Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007112.1 Hibiscus syriacus cultivar Beakdansim tig00018585_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: 83161
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4533 original size:24 final size:24
Alignment explanation
Indices: 4489--4534 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4479 TAAGAATAAT
*
4489 TTTATCTTTGTGACACGTTTTTTC
1 TTTATCTTTGTGACACATTTTTTC
* *
4513 TTTATCTTTGTGGCATATTTTT
1 TTTATCTTTGTGACACATTTTT
4535 CATCTTTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (24 bp):
TTTATCTTTGTGACACATTTTTTC
Found at i:4753 original size:3 final size:3
Alignment explanation
Indices: 4745--4785 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
4735 TTTTTCAGCA
*
4745 TAT TAT TAT TAT T-T TAT TAT TAT TAC TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4786 AAATAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4814 original size:16 final size:17
Alignment explanation
Indices: 4793--4825 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4783 TATAAATAAA
4793 AAATATA-TACAAACCC
1 AAATATATTACAAACCC
4809 AAATATATTACAAACCC
1 AAATATATTACAAACCC
4826 GAAGCCCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATATATTACAAACCC
Found at i:6044 original size:23 final size:22
Alignment explanation
Indices: 6002--6073 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
5992 ACATGTTTAA
*
6002 ATTATTGCTTTAATTATTATTT
1 ATTATTACTTTAATTATTATTT
*
6024 ATTATTACTTTTA-TA-T-TTT
1 ATTATTACTTTAATTATTATTT
*
6043 ATTTATTGCTTTAATTATTATTT
1 A-TTATTACTTTAATTATTATTT
6066 AATTATTA
1 -ATTATTA
6074 TTTTTATCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.10
20 11 0.28
21 4 0.10
22 12 0.30
23 8 0.20
24 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (22 bp):
ATTATTACTTTAATTATTATTT
Found at i:6066 original size:11 final size:11
Alignment explanation
Indices: 6010--6076 Score: 61
Period size: 11 Copynumber: 6.3 Consensus size: 11
6000 AAATTATTGC
6010 TTTAATTATTA
1 TTTAATTATTA
6021 TTT-ATTATTA
1 TTTAATTATTA
*
6031 CTT--TTA-TA
1 TTTAATTATTA
* *
6039 TTTTATTTATTGC
1 -TTTAATTATT-A
6052 TTTAATTATTA
1 TTTAATTATTA
6063 TTTAATTATTA
1 TTTAATTATTA
6074 TTT
1 TTT
6077 TTATCTTAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
8 2 0.04
9 5 0.11
10 9 0.20
11 20 0.43
12 10 0.22
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:6157 original size:25 final size:26
Alignment explanation
Indices: 6091--6169 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 26
6081 CTTAGTCTTA
*
6091 TATATATATATATATATATATATATT
1 TATATAAATATATATATATATATATT
*
6117 ATATATATATATATATATATATATATT
1 -TATATAAATATATATATATATATATT
* * * *
6144 TGTTTAAATA-ATATATTTATTTATT
1 TATATAAATATATATATATATATATT
6169 T
1 T
6170 TTAATATCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 14 0.30
26 7 0.15
27 26 0.55
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TATATAAATATATATATATATATATT
Found at i:6159 original size:2 final size:2
Alignment explanation
Indices: 6089--6142 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
6079 ATCTTAGTCT
6089 TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
6130 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
6143 TTGTTTAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6550 original size:23 final size:21
Alignment explanation
Indices: 6518--6559 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
6508 CATTTTCTAA
*
6518 TATTTTTAAATAATTAAATATCT
1 TATTTATAAAT-A-TAAATATCT
6541 TATTTATAAATATAAATAT
1 TATTTATAAATATAAATAT
6560 TTTCTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTATAAATATAAATATCT
Found at i:7113 original size:24 final size:24
Alignment explanation
Indices: 7060--7114 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
7050 TATAATTCTT
*
7060 TTCTTT-TAAATTTTTTATACTTA
1 TTCTTTATAAATTTTATATACTTA
* *
7083 TTATTTATAATATTTTATATA-TTC
1 TTCTTTATAA-ATTTTATATACTTA
7107 TTCTTTAT
1 TTCTTTAT
7115 GATTGTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.19
24 12 0.46
25 9 0.35
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.65
Consensus pattern (24 bp):
TTCTTTATAAATTTTATATACTTA
Found at i:15986 original size:73 final size:73
Alignment explanation
Indices: 15879--16261 Score: 649
Period size: 73 Copynumber: 5.2 Consensus size: 73
15869 TCATAGTTCT
* *
15879 GACCTACAGTGCATGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTC
1 GACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCCTAAAGCCTCAGGGTC
*
15944 ATCAGTAA
66 ATCTGTAA
* * * *
15952 TACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCCTAAAACCTTAGGGTT
1 GACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCCTAAAGCCTCAGGGTC
16017 ATCTGTAA
66 ATCTGTAA
* * *
16025 GACCTACAGTGCATAATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATCCTAAAACCTCAGGGTC
1 GACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCCTAAAGCCTCAGGGTC
16090 ATCTGTAA
66 ATCTGTAA
16098 GACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCCTAAAGCCTCAGGGTC
1 GACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCCTAAAGCCTCAGGGTC
16163 ATCTGTAA
66 ATCTGTAA
*
16171 GACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTC
1 GACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCCTAAAGCCTCAGGGTC
16236 ATCTGTAA
66 ATCTGTAA
* *
16244 GACCTACATTGCAGGATG
1 GACCTACAGTGCATGATG
16262 ATAGGACATT
Statistics
Matches: 292, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 292 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (73 bp):
GACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCCTAAAGCCTCAGGGTC
ATCTGTAA
Found at i:16420 original size:3 final size:3
Alignment explanation
Indices: 16412--16458 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
16402 TTTTTAAGCA
* *
16412 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16459 AATAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:16868 original size:13 final size:14
Alignment explanation
Indices: 16850--16882 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16840 CCTCACCTGC
16850 AAAAGAAGA-AAAA
1 AAAAGAAGAGAAAA
*
16863 AAAAGAATAGAAAA
1 AAAAGAAGAGAAAA
16877 AAAAGA
1 AAAAGA
16883 GGACAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (14 bp):
AAAAGAAGAGAAAA
Found at i:17730 original size:43 final size:41
Alignment explanation
Indices: 17679--17772 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 41
17669 TTTCATTTTG
17679 TTTTTATTACTTTCAATATGTTTAAATTATTGCTTTAATTATTA
1 TTTTTATTACTTT-AATAT-TTT-AATTATTGCTTTAATTATTA
*
17723 TTTTATTATTACTTTTATATTTTAATTATTGCTTTAATTATTA
1 -TTT-TTATTACTTTAATATTTTAATTATTGCTTTAATTATTA
17766 TTTTTAT
1 TTTTTAT
17773 CTTAGTCTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.09
42 3 0.06
43 20 0.43
44 3 0.06
45 7 0.15
46 10 0.21
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (41 bp):
TTTTTATTACTTTAATATTTTAATTATTGCTTTAATTATTA
Found at i:17740 original size:20 final size:21
Alignment explanation
Indices: 17717--17764 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
17707 ATTGCTTTAA
17717 TTATTATTTT-ATTATTACTT
1 TTATTATTTTAATTATTACTT
*
17737 TTA-TATTTTAATTATTGCTT
1 TTATTATTTTAATTATTACTT
*
17757 TAATTATT
1 TTATTATT
17765 ATTTTTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 14 0.58
21 4 0.17
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTATTTTAATTATTACTT
Found at i:17748 original size:31 final size:32
Alignment explanation
Indices: 17712--17772 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
17702 AAATTATTGC
*
17712 TTTAATTATT-ATTTTATTATTACTTTTATAT
1 TTTAATTATTGATTTAATTATTACTTTTATAT
* *
17743 TTTAATTATTGCTTTAATTATTATTTTTAT
1 TTTAATTATTGATTTAATTATTACTTTTAT
17773 CTTAGTCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (32 bp):
TTTAATTATTGATTTAATTATTACTTTTATAT
Found at i:18213 original size:23 final size:21
Alignment explanation
Indices: 18181--18222 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
18171 CATTTTCTAA
*
18181 TATTTCTAAATAATTAAATATCT
1 TATTTATAAAT-A-TAAATATCT
18204 TATTTATAAATATAAATAT
1 TATTTATAAATATAAATAT
18223 TTTCTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTTATAAATATAAATATCT
Found at i:27089 original size:18 final size:18
Alignment explanation
Indices: 27062--27099 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
27052 AATGATAATT
27062 GTCGACAATATTTAAATA
1 GTCGACAATATTTAAATA
*
27080 GTCGATAATATTTAAATA
1 GTCGACAATATTTAAATA
27098 GT
1 GT
27100 TAAGTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (18 bp):
GTCGACAATATTTAAATA
Found at i:31242 original size:14 final size:15
Alignment explanation
Indices: 31223--31251 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31213 CACGTTATCT
31223 ATTTATTA-TTTTAA
1 ATTTATTAGTTTTAA
31237 ATTTATTAGTTTTAA
1 ATTTATTAGTTTTAA
31252 GAAAATCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTATTAGTTTTAA
Found at i:32484 original size:16 final size:15
Alignment explanation
Indices: 32465--32523 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
32455 AATATAATTA
32465 ATAATATATATTATTT
1 ATAATATA-ATTATTT
*
32481 ATAATATACTTATTT
1 ATAATATAATTATTT
*
32496 -TAATA-AATAATTT
1 ATAATATAATTATTT
*
32509 ATAATATGATTATTT
1 ATAATATAATTATTT
32524 CAATAGAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 6 0.17
14 10 0.28
15 12 0.33
16 8 0.22
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
ATAATATAATTATTT
Found at i:32487 original size:14 final size:14
Alignment explanation
Indices: 32470--32523 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
32460 AATTAATAAT
32470 ATATATTATTTATA
1 ATATATTATTTATA
32484 ATATACTTATTT-TA
1 ATATA-TTATTTATA
* *
32498 ATAAATAATTTATA
1 ATATATTATTTATA
32512 ATATGATTATTT
1 ATAT-ATTATTT
32524 CAATAGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 5 0.15
14 16 0.48
15 12 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
ATATATTATTTATA
Found at i:32508 original size:28 final size:29
Alignment explanation
Indices: 32477--32533 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
32467 AATATATATT
*
32477 ATTTATAATAT-ACTTATTTTAATA-AATA
1 ATTTATAATATGA-TTATTTCAATAGAATA
32505 ATTTATAATATGATTATTTCAATAGAATA
1 ATTTATAATATGATTATTTCAATAGAATA
32534 TACTAATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (29 bp):
ATTTATAATATGATTATTTCAATAGAATA
Found at i:32602 original size:15 final size:15
Alignment explanation
Indices: 32567--32608 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
32557 AAAATTGTAG
**
32567 AAATAATATTTTAAT
1 AAATAATATTGAAAT
32582 -AATAATATTGAAAT
1 AAATAATATTGAAAT
32596 AAATAATATTGAA
1 AAATAATATTGAA
32609 TAGATTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
AAATAATATTGAAAT
Found at i:35215 original size:71 final size:71
Alignment explanation
Indices: 34998--35217 Score: 163
Period size: 71 Copynumber: 3.1 Consensus size: 71
34988 CCATATTCCT
*
34998 TTATATTTGCATGTGATTGATTCTTTGGATTTGTTTTCCATACATATTTAAGCATTTGGTGTATT
1 TTATATTTGCATGTAATTGATTCTTTGGATTTGTTTTCCATACATATTTAAGCATTTGGTGTATT
35063 CATATA
66 CATATA
* ** * *** * *
35069 TTATATTTATTGTATAAAAATTTGATTAGGTTCGTTTCTTTGTTTACCAT--ATATTT--G--TA
1 TTATA--T-TTGCAT-GTAA-TTGATT--CTT--TGGATTTGTTTTCCATACATATTTAAGCATT
*** *
35128 T-CCATATTC--CT-
57 TGGTGTATTCATATA
35139 TTATATTTGCATGTAATTGATTCTTTGGATTTGTTTTCCATACATATTTAAGCATTTGGTGTATT
1 TTATATTTGCATGTAATTGATTCTTTGGATTTGTTTTCCATACATATTTAAGCATTTGGTGTATT
35204 CATATA
66 CATATA
35210 TTATATTT
1 TTATATTT
35218 ATTGTATAAA
Statistics
Matches: 103, Mismatches: 27, Indels: 38
0.61 0.16 0.23
Matches are distributed among these distances:
61 12 0.12
63 8 0.08
65 7 0.07
66 2 0.02
67 7 0.07
68 6 0.06
70 6 0.06
71 14 0.14
73 6 0.06
74 7 0.07
75 1 0.01
76 7 0.07
78 8 0.08
80 12 0.12
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (71 bp):
TTATATTTGCATGTAATTGATTCTTTGGATTTGTTTTCCATACATATTTAAGCATTTGGTGTATT
CATATA
Found at i:35241 original size:141 final size:141
Alignment explanation
Indices: 34987--35265 Score: 549
Period size: 141 Copynumber: 2.0 Consensus size: 141
34977 TTGTTTAGTC
*
34987 TCCATATTCCTTTATATTTGCATGTGATTGATTCTTTGGATTTGTTTTCCATACATATTTAAGCA
1 TCCATATTCCTTTATATTTGCATGTAATTGATTCTTTGGATTTGTTTTCCATACATATTTAAGCA
35052 TTTGGTGTATTCATATATTATATTTATTGTATAAAAATTTGATTAGGTTCGTTTCTTTGTTTACC
66 TTTGGTGTATTCATATATTATATTTATTGTATAAAAATTTGATTAGGTTCGTTTCTTTGTTTACC
35117 ATATATTTGTA
131 ATATATTTGTA
35128 TCCATATTCCTTTATATTTGCATGTAATTGATTCTTTGGATTTGTTTTCCATACATATTTAAGCA
1 TCCATATTCCTTTATATTTGCATGTAATTGATTCTTTGGATTTGTTTTCCATACATATTTAAGCA
35193 TTTGGTGTATTCATATATTATATTTATTGTATAAAAATTTGATTAGGTTCGTTTCTTTGTTTACC
66 TTTGGTGTATTCATATATTATATTTATTGTATAAAAATTTGATTAGGTTCGTTTCTTTGTTTACC
35258 ATATATTT
131 ATATATTT
35266 TAATAATACT
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 137 1.00
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (141 bp):
TCCATATTCCTTTATATTTGCATGTAATTGATTCTTTGGATTTGTTTTCCATACATATTTAAGCA
TTTGGTGTATTCATATATTATATTTATTGTATAAAAATTTGATTAGGTTCGTTTCTTTGTTTACC
ATATATTTGTA
Found at i:43070 original size:20 final size:20
Alignment explanation
Indices: 43047--43377 Score: 452
Period size: 20 Copynumber: 16.6 Consensus size: 20
43037 CGCGAACACA
43047 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
43067 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
**
43087 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
43107 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
43127 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
43147 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
43167 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
43187 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
43207 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
43227 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
43247 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
43267 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
43287 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
43307 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
43327 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
43347 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
43367 TAAATCACAAC
1 TAAATCGCAAC
43378 ACTGAAATTT
Statistics
Matches: 276, Mismatches: 29, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.01
20 273 0.99
21 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:44098 original size:24 final size:24
Alignment explanation
Indices: 44059--44105 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44049 AAATTTGGTC
44059 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
44083 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
44106 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:44297 original size:12 final size:12
Alignment explanation
Indices: 44280--44304 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44270 ATATAATCCT
44280 GAAGAAGAAAAA
1 GAAGAAGAAAAA
44292 GAAGAAGAAAAA
1 GAAGAAGAAAAA
44304 G
1 G
44305 TCCCGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:46599 original size:19 final size:19
Alignment explanation
Indices: 46577--46874 Score: 304
Period size: 19 Copynumber: 17.4 Consensus size: 19
46567 CGGAAAATAC
*
46577 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
46596 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
46610 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
46630 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
46644 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
46663 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
46682 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
46696 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
46715 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
46733 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
46747 AATCGCAATGCGAAA--AA
1 AATCGCAATGCGAAATGAA
46764 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
46783 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
46797 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
46815 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
46829 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
46848 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
46867 AATCGCAA
1 AATCGCAA
46875 CGAGATAATC
Statistics
Matches: 240, Mismatches: 8, Indels: 62
0.77 0.03 0.20
Matches are distributed among these distances:
14 56 0.23
15 4 0.02
16 29 0.12
17 26 0.11
18 20 0.08
19 92 0.38
20 13 0.05
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:46664 original size:33 final size:33
Alignment explanation
Indices: 46577--46896 Score: 201
Period size: 33 Copynumber: 9.5 Consensus size: 33
46567 CGGAAAATAC
* *
46577 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
46610 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
46644 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
46682 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
46715 AATCGCAATGCGAAATG-AAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
46747 AATCGCAATGCGAAA--AAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
46783 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAGA--A
46815 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
46848 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
46881 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
46897 TATAAACGCA
Statistics
Matches: 245, Mismatches: 13, Indels: 58
0.78 0.04 0.18
Matches are distributed among these distances:
30 1 0.00
31 10 0.04
32 43 0.18
33 97 0.40
34 37 0.15
35 14 0.06
36 14 0.06
37 10 0.04
38 19 0.08
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:46692 original size:52 final size:52
Alignment explanation
Indices: 46605--46874 Score: 396
Period size: 52 Copynumber: 5.2 Consensus size: 52
46595 AAATCCCAAC
46605 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
46658 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
46710 ATGAAAATCGCAATGCGAAATG-AAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
46761 A--AAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
46811 ATG-AAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
46862 ATGAAAATCGCAA
1 ATGAAAATCGCAA
46875 CGAGATAATC
Statistics
Matches: 204, Mismatches: 4, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
46 8 0.04
48 3 0.01
49 24 0.12
50 30 0.15
51 56 0.27
52 67 0.33
53 16 0.08
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:46894 original size:84 final size:82
Alignment explanation
Indices: 46663--46896 Score: 330
Period size: 84 Copynumber: 2.8 Consensus size: 82
46653 GCGAAATGAA
* * * * *
46663 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAAAATCGCAATGCG
*
46727 AAATGAAATCGCAACGACAG
63 AAATGAAATCGCAACGAAAG
46747 AATCGCAATGCGAAA--AAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACG-AA-AATCGCAATGCGA
46810 AATGAAATCGCAACGAAAG
64 AATGAAATCGCAACGAAAG
46829 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGA
46894 AAT
64 AAT
46897 TATAAACGCA
Statistics
Matches: 137, Mismatches: 7, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
80 6 0.04
81 8 0.06
82 59 0.43
83 1 0.01
84 63 0.46
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (82 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAATCGCAATGCGAAA
TGAAATCGCAACGAAAG
Found at i:47012 original size:19 final size:19
Alignment explanation
Indices: 46903--47004 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
46893 AAATTATAAA
46903 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
46922 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
46942 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
46958 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
46975 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
46994 CGCATTGCGAT
1 CGCATTGCGAT
47005 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:47130 original size:14 final size:14
Alignment explanation
Indices: 47111--47147 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
47101 CATCAATTAC
47111 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
47125 ACAAATCATCTTTT
1 ACAAATCAACTTTT
47139 ACAAATCAA
1 ACAAATCAA
47148 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:49143 original size:33 final size:33
Alignment explanation
Indices: 49097--49189 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
49087 GCGAAACCAA
*
49097 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
49130 AATCGTAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
49163 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
49190 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:49168 original size:14 final size:14
Alignment explanation
Indices: 49116--49172 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
49106 GCGAAATGAA
*
49116 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
49130 AATCGTAATGCGAAATG
1 AATCGCAA--CGAAA-G
49147 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
49163 AATCGCAACG
1 AATCGCAACG
49173 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:49187 original size:19 final size:19
Alignment explanation
Indices: 49060--49194 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
49050 TAGTTTACTT
* *
49060 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
49080 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
49099 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
49118 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
* *
49132 TCGTAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
49151 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
49165 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
49184 TCGCAATGCGA
1 TCGCAACGCGA
49195 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:49212 original size:19 final size:19
Alignment explanation
Indices: 49190--49318 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
49180 AAAATCGCAA
49190 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
49209 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
49223 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
49242 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
49256 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
49275 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
49294 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
49314 TGCGA
1 TGCGA
49319 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:49232 original size:33 final size:33
Alignment explanation
Indices: 49190--49281 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
49180 AAAATCGCAA
49190 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
49223 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
49256 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
49282 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:49523 original size:92 final size:93
Alignment explanation
Indices: 49362--49738 Score: 701
Period size: 92 Copynumber: 4.1 Consensus size: 93
49352 TTGAATGGAT
49362 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
49427 -GTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
49454 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA-ACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
49518 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
49546 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
49608 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
49636 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAATACTATTTCACAGTGTTAAAGAATACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AAATACTATTTCACAGTGTTAAAGAATACA
*
49701 CAGTTTAGCAGAATTGGCAGCAACCGAAT
65 CAGTTTAGCAGAATTGGCAGCAACCGAAC
49730 AAATTTACT
1 AAATTTACT
49739 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 1, Indels: 10
0.96 0.00 0.03
Matches are distributed among these distances:
89 17 0.06
90 68 0.24
91 8 0.03
92 125 0.45
93 2 0.01
94 58 0.21
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:51379 original size:14 final size:14
Alignment explanation
Indices: 51360--51449 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
51350 TTGAAATGAA
51360 AATCGCAACGAGAG
1 AATCGCAACGAGAG
51374 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
51391 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
51407 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
51426 AATCGCAACGAGAG
1 AATCGCAACGAGAG
51440 AATCGCAACG
1 AATCGCAACG
51450 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:51397 original size:33 final size:33
Alignment explanation
Indices: 51352--51466 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
51342 TCTTTTGGTT
51352 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
51385 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
51418 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
51451 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
51467 TGCGATTGCG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:51398 original size:19 final size:18
Alignment explanation
Indices: 51359--51471 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
51349 GTTGAAATGA
51359 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
51374 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
51391 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
51407 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
51424 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
51440 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
51457 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
51472 TTGCGATTTT
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:51508 original size:14 final size:14
Alignment explanation
Indices: 51489--51543 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
51479 TTTGGTTTCG
51489 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
51503 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
51522 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
51536 CGTTGCGA
1 CGTTGCGA
51544 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:51514 original size:33 final size:33
Alignment explanation
Indices: 51472--51543 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
51462 CGCAATGCGA
**
51472 TTGCGATTTTGGTTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
51505 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
51538 TTGCGA
1 TTGCGA
51544 CAGTCATTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.08, C:0.22, G:0.25, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:51551 original size:33 final size:33
Alignment explanation
Indices: 51484--51565 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
51474 GCGATTTTGG
***
51484 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
51517 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
51550 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
51566 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:51570 original size:20 final size:20
Alignment explanation
Indices: 51496--51584 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
51486 TCGCGTTGCG
51496 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
51516 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
51529 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
51549 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
51569 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
51585 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:51705 original size:33 final size:33
Alignment explanation
Indices: 51663--51733 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
51653 AATACTAACT
*
51663 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
51696 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
51729 TGAAA
1 TGAAA
51734 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:51967 original size:22 final size:22
Alignment explanation
Indices: 51915--51969 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
51905 TGGTTGTGAG
**
51915 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
51937 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
51959 GGATTTCTTCG
1 GGATTTCTTCG
51970 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:52137 original size:20 final size:20
Alignment explanation
Indices: 52112--52304 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
52102 CTTTAAATAT
52112 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
52132 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
52154 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
52173 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
52193 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
52213 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
52233 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
52253 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
52273 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
52293 CGCGTTGCGATT
1 CGCGTTGCGATT
52305 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:52299 original size:60 final size:60
Alignment explanation
Indices: 52112--52304 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
52102 CTTTAAATAT
**
52112 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
52173 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
52233 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
52293 CGCGTTGCGATT
1 CGCGTTGCGATT
52305 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:52385 original size:20 final size:20
Alignment explanation
Indices: 52360--52411 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
52350 AAGAATCGCG
*
52360 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
52380 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
52400 TTGCGATTCTGG
1 TTGCGATTCTGG
52412 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:53157 original size:4 final size:4
Alignment explanation
Indices: 53148--53174 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53138 TGTAACTATG
53148 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
53175 ATACATGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:59265 original size:246 final size:244
Alignment explanation
Indices: 58819--60037 Score: 1670
Period size: 246 Copynumber: 5.0 Consensus size: 244
58809 TCTTGATCCA
*
58819 AAAGCAACACCGTTGACATCTACAGGGGGTAAAGAAATCTCACTAGGAGATGCTAAATGGCCATT
1 AAAGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCAC-AGGAGATGCTAAATGGCCATT
58884 TTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTCGACATGAATAT
65 TTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTCGACATGAATAT
* * * * * *
58949 GTGAAATGCCAACAGAATCTGTCTTTTCAGATATCTGTTCATCTGAACCATTATGTATTCCCCGA
130 GCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCGA
* * * *
59014 GTCTTAGAATCTTCCATCAGTTTACCCTGACTATCTTTCTCCGTTTCACC
195 GTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
* * *
59064 GAAAGAAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCAGCAGGAGATGTTAAACGGCCAT
1 -AAAGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCA-CAGGAGATGCTAAATGGCCAT
* *
59129 TTTCAAAATCTCCGATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTCAACATGAATA
64 TTTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTCGACATGAATA
* * * * *
59194 TGCGAAATGCCAACAGAACCGGTCTTTTGAGATATCTGCTCATCTGAAACGTCATGTATCCCCCA
129 TGCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCG
* *
59259 AGTCTTAGAATCTTCCATCAGTCTACCCTGGTTATCTTTCTCAGTTTGATC
194 AGTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
* * * *
59310 AACAGCAACCCCGTTGACATCTACAAGGGGTAAAGAAATCTCACTAGGAAATGTTAAATGGCTAT
1 AA-AGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCAC-AGGAGATGCTAAATGGCCAT
* * *
59375 TTTCAAAATCTCCAATCGTTGGATTGGAAGCAGTAGGAAGAGCACTTCGGTCCTCGACATGTATA
64 TTTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTCGACATGAATA
* * * *
59440 TGCGAAATGCTAACAGAACCGGTCTTTTGAGATATCTGTTCATCTGAAACTTCATGTATTCCCTG
129 TGCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCG
* **
59505 AGTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCGGTACCATC
194 AGTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
* *
59556 AAAACCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCAGCAGGAGATGCTAAATGGTCAT
1 -AAAGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCA-CAGGAGATGCTAAATGGCCAT
* * * *
59621 TTTCAAAATCACCAATCTTTGGTTTGGAAGTAGTAGGAAGAGCACTTCCG---TCGACATGCATA
64 TTTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTCGACATGAATA
* * * * *
59683 TGTGAAATGACAACAGAACCATTCTTTTGAGATATTTGTTCATCTG-AAC--CAT-CA-T----G
129 TGCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCG
* * * ** * *
59739 AGTCTTATATTCTTCCGTCAGGGTAGCCTGATTATCTTTCTCAGTTTGATC
194 AGTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
* *
59790 AACAGCAACCCCGTTGACATCTACAGGGGGTGAAGAAATCTCTCCAGGAGATGCTAAATGGCCAT
1 AA-AGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTC-ACAGGAGATGCTAAATGGCCAT
* * * *
59855 TTTCAAAATCTTCAATCTTTGGATTGGAAGCAGTAGAAAGAGCACATCCGTCCTCAACATGAATA
64 TTTCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTCGACATGAATA
* * *
59920 TGCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTTATCTGAACCATCCTGTATTCCCCG
129 TGCGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCG
* * *
59985 AGTCATATAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTGATC
194 AGTCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
60036 AA
1 AA
60038 TTTCAGGTGA
Statistics
Matches: 856, Mismatches: 98, Indels: 38
0.86 0.10 0.04
Matches are distributed among these distances:
233 2 0.00
234 143 0.17
237 51 0.06
238 3 0.00
239 1 0.00
240 5 0.01
241 1 0.00
242 4 0.00
243 51 0.06
245 3 0.00
246 588 0.69
247 4 0.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (244 bp):
AAAGCAACCCCGTTGACATCTACAGGGGGTAAAGAAATCTCACAGGAGATGCTAAATGGCCATTT
TCAAAATCTCCAATCTTTGGATTGGAAGCAGTAGGAAGAGCACTTCCGTCCTCGACATGAATATG
CGAAATGCCAACAGAACCAGTCTTTTGAGATATCTGTTCATCTGAAACATCATGTATTCCCCGAG
TCTTAGAATCTTCCATCAGTCTACCCTGATTATCTTTCTCAGTTTCATC
Found at i:61633 original size:20 final size:21
Alignment explanation
Indices: 61597--61640 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
61587 TCGATCGATA
*
61597 TTCTTTATTATC-CTTTTATT
1 TTCTTTATTATCATTTTTATT
61617 TTCTTATATTA-CATTTTTATT
1 TTCTT-TATTATCATTTTTATT
61638 TTC
1 TTC
61641 AATAAGTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (21 bp):
TTCTTTATTATCATTTTTATT
Found at i:62990 original size:42 final size:42
Alignment explanation
Indices: 62914--63010 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
62904 GTTAAAAGTT
* * * * *
62914 ATGATTTTTAGCGGCATTTTTTTATAAACTCCGCTAAAGGTG
1 ATGATATTTAGCGACATTTTGTTACAAACACCGCTAAAGGTG
* * *
62956 ATGGTATTTAGCGACGTTTTGTTACAAACACCGCTAAAGGTT
1 ATGATATTTAGCGACATTTTGTTACAAACACCGCTAAAGGTG
62998 ATGATATTTAGCG
1 ATGATATTTAGCG
63011 GCGCTTTTTC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (42 bp):
ATGATATTTAGCGACATTTTGTTACAAACACCGCTAAAGGTG
Found at i:63396 original size:21 final size:21
Alignment explanation
Indices: 63370--63428 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
63360 ATTATCCAAT
*
63370 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
63391 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
63412 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
63429 TAATAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.51, C:0.22, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:70040 original size:42 final size:42
Alignment explanation
Indices: 69993--70101 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
69983 AATTGGTAAG
* *
69993 TCCTTCGGGCCATC-AGTAAGTC-TTTCGAGAATGATGATTAAA
1 TCCTTCGGGCCATCTA-TAAGCCTTTTCGAGAAAGATGA-TAAA
* * *
70035 TCCTTCAGGTCATCTATAAGCCTTTTCGAGAAAGATGATAAG
1 TCCTTCGGGCCATCTATAAGCCTTTTCGAGAAAGATGATAAA
*
70077 TCCTTCGGGCCATCCATAAGACCTT
1 TCCTTCGGGCCATCTATAAG-CCTT
70102 CGAGCAGGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 37 0.66
43 19 0.34
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (42 bp):
TCCTTCGGGCCATCTATAAGCCTTTTCGAGAAAGATGATAAA
Found at i:70355 original size:41 final size:42
Alignment explanation
Indices: 70249--70360 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
70239 CAAAAATTGG
* *
70249 TAAGTCCTTCGGGCCAT-CAGTAGGCCTTTCAAGCATGATGAT
1 TAAGTCCTTCGGGCCATCCA-TAAGCCTTTCAAGCAAGATGAT
* * * *
70291 TAAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGA-
1 TAAGTCCTTCGGGCCATCCATAAGCCTTTCAAGCAAGATGAT
70332 TAAGTCCTTCGGGCCATCCATAAGACCTT
1 TAAGTCCTTCGGGCCATCCATAAG-CCTT
70361 CGGTCAGGAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 21 0.36
42 37 0.63
43 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCCATAAGCCTTTCAAGCAAGATGAT
Found at i:70502 original size:255 final size:254
Alignment explanation
Indices: 69481--70521 Score: 1536
Period size: 255 Copynumber: 4.1 Consensus size: 254
69471 TTCTTACTTA
* * *
69481 GTAAGTCCTTCGGGCTATTAGTAAGTCTTTCTAACATGATGATTAAA-CCTTTCGGGTCATCTAT
1 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTC-AACATGATGATTAAATCC-TTCGGGTCATCTAT
* ** * * *
69545 AAGCCTTTCGGGCAAGACAATAAGTCCTTCGAGCCATCCATAAGGCTTTCGGGTAGGTTGTTTTC
64 AAGCCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTC
* * *
69610 ACATGTTTTTCGAAAAATGCGAAAACGATTTCCAAAGTTTATCATTTAAATCTGAAAATTGAAAA
129 ACATGTTTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCTGAAAATTGAAAT
* **
69675 TTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCCGACCTAGTAAACTATTTCCAAAATTG
194 TTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* * ** * *
69736 GTATGTCATTCGGGCCATCAACAAGTCTTTTGAACATGATGATTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAG-CCTTTCAACATGATGATTAAATCCTTCGGGTCATCTATA
*
69801 AGCCTTTCGAGCAAGATGAT-AGTCCTTCGAGCCATTCATAAGACCTTCGGGTAGGA--TTTTCA
65 AGCCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTCA
* *
69863 CATGTTTTTCGAAAAATGAGAAAACGTTTTCTAAAGTTTCTCATTTAAATCTGAAAATTGAAATT
130 CATGTTTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCTGAAAATTGAAATT
* *
69928 TTTTAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCTAAAATTG
195 TTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* *
69988 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGA-ATGATGATTAAATCCTTCAGGTCATCTAT
1 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTC-A-ACATGATGATTAAATCCTTCGGGTCATCTAT
* * * *
70052 AAGCCTTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGAGCAGGATGTTTT
64 AAGCC-TTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTT
** ** *
70117 CACATGTTTTTCGAAAAAAAACAAGAAAATAAATTTCTAAAGTTTCTCATTTAAATCTGAAAATT
128 CACATGTTTTTCG---AAAAATGAGAAAA-CGATTTCCAAAGTTTCTCATTTAAATCTGAAAATT
* * *
70182 GAAATTTTTGAAAAGTAAGAAAATGATCTCCAAAGTTTCTTACCTAGTAAACTATTGCAAAAATT
189 GAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATT
70247 G
254 G
*
70248 GTAAGTCCTTCGGGCCATCAGTAGGCCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTCAA-CATGATGATTAAATCCTTCGGGTCATCTATA
*
70313 AGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTC-GGTCAGGATGTTTTC
65 AGCCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGT-AGGATGTTTTC
* *
70377 ACATGTTTTTCGAAAAATGAGAAAACGATTTCCAAAATTTCTCATTTAAATTTGAAAATTGAAAT
129 ACATGTTTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCTGAAAATTGAAAT
70442 TTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
194 TTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
70503 GTAAGTCCTTCGGGCCATC
1 GTAAGTCCTTCGGGCCATC
70522 TATTAGTCTT
Statistics
Matches: 707, Mismatches: 64, Indels: 30
0.88 0.08 0.04
Matches are distributed among these distances:
251 3 0.00
252 176 0.25
253 16 0.02
254 64 0.09
255 178 0.25
256 33 0.05
258 2 0.00
259 79 0.11
260 156 0.22
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (254 bp):
GTAAGTCCTTCGGGCCATCAGTAAGCCTTTCAACATGATGATTAAATCCTTCGGGTCATCTATAA
GCCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAC
ATGTTTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCTGAAAATTGAAATTT
TTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
Found at i:70803 original size:3 final size:3
Alignment explanation
Indices: 70795--70830 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
70785 GGGTTTTTAA
70795 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
70831 ATTTATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:71365 original size:31 final size:30
Alignment explanation
Indices: 71327--71399 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 30
71317 GGGGAAATCG
*
71327 GAGAGAAAAAAGGAGGGGTCTTTTCTTTTC
1 GAGAGAAAAAAGGAGGGGTCTTTGCTTTTC
71357 AGAGAGAAAAAAGGAGGGGTCTTTGCTTTTC
1 -GAGAGAAAAAAGGAGGGGTCTTTGCTTTTC
71388 G-GAGAAAAAAGG
1 GAGAGAAAAAAGG
71400 GAAAAGTCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 11 0.27
30 1 0.02
31 29 0.71
ACGTcount: A:0.36, C:0.08, G:0.33, T:0.23
Consensus pattern (30 bp):
GAGAGAAAAAAGGAGGGGTCTTTGCTTTTC
Found at i:72461 original size:2 final size:2
Alignment explanation
Indices: 72449--72491 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
72439 TTATTTCATT
72449 TA TA T- 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
72490 TA
1 TA
72492 CATGTGTGCG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:73994 original size:15 final size:14
Alignment explanation
Indices: 73960--73993 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
73950 GAGACGATAT
*
73960 CTTTTAAAAAATCA
1 CTTTTTAAAAATCA
73974 CTTTTTAAAAATCA
1 CTTTTTAAAAATCA
*
73988 ATTTTT
1 CTTTTT
73994 TTTAAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (14 bp):
CTTTTTAAAAATCA
Found at i:76769 original size:11 final size:10
Alignment explanation
Indices: 76755--76813 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
76745 TTTATGTGAC
76755 TAATATGAAAA
1 TAATAT-AAAA
76766 TAATAATAAAA
1 TAAT-ATAAAA
76777 TAATATAAAA
1 TAATATAAAA
*
76787 GTAATAACAAAA
1 -TAAT-ATAAAA
*
76799 TAATAAATAAA
1 TAATATA-AAA
76810 TAAT
1 TAAT
76814 GATTAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.19
11 27 0.64
12 7 0.17
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (10 bp):
TAATATAAAA
Found at i:76813 original size:22 final size:22
Alignment explanation
Indices: 76755--76813 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
76745 TTTATGTGAC
* *
76755 TAATATGAAAATAATAATAAAA
1 TAATATAAAAATAATAACAAAA
*
76777 TAATATAAAAGTAATAACAAAA
1 TAATATAAAAATAATAACAAAA
76799 TAATA-AATAAATAAT
1 TAATATAA-AAATAAT
76814 GATTAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (22 bp):
TAATATAAAAATAATAACAAAA
Found at i:78608 original size:111 final size:112
Alignment explanation
Indices: 78428--78832 Score: 581
Period size: 111 Copynumber: 3.7 Consensus size: 112
78418 TAGAGTTATG
** * *
78428 CAAAAGGTTGAACAAGCTCTTCTCCTTATGAACTTCTTCTTCTTCTTCAGATAAGTTC-TCTCAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
78492 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
66 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
* *
78539 CAAAA-GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGACGAGTT-TTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCA
* * * * * *
78602 TTATGAACTTAC-CTGGCAATGTTGATCCATCAAATGATGAATTTAAA
65 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
78649 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
**
78714 TTATGAAC-TTCTCTGGAAAAACTGATCCATCGAGTGATGAATTCAAA
65 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
* * *
78761 CAAAA-GTTGAACAAATTCTTCTCATTATAAATTTCTTCTTTCTTCTTCAAAT-AGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCA
78824 TTATGAACT
65 TTATGAACT
78833 CTAACTGGCA
Statistics
Matches: 261, Mismatches: 25, Indels: 16
0.86 0.08 0.05
Matches are distributed among these distances:
110 86 0.33
111 125 0.48
112 50 0.19
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
Found at i:78751 original size:222 final size:222
Alignment explanation
Indices: 78428--78853 Score: 680
Period size: 222 Copynumber: 1.9 Consensus size: 222
78418 TAGAGTTATG
* *
78428 CAAAAGGTTGAACAAGCTCTTCTCCTTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTCTCATT
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTCTCATT
**
78493 ATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGTTGAACAAATTCT
66 ATGAACTTTCTCTGGAAAAACTGATCCATCGAGTGATGAATTCAAACAAAAGTTGAACAAATTCT
* * *
78558 TCTCATTATGAATTTCTTC-TTCATTCTTCAGACGAGTT-TTCTCATTATGAACT-TACCTGGCA
131 TCTCATTATAAATTTCTTCTTTC-TTCTTCA-AAGAGTTCTTCTCATTATGAACTCTAACTGGCA
*
78620 ATGTTGATCCATCAAATGATGAATTTAAA
194 ATGCTGATCCATCAAATGATGAATTTAAA
* *
78649 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTC-TCTCA
78714 TTATGAAC-TTCTCTGGAAAAACTGATCCATCGAGTGATGAATTCAAACAAAAGTTGAACAAATT
64 TTATGAACTTTCTCTGGAAAAACTGATCCATCGAGTGATGAATTCAAACAAAAGTTGAACAAATT
*
78778 CTTCTCATTATAAATTTCTTCTTTCTTCTTCAAATAGTTCTTCTCATTATGAACTCTAACTGGCA
129 CTTCTCATTATAAATTTCTTCTTTCTTCTTCAAAGAGTTCTTCTCATTATGAACTCTAACTGGCA
*
78843 TTGCTGATCCA
194 ATGCTGATCCA
78854 CCGAAGGTTT
Statistics
Matches: 188, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
221 43 0.23
222 112 0.60
223 33 0.18
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (222 bp):
CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTCTCATT
ATGAACTTTCTCTGGAAAAACTGATCCATCGAGTGATGAATTCAAACAAAAGTTGAACAAATTCT
TCTCATTATAAATTTCTTCTTTCTTCTTCAAAGAGTTCTTCTCATTATGAACTCTAACTGGCAAT
GCTGATCCATCAAATGATGAATTTAAA
Found at i:78877 original size:111 final size:109
Alignment explanation
Indices: 78429--78877 Score: 396
Period size: 111 Copynumber: 4.1 Consensus size: 109
78419 AGAGTTATGC
* ** * * *
78429 AAAAGGTTGAACAAGCTCTTCTCCTTATGAACTTCTTC-TTCTTCTTCAGATAAGTTC-TCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAAAT-AGTTCTTCTCAT
* * * **
78492 TATGAACTTTCT-CTGGAAAAGTTGATCCATCG-AGTGATGAATTCAA
65 TATGAAC--TCTACTGGCAATGCTGATCCATCGAAGT-ATGAAAACAA
**
78538 ACAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTC-TTCATTCTTCAGACGAGTT-TTCTC
1 A-AAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTC-TTCTTCA-AATAGTTCTTCTC
* * ***
78601 ATTATGAACT-TACCTGGCAATGTTGATCCATC-AAATGATGAATTTAA
63 ATTATGAACTCTA-CTGGCAATGCTGATCCATCGAAGT-ATGAAAACAA
* * *
78648 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 A-AAAA-GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAAAT-AGTTCTTCTC
* ** **
78713 ATTATGAACTTCT-CTGGAAAAACTGATCCATCG-AGTGATGAATTCAA
63 ATTATGAAC-TCTACTGGCAATGCTGATCCATCGAAGT-ATGAAAACAA
*
78760 ACAAAAGTTGAACAAATTCTTCTCATTATAAATTTCTTCTTTCTTCTTCAAATAGTTCTTCTCAT
1 A-AAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAAATAGTTCTTCTCAT
* * * *
78825 TATGAACTCTAACTGGCATTGCTGATCCACCGAAGGTTTGAAAACAT
65 TATGAACTCT-ACTGGCAATGCTGATCCATCGAA-GTATGAAAACAA
78872 AAAAAG
1 AAAAAG
78878 ATCCCGAAGG
Statistics
Matches: 286, Mismatches: 36, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
108 1 0.00
109 5 0.02
110 89 0.31
111 130 0.45
112 57 0.20
113 3 0.01
114 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (109 bp):
AAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAAATAGTTCTTCTCATT
ATGAACTCTACTGGCAATGCTGATCCATCGAAGTATGAAAACAA
Found at i:79027 original size:75 final size:75
Alignment explanation
Indices: 78857--79075 Score: 372
Period size: 75 Copynumber: 2.9 Consensus size: 75
78847 TGATCCACCG
* *
78857 AAGG-TTTGAAAACAT-AAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCAATGTAGGACTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGC-ACGTAGGACTTA
78920 CAGATGACCCT
65 CAGATGACCCT
78931 AAGGCTTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACGTAGGACTTAC
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACGTAGGACTTAC
78995 AGATGACCCT
66 AGATGACCCT
*
79005 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC-GTAGGACTTA
79070 CAGATG
65 CAGATG
79076 TAGGAAATAG
Statistics
Matches: 138, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
74 43 0.31
75 80 0.58
76 15 0.11
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (75 bp):
AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACGTAGGACTTAC
AGATGACCCT
Found at i:79829 original size:17 final size:16
Alignment explanation
Indices: 79807--79840 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
79797 TAAAAACAGT
79807 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
79824 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
79840 A
1 A
79841 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Done.