Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008332.1 Hibiscus syriacus cultivar Beakdansim tig00111045_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: 268411
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:910 original size:11 final size:13
Alignment explanation
Indices: 878--907 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
868 TGGCCAAAGA
878 TGAAAAGGTATGT
1 TGAAAAGGTATGT
891 TGAAAAGGTATG-
1 TGAAAAGGTATGT
903 TGAAA
1 TGAAA
908 GGTGTAGTAT
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:8040 original size:13 final size:13
Alignment explanation
Indices: 8024--8063 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
8014 CTTTTGTTTC
8024 TTTCTTTTTTGTT
1 TTTCTTTTTTGTT
* *
8037 TTTCTTCTTTCTT
1 TTTCTTTTTTGTT
8050 TTTCTCTTTTTGTT
1 TTTCT-TTTTTGTT
8064 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:8302 original size:16 final size:16
Alignment explanation
Indices: 8264--8294 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8254 AGAATATGAA
8264 ATAAG-AAAGGAAATG
1 ATAAGAAAAGGAAATG
8279 ATAAGAAAAGGAAATG
1 ATAAGAAAAGGAAATG
8295 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:8508 original size:13 final size:13
Alignment explanation
Indices: 8490--8514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8480 ATAGGCGTGA
8490 AAAATGGTGATGG
1 AAAATGGTGATGG
8503 AAAATGGTGATG
1 AAAATGGTGATG
8515 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:9414 original size:19 final size:20
Alignment explanation
Indices: 9377--9417 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
9367 GGATAATAAT
9377 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
9397 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
9416 AT
1 AT
9418 GAAAGGATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 10 0.50
20 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:9870 original size:19 final size:20
Alignment explanation
Indices: 9829--9871 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
9819 GAAACCCCTT
* *
9829 TGAAAATACATGATTTTTGA
1 TGAAAATACATGAATTTTAA
9849 TGAAAATACAT-AATTTTAA
1 TGAAAATACATGAATTTTAA
9868 TGAA
1 TGAA
9872 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:13539 original size:19 final size:20
Alignment explanation
Indices: 13502--13541 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
13492 GGATAATAAT
13502 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
13522 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
13541 A
1 A
13542 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:13995 original size:19 final size:20
Alignment explanation
Indices: 13955--14004 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
13945 AAACCCCTTA
* *
13955 GAAAATGCATGATTTTTGAT
1 GAAAATACATGATTTTTAAT
13975 GAAAATACATGA-TTTTAAT
1 GAAAATACATGATTTTTAAT
*
13994 GAAGATACATG
1 GAAAATACATG
14005 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (20 bp):
GAAAATACATGATTTTTAAT
Found at i:14834 original size:17 final size:17
Alignment explanation
Indices: 14812--14847 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
14802 AACAATATAA
*
14812 TGCATATAATAATGATG
1 TGCATATAATAAAGATG
*
14829 TGCATATTATAAAGATG
1 TGCATATAATAAAGATG
14846 TG
1 TG
14848 AACTATAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (17 bp):
TGCATATAATAAAGATG
Found at i:16011 original size:759 final size:757
Alignment explanation
Indices: 14436--16659 Score: 3248
Period size: 755 Copynumber: 2.9 Consensus size: 757
14426 ATAGGTGAAT
* ** * * * * *
14436 TACATGAAGATGAGTCTTTGGCCAGCTCCTTGTGAAAAGGCACCTCTTGGAATGGCAACTCTTCG
1 TACATGATGATGAGTCTTAAGACAGCTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
* * * * * **
14501 CGAAAAGGTACGAATCCACAAAAATTGACTTAGACCATATTTGAAGTACTCTATGTGGTGGTGAT
66 CGAAAAGGTACGAATTCAC-AAAATTGACCTAGACCATATTTGTAGTGCTCTGTGTGGTGAAGAT
* * * *
14566 GATGGTGCAACTCTCCAGCTGAAATGAGGTCTCTAGCTAGCTTAAAGGTCCAGCTCAAGTGAGCT
130 GATGGTGCAACTCTCCAGCTGAAAAGAGGTCTCTA-CTAGCTCAAAAGTCCAACTCAAGTGAGCT
* * * * ** * * * * **
14631 ATGAGCTCGGGGGTCAGCTGATAAGTTT-TCACAATTTGTTCTTCATGATCTCCC-GAGTCATCC
194 ATGAGCTCGGAGGTCAGCTGACAACTTTGTCTCAAAATGTCCTTGA-GCTATCCCGGAGTTGTCC
* * * * * * * *
14694 TA-TGTAAGTTTTCC-TAGCTC-CTTA-TCC-TTAGTTAAGC-TCAAATGTAGATCCCA--AGTG
258 TACT-CAAG-TTTCCTTAGCTCAATGATTCCAAT-GCT-AGCTTTAAAT-CAGCTCCCATCA-T-
* * * * * *
14751 TTGGCCGAATAT--TCCTAT--ATGCATAA-CATAAAGAAATAAACTAAGTATAT-AAACAATAT
316 TTGGCCGAACATGCACCTATAAAAG-A-AAGCAT--A-ATATAAACTAAGTATATGAAATATTAT
* *
14810 AATGCATATAATAATGATGTGCATATTATAAAGATGTGAACTATAGG-T-T-ATAATAACTCATG
376 AAAGCA-ATAA-GA--ATGTGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATG
* *
14872 CATCATATGATTATGAATGAATATTAATATTATAACTATAGATTATATACATGAATATCAATCAA
437 CATCATATGATAATGAATGAATATTAATATTATAACTATAGATTATATGCATGAATATCAATCAA
* * *
14937 TGATACAAACCATAGGATATAATGAATGAATACACATACTATGATAAATCAACTATAGTCTAATA
502 TGATACAAACCATAGGATATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAATA
* *
15002 TGCAAATGTATGCTC---ATAATATATATAGTGCATGAATAAGTAAATATAATATAAAGTATGGT
567 TGCAAATGTATGCTCATAATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATAGT
15064 AGAACT-CCTTATATTGAGTTTGATGGTTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTGGT
632 AGAACTCCCTTATATTGAGTTTGATGGTTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTGGT
* * *
15128 GCTAAACAGGATCACATAATCCCATGTGTTTGAGATGAAGATGAGCTGGCCATAGATGCAA
697 GCTAAACAGGATCACATCATCCCATGTGTTTGAGATGAAGATGAGCTGGACATAGAAGCAA
* *
15189 TACATAATGATGAGTCTTAAGACAGTTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
1 TACATGATGATGAGTCTTAAGACAGCTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
15254 CGAAAAGGTACGAATTCACAAAATTCGACCTAGACCATATTTGTAGTGCTCTGTGTGGTGAAGAT
66 CGAAAAGGTACGAATTCACAAAATT-GACCTAGACCATATTTGTAGTGCTCTGTGTGGTGAAGAT
*
15319 GATGGTACAACTCTCCAGCTGAAAAGAGGTCTCTAACTAGCTCAAAAGTCCAACTCAAGTGAGCT
130 GATGGTGCAACTCTCCAGCTGAAAAGAGGTCTCT-ACTAGCTCAAAAGTCCAACTCAAGTGAGCT
* *
15384 ATGAGCTCGGAGATCAGCTGACAACTTTGTCTCAAAATGTCCTTGAGCTGTCCCGGAGTTGTCCT
194 ATGAGCTCGGAGGTCAGCTGACAACTTTGTCTCAAAATGTCCTTGAGCTATCCCGGAGTTGTCCT
15449 ACTCAAGTTTCCTTAGCTCAATGATTCCAATGCTAGCTTTAAATCAGCTCCCATCATTTGGCCGA
259 ACTCAAGTTTCCTTAGCTCAATGATTCCAATGCTAGCTTTAAATCAGCTCCCATCATTTGGCCGA
15514 ACATGCACCTATAAAAGAAAGCATAATATAAACTAAGTATATGAAATATTATAAAGCAATAAGAA
324 ACATGCACCTATAAAAGAAAGCATAATATAAACTAAGTATATGAAATATTATAAAGCAATAAGAA
*
15579 TGTGCGTATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATGCATCATATGATAATGAA
389 TGTGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATGCATCATATGATAATGAA
15644 TGAATATTAATATTATAACTATAGATTATATGCATGAATATCAATCAATGATACAAACCATAGGA
454 TGAATATTAATATTATAACTATAGATTATATGCATGAATATCAATCAATGATACAAACCATAGGA
15709 TATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAATATGCAAATGTATGCTCAT
519 TATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAATATGCAAATGTATGCTCAT
15774 AATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATAGTAGAACTCCCTTATATTG
584 AATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATAGTAGAACTCCCTTATATTG
*
15839 AGTTTGATGGTTCTTCAATGACGTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACAT
649 AGTTTGATGGTTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACAT
15904 CATCCCATGTGTTTGAGATGAAGATGAGCTGGACATAGAAGCAA
714 CATCCCATGTGTTTGAGATGAAGATGAGCTGGACATAGAAGCAA
15948 TACATGATGATGAGTCTTAAGACAGCTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
1 TACATGATGATGAGTCTTAAGACAGCTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
*
16013 CGAAAAGGTACGAATTCACAAAATTTGACCTAGAACATATTTGTAGTGCTCTGTGTGGTGAAGAT
66 CGAAAAGGTACGAATTCACAAAA-TTGACCTAGACCATATTTGTAGTGCTCTGTGTGGTGAAGAT
16078 GATGGTGCAACTCTCCAGCTGAAAAGAGG--TCT-CTAGCTCAAAAGTCCAACTCAAGTGAGCTA
130 GATGGTGCAACTCTCCAGCTGAAAAGAGGTCTCTACTAGCTCAAAAGTCCAACTCAAGTGAGCTA
*
16140 TGAGCTCGTAGGTCAGCTGACAACTTTGTCTCAAAATGTCCTTGAGCTATCCCGGAGTTGTCCTA
195 TGAGCTCGGAGGTCAGCTGACAACTTTGTCTCAAAATGTCCTTGAGCTATCCCGGAGTTGTCCTA
16205 CTCAAGTTTCCTTAGCTCAATGATTCCAATGCTAGCTTTAAATCAGCTCCCATCATTTGGCCGAA
260 CTCAAGTTTCCTTAGCTCAATGATTCCAATGCTAGCTTTAAATCAGCTCCCATCATTTGGCCGAA
* * *
16270 CATGCACCTACAAAAGAAAGCATAATAAAAACTAAGTATATGAATTATTATAAAGCAATAAGAAT
325 CATGCACCTATAAAAGAAAGCATAATATAAACTAAGTATATGAAATATTATAAAGCAATAAGAAT
*
16335 GTGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATACATCATATGATAATGAAT
390 GTGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATGCATCATATGATAATGAAT
* * * * * *
16400 TAATATTATTATTACAACTATAGATTATATGCATGAATATCAATCAATGATGCAAACCATTGGAC
455 GAATATTAATATTATAACTATAGATTATATGCATGAATATCAATCAATGATACAAACCATAGGAT
** * *
16465 ATAATGAATGAATGCACATGTTATGATAATTCAAGCATAGTCTAATATGAAAATGTATGCTCATA
520 ATAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATA
* * *
16530 AT-A-ATATATAGTGCATAAATGAGTAAATATAATATAAAGTA-AGGTAGAAATCCCTTATACTG
585 ATAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATA-GTAGAACTCCCTTATATTG
* * *
16592 AGATTGATGGATT-TTCAATGATGTGAGTATGTCATGCAGAAAGTTGGTGCTAGACATGATCACA
649 AGTTTGATGG-TTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACA
16656 TCAT
713 TCAT
16660 GTTCCACCTT
Statistics
Matches: 1351, Mismatches: 92, Indels: 56
0.90 0.06 0.04
Matches are distributed among these distances:
752 37 0.03
753 315 0.23
754 36 0.03
755 601 0.44
756 24 0.02
757 12 0.01
758 55 0.04
759 269 0.20
760 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (757 bp):
TACATGATGATGAGTCTTAAGACAGCTCCTTGTGAAAGGGCACTTCTCGGATTGGCAACTCTTCG
CGAAAAGGTACGAATTCACAAAATTGACCTAGACCATATTTGTAGTGCTCTGTGTGGTGAAGATG
ATGGTGCAACTCTCCAGCTGAAAAGAGGTCTCTACTAGCTCAAAAGTCCAACTCAAGTGAGCTAT
GAGCTCGGAGGTCAGCTGACAACTTTGTCTCAAAATGTCCTTGAGCTATCCCGGAGTTGTCCTAC
TCAAGTTTCCTTAGCTCAATGATTCCAATGCTAGCTTTAAATCAGCTCCCATCATTTGGCCGAAC
ATGCACCTATAAAAGAAAGCATAATATAAACTAAGTATATGAAATATTATAAAGCAATAAGAATG
TGCATATTATAAAGATGTGAACTATAGGTTATAATAATAACTCATGCATCATATGATAATGAATG
AATATTAATATTATAACTATAGATTATATGCATGAATATCAATCAATGATACAAACCATAGGATA
TAATGAATGAATGCACATACTATGATAATTCAAGTATAGTCTAATATGCAAATGTATGCTCATAA
TAATATATATAGTGCATAAATAAGTAAATATAATATAAAGTATAGTAGAACTCCCTTATATTGAG
TTTGATGGTTCTTCAATGATGTGAGTATGTCATGCAGAAAGTTGGTGCTAAACAGGATCACATCA
TCCCATGTGTTTGAGATGAAGATGAGCTGGACATAGAAGCAA
Found at i:19808 original size:10 final size:10
Alignment explanation
Indices: 19793--19819 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
19783 CTCAACTCCT
19793 CAGCTACTTC
1 CAGCTACTTC
19803 CAGCTACTTC
1 CAGCTACTTC
19813 CAGCTAC
1 CAGCTAC
19820 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:19832 original size:21 final size:20
Alignment explanation
Indices: 19793--19832 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19783 CTCAACTCCT
*
19793 CAGCTACTTCCAGCTACTTC
1 CAGCTACCTCCAGCTACTTC
*
19813 CAGCTACCTCTAGTCTACTT
1 CAGCTACCTCCAG-CTACTT
19833 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:25088 original size:5 final size:5
Alignment explanation
Indices: 25078--25103 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
25068 CTTCAACTTC
25078 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
25104 CTTTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:36519 original size:20 final size:20
Alignment explanation
Indices: 36480--36543 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 20
36470 ATTGGCGTGC
36480 AAAG-CAAAAAGAA-AAGAAA
1 AAAGACAAAAAGAAGAA-AAA
36499 AAAGACAAAAAGAAG-AAAA
1 AAAGACAAAAAGAAGAAAAA
*
36518 AAA-TCAGAAAAGAAGAAAATA
1 AAAGACA-AAAAGAAGAAAA-A
36539 AAAGA
1 AAAGA
36544 AATTCAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 2 0.05
19 18 0.49
20 13 0.35
21 4 0.11
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.03
Consensus pattern (20 bp):
AAAGACAAAAAGAAGAAAAA
Found at i:36520 original size:19 final size:18
Alignment explanation
Indices: 36480--36536 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 18
36470 ATTGGCGTGC
*
36480 AAAGCAAAAAGAAAAGAAA
1 AAAGCAAAAAGAAGA-AAA
36499 AAAGACAAAAAGAAGAAAA
1 AAAG-CAAAAAGAAGAAAA
*
36518 AAATCAGAAAAGAAGAAAA
1 AAAGCA-AAAAGAAGAAAA
36537 TAAAAGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.06
19 22 0.65
20 10 0.29
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAGCAAAAAGAAGAAAA
Found at i:52281 original size:74 final size:73
Alignment explanation
Indices: 52162--52319 Score: 187
Period size: 74 Copynumber: 2.1 Consensus size: 73
52152 TGAATAAATC
** *
52162 TTCATGAATGTATCTTTATGGCTGAATTCTTCCTCCCATGTGTGAACATGTTTGATTTGTCTTCT
1 TTCATGAATGTATC-TTATGGCTGAATTCTTCCTCCCATGTGTGAACATGACT-ATTTGGCTTCT
* *
52227 ATGGATGAATG
64 -TGCATGAATA
*
52238 TTCATGAATGTATC-T-TGGCTGAAATTCTT-CTCCCCTTGTGTGAACATGACTATTTGGCTTCT
1 TTCATGAATGTATCTTATGGCTG-AATTCTTCCT-CCCATGTGTGAACATGACTATTTGGCTTCT
52300 TGCATGAATA
64 TGCATGAATA
*
52310 TGCATGAATG
1 TTCATGAATG
52320 GATGAACTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
72 17 0.23
73 18 0.25
74 24 0.33
76 14 0.19
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (73 bp):
TTCATGAATGTATCTTATGGCTGAATTCTTCCTCCCATGTGTGAACATGACTATTTGGCTTCTTG
CATGAATA
Found at i:54861 original size:19 final size:20
Alignment explanation
Indices: 54837--54876 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
54827 TATCATTTCT
54837 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
54856 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
54876 T
1 T
54877 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:54879 original size:19 final size:18
Alignment explanation
Indices: 54833--54879 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
54823 TCTCTATCAT
54833 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
54850 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
54869 TTACTTATATT
1 TT-CTTATATT
54880 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:55898 original size:14 final size:15
Alignment explanation
Indices: 55868--55905 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
55858 AATCACTCAA
55868 AAAGAAGAAAAATAAG
1 AAAGAA-AAAAATAAG
55884 AAAGAAAAAAA-AAG
1 AAAGAAAAAAATAAG
55898 AAAGAAAA
1 AAAGAAAA
55906 GTTGAAGCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 11 0.50
15 5 0.23
16 6 0.27
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (15 bp):
AAAGAAAAAAATAAG
Found at i:60840 original size:12 final size:12
Alignment explanation
Indices: 60823--60863 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
60813 AAATTTTGGC
60823 TTTTTTGGCTCT
1 TTTTTTGGCTCT
*
60835 TTTTTTGCCT-T
1 TTTTTTGGCTCT
*
60846 TTTTTTTGC-CT
1 TTTTTTGGCTCT
60857 TTTTTTG
1 TTTTTTG
60864 TTTTTTGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.00, C:0.15, G:0.12, T:0.73
Consensus pattern (12 bp):
TTTTTTGGCTCT
Found at i:60846 original size:10 final size:10
Alignment explanation
Indices: 60816--60863 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
60806 TTTTTTGAAA
*
60816 TTTTGGCTTT
1 TTTTGCCTTT
*
60826 TTTGGCTCTTT
1 TTTTGC-CTTT
60837 TTTTGCCTTTTT
1 TTTTGCC--TTT
60849 TTTTGCCTTT
1 TTTTGCCTTT
60859 TTTTG
1 TTTTG
60864 TTTTTTGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 13 0.41
11 9 0.28
12 10 0.31
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.71
Consensus pattern (10 bp):
TTTTGCCTTT
Found at i:60850 original size:11 final size:11
Alignment explanation
Indices: 60823--60862 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
60813 AAATTTTGGC
*
60823 TTTTTTGGCTCT
1 TTTTTTGCCT-T
60835 TTTTTTGCCTTT
1 TTTTTTGCC-TT
60847 TTTTTTGCCTT
1 TTTTTTGCCTT
60858 TTTTT
1 TTTTT
60863 GTTTTTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.27
12 18 0.69
13 1 0.04
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.75
Consensus pattern (11 bp):
TTTTTTGCCTT
Found at i:61682 original size:43 final size:47
Alignment explanation
Indices: 61629--61730 Score: 115
Period size: 50 Copynumber: 2.2 Consensus size: 47
61619 AAATAAAAAG
*
61629 AAATATTAATAAACT-AAACA-TGTTTTAA-C-CC-TAATTCCTAATA
1 AAATAATAAT-AACTAAAACATTGTTTTAACCACCTTAATTCCTAATA
*
61672 AAATAATAATAACTAAAAATATTGTTTTAACCCAACCTTAATTCCTAATA
1 AAATAATAATAACT-AAAACATTGTTTTAA-CC-ACCTTAATTCCTAATA
61722 AAATAATAA
1 AAATAATAA
61731 ATCTGATCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
42 4 0.08
43 9 0.18
44 4 0.08
45 8 0.16
47 1 0.02
49 2 0.04
50 21 0.43
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (47 bp):
AAATAATAATAACTAAAACATTGTTTTAACCACCTTAATTCCTAATA
Found at i:64841 original size:13 final size:13
Alignment explanation
Indices: 64811--64835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64801 TGATAGTTAT
64811 ATTTAAATTATGC
1 ATTTAAATTATGC
64824 ATTTAAATTATG
1 ATTTAAATTATG
64836 TTTTTAGGGA
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:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
ATTTAAATTATGC
Found at i:68276 original size:24 final size:21
Alignment explanation
Indices: 68242--68284 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
68232 TCCACAAGAC
*
68242 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
68264 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
68285 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:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:70933 original size:19 final size:20
Alignment explanation
Indices: 70909--70954 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
70899 CAGCCAAGAG
*
70909 CATGTATCTTCAT-TAAAAT
1 CATGTATCTTCATAAAAAAT
*
70928 CATGTATTTTCATAAAAAAT
1 CATGTATCTTCATAAAAAAT
70948 CATGTAT
1 CATGTAT
70955 TTTTAAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (20 bp):
CATGTATCTTCATAAAAAAT
Found at i:70948 original size:20 final size:19
Alignment explanation
Indices: 70909--70957 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
70899 CAGCCAAGAG
* *
70909 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
70928 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCAT-AAAAAT
70948 CATGTATTTT
1 CATGTATTTT
70958 TAAAGGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:70961 original size:18 final size:19
Alignment explanation
Indices: 70923--70961 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
70913 TATCTTCATT
70923 AAAATCATGTATTTTCATAA
1 AAAATCATGTATTTT-ATAA
70943 AAAATCATGTATTTT-TAA
1 AAAATCATGTATTTTATAA
70961 A
1 A
70962 GGGGTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
20 15 0.79
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (19 bp):
AAAATCATGTATTTTATAA
Found at i:71414 original size:23 final size:23
Alignment explanation
Indices: 71371--71417 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
71361 CTATCCTTTC
* *
71371 TTTATTTCATTTCATTCTTATTA
1 TTTATTTCATTACATTATTATTA
71394 TTTATTTTCATTAC-TTATTATTA
1 TTTA-TTTCATTACATTATTATTA
71417 T
1 T
71418 CCCTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTCATTACATTATTATTA
Found at i:73113 original size:24 final size:25
Alignment explanation
Indices: 73078--73132 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
73068 ACTTGAAGCC
*
73078 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
73102 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
73126 TCAAGTG
1 TCAAGTG
73133 GCATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:78729 original size:2 final size:2
Alignment explanation
Indices: 78722--78752 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
78712 TGGTAGCGAA
78722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78753 AGTTGGTGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79068 original size:15 final size:15
Alignment explanation
Indices: 79048--79086 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
79038 TAAATGGAAG
79048 AAGAAATGAAAT-GA
1 AAGAAATGAAATGGA
*
79062 TAAGAAAGGAAATGGA
1 -AAGAAATGAAATGGA
79078 AAGAAATGA
1 AAGAAATGA
79087 TATCAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (15 bp):
AAGAAATGAAATGGA
Found at i:90262 original size:24 final size:20
Alignment explanation
Indices: 90231--90280 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 20
90221 TAGGAAAGGT
90231 TAAGAAAAAGATAAGGAAATGAAA
1 TAAGAAAAAGAT---GAAA-GAAA
90255 TAAG-AAAAGATGAAAGAAA
1 TAAGAAAAAGATGAAAGAAA
90274 TAAGAAA
1 TAAGAAA
90281 TGAAATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 8 0.32
20 6 0.24
23 7 0.28
24 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (20 bp):
TAAGAAAAAGATGAAAGAAA
Found at i:90272 original size:36 final size:33
Alignment explanation
Indices: 90232--90301 Score: 79
Period size: 36 Copynumber: 2.0 Consensus size: 33
90222 AGGAAAGGTT
90232 AAGAAA-AAGATAAGGAAATGAAATAAGAAAAGATGA
1 AAGAAATAAGA-AAGGAAAT--AATAAGAAAA-ATGA
* *
90268 AAGAAATAAGAAATGAAATAGTAAGAAAAATGA
1 AAGAAATAAGAAAGGAAATAATAAGAAAAATGA
90301 A
1 A
90302 GATAACTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 5 0.16
34 9 0.29
36 13 0.42
37 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (33 bp):
AAGAAATAAGAAAGGAAATAATAAGAAAAATGA
Found at i:90531 original size:13 final size:11
Alignment explanation
Indices: 90502--90545 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
90492 TGTAGGAGTC
90502 TTTTCTTTTGTT
1 TTTTCTTTT-TT
90514 TTTTCTTTTTCT
1 TTTTCTTTTT-T
90526 TCTTTC-TTTTT
1 T-TTTCTTTTTT
90537 TTTTCTTTT
1 TTTTCTTTT
90546 GTTGCAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.14
11 6 0.21
12 15 0.52
13 4 0.14
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:93133 original size:12 final size:12
Alignment explanation
Indices: 93114--93156 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
93104 CAAAAGCAAC
93114 AAAA-AAAGAGA
1 AAAAGAAAGAGA
93125 AAAAGAAAGAAGA
1 AAAAGAAAG-AGA
*
93138 AAAAGAAAAAG-
1 AAAAGAAAGAGA
93149 AAAAGAAA
1 AAAAGAAA
93157 AATACTCCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 12 0.41
12 6 0.21
13 11 0.38
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAGA
Found at i:93143 original size:6 final size:6
Alignment explanation
Indices: 93117--93158 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
93107 AAGCAACAAA
93117 AAAAGAG AAAAAG AAAGAAG AAAAAG AAAAAG -AAAAG AAAAA
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAA
93159 TACTCCTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:94555 original size:19 final size:18
Alignment explanation
Indices: 94531--94597 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 18
94521 ATTGGAGTGC
94531 AAAAAGAAAGAAATACACA
1 AAAAAGAAA-AAATACACA
*
94550 AAAAAGAGAAAAAT-CAGA
1 AAAAAGA-AAAAATACACA
94568 AAAGAAGAAAAGAATA-ACA
1 AAA-AAGAAAA-AATACACA
*
94587 TAAAAGAAAAA
1 AAAAAGAAAAA
94598 GAGAAGTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
17 1 0.02
18 16 0.39
19 22 0.54
20 2 0.05
ACGTcount: A:0.75, C:0.06, G:0.13, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAAAATACACA
Found at i:98559 original size:22 final size:22
Alignment explanation
Indices: 98532--98581 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
98522 AAAATCGAGC
98532 AAAGAAAATCAAAGCACTCAAA
1 AAAGAAAATCAAAGCACTCAAA
* * *
98554 TAAGAAATTGAAAGCACTCAAA
1 AAAGAAAATCAAAGCACTCAAA
98576 AAAGAA
1 AAAGAA
98582 GAAAAAGCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.62, C:0.14, G:0.12, T:0.12
Consensus pattern (22 bp):
AAAGAAAATCAAAGCACTCAAA
Found at i:98590 original size:21 final size:21
Alignment explanation
Indices: 98532--98590 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
98522 AAAATCGAGC
*
98532 AAAGAAAATCAAAGCACTCAAA
1 AAAG-AAATAAAAGCACTCAAA
* *
98554 TAAGAAATTGAAAGCACTCAAA
1 AAAGAAA-TAAAAGCACTCAAA
98576 AAAGAAGA-AAAAGCA
1 AAAGAA-ATAAAAGCA
98591 AAGAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 9 0.29
22 21 0.68
23 1 0.03
ACGTcount: A:0.63, C:0.14, G:0.14, T:0.10
Consensus pattern (21 bp):
AAAGAAATAAAAGCACTCAAA
Found at i:104036 original size:2 final size:2
Alignment explanation
Indices: 104029--104059 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
104019 TGATAGCGGA
104029 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
104060 AGTTGGTGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:107432 original size:27 final size:27
Alignment explanation
Indices: 107410--107461 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
107400 TTTTTTTTGA
*
107410 ATTTTTTT-TTCTTTTTTTCTTTTCTG
1 ATTTTTTTCTTCTTTTTGTCTTTTCTG
107436 ATTTTTTTCTTCTTTTTGTCTTTTCT
1 ATTTTTTTCTTCTTTTTGTCTTTTCT
107462 TTGCTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.79
Consensus pattern (27 bp):
ATTTTTTTCTTCTTTTTGTCTTTTCTG
Found at i:111026 original size:21 final size:23
Alignment explanation
Indices: 111002--111044 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
110992 TGAGGCATTG
*
111002 AAGCATATC-AAAGG-ACGCCAC
1 AAGCATAACAAAAGGCACGCCAC
*
111023 AAGCTTAACAAAAGGCACGCCA
1 AAGCATAACAAAAGGCACGCCA
111045 ATTGGGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (23 bp):
AAGCATAACAAAAGGCACGCCAC
Found at i:111504 original size:12 final size:12
Alignment explanation
Indices: 111487--111527 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
111477 TTAATAAGGG
111487 AATAATAAATGA
1 AATAATAAATGA
111499 AATAATAAGAT-A
1 AATAATAA-ATGA
111511 AATAATGAAATGA
1 AATAAT-AAATGA
111524 AATA
1 AATA
111528 GGAGGGATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (12 bp):
AATAATAAATGA
Found at i:112632 original size:15 final size:15
Alignment explanation
Indices: 112597--112625 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
112587 GTGCTTCAAC
112597 TTCTTT-CTTTTTTT
1 TTCTTTGCTTTTTTT
112611 TTCTTTGCTTTTTTT
1 TTCTTTGCTTTTTTT
112626 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (15 bp):
TTCTTTGCTTTTTTT
Found at i:115051 original size:274 final size:273
Alignment explanation
Indices: 114673--115211 Score: 900
Period size: 274 Copynumber: 2.0 Consensus size: 273
114663 ATAAATGAAA
114673 ACATGTAATAATAATATCCTAGAAATGATATGTAATCATAGCATATATTTGAATAATATGAAACA
1 ACATGTAATAATAATATCCTAGAAATGATATGTAATCATAGCATATATTTGAATAATATGAAACA
* * *
114738 CATGATCAAATAAGCATATGATGGAAATAATAATATGATAATTTTTACTAACATGTGAATGCTTG
66 CATGATCAAATAAGCATAAGATGGAAATAATAATATGATAATTTATACTAACATGTGAATGCATG
* * *
114803 CTTATGATAGAATATAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAACTCCCTTAGA
131 CTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGGTAAGGAAGAACTCCCTTAGA
* * * *
114868 AATAACTATGAAGAACATCCATGGTGTGTTCAAGTCATGGAAAAAGTTGGAGCTTGTTTGGATCG
196 AACAACAATGAAGAACATCCATCGTGTGTTCAAGTCATGGAAAAAGTTGGAGCTAGTTTGGATCG
114933 TATCAATCACATC
261 TATCAATCACATC
*
114946 ACATGTAATAATAATATCCTAAGAAATGATATGTAATCATAGCATATATTTGAATGATATGGAAA
1 ACATGTAATAATAATATCCT-AGAAATGATATGTAATCATAGCATATATTTGAATAATAT-GAAA
*
115011 -ACATGATCAAATAAGCATAAGATGGAAATAATAATATGATAATTTATACTAACATGTGAATTCA
64 CACATGATCAAATAAGCATAAGATGGAAATAATAATATGATAATTTATACTAACATGTGAATGCA
* * *
115075 TGGTTATGATAGAATAGAATTTATAAATGATATAATATAAGATAGGGTAAGGAAGCACTCCCTTA
129 TGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGGTAAGGAAGAACTCCCTTA
* *
115140 GAAGCAACAATGAAGAACATCCATCGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTAGTTTGGAT
194 GAAACAACAATGAAGAACATCCATCGTGTGTTCAAGTCATGGAAAAAGTTGGAGCTAGTTTGGAT
115205 CGTATCA
259 CGTATCA
115212 TCCTCCCCTT
Statistics
Matches: 247, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
273 20 0.08
274 223 0.90
275 4 0.02
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (273 bp):
ACATGTAATAATAATATCCTAGAAATGATATGTAATCATAGCATATATTTGAATAATATGAAACA
CATGATCAAATAAGCATAAGATGGAAATAATAATATGATAATTTATACTAACATGTGAATGCATG
CTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGGTAAGGAAGAACTCCCTTAGA
AACAACAATGAAGAACATCCATCGTGTGTTCAAGTCATGGAAAAAGTTGGAGCTAGTTTGGATCG
TATCAATCACATC
Found at i:115870 original size:24 final size:21
Alignment explanation
Indices: 115835--115877 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
115825 GGCACATTCT
*
115835 TTTGAATTTCAAGAGGTACATCA
1 TTTGAATGTCAA-AGG-ACATCA
115858 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
115878 GTCTTGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCA
Found at i:118295 original size:33 final size:33
Alignment explanation
Indices: 118253--118321 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
118243 GTTGATGAAT
*
118253 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
118286 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
118319 GAA
1 GAA
118322 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:123954 original size:33 final size:33
Alignment explanation
Indices: 123912--123980 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
123902 GTTGATGAAT
*
123912 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* *
123945 GAAGGATGATGTTATTGGCGTGATATGGTAATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
123978 GAA
1 GAA
123981 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:124000 original size:35 final size:33
Alignment explanation
Indices: 123936--124004 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 33
123926 TGGTGATGAA
* *
123936 ATGGTAATGGAAGGATGATGTTATTGGCGTGAT
1 ATGGTAATGGAAGGATGATGATATAGGCGTGAT
123969 ATGGTAATGGAATATGG-TGATGATATAGGCGTGAT
1 ATGGTAATGG-A-A-GGATGATGATATAGGCGTGAT
124004 A
1 A
124005 ATGGCGATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 10 0.32
34 1 0.03
35 18 0.58
36 2 0.06
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.32
Consensus pattern (33 bp):
ATGGTAATGGAAGGATGATGATATAGGCGTGAT
Found at i:128588 original size:35 final size:36
Alignment explanation
Indices: 128501--128588 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 36
128491 TACAATATGT
*
128501 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
* * * * *
128537 TAATCCCCATAGTCCATCATCA-TATCACGTCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
128572 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
128589 TTCCATTTCT
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
35 25 0.60
36 17 0.40
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:130471 original size:18 final size:18
Alignment explanation
Indices: 130448--130483 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
130438 ACTTAAGAAA
130448 AAAAGAAAA-AAAGCAAAG
1 AAAAGAAAAGAAA-CAAAG
130466 AAAAGAAAAGAAACAAAG
1 AAAAGAAAAGAAACAAAG
130484 TTGAAGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.78, C:0.06, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAACAAAG
Found at i:131665 original size:13 final size:12
Alignment explanation
Indices: 131646--131730 Score: 65
Period size: 11 Copynumber: 7.2 Consensus size: 12
131636 TTATTGGCGT
131646 GATATGGTGATG
1 GATATGGTGATG
131658 GAATATGGTGAT-
1 G-ATATGGTGATG
*
131670 GATATAGGCG-T-
1 GATAT-GGTGATG
131681 GATAATGGTGATG
1 GAT-ATGGTGATG
131694 GACTATGGTGAT-
1 GA-TATGGTGATG
*
131706 GATATAGGCG-T-
1 GATAT-GGTGATG
131717 GATATGGTGATG
1 GATATGGTGATG
131729 GA
1 GA
131731 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.05
11 21 0.35
12 15 0.25
13 20 0.33
14 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:131731 original size:35 final size:35
Alignment explanation
Indices: 131631--131731 Score: 166
Period size: 36 Copynumber: 2.9 Consensus size: 35
131621 AATGTAAGGA
* * *
131631 TGATGTTATTGGCGTGATATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATATGGTGATGGACTATGG
131666 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGAT-ATGGTGATGGACTATGG
131702 TGATGATATAGGCGTGATATGGTGATGGAC
1 TGATGATATAGGCGTGATATGGTGATGGAC
131732 AGATTGTATC
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 28 0.45
36 34 0.55
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.33
Consensus pattern (35 bp):
TGATGATATAGGCGTGATATGGTGATGGACTATGG
Found at i:136077 original size:34 final size:33
Alignment explanation
Indices: 136009--136077 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
135999 GTTGATGAAT
136009 GAAGGATGATTTAATGGAGATGAAATGGTAATG
1 GAAGGATGATTTAATGGAGATGAAATGGTAATG
* * *
136042 GAAGGATGATGTTATTGGCG-TGATAATGGTGATG
1 GAAGGATGAT-TTAATGGAGATGA-AATGGTAATG
136076 GA
1 GA
136078 CATTGTATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.29
Consensus pattern (33 bp):
GAAGGATGATTTAATGGAGATGAAATGGTAATG
Found at i:145043 original size:5 final size:5
Alignment explanation
Indices: 145029--145058 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
145019 GTGCTTCAAC
145029 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
145059 CTTTTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:152391 original size:12 final size:13
Alignment explanation
Indices: 152361--152389 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
152351 AAGAAAAATA
152361 CAAAAG-GAAGTG
1 CAAAAGTGAAGTG
152373 CAAAAGTGAAGTG
1 CAAAAGTGAAGTG
152386 CAAA
1 CAAA
152390 GTCAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.52, C:0.10, G:0.28, T:0.10
Consensus pattern (13 bp):
CAAAAGTGAAGTG
Found at i:161408 original size:18 final size:17
Alignment explanation
Indices: 161370--161402 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
161360 GTGCAAAAAG
161370 AAAGAAAATCAGAAAATA
1 AAAGAAAA-CAGAAAATA
161388 AAAGAAAA-AGAAAAT
1 AAAGAAAACAGAAAAT
161403 TCAAAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (17 bp):
AAAGAAAACAGAAAATA
Found at i:169982 original size:65 final size:64
Alignment explanation
Indices: 169784--169993 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
169774 TACACTAAGA
* * * *
169784 GTGCAGCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGT-GTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCCA-TAGTGCATCGATGCATGGTT
169847 G
64 G
* * *
169848 GTGCATTGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCATAGTGCATCGATGCATGGT-T
169913 -
64 G
* ** * *
169913 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG-TT
169977 G
64 G
*
169978 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
169994 CTTTGATAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
63 3 0.02
64 50 0.41
65 65 0.53
66 4 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCATAGTGCATCGATGCATGGTTG
Found at i:171060 original size:21 final size:21
Alignment explanation
Indices: 171036--171079 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
171026 AAGGAGGAGG
*
171036 AGGAGGAGCACGA-GAAGAGCT
1 AGGAGCAGCAC-ATGAAGAGCT
*
171057 AGGAGCAGCTCATGAAGAGCT
1 AGGAGCAGCACATGAAGAGCT
171078 AG
1 AG
171080 CTCCCGGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACATGAAGAGCT
Found at i:172637 original size:23 final size:22
Alignment explanation
Indices: 172610--172705 Score: 94
Period size: 23 Copynumber: 4.5 Consensus size: 22
172600 TGACCCTGTA
172610 CATCGATGCACATTCAAGGTGT
1 CATCGATGCACATTCAAGGTGT
* * *
172632 GCATCGGTGCACCTTCATGGTGT
1 -CATCGATGCACATTCAAGGTGT
172655 -ATCGATGCACATTCAAGGATG-
1 CATCGATGCACATTCAAGG-TGT
*
172676 CATTGATGCACTATT--AGGTGT
1 CATCGATGCAC-ATTCAAGGTGT
172697 -ATCGATGCA
1 CATCGATGCA
172706 TGAAGCACAA
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
20 10 0.16
21 18 0.30
22 11 0.18
23 22 0.36
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGTGT
Found at i:172660 original size:44 final size:42
Alignment explanation
Indices: 172611--172705 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
172601 GACCCTGTAC
* *
172611 ATCGATGCACATTCAAGGTGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCA-CTATCA-GGTGT
* *
172655 ATCGATGCACATTCAAGGATGCATTGATGCACTATTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTATCAGGTGT
172697 ATCGATGCA
1 ATCGATGCA
172706 TGAAGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 16 0.35
43 12 0.26
44 18 0.39
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTATCAGGTGT
Found at i:174997 original size:9 final size:9
Alignment explanation
Indices: 174983--175008 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
174973 GAAGAGGTAT
174983 TACCTATAG
1 TACCTATAG
174992 TACCTATAG
1 TACCTATAG
175001 TACCTATA
1 TACCTATA
175009 CCTTCGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (9 bp):
TACCTATAG
Found at i:177744 original size:65 final size:65
Alignment explanation
Indices: 177608--177767 Score: 164
Period size: 65 Copynumber: 2.5 Consensus size: 65
177598 TGCACTAAGA
* * * *
177608 GTGCATCGATGTATCAAGTGTATTCGATG-TTTCAAAATAGCCAGAGTGCATCAATGCATGGCTG
1 GTGCATCGATGCATCAAATGAATTCGATGTTTTCAAAATAGCCACAGTGCATCAATGCATGGCTG
* * * * **
177672 GTACATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGAATTCGATGTTTTCA-AAATAGCCACAGTGCATCAATGCATGGCT
*
177735 AT
65 -G
* *
177737 GTGCATCGATACATGAAATGAATTCGATGTT
1 GTGCATCGATGCATCAAATGAATTCGATGTT
177768 CAATTTAATT
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
64 26 0.33
65 50 0.63
66 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGAATTCGATGTTTTCAAAATAGCCACAGTGCATCAATGCATGGCTG
Found at i:186860 original size:34 final size:34
Alignment explanation
Indices: 186806--186908 Score: 104
Period size: 34 Copynumber: 3.0 Consensus size: 34
186796 ATACAATCTG
*
186806 TCCATCACCATTATCACGCC-ATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T-T
186841 TCCATCACCATATCACGCCAATAACATCATCCTT
1 TCCATCACCATATCACGCCAATAACATCATCCTT
* * * *
186875 TCCATTACCATTTCATCACCATTAA-ATCATCCTT
1 TCCATCACCATATCA-CGCCAATAACATCATCCTT
186909 CATTCATCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
34 32 0.53
35 26 0.43
36 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (34 bp):
TCCATCACCATATCACGCCAATAACATCATCCTT
Found at i:191321 original size:34 final size:34
Alignment explanation
Indices: 191267--191369 Score: 104
Period size: 34 Copynumber: 3.0 Consensus size: 34
191257 ATACAATCTG
*
191267 TCCATCACCATTATCACGCC-ATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T-T
191302 TCCATCACCATATCACGCCAATAACATCATCCTT
1 TCCATCACCATATCACGCCAATAACATCATCCTT
* * * *
191336 TCCATTACCATTTCATCACCATTAA-ATCATCCTT
1 TCCATCACCATATCA-CGCCAATAACATCATCCTT
191370 CATTCATCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
34 32 0.53
35 26 0.43
36 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (34 bp):
TCCATCACCATATCACGCCAATAACATCATCCTT
Found at i:194675 original size:19 final size:20
Alignment explanation
Indices: 194633--194683 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
194623 GAGACCCCTT
*
194633 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTAAA
*
194653 TGAAAATACATTA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
194672 TGAAGATACATG
1 TGAAAATACATG
194684 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:197610 original size:16 final size:16
Alignment explanation
Indices: 197579--197625 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
197569 TGGTAATGAA
197579 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
197596 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
197613 ATAAAAAAATGAA
1 ATAAAAAAATGAA
197626 GATAACTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:203882 original size:69 final size:69
Alignment explanation
Indices: 203770--203920 Score: 171
Period size: 69 Copynumber: 2.2 Consensus size: 69
203760 TTGGTGAAGT
* * * * *
203770 AAAGGACGTGACTTTTCAAAAATCAAGAGGTGCGACTATTGAAAAGCAAAGAGT-GGTAATTCTT
1 AAAGGACGTGACTCTTCAAAAATCAAGAGGTGCGACTAATGAAAACCAAA-AGTAAGCAATTCTT
203834 CATCC
65 CATCC
* * * *
203839 AAAGGACGTGA-TCCTTCAAGAATCAAGAGTTGTGCCTAATGAAAACCAAAAGTAAGCAATTCTT
1 AAAGGACGTGACT-CTTCAAAAATCAAGAGGTGCGACTAATGAAAACCAAAAGTAAGCAATTCTT
*
203903 TATCC
65 CATCC
*
203908 AAAGGGCGTGACT
1 AAAGGACGTGACT
203921 TGTGAGGACA
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
68 4 0.06
69 63 0.93
70 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (69 bp):
AAAGGACGTGACTCTTCAAAAATCAAGAGGTGCGACTAATGAAAACCAAAAGTAAGCAATTCTTC
ATCC
Found at i:207005 original size:12 final size:12
Alignment explanation
Indices: 206966--207006 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
206956 AAGATATGAT
206966 TAAATGGAAATAA
1 TAAAT-GAAATAA
*
206979 GAAATGAAATAAA
1 TAAATGAAAT-AA
206992 TAAATGAAATAA
1 TAAATGAAATAA
207004 TAA
1 TAA
207007 GAAATGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (12 bp):
TAAATGAAATAA
Found at i:208889 original size:24 final size:24
Alignment explanation
Indices: 208862--208949 Score: 77
Period size: 24 Copynumber: 3.4 Consensus size: 24
208852 TCAAGCTATA
208862 ACTCACCTAGTTAGCTACCAAGAC
1 ACTCACCTAGTTAGCTACCAAGAC
* * * * *
208886 ACTCACATATCTTGAGTTTATCAAGCTATA
1 ACTCACCTA-GTT-AG-CTACCAAG--A-C
208916 ACTCACCTAGTTAGCTACCAAGAC
1 ACTCACCTAGTTAGCTACCAAGAC
208940 ACTCACCTAG
1 ACTCACCTAG
208950 CTTACCTTGA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
24 18 0.38
25 3 0.06
26 2 0.04
27 12 0.25
28 2 0.04
29 3 0.06
30 8 0.17
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26
Consensus pattern (24 bp):
ACTCACCTAGTTAGCTACCAAGAC
Found at i:208909 original size:54 final size:54
Alignment explanation
Indices: 208843--208945 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
208833 GCTAACTAGA
208843 TTGAGTTCATCAAGCTATAACTCACCTAGTTAGCTACCAAGACACTCACATATC
1 TTGAGTTCATCAAGCTATAACTCACCTAGTTAGCTACCAAGACACTCACATATC
*
208897 TTGAGTTTATCAAGCTATAACTCACCTAGTTAGCTACCAAGACACTCAC
1 TTGAGTTCATCAAGCTATAACTCACCTAGTTAGCTACCAAGACACTCAC
208946 CTAGCTTACC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (54 bp):
TTGAGTTCATCAAGCTATAACTCACCTAGTTAGCTACCAAGACACTCACATATC
Found at i:209729 original size:19 final size:20
Alignment explanation
Indices: 209705--209744 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
209695 TATCCTTTCT
209705 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
209724 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
209744 T
1 T
209745 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:209962 original size:32 final size:33
Alignment explanation
Indices: 209901--209967 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
209891 ACAAAATTAA
* *
209901 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
209933 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGATAG
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGATAG
209966 AA
1 AA
209968 ATGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:210503 original size:19 final size:20
Alignment explanation
Indices: 210465--210507 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
210455 GAAATCCCTT
*
210465 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
210485 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
210504 TGAA
1 TGAA
210508 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:213483 original size:24 final size:24
Alignment explanation
Indices: 213463--213513 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
213453 ATCAGAAAAC
*
213463 AAAATGAAGCACTCAAAAGAAAGA
1 AAAATCAAGCACTCAAAAGAAAGA
213487 AAAATCAAGCACTCAAAAG-AAGA
1 AAAATCAAGCACTCAAAAGAAAGA
213510 AAAA
1 AAAA
213514 GCAAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.65, C:0.14, G:0.14, T:0.08
Consensus pattern (24 bp):
AAAATCAAGCACTCAAAAGAAAGA
Found at i:228718 original size:24 final size:21
Alignment explanation
Indices: 228683--228725 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
228673 GGCTCATTCT
*
228683 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
228706 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
228726 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:231242 original size:20 final size:22
Alignment explanation
Indices: 231213--231252 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
231203 AGGAGAATTT
231213 TGGACCAAA-GTA-CTGAAAAA
1 TGGACCAAAGGTAGCTGAAAAA
*
231233 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
231253 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAA
Found at i:232488 original size:15 final size:14
Alignment explanation
Indices: 232468--232499 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
232458 GCACTTAAAA
232468 AAAAGAAAAGCAAAG
1 AAAAGAAAAG-AAAG
232483 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
232497 AAA
1 AAA
232500 GTTGAAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:233745 original size:24 final size:21
Alignment explanation
Indices: 233711--233753 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
233701 TGCACAAGAT
*
233711 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
233733 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
233754 ATAATGAACC
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:236523 original size:15 final size:14
Alignment explanation
Indices: 236503--236534 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
236493 GCACTTAAAA
236503 AAAAGAAAAGCAAAG
1 AAAAGAAAAG-AAAG
236518 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
236532 AAA
1 AAA
236535 GTTGAAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:237781 original size:24 final size:21
Alignment explanation
Indices: 237747--237789 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
237737 TGCACAAGAT
*
237747 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
237769 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
237790 AGAATGAGAC
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:243076 original size:11 final size:13
Alignment explanation
Indices: 243044--243073 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
243034 TGGCCAAAGA
243044 TGAAAAGGTATGT
1 TGAAAAGGTATGT
243057 TGAAAAGGTATG-
1 TGAAAAGGTATGT
243069 TGAAA
1 TGAAA
243074 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:245941 original size:34 final size:34
Alignment explanation
Indices: 245902--245970 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
245892 TTGATGAATG
*
245902 AAGGATGAT-TTAATGGTGATGAAATGGTAATGGA
1 AAGGATGATGTTAATGGCG-TGAAATGGTAATGGA
* * *
245936 AAGGATGATGTTATTGGCGTGATATGGTGATGGA
1 AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
245970 A
1 A
245971 TATGGCGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 23 0.77
35 7 0.23
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (34 bp):
AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
Found at i:250403 original size:34 final size:34
Alignment explanation
Indices: 250364--250466 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
250354 TTGATGAATG
*
250364 AAGGATGAT-TTAATGGTGATGAAATGGTAATGGA
1 AAGGATGATGTTAATGGCG-TGAAATGGTAATGGA
* * *
250398 AAGGATGATGTTATTGGCGTGATATGGTGATGGA
1 AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
* *
250432 ATATGG-TGATGAT-ATGGCGTGATAATGGTGATGGA
1 A-A-GGATGATGTTAATGGCGTGA-AATGGTAATGGA
250467 CAGATTGTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
34 31 0.53
35 25 0.43
36 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (34 bp):
AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
Found at i:250460 original size:35 final size:35
Alignment explanation
Indices: 250386--250466 Score: 105
Period size: 34 Copynumber: 2.3 Consensus size: 35
250376 ATGGTGATGA
* *
250386 AATGGTAATGGAAAGGATGATGTTATTGGCGTGAT
1 AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
250421 -ATGGTGATGGAATATGG-TGATGATA-TGGCGTGAT
1 AATGGTGATGGAA-A-GGATGATGATATTGGCGTGAT
250455 AATGGTGATGGA
1 AATGGTGATGGA
250467 CAGATTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 20 0.49
35 19 0.46
36 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
Found at i:253800 original size:28 final size:26
Alignment explanation
Indices: 253769--253826 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
253759 TTTGAATGTA
253769 CTTTGCAA-CTTTCTTCACTTTTCTTTTT
1 CTTTG-AATCTTTCTTC-CTTTTC-TTTT
* *
253797 CTTTGAATTTTTCTTCTTTTTCTTTT
1 CTTTGAATCTTTCTTCCTTTTCTTTT
253823 CTTT
1 CTTT
253827 CTTTGGCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.30
27 7 0.26
28 12 0.44
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.67
Consensus pattern (26 bp):
CTTTGAATCTTTCTTCCTTTTCTTTT
Found at i:254663 original size:20 final size:19
Alignment explanation
Indices: 254635--254675 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
254625 ACCCCTTTGA
*
254635 AAAACACATGATTTTTAATG
1 AAAACACAT-AATTTTAATG
*
254655 AAAATACATAATTTTAATG
1 AAAACACATAATTTTAATG
254674 AA
1 AA
254676 GATAAATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (19 bp):
AAAACACATAATTTTAATG
Found at i:260380 original size:25 final size:22
Alignment explanation
Indices: 260331--260380 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 22
260321 AAACAAAATC
**
260331 AAAGCACTCAAAGAAGAAATTG
1 AAAGCACTCAAAGAAGAAAAAG
260353 AAAGCACTCAAAAAGGAAGAAAAAG
1 AAAGCACTC--AAA-GAAGAAAAAG
260378 AAA
1 AAA
260381 TGAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
24 3 0.13
25 11 0.48
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (22 bp):
AAAGCACTCAAAGAAGAAAAAG
Found at i:265664 original size:515 final size:512
Alignment explanation
Indices: 264684--265681 Score: 1412
Period size: 515 Copynumber: 1.9 Consensus size: 512
264674 TTAACAATTG
*
264684 ATTGTGGATCTAGGAAGGAAGCAAACAACCTGCACAAGTGAATGGCCTAAAAAGAGAGGGATAAG
1 ATTGTGGATCTAGGAAGGAAGCAAACAACCTGCACAAGTGAATGGCCTAAAAAGAAAGGGATAAG
** * * * *
264749 GGTGGTAGGCGTATGGTGAAATAGGTGGGCTGTTTAAAATGAGAGATGGAAGCGGAAAATGGTTG
66 GGTGGTAAACGTATGGTGAAATAGGTAGGATATTTAAAATGAGAGATGGAAGCGGAAAATGATTG
** * *
264814 ATAAGGCTATGGTTATGGTTTATGAAACAAAGGGATAGTTGTGAGGTTAGTATCTTAAAGAAGAC
131 ATAAGGCTATGGTTATGGTCGATGAAACAAAAGGATAGTTGTGAGGATAGTATCTTAAAGAAGAC
* *
264879 TCAAAGAAGAACCAATGCTATATAGAGCAAAGACCCAGACTTTATATTCTTTAAGGGGTGGTATT
196 TCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTCTTCAAGGGGTGGTATT
* *
264944 AAGTACTTTGACCCACTGTTATAAAGAATTAGGAACCAAAAGTATCAAGGTGAAAGAAGGGGTTG
261 AAGTACTTTGACCCACTGTTATAAAGAACTAGGAACCAAAAG-ATCAAGATGAAAGAAGGGGTTG
*
265009 ACGCCATAAGTATAAAAATACTTGATAAGTCGATAAAAGTCACCAGGACTTAAGGAAGAGAATAA
325 ACGCCACAAGTATAAAAATACTTGATAAGTCGATAAAAGTCACCAGGACTTAAGGAAGAGAATAA
* ** * *
265074 TATCACTTTAATTAAACAAAATTTCTGATTACAAATGAATTATAATGACTTATTTATAGTTTTTG
390 TATCACATTAATTAAACAAAAGGTCTGATTACAAATGAAATATAATGACATATTTATAGTTTTTG
* *
265139 AAGGGACTTGGCCGAATAGGTGCATGTTGTGATGTAAGGTAATCCTACCTTCTCATTTT
455 AAGAGACTTGG-CGAATAGGTACATGTTGTGATGTAAGGTAATCCTACCTTCTCATTTT
*
265198 ATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCACAAGTGAATGG-CTCAAAACA-AAATGGAT
1 ATTGTGGATCTAGGAAGGAAGC-AAACAACCTGCACAAGTGAATGGCCT-AAAA-AGAAAGGGAT
** *
265261 AAGGGTGGTAAACGTATGGTTTAATAGGTAGGATATTTAATAATGAGAGATGGAAGC-GAAGATG
63 AAGGGTGGTAAACGTATGGTGAAATAGGTAGGATATTTAA-AATGAGAGATGGAAGCGGAAAATG
* *
265325 ATTGA-AATGGCTATGGTTATGG-CGATGAAACAAAAGGATGGTTGTGAGGATAGTATCTTGAAG
127 ATTGATAA-GGCTATGGTTATGGTCGATGAAACAAAAGGATAGTTGTGAGGATAGTATCTTAAAG
*
265388 AACG-CTTAAAGAAG-ACCAATGCTATAGAGAGCAAAGACCCA-ATCTTTATATTGTTTCTTCAA
191 AA-GACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGA-CTTTATA----TTCTTCAA
* *
265450 GGGGTGGTGTTAAGTACTTTGACCCACTAGTTAT-ATGAACTA-GAACCAAAAG-TCAAGATGAA
250 GGGGTGGTATTAAGTACTTTGACCCACT-GTTATAAAGAACTAGGAACCAAAAGATCAAGATGAA
*
265512 AGAAGAGGG-TGACGCCACAAGTATAAATTATACTTGATAAGTCGATAAAAAGTCACCAGGACTT
314 AGAAG-GGGTTGACGCCACAAGTATAAA-AATACTTGATAAGTCGAT-AAAAGTCACCAGGACTT
* *
265576 AAGGAAGAGAATAATCTCA-ATTAATTAAACAAAAGGTCTGATTACAAATGAAATATAATGGCAT
376 AAGGAAGAGAATAATATCACATTAATTAAACAAAAGGTCTGATTACAAATGAAATATAATGACAT
*
265640 ATTTATAGTTTTTTG-AGAGACTTGGTGAATAGGTACATGTTG
441 ATTTATAG-TTTTTGAAGAGACTTGGCGAATAGGTACATGTTG
265682 GTTCGGCCAG
Statistics
Matches: 432, Mismatches: 36, Indels: 32
0.86 0.07 0.06
Matches are distributed among these distances:
512 1 0.00
513 33 0.08
514 118 0.27
515 167 0.39
516 68 0.16
517 40 0.09
518 5 0.01
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (512 bp):
ATTGTGGATCTAGGAAGGAAGCAAACAACCTGCACAAGTGAATGGCCTAAAAAGAAAGGGATAAG
GGTGGTAAACGTATGGTGAAATAGGTAGGATATTTAAAATGAGAGATGGAAGCGGAAAATGATTG
ATAAGGCTATGGTTATGGTCGATGAAACAAAAGGATAGTTGTGAGGATAGTATCTTAAAGAAGAC
TCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTCTTCAAGGGGTGGTATT
AAGTACTTTGACCCACTGTTATAAAGAACTAGGAACCAAAAGATCAAGATGAAAGAAGGGGTTGA
CGCCACAAGTATAAAAATACTTGATAAGTCGATAAAAGTCACCAGGACTTAAGGAAGAGAATAAT
ATCACATTAATTAAACAAAAGGTCTGATTACAAATGAAATATAATGACATATTTATAGTTTTTGA
AGAGACTTGGCGAATAGGTACATGTTGTGATGTAAGGTAATCCTACCTTCTCATTTT
Done.