Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009027.1 Hibiscus syriacus cultivar Beakdansim tig00112424_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: 69277
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2040 original size:237 final size:231
Alignment explanation
Indices: 1627--2095 Score: 843
Period size: 237 Copynumber: 2.0 Consensus size: 231
1617 GGCCATTCAT
1627 GAACATAGTCCTCCAAAAGGTTAGCAATGGAGTCTTAAGTAATCCCTCCAGCTTGATACGTTCTC
1 GAACATAGTCCTCCAAAAGGTTAGCAATGGAGTCTTAAGTAATCCCTCCAGCTTGATACGTTCTC
1692 GGTTTGCAAGTTGAAACTCTTGGGAAGTCTCGTCGTCTTCACTCATCGGAGTAGTTCTTCAATCG
66 GGTTTGCAAGTTGAAACTCTTGGGAAGTCTCGTCGTCTTCACTCATCGGAGTAGTTCTTCAATCG
1757 CTCCTTCTCCGGTAAACGGAAGAATTCTTTCGAGACGTGCGTCATCTTATCGATCACCTCGTTTG
131 CTCCTTCTCCGGTAAACGGAAGAATTCTTTCGAGACGTGCGTCATCTTATCGATCA---CG-TTG
1822 AAAGGCCGTGGTTTTTAACCTTCGCCACAGATTAATTAGC
192 AAAGGCCGTGGTTTTTAACCTTCGCCACAGATTAATTAGC
*
1862 GAACATAGTCCTCCAAAAGGTTAGCAATGGAGTCTTAAGTAATCCCTTCAGCTTGATACGTTCTC
1 GAACATAGTCCTCCAAAAGGTTAGCAATGGAGTCTTAAGTAATCCCTCCAGCTTGATACGTTCTC
1927 GG-TTGCAAGTTG-AACTCTTGGGAAGTCTCGTCGTCTTCATCGGATCATCGGAGTAGTTCTTCA
66 GGTTTGCAAGTTGAAACTCTTGGGAAGTCTCGTCGTCTTCA-C---TCATCGGAGTAGTTCTTCA
1990 ATCGCTCCTTCTCCGGTAAACGGAAGAATTCTTTCGAGACGTGCGTCATCTTATCGATCACGTTG
127 ATCGCTCCTTCTCCGGTAAACGGAAGAATTCTTTCGAGACGTGCGTCATCTTATCGATCACGTTG
2055 AAAGGCCGTGGTTTTTAACCTTCGCCACAGATTAATTAGC
192 AAAGGCCGTGGTTTTTAACCTTCGCCACAGATTAATTAGC
2095 G
1 G
2096 TTACAGCCGA
Statistics
Matches: 229, Mismatches: 1, Indels: 10
0.95 0.00 0.04
Matches are distributed among these distances:
233 71 0.31
234 13 0.06
235 66 0.29
237 79 0.34
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (231 bp):
GAACATAGTCCTCCAAAAGGTTAGCAATGGAGTCTTAAGTAATCCCTCCAGCTTGATACGTTCTC
GGTTTGCAAGTTGAAACTCTTGGGAAGTCTCGTCGTCTTCACTCATCGGAGTAGTTCTTCAATCG
CTCCTTCTCCGGTAAACGGAAGAATTCTTTCGAGACGTGCGTCATCTTATCGATCACGTTGAAAG
GCCGTGGTTTTTAACCTTCGCCACAGATTAATTAGC
Found at i:2967 original size:14 final size:14
Alignment explanation
Indices: 2943--2980 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2933 AGATTTCTTA
2943 TATTA-ATTATGAT
1 TATTATATTATGAT
2956 TATTATATTATGAT
1 TATTATATTATGAT
* *
2970 TCTTATGTTAT
1 TATTATATTAT
2981 AAATCTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.58
Consensus pattern (14 bp):
TATTATATTATGAT
Found at i:3456 original size:32 final size:32
Alignment explanation
Indices: 3420--3528 Score: 107
Period size: 32 Copynumber: 3.3 Consensus size: 32
3410 GTTCAACTCG
3420 TGCTCGTTAAGAAAATTTGTTGCTCGACTCAT
1 TGCTCGTTAAGAAAATTTGTTGCTCGACTCAT
* *
3452 TGCTCGTTAAACTCGTTAAAA-TT-TTGCTCGCCCCA-
1 TGCTCGTT-AA---G--AAAATTTGTTGCTCGACTCAT
* *
3487 TGCTCGTTAAGAAAATTTGTTACTCGACTCGT
1 TGCTCGTTAAGAAAATTTGTTGCTCGACTCAT
3519 TGCTCGTTAA
1 TGCTCGTTAA
3529 ACTCATCGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
29 4 0.06
30 2 0.03
31 9 0.15
32 18 0.29
33 2 0.03
34 2 0.03
35 8 0.13
36 11 0.18
37 2 0.03
38 4 0.06
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (32 bp):
TGCTCGTTAAGAAAATTTGTTGCTCGACTCAT
Found at i:11031 original size:13 final size:13
Alignment explanation
Indices: 10998--11031 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
10988 CTCTTTCTAT
*
10998 TCCATTAAAATTG
1 TCCATTTAAATTG
11011 TCCCATTTAAATTG
1 T-CCATTTAAATTG
11025 TCCATTT
1 TCCATTT
11032 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (13 bp):
TCCATTTAAATTG
Found at i:15893 original size:29 final size:29
Alignment explanation
Indices: 15841--15929 Score: 115
Period size: 29 Copynumber: 3.1 Consensus size: 29
15831 AATGTTGGCC
* * *
15841 GTAGGTCGCCATACCCTCCGGGCGACCTT
1 GTAGGTCGCCATGCACGCCGGGCGACCTT
* * *
15870 GTAGGTCGCCATGCACGCCAGGCGACATG
1 GTAGGTCGCCATGCACGCCGGGCGACCTT
*
15899 GTAGGTCGCCATGCACGCTGGGCGACCTT
1 GTAGGTCGCCATGCACGCCGGGCGACCTT
15928 GT
1 GT
15930 CCTGCGCCCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACGCCGGGCGACCTT
Found at i:16010 original size:22 final size:22
Alignment explanation
Indices: 15980--16026 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
15970 CTGCATGCAA
*
15980 GCGATCTCTTCCGACGTGCATG
1 GCGACCTCTTCCGACGTGCATG
16002 GCGACCTCTTCCGACGTGCATG
1 GCGACCTCTTCCGACGTGCATG
16024 GCG
1 GCG
16027 TATGCAAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.34, G:0.30, T:0.23
Consensus pattern (22 bp):
GCGACCTCTTCCGACGTGCATG
Found at i:16070 original size:31 final size:31
Alignment explanation
Indices: 16032--16091 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
16022 TGGCGTATGC
16032 AAAGCTTCATCCTCTCACCACAGCTCGTAGA
1 AAAGCTTCATCCTCTCACCACAGCTCGTAGA
**
16063 AAAGCTTCATCCTCTCGTCACAGCTCGTA
1 AAAGCTTCATCCTCTCACCACAGCTCGTA
16092 TAGAACACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25
Consensus pattern (31 bp):
AAAGCTTCATCCTCTCACCACAGCTCGTAGA
Found at i:20589 original size:40 final size:39
Alignment explanation
Indices: 20542--20796 Score: 194
Period size: 40 Copynumber: 6.4 Consensus size: 39
20532 TGCGATTTTC
** **
20542 CAAATTCGCAACATGATAGTCAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAAC-CGAATTT
* *
20582 CAAATTCGCAACGCGAAAGTCAAATTCGCAACTGAATTT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACCGAATTT
* * * *
20621 CAAATTCGCAACGCGA-ATTCCAATTTCGCAACCCAGTTT
1 CAAATTCGCAACGCGATAGT-CAAATTCGCAACCGAATTT
* *** *
20660 CTAATTTCGCAACGCGGATATGT-AAA-TCGCGTTGCGATTTT
1 C-AAATTCGCAACGC-GATA-GTCAAATTCGC-AACCGAATTT
** * *
20701 CCAAATTCGCAACATGATAGTCAAATGCGCAACGCG-ATAGT
1 -CAAATTCGCAACGCGATAGTCAAATTCGCAAC-CGAAT-TT
* * *
20742 CAAATGCGCAACGCGAAAGTCAAATTCGCAACTGAATTT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACCGAATTT
*
20781 CAAATTCGCAATGCGA
1 CAAATTCGCAACGCGA
20797 ATTTAATTTC
Statistics
Matches: 166, Mismatches: 37, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
38 2 0.01
39 54 0.33
40 82 0.49
41 25 0.15
42 2 0.01
43 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (39 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACCGAATTT
Found at i:20725 original size:160 final size:160
Alignment explanation
Indices: 20461--20811 Score: 605
Period size: 160 Copynumber: 2.2 Consensus size: 160
20451 AAATGACCAA
*
20461 CAAATTCGCAACGCGAATTCCAATTTCGTAACCCAATGTCCAATTTCGCAACGCGAATATGTAAA
1 CAAATTCGCAACGCGAATTCCAATTTCGCAACCCAATGTCCAATTTCGCAACGCGAATATGTAAA
* *
20526 TCGCGTTGCGATTTTCCAAATTCGCAACATGATAGTCAAATTCGCAACGCGAAAGTCAAATTCGC
66 TCGCGTTGCGATTTTCCAAATTCGCAACATGATAGTCAAATGCGCAACGCGAAAGTCAAATGCGC
20591 AACGCGAAAGTCAAATTCGCAACTGAATTT
131 AACGCGAAAGTCAAATTCGCAACTGAATTT
* * * *
20621 CAAATTCGCAACGCGAATTCCAATTTCGCAACCCAGTTTCTAATTTCGCAACGCGGATATGTAAA
1 CAAATTCGCAACGCGAATTCCAATTTCGCAACCCAATGTCCAATTTCGCAACGCGAATATGTAAA
*
20686 TCGCGTTGCGATTTTCCAAATTCGCAACATGATAGTCAAATGCGCAACGCGATAGTCAAATGCGC
66 TCGCGTTGCGATTTTCCAAATTCGCAACATGATAGTCAAATGCGCAACGCGAAAGTCAAATGCGC
20751 AACGCGAAAGTCAAATTCGCAACTGAATTT
131 AACGCGAAAGTCAAATTCGCAACTGAATTT
* *
20781 CAAATTCGCAATGCGAATT-TAATTTCGCAAC
1 CAAATTCGCAACGCGAATTCCAATTTCGCAAC
20812 AGGTTTTAGT
Statistics
Matches: 181, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
159 11 0.06
160 170 0.94
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (160 bp):
CAAATTCGCAACGCGAATTCCAATTTCGCAACCCAATGTCCAATTTCGCAACGCGAATATGTAAA
TCGCGTTGCGATTTTCCAAATTCGCAACATGATAGTCAAATGCGCAACGCGAAAGTCAAATGCGC
AACGCGAAAGTCAAATTCGCAACTGAATTT
Found at i:20800 original size:20 final size:20
Alignment explanation
Indices: 20461--20811 Score: 172
Period size: 20 Copynumber: 17.6 Consensus size: 20
20451 AAATGACCAA
20461 CAAATTCGCAACGCGAAT-T
1 CAAATTCGCAACGCGAATGT
* * *
20480 CCAATTTCGTAAC-CCAATGT
1 -CAAATTCGCAACGCGAATGT
*
20500 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCG-A-ATGT
*** * *
20523 -AAA-TCGCGTTGCGATTTT
1 CAAATTCGCAACGCGAATGT
**
20541 CCAAATTCGCAACATG-ATAGT
1 -CAAATTCGCAACGCGAAT-GT
*
20562 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAATGT
*
20582 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAATGT
* *
20602 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATGT
20621 CAAATTCGCAACGCGAAT-T
1 CAAATTCGCAACGCGAATGT
* * * *
20640 CCAATTTCGCAAC-CCAGTTT
1 -CAAATTCGCAACGCGAATGT
*
20660 CTAATTTCGCAACGCGGATATGT
1 C-AAATTCGCAACGC-GA-ATGT
*** * *
20683 -AAA-TCGCGTTGCGATTTT
1 CAAATTCGCAACGCGAATGT
**
20701 CCAAATTCGCAACATG-ATAGT
1 -CAAATTCGCAACGCGAAT-GT
*
20722 CAAATGCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-GT
* *
20742 CAAATGCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAATGT
* *
20762 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATGT
*
20781 CAAATTCGCAATGCGAAT-T
1 CAAATTCGCAACGCGAATGT
* *
20800 TAATTTCGCAAC
1 CAAATTCGCAAC
20812 AGGTTTTAGT
Statistics
Matches: 252, Mismatches: 57, Indels: 45
0.71 0.16 0.13
Matches are distributed among these distances:
18 4 0.02
19 53 0.21
20 167 0.66
21 20 0.08
22 2 0.01
23 6 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATGT
Found at i:24047 original size:18 final size:18
Alignment explanation
Indices: 24024--24059 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
24014 AAGCAAAAGG
*
24024 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
24042 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
24060 CAACTGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:24373 original size:20 final size:20
Alignment explanation
Indices: 24345--24390 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
24335 ATGTTGCGAT
* *
24345 CAACACGAAAGTCAAATTCG
1 CAACGCGAAAGACAAATTCG
24365 CAACGCGAAAGACAAATTCG
1 CAACGCGAAAGACAAATTCG
24385 CAACGC
1 CAACGC
24391 AAAATCGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.28, G:0.17, T:0.11
Consensus pattern (20 bp):
CAACGCGAAAGACAAATTCG
Found at i:24546 original size:25 final size:25
Alignment explanation
Indices: 24508--24557 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
24498 AAATCAATTA
*
24508 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
24533 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
24558 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:24963 original size:6 final size:6
Alignment explanation
Indices: 24944--25006 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
24934 GTAATTGGAG
* * * *
24944 TTTGAA TTTAAA TTTCAA TTTGAG TTTGAA TTTGAA TTTGAA TTTGAG
1 TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA
24992 TTTGAA TTTGAA TTT
1 TTTGAA TTTGAA TTT
25007 CAATATAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (6 bp):
TTTGAA
Found at i:24963 original size:24 final size:24
Alignment explanation
Indices: 24936--25010 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
24926 TTTCATATGT
* *
24936 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTGAATTTC
*
24960 AATTTGAGTTTGAATTTGAATTTG
1 AATTTGAGTTTGAATTTGAATTTC
24984 AATTTGAGTTTGAATTTGAATTTC
1 AATTTGAGTTTGAATTTGAATTTC
25008 AAT
1 AAT
25011 ATAAATTTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTGAATTTC
Found at i:25358 original size:39 final size:39
Alignment explanation
Indices: 25315--25401 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
25305 TCCGATGCTC
*
25315 ATCAAAATCCAAAGCTCATATGGTGCCAAGAAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTACCAAGAAAAAGGAA
* *
25354 ATCAAAATCCAAATCTCATATGGTACCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTACCAAGAAAAAGGAA
25393 ATCAAAATC
1 ATCAAAATC
25402 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTACCAAGAAAAAGGAA
Found at i:25602 original size:20 final size:20
Alignment explanation
Indices: 25577--25653 Score: 67
Period size: 20 Copynumber: 4.2 Consensus size: 20
25567 ATGTTGCGAT
25577 CAACGCGAAAGTTAAATTCG
1 CAACGCGAAAGTTAAATTCG
25597 CAACGCGAAA--T-AA---G
1 CAACGCGAAAGTTAAATTCG
** *
25611 CATTGCGATAGTTAAATTCG
1 CAACGCGAAAGTTAAATTCG
* *
25631 AAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTTAAATTCG
25651 CAA
1 CAA
25654 ACCGAAAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
14 8 0.19
16 1 0.02
17 4 0.10
18 1 0.02
20 28 0.67
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (20 bp):
CAACGCGAAAGTTAAATTCG
Found at i:25840 original size:14 final size:14
Alignment explanation
Indices: 25806--25859 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
25796 ATAATTCTTA
*
25806 TTTACAAATCAAAT
1 TTTACAAATCAACT
**
25820 TAAACAAATCAACT
1 TTTACAAATCAACT
*
25834 TTTACAAATCATCT
1 TTTACAAATCAACT
25848 TTTACAAATCAA
1 TTTACAAATCAA
25860 TTAATCAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:28672 original size:19 final size:20
Alignment explanation
Indices: 28650--28692 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
28640 AAATCGCAAC
28650 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
28669 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
28689 GCGA
1 GCGA
28693 ATTTGGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:28739 original size:13 final size:13
Alignment explanation
Indices: 28721--28752 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
28711 GGGTTACTTC
28721 AACAAAAAGACAA
1 AACAAAAAGACAA
28734 AACAAAAAGACAA
1 AACAAAAAGACAA
28747 AACAAA
1 AACAAA
28753 GACAAATACT
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:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:28755 original size:11 final size:12
Alignment explanation
Indices: 28725--28758 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
28715 TACTTCAACA
28725 AAAAGACAAAAC
1 AAAAGACAAAAC
28737 AAAAAGACAAAAC
1 -AAAAGACAAAAC
28750 -AAAGACAAA
1 AAAAGACAAA
28759 TACTAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
13 12 0.57
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:28993 original size:22 final size:22
Alignment explanation
Indices: 28965--29007 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28955 GAGATAGACG
*
28965 GATTTCGTCGGAAATGGGGACA
1 GATTTCGTCAGAAATGGGGACA
*
28987 GATTTCGTCAGAGATGGGGAC
1 GATTTCGTCAGAAATGGGGAC
29008 GGATGTCGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.37, T:0.23
Consensus pattern (22 bp):
GATTTCGTCAGAAATGGGGACA
Found at i:29164 original size:20 final size:20
Alignment explanation
Indices: 29139--29367 Score: 209
Period size: 20 Copynumber: 11.2 Consensus size: 20
29129 GCGTAAAAAC
29139 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
29159 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
29179 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
29199 ATTTGACTATCGCATTGCGA
1 ATTTGACTATCGCGTTGCGA
*
29219 ATTTGACTATCGCGTTACGA
1 ATTTGACTATCGCGTTGCGA
* *
29239 ATTTGACT-TCTGTGTTTCG-
1 ATTTGACTATC-GCGTTGCGA
* *
29258 ATTTACAAATTCGCTTTCGCGTTGCGA
1 ATTT---GA----CTATCGCGTTGCGA
29285 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
* *
29305 ATTTGGA--AACTGAGTTGCGAA
1 ATTT-GACTATC-GCGTTGCG-A
* *
29326 ATTGGAAT-TCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
* *
29345 ATTTGA-GATCGCTTTGCGA
1 ATTTGACTATCGCGTTGCGA
29364 ATTT
1 ATTT
29368 ATTGGTCATT
Statistics
Matches: 175, Mismatches: 18, Indels: 33
0.77 0.08 0.15
Matches are distributed among these distances:
19 28 0.16
20 124 0.71
21 7 0.04
22 1 0.01
24 1 0.01
26 8 0.05
27 6 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:29337 original size:66 final size:66
Alignment explanation
Indices: 29148--29325 Score: 158
Period size: 66 Copynumber: 2.8 Consensus size: 66
29138 CATTTGACTA
* * * *
29148 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA-TCGCGTTGCGAA-T-----TT-GA
1 TCGCATTGCGAATTTGACTATCGCGTTACGAATTTGACAACT-GAGTTGCGAATTACAAATTCG-
*
29205 CTA
64 CTT
** * * *
29208 TCGCATTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTTCGATTTACAAATTCGCT
1 TCGCATTGCGAATTTGACTATCGCGTTACGAATTTGACAACTGAGTTGCGAATTACAAATTCGCT
29273 T
66 T
* *
29274 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGGA-AACTGAGTTGCGAA
1 TCGCATTGCGAATTTGACTATCGCGTTACGAATTT-GACAACTGAGTTGCGAA
29326 ATTGGAATTC
Statistics
Matches: 95, Mismatches: 14, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
60 44 0.46
61 2 0.02
66 46 0.48
67 3 0.03
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (66 bp):
TCGCATTGCGAATTTGACTATCGCGTTACGAATTTGACAACTGAGTTGCGAATTACAAATTCGCT
T
Found at i:31635 original size:13 final size:14
Alignment explanation
Indices: 31617--31651 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
31607 TAAAACACAT
31617 GGGCTGCTAA-GGG
1 GGGCTGCTAAGGGG
31630 GGGCTGCTAAGGGG
1 GGGCTGCTAAGGGG
31644 GGGCTGCT
1 GGGCTGCT
31652 GTAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.11, C:0.17, G:0.54, T:0.17
Consensus pattern (14 bp):
GGGCTGCTAAGGGG
Found at i:32069 original size:16 final size:16
Alignment explanation
Indices: 32048--32081 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
32038 TTACTATTCA
*
32048 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
32064 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
32080 CG
1 CG
32082 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:32852 original size:15 final size:16
Alignment explanation
Indices: 32832--32863 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
32822 TGGCAGATCC
32832 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
32847 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
32863 A
1 A
32864 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:36143 original size:13 final size:13
Alignment explanation
Indices: 36125--36165 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
36115 TAAAACACAT
36125 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
36138 GGGCTGCTAA-GG
1 GGGCTGCTAAGGG
36150 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
36163 GGG
1 GGG
36166 GGCTGCTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (13 bp):
GGGCTGCTAAGGG
Found at i:36153 original size:12 final size:12
Alignment explanation
Indices: 36125--36164 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
36115 TAAAACACAT
36125 GGGCTGCTAAGGG
1 GGGCTGCTAA-GG
36138 GGGCTGCTAAGG
1 GGGCTGCTAAGG
36150 GGGCTGCTAAGG
1 GGGCTGCTAAGG
36162 GGG
1 GGG
36165 GGGCTGCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.15, C:0.15, G:0.55, T:0.15
Consensus pattern (12 bp):
GGGCTGCTAAGG
Found at i:36738 original size:20 final size:20
Alignment explanation
Indices: 36715--36802 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
36705 GTTTCCAATT
*
36715 TCGCAACGTGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
** * * **
36735 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATATGTAAA
*
36755 TTCGCAACGCGAATCTGTAAA
1 -TCGCAACGCGAATATGTAAA
*
36776 TCGCAACGCGAATGTGTAAA
1 TCGCAACGCGAATATGTAAA
36796 TCGCAAC
1 TCGCAAC
36803 ACAGAAGTCA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 39 0.74
21 14 0.26
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:36819 original size:20 final size:20
Alignment explanation
Indices: 36796--36883 Score: 88
Period size: 20 Copynumber: 4.3 Consensus size: 20
36786 AATGTGTAAA
36796 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
36816 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
36836 TCGCAATACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* ** *
36856 TTGCAATGCAGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
36877 TCGCAAC
1 TCGCAAC
36884 TGAATTTCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 41 0.75
21 12 0.22
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.22
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:36820 original size:40 final size:40
Alignment explanation
Indices: 36796--36883 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
36786 AATGTGTAAA
*
36796 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
* * * *
36836 TCGCAATACAAAAGTCAAATTTGCAATGCAGA-ATTTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGC-GATA-GTCAAAT
36877 TCGCAAC
1 TCGCAAC
36884 TGAATTTCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 26 0.65
41 14 0.35
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.22
Consensus pattern (40 bp):
TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:36890 original size:19 final size:20
Alignment explanation
Indices: 36865--36922 Score: 91
Period size: 19 Copynumber: 3.0 Consensus size: 20
36855 TTTGCAATGC
36865 AGAATTTCAAATTCGCAACT
1 AGAATTTCAAATTCGCAACT
36885 -GAATTTCAAATTCGCAACT
1 AGAATTTCAAATTCGCAACT
* *
36904 AGATTTTCGAATTCGCAAC
1 AGAATTTCAAATTCGCAAC
36923 AGTTTTTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (20 bp):
AGAATTTCAAATTCGCAACT
Found at i:37732 original size:12 final size:12
Alignment explanation
Indices: 37711--37744 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
37701 ACCACATTTC
*
37711 CAATACCAAACA
1 CAATATCAAACA
37723 CAATATCAAACA
1 CAATATCAAACA
*
37735 CAATCTCAAA
1 CAATATCAAA
37745 ACTCACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:37895 original size:24 final size:24
Alignment explanation
Indices: 37868--37923 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
37858 CAGTATTCGA
*
37868 ACTTTGATCTTGGTCAATACTCGG
1 ACTTTGATCTTGGTCAATACTCAG
37892 ACTTTGATCTTGGTCAATACTCAG
1 ACTTTGATCTTGGTCAATACTCAG
*
37916 ATTTTGAT
1 ACTTTGAT
37924 GATATGATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (24 bp):
ACTTTGATCTTGGTCAATACTCAG
Found at i:40523 original size:20 final size:20
Alignment explanation
Indices: 40498--40547 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
40488 ATGTTGCGAT
*
40498 CAACGTGAAAGTCAAATTCG
1 CAACGTGAAAGTAAAATTCG
*
40518 CAACGTGAAAGTAAAATTTG
1 CAACGTGAAAGTAAAATTCG
40538 CAACGTGAAA
1 CAACGTGAAA
40548 TCGCAAACCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (20 bp):
CAACGTGAAAGTAAAATTCG
Found at i:40639 original size:20 final size:20
Alignment explanation
Indices: 40614--40651 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
40604 GCAACGCTTA
40614 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
40634 TTTCGCGTTGCGAATTTG
1 TTTCGCGTTGCGAATTTG
40652 TACCTTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:40725 original size:14 final size:14
Alignment explanation
Indices: 40706--40742 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
40696 ATTTAAAACA
40706 ACAAATCAACTTTT
1 ACAAATCAACTTTT
40720 ACAAATCAACTTTT
1 ACAAATCAACTTTT
40734 ACAAATCAA
1 ACAAATCAA
40743 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:42501 original size:20 final size:20
Alignment explanation
Indices: 42444--42490 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
42434 CTAAAATCGC
42444 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
42464 GTTGCGATTTTCATTTTCTT
1 GTTGCGATTTTCATTTTCGT
42484 GTTGCGA
1 GTTGCGA
42491 ATTTAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.11, C:0.15, G:0.21, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:42867 original size:22 final size:22
Alignment explanation
Indices: 42840--42919 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
42830 GATGGAGATA
*
42840 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
42862 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
42884 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
42906 GACGGATGTCGTCG
1 GACGGATTTCGTCG
42920 TAGAGAGTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.17, C:0.15, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:43092 original size:21 final size:19
Alignment explanation
Indices: 43023--43104 Score: 101
Period size: 20 Copynumber: 4.1 Consensus size: 19
43013 AATATTGTGT
*
43023 TTCGCGTTGCGAATTTGAC
1 TTCGTGTTGCGAATTTGAC
43042 TATCGTGTTGCGAATTTGAC
1 T-TCGTGTTGCGAATTTGAC
* *
43062 TTTTGTGTTGCGAATTTGAAA
1 -TTCGTGTTGCGAATTTG-AC
43083 TTCAGTGTTGCGAATTTGAC
1 TTC-GTGTTGCGAATTTGAC
43103 TT
1 TT
43105 TTGTGTTACG
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.02
20 37 0.69
21 16 0.30
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.43
Consensus pattern (19 bp):
TTCGTGTTGCGAATTTGAC
Found at i:43099 original size:41 final size:40
Alignment explanation
Indices: 43028--43111 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 40
43018 TGTGTTTCGC
*
43028 GTTGCGAATTTGACTATCGTGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAATATCGTGTTGCGAATTTGACTTTTGT
43068 GTTGCGAATTTGAA-ATTCAGTGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAATA-TC-GTGTTGCGAATTTGACTTTTGT
43109 GTT
1 GTT
43112 ACGATTTACA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 1 0.02
40 15 0.37
41 25 0.61
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.45
Consensus pattern (40 bp):
GTTGCGAATTTGAATATCGTGTTGCGAATTTGACTTTTGT
Found at i:43125 original size:41 final size:40
Alignment explanation
Indices: 43044--43135 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 40
43034 AATTTGACTA
* *
43044 TCGTGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAAAT
1 TCGTGTTGCGAATTTGACTTTTGTGTTACGAATTTCAAAT
43084 TCAGTGTTGCGAATTTGACTTTTGTGTTACG-ATTTACAAAT
1 TC-GTGTTGCGAATTTGACTTTTGTGTTACGAATTT-CAAAT
*
43125 TCGCGTTGCGA
1 TCGTGTTGCGA
43136 TTTACAGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
40 14 0.30
41 33 0.70
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.42
Consensus pattern (40 bp):
TCGTGTTGCGAATTTGACTTTTGTGTTACGAATTTCAAAT
Found at i:43138 original size:20 final size:20
Alignment explanation
Indices: 43113--43196 Score: 78
Period size: 20 Copynumber: 4.2 Consensus size: 20
43103 TTTTGTGTTA
43113 CGATTTACAAATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
*
43133 CGATTTACAGATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
* ** * ***
43153 CGAATATGGAAAATCGCAACG
1 CG-ATTTACAAATTCGCGTTG
*
43174 CGATTTACATATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
43194 CGA
1 CGA
43197 AATTAGAAAC
Statistics
Matches: 46, Mismatches: 17, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 34 0.74
21 12 0.26
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTG
Found at i:47951 original size:24 final size:25
Alignment explanation
Indices: 47924--47973 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
47914 GTATTTGGAA
*
47924 ACTGCTTTTGATCC-TTCCTTTTCC
1 ACTGCTTTTGATCCACTCCTTTTCC
* *
47948 ACTGTTTTTGGTCCACTCCTTTTCC
1 ACTGCTTTTGATCCACTCCTTTTCC
47973 A
1 A
47974 AGTTTGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.10, C:0.32, G:0.10, T:0.48
Consensus pattern (25 bp):
ACTGCTTTTGATCCACTCCTTTTCC
Found at i:48852 original size:31 final size:32
Alignment explanation
Indices: 48814--48898 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 32
48804 TTATATATTT
*
48814 TTGAATTTTTTTGAC-TTTATATT-TTTTTGTA
1 TTGAATTTTTTTAACTTTTA-ATTCTTTTTGTA
* *
48845 TTGAATTTTATTAACTTTTAATTCTTTTTTTA
1 TTGAATTTTTTTAACTTTTAATTCTTTTTGTA
* *
48877 TTGCATTTTTAT-ACTTTTAATT
1 TTGAATTTTTTTAACTTTTAATT
48899 ACAATTGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 26 0.57
32 20 0.43
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (32 bp):
TTGAATTTTTTTAACTTTTAATTCTTTTTGTA
Found at i:48961 original size:21 final size:20
Alignment explanation
Indices: 48936--48995 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
48926 TTCACTTTTT
48936 TAAAAATCAATAAAAATGAAA
1 TAAAAATCAATAAAAATG-AA
** *
48957 TAAAAAAGAATTAAAAGTGAA
1 TAAAAATCAA-TAAAAATGAA
*
48978 TAAAATTCAATAAAAATG
1 TAAAAATCAATAAAAATG
48996 TCAACTTTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.23
21 17 0.55
22 7 0.23
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (20 bp):
TAAAAATCAATAAAAATGAA
Found at i:49164 original size:10 final size:10
Alignment explanation
Indices: 49149--49206 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
49139 TTATTTTTTA
49149 AAAAATCAAT
1 AAAAATCAAT
49159 AAAAATACAAT
1 AAAAAT-CAAT
**
49170 AAAAAAGAATT
1 AAAAATCAA-T
*
49181 AAAATTCAAT
1 AAAAATCAAT
*
49191 AAAATTCAAT
1 AAAAATCAAT
49201 ACAAAA
1 A-AAAA
49207 AGAATATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 20 0.51
11 19 0.49
ACGTcount: A:0.69, C:0.09, G:0.02, T:0.21
Consensus pattern (10 bp):
AAAAATCAAT
Found at i:49174 original size:21 final size:21
Alignment explanation
Indices: 49149--49206 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
49139 TTATTTTTTA
49149 AAAAATCAATAAAAATACAAT
1 AAAAATCAATAAAAATACAAT
** * *
49170 AAAAAAGAATTAAAATTCAAT
1 AAAAATCAATAAAAATACAAT
*
49191 AAAATTCAATACAAAA
1 AAAAATCAATA-AAAA
49207 AGAATATAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.69, C:0.09, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAAATCAATAAAAATACAAT
Found at i:49222 original size:32 final size:32
Alignment explanation
Indices: 49149--49222 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
49139 TTATTTTTTA
*
49149 AAAAATCAATAAAAATACAATAAAAAAGAATT
1 AAAAGTCAATAAAAATACAATAAAAAAGAATT
* *
49181 AAAATTCAAT-AAAATTCAATACAAAAAGAA-T
1 AAAAGTCAATAAAAATACAATA-AAAAAGAATT
49212 ATAAAGTCAAT
1 A-AAAGTCAAT
49223 TTTTTTCTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 12 0.32
32 25 0.68
ACGTcount: A:0.66, C:0.08, G:0.04, T:0.22
Consensus pattern (32 bp):
AAAAGTCAATAAAAATACAATAAAAAAGAATT
Found at i:50379 original size:17 final size:15
Alignment explanation
Indices: 50365--50404 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
50355 AGTAATATAA
50365 TTATATAAATAATAT
1 TTATATAAATAATAT
*
50380 TTTTATTAAAATAATAT
1 TTATA-T-AAATAATAT
50397 TTATATAA
1 TTATATAA
50405 TTGTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 6 0.29
16 2 0.10
17 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATAAATAATAT
Found at i:50601 original size:28 final size:31
Alignment explanation
Indices: 50568--50634 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
50558 TGTTAATATT
50568 TATTATTTTTAATT-TAAA-TTTATAATGAA
1 TATTATTTTTAATTATAAATTTTATAATGAA
* *
50597 T-TTA-TATTAATTATAAATTTTTATAATGCA
1 TATTATTTTTAATTATAAA-TTTTATAATGAA
50627 TATTATTT
1 TATTATTT
50635 AGGAAACTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.23
28 7 0.23
29 1 0.03
30 11 0.37
31 3 0.10
32 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (31 bp):
TATTATTTTTAATTATAAATTTTATAATGAA
Found at i:52237 original size:21 final size:21
Alignment explanation
Indices: 52211--52269 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
52201 ATCTCCGCAG
52211 GGTTACATTCCTAGCCCTCAA
1 GGTTACATTCCTAGCCCTCAA
*
52232 GGTTACATTCCTAGCCCTCCA
1 GGTTACATTCCTAGCCCTCAA
*
52253 GGTTACATGCCTAGCCC
1 GGTTACATTCCTAGCCC
52270 GTAGGGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.36, G:0.17, T:0.27
Consensus pattern (21 bp):
GGTTACATTCCTAGCCCTCAA
Found at i:52277 original size:21 final size:21
Alignment explanation
Indices: 52208--52277 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
52198 ACCATCTCCG
52208 CAGGGTTACATTCCTAGCCCT
1 CAGGGTTACATTCCTAGCCCT
*
52229 CAAGGTTACATTCCTAGCCCT
1 CAGGGTTACATTCCTAGCCCT
*
52250 CCA-GGTTACATGCCTAGCCCGT
1 -CAGGGTTACATTCCTAGCCC-T
52272 -AGGGTT
1 CAGGGTT
52278 TTATGACACC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
20 1 0.02
21 40 0.91
22 3 0.07
ACGTcount: A:0.20, C:0.31, G:0.21, T:0.27
Consensus pattern (21 bp):
CAGGGTTACATTCCTAGCCCT
Found at i:52831 original size:34 final size:34
Alignment explanation
Indices: 52787--52859 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
52777 TTTAATGTTT
*
52787 TTAATATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
52821 TTAAAATACAAATTATGGTATTTGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
52855 TTAAA
1 TTAAA
52860 TTCAACTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:52988 original size:14 final size:14
Alignment explanation
Indices: 52969--52995 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52959 TTATCCTTAA
52969 CATATACATTAAAG
1 CATATACATTAAAG
52983 CATATACATTAAA
1 CATATACATTAAA
52996 ACCAACTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.30
Consensus pattern (14 bp):
CATATACATTAAAG
Found at i:53167 original size:63 final size:63
Alignment explanation
Indices: 53063--53190 Score: 222
Period size: 63 Copynumber: 2.0 Consensus size: 63
53053 TTTCAATGTC
53063 ACAACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
1 ACAACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
* *
53126 ACAACCAA-TTGATCACTTCACATTTATTCAATTTATTCATAACATTTTATCCAATTTATTCAA
1 ACAACCAACTT-ATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
53189 AC
1 AC
53191 TTCACATAAC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
62 2 0.03
63 60 0.97
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.39
Consensus pattern (63 bp):
ACAACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
Found at i:53185 original size:23 final size:22
Alignment explanation
Indices: 53082--53187 Score: 80
Period size: 23 Copynumber: 4.9 Consensus size: 22
53072 TTATCACTTC
* *
53082 ACATTTATTCAATTTATCCATA
1 ACATTTATCCAATTTATTCATA
*
53104 ACATTTTATCCAATATATTCA-A
1 ACA-TTTATCCAATTTATTCATA
* *
53126 ACA---A-CCAATTGA-TCACTTC
1 ACATTTATCCAATTTATTCA--TA
*
53145 ACATTTATTCAATTTATTCATA
1 ACATTTATCCAATTTATTCATA
53167 ACATTTTATCCAATTTATTCA
1 ACA-TTTATCCAATTTATTCA
53188 AACTTCACAT
Statistics
Matches: 64, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
16 3 0.05
17 6 0.09
18 1 0.02
19 3 0.05
22 12 0.19
23 36 0.56
24 3 0.05
ACGTcount: A:0.37, C:0.20, G:0.01, T:0.42
Consensus pattern (22 bp):
ACATTTATCCAATTTATTCATA
Found at i:56781 original size:25 final size:25
Alignment explanation
Indices: 56744--56802 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
56734 TATGTACACC
* *
56744 TAAATAATTTTTTTTAATTTTTATT
1 TAAATAATTTTTTATAATATTTATT
*
56769 TAAA-AATTATTTTATGATATTTATT
1 TAAATAATT-TTTTATAATATTTATT
56794 TAATATAAT
1 TAA-ATAAT
56803 AATTAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.14
25 20 0.71
26 1 0.04
27 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TAAATAATTTTTTATAATATTTATT
Found at i:56836 original size:22 final size:22
Alignment explanation
Indices: 56785--56847 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
56775 TTATTTTATG
* **
56785 ATATTTATTTAATATAATAATTA
1 ATATTTATTTATTATAA-AAAAA
56808 ATA-TTATTTATTATAAAAAAA
1 ATATTTATTTATTATAAAAAAA
* *
56829 ATATTTATTAATTTTAAAA
1 ATATTTATTTATTATAAAA
56848 TATTATAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 6 0.18
22 25 0.74
23 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTTATTTATTATAAAAAAA
Found at i:56847 original size:18 final size:19
Alignment explanation
Indices: 56826--56861 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
56816 TATTATAAAA
*
56826 AAAATATT-TATTAATTTT
1 AAAATATTATAATAATTTT
56844 AAAATATTATAATAATTT
1 AAAATATTATAATAATTT
56862 CACCTTCTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATATTATAATAATTTT
Found at i:57770 original size:21 final size:20
Alignment explanation
Indices: 57732--57771 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
57722 AACAAAAGTT
* *
57732 AATATATTTTAATTATATTC
1 AATATATTTGAATAATATTC
57752 AATATAATTTGAATAATATT
1 AATAT-ATTTGAATAATATT
57772 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
AATATATTTGAATAATATTC
Found at i:59038 original size:91 final size:91
Alignment explanation
Indices: 58883--59065 Score: 330
Period size: 91 Copynumber: 2.0 Consensus size: 91
58873 AATCATTAGT
*
58883 TACATATTGATTACCAAATGACTAAGCAGTTTGAGATGTAATGGCTAGCCATATCTTACCATCGG
1 TACATATTGATTACCAAATGACTAAGCAGTTTGAGATGTAATGGCTAGACATATCTTACCATCGG
*
58948 AACGGAATCTTCAGCATTATCAGTTC
66 AACGGAATCTTCAGCAGTATCAGTTC
*
58974 TACATATTGATTACCAAATGACTAAGCAGTTTGAGATGTAATGGCTAGACATATCTTACTATCGG
1 TACATATTGATTACCAAATGACTAAGCAGTTTGAGATGTAATGGCTAGACATATCTTACCATCGG
*
59039 AACTGAATCTTCAGCAGTATCAGTTC
66 AACGGAATCTTCAGCAGTATCAGTTC
59065 T
1 T
59066 GGAATTAGAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (91 bp):
TACATATTGATTACCAAATGACTAAGCAGTTTGAGATGTAATGGCTAGACATATCTTACCATCGG
AACGGAATCTTCAGCAGTATCAGTTC
Found at i:66163 original size:19 final size:19
Alignment explanation
Indices: 66114--66191 Score: 111
Period size: 19 Copynumber: 4.1 Consensus size: 19
66104 ATATGAAATT
66114 TGTCCCAAAGGACCTCATGA
1 TGTCCCAAAGGACCTCAT-A
* *
66134 TATCCCAAAGGACCTCGTA
1 TGTCCCAAAGGACCTCATA
*
66153 TGTCCCGAAGGACCTCATA
1 TGTCCCAAAGGACCTCATA
*
66172 TGTCCCGAAGGACCTCATA
1 TGTCCCAAAGGACCTCATA
66191 T
1 T
66192 AACCCTCGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 37 0.70
20 16 0.30
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (19 bp):
TGTCCCAAAGGACCTCATA
Found at i:66168 original size:39 final size:38
Alignment explanation
Indices: 66114--66187 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
66104 ATATGAAATT
66114 TGTCCCAAAGGACCTCATGATATCCCAAAGGACCTCGTA
1 TGTCCCAAAGGACCTCAT-ATATCCCAAAGGACCTCGTA
* * *
66153 TGTCCCGAAGGACCTCATATGTCCCGAAGGACCTC
1 TGTCCCAAAGGACCTCATATATCCCAAAGGACCTC
66188 ATATAACCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 15 0.47
39 17 0.53
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.20
Consensus pattern (38 bp):
TGTCCCAAAGGACCTCATATATCCCAAAGGACCTCGTA
Found at i:68604 original size:18 final size:18
Alignment explanation
Indices: 68577--68611 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
68567 TGAATATTTA
68577 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
* *
68595 TCCCGGAGGACTACTAT
1 TCCCGAAGGACCACTAT
68612 TATAACACCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:69249 original size:38 final size:38
Alignment explanation
Indices: 69198--69277 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
69188 CTCGTATAAA
** *
69198 TGTCCCAAAGGACCTATCATATTGAAGGATGTCATCTG
1 TGTCCCAAAGGACCTATCATACCGAAGGATGTAATCTG
* * *
69236 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCAAAGGACCTATCATACCGAAGGATGTAATCTG
69274 TGTC
1 TGTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (38 bp):
TGTCCCAAAGGACCTATCATACCGAAGGATGTAATCTG
Done.