Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002170.1 Hibiscus syriacus cultivar Beakdansim tig00004426_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: 194103
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:17450 original size:36 final size:36
Alignment explanation
Indices: 17403--17473 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
17393 ACATTGAAAT
17403 GATTGGCAATGGAGAGTAAAACTCAACAATGTATAG
1 GATTGGCAATGGAGAGTAAAACTCAACAATGTATAG
*
17439 GATTGGCAATGGAGGGTAAAACTCAACAATGTATA
1 GATTGGCAATGGAGAGTAAAACTCAACAATGTATA
17474 TTTGAGGTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (36 bp):
GATTGGCAATGGAGAGTAAAACTCAACAATGTATAG
Found at i:30634 original size:22 final size:23
Alignment explanation
Indices: 30617--30682 Score: 102
Period size: 22 Copynumber: 3.0 Consensus size: 23
30607 CTCGTATAAA
30617 TGCA-CGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
30639 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
30661 TGCACCGTAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
30683 GATGTCCATA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 35 0.83
23 7 0.17
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:32397 original size:21 final size:21
Alignment explanation
Indices: 32373--32417 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32363 TCTTGTTCGT
* *
32373 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
32394 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
32415 TTG
1 TTG
32418 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:35523 original size:22 final size:22
Alignment explanation
Indices: 35482--35548 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
35472 CTCGTATAAA
35482 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
35505 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
35527 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
35549 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:37254 original size:21 final size:21
Alignment explanation
Indices: 37230--37274 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
37220 TCTTGTTCGT
* *
37230 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
37251 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
37272 TTG
1 TTG
37275 CCCAGAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:39052 original size:12 final size:12
Alignment explanation
Indices: 39035--39059 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39025 AAGATAAAAT
39035 TTATACATTAGA
1 TTATACATTAGA
39047 TTATACATTAGA
1 TTATACATTAGA
39059 T
1 T
39060 CAAAGTTTGT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTATACATTAGA
Found at i:39658 original size:81 final size:81
Alignment explanation
Indices: 39560--39720 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 81
39550 ACTCAAACTC
39560 AGGACCTCAATAAAAATGATATTC-TTTTAATCACTTAAATCAAATCACTAAGTTGAATTATTAT
1 AGGACCTCAATAAAAATGATATTCTTTTTAATCACTTAAATC-AATCACTAAGTTGAATTATTAT
39624 AATAAATGTAATTTTTT
65 AATAAATGTAATTTTTT
39641 AGGACCTCAATAAAAATGATATTCTTTTTAATCACTTAAATCAATCACTAAGTTGAATTATTATA
1 AGGACCTCAATAAAAATGATATTCTTTTTAATCACTTAAATCAATCACTAAGTTGAATTATTATA
39706 ATAAATGTAATTTTT
66 ATAAATGTAATTTTT
39721 GTTAAACTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 62 0.78
82 17 0.22
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (81 bp):
AGGACCTCAATAAAAATGATATTCTTTTTAATCACTTAAATCAATCACTAAGTTGAATTATTATA
ATAAATGTAATTTTTT
Found at i:45783 original size:28 final size:29
Alignment explanation
Indices: 45752--45827 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 29
45742 ACAAATGAAA
45752 TTAATTAATCTTTTGAAAAA-TTGA-AGAT
1 TTAATTAATCTTTTGAAAAATTTGAGAG-T
* *
45780 TTAA-TCAT-TTTTTATAAAATTTGAGAGT
1 TTAATTAATCTTTTGA-AAAATTTGAGAGT
* *
45808 TTATTTAATCTTTAGAAAAA
1 TTAATTAATCTTTTGAAAAA
45828 AATTAAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
26 5 0.14
27 7 0.19
28 12 0.32
29 9 0.24
30 4 0.11
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (29 bp):
TTAATTAATCTTTTGAAAAATTTGAGAGT
Found at i:45883 original size:24 final size:24
Alignment explanation
Indices: 45826--45883 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
45816 TCTTTAGAAA
45826 AAAAT-TAAATAAAATAAATTTAT
1 AAAATATAAATAAAATAAATTTAT
* *
45849 AAAATAAAAATATAATAAA-TTAT
1 AAAATATAAATAAAATAAATTTAT
45872 AAAACTATAAAT
1 AAAA-TATAAAT
45884 TTTAAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAATATAAATAAAATAAATTTAT
Found at i:46697 original size:21 final size:21
Alignment explanation
Indices: 46658--46697 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
46648 TTATTCACAT
* * *
46658 ATAAATTATTATATGAATATC
1 ATAAATTATCACATCAATATC
46679 ATAAATTATCACATCAATA
1 ATAAATTATCACATCAATA
46698 ATATAACAGT
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:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (21 bp):
ATAAATTATCACATCAATATC
Found at i:46703 original size:21 final size:20
Alignment explanation
Indices: 46656--46703 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
46646 TATTATTCAC
* * *
46656 ATATAAATTATTATATGAAT
1 ATATAAATTATCACATCAAT
46676 ATCATAAATTATCACATCAAT
1 AT-ATAAATTATCACATCAAT
46697 AATATAA
1 -ATATAA
46704 CAGTTAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (20 bp):
ATATAAATTATCACATCAAT
Found at i:51148 original size:64 final size:63
Alignment explanation
Indices: 51035--51155 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 63
51025 GCATAAATTC
* * * *
51035 CATTCGATGTTTGTATTTAAGGGGGTGCATCAATGCACTACTTGTGCATCGATACACTGATGA
1 CATTCGATGTTTGTATTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACACTGATGA
* * * *
51098 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATATACTTCATGTGCATCGATACAC
1 CATTCGATGTTTGTA-TTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACAC
51156 CTTGAACAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 14 0.29
64 35 0.71
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (63 bp):
CATTCGATGTTTGTATTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACACTGATGA
Found at i:63904 original size:29 final size:27
Alignment explanation
Indices: 63866--63934 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 27
63856 ATCGATATTT
63866 ATATTAAATTAGATTAAATAT-TATATATA
1 ATATTAAATTA-ATT-AAT-TCTATATATA
* *
63895 TTATTAAATTAATTTATTCTATATATA
1 ATATTAAATTAATTAATTCTATATATA
63922 ATATTAAAATTAA
1 ATATT-AAATTAA
63935 AAATTTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.03
27 14 0.40
28 10 0.29
29 10 0.29
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (27 bp):
ATATTAAATTAATTAATTCTATATATA
Found at i:63918 original size:25 final size:27
Alignment explanation
Indices: 63884--63934 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
63874 TTAGATTAAA
63884 TATTATATATAT-TATT-AAATTAATT
1 TATTATATATATATATTAAAATTAATT
*
63909 TATTCTATATATAATATTAAAATTAA
1 TATTATATATAT-ATATTAAAATTAA
63935 AAATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
27 4 0.18
28 7 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
TATTATATATATATATTAAAATTAATT
Found at i:64249 original size:23 final size:22
Alignment explanation
Indices: 64222--64270 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
64212 TCACCTAAGA
*
64222 TATTTATATACCTAAAATATTAT
1 TATTTAT-TACCTAAAATATCAT
*
64245 TATTT-TTATCTAAAATATCAT
1 TATTTATTACCTAAAATATCAT
64266 T-TTTA
1 TATTTA
64271 ACATTTTCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.13
21 14 0.61
22 1 0.04
23 5 0.22
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTATTACCTAAAATATCAT
Found at i:65094 original size:23 final size:24
Alignment explanation
Indices: 65050--65094 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
65040 TATTAAGAGG
* *
65050 TAAATTTTTAAAGTCTTTAAAAAA
1 TAAATTTTTAAAGTCATAAAAAAA
*
65074 TAAATTTTT-AAGTGATAAAAA
1 TAAATTTTTAAAGTCATAAAAA
65095 TAAATTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (24 bp):
TAAATTTTTAAAGTCATAAAAAAA
Found at i:70410 original size:60 final size:60
Alignment explanation
Indices: 70283--70410 Score: 132
Period size: 60 Copynumber: 2.1 Consensus size: 60
70273 TAGTTAAGTA
* * * * *** *
70283 ACCATTTTAAAATTTTTAATAGTCGAACGACTCAACAAAGAAATACCTTATAGTTAGGGG
1 ACCATTTTAAAATTTTTAATAATCGAACAACTAAACAAAGAAATACCCTATAACCAGAGG
* * **
70343 ACAATTTTATAATTTTTAATAATCGGGCAACTAAACAAA-ACAATACCCTATAACCAGAGG
1 ACCATTTTAAAATTTTTAATAATCGAACAACTAAACAAAGA-AATACCCTATAACCAGAGG
70403 ACCATTTT
1 ACCATTTT
70411 TGTGATTTAC
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (60 bp):
ACCATTTTAAAATTTTTAATAATCGAACAACTAAACAAAGAAATACCCTATAACCAGAGG
Found at i:70443 original size:15 final size:15
Alignment explanation
Indices: 70423--70455 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
70413 TGATTTACTC
70423 AAATTTTTAACGTTA
1 AAATTTTTAACGTTA
*
70438 AAA-TTTTACCGTTA
1 AAATTTTTAACGTTA
70452 AAAT
1 AAAT
70456 AAAATTAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.81
15 3 0.19
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (15 bp):
AAATTTTTAACGTTA
Found at i:75565 original size:2 final size:2
Alignment explanation
Indices: 75558--75617 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
75548 ATATTAACTC
75558 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75600 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
75618 CAATCTAGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89506 original size:31 final size:31
Alignment explanation
Indices: 89471--89529 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
89461 AAAAATAGAC
*
89471 GTTTAATGTTTTCTCTGTTACACTTTTATGT
1 GTTTAATATTTTCTCTGTTACACTTTTATGT
*
89502 GTTTAATATTTTTTCTGTTACACTTTTA
1 GTTTAATATTTTCTCTGTTACACTTTTA
89530 GGTGCTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.59
Consensus pattern (31 bp):
GTTTAATATTTTCTCTGTTACACTTTTATGT
Found at i:91725 original size:18 final size:18
Alignment explanation
Indices: 91702--91746 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
91692 AGAATTTCAT
*
91702 GGTGGCTGCCGTGGCTAC
1 GGTGGCCGCCGTGGCTAC
91720 GGTGGCCGCCGTGGCTAC
1 GGTGGCCGCCGTGGCTAC
*
91738 GGAGGCCGC
1 GGTGGCCGC
91747 GGAGGAAGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.07, C:0.31, G:0.47, T:0.16
Consensus pattern (18 bp):
GGTGGCCGCCGTGGCTAC
Found at i:96371 original size:30 final size:35
Alignment explanation
Indices: 96335--96411 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 35
96325 TAGTAATTAC
*
96335 TAATAATATA-A-CAT-ATA-TAAAT-ATAACTAA
1 TAATAATATAGATCATAATAGTAAATAAAAACTAA
96365 TAATAATATAGATCATAAATAGTAAATAAAAACTAA
1 TAATAATATAGATCAT-AATAGTAAATAAAAACTAA
96401 TAATTAATATA
1 TAA-TAATATA
96412 TTATTCACAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 10 0.26
31 1 0.03
32 3 0.08
34 3 0.08
35 5 0.13
36 10 0.26
37 7 0.18
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (35 bp):
TAATAATATAGATCATAATAGTAAATAAAAACTAA
Found at i:97916 original size:221 final size:218
Alignment explanation
Indices: 97508--97946 Score: 835
Period size: 221 Copynumber: 2.0 Consensus size: 218
97498 ATCCAACTTT
97508 AGTTTGGTTCATTTCTACACTACACCGAAACTAGAGCATGTGAGTATGTCTATTAAAGAATGCCC
1 AGTTTGGTTCATTTCTACACTACACCGAAACTAGAGCATGTGAGTATGTCTATTAAAGAATGCCC
97573 AATGATCGATCTCAACAATTTTTAGGATCTTGAATGCCGAAAAGGGGAGGGGATATAAAAGTTAT
66 AATGATCGATCTCAACAATTTTTAGGATCTTGAATGCCGAAAAGGGGAGGGGATATAAAAGTTAT
97638 TGGGACTTACCTTCAAGGTGGAGTCTTTACTTCCACTTAAAAGAAGCCTACTATCTGCAGACCAG
131 TGGGACTTACCTTCAAGGTGGAGTCTTTACTTCCACTTAAAAGAAGCCTACTATCTGCAGACCAG
97703 CTGAAGGGCAACATGCAAGATAC
196 CTGAAGGGCAACATGCAAGATAC
97726 AGTTTGGTTCATTTCTACAC-ACACCGAAACTAGAGCATGTGAGTATGTCTATTAAAGAATGCCC
1 AGTTTGGTTCATTTCTACACTACACCGAAACTAGAGCATGTGAGTATGTCTATTAAAGAATGCCC
97790 AATGATCGATCTCAACAATTTTTTAGGATCTTTGAATGCCGAAAAGGGGAGGGGGATATAAAAAG
66 AATGATCGATCTCAACAA-TTTTTAGGATC-TTGAATGCCGAAAAGGGGA-GGGGATAT-AAAAG
97855 TTATTGGGACTTACCTTCAAGGTGGAGTCTTTACTTCCACTTAAAAGAAGCCTACTATCTGCAGA
127 TTATTGGGACTTACCTTCAAGGTGGAGTCTTTACTTCCACTTAAAAGAAGCCTACTATCTGCAGA
97920 CCAGCTGAAGGGCAACATGCAAGATAC
192 CCAGCTGAAGGGCAACATGCAAGATAC
97947 TCATTAATCC
Statistics
Matches: 217, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
217 62 0.29
218 31 0.14
219 19 0.09
220 8 0.04
221 97 0.45
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (218 bp):
AGTTTGGTTCATTTCTACACTACACCGAAACTAGAGCATGTGAGTATGTCTATTAAAGAATGCCC
AATGATCGATCTCAACAATTTTTAGGATCTTGAATGCCGAAAAGGGGAGGGGATATAAAAGTTAT
TGGGACTTACCTTCAAGGTGGAGTCTTTACTTCCACTTAAAAGAAGCCTACTATCTGCAGACCAG
CTGAAGGGCAACATGCAAGATAC
Found at i:105135 original size:265 final size:264
Alignment explanation
Indices: 104663--105192 Score: 988
Period size: 265 Copynumber: 2.0 Consensus size: 264
104653 ATACAATTCC
104663 TTATTTTTATTAATAAAACAACTTAAATTTATTTAGTTTCACTTTTAACATAAAAATATTTAATT
1 TTATTTTTATTAATAAAACAACTTAAATTTATTTAGTTTCACTTTTAACATAAAAATATTTAATT
*
104728 AAGTATGTAAATAATTAACATAATCAAACATTAATTTAATTGACGCTATGATAATATATTTTCGT
66 AAGTATGTAAATAATTAACAGAATCAAACATTAATTTAATTGACGCTATGATAATATATTTTCGT
* *
104793 GAAAGTTGTCAGGTGTAAGTGGACTTAAAAATGCGTAAATGTCACATTCTGGAAAGGTGAGAGAT
131 GAAAGTTGTCAGGTGTAAGTGGACGTAAAAATGCATAAATGTCACATTCTGGAAAGGTGAGAGAT
104858 TAATTCTACATCAGAAAAGAAAGGTCATGAAATTTATAAACAATTGTCATGTTAATTCTATCAGA
196 TAATTCTACATCAGAAAAGAAAGGTCATGAAATTTATAAACAATTGTCATGTTAATTCTATCAGA
104923 TACA
261 TACA
104927 TTATTTTTATTAATAAAACAACTTAAATTTATTTAGTTTCACTTTTAACATAAAAAATATTTAAT
1 TTATTTTTATTAATAAAACAACTTAAATTTATTTAGTTTCACTTTTAACAT-AAAAATATTTAAT
104992 TAAGTATGTAAATAATTAACAGAATCAAACATTAATTTAATTGACGCTATGATAATATATTTTCG
65 TAAGTATGTAAATAATTAACAGAATCAAACATTAATTTAATTGACGCTATGATAATATATTTTCG
** *
105057 TGAAAGTTGTTGGGTGTGAGTGGACGTAAAAATGCATAAATGTCACATTCTGGAAAGGTGAGAGA
130 TGAAAGTTGTCAGGTGTAAGTGGACGTAAAAATGCATAAATGTCACATTCTGGAAAGGTGAGAGA
*
105122 TTAATTCTACATCAGAAAAGAAATGTCATGAAATTTATAAACAATTGTCATGTTAATTCTATCAG
195 TTAATTCTACATCAGAAAAGAAAGGTCATGAAATTTATAAACAATTGTCATGTTAATTCTATCAG
105187 ATACA
260 ATACA
105192 T
1 T
105193 CTTTTGAAAT
Statistics
Matches: 258, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
264 51 0.20
265 207 0.80
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (264 bp):
TTATTTTTATTAATAAAACAACTTAAATTTATTTAGTTTCACTTTTAACATAAAAATATTTAATT
AAGTATGTAAATAATTAACAGAATCAAACATTAATTTAATTGACGCTATGATAATATATTTTCGT
GAAAGTTGTCAGGTGTAAGTGGACGTAAAAATGCATAAATGTCACATTCTGGAAAGGTGAGAGAT
TAATTCTACATCAGAAAAGAAAGGTCATGAAATTTATAAACAATTGTCATGTTAATTCTATCAGA
TACA
Found at i:112420 original size:50 final size:51
Alignment explanation
Indices: 112366--112474 Score: 141
Period size: 50 Copynumber: 2.1 Consensus size: 51
112356 ACTCTATTTA
* *
112366 TATTATAAATAAGGTTAATATATATAAAAA-ATTATTTA-TATATTAATATG
1 TATTATAAATAAGATTAATATATACAAAAATATTATTTATTATATTAATA-G
* *
112416 TATTATAAATAATATTAATATATGCAAAAATATTATTTATTTATATTAATAG
1 TATTATAAATAAGATTAATATATACAAAAATATTATTTA-TTATATTAATAG
*
112468 TTTTATA
1 TATTATA
112475 TGTGATTTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
50 26 0.51
51 8 0.16
52 7 0.14
53 10 0.20
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.47
Consensus pattern (51 bp):
TATTATAAATAAGATTAATATATACAAAAATATTATTTATTATATTAATAG
Found at i:113902 original size:18 final size:18
Alignment explanation
Indices: 113881--113935 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
113871 ATTAAAATAT
113881 ATAAAATAAATATTAAAA
1 ATAAAATAAATATTAAAA
*
113899 ATAAAA-ATATTATTGAAAA
1 ATAAAATA-AATATT-AAAA
* *
113918 TTTAAATAAATATTAAAA
1 ATAAAATAAATATTAAAA
113936 TGTTACACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.03
18 15 0.50
19 13 0.43
20 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
ATAAAATAAATATTAAAA
Found at i:125560 original size:16 final size:16
Alignment explanation
Indices: 125538--125598 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
125528 TAATAAATAA
*
125538 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
125554 TCGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
125570 ACTAACATAAATGAAC
1 ACGAACATAAACGAAC
125586 ACGAACATAAACG
1 ACGAACATAAACG
125599 TTAGAGACTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.56, C:0.23, G:0.10, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:125585 original size:26 final size:26
Alignment explanation
Indices: 125534--125586 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
125524 CATTTAATAA
*
125534 ATAAACGAACATAAACAAACTCGAAC
1 ATAAACGAACATAAACAAAATCGAAC
125560 ATAAACGAACACT-AACATAAAT-GAAC
1 ATAAACGAACA-TAAACA-AAATCGAAC
125586 A
1 A
125587 CGAACATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.58, C:0.21, G:0.08, T:0.13
Consensus pattern (26 bp):
ATAAACGAACATAAACAAAATCGAAC
Found at i:126007 original size:19 final size:19
Alignment explanation
Indices: 125983--126025 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
125973 TTAATGGGTT
125983 CTTCCTGGAAAACCCATTA
1 CTTCCTGGAAAACCCATTA
*
126002 CTTCCTGGAAAACCTATTA
1 CTTCCTGGAAAACCCATTA
126021 CTTCC
1 CTTCC
126026 GCTATTACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (19 bp):
CTTCCTGGAAAACCCATTA
Found at i:126988 original size:29 final size:29
Alignment explanation
Indices: 126953--127034 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
126943 AAACTAAATT
*
126953 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
126982 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
127011 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
127035 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:131751 original size:29 final size:29
Alignment explanation
Indices: 131716--131797 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
131706 AAACTAAATT
*
131716 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
131745 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
131774 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
131798 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:133106 original size:26 final size:25
Alignment explanation
Indices: 133077--133154 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 25
133067 TTTAAATATT
133077 AAATAAATTATTACAATTATATTTTA
1 AAATAAATTATTA-AATTATATTTTA
133103 AAATTAAATTAGTT-AA--A-ATTTT-
1 AAA-TAAATTA-TTAAATTATATTTTA
133125 AAATAAATTATTATAATTATATTTTA
1 AAATAAATTATTA-AATTATATTTTA
133151 AAAT
1 AAAT
133155 TATTTTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
20 2 0.05
21 7 0.16
22 5 0.11
23 5 0.11
24 2 0.05
25 5 0.11
26 9 0.20
27 7 0.16
28 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (25 bp):
AAATAAATTATTAAATTATATTTTA
Found at i:133133 original size:21 final size:22
Alignment explanation
Indices: 133097--133142 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 22
133087 TTACAATTAT
133097 ATTTTAAAATTAAATTAGTTAAA
1 ATTTTAAAATTAAATTA-TTAAA
*
133120 ATTTT-AAA-TAAATTATTATA
1 ATTTTAAAATTAAATTATTAAA
133140 ATT
1 ATT
133143 ATATTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
22 3 0.14
23 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTTAAAATTAAATTATTAAA
Found at i:133157 original size:22 final size:22
Alignment explanation
Indices: 133081--133158 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
133071 AATATTAAAT
*
133081 AAATTATTACAATTATATTTTA
1 AAATTATTATAATTATATTTTA
* * *
133103 AAATTA-AATTAGTTAAAATTTTAAA
1 AAATTATTA-TAATT-ATATTTT--A
133128 TAAATTATTATAATTATATTTTA
1 -AAATTATTATAATTATATTTTA
133151 AAATTATT
1 AAATTATT
133159 TTTTTTGATT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
21 1 0.02
22 17 0.40
23 7 0.16
25 7 0.16
26 10 0.23
27 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (22 bp):
AAATTATTATAATTATATTTTA
Found at i:147379 original size:35 final size:35
Alignment explanation
Indices: 147257--147453 Score: 156
Period size: 35 Copynumber: 5.5 Consensus size: 35
147247 TTTGCAAATT
*
147257 GTTTTTGAAAATACATATATAATATATAGTTTAAAAC
1 GTTTTTGAAAAT--ATATATAATATATATTTTAAAAC
* * *
147294 ATTTTTGAAAATATGTATATTATAGT-TTTTAAATA-
1 GTTTTTGAAAATATATATAATATA-TATTTTAAA-AC
147329 -TTTTTGAAAAT-TATATAATATAGT-TTTTGAAAAC
1 GTTTTTGAAAATATATATAATATA-TATTTT-AAAAC
147363 GTTTTT-AAAATATATATAATATATACTTTTGAAAAC
1 GTTTTTGAAAATATATATAATATATA-TTTT-AAAAC
* *
147399 G-TTATGAAAACATTTATATAATATATAATTTTTAAAAAC
1 GTTTTTG-AAA-ATATATATAATATAT-A-TTTT-AAAAC
**
147438 CATTTTGAAAATATAT
1 GTTTTTGAAAATATAT
147454 TTTTTGAAAA
Statistics
Matches: 134, Mismatches: 13, Indels: 25
0.78 0.08 0.15
Matches are distributed among these distances:
33 16 0.12
34 20 0.15
35 35 0.26
36 13 0.10
37 14 0.10
38 19 0.14
39 13 0.10
40 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (35 bp):
GTTTTTGAAAATATATATAATATATATTTTAAAAC
Found at i:147400 original size:36 final size:36
Alignment explanation
Indices: 147257--147453 Score: 160
Period size: 34 Copynumber: 5.4 Consensus size: 36
147247 TTTGCAAATT
*
147257 GTTTTTGAAAATACATATATAATATATAGTTT-AAAAC
1 GTTTTTGAAAAT--ATATATAATATATATTTTGAAAAC
* * *
147294 ATTTTTGAAAATATGTAT-AT-TATAGTTTTTAAATA-
1 GTTTTTGAAAATATATATAATATATA-TTTTGAAA-AC
147329 -TTTTTGAAAAT-TATATAATATAGT-TTTTGAAAAC
1 GTTTTTGAAAATATATATAATATA-TATTTTGAAAAC
147363 GTTTTT-AAAATATATATAATATATACTTTTGAAAAC
1 GTTTTTGAAAATATATATAATATATA-TTTTGAAAAC
* * *
147399 G-TTATGAAAACATTTATATAATATATAATTTTTAAAAAC
1 GTTTTTG-AAA-ATATATATAATATAT-A-TTTTGAAAAC
**
147438 CATTTTGAAAATATAT
1 GTTTTTGAAAATATAT
147454 TTTTTGAAAA
Statistics
Matches: 132, Mismatches: 12, Indels: 31
0.75 0.07 0.18
Matches are distributed among these distances:
33 9 0.07
34 31 0.23
35 29 0.22
36 13 0.10
37 14 0.11
38 19 0.14
39 13 0.10
40 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
GTTTTTGAAAATATATATAATATATATTTTGAAAAC
Found at i:147435 original size:27 final size:27
Alignment explanation
Indices: 147405--147504 Score: 82
Period size: 26 Copynumber: 3.7 Consensus size: 27
147395 AAACGTTATG
147405 AAAACATTTATATAATATATAATTTTTA
1 AAAACATTT-TATAATATATAATTTTTA
*
147433 AAAACCATTTTGA-AA-ATAT-ATTTTTT
1 AAAA-CATTTT-ATAATATATAATTTTTA
* * * *
147459 GAAA-ATTATATAATATATAGTTTTTG
1 AAAACATTTTATAATATATAATTTTTA
* *
147485 AAAACGTTTTAAAATATATA
1 AAAACATTTTATAATATATA
147505 TAATATATAC
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
23 1 0.02
24 6 0.11
25 4 0.07
26 17 0.30
27 16 0.28
28 7 0.12
29 6 0.11
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (27 bp):
AAAACATTTTATAATATATAATTTTTA
Found at i:147460 original size:15 final size:16
Alignment explanation
Indices: 147440--147469 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
147430 TTAAAAACCA
147440 TTTTGAAAA-TATATT
1 TTTTGAAAATTATATT
147455 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
147470 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTGAAAATTATATT
Found at i:147476 original size:25 final size:25
Alignment explanation
Indices: 147412--147488 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
147402 ATGAAAACAT
*
147412 TTATATAATATATAATTTTTAAAAA
1 TTATATAATATATAATTTTTGAAAA
** * * *
147437 CCATTTTGAAAATATATTTTTTGAAAA
1 TTA-TAT-AATATATAATTTTTGAAAA
*
147464 TTATATAATATATAGTTTTTGAAAA
1 TTATATAATATATAATTTTTGAAAA
147489 CGTTTTAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 18 0.46
26 4 0.10
27 17 0.44
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (25 bp):
TTATATAATATATAATTTTTGAAAA
Found at i:147512 original size:126 final size:126
Alignment explanation
Indices: 147329--147580 Score: 463
Period size: 126 Copynumber: 2.0 Consensus size: 126
147319 TTTTTAAATA
147329 TTTTTGAAAATTATATAATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTTTG
1 TTTTTGAAAATTATATAATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTTTG
*
147394 AAAACGTTATGAAAACATTTATATAATATATAATTTTT-AAAAACCATTTTGAAAATATAT
66 AAAACGTTATGAAAACATTTACATAATATATAATTTTTAAAAAACCATTTTGAAAATATAT
147454 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACG-TTTTAAAATATATATAATATATACTTT
1 TTTTTGAAAATTATAT-A-ATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
147518 TGAAAACGTTATGAAAACATTTACATAATATATAATTTTTAAAAAACCATTTTGAAAATATAT
64 TGAAAACGTTATGAAAACATTTACATAATATATAATTTTTAAAAAACCATTTTGAAAATATAT
147581 ATAATTTATA
Statistics
Matches: 123, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
125 16 0.13
126 67 0.54
127 40 0.33
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.43
Consensus pattern (126 bp):
TTTTTGAAAATTATATAATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTTTG
AAAACGTTATGAAAACATTTACATAATATATAATTTTTAAAAAACCATTTTGAAAATATAT
Found at i:147546 original size:38 final size:35
Alignment explanation
Indices: 147460--147561 Score: 98
Period size: 38 Copynumber: 2.8 Consensus size: 35
147450 ATATTTTTTG
* * *
147460 AAAAT-TATATAATATATAGTTTTTGAAAACGTTTT
1 AAAATATACATAATATATA-ATTTTGAAAACGTTTA
* *
147495 AAAATATATATAATATATACTTTTGAAAACGTTATGA
1 AAAATATACATAATATATAATTTTGAAAACGTT-T-A
* *
147532 AAACATTTACATAATATATAATTTTTAAAA
1 AAA-ATATACATAATATATAATTTTGAAAA
147562 AACCATTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
35 18 0.32
36 14 0.25
37 3 0.05
38 22 0.39
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (35 bp):
AAAATATACATAATATATAATTTTGAAAACGTTTA
Found at i:147598 original size:41 final size:40
Alignment explanation
Indices: 147553--147636 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 40
147543 TAATATATAA
* *
147553 TTTTTAAAAAACCATTTTGAAAATATATATAATT-TATAGTT
1 TTTTTAAAAAAACATTTTAAAAATATATAT-ATTATAT-GTT
*
147594 TTTTTAAAAAAACATTTTAAAAATTTATATATTATATGTT
1 TTTTTAAAAAAACATTTTAAAAATATATATATTATATGTT
147634 TTT
1 TTT
147637 GAAAACGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 9 0.23
41 30 0.77
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (40 bp):
TTTTTAAAAAAACATTTTAAAAATATATATATTATATGTT
Found at i:149079 original size:30 final size:26
Alignment explanation
Indices: 149008--149065 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
148998 TTTTTTTCCC
149008 TTTTTCTTTTGTT-TTCATTTTGATTTTT
1 TTTTTCTTTT-TTATT-A-TTTGATTTTT
149036 TTTTTCTTTTTTATTATTTGATTTTT
1 TTTTTCTTTTTTATTATTTGATTTTT
149062 TTTT
1 TTTT
149066 CTAACATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 14 0.48
27 3 0.10
28 12 0.41
ACGTcount: A:0.09, C:0.05, G:0.05, T:0.81
Consensus pattern (26 bp):
TTTTTCTTTTTTATTATTTGATTTTT
Found at i:156078 original size:22 final size:20
Alignment explanation
Indices: 156041--156080 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
156031 TTCAAATGTT
156041 AGTTAATTTTAATTAAAAAA
1 AGTTAATTTTAATTAAAAAA
*
156061 AGTTATATGTTTAGTTAAAA
1 AGTTA-AT-TTTAATTAAAA
156081 GAATATGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (20 bp):
AGTTAATTTTAATTAAAAAA
Found at i:168209 original size:21 final size:21
Alignment explanation
Indices: 168183--168228 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
168173 AACCTGTAAA
168183 TGATCTGACTTGTTATTGAAC
1 TGATCTGACTTGTTATTGAAC
168204 TGATCTGACTTGTTATTGAAC
1 TGATCTGACTTGTTATTGAAC
168225 TGAT
1 TGAT
168229 TTGATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (21 bp):
TGATCTGACTTGTTATTGAAC
Found at i:169183 original size:2 final size:2
Alignment explanation
Indices: 169176--169209 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
169166 CCTTGCCATT
169176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
169210 ATTGTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:170272 original size:2 final size:2
Alignment explanation
Indices: 170265--170487 Score: 181
Period size: 2 Copynumber: 111.0 Consensus size: 2
170255 CTTTATACTT
* *
170265 TA TA TA TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
170307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
170349 TA TA CTT TA TA TT TA TA TT TA TA TA CA T- TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
170391 -A GTA TA TA CA TA TA CTG TA TCG TA TA -A TG TA CA T- TA TA TA
1 TA -TA TA TA TA TA TA -TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * * *
170431 TA CA TG CA TCA TA T- TA TCA TA -A TA TT TA TCA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA T-A TA TA TA TA TA T-A TA TA TA TA TA
170472 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
170488 ACTGTTTCAA
Statistics
Matches: 176, Mismatches: 30, Indels: 30
0.75 0.13 0.13
Matches are distributed among these distances:
1 7 0.04
2 158 0.90
3 11 0.06
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:170366 original size:21 final size:22
Alignment explanation
Indices: 170246--170360 Score: 51
Period size: 22 Copynumber: 5.1 Consensus size: 22
170236 AATTATAATT
*
170246 ATACT-TATACTTTATACTTTAT
1 ATACTATATACATTATA-TTTAT
**
170268 ATA-TATATATGTGTATATATATAT
1 ATACTATATACAT-TATAT-T-TAT
* *
170292 ATA-TATATATATATATATATAT
1 ATACTATATACAT-TATATTTAT
* *
170314 ATA-TATATATATATATATATAT
1 ATACTATATACAT-TATATTTAT
*
170336 ATATTTATATAC-TTATACTTTAT
1 ATA-CTATATACATTATA-TTTAT
170359 AT
1 AT
170361 TTATATTTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.01
22 41 0.52
23 12 0.15
24 25 0.32
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
ATACTATATACATTATATTTAT
Found at i:171217 original size:15 final size:16
Alignment explanation
Indices: 171180--171218 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
171170 GTTTTGACAT
*
171180 GAACTGACATTAATCC
1 GAACTGAAATTAATCC
171196 GAACTGAAATTAA-CC
1 GAACTGAAATTAATCC
*
171211 GACCTGAA
1 GAACTGAA
171219 CCCGAACTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (16 bp):
GAACTGAAATTAATCC
Found at i:171699 original size:2 final size:2
Alignment explanation
Indices: 171692--171717 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
171682 TATCTATACG
171692 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
171718 AAAACTGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:173915 original size:29 final size:29
Alignment explanation
Indices: 173880--173961 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
173870 AAACTAAATT
* *
173880 GATGTCATTACTTACATAATTTAATTAAA
1 GATGTCATTGCTTACATAATTTAAGTAAA
* * *
173909 GATGTCATTGCTTACCTCATTTAAGTAAT
1 GATGTCATTGCTTACATAATTTAAGTAAA
*
173938 GATGTCATTGCTTATATCAATTTA
1 GATGTCATTGCTTACAT-AATTTA
173962 GTTAGGTGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 39 0.89
30 5 0.11
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATAATTTAAGTAAA
Found at i:177025 original size:59 final size:59
Alignment explanation
Indices: 176898--177026 Score: 145
Period size: 59 Copynumber: 2.2 Consensus size: 59
176888 TTAGTGACAT
* * *
176898 ATTGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAATCATAGTTTGGGGGTGA
1 ATTGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAATCATAGTTTGAGGATAA
* * ** *
176957 ATATAAAATGTTCAAAAGTTT-GGGATCAATTTAGAATG-GAAGTCATGGTTTGAGGATAAA
1 AT-TGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAA-TCATAGTTTGAGGAT-AA
177017 ATTGAAATGT
1 ATTGAAATGT
177027 AAAAGAAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
58 3 0.05
59 35 0.60
60 20 0.34
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (59 bp):
ATTGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAATCATAGTTTGAGGATAA
Found at i:179438 original size:3 final size:3
Alignment explanation
Indices: 179430--179517 Score: 130
Period size: 3 Copynumber: 30.3 Consensus size: 3
179420 GACCGTTTGA
*
179430 TCT TCT TCT TCT TCT TCT TCT TCT TC- TCT TCT TCT TCT TCT TTT TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
179476 TCT TC- TCT TCT TCT TCT TCT CTCT TCT TCT TCT T-T TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT T
179518 TAAATCCACT
Statistics
Matches: 78, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
2 8 0.10
3 67 0.86
4 3 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:179461 original size:14 final size:14
Alignment explanation
Indices: 179430--179517 Score: 130
Period size: 14 Copynumber: 6.5 Consensus size: 14
179420 GACCGTTTGA
179430 TCTTCTTCTTCTTCT
1 TCTTCTTCTTC-TCT
179445 TCTTCTTCTTCTCT
1 TCTTCTTCTTCTCT
179459 TCTTCTTCTTCT-T
1 TCTTCTTCTTCTCT
179472 T-TTC-TCTTCTCT
1 TCTTCTTCTTCTCT
179484 TCTTCTTCTTCTC-
1 TCTTCTTCTTCTCT
*
179497 TCTTCTTCTTCTTT
1 TCTTCTTCTTCTCT
179511 TCTTCTT
1 TCTTCTT
179518 TAAATCCACT
Statistics
Matches: 68, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
11 6 0.09
12 5 0.07
13 17 0.25
14 29 0.43
15 11 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTCTTCTTCTCT
Found at i:187993 original size:4 final size:4
Alignment explanation
Indices: 187984--188015 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
187974 TAAACACCCA
*
187984 TATT TATT TATT TATT TATT TATT TATA TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
188016 CATATCTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TATT
Done.