
14150 TTTATTTATTAAAATAAA
1 TTTATTTTTTAAAATAAA
*
14168 -ATATTTTTTAAAA
1 TTTATTTTTTAAAA
14181 AAAACCCCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 11 0.41
18 3 0.11
19 13 0.48
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTATTTTTTAAAATAAA
Found at i:22568 original size:14 final size:14
Alignment explanation
Indices: 22546--22583 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
22536 TTTTTACCTT
*
22546 AAACTTTAAACCCA
1 AAACCTTAAACCCA
*
22560 AAACCTTAAACCCC
1 AAACCTTAAACCCA
22574 AAACCTTAAA
1 AAACCTTAAA
22584 GTTCAAGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
AAACCTTAAACCCA
Found at i:35743 original size:310 final size:311
Alignment explanation
Indices: 35180--35755 Score: 764
Period size: 310 Copynumber: 1.9 Consensus size: 311
35170 GTGTGTTTCA
* *
35180 AAATATTCCCTTAAACATTTATATGTTTCACATTTGGCAAATTCAATTTTAAGTAAAATTTCTTT
1 AAATATTCCCTTAAACATTTATAAGTTTCACATTTGGCAAATTCAATTTCAAGTAAAATTTCTTT
* * *
35245 TTATTTTCTAAAAAAATTAATTTTGGAGAATTGATGATTATAATATCTCTAATCACATAACGACT
66 TTATTTTCTAAAAAAATTAATTTTGGAGAATTGAAGATTATAATATCACTAATCACATAACAACT
* * * * *
35310 GAGAGAGAGATTAGGTCATAGACAGCCGAGAGTAAAAAGACCATAATCATCCTAACGAAAAGGGC
131 GAGAAAGAGACTAGGTCATAGACAACCGAGAGTAAAAAAACCATAATCACCCTAACGAAAAGGGC
** * * * *
35375 CACATTAAATCTTTTTCTTAGACTGTGAACAATTGTAAATAAGTGATACTACATATCATTAAAAA
196 CACATTAAATCCCTTTCTTAGACTGTCAACAATTGCAAAGAAGCGATACTACATATCATTAAAAA
35440 GTTGTTGGATTAGCTATCCATTGTGTAAAAATTATATATATATATGTTGTC
261 GTTGTTGGATTAGCTATCCATTGTGTAAAAATTATATATATATATGTTGTC
* * *
35491 AAATATTTCCTTAAACATTTATAAGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTT-TTT
1 AAATATTCCCTTAAACATTTATAAGTTTCACATTTGGCAAATTCAATTTCAAGTAAAATTTCTTT
* * * *
35555 TTCATTTTCT-AAAAAATTAATTTTGGAGAATTGACAG-TTATAATGTCACTGATCTCGTAACAA
66 TT-ATTTTCTAAAAAAATTAATTTTGGAGAATTGA-AGATTATAATATCACTAATCACATAACAA
* * * * *
35618 CTGAGAAAGAGACT-GTGTCATAGATAACCGAGAGTAAAAAAATCATAATTACCCTAGCGAAACG
129 CTGAGAAAGAGACTAG-GTCATAGACAACCGAGAGTAAAAAAACCATAATCACCCTAACGAAAAG
* * * ** ** * *
35682 GTCTACATTATATCCCTTTCTTAGTTTGTCAACGCTTGCAAAGAAGCGATGCTACATATCATTAG
193 GGCCACATTAAATCCCTTTCTTAGACTGTCAACAATTGCAAAGAAGCGATACTACATATCATTAA
35747 AAAGTTGTT
258 AAAGTTGTT
35756 ATGTAGCAAT
Statistics
Matches: 225, Mismatches: 37, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
309 1 0.00
310 160 0.71
311 64 0.28
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (311 bp):
AAATATTCCCTTAAACATTTATAAGTTTCACATTTGGCAAATTCAATTTCAAGTAAAATTTCTTT
TTATTTTCTAAAAAAATTAATTTTGGAGAATTGAAGATTATAATATCACTAATCACATAACAACT
GAGAAAGAGACTAGGTCATAGACAACCGAGAGTAAAAAAACCATAATCACCCTAACGAAAAGGGC
CACATTAAATCCCTTTCTTAGACTGTCAACAATTGCAAAGAAGCGATACTACATATCATTAAAAA
GTTGTTGGATTAGCTATCCATTGTGTAAAAATTATATATATATATGTTGTC
Found at i:36011 original size:288 final size:291
Alignment explanation
Indices: 35474--36519 Score: 941
Period size: 304 Copynumber: 3.5 Consensus size: 291
35464 GTAAAAATTA
* * * *
35474 TATATATATATGTTGTCAAATATTTCCTTAAACATTTATAAGTTTCACATTTGGTAAATTCAATT
1 TATATATATA-G-TGCCAAATATTCCCTTAAACATTTATATGTTCCACATTTGGTAAATTCAATT
* * *
35539 TCAAGTAAAGTTT-TTTTTCATTTTCTAAAAAATTAATTTTGGAGAATTGACAGTTATAATGTCA
64 TCAAGTAAAGTTTCTTTTT-ATTTGCTAAAAAATTAATTTTGAAGAATTGACAATTATAATGTCA
* * * * * *
35603 CTGATCTCGTAACAACTGAGAAAGAGACT-GTGT-CATAGATAACCGAGAGTAAAAAAATCATAA
128 CTGATCACGTAACAACTGAAAAAGAAACTGGTTTACA-A-ACAACCGAGAGTAAAAAAACCATAA
** * * ** ** * ** *
35666 TTACCCTAGCG-AAACGGTCTACATTATATCCCTTTCTTAGTTTGTCAACGCTTGCAAAGAAGCG
191 TCGCCCTAGCGAAAAGGGTC-ACATTAAAT-ATTTTCTTAGACTATCAACAATTGCAAATAAGCG
*
35730 ATGCTACATATCATTAGAAAGTTGTT-A-TGTAGCAAT
254 ATGCTACATGTCATTAGAAAGTTGTTCATTGTAGCAAT
*
35766 TATATATATAGTGCCAAATATTCCCTT-AA-ATTTATATGTTCCACATTTGGTAAATTCAATTTT
1 TATATATATAGTGCCAAATATTCCCTTAAACATTTATATGTTCCACATTTGGTAAATTCAATTTC
* * * *
35829 AAGTAAAGTTTCTTTTTGTTTGCTAAAAAAATAATTTTGGAGAATTGACAATTATAATGTTACTG
66 AAGTAAAGTTTCTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGACAATTATAATGTCACTG
* * * * * * * *
35894 ATCACATAACAACTAAAAAACAAATTGGTTTACAAACAATCGAGATTAAAAACACCATGATCGCC
131 ATCACGTAACAACTGAAAAAGAAACTGGTTTACAAACAACCGAGAGTAAAAAAACCATAATCGCC
* * * *
35959 CTAGCGAAAAGGGGCACATTACATATTTTTCTTAGACTATCAACAATTGCAAATAAGTGATGTTA
196 CTAGCGAAAAGGGTCACATTAAATA-TTTTCTTAGACTATCAACAATTGCAAATAAGCGATGCTA
*
36024 AATGTCATTAGAAAGCTATTCGATTAGCTATCCATTGTGTAGCAAT
260 CATGTCATTAG-AA---A---G-TT-G-T-T-CA-T-TGTAGCAAT
* * *
36070 TATATATAT--TGTCAAATATTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTC
1 TATATATATAGTGCCAAATATTCCCTTAAACATTTATATGTTCCACATTTGGTAAATTCAATTTC
* * * *
36133 AAGTAAAGTTTCTTTTTATTTTCTAAAAATTTAATTTTGAAAAATTGACATTTATAATGTCACTG
66 AAGTAAAGTTTCTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGACAATTATAATGTCACTG
* * * * * * * * * *
36198 ATCATGTAACGACTGAAAGAGAAACTGGATAATAGACAACCAAGAGTAAAAAGACCATAATCGCT
131 ATCACGTAACAACTGAAAAAGAAACTGGTTTACAAACAACCGAGAGTAAAAAAACCATAATCGCC
* ** * * *
36263 ATAATGAAAAGGGTCACATTAAATCATTTTCTTAGACTATCAACAATTGCATATAAGGGATGCCA
196 CTAGCGAAAAGGGTCACATTAAAT-ATTTTCTTAGACTATCAACAATTGCAAATAAGCGATGCTA
*
36328 CATGTCATTAGAAAGTTGTTGGATTAGCTACCCAATATGTGGCAAT
260 CATGTCATTAGAAA---GTT-G--T---T---C-AT-TGTAGCAAT
* *
36374 TATATATACATATTGCCAAATATTCCCTT-AA-ATTTATATGTTCCACATTTGATAAATTCAATT
1 TATATAT--ATAGTGCCAAATATTCCCTTAAACATTTATATGTTCCACATTTGGTAAATTCAATT
* * * *
36437 TCAAGTAAAATGTCTTTTTATTTGCTAAAAAATTAATTTTGAAGAATT-A-AAGGTTATAGTGAC
64 TCAAGTAAAGTTTCTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGACAA--TTATAATGTC
* *
36500 ACTCATCACGTAACGACTGA
127 ACTGATCACGTAACAACTGA
36520 GAGAGAGATT
Statistics
Matches: 617, Mismatches: 101, Indels: 58
0.80 0.13 0.07
Matches are distributed among these distances:
288 179 0.29
289 19 0.03
290 16 0.03
291 1 0.00
292 11 0.02
295 1 0.00
296 2 0.00
297 1 0.00
298 1 0.00
299 4 0.01
300 4 0.01
301 1 0.00
302 15 0.02
303 4 0.01
304 238 0.39
305 3 0.00
306 101 0.16
307 2 0.00
308 14 0.02
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (291 bp):
TATATATATAGTGCCAAATATTCCCTTAAACATTTATATGTTCCACATTTGGTAAATTCAATTTC
AAGTAAAGTTTCTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGACAATTATAATGTCACTG
ATCACGTAACAACTGAAAAAGAAACTGGTTTACAAACAACCGAGAGTAAAAAAACCATAATCGCC
CTAGCGAAAAGGGTCACATTAAATATTTTCTTAGACTATCAACAATTGCAAATAAGCGATGCTAC
ATGTCATTAGAAAGTTGTTCATTGTAGCAAT
Found at i:36338 original size:592 final size:602
Alignment explanation
Indices: 35180--36484 Score: 1555
Period size: 592 Copynumber: 2.2 Consensus size: 602
35170 GTGTGTTTCA
* *
35180 AAATATTCCCTTAAACATTTATATGTTTCACATTTGGCAAATTCAATTTTAAGTAAAATTTCTTT
1 AAATATTCCCTT-AA-ATTTATATGTTCCACATTTGGTAAATTCAATTTTAAGTAAAATTTCTTT
* ** *
35245 TTATTTTCTAAAAAAATTAATTTTGGAGAATTGATGATTATAATATCTCTAATCACATAACGACT
64 TTATTTGCTAAAAAAA-TAATTTTGGAGAATTGACAATTATAATATCTCTAATCACATAACAACT
* * * * * * * * * *
35310 GAGAGAGAGATTAGGTCATAGACAGCCGAGAGTAAAAAGACCATAATCATCCTAACGAAAAGGGC
128 AAAAAACAAATTAGGTCACAAACAACCGAGAGTAAAAACACCATAATCACCCTAACGAAAAGGGC
* * * * *
35375 CACATTAAATCTTTTTCTTAGACTGTGAACAATTGTAAATAAGTGATACTACATATCATTAAAAA
193 CACATTAAATATTTTTCTTAGACTATCAACAATTGCAAATAAGTGATACTAAATATCATTAAAAA
* * *
35440 GTTGTTGGATTAGCTATCCATTGTGTAAAAATTATATATATATATGTTGTCAAATATTTCCTTAA
258 GCTATTCGATTAGCTATCCATTGTGTAAAAA-TATATATATATA-GTTGTCAAATATTTCCTTAA
35505 ACATTTATAAGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTTTTTTCATTTTCTAAAAA
321 ACATTTATAAGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTTTTTTCATTTTCTAAAAA
* * *
35570 ATTAATTTTGGAGAATTGACAGTTATAATGTCACTGATCTCGTAACAACTGAGAAAGAGACTGTG
386 ATTAATTTTGAAAAATTGACAGTTATAATGTCACTGATCTCGTAACAACTGAGAAAGAAACTGTG
* * * * * * * * *
35635 TCATAGATAACCGAGAGTAAAAAAATCATAATTACCCTAGCGAAACGGTCTACATTATATCCCTT
451 TAATAGACAACCAAGAGTAAAAAAACCATAATCACCATAACGAAACGGTCTACATTAAATCACTT
** * ** *
35700 TCTTAGTTTGTCAACGCTTGCAAAGAAGCGATGCTACATATCATTAGAAAGTTGTT-A-T-G-TA
516 TCTTAGACTATCAACAATTGCAAAGAAGCGATGCCACATATCATTAGAAAGTTGTTGATTAGCTA
35761 -GCAATTATATAT-ATAGTGCC
581 GGCAATTATATATAATAGTGCC
*
35781 AAATATTCCCTTAAATTTATATGTTCCACATTTGGTAAATTCAATTTTAAGTAAAGTTTCTTTTT
1 AAATATTCCCTTAAATTTATATGTTCCACATTTGGTAAATTCAATTTTAAGTAAAATTTCTTTTT
* * *
35846 GTTTGCTAAAAAAATAATTTTGGAGAATTGACAATTATAATGT-TACTGATCACATAACAACTAA
66 ATTTGCTAAAAAAATAATTTTGGAGAATTGACAATTATAATATCT-CTAATCACATAACAACTAA
* * * * * * *
35910 AAAACAAATT-GGTTTACAAACAATCGAGATTAAAAACACCATGATCGCCCTAGCGAAAAGGGGC
130 AAAACAAATTAGG-TCACAAACAACCGAGAGTAAAAACACCATAATCACCCTAACGAAAAGGGCC
* ** * *
35974 ACATTACATATTTTTCTTAGACTATCAACAATTGCAAATAAGTGATGTTAAATGTCATTAGAAAG
194 ACATTAAATATTTTTCTTAGACTATCAACAATTGCAAATAAGTGATACTAAATATCATTAAAAAG
**
36039 CTATTCGATTAGCTATCCATTGTGT-AGCA-AT-TATATATA-TTGTCAAATATTTCCTTAAACA
259 CTATTCGATTAGCTATCCATTGTGTAAAAATATATATATATAGTTGTCAAATATTTCCTTAAACA
* *
36100 TTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTCTTTTT-ATTTTCTAAAAATT
324 TTTATAAGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTT-TTTTTCATTTTCTAAAAAAT
* *
36164 TAATTTTGAAAAATTGACATTTATAATGTCACTGATCAT-GTAACGACTGA-AAGAGAAACTG-G
388 TAATTTTGAAAAATTGACAGTTATAATGTCACTGATC-TCGTAACAACTGAGAA-AGAAACTGTG
* * * * * *
36226 ATAATAGACAACCAAGAGTAAAAAGACCATAATCGCTATAATGAAAAGGGTC-ACATTAAATCAT
451 -TAATAGACAACCAAGAGTAAAAAAACCATAATCACCATAACG-AAACGGTCTACATTAAATCAC
* * * *
36290 TTTCTTAGACTATCAACAATTGCATATAAGGGATGCCACATGTCATTAGAAAGTTGTTGGATTAG
514 TTTCTTAGACTATCAACAATTGCAAAGAAGCGATGCCACATATCATTAGAAAGTTGTT-GATTAG
*
36355 CTACCCAATATGTGGCAATTATATATACATATTGCC
578 -----C--TA---GGCAATTATATATA-ATAGTGCC
* * *
36391 AAATATTCCCTTAAATTTATATGTTCCACATTTGATAAATTCAATTTCAAGTAAAATGTCTTTTT
1 AAATATTCCCTTAAATTTATATGTTCCACATTTGGTAAATTCAATTTTAAGTAAAATTTCTTTTT
* *
36456 ATTTGCTAAAAAATTAATTTTGAAGAATT
66 ATTTGCTAAAAAAATAATTTTGGAGAATT
36485 AAAGGTTATA
Statistics
Matches: 597, Mismatches: 82, Indels: 41
0.83 0.11 0.06
Matches are distributed among these distances:
591 3 0.01
592 217 0.36
593 13 0.02
594 9 0.02
595 3 0.01
596 1 0.00
597 5 0.01
598 164 0.27
599 60 0.10
600 2 0.00
601 12 0.02
604 2 0.00
608 12 0.02
610 94 0.16
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (602 bp):
AAATATTCCCTTAAATTTATATGTTCCACATTTGGTAAATTCAATTTTAAGTAAAATTTCTTTTT
ATTTGCTAAAAAAATAATTTTGGAGAATTGACAATTATAATATCTCTAATCACATAACAACTAAA
AAACAAATTAGGTCACAAACAACCGAGAGTAAAAACACCATAATCACCCTAACGAAAAGGGCCAC
ATTAAATATTTTTCTTAGACTATCAACAATTGCAAATAAGTGATACTAAATATCATTAAAAAGCT
ATTCGATTAGCTATCCATTGTGTAAAAATATATATATATAGTTGTCAAATATTTCCTTAAACATT
TATAAGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTTTTTTCATTTTCTAAAAAATTAA
TTTTGAAAAATTGACAGTTATAATGTCACTGATCTCGTAACAACTGAGAAAGAAACTGTGTAATA
GACAACCAAGAGTAAAAAAACCATAATCACCATAACGAAACGGTCTACATTAAATCACTTTCTTA
GACTATCAACAATTGCAAAGAAGCGATGCCACATATCATTAGAAAGTTGTTGATTAGCTAGGCAA
TTATATATAATAGTGCC
Found at i:36516 original size:306 final size:303
Alignment explanation
Indices: 35755--36525 Score: 947
Period size: 304 Copynumber: 2.5 Consensus size: 303
35745 AGAAAGTTGT
*
35755 TATGTAGCAATTATATATATAGTGCCAAATATTCCCTTAAATTTATATGTTCCACATTTGGTAAA
1 TATGTAGCAATTATATATATATTGCCAAATATTCCCTTAAATTTATATGTTCCACATTTGGTAAA
* * * *
35820 TTCAATTTTAAGTAAAGTTTCTTTTTGTTTGCTAAAAAAATAATTTTGGAGAATTGACAATTATA
66 TTCAATTTCAAGTAAAGTTTCTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGA-AATTATA
* * * * * * * * * * * *
35885 ATGTTACTGATCACATAACAACTAAAAAACAAATTGGTTTACAAACAATCGAGATTAAAAACACC
130 ATGTCACTGATCACGTAACGACTGAAAGAGAAACTGGATAACAAACAACCAAGAGTAAAAACACC
* * * *
35950 ATGATCGCCCTAGCGAAAAGGGGCACATTACATATTTTTCTTAGACTATCAACAATTGCAAATAA
195 ATAATCGCCATAACGAAAAGGGGCACATTAAATATTTTTCTTAGACTATCAACAATTGCAAATAA
* ** * *
36015 GTGATGTTAAATGTCATTAGAAAGCTATTCGATTAGCTATCCAT
260 GGGATGCCAAATGTCATTAGAAAGCTATTCGATTAGCTACCCAA
* * * *
36059 TGTGTAGCAA-T-TATATATATTGTCAAATATTTCCTTAAACATTTATATGTTTCACATTTGGTA
1 TATGTAGCAATTATATATATATTGCCAAATATTCCCTT-AA-ATTTATATGTTCCACATTTGGTA
* * * *
36122 AATTCAATTTCAAGTAAAGTTTCTTTTTATTTTCTAAAAATTTAATTTTGAAAAATTGACATTTA
64 AATTCAATTTCAAGTAAAGTTTCTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGA-AATTA
* * * *
36187 TAATGTCACTGATCATGTAACGACTGAAAGAGAAACTGGATAATAGACAACCAAGAGTAAAAAGA
128 TAATGTCACTGATCACGTAACGACTGAAAGAGAAACTGGATAACAAACAACCAAGAGTAAAAACA
* * * *
36252 CCATAATCGCTATAATGAAAAGGGTCACATTAAATCA-TTTTCTTAGACTATCAACAATTGCATA
193 CCATAATCGCCATAACGAAAAGGGGCACATTAAAT-ATTTTTCTTAGACTATCAACAATTGCAAA
* * * *
36316 TAAGGGATGCCACATGTCATTAGAAAGTTGTTGGATTAGCTACCCAA
257 TAAGGGATGCCAAATGTCATTAGAAAGCTATTCGATTAGCTACCCAA
* *
36363 TATGTGGCAATTATATATACATATTGCCAAATATTCCCTTAAATTTATATGTTCCACATTTGATA
1 TATGTAGCAATTATATAT--ATATTGCCAAATATTCCCTTAAATTTATATGTTCCACATTTGGTA
* *
36428 AATTCAATTTCAAGTAAAATGTCTTTTTATTTGCTAAAAAATTAATTTTGAAGAATT-AAAGGTT
64 AATTCAATTTCAAGTAAAGTTTCTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGAAA--TT
* * * *
36492 ATAGTGACACTCATCACGTAACGACTGAGAGAGA
127 ATAATGTCACTGATCACGTAACGACTGAAAGAGA
36526 GATTGGGTCA
Statistics
Matches: 395, Mismatches: 63, Indels: 16
0.83 0.13 0.03
Matches are distributed among these distances:
302 22 0.06
303 3 0.01
304 238 0.60
305 3 0.01
306 109 0.28
307 2 0.01
308 18 0.05
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (303 bp):
TATGTAGCAATTATATATATATTGCCAAATATTCCCTTAAATTTATATGTTCCACATTTGGTAAA
TTCAATTTCAAGTAAAGTTTCTTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGAAATTATAA
TGTCACTGATCACGTAACGACTGAAAGAGAAACTGGATAACAAACAACCAAGAGTAAAAACACCA
TAATCGCCATAACGAAAAGGGGCACATTAAATATTTTTCTTAGACTATCAACAATTGCAAATAAG
GGATGCCAAATGTCATTAGAAAGCTATTCGATTAGCTACCCAA
Done.