Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005398.1 Hibiscus syriacus cultivar Beakdansim tig00012373_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: 88896
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5203 original size:51 final size:51
Alignment explanation
Indices: 5142--5240 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
5132 AATACTTCGC
* * *
5142 TTAGGATGAAAACCTGAAAGGGCATCCTAAGTCAAAAAAAAGGAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAGGAAAAACGT
* * * *
5193 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAATGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAGGAAAAA
5241 GGGAAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.15
Consensus pattern (51 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAGGAAAAACGT
Found at i:6198 original size:106 final size:106
Alignment explanation
Indices: 6013--6680 Score: 849
Period size: 106 Copynumber: 6.4 Consensus size: 106
6003 ACAATTTCCT
* * * * *
6013 AATTTCAACTTCACATCGAAGGATGTTGGACACGATAAAACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
6078 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTC
66 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTC
* * * **
6119 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAATACAAGTTTAACTTCACAATAAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
*
6184 GACGGCTGGTTGTCAACAAACAATCTCCCAATTTCAGAG--
66 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTC
*
6223 ----TCAA--T---AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
* * *
6279 GACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGGGTT
66 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTC
* * *
6320 AATTTCAACTTCACATCGAAGGATATTGGGCTCGAGAC--CATAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
* * * *
6383 GACGGCTGGTTGTTAACAAATAATTTCCAAATTTCAGAGCC
66 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTC
*
6424 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
* * *
6489 GACGGTTGGTTGTCAACAAATAATTTCCCAATTTCAGGGTC
66 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTC
* * * ** * *
6530 AATTTCAACTTCACATCGAATGATATTAGACTTAAGACAACACAAGCTCAACTTCACAGCGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
* * * * * * *
6595 GGCGGTTGGCTGTCAACAAACAATTTTCCAGTTCCAGAGCC
66 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTC
* * * *
6636 AATTTCAACTTCACGGCGGAGGATATTGGACTCGAAACAATACAA
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
6681 ACTACTTGGA
Statistics
Matches: 488, Mismatches: 61, Indels: 26
0.85 0.11 0.05
Matches are distributed among these distances:
95 81 0.17
98 1 0.00
100 4 0.01
101 4 0.01
103 1 0.00
104 96 0.20
106 301 0.62
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (106 bp):
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTC
Found at i:6479 original size:305 final size:294
Alignment explanation
Indices: 5937--6532 Score: 834
Period size: 305 Copynumber: 2.0 Consensus size: 294
5927 CTTCACAGTA
*
5937 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGATTGTCAACA
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTCAACA
*
6002 AACAATTTCCTAATTTCAACTTCACATCGAAGGATGTTGGACACGATAAAACACAAGTTCAACTT
66 AACAATTTCCTAATTTCAACTTCACATCGAAGGATATTGGACACGA-AAAACACAAGTTCAACTT
* *
6067 CACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCA
130 CACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAATTTCAGAGCCAATTTCAACTTCA
* * *
6132 CAGCGAAGGATATTGGACTCAAGACAATACAAGTTTAACTTCACAATAAAGGGACGGCTGGTTGT
195 CAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGT
6197 CAACAAACAATCTCCCAATTTCAGAGTCAATAGCG
260 CAACAAACAATCTCCCAATTTCAGAGTCAATAGCG
* * * *
6232 AAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACA
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTCAAC-
* * * * * *
6297 AATAATTTCCCAATTTCAGGGTTAATTTCAACTTCACATCGAAGGATATTGGGCTCG-AGACCAT
65 -A-AA-----CAATTTC----CTAATTTCAACTTCACATCGAAGGATATTGGACACGAAAAACAC
* *
6361 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTTAACAAATAATTTCCAAATTTCAGAGCCAA
119 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAATTTCAGAGCCAA
* * *
6426 TTTCAACTTCACAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGA
184 TTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGA
* * * *
6491 CGGTTGGTTGTCAACAAATAATTTCCCAATTTCAGGGTCAAT
249 CGGCTGGTTGTCAACAAACAATCTCCCAATTTCAGAGTCAAT
6533 TTCAACTTCA
Statistics
Matches: 263, Mismatches: 26, Indels: 14
0.87 0.09 0.05
Matches are distributed among these distances:
295 59 0.22
297 1 0.00
298 2 0.01
303 7 0.03
305 162 0.62
307 32 0.12
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (294 bp):
AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTCAACA
AACAATTTCCTAATTTCAACTTCACATCGAAGGATATTGGACACGAAAAACACAAGTTCAACTTC
ACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAAATTTCAGAGCCAATTTCAACTTCAC
AGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTC
AACAAACAATCTCCCAATTTCAGAGTCAATAGCG
Found at i:6501 original size:210 final size:211
Alignment explanation
Indices: 6228--6670 Score: 683
Period size: 210 Copynumber: 2.1 Consensus size: 211
6218 CAGAGTCAAT
6228 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
* * * *
6293 AACAAATAATTTCCCAATTTCAGGGTTAATTTCAACTTCACATCGAAGGATATTGGGCTCGAGAC
66 AACAAATAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTCAAGAC
* * * * * *
6358 -CATAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTTAACAAATAA-TTTCCAAATTTCAGA
131 ACACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATTTTCC-AATTCCAGA
6421 GCCAATTTCAACTTCAC
195 GCCAATTTCAACTTCAC
*
6438 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
* *
6503 AACAAATAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATCGAATGATATTAGACTTAAGAC
66 AACAAATAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTCAAGAC
* * * *
6568 AACACAAGCTCAACTTCACAGCGAAGGGGCGGTTGGCTGTCAACAAACAATTTTCCAGTTCCAGA
131 -ACACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATTTTCCAATTCCAGA
6633 GCCAATTTCAACTTCAC
195 GCCAATTTCAACTTCAC
* *
6650 GGCGGAGGATATTGGACTCGA
1 AGCGAAGGATATTGGACTCGA
6671 AACAATACAA
Statistics
Matches: 211, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
210 123 0.58
212 83 0.39
213 5 0.02
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (211 bp):
AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
AACAAATAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTCAAGAC
ACACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATTTTCCAATTCCAGAG
CCAATTTCAACTTCAC
Found at i:7201 original size:35 final size:35
Alignment explanation
Indices: 7153--7224 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
7143 CCAAAAAAGA
*
7153 AGAGTTGGTTTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
7188 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
7223 AG
1 AG
7225 GGTTTTTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:7620 original size:16 final size:18
Alignment explanation
Indices: 7597--7635 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
7587 ATTATATGGG
7597 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
7613 T-TTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
7630 TATTAT
1 TATTAT
7636 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.10
16 9 0.45
17 5 0.25
18 4 0.20
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:7640 original size:2 final size:2
Alignment explanation
Indices: 7633--7711 Score: 51
Period size: 2 Copynumber: 40.5 Consensus size: 2
7623 ATGTTATTAT
* *
7633 TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA T- TT TCA TT TGA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA
* * *
7673 TT TT TA CTA TA T- TT TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7712 TTCTTTAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
1 5 0.08
2 55 0.86
3 4 0.06
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (2 bp):
TA
Found at i:7923 original size:22 final size:22
Alignment explanation
Indices: 7884--7946 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
7874 ATAATTATAT
7884 ATATATATATATATTTTTTTTATT-
1 ATAT-TATAT-TA-TTTTTTTATTC
* *
7908 TTATTATTTTCA-TTTTTTATTC
1 ATATTATATT-ATTTTTTTATTC
7930 ATATTATATTATTTTTT
1 ATATTATATTATTTTTT
7947 AAAACCTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
21 10 0.31
22 14 0.44
23 5 0.16
24 3 0.09
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (22 bp):
ATATTATATTATTTTTTTATTC
Found at i:7924 original size:21 final size:21
Alignment explanation
Indices: 7888--7947 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
7878 TTATATATAT
7888 ATATATATATT-TTTTTTATT-
1 ATAT-TATATTATTTTTTATTC
* *
7908 TTATTATTTTCATTTTTTATTC
1 ATATTATATT-ATTTTTTATTC
7930 ATATTATATTATTTTTTA
1 ATATTATATTATTTTTTA
7948 AAACCTTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 17 0.52
22 8 0.24
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
ATATTATATTATTTTTTATTC
Found at i:16281 original size:16 final size:18
Alignment explanation
Indices: 16260--16297 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16250 CGAGTTTTGG
16260 TTATTTGA-A-GTGGTAT
1 TTATTTGACACGTGGTAT
*
16276 TTATTTGACACGTGGTTT
1 TTATTTGACACGTGGTAT
16294 TTAT
1 TTAT
16298 AGAGGGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (18 bp):
TTATTTGACACGTGGTAT
Found at i:24493 original size:101 final size:102
Alignment explanation
Indices: 24312--24576 Score: 370
Period size: 101 Copynumber: 2.6 Consensus size: 102
24302 TGATACGAAT
* * *
24312 AAATTTATATCACTTGAGATTGTTTTTATTAAAAGCAATTTCGTCTCACTTGAGACAGTTTCCCT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAATCAATTTCGTCTCACTTGAGACAGTTTCCCT
* * ** *
24377 TGAAGAACAAGTTTTGGAATTGCTTCACTTG-AAACA
66 TGAAGAACAAATTTTGAAATTGCTTCACCAGAAAAAA
* * * *
24413 AGATTTATCTCACTGGAGATTCTTTTTCTTAAAATCAATTTCGTCTCACTTGAGACCGTTTCCCT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAATCAATTTCGTCTCACTTGAGACAGTTTCCCT
* *
24478 TGAAGTACAAATTTTGAAATTGTTTCACCAGAAAAAAA
66 TGAAGAACAAATTTTGAAATTGCTTCACCAG-AAAAAA
* *
24516 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAATCAACTTCGTCTCGCTTGAGACAGTTT
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAATCAATTTCGTCTCACTTGAGACAGTTT
24577 TTCGCTCGAG
Statistics
Matches: 142, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
101 83 0.58
103 59 0.42
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (102 bp):
AAATTTATCTCACTTGAGATTGTTTTTCTTAAAATCAATTTCGTCTCACTTGAGACAGTTTCCCT
TGAAGAACAAATTTTGAAATTGCTTCACCAGAAAAAA
Found at i:24587 original size:17 final size:17
Alignment explanation
Indices: 24561--24595 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
24551 CAACTTCGTC
*
24561 TCGCTTGAGACAGTTTT
1 TCGCTCGAGACAGTTTT
24578 TCGCTCGAGACAGTTTT
1 TCGCTCGAGACAGTTTT
24595 T
1 T
24596 ATCTCACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (17 bp):
TCGCTCGAGACAGTTTT
Found at i:25051 original size:118 final size:118
Alignment explanation
Indices: 24776--25130 Score: 486
Period size: 118 Copynumber: 3.0 Consensus size: 118
24766 AAAAAAAAAT
* *
24776 TCAAATCCATCATATAAGGAGGTGGATCAACATTTCCAATGGAATG-GTTCATAATGAGAAGAAC
1 TCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATGGAA-GAGTTCATAATGAGAAGAAC
* * *
24840 TCGTCTG--AAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGATCTTTTGC
65 TCGTCCGAAAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC-ACCTTTTGC
* *
24893 TCAAATCCATCACAGAATGAGGTGGATCAATATTTCCAATGGAAGAGTTCATAATGAGAAGAACT
1 TCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACT
* *
24958 CGTCCGAAAAAGGA-AAAAAGTTCATAATGAGAAGAACTTGTTCACCATTTTTC
66 CGTCCGAAAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCACC-TTTTGC
* * * * *
25011 TCGATTCCATCACAGTAGGAGGTGGCTCAACATTTGCAATGGAAGAGTTCATAATGAGAAGAACT
1 TCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACT
* *
25076 CATCC-ATAAAAAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCACTCTTTTGC
66 CGTCCGA-AAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAC-CTTTTGC
25130 T
1 T
25131 AGATTCTATC
Statistics
Matches: 211, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
116 1 0.00
117 67 0.32
118 101 0.48
119 41 0.19
120 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (118 bp):
TCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACT
CGTCCGAAAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCACCTTTTGC
Found at i:25119 original size:20 final size:19
Alignment explanation
Indices: 25057--25120 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
25047 CAATGGAAGA
25057 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
25076 CATCCATAAAAAGAGAAGAA--
1 -GTTCAT--AATGAGAAGAACT
25096 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
25116 GTTCA
1 GTTCA
25121 CTCTTTTGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 10 0.30
19 4 0.12
20 9 0.27
22 10 0.30
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:25226 original size:163 final size:163
Alignment explanation
Indices: 25011--25418 Score: 545
Period size: 163 Copynumber: 2.5 Consensus size: 163
25001 ACCATTTTTC
* * * * * *
25011 TCGATTCCATCACAGTAGGAGGTGGCTCAACATTTGCAATGGAA-GAGTTCATAATGAGAAGAAC
1 TCGAATCCATCACAGAATGAGGTGGATCATCATTTCCAATGGAATG-GTTCATAATGAGAAGAAC
* * *
25075 TCATCCATAAA-A-AGAGAAGAAGTTCATAATGAGAAGAACTTGTTCACTCTTTTGCT-AGATTC
65 TCAT-C-TAAAGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGCTCACCCTTTTGCTCA-ACTC
*
25137 TATCGCAGAAGGAGATAAATCAACATCAACATTTTGA
127 TATCGCAGAAGGAGATAAACCAACATCAACATTTTGA
* * *
25174 TCGAATCCATCATAGAATGAGGTGGATCGTCATTTCCAATTGAATGGTTCATAATGAGAAGAACT
1 TCGAATCCATCACAGAATGAGGTGGATCATCATTTCCAATGGAATGGTTCATAATGAGAAGAACT
*
25239 CATCTAAAGAGTGAGAAGAAGTTCATAATGAGAAGAACTTGCTCACCCTTTTGCTCAACTCTATC
66 CATCTAAAGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGCTCACCCTTTTGCTCAACTCTATC
* * ** *
25304 GCTGAAGGAGATATACCAGTATCATCATTTTGA
131 GCAGAAGGAGATAAACCAACATCAACATTTTGA
*
25337 TCGAATCCATCACAGAATGAGGTGGATCATCATTTCCAATGGAATGATTCATAATGAGAAGAACT
1 TCGAATCCATCACAGAATGAGGTGGATCATCATTTCCAATGGAATGGTTCATAATGAGAAGAACT
* * *
25402 CGTCTGAAGAGTGAGAA
66 CATCTAAAGAGAGAGAA
25419 TGACTTCATA
Statistics
Matches: 216, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
161 4 0.02
162 2 0.01
163 208 0.96
164 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (163 bp):
TCGAATCCATCACAGAATGAGGTGGATCATCATTTCCAATGGAATGGTTCATAATGAGAAGAACT
CATCTAAAGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGCTCACCCTTTTGCTCAACTCTATC
GCAGAAGGAGATAAACCAACATCAACATTTTGA
Found at i:27094 original size:14 final size:14
Alignment explanation
Indices: 27075--27110 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
27065 TTTTTATTTA
27075 TTTAATTTCAGTAC
1 TTTAATTTCAGTAC
* *
27089 TTTAATTTCATTAT
1 TTTAATTTCAGTAC
27103 TTTAATTT
1 TTTAATTT
27111 TTCGTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:32493 original size:25 final size:25
Alignment explanation
Indices: 32464--32551 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 25
32454 ATAAATGCAT
32464 AATATTTTATATATATTAACATAAA
1 AATATTTTATATATATTAACATAAA
32489 AATATTTT-T-TATATTAACTTATTAAA
1 AATATTTTATATATATTAAC--A-TAAA
* * **
32515 TATATTTTATTATTATCTTAATTTAAA
1 AATATTTTA-TA-TATATTAACATAAA
32542 AATATTTTAT
1 AATATTTTAT
32552 TTTTATTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
23 9 0.18
24 1 0.02
25 9 0.18
26 12 0.24
27 12 0.24
28 1 0.02
30 7 0.14
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
AATATTTTATATATATTAACATAAA
Found at i:32527 original size:27 final size:27
Alignment explanation
Indices: 32464--32552 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 27
32454 ATAAATGCAT
32464 AATATTTTATATATATTAAC--A-TAAA
1 AATATTTTAT-TATATTAACTTATTAAA
32489 AATATTTT-TTATATTAACTTATTAAA
1 AATATTTTATTATATTAACTTATTAAA
* *
32515 TATATTTTA-T-TATTATCTTAATTTAAA
1 AATATTTTATTATATTAACTT-A-TTAAA
32542 AATATTTTATT
1 AATATTTTATT
32553 TTTATTTTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
23 9 0.17
24 1 0.02
25 17 0.31
26 13 0.24
27 13 0.24
28 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (27 bp):
AATATTTTATTATATTAACTTATTAAA
Found at i:32557 original size:27 final size:25
Alignment explanation
Indices: 32485--32573 Score: 81
Period size: 27 Copynumber: 3.4 Consensus size: 25
32475 TATATTAACA
*
32485 TAAAAATATTTT-TTATATTAACTTAT
1 TAAAAATATTTTATT-T-TTATCTTAT
* *
32511 TAAATATATTTTATTATTATCTTAATT
1 TAAAAATATTTTATTTTTATCTT-A-T
*
32538 TAAAAATATTTTATTTTTATTTTCACT
1 TAAAAATATTTTATTTTTATCTT-A-T
32565 TAAAAATAT
1 TAAAAATAT
32574 ATATTTTATA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
25 6 0.12
26 12 0.23
27 34 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
TAAAAATATTTTATTTTTATCTTAT
Found at i:32749 original size:31 final size:31
Alignment explanation
Indices: 32714--32777 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
32704 TGATGACCAC
32714 ATCTTAATCAAATAAAAACAAAAGTGATAAT
1 ATCTTAATCAAATAAAAACAAAAGTGATAAT
* * *
32745 ATCTTAATTAAATAAAAACGAAAGTGATCAT
1 ATCTTAATCAAATAAAAACAAAAGTGATAAT
32776 AT
1 AT
32778 ATTATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (31 bp):
ATCTTAATCAAATAAAAACAAAAGTGATAAT
Found at i:33453 original size:16 final size:16
Alignment explanation
Indices: 33432--33487 Score: 103
Period size: 16 Copynumber: 3.5 Consensus size: 16
33422 AATTTAGCAA
33432 AACCGAAAGCAACTTG
1 AACCGAAAGCAACTTG
*
33448 AACCGAAAGCAACCTG
1 AACCGAAAGCAACTTG
33464 AACCGAAAGCAACTTG
1 AACCGAAAGCAACTTG
33480 AACCGAAA
1 AACCGAAA
33488 TTAACCCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (16 bp):
AACCGAAAGCAACTTG
Found at i:33468 original size:32 final size:32
Alignment explanation
Indices: 33432--33552 Score: 118
Period size: 32 Copynumber: 3.8 Consensus size: 32
33422 AATTTAGCAA
33432 AACCGAAAGCAACTTGAACCGAAAGCAA-CCT
1 AACCGAAAGCAACTTGAACCGAAAGCAACCCT
**
33463 GAACCGAAAGCAACTTGAACCGAAATTAACCCT
1 -AACCGAAAGCAACTTGAACCGAAAGCAACCCT
* * ** ** * *
33496 AATCGAAAGTAACTTGAATTGAAATTAACACA
1 AACCGAAAGCAACTTGAACCGAAAGCAACCCT
**
33528 AACCGAAAGCAACCCGAACCGAAAG
1 AACCGAAAGCAACTTGAACCGAAAG
33553 AAATCTAACC
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
32 70 0.96
33 3 0.04
ACGTcount: A:0.46, C:0.25, G:0.16, T:0.13
Consensus pattern (32 bp):
AACCGAAAGCAACTTGAACCGAAAGCAACCCT
Found at i:34729 original size:20 final size:19
Alignment explanation
Indices: 34688--34731 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
34678 TAAATATAAA
*
34688 TAAAAATATTCAAATAAAT
1 TAAAAATATTCAAAGAAAT
**
34707 TAAAAATATTTTAAGAAACT
1 TAAAAATATTCAAAGAAA-T
34727 TAAAA
1 TAAAA
34732 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (19 bp):
TAAAAATATTCAAAGAAAT
Found at i:35724 original size:20 final size:20
Alignment explanation
Indices: 35699--35793 Score: 100
Period size: 21 Copynumber: 4.7 Consensus size: 20
35689 TTTTCCCAAT
*
35699 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
35719 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAATAAGTAAA
*
35739 TTCGCAATGCGAATAAGTAAA
1 -TCGCAACGCGAATAAGTAAA
** *
35760 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
35781 TCGCAACGCGAAT
1 TCGCAACGCGAAT
35794 TGGGAAAATC
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
20 28 0.46
21 33 0.54
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:35741 original size:41 final size:41
Alignment explanation
Indices: 35696--35793 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
35686 CGATTTTCCC
35696 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
35737 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
* *
35778 AAATCGCAACGCGAAT
1 AATTCGCAATGCGAAT
35794 TGGGAAAATC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:35745 original size:21 final size:20
Alignment explanation
Indices: 35716--35812 Score: 122
Period size: 21 Copynumber: 4.7 Consensus size: 20
35706 GCGAATAAGT
35716 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
* ** *
35736 AAATTCGCAATGCGAATAAGT
1 AAA-TCGCAACGCGAATTGGG
35757 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
35777 AAAATCGCAACGCGAATTGGG
1 -AAATCGCAACGCGAATTGGG
*
35798 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
35813 TACTGACTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.24
21 50 0.76
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (20 bp):
AAATCGCAACGCGAATTGGG
Found at i:35825 original size:41 final size:41
Alignment explanation
Indices: 35798--35875 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
35788 GCGAATTGGG
* * *
35798 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
35839 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
35876 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:35826 original size:20 final size:20
Alignment explanation
Indices: 35801--35894 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
35791 AATTGGGAAA
*
35801 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
35821 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
35842 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
35862 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
35882 TTCGCAACGCGAT
1 ATCGCAACGCGAT
35895 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:35843 original size:62 final size:61
Alignment explanation
Indices: 35699--35850 Score: 166
Period size: 62 Copynumber: 2.5 Consensus size: 61
35689 TTTTCCCAAT
* *
35699 TCGCAATGCG-AATAAGTAAATCGCAACGCGAATTGGGAAATTCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAAATAA-AAAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTAAA
* * ** * *
35760 TCGCAACGCGAATTGGGAAAATCGCAACGCGAATTGGGAAAATCGCAATGCG-AT-ACTGACTA
1 TCGCAATGCGAAAT-AAAAAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGT-A-AA
35822 TCGCAATGCGATAATAAAAAATCGCAACG
1 TCGCAATGCGA-AATAAAAAATCGCAACG
35851 AGATACTTAC
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
60 2 0.03
61 12 0.16
62 58 0.78
63 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.18
Consensus pattern (61 bp):
TCGCAATGCGAAATAAAAAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTAAA
Found at i:36470 original size:19 final size:19
Alignment explanation
Indices: 36410--36490 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
36400 TTCGAGAATG
36410 AAAATCGCAACGCGTAAATA
1 AAAATCGCAACGCG-AAATA
** *
36430 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
36446 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
36463 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
36482 AAAATCGCA
1 AAAATCGCA
36491 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 3 0.06
18 2 0.04
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:36551 original size:20 final size:19
Alignment explanation
Indices: 36486--36670 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
36476 GAAACCAAAA
*
36486 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36505 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
36524 TCGCGTTGTGATTTTTATT
1 TCGCGTTGCGATTTTCATT
36543 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
36563 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
36579 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
36596 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
36610 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
36629 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
36649 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
36669 TC
1 TC
36671 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 48 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:36561 original size:39 final size:38
Alignment explanation
Indices: 36486--36670 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
36476 GAAACCAAAA
*
36486 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
36524 TCGCGTTGTGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
36563 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
36596 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
36629 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
36669 TC
1 TC
36671 AACCAAAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 20 0.16
39 29 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:38727 original size:21 final size:21
Alignment explanation
Indices: 38703--38770 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
38693 TCATTCCTCG
38703 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
38724 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
38745 AGAGGTCCCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
38767 AGAG
1 AGAG
38771 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.24, C:0.37, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:40122 original size:13 final size:14
Alignment explanation
Indices: 40097--40131 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
40087 ATTGTTTAAT
40097 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
40111 TGATTTGT-AAAGT
1 TGATTTGTAAAAGG
40124 TGATTTGT
1 TGATTTGT
40132 TAATTGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:40355 original size:33 final size:32
Alignment explanation
Indices: 40313--40594 Score: 345
Period size: 33 Copynumber: 8.9 Consensus size: 32
40303 ATTAAATTCG
40313 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
40346 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
40379 CG-TGCGATTTTC----CGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
40407 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
40440 CGTTGCGATTTTCATTTCGCA-TGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
40472 CGTTGCGATTTTCATTTCGCATTGCGATTCC-
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCT
**
40503 C-TTGCGATTTTCATTT-GCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
40534 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
40567 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
40595 ATTAATTTCC
Statistics
Matches: 219, Mismatches: 9, Indels: 42
0.81 0.03 0.16
Matches are distributed among these distances:
26 3 0.01
28 12 0.05
29 18 0.08
30 18 0.08
31 8 0.04
32 52 0.24
33 102 0.47
35 6 0.03
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:40372 original size:19 final size:19
Alignment explanation
Indices: 40309--40372 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
40299 CGAAATTAAA
*
40309 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
40328 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
40344 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
40361 TTCGCATTGCGA
1 TTCGCATTGCGA
40373 AATTCGCGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.17
16 6 0.17
17 6 0.17
19 17 0.49
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:40479 original size:94 final size:93
Alignment explanation
Indices: 40308--40594 Score: 356
Period size: 94 Copynumber: 3.0 Consensus size: 93
40298 GCGAAATTAA
* **
40308 ATTCGCGTTGCGATTTTCATTTCGCATTGCG--ATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 ATTCCCGTTGCGATTTTCATTTCGCATTGCGAAATT--AGCGTTGCGATTTTCATTTCGCATTGC
*
40371 GAAATT-CGCG-TGCGATTTTC-CGCATTGCG
64 G--ATTCCTCGTTGCGATTTTCTCGCATTGCG
40400 ATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAGCGTTGCGATTTTCATTTCGCA-TGC
1 ATT-CC-CGTTGCGATTTTCATTTCGCATTGCGAAATTAGCGTTGCGATTTTCATTTCGCATTGC
40464 GATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
64 GATT-CCTCGTTGCGATTTTC---TCGCATTGCG
40498 ATTCCC-TTGCGATTTTCATTT-GCATTGCGAAATTAGCGTTGCGATTTTCATTTCGCATTGCGA
1 ATTCCCGTTGCGATTTTCATTTCGCATTGCGAAATTAGCGTTGCGATTTTCATTTCGCATTGCGA
40561 TTCTCTCGTTGCGATTTTCATTTCGCATTGCG
66 TTC-CTCGTTGCGATTTTC---TCGCATTGCG
40593 AT
1 AT
40595 ATTAATTTCC
Statistics
Matches: 178, Mismatches: 4, Indels: 23
0.87 0.02 0.11
Matches are distributed among these distances:
91 3 0.02
92 3 0.02
93 8 0.04
94 94 0.53
95 52 0.29
96 4 0.02
97 2 0.01
98 12 0.07
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (93 bp):
ATTCCCGTTGCGATTTTCATTTCGCATTGCGAAATTAGCGTTGCGATTTTCATTTCGCATTGCGA
TTCCTCGTTGCGATTTTCTCGCATTGCG
Found at i:40538 original size:127 final size:125
Alignment explanation
Indices: 40306--40594 Score: 406
Period size: 127 Copynumber: 2.3 Consensus size: 125
40296 ACGCGAAATT
40306 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
* **
40371 GAAATTCGCGTGCGATTTTCCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
66 G-AATTCCCGTGCGATTTTCCGCATTGCGATT-CAGCGTTGCGATTTTCATTTCGCATTGCG
*
40433 AAATTAGCGTTGCGATTTTCATTTCGCA-TGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
* *
40497 G-ATTCCCTTGCGATTTTCATTTGCATTGCGAAATT-AGCGTTGCGATTTTCATTTCGCATTGCG
66 GAATTCCCGTGCGATTTTC---CGCATTGCG--ATTCAGCGTTGCGATTTTCATTTCGCATTGCG
* *
40560 -ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 AAAT-TCGCGTTGCGATTTTCATTTCGCATTGCGAT
40595 ATTAATTTCC
Statistics
Matches: 146, Mismatches: 9, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
124 15 0.10
126 39 0.27
127 83 0.57
128 6 0.04
129 3 0.02
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.41
Consensus pattern (125 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
GAATTCCCGTGCGATTTTCCGCATTGCGATTCAGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:40613 original size:20 final size:19
Alignment explanation
Indices: 40567--40614 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
40557 GCGATTCTCT
* *
40567 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTAATTTCG
*
40586 CATTGCGATATTAATTTCCG
1 CGTTGCGATATTAATTT-CG
40606 CGTTGCGAT
1 CGTTGCGAT
40615 GGCATTAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.42
Consensus pattern (19 bp):
CGTTGCGATATTAATTTCG
Found at i:42877 original size:12 final size:12
Alignment explanation
Indices: 42860--42884 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42850 TCTTCGGGGA
42860 CTTTTTCTTCTT
1 CTTTTTCTTCTT
42872 CTTTTTCTTCTT
1 CTTTTTCTTCTT
42884 C
1 C
42885 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:43089 original size:24 final size:24
Alignment explanation
Indices: 43055--43108 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
43045 CTGAAACATC
* *
43055 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
43079 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
43103 ATCAAA
1 ATCAAA
43109 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:44167 original size:20 final size:20
Alignment explanation
Indices: 44142--44219 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
44132 ATTCATTTGA
44142 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
44162 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
44182 CTATCGCAACGCGAAAATAG
1 CTATCGCAACGCGAAAATGG
* *
44202 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
44220 CGCAATCTGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:44278 original size:19 final size:18
Alignment explanation
Indices: 44237--44290 Score: 71
Period size: 14 Copynumber: 3.2 Consensus size: 18
44227 TGAAATGAAA
44237 TCGCATTGCGATTTTC--
1 TCGCATTGCGATTTTCTT
44253 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTC-TT
44270 TCGCATTGCGATTTTCTT
1 TCGCATTGCGATTTTCTT
44288 TCG
1 TCG
44291 ATAGCCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 11 0.33
16 3 0.09
17 3 0.09
18 5 0.15
19 11 0.33
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.48
Consensus pattern (18 bp):
TCGCATTGCGATTTTCTT
Found at i:44302 original size:30 final size:32
Alignment explanation
Indices: 44237--44311 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 32
44227 TGAAATGAAA
***
44237 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTC-TTGCGATAGCCATT
44270 TCGCATTGCGATTTTCT-TT-CGATAGCCATT
1 TCGCATTGCGATTTTCTCTTGCGATAGCCATT
*
44300 TCGCGTTGCGAT
1 TCGCATTGCGAT
44312 AGTCTGTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 19 0.50
31 2 0.05
33 17 0.45
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (32 bp):
TCGCATTGCGATTTTCTCTTGCGATAGCCATT
Found at i:46299 original size:20 final size:19
Alignment explanation
Indices: 46264--46330 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
46254 CGAAACTTAA
46264 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
46283 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
46303 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
46322 ATCGCAACG
1 ATCGCAACG
46331 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:46338 original size:14 final size:14
Alignment explanation
Indices: 46319--46376 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
46309 ATGCGAAATG
46319 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
46333 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
46349 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
46365 AAAATCGCAACG
1 AAAATCGCAACG
46377 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:46361 original size:32 final size:33
Alignment explanation
Indices: 46303--46381 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
46293 GGAAATGGCT
*
46303 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
46336 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
46368 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
46382 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:46429 original size:14 final size:14
Alignment explanation
Indices: 46410--46467 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
46400 TTTTATTTCG
46410 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
46424 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
46440 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
46456 CGTTGCAATTTT
1 CGTTGCGATTTT
46468 TATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:46481 original size:33 final size:33
Alignment explanation
Indices: 46393--46483 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
46383 ACAAATCGCA
46393 TTGCGATTTTTATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTTATTTCGCGTTGCGATTTTGTCG
*
46426 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTTATTTCGCGTTGCGATTTTGTCG
* *
46458 TTGCAATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTTATTTCGCGTTGCGAT
46484 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.57
33 23 0.43
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTTATTTCGCGTTGCGATTTTGTCG
Found at i:46491 original size:19 final size:20
Alignment explanation
Indices: 46469--46511 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
46459 TGCAATTTTT
46469 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
46488 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
46508 ATTT
1 ATTT
46512 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:46502 original size:20 final size:20
Alignment explanation
Indices: 46477--46522 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
46467 TTATTTCGCA
46477 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
46497 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
46517 TTGCGA
1 TTGCGA
46523 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:47020 original size:18 final size:18
Alignment explanation
Indices: 46994--47038 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
46984 GTCGATCAGA
*
46994 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
47012 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
47030 TGATGGCTC
1 TGATGGCTC
47039 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:48369 original size:20 final size:20
Alignment explanation
Indices: 48344--48381 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48334 AATAGTTTCT
48344 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
48364 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
48382 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:49997 original size:25 final size:29
Alignment explanation
Indices: 49969--50028 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
49959 ATTGTAAATT
49969 ATATTAATT-TT-T-TTA-AAATTTCAGA
1 ATATTAATTATTATATTACAAATTTCAGA
* *
49994 ATATAAATTATTATATTACGAATTTCAGA
1 ATATTAATTATTATATTACAAATTTCAGA
50023 ATATTA
1 ATATTA
50029 GCCGAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 8 0.29
26 2 0.07
27 1 0.04
28 3 0.11
29 14 0.50
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (29 bp):
ATATTAATTATTATATTACAAATTTCAGA
Found at i:50629 original size:16 final size:17
Alignment explanation
Indices: 50608--50645 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
50598 ATACTTTTAC
*
50608 TATATTTTGAT-ATAAA
1 TATATTTAGATAATAAA
*
50624 TATATTTAGATAATACA
1 TATATTTAGATAATAAA
50641 TATAT
1 TATAT
50646 ATGTAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (17 bp):
TATATTTAGATAATAAA
Found at i:50668 original size:14 final size:16
Alignment explanation
Indices: 50617--50676 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 16
50607 CTATATTTTG
*
50617 ATATAA-ATATATTTA
1 ATATAATATATATGTA
50632 GATAATACATATATATGTA
1 -AT-ATA-ATATATATGTA
*
50651 ATATATTATATAT-T-
1 ATATAATATATATGTA
50665 ATATAATATATA
1 ATATAATATATA
50677 ATATTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 11 0.29
15 1 0.03
16 9 0.24
17 6 0.16
18 3 0.08
19 8 0.21
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (16 bp):
ATATAATATATATGTA
Found at i:50673 original size:19 final size:19
Alignment explanation
Indices: 50640--50698 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
50630 TAGATAATAC
* *
50640 ATATA-TATGTAATATATT
1 ATATATTATATAATATATA
50658 ATATATTATATAATATATA
1 ATATATTATATAATATATA
* * *
50677 ATATTTTTTAAAATATATA
1 ATATATTATATAATATATA
50696 ATA
1 ATA
50699 AATCCAAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
18 5 0.14
19 30 0.86
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTATATAATATATA
Found at i:50812 original size:19 final size:19
Alignment explanation
Indices: 50775--50823 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
50765 TTGCATTATG
*
50775 TTATATATTTTAAAAAATA
1 TTATATATATTAAAAAATA
* *
50794 TTATATATATTATATAATA
1 TTATATATATTAAAAAATA
*
50813 -TAAATATATTA
1 TTATATATATTA
50824 CACATATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATATATATTAAAAAATA
Found at i:51531 original size:26 final size:25
Alignment explanation
Indices: 51491--51548 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
51481 AGAGTCCATT
**
51491 AAAAAATAAGTTTTAAAAAAT-TAAA
1 AAAAAATAAAATTT-AAAAATGTAAA
*
51516 ATAAAAATAAAATTTATAAATGTAAA
1 A-AAAAATAAAATTTAAAAATGTAAA
51542 AAAAAAT
1 AAAAAAT
51549 TAGGTGGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (25 bp):
AAAAAATAAAATTTAAAAATGTAAA
Found at i:51535 original size:20 final size:20
Alignment explanation
Indices: 51505--51549 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
51495 AATAAGTTTT
51505 AAAAAA-TTA-AAATA-AAA
1 AAAAAATTTATAAATATAAA
* *
51522 ATAAAATTTATAAATGTAAA
1 AAAAAATTTATAAATATAAA
51542 AAAAAATT
1 AAAAAATT
51550 AGGTGGTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 5 0.23
18 3 0.14
19 4 0.18
20 10 0.45
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAAATTTATAAATATAAA
Found at i:52663 original size:18 final size:16
Alignment explanation
Indices: 52640--52675 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
52630 AATTTATTTA
52640 TTTATTTTTTAAAATATT
1 TTTA-TTTTT-AAATATT
52658 TTTATTTTTAAATATT
1 TTTATTTTTAAATATT
52674 TT
1 TT
52676 AGATGGCGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 5 0.28
18 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTTTTAAATATT
Found at i:53736 original size:5 final size:5
Alignment explanation
Indices: 53726--53777 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
53716 ATCAAAGATA
* *
53726 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAG AGCGAGAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A---AAAT AAAAT AAAAT
53774 AAAA
1 AAAA
53778 AGATAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 37 0.93
8 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:54611 original size:32 final size:32
Alignment explanation
Indices: 54527--54647 Score: 147
Period size: 32 Copynumber: 3.7 Consensus size: 32
54517 AATTAGCGGG
* *
54527 AATAAAATGTTAGTAA-ATTAGTAAGAACAATAAA
1 AATAAAA-GTTAG-AATGTTAGTATGAACAAT-AA
*
54561 AATAAAAAGTTAGTATGTTAGTATGAACAATAA
1 AAT-AAAAGTTAGAATGTTAGTATGAACAATAA
54594 AATAAAAGTTAGAATGTTAGT-TCGAACAATAA
1 AATAAAAGTTAGAATGTTAGTAT-GAACAATAA
*
54626 AATAAAGGTTAGAATGTTAGTA
1 AATAAAAGTTAGAATGTTAGTA
54648 AGTTAGTGAC
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
31 1 0.01
32 46 0.59
33 6 0.08
34 21 0.27
35 4 0.05
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (32 bp):
AATAAAAGTTAGAATGTTAGTATGAACAATAA
Found at i:55229 original size:12 final size:12
Alignment explanation
Indices: 55214--55257 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
55204 AAAATCCACA
*
55214 AAACCTTAACAT
1 AAACCTTAACCT
*
55226 AAACCTAAACCT
1 AAACCTTAACCT
*
55238 AAACTTTAACCT
1 AAACCTTAACCT
*
55250 AAAGCTTA
1 AAACCTTA
55258 CTTCCAAATG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (12 bp):
AAACCTTAACCT
Found at i:55237 original size:18 final size:18
Alignment explanation
Indices: 55214--55257 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
55204 AAAATCCACA
55214 AAACCTTAACATAAACCT
1 AAACCTTAACATAAACCT
* * *
55232 AAACCTAAACTTTAACCT
1 AAACCTTAACATAAACCT
*
55250 AAAGCTTA
1 AAACCTTA
55258 CTTCCAAATG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (18 bp):
AAACCTTAACATAAACCT
Found at i:56283 original size:52 final size:52
Alignment explanation
Indices: 56221--56323 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
56211 ACGGTCTCTC
56221 TGATTGTTTTGATATTGAGGATTAAGCCCTTTGCCATATAAAAATATACATA
1 TGATTGTTTTGATATTGAGGATTAAGCCCTTTGCCATATAAAAATATACATA
56273 TGATTGTTTTGATATTGAGGATTAAGCCCTTTGCCATATAAAAATATACAT
1 TGATTGTTTTGATATTGAGGATTAAGCCCTTTGCCATATAAAAATATACAT
56324 TATTCCTTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (52 bp):
TGATTGTTTTGATATTGAGGATTAAGCCCTTTGCCATATAAAAATATACATA
Found at i:56448 original size:24 final size:24
Alignment explanation
Indices: 56421--56468 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
56411 AGGACGACTA
56421 GTCGTGTTTCAATGATTTGACCCT
1 GTCGTGTTTCAATGATTTGACCCT
56445 GTCGTGTTTCAATGATTTGACCCT
1 GTCGTGTTTCAATGATTTGACCCT
56469 CCTATGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.42
Consensus pattern (24 bp):
GTCGTGTTTCAATGATTTGACCCT
Found at i:59196 original size:23 final size:23
Alignment explanation
Indices: 59166--59212 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
59156 TTGAAACCTT
59166 AAGTGATATAGAGGCTTAAGGAA
1 AAGTGATATAGAGGCTTAAGGAA
59189 AAGTGATATAGAGGCTTAAGGAA
1 AAGTGATATAGAGGCTTAAGGAA
59212 A
1 A
59213 GTTCAAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.30, T:0.21
Consensus pattern (23 bp):
AAGTGATATAGAGGCTTAAGGAA
Found at i:68578 original size:72 final size:71
Alignment explanation
Indices: 68453--68599 Score: 215
Period size: 72 Copynumber: 2.1 Consensus size: 71
68443 AGTTGGACTG
* * * *
68453 AGTTTATAGAGGATGTCCTATAGAGATTTATGATGAGACATTGGAGTTGATGAAGGCTTTATTCT
1 AGTTCATAGAGGATGTCCTATAGAGATTTATGATGAGACATTGGAGTCGATGAAAGCTCTATTCT
*
68518 CGCATT
66 CGCATC
*
68524 AGTTCATACGAGGATGTCCTATATG-GATTTATGATGATACATTGGAGTCGATGAAAGCTCTATT
1 AGTTCATA-GAGGATGTCCTATA-GAGATTTATGATGAGACATTGGAGTCGATGAAAGCTCTATT
68588 CTCGCATC
64 CTCGCATC
68596 AGTT
1 AGTT
68600 TAGACCAAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 7 0.10
72 60 0.88
73 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (71 bp):
AGTTCATAGAGGATGTCCTATAGAGATTTATGATGAGACATTGGAGTCGATGAAAGCTCTATTCT
CGCATC
Found at i:72801 original size:21 final size:21
Alignment explanation
Indices: 72775--72831 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
72765 GCACAACAGG
72775 ATGCATCGATGCACAACCTTA
1 ATGCATCGATGCACAACCTTA
* *
72796 ATGCATCGATGCACATCCTTG
1 ATGCATCGATGCACAACCTTA
*
72817 GTGCATCGATGCACA
1 ATGCATCGATGCACA
72832 GAAGGATGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (21 bp):
ATGCATCGATGCACAACCTTA
Found at i:72940 original size:21 final size:20
Alignment explanation
Indices: 72871--72969 Score: 128
Period size: 21 Copynumber: 4.8 Consensus size: 20
72861 CGGTGTTTAA
*
72871 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
72891 GTGCATGGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
72913 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
72933 GATGCATGGATGCACCGCAGGG
1 G-TGCATGGATGCACTGCA-GG
72955 GTGCATGGATGCACT
1 GTGCATGGATGCACT
72970 TTGACACCCT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
19 4 0.06
20 16 0.23
21 29 0.41
22 18 0.25
23 4 0.06
ACGTcount: A:0.21, C:0.20, G:0.37, T:0.21
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:73096 original size:30 final size:30
Alignment explanation
Indices: 73049--73107 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
73039 AAACTTTGAA
73049 TAAATTCAATTAAGTCCAAA-AACATTTTG
1 TAAATTCAATTAAGTCCAAACAACATTTTG
*
73078 TAAATTCAATTCAAGTCCAAACACCATTTT
1 TAAATTCAATT-AAGTCCAAACAACATTTT
73108 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 9 0.33
31 7 0.26
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAACAACATTTTG
Found at i:74413 original size:19 final size:20
Alignment explanation
Indices: 74370--74419 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
74360 TCTAAATCCT
*
74370 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATATCATTTTGG
* *
74390 CTTTCAAAATAT-ATTTTTG
1 TTTTCAAAATATCATTTTGG
74409 TTTTCAAAATA
1 TTTTCAAAATA
74420 AAATCGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGG
Found at i:75249 original size:34 final size:29
Alignment explanation
Indices: 75181--75240 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
75171 AAACTTTGAA
*
75181 TAAATTCAATTAATTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
*
75210 TAAATTCAATTCAAGTCCAAACACCATTTTG
1 TAAATTCAATT-AAGTCCAAA-AACATTTTG
75241 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 8 0.30
31 8 0.30
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:78928 original size:24 final size:24
Alignment explanation
Indices: 78892--78937 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
78882 GGTATAACCA
*
78892 AACCGAACCATTGACCATTGACCG
1 AACCAAACCATTGACCATTGACCG
*
78916 AACCAAACTATTGACCATTGAC
1 AACCAAACCATTGACCATTGAC
78938 TGCCGCCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20
Consensus pattern (24 bp):
AACCAAACCATTGACCATTGACCG
Found at i:83415 original size:11 final size:12
Alignment explanation
Indices: 83390--83419 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
83380 AATAATATAT
83390 AAATTATATTAA
1 AAATTATATTAA
83402 AAATTATATT-A
1 AAATTATATTAA
83413 AAATTAT
1 AAATTAT
83420 TTAGAGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATTATATTAA
Found at i:86340 original size:10 final size:10
Alignment explanation
Indices: 86325--86350 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
86315 GCTGGTACGT
86325 TCCCCGGCCG
1 TCCCCGGCCG
86335 TCCCCGGCCG
1 TCCCCGGCCG
86345 TCCCCG
1 TCCCCG
86351 TACCGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.62, G:0.27, T:0.12
Consensus pattern (10 bp):
TCCCCGGCCG
Found at i:86364 original size:14 final size:14
Alignment explanation
Indices: 86345--86374 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
86335 TCCCCGGCCG
86345 TCCCCGTACCGTCC
1 TCCCCGTACCGTCC
86359 TCCCCGTACCGTCC
1 TCCCCGTACCGTCC
86373 TC
1 TC
86375 GTGCCAGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.57, G:0.13, T:0.23
Consensus pattern (14 bp):
TCCCCGTACCGTCC
Found at i:87345 original size:27 final size:28
Alignment explanation
Indices: 87315--87383 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
87305 ATAAGGATGT
*
87315 AATCCCATACAAAACAAAT-CGGGAACA
1 AATCCCATACAAAACAAATACGAGAACA
* * *
87342 AATCCCATATAGAACAAATATGAGAACA
1 AATCCCATACAAAACAAATACGAGAACA
*
87370 AAACCCATACAAAA
1 AATCCCATACAAAA
87384 TCAGGATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 17 0.50
28 17 0.50
ACGTcount: A:0.55, C:0.23, G:0.09, T:0.13
Consensus pattern (28 bp):
AATCCCATACAAAACAAATACGAGAACA
Done.