Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009203.1 Hibiscus syriacus cultivar Beakdansim tig00112789_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: 338692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:264590 original size:75 final size:76
Alignment explanation
Indices: 264305--264598 Score: 497
Period size: 76 Copynumber: 3.9 Consensus size: 76
264295 CTTCAGTGCA
* * *
264305 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
264370 CGGGAGCTTTT
66 CGGGAGCTTTT
*
264381 TGATGTTTTCAAAGCC-TCAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTC-GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCT
264445 TCGGGAGCTTTT
65 TCGGGAGCTTTT
264457 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
264522 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
264533 TGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGTCTTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
264595 CGGG
66 CGGG
264599 TCATCTGTAA
Statistics
Matches: 209, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
73 8 0.04
74 4 0.02
75 44 0.21
76 151 0.72
77 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:264599 original size:45 final size:45
Alignment explanation
Indices: 264533--264645 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
264523 GGGAGCTTTT
* *
264533 TGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGTCTTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
264577 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
264622 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
264646 AGCTTTTTGA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
44 9 0.14
45 42 0.67
46 4 0.06
47 8 0.13
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:264637 original size:272 final size:273
Alignment explanation
Indices: 264184--264991 Score: 1482
Period size: 272 Copynumber: 3.0 Consensus size: 273
264174 CTTCAGTGCA
* *
264184 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
264249 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
* *
264314 CAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTT
131 CAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTT
*
264379 TTTGATGTTTTCAAAGCC-TCAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGC
196 TTTGATGTTTTCAAAGCCTTC-GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGC
264443 CTTCGGGAGCTTTT
260 CTTCGGGAGCTTTT
264457 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
264522 CGGGAGCTTTTTGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGTCTTTCAGTGCATGATGTTTT
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
264586 CAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTT
131 CAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTT
264651 TTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCC
196 TTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCC
264716 TTCGGGAGCTTTT
261 TTCGGGAGCTTTT
*
264729 TGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
264793 CAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
*
264858 CAAAACCTTCGGGTCATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTT
131 CAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTT
*
264923 TTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CC
196 TTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCC
264986 TTCGGG
261 TTCGGG
264992 TCATCTGTAA
Statistics
Matches: 522, Mismatches: 11, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
270 8 0.02
271 77 0.15
272 352 0.67
273 85 0.16
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (273 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
CAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTT
TTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCC
TTCGGGAGCTTTT
Found at i:264786 original size:75 final size:76
Alignment explanation
Indices: 264577--264870 Score: 531
Period size: 76 Copynumber: 3.9 Consensus size: 76
264567 TTTCAGTGCA
*
264577 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
264642 CGGGAGCTTTT
66 CGGGAGCTTTT
264653 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
264718 CGGGAGCTTTT
66 CGGGAGCTTTT
*
264729 TGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
264793 CAGGAGCTTTT
66 CGGGAGCTTTT
*
264804 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
264867 CGGG
66 CGGG
264871 TCATCTGTAA
Statistics
Matches: 211, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
74 7 0.03
75 77 0.36
76 127 0.60
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:264857 original size:45 final size:45
Alignment explanation
Indices: 264804--264917 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
264794 AGGAGCTTTT
264804 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
264849 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTTAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
264894 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
264918 AGCTTTTTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 52 0.83
47 11 0.17
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:264879 original size:121 final size:121
Alignment explanation
Indices: 264729--265105 Score: 677
Period size: 121 Copynumber: 3.1 Consensus size: 121
264719 GGGAGCTTTT
*
264729 TGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
264793 CAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
264849 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
264914 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
264970 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTTCCAAAAAGCCT
*
265035 TCGGGAGCTTTTTGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
65 TCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
265091 TGATGTTTTCCAAAA
1 TGATGTTTT-CAAAA
265106 AGCCTTTGGG
Statistics
Matches: 247, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
120 9 0.04
121 198 0.80
122 40 0.16
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:264929 original size:76 final size:74
Alignment explanation
Indices: 264849--264991 Score: 241
Period size: 76 Copynumber: 1.9 Consensus size: 74
264839 CTTCAGTGCA
*
264849 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAA-CCTT
264914 CGGGAGCTTTT
64 CGGGAGCTTTT
* *
264925 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACCTTCG
264990 GG
66 GG
264992 TCATCTGTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 8 0.12
75 4 0.06
76 52 0.81
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (74 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACCTTCG
GGAGCTTTT
Found at i:264978 original size:45 final size:45
Alignment explanation
Indices: 264925--265039 Score: 185
Period size: 45 Copynumber: 2.5 Consensus size: 45
264915 GGGAGCTTTT
*
264925 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
264970 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
265015 TGATGTTTTCCAAAAAGCCTTCGGG
1 TGATGTTTT-C--AAAGCCTTCGGG
265040 AGCTTTTTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
45 52 0.81
46 1 0.02
48 11 0.17
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:265097 original size:76 final size:76
Alignment explanation
Indices: 264970--265252 Score: 453
Period size: 76 Copynumber: 3.7 Consensus size: 76
264960 CTTCAGTGCA
*
264970 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
1 TGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
265035 TCGGGAGCTTTT
65 TCGGGAGCTTTT
265047 TGATGTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCTT
1 TGATGTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCTT
*
265112 TGGGAGCTTTT
66 CGGGAGCTTTT
* * * * *
265123 TGATGTTTTAAAGCCTTCGGGTCATCTGTAAGTCCTACAATGTATGAAG-TTTCCAAAAAGCCTT
1 TGATGTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCTT
265187 CGGGAGCTTTT
66 CGGGAGCTTTT
*
265198 TGATGTTCTCAAAGCC-TCAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC
1 TGATGTT-TTAAAGCCTTC-GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC
265253 AACATTTCCA
Statistics
Matches: 189, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
75 34 0.18
76 142 0.75
77 13 0.07
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
TGATGTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:265389 original size:3 final size:3
Alignment explanation
Indices: 265383--265503 Score: 127
Period size: 3 Copynumber: 39.7 Consensus size: 3
265373 TCATTTAAAT
* * *
265383 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA GTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
265428 TTA TTA TTA TTA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
265474 TTA TTA TTA ATA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
265504 TAATAAATAA
Statistics
Matches: 106, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
2 1 0.01
3 98 0.92
4 7 0.07
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:266916 original size:3 final size:3
Alignment explanation
Indices: 266908--266946 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
266898 TTTACTCTTA
*
266908 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
266947 TAGTCATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:267150 original size:2 final size:2
Alignment explanation
Indices: 267145--267177 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
267135 TTATTTTAAT
267145 TA TA TA TA TA TA TA TA T- TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
267178 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:267165 original size:9 final size:9
Alignment explanation
Indices: 267143--267177 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
267133 AATTATTTTA
267143 ATTATATAT
1 ATTATATAT
267152 A-TATATAT
1 ATTATATAT
267160 ATTATATAT
1 ATTATATAT
267169 ATTATATAT
1 ATTATATAT
267178 CAAAGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTATATAT
Found at i:267271 original size:17 final size:17
Alignment explanation
Indices: 267249--267286 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
267239 ATATTTTATT
267249 TATATTTTATATATAAA
1 TATATTTTATATATAAA
*
267266 TATATTTTATATATAAT
1 TATATTTTATATATAAA
267283 TATA
1 TATA
267287 ACTTTGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:272581 original size:34 final size:32
Alignment explanation
Indices: 272528--272597 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 32
272518 CCTTACAAAC
*
272528 TCCCTAGTTTTTCCGGGCTAAACTAGAATC-TT
1 TCCCTAGTTTTACCGGGCTAAACTAGAA-CATT
*
272560 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
272594 TCCC
1 TCCC
272598 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 7 0.21
33 6 0.18
34 20 0.61
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:273084 original size:19 final size:19
Alignment explanation
Indices: 273060--273099 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
273050 AAAACCTGTA
273060 GGGGGAATATGTACCCCCT
1 GGGGGAATATGTACCCCCT
*
273079 GGGGGAATCTGTACCCCCT
1 GGGGGAATATGTACCCCCT
273098 GG
1 GG
273100 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.28, G:0.35, T:0.20
Consensus pattern (19 bp):
GGGGGAATATGTACCCCCT
Found at i:273105 original size:18 final size:19
Alignment explanation
Indices: 273069--273107 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
273059 AGGGGGAATA
**
273069 TGTACCCCCTGGGGGAATC
1 TGTACCCCCTGGGACAATC
273088 TGTACCCCCT-GGACAATC
1 TGTACCCCCTGGGACAATC
273106 TG
1 TG
273108 ATTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (19 bp):
TGTACCCCCTGGGACAATC
Found at i:274013 original size:24 final size:24
Alignment explanation
Indices: 273972--274019 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
273962 TAATTTTGAA
*
273972 ATTTTAAAAAAATATAATTTTTTT
1 ATTTTAAAAAAACATAATTTTTTT
* *
273996 ATTTTAAAAAAGCCTAATTTTTTT
1 ATTTTAAAAAAACATAATTTTTTT
274020 CAAATCTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTTAAAAAAACATAATTTTTTT
Found at i:275330 original size:2 final size:2
Alignment explanation
Indices: 275323--275347 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
275313 TAAACAAGTT
275323 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 T
275348 TCTGAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:275829 original size:24 final size:25
Alignment explanation
Indices: 275788--275834 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
275778 GAACTCAAAA
275788 AAAATTAGAAGCTCGATTGAAGTCT
1 AAAATTAGAAGCTCGATTGAAGTCT
* *
275813 AAAATTCG-AGCTTGATTGAAGT
1 AAAATTAGAAGCTCGATTGAAGT
275835 GAAAGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGTCT
Found at i:279666 original size:60 final size:61
Alignment explanation
Indices: 279522--279706 Score: 150
Period size: 59 Copynumber: 3.1 Consensus size: 61
279512 TATATCATAT
* * * * * *
279522 ATCCTCAAAATATGACTC-TCATTTTAAATTGGTCCCTAAACT-TTT-AA-ATGTCCTAATTTT
1 ATCCCCAAACTATGAC-CATCATTCTAAATTAGTCCCCAAACTATTTGAACAT-T-CTAATTTC
* * * * *
279582 AT-CCTAAACTATGACTATCATTCTAAATTAGTTCTCAAAC-ATTTGAATATT-TCAATTTC
1 ATCCCCAAACTATGACCATCATTCTAAATTAGTCCCCAAACTATTTGAACATTCT-AATTTC
** * *
279641 ATCCCCAAACTATGACCATTTTTCTAAATTGGTCCCCAAACTTTTTGAACATTCTAATTTC
1 ATCCCCAAACTATGACCATCATTCTAAATTAGTCCCCAAACTATTTGAACATTCTAATTTC
279702 ATCCC
1 ATCCC
279707 AATTTCATCC
Statistics
Matches: 98, Mismatches: 19, Indels: 15
0.74 0.14 0.11
Matches are distributed among these distances:
58 1 0.01
59 38 0.39
60 36 0.37
61 22 0.22
62 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (61 bp):
ATCCCCAAACTATGACCATCATTCTAAATTAGTCCCCAAACTATTTGAACATTCTAATTTC
Found at i:279708 original size:60 final size:58
Alignment explanation
Indices: 279522--279708 Score: 164
Period size: 60 Copynumber: 3.1 Consensus size: 58
279512 TATATCATAT
* * * *
279522 ATCCTCAAAATATGACTC-TCATTTTAAATTGGTCCCTAAACTTTT-AAATGTCCTAATTTT
1 ATCC-CAAACTATGAC-CATCATTCTAAATTGGTCCCCAAACTTTTGAAAT-T-CTAATTTC
* * * * * *
279582 ATCCTAAACTATGACTATCATTCTAAATTAGTTCTCAAACATTTGAATATT-TCAATTTC
1 ATCCCAAACTATGACCATCATTCTAAATTGGTCCCCAAACTTTTGAA-ATTCT-AATTTC
**
279641 ATCCCCAAACTATGACCATTTTTCTAAATTGGTCCCCAAACTTTTTGAACATTCTAATTTC
1 AT-CCCAAACTATGACCATCATTCTAAATTGGTCCCCAAAC-TTTTGAA-ATTCTAATTTC
279702 ATCCCAA
1 ATCCCAA
279709 TTTCATCCAA
Statistics
Matches: 101, Mismatches: 19, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
58 1 0.01
59 37 0.37
60 43 0.43
61 19 0.19
62 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (58 bp):
ATCCCAAACTATGACCATCATTCTAAATTGGTCCCCAAACTTTTGAAATTCTAATTTC
Found at i:279929 original size:60 final size:61
Alignment explanation
Indices: 279817--279932 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 61
279807 TACAATTTGA
* * * * *
279817 GATGAAATTGGAATGTTCAAAAAGTTTGGGGATTAATTTAGAAAGAGGGTCATAGTTTAGG
1 GATGAAATTGAAATGTTCAAAAAGCTTGAGGACTAATTTAGAAAGAGAGTCATAGTTTAGG
* *
279878 GATGAAATTGAAATGTTC-AAAAGCTTGAGGACTAATTTAGAATGATAGTCATAGT
1 GATGAAATTGAAATGTTCAAAAAGCTTGAGGACTAATTTAGAAAGAGAGTCATAGT
279933 GTAAGGATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 31 0.65
61 17 0.35
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (61 bp):
GATGAAATTGAAATGTTCAAAAAGCTTGAGGACTAATTTAGAAAGAGAGTCATAGTTTAGG
Found at i:279960 original size:60 final size:59
Alignment explanation
Indices: 279817--279990 Score: 156
Period size: 60 Copynumber: 2.9 Consensus size: 59
279807 TACAATTTGA
* * * * * * * *
279817 GATGAAATTGGAATGTTCAAAAAGTTTGGGGATTAATTTAGAAAGAGGGTCATAGTTTAGG
1 GATGAAATTGAAATGTTC-AAAAGCTTGAGGACTAATTTAGAATGA-AGTCATAGTGTAAG
279878 GATGAAATTGAAATGTTCAAAAGCTTGAGGACTAATTTAGAATGATAGTCATAGTGTAAG
1 GATGAAATTGAAATGTTCAAAAGCTTGAGGACTAATTTAGAATGA-AGTCATAGTGTAAG
* * * *
279938 GAT-AAATGTGGAACAT-TT-AAAAGGTTAAGCACTAATTTAAAATGAAGATCATA
1 GATGAAAT-T-GAA-ATGTTCAAAAGCTTGAGGACTAATTTAGAATGAAG-TCATA
279991 CTTTGAGGAC
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
59 6 0.06
60 66 0.69
61 22 0.23
62 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.30
Consensus pattern (59 bp):
GATGAAATTGAAATGTTCAAAAGCTTGAGGACTAATTTAGAATGAAGTCATAGTGTAAG
Found at i:280726 original size:21 final size:21
Alignment explanation
Indices: 280702--280746 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
280692 ATTTTGAAAA
280702 AAAAATGA-ACGTTTAGGTACT
1 AAAAATGATA-GTTTAGGTACT
*
280723 AAAACTGATAGTTTAGGTACT
1 AAAAATGATAGTTTAGGTACT
280744 AAA
1 AAA
280747 CGCGTTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (21 bp):
AAAAATGATAGTTTAGGTACT
Found at i:281983 original size:59 final size:59
Alignment explanation
Indices: 281865--281985 Score: 136
Period size: 59 Copynumber: 2.1 Consensus size: 59
281855 ATATGACTAT
* * * * *
281865 TTTGTAATTTTTAATAGTAAAGGGACTTAATAAAGTAACATACTATAGCTAGAGTACCA
1 TTTGTAACTTTTAATAGTAAAGAGACTTAATAAAGCAACACACTATAGCTAGAGGACCA
** * * *
281924 TTTGTAACTTTTAATAGTTGAGAGACTTAATAAAGCAATACCCTATAG-TCGGAGGACCA
1 TTTGTAACTTTTAATAGTAAAGAGACTTAATAAAGCAACACACTATAGCT-AGAGGACCA
281983 TTT
1 TTT
281986 ATGTACTTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 50 0.98
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (59 bp):
TTTGTAACTTTTAATAGTAAAGAGACTTAATAAAGCAACACACTATAGCTAGAGGACCA
Found at i:286545 original size:50 final size:50
Alignment explanation
Indices: 286478--286577 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
286468 AATCCTACTC
286478 AAAGGGGAGGGAAATGAAATATTTTAGAAGAAGACAAGAAAATACTCTTA
1 AAAGGGGAGGGAAATGAAATATTTTAGAAGAAGACAAGAAAATACTCTTA
286528 AAAGGGGAGGGAAATGAAATATTTTAGAAGAAGACAAGAAAATACTCTTA
1 AAAGGGGAGGGAAATGAAATATTTTAGAAGAAGACAAGAAAATACTCTTA
286578 GTAGGTCTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.20
Consensus pattern (50 bp):
AAAGGGGAGGGAAATGAAATATTTTAGAAGAAGACAAGAAAATACTCTTA
Found at i:286568 original size:27 final size:27
Alignment explanation
Indices: 286488--286568 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
286478 AAAGGGGAGG
286488 GAAATGAAATATTTTAGAAGAAGACAA
1 GAAATGAAATATTTTAGAAGAAGACAA
* * ** **
286515 G--A--AAATACTCTTAAAAGGGGA-GG
1 GAAATGAAATA-TTTTAGAAGAAGACAA
286538 GAAATGAAATATTTTAGAAGAAGACAA
1 GAAATGAAATATTTTAGAAGAAGACAA
286565 GAAA
1 GAAA
286569 ATACTCTTAG
Statistics
Matches: 36, Mismatches: 12, Indels: 12
0.60 0.20 0.20
Matches are distributed among these distances:
23 6 0.17
24 9 0.25
25 2 0.06
26 9 0.25
27 10 0.28
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (27 bp):
GAAATGAAATATTTTAGAAGAAGACAA
Found at i:289049 original size:36 final size:35
Alignment explanation
Indices: 288970--289052 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 35
288960 TAAACCCAAC
*
288970 CCCGTCCCTGTCCCCATTTAACATAAACAATTTTT
1 CCCGTCCCCGTCCCCATTTAACATAAACAATTTTT
* * *
289005 CCCTGTCCCCGTCCCCGTTTAGCATAAACGATTTTTT
1 CCC-GTCCCCGTCCCCATTTAACATAAAC-AATTTTT
*
289042 TCCGTCCCCGT
1 CCCGTCCCCGT
289053 TTAATTCGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 3 0.07
36 30 0.73
37 8 0.20
ACGTcount: A:0.18, C:0.37, G:0.11, T:0.34
Consensus pattern (35 bp):
CCCGTCCCCGTCCCCATTTAACATAAACAATTTTT
Found at i:290169 original size:43 final size:44
Alignment explanation
Indices: 290102--290184 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 44
290092 ATATTTATCG
* *
290102 GATCAAAATGAATGGACGAAAAACAACAT-CCGACTCATAGCCA
1 GATCAAAATGAACGGACCAAAAACAACATGCCGACTCATAGCCA
* * *
290145 GATCAAATTGAACGGACCAGAAACAACATGGCGACTCATA
1 GATCAAAATGAACGGACCAAAAACAACATGCCGACTCATA
290185 TCCCTAGGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 25 0.74
44 9 0.26
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (44 bp):
GATCAAAATGAACGGACCAAAAACAACATGCCGACTCATAGCCA
Found at i:290399 original size:2 final size:2
Alignment explanation
Indices: 290392--290438 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
290382 CATCGAAATG
*
290392 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAG AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
290434 AT AT A
1 AT AT A
290439 CTTAAAGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:293742 original size:37 final size:36
Alignment explanation
Indices: 293671--293743 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
293661 CTTACTCAAG
*
293671 AATAAAAAAAATTATTAATAATATATTAATAATATA
1 AATAAAAAAAATTATTAATAATAGATTAATAATATA
*
293707 AATAATAAAATAA-TATTAATAAATAGATTTA-AATATA
1 AATAA-AAAA-AATTATTAAT-AATAGATTAATAATATA
293744 GATTAGTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 5 0.16
37 17 0.53
38 10 0.31
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (36 bp):
AATAAAAAAAATTATTAATAATAGATTAATAATATA
Found at i:294519 original size:16 final size:16
Alignment explanation
Indices: 294498--294547 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
294488 TCATTTAGCT
294498 TGTTCATATTTGTTTA
1 TGTTCATATTTGTTTA
** *
294514 TGTTCAT-TCAG-CT-
1 TGTTCATATTTGTTTA
294527 TGTTCATATTTGTTTA
1 TGTTCATATTTGTTTA
294543 TGTTC
1 TGTTC
294548 GTTCGTTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 7 0.28
14 3 0.12
15 3 0.12
16 12 0.48
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (16 bp):
TGTTCATATTTGTTTA
Found at i:294519 original size:29 final size:29
Alignment explanation
Indices: 294477--294547 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
294467 AACGGAATTT
* *
294477 TTTGTTCATGTTCATTTAGCTTGTTCATA
1 TTTGTTTATGTTCATTCAGCTTGTTCATA
294506 TTTGTTTATGTTCATTCAGCTTGTTCATA
1 TTTGTTTATGTTCATTCAGCTTGTTCATA
294535 TTTGTTTATGTTC
1 TTTGTTTATGTTC
294548 GTTCGTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.15, C:0.13, G:0.14, T:0.58
Consensus pattern (29 bp):
TTTGTTTATGTTCATTCAGCTTGTTCATA
Found at i:308829 original size:19 final size:20
Alignment explanation
Indices: 308795--308835 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
308785 CCCTTAAAAT
308795 ATATTTTATATATTAATGTA
1 ATATTTTATATATTAATGTA
* *
308815 ATATTTTA-ATTTTAATTTA
1 ATATTTTATATATTAATGTA
308834 AT
1 AT
308836 CAAATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
ATATTTTATATATTAATGTA
Found at i:311689 original size:3 final size:3
Alignment explanation
Indices: 311681--311735 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
311671 GTGGTACCAT
*
311681 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
311728 TATA TTA T
1 T-TA TTA T
311736 CAAATTTGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:313585 original size:34 final size:34
Alignment explanation
Indices: 313547--313614 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
313537 TATTTTATAA
313547 CTTTTAACAGTCAATAAACTCGATAAAATAATAT
1 CTTTTAACAGTCAATAAACTCGATAAAATAATAT
* * * *
313581 CTTTTAATAGTTAATTAACTTGATAAAATAATAT
1 CTTTTAACAGTCAATAAACTCGATAAAATAATAT
313615 ATATAATCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (34 bp):
CTTTTAACAGTCAATAAACTCGATAAAATAATAT
Found at i:317761 original size:2 final size:2
Alignment explanation
Indices: 317754--317783 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
317744 AGATGCTGAA
317754 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
317784 GGATCAGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:321081 original size:98 final size:101
Alignment explanation
Indices: 320907--321105 Score: 278
Period size: 98 Copynumber: 2.0 Consensus size: 101
320897 ATCTAGATTG
** * *
320907 AACTATAAATCCCTGAAAAATTCTCTGTCACTGCTAATAGCATTATTGCCAATACAAAGAATACA
1 AACTATAAATCCCTGAAAAATTCTCACTCACAGCCAATAGCATTATTGCCAATACAAAGAATACA
320972 AGCTCATGTAGCATATATGAATCAAGTTCATGCATT
66 AGCTCATGTAGCATATATGAATCAAGTTCATGCATT
* * * * * *
321008 AACTATAAATCCTTG-AAAATTCTCACTCTCAGCCAATAGCATTTTTTCC-A-ACACAGAATATA
1 AACTATAAATCCCTGAAAAATTCTCACTCACAGCCAATAGCATTATTGCCAATACAAAGAATACA
*
321070 AGCTCGTGTAGCATATATGAATCAAGTTCATGCATT
66 AGCTCATGTAGCATATATGAATCAAGTTCATGCATT
321106 CTACCCTAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
98 45 0.52
99 1 0.01
100 27 0.31
101 14 0.16
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.31
Consensus pattern (101 bp):
AACTATAAATCCCTGAAAAATTCTCACTCACAGCCAATAGCATTATTGCCAATACAAAGAATACA
AGCTCATGTAGCATATATGAATCAAGTTCATGCATT
Found at i:327937 original size:20 final size:20
Alignment explanation
Indices: 327912--328004 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
327902 TTTTCCCAAT
327912 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
327932 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
327952 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
327973 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
327994 TCGCAATGCGA
1 TCGCAATGCGA
328005 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:327954 original size:41 final size:41
Alignment explanation
Indices: 327909--328004 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
327899 CGATTTTCCC
327909 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
327950 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
327991 AAATCGCAATGCGA
1 AATTCGCAATGCGA
328005 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:327958 original size:21 final size:20
Alignment explanation
Indices: 327912--328004 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
327902 TTTTCCCAAT
*
327912 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
327932 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
327952 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
327973 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
327994 TCGCAATGCGA
1 TCGCAATGCGA
328005 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:328017 original size:41 final size:41
Alignment explanation
Indices: 327931--328066 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
327921 GAATAAGTAA
* * *
327931 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
327972 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * *** * * *
328013 ATCGCAATGCGATAATAAAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
328055 TTCGCAACGCGA
1 ATCGCAACGCGA
328067 TACTGACTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
40 4 0.05
41 43 0.54
42 32 0.41
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:328018 original size:20 final size:20
Alignment explanation
Indices: 327993--328087 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
327983 AATTGGGAAA
*
327993 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
328013 ATCGCAATGCGATAATAAAAAA
1 ATCGCAACGCGATACT--GACT
* *
328035 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
328055 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
328075 TTCGCAACGCGAT
1 ATCGCAACGCGAT
328088 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 46 0.77
22 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:328643 original size:19 final size:19
Alignment explanation
Indices: 328605--328671 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
328595 TTCGAGAATG
*
328605 AAAATCGCAAAGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
328625 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
328644 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
328663 AAAATCGCA
1 AAAATCGCA
328672 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:328689 original size:19 final size:19
Alignment explanation
Indices: 328667--328831 Score: 134
Period size: 19 Copynumber: 9.1 Consensus size: 19
328657 GAAACCAAAA
*
328667 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
328686 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
328705 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
328724 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
328738 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
328757 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
328771 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
328790 TCCGCGTTGCAATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
328810 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
328830 TC
1 TC
328832 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 18, Indels: 24
0.73 0.11 0.15
Matches are distributed among these distances:
14 18 0.16
16 4 0.03
17 5 0.04
19 60 0.52
20 28 0.24
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:328723 original size:38 final size:33
Alignment explanation
Indices: 328672--328806 Score: 144
Period size: 33 Copynumber: 3.9 Consensus size: 33
328662 CAAAATCGCA
*
328672 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
328710 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* ** *
328743 TCGCGATAGTCATTTCGCGTTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
328776 TTGCGATAGTCATTTCCGCGTTGCAATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
328807 ATTATCTCGT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 47 0.53
34 14 0.16
36 3 0.03
38 25 0.28
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:328808 original size:20 final size:20
Alignment explanation
Indices: 328785--328831 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
328775 ATTGCGATAG
328785 TCATTTCCGCGTTGCAATTC
1 TCATTTCCGCGTTGCAATTC
* * *
328805 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCAATTC
328825 TCATTTC
1 TCATTTC
328832 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:330879 original size:42 final size:42
Alignment explanation
Indices: 330819--330941 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
330809 GCCCGACTCG
* * *
330819 CCTATCATCCATCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
330861 CCTATCATTCC-TCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCA-TCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
330903 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCATCAAGA-GTCCACTCCCACCGTTCAAGAG
330942 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.03
42 58 0.87
43 7 0.10
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:330899 original size:21 final size:21
Alignment explanation
Indices: 330875--330941 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
330865 TCATTCCTCG
330875 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
330896 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
330917 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
330938 AGAG
1 AGAG
330942 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:332312 original size:14 final size:14
Alignment explanation
Indices: 332293--332328 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
332283 ATTGTTTAAT
332293 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
332307 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
332321 TGATTTGT
1 TGATTTGT
332329 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:332527 original size:19 final size:18
Alignment explanation
Indices: 332504--332601 Score: 68
Period size: 19 Copynumber: 5.8 Consensus size: 18
332494 GCGAAATTAA
332504 ATTCGCGTTGCGATTTTC
1 ATTCGCGTTGCGATTTTC
*
332522 ATTTCGCATTGCGA--TTC
1 A-TTCGCGTTGCGATTTTC
* *
332539 --CCTCGTTGCGATTTTC
1 ATTCGCGTTGCGATTTTC
*
332555 ATTTCGCATTGCGA--TTC
1 A-TTCGCGTTGCGATTTTC
*
332572 --TCTCGTTGCGATTTTC
1 ATTCGCGTTGCGATTTTC
*
332588 ATTCGCATTGCGAT
1 ATTCGCGTTGCGAT
332602 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
14 17 0.29
16 6 0.10
17 6 0.10
18 11 0.19
19 19 0.32
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.43
Consensus pattern (18 bp):
ATTCGCGTTGCGATTTTC
Found at i:332551 original size:33 final size:33
Alignment explanation
Indices: 332509--332601 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
332499 ATTAAATTCG
332509 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
332542 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
332575 CGTTGCGATTTTCA-TTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
332602 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 13 0.22
33 46 0.78
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:334887 original size:12 final size:12
Alignment explanation
Indices: 334870--334894 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
334860 TCTTCGGGGA
334870 CTTTTTCTTCTT
1 CTTTTTCTTCTT
334882 CTTTTTCTTCTT
1 CTTTTTCTTCTT
334894 C
1 C
334895 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:336212 original size:19 final size:19
Alignment explanation
Indices: 336184--336221 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
336174 TGGCTATCGC
*
336184 AACGAGAATCGCAATGCGA
1 AACGAAAATCGCAATGCGA
*
336203 AACGAAAATCGCATTGCGA
1 AACGAAAATCGCAATGCGA
336222 TTTCTCGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (19 bp):
AACGAAAATCGCAATGCGA
Found at i:336357 original size:14 final size:14
Alignment explanation
Indices: 336338--336374 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
336328 TACACATTAA
336338 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
336352 ACAAATCATCTTTT
1 ACAAATCAACATTT
336366 ACAAATCAA
1 ACAAATCAA
336375 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:336944 original size:14 final size:14
Alignment explanation
Indices: 336925--336961 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
336915 CATCAATTAA
336925 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
336939 ACAAATCATCTTTT
1 ACAAATCAACATTT
336953 ACAAATCAA
1 ACAAATCAA
336962 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:337167 original size:585 final size:589
Alignment explanation
Indices: 335973--338591 Score: 4859
Period size: 585 Copynumber: 4.5 Consensus size: 589
335963 TTTAACAATT
*
335973 ATTATTGAATTCTAGGTACTTAACCAAATA-TTTCAAA-CAAAGGAGTATATATGTTAACAAAAC
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAGGAGTATATATGTTAACAAAAC
336036 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTT-AGTTAGGCATGTATTAGTAACTTG
66 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
*
336100 AGTTTAAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
131 AGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
*
336165 ATGCGAAAATGGCTATCGCAACGAG--AATCGCAATGCGAAACGAAAATCGCATTGCGA-TTTCT
196 ATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTCT
336227 CGTTGCGATAGCCATTTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 CGTTGCGATAGCCA-TTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
336292 TC-ACAAATCAACTATTACATTTCAACACAAATTATGT--ACA-C-ATTAAACAAATCAACATTT
325 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
336352 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAAATAATAATAATTCTTATTTCTTCATC
390 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAAATAATAATAATTCTTATTTCTTCATC
*
336417 AATTATTGAATCAATGAATCAACAACTTTGTGATCCCGTACATCCATTTCACACAGCTCACTTAA
455 AATTATTGAATC-ATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAA
336482 GGATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAA
519 GGATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAA
336547 CA-CAA
584 CAGCAA
336552 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAGGA-TATATATGTTAAC-AAAC
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAGGAGTATATATGTTAACAAAAC
336615 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
66 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
*
336680 AGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTGGACATTCATTTGACTATCGCA
131 AGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
336745 ATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTCT
196 ATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTCT
336810 CGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
261 CGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
336875 CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTA
326 CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTA
336940 CAAATCATCTTTTACAAATCAATTAAACAATCAAAAAAATAAT-A-AATTCTTATTTCTTCATCA
391 CAAATCATCTTTTACAAATCAATTAAACAATCAAAAAAATAATAATAATTCTTATTTCTTCATCA
337003 ATTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
456 ATTATTGAATC-ATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAG
337068 GATTAACCTGCAGAAACC-AACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
520 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
337132 AGCAA
585 AGCAA
337137 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACC-AAAGGAGTATATATGTTAACAAAA
337202 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
65 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
337267 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
130 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
*
337332 AATGCG-AAATGGTTATCGCAACGCGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTT
195 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGA-TTTT
337396 CTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
259 CTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
337461 ATCAAC-AATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
324 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
337525 TACAAATCATCTTTTACAAATCAATT-AACAATC-AAAAAAT-ATAATAATTCTTATTTCTTCAT
389 TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAAATAATAATAATTCTTATTTCTTCAT
337587 CAATTATTGAATCATGAATCAACAAC-TTGTGACCCCGTACATCCATTTCACACAGCTCACTTAA
454 CAATTATTGAATCATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAA
337651 GGATTAACCTGCAGAAACC-AACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAA
519 GGATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAA
337715 CAGCAA
584 CAGCAA
*
337721 ATTATTGAATTCTAGGTACTTAACC-AACATTTTCAAACCAAAAGAGTATATATGTTAACAAAAC
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAGGAGTATATATGTTAACAAAAC
337785 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACA-TTTCAGTTAGGCATGTATTAGTAACTTG
66 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
337849 AGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
131 AGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
337914 ATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTCT
196 ATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTCT
337979 CGTTGCGATAGCCATTTCGCGTTGCGATAGTCTG-TTTGCCTTCAACATAAAGCAGATTGAAAAT
261 CGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
338043 CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTA
326 CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTA
338108 CAAATCATCTTTTACAAATCAATTAAACAATC-AAAAAATAATAATAATTCTTATTTCTTCATCA
391 CAAATCATCTTTTACAAATCAATTAAACAATCAAAAAAATAATAATAATTCTTATTTCTTCATCA
338172 ATTATTGAATCATGAATCAACAACTTTGTGACCCCGTACATCCA-TTCACA-A-CTCACTTAAGG
456 ATTATTGAATCATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAGG
338234 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
521 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
338299 GCAA
586 GCAA
338303 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACC-AAAGGAGTATATATGTTAACAAAA
338368 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
65 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
338433 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
130 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
*
338498 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
195 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
*** *
338563 TCGTTGCGATTTTCATTTCGCATTGCGAT
260 TCGTTGCGATAGCCATTTCGCGTTGCGAT
338592 TTTCATTTCG
Statistics
Matches: 1998, Mismatches: 15, Indels: 48
0.97 0.01 0.02
Matches are distributed among these distances:
579 73 0.04
580 165 0.08
581 257 0.13
582 287 0.14
583 136 0.07
584 261 0.13
585 349 0.17
586 45 0.02
587 212 0.11
588 213 0.11
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (589 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAGGAGTATATATGTTAACAAAAC
TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
AGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
ATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTCT
CGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTA
CAAATCATCTTTTACAAATCAATTAAACAATCAAAAAAATAATAATAATTCTTATTTCTTCATCA
ATTATTGAATCATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAGG
ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
GCAA
Found at i:337531 original size:14 final size:14
Alignment explanation
Indices: 337512--337548 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
337502 CATCAATTAA
337512 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
337526 ACAAATCATCTTTT
1 ACAAATCAACATTT
337540 ACAAATCAA
1 ACAAATCAA
337549 TTAACAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:338112 original size:14 final size:14
Alignment explanation
Indices: 338093--338129 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
338083 CATCAATTAA
338093 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
338107 ACAAATCATCTTTT
1 ACAAATCAACATTT
338121 ACAAATCAA
1 ACAAATCAA
338130 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:338588 original size:19 final size:19
Alignment explanation
Indices: 338547--338612 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
338537 GAAATGAAAA
338547 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
338563 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
338580 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
338599 TCGCATTGCGATTT
1 TCGCATTGCGATTT
338613 CTCGTTGCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 28 0.62
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Done.