Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008412.1 Hibiscus syriacus cultivar Beakdansim tig00111187_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: 114035
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:7008 original size:90 final size:91
Alignment explanation
Indices: 6827--7000 Score: 260
Period size: 90 Copynumber: 1.9 Consensus size: 91
6817 CCTAGAACAC
*
6827 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
6892 AAGAGTTCTCTCCCTATTCAACCAAG
66 AAGAGCTCTCTCCCTATTCAACCAAG
** * * * * *
6918 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
6982 AAGAGCTCTCTCCCTATTC
66 AAGAGCTCTCTCCCTATTC
7001 GGCCAAGCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 55 0.74
91 19 0.26
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCAACCAAG
Found at i:8181 original size:41 final size:44
Alignment explanation
Indices: 8130--8226 Score: 112
Period size: 47 Copynumber: 2.2 Consensus size: 44
8120 ACTAAAGAAT
* *
8130 AAATATTAATAAACTAAACA-TTTTAA-C-CC-TAATTCCTAATA
1 AAATAATAAT-AACTAAAAAGTTTTAACCACCTTAATTCCTAATA
8171 AAATAATAATAACTAAAAATGTTTTAACCCAACCTTAATTCCTAATA
1 AAATAATAATAACTAAAAA-GTTTTAA-CC-ACCTTAATTCCTAATA
8218 AAATAATAA
1 AAATAATAA
8227 ATCTGATCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
40 8 0.17
41 9 0.19
42 6 0.13
44 1 0.02
46 2 0.04
47 21 0.45
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (44 bp):
AAATAATAATAACTAAAAAGTTTTAACCACCTTAATTCCTAATA
Found at i:12025 original size:12 final size:12
Alignment explanation
Indices: 11985--12016 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
11975 TTTTTGCTTT
11985 CTTTTTTTTTGC
1 CTTTTTTTTTGC
11997 CTTTTTTTTTGC
1 CTTTTTTTTTGC
12009 CTTTTTTT
1 CTTTTTTT
12017 ACCTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (12 bp):
CTTTTTTTTTGC
Found at i:13261 original size:19 final size:18
Alignment explanation
Indices: 13239--13274 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13229 AAATTTTGGC
13239 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
*
13258 TTTTTTTGCCTTTTTTT
1 TTTTTTGGCCTTTTTTT
13275 TTTGCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:13275 original size:14 final size:14
Alignment explanation
Indices: 13253--13289 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
13243 TTGGCTCTTT
13253 TTTTGTTTTTTTGCC
1 TTTT-TTTTTTTGCC
13268 -TTTTTTTTTTGCC
1 TTTTTTTTTTTGCC
13281 TTTTTTTTT
1 TTTTTTTTT
13290 GTTTTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTTTGCC
Found at i:13290 original size:12 final size:13
Alignment explanation
Indices: 13258--13289 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
13248 TCTTTTTTTG
13258 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
13271 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
13284 TTTTTT
1 TTTTTT
13290 GTTTTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:13296 original size:20 final size:20
Alignment explanation
Indices: 13239--13275 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13229 AAATTTTGGC
*
13239 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTCTTTTTTTGT
13259 TTTTTTGCCT-TTTTTTT
1 TTTTTTGCCTCTTTTTTT
13276 TTGCCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (20 bp):
TTTTTTGCCTCTTTTTTTGT
Found at i:19692 original size:10 final size:10
Alignment explanation
Indices: 19677--19715 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
19667 TGCTTTCTTT
19677 CTTTTTTTGC
1 CTTTTTTTGC
19687 CTTTTTTTTTGC
1 C--TTTTTTTGC
*
19699 CTTTTTTTAC
1 CTTTTTTTGC
19709 CTTTTTT
1 CTTTTTT
19716 GTTTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 16 0.62
12 10 0.38
ACGTcount: A:0.03, C:0.18, G:0.05, T:0.74
Consensus pattern (10 bp):
CTTTTTTTGC
Found at i:19715 original size:12 final size:12
Alignment explanation
Indices: 19678--19706 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
19668 GCTTTCTTTC
19678 TTTTTTTGCCTT
1 TTTTTTTGCCTT
19690 TTTTTTTGCCTT
1 TTTTTTTGCCTT
19702 TTTTT
1 TTTTT
19707 ACCTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:25529 original size:11 final size:13
Alignment explanation
Indices: 25497--25526 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
25487 TGGCCAAACA
25497 TGAAAAGGTATGT
1 TGAAAAGGTATGT
25510 TGAAAAGGTATG-
1 TGAAAAGGTATGT
25522 TGAAA
1 TGAAA
25527 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:31082 original size:90 final size:91
Alignment explanation
Indices: 30928--31109 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
30918 CCTAGAACAC
* *
30928 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATG
* *
30993 AATAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * *
31019 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATG
31083 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
31109 C
1 C
31110 ATCATTTCCC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 62 0.77
91 19 0.23
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:32193 original size:19 final size:20
Alignment explanation
Indices: 32152--32202 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
32142 GAAACCCCTT
*
32152 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
32172 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
32191 TGAAGATACATG
1 TGAAAATACATG
32203 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:36366 original size:19 final size:20
Alignment explanation
Indices: 36325--36375 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
36315 GAAACCCCTT
*
36325 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
36345 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
36364 TGAAGATACATG
1 TGAAAATACATG
36376 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:37325 original size:30 final size:30
Alignment explanation
Indices: 37290--37346 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
37280 CTGCCATGAT
**
37290 ATCTAAATGAAATGAAAACATAATAAATTA
1 ATCTAAAACAAATGAAAACATAATAAATTA
* *
37320 ATCTAAAACATATGTAAACATAATAAA
1 ATCTAAAACAAATGAAAACATAATAAA
37347 AAGATGTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (30 bp):
ATCTAAAACAAATGAAAACATAATAAATTA
Found at i:38450 original size:19 final size:20
Alignment explanation
Indices: 38409--38459 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
38399 GAAACCCCTT
*
38409 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
38429 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
38448 TGAAGATACATG
1 TGAAAATACATG
38460 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:42607 original size:19 final size:20
Alignment explanation
Indices: 42566--42616 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
42556 GAAACCCCTT
*
42566 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
42586 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
42605 TGAAGATACATG
1 TGAAAATACATG
42617 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:44023 original size:35 final size:37
Alignment explanation
Indices: 43977--44056 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
43967 TTTGACAATT
*
43977 TGGTGATGATATAGCCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGCCGTGATAATGGAAGATGGACTA
* *
44012 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGCCGTGATAATGGAAGATGGACTA
44049 TGGTGATG
1 TGGTGATG
44057 GAAATAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGCCGTGATAATGGAAGATGGACTA
Found at i:49693 original size:12 final size:11
Alignment explanation
Indices: 49656--49701 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 11
49646 TTTGAGAATT
49656 TGGTGATGATA
1 TGGTGATGATA
*
49667 TAGGCG-TGATA
1 T-GGTGATGATA
49678 TGGTGATGACTA
1 TGGTGATGA-TA
49690 TGGTGATGATA
1 TGGTGATGATA
49701 T
1 T
49702 AGGCGTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 3 0.10
11 13 0.43
12 14 0.47
ACGTcount: A:0.26, C:0.04, G:0.35, T:0.35
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:51341 original size:19 final size:20
Alignment explanation
Indices: 51317--51367 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
51307 CGGCCAAGAG
* *
51317 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
51336 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
51356 CATGTATTTTCA
1 CATGTATTTTCA
51368 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:53731 original size:48 final size:48
Alignment explanation
Indices: 53660--53763 Score: 208
Period size: 48 Copynumber: 2.2 Consensus size: 48
53650 GTTGGATCTT
53660 CAAAAGACATGTCGTGTGGATCACCAAAGGTCATGACTATTGGTTCCC
1 CAAAAGACATGTCGTGTGGATCACCAAAGGTCATGACTATTGGTTCCC
53708 CAAAAGACATGTCGTGTGGATCACCAAAGGTCATGACTATTGGTTCCC
1 CAAAAGACATGTCGTGTGGATCACCAAAGGTCATGACTATTGGTTCCC
53756 CAAAAGAC
1 CAAAAGAC
53764 TTGTTTCTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (48 bp):
CAAAAGACATGTCGTGTGGATCACCAAAGGTCATGACTATTGGTTCCC
Found at i:53742 original size:24 final size:24
Alignment explanation
Indices: 53667--53742 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
53657 CTTCAAAAGA
53667 CATGTCGTGTGGATCACCAAAGGT
1 CATGTCGTGTGGATCACCAAAGGT
* * * * * *
53691 CATGAC-TATTGGTTCCCCAAAAGA
1 CATGTCGT-GTGGATCACCAAAGGT
53715 CATGTCGTGTGGATCACCAAAGGT
1 CATGTCGTGTGGATCACCAAAGGT
53739 CATG
1 CATG
53743 ACTATTGGTT
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (24 bp):
CATGTCGTGTGGATCACCAAAGGT
Found at i:53758 original size:24 final size:24
Alignment explanation
Indices: 53683--53759 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
53673 GTGTGGATCA
53683 CCAAAGGTCATGACTATTGGTTCC
1 CCAAAGGTCATGACTATTGGTTCC
* * * * * *
53707 CCAAAAGACATGTCGT-GTGGATCA
1 CCAAAGGTCATGAC-TATTGGTTCC
53731 CCAAAGGTCATGACTATTGGTTCC
1 CCAAAGGTCATGACTATTGGTTCC
53755 CCAAA
1 CCAAA
53760 AGACTTGTTT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
23 1 0.03
24 37 0.95
25 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (24 bp):
CCAAAGGTCATGACTATTGGTTCC
Found at i:55479 original size:19 final size:19
Alignment explanation
Indices: 55455--55504 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
55445 CGGCCAAGAG
*
55455 CATGTATCTTCAT-TAAAAT
1 CATGTAT-TTCATCAAAAAT
55474 CATGTATTTTCATCAAAAAT
1 CATGTA-TTTCATCAAAAAT
55494 CATGTATTTCA
1 CATGTATTTCA
55505 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (19 bp):
CATGTATTTCATCAAAAAT
Found at i:55494 original size:20 final size:19
Alignment explanation
Indices: 55455--55502 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
55445 CGGCCAAGAG
* *
55455 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
55474 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCAT-AAAAAT
55494 CATGTATTT
1 CATGTATTT
55503 CAAAGGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:57753 original size:48 final size:48
Alignment explanation
Indices: 57682--57785 Score: 208
Period size: 48 Copynumber: 2.2 Consensus size: 48
57672 GTTGGATCTT
57682 CAAAAGACATGTCGTGTGGATCACCAAAGGTCATGACTATTGGTTCCC
1 CAAAAGACATGTCGTGTGGATCACCAAAGGTCATGACTATTGGTTCCC
57730 CAAAAGACATGTCGTGTGGATCACCAAAGGTCATGACTATTGGTTCCC
1 CAAAAGACATGTCGTGTGGATCACCAAAGGTCATGACTATTGGTTCCC
57778 CAAAAGAC
1 CAAAAGAC
57786 TTGTTTCTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (48 bp):
CAAAAGACATGTCGTGTGGATCACCAAAGGTCATGACTATTGGTTCCC
Found at i:57764 original size:24 final size:24
Alignment explanation
Indices: 57689--57764 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
57679 CTTCAAAAGA
57689 CATGTCGTGTGGATCACCAAAGGT
1 CATGTCGTGTGGATCACCAAAGGT
* * * * * *
57713 CATGAC-TATTGGTTCCCCAAAAGA
1 CATGTCGT-GTGGATCACCAAAGGT
57737 CATGTCGTGTGGATCACCAAAGGT
1 CATGTCGTGTGGATCACCAAAGGT
57761 CATG
1 CATG
57765 ACTATTGGTT
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (24 bp):
CATGTCGTGTGGATCACCAAAGGT
Found at i:57780 original size:24 final size:24
Alignment explanation
Indices: 57705--57781 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
57695 GTGTGGATCA
57705 CCAAAGGTCATGACTATTGGTTCC
1 CCAAAGGTCATGACTATTGGTTCC
* * * * * *
57729 CCAAAAGACATGTCGT-GTGGATCA
1 CCAAAGGTCATGAC-TATTGGTTCC
57753 CCAAAGGTCATGACTATTGGTTCC
1 CCAAAGGTCATGACTATTGGTTCC
57777 CCAAA
1 CCAAA
57782 AGACTTGTTT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
23 1 0.03
24 37 0.95
25 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (24 bp):
CCAAAGGTCATGACTATTGGTTCC
Found at i:59698 original size:36 final size:36
Alignment explanation
Indices: 59651--59755 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
59641 GATACAATCT
59651 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
59687 GTCCATCACCATTATCACGCCTATGTCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
59723 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
59756 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:60401 original size:16 final size:16
Alignment explanation
Indices: 60382--60415 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
60372 TTTCTTACTA
60382 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
60398 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
60414 TT
1 TT
60416 GTTTCATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCATTTCTTTATTC
Found at i:63274 original size:19 final size:20
Alignment explanation
Indices: 63250--63300 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
63240 CGGCCAAGAG
* *
63250 CATGTATCTTCATT-TAAAT
1 CATGTATTTTCATTAAAAAT
63269 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
63289 CATGTATTTTCA
1 CATGTATTTTCA
63301 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:63686 original size:13 final size:11
Alignment explanation
Indices: 63645--63729 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
63635 ACAATCTGTC
63645 CATCACCATTAT
1 CATCACCA-TAT
*
63657 CA-CGCCTATAT
1 CATCACC-ATAT
63668 CATCACCATAGT
1 CATCACCATA-T
63680 CCATCACCATTAT
1 -CATCACCA-TAT
*
63693 CA-CGCCTATAT
1 CATCACC-ATAT
63704 CATCACCATATT
1 CATCACCATA-T
63716 CCATCACCATAT
1 -CATCACCATAT
63728 CA
1 CA
63730 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:63689 original size:36 final size:36
Alignment explanation
Indices: 63642--63746 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
63632 GATACAATCT
63642 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
63678 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
63714 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
63747 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:64145 original size:22 final size:19
Alignment explanation
Indices: 64117--64162 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
64107 GTGCTACAAC
*
64117 AAAAAAAGCAACAAGAAAGAAG
1 AAAAAAA-CAAAAAG-AA-AAG
64139 AAAAAAACAAAAAGAAAAG
1 AAAAAAACAAAAAGAAAAG
64158 AAAAA
1 AAAAA
64163 GACTCCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 2 0.09
21 6 0.26
22 7 0.30
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAGAAAAG
Found at i:64393 original size:16 final size:16
Alignment explanation
Indices: 64374--64407 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
64364 TTTCTTACTA
64374 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
64390 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
64406 TT
1 TT
64408 GTTTCATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCATTTCTTTATTC
Found at i:67266 original size:19 final size:20
Alignment explanation
Indices: 67242--67292 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
67232 CGGCCAAGAG
* *
67242 CATGTATCTTCATT-TAAAT
1 CATGTATTTTCATTAAAAAT
67261 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
67281 CATGTATTTTCA
1 CATGTATTTTCA
67293 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:67678 original size:13 final size:11
Alignment explanation
Indices: 67637--67738 Score: 84
Period size: 11 Copynumber: 8.7 Consensus size: 11
67627 ACAATCTGTC
67637 CATCACCATTAT
1 CATCACCA-TAT
67649 CA-CACCTATAT
1 CATCACC-ATAT
67660 CATCACCATAGT
1 CATCACCATA-T
67672 CCATCACCATTAT
1 -CATCACCA-TAT
*
67685 CA-CGCCTATAT
1 CATCACC-ATAT
67696 CATCACCATATT
1 CATCACCATA-T
67708 CCATCACCATAT
1 -CATCACCATAT
67720 CA-CACCTATAT
1 CATCACC-ATAT
*
67731 TATCACCA
1 CATCACCA
67739 ACTTATAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 23
0.75 0.03 0.23
Matches are distributed among these distances:
10 4 0.05
11 31 0.41
12 20 0.26
13 19 0.25
14 2 0.03
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:67681 original size:36 final size:36
Alignment explanation
Indices: 67634--67738 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
67624 GATACAATCT
67634 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACACCTATATCATCACCATA
*
67670 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACACCTATATCATCACCATA
* *
67706 TTCCATCACCA-TATCACACCTATATTATCACCA
1 GTCCATCACCATTATCACACCTATATCATCACCA
67739 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACACCTATATCATCACCATA
Found at i:70217 original size:10 final size:9
Alignment explanation
Indices: 70182--70280 Score: 81
Period size: 10 Copynumber: 10.3 Consensus size: 9
70172 GCTGCTGGAA
*
70182 ACCGGTTTA
1 ACCGGTTTG
*
70191 ACCGGTTTTCA
1 ACCGG-TTT-G
70202 ACCGGTTCTG
1 ACCGGTT-TG
70212 ACCGGTTTG
1 ACCGGTTTG
*
70221 ACCGGTTTCA
1 ACCGGTTT-G
*
70231 ACCGGTTCG
1 ACCGGTTTG
70240 AACCGGTTTG
1 -ACCGGTTTG
*
70250 ACCGGTCTG
1 ACCGGTTTG
*
70259 AATCGGTTTG
1 -ACCGGTTTG
*
70269 ACCGGTCTG
1 ACCGGTTTG
70278 ACC
1 ACC
70281 CGACCCGACC
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
9 33 0.45
10 34 0.46
11 7 0.09
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:70226 original size:19 final size:19
Alignment explanation
Indices: 70183--70280 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 19
70173 CTGCTGGAAA
* * *
70183 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
70203 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
70222 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
70242 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
70261 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
70279 CC
1 CC
70281 CGACCCGACC
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.07
19 39 0.58
20 15 0.22
21 8 0.12
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:70244 original size:29 final size:30
Alignment explanation
Indices: 70181--70280 Score: 118
Period size: 29 Copynumber: 3.4 Consensus size: 30
70171 GGCTGCTGGA
*
70181 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
70212 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
70240 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
70269 -ACCGGTCTGACC
1 AACCGGTTTGACC
70281 CGACCCGACC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.19
29 37 0.60
30 13 0.21
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:70287 original size:5 final size:5
Alignment explanation
Indices: 70277--70334 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
70267 TGACCGGTCT
* *
70277 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
70326 GACCC GACC
1 GACCC GACC
70335 GTTGATCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:70303 original size:22 final size:22
Alignment explanation
Indices: 70277--70339 Score: 126
Period size: 22 Copynumber: 2.9 Consensus size: 22
70267 TGACCGGTCT
70277 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
70299 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
70321 GACCCGACCCGACCGTTGA
1 GACCCGACCCGACCGTTGA
70340 TCGTTGACCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.19, C:0.48, G:0.24, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:70346 original size:7 final size:7
Alignment explanation
Indices: 70331--70368 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
70321 GACCCGACCC
70331 GACCGTT
1 GACCGTT
*
70338 GATCGTT
1 GACCGTT
70345 GACCGTT
1 GACCGTT
70352 GACCGTT
1 GACCGTT
*
70359 GACCATT
1 GACCGTT
70366 GAC
1 GAC
70369 TTTCTTTGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:77550 original size:10 final size:9
Alignment explanation
Indices: 77515--77613 Score: 72
Period size: 10 Copynumber: 10.3 Consensus size: 9
77505 GCTGCTGGAA
*
77515 ACCGGTTTA
1 ACCGGTTTG
*
77524 ACCGGTTTTCA
1 ACCGG-TTT-G
77535 ACCGGTTCTG
1 ACCGGTT-TG
77545 ACCGGTTTG
1 ACCGGTTTG
*
77554 ACCGGTTTCA
1 ACCGGTTT-G
*
77564 ACCGGTTCG
1 ACCGGTTTG
*
77573 AACTGGTTTG
1 -ACCGGTTTG
*
77583 ACCGGTCTG
1 ACCGGTTTG
*
77592 AATCGGTTTG
1 -ACCGGTTTG
*
77602 ACCGGTCTG
1 ACCGGTTTG
77611 ACC
1 ACC
77614 CGACCCGACC
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
9 32 0.44
10 33 0.46
11 7 0.10
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:77559 original size:19 final size:19
Alignment explanation
Indices: 77516--77613 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
77506 CTGCTGGAAA
* * *
77516 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
77536 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
77555 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
*
77575 CTGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
77594 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
77612 CC
1 CC
77614 CGACCCGACC
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
18 5 0.08
19 38 0.58
20 14 0.22
21 8 0.12
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.31
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:77580 original size:29 final size:29
Alignment explanation
Indices: 77515--77613 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
77505 GCTGCTGGAA
*
77515 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
77545 ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* * * *
77573 AACTGGTTTGACCGGTCTGAATCGGTT-TG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCTG
*
77602 ACCGGTCTGACC
1 ACCGGTTTGACC
77614 CGACCCGACC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 11 0.18
29 36 0.60
30 13 0.22
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:77620 original size:5 final size:5
Alignment explanation
Indices: 77610--77689 Score: 79
Period size: 5 Copynumber: 14.8 Consensus size: 5
77600 TGACCGGTCT
* *
77610 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
77659 GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
77690 GTTGATCGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
5 51 0.81
7 12 0.19
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:77631 original size:17 final size:15
Alignment explanation
Indices: 77608--77689 Score: 65
Period size: 17 Copynumber: 5.1 Consensus size: 15
77598 TTTGACCGGT
77608 CTGACCCGACCCGAC
1 CTGACCCGACCCGAC
77623 CGTTGACCCGACCCGAC
1 C--TGACCCGACCCGAC
* *
77640 CCGACCGTTGACCCGAC
1 CTGACC--CGACCCGAC
* *
77657 CCGACCCGACCGTTGAC
1 CTGACCCGACC--CGAC
*
77674 CCGACCCGACCCGAC
1 CTGACCCGACCCGAC
77689 C
1 C
77690 GTTGATCGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
15 13 0.23
17 43 0.77
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (15 bp):
CTGACCCGACCCGAC
Found at i:77636 original size:22 final size:22
Alignment explanation
Indices: 77610--77694 Score: 170
Period size: 22 Copynumber: 3.9 Consensus size: 22
77600 TGACCGGTCT
77610 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
77632 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
77654 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
77676 GACCCGACCCGACCGTTGA
1 GACCCGACCCGACCGTTGA
77695 TCGTTGACCG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.19, C:0.48, G:0.24, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:93506 original size:25 final size:20
Alignment explanation
Indices: 93450--93489 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
93440 AATGAAAATG
93450 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
93470 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
93490 TGAAATGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (20 bp):
AAATGGAAAAAGGAAAGAAT
Found at i:93721 original size:36 final size:36
Alignment explanation
Indices: 93647--93746 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 36
93637 AAATGGAATT
**
93647 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
93682 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
93718 TGGTGATG--ATAGGCGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGATAATGGTGATG
93747 AACAGATTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
34 21 0.34
35 21 0.34
36 20 0.32
ACGTcount: A:0.27, C:0.04, G:0.39, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
Found at i:97977 original size:20 final size:20
Alignment explanation
Indices: 97952--97991 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
97942 AATGAAAATG
97952 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
97972 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
97992 TGAATGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (20 bp):
AAATGGAAAAAGGAAAGAAT
Found at i:98185 original size:35 final size:36
Alignment explanation
Indices: 98138--98247 Score: 181
Period size: 34 Copynumber: 3.1 Consensus size: 36
98128 GGAATGGAAA
* *
98138 ATGGAATTTGGTGATGATATATGCGTGAT-ATGGTG
1 ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
98173 ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
1 ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
98209 ATGG-A-ATGGTGATGATATAGGCGTGATAATGGTG
1 ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
98243 ATGGA
1 ATGGA
98248 CAGATTGTAT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
34 33 0.46
35 28 0.39
36 10 0.14
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (36 bp):
ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
Found at i:98239 original size:23 final size:23
Alignment explanation
Indices: 98146--98245 Score: 86
Period size: 23 Copynumber: 4.3 Consensus size: 23
98136 AAATGGAATT
98146 TGGTGATGATATATGCGTGAT--A
1 TGGTGATGATATATG-GTGATGAA
98168 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATATGGTGATGA-A
*
98192 TAGGCG-TGATA-ATGGTGATGGAA
1 T-GGTGATGATATATGGTGAT-GAA
*
98215 TGGTGATGATATAGGCGTGAT-AA
1 TGGTGATGATATATG-GTGATGAA
98238 TGGTGATG
1 TGGTGATG
98246 GACAGATTGT
Statistics
Matches: 65, Mismatches: 3, Indels: 19
0.75 0.03 0.22
Matches are distributed among these distances:
21 5 0.08
22 15 0.23
23 29 0.45
24 8 0.12
25 8 0.12
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.32
Consensus pattern (23 bp):
TGGTGATGATATATGGTGATGAA
Found at i:99813 original size:16 final size:16
Alignment explanation
Indices: 99789--99821 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
99779 TAGTTAGCTC
99789 ATTTACATTCTAACAT
1 ATTTACATTCTAACAT
*
99805 ATTTGCATTCTAACAT
1 ATTTACATTCTAACAT
99821 A
1 A
99822 GGTGGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTTACATTCTAACAT
Found at i:105159 original size:16 final size:16
Alignment explanation
Indices: 105138--105170 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
105128 TAGTTAGCTC
105138 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
105154 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
105170 A
1 A
105171 GGTGGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:110185 original size:17 final size:19
Alignment explanation
Indices: 110150--110185 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
110140 ATCATTCACT
110150 TGCAACTATATGATTTTCA
1 TGCAACTATATGATTTTCA
110169 TGCAAC-ATATG-TTTTCA
1 TGCAACTATATGATTTTCA
110186 CATCTTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (19 bp):
TGCAACTATATGATTTTCA
Found at i:111187 original size:19 final size:20
Alignment explanation
Indices: 111163--111213 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
111153 CGGCCAAGAG
* *
111163 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
111182 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
111202 CATGTATTTTCA
1 CATGTATTTTCA
111214 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Done.