Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012096.1 Kokia drynarioides strain JFW-HI SEQ_127095, 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: 111318
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:984 original size:476 final size:475
Alignment explanation
Indices: 9--904 Score: 1643
Period size: 476 Copynumber: 1.9 Consensus size: 475
1 CAATCGAG
9 TTAAAATTCAATCGGCAAATTTAAGCAAATATTAAAAGCTTGATGATAAATTTGGCCACTAACAT
1 TTAAAATTCAATCGGCAAATTTAAGCAAATATTAAAAGCTTGATGATAAATTTGGCCACTAACAT
74 TTACATATTTTGTCAAAATGACCCTAATTGTATTTTTGAGTATTTTTTGGTCATCAACATTTATT
66 TTACATATTTTGTCAAAATGACCCTAATTGTATTTTTGAGTATTTTTTGGTCATCAACATTTATT
139 TTATTTTTTTCAAATTTCTTTTTCTATCATATTTGATGAAAGTACCGTTAAAAAATTAACGGGAT
131 TTATTTTTTTCAAATTTCTTTTTCTATCATATTTGATGAAAGTACCGTTAAAAAATTAACGGGAT
204 TTATGTGGAATATTTTAATCAGATGTAATTTATTACTTAGATAACCCAAAAAGATAATTATATGT
196 TTATGTGGAATATTTTAATCAGATGTAATTTATTACTTAGATAACCCAAAAAGATAATTATATGT
269 AAAAATAATAAAATAAATAAATTATACTCGAAATTAAAAAATAACTTTTAATTTAAAGAAAATAA
261 AAAAATAATAAAATAAATAAATTATACTCGAAATTAAAAAATAACTTTTAATTTAAAGAAAATAA
*
334 ATGTAATTATCTAAAAAAAGTTTCAAAATGAATTCATATATTTGTTTTCTAACAGGTTTCAAAAA
326 ATGTAATTATCTAAAAAAAGTTTCAAAATGAATTCATATATTTGTTTACTAACAGGTTTCAAAAA
* * ** *
399 GATAATCATAAATAAGAGAAAAATACGCTTCAGCGCACTCAAACCCATGTCTTTCTGCATTGACA
391 GATAATAATAAATAAGAAAAAAATACAATTCAGCGCACTCAAACCAATGTCTTTCT-CATTGACA
* * *
464 ATAATATCTATATCAATCGAG
455 ATAACATCTATATCAATCAAA
485 TTAAAATTCAATCGGCAAATTTAAGCAAATATTAAAAGCTTGATGATAAATTTGGCCACTAACAT
1 TTAAAATTCAATCGGCAAATTTAAGCAAATATTAAAAGCTTGATGATAAATTTGGCCACTAACAT
550 TTACATATTTTGTCAAAATGACCCTAATTGTATTTTTGAGTATTTTTTGGTCATCAACATTTATT
66 TTACATATTTTGTCAAAATGACCCTAATTGTATTTTTGAGTATTTTTTGGTCATCAACATTTATT
615 TTATTTTTTTCAAATTTCTTTTTCTATCATATTTGATGAAAGTACCGTTAAAAAATTAACGGGAT
131 TTATTTTTTTCAAATTTCTTTTTCTATCATATTTGATGAAAGTACCGTTAAAAAATTAACGGGAT
680 TTATGTGGAATATTTTTAATCAGATGTAATTTATTACTTAGATAACCCAAAAAGATAATTATATG
196 TTATGTGGAATA-TTTTAATCAGATGTAATTTATTACTTAGATAACCCAAAAAGATAATTATATG
*
745 TGAAAATAATAAAATAAATAAATTATACTCGAAATTAAAAAATAACTTTTAATTTAAAGAAAATA
260 TAAAAATAATAAAATAAATAAATTATACTCGAAATTAAAAAATAACTTTTAATTTAAAGAAAATA
810 AATGTAATTATCT-AAAAAAGTTTCAAAATGAATTCATATATTTGTTTACTAACAGGTTTCAAAA
325 AATGTAATTATCTAAAAAAAGTTTCAAAATGAATTCATATATTTGTTTACTAACAGGTTTCAAAA
874 AGATAATTAATAAATCAA-ACAAAAAATACAA
390 AGATAA-TAATAAAT-AAGA-AAAAAATACAA
905 AATGTATGCA
Statistics
Matches: 410, Mismatches: 6, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
476 263 0.64
477 137 0.33
478 10 0.02
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (475 bp):
TTAAAATTCAATCGGCAAATTTAAGCAAATATTAAAAGCTTGATGATAAATTTGGCCACTAACAT
TTACATATTTTGTCAAAATGACCCTAATTGTATTTTTGAGTATTTTTTGGTCATCAACATTTATT
TTATTTTTTTCAAATTTCTTTTTCTATCATATTTGATGAAAGTACCGTTAAAAAATTAACGGGAT
TTATGTGGAATATTTTAATCAGATGTAATTTATTACTTAGATAACCCAAAAAGATAATTATATGT
AAAAATAATAAAATAAATAAATTATACTCGAAATTAAAAAATAACTTTTAATTTAAAGAAAATAA
ATGTAATTATCTAAAAAAAGTTTCAAAATGAATTCATATATTTGTTTACTAACAGGTTTCAAAAA
GATAATAATAAATAAGAAAAAAATACAATTCAGCGCACTCAAACCAATGTCTTTCTCATTGACAA
TAACATCTATATCAATCAAA
Found at i:1666 original size:20 final size:21
Alignment explanation
Indices: 1628--1666 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1618 TAAAATGAAA
**
1628 AATTTTATTTTTAGGTTTTTT
1 AATTTTATTTTTAAATTTTTT
1649 AATTTT-TTTTTAAATTTT
1 AATTTTATTTTTAAATTTT
1667 AAATTAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (21 bp):
AATTTTATTTTTAAATTTTTT
Found at i:3775 original size:17 final size:16
Alignment explanation
Indices: 3750--3784 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3740 CATTTTGAGT
3750 TTTAATTTACTTTAAA
1 TTTAATTTACTTTAAA
*
3766 TTTAAGTTTATTTTAAA
1 TTTAA-TTTACTTTAAA
3783 TT
1 TT
3785 AAAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTAATTTACTTTAAA
Found at i:5459 original size:29 final size:28
Alignment explanation
Indices: 5411--5959 Score: 304
Period size: 29 Copynumber: 18.8 Consensus size: 28
5401 GAGGTCCCTA
*
5411 AACTGTTCAAAAATTTCATTTTTATCCCCG
1 AACT-TTCAAAAATTCCATTTTTA-CCCCG
* *
5441 AACTTTCAAAAATTCCATTTTCGACCCCA
1 AACTTTCAAAAATTCCATTTT-TACCCCG
* * **
5470 AAATTTCCAAAAATTCCATTTTCGACCCTAA
1 AACTTT-CAAAAATTCCATTTT-TACCC-CG
*
5501 AAC-TTCTAAAAATTCCATTTTTACCCCA
1 AACTTTC-AAAAATTCCATTTTTACCCCG
* ** * *
5529 AAC-TTCCAAAATTTTATTTTGACCCCTA
1 AACTTTCAAAAATTCCATTTTTACCCC-G
* *
5557 AACTTCCAAAAATTCCATTTTGACCCCCG
1 AACTTTCAAAAATTCCATTTTTA-CCCCG
* * * *
5586 AACTTCCATAAATTCCATTTTGACCTCG
1 AACTTTCAAAAATTCCATTTTTACCCCG
** * * *
5614 AAAATTCTAAAAATTCAAATTTTACCCCT
1 AACTTTC-AAAAATTCCATTTTTACCCCG
* **
5643 AAC-TTCGAAAAATTACATTTTTGACATCG
1 AACTTTC-AAAAATTCCATTTTT-ACCCCG
*
5672 AAACTTCCAAAAATTTCCATTTTTACCCCCG
1 -AACTTTCAAAAA-TTCCATTTTTA-CCCCG
* *
5703 AACTTCCAAAAATTCCATTTTTAGCCCG
1 AACTTTCAAAAATTCCATTTTTACCCCG
*
5731 AAACTTTC-AAAATTTCATTTTTACCCTCG
1 -AACTTTCAAAAATTCCATTTTTACCC-CG
* * ** **
5760 ATC-TTCTAAAAATTCAATTCTCAACCTCAA
1 AACTTTC-AAAAATTCCATT-TTTACC-CCG
* *
5790 AACTTCCAAAAATTACATTTTTACCCTCG
1 AACTTTCAAAAATTCCATTTTTACCC-CG
* * * **
5819 AACCTCCAAAATTTCCATTTTTGACCCTAA
1 AACTTTCAAAAATTCCATTTTT-ACCC-CG
*
5849 AACTTTCAAAAATTACCATTTTTTCCCCG
1 AACTTTCAAAAATT-CCATTTTTACCCCG
* * * * *
5878 AA-TATCCAAAAACTCTATTTTCAACCTCG
1 AACT-TTCAAAAATTCCATTTT-TACCCCG
*
5907 AAAC-TCCAAAAATTCCATTTTTACCCCCG
1 -AACTTTCAAAAATTCCATTTTTA-CCCCG
*
5936 AA-TGTCTAAAAATTCCATCTTTTA
1 AACTTTC-AAAAATTCCAT-TTTTA
5960 ACCTTGAACT
Statistics
Matches: 406, Mismatches: 82, Indels: 62
0.74 0.15 0.11
Matches are distributed among these distances:
27 19 0.05
28 68 0.17
29 182 0.45
30 109 0.27
31 28 0.07
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (28 bp):
AACTTTCAAAAATTCCATTTTTACCCCG
Found at i:5559 original size:28 final size:28
Alignment explanation
Indices: 5449--5870 Score: 219
Period size: 30 Copynumber: 14.5 Consensus size: 28
5439 CGAACTTTCA
* *
5449 AAAATTCCATTTTCGACCCCAAAATTTCC
1 AAAATTCCATTTT-GACCCCTAAACTTCC
*
5478 AAAAATTCCATTTTCGA-CCCTAAAACTTCTA
1 -AAAATTCCATTTT-GACCCCT-AAACTTC-C
*
5509 AAAATTCCATTTTTACCCC-AAACTTCC
1 AAAATTCCATTTTGACCCCTAAACTTCC
**
5536 AAAATTTTATTTTGACCCCTAAACTTCC
1 AAAATTCCATTTTGACCCCTAAACTTCC
**
5564 AAAAATTCCATTTTGACCCCCGAACTTCC
1 -AAAATTCCATTTTGACCCCTAAACTTCC
* * * *
5593 ATAAATTCCATTTTGACCTCGAAAATTCTA
1 A-AAATTCCATTTTGACCCCTAAACTTC-C
* *
5623 AAAATTCAAATTTT-ACCCCT-AACTTCGA
1 AAAATTC-CATTTTGACCCCTAAACTTC-C
* ** *
5651 AAAATTACATTTTTGACATCGAAACTTCC
1 AAAATTCCA-TTTTGACCCCTAAACTTCC
* **
5680 AAAAATTTCCATTTTTACCCCCGAACTTCC
1 -AAAA-TTCCATTTTGACCCCTAAACTTCC
* * * *
5710 AAAAATTCCATTTTTAGCCCGAAACTTTC
1 -AAAATTCCATTTTGACCCCTAAACTTCC
* * * * *
5739 AAAATTTCATTTTTA-CCCTCGATCTTCTA
1 AAAATTCCATTTTGACCCCT-AAACTTC-C
* ** * *
5768 AAAATTCAATTCTCAACCTCAAAACTTCC
1 AAAATTCCATT-TTGACCCCTAAACTTCC
* * * *
5797 AAAAATTACATTTTTA-CCCTCGAACCTCC
1 -AAAATTCCATTTTGACCCCT-AAACTTCC
*
5826 AAAATTTCCATTTTTGA-CCCTAAAACTTTCA
1 AAAA-TTCCA-TTTTGACCCCT-AAAC-TTCC
5857 AAAATTACCATTTT
1 AAAATT-CCATTTT
5871 TTCCCCGAAT
Statistics
Matches: 302, Mismatches: 67, Indels: 46
0.73 0.16 0.11
Matches are distributed among these distances:
27 20 0.07
28 56 0.19
29 104 0.34
30 107 0.35
31 15 0.05
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAATTCCATTTTGACCCCTAAACTTCC
Found at i:5793 original size:117 final size:116
Alignment explanation
Indices: 5441--5959 Score: 443
Period size: 117 Copynumber: 4.4 Consensus size: 116
5431 TTTATCCCCG
* * ** * * *
5441 AACTTTCAAAAATTCCATTTTCGACCCCAAAATTTCCAAAAATTCCA-TTTTCGACCCTAAAAC-
1 AACTTCCAAAAATTCCATTTT-TACCCCCGAACTTCCAAAAATTCCATTTTTAG-CCC-GAAACT
* * * ** * * *
5504 TTCTAAAAATTCCATTTTTACCCCAAACTTCC-AAAATTTTATTTT-GACCCCTA
63 TTC-AAAAATTTCATTTTTACCCCGATCTTCCAAAAATTCAATTTTCAACCTCGA
* * * *
5557 AACTTCCAAAAATTCCATTTTGACCCCCGAACTTCCATAAATTCCATTTTGA-CCTCGAAA-ATT
1 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAGCC-CGAAACTTT
* * * * ** *
5620 CTAAAAA-TTCAAATTTTACCCCTAACTTCGAAAAATT-ACATTTTTGACATCGA
65 C-AAAAATTTC-ATTTTTACCCCGATCTTCCAAAAATTCA-ATTTTCAACCTCGA
5673 AACTTCCAAAAATTTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAGCCCGAAACTTT
1 AACTTCCAAAAA-TTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAGCCCGAAACTTT
* * *
5738 C-AAAATTTCATTTTTACCCTCGATCTTCTAAAAATTCAATTCTCAACCTCAA
65 CAAAAATTTCATTTTTACCC-CGATCTTCCAAAAATTCAATTTTCAACCTCGA
* * * * *
5790 AACTTCCAAAAATTACATTTTTACCCTCGAACCTCCAAAATTTCCATTTTT-GACCCTAAAACTT
1 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAG-CCC-GAAACTT
* * * * *
5854 TCAAAAATTACCATTTTTTCCCCGAAT-ATCCAAAAACTCTATTTTCAACCTCGA
64 TCAAAAATT-TCATTTTTACCCCG-ATCTTCCAAAAATTCAATTTTCAACCTCGA
*
5908 AAC-TCCAAAAATTCCATTTTTACCCCCGAA-TGTCTAAAAATTCCATCTTTTA
1 AACTTCCAAAAATTCCATTTTTACCCCCGAACT-TCCAAAAATTCCAT-TTTTA
5960 ACCTTGAACT
Statistics
Matches: 335, Mismatches: 47, Indels: 39
0.80 0.11 0.09
Matches are distributed among these distances:
113 2 0.01
114 30 0.09
115 34 0.10
116 91 0.27
117 124 0.37
118 42 0.13
119 12 0.04
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (116 bp):
AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAGCCCGAAACTTTC
AAAAATTTCATTTTTACCCCGATCTTCCAAAAATTCAATTTTCAACCTCGA
Found at i:5996 original size:59 final size:57
Alignment explanation
Indices: 5669--6005 Score: 179
Period size: 59 Copynumber: 5.7 Consensus size: 57
5659 ATTTTTGACA
* * * *
5669 TCGAAACTTCCAAAAATTTCCATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTTAGCC
1 TCGAAAC-TCCAAAAATTACCATTTTT--CCCCGAA-TGTCCAAAAACTCCATTTTCAACC
* * * * * * *
5729 -CGAAACTTTC-AAAATT-TCATTTTTACCCTCG-ATCTTCTAAAAATTCAATTCTCAACC
1 TCGAAAC-TCCAAAAATTACCATTTTT-CCC-CGAAT-GTCCAAAAACTCCATTTTCAACC
* ** ** **
5786 TCAAAACTTCCAAAAATTA-CATTTTTACCCTCGAACCTCCAAAATTTCCATTTTTGACC
1 TCGAAAC-TCCAAAAATTACCATTTTT-CCC-CGAATGTCCAAAAACTCCATTTTCAACC
* * * *
5845 -CTAAAACTTTCAAAAATTACCATTTTTTCCCCGAATATCCAAAAACTCTATTTTCAACC
1 TC-GAAAC-TCCAAAAATTACCA-TTTTTCCCCGAATGTCCAAAAACTCCATTTTCAACC
* * *
5904 TCGAAACTCCAAAAATT-CCATTTTTACCCCCGAATGTCTAAAAATTCCATCTTTTAACC
1 TCGAAACTCCAAAAATTACCATTTTT--CCCCGAATGTCCAAAAACTCCAT-TTTCAACC
* * * *
5963 TTG-AACTTCCCCAAAATTACCATCTTTCCCCGAAAGTCCAAAA
1 TCGAAAC-T-CCAAAAATTACCATTTTTCCCCGAATGTCCAAAA
6006 TTACCATTTT
Statistics
Matches: 222, Mismatches: 38, Indels: 35
0.75 0.13 0.12
Matches are distributed among these distances:
55 1 0.00
56 9 0.04
57 29 0.13
58 46 0.21
59 110 0.50
60 15 0.07
61 12 0.05
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (57 bp):
TCGAAACTCCAAAAATTACCATTTTTCCCCGAATGTCCAAAAACTCCATTTTCAACC
Found at i:11464 original size:17 final size:18
Alignment explanation
Indices: 11442--11477 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11432 TAAGCTAGTT
11442 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
11459 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
11477 A
1 A
11478 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:11796 original size:18 final size:18
Alignment explanation
Indices: 11773--11807 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11763 TTTGTGATCA
11773 AAATTGAAAGTGAAAGTT
1 AAATTGAAAGTGAAAGTT
* *
11791 AAATTGGAATTGAAAGT
1 AAATTGAAAGTGAAAGT
11808 GATATGAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTT
Found at i:15051 original size:13 final size:13
Alignment explanation
Indices: 15033--15061 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
15023 CATTTTAGCC
15033 CATTGTAGACTTT
1 CATTGTAGACTTT
15046 CATTGTAGACTTT
1 CATTGTAGACTTT
15059 CAT
1 CAT
15062 AGAACCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (13 bp):
CATTGTAGACTTT
Found at i:15166 original size:25 final size:25
Alignment explanation
Indices: 15122--15226 Score: 144
Period size: 25 Copynumber: 4.3 Consensus size: 25
15112 AAGGTACATA
*
15122 AGTGCTGGGGAAACAGAAGCACACAC
1 AGTGCT-GGGTAACAGAAGCACACAC
15148 AGTGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
15173 AATGCT--G-AACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
15195 AGTGCTGGGTAATAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
15220 AATGCTG
1 AGTGCTG
15227 AACAGAAGCG
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
22 20 0.28
23 1 0.01
24 1 0.01
25 43 0.61
26 6 0.08
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (25 bp):
AGTGCTGGGTAACAGAAGCACACAC
Found at i:15184 original size:47 final size:47
Alignment explanation
Indices: 15133--15235 Score: 197
Period size: 47 Copynumber: 2.2 Consensus size: 47
15123 GTGCTGGGGA
15133 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAATGCTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAATGCTG
*
15180 AACAGAAGCACACACAGTGCTGGGTAATAGAAGCACACACAATGCTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAATGCTG
15227 AACAGAAGC
1 AACAGAAGC
15236 GCGCTAGCAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.42, C:0.24, G:0.23, T:0.11
Consensus pattern (47 bp):
AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAATGCTG
Found at i:15443 original size:21 final size:21
Alignment explanation
Indices: 15419--15459 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15409 TGTCACAAAT
*
15419 TAATTACACA-ATCAATATTTA
1 TAATTAAACACAT-AATATTTA
15440 TAATTAAACACATAATATTT
1 TAATTAAACACATAATATTT
15460 CACATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTAAACACATAATATTTA
Found at i:17971 original size:26 final size:26
Alignment explanation
Indices: 17942--17993 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
17932 TATTGTTTTA
17942 TTTTAATAT-TTAATAATTTTATATAT
1 TTTTAATATATTAA-AATTTTATATAT
* * *
17968 TTTTTATTTATTAAAATTTTTTATAT
1 TTTTAATATATTAAAATTTTATATAT
17994 ATTAGTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTAATATATTAAAATTTTATATAT
Found at i:17976 original size:16 final size:16
Alignment explanation
Indices: 17930--17976 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
17920 AATATATATT
17930 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
17947 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
17963 TATATTTTTTATTT
1 TATATTTTTTATTT
17977 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:22081 original size:21 final size:23
Alignment explanation
Indices: 22044--22100 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
22034 TTAGTAAAAT
* *
22044 AATAATAATAATATTATATATCAA
1 AATAATATTATTATTAT-TATCAA
*
22068 AATAATATTTTTATTTATTTATCAA
1 AATAATATTATTA-TTA-TTATCAA
22093 AATAATAT
1 AATAATAT
22101 ACTTGAGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 10 0.36
25 17 0.61
26 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
AATAATATTATTATTATTATCAA
Found at i:23664 original size:23 final size:23
Alignment explanation
Indices: 23632--23734 Score: 120
Period size: 23 Copynumber: 4.5 Consensus size: 23
23622 AAGTACTTAA
* *
23632 CAGTAAGCACACACAATGCAATC
1 CAGTAGGCACACACAGTGCAATC
23655 CAGTAGGCACACACAGTGCAATC
1 CAGTAGGCACACACAGTGCAATC
23678 CAGTAGGCACACACAGTGCAAT-
1 CAGTAGGCACACACAGTGCAATC
* ** * *
23700 TAGTAGGCGTACATAGAGCAAAT-
1 CAGTAGGCACACACAGTGC-AATC
23723 CAGTAGGCACAC
1 CAGTAGGCACAC
23735 GAAGTGCGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
22 14 0.20
23 55 0.80
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (23 bp):
CAGTAGGCACACACAGTGCAATC
Found at i:23727 original size:45 final size:46
Alignment explanation
Indices: 23632--23734 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 46
23622 AAGTACTTAA
* *
23632 CAGTAAGCACACACAATGCAATCCAGTAGGCACACACAGTGCAATC
1 CAGTAGGCACACACAATGCAATCCAGTAGGCACACACAGAGCAATC
* * ** *
23678 CAGTAGGCACACACAGTGCAAT-TAGTAGGCGTACATAGAGCAAAT-
1 CAGTAGGCACACACAATGCAATCCAGTAGGCACACACAGAGC-AATC
23723 CAGTAGGCACAC
1 CAGTAGGCACAC
23735 GAAGTGCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
45 26 0.53
46 23 0.47
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (46 bp):
CAGTAGGCACACACAATGCAATCCAGTAGGCACACACAGAGCAATC
Found at i:23749 original size:23 final size:23
Alignment explanation
Indices: 23723--23776 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
23713 TAGAGCAAAT
*
23723 CAGTAGGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
23746 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
23769 CAGTAAGC
1 CAGTAAGC
23777 GCGCTAGCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.41, C:0.22, G:0.28, T:0.09
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:25418 original size:21 final size:21
Alignment explanation
Indices: 25377--25418 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
25367 CAAACACACA
*
25377 GATGTTACATATATATATTGT
1 GATGTTACATATAAATATTGT
*
25398 GATGCTTACATA-AAATTTTGT
1 GATG-TTACATATAAATATTGT
25419 TATCTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (21 bp):
GATGTTACATATAAATATTGT
Found at i:30963 original size:25 final size:25
Alignment explanation
Indices: 30917--30965 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
30907 CTTCTGTTTC
*
30917 CTTTTCTTCTTCAAAACTTTTGCTT
1 CTTTTCTTCTTCAAAACATTTGCTT
30942 CTTTTCTTTCTTCAAAA-ATTTGCT
1 CTTTTC-TTCTTCAAAACATTTGCT
30966 GTTAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.55
Consensus pattern (25 bp):
CTTTTCTTCTTCAAAACATTTGCTT
Found at i:32671 original size:3 final size:3
Alignment explanation
Indices: 32663--32687 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
32653 TCTATTTTGA
32663 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
32688 TTAGGATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:34258 original size:17 final size:16
Alignment explanation
Indices: 34231--34264 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
34221 TTTGAATTTG
*
34231 ATATCAAATTCGATAA
1 ATATCAAATTCAATAA
34247 ATATCTAAATTCAATAA
1 ATATC-AAATTCAATAA
34264 A
1 A
34265 CTAGAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (16 bp):
ATATCAAATTCAATAA
Found at i:35454 original size:2 final size:2
Alignment explanation
Indices: 35447--35474 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35437 GATGAAAAAG
35447 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
35475 CTTATCCAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45967 original size:286 final size:286
Alignment explanation
Indices: 45455--46028 Score: 1121
Period size: 286 Copynumber: 2.0 Consensus size: 286
45445 AGTTAGCCGG
45455 TTCGATTAGATAAATATCTAAAAAAAATTTAATTTAGTCCAGGTCAATGTTCACAAGTCAATTGA
1 TTCGATTAGATAAATATCTAAAAAAAATTTAATTTAGTCCAGGTCAATGTTCACAAGTCAATTGA
45520 TTTAACCTCTCTCCAGATGTTGATTTCACAACTTTGGTGCTGGTTCAATGATGTTGGAATCAGAT
66 TTTAACCTCTCTCCAGATGTTGATTTCACAACTTTGGTGCTGGTTCAATGATGTTGGAATCAGAT
*
45585 TGGTTGATCGGATTAGTTGGATTGAGAACTAGCAAAAGTACCAATTTGAATAATGGCATTGAATC
131 TGGTTGATCGGATTAGTTGGATTGAGAACTAGCAAAAGTACCAATTTGAATAATGACATTGAATC
*
45650 GGTTAAATTGAAAGAACTGATTAAAGGTAAGTTGAGTTGATTGTGGGATCGAATTTTTAACATAT
196 GGTTAAATTGAAAGAACTGATTAAAGGTAAGTTGAGTTGATTGTGGGATCAAATTTTTAACATAT
45715 TTTTTGATTTTTTATTTTTCGATGAC
261 TTTTTGATTTTTTATTTTTCGATGAC
45741 TTCGATTAGATAAATATCTAAAAAAAATTTAATTTAGTCCAGGTCAATGTTCACAAGTCAATTGA
1 TTCGATTAGATAAATATCTAAAAAAAATTTAATTTAGTCCAGGTCAATGTTCACAAGTCAATTGA
45806 TTTAACCTCTCTCCAGATGTTGATTTCACAACTTTGGTGCTGGTTCAATGATGTTGGAATCAGAT
66 TTTAACCTCTCTCCAGATGTTGATTTCACAACTTTGGTGCTGGTTCAATGATGTTGGAATCAGAT
*
45871 TGGTTGATCGGATTAGTTGGATTGAGAACTAGCAAAAGTACCAATTTGAATAATGACATTGTATC
131 TGGTTGATCGGATTAGTTGGATTGAGAACTAGCAAAAGTACCAATTTGAATAATGACATTGAATC
45936 GGTTAAATTGAAAGAACTGATTAAAGGTAAGTTGAGTTGATTGTGGGATCAAATTTTTAACATAT
196 GGTTAAATTGAAAGAACTGATTAAAGGTAAGTTGAGTTGATTGTGGGATCAAATTTTTAACATAT
46001 TTTTTGATTTTTTATTTTTCGATGAC
261 TTTTTGATTTTTTATTTTTCGATGAC
46027 TT
1 TT
46029 GACTGTTTTG
Statistics
Matches: 285, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
286 285 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (286 bp):
TTCGATTAGATAAATATCTAAAAAAAATTTAATTTAGTCCAGGTCAATGTTCACAAGTCAATTGA
TTTAACCTCTCTCCAGATGTTGATTTCACAACTTTGGTGCTGGTTCAATGATGTTGGAATCAGAT
TGGTTGATCGGATTAGTTGGATTGAGAACTAGCAAAAGTACCAATTTGAATAATGACATTGAATC
GGTTAAATTGAAAGAACTGATTAAAGGTAAGTTGAGTTGATTGTGGGATCAAATTTTTAACATAT
TTTTTGATTTTTTATTTTTCGATGAC
Found at i:47444 original size:111 final size:111
Alignment explanation
Indices: 47309--47514 Score: 299
Period size: 111 Copynumber: 1.9 Consensus size: 111
47299 ACATTATGAA
* * *
47309 CAACAGAGATACTGTTCCTGTCCTCCATGTTTGCAGGCTCGGAAGAAACCTTATCGAGTTCAGGA
1 CAACAGAGATACTGTTCCTATCCTCCATGGTTGCAGGCTCGGAAGAAACCTTATCAAGTTCAGGA
*
47374 GCAGCTTCTTCCGATCT-ATTTTCACTATCATCTGCAATGTTATTAG
66 GCAGATTCTTCCGAT-TGATTTTCACTATCATCTGCAATGTTATTAG
* * *
47420 CAACAGAGATATTGTTTCC-ATCCTCCTTGGTTGCAGGCTCGGAAGAAACGTTATCAAGTTCAGG
1 CAACAGAGATACTG-TTCCTATCCTCCATGGTTGCAGGCTCGGAAGAAACCTTATCAAGTTCAGG
* *
47484 AGCAGATTCTTCTGATTGATTTTCGCTATCA
65 AGCAGATTCTTCCGATTGATTTTCACTATCA
47515 CAAGTTCCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
110 1 0.01
111 79 0.94
112 4 0.05
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (111 bp):
CAACAGAGATACTGTTCCTATCCTCCATGGTTGCAGGCTCGGAAGAAACCTTATCAAGTTCAGGA
GCAGATTCTTCCGATTGATTTTCACTATCATCTGCAATGTTATTAG
Found at i:47728 original size:39 final size:39
Alignment explanation
Indices: 47674--47751 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
47664 TGGAGGTGAT
47674 ACAGCTACTTCTTTGTAAGAAAGACATTTCGAAGCAATG
1 ACAGCTACTTCTTTGTAAGAAAGACATTTCGAAGCAATG
47713 ACAGCTACTTCTTTGTAAGAAAGACATTTCGAAGCAATG
1 ACAGCTACTTCTTTGTAAGAAAGACATTTCGAAGCAATG
47752 GCACTGAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (39 bp):
ACAGCTACTTCTTTGTAAGAAAGACATTTCGAAGCAATG
Found at i:54417 original size:15 final size:14
Alignment explanation
Indices: 54396--54437 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
54386 TTTATTTCAG
54396 ATTATATTTTAATT
1 ATTATATTTTAATT
*
54410 ATTTATATTTTAAAT
1 A-TTATATTTTAATT
54425 ATTATATTTTAAT
1 ATTATATTTTAAT
54438 CACTTACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATATTTTAATT
Found at i:57394 original size:164 final size:164
Alignment explanation
Indices: 57123--57453 Score: 644
Period size: 164 Copynumber: 2.0 Consensus size: 164
57113 TTGTTAGATG
*
57123 TTTGGGTCCCTTTCGTTTTTGCATCGCACTATGAGTTTTCGACTGTTGGATGAAGATGCCTCATT
1 TTTGGGTCCCTTTCATTTTTGCATCGCACTATGAGTTTTCGACTGTTGGATGAAGATGCCTCATT
57188 GGATATGCATATATTGAAAATTAGATTTGAATTTTAATTAATTTTATGTTTTTAATTGTTTTTAA
66 GGATATGCATATATTGAAAATTAGATTTGAATTTTAATTAATTTTATGTTTTTAATTGTTTTTAA
57253 AATTGTTATTTTAATTAAATATATTAATATAATT
131 AATTGTTATTTTAATTAAATATATTAATATAATT
57287 TTTGGGTCCCTTTCATTTTTGCATCGCACTATGAGTTTTCGACTGTTGGATGAAGATGCCTCATT
1 TTTGGGTCCCTTTCATTTTTGCATCGCACTATGAGTTTTCGACTGTTGGATGAAGATGCCTCATT
57352 GGATATGCATATATTGAAAATTAGATTTGAATTTTAATTAATTTTATGTTTTTAATTGTTTTTAA
66 GGATATGCATATATTGAAAATTAGATTTGAATTTTAATTAATTTTATGTTTTTAATTGTTTTTAA
*
57417 AATTTTTATTTTAATTAAATATATTAATATAATT
131 AATTGTTATTTTAATTAAATATATTAATATAATT
57451 TTT
1 TTT
57454 CTTTCTTTAT
Statistics
Matches: 165, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 165 1.00
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (164 bp):
TTTGGGTCCCTTTCATTTTTGCATCGCACTATGAGTTTTCGACTGTTGGATGAAGATGCCTCATT
GGATATGCATATATTGAAAATTAGATTTGAATTTTAATTAATTTTATGTTTTTAATTGTTTTTAA
AATTGTTATTTTAATTAAATATATTAATATAATT
Found at i:60655 original size:7 final size:7
Alignment explanation
Indices: 60643--60667 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
60633 AGGGGAAAAA
60643 TTAAATT
1 TTAAATT
60650 TTAAATT
1 TTAAATT
60657 TTAAATT
1 TTAAATT
60664 TTAA
1 TTAA
60668 TAGTCTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:60916 original size:6 final size:6
Alignment explanation
Indices: 60907--61013 Score: 105
Period size: 6 Copynumber: 18.0 Consensus size: 6
60897 GATTTATTTC
* **
60907 TAAATT TAAATT T-AATT TAAATT TAAATT TAAATT TAAATT CATTTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
60954 TAAATT TAAATT T-AATT TAAATT TGAAA-- TAATTT TAAAACT TAAACTT
1 TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT T-AAATT TAAA-TT
*
61002 TAAAAT TAAATT
1 TAAATT TAAATT
61014 CAAAGTCTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
4 2 0.02
5 11 0.13
6 57 0.70
7 12 0.15
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:60930 original size:29 final size:29
Alignment explanation
Indices: 60883--60977 Score: 115
Period size: 29 Copynumber: 3.3 Consensus size: 29
60873 TACTTTTGAG
* *
60883 TTTAAA-TTATTTTAGATTT-ATTTCTAAA
1 TTTAAATTTATTTTAAATTTAAATT-TAAA
*
60911 TTTAAATTTAATTTAAATTTAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAATTTAAA
*
60940 TTTAAATTCATTTTTAAATTTAAATTT-AA
1 TTTAAATTTA-TTTTAAATTTAAATTTAAA
60969 TTTAAATTT
1 TTTAAATTT
60978 GAAATAATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.10
29 34 0.59
30 18 0.31
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (29 bp):
TTTAAATTTATTTTAAATTTAAATTTAAA
Found at i:60989 original size:17 final size:17
Alignment explanation
Indices: 60907--60991 Score: 77
Period size: 17 Copynumber: 4.9 Consensus size: 17
60897 GATTTATTTC
*
60907 TAAATTTAAATTT-AATT
1 TAAA-TTAATTTTAAATT
*
60924 TAAATTTAAATTTAAATT
1 TAAA-TTAATTTTAAATT
*
60942 TAAATTCATTTTTAAATT
1 TAAATT-AATTTTAAATT
60960 TAAATTTAA-TTTAAATT
1 TAAA-TTAATTTTAAATT
60977 TGAAA-TAATTTTAAA
1 T-AAATTAATTTTAAA
60992 ACTTAAACTT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.05
17 30 0.50
18 25 0.42
19 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
TAAATTAATTTTAAATT
Found at i:61699 original size:13 final size:13
Alignment explanation
Indices: 61681--61711 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
61671 ATTACCTGTA
61681 TTATTATTATCAT
1 TTATTATTATCAT
*
61694 TTATTATTCTCAT
1 TTATTATTATCAT
61707 TTATT
1 TTATT
61712 TCCAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTATTATCAT
Found at i:62892 original size:29 final size:29
Alignment explanation
Indices: 62843--63119 Score: 147
Period size: 29 Copynumber: 9.4 Consensus size: 29
62833 GAAGGTCCCC
* **
62843 AAACTTCTCCAAAATTTTATTTTGACCTCG
1 AAACTTC-CAAAAATTACATTTTGACCTCG
* *
62873 AAACTTCCAAAAATTATATTTTTATCC-CTG
1 AAACTTCCAAAAATTACATTTTGA-CCTC-G
* * *
62903 -AACTTCCAAAAATTCCATTTTGACCCCA
1 AAACTTCCAAAAATTACATTTTGACCTCG
* * *
62931 AAATTTCCAAAAATTACATTTTTATCTCCG
1 AAACTTCCAAAAATTACATTTTGACCT-CG
* * * *
62961 -AACTTTCAAAAATCCAGATTTTGACCTTG
1 AAACTTCCAAAAAT-TACATTTTGACCTCG
* * *
62990 AAAC-TCTC-AAAATTACCATCTT-ACCCCT
1 AAACTTC-CAAAAATTA-CATTTTGACCTCG
* *
63018 AAACTTCCAAAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTACA-TTTTGACCTCG
* * *
63048 AAACTTCCCAAAATTACCATTTTGCCCCCG
1 AAACTTCCAAAAATTA-CATTTTGACCTCG
* * * *
63078 -AA-TGTCCAAAATTTTCATTTTTAACCCCG
1 AAACT-TCCAAAAATTACA-TTTTGACCTCG
*
63107 AAACTTTCAAAAA
1 AAACTTCCAAAAA
63120 AATACCCTTT
Statistics
Matches: 186, Mismatches: 43, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
28 16 0.09
29 109 0.59
30 58 0.31
31 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTGACCTCG
Found at i:63086 original size:59 final size:59
Alignment explanation
Indices: 62862--63161 Score: 238
Period size: 58 Copynumber: 5.1 Consensus size: 59
62852 CAAAATTTTA
* * *
62862 TTTTGACCTCGAAACTTCCAAAAATTA-TATTTTTATCCCTGAACTTCCAAAAATTCCA-
1 TTTTGACCTCGAAACTTCCAAAAATTACCA-TTTTACCCCCGAACTTCCAAAAATTCCAT
* * * * * * *
62920 TTTTGACCCCAAAATTTCCAAAAATTA-CATTTTTATCTCCGAACTTTCAAAAA-TCCAGA
1 TTTTGACCTCGAAACTTCCAAAAATTACCA-TTTTACCCCCGAACTTCCAAAAATTCCA-T
* * **
62979 TTTTGACCTTGAAAC-TCTC-AAAATTACCATCTTACCCCTAAACTTCCAAAAATTCCAT
1 TTTTGACCTCGAAACTTC-CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCAT
* * * * *
63037 TTTTAACCTCGAAACTTCCCAAAATTACCATTTTGCCCCCGAA-TGTCCAAAATTTTCAT
1 TTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCGAACT-TCCAAAAATTCCAT
* * * * * * * *
63096 TTTTAACCCCGAAACTTTCAAAAAAATACCCTTTTACTCTCGAA-TGTCCAAAAATTCTAT
1 TTTTGACCTCGAAAC-TTCCAAAAATTACCATTTTACCCCCGAACT-TCCAAAAATTCCAT
63156 TTTTGA
1 TTTTGA
63162 TCCCGATTTT
Statistics
Matches: 195, Mismatches: 38, Indels: 16
0.78 0.15 0.06
Matches are distributed among these distances:
57 4 0.02
58 87 0.45
59 65 0.33
60 39 0.20
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (59 bp):
TTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCAT
Found at i:63159 original size:60 final size:59
Alignment explanation
Indices: 63023--63159 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 59
63013 CCCCTAAACT
* * ** * *
63023 TCCAAAAATTCCATTTTTAACCTCGAAACTTCCCAAAATTACCATTTTGCCCCCGAATG
1 TCCAAAAATTCTATTTTTAACCCCGAAACTTCAAAAAAATACCATTTTACCCCCGAATG
* * * *
63082 TCC-AAAATTTTCATTTTTAACCCCGAAACTTTCAAAAAAATACCCTTTTACTCTCGAATG
1 TCCAAAAATTCT-ATTTTTAACCCCGAAAC-TTCAAAAAAATACCATTTTACCCCCGAATG
63142 TCCAAAAATTCTATTTTT
1 TCCAAAAATTCTATTTTT
63160 GATCCCGATT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
58 6 0.09
59 19 0.30
60 32 0.50
61 7 0.11
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (59 bp):
TCCAAAAATTCTATTTTTAACCCCGAAACTTCAAAAAAATACCATTTTACCCCCGAATG
Found at i:63243 original size:59 final size:61
Alignment explanation
Indices: 62997--63254 Score: 196
Period size: 59 Copynumber: 4.3 Consensus size: 61
62987 TTGAAACTCT
* *
62997 CAAAATTACCATCTTACCCCT-AAACT-TCCAAAAATTCCATTTTTAA-CCTCGAAAC-TTCC
1 CAAAATTACCATTTTACCCCTCGAA-TGTCCAAAAATTCCATTTTTAACCCT-GAAACTTTCC
* * * * *
63056 CAAAATTACCATTTTGCCCC-CGAATGTCCAAAATTTTCATTTTTAACCCCGAAACTTTCA
1 CAAAATTACCATTTTACCCCTCGAATGTCCAAAAATTCCATTTTTAACCCTGAAACTTTCC
* * * * * * * **
63116 AAAAAATACCCTTTTA-CTCTCGAATGTCCAAAAATTCTATTTTTGATCCC-G--ATTTTTT
1 CAAAATTACCATTTTACCCCTCGAATGTCCAAAAATTCCATTTTT-AACCCTGAAACTTTCC
* * * * *
63174 TAAAAGTTACCGTTTTACCCCTAG-GTGTCTAAAAATTCCATTTTTAACCCTG-AACTTTCC
1 CAAAA-TTACCATTTTACCCCTCGAATGTCCAAAAATTCCATTTTTAACCCTGAAACTTTCC
*
63234 CAAAATTACCAATTTTCCCCC
1 CAAAATTACC-ATTTTACCCC
63255 CCGGGTATCC
Statistics
Matches: 154, Mismatches: 34, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
58 13 0.08
59 78 0.51
60 59 0.38
61 4 0.03
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.35
Consensus pattern (61 bp):
CAAAATTACCATTTTACCCCTCGAATGTCCAAAAATTCCATTTTTAACCCTGAAACTTTCC
Found at i:64847 original size:17 final size:18
Alignment explanation
Indices: 64825--64866 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
64815 TCAGATGAAT
*
64825 AAGAAAAGAAA-AAGAAA
1 AAGAAAAGAAATAACAAA
*
64842 AAGAAAAGAAATAACTAA
1 AAGAAAAGAAATAACAAA
64860 AAGAAAA
1 AAGAAAA
64867 TTTTACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (18 bp):
AAGAAAAGAAATAACAAA
Found at i:65199 original size:16 final size:16
Alignment explanation
Indices: 65158--65200 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
65148 TTTTTTTCTT
*
65158 AATAATAATTCTAAAA
1 AATAAAAATTCTAAAA
*
65174 AATTTAAAAATTCTTAAA
1 AA--TAAAAATTCTAAAA
65192 AATAAAAAT
1 AATAAAAAT
65201 AAATTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAAATTCTAAAA
Found at i:72251 original size:16 final size:16
Alignment explanation
Indices: 72230--72290 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
72220 TTTTTAAGAT
*
72230 AATTACTCATTTTAAA
1 AATTACTTATTTTAAA
72246 AATTACTTTATTTTTAATA
1 AATTAC-TTA-TTTTAA-A
72265 AATTA-TTATTTTAAA
1 AATTACTTATTTTAAA
72280 AA-TA-TTATTTT
1 AATTACTTATTTT
72291 TTTATCGAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 9 0.22
15 3 0.07
16 12 0.29
17 5 0.12
18 6 0.15
19 6 0.15
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTACTTATTTTAAA
Found at i:72273 original size:17 final size:16
Alignment explanation
Indices: 72239--72291 Score: 65
Period size: 15 Copynumber: 3.2 Consensus size: 16
72229 TAATTACTCA
72239 TTTTAAAAATTACTTTAT
1 TTTTAAAAATTA--TTAT
72257 TTTTAATAAATTATTA-
1 TTTTAA-AAATTATTAT
72273 TTTTAAAAA-TATTAT
1 TTTTAAAAATTATTAT
72288 TTTT
1 TTTT
72292 TTATCGAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 6 0.18
17 3 0.09
18 6 0.18
19 6 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTAAAAATTATTAT
Found at i:72285 original size:14 final size:15
Alignment explanation
Indices: 72238--72290 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 15
72228 ATAATTACTC
72238 ATTTTAAAAATTACTTT
1 ATTTTAAAAATTA--TT
72255 ATTTTTAATAAATTATT
1 A-TTTTAA-AAATTATT
72272 ATTTTAAAAA-TATT
1 ATTTTAAAAATTATT
72286 ATTTT
1 ATTTT
72291 TTTATCGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.26
15 3 0.09
16 6 0.18
17 4 0.12
18 6 0.18
19 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTAAAAATTATT
Found at i:72293 original size:17 final size:16
Alignment explanation
Indices: 72256--72294 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
72246 AATTACTTTA
*
72256 TTTTTAATAAATTATT
1 TTTTTAAAAAATTATT
*
72272 ATTTTAAAAATATTATT
1 TTTTTAAAAA-ATTATT
72289 TTTTTA
1 TTTTTA
72295 TCGAGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAAAAAATTATT
Found at i:75811 original size:3 final size:3
Alignment explanation
Indices: 75803--75834 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
75793 TCACAACCAC
75803 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
75835 CAACTGTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:87917 original size:15 final size:15
Alignment explanation
Indices: 87897--87927 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
87887 CTGCCTCCCC
87897 TCCAAGCTTCTTAAT
1 TCCAAGCTTCTTAAT
87912 TCCAAGCTTCTTAAT
1 TCCAAGCTTCTTAAT
87927 T
1 T
87928 GAAAGACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (15 bp):
TCCAAGCTTCTTAAT
Found at i:89362 original size:16 final size:17
Alignment explanation
Indices: 89331--89365 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
89321 TTAAAAACCC
89331 AAAAAATAAAACAAAAT
1 AAAAAATAAAACAAAAT
*
89348 AAAAGATAAAA-AAAAT
1 AAAAAATAAAACAAAAT
89364 AA
1 AA
89366 GTCTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (17 bp):
AAAAAATAAAACAAAAT
Found at i:98304 original size:2 final size:2
Alignment explanation
Indices: 98288--98332 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
98278 TTTTTGAATT
*
98288 TA TA -A TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
98330 TA T
1 TA T
98333 TTAAATATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:98337 original size:10 final size:10
Alignment explanation
Indices: 98297--98341 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
98287 TTATAATATC
*
98297 ATATATATAT
1 ATATATATAA
*
98307 ATATATATAT
1 ATATATATAA
98317 ATATATATAA
1 ATATATATAA
*
98327 ATATATTTAA
1 ATATATATAA
98337 ATATA
1 ATATA
98342 CTGATGTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATATATATAA
Found at i:104520 original size:12 final size:12
Alignment explanation
Indices: 104502--104536 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
104492 GTTAGAATGA
104502 ACATACATATAT
1 ACATACATATAT
* *
104514 GCATACATACAT
1 ACATACATATAT
104526 ACATACATATA
1 ACATACATATA
104537 CATGTGTCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.29
Consensus pattern (12 bp):
ACATACATATAT
Found at i:106353 original size:2 final size:2
Alignment explanation
Indices: 106346--106370 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
106336 TTTTCCTATG
106346 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 T
106371 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:111155 original size:4 final size:4
Alignment explanation
Indices: 111139--111205 Score: 64
Period size: 4 Copynumber: 16.2 Consensus size: 4
111129 ACGAAAAATG
* * *
111139 AAGA AAAA AAGA AAGA AAAA AGAGA AAGA AAGAA AAAA AAGA AAGA AAG-
1 AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAG-A AAGA AAGA AAGA AAGA
*
111188 AAGG AAGA AAGA GAAGA A
1 AAGA AAGA AAGA -AAGA A
111206 GGGGAAGAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
3 3 0.06
4 39 0.75
5 10 0.19
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:111168 original size:17 final size:17
Alignment explanation
Indices: 111142--111189 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
111132 AAAAATGAAG
111142 AAAA-AAAGAAAGAAAA
1 AAAAGAAAGAAAGAAAA
*
111158 AAGAGAAAGAAAGAAAA
1 AAAAGAAAGAAAGAAAA
111175 AAAAGAAAGAAAGAA
1 AAAAGAAAGAAAGAA
111190 GGAAGAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 3 0.10
17 26 0.90
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGAAAGAAAA
Found at i:111202 original size:17 final size:17
Alignment explanation
Indices: 111146--111207 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 17
111136 ATGAAGAAAA
*
111146 AAAGAAAGAAAAAAGAG
1 AAAGAAGGAAAAAAGAG
*
111163 AAAGAAAGAAAAAAAAGAAAG
1 AAAG-AAG-GAAAAAAG--AG
*
111184 AAAGAAGGAAGAAAGAG
1 AAAGAAGGAAAAAAGAG
111201 -AAGAAGG
1 AAAGAAGG
111208 GGAAGAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
16 7 0.19
17 6 0.16
18 2 0.05
19 13 0.35
20 3 0.08
21 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
AAAGAAGGAAAAAAGAG
Found at i:111202 original size:21 final size:19
Alignment explanation
Indices: 111146--111235 Score: 70
Period size: 17 Copynumber: 4.9 Consensus size: 19
111136 ATGAAGAAAA
111146 AAAGAAAG-A-AAAAAGAG
1 AAAGAAAGAAGAAAAAGAG
111163 AAAGAAAGAA-AAAAA-AG
1 AAAGAAAGAAGAAAAAGAG
111180 AAAGAAAGAAGGAAGAAAGAG
1 AAAGAAAGAA-GAA-AAAGAG
* *
111201 -AAGAAGGGGAAGAAGAAGAG
1 AAAGAA--AGAAGAAAAAGAG
111221 AAA-AAA-AA-AAAAAGA
1 AAAGAAAGAAGAAAAAGA
111236 ATGTGTTTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
16 6 0.10
17 22 0.36
18 6 0.10
19 2 0.03
20 15 0.25
21 7 0.11
22 3 0.05
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAGAAAAAGAG
Done.