Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000828.1 Hibiscus syriacus cultivar Beakdansim tig00001602_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: 112029
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:4254 original size:11 final size:11
Alignment explanation
Indices: 4238--4269 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
4228 TCACGTCATG
4238 AATCATGACAA
1 AATCATGACAA
4249 AATCATGACAA
1 AATCATGACAA
4260 AATCATGACA
1 AATCATGACA
4270 TTTTACTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (11 bp):
AATCATGACAA
Found at i:21539 original size:3 final size:3
Alignment explanation
Indices: 21525--21588 Score: 53
Period size: 3 Copynumber: 21.3 Consensus size: 3
21515 TAAACCGAAA
* * *
21525 AAT AAT ATT AAT AAT AAT -AT AAT AAA AAT AAT AAAT AAT ACT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
21569 AAAT AAT ATAT AAT -AT AAT A
1 -AAT AAT A-AT AAT AAT AAT A
21589 CATACTATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
2 5 0.10
3 36 0.73
4 8 0.16
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:21561 original size:24 final size:25
Alignment explanation
Indices: 21522--21597 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 25
21512 GAATAAACCG
*
21522 AAAAATAATATTAATAATAATATAAT
1 AAAAATAATA-TAATAATACTATAAT
21548 AAAAATAATA-AATAATACTATAAAT
1 AAAAATAATATAATAATACTAT-AAT
*
21573 AATATATAATATAATACATACTATA
1 AA-AAATAATATAATA-ATACTATA
21598 TATTTATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 10 0.23
25 5 0.11
26 17 0.39
27 5 0.11
28 7 0.16
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAAATAATATAATAATACTATAAT
Found at i:21574 original size:19 final size:16
Alignment explanation
Indices: 21524--21583 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 16
21514 ATAAACCGAA
**
21524 AAATAATATTAATAAT
1 AAATAATAAAAATAAT
21540 AATATAATAAAAATAAT
1 AA-ATAATAAAAATAAT
21557 AAATAATACTATAAATAAT
1 AAATAATA--A-AAATAAT
*
21576 ATATAATA
1 AAATAATA
21584 TAATACATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.22
17 14 0.38
18 1 0.03
19 14 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAATAAAAATAAT
Found at i:21631 original size:31 final size:29
Alignment explanation
Indices: 21588--21648 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 29
21578 ATAATATAAT
*
21588 ACATACTATATATTTATTTAAAAACTATATA
1 ACATACTATATA-TT-TTCAAAAACTATATA
21619 ACATA-TATTATATTTTCAAAAACTATATA
1 ACATACTA-TATATTTTCAAAAACTATATA
21648 A
1 A
21649 TATGTTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 15 0.54
30 4 0.14
31 9 0.32
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (29 bp):
ACATACTATATATTTTCAAAAACTATATA
Found at i:21646 original size:22 final size:23
Alignment explanation
Indices: 21621--21672 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
21611 ACTATATAAC
21621 ATATATTATAT-TTTC-AAAAACT
1 ATATA-TATATGTTTCTAAAAACT
*
21643 ATATA-ATATGTTTCTAAAAATT
1 ATATATATATGTTTCTAAAAACT
21665 ATATATAT
1 ATATATAT
21673 TATATACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 16 0.62
23 2 0.08
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATATATATGTTTCTAAAAACT
Found at i:21651 original size:27 final size:26
Alignment explanation
Indices: 21595--21648 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 26
21585 AATACATACT
21595 ATATATTTATTTAAAAACTATATAAC
1 ATATATTTATTTAAAAACTATATAAC
21621 ATATATTATATTTTCAAAAACTATATAA
1 ATATATT-TA-TTT-AAAAACTATATAA
21649 TATGTTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 7 0.28
27 2 0.08
28 3 0.12
29 13 0.52
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATATTTATTTAAAAACTATATAAC
Found at i:21808 original size:77 final size:71
Alignment explanation
Indices: 21704--21889 Score: 191
Period size: 77 Copynumber: 2.5 Consensus size: 71
21694 TTTTAAAACG
* *
21704 ATATCTATTTGTTTTCAAAATATGTTTTCAAAACTATAT-TATATACGTTTTCAAAAAAACCGAT
1 ATAT-TATATGTTTTCAAAATACGTTTTCAAAACTATATAT-TATACGTTTTC---AAAACC-AT
21768 TTTTTAAAAACTAT
60 TTTTT--AAACTAT
* * *
21782 ATATTATATGTTTTCAAAA-ACCGTTTTTAAAACTATATATTATATGTTTTCAAAACCCTTTTTT
1 ATATTATATGTTTTCAAAATA-CGTTTTCAAAACTATATATTATACGTTTTCAAAACCATTTTTT
*
21846 TAACTAT
65 AAACTAT
21853 ATATTATATGTTTTCAACAATA--TTTTCAAAAACTATA
1 ATATTATATGTTTTCAA-AATACGTTTTC-AAAACTATA
21890 CAATATATCT
Statistics
Matches: 96, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
70 4 0.04
71 32 0.33
72 2 0.02
73 7 0.07
74 6 0.06
76 1 0.01
77 39 0.41
78 5 0.05
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (71 bp):
ATATTATATGTTTTCAAAATACGTTTTCAAAACTATATATTATACGTTTTCAAAACCATTTTTTA
AACTAT
Found at i:21814 original size:36 final size:36
Alignment explanation
Indices: 21666--21869 Score: 193
Period size: 35 Copynumber: 5.6 Consensus size: 36
21656 CTAAAAATTA
* *
21666 TATATATTATATACATTTTCAAAAGCCG-TTTTAAAAC
1 TATATATTATAT--GTTTTCAAAAACCGTTTTTAAAAC
* * * * *
21703 GATAT-CTATTTGTTTTCAAAATA-TGTTTTCAAAAC
1 TATATATTATATGTTTTCAAAA-ACCGTTTTTAAAAC
*
21738 TATAT-TATATACGTTTTCAAAAAAACCGATTTTTTAAAAAC
1 TATATAT-TATATGTTTTC--AAAAACCG--TTTTT-AAAAC
21779 TATATATTATATGTTTTCAAAAACCGTTTTTAAAAC
1 TATATATTATATGTTTTCAAAAACCGTTTTTAAAAC
* **
21815 TATATATTATATGTTTTC-AAAACCCTTTTTTTAAC
1 TATATATTATATGTTTTCAAAAACCGTTTTTAAAAC
21850 TATATATTATATGTTTTCAA
1 TATATATTATATGTTTTCAA
21870 CAATATTTTC
Statistics
Matches: 139, Mismatches: 17, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
34 10 0.07
35 44 0.32
36 37 0.27
37 10 0.07
38 5 0.04
39 8 0.06
40 4 0.03
41 20 0.14
42 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (36 bp):
TATATATTATATGTTTTCAAAAACCGTTTTTAAAAC
Found at i:21894 original size:20 final size:22
Alignment explanation
Indices: 21869--21911 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21859 TATGTTTTCA
21869 ACAATAT-T-TTCAAAAACTAT
1 ACAATATATCTTCAAAAACTAT
*
21889 ACAATATATCTTCAAAATCTAT
1 ACAATATATCTTCAAAAACTAT
21911 A
1 A
21912 TGTATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 1 0.05
22 12 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (22 bp):
ACAATATATCTTCAAAAACTAT
Found at i:23958 original size:12 final size:12
Alignment explanation
Indices: 23941--23995 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
23931 TTTTTCCTTC
23941 TCCTATTGAAAA
1 TCCTATTGAAAA
*
23953 TCCTATTGAACA
1 TCCTATTGAAAA
* *
23965 TCCTATTGATAT
1 TCCTATTGAAAA
**
23977 TTTTATTGAAAA
1 TCCTATTGAAAA
23989 TCCTATT
1 TCCTATT
23996 CATCACTCTG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (12 bp):
TCCTATTGAAAA
Found at i:27036 original size:21 final size:21
Alignment explanation
Indices: 26939--27119 Score: 141
Period size: 21 Copynumber: 8.9 Consensus size: 21
26929 ATAACCAATA
*
26939 AATTCGCAACTC--AATTTCG
1 AATTCGCAACACAGAATTTCG
* *
26958 AATTCGCAACAC-GAA-CTCC
1 AATTCGCAACACAGAATTTCG
26977 AATTTCGCAACACAG--TTTCCG
1 AA-TTCGCAACACAGAATTT-CG
* *
26998 AATTCGCAACTC-GAATTTGG
1 AATTCGCAACACAGAATTTCG
*
27018 AATTCGCAACACAGAATTTGG
1 AATTCGCAACACAGAATTTCG
* * *
27039 AATTTGCAACACAAAATTTGG
1 AATTCGCAACACAGAATTTCG
*
27060 AATTCGCAACACAGAA-GTCG
1 AATTCGCAACACAGAATTTCG
*
27080 AATTCGCAACTC-GAATTT-G
1 AATTCGCAACACAGAATTTCG
27099 ACAATTTCGCAACACA-AATTT
1 --AA-TTCGCAACACAGAATTT
27120 ATTTTTCGCA
Statistics
Matches: 132, Mismatches: 17, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
19 20 0.15
20 48 0.36
21 50 0.38
22 14 0.11
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (21 bp):
AATTCGCAACACAGAATTTCG
Found at i:27240 original size:20 final size:20
Alignment explanation
Indices: 26939--27252 Score: 126
Period size: 20 Copynumber: 15.6 Consensus size: 20
26929 ATAACCAATA
* *
26939 AATTCGCAACTC-AATTTCG
1 AATTCGCAACACGAATTTTG
* **
26958 AATTCGCAACACGAA-CTCC
1 AATTCGCAACACGAATTTTG
* *
26977 AATTTCGCAACAC-AGTTTCCG
1 AA-TTCGCAACACGAATTT-TG
* *
26998 AATTCGCAACTCGAATTTGG
1 AATTCGCAACACGAATTTTG
*
27018 AATTCGCAACACAGAATTTGG
1 AATTCGCAACAC-GAATTTTG
* * *
27039 AATTTGCAACACAAAATTTGG
1 AATTCGCAACAC-GAATTTTG
* *
27060 AATTCGCAACACAGAA-GTCG
1 AATTCGCAACAC-GAATTTTG
*
27080 AATTCGCAACTCGAA-TTTG
1 AATTCGCAACACGAATTTTG
*
27099 ACAATTTCGCAACACAAATTTAT-
1 --AA-TTCGCAACACGAATTT-TG
** * * * *
27122 TTTTCGCAACTCTATTTTTA
1 AATTCGCAACACGAATTTTG
* * *
27142 AATTCGCAACAAGATTTTTT
1 AATTCGCAACACGAATTTTG
* * *
27162 AATTCGTAACACG-AGTTTC
1 AATTCGCAACACGAATTTTG
* * *
27181 ATTTTCACAACACGAA-TTTC
1 A-ATTCGCAACACGAATTTTG
* * *
27201 ATTTTAGCAACTC-AATTTTTG
1 A-ATTCGCAACACGAA-TTTTG
27222 AATTCGCAACACGAATTTT-
1 AATTCGCAACACGAATTTTG
27241 AATTTCGCAACA
1 AA-TTCGCAACA
27253 AAGCTTTTAT
Statistics
Matches: 230, Mismatches: 47, Indels: 35
0.74 0.15 0.11
Matches are distributed among these distances:
19 30 0.13
20 129 0.56
21 57 0.25
22 11 0.05
23 2 0.01
24 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (20 bp):
AATTCGCAACACGAATTTTG
Found at i:27266 original size:19 final size:19
Alignment explanation
Indices: 27237--27312 Score: 125
Period size: 19 Copynumber: 3.9 Consensus size: 19
27227 GCAACACGAA
27237 TTTTAATTTCGCAACAAAGC
1 TTTT-ATTTCGCAACAAAGC
27257 TTTTATTTCGCAACAAAGC
1 TTTTATTTCGCAACAAAGC
27276 TTTTATTTCGCAACAAAGC
1 TTTTATTTCGCAACAAAGC
*
27295 TTTTATTTTTGCAACAAA
1 TTTTA-TTTCGCAACAAA
27313 AATGTTTTGG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 39 0.72
20 15 0.28
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (19 bp):
TTTTATTTCGCAACAAAGC
Found at i:31871 original size:80 final size:80
Alignment explanation
Indices: 31725--31888 Score: 231
Period size: 80 Copynumber: 2.0 Consensus size: 80
31715 CCTTACAGAC
* * * *
31725 CTAAGGATATCTTGGGTAGGCCCCAAGGCATATCCTTAGGTTGATTCCCTTTATTGTGTGCATAA
1 CTAAGGATACCTTAGGTAGGCCCCAAGGCATATCCTTAGGTTGATTCCCTTTACTGTGCGCATAA
31790 GGTAACCCTAAAGAT
66 GGTAACCCTAAAGAT
* * *
31805 CTAAGGATACCCTTAGGTAGG-CCCAAGGCATATCCTTAGGTTGGTTCCCTTTGCTGTGCGCTTA
1 CTAAGGATA-CCTTAGGTAGGCCCCAAGGCATATCCTTAGGTTGATTCCCTTTACTGTGCGCATA
**
31869 AGGTAACCCTACGGAT
65 AGGTAACCCTAAAGAT
31885 CTAA
1 CTAA
31889 ACCCAAGGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 65 0.88
81 9 0.12
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (80 bp):
CTAAGGATACCTTAGGTAGGCCCCAAGGCATATCCTTAGGTTGATTCCCTTTACTGTGCGCATAA
GGTAACCCTAAAGAT
Found at i:31904 original size:64 final size:65
Alignment explanation
Indices: 31826--31953 Score: 204
Period size: 65 Copynumber: 2.0 Consensus size: 65
31816 CTTAGGTAGG
*
31826 CCCAAGGCATATCCTTAGGTTG-GTTCCCTTTGCTGTGCGCTTAAGGTAACCCTACGGATCTAAA
1 CCCAAGGCATATCCTTAGATTGAGTTCCCTTTGCTGTGCGCTTAAGGTAACCCTACGGATCTAAA
* * * *
31890 CCCAAGGTATATCCTTAGATTGATTTCCTTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTAA
1 CCCAAGGCATATCCTTAGATTGAGTTCCCTTTGCTGTGCGCTTAAGGTAACCCTACGGATCTAA
31954 GGATATCCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
64 20 0.34
65 38 0.66
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (65 bp):
CCCAAGGCATATCCTTAGATTGAGTTCCCTTTGCTGTGCGCTTAAGGTAACCCTACGGATCTAAA
Found at i:34639 original size:2 final size:2
Alignment explanation
Indices: 34634--34670 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34624 CTGTTTACTT
34634 TA TA TA TA 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 TA TA TA TA T
34671 CATTTTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34725 original size:2 final size:2
Alignment explanation
Indices: 34718--34752 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34708 TTTACATTGT
34718 TA TA TA 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 TA TA TA T
34753 TATCATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35270 original size:6 final size:6
Alignment explanation
Indices: 35259--35286 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
35249 ATCGAGTTTT
35259 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
35287 TCATAATTAA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:38795 original size:64 final size:64
Alignment explanation
Indices: 38694--39244 Score: 850
Period size: 64 Copynumber: 8.6 Consensus size: 64
38684 TGTAGCTTTT
* *
38694 AGAGTCAATTTCAACTTCACAACGAAAGATATTGGACTCAACAAACAACGTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
*
38758 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * *
38822 AAAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAATAACGTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
38886 AGAGTCAATTTCAACTTCACAACGAATGATATTAGACTCAACAAATAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * *
38950 AGAGTTAATTTTAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAATTTCATTT
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
39014 AGAGTAAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAATAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
39078 AGAATCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAATAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* ** *
39142 AGAGTCAATTTCAACTTCACAGCGAACAATATTGGACTCAACAAACAACTTTCCAGTTTCAATC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
** * *
39206 AGAGTCAATTTCAACTTCACAGTGGAGTATATTGGACTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
39245 GAAAAAATAC
Statistics
Matches: 446, Mismatches: 41, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 446 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:39359 original size:65 final size:64
Alignment explanation
Indices: 39255--39431 Score: 236
Period size: 65 Copynumber: 2.8 Consensus size: 64
39245 GAAAAAATAC
* * *
39255 AACTTACACGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACTAATTTGGTGA
1 AACTTACTC-AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTGA
39320 AACTTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTGA
1 AACTTACTC-AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTGA
* * * * *
39385 AAC--AATC--CTTGGATTTCAACTTCATGACGAAGGATATCTAATTCAAA
1 AACTTACTCAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAA
39432 GCTCAACTTC
Statistics
Matches: 103, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
60 36 0.35
63 3 0.03
65 64 0.62
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (64 bp):
AACTTACTCAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTGA
Found at i:39539 original size:121 final size:121
Alignment explanation
Indices: 39391--39609 Score: 366
Period size: 121 Copynumber: 1.8 Consensus size: 121
39381 GTGAAACAAT
* * * *
39391 CCTTGGATTTCAACTTCATGACGAAGGATATCTAATTCAAAGCTCAACTTCACAACGAATTAGCC
1 CCTTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCC
* *
39456 ATCCATGATTTCAACTTCACGATGAAGAATATCGTGCCCACAAGAAGCAATGCAAC
66 ATCCACGATTTCAACTTCACGACGAAGAATATCGTGCCCACAAGAAGCAATGCAAC
*
39512 CCTTGGATTTCAACTTCACGATAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCC
1 CCTTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCC
*
39577 ATCCACGATTTCAACTTCACGACGAAGGATATC
66 ATCCACGATTTCAACTTCACGACGAAGAATATC
39610 CAATTCAAAG
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 90 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.25
Consensus pattern (121 bp):
CCTTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCC
ATCCACGATTTCAACTTCACGACGAAGAATATCGTGCCCACAAGAAGCAATGCAAC
Found at i:39596 original size:32 final size:32
Alignment explanation
Indices: 39555--39664 Score: 123
Period size: 32 Copynumber: 3.4 Consensus size: 32
39545 AATTCAAAGC
*
39555 TCAACTTCACAACGAATGAGCCATCCACGATT
1 TCAACTTCACAACGAAGGAGCCATCCACGATT
* * * * **
39587 TCAACTTCACGACGAAGGATATCCAATTCA-AAGC
1 TCAACTTCACAACGAAGG--AGCC-ATCCACGATT
39621 TCAACTTCACAACGAAGGAGCCATCCACGATT
1 TCAACTTCACAACGAAGGAGCCATCCACGATT
39653 TCAACTTCACAA
1 TCAACTTCACAA
39665 TAAAGGATAT
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
31 4 0.07
32 32 0.52
34 21 0.34
35 4 0.07
ACGTcount: A:0.36, C:0.30, G:0.13, T:0.21
Consensus pattern (32 bp):
TCAACTTCACAACGAAGGAGCCATCCACGATT
Found at i:39623 original size:66 final size:66
Alignment explanation
Indices: 39517--39983 Score: 313
Period size: 66 Copynumber: 7.4 Consensus size: 66
39507 GCAACCCTTG
* *
39517 GATTTCAACTTCACGATAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
39582 C
66 C
*
39583 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
1 GATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
39648 C
66 C
* * * *
39649 GATTTCAACTTCACAATAAAGGATAT-C-ATGCCCACAAGCAGCAA--T-ACAAC-------CC-
1 GATTTCAACTTCACGACAAAGGATATCCAAT--TCA-AAGC-TCAACTTCACAACGAAGGAGCCA
**
39701 T--TG
62 TCCAC
* * *
39704 TATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
*
39769 T
66 C
* * * * * * ** * * * *
39770 AATATCAATTTCACGACGAAGGATAT-C-GTGCCCA--T-AA--GCAGCAATGCA--A-CC--CT
1 GATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCA-CAACGAAGGAGCCATCC
**
39823 TG
65 AC
** * *
39825 GATTTCAACTTCACGATGAAGGATATCCAATTCAAATCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
*
39890 T
66 C
** * * * *
39891 GATTTCAACTTCACGATGAAGGATATCCAATTTAAAGTTCAACTTCGCAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
39956 C
66 C
* * * **
39957 AATTTTAACTTTACGATGAAGGATATC
1 GATTTCAACTTCACGACAAAGGATATC
39984 GTGCCTAACG
Statistics
Matches: 316, Mismatches: 53, Indels: 64
0.73 0.12 0.15
Matches are distributed among these distances:
53 3 0.01
54 4 0.01
55 48 0.15
56 7 0.02
57 8 0.03
58 3 0.01
59 3 0.01
60 7 0.02
61 7 0.02
62 3 0.01
63 3 0.01
64 8 0.03
65 7 0.02
66 198 0.63
67 4 0.01
68 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (66 bp):
GATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
C
Found at i:39623 original size:187 final size:187
Alignment explanation
Indices: 39396--39796 Score: 640
Period size: 187 Copynumber: 2.1 Consensus size: 187
39386 ACAATCCTTG
* * **
39396 GATTTCAACTTCATGACGAAGGATATCTAATTCAAAGCTCAACTTCACAACGAATTAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
* * * * *
39461 TGATTTCAACTTCACGATGAAGAATATCGTGCCCACAAGAAGCAATGCAACCCTTGGATTTCAAC
66 CGATTTCAACTTCACAATAAAGAATATCATGCCCACAAGAAGCAATACAACCCTTGGATTTCAAC
*
39526 TTCACGATAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
131 TTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
39583 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
* * *
39648 CGATTTCAACTTCACAATAAAGGATATCATGCCCACAAGCAGCAATACAACCCTTGTATTTCAAC
66 CGATTTCAACTTCACAATAAAGAATATCATGCCCACAAGAAGCAATACAACCCTTGGATTTCAAC
* *
39713 TTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAT
131 TTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
* * *
39770 AATATCAATTTCACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
39797 GTGCCCATAA
Statistics
Matches: 196, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
187 196 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (187 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
CGATTTCAACTTCACAATAAAGAATATCATGCCCACAAGAAGCAATACAACCCTTGGATTTCAAC
TTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
Found at i:39636 original size:34 final size:34
Alignment explanation
Indices: 39521--39639 Score: 118
Period size: 34 Copynumber: 3.6 Consensus size: 34
39511 CCCTTGGATT
* **
39521 TCAACTTCACGATAAAGGATATCCAATTCAAAGC
1 TCAACTTCACAACGAAGGATATCCAATTCAAAGC
* * * * **
39555 TCAACTTCACAACGAATG--AGCC-ATCCACGATT
1 TCAACTTCACAACGAAGGATATCCAATTCA-AAGC
*
39587 TCAACTTCACGACGAAGGATATCCAATTCAAAGC
1 TCAACTTCACAACGAAGGATATCCAATTCAAAGC
39621 TCAACTTCACAACGAAGGA
1 TCAACTTCACAACGAAGGA
39640 GCCATCCACG
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
31 4 0.06
32 20 0.31
34 36 0.56
35 4 0.06
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (34 bp):
TCAACTTCACAACGAAGGATATCCAATTCAAAGC
Found at i:39738 original size:308 final size:308
Alignment explanation
Indices: 39386--39988 Score: 972
Period size: 308 Copynumber: 2.0 Consensus size: 308
39376 ATTTGGTGAA
* * *
39386 ACAATCCTTGGATTTCAACTTCATGACGAAGGATATCTAATTCAAAGCTCAACTTCACAACGAAT
1 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAT
* * * *
39451 TAGCCATCCATGATTTCAACTTCACGATGAAGAATATCGTGCCCACAAGAAGCAATGCAACCCTT
66 GAGCCATCCATAATATCAACTTCACGACGAAGAATATCGTGCCCACAAGAAGCAATGCAACCCTT
39516 GGATTTCAACTTCACGATAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCC
131 GGATTTCAACTTCACGATAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCC
39581 ACGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATC
196 ACGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATC
*
39646 CACGATTTCAACTTCACAATAAAGGATATCATGCCCACAAGCAGCAAT
261 CACAATTTCAACTTCACAATAAAGGATATCATGCCCACAAGCAGCAAT
*
39694 ACAACCCTTGTATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAT
1 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAT
* * * *
39759 GAGCCATCCATAATATCAATTTCACGACGAAGGATATCGTGCCCATAAGCAGCAATGCAACCCTT
66 GAGCCATCCATAATATCAACTTCACGACGAAGAATATCGTGCCCACAAGAAGCAATGCAACCCTT
* *
39824 GGATTTCAACTTCACGATGAAGGATATCCAATTCAAATCTCAACTTCACAACGAATGAGCCATCC
131 GGATTTCAACTTCACGATAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCC
* * * * * *
39889 ATGATTTCAACTTCACGATGAAGGATATCCAATTTAAAGTTCAACTTCGCAACGAATGAGCCATC
196 ACGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATC
* * * * *
39954 CACAATTTTAACTTTACGATGAAGGATATCGTGCC
261 CACAATTTCAACTTCACAATAAAGGATATCATGCC
39989 TAACGGATCG
Statistics
Matches: 269, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
308 269 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (308 bp):
ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAT
GAGCCATCCATAATATCAACTTCACGACGAAGAATATCGTGCCCACAAGAAGCAATGCAACCCTT
GGATTTCAACTTCACGATAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCC
ACGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATC
CACAATTTCAACTTCACAATAAAGGATATCATGCCCACAAGCAGCAAT
Found at i:39802 original size:121 final size:121
Alignment explanation
Indices: 39583--39917 Score: 544
Period size: 121 Copynumber: 2.8 Consensus size: 121
39573 AGCCATCCAC
*
39583 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
* * *
39648 CGATTTCAACTTCACAATAAAGGATATCATGCCCACAAGCAGCAATACAACCCTTG
66 TGATTTCAACTTCACGATGAAGGATATCATGCCCACAAGCAGCAATACAACCCTTG
*
39704 TATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
* * * * * * *
39769 TAATATCAATTTCACGACGAAGGATATCGTGCCCATAAGCAGCAATGCAACCCTTG
66 TGATTTCAACTTCACGATGAAGGATATCATGCCCACAAGCAGCAATACAACCCTTG
* *
39825 GATTTCAACTTCACGATGAAGGATATCCAATTCAAATCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
39890 TGATTTCAACTTCACGATGAAGGATATC
66 TGATTTCAACTTCACGATGAAGGATATC
39918 CAATTTAAAG
Statistics
Matches: 195, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 195 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.23
Consensus pattern (121 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
TGATTTCAACTTCACGATGAAGGATATCATGCCCACAAGCAGCAATACAACCCTTG
Found at i:39872 original size:34 final size:33
Alignment explanation
Indices: 39828--39936 Score: 98
Period size: 34 Copynumber: 3.3 Consensus size: 33
39818 ACCCTTGGAT
39828 TTCAACTTCACGATGAAGGATATCCAATTCAAA
1 TTCAACTTCACGATGAAGGATATCCAATTCAAA
* * ** * *
39861 TCTCAACTTCACAACGAATGAGCCATCC-A-T-GAT
1 T-TCAACTTCACGATGAA-G-GATATCCAATTCAAA
*
39894 TTCAACTTCACGATGAAGGATATCCAATTTAAA
1 TTCAACTTCACGATGAAGGATATCCAATTCAAA
39927 GTTCAACTTC
1 -TTCAACTTC
39937 GCAACGAATG
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
30 5 0.09
31 2 0.04
32 15 0.26
33 4 0.07
34 24 0.42
35 2 0.04
36 5 0.09
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (33 bp):
TTCAACTTCACGATGAAGGATATCCAATTCAAA
Found at i:40200 original size:86 final size:86
Alignment explanation
Indices: 40047--40341 Score: 436
Period size: 85 Copynumber: 3.5 Consensus size: 86
40037 AGTCCAGTGT
* * *
40047 AGCATAACTCAAGGCGAGAAGGGTTATCTGTC-ATAAAAGACCTTCGAGTTCGATTACACTCAGC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACTTTCGAGTTCGATTACACTCTGC
*
40111 TCAAAAGCACATCCAATTTAC
66 TCAAAGGCACATCCAATTTAC
*
40132 AGCATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACTTTCGAGTTCGATTACACTCTGC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACTTTCGAGTTCGATTACACTCTGC
*
40197 TCAAAGGCATATCCAATTTAC
66 TCAAAGGCACATCCAATTTAC
* *
40218 AGCATAACTCAAGGCGAGAAAGGTTATCTGTCAAC-CAAGACCTTT-GAGTTCGATTACACT-TA
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGA-CTTTCGAGTTCGATTACACTCT-
*
40280 GCTCAAAGGCACATCAAATTTAC
64 GCTCAAAGGCACATCCAATTTAC
* * *
40303 AGCATAGCTCAATGCGAGAAGGGCTATCTGTCAACAAAA
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAA
40342 CTGTCAAGTT
Statistics
Matches: 190, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
84 1 0.01
85 102 0.54
86 87 0.46
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (86 bp):
AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACTTTCGAGTTCGATTACACTCTGC
TCAAAGGCACATCCAATTTAC
Found at i:42487 original size:18 final size:20
Alignment explanation
Indices: 42459--42504 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
42449 TATATATATA
*
42459 TATTATCTTTTT-TTTTTGT
1 TATTATTTTTTTATTTTTGT
42478 T-TTATTTTTTTTATTTTTGT
1 TATTA-TTTTTTTATTTTTGT
42498 TATTATT
1 TATTATT
42505 ATTATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 3 0.13
19 7 0.30
20 10 0.43
21 3 0.13
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (20 bp):
TATTATTTTTTTATTTTTGT
Found at i:42494 original size:20 final size:20
Alignment explanation
Indices: 42466--42504 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
42456 ATATATTATC
42466 TTTTTTTTTTGTT-TTATTT
1 TTTTTTTTTTGTTATTATTT
42485 TTTTTATTTTTGTTATTATT
1 TTTTT-TTTTTGTTATTATT
42505 ATTATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.10, C:0.00, G:0.05, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTTGTTATTATTT
Found at i:42645 original size:18 final size:16
Alignment explanation
Indices: 42623--42681 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 16
42613 TTTTTTTCAA
42623 ATTTTTTCAACCTTTTCT
1 ATTTTTTCAA-CTTTT-T
* *
42641 TTTTTTTCAACTATTT
1 ATTTTTTCAACTTTTT
42657 ATTTTTTCAAACTTTTT
1 ATTTTTTC-AACTTTTT
42674 GATTTTTT
1 -ATTTTTT
42682 TCTTTTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 8 0.23
17 11 0.31
18 16 0.46
ACGTcount: A:0.19, C:0.14, G:0.02, T:0.66
Consensus pattern (16 bp):
ATTTTTTCAACTTTTT
Found at i:43554 original size:18 final size:18
Alignment explanation
Indices: 43531--43583 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
43521 AAAGTCTATC
43531 TTTGATTTTGAAAAATAT
1 TTTGATTTTGAAAAATAT
43549 TTTGATTTTGAAAAATAT
1 TTTGATTTTGAAAAATAT
43567 TTTGATTTTGAAAAATA
1 TTTGATTTTGAAAAATA
43584 AGCGCAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTGATTTTGAAAAATAT
Found at i:48172 original size:128 final size:123
Alignment explanation
Indices: 47949--48186 Score: 332
Period size: 128 Copynumber: 1.9 Consensus size: 123
47939 TTGGTCACTG
* *
47949 CTAACTGCTAACTTTTATTTTATTGCATTCTAACCATTATTTATTTATTGTTTTTATTATTCGAT
1 CTAACTACTAACTTTTATTTTATTGCACTCTAACCATTATTTATTTATTGTTTTTATTATTCGAT
*
48014 TCGACCTTGTGGTGATCAGATCCGGGGTATGATCCACATTATTATTGTTCGAACTCTT
66 TCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATTGTTCGAACTCTT
* * * *
48072 CTAACTACTGACTTTTATTTTTATTGCGCTCTAACCTTTGTTTATTTATTTGTTGTTTCTATTAT
1 CTAACTACTAACTTTTA-TTTTATTGCACTCTAACCATTATTTATTTA-TTG-T-TTT-TATTAT
* * * *
48137 TCGATTCGGCCTTGTGGTGACCCGATTCGGGGTATGATCCGCATTATTAT
61 TCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTAT
48187 GGTCCGGACT
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
123 15 0.15
124 26 0.26
125 3 0.03
126 1 0.01
127 3 0.03
128 51 0.52
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.47
Consensus pattern (123 bp):
CTAACTACTAACTTTTATTTTATTGCACTCTAACCATTATTTATTTATTGTTTTTATTATTCGAT
TCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATTGTTCGAACTCTT
Found at i:52326 original size:25 final size:25
Alignment explanation
Indices: 52286--52424 Score: 116
Period size: 26 Copynumber: 5.7 Consensus size: 25
52276 AAGAGACAAG
*
52286 AAAAACAAACATAAAAGAAGCAAAGA
1 AAAAACAAAGA-AAAAGAAGCAAAGA
52312 AAAAACAAAGAAAAAG-A--AAA-A
1 AAAAACAAAGAAAAAGAAGCAAAGA
* *
52333 AAGAACAAAG---AA-TAGCAAAGA
1 AAAAACAAAGAAAAAGAAGCAAAGA
*
52354 AAAAACAAAGAAAAA-AGTGCAAAGA
1 AAAAACAAAGAAAAAGA-AGCAAAGA
*
52379 AAAAAGCAAAGAGAAAAGAAACAAAGA
1 AAAAA-CAAAGA-AAAAGAAGCAAAGA
*
52406 AAAAATCAAAGCAAAAGAA
1 AAAAA-CAAAGAAAAAGAA
52425 AAAACAAAGA
Statistics
Matches: 93, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
18 3 0.03
20 3 0.03
21 20 0.22
22 3 0.03
24 3 0.03
25 17 0.18
26 23 0.25
27 20 0.22
28 1 0.01
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.03
Consensus pattern (25 bp):
AAAAACAAAGAAAAAGAAGCAAAGA
Found at i:52341 original size:21 final size:22
Alignment explanation
Indices: 52303--52434 Score: 114
Period size: 21 Copynumber: 5.9 Consensus size: 22
52293 AACATAAAAG
52303 AAGCAAAGAAAAAACAAAGAAA
1 AAGCAAAGAAAAAACAAAGAAA
52325 AAG-AAA-AAAAGAACAAAG-AA
1 AAGCAAAGAAAA-AACAAAGAAA
*
52345 TAGCAAAGAAAAAACAAAGAAAA
1 AAGCAAAGAAAAAACAAAG-AAA
52368 AAGTGCAAAGAAAAAAGCAAAGAGAA
1 AA--GCAAAGAAAAAA-CAAAGA-AA
* **
52394 AAG-AAACAAAGAAA-AAA-TCA
1 AAGCAAAGAAA-AAACAAAGAAA
52414 AAGCAAAAGAAAAAACAAAGA
1 AAGC-AAAGAAAAAACAAAGA
52435 GCAAAAAAGA
Statistics
Matches: 89, Mismatches: 7, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
20 12 0.13
21 23 0.26
22 19 0.21
23 9 0.10
24 4 0.04
25 13 0.15
26 9 0.10
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.02
Consensus pattern (22 bp):
AAGCAAAGAAAAAACAAAGAAA
Found at i:52378 original size:14 final size:12
Alignment explanation
Indices: 52298--52421 Score: 93
Period size: 11 Copynumber: 10.3 Consensus size: 12
52288 AAACAAACAT
52298 AAAAGAAGCAAAG
1 AAAA-AAGCAAAG
52311 AAAAAA-CAAAG
1 AAAAAAGCAAAG
52322 -AAAAAG-AAA-
1 AAAAAAGCAAAG
52331 AAAAGAA-CAAAG
1 AAAA-AAGCAAAG
*
52343 --AATAGCAAAG
1 AAAAAAGCAAAG
52353 AAAAAA-CAAAG
1 AAAAAAGCAAAG
52364 AAAAAAGTGCAAAG
1 AAAAAA--GCAAAG
52378 AAAAAAGCAAAGAG
1 AAAAAAGC-AA-AG
*
52392 AAAAGAAACAAAG
1 AAAA-AAGCAAAG
*
52405 AAAAAATCAAAG
1 AAAAAAGCAAAG
52417 CAAAA
1 -AAAA
52422 GAAAAAACAA
Statistics
Matches: 92, Mismatches: 4, Indels: 30
0.73 0.03 0.24
Matches are distributed among these distances:
9 1 0.01
10 18 0.20
11 21 0.23
12 14 0.15
13 16 0.17
14 19 0.21
15 3 0.03
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAAAAGCAAAG
Found at i:52415 original size:27 final size:26
Alignment explanation
Indices: 52306--52447 Score: 112
Period size: 27 Copynumber: 5.3 Consensus size: 26
52296 ATAAAAGAAG
* *
52306 CAAAGAAAAAACAAAGAAA-AAGAAAA
1 CAAAGAAAAAAGAAACAAAGAA-AAAA
*
52332 -AAAGAACAAAGAATAGCAAAGAAAAAA
1 CAAAGAAAAAAGAA-A-CAAAGAAAAAA
**
52359 CAAAGAAAAAAG-TGCAAAGAAAAAA
1 CAAAGAAAAAAGAAACAAAGAAAAAA
*
52384 GCAAAGAGAAAAGAAACAAAGAAAAAA
1 -CAAAGAAAAAAGAAACAAAGAAAAAA
* **
52411 TCAAAGCAAAAGAAAAAACAAAGAGCAAA
1 -CAAAG-AAAA-AAGAAACAAAGAAAAAA
52440 -AAAGAAAA
1 CAAAGAAAA
52448 CAAGGAGCAT
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
25 22 0.23
26 16 0.17
27 27 0.29
28 15 0.16
29 14 0.15
ACGTcount: A:0.75, C:0.08, G:0.15, T:0.02
Consensus pattern (26 bp):
CAAAGAAAAAAGAAACAAAGAAAAAA
Found at i:52425 original size:26 final size:25
Alignment explanation
Indices: 52339--52424 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 25
52329 AAAAAAGAAC
52339 AAAGAATAGCAAAGAAAAAACAAAGA
1 AAAGAATA-CAAAGAAAAAACAAAGA
*
52365 AAA-AAGTGCAAAGAAAAAAGCAAAGAGA
1 AAAGAA-TACAAAGAAAAAA-C-AA-AGA
52393 AAAGAA-ACAAAGAAAAAATCAAAGCA
1 AAAGAATACAAAGAAAAAA-CAAAG-A
52419 AAAGAA
1 AAAGAA
52425 AAAACAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
25 15 0.29
26 14 0.27
27 14 0.27
28 6 0.12
29 2 0.04
ACGTcount: A:0.72, C:0.08, G:0.16, T:0.03
Consensus pattern (25 bp):
AAAGAATACAAAGAAAAAACAAAGA
Found at i:52455 original size:19 final size:19
Alignment explanation
Indices: 52401--52456 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
52391 GAAAAGAAAC
52401 AAAGAAAAAATC-AA-AGCA
1 AAAGAAAAAA-CAAAGAGCA
52419 AAAGAAAAAACAAAGAGCA
1 AAAGAAAAAACAAAGAGCA
*
52438 AAA-AAGAAAACAAGGAGCA
1 AAAGAA-AAAACAAAGAGCA
52457 TAGACAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 1 0.03
18 14 0.41
19 19 0.56
ACGTcount: A:0.71, C:0.11, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAACAAAGAGCA
Found at i:53541 original size:4 final size:4
Alignment explanation
Indices: 53534--53889 Score: 712
Period size: 4 Copynumber: 89.0 Consensus size: 4
53524 TCTCTGCATG
53534 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53582 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53630 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53678 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53726 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53774 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53822 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53870 CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA
53890 AAAGTTGCAT
Statistics
Matches: 352, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 352 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:54545 original size:37 final size:35
Alignment explanation
Indices: 54504--54625 Score: 113
Period size: 35 Copynumber: 3.4 Consensus size: 35
54494 ACAAAGTTGA
54504 TCTCACTTGAGATC-GTTTTCTCACAAAACAAACTTTG
1 TCTCACTTGAGA-CAGTTTTCT-A-AAAACAAACTTTG
*
54541 TCTCACTTGAGACAGTTTTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAGTTTTCTAAAAACAAACTTTG
** * * * *
54576 TCTCGTTTAAAACAATTTCTCTTAAAACAAA-TGTTG
1 TCTCACTTGAGACAGTTT-TCTAAAAACAAACT-TTG
*
54612 TCTCAGTTGAGACA
1 TCTCACTTGAGACA
54626 ATTCTCCAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
35 26 0.37
36 26 0.37
37 19 0.27
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (35 bp):
TCTCACTTGAGACAGTTTTCTAAAAACAAACTTTG
Found at i:54627 original size:36 final size:36
Alignment explanation
Indices: 54492--54628 Score: 120
Period size: 36 Copynumber: 3.8 Consensus size: 36
54482 ATTTCACATT
**
54492 AAACAAA-GTTGATCTCACTTGAGATCGTTTTCTC-ACA
1 AAACAAATGTTG-TCTCACTTGAGA-CAATTTCTCTA-A
*
54529 AAACAAACT-TTGTCTCACTTGAGACAGTTT-TCTAA
1 AAACAAA-TGTTGTCTCACTTGAGACAATTTCTCTAA
* ** * * *
54564 AAACAAATTTTGTCTCGTTTAAAACAATTTCTCTTA
1 AAACAAATGTTGTCTCACTTGAGACAATTTCTCTAA
*
54600 AAACAAATGTTGTCTCAGTTGAGACAATT
1 AAACAAATGTTGTCTCACTTGAGACAATT
54629 CTCCAAATTA
Statistics
Matches: 82, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
34 1 0.01
35 26 0.32
36 33 0.40
37 19 0.23
38 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (36 bp):
AAACAAATGTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:54872 original size:31 final size:31
Alignment explanation
Indices: 54837--54897 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
54827 CCTTGAGGAA
*
54837 GTTTCTCTAGAAAATCAAA-ATCTTTGAGTTT
1 GTTTCTCTAG-AAATAAAACATCTTTGAGTTT
*
54868 GTTTCTCTTGAAATAAAATCATCTTTGAGT
1 GTTTCTCTAGAAATAAAA-CATCTTTGAGT
54898 CGTTTCCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 9 0.35
32 10 0.38
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (31 bp):
GTTTCTCTAGAAATAAAACATCTTTGAGTTT
Found at i:54979 original size:32 final size:32
Alignment explanation
Indices: 54856--54980 Score: 103
Period size: 32 Copynumber: 3.9 Consensus size: 32
54846 GAAAATCAAA
* *
54856 ATCTTTGAGTTTGTTTCTCTTGAAATAAAATC
1 ATCTTTGAGTTTGTTTCTCTTGAAACAATATC
* * * *
54888 ATCTTTGAG-TCGTTTCCCTTGAAACGAATTTTG
1 ATCTTTGAGTTTGTTTCTCTTGAAAC-AA-TATC
* * *
54921 A-CTATTAAGATAT-TTTCTCTTAAAACAATATC
1 ATCT-TTGAG-TTTGTTTCTCTTGAAACAATATC
*
54953 ATCTTTGAGTTTGTTTCTCTGGAAACAA
1 ATCTTTGAGTTTGTTTCTCTTGAAACAA
54981 GGTTTTATCC
Statistics
Matches: 69, Mismatches: 17, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
31 15 0.22
32 33 0.48
33 10 0.14
34 11 0.16
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (32 bp):
ATCTTTGAGTTTGTTTCTCTTGAAACAATATC
Found at i:55164 original size:64 final size:64
Alignment explanation
Indices: 55077--55216 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 64
55067 ATTTTCTGAA
* *
55077 AAACAAAGTTTTGTCTATCTTGAGACAATTTCTTTT-GAAAAATCATTGAATATGTTTCTTTGGG
1 AAACAAAATTTTGTCTATCTTGAGACAATTTATTTTAGAAAAATCATTGAATATGTTTCTTT-GG
* * * * * * * *
55141 AAATAAAATTTTGTCTCTTTTGAGATAGTTTATTTTAAGAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAACAAAATTTTGTCTATCTTGAGACAATTTATTTT-AGAAAAATCATTGAATATGTTTCTTTGG
55206 AAACAAAATTT
1 AAACAAAATTT
55217 ACCATCTTTG
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
64 29 0.46
65 12 0.19
66 22 0.35
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (64 bp):
AAACAAAATTTTGTCTATCTTGAGACAATTTATTTTAGAAAAATCATTGAATATGTTTCTTTGG
Found at i:55416 original size:29 final size:29
Alignment explanation
Indices: 55373--55438 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
55363 GACAGTTGCT
55373 TTTGAAAACATCATCCTTGAGTCT-GTTTCC
1 TTTG-AAACATCATCCTTGAGT-TGGTTTCC
* *
55403 TTTGAAACATCATCTTTGAGTTGGTTTCT
1 TTTGAAACATCATCCTTGAGTTGGTTTCC
55432 TTTGAAA
1 TTTGAAA
55439 TTAGTATCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.85
30 4 0.12
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (29 bp):
TTTGAAACATCATCCTTGAGTTGGTTTCC
Found at i:55517 original size:40 final size:40
Alignment explanation
Indices: 55458--55569 Score: 197
Period size: 40 Copynumber: 2.8 Consensus size: 40
55448 CTAAAGATGG
*
55458 CCAGAACTCTTCATCACGTATGAGTCGTGTCATCCACCGA
1 CCAGATCTCTTCATCACGTATGAGTCGTGTCATCCACCGA
*
55498 CCAGATCTCTTCATAACGTATGAGTCGTGTCATCCACCGA
1 CCAGATCTCTTCATCACGTATGAGTCGTGTCATCCACCGA
*
55538 CCAGATCTCTTCATCACGTAGGAGTCGTGTCA
1 CCAGATCTCTTCATCACGTATGAGTCGTGTCA
55570 ACCATAGATA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (40 bp):
CCAGATCTCTTCATCACGTATGAGTCGTGTCATCCACCGA
Found at i:55738 original size:39 final size:39
Alignment explanation
Indices: 55632--55741 Score: 148
Period size: 39 Copynumber: 2.8 Consensus size: 39
55622 CTAAAGATGG
* * ** *
55632 CCAGAACTATTCATCACGTATAAGCCGTATCATCCACCA
1 CCAGATCTCTTCATCACGTAGGAGCCGTGTCATCCACCA
* **
55671 CCAGATCTCTTTATCAAATAGGAGCCGTGTCATCCACCA
1 CCAGATCTCTTCATCACGTAGGAGCCGTGTCATCCACCA
55710 CCAGATCTCTTCATCACGTAGGAGCCGTGTCA
1 CCAGATCTCTTCATCACGTAGGAGCCGTGTCA
55742 ACCATATATA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (39 bp):
CCAGATCTCTTCATCACGTAGGAGCCGTGTCATCCACCA
Found at i:55755 original size:172 final size:174
Alignment explanation
Indices: 55445--55875 Score: 688
Period size: 172 Copynumber: 2.5 Consensus size: 174
55435 GAAATTAGTA
*
55445 TCCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCACCGACCAGATCTCTTC
1 TCCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACCAGATCTCTTC
* * *
55510 AT-AACGTATGAGTCGTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAGTCGTGTCAACCA
66 ATCAA-GTAGGAGCCGTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCA
*
55574 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCC
130 TAGATAACCAGCCGTCATCATCACGTAGGAACCGAGTTATCACCC
* * * *
55619 TCCCTAAAGATGGCCAGAACTATTCATCACGTATAAGCCGTATCATCCACC-ACCAGATCTCTTT
1 TCCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACCAGATCTCTTC
*
55683 ATCAAATAGGAGCCGTGTCATCCACC-ACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
66 ATCAAGTAGGAGCCGTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
* *
55747 ATATAACCAGCCGTCATCATCACGTAGGAACCGAGTTTTCACCC
131 AGATAACCAGCCGTCATCATCACGTAGGAACCGAGTTATCACCC
* * *
55791 TTCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCCACCGACCATATCTCTTC
1 TCCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACCAGATCTCTTC
*
55856 ATCACGTAGGAGCCGTGTCA
66 ATCAAGTAGGAGCCGTGTCA
55876 ACCATAGATA
Statistics
Matches: 234, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
172 124 0.53
173 61 0.26
174 49 0.21
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (174 bp):
TCCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACCAGATCTCTTC
ATCAAGTAGGAGCCGTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
AGATAACCAGCCGTCATCATCACGTAGGAACCGAGTTATCACCC
Found at i:55910 original size:134 final size:134
Alignment explanation
Indices: 55692--56000 Score: 505
Period size: 134 Copynumber: 2.3 Consensus size: 134
55682 TATCAAATAG
*
55692 GAGCCGTGTCATCCACC-ACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATATATAACCA
1 GAGCCGTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCA
*
55756 GCCGTCATCATCACGTAGGAACCGAGTTTTCACCCTTCCTAAAGATGGCCAGAACTCTTCATCAC
66 GCCGTCATCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAACTCTTCATCAC
55821 GTAT
131 GTAT
* *
55825 GAGCAGTGTCATCCACCGACCATATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCA
1 GAGCCGTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCA
* ** *
55890 GCCGTCCTCATCGTGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCATAACTCTTCATCAC
66 GCCGTCATCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAACTCTTCATCAC
55955 GTAT
131 GTAT
* * *
55959 GAGCCGTGTCATCC-CTGACCAGACCTCCTCATCACGTAGGAG
1 GAGCCGTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAG
56001 TTGTGTCACT
Statistics
Matches: 162, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
133 40 0.25
134 122 0.75
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (134 bp):
GAGCCGTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCA
GCCGTCATCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAACTCTTCATCAC
GTAT
Found at i:57249 original size:4 final size:4
Alignment explanation
Indices: 57240--57264 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
57230 ATTCTAACCA
57240 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
57265 GTTTCTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:57383 original size:136 final size:127
Alignment explanation
Indices: 57201--57471 Score: 326
Period size: 128 Copynumber: 2.1 Consensus size: 127
57191 AATTTGGTCA
* *
57201 CTGCTAACTGCTAACTTTTATTTTATTGCATTCTAACCATTATTTATTTATTTATTTATTTATTG
1 CTGCTAACTACTAACTTTTATTTTATTGCACTCTAACC-------A-TTATTTATTTATTTATTG
* * *
57266 TTTCTATTATTCGATTTGACCTTGTGGTGATCAGATCCGGGGTATGATCCACATTATTATGGTTC
58 TTTCTATTATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTCC
57331 GGACT
123 GGACT
* * * * *
57336 CTGCTAACTACTGACTTTTATTTTTATTGCGCTCTAACCTTTGTTTATTTATTTGTTGTTTCTAT
1 CTGCTAACTACTAACTTTTA-TTTTATTGCACTCTAACCATTATTTATTTATTTATTGTTTCTAT
* * * *
57401 TATTCGATTCGGCCTTGTGGTGACCCGATTCGGGGTATGATCCGCATTATTATGGTCCGGACT
65 TATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTCCGGACT
*
57464 CTGTTAAC
1 CTGCTAAC
57472 CGTTAATTTT
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
128 86 0.72
135 18 0.15
136 16 0.13
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.46
Consensus pattern (127 bp):
CTGCTAACTACTAACTTTTATTTTATTGCACTCTAACCATTATTTATTTATTTATTGTTTCTATT
ATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTCCGGACT
Found at i:64469 original size:12 final size:12
Alignment explanation
Indices: 64452--64477 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
64442 GTCCTCTCAA
64452 GTATGATCATAG
1 GTATGATCATAG
64464 GTATGATCATAG
1 GTATGATCATAG
64476 GT
1 GT
64478 CAAGCATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.35
Consensus pattern (12 bp):
GTATGATCATAG
Found at i:67047 original size:2 final size:2
Alignment explanation
Indices: 67040--67065 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
67030 GAGGTGTGAA
67040 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
67066 GAAATTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67170 original size:27 final size:27
Alignment explanation
Indices: 67135--67188 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
67125 TTGAATTCAC
67135 CAATGTTATATA-AATATTTTTTATTAT
1 CAATGTTATATATAAT-TTTTTTATTAT
* *
67162 CAATTTTATATATGATTTTTTTATTAT
1 CAATGTTATATATAATTTTTTTATTAT
67189 GAACAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (27 bp):
CAATGTTATATATAATTTTTTTATTAT
Found at i:67189 original size:14 final size:14
Alignment explanation
Indices: 67150--67191 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
67140 TTATATAAAT
*
67150 ATTTTTTATTATCA
1 ATTTTTTATTATGA
*
67164 ATTTTATA-TATGA
1 ATTTTTTATTATGA
*
67177 TTTTTTTATTATGA
1 ATTTTTTATTATGA
67191 A
1 A
67192 CAGTAAAGAG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (14 bp):
ATTTTTTATTATGA
Found at i:67457 original size:16 final size:16
Alignment explanation
Indices: 67416--67462 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
67406 TGTAAATAAT
* *
67416 CCGACTTGTTATTGAC
1 CCGACTTGATATTTAC
*
67432 CTGA-TCTGATATTTAC
1 CCGACT-TGATATTTAC
67448 CCGACTTGATATTTA
1 CCGACTTGATATTTA
67463 ACTTACTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (16 bp):
CCGACTTGATATTTAC
Found at i:67961 original size:19 final size:20
Alignment explanation
Indices: 67934--67974 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
67924 TTGGGAAGTT
*
67934 GAGACATTGA-AAATTTAGA
1 GAGAAATTGAGAAATTTAGA
*
67953 GAGAAATTGAGAAATTTTGA
1 GAGAAATTGAGAAATTTAGA
67973 GA
1 GA
67975 ATAGAGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.46, C:0.02, G:0.24, T:0.27
Consensus pattern (20 bp):
GAGAAATTGAGAAATTTAGA
Found at i:68005 original size:46 final size:46
Alignment explanation
Indices: 67900--68031 Score: 144
Period size: 45 Copynumber: 2.9 Consensus size: 46
67890 TTTATTTGGG
* * * *
67900 AATTTAGAGGGAAATCGAGAAATTTTGGGAAGTTGA-G-ACATTGAA
1 AATTTAGAGGGAAATTGAGAAATTTTGGGAA-TAGAGGAAAAATGAA
* * *
67945 AATTTAGAGAGAAATTGAGAAATTTTGAGAATAGAGGAAAAATGAT
1 AATTTAGAGGGAAATTGAGAAATTTTGGGAATAGAGGAAAAATGAA
*
67991 AATTTAGAGGGAAATT-AGAGAATTTTGGGAATGAAAGGAAA
1 AATTTAGAGGGAAATTGAGA-AATTTTGGGAAT-AGAGGAAA
68032 TTGAGAAATT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 3 0.04
45 32 0.44
46 31 0.42
47 7 0.10
ACGTcount: A:0.45, C:0.02, G:0.27, T:0.26
Consensus pattern (46 bp):
AATTTAGAGGGAAATTGAGAAATTTTGGGAATAGAGGAAAAATGAA
Found at i:68477 original size:20 final size:19
Alignment explanation
Indices: 68461--68499 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
68451 GTATATATTA
68461 TAGACTTATATTCTATACTT
1 TAGACTTATATT-TATACTT
*
68481 TATACTTATATTTATACTT
1 TAGACTTATATTTATACTT
68500 CTGTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.31, C:0.13, G:0.03, T:0.54
Consensus pattern (19 bp):
TAGACTTATATTTATACTT
Found at i:68606 original size:16 final size:16
Alignment explanation
Indices: 68581--68617 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
68571 GTACACTTTT
*
68581 ATATATATAAGTATAA
1 ATATACATAAGTATAA
*
68597 ATATACATAAGTATAT
1 ATATACATAAGTATAA
68613 ATATA
1 ATATA
68618 ATATTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (16 bp):
ATATACATAAGTATAA
Found at i:69237 original size:24 final size:24
Alignment explanation
Indices: 69160--69252 Score: 102
Period size: 24 Copynumber: 3.8 Consensus size: 24
69150 AACATTATTA
*
69160 TTTCTATCGGTTTTGTTATTATTGGGTG
1 TTTCTATCGGTTTTGTTATT-TT---TT
*
69188 CTT-TATCGGTTTTGTTA--TTTT
1 TTTCTATCGGTTTTGTTATTTTTT
69209 TTTCTATCGGTTTTGTTATTTTTT
1 TTTCTATCGGTTTTGTTATTTTTT
*
69233 TTTCTACCGGTTTTGTTATT
1 TTTCTATCGGTTTTGTTATT
69253 ATTAGGCACT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
21 3 0.05
22 14 0.24
24 25 0.43
27 14 0.24
28 2 0.03
ACGTcount: A:0.10, C:0.10, G:0.17, T:0.63
Consensus pattern (24 bp):
TTTCTATCGGTTTTGTTATTTTTT
Found at i:77898 original size:18 final size:18
Alignment explanation
Indices: 77864--77898 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
77854 ATGTGTTATA
* *
77864 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTACGAGACAT
77882 AGTGGTCCTACGAGACA
1 AGTGGTCCTACGAGACA
77899 AATTCTACGC
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:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (18 bp):
AGTGGTCCTACGAGACAT
Found at i:78228 original size:18 final size:20
Alignment explanation
Indices: 78190--78231 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
78180 ATATGCTTAT
*
78190 ATAATAAAAATGAATTAATG
1 ATAATAAAAATGAAGTAATG
78210 ATAAT-AAAAT-AAGTAATG
1 ATAATAAAAATGAAGTAATG
78228 ATAA
1 ATAA
78232 GCATGTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 5 0.24
20 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (20 bp):
ATAATAAAAATGAAGTAATG
Found at i:84159 original size:17 final size:17
Alignment explanation
Indices: 84137--84171 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
84127 TATTATACTA
84137 ATATTTAAATTTAAAAT
1 ATATTTAAATTTAAAAT
*
84154 ATATTTAAATTTATAAT
1 ATATTTAAATTTAAAAT
84171 A
1 A
84172 GTAAAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTTAAATTTAAAAT
Found at i:84248 original size:47 final size:48
Alignment explanation
Indices: 84195--84290 Score: 149
Period size: 47 Copynumber: 2.0 Consensus size: 48
84185 GAATTTATTA
* *
84195 TAAATATTAAATCCATAAATTAAATTCACCTTTTT-CTAACACTTTAT
1 TAAATATTAAATCCATAAATTAAATTCACATTTTTACCAACACTTTAT
* *
84242 TAAATATTAAATCCATCAATTCAATTCACATTTTTACCAACACTTTAT
1 TAAATATTAAATCCATAAATTAAATTCACATTTTTACCAACACTTTAT
84290 T
1 T
84291 CACAATAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 32 0.73
48 12 0.27
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.42
Consensus pattern (48 bp):
TAAATATTAAATCCATAAATTAAATTCACATTTTTACCAACACTTTAT
Found at i:88542 original size:2 final size:2
Alignment explanation
Indices: 88535--88581 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
88525 AAATTTCAAT
88535 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88577 TA TA T
1 TA TA T
88582 GTACGAACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:101550 original size:18 final size:18
Alignment explanation
Indices: 101527--101562 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
101517 TAAAATAATT
101527 TCAAAACAATTTTACAAA
1 TCAAAACAATTTTACAAA
101545 TCAAAACAATTTTACAAA
1 TCAAAACAATTTTACAAA
101563 GTATTTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.28
Consensus pattern (18 bp):
TCAAAACAATTTTACAAA
Found at i:104736 original size:20 final size:18
Alignment explanation
Indices: 104692--104728 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
104682 GATTTAACAA
**
104692 AAAGGGGAGAAGTGTTTT
1 AAAGGGGAGAAGTGTTAG
104710 AAAGGGGAGAAGTGTTAG
1 AAAGGGGAGAAGTGTTAG
104728 A
1 A
104729 GTAAGGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.22
Consensus pattern (18 bp):
AAAGGGGAGAAGTGTTAG
Done.