Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006252.1 Hibiscus syriacus cultivar Beakdansim tig00014922_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: 90477
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:11376 original size:7 final size:7
Alignment explanation
Indices: 11362--11400 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
11352 CTCTGGGTTG
11362 TAATTAT
1 TAATTAT
*
11369 TTATTAT
1 TAATTAT
11376 T-ATTAT
1 TAATTAT
11382 TAATTAT
1 TAATTAT
11389 TAATTA-
1 TAATTAT
11395 TAATTA
1 TAATTA
11401 GGGTAAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAATTAT
Found at i:11387 original size:20 final size:20
Alignment explanation
Indices: 11362--11400 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11352 CTCTGGGTTG
* *
11362 TAATTATTTATTATTATTAT
1 TAATTATTAATTATAATTAT
11382 TAATTATTAATTATAATTA
1 TAATTATTAATTATAATTA
11401 GGGTAAAGTA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATTATTAATTATAATTAT
Found at i:11514 original size:31 final size:31
Alignment explanation
Indices: 11472--11545 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
11462 TTAAAACTTG
* * *
11472 CAATATAGTCCCCTAACATTTAGTCTGTTTGT
1 CAATATGGTCCCCCAACATTTAGTCTATTT-T
*
11504 -AATATGGTCCCCCAATATTTAGTCTATTTT
1 CAATATGGTCCCCCAACATTTAGTCTATTTT
11534 CAATATGGTCCC
1 CAATATGGTCCC
11546 TGACGTAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 1 0.03
31 36 0.97
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (31 bp):
CAATATGGTCCCCCAACATTTAGTCTATTTT
Found at i:13555 original size:31 final size:31
Alignment explanation
Indices: 13517--13582 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
13507 CAGTTACGTC
*** *
13517 GGGACCATATTGTAAATGGACTAAATGTTGG
1 GGGACCATATTGTAAAAAAACTAAATGTTAG
13548 GGGACCATATTGTAAAAAAACTAAATGTTAG
1 GGGACCATATTGTAAAAAAACTAAATGTTAG
13579 GGGA
1 GGGA
13583 TTGTATTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.26
Consensus pattern (31 bp):
GGGACCATATTGTAAAAAAACTAAATGTTAG
Found at i:19597 original size:18 final size:17
Alignment explanation
Indices: 19532--19602 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 17
19522 GGATTATCAG
*
19532 TGGTCCTTCGGGATATAA
1 TGGT-CTTCGGGACATAA
* *
19550 TGGTTCTTCGGAACAATCAG
1 TGG-TCTTCGGGAC-AT-AA
19570 TGGTCTTTCGGGACATAA
1 TGGTC-TTCGGGACATAA
19588 TGGTCATTCGGGACA
1 TGGTC-TTCGGGACA
19603 AATATTCAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 25 0.58
19 7 0.16
20 11 0.26
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (17 bp):
TGGTCTTCGGGACATAA
Found at i:29869 original size:21 final size:21
Alignment explanation
Indices: 29843--29882 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29833 CCCCCTTTGA
29843 AGGGGAACCGATACCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
29864 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
29883 TGGGGTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.40, G:0.25, T:0.07
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:31879 original size:15 final size:15
Alignment explanation
Indices: 31839--31879 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
31829 TTGTTTCAAC
* *
31839 ATTTTGAATTGTTTG
1 ATTTTGGATTGTTGG
31854 ATTTGTGGATTGTTGG
1 ATTT-TGGATTGTTGG
31870 ATTTTGGATT
1 ATTTTGGATT
31880 TATGAATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:34944 original size:22 final size:20
Alignment explanation
Indices: 34911--34950 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
34901 TAATTAAGAC
34911 ATATGAAATGTTAGAATTAG
1 ATATGAAATGTTAGAATTAG
*
34931 ATATAGAACATGTTGGAATT
1 ATAT-GAA-ATGTTAGAATT
34951 TGAGGGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (20 bp):
ATATGAAATGTTAGAATTAG
Found at i:35349 original size:64 final size:63
Alignment explanation
Indices: 35218--35357 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 63
35208 TGAGGTGTGT
* * * *
35218 ATCGATGTACTCCTTTAAAATAAAAACATCGAATGGCATTAGTGTATCGATGTACAAGTAGTGC
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGGCATTAGTGTACCGATG-ACAAGTAGTGC
* * * *
35282 ATCGATGCACCCCCTTAAAATACAAACATCGAATGGTATTTA-TGTACCGATG-CATAGATTGTT
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGGCA-TTAGTGTACCGATGACA-AG-TAGTG
35345 C
63 C
35346 ATCGATGCACCC
1 ATCGATGCACCC
35358 GTCAAGGGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 2 0.03
63 2 0.03
64 58 0.89
65 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (63 bp):
ATCGATGCACCCCCTTAAAATAAAAACATCGAATGGCATTAGTGTACCGATGACAAGTAGTGC
Found at i:35954 original size:18 final size:19
Alignment explanation
Indices: 35928--35985 Score: 82
Period size: 18 Copynumber: 3.1 Consensus size: 19
35918 TTGAGGGATT
35928 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
* *
35947 AT-AGTGGTTCTTCGGAAC
1 ATCAGTGGTCCTTCGGGAC
35965 AATCAGTGGTCCTTCGGGAC
1 -ATCAGTGGTCCTTCGGGAC
35985 A
1 A
35986 AATATTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 14 0.42
19 5 0.15
20 14 0.42
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:35974 original size:20 final size:20
Alignment explanation
Indices: 35928--35986 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
35918 TTGAGGGATT
35928 ATCAGTGGTCCTTCGGGAC-
1 ATCAGTGGTCCTTCGGGACA
* *
35947 AT-AGTGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGGGACA
35966 ATCAGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTCGGGACA
35986 A
1 A
35987 ATATTCAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 14 0.41
19 4 0.12
20 16 0.47
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCAGTGGTCCTTCGGGACA
Found at i:36243 original size:2 final size:2
Alignment explanation
Indices: 36236--36260 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36226 AATACATTGT
36236 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
36261 TATGCCTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37932 original size:19 final size:20
Alignment explanation
Indices: 37897--37948 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
37887 AAAATGACCA
*
37897 AAATATTCGCAACGCGATCTC
1 AAAT-TTCGCAACGCGAACTC
*
37918 AAATTT-GCAATGCGAACTC
1 AAATTTCGCAACGCGAACTC
*
37937 CAATTTCGCAAC
1 AAATTTCGCAAC
37949 CCAATTTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 16 0.62
20 6 0.23
21 4 0.15
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (20 bp):
AAATTTCGCAACGCGAACTC
Found at i:38008 original size:20 final size:20
Alignment explanation
Indices: 37982--38250 Score: 163
Period size: 20 Copynumber: 13.3 Consensus size: 20
37972 AATATGTAAA
37982 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
** *** *
38002 TTACAACGTGGTAGTCAAA-
1 TCGCAACACAGAAGTCAAAT
* *
38021 TCTGCAACAAAAAAGTCAAAT
1 TC-GCAACACAGAAGTCAAAT
* *
38042 TCGCAACAAAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
38062 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
38082 TCGCAACACTGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
** *
38103 TCATAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
38123 TCGCAATGC-GACAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
38143 TCGTAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
38163 TCGTAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* * *
38183 TCGCAACACTGAATTTTAAAT
1 TCGCAACACAGAA-GTCAAAT
38204 TCGCAACACA-ATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* * *
38224 GCGCAACGCAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
38244 TCACAAC
1 TCGCAAC
38251 GCGAAACACA
Statistics
Matches: 197, Mismatches: 42, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.02
20 157 0.80
21 37 0.19
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.21
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:38204 original size:81 final size:80
Alignment explanation
Indices: 38025--38255 Score: 239
Period size: 81 Copynumber: 2.9 Consensus size: 80
38015 GTCAAATCTG
* * * *
38025 CAACAAAAAAGTCAAATTCGCAACAAAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACA
1 CAACACAAAAGTCAAATTCGCAACACAACAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACG
*
38090 CTGAATTTCAAATTCA
66 C-GAATGTCAAATTCA
* ** * * *
38106 TAACACAAAAGTCAAATTCGCAATGCGACAGTCAAATTCGTAACGCGATAGTCAAATTCGTAACG
1 CAACACAAAAGTCAAATTCGCAACACAACAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACG
*
38171 CG-ATAGTCAAATTCG
66 CGAAT-GTCAAATTCA
* ** * * * * * *
38186 CAACACTGAATTTTAAATTCGCAACACAATAGTCAAATGCGCAACGCAAAAGTCAAATTCACAAC
1 CAACAC-AAAAGTCAAATTCGCAACACAACAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAC
38251 GCGAA
65 GCGAA
38256 ACACAATATT
Statistics
Matches: 120, Mismatches: 27, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
79 2 0.02
80 14 0.12
81 103 0.86
82 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (80 bp):
CAACACAAAAGTCAAATTCGCAACACAACAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACG
CGAATGTCAAATTCA
Found at i:38251 original size:20 final size:20
Alignment explanation
Indices: 38032--38256 Score: 191
Period size: 20 Copynumber: 11.2 Consensus size: 20
38022 CTGCAACAAA
***
38032 AAAGTCAAATTCGCAACAAA
1 AAAGTCAAATTCGCAACGCG
38052 AAAGTCAAATTCGCAACGCG
1 AAAGTCAAATTCGCAACGCG
* *
38072 ATAGTCAAATTCGCAACACTG
1 AAAGTCAAATTCGCAACGC-G
** ** * *
38093 AATTTCAAATTCATAACACA
1 AAAGTCAAATTCGCAACGCG
*
38113 AAAGTCAAATTCGCAATGCG
1 AAAGTCAAATTCGCAACGCG
* *
38133 ACAGTCAAATTCGTAACGCG
1 AAAGTCAAATTCGCAACGCG
* *
38153 ATAGTCAAATTCGTAACGCG
1 AAAGTCAAATTCGCAACGCG
* *
38173 ATAGTCAAATTCGCAACACTG
1 AAAGTCAAATTCGCAACGC-G
** * *
38194 AATTTTAAATTCGCAACAC-
1 AAAGTCAAATTCGCAACGCG
* *
38213 AATAGTCAAATGCGCAACGCA
1 AA-AGTCAAATTCGCAACGCG
*
38234 AAAGTCAAATTCACAACGCG
1 AAAGTCAAATTCGCAACGCG
38254 AAA
1 AAA
38257 CACAATATTA
Statistics
Matches: 165, Mismatches: 36, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
19 2 0.01
20 130 0.79
21 33 0.20
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (20 bp):
AAAGTCAAATTCGCAACGCG
Found at i:38252 original size:101 final size:100
Alignment explanation
Indices: 38013--38256 Score: 317
Period size: 101 Copynumber: 2.4 Consensus size: 100
38003 TACAACGTGG
** ***
38013 TAGTCAAATCTGCAACAAAAAAGTCAAATTCGCAACAAAAAAGTCAAATTCGCAACGCGATAGTC
1 TAGTCAAATC-GCAACGCAAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGATAGTC
*
38078 AAATTCGCAACACTGAATTTCAAATTCATAACACAA
65 AAATTCGCAACACTGAATTTCAAATTCACAACACAA
* * * * * * *
38114 AAGTCAAATTCGCAATGCGACAGTCAAATTCGTAACGCGATAGTCAAATTCGTAACGCGATAGTC
1 TAGTCAAA-TCGCAACGCAAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGATAGTC
* *
38179 AAATTCGCAACACTGAATTTTAAATTCGCAACACAA
65 AAATTCGCAACACTGAATTTCAAATTCACAACACAA
*
38215 TAGTCAAATGCGCAACGCAAAAGTCAAATTCACAACGCGAAA
1 TAGTCAAAT-CGCAACGCAAAAGTCAAATTCGCAACGCGAAA
38257 CACAATATTA
Statistics
Matches: 119, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
100 1 0.01
101 116 0.97
102 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (100 bp):
TAGTCAAATCGCAACGCAAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGATAGTCA
AATTCGCAACACTGAATTTCAAATTCACAACACAA
Found at i:38413 original size:22 final size:22
Alignment explanation
Indices: 38359--38401 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
38349 TCACTCTCTA
* *
38359 CGACGACATCCGTCCCCATCTT
1 CGACGAAATCCATCCCCATCTT
38381 CGACGAAATCCATCCCCATCT
1 CGACGAAATCCATCCCCATCT
38402 CTGGCGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (22 bp):
CGACGAAATCCATCCCCATCTT
Found at i:38809 original size:20 final size:20
Alignment explanation
Indices: 38762--38810 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
38752 AAACTTAAAT
*
38762 TCGCAACACGAAAACCAAAA
1 TCGCAACGCGAAAACCAAAA
**
38782 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAACCAAAA
38802 TCGCAACGC
1 TCGCAACGC
38811 AATTTTAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.08
Consensus pattern (20 bp):
TCGCAACGCGAAAACCAAAA
Found at i:38844 original size:20 final size:20
Alignment explanation
Indices: 38819--38856 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38809 GCAATTTTAG
*
38819 TTTCGCGTTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
38839 TTTCGCATTGCGATTTTC
1 TTTCGCATTGCGATTTTC
38857 TCGTTGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTCAT
Found at i:38854 original size:14 final size:14
Alignment explanation
Indices: 38837--38884 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
38827 TGCGATTTTC
*
38837 ATTTTCGCATTGCG
1 ATTTTCGCGTTGCG
*
38851 ATTTTCTCGTTGCG
1 ATTTTCGCGTTGCG
* *
38865 ATTTTGGTGTTGCG
1 ATTTTCGCGTTGCG
38879 ATTTTC
1 ATTTTC
38885 ATTTTCGTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.10, C:0.17, G:0.23, T:0.50
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:41101 original size:21 final size:21
Alignment explanation
Indices: 41062--41101 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41052 TGCACCTATC
* *
41062 ATCATTCAAGAGGCGCCTTTT
1 ATCATTCAAGAGACCCCTTTT
41083 ATCATTCAAGAGACCCCTT
1 ATCATTCAAGAGACCCCTT
41102 CCACCGTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (21 bp):
ATCATTCAAGAGACCCCTTTT
Found at i:41111 original size:21 final size:21
Alignment explanation
Indices: 41087--41157 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
41077 CCTTTTATCA
41087 TTCAAGAGACCCCT-TCCACCG
1 TTCAAGAGACCCCTGT-CACCG
* *
41108 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGACCCCTGTCACCG
**
41129 TTCAAGAGGTCCC-GTCAGCCG
1 TTCAAGAGACCCCTGTCA-CCG
41150 TTCAAGAG
1 TTCAAGAG
41158 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.09
21 39 0.89
22 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.21
Consensus pattern (21 bp):
TTCAAGAGACCCCTGTCACCG
Found at i:42560 original size:69 final size:66
Alignment explanation
Indices: 42479--42654 Score: 248
Period size: 66 Copynumber: 2.6 Consensus size: 66
42469 TGGGGTACAC
*
42479 TTTTTTTGCTTGTTTAATTGAATTTTACATTGAAAGTTGATTTGTTTAA-TTGATGAGGAAATAA
1 TTTTTTTGCTTGTTTAATTGAATTGT--A---AAAGTTGATTTGTTTAATTTGATGAGGAAATAA
*
42543 GAATTA
61 GAATGA
* *
42549 -TTTTTTGCTTGTTTAATTGAATTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATG
1 TTTTTTTGCTTGTTTAATTGAATTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATG
42613 A
66 A
*
42614 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGAATTGTAAAAGTTGATTTGTT
42655 GTTTTAAATT
Statistics
Matches: 99, Mismatches: 5, Indels: 8
0.88 0.04 0.07
Matches are distributed among these distances:
64 17 0.17
65 18 0.18
66 39 0.39
67 1 0.01
69 24 0.24
ACGTcount: A:0.28, C:0.02, G:0.18, T:0.52
Consensus pattern (66 bp):
TTTTTTTGCTTGTTTAATTGAATTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATG
A
Found at i:42740 original size:20 final size:21
Alignment explanation
Indices: 42702--42816 Score: 141
Period size: 20 Copynumber: 5.7 Consensus size: 21
42692 AGACCTGTTG
** *
42702 AAGGTACAAATTCATAACGCAA
1 AAGGT-CAAATTCGCAACGCGA
*
42724 AAGGT-AAATTTGCAACGCGA
1 AAGGTCAAATTCGCAACGCGA
42744 AAGGT-AAATTCGCAACGCGA
1 AAGGTCAAATTCGCAACGCGA
*
42764 AA-GTCAAATTCGCAACACGA
1 AAGGTCAAATTCGCAACGCGA
42784 AA-GTCAAATTCGCAACGCGA
1 AAGGTCAAATTCGCAACGCGA
42804 AA-GTCAAATTCGC
1 AAGGTCAAATTCGC
42817 GTTGCAATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 2 0.02
20 78 0.92
22 5 0.06
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (21 bp):
AAGGTCAAATTCGCAACGCGA
Found at i:43199 original size:18 final size:18
Alignment explanation
Indices: 43176--43211 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43166 AAGTCGGTTG
*
43176 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
43194 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
43212 CCTTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:45318 original size:24 final size:24
Alignment explanation
Indices: 45268--45318 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
45258 TCCAAGTATG
** *
45268 GACCAAGATCAAAGTCTGGGTATT
1 GACCAAGATCAAAGTCTGAATACT
* *
45292 GACCAAGATCAAATTTTGAATACT
1 GACCAAGATCAAAGTCTGAATACT
45316 GAC
1 GAC
45319 TAATACTCAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (24 bp):
GACCAAGATCAAAGTCTGAATACT
Found at i:45825 original size:19 final size:19
Alignment explanation
Indices: 45765--45877 Score: 156
Period size: 19 Copynumber: 5.9 Consensus size: 19
45755 ACTAAAACCT
* *
45765 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTC-A
* * *
45784 GTTACGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTC-A
45804 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
45823 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
45842 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
45861 GTTGCGAATTTGAAATT
1 GTTGCGAATTTGAAATT
45878 TCTCTTTGCG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
19 64 0.76
20 20 0.24
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:45850 original size:38 final size:39
Alignment explanation
Indices: 45765--45891 Score: 159
Period size: 38 Copynumber: 3.3 Consensus size: 39
45755 ACTAAAACCT
* * * * *
45765 GTTGCGAAATT-AAATTCGTGTTACGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCTA
45804 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAAATTCTA
*
45842 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAAATTTCTC
1 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAAA-TTCTA
*
45882 TTTGCGAATT
1 GTTGCGAATT
45892 CGACTTTTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
38 35 0.45
39 28 0.36
40 15 0.19
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.38
Consensus pattern (39 bp):
GTTGCGAATTTGAAATTCAGTTGCGAATTTGAAATTCTA
Found at i:45873 original size:57 final size:58
Alignment explanation
Indices: 45765--45877 Score: 158
Period size: 58 Copynumber: 2.0 Consensus size: 58
45755 ACTAAAACCT
*
45765 GTTGCGAAATTAAATTCGTGTTACGAATTCGAAAATCTAGTTGCGAATTTGAAATTCA
1 GTTGCGAAATTAAATTCGAGTTACGAATTCGAAAATCTAGTTGCGAATTTGAAATTCA
* * * *
45823 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATT
1 GTTGCGAAATT-AAATTCGAGTTACGAATTCGAAAATCTAGTTGCGAATTTGAAATT
45878 TCTCTTTGCG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 18 0.37
58 25 0.51
59 6 0.12
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (58 bp):
GTTGCGAAATTAAATTCGAGTTACGAATTCGAAAATCTAGTTGCGAATTTGAAATTCA
Found at i:45908 original size:20 final size:20
Alignment explanation
Indices: 45861--46068 Score: 188
Period size: 20 Copynumber: 10.3 Consensus size: 20
45851 TTGAAATTCA
* *
45861 GTTGCGAATTTGAAATTTCTCT
1 GTTGCGAATTTG-ACTTT-TGT
*
45883 -TTGCGAATTCGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
45902 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
45922 GTTGCGAAATTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
45942 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC--TTTTGT
* * * *
45962 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
45982 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
46002 GTTACGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
46022 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
46042 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
46062 GTTGCGA
1 GTTGCGA
46069 TTTACAAATT
Statistics
Matches: 150, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
18 2 0.01
19 5 0.03
20 127 0.85
21 14 0.09
22 2 0.01
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:45927 original size:40 final size:40
Alignment explanation
Indices: 45883--46068 Score: 232
Period size: 40 Copynumber: 4.7 Consensus size: 40
45873 AAATTTCTCT
*
45883 TTGCGAATTCGACTTTTGTGTTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
* *
45923 TTGCGAAATTGACTTTTGTGTTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-TA-TCGCG
* * * * * * *
45963 TTGCAAATTTGACTATCGCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
*
46003 TTACGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
*
46043 TTGCGAATTTGACTTCTGTGTTGCGA
1 TTGCGAATTTGACTTTTGTGTTGCGA
46069 TTTACAAATT
Statistics
Matches: 120, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
38 2 0.02
39 5 0.04
40 107 0.89
41 4 0.03
42 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (40 bp):
TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
Found at i:45947 original size:60 final size:60
Alignment explanation
Indices: 45861--46068 Score: 269
Period size: 60 Copynumber: 3.5 Consensus size: 60
45851 TTGAAATTCA
* *
45861 GTTGCGAATTTGAAATTTCTCT-TTGCGAATTCGACTTTTGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTG-ACTTT-TGTGTTGCGAATTCGACTTTTGTGTTGCGAATTTGACTATCGC
* * * * *
45922 GTTGCGAAATTGACTTTTGTGTTGCGATTTACAGA--TTCGCGTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATT-C-GACTTTTGTGTTGCGAATTTGACTATCGC
* *
45982 GTTGCGAATTTGACTTTTGTGTTACGAATTTGACTTTTGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTCGACTTTTGTGTTGCGAATTTGACTATCGC
*
46042 GTTGCGAATTTGACTTCTGTGTTGCGA
1 GTTGCGAATTTGACTTTTGTGTTGCGA
46069 TTTACAAATT
Statistics
Matches: 126, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
58 2 0.02
59 2 0.02
60 108 0.86
61 12 0.10
62 2 0.02
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (60 bp):
GTTGCGAATTTGACTTTTGTGTTGCGAATTCGACTTTTGTGTTGCGAATTTGACTATCGC
Found at i:46085 original size:20 final size:20
Alignment explanation
Indices: 46062--46104 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
46052 TGACTTCTGT
*
46062 GTTGCGATTTACAAATTTGC
1 GTTGCGATTTACAAATTCGC
*
46082 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
46102 GTT
1 GTT
46105 ACGAAATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:46086 original size:60 final size:59
Alignment explanation
Indices: 45897--46088 Score: 269
Period size: 60 Copynumber: 3.2 Consensus size: 59
45887 GAATTCGACT
* *
45897 TTTGTGTTGCGAATTTGACTATCGCGTTGCGAAATTGACTTTTGTGTTGCGATTTACAGA
1 TTTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTACA-A
* * * *
45957 TTCGCGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTACGAATTTGAC-T
1 TTTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCG-ATTT-ACAA
* *
46017 TTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAA
1 TTTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTAC-AA
46077 TTTGCGTTGCGA
1 TTTGCGTTGCGA
46089 TTTACAGATT
Statistics
Matches: 115, Mismatches: 13, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
58 2 0.02
59 4 0.03
60 103 0.90
61 4 0.03
62 2 0.02
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (59 bp):
TTTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTACAA
Found at i:46088 original size:40 final size:41
Alignment explanation
Indices: 45823--46068 Score: 231
Period size: 40 Copynumber: 6.2 Consensus size: 41
45813 TTGAAATTCA
* * ** **
45823 GTTGCGAATTTGA-AATTC-AGTTGCGAATTTGA-AATTCA
1 GTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTTTGT
* * * *
45861 GTTGCGAATTTGA-AATTTCTCTTTGCGAATTCGACTTTTGT
1 GTTGCGAATTTGACTA-TTCGCGTTGCGAATTTGACTTTTGT
*
45902 GTTGCGAATTTGACTA-TCGCGTTGCGAAATTGACTTTTGT
1 GTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTTTGT
* * * * *
45942 GTTGCG-ATTT-ACAGATTCGCGTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGAC-TATTCGCGTTGCGAATTTGACTTTTGT
* * *
45982 GTTGCGAATTTGACT-TTTGTGTTACGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTTTGT
*
46022 GTTGCGAATTTGACTA-TCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTTTGT
46062 GTTGCGA
1 GTTGCGA
46069 TTTACAAATT
Statistics
Matches: 169, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
38 17 0.10
39 8 0.05
40 122 0.72
41 19 0.11
42 3 0.02
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (41 bp):
GTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTTTGT
Found at i:47949 original size:32 final size:32
Alignment explanation
Indices: 47913--47973 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
47903 TCAAATTACA
*
47913 TAGTCCAACATCTAAACATAATTAAAAAATGT
1 TAGTCCAACATCCAAACATAATTAAAAAATGT
47945 TAGTCCAACATCCAAACATAATTAAAAAA
1 TAGTCCAACATCCAAACATAATTAAAAAA
47974 AATGTCATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (32 bp):
TAGTCCAACATCCAAACATAATTAAAAAATGT
Found at i:48241 original size:68 final size:68
Alignment explanation
Indices: 48059--48327 Score: 363
Period size: 68 Copynumber: 4.0 Consensus size: 68
48049 ATTTTGAAAA
* *
48059 AAATTATAATTGAGTGACCAAAACATAAATTAGATAATATATAAGTGACC-AATAGGTAGTTTAC
1 AAATAATAATTGAGTGAACAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
48123 CCT
66 CCT
* ** * * * *
48126 AAATAA-AAAT-A-T-ATA-TGAA-TTATATTAGATAATATATAAGTGGCCAAATAGGTAGTTCA
1 AAATAATAATTGAGTGA-ACAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTA
48185 CCCT
65 CCCT
48189 AAATAATAATTGAGTGAACAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATTGAGTGAACAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
48254 CCT
66 CCT
* * * *
48257 AAATAATAATCGAGTGACCAAAACATAAGTTAGATAATATATAAGAGACCAAATAGGTAGTTTAC
1 AAATAATAATTGAGTGAACAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
48322 CCT
66 CCT
48325 AAA
1 AAA
48328 AATCGCTAAT
Statistics
Matches: 174, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
62 23 0.13
63 25 0.14
64 4 0.02
65 2 0.01
66 5 0.03
67 8 0.05
68 107 0.61
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.28
Consensus pattern (68 bp):
AAATAATAATTGAGTGAACAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
CCT
Found at i:48479 original size:14 final size:14
Alignment explanation
Indices: 48460--48496 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
48450 TCAGGTTGAG
*
48460 GGGTCGGGTCAATC
1 GGGTCGGGTCAACC
*
48474 GGGTCGGGTTAACC
1 GGGTCGGGTCAACC
48488 GGGTCGGGT
1 GGGTCGGGT
48497 ATTTTTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.19, G:0.49, T:0.22
Consensus pattern (14 bp):
GGGTCGGGTCAACC
Found at i:49958 original size:137 final size:137
Alignment explanation
Indices: 49692--50016 Score: 382
Period size: 137 Copynumber: 2.4 Consensus size: 137
49682 AGTCATCCTT
* * * * * *
49692 AACACGAAGGAATAATGTCGTTCACTGACCAGATCTCCTCAACGCAAAGGAGTAGTATCATCCTC
1 AACACAAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAATGCAAAGGAGCAGTATCATCCTC
* **
49757 AGACAATCAGACCTCCTCAACACGAAGGAATCACATTATCTCCAAATTATCCAAATATGGCTAGA
66 AGACAATCAGACCTCCTCAACACGAAGGAACCACATTATCTCCAAATTATCCAAATACAGCTAGA
*
49822 TGTCATC
131 AGTCATC
* * * *
49829 AACACAAAGGAACAATGTCATCCACCGACTAGATCTCCTCAATGCAAAGGAGCAGTGTCGTCCTC
1 AACACAAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAATGCAAAGGAGCAGTATCATCCTC
* * *** * *
49894 AGACAATCAGACTTCCTCAACATGAAGGAACCTTGTTGTCTCCAAATTATCCAAATACATCTAGA
66 AGACAATCAGACCTCCTCAACACGAAGGAACCACATTATCTCCAAATTATCCAAATACAGCTAGA
*
49959 AGTCCTC
131 AGTCATC
* * * * * *
49966 AACATGAAA-GAACGATGTTGTCCACCGACCAAATCTTCTTAATGCAAAGGA
1 AACA-CAAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAATGCAAAGGA
50017 ACCATGTTAT
Statistics
Matches: 157, Mismatches: 30, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
137 154 0.98
138 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (137 bp):
AACACAAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAATGCAAAGGAGCAGTATCATCCTC
AGACAATCAGACCTCCTCAACACGAAGGAACCACATTATCTCCAAATTATCCAAATACAGCTAGA
AGTCATC
Found at i:50397 original size:3 final size:3
Alignment explanation
Indices: 50384--50426 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
50374 CTGAGTTTTA
*
50384 ATT ATTT ATT ATT ATT ATT ATT AATT AGT ATT ATT AATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT -ATT ATT ATT ATT -ATT ATT A
50427 AAAAGGGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 26 0.74
4 9 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:50402 original size:13 final size:13
Alignment explanation
Indices: 50381--50426 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
50371 TGTCTGAGTT
50381 TTAATTA-T-TTA
1 TTAATTATTATTA
50392 TT-ATTATTATTA
1 TTAATTATTATTA
*
50404 TTAATTAGTATTA
1 TTAATTATTATTA
50417 TTAATTATTA
1 TTAATTATTA
50427 AAAAGGGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 4 0.13
11 3 0.10
12 5 0.17
13 18 0.60
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TTAATTATTATTA
Found at i:50405 original size:16 final size:16
Alignment explanation
Indices: 50384--50426 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
50374 CTGAGTTTTA
*
50384 ATTATTTATTATTATT
1 ATTATTTATTAGTATT
*
50400 ATTATTAATTAGTATT
1 ATTATTTATTAGTATT
*
50416 ATTAATTATTA
1 ATTATTTATTA
50427 AAAAGGGGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTATTTATTAGTATT
Found at i:55667 original size:2 final size:2
Alignment explanation
Indices: 55660--55692 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55650 GGTGATATGC
55660 AT AT 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 AT AT A
55693 ACATTATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56656 original size:21 final size:21
Alignment explanation
Indices: 56631--56677 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
56621 TTCACTTGTT
56631 TTATTTGTTGGCATTCTGGAG
1 TTATTTGTTGGCATTCTGGAG
56652 TTATTTGTTGGCATTCTGGAG
1 TTATTTGTTGGCATTCTGGAG
56673 TTATT
1 TTATT
56678 ATGCCCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.09, G:0.26, T:0.51
Consensus pattern (21 bp):
TTATTTGTTGGCATTCTGGAG
Found at i:71158 original size:18 final size:18
Alignment explanation
Indices: 71135--71169 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
71125 AAATGTTGTC
*
71135 TGAGGTTAGGGAATCATA
1 TGAGGTTAAGGAATCATA
71153 TGAGGTTAAGGAATCAT
1 TGAGGTTAAGGAATCAT
71170 TTGACATTAT
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:0.34, C:0.06, G:0.31, T:0.29
Consensus pattern (18 bp):
TGAGGTTAAGGAATCATA
Found at i:83094 original size:26 final size:26
Alignment explanation
Indices: 83065--83145 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 26
83055 ACCCTTAAAT
*
83065 ATAACATATCACAATTTATTTGATTG
1 ATAAAATATCACAATTTATTTGATTG
* ** *
83091 ATAAAATATTAC-CCTTA----AAT-
1 ATAAAATATCACAATTTATTTGATTG
*
83111 ATAACATATCACAATTTATTTGATTG
1 ATAAAATATCACAATTTATTTGATTG
83137 ATAAAATAT
1 ATAAAATAT
83146 TGCGTGATCA
Statistics
Matches: 38, Mismatches: 11, Indels: 12
0.62 0.18 0.20
Matches are distributed among these distances:
20 10 0.26
21 5 0.13
25 5 0.13
26 18 0.47
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (26 bp):
ATAAAATATCACAATTTATTTGATTG
Found at i:83120 original size:46 final size:46
Alignment explanation
Indices: 83053--83146 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
83043 ATTGTATTGT
83053 TTACCCTTAAATATAACATATCACAATTTATTTGATTGATAAAATA
1 TTACCCTTAAATATAACATATCACAATTTATTTGATTGATAAAATA
83099 TTACCCTTAAATATAACATATCACAATTTATTTGATTGATAAAATA
1 TTACCCTTAAATATAACATATCACAATTTATTTGATTGATAAAATA
83145 TT
1 TT
83147 GCGTGATCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (46 bp):
TTACCCTTAAATATAACATATCACAATTTATTTGATTGATAAAATA
Found at i:85609 original size:17 final size:16
Alignment explanation
Indices: 85582--85613 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
85572 TGGTAGGGAG
85582 ATTTTTTTTAAATAAT
1 ATTTTTTTTAAATAAT
85598 ATTTTATTTTAAATAA
1 ATTTT-TTTTAAATAA
85614 AAACTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTTTTAAATAAT
Done.