Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006708.1 Hibiscus syriacus cultivar Beakdansim tig00016717_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: 104053
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1076 original size:11 final size:11
Alignment explanation
Indices: 1060--1085 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1050 TTCACATTAA
1060 ATTAAATATTT
1 ATTAAATATTT
1071 ATTAAATATTT
1 ATTAAATATTT
1082 ATTA
1 ATTA
1086 GAAAATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTAAATATTT
Found at i:1720 original size:12 final size:12
Alignment explanation
Indices: 1703--1736 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1693 CTAACATTCG
1703 CAATTCTTCCCC
1 CAATTCTTCCCC
1715 CAATTCTTCCCC
1 CAATTCTTCCCC
1727 CAATTCTTCC
1 CAATTCTTCC
1737 TCGCGTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.35
Consensus pattern (12 bp):
CAATTCTTCCCC
Found at i:7072 original size:16 final size:15
Alignment explanation
Indices: 7051--7091 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
7041 ATGAGGTGAA
7051 AAAATAATATTATTGT
1 AAAATAATATTATT-T
7067 AAAAT-ATGATTATTT
1 AAAATAAT-ATTATTT
7082 AAAATAATAT
1 AAAATAATAT
7092 CTATCACCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (15 bp):
AAAATAATATTATTT
Found at i:9588 original size:31 final size:31
Alignment explanation
Indices: 9553--9614 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
9543 TGATAGTTTA
*
9553 AGTACTAAATGTGTAATTTATCCTTTAGTAT
1 AGTACTAAATGTGTAATTTACCCTTTAGTAT
9584 AGTACTAAATGTGTAATTTACCCTTTAGTAT
1 AGTACTAAATGTGTAATTTACCCTTTAGTAT
9615 GTTGTGCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (31 bp):
AGTACTAAATGTGTAATTTACCCTTTAGTAT
Found at i:9782 original size:42 final size:41
Alignment explanation
Indices: 9701--9802 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 41
9691 TCTTAAATTG
*
9701 ACATTCAAACATAAT--CAC-ATAAAACATTGGGAATCATT
1 ACATTCAAACATAATCACACAATAAAACACTGGGAATCATT
*
9739 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
1 ACATTCAAACATAATCACACAATAA-AACACTGGGAATCATT
9781 ACATTCAAACATAATCACACAA
1 ACATTCAAACATAATCACACAA
9803 ATCCATTAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
38 14 0.25
40 3 0.05
41 4 0.07
42 36 0.63
ACGTcount: A:0.49, C:0.21, G:0.07, T:0.24
Consensus pattern (41 bp):
ACATTCAAACATAATCACACAATAAAACACTGGGAATCATT
Found at i:12498 original size:13 final size:13
Alignment explanation
Indices: 12480--12504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12470 GTATATATGC
12480 AAAAATTAAAATA
1 AAAAATTAAAATA
12493 AAAAATTAAAAT
1 AAAAATTAAAAT
12505 CTTGATATGA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAAAATA
Found at i:13003 original size:11 final size:11
Alignment explanation
Indices: 12974--13012 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
12964 CTCCGGCAGT
12974 AAAATAA-AAA
1 AAAATAATAAA
12984 TAAAA-AATAAA
1 -AAAATAATAAA
12995 AAAATAATAAA
1 AAAATAATAAA
13006 AAAATAA
1 AAAATAA
13013 AGATAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAATAAA
Found at i:13003 original size:18 final size:19
Alignment explanation
Indices: 12973--13020 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
12963 CCTCCGGCAG
12973 TAAAATAAAAAT-AAAAAA
1 TAAAATAAAAATAAAAAAA
12991 TAAAA-AAATAATAAAAAAA
1 TAAAATAAA-AATAAAAAAA
13010 TAAAGATAAAA
1 TAAA-ATAAAA
13021 TACAATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 8 0.31
19 10 0.38
20 2 0.08
21 3 0.12
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (19 bp):
TAAAATAAAAATAAAAAAA
Found at i:24392 original size:15 final size:15
Alignment explanation
Indices: 24381--24417 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
24371 ACTAAATTTG
24381 AATAAAACAAATTCA
1 AATAAAACAAATTCA
24396 AATAAAACAAATTCA
1 AATAAAACAAATTCA
24411 AATAAAA
1 AATAAAA
24418 TTTGAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAAACAAATTCA
Found at i:25927 original size:20 final size:18
Alignment explanation
Indices: 25904--25955 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
25894 TTTTAATATT
25904 TAAAAAATGATTTTTGAAAA
1 TAAAAAATGATTTTT--AAA
*
25924 TAAAAAA-G-TATTTAAA
1 TAAAAAATGATTTTTAAA
25940 TAAAAAAATGATTTTT
1 T-AAAAAATGATTTTT
25956 CCCTCTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 4 0.15
17 6 0.22
18 5 0.19
19 5 0.19
20 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (18 bp):
TAAAAAATGATTTTTAAA
Found at i:29665 original size:14 final size:14
Alignment explanation
Indices: 29616--29688 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
29606 CTTTTTAGGA
*
29616 TTAGGATTTAGGGT
1 TTAGGATTTAGAGT
*
29630 TTAAGATTTA-AGTT
1 TTAGGATTTAGAG-T
29644 TTAAGG-TTTAGAGT
1 TT-AGGATTTAGAGT
* * *
29658 TTAGGGTTTATAAT
1 TTAGGATTTAGAGT
*
29672 TTATGATTTAGAGT
1 TTAGGATTTAGAGT
29686 TTA
1 TTA
29689 TGGTTTAAGG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
13 4 0.09
14 38 0.83
15 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (14 bp):
TTAGGATTTAGAGT
Found at i:29667 original size:21 final size:21
Alignment explanation
Indices: 29648--29707 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
29638 TAAGTTTTAA
*
29648 GGTTT-AGAGTTTAGGGTTTAT
1 GGTTTAAGA-TTTAGAGTTTAT
** *
29669 AATTTATGATTTAGAGTTTAT
1 GGTTTAAGATTTAGAGTTTAT
*
29690 GGTTTAAGGTTTAG-GTTT
1 GGTTTAAGATTTAGAGTTT
29708 GGGATTGAGG
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 4 0.13
21 24 0.80
22 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (21 bp):
GGTTTAAGATTTAGAGTTTAT
Found at i:29695 original size:14 final size:14
Alignment explanation
Indices: 29643--29707 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
29633 AGATTTAAGT
*
29643 TTTAAGGTTTAGAG
1 TTTATGGTTTAGAG
* * *
29657 TTTAGGGTTTATAA
1 TTTATGGTTTAGAG
*
29671 TTTATGATTTAGAG
1 TTTATGGTTTAGAG
29685 TTTATGGTTTA-AGG
1 TTTATGGTTTAGA-G
29699 TTTA-GGTTT
1 TTTATGGTTT
29708 GGGATTGAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 6 0.14
14 36 0.86
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (14 bp):
TTTATGGTTTAGAG
Found at i:29879 original size:2 final size:2
Alignment explanation
Indices: 29872--29904 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29862 TCCGACCTTT
29872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29905 GCGCGCGCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30040 original size:55 final size:55
Alignment explanation
Indices: 29955--30060 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
29945 TATATATATA
* *
29955 TGTGTGTATGCATGAACGTGATAGGCTGTTTATGAATAATTTTTGCATTATCATG
1 TGTGTATATGCATGAACGTGATAGGCTGTTTATGAATAATTTCTGCATTATCATG
* * * * *
30010 TGTGTATATGCTTGAATGTGATAGGTTGTTTGTGAATAATTTCTGTATTAT
1 TGTGTATATGCATGAACGTGATAGGCTGTTTATGAATAATTTCTGCATTAT
30061 TATTGGACAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.45
Consensus pattern (55 bp):
TGTGTATATGCATGAACGTGATAGGCTGTTTATGAATAATTTCTGCATTATCATG
Found at i:34837 original size:2 final size:2
Alignment explanation
Indices: 34830--34857 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34820 TTATATTGTA
34830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34858 GAGTTACGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35189 original size:28 final size:29
Alignment explanation
Indices: 35156--35245 Score: 96
Period size: 30 Copynumber: 3.2 Consensus size: 29
35146 TAGTCATACT
* *
35156 TTTAATAAATTAAAATAAA-TTTAATTTA
1 TTTAATAAATTAAAATAAAGTATAATATA
*
35184 TTTAATAATTTAAAATAATAGTATAATATA
1 TTTAATAAATTAAAATAA-AGTATAATATA
* * *
35214 TTTAGTAAATTAAGATAAAATAT-ATA-A
1 TTTAATAAATTAAAATAAAGTATAATATA
35241 TTTAA
1 TTTAA
35246 ACATTTCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 5 0.10
28 20 0.38
29 5 0.10
30 22 0.42
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTAATAAATTAAAATAAAGTATAATATA
Found at i:38006 original size:6 final size:6
Alignment explanation
Indices: 37995--38040 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
37985 TGTTGGTAAG
* * * *
37995 ATATAC ATATAC ATACAT ATATAT GTATAT ATATAT ATATAT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
38041 GAACTCTCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:38018 original size:4 final size:4
Alignment explanation
Indices: 37995--38040 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
37985 TGTTGGTAAG
* * * *
37995 ATAT ACAT ATAC ATAC ATAT ATAT GTAT ATAT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
38041 GAACTCTCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:38039 original size:10 final size:10
Alignment explanation
Indices: 37995--38040 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
37985 TGTTGGTAAG
*
37995 ATATACATAT
1 ATATATATAT
* *
38005 ACATACATAT
1 ATATATATAT
*
38015 ATATGTATAT
1 ATATATATAT
38025 ATATATATAT
1 ATATATATAT
38035 ATATAT
1 ATATAT
38041 GAACTCTCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (10 bp):
ATATATATAT
Found at i:41291 original size:32 final size:31
Alignment explanation
Indices: 41218--41308 Score: 146
Period size: 31 Copynumber: 2.9 Consensus size: 31
41208 TCATACCTAA
* **
41218 CGTTTACTTTTTGTTTCATTTTAGTACCCTT
1 CGTTAACTTTTTGTTTCATTTTAGTACCCCG
41249 CGTTAACTTTTTGTTTCATTTTAGTACCCCG
1 CGTTAACTTTTTGTTTCATTTTAGTACCCCG
41280 CTGTTAACTTTTTGTTTCATTTTAGTACC
1 C-GTTAACTTTTTGTTTCATTTTAGTACC
41309 TAAATTTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 29 0.52
32 27 0.48
ACGTcount: A:0.15, C:0.20, G:0.11, T:0.54
Consensus pattern (31 bp):
CGTTAACTTTTTGTTTCATTTTAGTACCCCG
Found at i:43992 original size:24 final size:24
Alignment explanation
Indices: 43947--43993 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
43937 TACTCAGATA
* *
43947 ATTTGATTTATATTTCTAAAAAAT
1 ATTTAATTTATATTTATAAAAAAT
* *
43971 ATTTAATTTATTTTTATTAAAAA
1 ATTTAATTTATATTTATAAAAAA
43994 GTGGATTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTTAATTTATATTTATAAAAAAT
Found at i:50657 original size:21 final size:21
Alignment explanation
Indices: 50628--50766 Score: 120
Period size: 21 Copynumber: 6.7 Consensus size: 21
50618 ATTCTGACTA
50628 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
50649 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGA-TTTCCCAAAT
* *
50670 TCACATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
50691 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
* * **
50712 TCACATTGCGATTTACGTAA-
1 TCGCATTGCGATTTCCCAAAT
* * *
50732 TCGCATTGCAATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
50753 TCGTATTGCGATTT
1 TCGCATTGCGATTT
50767 AGTAAATCGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
20 23 0.24
21 65 0.68
22 8 0.08
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:50689 original size:42 final size:42
Alignment explanation
Indices: 50631--50767 Score: 186
Period size: 42 Copynumber: 3.3 Consensus size: 42
50621 CTGACTATCG
* *
50631 CATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAAATCA
1 CATTGCGATTTACCAAATTCGCGTTGCGATTTTCCTAATTCA
*
50673 CATTGCGATTTTCCAAATTCGCGTTGCGATTTTCCTAATTCA
1 CATTGCGATTTACCAAATTCGCGTTGCGATTTTCCTAATTCA
** * * *
50715 CATTGCGATTTACGTAA-TCGCATTGCAATTTTCCTAATTCG
1 CATTGCGATTTACCAAATTCGCGTTGCGATTTTCCTAATTCA
*
50756 TATTGCGATTTA
1 CATTGCGATTTA
50768 GTAAATCGCA
Statistics
Matches: 86, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 32 0.37
42 54 0.63
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (42 bp):
CATTGCGATTTACCAAATTCGCGTTGCGATTTTCCTAATTCA
Found at i:51663 original size:24 final size:24
Alignment explanation
Indices: 51636--51689 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
51626 AGTATTCGAA
51636 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
51660 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
51684 TTTGAT
1 TTTGAT
51690 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:53984 original size:20 final size:20
Alignment explanation
Indices: 53917--53989 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
53907 GGCATTCATT
53917 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
**
53937 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-CA-CGGAAA
* *
53958 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACACGGAAA
53978 TGACTATCGCAA
1 TGACTATCGCAA
53990 TGCAAAATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.02
20 25 0.61
21 14 0.34
22 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:53999 original size:19 final size:20
Alignment explanation
Indices: 53956--54010 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
53946 CAATCATCTT
* * *
53956 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAATGCGAA
53976 AATGACTATCGCAATGC-AA
1 AATGACTATCGCAATGCGAA
**
53995 AATGAAAATCGCAATG
1 AATGACTATCGCAATG
54011 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAATGCGAA
Found at i:54020 original size:33 final size:33
Alignment explanation
Indices: 53983--54107 Score: 196
Period size: 33 Copynumber: 3.8 Consensus size: 33
53973 GGAAATGACT
* *
53983 ATCGCAATGCAAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAAAGAGAGA
*
54016 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAAAGAGAGA
* *
54049 ATCGTAATGCGAAATGAAAATCGCAAAGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAAAGAGAGA
*
54082 ATCGCAAAGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
54108 CGCGAATTTA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAAAGAGAGA
Found at i:54039 original size:19 final size:19
Alignment explanation
Indices: 53963--54074 Score: 82
Period size: 19 Copynumber: 6.4 Consensus size: 19
53953 CTTAATGTCT
* **
53963 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
*
53983 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
54002 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
54016 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
54035 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
54049 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
54068 ATCGCAA
1 ATCGCAA
54075 AGAGGGAATC
Statistics
Matches: 71, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
14 20 0.28
15 2 0.03
16 3 0.04
17 2 0.03
18 2 0.03
19 33 0.46
20 9 0.13
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:54105 original size:19 final size:19
Alignment explanation
Indices: 54015--54113 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 19
54005 GCAATGAGAG
*
54015 AATCGCAATGCGAAATGAA
1 AATCGCAAAGCGAAATGAA
*
54034 AATCGC-AA-CG--A-GAG
1 AATCGCAAAGCGAAATGAA
* *
54048 AATCGTAATGCGAAATGAA
1 AATCGCAAAGCGAAATGAA
**
54067 AATCGCAAA--G--A-GGG
1 AATCGCAAAGCGAAATGAA
54081 AATCGCAAAGCGAAATGAA
1 AATCGCAAAGCGAAATGAA
*
54100 AATCGCAACGCGAA
1 AATCGCAAAGCGAA
54114 TTTAGTTTCG
Statistics
Matches: 58, Mismatches: 12, Indels: 20
0.64 0.13 0.22
Matches are distributed among these distances:
14 17 0.29
15 3 0.05
16 3 0.05
17 3 0.05
18 3 0.05
19 29 0.50
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.12
Consensus pattern (19 bp):
AATCGCAAAGCGAAATGAA
Found at i:54163 original size:33 final size:33
Alignment explanation
Indices: 54119--54229 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
54109 GCGAATTTAG
* *
54119 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
54152 TTTCGCATTGCGA--TTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
*
54183 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
54216 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
54230 AGTCTTTTTG
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
31 30 0.41
33 43 0.59
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
Found at i:54353 original size:13 final size:13
Alignment explanation
Indices: 54335--54369 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
54325 TATCAATTAA
54335 ACAATCAACTTTT
1 ACAATCAACTTTT
*
54348 ACAATCATCTTTT
1 ACAATCAACTTTT
54361 ACAAATCAA
1 AC-AATCAA
54370 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (13 bp):
ACAATCAACTTTT
Found at i:54400 original size:39 final size:39
Alignment explanation
Indices: 54326--54400 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
54316 TTATGTTCAT
**** *
54326 ATCAATTAAACAATCAACTTTTACAATCATCTTTTACAA
1 ATCAATTAAACAATCAAAAAATACAATAATCTTTTACAA
54365 ATCAATTAAACAATCAAAAAATAGCAATAAT-TTTTA
1 ATCAATTAAACAATCAAAAAATA-CAATAATCTTTTA
54401 TTTCCTCTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 24 0.80
40 6 0.20
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.33
Consensus pattern (39 bp):
ATCAATTAAACAATCAAAAAATACAATAATCTTTTACAA
Found at i:55723 original size:21 final size:21
Alignment explanation
Indices: 55657--55723 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
55647 GTGAATCGGG
*
55657 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
55677 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
55699 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
55720 CTCT
1 CTCT
55724 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:55931 original size:21 final size:21
Alignment explanation
Indices: 55864--55931 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
55854 GTGAATCGGG
* *
55864 CTCTTGAATGGTGGGGGAGGGA
1 CTCTTGAACGGTGGGAG-GGGA
* * ** * *
55886 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA
55907 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
55928 CTCT
1 CTCT
55932 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 14, Indels: 1
0.68 0.30 0.02
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:56321 original size:19 final size:18
Alignment explanation
Indices: 56299--56399 Score: 74
Period size: 19 Copynumber: 5.9 Consensus size: 18
56289 AACTTAGTAT
56299 GAAAATCGCAACGCGAAA
1 GAAAATCGCAACGCGAAA
56317 CGAAAATCGCAA--CG--A
1 -GAAAATCGCAACGCGAAA
*
56332 GAGAATCGCAACGCGAAA
1 GAAAATCGCAACGCGAAA
*
56350 TGAAAATCGCAA--TG--A
1 -GAAAATCGCAACGCGAAA
* * *
56365 GAGAATCGCAATGCGGAAT
1 GAAAATCGCAACGC-GAAA
56384 GAAAATCGCAACGCGA
1 GAAAATCGCAACGCGA
56400 TTATAATTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 21
0.69 0.09 0.23
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 2 0.03
17 4 0.06
18 3 0.05
19 33 0.52
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (18 bp):
GAAAATCGCAACGCGAAA
Found at i:56344 original size:33 final size:33
Alignment explanation
Indices: 56302--56396 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
56292 TTAGTATGAA
*
56302 AATCGCAACGCGAAACGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
56335 AATCGCAACGCGAAATGAAAATCGCAATGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
56368 AATCGCAATGCGGAATGAAAATCGCAACG
1 AATCGCAACGCGAAATGAAAATCGCAACG
56397 CGATTATAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:56468 original size:33 final size:33
Alignment explanation
Indices: 56426--56509 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
56416 CGATTTTTGG
* *
56426 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTTTCTCATTGTGATTTTCA
* *
56459 TTTCGCGTTGCGATTCTCTCATTGTGATTTTCG
1 TTTCGCGTTGCGATTTTCTCATTGTGATTTTCA
56492 TTTCGCGTTGCGATTTTC
1 TTTCGCGTTGCGATTTTC
56510 ATTCTCTCGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.08, C:0.19, G:0.23, T:0.50
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTCTCATTGTGATTTTCA
Found at i:56522 original size:20 final size:20
Alignment explanation
Indices: 56471--56532 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
56461 TCGCGTTGCG
* *
56471 ATTCTCTCATTGTGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
56491 GTT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
56510 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
56530 ATT
1 ATT
56533 TCAACCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 15 0.43
20 20 0.57
ACGTcount: A:0.11, C:0.21, G:0.16, T:0.52
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:56987 original size:93 final size:94
Alignment explanation
Indices: 56625--57089 Score: 752
Period size: 94 Copynumber: 5.1 Consensus size: 94
56615 ATGGATTGCA
* *
56625 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
56689 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
56718 TTACTTTCAACCAAAGGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
56783 TTAGCAGAATTGGTAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
56812 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
56877 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
56906 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATATTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
56970 TTAGCAGAATTGGCAGCAACCG-A-AAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
56997 TTAC-TTCAACCAAAAGACAACA-AAAGACAAATACTAACTTCACAGTGTT----AATAAACATT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
57056 TTAGCAGTATTAGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
57085 TTACT
1 TTACT
57090 AAGCAATCTA
Statistics
Matches: 353, Mismatches: 14, Indels: 14
0.93 0.04 0.04
Matches are distributed among these distances:
86 28 0.08
87 1 0.00
88 8 0.02
89 6 0.02
90 36 0.10
91 8 0.02
92 1 0.00
93 59 0.17
94 206 0.58
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:58711 original size:20 final size:20
Alignment explanation
Indices: 58686--58786 Score: 109
Period size: 20 Copynumber: 5.2 Consensus size: 20
58676 TTTTTGTTGA
58686 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* *
58706 AATGAAAATCACAACGCG-G
1 AATGAAAATCGCAACGAGAG
** *
58725 AAATGACTATCGCAACGCGA-
1 -AATGAAAATCGCAACGAGAG
*
58745 AATGAAAATCGCAGCGAGA-
1 AATGAAAATCGCAACGAGAG
*
58764 AATTAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
58784 AAT
1 AAT
58787 CGCAACGCGA
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 33 0.49
20 34 0.51
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:58748 original size:19 final size:19
Alignment explanation
Indices: 58684--58815 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
58674 TCTTTTTGTT
*
58684 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
58703 GAGAATGAAAATCACAACGC
1 GA-AATGAAAATCGCAACGC
**
58723 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
* *
58743 GAAATGAAAATCGCAGCGA
1 GAAATGAAAATCGCAACGC
*
58762 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
58779 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
58795 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
58814 GA
1 GA
58816 TTTTGGTTTC
Statistics
Matches: 90, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 45 0.50
20 29 0.32
21 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:58844 original size:19 final size:20
Alignment explanation
Indices: 58822--58932 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
58812 GCGATTTTGG
58822 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
58841 TTTCGCGTTGCGA--TTC--
1 TTTCGCGTTGCGATTTTCAT
*
58857 --TCTCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
* **
58875 TTCTCTCGTTGCGATAGTCAT
1 TT-TCGCGTTGCGATTTTCAT
*
58896 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
**
58916 TTTCATGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
58933 AAGTTTAGAA
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 13 0.17
20 30 0.39
21 18 0.23
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:60035 original size:25 final size:25
Alignment explanation
Indices: 60007--60084 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
59997 ACACGTGTCC
60007 CTTAATTTGATATACTGATTTATGG
1 CTTAATTTGATATACTGATTTATGG
* **
60032 CTT-ATTT-ACTTTCAC--ATTTGATCC
1 CTTAATTTGA-TAT-ACTGATTT-ATGG
60056 CTTAATTTGATATACTGATTTATGG
1 CTTAATTTGATATACTGATTTATGG
60081 CTTA
1 CTTA
60085 TTTACTTTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
23 5 0.12
24 13 0.32
25 17 0.43
26 5 0.12
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (25 bp):
CTTAATTTGATATACTGATTTATGG
Found at i:60038 original size:24 final size:24
Alignment explanation
Indices: 60011--60087 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
60001 GTGTCCCTTA
60011 ATTTGATATACTGATTTATGGCTT
1 ATTTGATATACTGATTTATGGCTT
* **
60035 ATTT-ACTTTCAC--ATTTGATCCCTT
1 ATTTGA-TAT-ACTGATTT-ATGGCTT
60059 AATTTGATATACTGATTTATGGCTT
1 -ATTTGATATACTGATTTATGGCTT
60084 ATTT
1 ATTT
60088 ACTTTCACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
23 5 0.12
24 17 0.43
25 13 0.32
26 5 0.12
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.51
Consensus pattern (24 bp):
ATTTGATATACTGATTTATGGCTT
Found at i:60058 original size:49 final size:49
Alignment explanation
Indices: 60004--60102 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
59994 GTGACACGTG
60004 TCCCTTAATTTGATATACTGATTTATGGCTTATTTACTTTCACATTTGA
1 TCCCTTAATTTGATATACTGATTTATGGCTTATTTACTTTCACATTTGA
60053 TCCCTTAATTTGATATACTGATTTATGGCTTATTTACTTTCACATTTGA
1 TCCCTTAATTTGATATACTGATTTATGGCTTATTTACTTTCACATTTGA
60102 T
1 T
60103 GTATAAAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.49
Consensus pattern (49 bp):
TCCCTTAATTTGATATACTGATTTATGGCTTATTTACTTTCACATTTGA
Found at i:70250 original size:58 final size:58
Alignment explanation
Indices: 70160--70385 Score: 310
Period size: 58 Copynumber: 3.9 Consensus size: 58
70150 ATGTGCATCT
* * * * * *
70160 TTCGGGTTTTGAGCTCGACATAGACTCGATTTTAGGGTAGTCAACGAGAAGTTTACCG
1 TTCGGGTTTCGAGCTCGAAATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTAACTG
* *
70218 TTCGGGTTTCGAGCTCGACATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTCACTG
1 TTCGGGTTTCGAGCTCGAAATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTAACTG
**
70276 TTC-ATTTTCGAGCTCGAAATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTAACTG
1 TTCGGGTTTCGAGCTCGAAATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTAACTG
* * * * *
70333 TTTGGTTTTCGAGCTCGAAATAGACTTGATTTTAGCGTAGTCAGCCAAAAGTT
1 TTCGGGTTTCGAGCTCGAAATAGACTCGATTTTAGGGTAGTCAACCAAAAGTT
70386 CACCGGTCAG
Statistics
Matches: 153, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
57 52 0.34
58 101 0.66
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (58 bp):
TTCGGGTTTCGAGCTCGAAATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTAACTG
Found at i:70373 original size:115 final size:114
Alignment explanation
Indices: 70166--70388 Score: 338
Period size: 115 Copynumber: 1.9 Consensus size: 114
70156 ATCTTTCGGG
* * * *
70166 TTTTGAGCTCGACATAGACTCGATTTTAGGGTAGTCAACGAGAAGTTTACCGTTCGGGTTTCGAG
1 TTTTGAGCTCGAAATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTAACCGTTCGGGTTTCGAG
* *
70231 CTCGACATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTCACTGTTCA
66 CTCGAAATAGACTCGATTTTAGCGTAGTCAACCAAAAGTTCACTGTTCA
* * *
70280 TTTTCGAGCTCGAAATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTAACTGTTTGGTTTTCGA
1 TTTT-GAGCTCGAAATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTAACCGTTCGGGTTTCGA
* *
70345 GCTCGAAATAGACTTGATTTTAGCGTAGTCAGCCAAAAGTTCAC
65 GCTCGAAATAGACTCGATTTTAGCGTAGTCAACCAAAAGTTCAC
70389 CGGTCAGCCA
Statistics
Matches: 97, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
114 4 0.04
115 93 0.96
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (114 bp):
TTTTGAGCTCGAAATAGACTCGATTTTAGGGTAGTCAACCAAAAGTTAACCGTTCGGGTTTCGAG
CTCGAAATAGACTCGATTTTAGCGTAGTCAACCAAAAGTTCACTGTTCA
Found at i:70396 original size:19 final size:19
Alignment explanation
Indices: 70372--70409 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
70362 TTTTAGCGTA
70372 GTCAGCCAAAAGTTCACCG
1 GTCAGCCAAAAGTTCACCG
70391 GTCAGCCAAAAGTTCACCG
1 GTCAGCCAAAAGTTCACCG
70410 TTTGGGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.16
Consensus pattern (19 bp):
GTCAGCCAAAAGTTCACCG
Found at i:71784 original size:4 final size:4
Alignment explanation
Indices: 71775--71801 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
71765 AGCTTTCATT
71775 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
71802 GCATATATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:77951 original size:19 final size:19
Alignment explanation
Indices: 77927--77963 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
77917 AAATGAAGGT
*
77927 TTTCAAAGTTTAAGTGTTA
1 TTTCAAAATTTAAGTGTTA
*
77946 TTTCAAAATTTATGTGTT
1 TTTCAAAATTTAAGTGTT
77964 TTTTTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (19 bp):
TTTCAAAATTTAAGTGTTA
Found at i:78142 original size:26 final size:25
Alignment explanation
Indices: 78110--78174 Score: 112
Period size: 26 Copynumber: 2.6 Consensus size: 25
78100 CACCCGAATG
78110 GACAAAAAAATATAGGTACTTATTT
1 GACAAAAAAATATAGGTACTTATTT
*
78135 GACAAAAAAAATATAGGTATTTATTT
1 GAC-AAAAAAATATAGGTACTTATTT
78161 GACAAAAAAATATA
1 GACAAAAAAATATA
78175 ATTTAGGCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 14 0.37
26 24 0.63
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (25 bp):
GACAAAAAAATATAGGTACTTATTT
Found at i:83158 original size:12 final size:12
Alignment explanation
Indices: 83141--83168 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
83131 GGTTTTGGCT
83141 TCTTTTCTGGTC
1 TCTTTTCTGGTC
83153 TCTTTTCTGGTC
1 TCTTTTCTGGTC
83165 TCTT
1 TCTT
83169 GCGTGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.25, G:0.14, T:0.61
Consensus pattern (12 bp):
TCTTTTCTGGTC
Found at i:84292 original size:15 final size:15
Alignment explanation
Indices: 84269--84354 Score: 122
Period size: 15 Copynumber: 5.7 Consensus size: 15
84259 TATGCACACA
84269 CCTATCAGCCTATCAG
1 CCTATCAGCCTATC-G
*
84285 -CAATCAGCCTATCG
1 CCTATCAGCCTATCG
*
84299 CCTATCAGCCAATCAG
1 CCTATCAGCCTATC-G
84315 CCTATC-GCCTATCG
1 CCTATCAGCCTATCG
84329 CCTATCAGCCTATCG
1 CCTATCAGCCTATCG
84344 CCTATCAGCCT
1 CCTATCAGCCT
84355 GTTTGTGGTT
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
14 8 0.13
15 48 0.76
16 7 0.11
ACGTcount: A:0.23, C:0.40, G:0.13, T:0.24
Consensus pattern (15 bp):
CCTATCAGCCTATCG
Found at i:85011 original size:70 final size:70
Alignment explanation
Indices: 84898--85039 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
84888 CTCATTGTTC
84898 GCTTCTGACCACAGCTCTCAGTGAACAGCTGAAGAAGGAAGTAGAGACGCTCAAGATTGCCACCA
1 GCTTCTGACCACAGCTCTCAGTGAACAGCTGAAGAAGGAAGTAGAGACGCTCAAGATTGCCACCA
84963 GAGAA
66 GAGAA
*
84968 GCTTCTGACCACAGCTCTCAGTGAACAGCTGAAGAAGGAAGTAGAGACGCTCAAGATTGCCACCG
1 GCTTCTGACCACAGCTCTCAGTGAACAGCTGAAGAAGGAAGTAGAGACGCTCAAGATTGCCACCA
85033 GAGAA
66 GAGAA
85038 GC
1 GC
85040 AACGACACCC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (70 bp):
GCTTCTGACCACAGCTCTCAGTGAACAGCTGAAGAAGGAAGTAGAGACGCTCAAGATTGCCACCA
GAGAA
Found at i:90289 original size:126 final size:126
Alignment explanation
Indices: 90085--90376 Score: 383
Period size: 126 Copynumber: 2.3 Consensus size: 126
90075 ATATAGCGTA
* * *
90085 TGTCTTCGATCCCGGGACTTAGATAAGTTGATTTTGATTTTTACCGTTACTTTTAAGAGATGACA
1 TGTCTTCGATCCCGGAACTTAGATAAGTTGATTTTGATTCTTACCGTTACTTTTAAGAGACGACA
* *
90150 TCTAATGGATTATGTGAATAGGGATGTTGAAACATAGGAGATTGAATAAG-AACAT-ACAATG
66 TCTAATGGATTATGTGAATAGGGATGCTGAAACATAGGAGACTGAATAAGTAA-ATAAC-ATG
* * *
90211 TGTCTTCGATCCCGGAACTTAGATCAGTTGATTTTGATTCTTATCGTTACTTTTAAGAGCCGACA
1 TGTCTTCGATCCCGGAACTTAGATAAGTTGATTTTGATTCTTACCGTTACTTTTAAGAGACGACA
* * * *
90276 T-TGAATGGGTTATGTGAGTTGGGATGCTGGAACATAGGAGACTGAATAAGTAAATAACATG
66 TCT-AATGGATTATGTGAATAGGGATGCTGAAACATAGGAGACTGAATAAGTAAATAACATG
* * * *
90337 TGGCTTCGATACCTGAACTTAGATAAGTTTGGTTTTGATT
1 TGTCTTCGATCCCGGAACTTAGATAAG-TTGATTTTGATT
90377 TTGTGTTATT
Statistics
Matches: 145, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
125 1 0.01
126 129 0.89
127 15 0.10
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.35
Consensus pattern (126 bp):
TGTCTTCGATCCCGGAACTTAGATAAGTTGATTTTGATTCTTACCGTTACTTTTAAGAGACGACA
TCTAATGGATTATGTGAATAGGGATGCTGAAACATAGGAGACTGAATAAGTAAATAACATG
Done.