Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005610.1 Hibiscus syriacus cultivar Beakdansim tig00013046_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: 79861
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7495 original size:13 final size:13
Alignment explanation
Indices: 7479--7508 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
7469 ATCTTATCTT
*
7479 CTTTTCACTTTTA
1 CTTTTCACTTTCA
7492 CTTTTCACTTTCA
1 CTTTTCACTTTCA
7505 CTTT
1 CTTT
7509 CTTTCATCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (13 bp):
CTTTTCACTTTCA
Found at i:9576 original size:15 final size:16
Alignment explanation
Indices: 9556--9586 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9546 CCCTTTTACC
9556 TAGAGTG-TGGGATGA
1 TAGAGTGATGGGATGA
9571 TAGAGTGATGGGATGA
1 TAGAGTGATGGGATGA
9587 CTCCCCTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (16 bp):
TAGAGTGATGGGATGA
Found at i:25962 original size:18 final size:17
Alignment explanation
Indices: 25922--25969 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
25912 GATCATAAAA
* *
25922 ATAAATAAACAAATAATT
1 ATAAATAAA-AAACAATG
25940 ATAAATAAAAAACAATG
1 ATAAATAAAAAACAATG
25957 ATTAAATTAAAAA
1 A-TAAA-TAAAAA
25970 TTATTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 7 0.27
18 13 0.50
19 6 0.23
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (17 bp):
ATAAATAAAAAACAATG
Found at i:25970 original size:25 final size:22
Alignment explanation
Indices: 25917--25962 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
25907 TGTTAGATCA
25917 TAAAAATAAATAAACAAATAAT
1 TAAAAATAAATAAACAAATAAT
* *
25939 TATAAATAAA-AAAC-AATGAT
1 TAAAAATAAATAAACAAATAAT
25959 TAAA
1 TAAA
25963 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 8 0.38
21 4 0.19
22 9 0.43
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAAATAAATAAACAAATAAT
Found at i:26009 original size:17 final size:17
Alignment explanation
Indices: 25987--26021 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25977 AAGAGAGGTT
25987 AAAATGATAAAAAAACA
1 AAAATGATAAAAAAACA
* *
26004 AAAATGTTTAAAAAACA
1 AAAATGATAAAAAAACA
26021 A
1 A
26022 TATAAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAATGATAAAAAAACA
Found at i:26120 original size:19 final size:19
Alignment explanation
Indices: 26074--26121 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
26064 GCAAATTTTT
26074 AATTTAAAAGAAATAAATAA
1 AATTT-AAAGAAATAAATAA
* *
26094 AGA-GTAAATAAATAAATAA
1 A-ATTTAAAGAAATAAATAA
26113 AATTTAAAG
1 AATTTAAAG
26122 GATCAAATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 5
0.71 0.13 0.16
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 2 0.09
21 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (19 bp):
AATTTAAAGAAATAAATAA
Found at i:27375 original size:16 final size:16
Alignment explanation
Indices: 27334--27366 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
27324 AAATACAAAT
27334 AAATAC-AAAAACTAA
1 AAATACAAAAAACTAA
27349 AAATACAAAAAACTAA
1 AAATACAAAAAACTAA
27365 AA
1 AA
27367 TACTGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (16 bp):
AAATACAAAAAACTAA
Found at i:27492 original size:23 final size:23
Alignment explanation
Indices: 27442--27498 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 23
27432 TTCAAAAATA
*
27442 TTTTAAAAACTATATATTATATG
1 TTTTCAAAACTATATATTATATG
27465 TTTTCAAAACTATATATTATATG
1 TTTTCAAAACTATATATTATATG
27488 TTTTCCAAAAC
1 TTTT-CAAAAC
27499 CGATTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 26 0.81
24 6 0.19
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.46
Consensus pattern (23 bp):
TTTTCAAAACTATATATTATATG
Found at i:27513 original size:39 final size:39
Alignment explanation
Indices: 27465--27708 Score: 202
Period size: 39 Copynumber: 6.4 Consensus size: 39
27455 ATATTATATG
* * *
27465 TTTTCAAAACTATATATTATATGTTTTCCAAAACCGATT
1 TTTTAAAAACTATATATTATATGTTTTCAAAAATCGATT
*
27504 TTTTAAAAACTATATATTATATACGTTTTCAAAAAT--ATG
1 TTTTAAAAACTATATATTATAT--GTTTTCAAAAATCGATT
* * * *
27543 TTTTCAAAACCATAAATTATATGTTTTCAAAAAAT-G-TG
1 TTTTAAAAACTATATATTATATGTTTTC-AAAAATCGATT
* * * *
27581 TTTTCAAAACCATGT-TATATATATTTTCAAAAATCG-TT
1 TTTTAAAAACTATATAT-TATATGTTTTCAAAAATCGATT
* *
27619 TTTTAAAAAACTATAAATTATATGCTTTCAAAAATC-ATT
1 TTTT-AAAAACTATATATTATATGTTTTCAAAAATCGATT
* * *
27658 TTCTAAAAATTATATGTTATATGTTTTTCAAAAAT-G--T
1 TTTTAAAAACTATATATTATATG-TTTTCAAAAATCGATT
*
27695 TTTCAAAAACTATA
1 TTTTAAAAACTATA
27709 CTATATTATT
Statistics
Matches: 169, Mismatches: 25, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
37 25 0.15
38 53 0.31
39 80 0.47
40 1 0.01
41 10 0.06
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (39 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAAATCGATT
Found at i:27679 original size:77 final size:73
Alignment explanation
Indices: 27465--27708 Score: 222
Period size: 77 Copynumber: 3.2 Consensus size: 73
27455 ATATTATATG
* * *
27465 TTTTCAAAACTATATATTATATGTTTTCCAAAACCGATTTTTTAAAAACTATATATTATATACGT
1 TTTTAAAAACTATAAATTATATGTTTT-CAAAAAC-ATTTTTTAAAAACTATAT-TTATATA--T
* *
27530 TTTCAAAAATATG
61 TTTCAAAAATGTT
* * * * *
27543 TTTTCAAAACCATAAATTATATGTTTTCAAAAA-ATGTGTTTTCAAAACCATGTTATATATATTT
1 TTTTAAAAACTATAAATTATATGTTTTCAAAAACAT-T-TTTTAAAAACTATATT-TATATATTT
27607 TCAAAAATCGTT
63 TCAAAAAT-GTT
* * * *
27619 TTTTAAAAAACTATAAATTATATGCTTTCAAAAATCATTTTCTAAAAATTATATGTTATATGTTT
1 TTTT-AAAAACTATAAATTATATGTTTTCAAAAA-CATTTTTTAAAAACTATAT-TTATAT-ATT
27684 TTCAAAAATG-T
62 TTCAAAAATGTT
*
27695 TTTCAAAAACTATA
1 TTTTAAAAACTATA
27709 CTATATTATT
Statistics
Matches: 139, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
75 23 0.17
76 11 0.08
77 65 0.47
78 38 0.27
79 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (73 bp):
TTTTAAAAACTATAAATTATATGTTTTCAAAAACATTTTTTAAAAACTATATTTATATATTTTCA
AAAATGTT
Found at i:28551 original size:3 final size:3
Alignment explanation
Indices: 28538--28595 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
28528 AATACCTTTT
28538 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28585 TTA TTA TTA TT
1 TTA TTA TTA TT
28596 TTCCTTTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31906 original size:36 final size:36
Alignment explanation
Indices: 31866--31941 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
31856 CTAACAATCC
*
31866 ACAAATACACCAAACTAACATAGTAAAACAAAAGTA
1 ACAAATACACCAAACTAACATAGTAAAACAAAAGCA
** * *
31902 ACAAATTTACCAAACTAACATATTAAAACTAAAGCA
1 ACAAATACACCAAACTAACATAGTAAAACAAAAGCA
31938 ACAA
1 ACAA
31942 TCCATAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (36 bp):
ACAAATACACCAAACTAACATAGTAAAACAAAAGCA
Found at i:32392 original size:39 final size:39
Alignment explanation
Indices: 32348--32428 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
32338 TATTACTAGT
* *
32348 TATATA-AGCATTAATTATTAGTTATTAGTTATGCATATG
1 TATATATAGCATTAATTATTA-TCATTAGTTAAGCATATG
**
32387 TATATATATTATTAATTATTATCATTAGTTAAGCATATG
1 TATATATAGCATTAATTATTATCATTAGTTAAGCATATG
32426 TAT
1 TAT
32429 TAATTATTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 25 0.68
40 12 0.32
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (39 bp):
TATATATAGCATTAATTATTATCATTAGTTAAGCATATG
Found at i:32585 original size:23 final size:24
Alignment explanation
Indices: 32536--32586 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
32526 TATGGAAATG
**
32536 GTGGCTTATATATATTTCGGTGGGT
1 GTGGCTTATATATAAATC-GTGGGT
*
32561 GTGGCTTATATATAAAT-GTGTGT
1 GTGGCTTATATATAAATCGTGGGT
32584 GTG
1 GTG
32587 AGAGAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.35
25 15 0.65
ACGTcount: A:0.20, C:0.06, G:0.31, T:0.43
Consensus pattern (24 bp):
GTGGCTTATATATAAATCGTGGGT
Found at i:34655 original size:184 final size:185
Alignment explanation
Indices: 34346--34734 Score: 658
Period size: 184 Copynumber: 2.1 Consensus size: 185
34336 TTTTCTAATT
* * *
34346 TATATAA-AAATTAAATATTTTATAATTCAAAAATCAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTATAATTCAAAAATCAGTTTACAATTAATTTAAATAATATATAA
*
34410 TTGTAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
* * *
34475 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTAAGCCCATATGTTA
131 TAGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTAAGCCCATATGTTA
*
34530 TATATAATATATTTAATATTTTTTAATTCAGAAAA-CAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCA-AAAATCAGTTTACAATTAATTTAAATAATATATA
34594 ATTATAAAAT-AAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
*
34658 TTAGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTGAGCCCATATGTTA
130 TTAGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTAAGCCCATATGTTA
*
34714 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
34735 AAAATTTTAA
Statistics
Matches: 193, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
184 133 0.69
185 56 0.29
186 4 0.02
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTATAATTCAAAAATCAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TAGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTAAGCCCATATGTTA
Found at i:40993 original size:7 final size:7
Alignment explanation
Indices: 40981--41127 Score: 108
Period size: 7 Copynumber: 20.9 Consensus size: 7
40971 AGTATTATAC
40981 TATATTA
1 TATATTA
40988 TATATTA
1 TATATTA
40995 TATATTA
1 TATATTA
*
41002 T-T-TCA
1 TATATTA
*
41007 TATATCA
1 TATATTA
*
41014 TATAGTA
1 TATATTA
*
41021 TATAGTA
1 TATATTA
41028 TGATATTA
1 T-ATATTA
*
41036 TATAGCATA
1 TATA--TTA
41045 TATATTA
1 TATATTA
41052 TAATATTTA
1 T-ATA-TTA
*
41061 TATAGTA
1 TATATTA
41068 TATAATTA
1 TAT-ATTA
*
41076 TATAGTA
1 TATATTA
41083 TATTATTA
1 TA-TATTA
41091 TATA-TA
1 TATATTA
**
41097 T-TACAA
1 TATATTA
41103 TATATT-
1 TATATTA
41109 TATATTA
1 TATATTA
41116 TATA-TA
1 TATATTA
41122 TATATT
1 TATATT
41128 GTAATAATCA
Statistics
Matches: 114, Mismatches: 13, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
5 5 0.04
6 19 0.17
7 56 0.49
8 24 0.21
9 10 0.09
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (7 bp):
TATATTA
Found at i:40998 original size:2 final size:2
Alignment explanation
Indices: 40967--41126 Score: 87
Period size: 2 Copynumber: 82.0 Consensus size: 2
40957 TTTTTATTCA
*
40967 AT AT AGT AT -T AT ACT AT AT -T AT AT AT -T AT AT AT -T AT TT CAT
1 AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
41008 AT AT CAT AT AGT AT AT AGT AT GAT AT -T AT AT AGC AT AT AT AT -T
1 AT AT -AT AT A-T AT AT A-T AT -AT AT AT AT AT A-T AT AT AT AT AT
*
41051 AT A- AT AT TT AT AT AGT AT AT A- AT -T AT AT AGT AT AT -T AT -T
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
41090 AT AT AT AT -T AC A- AT AT AT TT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41127 TGTAATAATC
Statistics
Matches: 125, Mismatches: 9, Indels: 48
0.69 0.05 0.26
Matches are distributed among these distances:
1 14 0.11
2 93 0.74
3 18 0.14
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41039 original size:15 final size:14
Alignment explanation
Indices: 40967--41127 Score: 107
Period size: 15 Copynumber: 12.0 Consensus size: 14
40957 TTTTTATTCA
40967 ATATAGTAT-TA-T
1 ATATAGTATATATT
*
40979 ACTATATTATATATT
1 A-TATAGTATATATT
40994 ATATA-T-TAT-TT
1 ATATAGTATATATT
*
41005 CATATA-TCATATAGT
1 -ATATAGT-ATATATT
41020 ATATAGTATGATATT
1 ATATAGTAT-ATATT
*
41035 ATATAGCATATA-T
1 ATATAGTATATATT
41048 AT-TA-TA-ATATTT
1 ATATAGTATATA-TT
41060 ATATAGTATATAATT
1 ATATAGTATAT-ATT
41075 ATATAGTATATTATT
1 ATATAGTATA-TATT
**
41090 ATATA-TAT-TACA
1 ATATAGTATATATT
*
41102 ATATA-TTTATATT
1 ATATAGTATATATT
41115 ATATA-TATATATT
1 ATATAGTATATATT
41128 GTAATAATCA
Statistics
Matches: 121, Mismatches: 11, Indels: 33
0.73 0.07 0.20
Matches are distributed among these distances:
10 3 0.02
11 3 0.02
12 24 0.20
13 27 0.22
14 24 0.20
15 38 0.31
16 2 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (14 bp):
ATATAGTATATATT
Found at i:41068 original size:40 final size:40
Alignment explanation
Indices: 41019--41098 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
41009 TATCATATAG
41019 TATATAGTATGAT-ATTATATAGCATATATATTATA-ATATT
1 TATATAGTAT-ATAATTATATAGCATAT-TATTATATATATT
*
41059 TATATAGTATATAATTATATAGTATATTATTATATATATT
1 TATATAGTATATAATTATATAGCATATTATTATATATATT
41099 ACAATATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 9 0.24
40 28 0.76
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.50
Consensus pattern (40 bp):
TATATAGTATATAATTATATAGCATATTATTATATATATT
Found at i:41078 original size:55 final size:57
Alignment explanation
Indices: 40986--41094 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 57
40976 TATACTATAT
40986 TATATATTATATATTATTTCATATATCATATAGTATATAGTATGA-TATTATATAGCA
1 TATATATTATATATTATTTCATATATCATATAGTATATAGTAT-ATTATTATATAGCA
*
41043 TATATATTATA-A-TATTT-ATATAGT-ATATAATTATATAGTATATTATTATATA
1 TATATATTATATATTATTTCATATA-TCATAT-AGTATATAGTATATTATTATATA
41095 TATTACAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
54 10 0.21
55 26 0.54
56 1 0.02
57 11 0.23
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (57 bp):
TATATATTATATATTATTTCATATATCATATAGTATATAGTATATTATTATATAGCA
Found at i:46342 original size:3 final size:3
Alignment explanation
Indices: 46334--46375 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
46324 ACATGTAAAC
46334 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46376 ATATAATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:46921 original size:133 final size:133
Alignment explanation
Indices: 46584--47269 Score: 914
Period size: 133 Copynumber: 5.1 Consensus size: 133
46574 TGGTCTTCTA
** * ** **
46584 AGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACTACTCATTTGTGATG
1 AGGGTGACACGGTTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATG
*
46649 AAGAGTTTTTGGCCATCTTTA-GGAAGGGTGATAAC-TCGGTTCCTAC-ATGATGAGGACGTCTG
66 AAGAG-TTTTGGCCATCTTTAGGGAA-GGTGATAACAT-GGTTCCTACGA-GATGAGGACGGCTG
46711 GTTATCT
127 GTTATCT
* * * *
46718 GAGTGTGACACGGTTCCTACGTGATGAGAAGATCTAGTCGGTAGATGACACGGCTCATACGTGAT
1 -AGGGTGACACGGTTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGAT
*
46783 GAAGAGTTTTGGCCATCTTTAGGGAAGGTGATAACATGGTTCCTACGAGATGAGGACGGTTGGTT
65 GAAGAGTTTTGGCCATCTTTAGGGAAGGTGATAACATGGTTCCTACGAGATGAGGACGGCTGGTT
46848 ATCT
130 ATCT
* * * * * *
46852 AGGGTGACACAGTTCCTACGCGATGAGGATAACTGGTCGGTGGATGACACGACTCATAGGTGATG
1 AGGGTGACACGGTTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATG
* * *
46917 AAGAGTTTTAGCCATCTTTAGGGAAGGTGATAACATGGTTCTTACGTGATGAGGACGGCTGGTTA
66 AAGAGTTTTGGCCATCTTTAGGGAAGGTGATAACATGGTTCCTACGAGATGAGGACGGCTGGTTA
46982 TCT
131 TCT
* * * * * *
46985 GAGGGTGACAAGGTTCCTACGTGATGAGGAGATCTAGTCGATAGATGACATGGCTCATACTTGAT
1 -AGGGTGACACGGTTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGAT
* * * *
47050 GAAGAGTTGTGGCCATCTTTAGGG-AGGTGATAACATGGTTCCTACGCGATGAGGATGGCTGGCT
65 GAAGAGTTTTGGCCATCTTTAGGGAAGGTGATAACATGGTTCCTACGAGATGAGGACGGCTGGTT
47114 ATCT
130 ATCT
* * * *
47118 AGGGTAACACGGTTCCTACATGATGAGGACG-GCTGGTCAGTGGATGACACGGCTCATACGTGAT
1 AGGGTGACACGGTTCCTACGTGATGAGGA-GATCTGGTCGGTGGATGACACGGCTCATACGTGAT
* ** *
47182 GAAGAGTTCTGGCCATCTTTAGGGAAGGTGATAACACAGTTCCTACGTGATGAGGACGGCTGGTT
65 GAAGAGTTTTGGCCATCTTTAGGGAAGGTGATAACATGGTTCCTACGAGATGAGGACGGCTGGTT
47247 ATCT
130 ATCT
47251 AGGGTGACACGGTTCCTAC
1 AGGGTGACACGGTTCCTAC
47270 TAGAGGTGGG
Statistics
Matches: 483, Mismatches: 62, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
132 75 0.16
133 217 0.45
134 126 0.26
135 65 0.13
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (133 bp):
AGGGTGACACGGTTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATG
AAGAGTTTTGGCCATCTTTAGGGAAGGTGATAACATGGTTCCTACGAGATGAGGACGGCTGGTTA
TCT
Found at i:47634 original size:2 final size:2
Alignment explanation
Indices: 47627--47671 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
47617 TTAATCATTA
47627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47669 AT A
1 AT A
47672 ACGATACAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48823 original size:66 final size:68
Alignment explanation
Indices: 48745--48903 Score: 168
Period size: 68 Copynumber: 2.4 Consensus size: 68
48735 ATTTGTTTTG
*
48745 TTTCAAGGGAAACAGACTCAAAGATGAATA-T-TTCACGAGAAACTA-TCTCAAGAAAAATAAGA
1 TTTCAAGAGAAACAGACTCAAAGATGAATATTGTTCACGAGAAAC-AGTCTCAAGAAAAATAAGA
48807 ATTA
65 ATTA
** * * *
48811 TTTCAAGAGAAACA-ATCTCAAAGATGGTTATTGTTTATGAGAAACAGTCTCAAGGAAAATAAGA
1 TTTCAAGAGAAACAGA-CTCAAAGATGAATATTGTTCACGAGAAACAGTCTCAAGAAAAATAAGA
* *
48875 TTTG
65 ATTA
*
48879 TTTCAAGA-AAAGC-GTCTCAAAGATG
1 TTTCAAGAGAAA-CAGACTCAAAGATG
48904 GTTGTTGTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
65 1 0.01
66 25 0.32
67 15 0.19
68 37 0.47
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (68 bp):
TTTCAAGAGAAACAGACTCAAAGATGAATATTGTTCACGAGAAACAGTCTCAAGAAAAATAAGAA
TTA
Found at i:48874 original size:68 final size:67
Alignment explanation
Indices: 48781--48913 Score: 180
Period size: 68 Copynumber: 2.0 Consensus size: 67
48771 AATATTTCAC
48781 GAGAAACTATCTCAAGAAAAATAAGAATTATTTCAAGAGAAA-CAATCTCAAAGATGGTTATTGT
1 GAGAAACTATCTCAAGAAAAATAAGAATTATTTCAAGA-AAAGC-ATCTCAAAGATGGTTATTGT
48845 TTAT
64 TTAT
* * * * *
48849 GAGAAAC-AGTCTCAAGGAAAATAAGATTTGTTTCAAGAAAAGCGTCTCAAAGATGGTTGTTGTT
1 GAGAAACTA-TCTCAAGAAAAATAAGAATTATTTCAAGAAAAGCATCTCAAAGATGGTTATTGTT
48913 T
65 T
48914 CCAGTGAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
67 24 0.41
68 34 0.59
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (67 bp):
GAGAAACTATCTCAAGAAAAATAAGAATTATTTCAAGAAAAGCATCTCAAAGATGGTTATTGTTT
AT
Found at i:49156 original size:36 final size:36
Alignment explanation
Indices: 49116--49186 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
49106 AGAGGAAAAA
*
49116 TGTCTCAAGCGAGACGAAATTCGTTTTGAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTCGTTTTGAGAGAAAT
* * *
49152 TGTCTCAAGTGAGACAAAATTTGTTTTGAGCGAAA
1 TGTCTCAAGCGAGACAAAATTCGTTTTGAGAGAAA
49187 CAATTTCAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.30
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTCGTTTTGAGAGAAAT
Found at i:49196 original size:36 final size:36
Alignment explanation
Indices: 49118--49196 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 36
49108 AGGAAAAATG
* ***
49118 TCTCAAGCGAGACGAAATTCGTTTTGAGAGAAATTG
1 TCTCAAGCGAGACAAAATTCGTTTTGAGAGAAACAA
* * *
49154 TCTCAAGTGAGACAAAATTTGTTTTGAGCGAAACAA
1 TCTCAAGCGAGACAAAATTCGTTTTGAGAGAAACAA
*
49190 TTTCAAG
1 TCTCAAG
49197 GACGATCGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (36 bp):
TCTCAAGCGAGACAAAATTCGTTTTGAGAGAAACAA
Found at i:54838 original size:22 final size:20
Alignment explanation
Indices: 54810--54868 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
54800 GAAAATATTT
54810 GATAAATTAAAATTAATAAATA
1 GATAAATTAAAATTAA-AAA-A
* *
54832 GATAAATAAAAATTAAACAA
1 GATAAATTAAAATTAAAAAA
*
54852 GATAAAATAAAA-TAAAA
1 GATAAATTAAAATTAAAA
54869 TGATAATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 4 0.12
20 11 0.34
21 2 0.06
22 15 0.47
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (20 bp):
GATAAATTAAAATTAAAAAA
Found at i:56341 original size:3 final size:3
Alignment explanation
Indices: 56333--56358 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56323 AAGATAAAAT
56333 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
56359 CTAAATATAA
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:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56375 original size:9 final size:10
Alignment explanation
Indices: 56326--56374 Score: 52
Period size: 9 Copynumber: 5.3 Consensus size: 10
56316 GTAAAATAAG
56326 ATAA-AATTA
1 ATAATAATTA
56335 ATAATAA-TA
1 ATAATAATTA
56344 ATAATAA-TA
1 ATAATAATTA
* *
56353 ATAATACTAA
1 ATAATAATTA
56363 AT-ATAATTA
1 ATAATAATTA
56372 ATA
1 ATA
56375 TTTTTTCGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 28 0.85
10 5 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
ATAATAATTA
Found at i:56414 original size:2 final size:2
Alignment explanation
Indices: 56407--56569 Score: 118
Period size: 2 Copynumber: 86.0 Consensus size: 2
56397 GAGTGTCTAC
56407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
56449 AT AT AT TT AT AT AT -T AT AGT AA AT AT TT AT AT AGT AT GT -T AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT
* * * *
56491 AC AT AT -T AT AT -T A- AT AT CT -T AT AC GT AT AT -T AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
56529 AT AT -T AA AGT -T AT AT AT -T AT AT -T AT AT -T AT AT AT -T AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56566 AT AT
1 AT AT
56570 TTATTTATTT
Statistics
Matches: 128, Mismatches: 16, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
1 13 0.10
2 109 0.85
3 6 0.05
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:57012 original size:20 final size:20
Alignment explanation
Indices: 56987--57035 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
56977 CCCTATTTTC
56987 AGTGACGAGATCAACAAAGG
1 AGTGACGAGATCAACAAAGG
57007 AGTGACGAGATCAACAAAGG
1 AGTGACGAGATCAACAAAGG
*
57027 AGCGACGAG
1 AGTGACGAG
57036 TTCCAAACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.43, C:0.16, G:0.33, T:0.08
Consensus pattern (20 bp):
AGTGACGAGATCAACAAAGG
Found at i:57835 original size:21 final size:20
Alignment explanation
Indices: 57809--57854 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
57799 TTAACATTTA
57809 TTTTTTAA-ATTTAATACTTAT
1 TTTTTTAACA-TTAAT-CTTAT
*
57830 TTTTTTAACATTAATTTTAT
1 TTTTTTAACATTAATCTTAT
57850 TTTTT
1 TTTTT
57855 GGCAGTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 13 0.57
22 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTTAACATTAATCTTAT
Found at i:57849 original size:20 final size:21
Alignment explanation
Indices: 57798--57854 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
57788 TTAATCATTC
*
57798 TTTAACATTTA-TTTTTTAAA
1 TTTAATATTTATTTTTTTAAA
*
57818 TTTAATACTTATTTTTTTAACA
1 TTTAATATTTATTTTTTTAA-A
57840 -TTAAT-TTTATTTTTT
1 TTTAATATTTATTTTTT
57855 GGCAGTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 18 0.56
21 13 0.41
22 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTAATATTTATTTTTTTAAA
Found at i:58678 original size:21 final size:23
Alignment explanation
Indices: 58654--58696 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
58644 TATTCAATAA
58654 GAATTAAATAAA-ACT-ATAATT
1 GAATTAAATAAAGACTAATAATT
*
58675 GAATTGAATAAAGACTAATAAT
1 GAATTAAATAAAGACTAATAAT
58697 AGTTTAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
GAATTAAATAAAGACTAATAATT
Found at i:60959 original size:31 final size:32
Alignment explanation
Indices: 60888--60964 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
60878 TTAATAATTC
* *
60888 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAAT-ATTACATAAATATTATTATAA
60922 TAAAAAATAATATTACATAAATA-TATTA-ATA
1 TAAAAAATAATATTACATAAATATTATTATA-A
60953 TAAAAAATAATA
1 TAAAAAATAATA
60965 ACTATTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 1 0.03
31 17 0.43
32 11 0.28
33 7 0.17
34 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAATATTACATAAATATTATTATAA
Found at i:60965 original size:34 final size:33
Alignment explanation
Indices: 60889--60970 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 33
60879 TAATAATTCT
*
60889 AAATAAATAATAATTATATAAATATTATTTTAATA
1 AAAT-AATAAT-ATTACATAAATATTATTTTAATA
60924 AAA-AATAATATTACATAAATA-TATTAATATAA-A
1 AAATAATAATATTACATAAATATTATT--T-TAATA
60957 AAATAATAACTATT
1 AAATAATAA-TATT
60971 TAAAAAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 11 0.27
34 8 0.20
35 7 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (33 bp):
AAATAATAATATTACATAAATATTATTTTAATA
Found at i:62722 original size:17 final size:15
Alignment explanation
Indices: 62686--62720 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
62676 TAAGTTAACG
*
62686 TATATTTAATATATC
1 TATATTTAATATATA
62701 TATATTTAATATATA
1 TATATTTAATATATA
62716 TATAT
1 TATAT
62721 ATACATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATTTAATATATA
Found at i:66542 original size:18 final size:18
Alignment explanation
Indices: 66511--66597 Score: 84
Period size: 18 Copynumber: 4.6 Consensus size: 18
66501 AACCATTTTC
*
66511 GTATCGATGCTCATGGGA
1 GTATCGATACTCATGGGA
* *
66529 GTATTGATAGTCATGGGA
1 GTATCGATACTCATGGGA
66547 GTATCGATACTCATGGTAGA
1 GTATCGATACTCATGG--GA
* *
66567 GTATCAATACTTACGATAGGA
1 GTATCGATAC-T-C-ATGGGA
66588 GTATCGATAC
1 GTATCGATAC
66598 CAAGCTACTT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
18 29 0.52
20 11 0.20
21 12 0.21
22 1 0.02
23 3 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (18 bp):
GTATCGATACTCATGGGA
Found at i:76355 original size:15 final size:15
Alignment explanation
Indices: 76337--76379 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
76327 CAAAAAATAA
76337 TAAAATGATAAATGG
1 TAAAATGATAAATGG
*
76352 TAAAAAT-ATAAAAGG
1 T-AAAATGATAAATGG
76367 -AAAATGATAAATG
1 TAAAATGATAAATG
76380 ATGATAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 5 0.21
14 6 0.25
15 8 0.33
16 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.23
Consensus pattern (15 bp):
TAAAATGATAAATGG
Found at i:76393 original size:29 final size:29
Alignment explanation
Indices: 76338--76403 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
76328 AAAAAATAAT
* *
76338 AAAATGATAAATGGTAAAAATATAAAAGG
1 AAAATGATAAATGATAAAAATAGAAAAGG
* *
76367 AAAATGATAAATGATGATAAAT-GAAAAGT
1 AAAATGATAAATGAT-AAAAATAGAAAAGG
76396 AAATATGA
1 AAA-ATGA
76404 GTTAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.23
Consensus pattern (29 bp):
AAAATGATAAATGATAAAAATAGAAAAGG
Found at i:78435 original size:138 final size:139
Alignment explanation
Indices: 78216--78477 Score: 307
Period size: 138 Copynumber: 1.9 Consensus size: 139
78206 GAGAAATACC
* * *
78216 TCAAGTGAGAAAAAATTTTGTTTCAAGAGAAACTATCTCGAGTAAGACAAAAATTTTAAGAGAAA
1 TCAAGTGAGAAAAAATTTTGTTTCAAGAGAAACTATCTCGAGCAAGAAAAAAATTTCAAGAGAAA
** * * *
78281 TTTATCTCAAGCGAGAT-AATT-TTTTTCGAGAGAATCCATATCGAGTGAGACGAAAATTCAAGG
66 AATATCTCAAGCGAGATAAATTATGTTTCAAGAGAAACCATATCGAGTGAGACGAAAATTCAAGG
78344 GAAAATATT
131 GAAAATATT
* ** *
78353 TCAAGTGAGATAAAATTTTTGTTTTGAGAGAAACTCA-CTCGAGCGAGAAAAAACATTTCAAG-G
1 TCAAGTGAGA-AAAAATTTTGTTTCAAGAGAAACT-ATCTCGAGCAAGAAAAAA-ATTTCAAGAG
* * * * *
78416 AAAAATATCTGAAGTGAGATGAAATTATGTTTCAAGAGAAACTATCTCGAGTGAGATGAAAA
63 AAAAATATCTCAAGCGAGAT-AAATTATGTTTCAAGAGAAACCATATCGAGTGAGACGAAAA
78478 ACAACCTCAA
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
137 10 0.10
138 51 0.50
139 8 0.08
140 4 0.04
141 29 0.28
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.27
Consensus pattern (139 bp):
TCAAGTGAGAAAAAATTTTGTTTCAAGAGAAACTATCTCGAGCAAGAAAAAAATTTCAAGAGAAA
AATATCTCAAGCGAGATAAATTATGTTTCAAGAGAAACCATATCGAGTGAGACGAAAATTCAAGG
GAAAATATT
Found at i:78465 original size:71 final size:70
Alignment explanation
Indices: 78209--78471 Score: 257
Period size: 71 Copynumber: 3.8 Consensus size: 70
78199 TTTTTAAGAG
* * * * *
78209 AAATACCTCAAGTGAGAAAAAATTTTGTTTCAAGAGAAACTATCTCGAGTAAGACAAAAATTTTA
1 AAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTATCTCGAGTGAGAAAAAAATTTCA
78274 AGAGAA
66 AG-GAA
** * * * * * **
78280 ATTTATCTCAAGCGAGAT--AATTTT-TTTCGAGAGAATCCATATCGAGTGAGACGAAAA-TTCA
1 AAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTATCTCGAGTGAGAAAAAAATTTCA
*
78341 AGGGA
66 AGGAA
* ** *
78346 AAATATTTCAAGTGAGATAAAATTTTTGTTTTGAGAGAAACTCA-CTCGAGCGAGAAAAAACATT
1 AAATATCTCAAGTGAGATAAAA-TTTTGTTTCAAGAGAAACT-ATCTCGAGTGAGAAAAAA-ATT
78410 TCAAGGAA
63 TCAAGGAA
* * *
78418 AAATATCTGAAGTGAGATGAAATTATGTTTCAAGAGAAACTATCTCGAGTGAGA
1 AAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTATCTCGAGTGAGA
78472 TGAAAAACAA
Statistics
Matches: 152, Mismatches: 32, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
66 16 0.11
67 5 0.03
68 29 0.19
69 10 0.07
70 24 0.16
71 41 0.27
72 27 0.18
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.27
Consensus pattern (70 bp):
AAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTATCTCGAGTGAGAAAAAAATTTCA
AGGAA
Found at i:78590 original size:36 final size:38
Alignment explanation
Indices: 78550--78641 Score: 134
Period size: 38 Copynumber: 2.5 Consensus size: 38
78540 ATTTGAAGAA
78550 AAACTATCTCAAGTGAGAT-AAATTTTT-TTTCAAAAG
1 AAACTATCTCAAGTGAGATAAAATTTTTGTTTCAAAAG
* *
78586 AAACTATATCAAGGGAGATAAAATTTTTGTTTCAAAAG
1 AAACTATCTCAAGTGAGATAAAATTTTTGTTTCAAAAG
* *
78624 AAACTTTCTCGAGTGAGA
1 AAACTATCTCAAGTGAGA
78642 CGAAAATTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
36 17 0.35
37 8 0.17
38 23 0.48
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (38 bp):
AAACTATCTCAAGTGAGATAAAATTTTTGTTTCAAAAG
Found at i:78619 original size:38 final size:36
Alignment explanation
Indices: 78550--78628 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 36
78540 ATTTGAAGAA
* *
78550 AAACTATCTCAAGTGAGATAAATTTTTTTTCAAAAG
1 AAACTATATCAAGGGAGATAAATTTTTTTTCAAAAG
78586 AAACTATATCAAGGGAGATAAAATTTTTGTTTCAAAAG
1 AAACTATATCAAGGGAGAT-AAATTTTT-TTTCAAAAG
78624 AAACT
1 AAACT
78629 TTCTCGAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 17 0.44
37 8 0.21
38 14 0.36
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (36 bp):
AAACTATATCAAGGGAGATAAATTTTTTTTCAAAAG
Done.