Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000538.1 Hibiscus syriacus cultivar Beakdansim tig00001040_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: 296388
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:703 original size:81 final size:81
Alignment explanation
Indices: 609--869 Score: 368
Period size: 80 Copynumber: 3.3 Consensus size: 81
599 ATCTTGCATG
* * * *
609 ATTGTCACCTTTCTGCCAAATGCACAGCTAGGGTATTAATCTTTTACTCAAAGGTATTTAACCTT
1 ATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTT
674 TCATCTAACTGGAATC
66 TCATCTAACTGGAATC
*
690 ATTGACACCTTTCTGTCAAATACACAACTAGGCTATTAATC-TTTACTCAAAGGTATTTAACCTT
1 ATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTT
*
754 TCATCTAA-TTGACATC
66 TCATCTAACTGGA-ATC
* * * * *
770 ATTGACACCTTTCTATCAAATGAACAACTAGGCTATTAATCTCTTACTCAATGGTATTTAACCAT
1 ATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTT
*
835 TCATCTAACTGGCATC
66 TCATCTAACTGGAATC
*
851 A-TGACACCTTT-TTTCAAAT
1 ATTGACACCTTTCTGTCAAAT
870 ACATAGTTAG
Statistics
Matches: 162, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
79 10 0.06
80 82 0.51
81 68 0.42
82 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (81 bp):
ATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTT
TCATCTAACTGGAATC
Found at i:1001 original size:68 final size:68
Alignment explanation
Indices: 834--1354 Score: 746
Period size: 68 Copynumber: 7.7 Consensus size: 68
824 TATTTAACCA
* * * * *
834 TTCATCTAACTGGCATCA-TGACACCTTT-TTTCAAATACATAGTTAGGCCTCAACGGCACTT-G
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
896 -CT
66 CCT
* * * *
898 TCCAT-TCAACTGGCATGATTGACACATTTCCGTCAAATGCACAGTTAGGCCTCAAAGGGACTTA
1 TTCATCT-AACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
*
962 GCTT
65 GCCT
* *
966 TTCATCTAATTAGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
1031 CCA
66 CCT
* * *
1034 TTCATTTAACTGACATGATTGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1099 CCT
66 CCT
* *
1102 TTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1167 CCT
66 CCT
* * * * *
1170 TTCATCTAACTGACATGATTGACACCTTTCTGTCAAATACATAGTTAGGCCTCAAAGGTACTTAT
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
1235 CAT
66 CCT
* *
1238 TTCATCTAACTGGCATGATTGACACCTTTTTGTCAAATGCACAGTTAGACCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1303 CCT
66 CCT
* *
1306 TTCATCTAACTGGCATGATTCACACCTTTCTGTCAAATGCATAGTTAGG
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGG
1355 TCATTATCTT
Statistics
Matches: 402, Mismatches: 49, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
63 1 0.00
64 14 0.03
65 9 0.02
66 27 0.07
67 1 0.00
68 349 0.87
69 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:2100 original size:20 final size:20
Alignment explanation
Indices: 2075--2126 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2065 TTTTGATCAA
*
2075 TGGTATCGATACCATCCT-CT
1 TGGTATCGATACCA-CCTAAT
*
2095 TGGTATCGATACCACTTAAT
1 TGGTATCGATACCACCTAAT
2115 TGGTATCGATAC
1 TGGTATCGATAC
2127 TCTCAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (20 bp):
TGGTATCGATACCACCTAAT
Found at i:2913 original size:82 final size:85
Alignment explanation
Indices: 2686--2914 Score: 281
Period size: 84 Copynumber: 2.7 Consensus size: 85
2676 GGCTTTCTCA
** * * * *
2686 CAAAGAGGAGTCACTTGAAGAATATCCCACTTGACTTT-CTCGTAAAGGGGAGTCATCCAAAGAT
1 CAAAGAGGAACCACTTGAAGAATATACCACTTGGCTTTCCT-GTGAAGGGGAGTCATCTAAAGAT
*
2750 CATCTCACTGGTTCAGACCCG
65 CATCCCACTGGTTCAGACCCG
* * *
2771 CAAAGAGGAACCACCTGAAGAATATACCACAT-GATTTCCTGTGAAGGGGAGTCATCTAAAGATC
1 CAAAGAGGAACCACTTGAAGAATATACCACTTGGCTTTCCTGTGAAGGGGAGTCATCTAAAGATC
2835 A-CCCACCTGGTTCAGACCCG
66 ATCCCA-CTGGTTCAGACCCG
* * *
2855 CGAAG-GGAACC-GTTGAAGAATA-ACCACTTGGCTTTCCTGTGAAGGGGAGTCATTTAAAGA
1 CAAAGAGGAACCACTTGAAGAATATACCACTTGGCTTTCCTGTGAAGGGGAGTCATCTAAAGA
2915 ATTATGATCG
Statistics
Matches: 125, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
81 6 0.05
82 37 0.30
83 9 0.07
84 44 0.35
85 29 0.23
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (85 bp):
CAAAGAGGAACCACTTGAAGAATATACCACTTGGCTTTCCTGTGAAGGGGAGTCATCTAAAGATC
ATCCCACTGGTTCAGACCCG
Found at i:3313 original size:197 final size:194
Alignment explanation
Indices: 2967--3537 Score: 682
Period size: 197 Copynumber: 2.9 Consensus size: 194
2957 TAGAGGAAAT
* *
2967 AGCATAGCTTAAGGCGAGAAGGGTTATCTGTCAACAAAAACTTTCGAGTTCGATTCCATTCAGCT
1 AGCATAGCTCAAGGCGAGAAGGGTTATCTGTAAAC-AAAACTTTCGAGTTCGATTCCATTCAGCT
* * * * *
3032 CGATGACATATCAACCGCATGGTAGC-AATGAACTACTTTCCGGTTGAAGTTTAAACTAAGGTCT
65 CGAAGGCATATCAACCGCATGGTAGCAAAGGAACTACTTTCCGGTTGAAATTTAAACTGAGGTCT
* *
3096 TTAAGTCAAGAAGAAGACCTAGGTTTGCTGCGATTTAGCAACAAGGAACTATCTCCTAGCCGAAT
130 TTAAG---AGAAGAAGACCTAGGTTTGCTGCGATTTAGCAACAAGGAACTAT-TCCCAGCCAAAT
3161 TTAC
191 TTAC
* *
3165 AGCATAACTCAAGGCGAGAAGGGTTATCTGTTAACAAAACTTTCGAGTTCGATTCCATTCAGCTC
1 AGCATAGCTCAAGGCGAGAAGGGTTATCTGTAAACAAAACTTTCGAGTTCGATTCCATTCAGCTC
* * * *
3230 AAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCAGTTGAAATTTAAACTGTGATC
66 GAAGGCATATCAACCGCATGGTAGCAA--AGGAACTACTTTCCGGTTGAAATTTAAACTGAGGTC
* *
3295 TTTAAGAGAAGAAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTATTCCCAGCCAAATTTA
129 TTTAAGAGAAGAAGACCTAGGTTTGCTGCGATTTAGCAACAAGGAACTATTCCCAGCCAAATTTA
3360 C
194 C
* * * * * *
3361 AGCATAGCTCAAGGCGAGAA--GCTATCTATAAAAAAAAGCCTTCGAGTTCGATTTCATTTAGCT
1 AGCATAGCTCAAGGCGAGAAGGGTTATCTGTAAACAAAA-CTTTCGAGTTCGATTCCATTCAGCT
* ** * *
3424 CGAGGGCATATCAACCATATGGTAGCATAAAAGGAACTACTTTCTGGTTGAATTTTCAAACTGAG
65 CGAAGGCATATCAACCGCATGGTAGC---AAAGGAACTACTTTCCGGTTGAAATTT-AAACTGAG
* * * *
3489 GTCCTTAAACTGAGAAGAAGACCAAGG-TTGTCTACGATTTGGCAACAAG
126 GT-CTTTAA--GAGAAGAAGACCTAGGTTTG-CTGCGATTTAGCAACAAG
3538 AAGCCACCTT
Statistics
Matches: 322, Mismatches: 39, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
194 13 0.04
195 44 0.14
196 55 0.17
197 102 0.32
198 40 0.12
199 2 0.01
200 66 0.20
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (194 bp):
AGCATAGCTCAAGGCGAGAAGGGTTATCTGTAAACAAAACTTTCGAGTTCGATTCCATTCAGCTC
GAAGGCATATCAACCGCATGGTAGCAAAGGAACTACTTTCCGGTTGAAATTTAAACTGAGGTCTT
TAAGAGAAGAAGACCTAGGTTTGCTGCGATTTAGCAACAAGGAACTATTCCCAGCCAAATTTAC
Found at i:4399 original size:17 final size:18
Alignment explanation
Indices: 4377--4420 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
4367 CTTTAGATTA
*
4377 TTTATTTAATTATTTTC-
1 TTTATTTAATTATTATCT
*
4394 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
4412 TTTATTTAA
1 TTTATTTAA
4421 AACAACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:4507 original size:20 final size:22
Alignment explanation
Indices: 4470--4510 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
4460 TATTATTATT
4470 TTATTATATTTCTCTTTATTTA
1 TTATTATATTTCTCTTTATTTA
*
4492 TTATTAT-TTTGT-TTTATTT
1 TTATTATATTTCTCTTTATTT
4511 TTTTCCCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (22 bp):
TTATTATATTTCTCTTTATTTA
Found at i:9813 original size:42 final size:42
Alignment explanation
Indices: 9755--9943 Score: 172
Period size: 41 Copynumber: 4.5 Consensus size: 42
9745 AAGATATTAG
*
9755 CGGCATTTTTAC-ATACAAACGCCG-TAAAGGTCTGGTATATA
1 CGGCATTTTT-CGATACAAACGCCGCCAAAGGTCTGGTATATA
9796 CGGCATTTTTCGTATACAAACG-CGCCAAAGGTCTGGTATATA
1 CGGCATTTTTCG-ATACAAACGCCGCCAAAGGTCTGGTATATA
* * * * *
9838 GCGGCGTTTTTTGCATACAAACTCCGCCAAATGTCTGGT-TA-G
1 -CGGCATTTTTCG-ATACAAACGCCGCCAAAGGTCTGGTATATA
* ** *
9880 CGGCATTTTTCGGATACAAACGCTGCCAAATATATGGTATATAA
1 CGGCATTTTTC-GATACAAACGCCGCCAAAGGTCTGGTATAT-A
** *
9924 CGGTTTTTTTGGATACAAAC
1 CGGCATTTTTCGATACAAAC
9944 ACACCAATAT
Statistics
Matches: 122, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
40 1 0.01
41 42 0.34
42 28 0.23
43 29 0.24
44 22 0.18
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (42 bp):
CGGCATTTTTCGATACAAACGCCGCCAAAGGTCTGGTATATA
Found at i:9884 original size:84 final size:85
Alignment explanation
Indices: 9752--9943 Score: 228
Period size: 84 Copynumber: 2.3 Consensus size: 85
9742 GTTAAGATAT
* * * *
9752 TAGCGGCATTTTTACATACAAACGCCGTAAAGGTCTGGTATATACGGCATTTTTCGTATACAAAC
1 TAGCGGCTTTTTTGCATACAAACGCCGCAAAGGTCTGGTATATACGGCATTTTTCGGATACAAAC
* *
9817 GC-GCCAAAGGTCTGGTATA
66 GCTGCCAAAGATATGGTATA
* * *
9836 TAGCGGCGTTTTTTGCATACAAACTCCGCCAAATGTCTGGT-TA-GCGGCATTTTTCGGATACAA
1 TAGCGGC-TTTTTTGCATACAAACGCCG-CAAAGGTCTGGTATATACGGCATTTTTCGGATACAA
*
9899 ACGCTGCCAAATATATGGTATA
64 ACGCTGCCAAAGATATGGTATA
* * *
9921 TAACGGTTTTTTTGGATACAAAC
1 TAGCGGCTTTTTTGCATACAAAC
9944 ACACCAATAT
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
84 44 0.48
85 38 0.41
86 10 0.11
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (85 bp):
TAGCGGCTTTTTTGCATACAAACGCCGCAAAGGTCTGGTATATACGGCATTTTTCGGATACAAAC
GCTGCCAAAGATATGGTATA
Found at i:9933 original size:85 final size:84
Alignment explanation
Indices: 9760--9943 Score: 219
Period size: 85 Copynumber: 2.2 Consensus size: 84
9750 ATTAGCGGCA
* * *
9760 TTTTTACATACAAACGCCGTAAAGGTCTGGTATATACGGCATTTTTCGTATACAAACGCGCCAAA
1 TTTTTGCATACAAACGCCGCAAAGGTCTGGTATATACGGCATTTTTCGGATACAAACGCGCCAAA
* * *
9825 GGTCTGGTATATAGCGGCGT
66 GATATGGTATATAACGG-GT
* * *
9845 TTTTTGCATACAAACTCCGCCAAATGTCTGGT-TA-GCGGCATTTTTCGGATACAAACGCTGCCA
1 TTTTTGCATACAAACGCCG-CAAAGGTCTGGTATATACGGCATTTTTCGGATACAAACGC-GCCA
* *
9908 AATATATGGTATATAACGGTT
64 AAGATATGGTATATAACGGGT
*
9929 TTTTTGGATACAAAC
1 TTTTTGCATACAAAC
9944 ACACCAATAT
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
84 37 0.44
85 38 0.45
86 10 0.12
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (84 bp):
TTTTTGCATACAAACGCCGCAAAGGTCTGGTATATACGGCATTTTTCGGATACAAACGCGCCAAA
GATATGGTATATAACGGGT
Found at i:10362 original size:21 final size:21
Alignment explanation
Indices: 10338--10393 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
10328 TATGCTGATA
*
10338 TGTTGCTTCTCTTTGTGCTTC
1 TGTTGCTTCTCTCTGTGCTTC
*
10359 TGTTTCTTCTCTCTGTGCTTC
1 TGTTGCTTCTCTCTGTGCTTC
* *
10380 TGCTGCTTTTCTCT
1 TGTTGCTTCTCTCT
10394 CTCCTTCCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.00, C:0.27, G:0.16, T:0.57
Consensus pattern (21 bp):
TGTTGCTTCTCTCTGTGCTTC
Found at i:17066 original size:16 final size:16
Alignment explanation
Indices: 17045--17079 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17035 TAATCACTCC
17045 TAAATT-ATAAAACTTT
1 TAAATTGATAAAA-TTT
17061 TAAATTGATAAAATTT
1 TAAATTGATAAAATTT
17077 TAA
1 TAA
17080 GGGAGCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (16 bp):
TAAATTGATAAAATTT
Found at i:19488 original size:41 final size:40
Alignment explanation
Indices: 19434--19545 Score: 145
Period size: 41 Copynumber: 2.8 Consensus size: 40
19424 GCGGTGTTTA
* *
19434 TATTAAAAACGCCATTAAGGGA-AAAATCTACTGTGGCATT
1 TATTAAAAACGCCACTAAGGGACAAAA-CTACTGCGGCATT
*
19474 TATTACAAAACGCCACTAAGGGACAAAACTACTGCGGCGTT
1 TATTA-AAAACGCCACTAAGGGACAAAACTACTGCGGCATT
**
19515 TATTAAAAAACGCCACTAAAAGACAAAACTA
1 TATT-AAAAACGCCACTAAGGGACAAAACTA
19546 TTACGGCGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
40 5 0.08
41 54 0.84
42 5 0.08
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (40 bp):
TATTAAAAACGCCACTAAGGGACAAAACTACTGCGGCATT
Found at i:19553 original size:41 final size:41
Alignment explanation
Indices: 19472--19617 Score: 143
Period size: 41 Copynumber: 3.5 Consensus size: 41
19462 TACTGTGGCA
* ** *
19472 TTTATTACAAAACGCCACTAAGGGACAAAACTACTGCGGCG
1 TTTATTAAAAAACGCCACTAAAAGACAAAACTATTGCGGCG
*
19513 TTTATTAAAAAACGCCACTAAAAGACAAAACTATTACGGCG
1 TTTATTAAAAAACGCCACTAAAAGACAAAACTATTGCGGCG
* **
19554 TTTACGTCAAAAAA-GCCACT-AAAGCACATGACTATTGCGGCG
1 TTTA--TTAAAAAACGCCACTAAAAG-ACAAAACTATTGCGGCG
** * *
19596 TTTGGTCACAAACGCCACTAAA
1 TTTATTAAAAAACGCCACTAAA
19618 TTAAGAGTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
40 4 0.05
41 50 0.58
42 25 0.29
43 7 0.08
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.21
Consensus pattern (41 bp):
TTTATTAAAAAACGCCACTAAAAGACAAAACTATTGCGGCG
Found at i:22068 original size:60 final size:61
Alignment explanation
Indices: 21969--22152 Score: 198
Period size: 60 Copynumber: 3.1 Consensus size: 61
21959 GAATGAATTT
* * * * * *
21969 GGGATGAGATTGGAATGTTCAAAAAGTTT-GGGACCAATTTAGAAAT-AGAGTCATAGTTTA
1 GGGATGAAATTGAAATATTC-AAAAGTTTAAGGACTAATTTAGAAATGAGAGTTATAGTTTA
* * * * *
22029 GGGATGAAATTGAAATGTTTAATAGTTTAAGGACTAATTTAG-AATGAGAGTTATAATTTG
1 GGGATGAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAGAAATGAGAGTTATAGTTTA
* *
22089 GGGATGAAATTGAAATATTCAAAATTTTAAAGA-TCAATTTA-AAATGAGAGTTATAGTTTA
1 GGGATGAAATTGAAATATTCAAAAGTTTAAGGACT-AATTTAGAAATGAGAGTTATAGTTTA
22149 GGGA
1 GGGA
22153 CATATGATGC
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
59 11 0.11
60 93 0.89
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (61 bp):
GGGATGAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAGAAATGAGAGTTATAGTTTA
Found at i:25882 original size:42 final size:41
Alignment explanation
Indices: 25821--26003 Score: 140
Period size: 42 Copynumber: 4.5 Consensus size: 41
25811 GCGGTGTTTA
* * * ** *
25821 TATT-AAAAACACCATTAAGGGAAAAAACTATTGTGGTATT
1 TATTAAAAAACGCCACTAAGGGACAAAACTATTACGGCATT
* *
25861 TATTACAAAAACGCCACTAAGGGACAAAACTACTACGGCGTT
1 TATTA-AAAAACGCCACTAAGGGACAAAACTATTACGGCATT
** *
25903 TATTAAAAAACGCCACTAAAAGACAAAACTATTACGGCGTT
1 TATTAAAAAACGCCACTAAGGGACAAAACTATTACGGCATT
* * * ** * *
25944 TACGTCAAAAAA-GCCACTAAAGCACATGACTATTGCGGC-GT
1 TA--TTAAAAAACGCCACTAAGGGACAAAACTATTACGGCATT
25985 T-TTATAAAAACGCCACTAA
1 TATTA-AAAAACGCCACTAA
26004 AGTACAAGTT
Statistics
Matches: 118, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.02
39 5 0.04
40 12 0.10
41 37 0.31
42 55 0.47
43 7 0.06
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.23
Consensus pattern (41 bp):
TATTAAAAAACGCCACTAAGGGACAAAACTATTACGGCATT
Found at i:25928 original size:41 final size:42
Alignment explanation
Indices: 25859--26004 Score: 158
Period size: 41 Copynumber: 3.5 Consensus size: 42
25849 TATTGTGGTA
** *
25859 TTTATTACAAAAACGCCACTAAGGGACAAAACTACTACGGCG
1 TTTATTACAAAAACGCCACTAAAAGACAAAACTATTACGGCG
25901 TTTATTA-AAAAACGCCACTAAAAGACAAAACTATTACGGCG
1 TTTATTACAAAAACGCCACTAAAAGACAAAACTATTACGGCG
* * ** *
25942 TTTACGT-CAAAAAAGCCACT-AAAGCACATGACTATTGCGGCG
1 TTTA-TTACAAAAACGCCACTAAAAG-ACAAAACTATTACGGCG
*
25984 -TT-TTATAAAAACGCCACTAAA
1 TTTATTACAAAAACGCCACTAAA
26005 GTACAAGTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
39 1 0.01
40 11 0.12
41 43 0.49
42 33 0.38
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (42 bp):
TTTATTACAAAAACGCCACTAAAAGACAAAACTATTACGGCG
Found at i:27643 original size:60 final size:62
Alignment explanation
Indices: 27566--27748 Score: 227
Period size: 60 Copynumber: 3.1 Consensus size: 62
27556 GAATGAATTT
* * * *
27566 GGGATGAGATTGGAATGTTCAAAAAGTTT-GGGACTAATTTAGAAAT-AGAGTCATAGTTTA
1 GGGATGAAATTGAAATGTTCAAAAAGTTTAAGGACTAATTTAGAAATGAGAGTTATAGTTTA
* * *
27626 GGGATGAAATTGAAATGTTC-AATAGTTTAAGGACTAATTTAG-AATGAGAGTTATAATTTG
1 GGGATGAAATTGAAATGTTCAAAAAGTTTAAGGACTAATTTAGAAATGAGAGTTATAGTTTA
* * *
27686 GGGATGAAATTGAAAT-ATCAAAAA-TTTAAAGACCAATTTA-AAATGAGAGTTATAGTTTA
1 GGGATGAAATTGAAATGTTCAAAAAGTTTAAGGACTAATTTAGAAATGAGAGTTATAGTTTA
27745 GGGA
1 GGGA
27749 CATATGATGC
Statistics
Matches: 106, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
59 46 0.43
60 60 0.57
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.32
Consensus pattern (62 bp):
GGGATGAAATTGAAATGTTCAAAAAGTTTAAGGACTAATTTAGAAATGAGAGTTATAGTTTA
Found at i:40879 original size:65 final size:64
Alignment explanation
Indices: 40756--40906 Score: 189
Period size: 65 Copynumber: 2.3 Consensus size: 64
40746 TGCACTAAGG
* * * * *
40756 GTGCATTGATGCATAAAATGCATTCGATGTTTTAAACAAGCCTGGAGTGCATCGATGCATGGTCT
1 GTGCATCGATGCATAAAATGCAATCGATGTTTCAAACAAGCCTGGAGTACATCCATGCATGG-CT
**
40821 GTGCATCGATGCATAAAATGCAATCGATGTTTCCATAA-AATTCT-GAGTACATCCATGCATGGC
1 GTGCATCGATGCATAAAATGCAATCGATGTTT-CA-AACAAGCCTGGAGTACATCCATGCATGGC
40884 T
64 T
*
40885 ATGCATCGATGCATAAAATGCA
1 GTGCATCGATGCATAAAATGCA
40907 TTCAAAATGG
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 23 0.30
65 46 0.61
66 5 0.07
67 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCAATCGATGTTTCAAACAAGCCTGGAGTACATCCATGCATGGCT
Found at i:43582 original size:23 final size:23
Alignment explanation
Indices: 43542--43585 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
43532 ATGCACAGCT
**
43542 GAGTGCATCGATGTATATTCAAG
1 GAGTGCATCGATACATATTCAAG
*
43565 GAGTGCATCGGTACATATTCA
1 GAGTGCATCGATACATATTCA
43586 CGATGTATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (23 bp):
GAGTGCATCGATACATATTCAAG
Found at i:47485 original size:20 final size:20
Alignment explanation
Indices: 47443--47485 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
47433 TTATTTTCAT
* *
47443 TTTTTAATTTTGAAATATCA
1 TTTTTAATTTTGAAAAATAA
47463 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
47483 TTT
1 TTT
47486 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:49103 original size:64 final size:65
Alignment explanation
Indices: 48950--49104 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 65
48940 GCACTAAGGG
* * * *
48950 TGCATCGATGCATAAAATGCATTCAATGTTTTAAACAAACCTGGAGTGCATCGGTGCATGGTCTG
1 TGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGGAGTGCATCGATGCATGGTCTA
* *
49015 TGCATCGATTCATAAAATGCATTCGATGTTTCCATAA-AATCCT-GAGTGCATCGATGCATGG-C
1 TGCATCGATGCATAAAATGCATTCGATGTTT-CA-AACAAACCTGGAGTGCATCGATGCATGGTC
49077 TA
64 TA
49079 TGCATCGATGCATAAAATGCATTCGA
1 TGCATCGATGCATAAAATGCATTCGA
49105 AATGGGTGTG
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 27 0.33
65 46 0.57
66 6 0.07
67 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (65 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGGAGTGCATCGATGCATGGTCTA
Found at i:58322 original size:199 final size:200
Alignment explanation
Indices: 57972--58489 Score: 696
Period size: 199 Copynumber: 2.6 Consensus size: 200
57962 CATTTATTGG
* * *
57972 AAATTTACAGCATAACTCAAGGTGAGAAGGGTTATCTGTCAACAAAAACTTTCGAGTTCGATTCC
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATTCC
* * * * * *
58037 ATTCAGCTCGATGACATATCAACTGC-ATGGTAGCAGCGAGGAACTACTTTCCGGTTGAAGTTTA
66 ATTCAGCTTGA-GGCATATCAAC-CCTATGGTAGCAACAAGGAACTACTTTCCGGTTGAAATTTA
* * *
58101 AACTAATTTCTTTAACTCAAGAAGAATACCTAGGTTTGCTGCAATTTAGCAACAAGGAACTATCT
129 AACTAATGTCTTTAACTCAAGAAGAAGACCTAGGTTAGCTGCAATTTAGCAACAAGGAACTATCT
58166 CCCAGCC
194 CCCAGCC
*
58173 GAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAACTTTCGAGTTCGATT-C
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATTCC
58236 ATTCAGCTTGAAGGCATATCAACCCTATGGTAGCAACAAGGAACTACTTTCCGGTTGAAATTTAA
66 ATTCAGCTTG-AGGCATATCAACCCTATGGTAGCAACAAGGAACTACTTTCCGGTTGAAATTTAA
* * **
58301 ACT-GTGGTCTTTAAGTCAAGAAGAAGACCTAGGTTAGCTGTGATTTAGCAACAAGGAACTATCT
130 ACTAAT-GTCTTTAACTCAAGAAGAAGACCTAGGTTAGCTGCAATTTAGCAACAAGGAACTATCT
*
58365 CTCAGCC
194 CCCAGCC
* * * *
58372 AAATTCATAGCATAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCC
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATT-C
* * *
58437 CA-TCAGC-T--CG-A-ATCAACCATATGGTAGCATCAAGGAACTACTTTCCGGTTGAA
65 CATTCAGCTTGAGGCATATCAACCCTATGGTAGCAACAAGGAACTACTTTCCGGTTGAA
58490 TTTTCTGATT
Statistics
Matches: 285, Mismatches: 26, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
195 40 0.14
196 1 0.00
197 1 0.00
198 2 0.01
199 156 0.55
200 39 0.14
201 44 0.15
202 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (200 bp):
AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATTCC
ATTCAGCTTGAGGCATATCAACCCTATGGTAGCAACAAGGAACTACTTTCCGGTTGAAATTTAAA
CTAATGTCTTTAACTCAAGAAGAAGACCTAGGTTAGCTGCAATTTAGCAACAAGGAACTATCTCC
CAGCC
Found at i:69603 original size:18 final size:18
Alignment explanation
Indices: 69580--69614 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
69570 TTCCATCCGG
*
69580 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
69598 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
69615 GTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:80926 original size:19 final size:18
Alignment explanation
Indices: 80889--80927 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
80879 AATTTAAAGT
*
80889 ATAAAAAAATAAAGGAAA
1 ATAAAAAAATAAAAGAAA
*
80907 ATAATAAAAATAAAATAAA
1 ATAA-AAAAATAAAAGAAA
80926 AT
1 AT
80928 TGTAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (18 bp):
ATAAAAAAATAAAAGAAA
Found at i:82534 original size:118 final size:118
Alignment explanation
Indices: 82327--82621 Score: 400
Period size: 118 Copynumber: 2.5 Consensus size: 118
82317 TCTGAGCTAT
* *
82327 AAGTTCTTCTCATTATGAAC-TTTTC-TCTCACTTCGGACGAGTTCTTCTTATTATGAACTTTTC
1 AAGTTCTTCTCATTATGAACTTTTTCTTC-CTCTTCGGACGAGTTCTTCTCATTATGAACTTTTC
** *
82390 CATTAGGAATGATGATTTATCTCTTTCTATGATAGAATCAAACTAACATTGAAC
65 CATTAGGAATGATGATCCATCACTTTCTATGATAGAATCAAACTAACATTGAAC
* * *
82444 AAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCGGATGAGTTATTCTCATTATGAACTTTTTC
1 AAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCGGACGAGTTCTTCTCATTATGAACTTTTCC
* * * **
82509 GTT-GGAAAT-ATTGATCCATCACTTTCTATGATGGAATCGAACTAAGGTTGAAC
66 ATTAGG-AATGA-TGATCCATCACTTTCTATGATAGAATCAAACTAACATTGAAC
**
82562 AAGTTCTTCTCATTATGAACTACTTCTTCCTCTTCGGACGAGTTCTTCTCATTATGAACT
1 AAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCGGACGAGTTCTTCTCATTATGAACT
82622 CTCCATTGAA
Statistics
Matches: 157, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
117 23 0.15
118 132 0.84
119 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (118 bp):
AAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCGGACGAGTTCTTCTCATTATGAACTTTTCC
ATTAGGAATGATGATCCATCACTTTCTATGATAGAATCAAACTAACATTGAAC
Found at i:82588 original size:20 final size:20
Alignment explanation
Indices: 82565--82621 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
82555 GTTGAACAAG
82565 TTCTTCTCATTATGAACTAC
1 TTCTTCTCATTATGAACTAC
* * * *
82585 TTCTTCCTC-TT-CGGACGAG
1 TTCTT-CTCATTATGAACTAC
82604 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
82622 CTCCATTGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
18 3 0.11
19 11 0.41
20 10 0.37
21 3 0.11
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.44
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTAC
Found at i:85499 original size:134 final size:134
Alignment explanation
Indices: 85297--85870 Score: 665
Period size: 134 Copynumber: 4.3 Consensus size: 134
85287 ATCGAGAAAC
* * * *
85297 GTTGATTCATTCCACTGTTCTTCATGGAAGATTGAATTGAGGCACATTTGTTCCACTGTTACTTA
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCACACTTGTTCCACTATTACTTA
* * ** * *
85362 GGGAATATCAAATCTCAAAAGAGAGGGATCTATTTTGTTTTTTCTTGAGGGAAAATCAAATATAG
66 GGGAATATCAAATCTCGAAAGAGAGGGATTTATTCCGTTTCTTCTTGAGGGAAAATCAAATCTAG
85427 GGAT
131 GGAT
* * * * * *
85431 GTTGATTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGTCAGACTTGTTCCACTGTTACTCA
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCACACTTGTTCCACTATTACTTA
* * * * * * * * * *
85496 GGGAATGTCAAATCTTGAAAGAGGGGGATTTGTTCTGCTTCTT-TCTGAGGGAAAATTAGATGTG
66 GGGAATATCAAATCTCGAAAGAGAGGGATTTATTCCGTTTCTTCT-TGAGGGAAAATCAAATCTA
85560 GGGAT
130 GGGAT
*
85565 GTTGATTCATTCCACTGTTAC-TCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTATTACTT
1 GTTGATTCATTCCACTGTT-CTTCAGGGAAGATTGAATCGAGGCACACTTGTTCCACTATTACTT
* * * *
85629 GGGGAATATCAAATC-CTGAAAGAGATGG-TTATGTTCC-TCTTCTTCTTGAGGAAAAATCAAAT
65 AGGGAATATCAAATCTC-GAAAGAGAGGGATT-TATTCCGT-TTCTTCTTGAGGGAAAATCAAAT
*
85691 CTAGGGAC
127 CTAGGGAT
*
85699 GTTGATTCATTCCACTGATTCTT-AGGGAAGATTGAATCGAGACACACTTGTTCCACTATTACTT
1 GTTGATTCATTCCACTG-TTCTTCAGGGAAGATTGAATCGAGGCACACTTGTTCCACTATTACTT
** * * * * * *
85763 AGGGAATATCAAATCTTTAAAGAGGGGGATTTGTTCCGCTTCTTCCTGATGGAAAATCAGATCTA
65 AGGGAATATCAAATCTCGAAAGAGAGGGATTTATTCCGTTTCTTCTTGAGGGAAAATCAAATCTA
85828 GGGAT
130 GGGAT
* *
85833 GTTGATTAATTCCACTGTTATTCAGGGAAGATTGAATC
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATC
85871 AAGTTTGATT
Statistics
Matches: 374, Mismatches: 54, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
133 7 0.02
134 360 0.96
135 7 0.02
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (134 bp):
GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCACACTTGTTCCACTATTACTTA
GGGAATATCAAATCTCGAAAGAGAGGGATTTATTCCGTTTCTTCTTGAGGGAAAATCAAATCTAG
GGAT
Found at i:85777 original size:268 final size:268
Alignment explanation
Indices: 85297--85870 Score: 807
Period size: 268 Copynumber: 2.1 Consensus size: 268
85287 ATCGAGAAAC
* * * * *
85297 GTTGATTCATTCCACTGTT-CTTCATGGAAGATTGAATTGAGGCACATTTGTTCCACTGTTACTT
1 GTTGATTCATTCCACTGTTAC-TCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTATTACTT
** * *
85361 AGGGAATATCAAATCTCAAAAGAGAGGGATCTATTTTGTTTTTTCTTGAGGGAAAATCAAATATA
65 AGGGAATATCAAATCTCAAAAGAGAGGGATCTATTTCCTTTCTTCTTGAGGAAAAATCAAATATA
* * * *
85426 GGGATGTTGATTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGTCAGACTTGTTCCACTGTT
130 GGGACGTTGATTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGACACACTTGTTCCACTATT
* * * *
85491 ACTCAGGGAATGTCAAATCTTGAAAGAGGGGGATTTGTTCTGCTTCTTTCTGAGGGAAAATTAGA
195 ACTCAGGGAATATCAAATCTTGAAAGAGGGGGATTTGTTCCGCTTCTTCCTGAGGGAAAATCAGA
* *
85556 TGTGGGGAT
260 TCTAGGGAT
*
85565 GTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTATTACTTG
1 GTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTATTACTTA
* * *
85630 GGGAATATCAAATC-CTGAAAGAGATGG-T-TATGTTCCTCTTCTTCTTGAGGAAAAATCAAATC
66 GGGAATATCAAATCTC-AAAAGAGAGGGATCTAT-TTCCT-TTCTTCTTGAGGAAAAATCAAATA
*
85692 TAGGGACGTTGATTCATTCCACTGATTCTT-AGGGAAGATTGAATCGAGACACACTTGTTCCACT
128 TAGGGACGTTGATTCATTCCACT-ATTCTTCAAGGAAGATTGAATCGAGACACACTTGTTCCACT
* * *
85756 ATTACTTAGGGAATATCAAATCTTTAAAGAGGGGGATTTGTTCCGCTTCTTCCTGATGGAAAATC
192 ATTACTCAGGGAATATCAAATCTTGAAAGAGGGGGATTTGTTCCGCTTCTTCCTGAGGGAAAATC
85821 AGATCTAGGGAT
257 AGATCTAGGGAT
* *
85833 GTTGATTAATTCCACTGTTATTCAGGGAAGATTGAATC
1 GTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATC
85871 AAGTTTGATT
Statistics
Matches: 272, Mismatches: 29, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
266 3 0.01
267 5 0.02
268 257 0.94
269 7 0.03
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (268 bp):
GTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTATTACTTA
GGGAATATCAAATCTCAAAAGAGAGGGATCTATTTCCTTTCTTCTTGAGGAAAAATCAAATATAG
GGACGTTGATTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGACACACTTGTTCCACTATTA
CTCAGGGAATATCAAATCTTGAAAGAGGGGGATTTGTTCCGCTTCTTCCTGAGGGAAAATCAGAT
CTAGGGAT
Found at i:92530 original size:13 final size:13
Alignment explanation
Indices: 92512--92557 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
92502 GTCATAAATC
92512 TATGACGCGCATT
1 TATGACGCGCATT
* *
92525 TATGACACACATT
1 TATGACGCGCATT
*
92538 TATGACGCGTATT
1 TATGACGCGCATT
92551 TATGACG
1 TATGACG
92558 TTCCTTGAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:93276 original size:14 final size:14
Alignment explanation
Indices: 93257--93287 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
93247 TTCATCCCCC
93257 ATTATTTAGAAAAA
1 ATTATTTAGAAAAA
93271 ATTATTTAGAAAAA
1 ATTATTTAGAAAAA
93285 ATT
1 ATT
93288 TTCATCCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (14 bp):
ATTATTTAGAAAAA
Found at i:96624 original size:91 final size:90
Alignment explanation
Indices: 96464--96638 Score: 244
Period size: 91 Copynumber: 1.9 Consensus size: 90
96454 CAATAAACTC
* *
96464 ATGTAACATTCTCGGTTGTAACCAAAATTATTACCAATTATGTAACTTTTTAGAGTAGACATGGT
1 ATGTAACATTCTAGGTTGTAACCAAAATTATTACCAATTATGTAACTTTTTAGAGTAAACAT-GT
*
96529 AACATTTTAGGTTAAAATCGGTCGCA
65 AACATTTTAGGATAAAATCGGTCGCA
* * * * *
96555 ATGTAACATTCTAGGTTGTAACCAAGATTGTTTCCAATTGTTTAACTTTTTAGAGTAAACAAT-T
1 ATGTAACATTCTAGGTTGTAACCAAAATTATTACCAATTATGTAACTTTTTAGAGTAAAC-ATGT
96619 AAACATTTTAGGATAAAATC
65 -AACATTTTAGGATAAAATC
96639 CAACGCAAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 71 0.96
92 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (90 bp):
ATGTAACATTCTAGGTTGTAACCAAAATTATTACCAATTATGTAACTTTTTAGAGTAAACATGTA
ACATTTTAGGATAAAATCGGTCGCA
Found at i:98526 original size:85 final size:85
Alignment explanation
Indices: 98367--98527 Score: 207
Period size: 85 Copynumber: 1.9 Consensus size: 85
98357 TGTAAGTCAT
* * * *
98367 ACAAATGTGTGTCATCTTCATTTAAGACGGGGGCTTCAATGACACGCAATGTAAGTCATAAATGC
1 ACAAATGCGTGCCATCTTAATTTAAGACAGGGGCTTCAATGACACGCAATGTAAGTCATAAATGC
* *
98432 GTGTTATAAATTTATGACAC
66 GAGTCATAAATTTATGACAC
* * * *
98452 ACAAATGCGTGCCATCTTAATTTATGACAGGGGCTTCAATGACGCTCAATG-AGCGTCATAAATG
1 ACAAATGCGTGCCATCTTAATTTAAGACAGGGGCTTCAATGACACGCAATGTA-AGTCATAAATG
*
98516 TGAGTCATAAAT
65 CGAGTCATAAAT
98528 GCTTGTCATC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
84 1 0.02
85 63 0.98
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (85 bp):
ACAAATGCGTGCCATCTTAATTTAAGACAGGGGCTTCAATGACACGCAATGTAAGTCATAAATGC
GAGTCATAAATTTATGACAC
Found at i:98548 original size:13 final size:13
Alignment explanation
Indices: 98499--98550 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
98489 AATGACGCTC
*
98499 AATGAGCGTCATA
1 AATGCGCGTCATA
* *
98512 AATGTGAGTCATA
1 AATGCGCGTCATA
** *
98525 AATGCTTGTCATC
1 AATGCGCGTCATA
98538 AATGCGCGTCATA
1 AATGCGCGTCATA
98551 GATTTATGAC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:111726 original size:18 final size:18
Alignment explanation
Indices: 111703--111741 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
111693 AAGACAAAAC
111703 AAAAGAATTCCATGATCG
1 AAAAGAATTCCATGATCG
111721 AAAAGAATTCCATGATCG
1 AAAAGAATTCCATGATCG
111739 AAA
1 AAA
111742 TGGAGTGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (18 bp):
AAAAGAATTCCATGATCG
Found at i:121551 original size:42 final size:42
Alignment explanation
Indices: 121504--121588 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
121494 TCTAATTGTT
121504 GAGCTCCCATTGTGGTTAAATGGGACTCTATAGAAGTAAAGC
1 GAGCTCCCATTGTGGTTAAATGGGACTCTATAGAAGTAAAGC
121546 GAGCTCCCATTGTGGTTAAATGGGACTCTATAGAAGTAAAGC
1 GAGCTCCCATTGTGGTTAAATGGGACTCTATAGAAGTAAAGC
121588 G
1 G
121589 CGAATCTATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (42 bp):
GAGCTCCCATTGTGGTTAAATGGGACTCTATAGAAGTAAAGC
Found at i:123399 original size:20 final size:20
Alignment explanation
Indices: 123320--123407 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 20
123310 ATAACCAGAA
123320 CCCTCA-GGGGGTATCGATT
1 CCCTCATGGGGGTATCGATT
*
123339 CCC-C-TAGTGGGGTAATCGGTT
1 CCCTCAT-G-GGGGT-ATCGATT
* * *
123360 CCCCTTCAAAGGGGGAATCGGTT
1 -CCC-TC-ATGGGGGTATCGATT
123383 CCCTCATGGGGGTATCGATT
1 CCCTCATGGGGGTATCGATT
123403 CCCTC
1 CCCTC
123408 TGCACCAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
18 1 0.02
19 4 0.07
20 22 0.41
21 8 0.15
22 6 0.11
23 7 0.13
24 5 0.09
25 1 0.02
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (20 bp):
CCCTCATGGGGGTATCGATT
Found at i:127251 original size:22 final size:21
Alignment explanation
Indices: 127209--127248 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
127199 GAGTTTATTT
*
127209 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
127230 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
127249 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:131898 original size:16 final size:16
Alignment explanation
Indices: 131877--131907 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
131867 TTGATGCTTA
*
131877 TGGATGTTTGAATTTT
1 TGGATGTTTAAATTTT
131893 TGGATGTTTAAATTT
1 TGGATGTTTAAATTT
131908 GTTTTAGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (16 bp):
TGGATGTTTAAATTTT
Found at i:133864 original size:14 final size:14
Alignment explanation
Indices: 133841--133874 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
133831 GTTCGAATGT
133841 AAAA-AAGAAAAGA
1 AAAAGAAGAAAAGA
133854 AAAAGAAGAAAAGA
1 AAAAGAAGAAAAGA
*
133868 AAGAGAA
1 AAAAGAA
133875 TTTGTTCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAGA
Found at i:140478 original size:3 final size:3
Alignment explanation
Indices: 140472--140525 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
140462 AATTAATTAT
* *
140472 TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
140520 TAA TAA
1 TAA TAA
140526 AAGCGGGACG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:141586 original size:3 final size:3
Alignment explanation
Indices: 141580--141632 Score: 63
Period size: 3 Copynumber: 17.0 Consensus size: 3
141570 ATTTGGTTTT
*
141580 TTA TTA TTTA TTA TTA TTA TTA TTA ATA TTA TTA TTTA TTA TTAA TT-
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TT-A TTA
141627 TTA TTA
1 TTA TTA
141633 CAGGCCCAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 2 0.05
3 33 0.75
4 9 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:141604 original size:19 final size:19
Alignment explanation
Indices: 141580--141632 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
141570 ATTTGGTTTT
141580 TTATTATTTATTATTA-TTA
1 TTATTA-TTATTATTATTTA
*
141599 TTATTAATATTATTATTTA
1 TTATTATTATTATTATTTA
141618 TTATTAATT-TTATTA
1 TTATT-ATTATTATTA
141633 CAGGCCCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 8 0.27
19 20 0.67
20 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTATTATTATTATTTA
Found at i:147151 original size:15 final size:15
Alignment explanation
Indices: 147131--147162 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
147121 ATCAATACCT
147131 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
147146 TTTTGCATACATTCA
1 TTTTGCATACATGCA
147161 TT
1 TT
147163 GCATTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:153629 original size:253 final size:256
Alignment explanation
Indices: 153181--153694 Score: 914
Period size: 253 Copynumber: 2.0 Consensus size: 256
153171 ATGGAGACTA
153181 TGTATAGAAAAGCAATGATCAAATGCTATTGAGATGTTTAAATACAGCGAAGCCAGAAACATCAT
1 TGTATAGAAAAGCAATGATCAAATGCTATTGAGATGTTTAAATACAGCGAAGCCAGAAACATCAT
153246 TGAAGAAGTACACAGTGGAATATGTGAACACATGCAAATGGTCTTTCCATGGCTAGAAAAATAAT
66 TGAAGAAGTA-ACAGTGGAATATGTGAACACATGCAAATGGTCTTTCCATGGCTAGAAAAATAAT
153311 GAGATATGATACTATTGGGCTACCATGCACACAGATTGCATTGATTATGCAAGGAAATGTCATAA
130 GAGATATGATACTATTGGGCTACCATGCACACAGATTGCATTGATTATGCAAGGAAATGTCATAA
153376 ATGCCAGATATATGC-A-AAGATTCATGTA-CCCC-CTCCTTTACATGTAATGACAGCACCC
195 ATGCCAGATATATGCAATAAGATTCATGTACCCCCACTCCTTTACATGTAATGACAGCACCC
*
153434 TGTATAGAAGAAGCAATGATCAAATGCTATTGAGATGTTTAAATACAGCGAAGCCAGAAGCATCA
1 TGTATAGAA-AAGCAATGATCAAATGCTATTGAGATGTTTAAATACAGCGAAGCCAGAAACATCA
*
153499 -TGAAGAAGT-ACAGTGGAATATGTGGAATACATGCAAATGGTCTTTCCATGGCTAGAAAAATAA
65 TTGAAGAAGTAACAGTGGAATATGT-GAACACATGCAAATGGTCTTTCCATGGCTAGAAAAATAA
153562 TGAGATATGGATACTATTGGGCTACCATGCACACAGATTGCATTGATTATGCAAGGAAATGTCAT
129 TGAGATAT-GATACTATTGGGCTACCATGCACACAGATTGCATTGATTATGCAAGGAAATGTCAT
153627 AAATGCCAGATATATGCAAATAAGATTCATGTACCCCCATCTCCTTTACATGTAATGACAGCACC
193 AAATGCCAGATATATGC-AATAAGATTCATGTACCCCCA-CTCCTTTACATGTAATGACAGCACC
153692 C
256 C
153693 TG
1 TG
153695 GCCATTTTCT
Statistics
Matches: 250, Mismatches: 2, Indels: 12
0.95 0.01 0.05
Matches are distributed among these distances:
251 14 0.06
252 46 0.18
253 91 0.36
254 54 0.22
255 1 0.00
256 12 0.05
257 4 0.02
259 28 0.11
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (256 bp):
TGTATAGAAAAGCAATGATCAAATGCTATTGAGATGTTTAAATACAGCGAAGCCAGAAACATCAT
TGAAGAAGTAACAGTGGAATATGTGAACACATGCAAATGGTCTTTCCATGGCTAGAAAAATAATG
AGATATGATACTATTGGGCTACCATGCACACAGATTGCATTGATTATGCAAGGAAATGTCATAAA
TGCCAGATATATGCAATAAGATTCATGTACCCCCACTCCTTTACATGTAATGACAGCACCC
Found at i:155333 original size:35 final size:36
Alignment explanation
Indices: 155271--155342 Score: 137
Period size: 35 Copynumber: 2.0 Consensus size: 36
155261 GTGTTCTTTG
155271 AGTTATCTGATCTGATTTGGTATGAACCCCAAAATC
1 AGTTATCTGATCTGATTTGGTATGAACCCCAAAATC
155307 AGTTATCTGATCTGA-TTGGTATGAACCCCAAAATC
1 AGTTATCTGATCTGATTTGGTATGAACCCCAAAATC
155342 A
1 A
155343 ATCATTGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 21 0.58
36 15 0.42
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (36 bp):
AGTTATCTGATCTGATTTGGTATGAACCCCAAAATC
Found at i:156735 original size:112 final size:113
Alignment explanation
Indices: 156162--156722 Score: 778
Period size: 113 Copynumber: 5.0 Consensus size: 113
156152 TAGCAAAGAT
* * *
156162 TCAAATCCATCAC--AATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
156225 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* *
156273 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
156338 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* *
156386 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
* *
156451 AGAAGGAAAAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * * * * *
156499 TTAAATTCATCATTTGATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACT--T-AT
* ** * *
156563 CTGAAGAA-GAAG-A-AA-TTCAAAATGAGAAGAATTTGTTCAACTTTTTGT
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * * *
156611 TTGAATTCATCACTCGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
* * *
156676 AGAA-GAAGAAGAAGCTCATAATGAAAAGAGCCTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
156723 ATAACTCTAT
Statistics
Matches: 405, Mismatches: 35, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
109 14 0.03
110 2 0.00
111 15 0.04
112 103 0.25
113 256 0.63
114 1 0.00
115 4 0.01
116 10 0.02
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
Found at i:157064 original size:3 final size:3
Alignment explanation
Indices: 157058--157126 Score: 95
Period size: 3 Copynumber: 22.0 Consensus size: 3
157048 ATTTGGCTTT
157058 TTA TTA TTTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
157105 TTA TTTA TTA TTAA TT- TTA TTA
1 TTA -TTA TTA TT-A TTA TTA TTA
157127 CAGGCCCAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.03
3 47 0.77
4 12 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:157103 original size:31 final size:32
Alignment explanation
Indices: 157058--157126 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
157048 ATTTGGCTTT
157058 TTATTATTTATTATTATTATTTATTATT-ATT
1 TTATTATTTATTATTATTATTTATTATTAATT
157089 ATTATTA-TTATTATTATTATTTATTATTAATT
1 -TTATTATTTATTATTATTATTTATTATTAATT
157121 TTATTA
1 TTATTA
157127 CAGGCCCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
31 27 0.75
32 9 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (32 bp):
TTATTATTTATTATTATTATTTATTATTAATT
Found at i:158697 original size:119 final size:118
Alignment explanation
Indices: 158559--158792 Score: 294
Period size: 119 Copynumber: 2.0 Consensus size: 118
158549 TTTAATCCTA
* * * * *
158559 TTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAATAACTGGATGTCCAT
1 TTTTAATATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-CA-
* *
158622 TTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAAT-TATATATTAACTG
64 TTTCTGATATTTCTAAATAAATAAATATCTTA-TTTATAAATATATAAATTAACTG
* * ** *
158677 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCAT
1 TTTTAA-TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
*
158742 TTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAA
65 TTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAA
158793 TATATATTTT
Statistics
Matches: 99, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
118 15 0.15
119 59 0.60
120 5 0.05
121 20 0.20
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (118 bp):
TTTTAATATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATT
TCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAACTG
Found at i:161478 original size:2 final size:2
Alignment explanation
Indices: 161471--161499 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
161461 CAATGTTAAT
161471 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
161500 TCGTGTCAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:166158 original size:16 final size:17
Alignment explanation
Indices: 166134--166167 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
166124 AACCTAAATC
166134 AAAATTAACTCGAACCG
1 AAAATTAACTCGAACCG
*
166151 AAAA-TAACTTGAACCG
1 AAAATTAACTCGAACCG
166167 A
1 A
166168 TAACAACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.50, C:0.21, G:0.12, T:0.18
Consensus pattern (17 bp):
AAAATTAACTCGAACCG
Found at i:166757 original size:17 final size:18
Alignment explanation
Indices: 166712--166760 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
166702 AGAATCCATT
*
166712 TTAATTTAAACTATCATAG
1 TTAATTTAAA-TAACATAG
**
166731 TTGTTTTAAATAACATA-
1 TTAATTTAAATAACATAG
166748 TTAATTTAAATAA
1 TTAATTTAAATAA
166761 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 11 0.44
18 6 0.24
19 8 0.32
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (18 bp):
TTAATTTAAATAACATAG
Found at i:180144 original size:15 final size:15
Alignment explanation
Indices: 180120--180162 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
180110 TGAGTGTTTG
180120 TTTG-TTTATTTTTA
1 TTTGTTTTATTTTTA
180134 TTTGTTTTATTTTT-
1 TTTGTTTTATTTTTA
* *
180148 TTAGTTTTAATTTTA
1 TTTGTTTTATTTTTA
180163 ATATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTGTTTTATTTTTA
Found at i:188166 original size:201 final size:200
Alignment explanation
Indices: 187822--188221 Score: 737
Period size: 201 Copynumber: 2.0 Consensus size: 200
187812 ATTGGGAAAG
187822 TGTTGTTTGGCATTGCTTAAAGACAAGCAACAGTTCAAGTTTTTTTTTTTTTGGATAATTATGAT
1 TGTTGTTTGGCATTGCTTAAAGACAAGCAACAGTTCAAGTTTTTTTTTTTTTGGATAATTATGAT
*
187887 TTTTATTACCCAAAATAGCAAAGTTTTGCTACAATCAATCAACCAATAAGTACAAAAAGAAATCT
66 TTTTATTACCCAAAATAGCAAAGTTTTGCTACAACCAATCAACCAATAAGTACAAAAAGAAATCT
*
187952 ATGCACAACCTATACAAAATCAATGATTGGTAAAACTATAGGCCCCAAACATTACAAAGGAAAAG
131 ATGCACAACCTATACAAAATCAATGATTGGTAAAACTATAAGCCCCAAACATTACAAAGGAAAAG
188017 GTTAC
196 GTTAC
*
188022 TGTTGTTTGGCATTGCTTAAAGACAAGCAACGGTTCAAGTTTTTTTTTTTTTTGGATAATTATGA
1 TGTTGTTTGGCATTGCTTAAAGACAAGCAACAGTTCAAG-TTTTTTTTTTTTTGGATAATTATGA
* *
188087 TTTTTATTACCCAAGATAGCAAAGTTTTGCTACAACCAATCAACCAATCAGTACAAAAAGAAATC
65 TTTTTATTACCCAAAATAGCAAAGTTTTGCTACAACCAATCAACCAATAAGTACAAAAAGAAATC
*
188152 TATGCACAACCTATACAAAATCAATGATTGGTAAAACTATAAGCCCTAAACATTACAAAGGAAAA
130 TATGCACAACCTATACAAAATCAATGATTGGTAAAACTATAAGCCCCAAACATTACAAAGGAAAA
188217 GGTTA
195 GGTTA
188222 GTGCTATTTA
Statistics
Matches: 193, Mismatches: 6, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
200 38 0.20
201 155 0.80
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (200 bp):
TGTTGTTTGGCATTGCTTAAAGACAAGCAACAGTTCAAGTTTTTTTTTTTTTGGATAATTATGAT
TTTTATTACCCAAAATAGCAAAGTTTTGCTACAACCAATCAACCAATAAGTACAAAAAGAAATCT
ATGCACAACCTATACAAAATCAATGATTGGTAAAACTATAAGCCCCAAACATTACAAAGGAAAAG
GTTAC
Found at i:200442 original size:22 final size:21
Alignment explanation
Indices: 200389--200442 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
200379 GAAGAATGGG
* *
200389 TGGTATCGATACTTTTAGCCA
1 TGGTATCAATACTTTTAACCA
* * *
200410 GGGTATTAATACTTTTGAACTA
1 TGGTATCAATACTTTT-AACCA
200432 TGGTATCAATA
1 TGGTATCAATA
200443 TTATCCTAAG
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (21 bp):
TGGTATCAATACTTTTAACCA
Found at i:209550 original size:21 final size:21
Alignment explanation
Indices: 209526--209565 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
209516 CAGATTGCTC
209526 AGAGGGAACCGATTCCCCCCA
1 AGAGGGAACCGATTCCCCCCA
*
209547 AGAGGGTACCGATTCCCCC
1 AGAGGGAACCGATTCCCCC
209566 TGAATGGTTT
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:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGAGGGAACCGATTCCCCCCA
Found at i:210411 original size:22 final size:22
Alignment explanation
Indices: 210367--210421 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
210357 TAGCATGTTT
*
210367 AAAAAT-AAAACTTAGAATAAA
1 AAAAATGAAAACTTAGAAAAAA
210388 AAAAATGAAAACTT-GAAAAGAA
1 AAAAATGAAAACTTAGAAAA-AA
*
210410 AATAAAAGAAAA
1 AA-AAATGAAAA
210422 GAAATAACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 10 0.34
22 11 0.38
23 8 0.28
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.15
Consensus pattern (22 bp):
AAAAATGAAAACTTAGAAAAAA
Found at i:223419 original size:6 final size:6
Alignment explanation
Indices: 223408--223435 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
223398 AGTACCTCTC
223408 TTTGCA TTTGCA TTTGCA TTTGCA TTTG
1 TTTGCA TTTGCA TTTGCA TTTGCA TTTG
223436 AATTCATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (6 bp):
TTTGCA
Found at i:225456 original size:43 final size:42
Alignment explanation
Indices: 225407--225491 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 42
225397 CAGGATATGG
225407 TGAAATCTTCCTTCTTCAAGGACATATTTCCAGTAACCCTCAA
1 TGAAATCTTCCTTCTTCAAGGACATATTTCCAGTAA-CCTCAA
225450 TGAAATCTTCCTTCTTCAAGGACATATTTCCAGTAACCTCAA
1 TGAAATCTTCCTTCTTCAAGGACATATTTCCAGTAACCTCAA
225492 GAAGAAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 6 0.14
43 36 0.86
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (42 bp):
TGAAATCTTCCTTCTTCAAGGACATATTTCCAGTAACCTCAA
Found at i:225491 original size:23 final size:23
Alignment explanation
Indices: 225422--225492 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
225412 TCTTCCTTCT
225422 TCAAGGACATATTTCCAGTAACCC
1 TCAAGGACATATTTCCAGTAA-CC
* * *
225446 TCAATGA-A-ATCTTCC--T-TCT
1 TCAAGGACATAT-TTCCAGTAACC
225465 TCAAGGACATATTTCCAGTAACC
1 TCAAGGACATATTTCCAGTAACC
225488 TCAAG
1 TCAAG
225493 AAGAAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 13
0.65 0.11 0.24
Matches are distributed among these distances:
19 7 0.20
20 5 0.14
21 3 0.09
22 3 0.09
23 11 0.31
24 6 0.17
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (23 bp):
TCAAGGACATATTTCCAGTAACC
Found at i:232833 original size:36 final size:36
Alignment explanation
Indices: 232750--232930 Score: 267
Period size: 36 Copynumber: 5.1 Consensus size: 36
232740 AGATGAATAA
* *
232750 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-AC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
*
232785 TTGAATCAAAAGTGCCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
*
232821 TTGAATCGAAAGTGCCGATGCTTCTTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
* *
232857 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-AC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
* *
232892 TTTGAATCGAAAGTGCTGATGCTTCCTTTCGTTTTTC
1 -TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
232929 TT
1 TT
232931 ATTCACCTTC
Statistics
Matches: 131, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
35 32 0.24
36 98 0.75
37 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
Found at i:236897 original size:216 final size:218
Alignment explanation
Indices: 236523--236959 Score: 734
Period size: 216 Copynumber: 2.0 Consensus size: 218
236513 CAACATGTCA
*
236523 CCTCTGATGGCATGAACATCTCACAGACAGTGGACTTTAATAATCTAGGTAAATTAATAGTTGGT
1 CCTCTGATGGCATGAACATCTCACAGACAGTGGACTTTAATAATCCAGGTAAATTAATAGTTGGT
*
236588 GATGGTGGTACTTTAGATGTTAAATCTGTTAGTAGATCTCCTCTATTTACATCATCGCGTGTACT
66 GATGGTGGTACTTTAGATGTTAAATCTGTTAGTAGATCTCCTCTATTTACATAATCGCGTGTACT
236653 GTTGTTAACCGATTTGTTGCATGT-G-CCAAGAATCTACTATCGGTGTCAAAGCTTGCTAGGGAT
131 GTTGTTAACCGATTTGTTGCATGTAGACCAAGAATCTACTATCGGTGTCAAAGCTTGCTAGGGAT
236716 AACAACGTTTTCCTTGAATTCTT
196 AACAACGTTTTCCTTGAATTCTT
236739 CCTCTGATGGCATGAACATCTCACAGACAGTGGACTTTAATAATCCAGGTAAATTAATAGTTGGT
1 CCTCTGATGGCATGAACATCTCACAGACAGTGGACTTTAATAATCCAGGTAAATTAATAGTTGGT
* * * *
236804 GATGGTGGTGCTTTAGATGTTAAATCTGTTAGTAGATCTCCTTTATTTACATAATCGTGTGTATT
66 GATGGTGGTACTTTAGATGTTAAATCTGTTAGTAGATCTCCTCTATTTACATAATCGCGTGTACT
236869 GTTGTTAACCGATTTGTTGCATGTGCCAAGAATAACCAAGAATCTACTATCGGTGTCAAAGCTTG
131 GTTGTTAACCGATTTGTTGCATGT----AG----ACCAAGAATCTACTATCGGTGTCAAAGCTTG
236934 CTAGGGATAACAACGTTTTCCTTGAA
188 CTAGGGATAACAACGTTTTCCTTGAA
236960 GTCCATGCAC
Statistics
Matches: 205, Mismatches: 6, Indels: 10
0.93 0.03 0.05
Matches are distributed among these distances:
216 148 0.72
221 1 0.00
226 56 0.27
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (218 bp):
CCTCTGATGGCATGAACATCTCACAGACAGTGGACTTTAATAATCCAGGTAAATTAATAGTTGGT
GATGGTGGTACTTTAGATGTTAAATCTGTTAGTAGATCTCCTCTATTTACATAATCGCGTGTACT
GTTGTTAACCGATTTGTTGCATGTAGACCAAGAATCTACTATCGGTGTCAAAGCTTGCTAGGGAT
AACAACGTTTTCCTTGAATTCTT
Found at i:240234 original size:21 final size:20
Alignment explanation
Indices: 240210--240276 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
240200 ATAGTTTTAA
*
240210 TATTAAATATTATAGTAGAAT
1 TATTAAATATTATATTA-AAT
240231 TATT-AATATTAATATTAAAT
1 TATTAAATATT-ATATTAAAT
* *
240251 TAGTAATTATTTATATTAAAT
1 TATTAAATA-TTATATTAAAT
240272 TATTA
1 TATTA
240277 GTAAATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 12 0.31
21 25 0.64
22 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
TATTAAATATTATATTAAAT
Found at i:240276 original size:24 final size:26
Alignment explanation
Indices: 240206--240291 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 26
240196 TCATATAGTT
*
240206 TTAATATTAAATATTATAGTAG-AATTA
1 TTAATATT-AATATTA-ATTAGTAATTA
240233 TTAATATTAATATTAAATTAGTAATTA
1 TTAATATTAATATT-AATTAGTAATTA
*
240260 TTTATATTAA-ATT-ATTAGTAA--A
1 TTAATATTAATATTAATTAGTAATTA
240282 TTAA-ATTAAT
1 TTAATATTAAT
240292 TACAAGTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
21 5 0.09
22 4 0.08
24 8 0.15
26 13 0.25
27 23 0.43
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (26 bp):
TTAATATTAATATTAATTAGTAATTA
Found at i:240289 original size:21 final size:21
Alignment explanation
Indices: 240228--240290 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
240218 ATTATAGTAG
240228 AATTATTAAT--ATTAATATTA
1 AATTATTAATAAATTAA-ATTA
* * * *
240248 AATTAGTAATTATTTATATTA
1 AATTATTAATAAATTAAATTA
*
240269 AATTATTAGTAAATTAAATTA
1 AATTATTAATAAATTAAATTA
240290 A
1 A
240291 TTACAAGTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
20 9 0.27
21 21 0.64
22 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
AATTATTAATAAATTAAATTA
Found at i:250553 original size:14 final size:14
Alignment explanation
Indices: 250534--250589 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 14
250524 CGTTCGTGAA
*
250534 CGTTCGGTTATGTT
1 CGTTCGTTTATGTT
250548 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
*
250562 CGTTCATTTATGTT
1 CGTTCGTTTATGTT
* *
250576 TGTTCATTTATGTT
1 CGTTCGTTTATGTT
250590 TAATCCAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:250590 original size:14 final size:14
Alignment explanation
Indices: 250541--250589 Score: 80
Period size: 14 Copynumber: 3.5 Consensus size: 14
250531 GAACGTTCGG
*
250541 TTATGTTCGTTCGT
1 TTATGTTCGTTCAT
250555 TTATGTTCGTTCAT
1 TTATGTTCGTTCAT
*
250569 TTATGTTTGTTCAT
1 TTATGTTCGTTCAT
250583 TTATGTT
1 TTATGTT
250590 TAATCCAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.61
Consensus pattern (14 bp):
TTATGTTCGTTCAT
Found at i:251690 original size:16 final size:14
Alignment explanation
Indices: 251669--251703 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
251659 GTCTCCAACG
251669 TTTATGTTCGTGTTCA
1 TTTATGTTCGT-TT-A
251685 TTTATGTTCGTTTA
1 TTTATGTTCGTTTA
251699 TTTAT
1 TTTAT
251704 TAAATGAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 2 0.11
16 11 0.58
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (14 bp):
TTTATGTTCGTTTA
Found at i:251785 original size:16 final size:16
Alignment explanation
Indices: 251764--251796 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
251754 AAAAAAAATT
251764 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
251780 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
251796 T
1 T
251797 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:252594 original size:21 final size:22
Alignment explanation
Indices: 252557--252598 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
252547 ATTTAAAAAT
*
252557 ATTAAAGGAAGTACCGATACTC
1 ATTAAAGGAACTACCGATACTC
252579 ATTAAA-GAACTACCGATACT
1 ATTAAAGGAACTACCGATACT
252599 ACCTGTCCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (22 bp):
ATTAAAGGAACTACCGATACTC
Found at i:252892 original size:30 final size:30
Alignment explanation
Indices: 252857--252920 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
252847 TTCCTTTTGT
252857 AAAGGGTTTTGGTTCTAGCTAAGCCTTTAA
1 AAAGGGTTTTGGTTCTAGCTAAGCCTTTAA
252887 AAAGGGTTTTGGTTCTAGCTAAGCCTTTAA
1 AAAGGGTTTTGGTTCTAGCTAAGCCTTTAA
252917 AAAG
1 AAAG
252921 CTAAGGAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.34
Consensus pattern (30 bp):
AAAGGGTTTTGGTTCTAGCTAAGCCTTTAA
Found at i:255564 original size:20 final size:20
Alignment explanation
Indices: 255535--255681 Score: 137
Period size: 20 Copynumber: 7.7 Consensus size: 20
255525 CTATCGCAAA
255535 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
*
255555 TTCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
*
255575 TTCGCATTGCGA---T--A-
1 TTCGCGTTGCGATTTTCCAT
* *
255589 ATCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATTTTCCAT
* ** *
255609 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
* * *
255630 ATCGCATTACGATTTTCCA-
1 TTCGCGTTGCGATTTTCCAT
255649 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
255669 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
255682 AGTCTACAGT
Statistics
Matches: 102, Mismatches: 17, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
14 10 0.10
15 1 0.01
17 2 0.02
19 17 0.17
20 59 0.58
21 13 0.13
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.39
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:255604 original size:34 final size:34
Alignment explanation
Indices: 255556--255622 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
255546 ATTTTCCATT
*
255556 TCGCATTGCGATTTTCCATTTCGCATTGCGATAA
1 TCGCATTGCGATTTTCCAGTTCGCATTGCGATAA
* *
255590 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATA
1 TCGCATTGCGATTTTCCAGTTCGCATTGCGATA
255623 GTTGAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.37
Consensus pattern (34 bp):
TCGCATTGCGATTTTCCAGTTCGCATTGCGATAA
Found at i:255731 original size:22 final size:22
Alignment explanation
Indices: 255673--255725 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
255663 TTCCATTTCG
* *
255673 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCCACAGTGGT
*
255695 TGTTGCGATAGTCCACAGTGGT
1 CGTTGCGATAGTCCACAGTGGT
255717 CGTTGCGAT
1 CGTTGCGAT
255726 TTTCCAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (22 bp):
CGTTGCGATAGTCCACAGTGGT
Found at i:255847 original size:6 final size:6
Alignment explanation
Indices: 255836--255895 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
255826 AGACACGTAT
255836 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
255883 GACC-C GACC-C GAC
1 GACCAC GACCAC GAC
255896 TCGAGACGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 14 0.26
6 40 0.74
ACGTcount: A:0.30, C:0.52, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:256421 original size:6 final size:6
Alignment explanation
Indices: 256400--256448 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
256390 GTCCGTCTCG
256400 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
256446 GGT
1 GGT
256449 AATACGTGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.23
6 33 0.77
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:256587 original size:22 final size:22
Alignment explanation
Indices: 256561--256613 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
256551 AATTTGGAAA
256561 ATCGCAATGACAACTGTAGACT
1 ATCGCAATGACAACTGTAGACT
** *
256583 ATCGCAACAACAACTGTAGATT
1 ATCGCAATGACAACTGTAGACT
*
256605 ATTGCAATG
1 ATCGCAATG
256614 CGAAATGGAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (22 bp):
ATCGCAATGACAACTGTAGACT
Found at i:256917 original size:25 final size:25
Alignment explanation
Indices: 256888--256936 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
256878 TAGGATTGAA
256888 AAATTCAATTTCAAGAATGAAAAAT
1 AAATTCAATTTCAAGAATGAAAAAT
256913 AAATTCAATTTCAAGAATGAAAAA
1 AAATTCAATTTCAAGAATGAAAAA
256937 GTTGGAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (25 bp):
AAATTCAATTTCAAGAATGAAAAAT
Found at i:261724 original size:22 final size:21
Alignment explanation
Indices: 261674--261737 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
261664 AGTCGAGGGT
* *
261674 TTCATAGGTCCTCCGGGACAA
1 TTCATAGGTCATTCGGGACAA
*
261695 CTCATAGGTCATTCGGGACATA
1 TTCATAGGTCATTCGGGACA-A
261717 TTCATAGGTCATTCGGGACAA
1 TTCATAGGTCATTCGGGACAA
261738 ATTTCATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 18 0.47
22 20 0.53
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCATTCGGGACAA
Found at i:263033 original size:16 final size:16
Alignment explanation
Indices: 263012--263042 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
263002 AGTTGGTGAT
263012 TATATAGAAAGATGCC
1 TATATAGAAAGATGCC
263028 TATATAGAAAGATGC
1 TATATAGAAAGATGC
263043 ATGTGAGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (16 bp):
TATATAGAAAGATGCC
Found at i:268876 original size:12 final size:12
Alignment explanation
Indices: 268859--268885 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
268849 TCAGATCTAA
268859 ATATTTTGGAAT
1 ATATTTTGGAAT
268871 ATATTTTGGAAT
1 ATATTTTGGAAT
268883 ATA
1 ATA
268886 GACATGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (12 bp):
ATATTTTGGAAT
Found at i:271354 original size:29 final size:29
Alignment explanation
Indices: 271318--271458 Score: 228
Period size: 29 Copynumber: 4.8 Consensus size: 29
271308 CAAACTAAAT
* *
271318 TGATGTCATTACTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAAGTAA
** *
271347 AAATGTCATTGCTTATATCATTTAAGTAA
1 TGATGTCATTGCTTACATCATTTAAGTAA
271376 TGATGTCATTGCTTACATCATTTAAGTAA
1 TGATGTCATTGCTTACATCATTTAAGTAA
271405 TGATGTCATTGCTTACATCATTTAAGTAA
1 TGATGTCATTGCTTACATCATTTAAGTAA
271434 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
271459 GTTAGGTGAG
Statistics
Matches: 103, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 98 0.95
30 5 0.05
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAAGTAA
Found at i:276012 original size:29 final size:29
Alignment explanation
Indices: 275977--276058 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
275967 AAACTAAATT
* *
275977 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
276006 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
276035 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
276059 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:284344 original size:17 final size:18
Alignment explanation
Indices: 284324--284357 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
284314 GAAAGTCAAC
284324 GGTCAAC-GGTCGGGTCA
1 GGTCAACGGGTCGGGTCA
284341 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
284358 GGTTCAGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCA
Found at i:291606 original size:17 final size:17
Alignment explanation
Indices: 291586--291622 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
291576 GGAAGTCAAC
291586 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
291603 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
291620 GGT
1 GGT
291623 TGGGTCAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:291607 original size:24 final size:24
Alignment explanation
Indices: 291580--291648 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
291570 GTCAAAGGAA
291580 GTCAACGGTCAACGGTCGGGTCGG
1 GTCAACGGTCAACGGTCGGGTCGG
* *
291604 GTCAACGGTC--GGGTCGGGTTGG
1 GTCAACGGTCAACGGTCGGGTCGG
291626 GTCAGACCGGTCAAACCGGTCGG
1 GTCA-A-CGGTC-AA-CGGTCGG
291649 AACTGGTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 14 0.39
23 1 0.03
24 15 0.42
28 6 0.17
ACGTcount: A:0.16, C:0.25, G:0.42, T:0.17
Consensus pattern (24 bp):
GTCAACGGTCAACGGTCGGGTCGG
Found at i:293296 original size:11 final size:11
Alignment explanation
Indices: 293282--293307 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
293272 TATATAAATT
293282 AATTATAGTAG
1 AATTATAGTAG
293293 AATTATAGTAG
1 AATTATAGTAG
293304 AATT
1 AATT
293308 CAACTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (11 bp):
AATTATAGTAG
Done.