Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008063.1 Hibiscus syriacus cultivar Beakdansim tig00110560_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: 602526
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 2
Found at i:239 original size:25 final size:25
Alignment explanation
Indices: 205--254 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
195 TGGTGACATG
205 GTTAAAGGAAAAAACAACACACAAC
1 GTTAAAGGAAAAAACAACACACAAC
230 GTTAAAGGAAAAAACAACACACAAC
1 GTTAAAGGAAAAAACAACACACAAC
255 AATTTGAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.12, T:0.08
Consensus pattern (25 bp):
GTTAAAGGAAAAAACAACACACAAC
Found at i:10824 original size:20 final size:20
Alignment explanation
Indices: 10799--10837 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10789 TATTTTTAGC
10799 AAAAAA-AAATCTTTAGATAT
1 AAAAAATAAAT-TTTAGATAT
*
10819 AAAAAATCAATTTTAGATA
1 AAAAAATAAATTTTAGATA
10838 CAATTTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAAAATAAATTTTAGATAT
Found at i:18963 original size:20 final size:20
Alignment explanation
Indices: 18938--18975 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18928 TTTTGGTGCA
*
18938 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
18958 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
18976 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:25308 original size:14 final size:14
Alignment explanation
Indices: 25289--25324 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
25279 TAAATGATTC
25289 AATAAAATAAAAAA
1 AATAAAATAAAAAA
*
25303 AATAAAATAAAATA
1 AATAAAATAAAAAA
*
25317 AATTAAAT
1 AATAAAAT
25325 TATTCTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAATAAAAAA
Found at i:25326 original size:5 final size:5
Alignment explanation
Indices: 25289--25323 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
25279 TAAATGATTC
*
25289 AATAA AATAA AA-AA AATAA AATAA AATAA ATTAA A
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA A
25324 TTATTCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:27945 original size:2 final size:2
Alignment explanation
Indices: 27938--27977 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
27928 GCATTTTCCG
27938 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
27978 ACCCTATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:38050 original size:27 final size:26
Alignment explanation
Indices: 38020--38098 Score: 113
Period size: 27 Copynumber: 3.0 Consensus size: 26
38010 AAAAACACGG
38020 TTTTCTTTTTCTTTTCTTTTCTCTTC
1 TTTTCTTTTTCTTTTCTTTTCTCTTC
* *
38046 TTTTTTCTTTTCTTTTCTTTTCTTTTC
1 TTTTCT-TTTTCTTTTCTTTTCTCTTC
*
38073 TTTTCTTTTTTCTTTTCTTTTTTCTT
1 TTTTC-TTTTTCTTTTCTTTTCTCTT
38099 TTACTTGGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.11
27 40 0.87
28 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTCTTTTTCTTTTCTTTTCTCTTC
Found at i:38066 original size:32 final size:32
Alignment explanation
Indices: 38020--38093 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
38010 AAAAACACGG
38020 TTTTCTTTTTCTTTTCTTTTCTCTTCTTTTTTC
1 TTTTC-TTTTCTTTTCTTTTCTCTTCTTTTTTC
*
38053 TTTTCTTTTCTTTTCTTTTCTTTTCTTTTTTC
1 TTTTCTTTTCTTTTCTTTTCTCTTCTTTTTTC
38085 TTTTCTTTT
1 TTTTCTTTT
38094 TTCTTTTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 35 0.88
33 5 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (32 bp):
TTTTCTTTTCTTTTCTTTTCTCTTCTTTTTTC
Found at i:38100 original size:5 final size:5
Alignment explanation
Indices: 38020--38093 Score: 94
Period size: 5 Copynumber: 13.8 Consensus size: 5
38010 AAAAACACGG
*
38020 TTTTC TTTTTC TTTTC TTTTC TCTTCTT TTTTC TTTTC TTTTC TTTTC
1 TTTTC -TTTTC TTTTC TTTTC T-TT-TC TTTTC TTTTC TTTTC TTTTC
38068 TTTTC TTTTC TTTTTTC TTTTC TTTT
1 TTTTC TTTTC --TTTTC TTTTC TTTT
38094 TTCTTTTACT
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
5 46 0.74
6 9 0.15
7 7 0.11
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:42295 original size:2 final size:2
Alignment explanation
Indices: 42288--42334 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
42278 TTTCTCCTTT
42288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42330 TA TA T
1 TA TA T
42335 TTGTTCAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63035 original size:16 final size:18
Alignment explanation
Indices: 63003--63035 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
62993 ACTTTAGAAA
63003 CTAAAACTATAATTTACC
1 CTAAAACTATAATTTACC
63021 CTAAAA-TAT-ATTTAC
1 CTAAAACTATAATTTAC
63036 GCTTAAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (18 bp):
CTAAAACTATAATTTACC
Found at i:63260 original size:33 final size:33
Alignment explanation
Indices: 63204--63287 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
63194 GCCCCGATTA
63204 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATA-TTTATATTTTTTATATTAAT
63238 TATATATATAATATTTATATTTTTTATATTAAT
1 TATATATATAATATTTATATTTTTTATATTAAT
*
63271 TATATATTAAAATATTT
1 TATATA-TATAATATTT
63288 TCGGATTCGG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 26 0.54
34 22 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TATATATATAATATTTATATTTTTTATATTAAT
Found at i:63276 original size:11 final size:11
Alignment explanation
Indices: 63229--63280 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
63219 TTATATTTTT
63229 TATATTAATTA
1 TATATTAATTA
*
63240 TATATATAATATT
1 TATAT-TAAT-TA
*
63253 TATATT--TTT
1 TATATTAATTA
63262 TATATTAATTA
1 TATATTAATTA
63273 TATATTAA
1 TATATTAA
63281 AATATTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
9 8 0.23
10 1 0.03
11 15 0.43
12 5 0.14
13 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATATTAATTA
Found at i:64448 original size:67 final size:71
Alignment explanation
Indices: 64361--64526 Score: 232
Period size: 73 Copynumber: 2.4 Consensus size: 71
64351 AGACTAAGGG
* * *
64361 CTAACATACGTATTGCTCTAAAGACTGATATTAC-T-GAGAG-A-GTATAACCAAAAGCAGAGCA
1 CTAACATAAGTATTGCTCTAAAGACTGACATTACTTAGAGAGTATATATAACCAAAAGCAGAGCA
64422 TTGAGA
66 TTGAGA
* *
64428 CTAACATAAGTATTGATCTAAAGACTGACATTACTTATAGATAGTATATATAACCAAAAGCAGAG
1 CTAACATAAGTATTGCTCTAAAGACTGACATTAC-T-TAGAGAGTATATATAACCAAAAGCAGAG
64493 CATTGAGA
64 CATTGAGA
*
64501 CTAACATAAGTCTTGCTCTAAAGACT
1 CTAACATAAGTATTGCTCTAAAGACT
64527 CACGTCAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
67 31 0.36
70 1 0.01
71 4 0.05
72 1 0.01
73 49 0.57
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (71 bp):
CTAACATAAGTATTGCTCTAAAGACTGACATTACTTAGAGAGTATATATAACCAAAAGCAGAGCA
TTGAGA
Found at i:68442 original size:25 final size:25
Alignment explanation
Indices: 68394--68442 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
68384 AAATTTATAA
*
68394 AATTTTAGAGAAAATAAACTTAAAG
1 AATTTTAGAGAAAATAAACATAAAG
*
68419 AATTTTATAGAAACATAAA-ATAAA
1 AATTTTAGAGAAA-ATAAACATAAA
68443 TTACTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (25 bp):
AATTTTAGAGAAAATAAACATAAAG
Found at i:69490 original size:15 final size:14
Alignment explanation
Indices: 69465--69494 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
69455 ATGCGGACTT
69465 TTTAACCCGCACCG
1 TTTAACCCGCACCG
69479 TTTAAGCCCGCACCG
1 TTTAA-CCCGCACCG
69494 T
1 T
69495 CAAAACCCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.40, G:0.17, T:0.23
Consensus pattern (14 bp):
TTTAACCCGCACCG
Found at i:72216 original size:29 final size:31
Alignment explanation
Indices: 72149--72222 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 31
72139 TTGTTTCGTC
*
72149 ATTAATTATTATTTTTAATAACAGTTAATAAT
1 ATTAA-TATTATTTTTAATAACAATTAATAAT
72181 ATT--TATTCATTTTTAATAA-AATTAA-AA-
1 ATTAATATT-ATTTTTAATAACAATTAATAAT
72208 ATTAATATTTATTTT
1 ATTAATA-TTATTTT
72223 ATATTTTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 16 0.43
30 13 0.35
32 3 0.08
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (31 bp):
ATTAATATTATTTTTAATAACAATTAATAAT
Found at i:73080 original size:12 final size:12
Alignment explanation
Indices: 73062--73097 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
73052 CATATATGTT
73062 CATGTGATATGA
1 CATGTGATATGA
*
73074 TATGTGATATGA
1 CATGTGATATGA
73086 CATGTGATATGA
1 CATGTGATATGA
73098 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:73148 original size:29 final size:29
Alignment explanation
Indices: 73113--73176 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
73103 TGATATGAAG
73113 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
73142 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
73171 TGACAT
1 TGACAT
73177 AAGTACACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:73392 original size:15 final size:15
Alignment explanation
Indices: 73372--73413 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
73362 CTTAAGGAGA
73372 AGTCCTTCGGGACAT
1 AGTCCTTCGGGACAT
73387 AGTCCTTCGGGACAT
1 AGTCCTTCGGGACAT
73402 AGTCCTTCGGGA
1 AGTCCTTCGGGA
73414 TGTAGGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (15 bp):
AGTCCTTCGGGACAT
Found at i:91144 original size:35 final size:37
Alignment explanation
Indices: 91105--91174 Score: 92
Period size: 35 Copynumber: 1.9 Consensus size: 37
91095 ATTTAATGAG
91105 TTTAACGAG-CGACACGAGC-ACGAGTCGAA-CAAAAT
1 TTTAACGAGTCGA-ACGAGCAACGAGTCGAATCAAAAT
**
91140 TTTAACGAGTTTAACGAGCAACGAGTCGAATCAAA
1 TTTAACGAGTCGAACGAGCAACGAGTCGAATCAAA
91175 TTTATCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 15 0.50
36 11 0.37
37 4 0.13
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (37 bp):
TTTAACGAGTCGAACGAGCAACGAGTCGAATCAAAAT
Found at i:97402 original size:16 final size:18
Alignment explanation
Indices: 97370--97402 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
97360 TACTTAGAAA
97370 CTAAAACTATAATTTACC
1 CTAAAACTATAATTTACC
97388 CTAAAA-TAT-ATTTAC
1 CTAAAACTATAATTTAC
97403 GCTTAAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (18 bp):
CTAAAACTATAATTTACC
Found at i:97612 original size:33 final size:34
Alignment explanation
Indices: 97572--97656 Score: 145
Period size: 33 Copynumber: 2.5 Consensus size: 34
97562 CCCGATTATA
97572 TATATATAATAATATTTTATATTTTTTATATTAAT
1 TATATAT-ATAATATTTTATATTTTTTATATTAAT
97607 TATATATATAATA-TTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
97640 TATATATAAAATATTTT
1 TATATATATAATATTTT
97657 CGGATTCGGA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 32 0.67
34 9 0.19
35 7 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:98819 original size:67 final size:70
Alignment explanation
Indices: 98732--98895 Score: 244
Period size: 71 Copynumber: 2.4 Consensus size: 70
98722 AGACTAAGGG
* *
98732 CTAACATACGTATTGCTCTAAAGACTGATATTAC-T-GAGAGAG-TATAACCAAAAGCAGAGCAT
1 CTAACATAAGTATTGCTCTAAAGACTGACATTACTTAGAGAGAGATATAACCAAAAGCAGAGCAT
98794 TGAGA
66 TGAGA
* * *
98799 CTAACATAAGTATTGATCTAAAGACTGACATTACTTATAGATAGTATATAACCAAAAGCAGAGCA
1 CTAACATAAGTATTGCTCTAAAGACTGACATTACTTAGAGAGAG-ATATAACCAAAAGCAGAGCA
98864 TTGAGA
65 TTGAGA
*
98870 CTAACATAAGTCTTGCTCTAAAGACT
1 CTAACATAAGTATTGCTCTAAAGACT
98896 CACGTCAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
67 31 0.36
68 1 0.01
69 5 0.06
71 49 0.57
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (70 bp):
CTAACATAAGTATTGCTCTAAAGACTGACATTACTTAGAGAGAGATATAACCAAAAGCAGAGCAT
TGAGA
Found at i:102814 original size:25 final size:25
Alignment explanation
Indices: 102766--102814 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
102756 AAATTTATAA
*
102766 AATTTTAGAGAAAATAAACTTAAAG
1 AATTTTAGAGAAAATAAACATAAAG
*
102791 AATTTTATAGAAACATAAA-ATAAA
1 AATTTTAGAGAAA-ATAAACATAAA
102815 TTACTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (25 bp):
AATTTTAGAGAAAATAAACATAAAG
Found at i:103854 original size:15 final size:14
Alignment explanation
Indices: 103829--103858 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
103819 ATGCGGACTT
103829 TTTAACCCGCACCG
1 TTTAACCCGCACCG
103843 TTTAAGCCCGCACCG
1 TTTAA-CCCGCACCG
103858 T
1 T
103859 CAAAACCCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.40, G:0.17, T:0.23
Consensus pattern (14 bp):
TTTAACCCGCACCG
Found at i:106601 original size:29 final size:31
Alignment explanation
Indices: 106534--106607 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 31
106524 TTGTTTCGTC
*
106534 ATTAATTATTATTTTTAATAACAGTTAATAAT
1 ATTAA-TATTATTTTTAATAACAATTAATAAT
106566 ATT--TATTCATTTTTAATAA-AATTAA-AA-
1 ATTAATATT-ATTTTTAATAACAATTAATAAT
106593 ATTAATATTTATTTT
1 ATTAATA-TTATTTT
106608 ATATTTTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 16 0.43
30 13 0.35
32 3 0.08
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (31 bp):
ATTAATATTATTTTTAATAACAATTAATAAT
Found at i:107472 original size:12 final size:12
Alignment explanation
Indices: 107454--107489 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
107444 TATATATGTT
107454 CATGTGATATGA
1 CATGTGATATGA
*
107466 TATGTGATATGA
1 CATGTGATATGA
107478 CATGTGATATGA
1 CATGTGATATGA
107490 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:107540 original size:29 final size:29
Alignment explanation
Indices: 107505--107578 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
107495 TGATATGAAG
107505 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
107534 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
107563 TGACATAAG-TACATGA
1 TGACATGAGCTACATGA
107579 ACGTATGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:107784 original size:15 final size:15
Alignment explanation
Indices: 107764--107805 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
107754 CTTAAGGAGA
107764 AGTCCTTCGGGACAT
1 AGTCCTTCGGGACAT
107779 AGTCCTTCGGGACAT
1 AGTCCTTCGGGACAT
107794 AGTCCTTCGGGA
1 AGTCCTTCGGGA
107806 TGTAGGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (15 bp):
AGTCCTTCGGGACAT
Found at i:125784 original size:35 final size:37
Alignment explanation
Indices: 125745--125814 Score: 92
Period size: 35 Copynumber: 1.9 Consensus size: 37
125735 ATTTAATGAG
125745 TTTAACGAG-CGACACGAGC-ACGAGTCGAA-CAAAAT
1 TTTAACGAGTCGA-ACGAGCAACGAGTCGAATCAAAAT
**
125780 TTTAACGAGTTTAACGAGCAACGAGTCGAATCAAA
1 TTTAACGAGTCGAACGAGCAACGAGTCGAATCAAA
125815 TAATAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 15 0.50
36 11 0.37
37 4 0.13
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (37 bp):
TTTAACGAGTCGAACGAGCAACGAGTCGAATCAAAAT
Found at i:126154 original size:2 final size:2
Alignment explanation
Indices: 126125--126173 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
126115 AAGTTGTAAA
*
126125 AT AT AT AA AT AT A- AT -T AT A- AT A- 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
126163 AT AT AT AT AT A
1 AT AT AT AT AT A
126174 AATTCTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 37 0.90
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:126353 original size:12 final size:12
Alignment explanation
Indices: 126336--126361 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
126326 TTTAAATATC
126336 ATCAATTATTTG
1 ATCAATTATTTG
126348 ATCAATTATTTG
1 ATCAATTATTTG
126360 AT
1 AT
126362 AATGAACACT
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:0.08, G:0.08, T:0.50
Consensus pattern (12 bp):
ATCAATTATTTG
Found at i:127670 original size:21 final size:21
Alignment explanation
Indices: 127632--127671 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
127622 GTCGACCGTT
* * *
127632 ACGGTGCTGATATGACAGTTC
1 ACGGTGCTAACATAACAGTTC
127653 ACGGTGCTAACATAACAGT
1 ACGGTGCTAACATAACAGT
127672 ATATGGTAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (21 bp):
ACGGTGCTAACATAACAGTTC
Found at i:131239 original size:20 final size:20
Alignment explanation
Indices: 131214--131260 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
131204 CATCCCACAC
*
131214 GTATCTAGGCACATGTGCAT
1 GTATCTAGGCACATGCGCAT
131234 GTATCTAGGCACATGCGCAT
1 GTATCTAGGCACATGCGCAT
131254 GTATCTA
1 GTATCTA
131261 ATTGTGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (20 bp):
GTATCTAGGCACATGCGCAT
Found at i:137260 original size:60 final size:60
Alignment explanation
Indices: 137182--137319 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
137172 AAAGAAAGGG
* * *
137182 AAAAG-TACACAAATGGTCCCCCAATTATAGGATATTACTTTATTAAGTCCCTCAACTATT
1 AAAAGTTACA-AAATGGTCCCCCAACTATAGAATATTACTTTATTAAGTCCCGCAACTATT
* * ** * ** * *
137242 AAAAGTTACAGAATGGTCCTCTGACTATAGAATGTTGGTTTATTAAGTCTCGCGACTATT
1 AAAAGTTACAAAATGGTCCCCCAACTATAGAATATTACTTTATTAAGTCCCGCAACTATT
137302 AAAAGTTACAAAATGGTC
1 AAAAGTTACAAAATGGTC
137320 ACCTGACTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 60 0.94
61 4 0.06
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (60 bp):
AAAAGTTACAAAATGGTCCCCCAACTATAGAATATTACTTTATTAAGTCCCGCAACTATT
Found at i:138113 original size:2 final size:2
Alignment explanation
Indices: 138075--138101 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
138065 CTTTTAACCA
138075 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
138102 CAAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:138279 original size:23 final size:23
Alignment explanation
Indices: 138230--138291 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
138220 TGTTATTAAT
* * ** *
138230 TATGGTATATAATTTATATGTAT
1 TATGTTATATAATATATACATAC
138253 TATGTTATATAATATATACATAC
1 TATGTTATATAATATATACATAC
*
138276 TATGTTATATACTATA
1 TATGTTATATAATATA
138292 ATTATATAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (23 bp):
TATGTTATATAATATATACATAC
Found at i:140346 original size:29 final size:29
Alignment explanation
Indices: 140311--140368 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
140301 AACATTTTTG
*
140311 AAACTTGC-ATTTAGGTCCCCCAACATTTA
1 AAACTTGCAATATA-GTCCCCCAACATTTA
140340 AAACTTGCAATATAGTCCCCCAACATTTA
1 AAACTTGCAATATAGTCCCCCAACATTTA
140369 TTCCGTTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.29
Consensus pattern (29 bp):
AAACTTGCAATATAGTCCCCCAACATTTA
Found at i:140572 original size:35 final size:35
Alignment explanation
Indices: 140499--140584 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
140489 AAAACAGACA
* * *
140499 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * * *
140534 TCAATTTTATTCTAAATCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
140569 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
140585 ATACTTCAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:140578 original size:21 final size:21
Alignment explanation
Indices: 140553--140595 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
140543 TTCTAAATCC
140553 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
140574 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
140595 T
1 T
140596 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:140749 original size:16 final size:18
Alignment explanation
Indices: 140717--140750 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
140707 TATTAATGTA
140717 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
140735 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
140751 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:141417 original size:130 final size:130
Alignment explanation
Indices: 141214--141461 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
141204 AATTTTCTTC
* * *
141214 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
141279 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
141344 TAATTAGGTGGTAACACGTGTCACCAATGACACATGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
141409 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
141462 TATATAAATA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:145200 original size:23 final size:22
Alignment explanation
Indices: 145174--145219 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
145164 TCATTAAGTG
*
145174 ACTAAAATATTAAAATTTTAAAA
1 ACTAAAAGATT-AAATTTTAAAA
*
145197 ACTAAACGATTAAATTTTAAAA
1 ACTAAAAGATTAAATTTTAAAA
145219 A
1 A
145220 ATTAACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
ACTAAAAGATTAAATTTTAAAA
Found at i:146293 original size:21 final size:21
Alignment explanation
Indices: 146263--146317 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
146253 GATTTACATA
*
146263 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
146284 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
146305 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
146318 TTATTTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:146648 original size:6 final size:6
Alignment explanation
Indices: 146637--146661 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
146627 CCGTCTCGTC
146637 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
146662 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:147132 original size:28 final size:28
Alignment explanation
Indices: 147095--147152 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
147085 AAACTTATCT
*
147095 TTTTTAGTCAAAATAAGTACATAAAGTA
1 TTTTTAGTCAAAACAAGTACATAAAGTA
* * *
147123 TTTTTGGTCAAAACATGTACCTAAAGTA
1 TTTTTAGTCAAAACAAGTACATAAAGTA
147151 TT
1 TT
147153 CAAAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (28 bp):
TTTTTAGTCAAAACAAGTACATAAAGTA
Found at i:149650 original size:6 final size:6
Alignment explanation
Indices: 149641--149684 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
149631 TCATCGTCCT
149641 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
149685 CTCACACTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CCTCCA
Found at i:152773 original size:31 final size:32
Alignment explanation
Indices: 152737--152799 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
152727 TTAAAGAAAA
152737 TTTTCTATATTAGAGAACA-TCATGCAATGTT
1 TTTTCTATATTAGAGAACATTCATGCAATGTT
*
152768 TTTTCTATATTAGATAACATTCATGCAATGTT
1 TTTTCTATATTAGAGAACATTCATGCAATGTT
152800 ATATTTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (32 bp):
TTTTCTATATTAGAGAACATTCATGCAATGTT
Found at i:167229 original size:2 final size:2
Alignment explanation
Indices: 167222--167248 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
167212 TAGATATACA
167222 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
167249 AATTATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:170969 original size:2 final size:2
Alignment explanation
Indices: 170964--170989 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
170954 AATTATCATA
170964 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
170990 GTCGTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:171980 original size:4 final size:4
Alignment explanation
Indices: 171922--171960 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
171912 ATATATATAT
171922 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
171961 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:171981 original size:8 final size:8
Alignment explanation
Indices: 171911--171980 Score: 77
Period size: 8 Copynumber: 8.8 Consensus size: 8
171901 AAAATTTATC
*
171911 TATATATA
1 TATATACA
171919 TATATACA
1 TATATACA
*
171927 TACATACA
1 TATATACA
*
171935 TACATACA
1 TATATACA
*
171943 TACATACA
1 TATATACA
*
171951 TACATACA
1 TATATACA
*
171959 TATATATA
1 TATATACA
*
171967 TATATATA
1 TATATACA
171975 TATATA
1 TATATA
171981 TCCAGATCGG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 58 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (8 bp):
TATATACA
Found at i:175977 original size:24 final size:26
Alignment explanation
Indices: 175939--175988 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
175929 TATAATAATT
**
175939 GAGTATTTATTATAAA-A-TATTTTA
1 GAGTATTTAAAATAAATATTATTTTA
175963 GAGTATTTAAAATAAATATTATTTTA
1 GAGTATTTAAAATAAATATTATTTTA
175989 TAATCATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.64
25 1 0.05
26 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (26 bp):
GAGTATTTAAAATAAATATTATTTTA
Found at i:181201 original size:9 final size:9
Alignment explanation
Indices: 181189--181240 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
181179 TAATATTTTG
181189 TATTTAATT
1 TATTTAATT
*
181198 TATTTAA-G
1 TATTTAATT
181206 TATTTAATT
1 TATTTAATT
181215 TATTTAA--
1 TATTTAATT
*
181222 TATTTTATT
1 TATTTAATT
*
181231 TAATTAATT
1 TATTTAATT
181240 T
1 T
181241 TTTTTGTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:181210 original size:17 final size:17
Alignment explanation
Indices: 181188--181237 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
181178 TTAATATTTT
181188 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
181205 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
181222 -TATTTTATTTAATTAA
1 GTATTTAATTTATTTAA
181238 TTTTTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:186554 original size:20 final size:21
Alignment explanation
Indices: 186515--186554 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
186505 AATTTTAAGT
*
186515 TATTAAAAAATACATCTTATA
1 TATTAAAAAATACATATTATA
*
186536 TATTAAAAATTA-ATATTAT
1 TATTAAAAAATACATATTAT
186555 TTGTCTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
TATTAAAAAATACATATTATA
Found at i:186588 original size:17 final size:17
Alignment explanation
Indices: 186568--186600 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
186558 TCTATTTAAA
186568 ATATTA-ATTTTCATATT
1 ATATTATATTTT-ATATT
186585 ATATTATATTTTATAT
1 ATATTATATTTTATAT
186601 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:193128 original size:20 final size:18
Alignment explanation
Indices: 193090--193129 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
193080 TTTAAAATTA
*
193090 AATGAGTAAATATAGGAT
1 AATGAGTAAATAAAGGAT
193108 AATGAGTAAATTTAAAGGAT
1 AATGAGTAAA--TAAAGGAT
193128 AA
1 AA
193130 AATTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.28
Consensus pattern (18 bp):
AATGAGTAAATAAAGGAT
Found at i:193954 original size:2 final size:2
Alignment explanation
Indices: 193947--193992 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
193937 TGTTGTGTTC
193947 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
193989 AT AT
1 AT AT
193993 TTTAATTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194099 original size:11 final size:12
Alignment explanation
Indices: 194077--194101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
194067 TTCACTTATA
194077 TTTTAGATTTTT
1 TTTTAGATTTTT
194089 TTTTAGATTTTT
1 TTTTAGATTTTT
194101 T
1 T
194102 ATTGATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTAGATTTTT
Found at i:196188 original size:60 final size:60
Alignment explanation
Indices: 196109--196280 Score: 186
Period size: 60 Copynumber: 2.9 Consensus size: 60
196099 CAAGTCCTTC
* * * * * *
196109 AATTATGATCTTCCTTCTAAATTAATTC-TTAAAGTTTTAAATATTTTAATTCCATCCCTA
1 AATTATGATCTTCATTCTAAATT-AGTCATCAAACTTTTAAATATTTCAATTCCATCCCCA
* *
196169 AATTATGA-CTATCATTCTAAATTAGTCATCAAACTTTTGAATATTTCAATTTCATCCCCA
1 AATTATGATCT-TCATTCTAAATTAGTCATCAAACTTTTAAATATTTCAATTCCATCCCCA
* ** * *
196229 AACTATGATCTTCATTCTAAATGGGTCATCAAACTTTTTGAACATTTCAATT
1 AATTATGATCTTCATTCTAAATTAGTCATCAAAC-TTTTAAATATTTCAATT
196281 TCATACCACA
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
59 5 0.05
60 73 0.76
61 18 0.19
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (60 bp):
AATTATGATCTTCATTCTAAATTAGTCATCAAACTTTTAAATATTTCAATTCCATCCCCA
Found at i:198248 original size:9 final size:9
Alignment explanation
Indices: 198209--198249 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
198199 CCGGTTTTCA
198209 ACCGGTTCTG
1 ACCGG-TCTG
198219 ACCGGTCTG
1 ACCGGTCTG
*
198228 AACCGGTTTG
1 -ACCGGTCTG
198238 ACCGGTCTG
1 ACCGGTCTG
198247 ACC
1 ACC
198250 CGACCAGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 15 0.54
10 13 0.46
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.24
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:198271 original size:5 final size:5
Alignment explanation
Indices: 198263--198320 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
198253 CCAGACCGTT
* *
198263 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
198312 GACCC GACC
1 GACCC GACC
198321 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:198272 original size:22 final size:22
Alignment explanation
Indices: 198263--198327 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
198253 CCAGACCGTT
198263 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
198285 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
198307 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
198328 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:198327 original size:17 final size:17
Alignment explanation
Indices: 198245--198293 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
198235 TTGACCGGTC
*
198245 TGACCCGACCAGACCGT
1 TGACCCGACCCGACCGT
198262 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
198279 TGACCCGACCCGACC
1 TGACCCGACCCGACC
198294 CGACCGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.20, C:0.47, G:0.22, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:205514 original size:20 final size:21
Alignment explanation
Indices: 205489--205547 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
205479 GGCTGCTGGA
205489 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
205509 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
205529 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
205548 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:205525 original size:10 final size:10
Alignment explanation
Indices: 205510--205579 Score: 62
Period size: 10 Copynumber: 7.3 Consensus size: 10
205500 CCGGTTTTCA
205510 ACCGGTTCTG
1 ACCGGTTCTG
*
205520 ACCGGTT-TCA
1 ACCGGTTCT-G
205530 ACCGGTTC-G
1 ACCGGTTCTG
205539 AACCGGTT-TG
1 -ACCGGTTCTG
205549 ACCGG-TCTG
1 ACCGGTTCTG
205558 AACCGGTT-TG
1 -ACCGGTTCTG
205568 ACCGG-TCTG
1 ACCGGTTCTG
205577 ACC
1 ACC
205580 CGACCAGACC
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
8 2 0.04
9 18 0.36
10 29 0.58
11 1 0.02
ACGTcount: A:0.16, C:0.30, G:0.29, T:0.26
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:205554 original size:19 final size:20
Alignment explanation
Indices: 205510--205577 Score: 90
Period size: 19 Copynumber: 3.5 Consensus size: 20
205500 CCGGTTTTCA
*
205510 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
205530 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
205549 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
205568 ACCGG-TCTGA
1 ACCGGTTCTGA
205578 CCCGACCAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
18 2 0.04
19 27 0.60
20 16 0.36
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.26
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:205578 original size:9 final size:9
Alignment explanation
Indices: 205540--205579 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
205530 ACCGGTTCGA
*
205540 ACCGGTTTG
1 ACCGGTCTG
205549 ACCGGTCTG
1 ACCGGTCTG
*
205558 AACCGGTTTG
1 -ACCGGTCTG
205568 ACCGGTCTG
1 ACCGGTCTG
205577 ACC
1 ACC
205580 CGACCAGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:205602 original size:22 final size:21
Alignment explanation
Indices: 205576--205635 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
205566 TGACCGGTCT
205576 GACCCGACCAGACCGTTGACCC
1 GACCCGACC-GACCGTTGACCC
205598 GA--C--CCGACCGTTGACCC
1 GACCCGACCGACCGTTGACCC
205615 GACCCGACCCGACCGTTGACC
1 GACCCGA-CCGACCGTTGACC
205636 GTTGACCGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 14 0.42
18 2 0.06
19 1 0.03
20 1 0.03
22 15 0.45
ACGTcount: A:0.20, C:0.47, G:0.23, T:0.10
Consensus pattern (21 bp):
GACCCGACCGACCGTTGACCC
Found at i:205635 original size:17 final size:17
Alignment explanation
Indices: 205575--205623 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
205565 TTGACCGGTC
*
205575 TGACCCGACCAGACCGT
1 TGACCCGACCCGACCGT
205592 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
205609 TGACCCGACCCGACC
1 TGACCCGACCCGACC
205624 CGACCGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.20, C:0.47, G:0.22, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:205637 original size:7 final size:7
Alignment explanation
Indices: 205625--205655 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
205615 GACCCGACCC
205625 GACCGTT
1 GACCGTT
205632 GACCGTT
1 GACCGTT
205639 GACCGTT
1 GACCGTT
205646 GACCGTT
1 GACCGTT
205653 GAC
1 GAC
205656 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:208031 original size:20 final size:19
Alignment explanation
Indices: 208002--208043 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
207992 AGTAATCATA
*
208002 TTCCCTGGTAATCTTACAT
1 TTCCCTGGTAATCTTAAAT
208021 TTCCACTGGTAATCTTAAAT
1 TTCC-CTGGTAATCTTAAAT
208041 TTC
1 TTC
208044 GTGAACCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.43
Consensus pattern (19 bp):
TTCCCTGGTAATCTTAAAT
Found at i:208585 original size:19 final size:20
Alignment explanation
Indices: 208561--208599 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
208551 AAGTATATAA
*
208561 AAAATTAT-AATTTATTTTT
1 AAAATTATAAATATATTTTT
208580 AAAATTATAAATATATTTTT
1 AAAATTATAAATATATTTTT
208600 TAAACCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAAATTATAAATATATTTTT
Found at i:222447 original size:33 final size:34
Alignment explanation
Indices: 222405--222470 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
222395 AAACTAATTT
* *
222405 GATGTCATTGCTTACAT-AATTTTGTTAGGTGAA
1 GATGTCATTGCTTACATCAAATTAGTTAGGTGAA
222438 GATGTCATTGCTTACATCAAATTAGTTAGGTGA
1 GATGTCATTGCTTACATCAAATTAGTTAGGTGA
222471 GAGTTAGGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (34 bp):
GATGTCATTGCTTACATCAAATTAGTTAGGTGAA
Found at i:223378 original size:16 final size:17
Alignment explanation
Indices: 223357--223392 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
223347 TTAATGTTAT
223357 TTTAAAATTAAATT-AA
1 TTTAAAATTAAATTGAA
*
223373 TTTAAATTTAAATTGAA
1 TTTAAAATTAAATTGAA
223390 TTT
1 TTT
223393 TTTCTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAAATTAAATTGAA
Found at i:228206 original size:33 final size:36
Alignment explanation
Indices: 228169--228244 Score: 95
Period size: 39 Copynumber: 2.1 Consensus size: 36
228159 GTTCATCAAT
*
228169 ATTATTAAC-AT-A-AACTTTTTATAATATGTACAA
1 ATTATTAACAATAATAACTTTTTATAATATGAACAA
228202 ATTATTAACAATAACATTAACTTTTTATAATATGAACAA
1 ATTATTAACAAT-A-A-TAACTTTTTATAATATGAACAA
228241 ATTA
1 ATTA
228245 ATTATTGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 9 0.25
34 2 0.06
37 1 0.03
39 24 0.67
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (36 bp):
ATTATTAACAATAATAACTTTTTATAATATGAACAA
Found at i:228239 original size:22 final size:21
Alignment explanation
Indices: 228175--228239 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 21
228165 CAATATTATT
228175 AACATAAACTTTTTATAATATG
1 AACAT-AACTTTTTATAATATG
* *
228197 TACA-AA-TTATTA-ACA-AT-
1 AACATAACTTTTTATA-ATATG
228214 AACATTAACTTTTTATAATATG
1 AACA-TAACTTTTTATAATATG
228236 AACA
1 AACA
228240 AATTAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
17 3 0.09
18 3 0.09
19 8 0.25
20 8 0.25
21 3 0.09
22 7 0.22
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (21 bp):
AACATAACTTTTTATAATATG
Found at i:234823 original size:2 final size:2
Alignment explanation
Indices: 234816--234844 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
234806 TCATTTAATA
234816 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
234845 AATAAACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:238135 original size:27 final size:26
Alignment explanation
Indices: 238082--238136 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 26
238072 CTCTCTCTGT
*
238082 TCATTTTTTTTCATTCTATATATAATA
1 TCATTTTTTTTCA-TCTACATATAATA
238109 TCATTTTTTTTC-TCTACCATATGAATA
1 TCATTTTTTTTCATCTA-CATAT-AATA
238136 T
1 T
238137 TACCAATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 4 0.16
26 4 0.16
27 17 0.68
ACGTcount: A:0.27, C:0.15, G:0.02, T:0.56
Consensus pattern (26 bp):
TCATTTTTTTTCATCTACATATAATA
Found at i:247359 original size:21 final size:21
Alignment explanation
Indices: 247335--247375 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
247325 GATTAAGAAT
*
247335 TATTTAAAATATTATTATTTA
1 TATTTAAAATATTAATATTTA
247356 TATTTAAAATATTAATATTT
1 TATTTAAAATATTAATATTT
247376 TTTAATATTT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTAAAATATTAATATTTA
Found at i:253944 original size:24 final size:24
Alignment explanation
Indices: 253912--253970 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
253902 ATCGATTAAA
* *
253912 TTTGGTTCATTTCGTTAGTTCGTC
1 TTTGATTCATTTCGTTAGTTCGGC
253936 TTTGATTCATTTCGTTAGTTCGGC
1 TTTGATTCATTTCGTTAGTTCGGC
253960 TTTGATTCATT
1 TTTGATTCATT
253971 AATGGTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.12, C:0.15, G:0.19, T:0.54
Consensus pattern (24 bp):
TTTGATTCATTTCGTTAGTTCGGC
Found at i:256227 original size:57 final size:57
Alignment explanation
Indices: 256157--256274 Score: 175
Period size: 57 Copynumber: 2.1 Consensus size: 57
256147 AGGCAATGTT
* * * *
256157 GGCATACTCGGAAGTGGAGGTAGAGCT-CCAGGCTTGGGTAACGATGGCTGTGTTGTC
1 GGCATACTAGGAAGTGGAGGAAGAGCTCCCAGG-TTGGGTAACGACGGCTGCGTTGTC
*
256214 GGCATGCTAGGAAGTGGAGGAAGAGCTCCCAGGTTGGGTAACGACGGCTGCGTTGTC
1 GGCATACTAGGAAGTGGAGGAAGAGCTCCCAGGTTGGGTAACGACGGCTGCGTTGTC
256271 GGCA
1 GGCA
256275 ATGTCGGTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 50 0.91
58 5 0.09
ACGTcount: A:0.20, C:0.19, G:0.40, T:0.21
Consensus pattern (57 bp):
GGCATACTAGGAAGTGGAGGAAGAGCTCCCAGGTTGGGTAACGACGGCTGCGTTGTC
Found at i:269894 original size:83 final size:81
Alignment explanation
Indices: 269757--269924 Score: 257
Period size: 83 Copynumber: 2.0 Consensus size: 81
269747 TATAGACCAT
* *
269757 TAGAAGAAATTACTTGCAAAGAAAGATAACTAGAGTCATTTATCAAGAAAAGCATCTTACGAGAT
1 TAGAAGAAATTACTTGCAAAGAAAGATAACTAGACTCATTTATCAAGAAAAGCATCTTACGAGAA
* *
269822 ATGATCTTACCAGAGC
66 ATGAACTTACCAAAGC
*
269838 TAGAAGAAATTACATAAT-CAAAGAAAGATAACTAGACTCGTTTATCAAGAAAAGCATCTTACGA
1 TAGAAGAAATTAC-T--TGCAAAGAAAGATAACTAGACTCATTTATCAAGAAAAGCATCTTACGA
269902 GAAATGAACTTACCAAAGC
63 GAAATGAACTTACCAAAGC
269921 TAGA
1 TAGA
269925 TGACAAGGCA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
81 13 0.16
82 1 0.01
83 64 0.81
84 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (81 bp):
TAGAAGAAATTACTTGCAAAGAAAGATAACTAGACTCATTTATCAAGAAAAGCATCTTACGAGAA
ATGAACTTACCAAAGC
Found at i:279199 original size:10 final size:9
Alignment explanation
Indices: 279174--279198 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
279164 CACAGATACA
279174 TTTTTTTAT
1 TTTTTTTAT
279183 TTTTTTTAT
1 TTTTTTTAT
279192 TTTTTTT
1 TTTTTTT
279199 TGGGAGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:283452 original size:21 final size:21
Alignment explanation
Indices: 283428--283472 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
283418 ACATGACAGA
* *
283428 TAAACTATAACGTCAGTATCG
1 TAAACCATAACGTCAGAATCG
* *
283449 TAAACCGTTACGTCAGAATCG
1 TAAACCATAACGTCAGAATCG
283470 TAA
1 TAA
283473 CGGTCAATCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (21 bp):
TAAACCATAACGTCAGAATCG
Found at i:286764 original size:22 final size:22
Alignment explanation
Indices: 286737--286808 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
286727 TAGAGTATTA
286737 TTTTATTCCAATTTAAATGGCT
1 TTTTATTCCAATTTAAATGGCT
* *
286759 TTTTATAAT-C-ATATAAGAT--AT
1 TTTTAT--TCCAATTTAA-ATGGCT
286780 ATTTTATTCCAATTTAAATGGCT
1 -TTTTATTCCAATTTAAATGGCT
286803 TTTTAT
1 TTTTAT
286809 AATCATATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
20 1 0.03
21 4 0.11
22 28 0.74
23 4 0.11
24 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTTATTCCAATTTAAATGGCT
Found at i:286785 original size:44 final size:44
Alignment explanation
Indices: 286735--286824 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
286725 ATTAGAGTAT
286735 TATTTTATTCCAATTTAAATGGCTTTTTATAATCATATAAGATA
1 TATTTTATTCCAATTTAAATGGCTTTTTATAATCATATAAGATA
*
286779 TATTTTATTCCAATTTAAATGGCTTTTTATAATCATATACGATA
1 TATTTTATTCCAATTTAAATGGCTTTTTATAATCATATAAGATA
286823 TA
1 TA
286825 CATATATATC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (44 bp):
TATTTTATTCCAATTTAAATGGCTTTTTATAATCATATAAGATA
Found at i:292600 original size:20 final size:19
Alignment explanation
Indices: 292575--292612 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
292565 TTCATACTCT
*
292575 AAAAAATTTAAATTTCTTA
1 AAAAAAATTAAATTTCTTA
292594 AAAAAAATTAAATTTCTTA
1 AAAAAAATTAAATTTCTTA
292613 TATTTTAAAT
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:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAAAATTAAATTTCTTA
Found at i:300223 original size:30 final size:29
Alignment explanation
Indices: 300163--300248 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 29
300153 TAAATTTTAG
* **
300163 TTAGTGACTAAAATATAAGTTTTGAAAGT
1 TTAGTGACTAAAATATAACTTTAAAAAGT
*
300192 TTAGTGGCTAAAATATAAACTTTAAAAAGT
1 TTAGTGACTAAAATAT-AACTTTAAAAAGT
* * * *
300222 TTAGGGACCAAAAGTGTAATTTTAAAA
1 TTAGTGACTAAAA-TATAACTTTAAAA
300249 GGTTATATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 15 0.33
30 29 0.63
31 2 0.04
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (29 bp):
TTAGTGACTAAAATATAACTTTAAAAAGT
Found at i:305074 original size:21 final size:22
Alignment explanation
Indices: 305039--305079 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
305029 AGTAAGTTTG
*
305039 ATTATATATAAATTTTGGGAAT
1 ATTATACATAAATTTTGGGAAT
305061 ATTATACA-AAATTTTGGGA
1 ATTATACATAAATTTTGGGA
305080 TTAAAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.41
Consensus pattern (22 bp):
ATTATACATAAATTTTGGGAAT
Found at i:316499 original size:90 final size:90
Alignment explanation
Indices: 316389--316569 Score: 362
Period size: 90 Copynumber: 2.0 Consensus size: 90
316379 TTGAATATGT
316389 AATTGACTAAGAATAGTCTTCTTTATGGTTCTATTATTCCTAAAAGAACTTCCATCATAATGAAC
1 AATTGACTAAGAATAGTCTTCTTTATGGTTCTATTATTCCTAAAAGAACTTCCATCATAATGAAC
316454 ACACTATGCTTTCTGCTCCATCCGA
66 ACACTATGCTTTCTGCTCCATCCGA
316479 AATTGACTAAGAATAGTCTTCTTTATGGTTCTATTATTCCTAAAAGAACTTCCATCATAATGAAC
1 AATTGACTAAGAATAGTCTTCTTTATGGTTCTATTATTCCTAAAAGAACTTCCATCATAATGAAC
316544 ACACTATGCTTTCTGCTCCATCCGA
66 ACACTATGCTTTCTGCTCCATCCGA
316569 A
1 A
316570 GCCAAATAAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.35
Consensus pattern (90 bp):
AATTGACTAAGAATAGTCTTCTTTATGGTTCTATTATTCCTAAAAGAACTTCCATCATAATGAAC
ACACTATGCTTTCTGCTCCATCCGA
Found at i:328633 original size:26 final size:25
Alignment explanation
Indices: 328594--328643 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
328584 AAAGTTTTGA
* **
328594 TATTTTTTTAAATTTTGAAAAAAAT
1 TATTTTTTAAAATTTAAAAAAAAAT
328619 TATTTTTTAATAATTTAAAAAAAAA
1 TATTTTTTAA-AATTTAAAAAAAAA
328644 ATCAATATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TATTTTTTAAAATTTAAAAAAAAAT
Found at i:340048 original size:36 final size:36
Alignment explanation
Indices: 339803--340046 Score: 362
Period size: 36 Copynumber: 6.8 Consensus size: 36
339793 TCTATGAGAG
*
339803 GATCTTACAGGACTTCTGCTGATGCTTCGCCTCGAA
1 GATCTTACAGGACTTCTGCCGATGCTTCGCCTCGAA
*
339839 GATCTTACAGGACTTCTGCCGATGCTCCGCCTCGAA
1 GATCTTACAGGACTTCTGCCGATGCTTCGCCTCGAA
* *
339875 GATCTTACAGGACTTGTGCCGATGCTCCGCCTCGAA
1 GATCTTACAGGACTTCTGCCGATGCTTCGCCTCGAA
* * * *
339911 GATCTTACAGGACTTGTGCCGATGCTCCACCTGGAA
1 GATCTTACAGGACTTCTGCCGATGCTTCGCCTCGAA
* *
339947 GAACTTACAGGACTTGTGCCGATGCTTCGCCTCGAA
1 GATCTTACAGGACTTCTGCCGATGCTTCGCCTCGAA
* * *
339983 GATCTTACAGGACTTCTGCTGATGCTTCTCCTTGAA
1 GATCTTACAGGACTTCTGCCGATGCTTCGCCTCGAA
*
340019 GATCTTACAGGACTTCTGCTGATGCTTC
1 GATCTTACAGGACTTCTGCCGATGCTTC
340047 TCTGAGAACG
Statistics
Matches: 194, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 194 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.29
Consensus pattern (36 bp):
GATCTTACAGGACTTCTGCCGATGCTTCGCCTCGAA
Found at i:342974 original size:19 final size:19
Alignment explanation
Indices: 342937--342974 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
342927 GGTACCGCCG
*
342937 GCGAGGAGAAGAGAAGGCA
1 GCGAGGAGAAAAGAAGGCA
*
342956 GCGAGGAGAAAAGATGGCA
1 GCGAGGAGAAAAGAAGGCA
342975 AGATGGTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.45, T:0.03
Consensus pattern (19 bp):
GCGAGGAGAAAAGAAGGCA
Found at i:342995 original size:33 final size:33
Alignment explanation
Indices: 342956--343043 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 33
342946 AGAGAAGGCA
* * * *
342956 GCGAGGAGAAAAGATGGCAAGATGGTACTGTCG
1 GCGAGGAGAAGAGAAGGCAAGATGGTACCGCCG
* *
342989 GTGAGGAGAAGAGAAGACAAGATGGTACCGCCG
1 GCGAGGAGAAGAGAAGGCAAGATGGTACCGCCG
343022 GCGAGGAGAAGAGAAGGCAAGA
1 GCGAGGAGAAGAGAAGGCAAGA
343044 AAATATTCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.38, C:0.12, G:0.41, T:0.09
Consensus pattern (33 bp):
GCGAGGAGAAGAGAAGGCAAGATGGTACCGCCG
Found at i:355191 original size:19 final size:20
Alignment explanation
Indices: 355153--355196 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
355143 CAACAGTCAT
*
355153 TTTTAAAATTATTTTAATAA
1 TTTTAAAATTATTATAATAA
*
355173 TTTTAAAA-TATTATCATAA
1 TTTTAAAATTATTATAATAA
355192 TTTTA
1 TTTTA
355197 TTTATTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAAAATTATTATAATAA
Found at i:362957 original size:31 final size:31
Alignment explanation
Indices: 362919--362982 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
362909 TTTTCAATAG
* * *
362919 TAGGGTTTAGAAAATGGGACTAAAACTAAAT
1 TAGGGTTTAGAAAAAGGGACGAAAACAAAAT
*
362950 TAGGGTTTAGAAAAAGGGAGGAAAACAAAAT
1 TAGGGTTTAGAAAAAGGGACGAAAACAAAAT
362981 TA
1 TA
362983 TACGGTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.05, G:0.25, T:0.22
Consensus pattern (31 bp):
TAGGGTTTAGAAAAAGGGACGAAAACAAAAT
Found at i:364376 original size:22 final size:22
Alignment explanation
Indices: 364348--364419 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
364338 GTGAAAAGGA
364348 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGATCTTCCAAG
364370 AATCGCAACGCGAT-TT--AGAG
1 AATCGCAACGCGATCTTCCA-AG
*
364390 AATCGCAATGCGATCTTCCAAG
1 AATCGCAACGCGATCTTCCAAG
364412 AATCGCAA
1 AATCGCAA
364420 AACGGTCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
19 1 0.02
20 15 0.33
21 4 0.09
22 24 0.53
23 1 0.02
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (22 bp):
AATCGCAACGCGATCTTCCAAG
Found at i:364529 original size:6 final size:6
Alignment explanation
Indices: 364518--364548 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
364508 GACACGTATT
364518 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
364549 GACGGCGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:365257 original size:6 final size:6
Alignment explanation
Indices: 365223--365260 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
365213 TCTCGTCTCG
*
365223 GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
365261 AATACGTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.00, C:0.16, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:365388 original size:20 final size:20
Alignment explanation
Indices: 365365--365474 Score: 143
Period size: 20 Copynumber: 5.4 Consensus size: 20
365355 TTTGACCGTT
365365 TTGCGATTCTCT-GAGTCGCA
1 TTGCGATTCT-TGGAGTCGCA
365385 TTGCGATTCTTGGAGTCGCA
1 TTGCGATTCTTGGAGTCGCA
365405 TTGCGATTCTCT-GAGTCGCA
1 TTGCGATTCT-TGGAGTCGCA
* *
365425 TTGCAATTCTTGGAATCGCA
1 TTGCGATTCTTGGAGTCGCA
*
365445 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-AG-TCGCA
365467 TTGCGATT
1 TTGCGATT
365475 TCTGAATCGC
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.03
20 64 0.80
21 2 0.03
22 12 0.15
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATTCTTGGAGTCGCA
Found at i:366599 original size:13 final size:13
Alignment explanation
Indices: 366581--366605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
366571 ATAGTTGAAC
366581 AGTCTTCATATGT
1 AGTCTTCATATGT
366594 AGTCTTCATATG
1 AGTCTTCATATG
366606 CGAATCTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
AGTCTTCATATGT
Found at i:370733 original size:30 final size:30
Alignment explanation
Indices: 370693--370764 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
370683 GTTAACATTG
* *
370693 AGTGACCATTTTGTAATAAATAATAATATT
1 AGTGACCATTTTATAATAAATAATAAAATT
* *
370723 AGTGATCATTTTATAATAAATGATAAAATT
1 AGTGACCATTTTATAATAAATAATAAAATT
370753 AGTGACCGATTT
1 AGTGACC-ATTT
370765 AAGATTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (30 bp):
AGTGACCATTTTATAATAAATAATAAAATT
Found at i:374888 original size:18 final size:18
Alignment explanation
Indices: 374862--374896 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
374852 CGAGGGTTAC
*
374862 AGTGTTCCTACGGGACAT
1 AGTGGTCCTACGGGACAT
*
374880 AGTGGTCCTTCGGGACA
1 AGTGGTCCTACGGGACA
374897 AATTTCAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:375427 original size:21 final size:21
Alignment explanation
Indices: 375403--375467 Score: 121
Period size: 21 Copynumber: 3.1 Consensus size: 21
375393 TTACGAAAAT
375403 CACTGTAGCAGTACATCGATG
1 CACTGTAGCAGTACATCGATG
375424 CACTGTAGCAGTACATCGATG
1 CACTGTAGCAGTACATCGATG
*
375445 CACTGTAGCAGTGCATCGATG
1 CACTGTAGCAGTACATCGATG
375466 CA
1 CA
375468 TAATTTTGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
CACTGTAGCAGTACATCGATG
Found at i:377763 original size:32 final size:32
Alignment explanation
Indices: 377705--377766 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
377695 TAACGCGACC
* *
377705 CTTGGGTAGACTCTTATGCCCTAAGGTACTAT
1 CTTGGGTAGACTCTAATGCCCCAAGGTACTAT
*
377737 CTTGGGTAGGCTCTGAAT-CCCCAAGGTACT
1 CTTGGGTAGACTCT-AATGCCCCAAGGTACT
377767 CTTTTATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (32 bp):
CTTGGGTAGACTCTAATGCCCCAAGGTACTAT
Found at i:380890 original size:29 final size:29
Alignment explanation
Indices: 380814--380890 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
380804 CTTCCCAGCA
*
380814 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
380843 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
380872 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
380891 CCTGCTCCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:389849 original size:14 final size:14
Alignment explanation
Indices: 389830--389878 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
389820 CTCATAAAAT
389830 TTTATAAATTTAAG
1 TTTATAAATTTAAG
*
389844 TTTATAATTTTAAAG
1 TTTATAAATTT-AAG
*
389859 TTTTATAAATTTAAA
1 -TTTATAAATTTAAG
389874 TTTAT
1 TTTAT
389879 TTATTCTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 15 0.50
15 5 0.17
16 10 0.33
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (14 bp):
TTTATAAATTTAAG
Found at i:389865 original size:16 final size:16
Alignment explanation
Indices: 389824--389873 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
389814 TCTCATCTCA
*
389824 TAAAATTTTATAAATT
1 TAAAGTTTTATAAATT
*
389840 T-AAG-TTTATAATTT
1 TAAAGTTTTATAAATT
389854 TAAAGTTTTATAAATT
1 TAAAGTTTTATAAATT
389870 TAAA
1 TAAA
389874 TTTATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.34
15 5 0.17
16 14 0.48
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
TAAAGTTTTATAAATT
Found at i:403310 original size:3 final size:3
Alignment explanation
Indices: 403302--403331 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
403292 TATCTGTGGA
*
403302 ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
403332 TCGTTGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:404059 original size:58 final size:60
Alignment explanation
Indices: 403940--404059 Score: 210
Period size: 58 Copynumber: 2.0 Consensus size: 60
403930 ATCCATGTCA
403940 AATGATCTTGGGTTGCAGTTTCTTTGGCGCAGACTCAGCAAGGTGGAAACTCGAAGTCCC
1 AATGATCTTGGGTTGCAGTTTCTTTGGCGCAGACTCAGCAAGGTGGAAACTCGAAGTCCC
404000 AATGATC-TGGGTTGCAGTTTTCTTT-GCGCAGACTCA-CAAGGTGGAAACTCGAAGTCCC
1 AATGATCTTGGGTTGCAG-TTTCTTTGGCGCAGACTCAGCAAGGTGGAAACTCGAAGTCCC
404058 AA
1 AA
404060 ACATAACTCA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
58 24 0.41
59 21 0.36
60 14 0.24
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (60 bp):
AATGATCTTGGGTTGCAGTTTCTTTGGCGCAGACTCAGCAAGGTGGAAACTCGAAGTCCC
Found at i:404141 original size:51 final size:51
Alignment explanation
Indices: 404036--404476 Score: 510
Period size: 51 Copynumber: 8.9 Consensus size: 51
404026 CGCAGACTCA
* * * *
404036 CAAGGTGGAAAC-TCGAAGTCCCAAACATA-ACTCAACTACCTCAACAGCAG
1 CAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAGCAG
* *
404086 CAAGGTGGAAACTTTGGATCCCAAACATATACTCAGCTACCGCAACAGCAG
1 CAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAGCAG
*
404137 CAAGGTGGAAACATTGGATCCCAAA-ATATA-TCATCTA-C-C-ACAGCAG
1 CAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAGCAG
* *
404183 C-A-GTGGAAACATT-GATTCCC-AA-ATATACTCTGCTACCACATCAGCAG
1 CAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAGCAG
*
404230 CAA-GTGGAAACAATGGATCCCAAACAT-T-CTCAGCTACCACAACAGCAG
1 CAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAGCAG
* *
404278 CAAGGTGGAAACATAT--ATTCCC-AACATA-ACTCTGCTACCACATCAGCAG
1 CAAGGTGGAAACAT-TGGA-TCCCAAACATATACTCAGCTACCACAACAGCAG
* *
404327 CAAGGTGGAAACAATGGATCCCAAACATATACTCAGCTACCACAACAGAAG
1 CAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAGCAG
* * * *
404378 CAAGTTGGAAACATTGATATCCAAAACATTTACTCTA-CTACCACAACAGCAG
1 CAAGGTGGAAACATTG-GATCCCAAACATATACTC-AGCTACCACAACAGCAG
*
404430 CAAGGTGGAAA-ATTGGTTCCCAAACATATACTCAGCTACCACAACAG
1 CAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
404477 ATGTTAATGT
Statistics
Matches: 338, Mismatches: 30, Indels: 46
0.82 0.07 0.11
Matches are distributed among these distances:
43 9 0.03
44 20 0.06
45 2 0.01
46 9 0.03
47 8 0.02
48 44 0.13
49 60 0.18
50 64 0.19
51 82 0.24
52 39 0.12
53 1 0.00
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (51 bp):
CAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAGCAG
Found at i:404388 original size:100 final size:101
Alignment explanation
Indices: 404054--404476 Score: 545
Period size: 97 Copynumber: 4.3 Consensus size: 101
404044 AAACTCGAAG
* * *
404054 TCCCAAACATA-ACTCAACTACCTCAACAGCAGCAAGGTGGAAACTTTGGA-TCCCAAACATATA
1 TCCCAAACATATACTCAGCTACCACAACAGCAGCAAGGTGGAAACATT-GATTCCC-AACATATA
* * *
404117 CTCAGCTACCGCAACAGCAGCAAGGTGGAAACATTGGA
64 CTCTGCTACCACAACAGCAGCAAGGTGGAAACAATGGA
*
404155 TCCCAAA-ATATA-TCATCTA-C-C-ACAGCAGC-A-GTGGAAACATTGATTCCCAA-ATATACT
1 TCCCAAACATATACTCAGCTACCACAACAGCAGCAAGGTGGAAACATTGATTCCCAACATATACT
*
404212 CTGCTACCACATCAGCAGCAA-GTGGAAACAATGGA
66 CTGCTACCACAACAGCAGCAAGGTGGAAACAATGGA
404247 TCCCAAACAT-T-CTCAGCTACCACAACAGCAGCAAGGTGGAAACATAT-ATTCCCAACATA-AC
1 TCCCAAACATATACTCAGCTACCACAACAGCAGCAAGGTGGAAACAT-TGATTCCCAACATATAC
*
404308 TCTGCTACCACATCAGCAGCAAGGTGGAAACAATGGA
65 TCTGCTACCACAACAGCAGCAAGGTGGAAACAATGGA
* * * *
404345 TCCCAAACATATACTCAGCTACCACAACAGAAGCAAGTTGGAAACATTGATATCCAAAACATTTA
1 TCCCAAACATATACTCAGCTACCACAACAGCAGCAAGGTGGAAACATTGAT-TCC-CAACATATA
* * *
404410 CTCTACTACCACAACAGCAGCAAGGTGGAAA-ATTGGT
64 CTCTGCTACCACAACAGCAGCAAGGTGGAAACAATGGA
404447 TCCCAAACATATACTCAGCTACCACAACAG
1 TCCCAAACATATACTCAGCTACCACAACAG
404477 ATGTTAATGT
Statistics
Matches: 289, Mismatches: 15, Indels: 35
0.85 0.04 0.10
Matches are distributed among these distances:
92 27 0.09
93 28 0.10
94 5 0.02
95 22 0.08
96 2 0.01
97 50 0.17
98 29 0.10
99 3 0.01
100 43 0.15
101 11 0.04
102 39 0.13
103 30 0.10
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.19
Consensus pattern (101 bp):
TCCCAAACATATACTCAGCTACCACAACAGCAGCAAGGTGGAAACATTGATTCCCAACATATACT
CTGCTACCACAACAGCAGCAAGGTGGAAACAATGGA
Found at i:416164 original size:22 final size:22
Alignment explanation
Indices: 416127--416183 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
416117 TCTTTAAGTT
*
416127 TTTAAA-TATTTCAAATTTATC
1 TTTAAACTATTTCAAATTAATC
*
416148 TTTAAACTATTAT-AAATTAATT
1 TTTAAACTATT-TCAAATTAATC
416170 TTTAAAC-ATTTCAA
1 TTTAAACTATTTCAA
416184 TTCTACCCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.35
22 18 0.58
23 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAAACTATTTCAAATTAATC
Found at i:416494 original size:12 final size:12
Alignment explanation
Indices: 416477--416501 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
416467 TGATTTCTTA
416477 GTAAAATTGGAT
1 GTAAAATTGGAT
416489 GTAAAATTGGAT
1 GTAAAATTGGAT
416501 G
1 G
416502 GTGGGGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (12 bp):
GTAAAATTGGAT
Found at i:426871 original size:23 final size:23
Alignment explanation
Indices: 426841--426884 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
426831 CTCAAAGTTT
426841 GGCAGACATGTTGAAAAAAATTC
1 GGCAGACATGTTGAAAAAAATTC
426864 GGCAGACATGTTGAAAAAAAT
1 GGCAGACATGTTGAAAAAAAT
426885 CAGTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.20
Consensus pattern (23 bp):
GGCAGACATGTTGAAAAAAATTC
Found at i:426990 original size:37 final size:38
Alignment explanation
Indices: 426932--427016 Score: 113
Period size: 37 Copynumber: 2.3 Consensus size: 38
426922 TGACAACCAA
426932 CTTTGAAAAA-AATGATGTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAAT-ATGTTCAAAGTTTGGTAAATGTTT
* *
426970 CTTTGAAAAATAAT-TTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAATATGTTCAAAGTTTGGTAAATGTTT
*
427007 -ATTGAAAAAT
1 CTTTGAAAAAT
427017 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 9 0.21
37 21 0.49
38 10 0.23
39 3 0.07
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (38 bp):
CTTTGAAAAATAATATGTTCAAAGTTTGGTAAATGTTT
Found at i:431132 original size:7 final size:7
Alignment explanation
Indices: 431120--431145 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
431110 AATAGATGTG
431120 TGTAAAT
1 TGTAAAT
431127 TGTAAAT
1 TGTAAAT
431134 TGTAAAT
1 TGTAAAT
431141 TGTAA
1 TGTAA
431146 TGTAGCTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (7 bp):
TGTAAAT
Done.