Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006340.1 Hibiscus syriacus cultivar Beakdansim tig00015154_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: 79500
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2007 original size:14 final size:14
Alignment explanation
Indices: 1988--2014 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1978 TATTTACTTT
1988 AATAAACGAACATA
1 AATAAACGAACATA
2002 AATAAACGAACAT
1 AATAAACGAACAT
2015 GAACGAGCTT
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:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (14 bp):
AATAAACGAACATA
Found at i:2054 original size:23 final size:23
Alignment explanation
Indices: 2027--2080 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
2017 ACGAGCTTTA
2027 ACCGAACGGTTCACGAACAATTC
1 ACCGAACGGTTCACGAACAATTC
*
2050 ACCGAACGGTTCACGAATAATTC
1 ACCGAACGGTTCACGAACAATTC
2073 ACCGAACG
1 ACCGAACG
2081 TTTTTTTCAT
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:0.35, C:0.30, G:0.19, T:0.17
Consensus pattern (23 bp):
ACCGAACGGTTCACGAACAATTC
Found at i:3086 original size:27 final size:27
Alignment explanation
Indices: 3056--3135 Score: 70
Period size: 30 Copynumber: 2.9 Consensus size: 27
3046 AGCCAAGGGA
*
3056 GCAGGCGGTGGGGTAGCTGGAGGAGTT
1 GCAGGCGGTGGAGTAGCTGGAGGAGTT
* * **
3083 GCAGGTGGTGGAGTTGCTGGTGGAGGAGAA
1 GCAGGCGGTGGAGTAGC---TGGAGGAGTT
* *
3113 GCAGGTGGTGGAGTAGCGGGAGG
1 GCAGGCGGTGGAGTAGCTGGAGG
3136 GGGAGATGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
27 19 0.44
30 24 0.56
ACGTcount: A:0.17, C:0.09, G:0.56, T:0.17
Consensus pattern (27 bp):
GCAGGCGGTGGAGTAGCTGGAGGAGTT
Found at i:3097 original size:15 final size:15
Alignment explanation
Indices: 3083--3195 Score: 82
Period size: 15 Copynumber: 7.5 Consensus size: 15
3073 TGGAGGAGTT
**
3083 GCAGGTGGTGGAGTT
1 GCAGGTGGTGGAGAA
* *
3098 GCTGGTGGAGGAGAA
1 GCAGGTGGTGGAGAA
*
3113 GCAGGTGGTGGAGTA
1 GCAGGTGGTGGAGAA
* * * *
3128 GCGGGAGGGGGAGAT
1 GCAGGTGGTGGAGAA
* *
3143 GCTGGTGGAGGAGAA
1 GCAGGTGGTGGAGAA
* **
3158 GCAGGTGGTGGGGTG
1 GCAGGTGGTGGAGAA
* *
3173 GCGGGAGGTGGAGAA
1 GCAGGTGGTGGAGAA
3188 GCAGGTGG
1 GCAGGTGG
3196 AGGCGGAGTT
Statistics
Matches: 70, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 70 1.00
ACGTcount: A:0.19, C:0.07, G:0.58, T:0.15
Consensus pattern (15 bp):
GCAGGTGGTGGAGAA
Found at i:3141 original size:30 final size:30
Alignment explanation
Indices: 3074--3155 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
3064 TGGGGTAGCT
** * * *
3074 GGAGGAGTTGCAGGTGGTGGAGTTGCTGGT
1 GGAGGAGAAGCAGGTGGTGGAGTAGCGGGA
3104 GGAGGAGAAGCAGGTGGTGGAGTAGCGGGA
1 GGAGGAGAAGCAGGTGGTGGAGTAGCGGGA
* * * *
3134 GGGGGAGATGCTGGTGGAGGAG
1 GGAGGAGAAGCAGGTGGTGGAG
3156 AAGCAGGTGG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.20, C:0.06, G:0.57, T:0.17
Consensus pattern (30 bp):
GGAGGAGAAGCAGGTGGTGGAGTAGCGGGA
Found at i:3146 original size:45 final size:45
Alignment explanation
Indices: 3092--3198 Score: 160
Period size: 45 Copynumber: 2.4 Consensus size: 45
3082 TGCAGGTGGT
*
3092 GGAGTTGCTGGTGGAGGAGAAGCAGGTGGTGGAGTAGCGGGAGGG
1 GGAGATGCTGGTGGAGGAGAAGCAGGTGGTGGAGTAGCGGGAGGG
* * *
3137 GGAGATGCTGGTGGAGGAGAAGCAGGTGGTGGGGTGGCGGGAGGT
1 GGAGATGCTGGTGGAGGAGAAGCAGGTGGTGGAGTAGCGGGAGGG
* *
3182 GGAGAAGCAGGTGGAGG
1 GGAGATGCTGGTGGAGG
3199 CGGAGTTGCT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.21, C:0.07, G:0.59, T:0.14
Consensus pattern (45 bp):
GGAGATGCTGGTGGAGGAGAAGCAGGTGGTGGAGTAGCGGGAGGG
Found at i:3213 original size:33 final size:32
Alignment explanation
Indices: 3135--3233 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 32
3125 GTAGCGGGAG
* *
3135 GGGGAGATGCTGGTGGAGGAGAAGCAGGTGG-
1 GGGGAGTTGCTGGAGGAGGAGAAGCAGGTGGA
* * * *
3166 TGGG-GTGGCGGGAGGTGGAGAAGCAGGTGGA
1 GGGGAGTTGCTGGAGGAGGAGAAGCAGGTGGA
3197 GGCGGAGTTGCTGGAGGAGGAG-AGCTAGGTGGA
1 GG-GGAGTTGCTGGAGGAGGAGAAGC-AGGTGGA
3230 GGGG
1 GGGG
3234 TTGAAACTGG
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
30 21 0.39
31 4 0.07
32 7 0.13
33 22 0.41
ACGTcount: A:0.20, C:0.07, G:0.60, T:0.13
Consensus pattern (32 bp):
GGGGAGTTGCTGGAGGAGGAGAAGCAGGTGGA
Found at i:7657 original size:23 final size:23
Alignment explanation
Indices: 7640--7772 Score: 221
Period size: 23 Copynumber: 5.8 Consensus size: 23
7630 AATAACATAT
*
7640 TAGGTACCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
7663 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
7686 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
7709 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
*
7732 TAGTTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
** *
7755 TATATATCGCTTATATAA
1 TAGGTAGCGCTTATATAA
7773 AATAGGTTAA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 105 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:7833 original size:23 final size:23
Alignment explanation
Indices: 7807--7855 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
7797 ATCAAGCACA
*
7807 ATAACATATTAGGTACCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
** *
7830 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
7853 ATA
1 ATA
7856 CTAAAATAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTACCGCTTAT
Found at i:7863 original size:23 final size:23
Alignment explanation
Indices: 7816--7866 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
7806 AATAACATAT
**
7816 TAGGTACCGCTTATATAATGTAA
1 TAGGTACCGCTTATATAATAAAA
* *
7839 TAGGTAGCGCTTATATACTAAAA
1 TAGGTACCGCTTATATAATAAAA
7862 TAGGT
1 TAGGT
7867 TAATTACTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (23 bp):
TAGGTACCGCTTATATAATAAAA
Found at i:7885 original size:87 final size:86
Alignment explanation
Indices: 7565--7942 Score: 417
Period size: 87 Copynumber: 4.3 Consensus size: 86
7555 ACATGTAAAA
*
7565 ATATGATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAGCAC
1 ATATAATGTAATAGGTAGCGCTTATAT-ATAAAATAGGTTAATTACTGGAAACATTATCAAGCAC
7630 AATAACATATTAGGTACCGCTT
65 AATAACATATTAGGTACCGCTT
* * * **
7652 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGCTT-ATATAATGTAATA-GGTA
1 ATATAATGTAATAGGTAGCGCTTATAT-A--TAA-A-ATAG-G-TTAAT-TACTGGAA-ACATTA
* ** ** * * *
7715 GC--GCTTATATAATGTAATAGTTAGCGCTT
57 TCAAGCACA-ATAACATATTAGGTACCGCTT
** * *
7744 ATATAATGTAATATATATCGC-T-TATATAAAATAGGTTAATTACTGAAAACATTATCAAGCACA
1 ATATAATGTAATAGGTAGCGCTTATATATAAAATAGGTTAATTACTGGAAACATTATCAAGCACA
7807 ATAACATATTAGGTACCGCTT
66 ATAACATATTAGGTACCGCTT
7828 ATATAATGTAATAGGTAGCGCTTATATACTAAAATAGGTTAATTACTGGAAACATTATCAAGCAC
1 ATATAATGTAATAGGTAGCGCTTATATA-TAAAATAGGTTAATTACTGGAAACATTATCAAGCAC
*
7893 AATAACATATTAGGTAGCGCTT
65 AATAACATATTAGGTACCGCTT
* *
7915 ATATAACGTAATAGGCAGCGCTTATATA
1 ATATAATGTAATAGGTAGCGCTTATATA
7943 ACGTAATAGG
Statistics
Matches: 238, Mismatches: 37, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
82 1 0.00
83 11 0.05
84 37 0.16
85 7 0.03
86 5 0.02
87 113 0.47
89 4 0.02
90 4 0.02
91 7 0.03
92 37 0.16
93 11 0.05
94 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (86 bp):
ATATAATGTAATAGGTAGCGCTTATATATAAAATAGGTTAATTACTGGAAACATTATCAAGCACA
ATAACATATTAGGTACCGCTT
Found at i:7975 original size:23 final size:23
Alignment explanation
Indices: 7894--7966 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
7884 ATCAAGCACA
* * *
7894 ATAACATATTAGGTAGCGCTTAT
1 ATAACGTAATAGGCAGCGCTTAT
7917 ATAACGTAATAGGCAGCGCTTAT
1 ATAACGTAATAGGCAGCGCTTAT
*
7940 ATAACGTAATAGGCATCGCTTAT
1 ATAACGTAATAGGCAGCGCTTAT
7963 ATAA
1 ATAA
7967 TAAAATAGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (23 bp):
ATAACGTAATAGGCAGCGCTTAT
Found at i:8307 original size:15 final size:14
Alignment explanation
Indices: 8270--8389 Score: 52
Period size: 14 Copynumber: 8.6 Consensus size: 14
8260 ATTTTTAAAA
8270 TATTAAAATA--AT
1 TATTAAAATATTAT
*
8282 TATT-TAATATTAT
1 TATTAAAATATTAT
* *
8295 TTTTGTAAATATTAT
1 TATT-AAAATATTAT
8310 TATTAAAATATTA-
1 TATTAAAATATTAT
* *
8323 TATCTATAATTTTAT
1 TAT-TAAAATATTAT
* * *
8338 AAATAAAAAAATTAT
1 -TATTAAAATATTAT
* **
8353 GATTATTATATT-T
1 TATTAAAATATTAT
**
8366 TATTAAAATAAAAT
1 TATTAAAATATTAT
8380 TATTATAAAT
1 TATTA-AAAT
8390 TATATTTTTT
Statistics
Matches: 77, Mismatches: 22, Indels: 15
0.68 0.19 0.13
Matches are distributed among these distances:
11 4 0.05
12 4 0.05
13 16 0.21
14 29 0.38
15 22 0.29
16 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (14 bp):
TATTAAAATATTAT
Found at i:8346 original size:29 final size:32
Alignment explanation
Indices: 8314--8397 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 32
8304 TATTATTATT
8314 AAAATATTATATCTA-TA-ATTTTA-T-AAATA
1 AAAATATTATAT-TATTATATTTTATTAAAATA
*
8343 AAAAAATTATGATTATTATATTTTATTAAAATA
1 AAAATATTAT-ATTATTATATTTTATTAAAATA
* *
8376 AAATTATTATA-AATTATATTTT
1 AAAATATTATATTATTATATTTT
8398 TTATTTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 11 0.24
30 4 0.09
31 16 0.35
32 2 0.04
33 13 0.28
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (32 bp):
AAAATATTATATTATTATATTTTATTAAAATA
Found at i:9175 original size:16 final size:16
Alignment explanation
Indices: 9134--9180 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
9124 AATTATGATT
9134 ATTATATTTTATTA-AA
1 ATTATA-TTTATTATAA
* *
9150 A-TAAAATTATTATAA
1 ATTATATTTATTATAA
9165 ATTATATTTATTATAA
1 ATTATATTTATTATAA
9181 TAAGAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.24
15 6 0.24
16 13 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTATATTTATTATAA
Found at i:9183 original size:30 final size:30
Alignment explanation
Indices: 9109--9183 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
9099 TATATCTATA
* *
9109 ATTTTATAAATAA-AAAATTATGATTATTAT
1 ATTTTAT-TATAATAAAATTATGATAATTAT
* *
9139 ATTTTATTAAAATAAAATTATTATAAATTAT
1 ATTTTATTATAATAAAATTATGAT-AATTAT
9170 A-TTTATTATAATAA
1 ATTTTATTATAATAA
9184 GAATAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 3 0.08
30 29 0.76
31 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
ATTTTATTATAATAAAATTATGATAATTAT
Found at i:9949 original size:198 final size:196
Alignment explanation
Indices: 9277--9950 Score: 947
Period size: 198 Copynumber: 3.4 Consensus size: 196
9267 TGTTACATCG
* * * *
9277 AAACCGATAATTATAATGTAATAGGTAAATTTACAATATAACCAGTATAAATATACCGGTTTTAT
1 AAACCGATAATTACAATGTAATAGGTAAATTTACAATGT-ACCGGTAGAAATATACCGGTTTTAT
* * * *** *
9342 GAGAGAATATGTCTACATAATGTATCGACACAAATTTAA-AAAGTGTCGATACATTTTGTCCAGA
65 GAGAAAATAGGTCTACATAATGTATCGACAC-ATTTTAAGTTTGTGTCGATAC-TTTTTTCCAGA
** * * *
9406 ATGAATGCTAAACGAGGTGCAAGCATAAAGTGTCGATAAATTTATTAAAAGTATTGATCCCAAAA
128 ATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA-TAAAAGTATCGATCCCAAAA
*
9471 ACATCG
192 A-ATCA
*
9477 AAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACTCGGTAGAAATATATCGGTTTTAT
1 AAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAC-CGGTAGAAATATACCGGTTTTAT
*
9542 GAGAAAATAGATCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTCCAGAAT
65 GAGAAAATAGGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTCCAGAAT
* * * *
9607 GAATGTCCAACGAGGTTCACACATAAAGTGTCGACACATTTATTAAAAGTATCGATCCCAAAAAA
130 GAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAAA
*
9672 TCC
194 TCA
9675 AAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCCGGTAGAAATATACCGGTTTTAT
1 AAACCGATAATTACAATGTAATAGGTAAATTTACAATGTA-CCGGTAGAAATATACCGGTTTTAT
*
9740 GAGAAAATAGGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTCCAGAAT
65 GAGAAAATAGGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTCCAGAAT
*
9805 GAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA-AAATTGTATCGATCCCAAAAAT
130 GAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATAAA-AGTATCGATCCCAAAAA-
9869 ATCA
193 ATCA
* * * *
9873 AAACCGATAATTATAATATAATAGGTAAATTTACAATGTTACCGGTATAAATATACCGATTTTAT
1 AAACCGATAATTACAATGTAATAGGTAAATTTACAATG-TACCGGTAGAAATATACCGGTTTTAT
* *
9938 GATATAATAGGTC
65 GAGAAAATAGGTC
9951 AATATAAGCG
Statistics
Matches: 430, Mismatches: 38, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
196 3 0.01
197 16 0.04
198 238 0.55
199 78 0.18
200 95 0.22
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (196 bp):
AAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCGGTAGAAATATACCGGTTTTATG
AGAAAATAGGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTCCAGAATG
AATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATAAAAGTATCGATCCCAAAAAATC
A
Found at i:10030 original size:23 final size:23
Alignment explanation
Indices: 10004--10054 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
9994 ATAGTAATTA
**
10004 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
10027 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
10050 ACCTA
1 ACCTA
10055 ATATGTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:11013 original size:15 final size:15
Alignment explanation
Indices: 10993--11031 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
10983 AAAGTTTAGT
10993 AATTAAAATTAAAAA
1 AATTAAAATTAAAAA
* * *
11008 AATTAAAAGTACAAT
1 AATTAAAATTAAAAA
11023 AATTAAAAT
1 AATTAAAAT
11032 ATAAGACAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (15 bp):
AATTAAAATTAAAAA
Found at i:25657 original size:73 final size:73
Alignment explanation
Indices: 25573--25718 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
25563 TTAATTGTTA
25573 AAAAAAATTCTGAACAAATATTAAATTATATTCATAGCAGACTATTCAAAAAATAAATAAAAAAA
1 AAAAAAATTCTGAACAAATATTAAATTATATTCATAGCAGACTATTCAAAAAATAAATAAAAAAA
25638 ATAACTAT
66 ATAACTAT
* *
25646 AAAAAATTTCTGAACAAATATTAAATTATATTCATAGCAGACTATTCAAAAAATAAATAAATAAA
1 AAAAAAATTCTGAACAAATATTAAATTATATTCATAGCAGACTATTCAAAAAATAAATAAAAAAA
25711 ATAACTAT
66 ATAACTAT
25719 CGGATGAAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.29
Consensus pattern (73 bp):
AAAAAAATTCTGAACAAATATTAAATTATATTCATAGCAGACTATTCAAAAAATAAATAAAAAAA
ATAACTAT
Found at i:25700 original size:35 final size:35
Alignment explanation
Indices: 25588--25700 Score: 86
Period size: 36 Copynumber: 3.1 Consensus size: 35
25578 AATTCTGAAC
25588 AAATATTAAATTATATTCATAGCAGACTATTCAAA
1 AAATATTAAATTATATTCATAGCAGACTATTCAAA
* ** * * * * * *
25623 AAATAAATAAAAAAAATAACTATA-AAAAAT-TTCTGAAC
1 AAAT-ATTAAATTATAT-TC-ATAGCAGACTATTC--AAA
25661 AAATATTAAATTATATTCATAGCAGACTATTCAAA
1 AAATATTAAATTATATTCATAGCAGACTATTCAAA
25696 AAATA
1 AAATA
25701 AATAAATAAA
Statistics
Matches: 53, Mismatches: 18, Indels: 14
0.62 0.21 0.16
Matches are distributed among these distances:
35 14 0.26
36 15 0.28
37 15 0.28
38 9 0.17
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.30
Consensus pattern (35 bp):
AAATATTAAATTATATTCATAGCAGACTATTCAAA
Found at i:32862 original size:22 final size:24
Alignment explanation
Indices: 32818--32865 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
32808 TAAAATCTTT
32818 ATAAAATTATAATTTAATACAATA
1 ATAAAATTATAATTTAATACAATA
*
32842 ATAAAATTAT-A-TTAATCCAATA
1 ATAAAATTATAATTTAATACAATA
32864 AT
1 AT
32866 TTTATTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.52
23 1 0.04
24 10 0.43
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAAAATTATAATTTAATACAATA
Found at i:33936 original size:83 final size:82
Alignment explanation
Indices: 33801--34092 Score: 365
Period size: 82 Copynumber: 3.5 Consensus size: 82
33791 AGTGGGTTTT
* * *
33801 TTTTTATATAAACGCCGTTAAAGACTCGTACTTTAGTGGCGTTTTTTGTACAAACGTCGTTAAAA
1 TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTT-TACAAACGTCGTTAAAG
** *
33866 ACAAGTTATTTAGTGGCG
65 ACTCGTTATTCAGTGGCG
*
33884 TTTTTATACAAACGCCGCTAACGACT-GTACTTTAGTGGCGTTTGTGTTTACAAACG-CTGTTAA
1 TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTT-T-TTTACAAACGTC-GTTAA
*
33947 AGACTCGTAATTCAGTGGCG
63 AGACTCGTTATTCAGTGGCG
* * * * * * *
33967 TTTTTATATAAACGCCTCTATAGACTCATACTTCAGTGGCGTTTTTATACAAACGTCGCTAAAGA
1 TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTTTACAAACGTCGTTAAAGA
34032 CTCG-TACTTCAGTGGCG
66 CTCGTTA-TTCAGTGGCG
* *
34049 TTTTTATACAAACGCTGCTAAAGACTTGTACTTTAGTGGCGTTT
1 TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTT
34093 GTAAACACAA
Statistics
Matches: 179, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
81 1 0.01
82 85 0.47
83 76 0.42
84 17 0.09
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (82 bp):
TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTTTACAAACGTCGTTAAAGA
CTCGTTATTCAGTGGCG
Found at i:33992 original size:41 final size:41
Alignment explanation
Indices: 33670--34092 Score: 294
Period size: 41 Copynumber: 10.3 Consensus size: 41
33660 AGTTCATCAA
* * * * *
33670 TAGTGGCGTTTGTTATAAAAACGCCAC-AAAAACAT-GTGCTA
1 TAGTGGCGTTT-TTATACAAACGCCTCTAAAGAC-TCGTACTT
* * * * * * *
33711 TAGTGGTGTTTTT-T-TAAATGCCGCTAAATACTCATATTT
1 TAGTGGCGTTTTTATACAAACGCCTCTAAAGACTCGTACTT
* * * * * *
33750 TAGTGGCATTTTTATATAAATGCCGCTAAAGA-TTGTAATT
1 TAGTGGCGTTTTTATACAAACGCCTCTAAAGACTCGTACTT
*
33790 TAGTGG-GTTTTTTTTTATATAAACGCCGT-TAAAGACTCGTACTT
1 TAGTGGCG----TTTTTATACAAACGCC-TCTAAAGACTCGTACTT
* * * **
33834 TAGTGGCGTTTTTTGTACAAACGTCGT-TAAAAACAAGTTA-TT
1 TAGTGGCG-TTTTTATACAAACG-CCTCTAAAGACTCG-TACTT
* *
33876 TAGTGGCGTTTTTATACAAACGCCGCTAACGACT-GTACTT
1 TAGTGGCGTTTTTATACAAACGCCTCTAAAGACTCGTACTT
* * *
33916 TAGTGGCGTTTGTGTTTACAAACG-CTGTTAAAGACTCGTAATT
1 TAGTGGCGTTT-T-TATACAAACGCCT-CTAAAGACTCGTACTT
* * * *
33959 CAGTGGCGTTTTTATATAAACGCCTCTATAGACTCATACTT
1 TAGTGGCGTTTTTATACAAACGCCTCTAAAGACTCGTACTT
* * *
34000 CAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCTCTAAAGACTCGTACTT
* *
34041 CAGTGGCGTTTTTATACAAACG-CTGCTAAAGACTTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCT-CTAAAGACTCGTACTT
34082 TAGTGGCGTTT
1 TAGTGGCGTTT
34093 GTAAACACAA
Statistics
Matches: 309, Mismatches: 52, Indels: 42
0.77 0.13 0.10
Matches are distributed among these distances:
38 8 0.03
39 21 0.07
40 30 0.10
41 148 0.48
42 50 0.16
43 39 0.13
44 12 0.04
45 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCTCTAAAGACTCGTACTT
Found at i:34105 original size:166 final size:166
Alignment explanation
Indices: 33801--34106 Score: 429
Period size: 166 Copynumber: 1.8 Consensus size: 166
33791 AGTGGGTTTT
* * * *
33801 TTTTTATATAAACGCCGTTAAAGACTCGTACTTTAGTGGCGTTTTTTGTACAAACGTCGTTAAAA
1 TTTTTATATAAACGCCGTTAAAGACTCATACTTCAGTGGCGTTTTTTATACAAACGTCGCTAAAA
* * **
33866 ACAAGTTATTTAGTGGCGTTTTTATACAAACGCCGCTAACGACTGTACTTTAGTGGCGTTTGTGT
66 ACAAGTTATTCAGTGGCGTTTTTATACAAACGCCGCTAAAGACTGTACTTTAGTGGCGTTTGTAA
**
33931 TTACAAACGCTGTTAAAGACTCGTAATTCAGTGGCG
131 ACACAAACGCTGTTAAAGACTCGTAATTCAGTGGCG
*
33967 TTTTTATATAAACGCC-TCTATAGACTCATACTTCAGTGGCG-TTTTTATACAAACGTCGCTAAA
1 TTTTTATATAAACGCCGT-TAAAGACTCATACTTCAGTGGCGTTTTTTATACAAACGTCGCTAAA
* ** *
34030 GACTCG-TACTTCAGTGGCGTTTTTATACAAACGCTGCTAAAGACTTGTACTTTAGTGGCGTTTG
65 AACAAGTTA-TTCAGTGGCGTTTTTATACAAACGCCGCTAAAGAC-TGTACTTTAGTGGCGTTTG
34094 TAAACACAAACGC
128 TAAACACAAACGC
34107 CGCAAGTTTA
Statistics
Matches: 122, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
164 2 0.02
165 56 0.46
166 64 0.52
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (166 bp):
TTTTTATATAAACGCCGTTAAAGACTCATACTTCAGTGGCGTTTTTTATACAAACGTCGCTAAAA
ACAAGTTATTCAGTGGCGTTTTTATACAAACGCCGCTAAAGACTGTACTTTAGTGGCGTTTGTAA
ACACAAACGCTGTTAAAGACTCGTAATTCAGTGGCG
Found at i:37162 original size:43 final size:44
Alignment explanation
Indices: 37036--37190 Score: 210
Period size: 42 Copynumber: 3.6 Consensus size: 44
37026 TTGTGGATAC
*
37036 AAACGCCGCTATAGATATTGACTTTTTGTGGCGTTTGT-TCC-A
1 AAACGCCGCTATAGATATTGACTTTTTGAGGCGTTTGTATCCAA
37078 AAACGCCGCTATAGATATTGACTTTTTGAGGCGTTTG-ATCCAA
1 AAACGCCGCTATAGATATTGACTTTTTGAGGCGTTTGTATCCAA
* * * * *
37121 AAACGCAGCTATAGATCTT-TCTTTTCGCGGCGTTTGTATCCAA
1 AAACGCCGCTATAGATATTGACTTTTTGAGGCGTTTGTATCCAA
* *
37164 AAACGCCGCTATAGATATCGACCTTTT
1 AAACGCCGCTATAGATATTGACTTTTT
37191 ACGACGTTGG
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
42 53 0.55
43 40 0.41
44 4 0.04
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (44 bp):
AAACGCCGCTATAGATATTGACTTTTTGAGGCGTTTGTATCCAA
Found at i:38618 original size:2 final size:2
Alignment explanation
Indices: 38613--38652 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
38603 AAAAATTCTT
*
38613 TA TA TA AA T- TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38653 AATAAAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:39005 original size:2 final size:2
Alignment explanation
Indices: 38998--39041 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
38988 AAAACAGGGT
38998 TA TA TA TA 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 TA TA TA TA
39040 TA
1 TA
39042 GAAGTGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39620 original size:20 final size:20
Alignment explanation
Indices: 39597--39638 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
39587 AAACAATGCT
39597 AATA-ATAAAAAATAAATAAA
1 AATAGATAAAAAA-AAATAAA
* *
39617 AATAGGTAAAAAAATATAAA
1 AATAGATAAAAAAAAATAAA
39637 AA
1 AA
39639 CTTAGGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (20 bp):
AATAGATAAAAAAAAATAAA
Found at i:40946 original size:3 final size:3
Alignment explanation
Indices: 40916--40980 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
40906 GAAAAATTAA
* * *
40916 AAT AA- AAT AAGT AAT AA- AAT ATT AAT AAT AAT AGT GAT AAT AAAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
40961 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
40981 ATATAAAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40963 original size:19 final size:19
Alignment explanation
Indices: 40920--40977 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
40910 AATTAAAATA
40920 AAATAAGTAATAA-AAT-AT
1 AAATAA-TAATAATAATAAT
* * *
40938 TAATAATAATAGTGATAAT
1 AAATAATAATAATAATAAT
40957 AAATAATAATAATAATAAT
1 AAATAATAATAATAATAAT
40976 AA
1 AA
40978 TAAATATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 5 0.16
18 7 0.22
19 20 0.62
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAATAATAATAATAATAAT
Found at i:40966 original size:22 final size:22
Alignment explanation
Indices: 40915--40983 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
40905 GGAAAAATTA
40915 AAATAA-AATAAGTAATAA-AAT
1 AAATAATAATAA-TAATAATAAT
* * *
40936 -ATTAATAATAATAGTGATAAT
1 AAATAATAATAATAATAATAAT
40957 AAATAATAATAATAATAATAAT
1 AAATAATAATAATAATAATAAT
40979 AAATA
1 AAATA
40984 TAAAAACTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 8 0.21
21 8 0.21
22 23 0.59
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATAATAATAATAATAATAAT
Found at i:41079 original size:31 final size:30
Alignment explanation
Indices: 41019--41128 Score: 123
Period size: 32 Copynumber: 3.5 Consensus size: 30
41009 AAACCGTTTC
*
41019 TTTTAAAAATTATATATAAATTTCCAAAAATAT
1 TTTTAAAAA--ATATAT-AATTTTCAAAAATAT
*
41052 TTTTAAAAAATGTATAATTTTCAAAAAATATT
1 TTTTAAAAAATATATAATTTTC-AAAAATA-T
**
41084 TTTTAAAAACCATATAATTTTCAAAAATA-
1 TTTTAAAAAATATATAATTTTCAAAAATAT
*
41113 TTTTAAAAATTATATA
1 TTTTAAAAAATATATA
41129 TTATATATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
29 14 0.21
30 6 0.09
31 19 0.28
32 20 0.29
33 9 0.13
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (30 bp):
TTTTAAAAAATATATAATTTTCAAAAATAT
Found at i:41167 original size:40 final size:38
Alignment explanation
Indices: 41117--41335 Score: 228
Period size: 40 Copynumber: 5.6 Consensus size: 38
41107 AAAATATTTT
*
41117 AAAAATTATATATTATATATTTATTTTCAAAATGTTTAA
1 AAAAACTATATATTATATATTT-TTTTCAAAATGTTTAA
41156 GAAAAACTATATATTATATATTTATTTTCAAAATGTTTTAA
1 -AAAAACTATATATTATATATTT-TTTTCAAAATG-TTTAA
* *
41197 AAAAACTATATAATATATATATTTTTTCAAAAATGTTT-T
1 AAAAACTATATATTATATAT-TTTTTTC-AAAATGTTTAA
* * *
41236 GAAAACTATATATTATAT-TTTTTTGTAAAAACGTTTTAA
1 AAAAACTATATATTATATATTTTTT-TCAAAATG-TTTAA
* * * * * *
41275 ACAAATTATATAATATATAAATGTTTTCAAAATGTTT-T
1 AAAAACTATATATTATAT-ATTTTTTTCAAAATGTTTAA
41313 AAAAACTATATATTATATATTTT
1 AAAAACTATATATTATATATTTT
41336 CAAAATGTTT
Statistics
Matches: 149, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
37 13 0.09
38 20 0.13
39 33 0.22
40 66 0.44
41 17 0.11
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (38 bp):
AAAAACTATATATTATATATTTTTTTCAAAATGTTTAA
Found at i:41195 original size:78 final size:76
Alignment explanation
Indices: 41100--41334 Score: 271
Period size: 78 Copynumber: 3.0 Consensus size: 76
41090 AAACCATATA
* *
41100 ATTTTCAAAAATATTTT-AAAAATTATATATTATATATTTATTTTCAAAATGTTTAAGAAAAACT
1 ATTTTC-AAAATGTTTTAAAAAATTATATAATATATATTT-TTTTCAAAATGTTT--GAAAAACT
41164 ATATATTATATATTT
62 ATATATTATATATTT
*
41179 ATTTTCAAAATGTTTTAAAAAAACTATATAATATATATATTTTTTCAAAAATGTTTTG-AAAACT
1 ATTTTCAAAATGTTTT-AAAAAATTATATAATATATAT-TTTTTTC-AAAATG-TTTGAAAAACT
41243 ATATATTATAT-TTT
62 ATATATTATATATTT
* * * * *
41257 -TTTGTAAAAACGTTTTAAACAAATTATATAATATATAAATGTTTTCAAAATGTTTTAAAAACTA
1 ATTT-TCAAAATGTTTTAAA-AAATTATATAATATAT-ATTTTTTTCAAAATGTTTGAAAAACTA
41321 TATATTATATATTT
63 TATATTATATATTT
41335 TCAAAATGTT
Statistics
Matches: 137, Mismatches: 9, Indels: 21
0.82 0.05 0.13
Matches are distributed among these distances:
76 3 0.02
77 29 0.21
78 46 0.34
79 24 0.18
80 24 0.18
81 8 0.06
82 3 0.02
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (76 bp):
ATTTTCAAAATGTTTTAAAAAATTATATAATATATATTTTTTTCAAAATGTTTGAAAAACTATAT
ATTATATATTT
Found at i:41257 original size:34 final size:36
Alignment explanation
Indices: 41101--41346 Score: 173
Period size: 40 Copynumber: 6.4 Consensus size: 36
41091 AACCATATAA
* *
41101 TTTTCAAAAATATTTT-AAAAATTATATATTATATATTT
1 TTTTCAAAAATGTTTTAAAAAACTATATA-T-TATA-TT
*
41139 ATTTTC-AAAATGTTTAAGAAAAACTATATATTATATATTT
1 -TTTTCAAAAATGTTTTA-AAAAACTATATA-T-TATA-TT
41179 ATTTTC-AAAATGTTTTAAAAAAACTATATAATATATATATT
1 -TTTTCAAAAATGTTTT-AAAAAAC--TAT-ATAT-TATATT
*
41220 TTTTCAAAAATGTTTT-GAAAACTATATATTATATTT
1 TTTTCAAAAATGTTTTAAAAAACTATATATTATA-TT
* * * *
41256 TTTTGTAAAAACGTTTTAAACAAATTATATAATATATAAATG
1 TTTT-CAAAAATGTTTTAAA-AAACTATAT-AT-TAT--ATT
*
41298 TTTTC-AAAATGTTTT-AAAAACTATATATTATATA
1 TTTTCAAAAATGTTTTAAAAAACTATATATTATATT
41332 TTTTC-AAAATGTTTT
1 TTTTCAAAAATGTTTT
41347 CGAAAATATA
Statistics
Matches: 178, Mismatches: 14, Indels: 35
0.78 0.06 0.15
Matches are distributed among these distances:
34 17 0.10
35 4 0.02
36 13 0.07
37 15 0.08
38 17 0.10
39 20 0.11
40 58 0.33
41 16 0.09
42 14 0.08
43 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTTCAAAAATGTTTTAAAAAACTATATATTATATT
Found at i:42123 original size:84 final size:81
Alignment explanation
Indices: 41983--42824 Score: 804
Period size: 84 Copynumber: 10.2 Consensus size: 81
41973 TTGAATATAA
* * *
41983 TCGAACTCAAAGGTCTTTAG-CAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
*
42047 TTGGAGCTGAGCGGAG
66 TTGGAGCTGAGCGTAG
* * * * *
42063 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
42128 GCCGTT-GAGCTGAGCGTAG
63 GCC-TTGGAGCTGAGCGTAG
* * * * *
42147 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTC-TTTG--GTCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
*** * *
42212 GCCCTCAAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
** * *
42232 TCGAACTCGGGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
42296 GTT-GAGCTGAGCGTAG
66 -TTGGAGCTGAGCGTAG
* * * * * * * * *
42312 TCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTAT
1 TCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * *
42377 GCCCTTGAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
** * *
42397 TCGAACTCGGGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
42461 GTT-GAGCTGAGCGTAG
66 -TTGGAGCTGAGCGTAG
* * * * * * * * *
42477 TCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTAT
1 TCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * *
42542 GCCCTTGAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
* * * * * *
42562 TCGAACT-TAAGGGTCTTTGG-CAGATAGCTCTTCTTGACTTAAGTTATTCTGCAAATGATGTGC
1 TCGAACTCGAA-GGTCTTTGGTCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
42625 CTTGGAGCTGAGCGTAG
65 CTTGGAGCTGAGCGTAG
*
42642 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTTAAGCTATGCTGCAAATGATG
1 TCGAACTCGAAGGTCTTTGG-T--CAGATAACCCTTCTCGAC-TTAAGCTATGCTGCAAATGATG
* * * *
42707 TGCCCTCGAAGCTGAGTGTAA
62 TG-CCTTGGAGCTGAGCGTAG
* * *
42728 TCGAACT-TAAGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGC
1 TCGAACTCGAA-GGTCTTTGGTCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
42791 CTTGGAGCTGAGCGTAG
65 CTTGGAGCTGAGCGTAG
42808 TCGAACTCGAAGGTCTT
1 TCGAACTCGAAGGTCTT
42825 GGTGATAGGT
Statistics
Matches: 620, Mismatches: 109, Indels: 66
0.78 0.14 0.08
Matches are distributed among these distances:
80 120 0.19
81 144 0.23
82 18 0.03
84 209 0.34
85 98 0.16
86 31 0.05
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (81 bp):
TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAG
Found at i:42257 original size:249 final size:247
Alignment explanation
Indices: 41980--42824 Score: 1017
Period size: 249 Copynumber: 3.4 Consensus size: 247
41970 AAGTTGAATA
* *
41980 TAATCGAACTCAAAGGTCTTTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
42045 CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGT-ACAGATAACCCTTCTAGCCTTGAG
42110 TTATGCTGTAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGA
130 TTATGCTGTAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGA
* * * *
42175 TAACCCTTCTTGACTTAAGTTATGCTGTAAATGATATGCCCTCAAAGCTGAGTG
194 TAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTG
*** * *
42229 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* *
42294 CCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGA
66 CC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGT-ACAGATAACCCTTCTAGCCTTGA
* * * * **
42358 GTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTC---T-TTGGCA
129 GTTATGCTGTAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCA
* * * ** *
42419 GATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGT-TGAGCTGAGCG
192 GATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTG
* * * * * * * *
42474 TAGTCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGT
1 TAATCGAACTCAAAGGTC-TTTG---GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * * * * * * *
42539 TATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTC-TTTGG--CAGATAGCTCTTCTTGAC
62 TGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTTGGTACAGATAACCCTTCTAGCC
* * * * *
42600 TTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTG
125 TTGAGTTATGCTGTAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTG
*
42665 GCAGATAACCCTTCTCGACTTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
189 GCAGATAACCCTTCTCGAC-TTAAGCTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTG
* * * *
42725 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
42790 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
42825 GGTGATAGGT
Statistics
Matches: 493, Mismatches: 84, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
245 48 0.10
246 107 0.22
247 37 0.08
249 198 0.40
250 80 0.16
251 23 0.05
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (247 bp):
TAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTACAGATAACCCTTCTAGCCTTGAGT
TATGCTGTAAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATA
ACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTG
Found at i:42314 original size:165 final size:165
Alignment explanation
Indices: 41983--42824 Score: 1122
Period size: 165 Copynumber: 5.1 Consensus size: 165
41973 TTGAATATAA
* * * *
41983 TCGAACTCAAAGGTC--TT--TAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCAAAGGTCTTTTGCTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATAT
* * * * * * * * *
42044 G-CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTG
66 GCCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTA
* * *
42108 AGTTATGCTGTAAATGATGTGCCGTTGAGCTGAGCGTAG
127 AGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
* * * *
42147 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCAAAGGTCTTTTGCTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATAT
** *
42212 GCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
66 GCCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
42277 ATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
131 ATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
* * * *
42312 TCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTAT
1 TCGAACTCAAAGGTCTTTTGCTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATAT
*
42377 GCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
66 GCCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
42442 ATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
131 ATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
* * * *
42477 TCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTAT
1 TCGAACTCAAAGGTCTTTTGCTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATAT
** * * *
42542 GCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTCTTGACTTAAGTT
66 GCCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
*
42607 ATTCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAG
131 ATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAG
* * * * * * *
42642 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTTAAGCTATGCTGCAAATGATG
1 TCGAACTCAAAGGTCTTTTGCTAGCAGATAACCCTTCTAGAC-TTAAGTTATGCTGTAAATGATA
* **
42707 TGCCCTCGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
65 TGCCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
*
42772 TATTCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAG
130 TATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAG
*
42808 TCGAACTCGAAGGTCTT
1 TCGAACTCAAAGGTCTT
42825 GGTGATAGGT
Statistics
Matches: 618, Mismatches: 53, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
164 16 0.03
165 399 0.65
166 132 0.21
168 46 0.07
169 25 0.04
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (165 bp):
TCGAACTCAAAGGTCTTTTGCTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATAT
GCCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
ATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
Found at i:46258 original size:18 final size:19
Alignment explanation
Indices: 46217--46261 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
46207 AGTTAATGTG
46217 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
* *
46236 AATGCACAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
46254 AATGCAAA
1 AATGCAAA
46262 ATGTCTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.64, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:49313 original size:3 final size:3
Alignment explanation
Indices: 49283--49347 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
49273 GAAAAATTAA
* * *
49283 AAT AA- AAT AAGT AAT AA- AAT ATT AAT AAT AAT AGT GAT AAT AAAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
49328 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
49348 ATATAAAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49330 original size:19 final size:19
Alignment explanation
Indices: 49287--49344 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
49277 AATTAAAATA
49287 AAATAAGTAATAA-AAT-AT
1 AAATAA-TAATAATAATAAT
* * *
49305 TAATAATAATAGTGATAAT
1 AAATAATAATAATAATAAT
49324 AAATAATAATAATAATAAT
1 AAATAATAATAATAATAAT
49343 AA
1 AA
49345 TAAATATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 5 0.16
18 7 0.22
19 20 0.62
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAATAATAATAATAATAAT
Found at i:49333 original size:22 final size:22
Alignment explanation
Indices: 49282--49350 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
49272 GGAAAAATTA
49282 AAATAA-AATAAGTAATAA-AAT
1 AAATAATAATAA-TAATAATAAT
* * *
49303 -ATTAATAATAATAGTGATAAT
1 AAATAATAATAATAATAATAAT
49324 AAATAATAATAATAATAATAAT
1 AAATAATAATAATAATAATAAT
49346 AAATA
1 AAATA
49351 TAAAAACTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 8 0.21
21 8 0.21
22 23 0.59
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATAATAATAATAATAATAAT
Found at i:49448 original size:31 final size:30
Alignment explanation
Indices: 49388--49497 Score: 123
Period size: 32 Copynumber: 3.5 Consensus size: 30
49378 AAACCGTTTC
*
49388 TTTTAAAAATTATATATAAATTTCCAAAAATAT
1 TTTTAAAAA--ATATAT-AATTTTCAAAAATAT
*
49421 TTTTAAAAAATGTATAATTTTCAAAAAATATT
1 TTTTAAAAAATATATAATTTTC-AAAAATA-T
**
49453 TTTTAAAAACCATATAATTTTCAAAAATA-
1 TTTTAAAAAATATATAATTTTCAAAAATAT
*
49482 TTTTAAAAATTATATA
1 TTTTAAAAAATATATA
49498 TTATATATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
29 14 0.21
30 6 0.09
31 19 0.28
32 20 0.29
33 9 0.13
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (30 bp):
TTTTAAAAAATATATAATTTTCAAAAATAT
Found at i:49577 original size:41 final size:39
Alignment explanation
Indices: 49470--49716 Score: 244
Period size: 40 Copynumber: 6.4 Consensus size: 39
49460 AACCATATAA
* *
49470 TTTTCAAAAATATTTT--AAAAATTATATATTATATATTT
1 TTTTC-AAAATGTTTTAAAAAAACTATATATTATATATTT
*
49508 ATTTTCAAAATGTTTAAAAAAAACTATATATTATATATTT
1 -TTTTCAAAATGTTTTAAAAAAACTATATATTATATATTT
*
49548 ATTTTCAAAATGTTTTAAAAAAAACTATATAATATATATATT
1 -TTTTCAAAATGTTTT-AAAAAAACTATATATTATATAT-TT
*
49590 TTTTCAAAAATGTTTT--GAAAACTATATATTATAT-TTT
1 TTTTC-AAAATGTTTTAAAAAAACTATATATTATATATTT
* * * * * * *
49627 TTTGTAAAAACGTTTTAAACAAATTATATAATATATAAATG
1 TTT-TCAAAATGTTTTAAAAAAACTATATATTATAT-ATTT
49668 TTTTCAAAATGTTTT--AAAAACTATATATTATATA---
1 TTTTCAAAATGTTTTAAAAAAACTATATATTATATATTT
49702 TTTTCAAAATGTTTT
1 TTTTCAAAATGTTTT
49717 CGAAAATATA
Statistics
Matches: 178, Mismatches: 20, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
34 15 0.08
37 15 0.08
38 25 0.14
39 35 0.20
40 46 0.26
41 30 0.17
42 12 0.07
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (39 bp):
TTTTCAAAATGTTTTAAAAAAACTATATATTATATATTT
Found at i:61610 original size:23 final size:23
Alignment explanation
Indices: 61584--61630 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
61574 AATATGCTTA
* *
61584 TCTCTGACTTTATGACACGTTTT
1 TCTCTGACTCTATAACACGTTTT
* *
61607 TCTCTGTCTCTGTAACACGTTTT
1 TCTCTGACTCTATAACACGTTTT
61630 T
1 T
61631 TGTCTTCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.15, C:0.23, G:0.13, T:0.49
Consensus pattern (23 bp):
TCTCTGACTCTATAACACGTTTT
Found at i:62950 original size:3 final size:3
Alignment explanation
Indices: 62936--62965 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
62926 AGAAACCCTT
62936 TTC TTC TCTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC T-TC TTC TTC TTC TTC TTC TTC TT
62966 TCAAGAACCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:65767 original size:18 final size:19
Alignment explanation
Indices: 65732--65770 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
65722 ATATTAAAAG
*
65732 TTTTAAAATAAATCTTAAT
1 TTTTAAAATAAATATTAAT
65751 TTTTAAAATAAA-ATTAAT
1 TTTTAAAATAAATATTAAT
65769 TT
1 TT
65771 AATCGAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTAAAATAAATATTAAT
Found at i:65865 original size:18 final size:19
Alignment explanation
Indices: 65814--65868 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
65804 CAATCAAATC
* *
65814 ATATTAATTAAATTACTTG
1 ATATTAATTAAATTAATAG
*
65833 ATAATT-ATAAAATTAATAG
1 AT-ATTAATTAAATTAATAG
65852 -TATTAATTAAATTAATA
1 ATATTAATTAAATTAATA
65869 TTCAAGCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.10
18 12 0.40
19 12 0.40
20 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (19 bp):
ATATTAATTAAATTAATAG
Found at i:67583 original size:60 final size:61
Alignment explanation
Indices: 67500--67616 Score: 191
Period size: 60 Copynumber: 1.9 Consensus size: 61
67490 TTCTTTTATT
* * * *
67500 ATAACAATCAATTAAGTTGTGACATGTATAATTTAAT-AAATTAATATTATATTAATCAAA
1 ATAACAATCAATCAAATTATGACACGTATAATTTAATAAAATTAATATTATATTAATCAAA
67560 ATAACAATCAATCAAATTATGACACGTATAATTTAATAAAATTAATATTATATTAAT
1 ATAACAATCAATCAAATTATGACACGTATAATTTAATAAAATTAATATTATATTAAT
67617 AATTTGATTG
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 33 0.63
61 19 0.37
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.38
Consensus pattern (61 bp):
ATAACAATCAATCAAATTATGACACGTATAATTTAATAAAATTAATATTATATTAATCAAA
Found at i:69115 original size:60 final size:60
Alignment explanation
Indices: 69050--69204 Score: 211
Period size: 61 Copynumber: 2.6 Consensus size: 60
69040 AGATTGGTCA
69050 TTAAACTTTTGAATATTTCAATTTCATCCCCAAACTATGACTCTCATTCTAAATTAGTCC
1 TTAAACTTTTGAATATTTCAATTTCATCCCCAAACTATGACTCTCATTCTAAATTAGTCC
* * * * *
69110 TTAAACTTTTTGAACATTTTAATTTCATCCCTAAACTATGACTCTCTTTCTAAATTGGTCC
1 TTAAAC-TTTTGAATATTTCAATTTCATCCCCAAACTATGACTCTCATTCTAAATTAGTCC
** * * *
69171 CCAAACTTTTAAATATTCCAATTACATCCCCAAA
1 TTAAACTTTTGAATATTTCAATTTCATCCCCAAA
69205 TTCATCCAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 28 0.35
61 53 0.65
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
TTAAACTTTTGAATATTTCAATTTCATCCCCAAACTATGACTCTCATTCTAAATTAGTCC
Found at i:69494 original size:60 final size:60
Alignment explanation
Indices: 69369--69486 Score: 157
Period size: 60 Copynumber: 1.9 Consensus size: 60
69359 GTTAAGGATC
*** * *
69369 AATTTAGAATGAAGGTCATAGTTTAGGGATGAAAATGAAATGTTTAAGAGTTTGAGAACA
1 AATTTAGAATGAAGGTCATAGTTTAGGGATGAAAATGAAACACTTAAAAATTTGAGAACA
*
69429 AATTTAGAATGACGGTCATAGTTTAGGGAT-AAAATTGAAACACTTAAAAATTTAGAGA
1 AATTTAGAATGAAGGTCATAGTTTAGGGATGAAAA-TGAAACACTTAAAAATTT-GAGA
69487 TTAATTTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 4 0.08
60 42 0.84
61 4 0.08
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (60 bp):
AATTTAGAATGAAGGTCATAGTTTAGGGATGAAAATGAAACACTTAAAAATTTGAGAACA
Found at i:71843 original size:12 final size:12
Alignment explanation
Indices: 71826--71853 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
71816 CAACTTTACA
71826 GTTGAAGTTGAT
1 GTTGAAGTTGAT
71838 GTTGAAGTTGAT
1 GTTGAAGTTGAT
71850 GTTG
1 GTTG
71854 GTCTCTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (12 bp):
GTTGAAGTTGAT
Found at i:76524 original size:8 final size:9
Alignment explanation
Indices: 76496--76525 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
76486 TACCCCAAAC
76496 TTTCTAATT
1 TTTCTAATT
*
76505 TTTCCAATT
1 TTTCTAATT
76514 TTTCTAATT
1 TTTCTAATT
76523 TTT
1 TTT
76526 ATATATACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTCTAATT
Found at i:76853 original size:31 final size:31
Alignment explanation
Indices: 76809--76881 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
76799 ATTGACCCTC
* * *
76809 AGTGACCACATCTTAATTACATTAAAACGAA
1 AGTGACCAAATCTTAATTAAATAAAAACGAA
*
76840 AGTGATCAAATCTTAATTAAATAAAAACGAA
1 AGTGACCAAATCTTAATTAAATAAAAACGAA
**
76871 AACGACCAAAT
1 AGTGACCAAAT
76882 ATAATGGTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.23
Consensus pattern (31 bp):
AGTGACCAAATCTTAATTAAATAAAAACGAA
Done.