Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008331.1 Hibiscus syriacus cultivar Beakdansim tig00111044_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: 68068
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1363 original size:22 final size:23
Alignment explanation
Indices: 1337--1380 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1327 AAAATTCAAC
1337 AAGAAATCG-AAGCACTCAAAAG
1 AAGAAATCGAAAGCACTCAAAAG
*
1359 AAGAAATTGAAAGCACTCAAAA
1 AAGAAATCGAAAGCACTCAAAA
1381 AGAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.11
Consensus pattern (23 bp):
AAGAAATCGAAAGCACTCAAAAG
Found at i:7024 original size:22 final size:23
Alignment explanation
Indices: 6998--7040 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
6988 AATCCAACAA
6998 AGAAATCG-AAGCACTCAAAAGG
1 AGAAATCGAAAGCACTCAAAAGG
*
7020 AGAAATTGAAAGCACTCAAAA
1 AGAAATCGAAAGCACTCAAAA
7041 AGAAGAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.53, C:0.16, G:0.19, T:0.12
Consensus pattern (23 bp):
AGAAATCGAAAGCACTCAAAAGG
Found at i:7047 original size:24 final size:22
Alignment explanation
Indices: 6997--7048 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
6987 AAATCCAACA
6997 AAGAAATCGAAGCACTCAAAAG
1 AAGAAATCGAAGCACTCAAAAG
* *
7019 GAGAAATTGAAAGCACTCAAAAAG
1 AAGAAATCG-AAGCACTC-AAAAG
7043 AAGAAA
1 AAGAAA
7049 AGAAGAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.28
23 8 0.32
24 10 0.40
ACGTcount: A:0.58, C:0.13, G:0.19, T:0.10
Consensus pattern (22 bp):
AAGAAATCGAAGCACTCAAAAG
Found at i:8608 original size:35 final size:35
Alignment explanation
Indices: 8496--8607 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
8486 TAAGATACAA
*
8496 CCTATAACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATTACCA-TTTCACG
*
8532 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATTACCATTTCACG
* * *
8567 CCTATATCATTACCATATTCCATTACCATTTCACG
1 CCTATAACATCACCATCTTCCATTACCATTTCACG
8602 CCTATA
1 CCTATA
8608 TAACCACCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 43 0.61
36 27 0.39
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATTACCATTTCACG
Found at i:9071 original size:11 final size:11
Alignment explanation
Indices: 9055--9081 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9045 ATTGGAGTGC
9055 AAAAGAAAAAG
1 AAAAGAAAAAG
9066 AAAAGAAAAAG
1 AAAAGAAAAAG
9077 AAAAG
1 AAAAG
9082 TGAAGAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:12674 original size:35 final size:35
Alignment explanation
Indices: 12588--12700 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
12578 TAAGATATAA
* * * *
12588 CCTATAACATCACCATATTCCATCACCATTTTCATG
1 CCTATATCATCACCATCTTCCATTACCA-TTTCACG
* *
12624 CCTATAGCATCACCATCTTCCATTACCATTGCACG
1 CCTATATCATCACCATCTTCCATTACCATTTCACG
* *
12659 CCTATATCATTACCATCTTCCATTACCATTTCACA
1 CCTATATCATCACCATCTTCCATTACCATTTCACG
12694 CCTATAT
1 CCTATAT
12701 AACCACCAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 43 0.63
36 25 0.37
ACGTcount: A:0.28, C:0.35, G:0.04, T:0.34
Consensus pattern (35 bp):
CCTATATCATCACCATCTTCCATTACCATTTCACG
Found at i:14719 original size:35 final size:35
Alignment explanation
Indices: 14607--14718 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
14597 TAAGATACAA
* *
14607 CCTATAACATCACCATCTTCCATCACCGTTTTCACG
1 CCTATAACATCACCATCTTCCATTACC-ATTTCACG
*
14643 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATTACCATTTCACG
* * * *
14678 CCTATATCATTACCATCTTCCATTGCCATTTCATG
1 CCTATAACATCACCATCTTCCATTACCATTTCACG
14713 CCTATA
1 CCTATA
14719 TAACCACCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 42 0.62
36 26 0.38
ACGTcount: A:0.26, C:0.36, G:0.05, T:0.33
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATTACCATTTCACG
Found at i:14881 original size:10 final size:11
Alignment explanation
Indices: 14868--14908 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
14858 TTTGATAACT
14868 TTTC-TTTCTA
1 TTTCATTTCTA
*
14878 TTTCAATTCT-
1 TTTCATTTCTA
14888 TTTCATTTCTA
1 TTTCATTTCTA
*
14899 TTTCTTTTCT
1 TTTCATTTCT
14909 TAATTATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 13 0.50
11 13 0.50
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTCATTTCTA
Found at i:16750 original size:35 final size:35
Alignment explanation
Indices: 16638--16749 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
16628 TAAGATACAA
*
16638 CCTATAACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATTACCA-TTTCACG
* *
16674 CCTATAACATCACCATATTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATTACCATTTCACG
* * *
16709 CCTATATCATTACCATCTTCCATTACCATTTCATG
1 CCTATAACATCACCATCTTCCATTACCATTTCACG
16744 CCTATA
1 CCTATA
16750 TAACCACCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 42 0.62
36 26 0.38
ACGTcount: A:0.29, C:0.35, G:0.04, T:0.33
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATTACCATTTCACG
Found at i:16911 original size:10 final size:11
Alignment explanation
Indices: 16898--16938 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
16888 TTTTGATACT
16898 TTTC-TTTCTA
1 TTTCATTTCTA
*
16908 TTTCAATTCT-
1 TTTCATTTCTA
16918 TTTCATTTCTA
1 TTTCATTTCTA
*
16929 TTTCTTTTCT
1 TTTCATTTCT
16939 TAATTATCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 13 0.50
11 13 0.50
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTCATTTCTA
Found at i:20277 original size:24 final size:21
Alignment explanation
Indices: 20243--20285 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
20233 TCCACAAGAC
*
20243 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
20265 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
20286 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:23879 original size:28 final size:26
Alignment explanation
Indices: 23842--23908 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 26
23832 AGAGAATCAG
*
23842 AAAAAAAGAAATTGAAGCACTCCAAAA
1 AAAAAAAGAAATTCAAGCACT-CAAAA
* *
23869 AAAATAAAGAAATTCCAGCACTTAAAA
1 AAAA-AAAGAAATTCAAGCACTCAAAA
23896 AAAAGCAAAGAAA
1 AAAA--AAAGAAA
23909 AGAAAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.64, C:0.13, G:0.10, T:0.12
Consensus pattern (26 bp):
AAAAAAAGAAATTCAAGCACTCAAAA
Found at i:30678 original size:11 final size:13
Alignment explanation
Indices: 30646--30675 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30636 TGGCCAAAGA
30646 TGAAAAGGTATGT
1 TGAAAAGGTATGT
30659 TGAAAAGGTATG-
1 TGAAAAGGTATGT
30671 TGAAA
1 TGAAA
30676 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:37832 original size:13 final size:13
Alignment explanation
Indices: 37816--37855 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
37806 CTTTTGTTTC
37816 TTTCTTTTTTGTT
1 TTTCTTTTTTGTT
* *
37829 TTTCTTCTTTCTT
1 TTTCTTTTTTGTT
37842 TTTCTCTTTTTGTT
1 TTTCT-TTTTTGTT
37856 GCTTTTGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (13 bp):
TTTCTTTTTTGTT
Found at i:38094 original size:16 final size:16
Alignment explanation
Indices: 38056--38086 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38046 AGAATATGAA
38056 ATAAG-AAAGGAAATG
1 ATAAGAAAAGGAAATG
38071 ATAAGAAAAGGAAATG
1 ATAAGAAAAGGAAATG
38087 GATAGAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (16 bp):
ATAAGAAAAGGAAATG
Found at i:38300 original size:13 final size:13
Alignment explanation
Indices: 38282--38306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38272 ATAGGCGTGA
38282 AAAATGGTGATGG
1 AAAATGGTGATGG
38295 AAAATGGTGATG
1 AAAATGGTGATG
38307 AACATATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (13 bp):
AAAATGGTGATGG
Found at i:39198 original size:18 final size:20
Alignment explanation
Indices: 39167--39206 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
39157 GGATAATAAT
39167 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
*
39187 ATAAG-AAT-AAAATGAATA
1 ATAAGTAATGAAAATAAATA
39205 AT
1 AT
39207 GAAAGGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 3 0.16
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:39658 original size:19 final size:20
Alignment explanation
Indices: 39617--39659 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39607 GAAACCCCTT
* *
39617 TGAAAATACATGATTTTTGA
1 TGAAAATACATGAATTTTAA
39637 TGAAAATACAT-AATTTTAA
1 TGAAAATACATGAATTTTAA
39656 TGAA
1 TGAA
39660 GATATATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGAATTTTAA
Found at i:43001 original size:19 final size:21
Alignment explanation
Indices: 42977--43015 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
42967 CTTGCTTCCT
42977 TTTGAA-TTTCTT-TTCTTTC
1 TTTGAATTTTCTTCTTCTTTC
42996 TTTGAATTTTCTTCTTCTTT
1 TTTGAATTTTCTTCTTCTTT
43016 TTGTCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.10, C:0.15, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTGAATTTTCTTCTTCTTTC
Found at i:43018 original size:19 final size:18
Alignment explanation
Indices: 42971--43018 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
42961 CCTTGGCTTG
*
42971 CTTCCTTTTGAATTTCTT
1 CTTCTTTTTGAATTTCTT
42989 -TTCTTTCTTTGAATTTTCTT
1 CTTC-TT-TTTGAA-TTTCTT
43009 CTTCTTTTTG
1 CTTCTTTTTG
43019 TCTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 10 0.40
20 8 0.32
21 3 0.12
ACGTcount: A:0.08, C:0.19, G:0.06, T:0.67
Consensus pattern (18 bp):
CTTCTTTTTGAATTTCTT
Found at i:43318 original size:19 final size:20
Alignment explanation
Indices: 43281--43320 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
43271 GGATAATAAT
43281 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
43301 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
43320 A
1 A
43321 ATAAATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:43779 original size:19 final size:18
Alignment explanation
Indices: 43735--43780 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
43725 ACCCCTTAGA
* *
43735 AAATGCATGATTTTGATG
1 AAATACATGATTTTAATG
43753 AAATACATGATTTTAATG
1 AAATACATGATTTTAATG
43771 AAGATACATG
1 AA-ATACATG
43781 CTCTTGGCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (18 bp):
AAATACATGATTTTAATG
Found at i:45743 original size:758 final size:756
Alignment explanation
Indices: 44211--46441 Score: 3259
Period size: 758 Copynumber: 2.9 Consensus size: 756
44201 ATAGGTGAAT
* ** * * * * *
44211 TACATGAAGATGAGTCTTTGGCCAGCTCCTTGTGAAAAGGCACCTCTTGGAATGGCAACTCTTCG
1 TACATGATGATGAGTCTTAAGACAGCTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
* * * * * **
44276 CGAAAAGGTACGAATCCACAAAAATTGACTTAGACCATATTTGAAGTACTCTATGTGGTGGTGAT
66 CGAAAAGGTACGAATTCAC-AAAATTGACCTAGACCATATTTGTAGTGCTCTGTGTGGTGAAGAT
* * * *
44341 GATGGTGCAACTCTCCAGCTGAAATGAGGTCTCTAGCTAGCTTAAAGGTCCAGCTCAAGTGAGCT
130 GATGGTGCAACTCTCCAGCTGAAAAGAGGTCTCTA-CTAGCTCAAAAGTCCAACTCAAGTGAGCT
* * * * ** * * * * **
44406 ATGAGCTCGGGGGTCAGCTGATAAGTTT-TCACAATTTGTTCTTCATGATCTCCC-GAGTCATCC
194 ATGAGCTCGGAGGTCAGCTGACAACTTTGTCTCAAAATGTCCTTGA-GCTATCCCGGAGTTGTCC
* * * * * * * *
44469 TA-TGTAAGTTTTCC-TAGCTC-CTTA-TCC-TTAGTTAAGC-TCAAATGTAGATCCCA--AGTG
258 TACT-CAAG-TTTCCTTAGCTCAATGATTCCAAT-GCT-AGCTTTAAAT-CAGCTCCCATCA-T-
* * * * * *
44526 TTGGCCGAATAT--TCCTAT--ATGCATAA-CATAAAGAAATAAACTAAGTATAT-AAACAATAT
316 TTGGCCGAACATGCACCTATAAAAG-A-AAGCAT--A-ATATAAACTAAGTATATGAAATATTAT
* *
44585 AATGCATATAATATAATGATGTGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCA
376 AAAGCA-AT-A-A-GA--ATGTGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCA
*
44650 TGCATCATATGATTATGAATGAATATTAATATTATAACTATAGATTATATACATGAATATCAATC
435 TGCATCATATGA-TATGAATGAATATTAATATTATAACTATAGATTATATGCATGAATATCAATC
* * *
44715 AATGATACAAACCATAGGATATAATGAATGAATACACATACTATGATAAATCAACTATAGTCTAA
499 AATGATACAAACCATAGGATATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAA
* *
44780 TATGCAAATGTATGCTCATAATAATATATATAGTGCATGAATAAGTAAATATAATATAAAGTATG
564 TATGCAAATGTATGCTCATAATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATA
*
44845 GTAGAACTCCTTTATATTGAGTTTGATGGTTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTG
629 GTAGAACTCCCTTATATTGAGTTTGATGGTTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTG
* * *
44910 GTGCTAAACAGGATCACATAATCCCATGTGTTTGAGATGAAGATGAGCTGGCCATAGATGCAA
694 GTGCTAAACAGGATCACATCATCCCATGTGTTTGAGATGAAGATGAGCTGGACATAGAAGCAA
* *
44973 TACATAATGATGAGTCTTAAGACAGTTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
1 TACATGATGATGAGTCTTAAGACAGCTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
45038 CGAAAAGGTACGAATTCACAAAATTCGACCTAGACCATATTTGTAGTGCTCTGTGTGGTGAAGAT
66 CGAAAAGGTACGAATTCACAAAATT-GACCTAGACCATATTTGTAGTGCTCTGTGTGGTGAAGAT
*
45103 GATGGTACAACTCTCCAGCTGAAAAGAGGTCTCTAACTAGCTCAAAAGTCCAACTCAAGTGAGCT
130 GATGGTGCAACTCTCCAGCTGAAAAGAGGTCTCT-ACTAGCTCAAAAGTCCAACTCAAGTGAGCT
* *
45168 ATGAGCTCGGAGATCAGCTGACAACTTTGTCTCAAAATGTCCTTGAGCTGTCCCGGAGTTGTCCT
194 ATGAGCTCGGAGGTCAGCTGACAACTTTGTCTCAAAATGTCCTTGAGCTATCCCGGAGTTGTCCT
45233 ACTCAAGTTTCCTTAGCTCAATGATTCCAATGCTAGCTTTAAATCAGCTCCCATCATTTGGCCGA
259 ACTCAAGTTTCCTTAGCTCAATGATTCCAATGCTAGCTTTAAATCAGCTCCCATCATTTGGCCGA
45298 ACATGCACCTATAAAAGAAAGCATAATATAAACTAAGTATATGAAATATTATAAAGCAATAAGAA
324 ACATGCACCTATAAAAGAAAGCATAATATAAACTAAGTATATGAAATATTATAAAGCAATAAGAA
*
45363 TGTGCGTATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATGCATCATATGATAATGAA
389 TGTGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATGCATCATATGAT-ATGAA
45428 TGAATATTAATATTATAACTATAGATTATATGCATGAATATCAATCAATGATACAAACCATAGGA
453 TGAATATTAATATTATAACTATAGATTATATGCATGAATATCAATCAATGATACAAACCATAGGA
45493 TATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAATATGCAAATGT-TGCTCAT
518 TATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAATATGCAAATGTATGCTCAT
45557 AATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATAGTAGAACTCCCTTATATTG
583 AATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATAGTAGAACTCCCTTATATTG
*
45622 AGTTTGATGGTTCTTCAATGACGTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACAT
648 AGTTTGATGGTTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACAT
45687 CATCCCATGTGTTTGAGATGAAGATGAGCTGGACATAGAAGCAA
713 CATCCCATGTGTTTGAGATGAAGATGAGCTGGACATAGAAGCAA
45731 TACATGATGATGAGTCTTAAGACAGCTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
1 TACATGATGATGAGTCTTAAGACAGCTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
*
45796 CGAAAAGGTACGAATTCACAAAATTTGACCTAGAACATATTTGTAGTGCTCTGTGTGGTGAAGAT
66 CGAAAAGGTACGAATTCACAAAA-TTGACCTAGACCATATTTGTAGTGCTCTGTGTGGTGAAGAT
45861 GATGGTGCAACTCTCCAGCTGAAAAGAGG--TCT-CTAGCTCAAAAGTCCAACTCAAGTGAGCTA
130 GATGGTGCAACTCTCCAGCTGAAAAGAGGTCTCTACTAGCTCAAAAGTCCAACTCAAGTGAGCTA
*
45923 TGAGCTCGTAGGTCAGCTGACAACTTTGTCTCAAAATGTCCTTGAGCTATCCCGGAGTTGTCCTA
195 TGAGCTCGGAGGTCAGCTGACAACTTTGTCTCAAAATGTCCTTGAGCTATCCCGGAGTTGTCCTA
45988 CTCAAGTTTCCTTAGCTCAATGATTCCAATGCTAGCTTTAAATCAGCTCCCATCATTTGGCCGAA
260 CTCAAGTTTCCTTAGCTCAATGATTCCAATGCTAGCTTTAAATCAGCTCCCATCATTTGGCCGAA
* * *
46053 CATGCACCTACAAAAGAAAGCATAATAAAAACTAAGTATATGAATTATTATAAAGCAATAAGAAT
325 CATGCACCTATAAAAGAAAGCATAATATAAACTAAGTATATGAAATATTATAAAGCAATAAGAAT
* *
46118 GTGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATACATCATATGATATGAATT
390 GTGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATGCATCATATGATATGAATG
* * * * * *
46183 AATATTATTATTACAAATATAGATTATATGCATGAATATCAATCAATGATGCAAACCATTGGACA
455 AATATTAATATTATAACTATAGATTATATGCATGAATATCAATCAATGATACAAACCATAGGATA
** * *
46248 TAATGAATGAATGCACATGTTATGATAATTCAAGCATAGTCTAATATGAAAATGTATGCTCATAA
520 TAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATAA
* * *
46313 T-A-ATATATAGTGCATAAATGAGTAAATATAATATAAAGTA-AGGTAGAAATCCCTTATACTGA
585 TAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATA-GTAGAACTCCCTTATATTGA
* * *
46375 GATTGATGGATT-TTCAATGATGTGAGTATGTCATGCAGAAAGTTGGTGCTAGACATGATCACAT
649 GTTTGATGG-TTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACAT
46439 CAT
713 CAT
46442 GTTCCACCTT
Statistics
Matches: 1353, Mismatches: 93, Indels: 56
0.90 0.06 0.04
Matches are distributed among these distances:
751 1 0.00
752 115 0.08
753 119 0.09
754 285 0.21
756 3 0.00
758 327 0.24
759 183 0.14
761 7 0.01
762 200 0.15
763 32 0.02
764 42 0.03
765 24 0.02
766 9 0.01
767 4 0.00
768 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (756 bp):
TACATGATGATGAGTCTTAAGACAGCTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
CGAAAAGGTACGAATTCACAAAATTGACCTAGACCATATTTGTAGTGCTCTGTGTGGTGAAGATG
ATGGTGCAACTCTCCAGCTGAAAAGAGGTCTCTACTAGCTCAAAAGTCCAACTCAAGTGAGCTAT
GAGCTCGGAGGTCAGCTGACAACTTTGTCTCAAAATGTCCTTGAGCTATCCCGGAGTTGTCCTAC
TCAAGTTTCCTTAGCTCAATGATTCCAATGCTAGCTTTAAATCAGCTCCCATCATTTGGCCGAAC
ATGCACCTATAAAAGAAAGCATAATATAAACTAAGTATATGAAATATTATAAAGCAATAAGAATG
TGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATGCATCATATGATATGAATGA
ATATTAATATTATAACTATAGATTATATGCATGAATATCAATCAATGATACAAACCATAGGATAT
AATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATAAT
AATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATAGTAGAACTCCCTTATATTGAGT
TTGATGGTTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACATCAT
CCCATGTGTTTGAGATGAAGATGAGCTGGACATAGAAGCAA
Found at i:47309 original size:10 final size:10
Alignment explanation
Indices: 47294--47318 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
47284 TTCTTTTTAA
47294 TTTTTCTTTT
1 TTTTTCTTTT
47304 TTTTTCTTTT
1 TTTTTCTTTT
47314 TTTTT
1 TTTTT
47319 TCAGATTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:49570 original size:10 final size:10
Alignment explanation
Indices: 49555--49581 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49545 CTCAACTCCT
49555 CAGCTACTTC
1 CAGCTACTTC
49565 CAGCTACTTC
1 CAGCTACTTC
49575 CAGCTAC
1 CAGCTAC
49582 CTCTAGTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.41, G:0.11, T:0.26
Consensus pattern (10 bp):
CAGCTACTTC
Found at i:49594 original size:21 final size:20
Alignment explanation
Indices: 49555--49594 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49545 CTCAACTCCT
*
49555 CAGCTACTTCCAGCTACTTC
1 CAGCTACCTCCAGCTACTTC
*
49575 CAGCTACCTCTAGTCTACTT
1 CAGCTACCTCCAG-CTACTT
49595 TTCAGTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.20, C:0.38, G:0.10, T:0.33
Consensus pattern (20 bp):
CAGCTACCTCCAGCTACTTC
Found at i:65872 original size:19 final size:20
Alignment explanation
Indices: 65848--65887 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
65838 TATCATTTCT
65848 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
65867 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
65887 T
1 T
65888 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:65890 original size:19 final size:18
Alignment explanation
Indices: 65844--65890 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
65834 TCTCTATCAT
65844 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
65861 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
65880 TTACTTATATT
1 TT-CTTATATT
65891 ATTATTCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:66141 original size:19 final size:19
Alignment explanation
Indices: 66109--66164 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
66099 GTGCAAAGCA
66109 AAAAGAA-AAGAAAAAAGAC
1 AAAAGAAGAA-AAAAAAGAC
** *
66128 AAAAGAAGAAAAAAATCAG
1 AAAAGAAGAAAAAAAAGAC
*
66147 AAAAGAAGAAATAAAAGA
1 AAAAGAAGAAAAAAAAGA
66165 AATTCAAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 28 0.93
20 2 0.07
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAAGAAGAAAAAAAAGAC
Done.