Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003126.1 Hibiscus syriacus cultivar Beakdansim tig00006547_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: 64817
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6974 original size:55 final size:55
Alignment explanation
Indices: 6860--7131 Score: 368
Period size: 55 Copynumber: 5.0 Consensus size: 55
6850 GATGCATGAA
* * * * *
6860 ACTCGCACAATCTTCAACAAACGTCTCTGCTCTCTA-TGCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTTTCTGCTCCCTATTTCTTCAGAGAGTATAAG
*
6914 ACTCGAACAATCTTCAACAATCGTTTCTGCTCCCTATTTCTTCAGAGAGTATTAG
1 ACTCGAACAATCTTCAACAATCGTTTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* * *
6969 ACTCGAACAATTTTCAACATTCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTTTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* * * *
7024 ACTCGAACATTCTTCAACAATCGTTTTTGTTCCCTATTTCTTCAAAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTTTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* * * *
7079 ACTCGAACAATCTTCAATAATCGGGTTC-GCTCCCTCTTTCTTCAGGGAGTATA
1 ACTCGAACAATCTTCAACAATC-GTTTCTGCTCCCTATTTCTTCAGAGAGTATA
7132 GAACCCTAAT
Statistics
Matches: 191, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
54 32 0.17
55 156 0.82
56 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGTTTCTGCTCCCTATTTCTTCAGAGAGTATAAG
Found at i:7245 original size:54 final size:54
Alignment explanation
Indices: 6898--8093 Score: 1172
Period size: 55 Copynumber: 22.1 Consensus size: 54
6888 GCTCTCTATG
* ** * * *
6898 CTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATC-GTTTCTGCTCCCTATTT
1 CTTCAGGGAGTATAGA-ACTCGAAC-ATCTTCTTCAAACGGGTTC-GCTCCCTCTTT
* * * *
6953 CTTCAGAGAGTATTAG-ACTCGAACA-ATT-TTCAACATTCGTG-TCTGCTCCCTATTT
1 CTTCAGGGAGTA-TAGAACTCGAACATCTTCTTCAA-A--CGGGTTC-GCTCCCTCTTT
* ** * ** * * *
7008 CTTCAGAGAGTATA-AGACTCGAACATTCTTCAACAATCGTTTTTGTTCCCTATTT
1 CTTCAGGGAGTATAGA-ACTCGAACA-TCTTCTTCAAACGGGTTCGCTCCCTCTTT
** * *
7063 CTTCAAAGAGTATA-AGACTCGAACAATCTTCAAT-AATCGGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGA-ACTCGAAC-ATCTTC-TTCAAACGGGTTCGCTCCCTCTTT
* * * *
7118 CTTCAGGGAGTATAGAACCCTAATAATCTTCTGT-AAACAGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGAA-CATCTTCT-TCAAACGGGTTCGCTCCCTCTTT
* * *
7173 CTTCAGGGAGTATAGAACTCGAACATTTTCTTCAAACGAGTTCTCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * * *
7227 C-TCTAGGGAGTATAGAACTTGGACATCTTCTTCAAACAGGTTCACTCCCTCTTT
1 CTTC-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
*
7281 CTTCAGGGAGTATAGAACTTGGAA-AT-TTCTTCAAACGGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGAAC-TCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* *
7334 C-TCTAGGGAGTAT-GTAACTCAAACATCTTCTTCAAACGGGTTCGCTTCGCTCTTT
1 CTTC-AGGGAGTATAG-AACTCGAACATCTTCTTCAAACGGGTTCGC-TCCCTCTTT
** *
7389 CTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* **
7444 CTTCAGGAAGTATAGAACTCGATA-ATCTTCTTCTTACGGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGA-ACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
*
7498 CTTCAGGGAGTATAGAACTCG---ATCTTCTTCAAACGGGTTCTCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
** * *
7549 CTTCAATGAATATAGAACTCGAAAATCTTC-T--AACGGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * * **
7600 CTTTAGAGAGTATAGAACTCGTACAATCTTCTGAAAACGGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* ** *
7655 CTTCAGGAAGTATAGAACTCGAGA-ATCTTCTTCTTACGGGTTCGCTTCGCTCTTT
1 CTTCAGGGAGTATAGAACTCGA-ACATCTTCTTCAAACGGGTTCGC-TCCCTCTTT
* * * *
7710 CTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACAGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGAA-CATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* *
7765 C-TCTAGGGAGTATGGAACTCAAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1 CTTC-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * *
7819 C-TCTAGGGAGTATGGAACTCGAACATCTTCTTTAAACGGGTTCTCTCCCTCTTT
1 CTTC-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
** *
7873 CTTCAATGAGTATAGAACTCGAAAATCTTC-T--AACGGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * **
7924 CTTTAGAGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* ** *
7979 CTTCAGGAAGTATAGAACTCGAGA-ATCTTCTTCTTACGGGTTCGCTTCGCTCTTT
1 CTTCAGGGAGTATAGAACTCGA-ACATCTTCTTCAAACGGGTTCGC-TCCCTCTTT
* * * *
8034 CTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACAGGTTCGCTCCCTCTTT
1 CTTCAGGGAGTATAGAACTCGAA-CATCTTCTTCAAACGGGTTCGCTCCCTCTTT
8089 CTTCA
1 CTTCA
8094 TACACGAAAA
Statistics
Matches: 970, Mismatches: 120, Indels: 102
0.81 0.10 0.09
Matches are distributed among these distances:
51 121 0.12
52 21 0.02
53 47 0.05
54 298 0.31
55 414 0.43
56 64 0.07
57 2 0.00
58 3 0.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (54 bp):
CTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
Found at i:7952 original size:324 final size:324
Alignment explanation
Indices: 7102--8093 Score: 1461
Period size: 324 Copynumber: 3.1 Consensus size: 324
7092 TCAATAATCG
* * *
7102 GGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACCCTAATAATCTTCTGT-AAACAGGTTCGCTC
1 GGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCT-TCAAACGGGTTCGCTC
* *
7166 CCTCTTTCTTCAGGGAGTATAGAACTCGAACATTTTCTTCAAACGAGTTCTCTCCCTCTTTC-TC
64 CCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTTC
** * * * * * * *
7230 TAGGGAGTATAGAACTTGGACATCTTCTTCAAACAGGTTCACTCCCTCTTTCTTCAGGGAGTATA
129 -AATGAGTATAGAACTCGAAAATCTTC-T--AACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATA
* * ** *
7295 GAACTTGGA-AAT-TTCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTAT-GTAACTC-A
190 GAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAG-AACTCGA
* ** * *
7355 AACATCTTCTTCAAACGGGTTCGCTTCGCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTC
253 GA-ATCTTCTTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTC
* **
7420 TGAAAATG
317 TGCAAACA
* * **
7428 GGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGATAATCTTCTTCTTACGGGTTCGCTCCC
1 GGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
7493 TCTTTCTTCAGGGAGTATAGAACTCG---ATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTTCAA
66 TCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTTCAA
*
7555 TGAATATAGAACTCGAAAATCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAGAACTC
131 TGAGTATAGAACTCGAAAATCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAGAACTC
*
7620 GTACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTC
196 GAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTC
7685 TTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACA
261 TTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACA
*
7749 GGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTC-AAACATCTTCTTCAAACGGGTTCGCTC
1 GGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAA-ATCTTCTTCAAACGGGTTCGCTC
* *
7812 CCTCTTTC-TCTAGGGAGTATGGAACTCGAACATCTTCTTTAAACGGGTTCTCTCCCTCTTTCTT
64 CCTCTTTCTTC-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTT
7876 CAATGAGTATAGAACTCGAAAATCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAGAA
128 CAATGAGTATAGAACTCGAAAATCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAGAA
7941 CTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATC
193 CTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATC
8006 TTCTTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAA
258 TTCTTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAA
8071 CA
323 CA
8073 GGTTCGCTCCCTCTTTCTTCA
1 GGTTCGCTCCCTCTTTCTTCA
8094 TACACGAAAA
Statistics
Matches: 611, Mismatches: 41, Indels: 30
0.90 0.06 0.04
Matches are distributed among these distances:
319 37 0.06
320 9 0.01
321 179 0.29
322 54 0.09
323 2 0.00
324 246 0.40
325 49 0.08
326 35 0.06
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (324 bp):
GGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
TCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTTCAA
TGAGTATAGAACTCGAAAATCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAGAACTC
GAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTC
TTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACA
Found at i:10784 original size:5 final size:5
Alignment explanation
Indices: 10774--10818 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
10764 ATTTTCAATT
10774 TTTTC TTTTC TTTTC TTTCTTC TTTTC TTTTCC TTTTC TCTTTC T
1 TTTTC TTTTC TTTTC -TT-TTC TTTTC TTTT-C TTTTC T-TTTC T
10819 ACATTTCTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 19 0.53
6 14 0.39
7 3 0.08
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:10796 original size:12 final size:11
Alignment explanation
Indices: 10774--10818 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
10764 ATTTTCAATT
10774 TTTTC-TTTTC
1 TTTTCTTTTTC
10784 TTTTCTTTCTTC
1 TTTTCTTT-TTC
*
10796 TTTTCTTTTCC
1 TTTTCTTTTTC
*
10807 TTTTCTCTTTC
1 TTTTCTTTTTC
10818 T
1 T
10819 ACATTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 5 0.17
11 14 0.47
12 11 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:10798 original size:17 final size:16
Alignment explanation
Indices: 10774--10818 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
10764 ATTTTCAATT
*
10774 TTTTCTTTTCTTTTCT
1 TTTTCTTTTCTTTTCC
10790 TTCTTCTTTTCTTTTCC
1 TT-TTCTTTTCTTTTCC
10807 TTTTCTCTTTCT
1 TTTTCT-TTTCT
10819 ACATTTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTCTTTTCC
Found at i:10818 original size:22 final size:22
Alignment explanation
Indices: 10774--10818 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
10764 ATTTTCAATT
*
10774 TTTTCTTTTCTTTTCTTTCTTC
1 TTTTCTTTTCTTTTCTCTCTTC
10796 TTTTCTTTTCCTTTTCTCT-TTC
1 TTTTCTTTT-CTTTTCTCTCTTC
10818 T
1 T
10819 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTCTTTTCTTTTCTCTCTTC
Found at i:10825 original size:25 final size:23
Alignment explanation
Indices: 10775--10838 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
10765 TTTTCAATTT
* *
10775 TTTCTTTTCTTT-TCTTTCTTCT
1 TTTCTTTTCTTTCTCTTTCTACA
10797 TTTCTTTTCCTTTTCTCTTTCTACA
1 TTTCTTTT-C-TTTCTCTTTCTACA
*
10822 TTTCTCTTCTTTCTCTT
1 TTTCTTTTCTTTCTCTT
10839 CATAATGACA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.22
23 9 0.25
24 4 0.11
25 15 0.42
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTCTTTTCTTTCTCTTTCTACA
Found at i:13411 original size:19 final size:20
Alignment explanation
Indices: 13386--13437 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
13376 CATGCGACGT
13386 GGTCTTCTCGTCTTTACGAA
1 GGTCTTCTCGTCTTTACGAA
*
13406 -GTCTTCTCGTC-TTATGAA
1 GGTCTTCTCGTCTTTACGAA
13424 GGTCTTCTCGTCTT
1 GGTCTTCTCGTCTT
13438 GATGGTCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 6 0.21
19 22 0.76
20 1 0.03
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
GGTCTTCTCGTCTTTACGAA
Found at i:13450 original size:16 final size:17
Alignment explanation
Indices: 13385--13457 Score: 76
Period size: 19 Copynumber: 4.1 Consensus size: 17
13375 CCATGCGACG
*
13385 TGGTCTTCTCGTCTTTA
1 TGGTCTTCTCGTCTTGA
*
13402 CGAAGTCTTCTCGTCTTATGA
1 TG--GTCTTCTCGTC-T-TGA
*
13423 AGGTCTTCTCGTCTTGA
1 TGGTCTTCTCGTCTTGA
13440 TGGTC-TCTCGTCTTGA
1 TGGTCTTCTCGTCTTGA
13456 TG
1 TG
13458 AATGCCCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
16 13 0.27
17 8 0.17
18 1 0.02
19 22 0.46
20 1 0.02
21 3 0.06
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (17 bp):
TGGTCTTCTCGTCTTGA
Found at i:13470 original size:21 final size:21
Alignment explanation
Indices: 13445--13493 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
13435 CTTGATGGTC
13445 TCTCGTCTTGATGAATGCCCT
1 TCTCGTCTTGATGAATGCCCT
*
13466 TCTCGTCTTGATGAATGCTCT
1 TCTCGTCTTGATGAATGCCCT
13487 TCTCGTC
1 TCTCGTC
13494 CTTGGTACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.12, C:0.29, G:0.18, T:0.41
Consensus pattern (21 bp):
TCTCGTCTTGATGAATGCCCT
Found at i:13475 original size:37 final size:35
Alignment explanation
Indices: 13410--13478 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
13400 TACGAAGTCT
**
13410 TCTCGTCTTATGAAGGTCTTCTCGTCTTGATGGTC
1 TCTCGTCTTATGAAGCCCTTCTCGTCTTGATGGTC
13445 TCTCGTCTTGATGAATGCCCTTCTCGTCTTGATG
1 TCTCGTCTT-ATGAA-GCCCTTCTCGTCTTGATG
13479 AATGCTCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 9 0.30
36 5 0.17
37 16 0.53
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.42
Consensus pattern (35 bp):
TCTCGTCTTATGAAGCCCTTCTCGTCTTGATGGTC
Found at i:18950 original size:64 final size:65
Alignment explanation
Indices: 18790--18951 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
18780 GAATTAATTG
* * **** *
18790 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
* * **
18855 AAACATCGAATGCATTTGATGCATCCATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
18919 AAACATCGAATGCATTTCATGCATCGATGCACA
1 AAACATCGAATGCATTTCATGCATCGATGCACA
18952 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 31 0.37
65 53 0.63
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:26342 original size:21 final size:21
Alignment explanation
Indices: 26300--26343 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
26290 ACCCCGGGAG
*
26300 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
26321 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
26342 CT
1 CT
26344 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:27082 original size:20 final size:21
Alignment explanation
Indices: 27045--27084 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
27035 AAATTAAGTT
27045 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
27066 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
27085 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:27461 original size:64 final size:65
Alignment explanation
Indices: 27301--27462 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
27291 GAATTAATTG
* * **** *
27301 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
* * **
27366 AAACATTGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
27430 AAACATCGAATGCATTTCATGCATCGATGCACA
1 AAACATCGAATGCATTTCATGCATCGATGCACA
27463 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 31 0.37
65 53 0.63
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:33571 original size:41 final size:37
Alignment explanation
Indices: 33525--33814 Score: 149
Period size: 37 Copynumber: 8.1 Consensus size: 37
33515 TGCAAATGGT
33525 TTTTGAATATATATATATATAATATATGGTTTTGAAAACA
1 TTTTGAA-A-ATATATATATAATATAT-GTTTTGAAAACA
* * * * * *
33565 TGTTTGAAAACATTTATATATTATATAATTTTTAAAATA
1 T-TTTGAAAATATATATATAATATAT-GTTTTGAAAACA
*
33604 TTTTGAAAATA-A-ATATAATATATAGTTTTTG-AAACGT
1 TTTTGAAAATATATATATAATATAT-G-TTTTGAAAAC-A
* * *
33641 TTTTGAAAA-CT-TATATAATACATAGTTTTGAAAATA
1 TTTTGAAAATATATATATAATATAT-GTTTTGAAAACA
*
33677 -TTT----ATATAT-TAT-ATA-AT-TTTTAAAAAACA
1 TTTTGAAAATATATATATAATATATGTTTT-GAAAACA
33706 TTTT-AAAA-ATATATATAATATATAGATTTT-AAAACA
1 TTTTGAAAATATATATATAATATAT-G-TTTTGAAAACA
33742 TTTTTGAAAATATATA-AT-ATATAT-TTTT-AAAACA
1 -TTTTGAAAATATATATATAATATATGTTTTGAAAACA
*** * * *
33776 TTTTTTTAAT-T-TATATATTATATGTTTTTAAAATA
1 TTTTGAAAATATATATATAATATATGTTTTGAAAACA
33811 TTTT
1 TTTT
33815 TTTTATTTTT
Statistics
Matches: 198, Mismatches: 26, Indels: 57
0.70 0.09 0.20
Matches are distributed among these distances:
28 4 0.02
29 5 0.03
30 5 0.03
31 6 0.03
32 11 0.06
33 17 0.09
34 17 0.09
35 14 0.07
36 25 0.13
37 38 0.19
38 19 0.10
39 29 0.15
40 2 0.01
41 6 0.03
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (37 bp):
TTTTGAAAATATATATATAATATATGTTTTGAAAACA
Found at i:33657 original size:37 final size:37
Alignment explanation
Indices: 33540--33815 Score: 153
Period size: 35 Copynumber: 7.8 Consensus size: 37
33530 AATATATATA
* *
33540 TATATAATATAT-GGTTTTGAAAACATGTTTGAAAACATT
1 TATATAATATATAGTTTTTG-AAACATTTTTGAAAAC--T
* *
33579 TATATATTATATAATTTTT-AAA-ATATTTTGAAAA-T
1 TATATAATATATAGTTTTTGAAACAT-TTTTGAAAACT
* *
33614 AAATATAATATATAGTTTTTGAAACGTTTTTGAAAACT
1 -TATATAATATATAGTTTTTGAAACATTTTTGAAAACT
* *
33652 TATATAATACATAG-TTTTGAAA-ATATTT----A--
1 TATATAATATATAGTTTTTGAAACATTTTTGAAAACT
* * *
33681 TATAT--TATATAATTTTTAAAAAACA-TTTT-AAAAAT
1 TATATAATATATAGTTTTT--GAAACATTTTTGAAAACT
* *
33716 ATATATAATATATAGATTTTAAAACATTTTTGAAAA--
1 -TATATAATATATAGTTTTTGAAACATTTTTGAAAACT
* ** *
33752 TATATAATATATA-TTTTTAAAACATTTTT-TTAATT
1 TATATAATATATAGTTTTTGAAACATTTTTGAAAACT
* * *
33787 TATATATTATAT-GTTTTTAAAATATTTTT
1 TATATAATATATAGTTTTTGAAACATTTTT
33816 TTTATTTTTT
Statistics
Matches: 191, Mismatches: 23, Indels: 50
0.72 0.09 0.19
Matches are distributed among these distances:
27 5 0.03
28 4 0.02
29 5 0.03
30 6 0.03
31 2 0.01
33 3 0.02
34 15 0.08
35 44 0.23
36 35 0.18
37 30 0.16
38 27 0.14
39 11 0.06
40 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (37 bp):
TATATAATATATAGTTTTTGAAACATTTTTGAAAACT
Found at i:33681 original size:100 final size:98
Alignment explanation
Indices: 33567--33778 Score: 300
Period size: 102 Copynumber: 2.1 Consensus size: 98
33557 TGAAAACATG
* * *
33567 TTTGAAAACATTTATATATTATATAATTTTT-AAAATATTTTGAAAATAAATATAATATATAGTT
1 TTTGAAAACATTTATATATTATATAATTTTTAAAAACATTTTAAAAATAAATATAATATATAGAT
* *
33631 TTTGAAACGTTTTTGAAAACTTATATAATACATAGT
66 TTTAAAACATTTTTGAAAA--TATATAATACATA-T
* *
33667 TTTGAAAATATTTATATATTATATAATTTTTAAAAAACATTTTAAAAATATATATAATATATAGA
1 TTTGAAAACATTTATATATTATATAATTTTT-AAAAACATTTTAAAAATAAATATAATATATAGA
*
33732 TTTTAAAACATTTTTGAAAATATATAATATATAT
65 TTTTAAAACATTTTTGAAAATATATAATACATAT
*
33766 TTTTAAAACATTT
1 TTTGAAAACATTT
33779 TTTTAATTTA
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
99 12 0.12
100 42 0.42
102 46 0.46
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (98 bp):
TTTGAAAACATTTATATATTATATAATTTTTAAAAACATTTTAAAAATAAATATAATATATAGAT
TTTAAAACATTTTTGAAAATATATAATACATAT
Found at i:33728 original size:38 final size:37
Alignment explanation
Indices: 33679--33773 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 37
33669 TGAAAATATT
*
33679 TATATATTATATAATTTTTAAAAAACATTTTAAAAATA
1 TATATAATATATAATTTTTAAAAAACATTTTAAAAA-A
**
33717 TATATAATATATAGA-TTTT--AAAACATTTTTGAAAA
1 TATATAATATATA-ATTTTTAAAAAACATTTTAAAAAA
33752 TATATAATATAT-ATTTTTAAAA
1 TATATAATATATAATTTTTAAAA
33774 CATTTTTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
33 1 0.02
34 4 0.08
35 13 0.26
36 15 0.30
38 16 0.32
39 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (37 bp):
TATATAATATATAATTTTTAAAAAACATTTTAAAAAA
Found at i:33823 original size:9 final size:9
Alignment explanation
Indices: 33809--33849 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
33799 GTTTTTAAAA
33809 TATTTTTTT
1 TATTTTTTT
33818 TATTTTTTT
1 TATTTTTTT
*
33827 TATTATTTAT
1 TATT-TTTTT
*
33837 TATTTTATT
1 TATTTTTTT
33846 TATT
1 TATT
33850 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TATTTTTTT
Found at i:33837 original size:16 final size:17
Alignment explanation
Indices: 33816--33862 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 17
33806 AAATATTTTT
33816 TTTATTTTT-TTTATTA
1 TTTATTTTTATTTATTA
33832 TTTATTATTTTATTTATTA
1 TTTA-T-TTTTATTTATTA
33851 TTTATTTTTATT
1 TTTATTTTTATT
33863 CGGTGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.14
17 8 0.29
18 5 0.18
19 11 0.39
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTTATTTATTA
Found at i:33839 original size:19 final size:19
Alignment explanation
Indices: 33817--33856 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
33807 AATATTTTTT
*
33817 TTATTTTTTTTATTATTTA
1 TTATTTTATTTATTATTTA
33836 TTATTTTATTTATTATTTA
1 TTATTTTATTTATTATTTA
33855 TT
1 TT
33857 TTTATTCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTATTTTATTTATTATTTA
Found at i:35172 original size:2 final size:2
Alignment explanation
Indices: 35165--35229 Score: 87
Period size: 2 Copynumber: 33.0 Consensus size: 2
35155 TTTTAATTTC
35165 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
* * * *
35207 -T AT TT TT AT AT AC AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
35230 TTATTATTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35319 original size:20 final size:20
Alignment explanation
Indices: 35281--35348 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
35271 TTTATTTTAT
* *
35281 TTTATCTTATATATATTTTTGG
1 TTTAT-TTA-ATATTTTTTTGA
*
35303 TTTATTTAATATTTTTTAT-T
1 TTTATTTAATATTTTTT-TGA
35323 TTTATTTAAT-TTTCTTTTGA
1 TTTATTTAATATTT-TTTTGA
35343 TTTATT
1 TTTATT
35349 CTTTTATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 4 0.10
20 27 0.68
21 4 0.10
22 5 0.12
ACGTcount: A:0.22, C:0.03, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTATTTAATATTTTTTTGA
Found at i:35373 original size:38 final size:39
Alignment explanation
Indices: 35317--35395 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
35307 TTTAATATTT
* *
35317 TTTATTTTTATTTAA-TTTTCTTTTGA-TTTATTCTTTTA
1 TTTATTTTTATTTAATTTTTC-CTTGATTTTATTATTTTA
*
35355 TTTA-TTTTACTTTCATTTTTCCTTGATTTTATTATTTTA
1 TTTATTTTTA-TTTAATTTTTCCTTGATTTTATTATTTTA
35394 TT
1 TT
35396 CATGTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
37 5 0.14
38 12 0.34
39 18 0.51
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (39 bp):
TTTATTTTTATTTAATTTTTCCTTGATTTTATTATTTTA
Found at i:38524 original size:93 final size:92
Alignment explanation
Indices: 38357--38539 Score: 258
Period size: 93 Copynumber: 2.0 Consensus size: 92
38347 ATAATATTAT
* * *
38357 TTATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGAT
1 TTATATACAATAAAGCTTGAGTTGTCCATCTAAAGCAATTGGTTAAACACCCCGACTTTATGGAT
* *
38422 AATATTCAGCTAGCCTGATAAAGGTGA
66 AAGATTCAGCTAACCTGATAAAGGTGA
* * * * * *
38449 TTATACTATAATAAAGCTTGAGTTGTCGATCTAAGGTAATTGGTTAAACACCCTGATTTTATGGA
1 TTATA-TACAATAAAGCTTGAGTTGTCCATCTAAAGCAATTGGTTAAACACCCCGACTTTATGGA
38514 TAAGATTCAGCTAACCTGATAAAGGT
65 TAAGATTCAGCTAACCTGATAAAGGT
38540 ATTTTCATAT
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
92 5 0.06
93 74 0.94
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (92 bp):
TTATATACAATAAAGCTTGAGTTGTCCATCTAAAGCAATTGGTTAAACACCCCGACTTTATGGAT
AAGATTCAGCTAACCTGATAAAGGTGA
Found at i:39997 original size:165 final size:164
Alignment explanation
Indices: 39768--40757 Score: 1116
Period size: 165 Copynumber: 6.0 Consensus size: 164
39758 ATATACCACC
* **
39768 AAGATCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
*
39833 AAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
66 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
39898 CAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCA
131 CAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCA
* * * * * * ** *
39932 AAGACCTGCGAGTTTGATTACACTTAGCTTCGAGGGCACATCATTTATAGCATAAATTAAGTCGA
1 AAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
* * *
39997 GAAGAGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATAATTT
65 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* ** *
40062 GCAGTATAGCTTAAGTTGAGAAGGGCTATCTGCTA
130 GCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCA
* * * * * * * ** * * *
40097 AAGAACC-TCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAAAATAACTCAAGGCT
1 AAG-ACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* *
40161 AGAAGGGTTATCTGTC-ACCAAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
64 AGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * * * *
40225 TTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCAAAGCA
128 TTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGC----CA
* * * *
40266 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* * * ** *
40331 AAGGGCTATCTG----CCAAAGACCCTCGAGTTCGA-TCACACTCAGCTATGAGGGCACATCATT
66 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT-ACGCTCAGCT-CCAAGGCACATCATT
* * * * * * *
40391 TACATCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
129 TGCAGCATAGCTTAAGTCAAGAAGGGCTATC--TG-CC-A
* * *
40431 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGCCGAG
1 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* * *
40496 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGACATATCATTTG
66 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
*
40561 CAGTATAGCTTAAGTCAAGAAGGGCTATCTGCCA
131 CAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCA
* *
40595 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATTATTTGCAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* * *
40660 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTTAGCT-CAGAGGCAAACCAAAT
66 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCA-AGGCACATC--AT
* * *
40724 TTACAGCATAGCTCAA-TACAAGGAGGGCTATCTG
128 TTGCAGCATAGCTTAAGT-CAAGAAGGGCTATCTG
40758 TCAACAAATT
Statistics
Matches: 701, Mismatches: 102, Indels: 44
0.83 0.12 0.05
Matches are distributed among these distances:
163 3 0.00
164 165 0.24
165 371 0.53
166 35 0.05
167 2 0.00
168 73 0.10
169 51 0.07
170 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (164 bp):
AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
CAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCA
Found at i:40221 original size:249 final size:248
Alignment explanation
Indices: 39724--40708 Score: 1142
Period size: 249 Copynumber: 4.0 Consensus size: 248
39714 TTTTAAACAA
* * * * * * * * * *
39724 ATCATTTGCAGCTTAGCTCAAGGCCATAAGGGTTATATACC-ACC-AAGATCTTCGAGTTCAACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* *
39787 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA--A
* * * * * * * *
39852 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAG
129 GA-ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAG
* * * * * * * *
39917 AAGGGCTATCTG---CCAAAGACCTGCGAGTTTGATTACACTTAGCTTCGAGGGCAC
193 AAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCAC
** * *
39971 ATCATTTATAGCATAAATTAAGTCGAGAAGAGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * * * *
40036 ACACTCAGCTCCAAGGCACATAATTTGCAGTATAGCTTAAGTTGAGAAGGGCTATCTGCTAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* * * * **
40101 ACC-TCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAAAATAACTCAAGGCTAGAA
131 ACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAA
*
40165 GGGTTATCTGTCACCAAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
195 GGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * * *
40220 ATCATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCAAAGCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* *
40285 ACGCTCAGCTCCAAGGCATATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG-
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* ** * *
40349 ACCCTCGAGTTCGA-TCACACTCAGCTATGAGGGCACATCATTTACATCATAACTCAAGGCTAGA
131 ACCTTCGAGTTCGACT-ACACTCAGCT-CCAAGGCACATCATTTACAGCATAACTCAAGGCTAGA
* * *
40413 AGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCAT
194 AGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * *
40469 ATCATTTGCAACATAACTTAAGCCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * * *
40534 ACGCTCAGCTCCAAGACATATCATTTGCAGTATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAG-
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* * * * * * * *
40598 ACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATTATTTGCAGCATAACTTAAGTCGAGAAG
131 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
* *
40663 GGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTTAGCTC
196 GGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
40709 AGAGGCAAAC
Statistics
Matches: 631, Mismatches: 95, Indels: 23
0.84 0.13 0.03
Matches are distributed among these distances:
245 18 0.03
246 41 0.06
247 31 0.05
248 75 0.12
249 442 0.70
250 24 0.04
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (248 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
GGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
Found at i:40715 original size:84 final size:84
Alignment explanation
Indices: 39724--40708 Score: 1040
Period size: 84 Copynumber: 11.9 Consensus size: 84
39714 TTTTAAACAA
* * * * * * * * * *
39724 ATCATTTGCAGCTTAGCTCAAGGCCATAAGGGTTATATACC-ACC-AAGATCTTCGAGTTCAACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
39787 ACGCTCAGCTCCAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
*
39806 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
39871 ACGCTCAGCTCCAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
* * * * * *
39890 ATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTG----CCAAAGACCTGCGAGTTTGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * * *
39951 ACACTTAGCTTCGAGGGCAC
66 ACGCTCAGC-TCCAAGGCAC
** * *
39971 ATCATTTATAGCATAAATTAAGTCGAGAAGAGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
40036 ACACTCAGCTCCAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
* * * * * * * *
40055 ATAATTTGCAGTATAGCTTAAGTTGAGAAGGGCTATCTGCTAA--AGA-ACC-TCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * * *
40116 ACACTCAGCTTCGAGGGTAC
66 ACGCTCAGC-TCCAAGGCAC
* ** * * * * *
40136 ATCATTTACAAAATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAATACCTTCGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGAC
40200 TACGCTCAGCTCCAAGGCAC
65 TACGCTCAGCTCCAAGGCAC
* * * *
40220 ATCATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCAAAGCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
40285 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * * *
40304 ATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGA-T
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* ** *
40364 CACACTCAGCTATGAGGGCAC
66 -ACGCTCAGCT-CCAAGGCAC
* * * * * ** *
40385 ATCATTTACATCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTTGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGAC
*
40449 TACGCTCAGCTCCAAGGCAT
65 TACGCTCAGCTCCAAGGCAC
* * *
40469 ATCATTTGCAACATAACTTAAGCCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* *
40534 ACGCTCAGCTCCAAGACAT
66 ACGCTCAGCTCCAAGGCAC
* * * * *
40553 ATCATTTGCAGTATAGCTTAAGTCAAGAAGGGCTATCTG----CCAAAGACCTTCGAGTTTGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
40614 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
*
40633 ATTATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
40698 ACGCTTAGCTC
66 ACGCTCAGCTC
40709 AGAGGCAAAC
Statistics
Matches: 744, Mismatches: 133, Indels: 50
0.80 0.14 0.05
Matches are distributed among these distances:
79 1 0.00
80 145 0.19
81 115 0.15
82 35 0.05
83 5 0.01
84 366 0.49
85 76 0.10
86 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (84 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCAC
Found at i:41456 original size:37 final size:37
Alignment explanation
Indices: 41345--41546 Score: 171
Period size: 37 Copynumber: 5.4 Consensus size: 37
41335 GGTTTTTGAA
* * * *
41345 AAAATATATATAATATATGGTTTTGAAAACATGTTTG
1 AAAATATATATAATAAATAGTTTTTAAAACATTTTTG
* * *
41382 AAAACATTTATATATTATATATA-TTTTTAAAA-TTTTTTG
1 -AAA-A--TATATATAATAAATAGTTTTTAAAACATTTTTG
* *
41421 AAAATAAATATAATAAATAGTTTTTAAAACGTTTTTG
1 AAAATATATATAATAAATAGTTTTTAAAACATTTTTG
* *
41458 AAAACT-TATATAATACATAGTTTTGAAAACATTTTTG
1 AAAA-TATATATAATAAATAGTTTTTAAAACATTTTTG
* * * *
41495 AAAACATTTATATATTATATAATTTTTAAAACATTTTT-
1 -AAA-ATATATATAATAAATAGTTTTTAAAACATTTTTG
41533 -AAATATATATAATA
1 AAAATATATATAATA
41547 TATAAATTAT
Statistics
Matches: 136, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
35 22 0.16
36 11 0.08
37 38 0.28
38 11 0.08
39 33 0.24
40 8 0.06
41 13 0.10
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
AAAATATATATAATAAATAGTTTTTAAAACATTTTTG
Found at i:41495 original size:12 final size:12
Alignment explanation
Indices: 41478--41503 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41468 TAATACATAG
41478 TTTTGAAAACAT
1 TTTTGAAAACAT
41490 TTTTGAAAACAT
1 TTTTGAAAACAT
41502 TT
1 TT
41504 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:41495 original size:113 final size:113
Alignment explanation
Indices: 41336--41546 Score: 320
Period size: 113 Copynumber: 1.9 Consensus size: 113
41326 TTTGCAAATG
* *
41336 GTTTTTGAAAAAATATATATAATATATGGTTTTGAAAACATGTTTGAAAACATTTATATATTATA
1 GTTTTTGAAAAAATATATATAATACATAGTTTTGAAAACATGTTTGAAAACATTTATATATTATA
*
41401 TATATTTTTAAAA-TTTTTTGAAAATAAATATAATAAATAGTTTTTAAAAC
66 TA-ATTTTTAAAACATTTTT--AAATAAATATAATAAATAGTTTTTAAAAC
* *
41451 GTTTTTG-AAAACT-TATATAATACATAGTTTTGAAAACATTTTTGAAAACATTTATATATTATA
1 GTTTTTGAAAAAATATATATAATACATAGTTTTGAAAACATGTTTGAAAACATTTATATATTATA
*
41514 TAATTTTTAAAACATTTTTAAATATATATAATA
66 TAATTTTTAAAACATTTTTAAATAAATATAATA
41547 TATAAATTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
111 13 0.15
112 10 0.11
113 54 0.61
114 5 0.06
115 7 0.08
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (113 bp):
GTTTTTGAAAAAATATATATAATACATAGTTTTGAAAACATGTTTGAAAACATTTATATATTATA
TAATTTTTAAAACATTTTTAAATAAATATAATAAATAGTTTTTAAAAC
Found at i:41594 original size:53 final size:53
Alignment explanation
Indices: 41502--41608 Score: 166
Period size: 55 Copynumber: 2.0 Consensus size: 53
41492 TTGAAAACAT
41502 TTATATATTATATAATTTTTAAAACATTTTT--AAATATATATAATATATAAA
1 TTATATATTATATAATTTTTAAAACATTTTTAAAAATATATATAATATATAAA
41553 TTATATATTATATAATTTTTAAAAAAACA-TTTTAAAAATATATATAATATATAAA
1 TTATATATTATATAATTTTT---AAAACATTTTTAAAAATATATATAATATATAAA
41608 T
1 T
41609 GTTTTCAAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
51 20 0.39
53 4 0.08
54 6 0.12
55 21 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (53 bp):
TTATATATTATATAATTTTTAAAACATTTTTAAAAATATATATAATATATAAA
Found at i:41745 original size:22 final size:20
Alignment explanation
Indices: 41694--41746 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
41684 TTTTAAAACA
*
41694 TTTTTTATTTTTTATTATTT
1 TTTTTTATTTATTATTATTT
41714 TTATTATTATTTATTATTTATTT
1 TT-TT-TTATTTATTA-TTATTT
41737 CTTTTTTATT
1 -TTTTTTATT
41747 CAGTGTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 14 0.50
23 8 0.29
24 2 0.07
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTATTTATTATTATTT
Found at i:43056 original size:2 final size:2
Alignment explanation
Indices: 43049--43101 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
43039 TTTAAATTTC
* *
43049 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
43090 AT AC AT AT AT AT
1 AT AT AT AT AT AT
43102 TATTATTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:43181 original size:20 final size:20
Alignment explanation
Indices: 43146--43213 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
43136 TTTATTTTAT
43146 TTTATCTTATATATATTTTTGA
1 TTTAT-TTA-ATATATTTTTGA
*
43168 TTTATTTAATATATTTTAT-T
1 TTTATTTAATATATTTT-TGA
*
43188 TTTATTTAAT-TTTCTTTTGA
1 TTTATTTAATATAT-TTTTGA
43208 TTTATT
1 TTTATT
43214 CTTTTATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.08
20 28 0.70
21 4 0.10
22 5 0.12
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTATTTAATATATTTTTGA
Found at i:46540 original size:19 final size:20
Alignment explanation
Indices: 46500--46550 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
46490 TTATTTTTAA
*
46500 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
46520 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
46539 CGTTGCGATTTT
1 CGTTGCGATTTT
46551 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:49721 original size:32 final size:31
Alignment explanation
Indices: 49680--49786 Score: 94
Period size: 31 Copynumber: 3.4 Consensus size: 31
49670 AGTCGAGGGT
49680 TTACCTATGTTCTACAGAACATATGGACAGAA
1 TTACCTATGTTCTACAGAACATATGGACAG-A
* * *
49712 TTACCTATG-TCTTTCGGGACATATGGACAG-
1 TTACCTATGTTC-TACAGAACATATGGACAGA
* * *
49742 TATACCTATGTTTTA-AGGAACATATGAACAGT
1 T-TACCTATGTTCTACA-GAACATATGGACAGA
*
49774 TTACCTAGGTTCT
1 TTACCTATGTTCT
49787 TAGGGACCTA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
30 1 0.02
31 33 0.55
32 26 0.43
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (31 bp):
TTACCTATGTTCTACAGAACATATGGACAGA
Found at i:49751 original size:31 final size:30
Alignment explanation
Indices: 49698--49802 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 30
49688 GTTCTACAGA
* *
49698 ACATATGGACAGAATTACCTATGTCTTTCGGG
1 ACATATGGACAGTA-TACCTATGT-TTTAGGG
*
49730 ACATATGGACAGTATACCTATGTTTTAAGGA
1 ACATATGGACAGTATACCTATGTTTT-AGGG
* * *
49761 ACATATGAACAGTTTACCTAGGTTCTTAGGG
1 ACATATGGACAGTATACCTATGTT-TTAGGG
*
49792 ACCTATGGACA
1 ACATATGGACA
49803 ATTTTCGAGG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
30 3 0.05
31 44 0.71
32 15 0.24
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (30 bp):
ACATATGGACAGTATACCTATGTTTTAGGG
Found at i:49764 original size:63 final size:62
Alignment explanation
Indices: 49681--49802 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 62
49671 GTCGAGGGTT
* * *
49681 TACCTATGTTCTACAGAACATATGGACAGAATTACCTATG-TCTTTCGGGACATATGGACAGTA
1 TACCTATGTTCTACAGAACATATGAACAG-ATTACCTAGGTTC-TTAGGGACATATGGACAGTA
* * *
49744 TACCTATGTTTTA-AGGAACATATGAACAGTTTACCTAGGTTCTTAGGGACCTATGGACA
1 TACCTATGTTCTACA-GAACATATGAACAGATTACCTAGGTTCTTAGGGACATATGGACA
49803 ATTTTCGAGG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
62 24 0.47
63 27 0.53
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (62 bp):
TACCTATGTTCTACAGAACATATGAACAGATTACCTAGGTTCTTAGGGACATATGGACAGTA
Found at i:50658 original size:19 final size:19
Alignment explanation
Indices: 50634--50683 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
50624 ATTGTTCACG
*
50634 ATACTGTTCATATCGTATA
1 ATACTGTTCATACCGTATA
50653 ATACTGTTCATACCGTATA
1 ATACTGTTCATACCGTATA
*
50672 ATATTGTTCATA
1 ATACTGTTCATA
50684 AATACGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (19 bp):
ATACTGTTCATACCGTATA
Found at i:56072 original size:14 final size:14
Alignment explanation
Indices: 56036--56069 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
56026 AAAATTGACA
56036 TAATTAATTAAATT
1 TAATTAATTAAATT
*
56050 TAATTAATTCAA-T
1 TAATTAATTAAATT
56063 TAATTAA
1 TAATTAA
56070 ATTTTGTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTAATTAAATT
Found at i:56323 original size:2 final size:2
Alignment explanation
Indices: 56306--56337 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
56296 TAACAATTTA
56306 AT AT A- AT AT AT A- 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 AT AT AT
56338 CAAACACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:62904 original size:2 final size:2
Alignment explanation
Indices: 62899--62930 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
62889 TCTCTCTCTT
*
62899 TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62931 CACACACCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Done.