Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003868.1 Hibiscus syriacus cultivar Beakdansim tig00008325_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: 81182
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1903 original size:20 final size:20
Alignment explanation
Indices: 1866--1904 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1856 GAAGTTTTAA
** *
1866 GATCATCATTTTCTTTTGAT
1 GATCATCATTGACCTTTGAT
1886 GATCATCATTGACCTTTGA
1 GATCATCATTGACCTTTGA
1905 AAGTAAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (20 bp):
GATCATCATTGACCTTTGAT
Found at i:2056 original size:22 final size:21
Alignment explanation
Indices: 2014--2053 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2004 GAGTTTATTT
*
2014 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2035 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2054 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:10909 original size:2 final size:2
Alignment explanation
Indices: 10902--10929 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10892 TTATTAAATA
10902 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
10930 TTTAAGTTTT
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:13393 original size:2 final size:2
Alignment explanation
Indices: 13386--13416 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13376 TAAAATATTC
13386 TA TA TA 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 TA TA TA T
13417 TTTTTTCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13715 original size:16 final size:16
Alignment explanation
Indices: 13676--13717 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
13666 CTACAAAAAA
13676 TATTATT-TTATTTAT
1 TATTATTATTATTTAT
13691 TATTATTATTATTATAT
1 TATTATTATTATT-TAT
*
13708 T-TTTTTATTA
1 TATTATTATTA
13718 AATCATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 13 0.54
17 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTATTATTTAT
Found at i:15178 original size:107 final size:107
Alignment explanation
Indices: 15060--15270 Score: 368
Period size: 107 Copynumber: 2.0 Consensus size: 107
15050 TTGTAATTAC
* * *
15060 TGTGTAGCCCTTTTAATTATTGTTGTTATTATCATTTTAGTCCTTGTAATTTTCAGGTACTCTCA
1 TGTGTAGCCCTTTTAATTATTGTTGTTATTATCATGTTAGTCCTTGTAATTCTCAGGAACTCTCA
15125 TTTTGACCATTGTATTTTGGTTTGTAATCTTCATTTGTTAAA
66 TTTTGACCATTGTATTTTGGTTTGTAATCTTCATTTGTTAAA
* *
15167 TGTGTAGCCCTTTTAGTTGTTGTTGTTATTATCATGTTAGTCCTTGTAATTCTCAGGAACTCTCA
1 TGTGTAGCCCTTTTAATTATTGTTGTTATTATCATGTTAGTCCTTGTAATTCTCAGGAACTCTCA
*
15232 TTTTGACCATTGTATTTTGGTTTGTAATCTTTATTTGTT
66 TTTTGACCATTGTATTTTGGTTTGTAATCTTCATTTGTT
15271 TTTTTATTTC
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 98 1.00
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (107 bp):
TGTGTAGCCCTTTTAATTATTGTTGTTATTATCATGTTAGTCCTTGTAATTCTCAGGAACTCTCA
TTTTGACCATTGTATTTTGGTTTGTAATCTTCATTTGTTAAA
Found at i:15415 original size:30 final size:30
Alignment explanation
Indices: 15376--15488 Score: 129
Period size: 30 Copynumber: 3.7 Consensus size: 30
15366 TTAATGGTTG
* *
15376 AGTCTTTTAAGTTTATGTATTTTCTATTTT
1 AGTCCTTTAACTTTATGTATTTTCTATTTT
* *
15406 AGTCCTTTAACTTTCTAT-TTTTAGCTATTTT
1 AGTCCTTTAACTTTATGTATTTT--CTATTTT
* * *
15437 AGTCCTTTAAGTTTTTGTATTTGCTATTTT
1 AGTCCTTTAACTTTATGTATTTTCTATTTT
*
15467 GGTCCTTTAACTTTATGTATTT
1 AGTCCTTTAACTTTATGTATTT
15489 ATTGTTTAGC
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 4 0.06
30 40 0.58
31 22 0.32
32 3 0.04
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.59
Consensus pattern (30 bp):
AGTCCTTTAACTTTATGTATTTTCTATTTT
Found at i:15435 original size:31 final size:30
Alignment explanation
Indices: 15393--15480 Score: 113
Period size: 31 Copynumber: 2.9 Consensus size: 30
15383 TAAGTTTATG
*
15393 TATTTTCTATTTTAGTCCTTTAACTTTCTA
1 TATTTGCTATTTTAGTCCTTTAACTTTCTA
* * * *
15423 TTTTTAGCTATTTTAGTCCTTTAAGTTTTTG
1 TATTT-GCTATTTTAGTCCTTTAACTTTCTA
*
15454 TATTTGCTATTTTGGTCCTTTAACTTT
1 TATTTGCTATTTTAGTCCTTTAACTTT
15481 ATGTATTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 24 0.49
31 25 0.51
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (30 bp):
TATTTGCTATTTTAGTCCTTTAACTTTCTA
Found at i:19437 original size:13 final size:13
Alignment explanation
Indices: 19410--19449 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
19400 CAAAGAGAAA
*
19410 AAAGGG-AAAATC
1 AAAGGGAAAAAAC
19422 AAAGGGAAAAAAC
1 AAAGGGAAAAAAC
*
19435 AAAGAGAAAAAAC
1 AAAGGGAAAAAAC
19448 AA
1 AA
19450 TGAGCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 6 0.24
13 19 0.76
ACGTcount: A:0.70, C:0.07, G:0.20, T:0.03
Consensus pattern (13 bp):
AAAGGGAAAAAAC
Found at i:19458 original size:13 final size:13
Alignment explanation
Indices: 19416--19459 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
19406 GAAAAAAGGG
* *
19416 AAAATCAAAGGGA
1 AAAAACAAAGAGA
19429 AAAAACAAAGAGA
1 AAAAACAAAGAGA
* *
19442 AAAAACAATGAGC
1 AAAAACAAAGAGA
19455 AAAAA
1 AAAAA
19460 GAAAATGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.70, C:0.09, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAAACAAAGAGA
Found at i:19459 original size:15 final size:13
Alignment explanation
Indices: 19427--19470 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
19417 AAATCAAAGG
*
19427 GAAAAAACAAAGA
1 GAAAAAACAATGA
19440 GAAAAAACAATGA
1 GAAAAAACAATGA
*
19453 GCAAAAAGAAAATGA
1 G-AAAAA-ACAATGA
19468 GAA
1 GAA
19471 GCACATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 13 0.48
14 7 0.26
15 7 0.26
ACGTcount: A:0.70, C:0.07, G:0.18, T:0.05
Consensus pattern (13 bp):
GAAAAAACAATGA
Found at i:20774 original size:66 final size:64
Alignment explanation
Indices: 20622--20777 Score: 199
Period size: 66 Copynumber: 2.4 Consensus size: 64
20612 ATCAGTATCA
* *
20622 TTTGAGT-TGTTTCTCTTGAAACAAATTTTGTCTCTCGAGATAATTTCTTTTGAGAAAAAAAATC
1 TTTGAGTCTGTTTCTCTCGAAACAAATTTTGTCTCTCGAGACAATTTCTTTTGAG-AAAAAAATC
* * * *
20686 TTTGATTCTTTTTCTATGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAG-AAAAAA
1 TTTGAGTCTGTTTCTCTCGAAACAAA-TTTTGTCTCTC--GAGACAATTTCTTTTGAGAAAAAAA
20750 TC
63 TC
*
20752 TTTGAGTCTGTTTCCCTCGAAACAAA
1 TTTGAGTCTGTTTCTCTCGAAACAAA
20778 ACACCCATCT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 6 0.08
65 15 0.19
66 40 0.51
68 17 0.22
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (64 bp):
TTTGAGTCTGTTTCTCTCGAAACAAATTTTGTCTCTCGAGACAATTTCTTTTGAGAAAAAAATC
Found at i:21203 original size:131 final size:130
Alignment explanation
Indices: 20898--21217 Score: 372
Period size: 131 Copynumber: 2.4 Consensus size: 130
20888 CGATCTTCCA
* ** * * *
20898 TTCTCATCATGTATAAACCGTGCCATTCCCCGACTAGACCTCCTCAATACGTAGGAGCCGCGTCA
1 TTCTCATCACGTAGGAACCGTGTCA-TCCCCGACCAGACCTCCTCATTACGTAGGAGCCGCGTCA
* *
20963 CCCCTGATAACCAGCCATCCTCATCGCATAGGAACCGTGTTATCACCCTTCCTAAAGATGGCCTA
65 CCCCTGATAACCAGCCATCCTCATCACATAGGAACCGTGTTATCA--CTTCCTAAAGATAGCCTA
21028 CCG
128 CCG
* * * ** * **
21031 TCCTCATCACGTAGGATCCATGTCATCCCCCTTCCATACCTCCTCATTACGTAGGAGCCTTGTCA
1 TTCTCATCACGTAGGAACCGTGTCAT-CCCCGACCAGACCTCCTCATTACGTAGGAGCCGCGTCA
* * * *
21096 CCCCTAGATAACCTGCCGTCCTCATCACGTAGGAACCGTGTTATCA-TTTCTAAAGATAGCCTAC
65 CCCCT-GATAACCAGCCATCCTCATCACATAGGAACCGTGTTATCACTTCCTAAAGATAGCCTAC
21160 CG
129 CG
* * *
21162 TTCTCATCACGTAGGAACCGTGTCATCCTCCGACCGGACCTCTTCATCACGTAGGA
1 TTCTCATCACGTAGGAACCGTGTCATCC-CCGACCAGACCTCCTCATTACGTAGGA
21218 ACCGTGTTAT
Statistics
Matches: 155, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
130 2 0.01
131 62 0.40
132 1 0.01
133 54 0.35
134 36 0.23
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (130 bp):
TTCTCATCACGTAGGAACCGTGTCATCCCCGACCAGACCTCCTCATTACGTAGGAGCCGCGTCAC
CCCTGATAACCAGCCATCCTCATCACATAGGAACCGTGTTATCACTTCCTAAAGATAGCCTACCG
Found at i:23119 original size:30 final size:30
Alignment explanation
Indices: 23084--23212 Score: 154
Period size: 30 Copynumber: 4.3 Consensus size: 30
23074 CTCTGATTTG
** *
23084 TTGTATTTACTGGTTGAGTCCTTTAAGTTT
1 TTGTATTTACTATTTGAGTCCTTTAACTTT
* *
23114 TTGTATTTTCTATTTTAGTCCTTTAACTTT
1 TTGTATTTACTATTTGAGTCCTTTAACTTT
* *
23144 TTGT-TTTAGCTATTTTAGTCCTTTAAGTTT
1 TTGTATTTA-CTATTTGAGTCCTTTAACTTT
*
23174 TTGTATTTTCTATTTTG-GTCCTTTAACTTT
1 TTGTATTTACTA-TTTGAGTCCTTTAACTTT
23204 TTGTATTTA
1 TTGTATTTA
23213 ATGTTCAACC
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.04
30 76 0.89
31 6 0.07
ACGTcount: A:0.16, C:0.11, G:0.12, T:0.60
Consensus pattern (30 bp):
TTGTATTTACTATTTGAGTCCTTTAACTTT
Found at i:23229 original size:60 final size:58
Alignment explanation
Indices: 23103--23226 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 58
23093 CTGGTTGAGT
* **
23103 CCTTTAAGTTTTTGTATTTTCTATTTTAGTCCTTTAACTTTTTGTTTTAGCTATTTTAGT
1 CCTTTAAGTTTTTGTATTTTCTATTTTAGTCCTTTAACTTTTTGTTTTA-C-ATTTCAAC
*
23163 CCTTTAAGTTTTTGTATTTTCTATTTTGGTCCTTTAACTTTTTGTATTTA-ATGTTCAAC
1 CCTTTAAGTTTTTGTATTTTCTATTTTAGTCCTTTAACTTTTTGT-TTTACAT-TTCAAC
23222 CCTTT
1 CCTTT
23227 TAATTATATT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
58 2 0.03
59 8 0.14
60 44 0.76
61 4 0.07
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.60
Consensus pattern (58 bp):
CCTTTAAGTTTTTGTATTTTCTATTTTAGTCCTTTAACTTTTTGTTTTACATTTCAAC
Found at i:29938 original size:135 final size:136
Alignment explanation
Indices: 29796--30039 Score: 368
Period size: 135 Copynumber: 1.8 Consensus size: 136
29786 TAAAATATTT
*
29796 TTTTATTAAATTTAAATTTAGCTATAATTCTATTTAATCAAAATTAAATTAATTAGAA-TCTTAT
1 TTTTATTAAATTTAAATTTAACTATAATTCTATTTAATCAAAATTAAATTAATTAGAATTC-TAT
* *
29860 TTAATTTTAAATTTAACTATAATTTT-TTCTCTTC-AAATCTTATATCAAGAGAAAAAAATATAA
65 TTAATTTTAAATTTAACTACAATTTTATT-TATTCGAAATCTTATATCAAGAGAAAAAAATATAA
29923 TTTTATAA
129 TTTTATAA
* ** * *
29931 TTTTATTAATTTTAGTTTTAATTATAATTCTATTTAATCAAAATTAAATTAATTAGAGTTCTATT
1 TTTTATTAAATTTAAATTTAACTATAATTCTATTTAATCAAAATTAAATTAATTAGAATTCTATT
*
29996 TAATTTTAAATTTAACTGCAATTTTATTTATTCGAAATCTTATA
66 TAATTTTAAATTTAACTACAATTTTATTTATTCGAAATCTTATA
30040 ATTAACTTAT
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
135 83 0.86
136 14 0.14
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (136 bp):
TTTTATTAAATTTAAATTTAACTATAATTCTATTTAATCAAAATTAAATTAATTAGAATTCTATT
TAATTTTAAATTTAACTACAATTTTATTTATTCGAAATCTTATATCAAGAGAAAAAAATATAATT
TTATAA
Found at i:35360 original size:18 final size:18
Alignment explanation
Indices: 35337--35371 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35327 GCACTTAAAA
35337 TTTGTCCCGAATGACCAT
1 TTTGTCCCGAATGACCAT
*
35355 TTTGTCCCGAATTACCA
1 TTTGTCCCGAATGACCA
35372 CTATCCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (18 bp):
TTTGTCCCGAATGACCAT
Found at i:35416 original size:31 final size:31
Alignment explanation
Indices: 35378--35465 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
35368 ACCACTATCC
35378 ATATGTCCCGAAGGACATAGGTAACCTGTCA
1 ATATGTCCCGAAGGACATAGGTAACCTGTCA
* * *
35409 ATATGTCCCGAAGGACGTAGGTAAACTGTCC
1 ATATGTCCCGAAGGACATAGGTAACCTGTCA
35440 ATATGTCCCGAAGGACATAGGTAACC
1 ATATGTCCCGAAGGACATAGGTAACC
35466 CTCGACTCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (31 bp):
ATATGTCCCGAAGGACATAGGTAACCTGTCA
Found at i:37323 original size:23 final size:23
Alignment explanation
Indices: 37262--37326 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
37252 ACATTATTAT
*
37262 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
** * *
37285 GCGACAC-TCTGATGCAATTCTAC
1 ATGGCACTTC-GGTGCAATTCTAC
37308 ATGGCACTTCGGTGCAATT
1 ATGGCACTTCGGTGCAATT
37327 ATACGAGTTG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
22 1 0.03
23 28 0.90
24 2 0.06
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:43415 original size:19 final size:20
Alignment explanation
Indices: 43368--43422 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
43358 ATTCTGGGCA
43368 ATGTGCATCGATGCACATTC
1 ATGTGCATCGATGCACATTC
43388 ATTGTGCATCGATGCACATGT-
1 A-TGTGCATCGATGCACAT-TC
43409 A-GTGCATCGATGCA
1 ATGTGCATCGATGCA
43423 TTAATTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 13 0.39
20 1 0.03
21 18 0.55
22 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
ATGTGCATCGATGCACATTC
Found at i:44168 original size:23 final size:23
Alignment explanation
Indices: 44134--44202 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
44124 CATTATTATA
44134 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
44157 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
44180 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
44203 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:45357 original size:2 final size:2
Alignment explanation
Indices: 45350--45379 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45340 TCTTATGTTC
45350 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
45380 CAAATGATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45928 original size:19 final size:21
Alignment explanation
Indices: 45900--45953 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 21
45890 ACTTAAAGTA
*
45900 GTATCAATACCCCT-GTAG-G
1 GTATCGATACCCCTAGTAGAG
*
45919 GTATCGATACTTCCCTAGTTGAG
1 GTATCGATAC--CCCTAGTAGAG
45942 GTATCGATACCC
1 GTATCGATACCC
45954 ATATTGCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 9 0.31
21 6 0.21
22 3 0.10
23 11 0.38
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (21 bp):
GTATCGATACCCCTAGTAGAG
Found at i:46269 original size:14 final size:14
Alignment explanation
Indices: 46250--46276 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46240 TAATACCTTT
46250 TCATCTTCAAAATC
1 TCATCTTCAAAATC
46264 TCATCTTCAAAAT
1 TCATCTTCAAAAT
46277 GGAAATCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (14 bp):
TCATCTTCAAAATC
Found at i:47295 original size:64 final size:65
Alignment explanation
Indices: 47197--47388 Score: 164
Period size: 64 Copynumber: 3.0 Consensus size: 65
47187 ATAATTATTC
* * * ** *
47197 TTTGAACATGTCAAATTAAAAG--GTATTACCTATTTAACTTTGAATATTAAAGATAATTATATC
1 TTTGAATATTTCAAATTAAAAGATATATTATATATTTAAATTTGAATATTAAAGATAATT-TAT-
47260 CT
64 CT
* * * *
47262 TTTGAAATATTTCAAATT-AAA-ATA-A-TATATATTTAAGTTTGAATAGTAAAAGGTGACTTTA
1 TTTG-AATATTTCAAATTAAAAGATATATTATATATTTAAATTTGAATA-TTAAAGAT-AATTTA
47323 TCT
63 TCT
* *
47326 TTTGAATATTTTAAATTAAAAGATATTATTTTATATTTAAATTTGAATATTAAAAGAT-ATTTA
1 TTTGAATATTTCAAATTAAAAGATA-TATTATATATTTAAATTTGAATATT-AAAGATAATTTA
47389 GTTGGAGTAA
Statistics
Matches: 101, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
63 12 0.12
64 26 0.26
65 20 0.20
66 18 0.18
67 2 0.02
68 23 0.23
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (65 bp):
TTTGAATATTTCAAATTAAAAGATATATTATATATTTAAATTTGAATATTAAAGATAATTTATCT
Found at i:48925 original size:109 final size:109
Alignment explanation
Indices: 48734--48953 Score: 431
Period size: 109 Copynumber: 2.0 Consensus size: 109
48724 GGGAGAATAA
48734 ACCATAATTTACTTTTTGTTTATTGTTGGAATTATTATTAATTCTAATTTCGTGTGCTAAACAAA
1 ACCATAATTTACTTTTTGTTTATTGTTGGAATTATTATTAATTCTAATTTCGTGTGCTAAACAAA
48799 ATCTTGATTGTCGGTGGTCATGAGCTACAATAAGAAACTTTGTT
66 ATCTTGATTGTCGGTGGTCATGAGCTACAATAAGAAACTTTGTT
*
48843 ACCATGATTTACTTTTTGTTTATTGTTGGAATTATTATTAATTCTAATTTCGTGTGCTAAACAAA
1 ACCATAATTTACTTTTTGTTTATTGTTGGAATTATTATTAATTCTAATTTCGTGTGCTAAACAAA
48908 ATCTTGATTGTCGGTGGTCATGAGCTACAATAAGAAACTTTGTT
66 ATCTTGATTGTCGGTGGTCATGAGCTACAATAAGAAACTTTGTT
48952 AC
1 AC
48954 AATGCAATTA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (109 bp):
ACCATAATTTACTTTTTGTTTATTGTTGGAATTATTATTAATTCTAATTTCGTGTGCTAAACAAA
ATCTTGATTGTCGGTGGTCATGAGCTACAATAAGAAACTTTGTT
Found at i:49420 original size:64 final size:65
Alignment explanation
Indices: 49289--49513 Score: 171
Period size: 64 Copynumber: 3.4 Consensus size: 65
49279 TAAAATTAAA
* * * * *
49289 ATTTTAATTTGAATATTAGTAGGATAA-TTAT-TCTTTGAACATGTCAAATTAAAAG--GTATTA
1 ATTTAAATTTGAATATTA--AAGATAATTTATCT-TTTGAATATTTCAAATTAAAAGATATATTA
**
49350 CCT
63 TAT
*
49353 ATTTAACTTTGAATATTAAAGATAATTATATCCTTTTGAAATATTTCAAATT-AAA-ATA-A-TA
1 ATTTAAATTTGAATATTAAAGATAATT-TAT-CTTTTG-AATATTTCAAATTAAAAGATATATTA
49414 TAT
63 TAT
* * * * * *
49417 ATTTAAGTTTGAATAGTAAAAGGTGACTTTATCTTTTGAATATTTTAAATTAAAAGATATTATTT
1 ATTTAAATTTGAATA-TTAAAGAT-AATTTATCTTTTGAATATTTCAAATTAAAAGATA-TATTA
49482 TAT
63 TAT
49485 ATTTAAATTTGAATATTAAAAGAT-ATTTA
1 ATTTAAATTTGAATATT-AAAGATAATTTA
49514 GTTGGAGTAA
Statistics
Matches: 128, Mismatches: 18, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
62 6 0.05
63 13 0.10
64 45 0.35
65 20 0.16
66 19 0.15
67 2 0.02
68 23 0.18
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.44
Consensus pattern (65 bp):
ATTTAAATTTGAATATTAAAGATAATTTATCTTTTGAATATTTCAAATTAAAAGATATATTATAT
Found at i:52875 original size:65 final size:58
Alignment explanation
Indices: 52733--52880 Score: 156
Period size: 64 Copynumber: 2.4 Consensus size: 58
52723 TAATTCATGT
* * *
52733 TCCTTTTGAATATTACAAATTAAAAGATATTTTTAATTTGAATATTAGTAGGATATTTA
1 TCCTTTTGAATATTTCAAATTAAAAGATATATTTAATTTGAATATTAG-AAGATATTTA
* *
52792 TTCTTTT-AATATATCAAATTAAAAGGTATTACCTATTTAACTTTGAATATTA-AAGATAATTAT
1 TCCTTTTGAATATTTCAAATTAAAA-G-A-TA--TATTTAA-TTTGAATATTAGAAGAT-ATT-T
52855 A
58 A
52856 TCCTTTTGAATATTTCAAATTAAAA
1 TCCTTTTGAATATTTCAAATTAAAA
52881 TAATATCAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
58 15 0.21
59 7 0.10
60 1 0.01
61 2 0.03
62 4 0.05
63 9 0.12
64 19 0.26
65 16 0.22
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (58 bp):
TCCTTTTGAATATTTCAAATTAAAAGATATATTTAATTTGAATATTAGAAGATATTTA
Found at i:60877 original size:35 final size:36
Alignment explanation
Indices: 60813--60885 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 36
60803 ATGAGTTATT
*
60813 CAAGGAGTATCGATACCTAAAGGGTAGTATCGATAC
1 CAAGGAGTATCGATACCTAAAGGGTAGTATAGATAC
*
60849 CAAGGA-TATCGATACCGT-TAGGCG-AGTATAGATAC
1 CAAGGAGTATCGATACC-TAAAGG-GTAGTATAGATAC
60884 CA
1 CA
60886 TTTTTGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 25 0.76
36 8 0.24
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (36 bp):
CAAGGAGTATCGATACCTAAAGGGTAGTATAGATAC
Found at i:64394 original size:2 final size:2
Alignment explanation
Indices: 64387--64449 Score: 90
Period size: 2 Copynumber: 31.0 Consensus size: 2
64377 ACATGTTACA
* * *
64387 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT TT GT GT 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
64430 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
64450 TGGATAAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 55 0.96
3 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:65964 original size:71 final size:70
Alignment explanation
Indices: 65867--66066 Score: 206
Period size: 71 Copynumber: 2.8 Consensus size: 70
65857 ATCGAAATGC
** ** *
65867 TAAACTCACACCAAATGGAA-TCAATCATATAATGTGGACGAACCCAAAAGTCCAAAT-GCATAC
1 TAAACTCACACCAAACAGAAGT-AATCACGTAAGGTGGACGAACCCAAAAGTCCAAATAGCAT-C
*
65930 TAAAATGT
64 -AAAATCT
* ** * * * * *
65938 TTAACTCACACCAAACAGAAGTAATCACGTAAGGTAAACAAATCCAAAGGTCAAAATACGCATCG
1 TAAACTCACACCAAACAGAAGTAATCACGTAAGGTGGACGAACCCAAAAGTCCAAATA-GCATCA
*
66003 GAATCT
65 AAATCT
*
66009 TAAACTCACACCAAACAGAAGTAATCACGTAAGGTGGACGAACCCGAAAGTCCAAATA
1 TAAACTCACACCAAACAGAAGTAATCACGTAAGGTGGACGAACCCAAAAGTCCAAATA
66067 CACAACTACT
Statistics
Matches: 103, Mismatches: 23, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
71 97 0.94
72 2 0.02
73 4 0.04
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (70 bp):
TAAACTCACACCAAACAGAAGTAATCACGTAAGGTGGACGAACCCAAAAGTCCAAATAGCATCAA
AATCT
Found at i:68866 original size:23 final size:22
Alignment explanation
Indices: 68839--68882 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
68829 ATATATAAAT
68839 TATTG-CAACTTTATATTCTAATA
1 TATTGACAA-TTTATATT-TAATA
68862 TATTGACAATTTATATTTAAT
1 TATTGACAATTTATATTTAAT
68883 CAAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (22 bp):
TATTGACAATTTATATTTAATA
Found at i:79969 original size:15 final size:15
Alignment explanation
Indices: 79949--79977 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
79939 AGTCATTTCA
79949 TCATCACCGTTACCG
1 TCATCACCGTTACCG
79964 TCATCACCGTTACC
1 TCATCACCGTTACC
79978 ATGATTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.41, G:0.10, T:0.28
Consensus pattern (15 bp):
TCATCACCGTTACCG
Done.