Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000820.1 Hibiscus syriacus cultivar Beakdansim tig00001587_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: 111424
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:12200 original size:135 final size:141
Alignment explanation
Indices: 12052--12337 Score: 370
Period size: 135 Copynumber: 2.0 Consensus size: 141
12042 TTTTTAATGT
** * **
12052 TAATATGGTTTTATCTTGTGGTGAGACATTAATAGCATCGTTAATTTTTTTAACGGTGGTGA-C-
1 TAATATGACTTTATCTTGTGGTGAGACATTAATAGCATCGTTAA-ATTTTTAACAATGGTGACCA
*
12115 C-A-AAACATAACATGAAGTATAA-TTT-AAAAAAA-ATAAATTATTAAAATAAAATTACGAGAA
65 CAAGAAACATAACATGAAGTATAATTTTAAAAAAAAGATAAATGATTAAAATAAAATTACGAGAA
*
12175 CAATTAACTGAC
130 CAATTAACCGAC
*
12187 TAATATGACTTTATCTTGTGGTGAGACATTAATAGTATCGTTAAATTTTTAACAATGGTGACCAA
1 TAATATGACTTTATCTTGTGGTGAGACATTAATAGCATCGTTAAATTTTTAACAATGGTGACC--
12252 AACAAAAAAGAAACATAACATGAAGTATAATTTTAAAAAAAAGATAAATGATTAAAATAAAATTA
64 -AC----AAGAAACATAACATGAAGTATAATTTTAAAAAAAAGATAAATGATTAAAATAAAATTA
*
12317 CGAGAATAATTAACCGAC
124 CGAGAACAATTAACCGAC
12335 TAA
1 TAA
12338 ATACGTAGTT
Statistics
Matches: 128, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
134 14 0.11
135 42 0.33
139 1 0.01
144 1 0.01
145 20 0.16
146 3 0.02
147 7 0.05
148 40 0.31
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.31
Consensus pattern (141 bp):
TAATATGACTTTATCTTGTGGTGAGACATTAATAGCATCGTTAAATTTTTAACAATGGTGACCAC
AAGAAACATAACATGAAGTATAATTTTAAAAAAAAGATAAATGATTAAAATAAAATTACGAGAAC
AATTAACCGAC
Found at i:13981 original size:2 final size:2
Alignment explanation
Indices: 13974--14009 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13964 TATACATCCC
13974 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
14010 GGGGGAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15355 original size:43 final size:43
Alignment explanation
Indices: 15304--15437 Score: 268
Period size: 43 Copynumber: 3.1 Consensus size: 43
15294 TTTTTGTGTA
15304 TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG
1 TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG
15347 TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG
1 TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG
15390 TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG
1 TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG
15433 TGATT
1 TGATT
15438 TTTTAAAAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (43 bp):
TGATTATGTATTATGAGCTTTTAAACTTTATGTATTTTCTATG
Found at i:16924 original size:28 final size:29
Alignment explanation
Indices: 16893--16954 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
16883 ATATAAAATT
* *
16893 ATATTTTTA-ATCAAAATATGTACCTAAA
1 ATATTTTTATATCAAAATAGGTACATAAA
*
16921 ATATTTTTATGTCAAAATAGGTACATAAA
1 ATATTTTTATATCAAAATAGGTACATAAA
*
16950 CTATT
1 ATATT
16955 CAAACGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (29 bp):
ATATTTTTATATCAAAATAGGTACATAAA
Found at i:17118 original size:31 final size:29
Alignment explanation
Indices: 17037--17126 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 29
17027 GAAAAAATCG
* *
17037 AATATTTTATGTGCTTATTTTGACTAAAA
1 AATATTTTATGTACTTATTTTGACCAAAA
*
17066 AATA-TTTAAGATA-TATATTTTGACCAAAA
1 AATATTTTATG-TACT-TATTTTGACCAAAA
*
17095 AGATAATTTTATGTACTTATTTTGACCGAAA
1 A-AT-ATTTTATGTACTTATTTTGACCAAAA
17126 A
1 A
17127 TGCTATAGGT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 6 0.12
29 19 0.38
30 2 0.04
31 17 0.34
32 6 0.12
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (29 bp):
AATATTTTATGTACTTATTTTGACCAAAA
Found at i:21463 original size:201 final size:201
Alignment explanation
Indices: 21118--21717 Score: 1173
Period size: 201 Copynumber: 3.0 Consensus size: 201
21108 TAAATATTTC
* *
21118 TATTTGTTTGTACTCGTTTGGATATGTATGTCTTTCTTGAATATTTATGTAATCTAAATTTATTT
1 TATTTGTTTGTACTTGTTTGGATATGCATGTCTTTCTTGAATATTTATGTAATCTAAATTTATTT
21183 TCAATGAAATTGTGTAAAATCAATTTTATGCAACGTCTAATGATGAATTAATGAAATTTTATTTT
66 TCAATGAAATTGTGTAAAATCAATTTTATGCAACGTCTAATGATGAATTAATGAAATTTTATTTT
21248 ATTATTCTATTTTTTAGTTGTAGATTCTCAAATATATTTTAGTTAAGAAAATATAGCAAAACATG
131 ATTATTCTATTTTTTAGTTGTAGATTCTCAAATATATTTTAGTTAAGAAAATATAGCAAAACATG
21313 AAAGTA
196 AAAGTA
21319 TATTTGTTTGTACTTGTTTGGATATGCATGTCTTTCTTGAATATTTATGTAATCTAAATTTATTT
1 TATTTGTTTGTACTTGTTTGGATATGCATGTCTTTCTTGAATATTTATGTAATCTAAATTTATTT
21384 TCAATGAAATTGTGTAAAATCAATTTTATGCAACGTCTAATGATGAATTAATGAAATTTTATTTT
66 TCAATGAAATTGTGTAAAATCAATTTTATGCAACGTCTAATGATGAATTAATGAAATTTTATTTT
21449 ATTATTCTATTTTTTAGTTGTAGATTCTCAAATATATTTTAGTTAAGAAAATATAGCAAAACATG
131 ATTATTCTATTTTTTAGTTGTAGATTCTCAAATATATTTTAGTTAAGAAAATATAGCAAAACATG
21514 AAAGTA
196 AAAGTA
21520 TATTTGTTTGTACTTGTTTGGATATGCATGTCTTTCTTGAATATTTATGTAATCTAAATTTATTT
1 TATTTGTTTGTACTTGTTTGGATATGCATGTCTTTCTTGAATATTTATGTAATCTAAATTTATTT
21585 TCAATGAAATTGTGTAAAATCAATTTTATGCAACGTCTAATGATGAATTAATGAAATTTTATTTT
66 TCAATGAAATTGTGTAAAATCAATTTTATGCAACGTCTAATGATGAATTAATGAAATTTTATTTT
*
21650 ATTATTCTATTTTTTAGTTGTAGATTCTCAAATATATTTTAGTTAAAAAAATATAGCAAAACATG
131 ATTATTCTATTTTTTAGTTGTAGATTCTCAAATATATTTTAGTTAAGAAAATATAGCAAAACATG
21715 AAA
196 AAA
21718 ATAAAAAAAA
Statistics
Matches: 396, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
201 396 1.00
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (201 bp):
TATTTGTTTGTACTTGTTTGGATATGCATGTCTTTCTTGAATATTTATGTAATCTAAATTTATTT
TCAATGAAATTGTGTAAAATCAATTTTATGCAACGTCTAATGATGAATTAATGAAATTTTATTTT
ATTATTCTATTTTTTAGTTGTAGATTCTCAAATATATTTTAGTTAAGAAAATATAGCAAAACATG
AAAGTA
Found at i:21982 original size:13 final size:13
Alignment explanation
Indices: 21934--21984 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
21924 TTTATATAAA
21934 CAGTTAATCAAAT
1 CAGTTAATCAAAT
* **
21947 CAATTTCTCAAAT
1 CAGTTAATCAAAT
*
21960 CAGCTAATCAAAT
1 CAGTTAATCAAAT
*
21973 CAGTTGATCAAA
1 CAGTTAATCAAA
21985 CCATTTACTA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (13 bp):
CAGTTAATCAAAT
Found at i:22255 original size:310 final size:311
Alignment explanation
Indices: 21778--22379 Score: 890
Period size: 310 Copynumber: 1.9 Consensus size: 311
21768 CAATCTCACT
* ****
21778 AAAGTATTTTATCTGAATAATTTCACCTCAATAAAGACTAAAGTATTGTAAAATATACATGTGCT
1 AAAGTATTTTATCTGAATAATTTCACCTCAATAAAGACTAAAGTATTGTAAAACATACACACACT
* * *
21843 TAACAATTAAATGTATCATACATTTATTTGTCATTTTACCCATATAAGCTATCAACTATTAGTTA
66 TAACAATTAAATATATCATACACTTATTTGTCATTTTACCCATATAAGCTATCAACTATCAGTTA
* *
21908 AATTTACCGAACACTTTTTATATAAACAGTTAATCAAATCAATTTCTCAAATCAGCTAATCAAAT
131 AATTTACCGAACACTTTTTATATAAACAATTAATCAAATCAATTTCTCAAATCAACTAATCAAAT
* * * * *
21973 CAGTTGATCAAACCATTTACTAGAATTAGCTA-AAAAAATCAACTATAAGTTATTTACCAAACA-
196 CAGTTGACCAAACCAATTACTAGAATCAACTACAAAAAACCAACTATAAGTTATTTA-CAAACAC
22036 CCCCAATATGTTCAAATAAGTGTCTAATAGTGATATTTGTAATTCTTAGTCA
260 CCCCAATATGTTCAAATAAGTGTCTAATAGTGATATTTGTAATTCTTAGTCA
*
22088 AAAGTATTTTATCTGAATAATTTTA-CTCCAATAAAGACTAAAGTATTGTAAAACATACACACAC
1 AAAGTATTTTATCTGAATAATTTCACCT-CAATAAAGACTAAAGTATTGTAAAACATACACACAC
* * ** *
22152 TTAACAATTAAATATATCATACCCTTATTTTTCATTTTACCCATATCAA-CTATCGGCTATCATT
65 TTAACAATTAAATATATCATACACTTATTTGTCATTTTACCCATAT-AAGCTATCAACTATCAGT
* * *
22216 TAAATTTTATCGAACAC-TTTTGTATAAACAATTAATCAAATTAATTTCTCAAATCAACTAATCA
129 TAAA-TTTACCGAACACTTTTTATATAAACAATTAATCAAATCAATTTCTCAAATCAACTAATCA
* **
22280 AATCAGTTGACCAAACCAATTACTAGAATCAACTACCAACTACCAACTATAAGTTATTTACAAAC
193 AATCAGTTGACCAAACCAATTACTAGAATCAACTACAAAAAACCAACTATAAGTTATTTACAAAC
22345 ACCCCCAATATGTTCAAATAAGTGTCTAATAGTGA
258 ACCCCCAATATGTTCAAATAAGTGTCTAATAGTGA
22380 AACATGTTGT
Statistics
Matches: 260, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
309 2 0.01
310 192 0.74
311 66 0.25
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (311 bp):
AAAGTATTTTATCTGAATAATTTCACCTCAATAAAGACTAAAGTATTGTAAAACATACACACACT
TAACAATTAAATATATCATACACTTATTTGTCATTTTACCCATATAAGCTATCAACTATCAGTTA
AATTTACCGAACACTTTTTATATAAACAATTAATCAAATCAATTTCTCAAATCAACTAATCAAAT
CAGTTGACCAAACCAATTACTAGAATCAACTACAAAAAACCAACTATAAGTTATTTACAAACACC
CCCAATATGTTCAAATAAGTGTCTAATAGTGATATTTGTAATTCTTAGTCA
Found at i:25393 original size:30 final size:30
Alignment explanation
Indices: 25323--25396 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
25313 ACCGGTAAAG
* *
25323 AACCGGT-AGAACCGACTGAGAACCGACAA
1 AACCGGTGTGAACCGACTGAAAACCGACAA
* ** * *
25352 AACTGAAGTGAACCGGCTGAAAACCGACCA
1 AACCGGTGTGAACCGACTGAAAACCGACAA
25382 AACCGGTGTGAACCG
1 AACCGGTGTGAACCG
25397 CCGGTTCTCT
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.38, C:0.27, G:0.26, T:0.09
Consensus pattern (30 bp):
AACCGGTGTGAACCGACTGAAAACCGACAA
Found at i:26402 original size:2 final size:2
Alignment explanation
Indices: 26395--26570 Score: 178
Period size: 2 Copynumber: 89.0 Consensus size: 2
26385 GGATTGGGTA
* * * *
26395 TC TC TC TC TC TC TC TC TC TT TC AC TC TA TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
26437 TC TC TC TC TC TC CC CC TC TC CC TC TC TC TC TC CC TC GC AC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
26479 CC TC GC TC TC TC TC TC TC TC TC TC AC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
26521 TC -C T- TC TC -C ATC GC TC TC AC TC TC TC TC TC TC TA TC TC TC
1 TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
26561 TC TC TC TC TC
1 TC TC TC TC TC
26571 ACACACACAC
Statistics
Matches: 141, Mismatches: 29, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
1 3 0.02
2 137 0.97
3 1 0.01
ACGTcount: A:0.04, C:0.51, G:0.02, T:0.44
Consensus pattern (2 bp):
TC
Found at i:27480 original size:20 final size:20
Alignment explanation
Indices: 27443--27480 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27433 CACAACTGGT
*
27443 CTGAGTCAACTCGAACCAGA
1 CTGAGTCAACTAGAACCAGA
*
27463 CTGAGTCAACTAGGACCA
1 CTGAGTCAACTAGAACCA
27481 AATCTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (20 bp):
CTGAGTCAACTAGAACCAGA
Found at i:27566 original size:18 final size:18
Alignment explanation
Indices: 27528--27571 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
27518 CCGGCCTGAC
*
27528 CCATTGACTTTGATCGAA
1 CCATTGACTTTGACCGAA
**
27546 CCATTGACTTTGACCTTA
1 CCATTGACTTTGACCGAA
27564 CCATTGAC
1 CCATTGAC
27572 ATGTTCAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (18 bp):
CCATTGACTTTGACCGAA
Found at i:32076 original size:20 final size:20
Alignment explanation
Indices: 32045--32175 Score: 86
Period size: 20 Copynumber: 6.9 Consensus size: 20
32035 GAGTATTTTG
32045 ACAAGAAGTTTCGAAACTTCT
1 ACAAG-AGTTTCGAAACTTCT
*
32066 ACAAGAGTTTCAAAACTT-T
1 ACAAGAGTTTCGAAACTTCT
* *
32085 TCAAGA----C-AGA-TTCCT
1 ACAAGAGTTTCGAAACTT-CT
* *
32100 A-AAAAGTTTCGATACTT-T
1 ACAAGAGTTTCGAAACTTCT
*
32118 TCAAGAGTTTCGAAACTATCT
1 ACAAGAGTTTCGAAACT-TCT
32139 -CAAGAGTTTCGAAACTATCT
1 ACAAGAGTTTCGAAACT-TCT
*
32159 -CAAGAGTTTCAAAACTT
1 ACAAGAGTTTCGAAACTT
32176 TCCTTAAAGT
Statistics
Matches: 89, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
13 2 0.02
14 5 0.06
15 2 0.02
18 2 0.02
19 22 0.25
20 50 0.56
21 6 0.07
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.31
Consensus pattern (20 bp):
ACAAGAGTTTCGAAACTTCT
Found at i:32195 original size:20 final size:20
Alignment explanation
Indices: 32104--32196 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
32094 ATTCCTAAAA
*
32104 AGTTTCGATACTTT-TCAAG
1 AGTTTCGAAACTTTCTCAAG
*
32123 AGTTTCGAAACTATCTCAAG
1 AGTTTCGAAACTTTCTCAAG
*
32143 AGTTTCGAAACTATCTCAAG
1 AGTTTCGAAACTTTCTCAAG
* *
32163 AGTTTCAAAACTTTCCTTAA-
1 AGTTTCGAAACTTT-CTCAAG
*
32183 AGTTTCGATACTTT
1 AGTTTCGAAACTTT
32197 GGCTCCAACG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.18
20 49 0.75
21 4 0.06
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (20 bp):
AGTTTCGAAACTTTCTCAAG
Found at i:33392 original size:25 final size:25
Alignment explanation
Indices: 33337--33393 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
33327 CCTTGTATGC
*
33337 TATATGATTATTTTATCTGTTTTGA
1 TATATGATTATTTTATCTGTTTGGA
* *
33362 -ATTATGGTTGTTTTATCTGTTTGGA
1 TA-TATGATTATTTTATCTGTTTGGA
33387 TATATGA
1 TATATGA
33394 ATGGATTATC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.04
25 24 0.92
26 1 0.04
ACGTcount: A:0.23, C:0.04, G:0.18, T:0.56
Consensus pattern (25 bp):
TATATGATTATTTTATCTGTTTGGA
Found at i:37403 original size:24 final size:24
Alignment explanation
Indices: 37361--37413 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 24
37351 TTTTATAAAG
37361 TTTTT-TTTTATTTTCAAGTTTTTA
1 TTTTTATTTTATTTTCAAG-TTTTA
37385 TTTTTATTTTATTTT-AAGTTTTA
1 TTTTTATTTTATTTTCAAGTTTTA
37408 TTTTTA
1 TTTTTA
37414 AACATGCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 11 0.39
24 8 0.29
25 9 0.32
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTTATTTTATTTTCAAGTTTTA
Found at i:37406 original size:12 final size:12
Alignment explanation
Indices: 37366--37411 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
37356 TAAAGTTTTT
37366 TTTTATTTTCAAG
1 TTTTATTTT-AAG
*
37379 TTTTTATTTTTA-
1 -TTTTATTTTAAG
37391 TTTTATTTTAAG
1 TTTTATTTTAAG
37403 TTTTATTTT
1 TTTTATTTT
37412 TAAACATGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.34
12 9 0.31
13 1 0.03
14 9 0.31
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTATTTTAAG
Found at i:37887 original size:140 final size:140
Alignment explanation
Indices: 37677--37961 Score: 525
Period size: 140 Copynumber: 2.0 Consensus size: 140
37667 GGCGAGATTG
37677 CCTTGCTAAGAGGGAATTAATATCGAAATTAGTAGTTATTAAAACAACAATACGAGTCGGTCTTA
1 CCTTGCTAAGAGGGAATTAATATCGAAATTAGTAGTTATTAAAACAACAATACGAGTCGGTCTTA
*
37742 ACGAACTTAAACGGTTATTGATCTACGATAATTGATGTTGATCAGATCAATTTCTGAAGTTGGAA
66 ACGAACTTAAACGGTTATTGATCTACGATAATTGATGTTGATCAGATCAATTTCTGAAGTTAGAA
37807 TCAAATATTA
131 TCAAATATTA
* *
37817 CCTTGCTAAGAGGGAATTGATATCGAAATTAGTAGTTATTGAAACAACAATACGAGTCGGTCTTA
1 CCTTGCTAAGAGGGAATTAATATCGAAATTAGTAGTTATTAAAACAACAATACGAGTCGGTCTTA
* *
37882 GCGAACTTAAACGGTTATTGATCTACGATAATTTATGTTGATCAGATCAATTTCTGAAGTTAGAA
66 ACGAACTTAAACGGTTATTGATCTACGATAATTGATGTTGATCAGATCAATTTCTGAAGTTAGAA
37947 TCAAATATTA
131 TCAAATATTA
37957 CCTTG
1 CCTTG
37962 AGTATTCTGT
Statistics
Matches: 140, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (140 bp):
CCTTGCTAAGAGGGAATTAATATCGAAATTAGTAGTTATTAAAACAACAATACGAGTCGGTCTTA
ACGAACTTAAACGGTTATTGATCTACGATAATTGATGTTGATCAGATCAATTTCTGAAGTTAGAA
TCAAATATTA
Found at i:41623 original size:20 final size:20
Alignment explanation
Indices: 41598--41638 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41588 GAAAAAATGT
41598 CATTTTATGGTTGATAAGGG
1 CATTTTATGGTTGATAAGGG
41618 CATTTTATGGTTGATAAGGG
1 CATTTTATGGTTGATAAGGG
41638 C
1 C
41639 TTAAGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.39
Consensus pattern (20 bp):
CATTTTATGGTTGATAAGGG
Found at i:42226 original size:298 final size:299
Alignment explanation
Indices: 41654--42252 Score: 1074
Period size: 298 Copynumber: 2.0 Consensus size: 299
41644 TTTATGCCAT
41654 ATTATTTCTTCAAAAGGAATTGTGGTAGAAAAAAGCGAAAATCGATATAGTACATTCACTTCCAT
1 ATTATTTCTTCAAAAGGAATTGTGGTAGAAAAAAGCGAAAATCGATATAGTACATTCACTTCCAT
* * *
41719 GCCCTACTACTGTGAGGGAAATCCACTCTTTTCTTGGTCATGTAGGATTTTACCGCATGTTCATC
66 GCCCTACAACTGTGAGGGAAATCCACTCTTTTCTTGGTCATGTAGGATTTTACCGCAGGTTAATC
**
41784 AAAATATTTTCCAAGGTGACACAACCATTATGTGAATTGTTGCAAAAAGATAAAAACTTTGATTT
131 AAAATATTTTCCAAGGTGACACAACCATTATACGAATTGTTGCAAAAAGATAAAAACTTTGATTT
*
41849 CGATCAAGAATGCAGAGAATCATTTGATGTTTTAAAGGAAAAGTTGGTTTCGGCACCCATAGTCT
196 CGATCAAGAATGCAGAGAATCATTTGATGTTTTAAAGGAAAAGTTGGTTTCGGCACCCATAGTCC
*
41914 AACTGCCAAATTGGTACTTCCCCTTTGAAGTCATATGTG
261 AACCGCCAAATTGGTACTTCCCCTTTGAAGTCATATGTG
* **
41953 ATTATTTCTTCAAAAGGAATTTTGGTAG-AAAAATTGAAAATCGATATAGTACATTCACTTCCAT
1 ATTATTTCTTCAAAAGGAATTGTGGTAGAAAAAAGCGAAAATCGATATAGTACATTCACTTCCAT
42017 GCCCTACAACTGTGAGGGAAATCCACTCTTTTCTTGGTCATGTAGGATTTTACCGCAGGTTAATC
66 GCCCTACAACTGTGAGGGAAATCCACTCTTTTCTTGGTCATGTAGGATTTTACCGCAGGTTAATC
42082 AAAATATTTTCCAAGGTGACACAACCATTATACGAATTGTTGCAAAAAGATAAAAACTTTGATTT
131 AAAATATTTTCCAAGGTGACACAACCATTATACGAATTGTTGCAAAAAGATAAAAACTTTGATTT
*
42147 CGATCAAGAATGCAGAGAATTATTTGATGTTTTAAAGGAAAAGTTGGTTTCGGCACCCATAGTCC
196 CGATCAAGAATGCAGAGAATCATTTGATGTTTTAAAGGAAAAGTTGGTTTCGGCACCCATAGTCC
**
42212 AACCGCTTAATTGGTACTTCCCCTTTGAAGTCATATGTG
261 AACCGCCAAATTGGTACTTCCCCTTTGAAGTCATATGTG
42251 AT
1 AT
42253 GCTTCGAATG
Statistics
Matches: 287, Mismatches: 13, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
298 260 0.91
299 27 0.09
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (299 bp):
ATTATTTCTTCAAAAGGAATTGTGGTAGAAAAAAGCGAAAATCGATATAGTACATTCACTTCCAT
GCCCTACAACTGTGAGGGAAATCCACTCTTTTCTTGGTCATGTAGGATTTTACCGCAGGTTAATC
AAAATATTTTCCAAGGTGACACAACCATTATACGAATTGTTGCAAAAAGATAAAAACTTTGATTT
CGATCAAGAATGCAGAGAATCATTTGATGTTTTAAAGGAAAAGTTGGTTTCGGCACCCATAGTCC
AACCGCCAAATTGGTACTTCCCCTTTGAAGTCATATGTG
Found at i:45448 original size:14 final size:14
Alignment explanation
Indices: 45419--45447 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
45409 TCATTTTTTG
45419 AAGAAAAGAGAAAA
1 AAGAAAAGAGAAAA
45433 AAGAAAAG-GAAAA
1 AAGAAAAGAGAAAA
45446 AA
1 AA
45448 ACAACAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAGAAAA
Found at i:46075 original size:31 final size:31
Alignment explanation
Indices: 46037--46095 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
46027 TTGGCTGATT
46037 TGATTATATCATACTTGAGGACAAGCATACA
1 TGATTATATCATACTTGAGGACAAGCATACA
46068 TGATTATATCATACTTGAGGACAAGCAT
1 TGATTATATCATACTTGAGGACAAGCAT
46096 GAGATAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (31 bp):
TGATTATATCATACTTGAGGACAAGCATACA
Found at i:46624 original size:24 final size:25
Alignment explanation
Indices: 46578--46625 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
46568 TAAAGTTATT
*
46578 TTTTCTTTTCAAGTTTTCATTTTTA
1 TTTTATTTTCAAGTTTTCATTTTTA
46603 TTTTATTTT-AAGTTTT-ATTTTTA
1 TTTTATTTTCAAGTTTTCATTTTTA
46626 AACATGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTTATTTTCAAGTTTTCATTTTTA
Found at i:46626 original size:13 final size:13
Alignment explanation
Indices: 46578--46626 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
46568 TAAAGTTATT
* *
46578 TTTTCTTTTCAAG
1 TTTTATTTTTAAG
46591 TTTTCATTTTT-A-
1 TTTT-ATTTTTAAG
46603 TTTTA-TTTTAAG
1 TTTTATTTTTAAG
46615 TTTTATTTTTAA
1 TTTTATTTTTAA
46627 ACATGCTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 2 0.07
12 9 0.30
13 11 0.37
14 4 0.13
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTAAG
Found at i:48001 original size:18 final size:18
Alignment explanation
Indices: 47978--48059 Score: 87
Period size: 18 Copynumber: 4.7 Consensus size: 18
47968 TGTTTATGAG
*
47978 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTCAA
*
47996 GGAATTGAAATCTGTCAA
1 GGAATTGGAATCTGTCAA
* * *
48014 -AAATTAGAATCTGTGAA
1 GGAATTGGAATCTGTCAA
* *
48031 GGAATTGAAATCTATCAA
1 GGAATTGGAATCTGTCAA
48049 -GAATTGGAATC
1 GGAATTGGAATC
48060 CAATTCCATA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 23 0.45
18 28 0.55
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTCAA
Found at i:48026 original size:35 final size:35
Alignment explanation
Indices: 47980--48059 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
47970 TTTATGAGGG
*
47980 AATTGGAATCTGTGAAGGAATTGAAATCTGTCAAA
1 AATTGGAATCTGTGAAGGAATTGAAATCTATCAAA
* *
48015 AATTAGAATCTGTGAAGGAATTGAAATCTATCAAG
1 AATTGGAATCTGTGAAGGAATTGAAATCTATCAAA
48050 AATTGGAATC
1 AATTGGAATC
48060 CAATTCCATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (35 bp):
AATTGGAATCTGTGAAGGAATTGAAATCTATCAAA
Found at i:48684 original size:33 final size:34
Alignment explanation
Indices: 48638--48718 Score: 146
Period size: 33 Copynumber: 2.4 Consensus size: 34
48628 CCTAAACCCG
48638 AACCCGACCCGACCCGAATATCACACTT-AAAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAAA
*
48671 AACCCGACTCGACCCGAATATCACACTTAAAAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAAA
48705 AACCCGACCCGACC
1 AACCCGACCCGACC
48719 TGAACAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 27 0.60
34 18 0.40
ACGTcount: A:0.41, C:0.38, G:0.10, T:0.11
Consensus pattern (34 bp):
AACCCGACCCGACCCGAATATCACACTTAAAAAA
Found at i:51503 original size:191 final size:194
Alignment explanation
Indices: 51159--51543 Score: 708
Period size: 190 Copynumber: 2.0 Consensus size: 194
51149 GTGAATACCT
51159 TGGGGTCATTAAGTAACGGAAAATCCGGCAAGATAGTCGATAACAATTTGAATCCTTAGCCTCCA
1 TGGGGTCATTAAGTAACGGAAAATCCGGCAAGATAGTCGATAACAATTTGAATCCTTAGCCTCCA
*
51224 TGAAAACATCGGGCCTTTAATCAGTTTATTCGATTGAAAATAAATTTTCTTATCTCAAAAATGAA
66 TGAAAACATCCGGCCTTTAATCAGTTTATTCGATTGAAAATAAATTTTCTTATCTCAAAAATGAA
51289 ACAGTTGCTAAGCCATCATATTCC-T-TATATTATTGTTGCCCT-ATCCTTAGGG-TTTCACGA
131 ACAGTTGCTAAGCCATCATATTCCTTATATATTATTGTTGCCCTAATCCTTAGGGTTTTCACGA
51349 TGGGGTCATTAAGTAACGGAAAATCCGGCAAGATAGTCGATAACAATTTGAATCCTTAGCCTCCA
1 TGGGGTCATTAAGTAACGGAAAATCCGGCAAGATAGTCGATAACAATTTGAATCCTTAGCCTCCA
51414 TGAAAACATCTCGGCCTTTAATCAGTTTATTCGATTGAAAATAAATTTTCTTATCTCAAAAACTG
66 TGAAAACATC-CGGCCTTTAATCAGTTTATTCGATTGAAAATAAATTTTCTTATCTCAAAAA-TG
51479 -AACAGTTGCTAAGCCATCATATTCCTTATATATTATTGTTGCCCTAATCCTTAGGGTTTTCACG
129 AAACAGTTGCTAAGCCATCATATTCCTTATATATTATTGTTGCCCTAATCCTTAGGGTTTTCACG
51543 A
194 A
51544 ATTATTATTA
Statistics
Matches: 188, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
190 75 0.40
191 75 0.40
192 3 0.02
193 17 0.09
194 10 0.05
195 8 0.04
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (194 bp):
TGGGGTCATTAAGTAACGGAAAATCCGGCAAGATAGTCGATAACAATTTGAATCCTTAGCCTCCA
TGAAAACATCCGGCCTTTAATCAGTTTATTCGATTGAAAATAAATTTTCTTATCTCAAAAATGAA
ACAGTTGCTAAGCCATCATATTCCTTATATATTATTGTTGCCCTAATCCTTAGGGTTTTCACGA
Found at i:59869 original size:12 final size:12
Alignment explanation
Indices: 59838--59882 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
59828 GTGCAAATAG
*
59838 TACCGTGAACAA
1 TACCATGAACAA
59850 TA--ATGAACAA
1 TACCATGAACAA
*
59860 TACCATGAACAG
1 TACCATGAACAA
59872 TACCATGAACA
1 TACCATGAACA
59883 GTACTGATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 9 0.31
12 20 0.69
ACGTcount: A:0.47, C:0.22, G:0.13, T:0.18
Consensus pattern (12 bp):
TACCATGAACAA
Found at i:59883 original size:12 final size:12
Alignment explanation
Indices: 59852--59886 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
59842 GTGAACAATA
*
59852 ATGAACAATACC
1 ATGAACAGTACC
59864 ATGAACAGTACC
1 ATGAACAGTACC
59876 ATGAACAGTAC
1 ATGAACAGTAC
59887 TGATGCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.17
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:60770 original size:31 final size:32
Alignment explanation
Indices: 60719--60812 Score: 111
Period size: 31 Copynumber: 3.0 Consensus size: 32
60709 CCTGAAGGAC
* * *
60719 CTATCCACATGTTCCTAAGAACATAGGTAA-A
1 CTATCCATATGTCCCGAAGAACATAGGTAATA
* *
60750 CTATCTATATGTCCCGAAGAACATAGGTAATC
1 CTATCCATATGTCCCGAAGAACATAGGTAATA
*
60782 CTGTCCATATGTCCCGAA-AGACATAGGTAAT
1 CTATCCATATGTCCCGAAGA-ACATAGGTAAT
60813 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 27 0.50
32 27 0.50
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (32 bp):
CTATCCATATGTCCCGAAGAACATAGGTAATA
Found at i:60797 original size:32 final size:32
Alignment explanation
Indices: 60718--60815 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
60708 TCCTGAAGGA
* * *
60718 CCTATCCACATGTTCCTAAGAACATAGGTAA-
1 CCTATCCATATGTCCCGAAGAACATAGGTAAT
* *
60749 ACTATCTATATGTCCCGAAGAACATAGGTAAT
1 CCTATCCATATGTCCCGAAGAACATAGGTAAT
*
60781 CCTGTCCATATGTCCCGAA-AGACATAGGTAAT
1 CCTATCCATATGTCCCGAAGA-ACATAGGTAAT
60813 CCT
1 CCT
60816 CGACTCTTGG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 27 0.47
32 30 0.53
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (32 bp):
CCTATCCATATGTCCCGAAGAACATAGGTAAT
Found at i:62979 original size:3 final size:3
Alignment explanation
Indices: 62971--63026 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
62961 CCATTTTTTG
* *
62971 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TATG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
63020 TTA TTA T
1 TTA TTA T
63027 ATTCTTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 46 0.96
4 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:70708 original size:77 final size:78
Alignment explanation
Indices: 70560--70708 Score: 180
Period size: 77 Copynumber: 1.9 Consensus size: 78
70550 AGTAAGTAAG
* *
70560 CATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATATAATTTGGAATAATTAAATA
1 CATTAAAAGAATGTAATTCAGATTACAACTCTATTAATTGATATATAATTTGGAATAATTAAATA
*
70625 GTTTTTAAATAAA
66 ATTTTTAAATAAA
* * * *
70638 CATT-AAAGATTGTAATTCAGATTATAAGTC-ATTAA-TGTATATTTAATTT-GAATTAATTAAA
1 CATTAAAAGAATGTAATTCAGATTACAACTCTATTAATTG-ATATATAATTTGGAA-TAATTAAA
70699 TAATATTTTA
64 TAAT-TTTTA
70709 TTTATTAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
75 5 0.08
76 25 0.41
77 27 0.44
78 4 0.07
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.43
Consensus pattern (78 bp):
CATTAAAAGAATGTAATTCAGATTACAACTCTATTAATTGATATATAATTTGGAATAATTAAATA
ATTTTTAAATAAA
Found at i:71479 original size:30 final size:30
Alignment explanation
Indices: 71445--71538 Score: 97
Period size: 29 Copynumber: 3.2 Consensus size: 30
71435 GTTTAGTCAC
71445 ATGGTTTATTTGATTAGGTACTTTTTCAAT
1 ATGGTTTATTTGATTAGGTACTTTTTCAAT
* * ** *
71475 ATGG-TTGTCTGCATATAGGT--TTAGTC-AC
1 ATGGTTTATTTG-AT-TAGGTACTTTTTCAAT
71503 ATGGTTTATTTGATTAGGTACTTTTTCAAT
1 ATGGTTTATTTGATTAGGTACTTTTTCAAT
71533 ATGGTT
1 ATGGTT
71539 GTCTGCAGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
27 5 0.10
28 7 0.15
29 18 0.38
30 13 0.27
31 5 0.10
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (30 bp):
ATGGTTTATTTGATTAGGTACTTTTTCAAT
Found at i:71503 original size:58 final size:58
Alignment explanation
Indices: 71413--71575 Score: 308
Period size: 58 Copynumber: 2.8 Consensus size: 58
71403 AATATACATA
*
71413 CAATATGGTTGTTTGCATATAGGTTTAGTCACATGGTTTATTTGATTAGGTACTTTTT
1 CAATATGGTTGTCTGCATATAGGTTTAGTCACATGGTTTATTTGATTAGGTACTTTTT
71471 CAATATGGTTGTCTGCATATAGGTTTAGTCACATGGTTTATTTGATTAGGTACTTTTT
1 CAATATGGTTGTCTGCATATAGGTTTAGTCACATGGTTTATTTGATTAGGTACTTTTT
*
71529 CAATATGGTTGTCTGCAGATAGGTTTAGTCACATGGTTTATTTGATT
1 CAATATGGTTGTCTGCATATAGGTTTAGTCACATGGTTTATTTGATT
71576 CGCAAGATAA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 103 1.00
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (58 bp):
CAATATGGTTGTCTGCATATAGGTTTAGTCACATGGTTTATTTGATTAGGTACTTTTT
Found at i:73459 original size:42 final size:42
Alignment explanation
Indices: 73372--73459 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
73362 GAAACATTAC
* * *
73372 ATTATTAAGAGAGAAAAATAAGATTTGAACATTGAATAAAAT
1 ATTATTAAGAGAAAAAAATAAGATTTGAAAACTGAATAAAAT
73414 ATTATTAAGAGAAACAAAATAA-ATATT-AAAACT-AATAAAAGT
1 ATTATTAAGAGAAA-AAAATAAGAT-TTGAAAACTGAATAAAA-T
73456 ATTA
1 ATTA
73460 ATATATTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 7 0.17
42 24 0.60
43 9 0.22
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.28
Consensus pattern (42 bp):
ATTATTAAGAGAAAAAAATAAGATTTGAAAACTGAATAAAAT
Found at i:78279 original size:12 final size:12
Alignment explanation
Indices: 78262--78306 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
78252 TACATTGGGC
*
78262 TATGAAAGTGAA
1 TATGAAAGTAAA
**
78274 TATGAAAACAAA
1 TATGAAAGTAAA
78286 TATGAAAGTAAA
1 TATGAAAGTAAA
*
78298 TGTGAAAGT
1 TATGAAAGT
78307 TATGACAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.20, T:0.24
Consensus pattern (12 bp):
TATGAAAGTAAA
Found at i:80613 original size:22 final size:22
Alignment explanation
Indices: 80588--80633 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
80578 CTCAACACTA
80588 ATACTAAAGTGCCTTAGT-ATTG
1 ATACTAAAGTGCCTTA-TCATTG
*
80610 ATACTAAAGTGTCTTATCATTG
1 ATACTAAAGTGCCTTATCATTG
80632 AT
1 AT
80634 GTAGATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (22 bp):
ATACTAAAGTGCCTTATCATTG
Found at i:84989 original size:17 final size:16
Alignment explanation
Indices: 84967--84998 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
84957 GTGGATCTAA
84967 AATTATTATGAAATAAT
1 AATTATTAT-AAATAAT
84984 AATTATTATAAATAA
1 AATTATTATAAATAA
84999 ATTCAGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTATTATAAATAAT
Found at i:85001 original size:14 final size:16
Alignment explanation
Indices: 84964--84999 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
84954 CATGTGGATC
84964 TAAAATTATTATGAAA
1 TAAAATTATTATGAAA
84980 TAATAATTATTAT-AAA
1 TAA-AATTATTATGAAA
84996 TAAA
1 TAAA
85000 TTCAGTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.05
16 9 0.47
17 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TAAAATTATTATGAAA
Found at i:85107 original size:17 final size:18
Alignment explanation
Indices: 85073--85116 Score: 81
Period size: 17 Copynumber: 2.5 Consensus size: 18
85063 TACAAAATAA
85073 AAAAATATAATTATAAAT
1 AAAAATATAATTATAAAT
85091 AAAAATATAATTA-AAAT
1 AAAAATATAATTATAAAT
85108 AAAAATATA
1 AAAAATATA
85117 TTTTATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATATAATTATAAAT
Found at i:85126 original size:18 final size:17
Alignment explanation
Indices: 85069--85126 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
85059 AAAGTACAAA
85069 ATAA-AAAAATATAATT
1 ATAATAAAAATATAATT
85085 ATAAATAAAAATATAATT
1 AT-AATAAAAATATAATT
* *
85103 AAAATAAAAATATATTTT
1 ATAATAAAAATATA-ATT
85121 ATAATA
1 ATAATA
85127 CCTCACTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 2 0.06
17 14 0.39
18 20 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAAAAATATAATT
Found at i:86514 original size:24 final size:24
Alignment explanation
Indices: 86471--86607 Score: 81
Period size: 24 Copynumber: 5.6 Consensus size: 24
86461 ATAAATAAAT
*
86471 AAATTAAATTAAAAT-GAAGAAAAA
1 AAATTAAA-TAAAATATAAGAAAAA
*
86495 AAATTAAATAAAAGATAAGATAAAGA
1 AAATTAAATAAAATATAAGA-AAA-A
** *
86521 AAACAAAGATAAAATAGTAAGTAAAAT
1 AAATTAA-ATAAAATA-TAAG-AAAAA
86548 AAATATAAA-AAAATA-AAG-AAAA
1 AAAT-TAAATAAAATATAAGAAAAA
* *
86570 AAATATAAATAAAACA-AATAAAAA
1 AAAT-TAAATAAAATATAAGAAAAA
86594 ATAA-TAAA-AAAATA
1 A-AATTAAATAAAATA
86608 AATAAATATA
Statistics
Matches: 91, Mismatches: 12, Indels: 22
0.73 0.10 0.18
Matches are distributed among these distances:
22 17 0.19
23 16 0.18
24 20 0.22
25 5 0.05
26 12 0.13
27 11 0.12
28 9 0.10
29 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (24 bp):
AAATTAAATAAAATATAAGAAAAA
Found at i:86551 original size:4 final size:4
Alignment explanation
Indices: 86544--86680 Score: 58
Period size: 4 Copynumber: 35.8 Consensus size: 4
86534 ATAGTAAGTA
* * * *
86544 AAAT AAAT --AT AAAA AAAT AAAG AAA- AAA- ATAT AAAT AAAAC AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT
* * * * * *
86589 AAA- AAAT -AAT AAAA AAAT AAAT AAAT ATAT ATAT ATAT ATAT ATAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
86635 AAAAT AAA- AAA- AAAT AAA- AAAT AGTAT ATAT ATAT AAAT TAAT AAA
1 -AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAA
86681 ATTGATAATA
Statistics
Matches: 108, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
2 2 0.02
3 20 0.19
4 77 0.71
5 9 0.08
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:86562 original size:14 final size:14
Alignment explanation
Indices: 86543--86611 Score: 68
Period size: 14 Copynumber: 4.7 Consensus size: 14
86533 AATAGTAAGT
86543 AAAATAAATATAAA
1 AAAATAAATATAAA
*
86557 AAAATAAAGA-AAA
1 AAAATAAATATAAA
*
86570 AAATATAAATAAAACA
1 AAA-ATAAATATAA-A
*
86586 AATAAAAAATAATAAA
1 AA-AATAAAT-ATAAA
86602 AAAATAAATA
1 AAAATAAATA
86612 AATATATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.13
14 16 0.36
15 8 0.18
16 11 0.24
17 4 0.09
ACGTcount: A:0.80, C:0.01, G:0.01, T:0.17
Consensus pattern (14 bp):
AAAATAAATATAAA
Found at i:86589 original size:37 final size:37
Alignment explanation
Indices: 86481--86615 Score: 116
Period size: 37 Copynumber: 3.6 Consensus size: 37
86471 AAATTAAATT
* * * *
86481 AAAATGAAGAAAAAAAATTAAATAAAAGATAAGATAAA
1 AAAATAAAGAAAAAAAAGTAAATAAAACA-AATATAAA
* * * * *
86519 GAAAACAAAGATAAAATAGTAAGTAAAATAAATATAAA
1 -AAAATAAAGAAAAAAAAGTAAATAAAACAAATATAAA
86557 AAAATAAAGAAAAAAATA-TAAATAAAACAAATA-AAA
1 AAAATAAAGAAAAAAA-AGTAAATAAAACAAATATAAA
*
86593 AATAATAAA-AAAATAAA-TAAATA
1 AA-AATAAAGAAAAAAAAGTAAATA
86616 TATATATATA
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
35 7 0.09
36 11 0.14
37 32 0.40
38 8 0.10
39 22 0.28
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (37 bp):
AAAATAAAGAAAAAAAAGTAAATAAAACAAATATAAA
Found at i:86663 original size:41 final size:40
Alignment explanation
Indices: 86586--86730 Score: 143
Period size: 41 Copynumber: 3.5 Consensus size: 40
86576 AAATAAAACA
*
86586 AATAAAAAATAATAAAAAAATAAATAAATATATATATATATAT
1 AATATAAAATAA-AAAAAAATAAA-AAATA-ATATATATATAT
*
86629 ATATATAAAATAAAAAAAAATAAAAAATAGTATATATATAT
1 A-ATATAAAATAAAAAAAAATAAAAAATAATATATATATAT
* * *
86670 AA-AT-TAATAAAATTGATAATAAAAAAATAATATATATATAT
1 AATATAAAATAAAA--AAAAAT-AAAAAATAATATATATATAT
* *
86711 AATCTAAAA-AAATAAAAATA
1 AATATAAAATAAAAAAAAATA
86731 TATACTAAAG
Statistics
Matches: 85, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
38 7 0.08
39 3 0.04
40 9 0.11
41 33 0.39
42 9 0.11
43 14 0.16
44 10 0.12
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (40 bp):
AATATAAAATAAAAAAAAATAAAAAATAATATATATATAT
Found at i:86724 original size:26 final size:26
Alignment explanation
Indices: 86689--86753 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
86679 AAATTGATAA
* *
86689 TAAAAAAATAATATATATATA-TAATC
1 TAAAAAAATAA-AAATATATACTAAAC
*
86715 TAAAAAAATAAAAATATATACTAAAG
1 TAAAAAAATAAAAATATATACTAAAC
*
86741 TAAAAAAAGAAAA
1 TAAAAAAATAAAA
86754 TGCATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 8 0.24
26 26 0.76
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (26 bp):
TAAAAAAATAAAAATATATACTAAAC
Found at i:87970 original size:21 final size:21
Alignment explanation
Indices: 87944--87983 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
87934 CAAGGGAAAC
87944 TGTCTCAAGAGAGACAAAATT
1 TGTCTCAAGAGAGACAAAATT
87965 TGTCTCAAGAGAGACAAAA
1 TGTCTCAAGAGAGACAAAA
87984 ACTTCTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (21 bp):
TGTCTCAAGAGAGACAAAATT
Found at i:88129 original size:36 final size:36
Alignment explanation
Indices: 88082--88252 Score: 117
Period size: 36 Copynumber: 4.9 Consensus size: 36
88072 AAGTTTATGC
* *
88082 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * **
88118 TTCAAGGGAAACTATCTCATGAGTGACAAAATTCAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * *
88154 TTCAAGGGAAA-TGTTTTC-A-A-TG-----TTTATGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT-TGT
* * *
88183 TTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTCGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT-GT
* *
88220 TTCAAGGGAACCTATCTCAAGAGAGACAAAATT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
88253 CATCTCAAGC
Statistics
Matches: 100, Mismatches: 23, Indels: 23
0.68 0.16 0.16
Matches are distributed among these distances:
28 2 0.02
29 14 0.14
30 3 0.03
32 1 0.01
33 2 0.02
34 1 0.01
35 1 0.01
36 44 0.44
37 32 0.32
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (36 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:88199 original size:101 final size:102
Alignment explanation
Indices: 88058--88315 Score: 410
Period size: 102 Copynumber: 2.5 Consensus size: 102
88048 TTGTTTTAAA
* *
88058 GGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-GTTTCA
1 GGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCGTTTCA
* * *
88122 AGGGAAACTATCTCATGAGTGACAAAATTCATTTCAAG
65 AGGGAAACTATCTCAAGAGAGACAAAATTCATCTCAAG
*
88160 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTCGTTTCAA
1 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCGTTTCAA
*
88225 GGGAACCTATCTCAAGAGAGACAAAATTCATCTCAAG
66 GGGAAACTATCTCAAGAGAGACAAAATTCATCTCAAG
* * *
88262 CGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
1 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
88316 CTTAGTTCCA
Statistics
Matches: 144, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
101 49 0.34
102 95 0.66
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (102 bp):
GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCGTTTCAA
GGGAAACTATCTCAAGAGAGACAAAATTCATCTCAAG
Found at i:88340 original size:102 final size:101
Alignment explanation
Indices: 88059--88354 Score: 394
Period size: 102 Copynumber: 2.9 Consensus size: 101
88049 TGTTTTAAAG
* * *
88059 GAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
1 GAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTAGTTTCAAG
* * * *
88124 GGAAACTATCTCATGAGTGACAAAATTCATTTCAAGG
65 GGAAACTATCTCAAGAGAGACAAAATTCATCTCAAGC
* *
88161 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTCGTTTCAAG
1 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTAGTTTCAAG
*
88226 GGAACCTATCTCAAGAGAGACAAAATTCATCTCAAGC
65 GGAAACTATCTCAAGAGAGACAAAATTCATCTCAAGC
* * * *
88263 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
1 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTAGTTTCAAG
* * * * *
88328 AGAAAATGTCTCAAGGGAGACGAAATT
65 GGAAACTATCTCAAGAGAGACAAAATT
88355 TGTTTCAATT
Statistics
Matches: 171, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
101 46 0.27
102 125 0.73
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (101 bp):
GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTAGTTTCAAGG
GAAACTATCTCAAGAGAGACAAAATTCATCTCAAGC
Found at i:88739 original size:106 final size:106
Alignment explanation
Indices: 88547--88869 Score: 441
Period size: 106 Copynumber: 3.0 Consensus size: 106
88537 TGTTTTGATC
* * * * **
88547 CGAGTCCAATATCC-TCTGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* * * * * *
88611 AGCCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGCTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
88653 CGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
88718 ACCAGCCGTTCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * *
88759 TTAGTCCAATATCCTTTGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
88824 ACCAGTCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
88865 CGAGT
1 CGAGT
88870 GGCACGATAT
Statistics
Matches: 190, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
106 188 0.99
107 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:89465 original size:32 final size:32
Alignment explanation
Indices: 89429--89537 Score: 121
Period size: 32 Copynumber: 3.4 Consensus size: 32
89419 CCTTCAAAAG
* * * *
89429 GTTGAATTTCCAAAGATGCCCTAATATTTGAT
1 GTTGAATTTCAAAAAATGCCCCAACATTTGAT
* *
89461 GTTGAATCTCAAAAAATTCCCCAACATTTGAT
1 GTTGAATTTCAAAAAATGCCCCAACATTTGAT
* **
89493 GTT-AAATAAAAAAAATGCCCCAACATTTGAT
1 GTTGAATTTCAAAAAATGCCCCAACATTTGAT
89524 GTTGAATCTTCAAA
1 GTTGAAT-TTCAAA
89538 GATGCCCTCA
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
31 26 0.43
32 31 0.51
33 4 0.07
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (32 bp):
GTTGAATTTCAAAAAATGCCCCAACATTTGAT
Found at i:89514 original size:31 final size:32
Alignment explanation
Indices: 89444--89531 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 32
89434 ATTTCCAAAG
* * * **
89444 ATGCCCTAATATTTGATGTTGAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTAAATCAAAAAAA
*
89476 ATTCCCCAACATTTGATGTTAAAT-AAAAAAA
1 ATGCCCCAACATTTGATGTTAAATCAAAAAAA
*
89507 ATGCCCCAACATTTGATGTTGAATC
1 ATGCCCCAACATTTGATGTTAAATC
89532 TTCAAAGATG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 27 0.57
32 20 0.43
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTAAATCAAAAAAA
Found at i:90580 original size:69 final size:69
Alignment explanation
Indices: 90464--90601 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
90454 TGTCTCTCTC
* * * * * *
90464 TTGATGCTCTATAATCTTCTAGTGGAGTGATTCAGTGATTCGGAAATGATTGTGCTTGGTCAATC
1 TTGATACTCTATAATCATCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
90529 TCAT
66 TCAT
* *
90533 TTGATACTCTATGATCATCGAGTGAAGTGATTCAGTGATTTGAAAATGATTGTGCTTGATCAATC
1 TTGATACTCTATAATCATCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
90598 TCAT
66 TCAT
90602 AGTTTGAATC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATACTCTATAATCATCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:90702 original size:20 final size:20
Alignment explanation
Indices: 90673--90710 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
90663 TTTTTCTTCA
90673 ATTTTCCTTTG-TTTTTTTT
1 ATTTTCCTTTGATTTTTTTT
90692 ATTTTCTCTTTGATTTTTT
1 ATTTTC-CTTTGATTTTTT
90711 CTCTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.76
Consensus pattern (20 bp):
ATTTTCCTTTGATTTTTTTT
Found at i:90717 original size:21 final size:20
Alignment explanation
Indices: 90660--90723 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
90650 CATCTTGTCT
* *
90660 TCTTT-TTTCTTCAATTTTC
1 TCTTTGTTTTTTCTATTTTC
*
90679 -CTTTGTTTTTTTTATTTTC
1 TCTTTGTTTTTTCTATTTTC
* *
90698 TCTTTGATTTTTTCTCTTTTT
1 TCTTTG-TTTTTTCTATTTTC
90719 TCTTT
1 TCTTT
90724 TTGTTCTGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 4 0.11
19 11 0.31
20 5 0.14
21 16 0.44
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (20 bp):
TCTTTGTTTTTTCTATTTTC
Found at i:93767 original size:23 final size:21
Alignment explanation
Indices: 93741--94007 Score: 91
Period size: 22 Copynumber: 12.1 Consensus size: 21
93731 AAAAGGTAAG
93741 AAATAAATAAATAAATAAAATTA
1 AAATAAATAAATAAA-AAAA-TA
*
93764 AAATGAATAAA-AAAATTAAATA
1 AAATAAATAAATAAAA--AAATA
*
93786 AAAGCTAAGATAAAGAAAGAAAAGATA
1 AAA--TAA-ATAAA-TAA-AAAA-ATA
* *
93813 AAAT-AGTAAGTAAAATAAATA
1 AAATAAATAAATAAAA-AAATA
* * *
93834 TAAAAAAATAAAGAAAAAGAAAA
1 -AAATAAATAAATAAAAA-AATA
*
93857 AAATATATAAATAAAACAAAT-
1 AAATAAATAAATAAAA-AAATA
93878 AAATAAAT-AATAATAAAAAGTA
1 AAATAAATAAATAA-AAAAA-TA
* * * * *
93900 AAA-ATATATATATATATATA
1 AAATAAATAAATAAAAAAATA
*
93920 TAAATAAA-AAATAAAAATAGTA
1 -AAATAAATAAATAAAAA-AATA
* * **
93942 AATATATATATATAAATTAATA
1 AA-ATAAATAAATAAAAAAATA
*
93964 AAACT-GAT-AATAAAAAAATA
1 AAA-TAAATAAATAAAAAAATA
* * **
93984 ATATATATATCTAAAAAAATA
1 AAATAAATAAATAAAAAAATA
94005 AAA
1 AAA
94008 ATATATTAAA
Statistics
Matches: 178, Mismatches: 40, Indels: 54
0.65 0.15 0.20
Matches are distributed among these distances:
19 1 0.01
20 23 0.13
21 48 0.27
22 51 0.29
23 34 0.19
24 3 0.02
25 6 0.03
26 2 0.01
27 8 0.04
28 2 0.01
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (21 bp):
AAATAAATAAATAAAAAAATA
Found at i:93877 original size:17 final size:16
Alignment explanation
Indices: 93824--93887 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
93814 AATAGTAAGT
93824 AAAATAAAT--ATAAA
1 AAAATAAATAAATAAA
* *
93838 AAAATAAAGAAAAAGAAA
1 AAAAT-AA-ATAAATAAA
*
93856 AAAATATATAAATAAA
1 AAAATAAATAAATAAA
93872 ACAAATAAATAAATAA
1 A-AAATAAATAAATAA
93888 TAATAAAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 9 0.23
17 14 0.36
18 9 0.23
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAATAAATAAATAAA
Found at i:93890 original size:46 final size:45
Alignment explanation
Indices: 93823--93933 Score: 127
Period size: 46 Copynumber: 2.4 Consensus size: 45
93813 AAATAGTAAG
93823 TAAAATAAATATAAAAA-AATAAAGAAAAAG-AAAAAAATATATAAA
1 TAAAATAAATA-AAAAATAAT-AAGAAAAAGTAAAAAAATATATAAA
* * * *
93868 TAAAACAAATAAATAAATAATAATAAAAAGTAAAAATATATATATA
1 TAAAATAAATAAA-AAATAATAAGAAAAAGTAAAAAAATATATAAA
*
93914 TATATATAAATAAAAAATAA
1 TA-AAATAAATAAAAAATAA
93934 AAATAGTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
44 2 0.04
45 21 0.38
46 24 0.43
47 9 0.16
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (45 bp):
TAAAATAAATAAAAAATAATAAGAAAAAGTAAAAAAATATATAAA
Found at i:95631 original size:21 final size:21
Alignment explanation
Indices: 95605--95663 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
95595 TAACACATTT
95605 ACTAAGAGGGGTTGGTTCAAG
1 ACTAAGAGGGGTTGGTTCAAG
95626 ACTAAGAGGGGTTGGTTCAAG
1 ACTAAGAGGGGTTGGTTCAAG
*
95647 GCTAAGAGGGGTTGGTT
1 ACTAAGAGGGGTTGGTT
95664 TAGGGTTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.08, G:0.41, T:0.25
Consensus pattern (21 bp):
ACTAAGAGGGGTTGGTTCAAG
Found at i:96644 original size:6 final size:6
Alignment explanation
Indices: 96633--96670 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
96623 ACGAAGGTAG
96633 GGTTGA GGTTGA GGTTGA GGTTGA GGTTGA GGTTGA GG
1 GGTTGA GGTTGA GGTTGA GGTTGA GGTTGA GGTTGA GG
96671 CCGAGGTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTTGA
Found at i:96676 original size:18 final size:18
Alignment explanation
Indices: 96637--96679 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
96627 AGGTAGGGTT
**
96637 GAGGTTGAGGTTGAGGTT
1 GAGGTTGAGGTTGAGGCC
96655 GAGGTTGAGGTTGAGGCC
1 GAGGTTGAGGTTGAGGCC
96673 GAGGTTG
1 GAGGTTG
96680 TAAGTATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.05, G:0.51, T:0.28
Consensus pattern (18 bp):
GAGGTTGAGGTTGAGGCC
Found at i:98898 original size:59 final size:61
Alignment explanation
Indices: 98787--98915 Score: 176
Period size: 59 Copynumber: 2.1 Consensus size: 61
98777 TATAATTTGA
* *
98787 GATGAAA-TTAGAATGTTCAAAAAATTTGAGGACCAATTTAGAATGAAGGTCATAGTTTAGG
1 GATGAAATTTAGAATGTTC-AAAAATTTAAGGACCAATTTAAAATGAAGGTCATAGTTTAGG
* *
98848 GATGAAATTTA-AATGTTC-AACATTTAAGGACTAATTTAAAATGACA-GTCATAGTTTAGG
1 GATGAAATTTAGAATGTTCAAAAATTTAAGGACCAATTTAAAATGA-AGGTCATAGTTTAGG
98907 GATGAAATT
1 GATGAAATT
98916 GGAACATTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
59 44 0.71
60 1 0.02
61 14 0.23
62 3 0.05
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (61 bp):
GATGAAATTTAGAATGTTCAAAAATTTAAGGACCAATTTAAAATGAAGGTCATAGTTTAGG
Found at i:106263 original size:21 final size:21
Alignment explanation
Indices: 106237--106308 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
106227 TAAATGTTAA
106237 TATCGATACTCATTCATAGAG
1 TATCGATACTCATTCATAGAG
** *
106258 TATCGATAC-CAAGGCA-GGAG
1 TATCGATACTC-ATTCATAGAG
*
106278 TATCGATACTC-TTCATAGGGG
1 TATCGATACTCATTCATA-GAG
106299 TATCGATACT
1 TATCGATACT
106309 GGGGTATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 25 0.62
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (21 bp):
TATCGATACTCATTCATAGAG
Found at i:110952 original size:29 final size:28
Alignment explanation
Indices: 110882--110965 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 28
110872 GCTAAAATAT
* * *
110882 AAATTTTAAAAATTATATTTTTGTCCCT
1 AAATTTTAAAAATTATACTTTAGTCCCC
110910 AAACTTTTACAAAATATATACTTTAG-CCACC
1 AAA-TTTTA-AAAAT-TATACTTTAGTCC-CC
*
110941 AAATTTTAAAAACTTCTA-TTTAGTC
1 AAATTTTAAAAA-TTATACTTTAGTC
110966 ACTAACCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
28 8 0.17
29 13 0.28
30 13 0.28
31 12 0.26
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.42
Consensus pattern (28 bp):
AAATTTTAAAAATTATACTTTAGTCCCC
Done.