Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008359.1 Hibiscus syriacus cultivar Beakdansim tig00111098_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: 1252926
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:888828 original size:19 final size:20
Alignment explanation
Indices: 888804--888853 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
888794 GATAAATTTA
*
888804 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
888823 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
888844 TT-ATAATTTT
1 TTAATAATTTT
888854 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:888856 original size:31 final size:30
Alignment explanation
Indices: 888771--888857 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
888761 TTCAATAATA
* *
888771 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
888802 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
888833 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
888858 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:889590 original size:31 final size:30
Alignment explanation
Indices: 889555--889641 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
889545 TCAATAAAGT
889555 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
889586 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
889617 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
889642 TATTATCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:889617 original size:20 final size:20
Alignment explanation
Indices: 889550--889617 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
889540 TTTCGTCAAT
*
889550 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
889568 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
889589 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
889608 ATAA-ATTTAT
1 A-AAGATTTAT
889618 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:892510 original size:21 final size:21
Alignment explanation
Indices: 892486--892543 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
892476 CCAAATGATA
* *
892486 AAAAATGTGTCATAAAAACAG
1 AAAAATATATCATAAAAACAG
* *
892507 AAAAATATATCATAAAAATAA
1 AAAAATATATCATAAAAACAG
892528 AAAAATATATCATAAA
1 AAAAATATATCATAAA
892544 GATAGAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (21 bp):
AAAAATATATCATAAAAACAG
Found at i:895509 original size:44 final size:44
Alignment explanation
Indices: 895446--895531 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
895436 ATATAGCAGA
895446 AAGGTTTAAAAGGCCGTGGTAGAAAGCTAATGATCAAGAAAGGT
1 AAGGTTTAAAAGGCCGTGGTAGAAAGCTAATGATCAAGAAAGGT
895490 AAGGTTTAAAAGGCCGTGGTAGAAAGCTAATGATCAAGAAAG
1 AAGGTTTAAAAGGCCGTGGTAGAAAGCTAATGATCAAGAAAG
895532 TGCGAGAGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.42, C:0.09, G:0.29, T:0.20
Consensus pattern (44 bp):
AAGGTTTAAAAGGCCGTGGTAGAAAGCTAATGATCAAGAAAGGT
Found at i:896078 original size:33 final size:33
Alignment explanation
Indices: 896041--896176 Score: 175
Period size: 33 Copynumber: 4.1 Consensus size: 33
896031 CAGCCAAGTA
*
896041 AAACAGATGGGGCTATAGCAAAAGAAGTTTAAT
1 AAACAGATGGGACTATAGCAAAAGAAGTTTAAT
* *
896074 AAACAGATGGAACTATAGCAAGAGAAGTTTAAT
1 AAACAGATGGGACTATAGCAAAAGAAGTTTAAT
* *
896107 AAACAGATGGGACTATAG-AAAGATAAGTTCAAT
1 AAACAGATGGGACTATAGCAAA-AGAAGTTTAAT
* * * *
896140 AAACAGATGGGGCTAGAGCAAGACAAGTTTAAT
1 AAACAGATGGGACTATAGCAAAAGAAGTTTAAT
896173 AAAC
1 AAAC
896177 CACCAACTAA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 2 0.02
33 85 0.96
34 2 0.02
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (33 bp):
AAACAGATGGGACTATAGCAAAAGAAGTTTAAT
Found at i:896124 original size:66 final size:66
Alignment explanation
Indices: 896041--896176 Score: 193
Period size: 66 Copynumber: 2.1 Consensus size: 66
896031 CAGCCAAGTA
* * * *
896041 AAACAGATGGGGCTATAGCAAA-AGAAGTTTAATAAACAGATGGAACTATAGCAAGAGAAGTTTA
1 AAACAGATGGGACTATAG-AAAGAGAAGTTCAATAAACAGATGGAACTAGAGCAAGACAAGTTTA
896105 AT
65 AT
* **
896107 AAACAGATGGGACTATAGAAAGATAAGTTCAATAAACAGATGGGGCTAGAGCAAGACAAGTTTAA
1 AAACAGATGGGACTATAGAAAGAGAAGTTCAATAAACAGATGGAACTAGAGCAAGACAAGTTTAA
896172 T
66 T
896173 AAAC
1 AAAC
896177 CACCAACTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 3 0.05
66 59 0.95
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (66 bp):
AAACAGATGGGACTATAGAAAGAGAAGTTCAATAAACAGATGGAACTAGAGCAAGACAAGTTTAA
T
Found at i:898085 original size:21 final size:21
Alignment explanation
Indices: 898033--898079 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
898023 GTTTCCAGAT
*
898033 TCGCAACGCGAACTTTGACTA
1 TCGCAACGCGAACTTCGACTA
898054 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
898075 TCGCA
1 TCGCA
898080 TTGCGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:898124 original size:21 final size:21
Alignment explanation
Indices: 898094--898230 Score: 111
Period size: 21 Copynumber: 6.6 Consensus size: 21
898084 GATTTACATA
*
898094 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
898115 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
898136 TTCGTGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
898157 TT--CGTTACGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
898176 TTCACGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
898199 TT--TGTTGCGATAGTGCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
898218 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
898231 TTATTACAAA
Statistics
Matches: 89, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
19 22 0.25
21 58 0.65
23 9 0.10
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:898210 original size:42 final size:42
Alignment explanation
Indices: 898119--898264 Score: 179
Period size: 42 Copynumber: 3.5 Consensus size: 42
898109 TCCAAGTTCG
* * *
898119 CGTTGCGATAGTCGAAGTTCGTGTTGCGA-TT-TTCCAAATT
1 CGTTACGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
898159 CGTTACGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATT
1 CGTTACGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* * * * *
898201 TGTTGCGATAGTGCAAGTTCGCATTGCGATTTATTACAAATT
1 CGTTACGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
898243 CGTTACGATAGTCGAAGATCGC
1 CGTTACGATAGTCCAAGTTCGC
898265 AACGACTGGT
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 25 0.28
41 2 0.02
42 62 0.70
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (42 bp):
CGTTACGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:898265 original size:42 final size:42
Alignment explanation
Indices: 898094--898265 Score: 174
Period size: 42 Copynumber: 4.1 Consensus size: 42
898084 GATTTACATA
* * *
898094 TTCGCATTGCGA--TAGTCCAAGTTCGCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATTTATTCCAAATT--CGTTACGATAGTCGAAG
** *
898136 TTCGTGTTGCGA-TT-TTCCAAATTCGTTACGATAGTCCAAG
1 TTCGCATTGCGATTTATTCCAAATTCGTTACGATAGTCGAAG
* * * *
898176 TTCACGTTGCGATTTATTCCAAATTTGTTGCGATAGT-GCAAG
1 TTCGCATTGCGATTTATTCCAAATTCGTTACGATAGTCG-AAG
*
898218 TTCGCATTGCGATTTATTACAAATTCGTTACGATAGTCGAAG
1 TTCGCATTGCGATTTATTCCAAATTCGTTACGATAGTCGAAG
*
898260 ATCGCA
1 TTCGCA
898266 ACGACTGGTG
Statistics
Matches: 108, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
40 25 0.23
41 2 0.02
42 79 0.73
43 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (42 bp):
TTCGCATTGCGATTTATTCCAAATTCGTTACGATAGTCGAAG
Found at i:898359 original size:6 final size:6
Alignment explanation
Indices: 898348--898384 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
898338 GACACGTATT
898348 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
898385 GACGGACGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:899121 original size:21 final size:19
Alignment explanation
Indices: 899088--899348 Score: 189
Period size: 21 Copynumber: 12.7 Consensus size: 19
899078 CGTTGCGATT
* *
899088 TTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
899107 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
899130 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
899149 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
899172 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
899191 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
899214 TTTGACTATCGCAACGCGAAC
1 TTGGAATATCGCAA--CGAAC
*
899235 TTGGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
899254 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* * * *
899277 TTCGACTATAGTAACGAAC
1 TTGGAATATCGCAACGAAC
*
899296 TTGGACTATCGCAATACGAAC
1 TTGGAATATCGC-A-ACGAAC
* *
899317 TTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
*
899336 TTGGAAAATCGCA
1 TTGGAATATCGCA
899349 TTGCGATAGT
Statistics
Matches: 200, Mismatches: 24, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
19 67 0.34
20 2 0.01
21 92 0.46
23 39 0.19
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (19 bp):
TTGGAATATCGCAACGAAC
Found at i:899153 original size:42 final size:42
Alignment explanation
Indices: 899091--899239 Score: 262
Period size: 42 Copynumber: 3.5 Consensus size: 42
899081 TGCGATTTTG
*
899091 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
899133 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
899175 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
899217 GACTATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
899240 CTATCGCAAC
Statistics
Matches: 103, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
42 93 0.90
44 10 0.10
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:899185 original size:63 final size:61
Alignment explanation
Indices: 899137--899348 Score: 227
Period size: 63 Copynumber: 3.4 Consensus size: 61
899127 AACTTCGACT
*
899137 ATCGCAA-CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACCGAACTTGGAAT--ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAAT-A
* *
899200 ATCGCAACGCGAACTTTGACTATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAA
1 ATCGCAAC-CGAACTTGGAATATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAAT-A
* * * * *
899263 ATCGCAACGCGAACTTCGACTATAGTAA--CGAACTTGGACTATCGCAATACGAACTTGGACT-
1 ATCGCAAC-CGAACTTGGAATATCGCAACGCGAACTTGGACTATCGC-A-ACGAACTTGGAATA
* *
899324 ATCGCAA-CGAATTTGGAAAATCGCA
1 ATCGCAACCGAACTTGGAATATCGCA
899349 TTGCGATAGT
Statistics
Matches: 132, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
59 12 0.09
61 24 0.18
62 1 0.01
63 85 0.64
65 10 0.08
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (61 bp):
ATCGCAACCGAACTTGGAATATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATA
Found at i:899267 original size:42 final size:42
Alignment explanation
Indices: 899221--899348 Score: 165
Period size: 40 Copynumber: 3.1 Consensus size: 42
899211 AACTTTGACT
899221 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAA
* * * *
899263 ATCGCAACGCGAACTTCGACTATAGTAACGAACTTGGACT--
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAA
** *
899303 ATCGCAATACGAACTTGGACTATCGCAACGAATTTGG-A-AA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAA
899343 ATCGCA
1 ATCGCA
899349 TTGCGATAGT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 37 0.51
42 36 0.49
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAA
Found at i:899318 original size:40 final size:40
Alignment explanation
Indices: 899088--899340 Score: 212
Period size: 42 Copynumber: 6.1 Consensus size: 40
899078 CGTTGCGATT
* *
899088 TTGGACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAACTTGGACT--ATCGCAA--CGAAC
* *
899130 TTCGACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAACTTGGACT--ATCGCAA--CGAAC
* *
899172 TTCGACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAACTTGGACT--ATCGCAA--CGAAC
*
899214 TTTGACTATCGCAACGCGAACTTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAAC
* * * *
899254 TTGGAATAAATCGCAACGCGAACTTCGACTATAGTAACGAAC
1 TTGGACT--ATCGCAACGCGAACTTGGACTATCGCAACGAAC
** *
899296 TTGGACTATCGCAATACGAACTTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAAC
899336 TTGGA
1 TTGGA
899341 AAATCGCATT
Statistics
Matches: 191, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
40 42 0.22
42 138 0.72
44 11 0.06
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (40 bp):
TTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAAC
Found at i:906698 original size:15 final size:15
Alignment explanation
Indices: 906678--906707 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
906668 ATCATCTAGT
*
906678 ATTATGTTATGTGAG
1 ATTATGTTATATGAG
906693 ATTATGTTATATGAG
1 ATTATGTTATATGAG
906708 CGTCTTTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (15 bp):
ATTATGTTATATGAG
Found at i:907536 original size:3 final size:3
Alignment explanation
Indices: 907530--907592 Score: 103
Period size: 3 Copynumber: 21.3 Consensus size: 3
907520 TATATAATAG
907530 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT -TAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
907574 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
907593 ATACTATTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 3 0.05
3 53 0.93
4 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:909271 original size:22 final size:22
Alignment explanation
Indices: 909246--909310 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
909236 TAACTCTAGC
909246 TTTAGTTCAACTCTTAAGGATA
1 TTTAGTTCAACTCTTAAGGATA
* *
909268 TTTATGAT-AACTC-T-A-G--C
1 TTTA-GTTCAACTCTTAAGGATA
*
909285 TTTAGTTCAATTCTTAAGGATA
1 TTTAGTTCAACTCTTAAGGATA
909307 TTTA
1 TTTA
909311 TGATGTGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 14
0.62 0.10 0.28
Matches are distributed among these distances:
16 2 0.06
17 8 0.26
18 1 0.03
19 2 0.06
20 2 0.06
21 1 0.03
22 13 0.42
23 2 0.06
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (22 bp):
TTTAGTTCAACTCTTAAGGATA
Found at i:909289 original size:39 final size:39
Alignment explanation
Indices: 909235--909314 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
909225 GTTACAACCA
909235 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
1 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
*
909274 ATAACTCTAGCTTTAGTTCAATTCTTAAGGATATTTATG
1 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
909313 AT
1 AT
909315 GTGATACATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (39 bp):
ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
Found at i:911382 original size:26 final size:26
Alignment explanation
Indices: 911353--911407 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
911343 ACATATTGTG
*
911353 CATT-TTGTTATTTTTCTTTACATTCA
1 CATTATTGTTACTTTT-TTTACATTCA
* *
911379 CATTATTTTTCCTTTTTTTACATTCA
1 CATTATTGTTACTTTTTTTACATTCA
911405 CAT
1 CAT
911408 GTCTCATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.60
Consensus pattern (26 bp):
CATTATTGTTACTTTTTTTACATTCA
Found at i:913610 original size:106 final size:106
Alignment explanation
Indices: 913425--914523 Score: 1763
Period size: 106 Copynumber: 10.5 Consensus size: 106
913415 TCTGTCAACA
* *
913425 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCCAGACAACGCAT
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
913490 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* *
913531 AACTTCTCAATTTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAT
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
913596 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* *
913637 AACTTCTCAATATCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAT
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
913702 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* * *
913743 AACTTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGTATATTGGACTCCAGACAACGCAA
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
* * * *
913808 GTTCAACTTCACAACGAAGGGTCCGATGGTTGTCAATAAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* * * *
913849 AACTTCCCAATTTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAT
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
913914 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* *
913955 AACTTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
*
914020 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* *
914061 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAT
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
914126 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* *
914167 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAA
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
914232 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* * *
914273 AACTTCCCGATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
*
914338 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-A-ATA-
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* * *
914376 AA-----CAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGTAA
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
* *
914432 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAT
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* * * * * *
914473 AATTTCCCAGTTCCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGAC
1 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
914524 CTGGAACAAT
Statistics
Matches: 928, Mismatches: 53, Indels: 24
0.92 0.05 0.02
Matches are distributed among these distances:
94 79 0.09
95 1 0.00
96 2 0.00
97 2 0.00
98 6 0.01
102 5 0.01
103 2 0.00
104 2 0.00
105 1 0.00
106 828 0.89
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
Found at i:914357 original size:43 final size:43
Alignment explanation
Indices: 914296--914451 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 43
914286 CAGAGCCAAT
914296 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
914339 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
* *
914390 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGTAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
914433 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
914452 GACCGCTGGT
Statistics
Matches: 82, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
43 36 0.44
44 3 0.04
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 3 0.04
51 20 0.24
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:914452 original size:94 final size:94
Alignment explanation
Indices: 914291--914481 Score: 355
Period size: 94 Copynumber: 2.0 Consensus size: 94
914281 GATTTCAGAG
914291 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
914356 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
* *
914385 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGTAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
914450 GGGACCGCTGGTTGTCAATAAATAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
914479 CCA
1 CCA
914482 GTTCCAGAGC
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (94 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTC
Found at i:914882 original size:83 final size:80
Alignment explanation
Indices: 914645--914889 Score: 267
Period size: 83 Copynumber: 3.0 Consensus size: 80
914635 AATCGTGCCA
* * * *
914645 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAAATCATTTACAGCATAGCTCAAGG
*
914710 CGAGAAA-GGCTATCT
66 C-AAAAAGGGCTATCT
* ** * * * * * *
914725 ACCAAGGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCAAATCATTTACAGCATAGCTCAAG
* * * *
914790 GCTAGAAGGGTTATTTGT
65 GCAAAAAGGGCTA--TCT
*
914808 GACCAAAGACCTTCGAGATCGACTACGCTCAGCTCCAAGGCAAATCATTTACAGCATAGCTCAAG
1 -ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAAATCATTTACAGCATAGCTCAAG
914873 GCAAAAAGGGCTATCT
65 GCAAAAAGGGCTATCT
914889 A
1 A
914890 TCAACAAAAT
Statistics
Matches: 129, Mismatches: 31, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
80 30 0.23
81 33 0.26
83 40 0.31
84 26 0.20
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (80 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAAATCATTTACAGCATAGCTCAAGG
CAAAAAGGGCTATCT
Found at i:915488 original size:3 final size:3
Alignment explanation
Indices: 915480--915521 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
915470 TATATAATAG
*
915480 ATT ATT ATT AAT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
915522 ATACTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:915496 original size:9 final size:9
Alignment explanation
Indices: 915482--915532 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
915472 TATAATAGAT
915482 TATTATTAA
1 TATTATTAA
*
915491 TATTATTAT
1 TATTATTAA
915500 TATTATT-A
1 TATTATTAA
915508 TATTA-T--
1 TATTATTAA
915514 TATTATTAA
1 TATTATTAA
*
915523 TACTATTAA
1 TATTATTAA
915532 T
1 T
915533 TTTGTTTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
6 5 0.14
7 2 0.06
8 5 0.14
9 24 0.67
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAA
Found at i:917217 original size:39 final size:39
Alignment explanation
Indices: 917163--917242 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
917153 GTTACAGCCA
917163 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
1 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
*
917202 ATAACTCTAGCTTTAGTTCAATTCTTAAGGATATTTATG
1 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
917241 AT
1 AT
917243 GTGATACATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (39 bp):
ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
Found at i:926760 original size:115 final size:114
Alignment explanation
Indices: 926580--926789 Score: 312
Period size: 115 Copynumber: 1.8 Consensus size: 114
926570 TATACATAAA
* * * * *
926580 TAAGATATTTACTTATTTAGAAATATAAAAAAAGGGCTTCTAGGTGCTTTAAGACAACTCTTTTC
1 TAAGATATTTACTTATTCAAAAATATAAAAAAAGAGCTTCTAGGTACCTTAAGACAACTCTTTTC
* *
926645 TTTGATATTAAAAAATAAATAAATATTAAAAATATTTTATTTTAATATAG
66 TTCGATATT-AAAAATAAATAAATATCAAAAATATTTTATTTTAATATAG
* * * *
926695 TAAGATATTTATTTATTCAAAAATATTAGAAAAGAGCTTCTAGGTACCTTAAGACAGCTCTTTTC
1 TAAGATATTTACTTATTCAAAAATATAAAAAAAGAGCTTCTAGGTACCTTAAGACAACTCTTTTC
926760 TTCGATATTAAAAATAAATAAATATCAAAA
66 TTCGATATTAAAAATAAATAAATATCAAAA
926790 TATAATTATT
Statistics
Matches: 84, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
114 20 0.24
115 64 0.76
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.38
Consensus pattern (114 bp):
TAAGATATTTACTTATTCAAAAATATAAAAAAAGAGCTTCTAGGTACCTTAAGACAACTCTTTTC
TTCGATATTAAAAATAAATAAATATCAAAAATATTTTATTTTAATATAG
Found at i:928382 original size:3 final size:3
Alignment explanation
Indices: 928368--928441 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
928358 GTTGTATCTG
* * *
928368 TAA TAA -AA TAA TAA TAA TAT TAA TAT TAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
928415 TAG TAA TAA AAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA
928442 AAAACCAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
2 3 0.05
3 54 0.93
4 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:928969 original size:113 final size:114
Alignment explanation
Indices: 928783--929646 Score: 1368
Period size: 113 Copynumber: 7.6 Consensus size: 114
928773 AGAATCATGC
* * *
928783 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTATTCTTCATTCTTTAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
928848 TATGAACTC-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCA
65 TATGAACTCAACTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCG
*
928897 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
928962 ATAAACTCAAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGTG
66 ATGAACTCAACTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCG
*
929010 AAAAGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
929075 ATGAACTCGAC-CTGGTAATGCTGATCCATTGAATGATGAATTCAAGCG
66 ATGAACTCAACTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCG
929123 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
929188 ATGAACTCAAC-CTGGTAATGCTGATCCATCGAATGATAAATTCAAGCG
66 ATGAACTCAACTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCG
*
929236 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
929301 ATGAACTCGACT-TGGTAATACTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCAACTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCG
929349 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* **
929414 ATGAACTC--TTCCAGAAATGCTGAAT-CATCGAATGATGAATTCAAGCG
66 ATGAACTCAACTCTGGAAATGCTG-ATCCATCGAATGATGAATTCAAGCG
929461 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
929526 ATGAACTCGA-TCTGGTAGTGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTCAACTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCG
*
929574 AAAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
929639 ATGAACTC
66 ATGAACTC
929647 TTCCAGAAAT
Statistics
Matches: 705, Mismatches: 38, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
111 1 0.00
112 104 0.15
113 594 0.84
114 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (114 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCAACTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCG
Found at i:930103 original size:22 final size:22
Alignment explanation
Indices: 930078--930132 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
930068 GATAAAGCTT
*
930078 TCATCTTTGAAAACAGAATCTG
1 TCATCTTTGAAAACAGAATCTA
* **
930100 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAACAGAATCTA
930122 TCATCTTTGAA
1 TCATCTTTGAA
930133 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAACAGAATCTA
Found at i:930580 original size:54 final size:54
Alignment explanation
Indices: 930498--930609 Score: 188
Period size: 54 Copynumber: 2.1 Consensus size: 54
930488 AGAATAACAG
* * *
930498 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCTCAGAT
*
930552 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCTCAGAT
930606 GTTC
1 GTTC
930610 TCAATCATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCTCAGAT
Found at i:940570 original size:115 final size:114
Alignment explanation
Indices: 940390--940599 Score: 312
Period size: 115 Copynumber: 1.8 Consensus size: 114
940380 TATACATAAA
* * * * * *
940390 TAAGATATTTACTTATTTAGAAATATAAAAAAAGGGCTTCTAGGTGCTTTAAGACAGCTCTTTTC
1 TAAGATATTTACTTATTCAAAAATATAAAAAAAGAGCTTCTAGATACCTTAAGACAGCTCTTTTC
* *
940455 TTTGATATTAAAAAATAAATAAATATTAAAAATATTTTATTTTAATATAG
66 TTCGATATT-AAAAATAAATAAATATCAAAAATATTTTATTTTAATATAG
* * *
940505 TAAGATATTTATTTATTCAAAAATATCAGAAAAGAGCTTCTAGATACCTTAAGACAGCTCTTTTC
1 TAAGATATTTACTTATTCAAAAATATAAAAAAAGAGCTTCTAGATACCTTAAGACAGCTCTTTTC
940570 TTCGATATTAAAAATAAATAAATATCAAAA
66 TTCGATATTAAAAATAAATAAATATCAAAA
940600 TATGATTATT
Statistics
Matches: 84, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
114 20 0.24
115 64 0.76
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (114 bp):
TAAGATATTTACTTATTCAAAAATATAAAAAAAGAGCTTCTAGATACCTTAAGACAGCTCTTTTC
TTCGATATTAAAAATAAATAAATATCAAAAATATTTTATTTTAATATAG
Found at i:942184 original size:3 final size:3
Alignment explanation
Indices: 942170--942252 Score: 89
Period size: 3 Copynumber: 28.0 Consensus size: 3
942160 GTTGTATCTG
* * * *
942170 TAA TAA -AA TAA TAA TAA TAA TAA TAT TAT TAA TAT TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
942217 TAA TAA TAA TAG TAA TAA AAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
942253 AAAACCAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
2 3 0.04
3 63 0.94
4 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:943503 original size:24 final size:24
Alignment explanation
Indices: 943460--943505 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
943450 ATGGTTAAAT
**
943460 TTGAGTCTCGCCTTTTTCAAGAGC
1 TTGAGTCTCGCCTTGATCAAGAGC
*
943484 TTGAGTCTCTCCTTGATCAAGA
1 TTGAGTCTCGCCTTGATCAAGA
943506 AGATGTCGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (24 bp):
TTGAGTCTCGCCTTGATCAAGAGC
Found at i:946216 original size:20 final size:21
Alignment explanation
Indices: 946193--946233 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
946183 ATTTATATGT
**
946193 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
946213 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
946234 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:947557 original size:3 final size:3
Alignment explanation
Indices: 947549--947634 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
947539 TTAATATATT
*
947549 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
947597 TAA TAA TAC CAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
947635 TGGATAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:948268 original size:224 final size:227
Alignment explanation
Indices: 947937--948471 Score: 791
Period size: 224 Copynumber: 2.4 Consensus size: 227
947927 TGTGATAGTA
*
947937 TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-T-TTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* ** * * ****
947999 T-TCATTATGAACTTTCTCTGG-AAAGGCTGATCCATCAATTGATGAATTCGGGTAAAAGGTTGA
66 TCTCATTATGAACCTTCTCTGGCAAAGAATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGA
948062 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
131 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
* *
948127 CTCTGG-AA-AATAATCCATCCAGTGATGAAT
196 CTCTGGCAATAATAATCCATCAAATGATGAAT
* ** * *
948157 TCAGATTAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
948222 TCTCATTATGAACCTTCTCTGGCAAA-AATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGA
66 TCTCATTATGAACCTTCTCTGGCAAAGAATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGA
948286 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
131 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
** *
948351 CTCTGGCAATGTTGATCCATCAAATGATGAAT
196 CTCTGGCAATAATAATCCATCAAATGATGAAT
* * *
948383 TTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
948448 TCTCATTATGAA-CTTATCTGGCAA
66 TCTCATTATGAACCTTCTCTGGCAA
948472 TGTTGATATC
Statistics
Matches: 280, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
220 4 0.01
221 38 0.14
222 1 0.00
223 15 0.05
224 120 0.43
225 16 0.06
226 86 0.31
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (227 bp):
TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACCTTCTCTGGCAAAGAATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGA
ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
CTCTGGCAATAATAATCCATCAAATGATGAAT
Found at i:948308 original size:113 final size:113
Alignment explanation
Indices: 947937--948471 Score: 771
Period size: 113 Copynumber: 4.8 Consensus size: 113
947927 TGTGATAGTA
**
947937 TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-T-TTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
** * *
947999 T-TCATTATGAACTTTCTCTGG-AAAGGCTGATCCATCAATTGATGAAT
66 TCTCATTATGAACTTTCTCTGGCAAA-AATAATCCATCAAGTGATGAAT
****
948046 TCGGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
948111 TCTCATTATGAACTTTCTCTGG--AAAATAATCCATCCAGTGATGAAT
66 TCTCATTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
* ** *
948157 TCAGATTAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
948222 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
66 TCTCATTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
948270 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*** * *
948335 TCTCATTATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAAT
66 TCTCATTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
* * * *
948383 TTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
948448 TCTCATTATGAAC-TTATCTGGCAA
66 TCTCATTATGAACTTTCTCTGGCAA
948472 TGTTGATATC
Statistics
Matches: 388, Mismatches: 32, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
109 2 0.01
110 39 0.10
111 100 0.26
112 27 0.07
113 220 0.57
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
Found at i:949358 original size:82 final size:82
Alignment explanation
Indices: 949216--950001 Score: 1421
Period size: 82 Copynumber: 9.5 Consensus size: 82
949206 CCTACTGAAT
* *
949216 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTTTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
*
949280 ATGATTGTTCTATCCAAC
65 ATGATTGTTCTGTCCAAC
949298 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
949363 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
949380 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
949445 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
949462 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
949527 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
949544 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
949609 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
949626 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
949691 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
* * * *
949708 CAGATCAGATAACTCAAAGAACACTTCCAAAAGATTCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCATCTTCTAAACTCA
949773 ATGATTGGTTCTGTCCAAC
65 ATGATT-GTTCTGTCCAAC
* *
949792 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCATCTTCTAAACTCA
949857 ATGATTGGTTCTGTCCAAC
65 ATGATT-GTTCTGTCCAAC
*
949876 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
949941 TGATTGGTTCTGTCCAAC
66 TGATT-GTTCTGTCCAAC
949959 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
950002 GCACATTATA
Statistics
Matches: 691, Mismatches: 10, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
82 445 0.64
83 109 0.16
84 137 0.20
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (82 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
TGATTGTTCTGTCCAAC
Found at i:954392 original size:162 final size:157
Alignment explanation
Indices: 954080--954400 Score: 597
Period size: 162 Copynumber: 2.0 Consensus size: 157
954070 TTGTAACAAC
954080 ATTTCTGGCCTCCGTCTGAGCTTTTGTTGGACTGGTTTATATTCAGGATTGATTGGAAGCTTGTG
1 ATTTCTGGCCTCCGTCTGAGCTTTTGTTGGACTGGTTTATATTCAGGATTGATTGGAAGCTTGTG
954145 TTCACTATATCTGTGCTCAAACCAGACATATCTGATAAGACCAGGCAAAGATATCTTTGAACTCT
66 TTCACTATATCTGTGCTCAAACCAGACATATCTGATAAGACCAGGCAAAGATATCTTTGAACTCT
954210 TGAAGGAGATTTATCAATTCTTGTTTT
131 TGAAGGAGATTTATCAATTCTTGTTTT
954237 ATTTCTGGCCTCCTTCGTCTGAGCTTTTGTTGGACTGGTTTATATTCAGGATTGATTGGAAGCTT
1 ATTTCTGGCCT-C--CGTCTGAGCTTTTGTTGGACTGGTTTATATTCAGGATTGATTGGAAGCTT
954302 GTGTATCACTATATCTGTGCTCAAACCAGACATATCTTGATAAGACCAGGCAAAGATATCTTTGA
63 GTGT-TCACTATATCTGTGCTCAAACCAGACATATC-TGATAAGACCAGGCAAAGATATCTTTGA
954367 ACTCTTGAAGGAGATTTATCAATTCTTGTTTT
126 ACTCTTGAAGGAGATTTATCAATTCTTGTTTT
954399 AT
1 AT
954401 CTGGAATGTC
Statistics
Matches: 159, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
157 11 0.07
158 1 0.01
160 54 0.34
161 31 0.19
162 62 0.39
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (157 bp):
ATTTCTGGCCTCCGTCTGAGCTTTTGTTGGACTGGTTTATATTCAGGATTGATTGGAAGCTTGTG
TTCACTATATCTGTGCTCAAACCAGACATATCTGATAAGACCAGGCAAAGATATCTTTGAACTCT
TGAAGGAGATTTATCAATTCTTGTTTT
Found at i:961772 original size:13 final size:15
Alignment explanation
Indices: 961750--961786 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
961740 TTTGACAGAA
961750 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
961762 AAATAAAATACTTGC
1 AAATAAAATACTTGC
961777 AAATAAAATA
1 AAATAAAATA
961787 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:961814 original size:16 final size:15
Alignment explanation
Indices: 961777--961825 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 15
961767 AAATACTTGC
961777 AAATAAAATAAAACATAT
1 AAAT-AAATAAAA-A-AT
*
961795 AAATATTATAAAAAAT
1 AAATA-AATAAAAAAT
961811 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
961826 TTGAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 9 0.32
16 7 0.25
17 2 0.07
18 10 0.36
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAATAAAAAAT
Found at i:963878 original size:11 final size:11
Alignment explanation
Indices: 963857--963886 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
963847 TGTAATTAAT
963857 TATTT-ATATA
1 TATTTAATATA
963867 TATTTAATATA
1 TATTTAATATA
963878 TATTTAATA
1 TATTTAATA
963887 ATAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTAATATA
Found at i:963890 original size:3 final size:3
Alignment explanation
Indices: 963882--963958 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
963872 AATATATATT
* *
963882 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
963930 CAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
963959 TGGATAAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:964946 original size:19 final size:19
Alignment explanation
Indices: 964909--964946 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
964899 GCGATTTTAA
*
964909 AAAATGTGTTACGATAGTT
1 AAAATGTGTTACGAGAGTT
*
964928 AAAATGTGTTGCGAGAGTT
1 AAAATGTGTTACGAGAGTT
964947 TGAAAAACGT
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:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (19 bp):
AAAATGTGTTACGAGAGTT
Found at i:964983 original size:19 final size:19
Alignment explanation
Indices: 964959--964995 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
964949 AAAAACGTGT
964959 TGTTGCGAAAGTGAAAAAG
1 TGTTGCGAAAGTGAAAAAG
*
964978 TGTTGCGATAGTGAAAAA
1 TGTTGCGAAAGTGAAAAA
964996 TCCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.30, T:0.24
Consensus pattern (19 bp):
TGTTGCGAAAGTGAAAAAG
Found at i:965314 original size:6 final size:6
Alignment explanation
Indices: 965298--965341 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
965288 TCTCGTCTCG
*
965298 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTTGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
965342 AATACGTGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.00, C:0.14, G:0.52, T:0.34
Consensus pattern (6 bp):
GGTCGT
Found at i:965489 original size:40 final size:41
Alignment explanation
Indices: 965434--965885 Score: 141
Period size: 40 Copynumber: 11.2 Consensus size: 41
965424 TGCGATTTTT
* *
965434 AATCGCAACGCGAACTTGGACTATATCAA-TGAATTTGGAA
1 AATCGCAACGCGAACTTGGACTATATCAACCGAACTTGGAA
* * *
965474 AATCGCAACGCGAACTTCGACTATCA-CAACGTGAACTTGGAC
1 AATCGCAACGCGAACTTGGACTAT-ATCAAC-CGAACTTGGAA
* * ** ** * *
965516 TATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTCGAC
1 AATCGCAACGCGAACTTGGACTATATCAAC-CGAACTTGGAA
* * * *
965556 TATCGCAACGTGAACTTGGACTAT-TGCAA-CGAATTTAGAA
1 AATCGCAACGCGAACTTGGACTATAT-CAACCGAACTTGGAA
* * ** * **
965596 AATCTCAACGCGAACTTCGACTATCGCAACGCGAACTTCGTC
1 AATCGCAACGCGAACTTGGACTATATCAAC-CGAACTTGGAA
* * ** ** *
965638 TATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTGGAT
1 AATCGCAACGCGAACTTGGACTATATCAAC-CGAACTTGGAA
* * * * *
965678 TATCGCAA--CGAATTTGGA--AAATC--GC-AAC--GCAA
1 AATCGCAACGCGAACTTGGACTATATCAACCGAACTTGGAA
* * ** * *
965710 ACTTCG-AACGTGAACTTGGACTATCGCAA-CGAATTTGAAA
1 A-ATCGCAACGCGAACTTGGACTATATCAACCGAACTTGGAA
* ** * *
965750 AATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGAC
1 AATCGCAACGCGAACTTGGACTATATCAAC-CGAACTTGGAA
* * ** * *
965792 TATCGCAACGTGAACTTGGACTATCGCAACGTGAACTTGGAC
1 AATCGCAACGCGAACTTGGACTATATCAAC-CGAACTTGGAA
* * ** * *
965834 TATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGAC
1 AATCGCAACGCGAACTTGGACTATATCAAC-CGAACTTGGAA
*
965876 TATCGCAACG
1 AATCGCAACG
965886 AATTTGGAAA
Statistics
Matches: 323, Mismatches: 66, Indels: 44
0.75 0.15 0.10
Matches are distributed among these distances:
32 4 0.01
33 3 0.01
34 11 0.03
35 1 0.00
36 2 0.01
37 1 0.00
38 4 0.01
39 3 0.01
40 157 0.49
41 1 0.00
42 136 0.42
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (41 bp):
AATCGCAACGCGAACTTGGACTATATCAACCGAACTTGGAA
Found at i:965509 original size:21 final size:21
Alignment explanation
Indices: 965475--965687 Score: 186
Period size: 21 Copynumber: 10.4 Consensus size: 21
965465 AATTTGGAAA
965475 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
965496 ATCACAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * **
965517 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
965536 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
965557 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * * **
965578 ATTGCAA--CGAATTTAGAAA
1 ATCGCAACGCGAACTTCGACT
*
965597 ATCTCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
965618 ATCGCAACGCGAACTTCGTCT
1 ATCGCAACGCGAACTTCGACT
* * **
965639 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
* *
965658 ATCGCAACGCGAACTTGGATT
1 ATCGCAACGCGAACTTCGACT
965679 ATCGCAACG
1 ATCGCAACG
965688 AATTTGGAAA
Statistics
Matches: 150, Mismatches: 36, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
19 41 0.27
21 109 0.73
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:965534 original size:61 final size:61
Alignment explanation
Indices: 965435--965957 Score: 519
Period size: 61 Copynumber: 8.6 Consensus size: 61
965425 GCGATTTTTA
* ** *
965435 ATCGCAACGCGAACTTGGACTATATCAATGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
*
965496 ATCACAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
* * *
965557 ATCGCAACGTGAACTTGGACTATTGCAACGAATTTAGAAAATCTCAACGCGAACTTCGACT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
* * * * *
965618 ATCGCAACGCGAACTTCGTCTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGATT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
* ** * ** * *
965679 ATCGCAAC--GAATTTGGAAAATCGCAACGCA-----AACTTCG-AACGTGAACTTGGACT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
* * ** * * ** * *
965732 ATCGCAAC--GAATTTGAAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACT
1 ATCGCAACGTGAACTTGGACTATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTCGACT
* **
965793 ATCGCAACGTGAACTTGGACTATCGCAACGTGAACTTGGACTATCGCAACGCGAACTTCGACT
1 ATCGCAACGTGAACTTGGACTATCGCAAC--GAATTTGGAAAATCGCAACGCGAACTTCGACT
* * * * *
965856 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCACATCGCGAACTTCGAACGCGA
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCG-A--C-T
*
965921 ACTTCG-AACGTGAACTTAGACTATCGCAACGAATTTG
1 A--TCGCAACGTGAACTTGGACTATCGCAACGAATTTG
965958 AACTAACGTA
Statistics
Matches: 395, Mismatches: 49, Indels: 31
0.83 0.10 0.07
Matches are distributed among these distances:
53 39 0.10
54 5 0.01
55 3 0.01
59 16 0.04
60 4 0.01
61 223 0.56
62 1 0.00
63 70 0.18
64 1 0.00
65 1 0.00
66 29 0.07
67 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (61 bp):
ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:965752 original size:53 final size:57
Alignment explanation
Indices: 965658--965864 Score: 206
Period size: 63 Copynumber: 3.5 Consensus size: 57
965648 AATTTGGAAA
* * *
965658 ATCGCAACGCGAACTTGGATTATCGCAACGAATTTGGAAAATCGCAACGC-AA-ACT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGCGAACACT
965713 -TCG-AACGTGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGCGAA---C-ACT
* * ** *
965772 ATCGCAACGTGAACTTGGACTATCGCAACGTGAACTTGGACTATCGCAACGTGAACTTGGACT
1 ATCGCAACGTGAACTTGGACTATCGCAAC--GAATTTGAAAAATCGCAACGCGAAC----ACT
* *
965835 ATCGCAACGCGAACTTCGACTATCGCAACG
1 ATCGCAACGTGAACTTGGACTATCGCAACG
965865 CGAACTTCGA
Statistics
Matches: 129, Mismatches: 10, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
53 42 0.33
54 5 0.04
59 3 0.02
60 4 0.03
61 25 0.19
63 50 0.39
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (57 bp):
ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGCGAACACT
Found at i:965775 original size:21 final size:21
Alignment explanation
Indices: 965751--965885 Score: 216
Period size: 21 Copynumber: 6.4 Consensus size: 21
965741 AATTTGAAAA
965751 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
965772 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* *
965793 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* *
965814 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
965835 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
965856 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
965877 ATCGCAACG
1 ATCGCAACG
965886 AATTTGGAAA
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 110 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:965807 original size:42 final size:42
Alignment explanation
Indices: 965716--965885 Score: 236
Period size: 42 Copynumber: 4.1 Consensus size: 42
965706 GCAAACTTCG
* * * * **
965716 AACGTGAACTTGGACTATCGCAAC--GAATTTGAAAAATCGC
1 AACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGC
965756 AACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGC
1 AACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGC
* *
965798 AACGTGAACTTGGACTATCGCAACGTGAACTTGGACTATCGC
1 AACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGC
* *
965840 AACGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGC
1 AACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGC
965882 AACG
1 AACG
965886 AATTTGGAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 22 0.19
42 94 0.81
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (42 bp):
AACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGC
Found at i:965840 original size:63 final size:62
Alignment explanation
Indices: 965716--965885 Score: 234
Period size: 63 Copynumber: 2.7 Consensus size: 62
965706 GCAAACTTCG
* * **
965716 AACGTGAACTTGGACTATCGCAAC-GAATTTGAAAAATCGCAACGCGAACTTCGACTATCGC
1 AACGTGAACTTGGACTATCGCAACGGAACTTGGACTATCGCAACGCGAACTTCGACTATCGC
* *
965777 AACGTGAACTTGGACTATCGCAACGTGAACTTGGACTATCGCAACGTGAACTTGGACTATCGC
1 AACGTGAACTTGGACTATCGCAACG-GAACTTGGACTATCGCAACGCGAACTTCGACTATCGC
* * *
965840 AACGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAACG
1 AACGTGAACTTGGACTATCGCAACG-GAACTTGGACTATCGCAACG
965886 AATTTGGAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
61 24 0.25
63 73 0.75
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (62 bp):
AACGTGAACTTGGACTATCGCAACGGAACTTGGACTATCGCAACGCGAACTTCGACTATCGC
Found at i:965921 original size:13 final size:13
Alignment explanation
Indices: 965903--965937 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
965893 AAAATCACAT
965903 CGCGAACTTCGAA
1 CGCGAACTTCGAA
965916 CGCGAACTTCGAA
1 CGCGAACTTCGAA
*
965929 CGTGAACTT
1 CGCGAACTT
965938 AGACTATCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (13 bp):
CGCGAACTTCGAA
Found at i:965992 original size:19 final size:19
Alignment explanation
Indices: 965968--966005 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
965958 AACTAACGTA
965968 AATTTGAAAAATCGCAACG
1 AATTTGAAAAATCGCAACG
*
965987 AATTTGGAAAATCGCAACG
1 AATTTGAAAAATCGCAACG
966006 CAAACTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (19 bp):
AATTTGAAAAATCGCAACG
Found at i:966485 original size:20 final size:21
Alignment explanation
Indices: 966460--966498 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
966450 CACGACAAAT
*
966460 AAAAATTGATT-TTCAAATCC
1 AAAAATTAATTCTTCAAATCC
966480 AAAAATTAATTCTTCAAAT
1 AAAAATTAATTCTTCAAAT
966499 AAAATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.36
Consensus pattern (21 bp):
AAAAATTAATTCTTCAAATCC
Found at i:966509 original size:21 final size:18
Alignment explanation
Indices: 966455--966502 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
966445 TATTACACGA
*
966455 CAAATAAAAATTGATTTT
1 CAAATAAAAATTAATTTT
966473 CAAATCCAAAAATTAATTCTT
1 CAAAT--AAAAATTAATT-TT
966494 CAAATAAAA
1 CAAATAAAA
966503 TAATTAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.19
19 4 0.15
20 10 0.38
21 7 0.27
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.31
Consensus pattern (18 bp):
CAAATAAAAATTAATTTT
Found at i:970135 original size:20 final size:20
Alignment explanation
Indices: 970107--970145 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
970097 AGGTAACGGG
* *
970107 ACAATAATGGCTTCCATGGT
1 ACAACAATGGCTGCCATGGT
970127 ACAACAATGGCTGCCATGG
1 ACAACAATGGCTGCCATGG
970146 CAAAGAGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (20 bp):
ACAACAATGGCTGCCATGGT
Found at i:974382 original size:22 final size:23
Alignment explanation
Indices: 974357--974417 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
974347 GTATATCTTA
974357 TTTAAGGTTTAGGATTATAC-AT
1 TTTAAGGTTTAGGATTATACAAT
*
974379 TTTAGGGTTTA-GATT-TACAAT
1 TTTAAGGTTTAGGATTATACAAT
*
974400 TTGAA-GTTTAGGGATTAT
1 TTTAAGGTTTA-GGATTAT
974418 TTAAATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 8 0.25
21 9 0.28
22 14 0.44
23 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (23 bp):
TTTAAGGTTTAGGATTATACAAT
Found at i:985131 original size:3 final size:3
Alignment explanation
Indices: 985123--985151 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
985113 TTGTTCTTCC
985123 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
985152 CCTCTTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:985461 original size:19 final size:19
Alignment explanation
Indices: 985437--985482 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
985427 GGTTAGGGCT
985437 GGTTTTGGCCCAAGTGTTA
1 GGTTTTGGCCCAAGTGTTA
985456 GGTTTTGGCCCAAGTGTTA
1 GGTTTTGGCCCAAGTGTTA
985475 GGTTTTGG
1 GGTTTTGG
985483 GATGAGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.13, C:0.13, G:0.35, T:0.39
Consensus pattern (19 bp):
GGTTTTGGCCCAAGTGTTA
Found at i:992099 original size:25 final size:25
Alignment explanation
Indices: 992045--992099 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
992035 AGTCACATTT
992045 CATATAACACTTATATTACATATTC
1 CATATAACACTTATATTACATATTC
*
992070 C-TATAATTACTTATATTA-ATA-TC
1 CATATAA-CACTTATATTACATATTC
992093 ACATATA
1 -CATATA
992100 TCACACGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.08
24 9 0.35
25 15 0.58
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (25 bp):
CATATAACACTTATATTACATATTC
Found at i:996788 original size:2 final size:2
Alignment explanation
Indices: 996781--996808 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
996771 ATGTACATGC
996781 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
996809 TAAGGTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:997216 original size:19 final size:19
Alignment explanation
Indices: 997187--997238 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
997177 ATGTGAAGTT
997187 AAAGTTCATATATGCATATC
1 AAAG-TCATATATGCATATC
997207 AAAGTCATATATGCATATC
1 AAAGTCATATATGCATATC
997226 AAAGTCATATATG
1 AAAGTCATATATG
997239 TTATAGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 28 0.88
20 4 0.12
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (19 bp):
AAAGTCATATATGCATATC
Found at i:1003290 original size:19 final size:19
Alignment explanation
Indices: 1003254--1003291 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1003244 TAATAAAAAA
*
1003254 TTAAATTTTTTTATATAAT
1 TTAAATTTTTTTAGATAAT
1003273 TTAAATTTTTATT-GATAAT
1 TTAAATTTTT-TTAGATAAT
1003292 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTAAATTTTTTTAGATAAT
Found at i:1004463 original size:11 final size:11
Alignment explanation
Indices: 1004439--1004472 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1004429 AGAATTTTGA
*
1004439 AAAAAAAAAAT
1 AAAAATAAAAT
*
1004450 AAAAATAAAGT
1 AAAAATAAAAT
1004461 AAAAATAAAAT
1 AAAAATAAAAT
1004472 A
1 A
1004473 TGAAAGATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1025708 original size:2 final size:2
Alignment explanation
Indices: 1025701--1025742 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1025691 TGTAATTACA
*
1025701 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1025743 TAAGCCCCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1026051 original size:16 final size:16
Alignment explanation
Indices: 1026026--1026060 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1026016 GTGATCACTC
* *
1026026 TAAAATTTTATCTTAT
1 TAAAAATTTATATTAT
1026042 TAAAAATTTATATTAT
1 TAAAAATTTATATTAT
1026058 TAA
1 TAA
1026061 TATATGCGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAAAATTTATATTAT
Found at i:1029642 original size:4 final size:4
Alignment explanation
Indices: 1029635--1029675 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
1029625 GAATATATAT
1029635 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1029676 AGGATTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1030745 original size:16 final size:16
Alignment explanation
Indices: 1030720--1030767 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1030710 ACGATTAAAT
1030720 AAAT-AATAAAAACAA
1 AAATAAATAAAAACAA
1030735 AAATAAATAAAAA-ATA
1 AAATAAATAAAAACA-A
1030751 AAA-AGAAT-AAAACAA
1 AAATA-AATAAAAACAA
1030766 AA
1 AA
1030768 TAATATGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.12
Consensus pattern (16 bp):
AAATAAATAAAAACAA
Found at i:1030880 original size:32 final size:34
Alignment explanation
Indices: 1030789--1031042 Score: 146
Period size: 35 Copynumber: 7.1 Consensus size: 34
1030779 GATATATATA
1030789 AAAAATCGTTTTAAAACTATATATA-ATATATATTTC
1 AAAAAT-GTTTTAAAACTATATATATATA-AT-TTTC
* * *
1030825 AAAGATATTTCCAAAA-TCATATATTATATAATTTT-
1 AAAAATGTTT-TAAAACT-ATATA-TATATAATTTTC
* * *
1030860 AAAAATGTTTTCAAACTATATGT-TATAGTTTTC
1 AAAAATGTTTTAAAACTATATATATATAATTTTC
* *
1030893 AAAAACGTTTTAAAACTATAT-TATAT-GTTTTC
1 AAAAATGTTTTAAAACTATATATATATAATTTTC
* *
1030925 AAAAATGTTTTTTTTAAATTATATATTATATAAATTTT-
1 AAAAATG---TTTTAAAACTATATA-TATAT-AATTTTC
* *
1030963 -AAAATGATTTTAAAAATATATATTATATAGTTTTC
1 AAAAATG-TTTTAAAACTATATA-TATATAATTTTC
* * *
1030998 AAAGGTATTTTTTAAAACATATATTATATATGTATTTTTC
1 AAA--AATGTTTTAAAAC-TATA-TATATA--TAATTTTC
1031038 AAAAA
1 AAAAA
1031043 CCATTTTGCT
Statistics
Matches: 172, Mismatches: 24, Indels: 42
0.72 0.10 0.18
Matches are distributed among these distances:
32 21 0.12
33 23 0.13
34 12 0.07
35 44 0.26
36 19 0.11
37 23 0.13
38 14 0.08
39 6 0.03
40 10 0.06
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (34 bp):
AAAAATGTTTTAAAACTATATATATATAATTTTC
Found at i:1030912 original size:103 final size:105
Alignment explanation
Indices: 1030789--1031028 Score: 251
Period size: 103 Copynumber: 2.3 Consensus size: 105
1030779 GATATATATA
*
1030789 AAAAATCGTTTTAAAACTATATATAATATATATTTCAAAGA-TATTTCCAAAATCATATATTATA
1 AAAAATCGTTTTAAAACTATAT-T-ATATAT-TTTCAAAAAGTATTTCCAAAATCATATATTATA
* *
1030853 T-AATTTTAAAAATG-TTTTCAAACTATAT-GT-TATAGTTTTC
63 TAAATTTT-AAAATGATTTTAAAAATATATAGTATATAGTTTTC
* * *** *
1030893 AAAAA-CGTTTTAAAACTATATTATATGTTTTCAAAAATGTTTTTTTTAAATTATATATTATATA
1 AAAAATCGTTTTAAAACTATATTATATATTTTCAAAAA-GTATTTCCAAAATCATATATTATATA
*
1030957 AATTTTAAAATGATTTTAAAAATATATATTATATAGTTTTC
65 AATTTTAAAATGATTTTAAAAATATATAGTATATAGTTTTC
* *
1030998 AAAGGTAT-TTTTTAAAACATATATTATATAT
1 AAA--AATCGTTTTAAAAC-TATATTATATAT
1031029 GTATTTTTCA
Statistics
Matches: 113, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
100 8 0.07
101 5 0.04
102 26 0.23
103 34 0.30
104 6 0.05
105 13 0.12
107 10 0.09
108 11 0.10
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (105 bp):
AAAAATCGTTTTAAAACTATATTATATATTTTCAAAAAGTATTTCCAAAATCATATATTATATAA
ATTTTAAAATGATTTTAAAAATATATAGTATATAGTTTTC
Found at i:1030953 original size:37 final size:36
Alignment explanation
Indices: 1030837--1031027 Score: 127
Period size: 32 Copynumber: 5.5 Consensus size: 36
1030827 AGATATTTCC
* * *
1030837 AAAATCATATATTATATAATTTTAAAAATG--TTTTC
1 AAAAT-ATATATTATATAGTTTTCAAAATGTTTTTTT
* * *
1030872 AAACTATAT-GT-TATAGTTTTCAAAAACG---TTTT
1 AAAATATATATTATATAGTTTTC-AAAATGTTTTTTT
*
1030904 AAAA-CTATATTATAT-GTTTTCAAAAATGTTTTTTTT
1 AAAATATATATTATATAGTTTTC-AAAATG-TTTTTTT
* * * *
1030940 AAATTATATATTATATAAATTTT-AAAATG-ATTTTA
1 AAAATATATATTATAT-AGTTTTCAAAATGTTTTTTT
*
1030975 AAAATATATATTATATAGTTTTC-AAAGGTATTTTTT
1 AAAATATATATTATATAGTTTTCAAAATGT-TTTTTT
*
1031011 AAAACATATATTATATA
1 AAAATATATATTATATA
1031028 TGTATTTTTC
Statistics
Matches: 122, Mismatches: 21, Indels: 25
0.73 0.12 0.15
Matches are distributed among these distances:
31 3 0.02
32 27 0.22
33 9 0.07
34 13 0.11
35 23 0.19
36 27 0.22
37 16 0.13
39 4 0.03
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (36 bp):
AAAATATATATTATATAGTTTTCAAAATGTTTTTTT
Found at i:1031585 original size:33 final size:33
Alignment explanation
Indices: 1031469--1031585 Score: 191
Period size: 33 Copynumber: 3.6 Consensus size: 33
1031459 CTCGAAGGTC
*
1031469 TTTGTGTTTCAAGAGAAACATTTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
** *
1031502 TTT-TGTTTCAAGAGAAATGAGTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
1031534 TTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
1031567 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
1031586 TATCTCCAGG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
32 28 0.37
33 48 0.63
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (33 bp):
TTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
Found at i:1031866 original size:21 final size:21
Alignment explanation
Indices: 1031842--1031906 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
1031832 GGAAACTGTC
1031842 TCAAGGGAGACGAAATTTGTT
1 TCAAGGGAGACGAAATTTGTT
* *
1031863 TCAA--G-G--GAAA-CTGTC
1 TCAAGGGAGACGAAATTTGTT
1031878 TCAAGGGAGACGAAATTTGTT
1 TCAAGGGAGACGAAATTTGTT
1031899 TCAAGGGA
1 TCAAGGGA
1031907 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 1 0.03
18 2 0.06
19 1 0.03
20 4 0.12
21 15 0.44
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (21 bp):
TCAAGGGAGACGAAATTTGTT
Found at i:1032124 original size:36 final size:36
Alignment explanation
Indices: 1031571--1032116 Score: 819
Period size: 36 Copynumber: 15.1 Consensus size: 36
1031561 AGGTTTTTTG
* * * * *
1031571 TGTTTCAAGAGAAACTATCTCCAGGGAGGCAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
1031607 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1031643 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1031679 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * *
1031715 TACTTT-AAGGGAAAGTGTCTCAAGGGAGACGAAATT
1 T-GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
1031751 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1031787 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
1031823 TGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
1031859 TGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1031895 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATT
* * *
1031932 TGTTTCAAAGGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
1031968 TGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
1032004 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAAATA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATT
1032041 TGTTTCAAGGGAAA--GTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
1032075 TGTTTCAAGGTAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
1032112 TGTTT
1 TGTTT
1032117 TGAGTAAATT
Statistics
Matches: 468, Mismatches: 35, Indels: 13
0.91 0.07 0.03
Matches are distributed among these distances:
34 18 0.04
35 17 0.04
36 370 0.79
37 63 0.13
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1032306 original size:34 final size:31
Alignment explanation
Indices: 1032227--1032312 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 31
1032217 GGGTAAGATT
*
1032227 CCCTTCGTCGTGAAGTTGAAACCGTGGATGGC
1 CCCTTCGTCGTGAAGTTG-AACCGTGGATGGA
*
1032259 CCCTTCGTTGTGAAGTTGAACC-TGGAATTGGATA
1 CCCTTCGTCGTGAAGTTGAACCGTGG-A-TGG--A
*
1032293 TCCTTCGTCGTGAAGTTGAA
1 CCCTTCGTCGTGAAGTTGAA
1032313 ATCCAGTATG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 3 0.07
31 5 0.11
32 20 0.43
34 18 0.39
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (31 bp):
CCCTTCGTCGTGAAGTTGAACCGTGGATGGA
Found at i:1032767 original size:106 final size:106
Alignment explanation
Indices: 1032582--1033471 Score: 1411
Period size: 106 Copynumber: 8.4 Consensus size: 106
1032572 GTATTGTTCC
* * * * * * *
1032582 GAGTCCAATATCCTCCATCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
1032647 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
*
1032688 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1032753 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * * * *
1032794 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
1032859 CCAGTGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
1032900 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
1032965 CCAGCTGTCCCTTCGTCGTGAATTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * * * *
1033006 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * *
1033071 CCAGTGGTCCCTTCGTCGTAAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
**
1033112 GAGTCCAATATATTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1033177 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
** * *
1033218 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
1033283 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
1033324 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
1033389 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* *
1033430 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
1033472 TAAAATTAGA
Statistics
Matches: 714, Mismatches: 70, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 714 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
Found at i:1033471 original size:212 final size:212
Alignment explanation
Indices: 1032582--1033471 Score: 1568
Period size: 212 Copynumber: 4.2 Consensus size: 212
1032572 GTATTGTTCC
* * *
1032582 GAGTCCAATATCC-TC-CATCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAC
** *
1032645 AACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
64 AACCAGTGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
*
1032710 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTAACAACCAGCGGTCCCTTCGTCGTGAA
129 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
1032775 GTTGAACATGCGTTGTCTG
194 GTTGAACATGCGTTGTCTG
*
1032794 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1032859 CCAGTGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGTGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* *
1032924 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCTGTCCCTTCGTCGTGAATT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1032989 TGAACATGCGTTGTCTG
196 TGAACATGCGTTGTCTG
*
1033006 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* **
1033071 CCAGTGGTCCCTTCGTCGTAAAGTTGAACTTGTGTTGTCTGGAGTCCAATATATTTCGTTGTGAA
66 CCAGTGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
1033136 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1033201 TGAACATGCGTTGTCTG
196 TGAACATGCGTTGTCTG
* *
1033218 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
1033283 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAA
66 CCAGTGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
1033348 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
1033413 TGAACATGCGTTATCTG
196 TGAACATGCGTTGTCTG
*
1033430 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
1033472 TAAAATTAGA
Statistics
Matches: 650, Mismatches: 26, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
212 646 0.99
213 3 0.00
214 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (212 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGTGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACATGCGTTGTCTG
Found at i:1033673 original size:16 final size:16
Alignment explanation
Indices: 1033648--1033678 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1033638 CATGGTTGAG
1033648 TTTGTGTTGAACTGGA
1 TTTGTGTTGAACTGGA
*
1033664 TTTGTTTTGAACTGG
1 TTTGTGTTGAACTGG
1033679 TTCTCGAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.29, T:0.48
Consensus pattern (16 bp):
TTTGTGTTGAACTGGA
Found at i:1037510 original size:4 final size:4
Alignment explanation
Indices: 1037496--1037529 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1037486 AAGAAACCAG
*
1037496 AATA TATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
1037530 AGGATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1038582 original size:7 final size:6
Alignment explanation
Indices: 1038569--1038613 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
1038559 AAAAACGATT
* *
1038569 AAATAA ATAATAA AAACAA AAATAA AAATAA ATA-AA AAATAA AAA
1 AAATAA A-AATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAA
1038614 GAATAAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 4 0.12
6 23 0.70
7 6 0.18
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:1038585 original size:21 final size:18
Alignment explanation
Indices: 1038569--1038613 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
1038559 AAAAACGATT
1038569 AAATAAATAATAAAAACAA
1 AAATAAA-AATAAAAACAA
*
1038588 AAATAAAAATAAATA-AA
1 AAATAAAAATAAAAACAA
1038605 AAATAAAAA
1 AAATAAAAA
1038614 GAATAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.44
18 7 0.28
19 7 0.28
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (18 bp):
AAATAAAAATAAAAACAA
Found at i:1038601 original size:25 final size:27
Alignment explanation
Indices: 1038569--1038631 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 27
1038559 AAAAACGATT
*
1038569 AAATAAATAATAAAA-ACAAA-AATAA
1 AAATAAATAATAAAATAAAAAGAATAA
1038594 AAATAAATAA-AAAATAAAAAGAATAA
1 AAATAAATAATAAAATAAAAAGAATAA
1038620 AACA-AAATAATA
1 AA-ATAAATAATA
1038632 TGATATGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.12
25 14 0.42
26 13 0.39
27 2 0.06
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (27 bp):
AAATAAATAATAAAATAAAAAGAATAA
Found at i:1038739 original size:32 final size:33
Alignment explanation
Indices: 1038648--1038887 Score: 141
Period size: 36 Copynumber: 6.8 Consensus size: 33
1038638 GATATATATA
1038648 AAAAATCGTTTTAAAACTATATATAATATA-TATTTC
1 AAAAAT-GTTTTAAAACTATAT-T-ATATAGT-TTTC
* * * * *
1038684 AAAGATATTTCCAAAATTATATATTATATAATTTT-
1 AAAAATGTTT-TAAAA--CTATATTATATAGTTTTC
*
1038719 AAAAATGTTTTCAAACTATATGT-TATAGTTTTC
1 AAAAATGTTTTAAAACTATAT-TATATAGTTTTC
*
1038752 AAAAACGTTTTAAAACTATATTATAT-GTTTTC
1 AAAAATGTTTTAAAACTATATTATATAGTTTTC
* *
1038784 AAAAATGTTTTTTTTAAAATTATATATTATATAAATTTT-
1 AAAAATG----TTTTAAAA--CTATATTATAT-AGTTTTC
*
1038823 -AAAATGATTTTAAAAATATATATTATATAGTTTTC
1 AAAAATG-TTTT-AAAA-CTATATTATATAGTTTTC
* *
1038858 AAAGGTATTTTTTAAAACATATATTATATA
1 AAA--AATGTTTTAAAAC-TATATTATATA
1038888 TGTATTTTTC
Statistics
Matches: 163, Mismatches: 20, Indels: 42
0.72 0.09 0.19
Matches are distributed among these distances:
32 26 0.16
33 23 0.14
34 8 0.05
35 27 0.17
36 46 0.28
37 6 0.04
38 23 0.14
40 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (33 bp):
AAAAATGTTTTAAAACTATATTATATAGTTTTC
Found at i:1038762 original size:33 final size:31
Alignment explanation
Indices: 1038710--1038794 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 31
1038700 TTATATATTA
* *
1038710 TATAATTTT-AAAAATGTTTTCAAACTATATGT
1 TATAGTTTTCAAAAATGTTTTAAAACTATA--T
*
1038742 TATAGTTTTCAAAAACGTTTTAAAACTATAT
1 TATAGTTTTCAAAAATGTTTTAAAACTATAT
1038773 TATATGTTTTCAAAAATGTTTT
1 TATA-GTTTTCAAAAATGTTTT
1038795 TTTTAAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
31 5 0.11
32 24 0.51
33 18 0.38
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (31 bp):
TATAGTTTTCAAAAATGTTTTAAAACTATAT
Found at i:1038762 original size:103 final size:106
Alignment explanation
Indices: 1038648--1038888 Score: 264
Period size: 103 Copynumber: 2.3 Consensus size: 106
1038638 GATATATATA
1038648 AAAAATCGTTTTAAAACTATATATAATATATATTTC-AAA-GATATTTCCAAAATTATATATTAT
1 AAAAATCGTTTTAAAACTATAT-T-ATATAT-TTTCAAAATGATATTTCCAAAATTATATATTAT
* *
1038711 AT-AATTTTAAAAATG-TTTTCAAACTATAT-GT-TATAGTTTTC
63 ATAAATTTT-AAAATGATTTTAAAAATATATAGTATATAGTTTTC
* * * **
1038752 AAAAA-CGTTTTAAAACTATATTATATGTTTTCAAAAATGTTTTTTTTAAAATTATATATTATAT
1 AAAAATCGTTTTAAAACTATATTATATATTTTC-AAAATGATATTTCCAAAATTATATATTATAT
*
1038816 AAATTTTAAAATGATTTTAAAAATATATATTATATAGTTTTC
65 AAATTTTAAAATGATTTTAAAAATATATAGTATATAGTTTTC
* *
1038858 AAAGGTAT-TTTTTAAAACATATATTATATAT
1 AAA--AATCGTTTTAAAAC-TATATTATATAT
1038889 GTATTTTTCA
Statistics
Matches: 115, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
100 4 0.03
101 5 0.04
102 4 0.03
103 44 0.38
104 23 0.20
105 1 0.01
106 13 0.11
108 10 0.09
109 11 0.10
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (106 bp):
AAAAATCGTTTTAAAACTATATTATATATTTTCAAAATGATATTTCCAAAATTATATATTATATA
AATTTTAAAATGATTTTAAAAATATATAGTATATAGTTTTC
Found at i:1038843 original size:35 final size:37
Alignment explanation
Indices: 1038794--1038887 Score: 113
Period size: 35 Copynumber: 2.6 Consensus size: 37
1038784 AAAAATGTTT
* *
1038794 TTTTTAAAATTATATATTATATAAATTTTAAAATG-A
1 TTTTTAAAAATATATATTATATAAATTTTAAAAGGTA
* *
1038830 -TTTTAAAAATATATATTATAT-AGTTTTCAAAGGTA
1 TTTTTAAAAATATATATTATATAAATTTTAAAAGGTA
* *
1038865 TTTTTTAAAACATATATTATATA
1 TTTTTAAAAATATATATTATATA
1038888 TGTATTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 9 0.18
35 21 0.43
36 19 0.39
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTTTAAAAATATATATTATATAAATTTTAAAAGGTA
Found at i:1038927 original size:2 final size:2
Alignment explanation
Indices: 1038916--1038962 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1038906 TTTTGCGAAC
* *
1038916 TA TA TA -A TA TA TA TG TA TA GA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1038957 TG TA TA
1 TA TA TA
1038963 AAGTAAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1041338 original size:11 final size:11
Alignment explanation
Indices: 1041322--1041348 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1041312 GAAAGAATAG
1041322 GAAAATAACAA
1 GAAAATAACAA
1041333 GAAAATAACAA
1 GAAAATAACAA
1041344 GAAAA
1 GAAAA
1041349 AGTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.07
Consensus pattern (11 bp):
GAAAATAACAA
Found at i:1055168 original size:3 final size:3
Alignment explanation
Indices: 1055160--1055200 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1055150 TAATTTCTAA
1055160 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1055201 AGTGACCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1055702 original size:24 final size:24
Alignment explanation
Indices: 1055668--1055724 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
1055658 TAGAACATTT
*
1055668 CATATAACAAAATACATACATGCA
1 CATATACCAAAATACATACATGCA
*
1055692 CATATACCAAAATGCATACATGCA
1 CATATACCAAAATACATACATGCA
1055716 CATATACCA
1 CATATACCA
1055725 TCATTATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.25, G:0.05, T:0.21
Consensus pattern (24 bp):
CATATACCAAAATACATACATGCA
Found at i:1058087 original size:4 final size:4
Alignment explanation
Indices: 1058078--1058119 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
1058068 ACAATTTTAA
1058078 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1058120 AAAGTTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1059151 original size:12 final size:12
Alignment explanation
Indices: 1059134--1059159 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1059124 ATCCACAGAC
1059134 ATTTTTTTAATA
1 ATTTTTTTAATA
1059146 ATTTTTTTAATA
1 ATTTTTTTAATA
1059158 AT
1 AT
1059160 GATTACGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTTTTAATA
Found at i:1059957 original size:14 final size:15
Alignment explanation
Indices: 1059927--1059965 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1059917 TATTTATTTG
1059927 AACCTTAAAATCTTA
1 AACCTTAAAATCTTA
* *
1059942 AAGCTTAAATTC-TA
1 AACCTTAAAATCTTA
1059956 AACCTTAAAA
1 AACCTTAAAA
1059966 AAGCCTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.31
Consensus pattern (15 bp):
AACCTTAAAATCTTA
Found at i:1061014 original size:29 final size:29
Alignment explanation
Indices: 1060957--1061014 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
1060947 TATATTACTT
*
1060957 TTTATTAAATTTTATTTTCTCTTATTTTA
1 TTTATTAAATTTTATTTTCTCTTAATTTA
*
1060986 TTTATTATACTTTTAATTTT-T-TTAATTTA
1 TTTATTA-AATTTT-ATTTTCTCTTAATTTA
1061015 CTCATTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 14 0.56
30 6 0.24
31 5 0.20
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTATTAAATTTTATTTTCTCTTAATTTA
Found at i:1062023 original size:30 final size:31
Alignment explanation
Indices: 1061962--1062026 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1061952 AAATGATACG
*
1061962 CTCTCAACCCGTAAACATTCACACAACAATC
1 CTCTCAACCCGTAAACATTAACACAACAATC
* * *
1061993 CTCTCAACCTGTAAACA-TAACCCGACAATC
1 CTCTCAACCCGTAAACATTAACACAACAATC
1062023 CTCT
1 CTCT
1062027 TATCTTTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.35, C:0.38, G:0.05, T:0.22
Consensus pattern (31 bp):
CTCTCAACCCGTAAACATTAACACAACAATC
Found at i:1062092 original size:16 final size:16
Alignment explanation
Indices: 1062068--1062108 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1062058 CGTCGTAAGG
*
1062068 TAATTTTTTTAATATA
1 TAATATTTTTAATATA
*
1062084 TAATATTTTTTATATA
1 TAATATTTTTAATATA
1062100 TGAATATTT
1 T-AATATTT
1062109 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TAATATTTTTAATATA
Found at i:1062094 original size:17 final size:16
Alignment explanation
Indices: 1062068--1062108 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
1062058 CGTCGTAAGG
1062068 TAAT-TTTTTTAATATA
1 TAATATTTTTT-ATATA
1062084 TAATATTTTTTATATA
1 TAATATTTTTTATATA
1062100 TGAATATTT
1 T-AATATTT
1062109 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TAATATTTTTTATATA
Found at i:1068035 original size:27 final size:27
Alignment explanation
Indices: 1068002--1068084 Score: 139
Period size: 27 Copynumber: 3.1 Consensus size: 27
1067992 CTGTTATCAC
1068002 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCATAGCAT
*
1068029 CACTTTGAACTTAAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCATAGCAT
* *
1068056 CACTTTGAACTTGAAAGTCCACAGCAT
1 CACTTTGAACTTGAAACTCCATAGCAT
1068083 CA
1 CA
1068085 AGTTCTTCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.28
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCATAGCAT
Found at i:1071368 original size:95 final size:95
Alignment explanation
Indices: 1071213--1071395 Score: 269
Period size: 95 Copynumber: 1.9 Consensus size: 95
1071203 TTAGTATCGA
* * ** *
1071213 TACTAAGAGAAAGTTATCGATACCTTGGAATCCAGAATGTAGAAATGGTATGGATACTGAAAGGG
1 TACTAAGAGAAAGGTATCGATACCATGGAATCCAGAATACAGAAATGGTATCGATACTGAAAGGG
1071278 AGTATC-AGTACCATAGTATAGAAGTATAGG
66 AGTATCGA-TACCATAGTATAGAAGTATAGG
* * * *
1071308 TACTAGGAGAAAGGTATCGATACCATGGATTCTAGAATACCGAAATGGTATCGATACTGAAAGGG
1 TACTAAGAGAAAGGTATCGATACCATGGAATCCAGAATACAGAAATGGTATCGATACTGAAAGGG
1071373 AGTATCGATACCATAGTATAGAA
66 AGTATCGATACCATAGTATAGAA
1071396 ATATCGATAC
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 77 0.99
96 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.25
Consensus pattern (95 bp):
TACTAAGAGAAAGGTATCGATACCATGGAATCCAGAATACAGAAATGGTATCGATACTGAAAGGG
AGTATCGATACCATAGTATAGAAGTATAGG
Found at i:1072664 original size:18 final size:18
Alignment explanation
Indices: 1072641--1072675 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1072631 ACGTAGGATT
*
1072641 TGTCCCGAATGACCACTA
1 TGTCCCAAATGACCACTA
1072659 TGTCCCAAATGACCACT
1 TGTCCCAAATGACCACT
1072676 CCTTAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.23
Consensus pattern (18 bp):
TGTCCCAAATGACCACTA
Found at i:1073709 original size:20 final size:20
Alignment explanation
Indices: 1073684--1073760 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
1073674 ATCAGATTGT
1073684 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
1073704 CCAGGGGGTATC-GATT---C
1 CCAGGGGGTA-CAGATTCCCC
* *
1073721 CC--TGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
1073739 CTCAGGGGGTACAGATTCCCC
1 C-CAGGGGGTACAGATTCCCC
1073760 C
1 C
1073761 TGCATGGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
14 1 0.02
15 8 0.18
17 3 0.07
18 2 0.04
19 1 0.02
20 14 0.31
21 16 0.36
ACGTcount: A:0.19, C:0.34, G:0.29, T:0.18
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:1073899 original size:21 final size:21
Alignment explanation
Indices: 1073873--1073913 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1073863 ATTTGAATAT
* *
1073873 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGATACCGATTCCC
1073894 TATGAAGGGATACCGATTCC
1 TATGAAGGGATACCGATTCC
1073914 TCCCATTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGATACCGATTCCC
Found at i:1073976 original size:21 final size:21
Alignment explanation
Indices: 1073943--1073982 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1073933 TTTTTGCAGA
*
1073943 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1073965 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1073983 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1075282 original size:3 final size:3
Alignment explanation
Indices: 1075255--1075313 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
1075245 TGAAGAAAGG
* * *
1075255 GAA G-A GAA GAA AAA CAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1075302 GAA GAA GAA GAA
1 GAA GAA GAA GAA
1075314 TGAGGACGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1077084 original size:20 final size:21
Alignment explanation
Indices: 1077044--1077122 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
1077034 ATCAGATTGT
1077044 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
1077065 CCAGGGGGTATC-GATT---CC
1 CCAGGGGGTA-CAGATTCCCCC
*
1077083 CC---GGGAACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
1077101 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
1077122 C
1 C
1077123 TGCATGGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
14 1 0.02
15 8 0.17
18 8 0.17
21 30 0.62
22 1 0.02
ACGTcount: A:0.19, C:0.38, G:0.28, T:0.15
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:1077260 original size:21 final size:21
Alignment explanation
Indices: 1077234--1077274 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1077224 ATTTGAATAT
*
1077234 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1077255 TATGAAGGGGTACCGATTCC
1 TATGAAGGGGTACCGATTCC
1077275 TCCCATTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1079067 original size:81 final size:81
Alignment explanation
Indices: 1078932--1079359 Score: 633
Period size: 81 Copynumber: 5.3 Consensus size: 81
1078922 GGATGTTACA
* * **
1078932 AAATGCCTTTGAGGAAAAGATTAATTGTCTAGCTATGCATTTGATAGAAAGGTGCCAATATTGCA
1 AAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCA
1078997 AGTTAGATGAAAGGCT
66 AGTTAGATGAAAGGCT
* ** *
1079013 AAATGCCTTTGAGTAAAAAATTAATTATCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTACA
1 AAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCA
*
1079078 AGTTAGATGAAAGGTT
66 AGTTAGATGAAAGGCT
* * * **
1079094 AAATGCCTTTGAGTAAAAAATTAATTGCCTAGTTATGCATTTGGCAG-AATGTGTTAATATTGCA
1 AAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCA
*
1079158 AGTTAGATGAAAGACT
66 AGTTAGATGAAAGGCT
* * * *
1079174 AAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCATAAAGGTACCGATATTGCA
1 AAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCA
1079239 AGTTAGATGAAAGGCT
66 AGTTAGATGAAAGGCT
* * * * *
1079255 AAATGCCTTTGAGTAAAAGATTAATTGACTAGCTGTGTATTTGACAGAAATGTGCCAATATTGCA
1 AAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCA
1079320 AGTTAGATGAAAGGCT
66 AGTTAGATGAAAGGCT
1079336 AAATGCCTTTGAGTAAAAGATTAA
1 AAATGCCTTTGAGTAAAAGATTAA
1079360 ATGCTTAACA
Statistics
Matches: 313, Mismatches: 33, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
80 70 0.22
81 243 0.78
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (81 bp):
AAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCA
AGTTAGATGAAAGGCT
Found at i:1079199 original size:161 final size:162
Alignment explanation
Indices: 1078932--1079359 Score: 651
Period size: 161 Copynumber: 2.6 Consensus size: 162
1078922 GGATGTTACA
* * * *
1078932 AAATGCCTTTGAGGAAAAGATTAATTGTCTAGCTATGCATTTGATAGAAAGGTGCCAATATTGCA
1 AAATGCCTTTGAGTAAAAGATTAATTGACTAGCTATGCATTTGACAGAAATGTGCCAATATTGCA
* *
1078997 AGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAAATTAATTATCTAGCTATGCATTTGGCAGAA
66 AGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTACCTAGCTATGCATTTGGCAGAA
* *
1079062 AGGTGCCAATATTACAAGTTAGATGAAAGGTT
131 AGGTACCAATATTACAAGTTAGATGAAAGGCT
* * * * **
1079094 AAATGCCTTTGAGTAAAAAATTAATTGCCTAGTTATGCATTTGGCAG-AATGTGTTAATATTGCA
1 AAATGCCTTTGAGTAAAAGATTAATTGACTAGCTATGCATTTGACAGAAATGTGCCAATATTGCA
* * * *
1079158 AGTTAGATGAAAGACTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCATAA
66 AGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTACCTAGCTATGCATTTGGCAGAA
* *
1079223 AGGTACCGATATTGCAAGTTAGATGAAAGGCT
131 AGGTACCAATATTACAAGTTAGATGAAAGGCT
* *
1079255 AAATGCCTTTGAGTAAAAGATTAATTGACTAGCTGTGTATTTGACAGAAATGTGCCAATATTGCA
1 AAATGCCTTTGAGTAAAAGATTAATTGACTAGCTATGCATTTGACAGAAATGTGCCAATATTGCA
1079320 AGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAA
66 AGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAA
1079360 ATGCTTAACA
Statistics
Matches: 237, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
161 142 0.60
162 95 0.40
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (162 bp):
AAATGCCTTTGAGTAAAAGATTAATTGACTAGCTATGCATTTGACAGAAATGTGCCAATATTGCA
AGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTACCTAGCTATGCATTTGGCAGAA
AGGTACCAATATTACAAGTTAGATGAAAGGCT
Found at i:1080377 original size:16 final size:16
Alignment explanation
Indices: 1080353--1080402 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1080343 AGACCCCTAT
*
1080353 TTTAGTTTATTTCTAA
1 TTTAATTTATTTCTAA
*
1080369 TTTAATTTAGTTCT--
1 TTTAATTTATTTCTAA
1080383 TTTAACTTTATTTACTAA
1 TTTAA-TTTATTT-CTAA
1080401 TT
1 TT
1080403 ATTTCACCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 14 0.52
18 2 0.07
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (16 bp):
TTTAATTTATTTCTAA
Found at i:1083493 original size:2 final size:2
Alignment explanation
Indices: 1083486--1083523 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1083476 TCATTTTATG
1083486 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1083524 AATGGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1085414 original size:16 final size:17
Alignment explanation
Indices: 1085393--1085437 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1085383 CCTATTTCAG
1085393 TTTATTTCTAATTTAA-
1 TTTATTTCTAATTTAAC
1085409 TTTATTTCT--TTTAAC
1 TTTATTTCTAATTTAAC
1085424 TTTATTTACTAATT
1 TTTATTT-CTAATT
1085438 ATTTCACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.20
15 7 0.28
16 11 0.44
18 2 0.08
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATTTCTAATTTAAC
Found at i:1088691 original size:21 final size:20
Alignment explanation
Indices: 1088667--1088710 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1088657 GATTTCTGGG
* *
1088667 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
1088688 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
1088708 CAA
1 CAA
1088711 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:1089622 original size:31 final size:31
Alignment explanation
Indices: 1089554--1089706 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
1089544 GGGTCGAGGG
1089554 TTACCTATGTTCTTCGGAACATATGGACTG-
1 TTACCTATGTTCTTCGGAACATATGGACTGT
1089584 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
1089615 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
1089646 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
1089677 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
1089707 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
30 30 0.26
31 84 0.73
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Done.