Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000511.1 Hibiscus syriacus cultivar Beakdansim tig00000973_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: 194173
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1527 original size:3 final size:3
Alignment explanation
Indices: 1519--1549 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1509 TCTTCAGGGA
*
1519 CTT CTT CTT CTT ATT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1550 AGGGTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:2718 original size:20 final size:19
Alignment explanation
Indices: 2672--2722 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
2662 ATTAAATTCT
*
2672 CGTTGCGAATTTGACTTTG
1 CGTTGCGAATTTGACTTCG
**
2691 TATTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACT-TCG
2711 CGTTGCGAATTT
1 CGTTGCGAATTT
2723 CCAAATTCGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.41
Consensus pattern (19 bp):
CGTTGCGAATTTGACTTCG
Found at i:2759 original size:20 final size:20
Alignment explanation
Indices: 2708--2759 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
2698 AATTTGACTA
*
2708 TCGCGTTGCGAATTTCCAAAT
1 TCGCGTTGCG-ATTTACAAAT
*** *
2729 TCGCAACGCGATTTACAGAT
1 TCGCGTTGCGATTTACAAAT
2749 TCGCGTTGCGA
1 TCGCGTTGCGA
2760 AATTAGAAAC
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (20 bp):
TCGCGTTGCGATTTACAAAT
Found at i:2796 original size:20 final size:21
Alignment explanation
Indices: 2747--2800 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
2737 CGATTTACAG
2747 ATTCGCGTTGCGAAATTAGAA
1 ATTCGCGTTGCGAAATTAGAA
* *
2768 ACT-GAGTTGCGAAATT-GAA
1 ATTCGCGTTGCGAAATTAGAA
*
2787 GTTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
2801 TTTGTTAGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.15
20 21 0.78
21 2 0.07
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTAGAA
Found at i:7901 original size:42 final size:42
Alignment explanation
Indices: 7842--7941 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
7832 AAAGCTAAAT
7842 GCCAAGTAATAGAAACAGAAAATGCAACCAAAAACGAAGGAG
1 GCCAAGTAATAGAAACAGAAAATGCAACCAAAAACGAAGGAG
* *
7884 GCCAAGTAGTAGAAACAGAAAATGCAACGAAAAACGAAGGAG
1 GCCAAGTAATAGAAACAGAAAATGCAACCAAAAACGAAGGAG
*
7926 GCCGAGTAATAGAAAC
1 GCCAAGTAATAGAAAC
7942 TTGGGTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.52, C:0.16, G:0.24, T:0.08
Consensus pattern (42 bp):
GCCAAGTAATAGAAACAGAAAATGCAACCAAAAACGAAGGAG
Found at i:22548 original size:59 final size:59
Alignment explanation
Indices: 22485--22599 Score: 230
Period size: 59 Copynumber: 1.9 Consensus size: 59
22475 TTATCTTTTA
22485 AAGGTTTAGGACATTAGATATATGATATGATCATTCAAATATAAAGGAAAATTTTATAG
1 AAGGTTTAGGACATTAGATATATGATATGATCATTCAAATATAAAGGAAAATTTTATAG
22544 AAGGTTTAGGACATTAGATATATGATATGATCATTCAAATATAAAGGAAAATTTTA
1 AAGGTTTAGGACATTAGATATATGATATGATCATTCAAATATAAAGGAAAATTTTA
22600 AAGATATAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (59 bp):
AAGGTTTAGGACATTAGATATATGATATGATCATTCAAATATAAAGGAAAATTTTATAG
Found at i:24178 original size:12 final size:12
Alignment explanation
Indices: 24161--24185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24151 ACAAAGCACC
24161 ATTTGGTGCCTA
1 ATTTGGTGCCTA
24173 ATTTGGTGCCTA
1 ATTTGGTGCCTA
24185 A
1 A
24186 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:31673 original size:18 final size:18
Alignment explanation
Indices: 31650--31689 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
31640 ATCCACTCTT
31650 CCTCTATATCCCCTCAAA
1 CCTCTATATCCCCTCAAA
31668 CCTCTATATCCCCTCAAA
1 CCTCTATATCCCCTCAAA
31686 CCTC
1 CCTC
31690 CTCAAAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.47, G:0.00, T:0.28
Consensus pattern (18 bp):
CCTCTATATCCCCTCAAA
Found at i:44319 original size:20 final size:20
Alignment explanation
Indices: 44281--44335 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
44271 CAACACTAAA
* *
44281 TTTCAAATTCGCAATTCGA-
1 TTTCGAATTCGCAACTCGAT
*
44300 TTTCTGAATTCACAACTCGAT
1 TTTC-GAATTCGCAACTCGAT
44321 TTTCGAATTCGCAAC
1 TTTCGAATTCGCAAC
44336 ACGAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTCGAATTCGCAACTCGAT
Found at i:44368 original size:17 final size:20
Alignment explanation
Indices: 44328--44373 Score: 71
Period size: 17 Copynumber: 2.5 Consensus size: 20
44318 GATTTTCGAA
44328 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
44348 TTCGCAACA-G-ATTTT-AT
1 TTCGCAACACGAATTTTAAT
44365 TTCGCAACA
1 TTCGCAACA
44374 TAAATGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.42
18 5 0.19
19 1 0.04
20 9 0.35
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:44531 original size:15 final size:16
Alignment explanation
Indices: 44511--44548 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
44501 TCCCCATCTC
*
44511 TAATTTT-TTTTTACA
1 TAATTTTATTTCTACA
*
44526 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
44542 TAATTTT
1 TAATTTT
44549 CAATGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:47612 original size:18 final size:18
Alignment explanation
Indices: 47578--47613 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47568 AAGCAAAAGG
**
47578 AAATCAAAATCGTAATCA
1 AAATCAAAATCCCAATCA
47596 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
47614 CAACCGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:47944 original size:20 final size:20
Alignment explanation
Indices: 47919--47983 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
47909 AAATCACAAC
* *
47919 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGATTTTCGTGTT
*
47939 GCGAATTTGATTTTTGTGTT
1 GCGAATTTGATTTTCGTGTT
47959 GCGAATTTGATTTTCGTGTT
1 GCGAATTTGATTTTCGTGTT
47979 GCGAA
1 GCGAA
47984 ATTGTACCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.17, C:0.12, G:0.26, T:0.45
Consensus pattern (20 bp):
GCGAATTTGATTTTCGTGTT
Found at i:49213 original size:18 final size:20
Alignment explanation
Indices: 49175--49215 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
49165 TTTGATCATA
*
49175 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
49195 ATATTTC-ATATG-ATATAT
1 ATATTTCAATATGCATATAT
49213 ATA
1 ATA
49216 ACCAAGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:49449 original size:18 final size:18
Alignment explanation
Indices: 49428--49463 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
49418 TATGTCCCGT
*
49428 AGGACCACTATGTCCGAA
1 AGGACCACTACGTCCGAA
*
49446 AGGACTACTACGTCCGAA
1 AGGACCACTACGTCCGAA
49464 GTACTACGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (18 bp):
AGGACCACTACGTCCGAA
Found at i:49470 original size:14 final size:15
Alignment explanation
Indices: 49451--49485 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
49441 CCGAAAGGAC
49451 TACTACGT-CCGAAG
1 TACTACGTCCCGAAG
49465 TACTACGTCCCGAAG
1 TACTACGTCCCGAAG
*
49480 GACTAC
1 TACTAC
49486 AATACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (15 bp):
TACTACGTCCCGAAG
Found at i:49742 original size:23 final size:22
Alignment explanation
Indices: 49716--49758 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
49706 TGTCTCAAAG
49716 CATATATCA-CATATGCATATAAT
1 CATATAT-ATCATAT-CATATAAT
49739 CATATATATCATATCATATA
1 CATATATATCATATCATATA
49759 TCTTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.37
Consensus pattern (22 bp):
CATATATATCATATCATATAAT
Found at i:50660 original size:117 final size:118
Alignment explanation
Indices: 50454--50686 Score: 443
Period size: 117 Copynumber: 2.0 Consensus size: 118
50444 GCATGATGAC
50454 AAGTCAAATTTAACTTCAAATTCAACTTATCAACTCTTTTCCATATTTCATATAAAAACCTTTTT
1 AAGTCAAATTTAACTTCAAATTCAACTTATCAACTCTTTTCCATATTTCATATAAAAACCTTTTT
50519 CTTTAATTTCTTATAACTTCTTCATC-TTTGATTATAAGACAACTTAAGCTGA
66 CTTTAATTTCTTATAACTTCTTCATCTTTTGATTATAAGACAACTTAAGCTGA
50571 AAGTCAAATTTAACTTCAAATTCAACTTATCAACTCTTTTCCATAATTTCATATAAAAACCTTTT
1 AAGTCAAATTTAACTTCAAATTCAACTTATCAACTCTTTTCCAT-ATTTCATATAAAAACCTTTT
50636 T-TTTAATTTCTTATAACTTCTTCATCTTTTGATTATAAGACAACTTAAGCT
65 TCTTTAATTTCTTATAACTTCTTCATCTTTTGATTATAAGACAACTTAAGCT
50687 TTCCTTAAGC
Statistics
Matches: 114, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
117 69 0.61
118 45 0.39
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.43
Consensus pattern (118 bp):
AAGTCAAATTTAACTTCAAATTCAACTTATCAACTCTTTTCCATATTTCATATAAAAACCTTTTT
CTTTAATTTCTTATAACTTCTTCATCTTTTGATTATAAGACAACTTAAGCTGA
Found at i:56168 original size:20 final size:20
Alignment explanation
Indices: 56128--56168 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
56118 TTTGATAATA
*
56128 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
56148 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
56168 A
1 A
56169 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:57080 original size:20 final size:20
Alignment explanation
Indices: 57055--57092 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
57045 TTTCATTTAA
*
57055 GGGGAATCTATACCCCCTAG
1 GGGGAATCGATACCCCCTAG
57075 GGGGAATCGATACCCCCT
1 GGGGAATCGATACCCCCT
57093 GAACATACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.32, G:0.26, T:0.18
Consensus pattern (20 bp):
GGGGAATCGATACCCCCTAG
Found at i:58725 original size:4 final size:4
Alignment explanation
Indices: 58704--58737 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
58694 CGGGCCGTTA
* *
58704 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
58738 TGCCGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:58871 original size:21 final size:21
Alignment explanation
Indices: 58847--58886 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58837 GTAGAGCGGC
* *
58847 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACCTAAAGTAGA
58868 TACCTCACCACCTAAAGTA
1 TACCTCACCACCTAAAGTA
58887 CCATTGTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.23
Consensus pattern (21 bp):
TACCTCACCACCTAAAGTAGA
Found at i:58980 original size:21 final size:21
Alignment explanation
Indices: 58956--59008 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
58946 TGAACCATTG
*
58956 TCATCACGTAAAGTACCGACC
1 TCATCACGTAAAGAACCGACC
* *
58977 TCATCACGCAAAGAACTGACC
1 TCATCACGTAAAGAACCGACC
*
58998 TCATCATGTAA
1 TCATCACGTAA
59009 CTCCCCTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.30, G:0.13, T:0.21
Consensus pattern (21 bp):
TCATCACGTAAAGAACCGACC
Found at i:63535 original size:20 final size:20
Alignment explanation
Indices: 63507--63557 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
63497 ACACAATTTC
63507 TAAATTCGCAACGCGAATATG
1 TAAA-TCGCAACGCGAATATG
*
63528 TAAATCGCAACGCGAATTTG
1 TAAATCGCAACGCGAATATG
*
63548 TAATTCGCAA
1 TAAATCGCAA
63558 TACAGAAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (20 bp):
TAAATCGCAACGCGAATATG
Found at i:63759 original size:22 final size:22
Alignment explanation
Indices: 63734--63776 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
63724 GCGACATGCG
63734 TCCCCATCTCCGACGAAATCCA
1 TCCCCATCTCCGACGAAATCCA
*
63756 TCCCCATCTCCGGCGAAATCC
1 TCCCCATCTCCGACGAAATCC
63777 GTCTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.47, G:0.12, T:0.19
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCCA
Found at i:64163 original size:19 final size:20
Alignment explanation
Indices: 64137--64185 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
64127 AAATTGCAAC
64137 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
* * *
64156 GTGATTTTCATTTTTGCGTT
1 GCGATTTTCAGTTTCGCGTT
64176 GCGATTTTCA
1 GCGATTTTCA
64186 TGGTTATGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.12, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:64844 original size:13 final size:13
Alignment explanation
Indices: 64826--64886 Score: 95
Period size: 13 Copynumber: 4.7 Consensus size: 13
64816 TGCGTCATAA
64826 ATTTATGACGCGC
1 ATTTATGACGCGC
* *
64839 ATTTATGACACGT
1 ATTTATGACGCGC
*
64852 ATTTATGACGTGC
1 ATTTATGACGCGC
64865 ATTTATGACGCGC
1 ATTTATGACGCGC
64878 ATTTATGAC
1 ATTTATGAC
64887 TTACATTGCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:64893 original size:26 final size:26
Alignment explanation
Indices: 64826--64893 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
64816 TGCGTCATAA
** *
64826 ATTTATGACGCGCATTTATGACACGT
1 ATTTATGACGTACATTTATGACACGC
* *
64852 ATTTATGACGTGCATTTATGACGCGC
1 ATTTATGACGTACATTTATGACACGC
*
64878 ATTTATGACTTACATT
1 ATTTATGACGTACATT
64894 GCGAGTCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (26 bp):
ATTTATGACGTACATTTATGACACGC
Found at i:65594 original size:20 final size:19
Alignment explanation
Indices: 65549--65596 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
65539 AATTTGACTT
*
65549 CTGTATTGCGAATTACAAA
1 CTGTGTTGCGAATTACAAA
* *
65568 TTCGTGTTGCGAATTTAGAAA
1 CT-GTGTTGCGAA-TTACAAA
65589 CTGTGTTG
1 CTGTGTTG
65597 TGAAATTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 15 0.65
21 7 0.30
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (19 bp):
CTGTGTTGCGAATTACAAA
Found at i:67413 original size:21 final size:21
Alignment explanation
Indices: 67369--67413 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
67359 GATTTCTGGG
* * *
67369 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
67390 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
67411 CAA
1 CAA
67414 ACGAACCATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:67486 original size:23 final size:22
Alignment explanation
Indices: 67438--67486 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
67428 ACAGAATGTC
67438 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
67459 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
67482 AAGGA
1 AAGGA
67487 AAAATGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:68505 original size:31 final size:31
Alignment explanation
Indices: 68467--68591 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
68457 AGGGTCGAGG
68467 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
68498 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
68529 GTTTACCTATGTTCTTCGGGACATATGGAAT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
68560 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
68591 G
1 G
68592 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:71599 original size:21 final size:21
Alignment explanation
Indices: 71555--71599 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
71545 GATTTCTGGG
* * *
71555 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
71576 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
71597 CAA
1 CAA
71600 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:71672 original size:23 final size:22
Alignment explanation
Indices: 71624--71672 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
71614 ACAGAATGTC
71624 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
71645 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
71668 AAGGA
1 AAGGA
71673 AAAATGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:72804 original size:62 final size:62
Alignment explanation
Indices: 72663--72808 Score: 204
Period size: 62 Copynumber: 2.4 Consensus size: 62
72653 GTTTACCTAT
* * * * *
72663 GTTCTTCGGGACATATGGACTGTTTAACTATGTTCTTCGGGACATATGGACTGTTTACCTAT
1 GTTCTTCAGAACATATGGACTGTTTAACTATGTTCTTCGGGACATATGGACTGATTACATAG
* * *
72725 GTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGATTACATAG
1 GTTCTTCAGAACATATGGACTGTTTAACTATGTTCTTCGGGACATATGGACTGATTACATAG
72787 GTTCTTCAGAATC-TATGGACTG
1 GTTCTTCAGAA-CATATGGACTG
72809 GTCCTTCGGG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
62 76 0.99
63 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (62 bp):
GTTCTTCAGAACATATGGACTGTTTAACTATGTTCTTCGGGACATATGGACTGATTACATAG
Found at i:72808 original size:31 final size:31
Alignment explanation
Indices: 72653--72793 Score: 246
Period size: 31 Copynumber: 4.5 Consensus size: 31
72643 AGGGTCAAGG
72653 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
72684 GTTTAACTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
72715 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
72746 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
72777 GATTACATAGGTTCTTC
1 GTTTACCTATGTTCTTC
72794 AGAATCTATG
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:74028 original size:13 final size:13
Alignment explanation
Indices: 74010--74036 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
74000 TTACAGACGA
74010 GCATATGAAGACT
1 GCATATGAAGACT
74023 GCATATGAAGACT
1 GCATATGAAGACT
74036 G
1 G
74037 TTTTAACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:74518 original size:43 final size:43
Alignment explanation
Indices: 74433--74518 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
74423 ATCTCACACC
* *
74433 CCTTAATATAATTTTTTATATTCGTCGCTCTCTAACACAAATT
1 CCTTAATATAATTTTTTATATTCGCCGCTCTCTAACAAAAATT
* * *
74476 CCTTAATATGATTTTTTATATTCGCCGCTCTCTTATAAAAATT
1 CCTTAATATAATTTTTTATATTCGCCGCTCTCTAACAAAAATT
74519 TTGCATCCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (43 bp):
CCTTAATATAATTTTTTATATTCGCCGCTCTCTAACAAAAATT
Found at i:77295 original size:249 final size:252
Alignment explanation
Indices: 76853--77355 Score: 633
Period size: 249 Copynumber: 2.0 Consensus size: 252
76843 AAGATTAAGA
* * * * * *
76853 AGTGGGATTACCTTTTCTGTCTCCGAAGTTTTAGGATCATCTGATTTAGCGTTTCCTTTTTCTGG
1 AGTGGGATTACCTTTTCTGTCACCGAAGTTTTAGGACCATCTGACTTAGCATTTCCTTATTCTGA
** * * * * *
76918 TTTTGATGGATCAGTTCCAAAGTTATGTTCAGTCAGTTTTTTCGATCCTCCAATATGCTCGTTAG
66 TTTTGATAAATCAGTTCCAAAGTTATGTACAGTCAGTTTTTTCGATCCTCCAAGAAGCTCGATAA
* * * * ** * *
76983 AATCGGGATTACTTTGACAATGTGGTTTTGATTCTTCTTTTGCACCCTTTGAACTCTTTGAAGTT
131 AATCAGGATTACTTTCACAAGGTGGTTTTGATGCTTCTTTCACACCCATTGAACTCGTTGAAGTT
* *
77048 TGTGATTCATCTTTACTGGA-TTT-CA-TAGAATCTTCCTTGCCATGTGTGCCTTCT
196 TGTGATTCATCTTTACTGGATTTTGCAGAAGAATCTTCCTTGCCATGAGTGCCTTCT
*
77102 AGTGGGATTACCTTTTCTGTCACC-ATAGTTTTAGGACCATCTGACTTAGCATTTTCTTCATT-T
1 AGTGGGATTACCTTTTCTGTCACCGA-AGTTTTAGGACCATCTGACTTAGCATTTCCTT-ATTCT
* *
77165 GATTTTGATAAATCAGTTCCAGAGTTATGTACAGTCAGATTTTTT-GATTCTCCAAGAAGCTCGA
64 GATTTTGATAAATCAGTTCCAAAGTTATGTACAGTCAG-TTTTTTCGATCCTCCAAGAAGCTCGA
* * * *
77229 TAAAATCAGGATTACTTTCAC-CGGATGGTTTTGATGGTTCTTTCACATCCATTGAATTCGTTGA
128 TAAAATCAGGATTACTTTCACAAGG-TGGTTTTGATGCTTCTTTCACACCCATTGAACTCGTTGA
* *
77293 AGTTTTTGATTCATCTTTACTGGATTTTGTAGAAGAATCTTCCTTGCCATGAGTGCCTTCT
192 AGTTTGTGATTCATCTTTACTGGATTTTGCAGAAGAATCTTCCTTGCCATGAGTGCCTTCT
77354 AG
1 AG
77356 GACAAGTTCA
Statistics
Matches: 215, Mismatches: 32, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
248 2 0.01
249 172 0.80
250 11 0.05
251 1 0.00
252 29 0.13
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (252 bp):
AGTGGGATTACCTTTTCTGTCACCGAAGTTTTAGGACCATCTGACTTAGCATTTCCTTATTCTGA
TTTTGATAAATCAGTTCCAAAGTTATGTACAGTCAGTTTTTTCGATCCTCCAAGAAGCTCGATAA
AATCAGGATTACTTTCACAAGGTGGTTTTGATGCTTCTTTCACACCCATTGAACTCGTTGAAGTT
TGTGATTCATCTTTACTGGATTTTGCAGAAGAATCTTCCTTGCCATGAGTGCCTTCT
Found at i:83252 original size:16 final size:17
Alignment explanation
Indices: 83202--83253 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
83192 AAAATAAATA
83202 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
83219 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
83234 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
83250 AATT
1 AATT
83254 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:108376 original size:34 final size:33
Alignment explanation
Indices: 108279--108377 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
108269 ATTTGGCAAG
*
108279 TTGGAAAGTTCATCTTGGTTGGTGGCCAATTTA
1 TTGGAAAGTTCATCTTGGTTGGTGGCCAACTTA
* *
108312 TTGGAAAATTCATCTTGGTTGGTGGGCAACTTA
1 TTGGAAAGTTCATCTTGGTTGGTGGCCAACTTA
**
108345 TTGGAAAGTTCATCTTTGGCAGGTGGCCAACTT
1 TTGGAAAGTTCATC-TTGGTTGGTGGCCAACTT
108378 TGCATATGGG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 43 0.74
34 15 0.26
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.36
Consensus pattern (33 bp):
TTGGAAAGTTCATCTTGGTTGGTGGCCAACTTA
Found at i:109732 original size:14 final size:14
Alignment explanation
Indices: 109705--109742 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
109695 AAAGCTGCTC
*
109705 CAGATGCATATGTTG
1 CAGA-GCATGTGTTG
109720 CAGAGCATGTGTTG
1 CAGAGCATGTGTTG
109734 CAGAGCATG
1 CAGAGCATG
109743 ATGCAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (14 bp):
CAGAGCATGTGTTG
Found at i:132173 original size:28 final size:28
Alignment explanation
Indices: 132140--132195 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
132130 TAAAACTTAT
132140 AATTTTAAGTGTTTCGAATGTAATAGTC
1 AATTTTAAGTGTTTCGAATGTAATAGTC
132168 AATTTTAAGTGTTTCGAATGTAATAGTC
1 AATTTTAAGTGTTTCGAATGTAATAGTC
132196 CTTAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (28 bp):
AATTTTAAGTGTTTCGAATGTAATAGTC
Found at i:132207 original size:25 final size:27
Alignment explanation
Indices: 132149--132207 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
132139 TAATTTTAAG
* * *
132149 TGTTTCGAATGTAATAGTCAATTTTAAG
1 TGTTTCGAATGTAATAGTC-ACTTAAAA
132177 TGTTTCGAATGTAATAGTC-CTTAAAA
1 TGTTTCGAATGTAATAGTCACTTAAAA
132203 T-TTTC
1 TGTTTC
132208 ATTAGATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.14
26 5 0.18
28 19 0.68
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (27 bp):
TGTTTCGAATGTAATAGTCACTTAAAA
Found at i:133311 original size:9 final size:9
Alignment explanation
Indices: 133273--133384 Score: 50
Period size: 9 Copynumber: 11.8 Consensus size: 9
133263 ACTAAAATGA
*
133273 TAAAATTAT
1 TAAATTTAT
133282 TAAATTTGATT
1 TAAATTT-A-T
133293 TAAA-TTAT
1 TAAATTTAT
133301 TAAATTTAT
1 TAAATTTAT
*
133310 TAGA-TT-T
1 TAAATTTAT
*
133317 TAAAGTTTAAG
1 TAAA-TTT-AT
*
133328 GAAATTTTATTT
1 TAAA-TTTA--T
**
133340 TAAAAAATAT
1 T-AAATTTAT
133350 TAAATTTGAT
1 TAAATTT-AT
*
133360 TAAAATTAT
1 TAAATTTAT
*
133369 TAAAATTAT
1 TAAATTTAT
133378 TAAATTT
1 TAAATTT
133385 TAAAATTTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 22
0.68 0.12 0.19
Matches are distributed among these distances:
7 4 0.05
8 7 0.09
9 37 0.47
10 14 0.18
11 11 0.14
12 2 0.03
13 3 0.04
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (9 bp):
TAAATTTAT
Found at i:133357 original size:68 final size:67
Alignment explanation
Indices: 133274--133415 Score: 203
Period size: 68 Copynumber: 2.1 Consensus size: 67
133264 CTAAAATGAT
* * * * * * *
133274 AAAATTATTAAATTTGATTTAAATTATTAAATTTATTAGATTTTAAAGTTTAAGGAAATTTTATT
1 AAAAATATTAAATTTGATTAAAATTATTAAAATTATTAAATTTTAAAATTTAAGAAAATTTTA-A
133339 TTA
65 TTA
*
133342 AAAAATATTAAATTTGATTAAAATTATTAAAATTATTAAATTTTAAAATTTTAGAAAATTTTAAT
1 AAAAATATTAAATTTGATTAAAATTATTAAAATTATTAAATTTTAAAATTTAAGAAAATTTTAAT
133407 TA
66 TA
133409 AAAAATA
1 AAAAATA
133416 AAAGATTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 10 0.15
68 56 0.85
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (67 bp):
AAAAATATTAAATTTGATTAAAATTATTAAAATTATTAAATTTTAAAATTTAAGAAAATTTTAAT
TA
Found at i:133361 original size:10 final size:9
Alignment explanation
Indices: 133342--133391 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
133332 TTTTATTTTA
*
133342 AAAAATATT
1 AAAATTATT
*
133351 AAATTTGATT
1 AAAATT-ATT
133361 AAAATTATT
1 AAAATTATT
133370 AAAATTATT
1 AAAATTATT
133379 -AAATT-TT
1 AAAATTATT
133386 AAAATT
1 AAAATT
133392 TTAGAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
7 2 0.06
8 10 0.28
9 16 0.44
10 8 0.22
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (9 bp):
AAAATTATT
Found at i:133369 original size:19 final size:18
Alignment explanation
Indices: 133342--133381 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
133332 TTTTATTTTA
*
133342 AAAAATATTAAATTTGATT
1 AAAAATATTAAAATT-ATT
*
133361 AAAATTATTAAAATTATT
1 AAAAATATTAAAATTATT
133379 AAA
1 AAA
133382 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAAATATTAAAATTATT
Found at i:133390 original size:8 final size:8
Alignment explanation
Indices: 133359--133405 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
133349 TTAAATTTGA
133359 TTAAAATT
1 TTAAAATT
133367 ATTAAAATT
1 -TTAAAATT
133376 ATT-AAATT
1 -TTAAAATT
133384 TTAAAATT
1 TTAAAATT
133392 TTAGAAAATT
1 TT--AAAATT
133402 TTAA
1 TTAA
133406 TTAAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 2 0.06
8 14 0.40
9 11 0.31
10 8 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
TTAAAATT
Found at i:137580 original size:18 final size:18
Alignment explanation
Indices: 137549--137590 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
137539 TCACTTTTTT
137549 TAAATAAAT-AAAAATGCAA
1 TAAA-AAATAAAAAATG-AA
*
137568 TAAAAAATTAAAAATGAA
1 TAAAAAATAAAAAATGAA
137586 TAAAA
1 TAAAA
137591 TTCAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (18 bp):
TAAAAAATAAAAAATGAA
Found at i:137721 original size:29 final size:29
Alignment explanation
Indices: 137672--137734 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
137662 TTAAAAATAT
*
137672 AAAATAAATATTAAATTTTAA-TTTTATTA
1 AAAATAAATA-TAAATTTTAACTGTTATTA
137701 AAAATAAATA-AACATTATTAACTGTTATTA
1 AAAATAAATATAA-ATT-TTAACTGTTATTA
137731 AAAA
1 AAAA
137735 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.07
28 3 0.10
29 14 0.47
30 11 0.37
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAATAAATATAAATTTTAACTGTTATTA
Found at i:137750 original size:14 final size:14
Alignment explanation
Indices: 137727--137757 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
137717 ATTAACTGTT
137727 ATTAAAAAATAATA
1 ATTAAAAAATAATA
*
137741 ATTAATAAATAATA
1 ATTAAAAAATAATA
137755 ATT
1 ATT
137758 CATTTGATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATTAAAAAATAATA
Found at i:138902 original size:11 final size:11
Alignment explanation
Indices: 138869--138905 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
138859 TTTACATTAT
138869 ATTTTTATTG-
1 ATTTTTATTGC
*
138879 AATTTTATT-C
1 ATTTTTATTGC
138889 ATTTTTATTGC
1 ATTTTTATTGC
138900 ATTTTT
1 ATTTTT
138906 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (11 bp):
ATTTTTATTGC
Found at i:142151 original size:23 final size:23
Alignment explanation
Indices: 142083--142143 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
142073 ACATTTTATA
142083 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
142106 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
142129 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
142144 TTTATACGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:143945 original size:31 final size:27
Alignment explanation
Indices: 143901--143975 Score: 73
Period size: 31 Copynumber: 2.7 Consensus size: 27
143891 AAAGCAAAGG
143901 AAAAT-AAGATAAAAAAGAAATGTGAATAAA
1 AAAATAAAG-TAAAAAA-AAA-GT-AATAAA
*
143931 ATAAATAAAGTAAAATAAAAGTAATAAA
1 A-AAATAAAGTAAAAAAAAAGTAATAAA
*
143959 AAAATAAA-TAAAGAAAA
1 AAAATAAAGTAAAAAAAA
143976 TATAGATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 7 0.17
27 7 0.17
28 7 0.17
29 2 0.05
30 4 0.10
31 10 0.25
32 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.17
Consensus pattern (27 bp):
AAAATAAAGTAAAAAAAAAGTAATAAA
Found at i:144260 original size:33 final size:31
Alignment explanation
Indices: 144244--144302 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
144234 AGAAAAATAT
144244 AGGTATATATATATATAATAAAACAAAAACA
1 AGGTATATATATATATAATAAAACAAAAACA
* * *
144275 ATGTATATATATATATAATTAAATAAAA
1 AGGTATATATATATATAATAAAACAAAA
144303 TATAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (31 bp):
AGGTATATATATATATAATAAAACAAAAACA
Found at i:145812 original size:102 final size:102
Alignment explanation
Indices: 145681--146100 Score: 716
Period size: 102 Copynumber: 4.1 Consensus size: 102
145671 ATATTTTGTG
** *
145681 TTTCAAGGGAAACATTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
145746 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * *
145783 TTTCAAGGGAAATGTTTTCAATGTCTATGTTTTAAGAGAAACTGTCTCAAGGGAGACACAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
145848 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
145885 TTTCAAGGGAAAT-ATTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
* *
145949 GTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
145986 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
** * *
146051 GTTTCAAGCAAAACTATCTCAAGCGAGATAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
146088 TTTCAAGGGAAAT
1 TTTCAAGGGAAAT
146101 ATTTCAAGAG
Statistics
Matches: 302, Mismatches: 15, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
101 95 0.31
102 207 0.69
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:145925 original size:64 final size:66
Alignment explanation
Indices: 145847--145970 Score: 180
Period size: 64 Copynumber: 1.9 Consensus size: 66
145837 GACACAATTT
* *
145847 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTCATTTCAAGGGAAA-TATTTCAATGTTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTCATTTCAAGGGAAACTATCTCAATGTTT
145910 A
66 A
* * **
145911 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTCATTTCAAGGGAAACTATCTCAA
145971 GCGAGATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 31 0.60
65 14 0.27
66 7 0.13
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTCATTTCAAGGGAAACTATCTCAATGTTT
A
Found at i:146052 original size:203 final size:203
Alignment explanation
Indices: 145681--146107 Score: 746
Period size: 203 Copynumber: 2.1 Consensus size: 203
145671 ATATTTTGTG
*
145681 TTTCAAGGGAAACATTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATA-TTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
145746 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTCTAT
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTCTAT
* * **
145811 GTTTTAAGAGAAACTGTCTCAAGGGAGACACAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
130 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGCAAAACTATCTCAAGAGAGA
145876 CAAAATTCA
195 CAAAATTCA
*
145885 TTTCAAGGGAAATATTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 TTTCAAGGGAAATATTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
* * *
145950 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
66 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTCTATG
* *
146015 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGCAAAACTATCTCAAGCGAGAT
131 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGCAAAACTATCTCAAGAGAGAC
146080 AAAATTCA
196 AAAATTCA
146088 TTTCAAGGGAAATATTTCAA
1 TTTCAAGGGAAATATTTCAA
146108 GAGAAATTGT
Statistics
Matches: 212, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
203 199 0.94
204 13 0.06
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (203 bp):
TTTCAAGGGAAATATTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTCTATG
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGCAAAACTATCTCAAGAGAGAC
AAAATTCA
Found at i:146107 original size:50 final size:50
Alignment explanation
Indices: 146052--146149 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 50
146042 CAAAATTTTG
* *
146052 TTTCAAGCA-AAACTATCTCAAGCGAGA-TAAAATTCATTTCAAGGGAAATA
1 TTTCAAG-AGAAACTATCTCAAGAGAGACAAAAATT-ATTTCAAGGGAAATA
* * *
146102 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAAATTGTTTCAAGGGAAA
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAAATTATTTCAAGGGAAA
146150 CTGTCTCAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
49 1 0.02
50 34 0.83
51 6 0.15
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (50 bp):
TTTCAAGAGAAACTATCTCAAGAGAGACAAAAATTATTTCAAGGGAAATA
Found at i:146137 original size:21 final size:21
Alignment explanation
Indices: 146111--146180 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
146101 ATTTCAAGAG
146111 AAATTGTCTCAAGAGAGACAA
1 AAATTGTCTCAAGAGAGACAA
*
146132 AAATTGTTTCAAG-G-G----
1 AAATTGTCTCAAGAGAGACAA
*
146147 AAACTGTCTCAAGAGAGACAA
1 AAATTGTCTCAAGAGAGACAA
* *
146168 AATTTGTTTCAAG
1 AAATTGTCTCAAG
146181 TTGGGTCAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
15 11 0.30
16 1 0.03
17 1 0.03
19 1 0.03
20 1 0.03
21 22 0.59
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (21 bp):
AAATTGTCTCAAGAGAGACAA
Found at i:146142 original size:36 final size:36
Alignment explanation
Indices: 146102--146180 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
146092 AAGGGAAATA
*
146102 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAAATTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTG
* *
146138 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTG
146174 TTTCAAG
1 TTTCAAG
146181 TTGGGTCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTG
Found at i:146180 original size:86 final size:87
Alignment explanation
Indices: 146015--146180 Score: 235
Period size: 86 Copynumber: 1.9 Consensus size: 87
146005 AATGTTTATG
* * * *
146015 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGCAAAACTATCTCAAGCGAGAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATATTGTTTCAAGCAAAACTATCTCAAGAGAGAC
146080 AAAATTCATTTCAAGGGAAATA
66 AAAATTCATTTCAAGGGAAATA
* ** *
146102 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAA-ATTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATATTGTTTCAAGCAAAACTATCTCAAGAGAGAC
**
146166 AAAATTTGTTTCAAG
66 AAAATTCATTTCAAG
146181 TTGGGTCAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
86 39 0.57
87 30 0.43
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (87 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATATTGTTTCAAGCAAAACTATCTCAAGAGAGAC
AAAATTCATTTCAAGGGAAATA
Found at i:146737 original size:106 final size:106
Alignment explanation
Indices: 146552--146919 Score: 524
Period size: 106 Copynumber: 3.5 Consensus size: 106
146542 GTATCGCTCC
* * * *
146552 GAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGTTATGGAACTGGGAAATTGCTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
* * *
146616 GTCAGCCACCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
65 ATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
* * * *
146658 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
146723 TCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGT-TT
66 TCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
** *
146763 GGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 -GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
* * *
146828 ACCAGCTGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTG
65 ATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
* * *
146870 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTCAAACTAGGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA
146920 TCCCCTTCGT
Statistics
Matches: 232, Mismatches: 27, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
105 2 0.01
106 228 0.98
107 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
TCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:148388 original size:95 final size:95
Alignment explanation
Indices: 148225--148403 Score: 306
Period size: 95 Copynumber: 1.9 Consensus size: 95
148215 TGTAAATACC
* * * *
148225 TTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCATTTGCCTTAGAGGGACA
1 TTTATCAGGCTACCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
148290 ACTCAAGCTTTATTGTATAGTATAATCACT
66 ACTCAAGCTTTATTGTATAGTATAATCACT
148320 TTTATCAGGCTACCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG-CTCTAGAGGGAC
1 TTTATCAGGCTACCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAGAGGGAC
148384 AACTCAAGCTTTATTGTATA
65 AACTCAAGCTTTATTGTATA
148404 TAAATATTAT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
94 2 0.03
95 77 0.97
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (95 bp):
TTTATCAGGCTACCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
ACTCAAGCTTTATTGTATAGTATAATCACT
Found at i:152066 original size:9 final size:9
Alignment explanation
Indices: 152052--152103 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
152042 AGAAAGATGG
152052 ATAAAATAA
1 ATAAAATAA
152061 ATAAAATAAA
1 ATAAAAT-AA
152071 ATAAAAGT-A
1 ATAAAA-TAA
152080 AT-AAATAA
1 ATAAAATAA
152088 AT-AAATAA
1 ATAAAATAA
*
152096 AGAAAATA
1 ATAAAATA
152104 TAGATAATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
7 1 0.03
8 13 0.34
9 15 0.39
10 8 0.21
11 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (9 bp):
ATAAAATAA
Found at i:152406 original size:21 final size:22
Alignment explanation
Indices: 152381--152437 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
152371 AGGTATATAT
* *
152381 ATATATATATAATTA-CACAAA
1 ATATATAAATAATAATCACAAA
152402 ATATA-AAATAATAATCACAAA
1 ATATATAAATAATAATCACAAA
152423 A-ATATAGTAATAATA
1 ATATATA--AATAATA
152438 GTAGGGATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 10 0.33
21 13 0.43
23 7 0.23
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
ATATATAAATAATAATCACAAA
Found at i:152406 original size:23 final size:22
Alignment explanation
Indices: 152389--152437 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
152379 ATATATATAT
*
152389 ATAATTACACAAAATATAAAATA
1 ATAATCACA-AAAATATAAAATA
*
152412 ATAATCACAAAAATATAGTAATA
1 ATAATCACAAAAATATA-AAATA
152435 ATA
1 ATA
152438 GTAGGGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (22 bp):
ATAATCACAAAAATATAAAATA
Found at i:152435 original size:20 final size:21
Alignment explanation
Indices: 152396--152437 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
152386 TATATAATTA
152396 CACAAAATATAAAATAATAAT
1 CACAAAATATAAAATAATAAT
*
152417 CACAAAAATATAGTAATAATA
1 CAC-AAAATATA-AAATAATA
152438 GTAGGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 8 0.44
23 7 0.39
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.24
Consensus pattern (21 bp):
CACAAAATATAAAATAATAAT
Found at i:159626 original size:17 final size:17
Alignment explanation
Indices: 159604--159643 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
159594 TTGCATTACT
*
159604 TGGAATGTTAATAGAAA
1 TGGAATGTTAACAGAAA
159621 TGGAATGTTAACAGAAA
1 TGGAATGTTAACAGAAA
159638 TGGAAT
1 TGGAAT
159644 TATAAACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.03, G:0.25, T:0.28
Consensus pattern (17 bp):
TGGAATGTTAACAGAAA
Found at i:163823 original size:19 final size:21
Alignment explanation
Indices: 163786--163828 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
163776 TAACTTTTTC
163786 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
163806 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
163826 TTT
1 TTT
163829 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:163834 original size:19 final size:20
Alignment explanation
Indices: 163785--163834 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
163775 TTAACTTTTT
*
163785 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
163805 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
163824 CTTTTACCTTT
1 CTTTTACCTTT
163835 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:168093 original size:22 final size:22
Alignment explanation
Indices: 168068--168112 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
168058 GATTGCAAAT
168068 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
*
168090 AGGGAACTGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
168112 A
1 A
168113 ATACTGCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTGCTAC
Found at i:168736 original size:23 final size:23
Alignment explanation
Indices: 168710--168755 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
168700 TGAAGGATCT
168710 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
168733 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
168756 TATAATATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:170476 original size:22 final size:22
Alignment explanation
Indices: 170448--170499 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
170438 CTTTATACTC
*
170448 ATTCACATTTACCATAACATAT
1 ATTCACATGTACCATAACATAT
170470 ATTCACATGTACCATAACATAT
1 ATTCACATGTACCATAACATAT
170492 ATTCACAT
1 ATTCACAT
170500 ATATTGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (22 bp):
ATTCACATGTACCATAACATAT
Found at i:171028 original size:64 final size:63
Alignment explanation
Indices: 170956--171076 Score: 197
Period size: 64 Copynumber: 1.9 Consensus size: 63
170946 GCACTAACTA
* *
170956 TGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAATGGGTGCATCGATACACTTCCTG
1 TGCATCGATACACAAATCACATTCAATGTTTCCA-TTTTAAGGGGTGCATCGATACACTTCCTG
* *
171020 TGCATCGATACACAAATTACATTCAATGTTTTCATTTTAAGGGGTGCATCGATACAC
1 TGCATCGATACACAAATCACATTCAATGTTTCCATTTTAAGGGGTGCATCGATACAC
171077 ACTAAATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
63 22 0.42
64 31 0.58
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (63 bp):
TGCATCGATACACAAATCACATTCAATGTTTCCATTTTAAGGGGTGCATCGATACACTTCCTG
Found at i:180931 original size:27 final size:29
Alignment explanation
Indices: 180884--180937 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
180874 TTATTTCACA
*
180884 GAAAATGTTTTTCGAAGAATG-AAATCTG
1 GAAAATGTTTTTAGAAGAATGTAAATCTG
180912 GAAAATGTTTTATAG-A-AATGTAAATC
1 GAAAATGTTTT-TAGAAGAATGTAAATC
180938 ATTTTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 4 0.17
28 17 0.74
29 2 0.09
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.33
Consensus pattern (29 bp):
GAAAATGTTTTTAGAAGAATGTAAATCTG
Found at i:181204 original size:15 final size:15
Alignment explanation
Indices: 181184--181212 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
181174 TACACTAGTT
181184 TAGGTTTATTTTATG
1 TAGGTTTATTTTATG
181199 TAGGTTTATTTTAT
1 TAGGTTTATTTTAT
181213 ATAATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (15 bp):
TAGGTTTATTTTATG
Found at i:184856 original size:13 final size:13
Alignment explanation
Indices: 184838--184876 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
184828 ATACTGAAAA
184838 CACATATATAATC
1 CACATATATAATC
184851 CACATATA-AA-C
1 CACATATATAATC
184862 CACATATATAATC
1 CACATATATAATC
184875 CA
1 CA
184877 TACAAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.38
12 4 0.17
13 11 0.46
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (13 bp):
CACATATATAATC
Done.