Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005796.1 Hibiscus syriacus cultivar Beakdansim tig00013586_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: 92566
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:11636 original size:25 final size:26
Alignment explanation
Indices: 11608--11663 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
11598 TCATAACAAA
*
11608 AATAATTATATTTAA-TTTAA-TTTAG
1 AATAATGAT-TTTAATTTTAATTTTAG
*
11633 AATAA-GATTTTAATTTTAATTTTAT
1 AATAATGATTTTAATTTTAATTTTAG
11658 AATAAT
1 AATAAT
11664 ATAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 7 0.27
25 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
AATAATGATTTTAATTTTAATTTTAG
Found at i:11900 original size:20 final size:22
Alignment explanation
Indices: 11877--11917 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
11867 AATTTTAAAA
11877 TAAATC-TA-AAAATAATAATG
1 TAAATCATATAAAATAATAATG
11897 TAAATCAATATAAAATAATAA
1 TAAATC-ATATAAAATAATAA
11918 CATATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
22 2 0.11
23 10 0.56
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAATCATATAAAATAATAATG
Found at i:12869 original size:25 final size:23
Alignment explanation
Indices: 12841--12886 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
12831 TGGTATTCAT
*
12841 TTTTAATTTAATTTAAAAATTAATA
1 TTTTAA-TTAAATT-AAAATTAATA
12866 TTTTAATTAAATTAAAATTAA
1 TTTTAATTAAATTAAAATTAA
12887 GATCAAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTAATTAAATTAAAATTAATA
Found at i:20018 original size:31 final size:31
Alignment explanation
Indices: 19920--20005 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 31
19910 CTTCAAACAA
*
19920 TACAAAATGGTAATTAAATTTATCGAACTGT
1 TACAAAATGGTAATTAAATTTATCGAAATGT
* *
19951 TACAAAATGATTATTAAATTTTATCGAAATGT
1 TACAAAATGGTAATTAAA-TTTATCGAAATGT
*
19983 TACAAAATGGTCATTAAATTTAT
1 TACAAAATGGTAATTAAATTTAT
20006 GGAATTTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
31 21 0.43
32 28 0.57
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38
Consensus pattern (31 bp):
TACAAAATGGTAATTAAATTTATCGAAATGT
Found at i:21054 original size:36 final size:36
Alignment explanation
Indices: 20992--21166 Score: 214
Period size: 36 Copynumber: 4.9 Consensus size: 36
20982 TCTGTTCTAG
* * *
20992 TTGAATCGGAAGTG-CAGACGCCTCCTTCCGGTC-GAC
1 TTGAATCGGAAGTGTC-GATGCTTCCTTCCGTTCAG-C
* *
21028 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAGT
1 TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCAGC
*
21064 TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCAGT
1 TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCAGC
*
21100 TTGAATCGGAAGTGTCGATGCTTTCTTCCGTTCA-C
1 TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCAGC
* *
21135 TTTGAATCGGAAGTG-CGACGTTTCCTTCCGTT
1 -TTGAATCGGAAGTGTCGATGCTTCCTTCCGTT
21167 ATTCTTGTTT
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
35 14 0.11
36 109 0.87
37 2 0.02
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (36 bp):
TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCAGC
Found at i:21113 original size:72 final size:71
Alignment explanation
Indices: 20992--21166 Score: 244
Period size: 72 Copynumber: 2.4 Consensus size: 71
20982 TCTGTTCTAG
* *
20992 TTGAATCGGAAGTGCAGACGCCTCCTTCCGGTCGACTTGAATCGAAAGTGTCGATGCTTCCTTCC
1 TTGAATCGGAAGTGC-GACGCTTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCTTCC
*
21057 GTTCAGT
65 GTTCACT
* * * *
21064 TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTC-AGTTTGAATCGGAAGTGTCGATGCTTTCTTC
1 TTGAATCGGAAGTG-CGACGCTTCCTTCCGTTCGA-CTTGAATCGAAAGTGTCGATGCTTCCTTC
21128 CGTTCACT
64 CGTTCACT
*
21136 TTGAATCGGAAGTGCGACGTTTCCTTCCGTT
1 TTGAATCGGAAGTGCGACGCTTCCTTCCGTT
21167 ATTCTTGTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
71 16 0.17
72 75 0.82
73 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (71 bp):
TTGAATCGGAAGTGCGACGCTTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCTTCCG
TTCACT
Found at i:21400 original size:44 final size:44
Alignment explanation
Indices: 21332--21423 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
21322 GTATAGTCTT
*
21332 CACAGCATGATTGTAGCACCATGAACTACAGGATCGTTTGTGGA
1 CACAACATGATTGTAGCACCATGAACTACAGGATCGTTTGTGGA
21376 CACAACATGATTGTAGCACCATGAACTACAGGATCGTTTGTGGA
1 CACAACATGATTGTAGCACCATGAACTACAGGATCGTTTGTGGA
21420 CACA
1 CACA
21424 GCTTACAGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (44 bp):
CACAACATGATTGTAGCACCATGAACTACAGGATCGTTTGTGGA
Found at i:22894 original size:21 final size:21
Alignment explanation
Indices: 22870--22961 Score: 109
Period size: 21 Copynumber: 4.4 Consensus size: 21
22860 TTGAAAATCG
*
22870 CGTTGCGATAGTTTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
22891 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
22912 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
22930 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
22953 CGTTGCGAT
1 CGTTGCGAT
22962 TTTCCATTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.03
19 4 0.07
20 9 0.15
21 38 0.64
22 4 0.07
23 2 0.03
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:22944 original size:41 final size:41
Alignment explanation
Indices: 22891--22972 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
22881 TTTACAGTGT
22891 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
22932 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
22973 ATAGTTGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
Found at i:23076 original size:40 final size:40
Alignment explanation
Indices: 22984--23080 Score: 126
Period size: 39 Copynumber: 2.4 Consensus size: 40
22974 TAGTTGAAAA
* * *
22984 TCGCATTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATT
1 TCGC-TTGCGATAGTCTACAGTGTCGTTGCGATTTTCAAAT
*
23025 TCGCATG-GATAGTCTACAGTGTCGTTGCGATTTTTCAAAT
1 TCGCTTGCGATAGTCTACAGTGTCGTTGCGA-TTTTCAAAT
23065 TCG-TTGCGATAGTCTA
1 TCGCTTGCGATAGTCTA
23081 TAGTAAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
39 24 0.49
40 21 0.43
41 4 0.08
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (40 bp):
TCGCTTGCGATAGTCTACAGTGTCGTTGCGATTTTCAAAT
Found at i:23766 original size:20 final size:20
Alignment explanation
Indices: 23741--23813 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
23731 AGAGAAAATT
23741 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * *
23761 ATCGCAA--CGACACTGTACACT
1 ATCGCAACGCGA-AATGGA-A-A
*
23782 ATCGCAACGCGAAATGGATA
1 ATCGCAACGCGAAATGGAAA
23802 ATCGCAACGCGA
1 ATCGCAACGCGA
23814 TTTTCAACTA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
18 3 0.07
19 4 0.10
20 20 0.49
21 7 0.17
22 4 0.10
23 3 0.07
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:23824 original size:41 final size:40
Alignment explanation
Indices: 23740--23880 Score: 160
Period size: 41 Copynumber: 3.4 Consensus size: 40
23730 TAGAGAAAAT
* *
23740 TATCGCAACGCGAAATGGAAAATCGCAACGAC-ACTGT-ACAC
1 TATCGCAACGCGAAATGG-AAATCGCAACG-CGATTTTCA-AC
23781 TATCGCAACGCGAAATGGATAATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGAAATGGA-AATCGCAACGCGATTTTCAAC
** **
23822 TATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGAAATGGAA--ATCGCAACGCGATTTTCAAC
23864 TATCGCAACGCGAAATG
1 TATCGCAACGCGAAATG
23881 CAGCGCGAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
40 3 0.03
41 48 0.56
42 35 0.41
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (40 bp):
TATCGCAACGCGAAATGGAAATCGCAACGCGATTTTCAAC
Found at i:23828 original size:21 final size:21
Alignment explanation
Indices: 23802--23876 Score: 150
Period size: 21 Copynumber: 3.6 Consensus size: 21
23792 GAAATGGATA
23802 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
23823 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
23844 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
23865 ATCGCAACGCGA
1 ATCGCAACGCGA
23877 AATGCAGCGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:24204 original size:38 final size:38
Alignment explanation
Indices: 24153--24230 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
24143 AAAGGTCGTT
*
24153 ATAAATACTCGAATCAAGATTGGAAAGGAGGATGGATC
1 ATAAATACTCGAATCAAGATGGGAAAGGAGGATGGATC
24191 ATAAATACTCGAATCAAGATGGGAAAGGAGGATGGATC
1 ATAAATACTCGAATCAAGATGGGAAAGGAGGATGGATC
24229 AT
1 AT
24231 GCATAATCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (38 bp):
ATAAATACTCGAATCAAGATGGGAAAGGAGGATGGATC
Found at i:29104 original size:51 final size:51
Alignment explanation
Indices: 29028--29130 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
29018 AAACGCATGT
29028 GTACATTTGGTCTGCATTGCTCAGAGCCTCAGGTTTAATGTATCCTTTTGG
1 GTACATTTGGTCTGCATTGCTCAGAGCCTCAGGTTTAATGTATCCTTTTGG
*
29079 GTACATTTGGTCTGCATTGCTCAGAGCCTCAGGTTTAATGTATCTTTTTGG
1 GTACATTTGGTCTGCATTGCTCAGAGCCTCAGGTTTAATGTATCCTTTTGG
29130 G
1 G
29131 ATATGTATTC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.40
Consensus pattern (51 bp):
GTACATTTGGTCTGCATTGCTCAGAGCCTCAGGTTTAATGTATCCTTTTGG
Found at i:31533 original size:21 final size:21
Alignment explanation
Indices: 31500--31544 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31490 GATTTTTAAA
*
31500 AAAATTGAAAGTTTAAATACT
1 AAAACTGAAAGTTTAAATACT
* **
31521 AAAACTGATAGTTTAGGTACT
1 AAAACTGAAAGTTTAAATACT
31542 AAA
1 AAA
31545 TACGTAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (21 bp):
AAAACTGAAAGTTTAAATACT
Found at i:33229 original size:14 final size:14
Alignment explanation
Indices: 33210--33236 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33200 TCCTGCCAAA
33210 GCCATGAAAACAAT
1 GCCATGAAAACAAT
33224 GCCATGAAAACAA
1 GCCATGAAAACAA
33237 CCCTCCGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.22, G:0.15, T:0.11
Consensus pattern (14 bp):
GCCATGAAAACAAT
Found at i:38770 original size:29 final size:29
Alignment explanation
Indices: 38728--38801 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
38718 TTTCATATGT
38728 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
38756 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
38785 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
38802 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:39337 original size:64 final size:62
Alignment explanation
Indices: 39160--39383 Score: 218
Period size: 64 Copynumber: 3.5 Consensus size: 62
39150 TAATGAAGGT
* * ** * * **
39160 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCAT-AATTGCATTCGATGT-TTATTATTAATGGG
* *
39224 ATGCATCGATGCACTCCTTATGCATCGATGCACTAATTACATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-TAATTGCATTCGATGTTT-ATTATTAATGGG
* **
39288 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTTGATGTTT-TTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCAT-AATTGCATTCGATGTTTATTA--TTAATGGG
** *
39351 AGTGCATCGATGCACTACCAATGCATTGATGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
39384 CATTCAAACA
Statistics
Matches: 136, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
62 3 0.02
63 4 0.03
64 128 0.94
65 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAATTGCATTCGATGTTTATTATTAATGGG
Found at i:39442 original size:21 final size:21
Alignment explanation
Indices: 39416--39471 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
39406 TTAACCTTGA
39416 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
*
39437 TGCATCGATGCACCATGAATG
1 TGCATCGATGCACTATGAATG
39458 TGCATCGATGCACT
1 TGCATCGATGCACT
39472 CTGCCCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCACTATGAATG
Found at i:39949 original size:3 final size:3
Alignment explanation
Indices: 39941--39966 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39931 TCTCGTACAT
39941 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
39967 GAATATCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43170 original size:29 final size:29
Alignment explanation
Indices: 43128--43201 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
43118 TTTCATATGT
43128 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
43156 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
43185 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
43202 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:43666 original size:64 final size:64
Alignment explanation
Indices: 43560--43783 Score: 238
Period size: 64 Copynumber: 3.5 Consensus size: 64
43550 TAATGAAAGT
* * ** **
43560 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATGT-GTCATTATTAATGGG
* ** *
43624 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGTATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATGTGTCATTATTAATGGG
* * * * **
43688 ATGCATCGATGCACTACTTATGAATCGATGCATAAATTGAATTCGATGTTTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATG-TGTCATTATTAATGGG
**
43751 AGTGCATCGATGCACTACCAATGCATCGATGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
43784 CATTCAAACA
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
63 3 0.02
64 127 0.93
65 6 0.04
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATGTGTCATTATTAATGGG
Found at i:44328 original size:3 final size:3
Alignment explanation
Indices: 44320--44372 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
44310 TCTCGTACAT
*
44320 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
44368 GAA GA
1 GAA GA
44373 GAATATCTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:47138 original size:61 final size:61
Alignment explanation
Indices: 47043--47169 Score: 245
Period size: 61 Copynumber: 2.1 Consensus size: 61
47033 GATCTCAGAA
47043 ATGTTTGAATGGTATAATCATTTGAGATTATGACATCAGATTTTATTATATCCCAGATAAC
1 ATGTTTGAATGGTATAATCATTTGAGATTATGACATCAGATTTTATTATATCCCAGATAAC
*
47104 ATGTTTGAATGGTATAATCATTTGAGATTATGACATCAGATTTTATTATATCCCAGATAGC
1 ATGTTTGAATGGTATAATCATTTGAGATTATGACATCAGATTTTATTATATCCCAGATAAC
47165 ATGTT
1 ATGTT
47170 AATGTTCAGC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (61 bp):
ATGTTTGAATGGTATAATCATTTGAGATTATGACATCAGATTTTATTATATCCCAGATAAC
Found at i:49108 original size:2 final size:2
Alignment explanation
Indices: 49101--49139 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
49091 ATCTTCTAGC
*
49101 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49140 ATTAACATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:57184 original size:81 final size:79
Alignment explanation
Indices: 57080--58540 Score: 586
Period size: 81 Copynumber: 18.3 Consensus size: 79
57070 GAAGACGGTT
* * * * * *
57080 GTTGTTGTTGTTTCTCTTGAGAAGCTGGCACTATTGAATCTTCTTTTTTGGAATCCTCATCTTGC
1 GTTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTA-TGAACCTTCCTTTTCGGAATCCTCATCTTGC
* * *
57145 TGAGGCTCCGAATAT
65 TGAGGCTCCAAAGAC
* * * ** * *
57160 GTTCGCTGTTGGTTCACTTGAGAAGATGGCGC--TGAACCTTCCTTTTCGGAATCATTGTCGTGG
1 GTT-GCTGTTGGTTCTCTTGAGAAGCTGGCGCTATGAACCTTCCTTTTCGGAATCCTCATCTTGC
57223 TG-GTGCTCCAAAGAC
65 TGAG-GCTCCAAAGAC
* * * ***
57238 GGCTGCTGTTGGCTCTGTTGAGAAGCTGGAATTGATGAACCTT-CTTTCTCGGAATCCTCATCTT
1 -GTTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTT-TCGGAATCCTCATCTT
*
57302 GCTGAGGCTCCAAAGTC
63 GCTGAGGCTCCAAAGAC
* * * * * * **
57319 GGTTGTTGTTGGTTCTCTTGAGAAGCTGGCGCTAAGGATCCATCCTTTTCAGAATCATTGTCTTG
1 -GTTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTCGGAATCCTCATCTTG
* *
57384 CTGAGGCTCCGAACAC
64 CTGAGGCTCCAAAGAC
* * * * *
57400 GATTGCTGTTGGTTCTCCTGAGAAGCTGGTGTTGATGAACCTTCCTTTTCGGAGTCTTCATCTTG
1 G-TTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTCGGAATCCTCATCTTG
* *
57465 GTGATGCTCCAAAGAC
64 CTGAGGCTCCAAAGAC
* * * *
57481 AATTGCAT-TTGGTTCTCTGGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCATCTT
1 -GTTGC-TGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTCGGAATCCTCATCTT
* *
57545 GCTGATGCTCCGAAGAC
63 GCTGAGGCTCCAAAGAC
* ** * * * * *
57562 AATTGCTGTTGGTTCTCTAAAGAAGCTGACTCTAATGATCCTTCCTTTCCGGAATCCT--T-GT-
1 -GTTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTCGGAATCCTCATCTTG
* *
57623 CT--TGCTCCGAAGAC
64 CTGAGGCTCCAAAGAC
* * ** *
57637 GATTGCTGTTGGTTCTCTCGAGAAGCTGGCTCTAATGGTCCATT-CTTTTCGGAATCCTCGTC-T
1 G-TTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACC-TTCCTTTTCGGAATCCTCATCTT
* *
57700 --T---GCTCCGAAGAT
63 GCTGAGGCTCCAAAGAC
* * * *
57712 GATTGCTGTTGGTTCTCTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTC-T-
1 G-TTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTCGGAATCCTCATCTTG
* *
57775 -T---GCTCCGAATAC
64 CTGAGGCTCCAAAGAC
* * *
57787 GATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTC-T-
1 G-TTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTCGGAATCCTCATCTTG
*
57850 -T---GCTCCGAAGAC
64 CTGAGGCTCCAAAGAC
* * **** *
57862 GATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTAAAAG-ATGGCTCTAATG
1 G-TTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTCGGAAT--C-C---TC
* ** * ** *
57926 ATCCTTCCTTTTCGGAATCC-TCGTC
58 AT-CTTGC--TGAGG-CTCCAAAGAC
** * ** * * ** * ***
57951 -TTGCTCCGAAGACGATTGCTGTTG-G-TTCT--C-TTGA-GAAGCTGGCTCTAATG-ATCCTTC
1 GTTGCT--GTTG--G-TT-CTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTCGGAATCC-TC
* * ** *
58008 CTTTTCGGAATCCTCGTCTTGCTCCGAAGAC
58 ATCTT--G----CT-G--AGGCTCCAAAGAC
* * *
58039 GATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATC-T-
1 G-TTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTCGGAATCCTCATCTTG
*
58102 -T---GCTCCGAAGAC
64 CTGAGGCTCCAAAGAC
* * * *
58114 GATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTCTCGGAATCCTCGTCTTG
1 G-TTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTCGGAATCCTCATCTTG
*
58179 CT----CT--GAAGAC
64 CTGAGGCTCCAAAGAC
* * * * * *
58189 AGTTGTTGTTGGTTCTCTTGACAAGCTGGCTCTGATGAATCTT-CTTTATTGGAATCCTCGTCTT
1 -GTTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTT-TCGGAATCCTCATCTT
58253 GCTGAGGCTCCAAAGAC
63 GCTGAGGCTCCAAAGAC
** * *
58270 AACTGCCGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTT-CTTTTCTGGAATCCTCATGTT
1 -GTTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTTTC-GGAATCCTCATCTT
* **
58334 GCTGAGGTTCTGAAGAC
63 GCTGAGGCTCCAAAGAC
** * * * ** *
58351 AACTGTTGTTGGTTCTCTTCAGAAGCTGGCTCTGATGAACCTT-CTTTCTTAGAATCCTCGTCTT
1 -GTTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTT-TCGGAATCCTCATCTT
*
58415 GCTGAGGCTCCGAAGAC
63 GCTGAGGCTCCAAAGAC
* * * * * **
58432 GATTGCTGTTGGCTGTCTTCAGAAGCTGGCTCTGATGAACCTT-CTTTCTTGGAATCCTTGTCTT
1 G-TTGCTGTTGGTTCTCTTGAGAAGCTGGCGCT-ATGAACCTTCCTTT-TCGGAATCCTCATCTT
*
58496 GCTGACGCTCCAAAGAC
63 GCTGAGGCTCCAAAGAC
** * *
58513 GATTTTTGTTGGTTCACTTTAGAAGCTG
1 G-TTGCTGTTGGTTCTCTTGAGAAGCTG
58541 CTGTTGAACC
Statistics
Matches: 1109, Mismatches: 198, Indels: 147
0.76 0.14 0.10
Matches are distributed among these distances:
74 7 0.01
75 388 0.35
76 6 0.01
77 8 0.01
78 56 0.05
79 5 0.00
80 12 0.01
81 531 0.48
82 10 0.01
84 6 0.01
85 5 0.00
86 4 0.00
87 20 0.02
88 8 0.01
89 9 0.01
90 19 0.02
91 7 0.01
92 3 0.00
93 5 0.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (79 bp):
GTTGCTGTTGGTTCTCTTGAGAAGCTGGCGCTATGAACCTTCCTTTTCGGAATCCTCATCTTGCT
GAGGCTCCAAAGAC
Found at i:57443 original size:162 final size:157
Alignment explanation
Indices: 57085--58540 Score: 1027
Period size: 162 Copynumber: 9.1 Consensus size: 157
57075 CGGTTGTTGT
* * * * * *
57085 TGTTGTTTCTCTTGAGAAGCTGGCACTATTGAATCTTCTTTTTTGGAATCCTCATCTTGCTGAGG
1 TGTTGGTTCTCTTGAGAAGCTGG-TCTAATGAACCTTCCTTTTCGGAATCCTCATCTTGCTGAGG
* * * * *
57150 CTCCGAA-TATG-TTCGCTGTTGGTTCACTTGAGAAGATGGCGCT---GAACCTTCCTTTTCGGA
65 CTCCGAAGT-CGATT-GCTGTTGGTTCTCTTGAGAAGCTGGCTCTAAGGATCCTTCCTTTTCGGA
* * * **
57210 ATCATTGTCGTGGTGGTGCTCCAAAGACGGCTGC
128 ATCCTCGTC-T-GT-G-GCTCCGAAGACGATTGC
* * *
57244 TGTTGGCTCTGTTGAGAAGCTGGAAT-TGATGAACCTT-CTTTCTCGGAATCCTCATCTTGCTGA
1 TGTTGGTTCTCTTGAGAAGCTGG--TCTAATGAACCTTCCTTT-TCGGAATCCTCATCTTGCTGA
* * * * * *
57307 GGCTCCAAAGTCGGTTGTTGTTGGTTCTCTTGAGAAGCTGGCGCTAAGGATCCATCCTTTTCAGA
63 GGCTCCGAAGTCGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAAGGATCCTTCCTTTTCGGA
* * *
57372 ATCATTGTCTTGCTGAGGCTCCGAACACGATTGC
128 ATCCTCGTC-TG-T--GGCTCCGAAGACGATTGC
* * * * * * *
57406 TGTTGGTTCTCCTGAGAAGCTGGTGTTGATGAACCTTCCTTTTCGGAGTCTTCATCTTGGTGATG
1 TGTTGGTTCTCTTGAGAAGCTGGT-CTAATGAACCTTCCTTTTCGGAATCCTCATCTTGCTGAGG
* * * * *
57471 CTCCAAAGACAATTGCAT-TTGGTTCTCTGGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAA
65 CTCCGAAGTCGATTGC-TGTTGGTTCTCTTGAGAAGCTGGCTCTAAGGATCCTTCCTTTTCGGAA
* *
57535 TCCTCATCTTGCTGATGCTCCGAAGACAATTGC
129 TCCTCGTC-TG-TG--GCTCCGAAGACGATTGC
** * * * * *
57568 TGTTGGTTCTCTAAAGAAGCTGACTCTAATGATCCTTCCTTTCCGGAATCCT--T-GT-CT--TG
1 TGTTGGTTCTCTTGAGAAGCTG-GTCTAATGAACCTTCCTTTTCGGAATCCTCATCTTGCTGAGG
* *
57627 CTCCGAAGACGATTGCTGTTGGTTCTCTCGAGAAGCTGGCTCTAATGG-TCCATT-CTTTTCGGA
65 CTCCGAAGTCGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAA-GGATCC-TTCCTTTTCGGA
*
57690 ATCCTCGTCT-T-GCTCCGAAGATGATTGC
128 ATCCTCGTCTGTGGCTCCGAAGACGATTGC
* * *
57718 TGTTGGTTCTCTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTC-T--T---G
1 TGTTGGTTCTCTTGAGAAGCTGG-TCTAATGAACCTTCCTTTTCGGAATCCTCATCTTGCTGAGG
*
57777 CTCCGAA-TACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAA
65 CTCCGAAGT-CGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAAGGATCCTTCCTTTTCGGAA
57841 TCCTCGTCT-T-GCTCCGAAGACGATTGC
129 TCCTCGTCTGTGGCTCCGAAGACGATTGC
* **
57868 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTAAAAGATGGCTCTAATGATCCTTC
1 TGTTGGTTCTCTTGAGAAGCTGG-TCTAATGAACCTTCCTT------T---TCGGA--ATCC-TC
* * * ** *
57933 CT-TTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCT
53 ATCTTGCTG-AGGCTC--C--G-----AAGTCGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCT
*
57997 AATGATCCTTCCTTTTCGGAATCCTCGTCT-T-GCTCCGAAGACGATTGC
108 AAGGATCCTTCCTTTTCGGAATCCTCGTCTGTGGCTCCGAAGACGATTGC
* *
58045 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATC-T--T---G
1 TGTTGGTTCTCTTGAGAAGCTGG-TCTAATGAACCTTCCTTTTCGGAATCCTCATCTTGCTGAGG
* * *
58104 CTCCGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTCTCGGAAT
65 CTCCGAAGTCGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAAGGATCCTTCCTTTTCGGAAT
* *
58169 CCTCGTCT-T-GCTCTGAAGAC-AGTTGT
130 CCTCGTCTGTGGCTCCGAAGACGA-TTGC
* * * * *
58195 TGTTGGTTCTCTTGACAAGCTGGCTCTGATGAATCTT-CTTTATTGGAATCCTCGTCTTGCTGAG
1 TGTTGGTTCTCTTGAGAAGCTGG-TCTAATGAACCTTCCTTT-TCGGAATCCTCATCTTGCTGAG
* * * * * * * * *
58259 GCTCCAAAGACAACTGCCGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTT-CTTTTCTGGA
64 GCTCCGAAGTCGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAAGGATCCTTCCTTTTC-GGA
* * * * * *
58323 ATCCTCATGTTGCTGAGGTTCTGAAGACAACTGT
128 ATCCTC--G-T-CTGTGGCTCCGAAGACGATTGC
* * ** *
58357 TGTTGGTTCTCTTCAGAAGCTGGCTCTGATGAACCTT-CTTTCTTAGAATCCTCGTCTTGCTGAG
1 TGTTGGTTCTCTTGAGAAGCTGG-TCTAATGAACCTTCCTTT-TCGGAATCCTCATCTTGCTGAG
* * * * * * * *
58421 GCTCCGAAGACGATTGCTGTTGGCTGTCTTCAGAAGCTGGCTCTGATGAACCTT-CTTTCTTGGA
64 GCTCCGAAGTCGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAAGGATCCTTCCTTT-TCGGA
* * **
58485 ATCCTTGTCTTGCTGACGCTCCAAAGACGATTTT
128 ATCCTCGTC-TG-TG--GCTCCGAAGACGATTGC
* *
58519 TGTTGGTTCACTTTAGAAGCTG
1 TGTTGGTTCTCTTGAGAAGCTG
58541 CTGTTGAACC
Statistics
Matches: 1090, Mismatches: 130, Indels: 151
0.80 0.09 0.11
Matches are distributed among these distances:
149 8 0.01
150 308 0.28
151 2 0.00
152 2 0.00
153 2 0.00
155 8 0.01
156 119 0.11
157 4 0.00
158 6 0.01
159 94 0.09
160 10 0.01
161 5 0.00
162 371 0.34
163 9 0.01
165 4 0.00
166 4 0.00
168 6 0.01
170 1 0.00
171 1 0.00
172 1 0.00
177 125 0.11
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (157 bp):
TGTTGGTTCTCTTGAGAAGCTGGTCTAATGAACCTTCCTTTTCGGAATCCTCATCTTGCTGAGGC
TCCGAAGTCGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAAGGATCCTTCCTTTTCGGAATC
CTCGTCTGTGGCTCCGAAGACGATTGC
Found at i:57670 original size:75 final size:75
Alignment explanation
Indices: 57325--57908 Score: 688
Period size: 75 Copynumber: 7.5 Consensus size: 75
57315 AGTCGGTTGT
* * * * *
57325 TGTTGGTTCTCTTGAGAAGCTGGCGCTAAGGATCCATCCTTTTCAGAATCATTGTCTTGCTGAGG
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTTGTC-T--T---G
*
57390 CTCCGAACACGATTGC
60 CTCCGAAGACGATTGC
* * * * * **
57406 TGTTGGTTCTCCTGAGAAGCTGG-TGTTGATGAACCTTCCTTTTCGGAGTCTTCATCTTGGTGAT
1 TGTTGGTTCTCTTGAGAAGCTGGCT-CTAATGATCCTTCCTTTTCGGA---ATC--CTT-GTCTT
* *
57470 GCTCCAAAGACAATTGC
59 GCTCCGAAGACGATTGC
* *
57487 AT-TTGGTTCTCTGGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCATCTTGCTGAT
1 -TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCT--T-GT-CT--T
*
57551 GCTCCGAAGACAATTGC
59 GCTCCGAAGACGATTGC
** * *
57568 TGTTGGTTCTCTAAAGAAGCTGACTCTAATGATCCTTCCTTTCCGGAATCCTTGTCTTGCTCCGA
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTTGTCTTGCTCCGA
57633 AGACGATTGC
66 AGACGATTGC
* * *
57643 TGTTGGTTCTCTCGAGAAGCTGGCTCTAATGGTCCATT-CTTTTCGGAATCCTCGTCTTGCTCCG
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCC-TTCCTTTTCGGAATCCTTGTCTTGCTCCG
*
57707 AAGATGATTGC
65 AAGACGATTGC
* *
57718 TGTTGGTTCTCTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGA
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTTGTCTTGCTCCGA
*
57783 ATACGATTGC
66 AGACGATTGC
*
57793 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGA
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTTGTCTTGCTCCGA
57858 AGACGATTGC
66 AGACGATTGC
57868 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTT
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTT
57909 AAAAGATGGC
Statistics
Matches: 440, Mismatches: 46, Indels: 40
0.84 0.09 0.08
Matches are distributed among these distances:
74 2 0.00
75 263 0.60
76 4 0.01
77 2 0.00
78 5 0.01
79 1 0.00
80 1 0.00
81 153 0.35
82 2 0.00
84 3 0.01
86 2 0.00
87 2 0.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (75 bp):
TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTTGTCTTGCTCCGA
AGACGATTGC
Found at i:57775 original size:150 final size:150
Alignment explanation
Indices: 57325--58498 Score: 982
Period size: 150 Copynumber: 7.4 Consensus size: 150
57315 AGTCGGTTGT
* * * * * *
57325 TGTTGGTTCTCTTGAGAAGCTGGCGCTAAGGATCCATCCTTTTCAGAATCATTGTCTTGCTGAGG
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTC-T--T---G
* * * * * *
57390 CTCCGAACACGATTGCTGTTGGTTCTCCTGAGAAGCTGG-TGTTGATGAACCTTCCTTTTCGGAG
60 CTCCGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCT-CTAATGATCCTTCCTTTTCGGAA
** * *
57454 TCTTCATCTTGGTGATGCTCCAAAGACAATTGC
124 TC--C-TC---GTCTTGCTCCGAAGACGATTGC
* *
57487 AT-TTGGTTCTCTGGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCATCTTGCTGAT
1 -TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAAT-C-C-TCGT-CT--T
* ** * *
57551 GCTCCGAAGACAATTGCTGTTGGTTCTCTAAAGAAGCTGACTCTAATGATCCTTCCTTTCCGGAA
59 GCTCCGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAA
*
57616 TCCTTGTCTTGCTCCGAAGACGATTGC
124 TCCTCGTCTTGCTCCGAAGACGATTGC
* *
57643 TGTTGGTTCTCTCGAGAAGCTGGCTCTAATGGTCCATT-CTTTTCGGAATCCTCGTCTTGCTCCG
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCC-TTCCTTTTCGGAATCCTCGTCTTGCTCCG
* *
57707 AAGATGATTGCTGTTGGTTCTCTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCG
65 AAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCG
*
57772 TCTTGCTCCGAATACGATTGC
130 TCTTGCTCCGAAGACGATTGC
57793 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGA
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGA
**
57858 AGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTAAAAGATGGCTCTA
66 AGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTT------T---TCGG
* * * ** * *
57923 ATGATCCTTCCTTTTCGGAATCC-TCGTCTTGCTCCGAAGACGATTGC
122 A--ATCC-TCGTCTT--G-CTCCGAAGAC--GAT-----------TGC
57970 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGA
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGA
* *
58035 AGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCAT
66 AGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGT
58100 CTTGCTCCGAAGACGATTGC
131 CTTGCTCCGAAGACGATTGC
* *
58120 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTCTCGGAATCCTCGTCTTGCTCTGA
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGA
* * * *
58185 AGAC-AGTTGTTGTTGGTTCTCTTGACAAGCTGGCTCTGATGAAT-CTT-CTTTATTGGAATCCT
66 AGACGA-TTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATG-ATCCTTCCTTT-TCGGAATCCT
* * *
58247 CGTCTTGCTGAGGCTCCAAAGACAACTGC
128 CGTC-T--T---GCTCCGAAGACGATTGC
* * * * *
58276 CGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTT-CTTTTCTGGAATCCTCATGTTGCTGAG
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTC-GGAATCCTC--G-T-CT--T
* * * * * * * * **
58340 GTTCTGAAGACAACTGTTGTTGGTTCTCTTCAGAAGCTGGCTCTGATGAACCTT-CTTTCTTAGA
59 GCTCCGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTT-TCGGA
58404 ATCCTCGTCTTGCTGAGGCTCCGAAGACGATTGC
123 ATCCTCGTC-T--T---GCTCCGAAGACGATTGC
* * * * * * *
58438 TGTTGGCTGTCTTCAGAAGCTGGCTCTGATGAACCTT-CTTTCTTGGAATCCTTGTCTTGCT
1 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTT-TCGGAATCCTCGTCTTGCT
58499 GACGCTCCAA
Statistics
Matches: 859, Mismatches: 96, Indels: 119
0.80 0.09 0.11
Matches are distributed among these distances:
149 7 0.01
150 309 0.36
151 3 0.00
152 2 0.00
153 4 0.00
154 1 0.00
155 7 0.01
156 119 0.14
157 2 0.00
158 3 0.00
159 6 0.01
160 4 0.00
161 7 0.01
162 232 0.27
163 8 0.01
164 2 0.00
165 13 0.02
166 7 0.01
168 3 0.00
171 1 0.00
177 119 0.14
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (150 bp):
TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGA
AGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGT
CTTGCTCCGAAGACGATTGC
Found at i:57989 original size:102 final size:102
Alignment explanation
Indices: 57813--58010 Score: 396
Period size: 102 Copynumber: 1.9 Consensus size: 102
57803 CTTGAGAAGC
57813 TGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
1 TGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
57878 CTTGAGAAGCTGGCTCTAATGATCCTTCCTTAAAAGA
66 CTTGAGAAGCTGGCTCTAATGATCCTTCCTTAAAAGA
57915 TGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
1 TGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
57980 CTTGAGAAGCTGGCTCTAATGATCCTTCCTT
66 CTTGAGAAGCTGGCTCTAATGATCCTTCCTT
58011 TTCGGAATCC
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (102 bp):
TGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
CTTGAGAAGCTGGCTCTAATGATCCTTCCTTAAAAGA
Found at i:58006 original size:75 final size:74
Alignment explanation
Indices: 57915--58498 Score: 605
Period size: 75 Copynumber: 7.5 Consensus size: 74
57905 CCTTAAAAGA
57915 TGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
1 TGGCTCTAATGATCCTT-CTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
57980 CTTGAGAAGC
65 CTTGAGAAGC
57990 TGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
1 TGGCTCTAATGATCCTT-CTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
58055 CTTGAGAAGC
65 CTTGAGAAGC
* *
58065 TGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATCTTGCTCCGAAGACGATTGCTGTTGGTTCT
1 TGGCTCTAATGATCCTT-CTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
58130 CTTGAGAAGC
65 CTTGAGAAGC
* * *
58140 TGGCTCTAATGATCCTTCCTTCTCGGAATCCTCGTCTTGCTCTGAAGAC-AGTTGTTGTTGGTTC
1 TGGCTCTAATGATCCTT-CTTTTCGGAATCCTCGTCTTGCTCCGAAGACGA-TTGCTGTTGGTTC
*
58204 TCTTGACAAGC
64 TCTTGAGAAGC
* * * * * *
58215 TGGCTCTGATGAAT-CTTCTTTATTGGAATCCTCGTCTTGCTGAGGCTCCAAAGACAACTGCCGT
1 TGGCTCTAATG-ATCCTTCTTT-TCGGAATCCTCGTC-T--T---GCTCCGAAGACGATTGCTGT
58279 TGGTTCTCTTGAGAAGC
58 TGGTTCTCTTGAGAAGC
* * * * * * * * *
58296 TGGCGCTGATGAACCTTCTTTTCTGGAATCCTCATGTTGCTGAGGTTCTGAAGACAACTGTTGTT
1 TGGCTCTAATGATCCTTCTTTTC-GGAATCCTC--G-T-CT--TGCTCCGAAGACGATTGCTGTT
*
58361 GGTTCTCTTCAGAAGC
59 GGTTCTCTTGAGAAGC
* * **
58377 TGGCTCTGATGAACCTTCTTTCTTAGAATCCTCGTCTTGCTGAGGCTCCGAAGACGATTGCTGTT
1 TGGCTCTAATGATCCTTCTTT-TCGGAATCCTCGTC-T--T---GCTCCGAAGACGATTGCTGTT
* * *
58442 GGCTGTCTTCAGAAGC
59 GGTTCTCTTGAGAAGC
* * * *
58458 TGGCTCTGATGAACCTTCTTTCTTGGAATCCTTGTCTTGCT
1 TGGCTCTAATGATCCTTCTTT-TCGGAATCCTCGTCTTGCT
58499 GACGCTCCAA
Statistics
Matches: 446, Mismatches: 42, Indels: 42
0.84 0.08 0.08
Matches are distributed among these distances:
74 4 0.01
75 244 0.55
76 3 0.01
77 1 0.00
78 5 0.01
79 1 0.00
80 3 0.01
81 178 0.40
82 2 0.00
83 1 0.00
84 3 0.01
85 1 0.00
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (74 bp):
TGGCTCTAATGATCCTTCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCTC
TTGAGAAGC
Found at i:58034 original size:177 final size:177
Alignment explanation
Indices: 57732--58085 Score: 690
Period size: 177 Copynumber: 2.0 Consensus size: 177
57722 GGTTCTCTTG
* *
57732 AAAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAATACGATTGCTGTT
1 AAAAGATGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTT
57797 GGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGAC
66 GGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGAC
57862 GATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTT
131 GATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTT
57909 AAAAGATGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTT
1 AAAAGATGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTT
57974 GGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGAC
66 GGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGAC
58039 GATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTT
131 GATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTT
58086 TTCAGAATCC
Statistics
Matches: 175, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 175 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (177 bp):
AAAAGATGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTT
GGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGAC
GATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTT
Found at i:58108 original size:252 final size:252
Alignment explanation
Indices: 57663--58160 Score: 926
Period size: 252 Copynumber: 2.0 Consensus size: 252
57653 CTCGAGAAGC
* *
57663 TGGCTCTAATGGTCCATTCTTTTCGGAATCCTCGTCTTGCTCCGAAGATGATTGCTGTTGGTTCT
1 TGGCTCTAATGATCCATTCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
*
57728 CTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAATACGATTGC
66 CTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGC
* *
57793 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGA
131 TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATCTTGCTCCGA
57858 AGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTAAAAGA
196 AGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTAAAAGA
57915 TGGCTCTAATGATCC-TTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTC
1 TGGCTCTAATGATCCATT-CTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTC
*
57979 TCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTG
65 TCTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTG
58044 CTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATCTTGCTCCG
130 CTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATCTTGCTCCG
58109 AAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTT
195 AAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTT
58161 CTCGGAATCC
Statistics
Matches: 239, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
251 2 0.01
252 237 0.99
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (252 bp):
TGGCTCTAATGATCCATTCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCT
CTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGC
TGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATCTTGCTCCGA
AGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTAAAAGA
Found at i:58201 original size:327 final size:327
Alignment explanation
Indices: 57591--58226 Score: 1114
Period size: 327 Copynumber: 1.9 Consensus size: 327
57581 AAGAAGCTGA
*
57591 CTCTAATGATCCTTCCTTTCCGGAATCCTTGTCTTGCTCCGAAGACGATTGCTGTTGGTTCTCTC
1 CTCTAATGATCCTTCCTTTCCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCTCTC
* *
57656 GAGAAGCTGGCTCTAATGGTCCATTCTTTTCGGAATCCTCGTCTTGCTCCGAAGATGATTGCTGT
66 GAGAAGCTGGCTCTAATGATCCATTCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGT
* * *
57721 TGGTTCTCTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAATA
131 TGGTTCTCTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATCTTGCTCCGAAGA
*
57786 CGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTT
196 CGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTCTCGGAATCCTCGTCTT
*
57851 GCTCCGAAGACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTAAAAGAT
261 GCTCCGAAGACGATTGCTGTTGGTTCTCTTGACAAGCTGGCTCTAATGATCCTTCCTTAAAAGAT
57916 GG
326 GG
* *
57918 CTCTAATGATCCTTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCTCTT
1 CTCTAATGATCCTTCCTTTCCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCTCTC
57983 GAGAAGCTGGCTCTAATGATCC-TTCCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTG
66 GAGAAGCTGGCTCTAATGATCCATT-CTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTG
*
58047 TTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATCTTGCTCCGAAG
130 TTGGTTCTCTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATCTTGCTCCGAAG
58112 ACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTCTCGGAATCCTCGTCT
195 ACGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTCTCGGAATCCTCGTCT
* * *
58177 TGCTCTGAAGAC-AGTTGTTGTTGGTTCTCTTGACAAGCTGGCTCTGATGA
260 TGCTCCGAAGACGA-TTGCTGTTGGTTCTCTTGACAAGCTGGCTCTAATGA
58227 ATCTTCTTTA
Statistics
Matches: 293, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
326 3 0.01
327 290 0.99
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (327 bp):
CTCTAATGATCCTTCCTTTCCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGTTGGTTCTCTC
GAGAAGCTGGCTCTAATGATCCATTCTTTTCGGAATCCTCGTCTTGCTCCGAAGACGATTGCTGT
TGGTTCTCTTGAAAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATCTTGCTCCGAAGA
CGATTGCTGTTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTCTCGGAATCCTCGTCTT
GCTCCGAAGACGATTGCTGTTGGTTCTCTTGACAAGCTGGCTCTAATGATCCTTCCTTAAAAGAT
GG
Found at i:59079 original size:18 final size:18
Alignment explanation
Indices: 59056--59109 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
59046 AAGGCTAGAG
59056 CCCTGGCTTGATGATGAT
1 CCCTGGCTTGATGATGAT
*
59074 CCCTGGCTAGATGATGAT
1 CCCTGGCTTGATGATGAT
*
59092 CCCTGGTTTGATGATGAT
1 CCCTGGCTTGATGATGAT
59110 GAGCGAACAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (18 bp):
CCCTGGCTTGATGATGAT
Found at i:63621 original size:28 final size:28
Alignment explanation
Indices: 63575--63671 Score: 106
Period size: 28 Copynumber: 3.4 Consensus size: 28
63565 GAAAAGGTTT
* * *
63575 AAATAGTTTATGTACCTATTTTGA-CATA
1 AAATACTTTAAGTATCTATTTTGACCA-A
63603 AAATACTTTAAGTATCTATTTTGACCAAAA
1 AAATACTTTAAGTATCTATTTTGACC--AA
*
63633 AAATAACTTTAAGTATTTATTTTGACCAA
1 AAAT-ACTTTAAGTATCTATTTTGACCAA
*
63662 AAATATTTTA
1 AAATACTTTA
63672 GGCACTTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
28 26 0.43
29 7 0.12
30 5 0.08
31 22 0.37
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (28 bp):
AAATACTTTAAGTATCTATTTTGACCAA
Found at i:63645 original size:31 final size:30
Alignment explanation
Indices: 63575--63664 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 30
63565 GAAAAGGTTT
* * * *
63575 AAATAGTTTATGTACCTATTTTGA-C-ATA
1 AAATACTTTAAGTATCTATTTTGACCAAAA
63603 AAATACTTTAAGTATCTATTTTGACCAAAA
1 AAATACTTTAAGTATCTATTTTGACCAAAA
*
63633 AAATAACTTTAAGTATTTATTTTGACCAAAA
1 AAAT-ACTTTAAGTATCTATTTTGACCAAAA
63664 A
1 A
63665 TATTTTAGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
28 21 0.39
29 1 0.02
30 6 0.11
31 26 0.48
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (30 bp):
AAATACTTTAAGTATCTATTTTGACCAAAA
Found at i:72601 original size:3 final size:3
Alignment explanation
Indices: 72593--72624 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
72583 TTATCGTAAT
72593 TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA T
72625 GCTATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:73352 original size:12 final size:13
Alignment explanation
Indices: 73335--73363 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
73325 CGTTCAGATT
73335 TTTTTAAA-AATA
1 TTTTTAAATAATA
73347 TTTTTAAATAATA
1 TTTTTAAATAATA
73360 TTTT
1 TTTT
73364 ACTTATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTTAAATAATA
Found at i:73886 original size:24 final size:23
Alignment explanation
Indices: 73840--73910 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 23
73830 AATGAAAATG
*
73840 AAATATTTTTAAATTAAGTTAATAGT
1 AAATATATTT-AA-TAAGTTAATA-T
73866 AAATATATTTAATAAGTTAATAT
1 AAATATATTTAATAAGTTAATAT
*
73889 AAAAATATTT--TAAGTTAATAT
1 AAATATATTTAATAAGTTAATAT
73910 A
1 A
73911 TAGAAGATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 12 0.28
23 10 0.23
24 10 0.23
25 2 0.05
26 9 0.21
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.44
Consensus pattern (23 bp):
AAATATATTTAATAAGTTAATAT
Found at i:74269 original size:39 final size:39
Alignment explanation
Indices: 74164--74269 Score: 112
Period size: 39 Copynumber: 2.7 Consensus size: 39
74154 TTTAAAAAAT
*
74164 AATTTAGAACGTCAAT-ATGAAATAATTTAAGAAATTAAG
1 AATTTAGAACGT-TATGATGAAATAATTTAAGAAATTAAG
* *
74203 AATTTAGAACGTTATGATGTCAA-AATTTAAGAAATTATG
1 AATTTAGAACGTTATGATG-AAATAATTTAAGAAATTAAG
*
74242 -ATTTCAGAATGTTA-GAGTGAAATAATTT
1 AATTT-AGAACGTTATGA-TGAAATAATTT
74270 GAGGATTATG
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
38 10 0.18
39 45 0.79
40 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (39 bp):
AATTTAGAACGTTATGATGAAATAATTTAAGAAATTAAG
Found at i:74729 original size:31 final size:31
Alignment explanation
Indices: 74671--74729 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
74661 ACCACATCTA
* * *
74671 AATTAAATAAAAATGAAAGTGATCATATATT
1 AATTAAATAAAAACGAAAGTAACCATATATT
*
74702 AATTAAATAAAAACGTAAGTAACCATAT
1 AATTAAATAAAAACGAAAGTAACCATAT
74730 CTTATGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.29
Consensus pattern (31 bp):
AATTAAATAAAAACGAAAGTAACCATATATT
Found at i:74778 original size:48 final size:48
Alignment explanation
Indices: 74726--74818 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
74716 GTAAGTAACC
74726 ATATCTTATGTATTTTGAAATCAGTGACAAAAAATGAATAAAACTAAA
1 ATATCTTATGTATTTTGAAATCAGTGACAAAAAATGAATAAAACTAAA
74774 ATATCTTATGTATTTTGAAATCAGTGACAAAAAATGAATAAAACT
1 ATATCTTATGTATTTTGAAATCAGTGACAAAAAATGAATAAAACT
74819 GAGAGATAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (48 bp):
ATATCTTATGTATTTTGAAATCAGTGACAAAAAATGAATAAAACTAAA
Found at i:75444 original size:14 final size:14
Alignment explanation
Indices: 75419--75456 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
75409 TTTTAAAGAT
*
75419 TAAAAA-AAATTAT
1 TAAAAATAAATTAA
*
75432 TAATAATAAATTAA
1 TAAAAATAAATTAA
75446 TAAAAATAAAT
1 TAAAAATAAAT
75457 AGTCGAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAAATAAATTAA
Found at i:75919 original size:2 final size:2
Alignment explanation
Indices: 75912--75946 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
75902 GACATTGTAC
75912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75947 CGTTGTGCCA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:84748 original size:17 final size:18
Alignment explanation
Indices: 84726--84759 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
84716 TCAGCCGGTC
84726 CGGTTT-GAACGGTTCAG
1 CGGTTTCGAACGGTTCAG
*
84743 CGGTTTCGACCGGTTCA
1 CGGTTTCGAACGGTTCA
84760 CTAATAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (18 bp):
CGGTTTCGAACGGTTCAG
Found at i:86621 original size:31 final size:31
Alignment explanation
Indices: 86586--86705 Score: 131
Period size: 31 Copynumber: 3.9 Consensus size: 31
86576 AATGATTTTT
*
86586 TTTGATAAATTTAAAGATTATTTTATAATAA
1 TTTGATAAATTTAATGATTATTTTATAATAA
* *
86617 TTTGAT-ATTTTAATGA--CTTTTATAATAA
1 TTTGATAAATTTAATGATTATTTTATAATAA
*
86645 TTTGATAAGATTTAATGATTATTTTATAACT-G
1 TTTGATAA-ATTTAATGATTATTTTATAA-TAA
* * *
86677 TTTGAGAACTTTAATGATTAGTTTATAAT
1 TTTGATAAATTTAATGATTATTTTATAAT
86706 TTTAAAGTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
28 17 0.23
29 1 0.01
30 17 0.23
31 24 0.32
32 15 0.20
33 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (31 bp):
TTTGATAAATTTAATGATTATTTTATAATAA
Found at i:89213 original size:2 final size:2
Alignment explanation
Indices: 89208--89233 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
89198 GCTGTGTGTG
89208 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
89234 CTTGTGATTA
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):
TA
Done.