Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001488.1 Hibiscus syriacus cultivar Beakdansim tig00002891_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: 146426
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1217 original size:22 final size:22
Alignment explanation
Indices: 1174--1219 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1164 CAGATCTAGC
*
1174 AAATTTTTAAATACTTTCTATA
1 AAATTTTTAAATACTTTATATA
*
1196 AAATTTTTATAA-ATTTTATATA
1 AAATTTTTA-AATACTTTATATA
1218 AA
1 AA
1220 TTTACTCAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATTTTTAAATACTTTATATA
Found at i:1934 original size:21 final size:22
Alignment explanation
Indices: 1910--1950 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1900 CAACATCCTC
1910 AAGACACC-GGAAATCCCAAAT
1 AAGACACCTGGAAATCCCAAAT
* *
1931 AAGACGCCTGGAGATCCCAA
1 AAGACACCTGGAAATCCCAA
1951 GCAAGACCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.41, C:0.29, G:0.20, T:0.10
Consensus pattern (22 bp):
AAGACACCTGGAAATCCCAAAT
Found at i:1956 original size:22 final size:21
Alignment explanation
Indices: 1909--1957 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
1899 CCAACATCCT
1909 CAAGACACCGGAAATCCCAAA
1 CAAGACACCGGAAATCCCAAA
* * * *
1930 TAAGACGCCTGGAGATCCCAAG
1 CAAGACACC-GGAAATCCCAAA
1952 CAAGAC
1 CAAGAC
1958 CCAAAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.41, C:0.31, G:0.20, T:0.08
Consensus pattern (21 bp):
CAAGACACCGGAAATCCCAAA
Found at i:5774 original size:18 final size:17
Alignment explanation
Indices: 5753--5788 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5743 TTTAAAGTAG
*
5753 TATTTTTTTTTACTTTTA
1 TATTGTTTTTT-CTTTTA
5771 TATTGTTTTTTCTTTTA
1 TATTGTTTTTTCTTTTA
5788 T
1 T
5789 CATTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.78
Consensus pattern (17 bp):
TATTGTTTTTTCTTTTA
Found at i:13212 original size:25 final size:27
Alignment explanation
Indices: 13184--13238 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
13174 TACAGTAAAA
* *
13184 AATTACAGAAATATCA-T-TTTTTTAC
1 AATTACAAAAATATCACTATTTTTAAC
13209 AATTACAAAAATATCACTATTTTTAAC
1 AATTACAAAAATATCACTATTTTTAAC
13236 AAT
1 AAT
13239 AATTACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 15 0.58
26 1 0.04
27 10 0.38
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (27 bp):
AATTACAAAAATATCACTATTTTTAAC
Found at i:13345 original size:56 final size:56
Alignment explanation
Indices: 13230--13391 Score: 206
Period size: 56 Copynumber: 2.9 Consensus size: 56
13220 TATCACTATT
*
13230 TTTAACAATAATTACTAAATATCACCG-TTTAACAATAATTACCAAAATAGCATCA
1 TTTAACAATAATTACCAAATATCACCGTTTTAACAATAATTACCAAAATAGCATCA
* * *
13285 TTTAACAATAATTACCAACATAGCACCGTTTTAACAATAATTACC-AAATATCA-CTG
1 TTTAACAATAATTACCAA-ATATCACCGTTTTAACAATAATTACCAAAATAGCATC-A
* *
13341 TTTAACAATAATTACCAAAATATTACCGTTTTAA-AATTAATTACAAAAATA
1 TTTAACAATAATTACC-AAATATCACCGTTTTAACAA-TAATTACCAAAATA
13392 ACACCCTTTT
Statistics
Matches: 94, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
55 20 0.21
56 51 0.54
57 23 0.24
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (56 bp):
TTTAACAATAATTACCAAATATCACCGTTTTAACAATAATTACCAAAATAGCATCA
Found at i:13383 original size:29 final size:29
Alignment explanation
Indices: 13209--13455 Score: 220
Period size: 29 Copynumber: 8.6 Consensus size: 29
13199 ATTTTTTTAC
* **
13209 AATTACAAAAATATCACTATTTTTAACAAT
1 AATTACCAAAATATCAC-CGTTTTAACAAT
*
13239 AATTA-CTAAATATCACCG-TTTAACAAT
1 AATTACCAAAATATCACCGTTTTAACAAT
* * *
13266 AATTACCAAAATAGCATC-ATTTAACAAT
1 AATTACCAAAATATCACCGTTTTAACAAT
* *
13294 AATTACCAACATAGCACCGTTTTAACAAT
1 AATTACCAAAATATCACCGTTTTAACAAT
*
13323 AATTACC-AAATATCACTG-TTTAACAAT
1 AATTACCAAAATATCACCGTTTTAACAAT
*
13350 AATTACCAAAATATTACCGTTTTAA-AATT
1 AATTACCAAAATATCACCGTTTTAACAA-T
* * * *
13379 AATTACAAAAATAACACCCTTTTTAAAAAT
1 AATTACCAAAATATCA-CCGTTTTAACAAT
* * * *
13409 AAATACAAAAATAACACAC-TTTTAAAAAT
1 AATTACCAAAATATCAC-CGTTTTAACAAT
* *
13438 AATTACGAAAATAACACC
1 AATTACCAAAATATCACC
13456 ATAACCGAAA
Statistics
Matches: 186, Mismatches: 22, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
27 30 0.16
28 54 0.29
29 70 0.38
30 30 0.16
31 2 0.01
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.30
Consensus pattern (29 bp):
AATTACCAAAATATCACCGTTTTAACAAT
Found at i:14015 original size:21 final size:21
Alignment explanation
Indices: 13971--14055 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
13961 CCACTTCATT
*
13971 TTATTTTATTCT-TAATGC-TA
1 TTATTTTATT-TATAGTGCTTA
**
13991 TTATAATATTTATAGTGCTTA
1 TTATTTTATTTATAGTGCTTA
14012 TTATTTTATTTATAGTGCTTA
1 TTATTTTATTTATAGTGCTTA
*
14033 TTATTTTATCTATAGTGC-TA
1 TTATTTTATTTATAGTGCTTA
14053 TTA
1 TTA
14056 GATATATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.02
20 18 0.32
21 38 0.67
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (21 bp):
TTATTTTATTTATAGTGCTTA
Found at i:14047 original size:42 final size:40
Alignment explanation
Indices: 13971--14055 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
13961 CCACTTCATT
*
13971 TTATTTTATTCTTAATGCTATTATAATATTTATAGTGCTTA
1 TTATTTTATTCTTAATGCTATTATAATATCTATAGTGC-TA
* **
14012 TTATTTTATT-TATAGTGCTTATTATTTTATCTATAGTGCTA
1 TTATTTTATTCT-TAATGC-TATTATAATATCTATAGTGCTA
14053 TTA
1 TTA
14056 GATATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 1 0.03
41 20 0.53
42 17 0.45
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (40 bp):
TTATTTTATTCTTAATGCTATTATAATATCTATAGTGCTA
Found at i:20821 original size:31 final size:30
Alignment explanation
Indices: 20781--20885 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 30
20771 ACGTATGTTA
*
20781 CATATACATTAATGATGATATAATATATAT
1 CATATACATTAATGATGATATAATGTATAT
**
20811 CATAGTACATTGGTAATGACTTGACGT-ATGT-TA-
1 CATA-TACA-T--TAATGA--TGATATAATGTATAT
20844 CATATACATTAATGATGATATAATGTATAT
1 CATATACATTAATGATGATATAATGTATAT
20874 CATAGTACATTA
1 CATA-TACATTA
20886 GTAATGACGT
Statistics
Matches: 60, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
27 4 0.07
28 4 0.07
29 8 0.13
30 8 0.13
31 12 0.20
32 5 0.08
33 4 0.07
34 8 0.13
35 3 0.05
36 4 0.07
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (30 bp):
CATATACATTAATGATGATATAATGTATAT
Found at i:20839 original size:63 final size:63
Alignment explanation
Indices: 20766--20934 Score: 275
Period size: 63 Copynumber: 2.7 Consensus size: 63
20756 ATCAATGATA
*
20766 ACTTGACGTATGTTACATATACATTAATGATGATATAATATATATCATAGTACATTGGTAATG
1 ACTTGACGTATGTTACATATACATTAATGATGATATAATATATATCATAGTACATTAGTAATG
*
20829 ACTTGACGTATGTTACATATACATTAATGATGATATAATGTATATCATAGTACATTAGTAATG
1 ACTTGACGTATGTTACATATACATTAATGATGATATAATATATATCATAGTACATTAGTAATG
* * * * *
20892 ACGTGACGTATGTTACATGTACATTAGTGATGACATAACATAT
1 ACTTGACGTATGTTACATATACATTAATGATGATATAATATAT
20935 GTTATATATG
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 98 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (63 bp):
ACTTGACGTATGTTACATATACATTAATGATGATATAATATATATCATAGTACATTAGTAATG
Found at i:20919 original size:32 final size:32
Alignment explanation
Indices: 20815--20938 Score: 108
Period size: 32 Copynumber: 3.9 Consensus size: 32
20805 ATATATCATA
* *
20815 GTACATTGGTAATGACTTGACGTATGTTACAT
1 GTACATTAGTAATGACATGACGTATGTTACAT
* * * * * * *
20847 ATACATTAATGATGATATAATGTAT-AT-CAT
1 GTACATTAGTAATGACATGACGTATGTTACAT
*
20877 AGTACATTAGTAATGACGTGACGTATGTTACAT
1 -GTACATTAGTAATGACATGACGTATGTTACAT
* * *
20910 GTACATTAGTGATGACATAACATATGTTA
1 GTACATTAGTAATGACATGACGTATGTTA
20939 TATATGGTAC
Statistics
Matches: 68, Mismatches: 21, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
30 3 0.04
31 19 0.28
32 43 0.63
33 3 0.04
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (32 bp):
GTACATTAGTAATGACATGACGTATGTTACAT
Found at i:28808 original size:29 final size:30
Alignment explanation
Indices: 28730--28809 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
28720 CGTTAACGAT
* *
28730 TTAACAGTTCAGTGATATAATTGAAACAAAA
1 TTAAAAGTTCAATGATATAATTG-AACAAAA
* *
28761 ATCAAAGTTCAAT-ACTATAATTG-ACAAAA
1 TTAAAAGTTCAATGA-TATAATTGAACAAAA
*
28790 TTAAAAGTTCAATGTTATAA
1 TTAAAAGTTCAATGATATAA
28810 ACGATATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
29 22 0.55
30 1 0.03
31 17 0.43
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (30 bp):
TTAAAAGTTCAATGATATAATTGAACAAAA
Found at i:28924 original size:31 final size:30
Alignment explanation
Indices: 28884--28959 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
28874 AACTACATCA
*
28884 GATATCACTAAACTTTAAATATTGTATT-ATT
1 GATAACACTAAACTTTAAAT-TT-TATTAATT
* * *
28915 GATACCACTAAATTTTTAATTTTATTAATT
1 GATAACACTAAACTTTAAATTTTATTAATT
*
28945 -ATAACACTGAACTTT
1 GATAACACTAAACTTT
28960 TATTTCCATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 16 0.42
30 5 0.13
31 17 0.45
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (30 bp):
GATAACACTAAACTTTAAATTTTATTAATT
Found at i:28952 original size:29 final size:31
Alignment explanation
Indices: 28884--28961 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
28874 AACTACATCA
* *
28884 GATATCACTAAACTTTAAATATTGTATTATT
1 GATAACACTAAACTTTTAATATTGTATTATT
* *
28915 GATACCACTAAATTTTTAAT-TT-TATTAATT
1 GATAACACTAAACTTTTAATATTGTATT-ATT
*
28945 -ATAACACTGAACTTTTA
1 GATAACACTAAACTTTTA
28962 TTTCCATTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 18 0.45
30 5 0.12
31 17 0.43
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (31 bp):
GATAACACTAAACTTTTAATATTGTATTATT
Found at i:40976 original size:31 final size:30
Alignment explanation
Indices: 40935--40998 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
40925 ATTTTAAAAG
40935 TTACAAATAACCATTA-AAT-TTATCAAATAA
1 TTACAAATAACCATTATAATATTAT--AATAA
*
40965 TTACAAAATAACTATTATAATATTATAATAA
1 TTAC-AAATAACCATTATAATATTATAATAA
40996 TTA
1 TTA
40999 TGGTAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 4 0.13
31 19 0.63
32 3 0.10
33 4 0.13
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (30 bp):
TTACAAATAACCATTATAATATTATAATAA
Found at i:41099 original size:31 final size:31
Alignment explanation
Indices: 41024--41113 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 31
41014 ATTAATTATA
* *
41024 TGATAAAGTTTAATAATCGTTTTATAATCATT
1 TGATAAA-TTTAATGATCGTTTTATAATAATT
** *
41056 CAATAAAATTTAATGATCATTTTATAATAATT
1 TGAT-AAATTTAATGATCGTTTTATAATAATT
41088 TGATAAATTTAATGATCGTTTTATAA
1 TGATAAATTTAATGATCGTTTTATAA
41114 CTATTTTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 21 0.43
32 25 0.51
33 3 0.06
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.46
Consensus pattern (31 bp):
TGATAAATTTAATGATCGTTTTATAATAATT
Found at i:41785 original size:16 final size:16
Alignment explanation
Indices: 41766--41799 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41756 CAATATACGA
41766 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
41782 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
41798 AT
1 AT
41800 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:41873 original size:16 final size:18
Alignment explanation
Indices: 41841--41874 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
41831 TATTAATTTA
41841 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
41859 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
41875 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:42543 original size:130 final size:130
Alignment explanation
Indices: 42338--42585 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
42328 AAATTTCTTC
* *
42338 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
42403 CATGGGTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CATAAGTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
42468 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCATAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* *
42533 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CATAAGTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
42586 TATATAAATA
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CATAAGTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:43032 original size:35 final size:35
Alignment explanation
Indices: 42982--43057 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
42972 AATTGAATTT
* *
42982 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
43017 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
43052 AATTGA
1 AATTGA
43058 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:43879 original size:35 final size:35
Alignment explanation
Indices: 43833--43908 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
43823 AAAACAGTCC
* *
43833 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
43868 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
43903 TCAATT
1 TCAATT
43909 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:44446 original size:130 final size:130
Alignment explanation
Indices: 44305--44552 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
44295 TATTTATATA
* **
44305 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATATGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTG
* *
44370 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
44435 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTG
* * *
44500 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
44553 GAAGAAATTT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:44908 original size:28 final size:27
Alignment explanation
Indices: 44877--44939 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
44867 AGTTGATACA
*
44877 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
44905 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
44933 ATATTTT
1 ATATTTT
44940 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:45040 original size:16 final size:18
Alignment explanation
Indices: 45019--45052 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
45009 ATTTCTTATT
45019 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
45035 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
45053 TAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:66271 original size:31 final size:31
Alignment explanation
Indices: 66249--66308 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
66239 GATATGACTT
*
66249 TTTTTGTTAATATATAATGATGATATATATC
1 TTTTTATTAATATATAATGATGATATATATC
* *
66280 TTTTTATTAATATTTAATTATGATATATA
1 TTTTTATTAATATATAATGATGATATATA
66309 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.55
Consensus pattern (31 bp):
TTTTTATTAATATATAATGATGATATATATC
Found at i:66316 original size:31 final size:31
Alignment explanation
Indices: 66250--66316 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
66240 ATATGACTTT
* *
66250 TTTTGTTAATATATAATGATGATATATATCT
1 TTTTATTAATATATAATGATGATATATATCA
* *
66281 TTTTATTAATATTTAATTATGATATATAAT-A
1 TTTTATTAATATATAATGATGATATAT-ATCA
66312 TTTTA
1 TTTTA
66317 AATAAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.55
Consensus pattern (31 bp):
TTTTATTAATATATAATGATGATATATATCA
Found at i:66383 original size:15 final size:16
Alignment explanation
Indices: 66365--66412 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
66355 TTTCTAAACC
*
66365 CTCAACTT-CTACCGT
1 CTCAACTTCCCACCGT
*
66380 CTCACCTTCCCACCGT
1 CTCAACTTCCCACCGT
* *
66396 CTCACCCTCCCACCGT
1 CTCAACTTCCCACCGT
66412 C
1 C
66413 ATTGTTTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 7 0.24
16 22 0.76
ACGTcount: A:0.15, C:0.54, G:0.06, T:0.25
Consensus pattern (16 bp):
CTCAACTTCCCACCGT
Found at i:66396 original size:16 final size:16
Alignment explanation
Indices: 66375--66412 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
66365 CTCAACTTCT
*
66375 ACCGTCTCACCTTCCC
1 ACCGTCTCACCCTCCC
66391 ACCGTCTCACCCTCCC
1 ACCGTCTCACCCTCCC
66407 ACCGTC
1 ACCGTC
66413 ATTGTTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.13, C:0.58, G:0.08, T:0.21
Consensus pattern (16 bp):
ACCGTCTCACCCTCCC
Found at i:73614 original size:5 final size:5
Alignment explanation
Indices: 73604--73632 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
73594 TTAAAACATC
73604 GAATG GAATG GAATG GAATG GAATG GAAT
1 GAATG GAATG GAATG GAATG GAATG GAAT
73633 TAGAGTGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (5 bp):
GAATG
Found at i:80004 original size:9 final size:9
Alignment explanation
Indices: 79980--80024 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
79970 TCTAGGAGGA
*
79980 CCACCAGAG
1 CCACCAAAG
*
79989 CCTCCAAAG
1 CCACCAAAG
* *
79998 CCCCCAAAA
1 CCACCAAAG
80007 CCACCAAAG
1 CCACCAAAG
80016 CCACCAAAG
1 CCACCAAAG
80025 GGGTCGCCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.40, C:0.47, G:0.11, T:0.02
Consensus pattern (9 bp):
CCACCAAAG
Found at i:85204 original size:19 final size:18
Alignment explanation
Indices: 85182--85224 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
85172 TTTAACATTG
85182 AAAATTA-ATTTTGGAAAAT
1 AAAATTAGA-TTT-GAAAAT
*
85201 AAAATTAGATTTGAGAAT
1 AAAATTAGATTTGAAAAT
85219 AAAATT
1 AAAATT
85225 TGGAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 10 0.45
20 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (18 bp):
AAAATTAGATTTGAAAAT
Found at i:101095 original size:182 final size:184
Alignment explanation
Indices: 100801--101173 Score: 614
Period size: 183 Copynumber: 2.0 Consensus size: 184
100791 ATAAAAATGA
* *
100801 AATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 AATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAATTATAAAATAAAAAT
*
100866 TTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTAT
66 TTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAATTAT
*
100931 TAATTGGGTTTTAAATG-TTTGGGCTT-AGCCCATATGTTATATATAATATATTT
131 TAATTGGGTTTTAAATGATTTAGG-TTGAGCCCATATGTTATATATAATATATTT
100984 AATATTTTTTAATT-AAAAAGCAA-TTTACAAATAATTTAAATAATATATAATTATAAAATTAAA
1 AATATTTTTTAATTCAAAAA--AAGTTTACAAATAATTTAAATAATATATAATTATAAAA-TAAA
*
101047 AA-TTTATAT-AATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAAT
63 AATTTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAAT
101110 TATTAATTGGGTTTTAAATGATTTAGGTTGAGCCCATATGTTATATATAATATATTT
128 TATTAATTGGGTTTTAAATGATTTAGGTTGAGCCCATATGTTATATATAATATATTT
*
101167 AAAATTT
1 AATATTT
101174 AATTTCGGTT
Statistics
Matches: 179, Mismatches: 6, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
182 80 0.45
183 91 0.51
184 8 0.04
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
AATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAATTATAAAATAAAAAT
TTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAATTAT
TAATTGGGTTTTAAATGATTTAGGTTGAGCCCATATGTTATATATAATATATTT
Found at i:101961 original size:41 final size:41
Alignment explanation
Indices: 101878--101961 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
101868 TATTAGGTAC
** * * *
101878 CGGCGGTTTGGCCGGTGTAGGTTCTCTCCTCTATGGGGCAT
1 CGGCGGTTTGGCCGGTAAAGGTTCTCTCCCCTATGAGACAT
*
101919 CGGCGGTTTGGCCGGTAAAGAGTT-TCTCCCCTATTAGACAT
1 CGGCGGTTTGGCCGGTAAAG-GTTCTCTCCCCTATGAGACAT
101960 CG
1 CG
101962 TGTTTTAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
41 33 0.92
42 3 0.08
ACGTcount: A:0.13, C:0.25, G:0.32, T:0.30
Consensus pattern (41 bp):
CGGCGGTTTGGCCGGTAAAGGTTCTCTCCCCTATGAGACAT
Found at i:103418 original size:2 final size:2
Alignment explanation
Indices: 103411--103441 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
103401 GGGTTTTTCT
103411 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
103442 TTTCATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:111832 original size:37 final size:36
Alignment explanation
Indices: 111723--111833 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 36
111713 TTTTAATTTA
* * * *
111723 AATATTAATTTTATCAACACTTTAAAGTAAATTAAAA
1 AATATTAATATTATGAACAATTTAAAGTAAATT-AAT
* ** * *
111760 AATATTAATGTTATGATTAGTTTAAATTAAATTAAT
1 AATATTAATATTATGAACAATTTAAAGTAAATTAAT
111796 AATCATTAATATTATGAACAATTTAAAGTAAATTAAT
1 AAT-ATTAATATTATGAACAATTTAAAGTAAATTAAT
111833 A
1 A
111834 TGAATGGGTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 5 0.08
37 56 0.92
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (36 bp):
AATATTAATATTATGAACAATTTAAAGTAAATTAAT
Found at i:119693 original size:24 final size:24
Alignment explanation
Indices: 119648--119693 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
119638 GGGACTAAAT
**
119648 AAAAAATAGAATATATTTTTACTA
1 AAAAAATAGAATATATAGTTACTA
119672 AAAAAATAAGAAT-TATAGTTAC
1 AAAAAAT-AGAATATATAGTTAC
119694 ATAGGTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (24 bp):
AAAAAATAGAATATATAGTTACTA
Found at i:120677 original size:19 final size:20
Alignment explanation
Indices: 120633--120684 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
120623 TTATCATTAA
*
120633 TTTTAAAAAATTATAACTTC
1 TTTTAAAAGATTATAACTTC
*
120653 TATTAAAAGATTATATA-TT-
1 TTTTAAAAGATTATA-ACTTC
120672 TTTTAAAAGATTA
1 TTTTAAAAGATTA
120685 GCGAATCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.43
20 15 0.54
21 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (20 bp):
TTTTAAAAGATTATAACTTC
Found at i:129370 original size:22 final size:21
Alignment explanation
Indices: 129345--129388 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
129335 TTCTCTCTAC
*
129345 TTCTACTTATTTTCCTCTACTT
1 TTCTACATATTTTCC-CTACTT
*
129367 TTCTCCATATTTTCCCTACTT
1 TTCTACATATTTTCCCTACTT
129388 T
1 T
129389 GCTCCAACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.14, C:0.30, G:0.00, T:0.57
Consensus pattern (21 bp):
TTCTACATATTTTCCCTACTT
Found at i:129387 original size:21 final size:22
Alignment explanation
Indices: 129352--129394 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
129342 TACTTCTACT
*
129352 TATTTTCCTCTACTTTTCTCCA
1 TATTTTCCTCTACTTTGCTCCA
129374 TATTTTCC-CTACTTTGCTCCA
1 TATTTTCCTCTACTTTGCTCCA
129395 ACAGAAGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.14, C:0.33, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTTCCTCTACTTTGCTCCA
Found at i:136014 original size:20 final size:20
Alignment explanation
Indices: 135989--136191 Score: 243
Period size: 20 Copynumber: 10.2 Consensus size: 20
135979 ATCTTCCAAG
*
135989 AATCGCAACGTGATTCAGAA
1 AATCGCAACGCGATTCAGAA
*
136009 AATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATT-CAGAA
*
136029 AATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCAGAA
*
136049 AATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATT-CAGAA
*
136069 AATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCAGAA
136089 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
* *
136109 AATCGTAACGCGATTCCA-AG
1 AATCGCAACGCGATT-CAGAA
*
136129 AATCGCAATGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
*
136149 AATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATT-CAGAA
**
136169 AATCGCAATACGATTCAGAA
1 AATCGCAACGCGATTCAGAA
136189 AAT
1 AAT
136192 GAGTAAATTC
Statistics
Matches: 156, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
19 6 0.04
20 143 0.92
21 7 0.04
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCAGAA
Found at i:136064 original size:60 final size:59
Alignment explanation
Indices: 135881--136191 Score: 231
Period size: 60 Copynumber: 5.1 Consensus size: 59
135871 AATGACCAAC
* * * * * **
135881 AAAATCGCAACGCGGTATCAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACGCGAT-TCAAGAATCGCAACGCGATTAAGAAAATCGCAACG-CGATTCAG
* *** *
135940 AAGATCGCAACGCGATCTTCCAAGAATCGCAATGCGACGATCTTCCAAGAATCGCAACGTGATTC
1 AAAATCGCAACGCGA--TT-CAAGAATCGCAA--CG-CGAT-TAAGAA-AATCGCAACGCGATTC
136005 AG
58 AG
136007 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CAG
* * *
136067 AGAATCGCAACGCGATT-AAGAAAATCGCAACGCGATTCAGAAAATCGTAACGCGATTCCA-
1 AAAATCGCAACGCGATTCAAG--AATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CAG
* * * **
136127 AGAATCGCAATGCGATTCAGAAAATCGCAACGCGATTCCAAG--AATCGCAATACGATTCAG
1 AAAATCGCAACGCGATTCA-AGAATCGCAACGCGATT--AAGAAAATCGCAACGCGATTCAG
136187 AAAAT
1 AAAAT
136192 GAGTAAATTC
Statistics
Matches: 211, Mismatches: 23, Indels: 35
0.78 0.09 0.13
Matches are distributed among these distances:
58 3 0.01
59 15 0.07
60 114 0.54
61 10 0.05
62 14 0.07
63 2 0.01
64 2 0.01
65 19 0.09
66 7 0.03
67 25 0.12
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (59 bp):
AAAATCGCAACGCGATTCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAG
Found at i:136165 original size:40 final size:40
Alignment explanation
Indices: 135938--136191 Score: 227
Period size: 40 Copynumber: 6.2 Consensus size: 40
135928 AACGTTGAAA
*
135938 AGAAGATCGCAACGCGATCTTCCAAGAATCGCAATGCGACGATCTTCC
1 AGAAAATCGCAACGCGA--TT-CAAGAATCGCAA--CG-CGA--TTCC
* * *
135986 A-AGAATCGCAACGTGATTCAGAAAATCGCAACGCGATTCC
1 AGAAAATCGCAACGCGATTCA-AGAATCGCAACGCGATTCC
*
136026 A-AGAATCGCAACGCGATT-AAGAAAATCGCAACGCGATTCC
1 AGAAAATCGCAACGCGATTCAAG--AATCGCAACGCGATTCC
*
136066 A-AGAATCGCAACGCGATT-AAGAAAATCGCAACGCGATT-C
1 AGAAAATCGCAACGCGATTCAAG--AATCGCAACGCGATTCC
* *
136105 AGAAAATCGTAACGCGATTCCAAGAATCGCAATGCGATT-C
1 AGAAAATCGCAACGCGATT-CAAGAATCGCAACGCGATTCC
**
136145 AGAAAATCGCAACGCGATTCCAAGAATCGCAATACGATT-C
1 AGAAAATCGCAACGCGATT-CAAGAATCGCAACGCGATTCC
136185 AGAAAAT
1 AGAAAAT
136192 GAGTAAATTC
Statistics
Matches: 189, Mismatches: 11, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
38 1 0.01
39 3 0.02
40 151 0.80
42 6 0.03
43 2 0.01
44 2 0.01
45 11 0.06
47 12 0.06
48 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (40 bp):
AGAAAATCGCAACGCGATTCAAGAATCGCAACGCGATTCC
Found at i:136290 original size:6 final size:6
Alignment explanation
Indices: 136279--136321 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
136269 TTCGACACGT
**
136279 ATTACC ATTACC ATTACC ACGACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC A
136322 CGACCACGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.35, C:0.35, G:0.02, T:0.28
Consensus pattern (6 bp):
ATTACC
Found at i:136306 original size:24 final size:24
Alignment explanation
Indices: 136279--136327 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
136269 TTCGACACGT
136279 ATTACCATTACCATTACCACGACC
1 ATTACCATTACCATTACCACGACC
136303 ATTACCATTACCATTACCACGACC
1 ATTACCATTACCATTACCACGACC
136327 A
1 A
136328 CGACCACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.37, G:0.04, T:0.24
Consensus pattern (24 bp):
ATTACCATTACCATTACCACGACC
Found at i:136327 original size:6 final size:6
Alignment explanation
Indices: 136318--136384 Score: 120
Period size: 6 Copynumber: 11.5 Consensus size: 6
136308 CATTACCATT
136318 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
136366 ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
136385 CGAGACGAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.16
6 51 0.84
ACGTcount: A:0.31, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:136908 original size:6 final size:6
Alignment explanation
Indices: 136899--136923 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
136889 GTCGTGGTCG
136899 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
136924 ACGTGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:137028 original size:20 final size:20
Alignment explanation
Indices: 137003--137200 Score: 162
Period size: 20 Copynumber: 9.8 Consensus size: 20
136993 ACAGCTTCTT
*
137003 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTTG
137023 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-TG
137043 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-TG
* *
137063 AATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTTG
*
137083 AAGATTGCGTTGCGATTCTCTT-
1 -A-ATCGCGTTGCGATTCT-TTG
* *
137105 AATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTTG
137125 AATATCGCGTTGCGATTTTCTTTTG
1 -A-ATCGCGTTGCGA--TTC-TTTG
*
137150 -A-C-CGTTGCGATT-TTCTA
1 AATCGCGTTGCGATTCTT-TG
137167 AATCGCGTTGCGA-T-TTTG
1 AATCGCGTTGCGATTCTTTG
137185 ATATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
137201 TTGTTGGTCA
Statistics
Matches: 148, Mismatches: 13, Indels: 34
0.76 0.07 0.17
Matches are distributed among these distances:
16 2 0.01
17 1 0.01
18 5 0.03
19 19 0.13
20 82 0.55
21 6 0.04
22 26 0.18
23 1 0.01
24 3 0.02
25 3 0.02
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.39
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTTTG
Found at i:137066 original size:40 final size:40
Alignment explanation
Indices: 136998--137202 Score: 165
Period size: 42 Copynumber: 5.0 Consensus size: 40
136988 ATGCAACAGC
* *
136998 TTCTTAATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATT
1 TTCTGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATT
*
137038 TTCTGAATCGCGTTGCGATTTTCTGAATCGCATTGCGATT
1 TTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT
* * * * *
137078 CTT-GGAAGATTGCGTTGCGATTCTCTTAATCGCATTGCGATT
1 -TTCTG-A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT
*
137120 CTT-GGAATATCGCGTTGCGATTTTCTTTTG-A-C-CGTTGCGATT
1 -TTCTG-A-ATCGCGTTGCGATTTTC---TGAATCGCGTTGCGATT
*
137162 TTCTAAATCGCGTTGCGA-TTT-TGATATCGCGTTGCGATT
1 TTCTGAATCGCGTTGCGATTTTCTGA-ATCGCGTTGCGATT
137201 TT
1 TT
137203 GTTGGTCATT
Statistics
Matches: 139, Mismatches: 14, Indels: 25
0.78 0.08 0.14
Matches are distributed among these distances:
35 2 0.01
37 1 0.01
38 1 0.01
39 17 0.12
40 47 0.34
41 6 0.04
42 62 0.45
43 1 0.01
44 1 0.01
45 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (40 bp):
TTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT
Found at i:137109 original size:42 final size:42
Alignment explanation
Indices: 137004--137146 Score: 170
Period size: 42 Copynumber: 3.5 Consensus size: 42
136994 CAGCTTCTTA
* *
137004 ATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATT-TTCTG-A-
1 ATCGCGTTGCGATTTTCTT--AATCGCATTGCGATTCTT-GGAAG
*
137044 ATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTTAATCGCATTGCGATTCTTGGAAG
* * *
137086 ATTGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGAAT
1 ATCGCGTTGCGATTTTCTTAATCGCATTGCGATTCTTGGAAG
137128 ATCGCGTTGCGATTTTCTT
1 ATCGCGTTGCGATTTTCTT
137147 TTGACCGTTG
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
40 27 0.30
41 3 0.03
42 59 0.66
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (42 bp):
ATCGCGTTGCGATTTTCTTAATCGCATTGCGATTCTTGGAAG
Found at i:137688 original size:12 final size:12
Alignment explanation
Indices: 137663--137703 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
137653 ATCATAAACA
137663 ATTTT-TTTTAT
1 ATTTTATTTTAT
*
137674 ATTTTATTTTCT
1 ATTTTATTTTAT
*
137686 ATTTTATTATAT
1 ATTTTATTTTAT
137698 -TTTTAT
1 ATTTTAT
137704 ACTATTGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTATTTTAT
Found at i:141514 original size:160 final size:161
Alignment explanation
Indices: 141196--141565 Score: 498
Period size: 161 Copynumber: 2.3 Consensus size: 161
141186 AATTATTGAT
* *
141196 AAAAGAAAACTATGAAGCAAACCAAGTCAGCAATTCCTCCAAATTGTGAGCAGTGTCCCACAAGC
1 AAAA-AAAACTATGAAGCAAACCAAGTAAGCAATTCCTCCAAATTGTGACCAGTGTCCCACAAGC
* * *
141261 TCCATTGCTCATTTGCTCTAACATTTGAAAGTTAACTAGGTTTCCTCATCCTCCCATGATGAGAA
65 TCCATTGCTCATTTGCTCCAACATTTGAAAGTTAACTAGGTTTCATCATCCTCCCATAATGAGAA
* *
141326 AAATAAAATGAAATAGAACTTATAGCAAAACC
130 AAATAAAATAAAATAGAACATATAGCAAAACC
* * *
141358 AAAAAAAAC-ATGAAGCAGACCAAGTAAGCAAATTCCTCCAAATTGTGACCAGTGTCTCACAAGT
1 AAAAAAAACTATGAAGCAAACCAAGTAAGC-AATTCCTCCAAATTGTGACCAGTGTCCCACAAGC
* *
141422 TCCATTGCTCATTTGCTCCAGCATTTGAAAGTTAACT-TGTTCTCATCATCCTCCCATAATGAG-
65 TCCATTGCTCATTTGCTCCAACATTTGAAAGTTAACTAGGTT-TCATCATCCTCCCATAATGAGA
141485 AAAATAAAATAAAATAGAACATATAGCAAAACCAC
129 AAAATAAAATAAAATAGAACATATAGCAAAA-C-C
* *
141520 AAAAAAAAAAAC-ATGAAGCAAACCAAGT-CGACAATTCTTCCAAATT
1 ---AAAAAAAACTATGAAGCAAACCAAGTAAG-CAATTCCTCCAAATT
141566 TTCATCCACA
Statistics
Matches: 185, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
160 50 0.27
161 91 0.49
162 5 0.03
164 14 0.08
165 25 0.14
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.24
Consensus pattern (161 bp):
AAAAAAAACTATGAAGCAAACCAAGTAAGCAATTCCTCCAAATTGTGACCAGTGTCCCACAAGCT
CCATTGCTCATTTGCTCCAACATTTGAAAGTTAACTAGGTTTCATCATCCTCCCATAATGAGAAA
AATAAAATAAAATAGAACATATAGCAAAACC
Done.