Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006611.1 Hibiscus syriacus cultivar Beakdansim tig00016226_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: 100985
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:17785 original size:16 final size:16
Alignment explanation
Indices: 17764--17801 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
17754 GTTACCTTAG
17764 AGAGGGGAGCCAAACC
1 AGAGGGGAGCCAAACC
17780 AGAGGGGAGCCAAACC
1 AGAGGGGAGCCAAACC
17796 AGAGGG
1 AGAGGG
17802 TTGTTTCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.21, G:0.42, T:0.00
Consensus pattern (16 bp):
AGAGGGGAGCCAAACC
Found at i:21220 original size:132 final size:131
Alignment explanation
Indices: 20984--21233 Score: 378
Period size: 132 Copynumber: 1.9 Consensus size: 131
20974 ATAATAACAT
* *
20984 TCGAATTAATATTGAATTTTAGGATGAAATAGTAGTATATCTTCATTTCAATTGGAGTAATGAAC
1 TCGAATTAATATTGAATTTTAGGATGAAATAGTAATATATCTTCATTTCAATTGGAGTAATAAAC
*
21049 GACTGCTTTAAAGCATGATAGGTCATTTATTCTTGATTGGAAATAATTAGATACTATCGTTTTCT
66 GACTGCTTTAAAGCATGAGAGGTCATTTATTCTTGATTGGAAATAATTAGATACTATCGTTTTCT
21114 C
131 C
* *
21115 TCGAATTAATATTGAATTTTATGATGAAAATAGTAATATCA-CTTCATTTCGATTGGAGTAATAA
1 TCGAATTAATATTGAATTTTAGGATG-AAATAGTAATAT-ATCTTCATTTCAATTGGAGTAATAA
** * *
21179 ATTATTGCTTTAAGGCATGAGAGGTCATTTATTCTAT-ATTGGAAATAATTAGATA
64 ACGACTGCTTTAAAGCATGAGAGGTCATTTATTCT-TGATTGGAAATAATTAGATA
21234 TTGTTGTTCT
Statistics
Matches: 107, Mismatches: 9, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
131 25 0.23
132 80 0.75
133 2 0.02
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (131 bp):
TCGAATTAATATTGAATTTTAGGATGAAATAGTAATATATCTTCATTTCAATTGGAGTAATAAAC
GACTGCTTTAAAGCATGAGAGGTCATTTATTCTTGATTGGAAATAATTAGATACTATCGTTTTCT
C
Found at i:22758 original size:20 final size:19
Alignment explanation
Indices: 22718--22759 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
22708 ACTAACTAAA
**
22718 TTTTATTTTGTCTTTTTTT
1 TTTTATTTTGTCTCATTTT
22737 TTTTATTTTGTTCTCATTTT
1 TTTTATTTTG-TCTCATTTT
22757 TTT
1 TTT
22760 CATTGTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.81
Consensus pattern (19 bp):
TTTTATTTTGTCTCATTTT
Found at i:33738 original size:13 final size:13
Alignment explanation
Indices: 33722--33746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33712 AGAAAAAGAA
33722 AAATAAATAAAAT
1 AAATAAATAAAAT
33735 AAATAAATAAAA
1 AAATAAATAAAA
33747 GGGTTTCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:37783 original size:131 final size:130
Alignment explanation
Indices: 37549--37942 Score: 601
Period size: 131 Copynumber: 3.0 Consensus size: 130
37539 CTAATAACAT
* *
37549 TCGAATTAATATTGAATTTTAGGATAAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAAT
1 TCGAATTAATATTGAATTTTAGGATGAAATAGTAATATCTCTTCATTTTGATTGGAGTAATAAAT
*
37614 GACTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCT
66 GACTGCTTTAAGGAATGAGA-GTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCT
37679 C
130 C
* * *
37680 TCGAATTAATATTGAATTTTAGGATGAAATAGTAATATCTCTTCATTTTGTTTAGAGTAATGAAT
1 TCGAATTAATATTGAATTTTAGGATGAAATAGTAATATCTCTTCATTTTGATTGGAGTAATAAAT
* * * *
37745 GATTGCTTTAAGGCATGAGATGTCATTTATTCTTGATTGGAAATAATTAGACATTATCGTTTTCT
66 GACTGCTTTAAGGAATGAGA-GTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCT
37810 C
130 C
* * * *
37811 TTGAATCAATATTTAATTTTAGGAAGAAATAGTAATATCTCTTCATTTTGATTGGAGTAATAAAT
1 TCGAATTAATATTGAATTTTAGGATGAAATAGTAATATCTCTTCATTTTGATTGGAGTAATAAAT
* * *
37876 GACTGCTTTAAGGAATGAGAGATCATTTATTCTCGATTAG-AATAATTAGATATTATCATTCTCT
66 GACTGCTTTAAGGAATGAGAG-TCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCT
37940 C
130 C
37941 TC
1 TC
37943 TTACAATTTA
Statistics
Matches: 237, Mismatches: 25, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
130 24 0.10
131 213 0.90
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (130 bp):
TCGAATTAATATTGAATTTTAGGATGAAATAGTAATATCTCTTCATTTTGATTGGAGTAATAAAT
GACTGCTTTAAGGAATGAGAGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTC
Found at i:39006 original size:23 final size:23
Alignment explanation
Indices: 38958--39007 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
38948 AATCAGGAGA
* * * *
38958 TCGATTGAAGCTCGAGCTCAAGC
1 TCGATTCAAGCTCGAACTAAAAC
38981 TCGATTCAAGCTCGAACTAAAAC
1 TCGATTCAAGCTCGAACTAAAAC
39004 TCGA
1 TCGA
39008 ATTTGAACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
TCGATTCAAGCTCGAACTAAAAC
Found at i:40025 original size:368 final size:367
Alignment explanation
Indices: 39343--40088 Score: 1429
Period size: 368 Copynumber: 2.0 Consensus size: 367
39333 TTTGATCATC
*
39343 ATGGTTATTTTTTTAGCACCATTTAGATTTGAATATATGGTTGGTTGGTCTTGATTTGGATTGAT
1 ATGGATATTTTTTTAGCACCATTTAGATTTGAATATATGGTTGGTTGGTCTTGATTTGGATTGAT
39408 TAATTAAGAATGTTTGATGTTGTTTATATAGTGGTTGATTTACTTACCATACATTAACTTGTATT
66 TAATTAAGAATGTTTGATGTTGTTTATATAGTGGTTGATTTACTTACCATACATTAACTTGTATT
39473 AAATTTTAATTGGTACTACAATGAATTTTGAGTTTTTAGATGTATGTATTATATTTATTTAGTTA
131 AAATTTTAATTGGTACTACAATGAATTTTGAGTTTTTAGATGTATGTATTATATTTATTTAGTTA
*
39538 CATTGTACATGAACATCATTCAATTAATCAATACAATATATATGTTTTATTCGTAAAAAATAATA
196 CATTGTACATGAACATCATTAAATTAATCAATACAATATATATGTTTTATTCGTAAAAAATAATA
39603 GGTTCGTTGAATTGAAAAAATCTCTTTAATTTAATAAATTATTAATTCCTCAATTAGTTAATACT
261 GGTTCGTTGAATTGAAAAAATCTCTTTAATTTAATAAATTATTAATTCCTCAATTAGTTAATACT
39668 TATTTAAATTAAAAAAATTATGTGATCCCAATTTATTAAAATT
326 TATTTAAATTAAAAAAATTATGTGATCCCAATTTATT-AAATT
39711 ATGGATATTTTTTTAGCACCATTTAGATTTGAATATATGGTTGGTTGGTCTTGATTTGGATTGAT
1 ATGGATATTTTTTTAGCACCATTTAGATTTGAATATATGGTTGGTTGGTCTTGATTTGGATTGAT
39776 TAATTAAGAATGTTTGATGTTGTTTATATAGTGGTTGATTTACTTACCATACATTAACTTGTATT
66 TAATTAAGAATGTTTGATGTTGTTTATATAGTGGTTGATTTACTTACCATACATTAACTTGTATT
*
39841 AAATTTTAATTGGTACTACAATGAATTTTGATTTTTTAGATGTATGTATTATATTTATTTAGTTA
131 AAATTTTAATTGGTACTACAATGAATTTTGAGTTTTTAGATGTATGTATTATATTTATTTAGTTA
*
39906 CATTGTACATGAACATCATTAAATTAATCAATACAATATATATGTTTTATTCGTGAAAAATAATA
196 CATTGTACATGAACATCATTAAATTAATCAATACAATATATATGTTTTATTCGTAAAAAATAATA
*
39971 GGTTCGTTGAATTGAAAAAATCTCTTTAATTTAATAAATTATTAATTTCTCAATTAGTTAATACT
261 GGTTCGTTGAATTGAAAAAATCTCTTTAATTTAATAAATTATTAATTCCTCAATTAGTTAATACT
*
40036 TATTTAAATTAAAAAAATTATGTGATCCCAATTTATTAATTT
326 TATTTAAATTAAAAAAATTATGTGATCCCAATTTATTAAATT
40078 ATGGATATTTT
1 ATGGATATTTT
40089 ACTGTAATTT
Statistics
Matches: 372, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
367 15 0.04
368 357 0.96
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.46
Consensus pattern (367 bp):
ATGGATATTTTTTTAGCACCATTTAGATTTGAATATATGGTTGGTTGGTCTTGATTTGGATTGAT
TAATTAAGAATGTTTGATGTTGTTTATATAGTGGTTGATTTACTTACCATACATTAACTTGTATT
AAATTTTAATTGGTACTACAATGAATTTTGAGTTTTTAGATGTATGTATTATATTTATTTAGTTA
CATTGTACATGAACATCATTAAATTAATCAATACAATATATATGTTTTATTCGTAAAAAATAATA
GGTTCGTTGAATTGAAAAAATCTCTTTAATTTAATAAATTATTAATTCCTCAATTAGTTAATACT
TATTTAAATTAAAAAAATTATGTGATCCCAATTTATTAAATT
Found at i:40473 original size:23 final size:21
Alignment explanation
Indices: 40427--40473 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
40417 AATAAAGGTA
**
40427 AAAGTTCTTTTACCTTTAATG
1 AAAGTTCTTTTACCCATAATG
40448 AAAGTTCTTTTTGACCCATAATG
1 AAAGTTC-TTTT-ACCCATAATG
40471 AAA
1 AAA
40474 CGTTTGGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 4 0.18
23 11 0.50
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (21 bp):
AAAGTTCTTTTACCCATAATG
Found at i:40815 original size:18 final size:18
Alignment explanation
Indices: 40794--40834 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
40784 TTTTTAACAA
*
40794 AATTAATAAATTGATAGT
1 AATTAATAAATTGAAAGT
40812 AATTAATAAATTGAAAGT
1 AATTAATAAATTGAAAGT
40830 AATTA
1 AATTA
40835 TTAATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (18 bp):
AATTAATAAATTGAAAGT
Found at i:42419 original size:12 final size:12
Alignment explanation
Indices: 42402--42427 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42392 CTGGTGTAAT
42402 TGGCCTTGGAGG
1 TGGCCTTGGAGG
42414 TGGCCTTGGAGG
1 TGGCCTTGGAGG
42426 TG
1 TG
42428 ATGAATTCTC
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:0.08, C:0.15, G:0.50, T:0.27
Consensus pattern (12 bp):
TGGCCTTGGAGG
Found at i:44322 original size:24 final size:24
Alignment explanation
Indices: 44285--44372 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 24
44275 TTCGATATCA
* *
44285 TAGATCTCCATCACCTGCGCGTCT
1 TAGATCTCCATCACCTACGCGTCG
* * *
44309 TTGATCTCCTTCACCTATGCGTCG
1 TAGATCTCCATCACCTACGCGTCG
** *
44333 TAGATCTCCATCACCTATACGTTG
1 TAGATCTCCATCACCTACGCGTCG
44357 TAGATCTCCATCACCT
1 TAGATCTCCATCACCT
44373 TTGCATTTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.19, C:0.34, G:0.14, T:0.33
Consensus pattern (24 bp):
TAGATCTCCATCACCTACGCGTCG
Found at i:47748 original size:30 final size:33
Alignment explanation
Indices: 47681--47762 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
47671 AGCCTCATGC
*
47681 ACCTGAATAACCTATAGCTCAACCGGTTGTGGT
1 ACCTGAACAACCTATAGCTCAACCGGTTGTGGT
* *
47714 ACCTGAACAGCCTATAGCTTAACCGG-T-T-GT
1 ACCTGAACAACCTATAGCTCAACCGGTTGTGGT
*
47744 ACCTGAACAACCTGTAGCT
1 ACCTGAACAACCTATAGCT
47763 GAGCTGATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 19 0.43
31 1 0.02
32 1 0.02
33 23 0.52
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (33 bp):
ACCTGAACAACCTATAGCTCAACCGGTTGTGGT
Found at i:51995 original size:40 final size:39
Alignment explanation
Indices: 51908--52034 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 39
51898 TTAAAAATAT
51908 ATATATTTTTATCTTAATTTTAAAATATTATAAGAATAAA
1 ATATA-TTTTATCTTAATTTTAAAATATTATAAGAATAAA
* **
51948 ATATATTTTATCTTAAATTTTAAAATATTTTAA-TTTAGAA
1 ATATATTTTATCTT-AATTTTAAAATATTATAAGAATA-AA
*
51988 ATTTATTTTTATTTTTATCTTAATTTTAAAATATTATAAGATTAAA
1 A--TA----TA-TTTTATCTTAATTTTAAAATATTATAAGAATAAA
52034 A
1 A
52035 AATAAATATT
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
39 11 0.15
40 25 0.35
42 2 0.03
46 22 0.31
47 12 0.17
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (39 bp):
ATATATTTTATCTTAATTTTAAAATATTATAAGAATAAA
Found at i:52104 original size:40 final size:40
Alignment explanation
Indices: 52059--52207 Score: 129
Period size: 40 Copynumber: 3.6 Consensus size: 40
52049 TTAAAGTAAG
52059 AATAAATTATATTTTTAAGTTAAATTAAAATTAAGATAAA
1 AATAAATTATATTTTTAAGTTAAATTAAAATTAAGATAAA
* *
52099 AATAAA-TATATTTTAAAATTAAAATATTTTAAAATTTAAGATAAA
1 AATAAATTATATTTTTAAGTT--AA-A--TTAAAA-TTAAGATAAA
* * * *** **
52144 AATATATTTTATTCTTATCATATTTTAAAATTAAGATAAA
1 AATAAATTATATTTTTAAGTTAAATTAAAATTAAGATAAA
*
52184 AATAAAATATATTTTTAATGTTAA
1 AATAAATTATATTTTTAA-GTTAA
52208 GATGTTAATT
Statistics
Matches: 82, Mismatches: 19, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
39 12 0.15
40 29 0.35
41 10 0.12
42 1 0.01
44 7 0.09
45 15 0.18
46 8 0.10
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (40 bp):
AATAAATTATATTTTTAAGTTAAATTAAAATTAAGATAAA
Found at i:52137 original size:17 final size:17
Alignment explanation
Indices: 52095--52134 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
52085 AAAATTAAGA
*
52095 TAAAAATAAATATATTT
1 TAAAATTAAATATATTT
52112 TAAAATTAAA-ATATTT
1 TAAAATTAAATATATTT
52128 TAAAATT
1 TAAAATT
52135 TAAGATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTAAATATATTT
Found at i:52146 original size:45 final size:44
Alignment explanation
Indices: 52083--52198 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 44
52073 TTAAGTTAAA
52083 TTAAAATTAAGATAAAAATAAATATATTTTAAAATTAAAATATT
1 TTAAAATTAAGATAAAAATAAATATATTTTAAAATTAAAATATT
*** **
52127 TTAAAATTTAAGAT---AA-AAATATATTTTATTCTTATCATATT
1 TTAAAA-TTAAGATAAAAATAAATATATTTTAAAATTAAAATATT
52168 TTAAAATTAAGATAAAAATAAAATATATTTT
1 TTAAAATTAAGATAAAAAT-AAATATATTTT
52199 TAATGTTAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
40 7 0.11
41 26 0.43
42 2 0.03
43 2 0.03
44 6 0.10
45 18 0.30
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (44 bp):
TTAAAATTAAGATAAAAATAAATATATTTTAAAATTAAAATATT
Found at i:52606 original size:61 final size:61
Alignment explanation
Indices: 52507--52631 Score: 205
Period size: 61 Copynumber: 2.0 Consensus size: 61
52497 CAGGTGACGA
* **
52507 TATGTGTCATGATGTTTGGTAATTAGTGCCATGTGGCATGATCTGATTTGAAGATTAAGTT
1 TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGAAGATTAAGTT
* *
52568 TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGATGATTGAGTT
1 TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGAAGATTAAGTT
52629 TAT
1 TAT
52632 TTGGATTTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (61 bp):
TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGAAGATTAAGTT
Found at i:62983 original size:16 final size:17
Alignment explanation
Indices: 62952--62987 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
62942 CGTATCGCCA
62952 ACAAAATTTCACTATTC
1 ACAAAATTTCACTATTC
62969 ACAAAATTT-ACTATTC
1 ACAAAATTTCACTATTC
62985 ACA
1 ACA
62988 TGAATAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:65746 original size:93 final size:93
Alignment explanation
Indices: 65648--65841 Score: 352
Period size: 93 Copynumber: 2.1 Consensus size: 93
65638 TTCAAAGTAT
* *
65648 ATGTTTATTTAACATTTTTTATGTTACTTTTTTAAGTGTCTAGATACCTAATTTATCATGATCGT
1 ATGTTTATTTAACATTTTTTATGTTACTTTTTTAAGTGCCTAGATACCTAATTCATCATGATCGT
65713 TAAAAAATTATGTTATCTAAAACATTTA
66 TAAAAAATTATGTTATCTAAAACATTTA
*
65741 ATGTTTATTTAACGTTTTTTATGTTACTTTTTTAAGTGCCTAGATACCTAATTCATCATGATCGT
1 ATGTTTATTTAACATTTTTTATGTTACTTTTTTAAGTGCCTAGATACCTAATTCATCATGATCGT
65806 TAAAAAATTATGTTATCTAAAACATTTA
66 TAAAAAATTATGTTATCTAAAACATTTA
*
65834 ATGCTTAT
1 ATGTTTAT
65842 GAAATTTTAT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 97 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.47
Consensus pattern (93 bp):
ATGTTTATTTAACATTTTTTATGTTACTTTTTTAAGTGCCTAGATACCTAATTCATCATGATCGT
TAAAAAATTATGTTATCTAAAACATTTA
Found at i:67926 original size:3 final size:3
Alignment explanation
Indices: 67918--67987 Score: 104
Period size: 3 Copynumber: 23.3 Consensus size: 3
67908 TTTGACGGAC
* *
67918 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
67966 TAA TAA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
67988 ATCAAGTATC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:68053 original size:21 final size:19
Alignment explanation
Indices: 68029--68098 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 19
68019 TTAAGGTTTC
68029 TTAAAAATTTTAAAAATTAA
1 TTAAAAATTTTAAAAATT-A
* *
68049 TTTAAAAATATTAAATATTA
1 -TTAAAAATTTTAAAAATTA
*
68069 TT-AAAATTATAAAAA-TA
1 TTAAAAATTTTAAAAATTA
* *
68086 TGAAAATTTTTAA
1 TTAAAAATTTTAA
68099 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
17 3 0.08
18 18 0.45
19 2 0.05
20 1 0.03
21 16 0.40
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (19 bp):
TTAAAAATTTTAAAAATTA
Found at i:71845 original size:2 final size:2
Alignment explanation
Indices: 71838--71865 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
71828 AAATTATTAG
71838 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
71866 GAATAGGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72069 original size:14 final size:14
Alignment explanation
Indices: 72050--72087 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
72040 CGTTCGATTA
72050 TATGTTCATTCATT
1 TATGTTCATTCATT
*
72064 TATGTTCGTTCATT
1 TATGTTCATTCATT
72078 TATGTTCATT
1 TATGTTCATT
72088 TATGTTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (14 bp):
TATGTTCATTCATT
Found at i:72086 original size:24 final size:23
Alignment explanation
Indices: 72058--72107 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
72048 TATATGTTCA
72058 TTCATTTATGTTCGTTCATTTATG
1 TTCATTTATGTTCGTT-ATTTATG
*
72082 TTCATTTATGTTCGTTATTTCTG
1 TTCATTTATGTTCGTTATTTATG
72105 TTC
1 TTC
72108 GAACAGAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (23 bp):
TTCATTTATGTTCGTTATTTATG
Found at i:72278 original size:27 final size:26
Alignment explanation
Indices: 72236--72289 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
72226 TTTTTTGTGT
* **
72236 TTGTGTTGTTCTTTTATGTTCGTTTA
1 TTGTGTTGTTCGTTTACATTCGTTTA
72262 TTGTGTTCGTTCGTTTACATTCGTTTA
1 TTGTGTT-GTTCGTTTACATTCGTTTA
72289 T
1 T
72290 GTTCGCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.09, C:0.11, G:0.19, T:0.61
Consensus pattern (26 bp):
TTGTGTTGTTCGTTTACATTCGTTTA
Found at i:72397 original size:16 final size:16
Alignment explanation
Indices: 72376--72406 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
72366 AAAAAAATTA
72376 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTG
72392 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
72407 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTG
Found at i:73990 original size:134 final size:134
Alignment explanation
Indices: 73588--74333 Score: 859
Period size: 134 Copynumber: 5.5 Consensus size: 134
73578 ACGAATCAAA
* *
73588 CTCGATTCAATCTTCCCTGAAGTGACAGTGGAATAAATCAACG-CCTCCATATCTGATTTTTCCC
1 CTCGATTCAATCTTCCCT-AAGTGACAGTGGAATGAATCAACGTCC-CCAGATCTGA-TTTTCCC
* * * * * *
73652 TCAAGAAGAAGCGAAACAGATCCCTTTCTTCCAAGATTTGATATTCCCTGGGTAATAGTGGAACA
63 TCAAGAAGAAGTGGAACAGATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
*
73717 AGTCTAC
128 AGTCTGC
* * * * *
73724 CTCAATTCAATCTTCCCTAAGTGACTA-TAGAATGAATCAACGTCCCCATATATGGTATTTCCCT
1 CTCGATTCAATCTTCCCTAAGTGAC-AGTGGAATGAATCAACGTCCCCAGATCTGAT-TTTCCCT
* * * * * *
73788 CAAGAAAAAGTGGAACATATTCATTTCTTCCAGGATTTGATATTCCATGAGTAACAGTGGAACAA
64 CAAGAAGAAGTGGAACAGATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
* *
73853 GTTTGT
129 GTCTGC
* * * * * *
73859 CTCGATTCAATCCTCCCTTAGTGATAGTAGAATGAATCAACGTCCCCATATATGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * * * *
73924 AGAAGAAGTAGAATAGATCCATCTCTTTCAAGATTTGATATTCCCTTAGTAACAGTAGAACAAGT
66 AGAAGAAGTGGAACAGATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
*
73989 TTGC
131 CTGC
* * * * *
73993 CTCGATTCAATCTTCCTTAAGTGACAGTGGAATGAATCAACATCCCGAGACCCGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * * * *
74058 ACAAGAAGTGAAACATAT-TATTTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACACG
66 AGAAGAAGTGGAACAGATCCA-TTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
74122 TCTGC
130 TCTGC
* *
74127 CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAATGTCTCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
** * * * * *
74192 AGAAGAAACGGAACATATCCCTCTCTTTCAAGATTTGTTATTCCTTGAGTAACAGTGGAACAAGT
66 AGAAGAAGTGGAACAGATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
74257 CTGC
131 CTGC
* ** * * * * *
74261 CTCGATTCAATCTTCCCTGAGCAAAAATGGAATGAATCGACGTTCCCAGATCTGATTTTCCCCCA
1 CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
*
74326 ACAAGAAG
66 AGAAGAAG
74334 CAAAACAAAT
Statistics
Matches: 518, Mismatches: 86, Indels: 14
0.84 0.14 0.02
Matches are distributed among these distances:
133 1 0.00
134 355 0.69
135 142 0.27
136 20 0.04
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
AGAAGAAGTGGAACAGATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTGC
Found at i:74486 original size:3 final size:3
Alignment explanation
Indices: 74478--74512 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
74468 CAATAGTTTA
74478 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
74513 CATCATCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:78940 original size:18 final size:17
Alignment explanation
Indices: 78906--78941 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
78896 ATATTTAAGG
78906 TAAAATATATTAAATAA
1 TAAAATATATTAAATAA
*
78923 TAAAATATAATTATATAA
1 TAAAATAT-ATTAAATAA
78941 T
1 T
78942 TATAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAATATATTAAATAA
Found at i:80225 original size:8 final size:8
Alignment explanation
Indices: 80214--80274 Score: 63
Period size: 8 Copynumber: 7.4 Consensus size: 8
80204 AATATTAGAT
80214 AAATAATA
1 AAATAATA
80222 AAATAAT-
1 AAATAATA
*
80229 AAATCAAAA
1 AAAT-AATA
80238 CAAATAATA
1 -AAATAATA
80247 AAA-AATTA
1 AAATAA-TA
80255 AAATAATAA
1 AAATAAT-A
80264 AAATAATA
1 AAATAATA
80272 AAA
1 AAA
80275 AATTAAATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
7 6 0.13
8 22 0.49
9 13 0.29
10 4 0.09
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.21
Consensus pattern (8 bp):
AAATAATA
Found at i:80242 original size:25 final size:25
Alignment explanation
Indices: 80214--80326 Score: 96
Period size: 25 Copynumber: 4.6 Consensus size: 25
80204 AATATTAGAT
80214 AAATAATAAAATAA-TAAATCAA-AA
1 AAATAATAAAA-AATTAAATCAATAA
80238 CAAATAATAAAAAATTAAAAT-AATAA
1 -AAATAATAAAAAATT-AAATCAATAA
*
80264 AAATAATAAAAAATTAAATCAGAGAA
1 AAATAATAAAAAATTAAATCA-ATAA
* *
80290 AAAT--TAAATAAA-TAAATTGAAAAA
1 AAATAATAAA-AAATTAAA-TCAATAA
80314 AAAT-ATAAAAAAT
1 AAATAATAAAAAAT
80327 AAGTCGAAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 18
0.78 0.03 0.19
Matches are distributed among these distances:
24 24 0.32
25 39 0.51
26 13 0.17
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (25 bp):
AAATAATAAAAAATTAAATCAATAA
Found at i:80315 original size:24 final size:24
Alignment explanation
Indices: 80214--80349 Score: 93
Period size: 24 Copynumber: 5.5 Consensus size: 24
80204 AATATTAGAT
*
80214 AAATAATAAAATAATAAATC-AAAAC
1 AAAT-ATAAAA-AATAAATCGAAAAA
*
80239 AAATAATAAAAAATTAAAAT--AATAA
1 AAAT-ATAAAAAA-T-AAATCGAAAAA
*
80264 AAATAATAAAAAATTAAATC-AGAGAA
1 AAAT-ATAAAAAA-TAAATCGA-AAAA
*
80290 AAAT-TAAATAAATAAATTGAAAAA
1 AAATATAAA-AAATAAATCGAAAAA
*
80314 AAATATAAAAAATAAGTCGAAAAA
1 AAATATAAAAAATAAATCGAAAAA
* *
80338 AAAGAAAAAAAA
1 AAATATAAAAAA
80350 AGAAAAAAAG
Statistics
Matches: 95, Mismatches: 9, Indels: 15
0.80 0.08 0.13
Matches are distributed among these distances:
24 45 0.47
25 39 0.41
26 11 0.12
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (24 bp):
AAATATAAAAAATAAATCGAAAAA
Found at i:80348 original size:10 final size:10
Alignment explanation
Indices: 80333--80358 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
80323 AAATAAGTCG
80333 AAAAAAAAGA
1 AAAAAAAAGA
80343 AAAAAAAAGA
1 AAAAAAAAGA
80353 AAAAAA
1 AAAAAA
80359 GTGAAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:80425 original size:13 final size:14
Alignment explanation
Indices: 80407--80436 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
80397 TTATATTTTG
80407 AAAT-AAAAAAATA
1 AAATAAAAAAAATA
80420 AAATAAAAAAAATA
1 AAATAAAAAAAATA
80434 AAA
1 AAA
80437 ATTGAGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (14 bp):
AAATAAAAAAAATA
Found at i:81784 original size:80 final size:78
Alignment explanation
Indices: 81700--81986 Score: 256
Period size: 80 Copynumber: 3.6 Consensus size: 78
81690 GCTATGATTT
* * * * *
81700 AAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGCATATAACTCTTCTCGA
1 AAATGATGTGCCTTGAAGCTGAGCGTAATCGAACTC-AAGGTCTTTGGCAGATAAC-CTTCTAGC
81765 CTTAAGCTATGCTGC
64 CTTAAGCTATGCTGC
*** * *
81780 AAATGATAGTGCCTTTG-AGCTGCTTGCAATCGAACTCTAA-GTCTTTGGTAGATAAACCTTCTA
1 AAATGAT-GTGCC-TTGAAGCTGAGCGTAATCGAACTC-AAGGTCTTTGGCAGAT-AACCTTCTA
* * *
81843 GCCTTGAGTTATGTTGC
62 GCCTTAAGCTATGCTGC
* * * *
81860 AAATGATATGCCCTTGAAGCTGAGTGTAATC-AACCTCAAGGGTCTTTGGCAGATAGCCCTTCTT
1 AAATGATGTG-CCTTGAAGCTGAGCGTAATCGAA-CTCAA-GGTCTTTGGCAGATA-ACCTTCTA
*
81924 GCCTTAAGCTATACTGC
62 GCCTTAAGCTATGCTGC
* * * *
81941 AAATGCTGAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
1 AAATGATGTGCCTTGAAGCTGAGCGTAATCGAACTC-AAGGTCTTT
81987 TGTTTCAAGA
Statistics
Matches: 165, Mismatches: 31, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
79 9 0.05
80 86 0.52
81 67 0.41
82 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (78 bp):
AAATGATGTGCCTTGAAGCTGAGCGTAATCGAACTCAAGGTCTTTGGCAGATAACCTTCTAGCCT
TAAGCTATGCTGC
Found at i:82196 original size:37 final size:36
Alignment explanation
Indices: 82108--82201 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 36
82098 AAACTGTCTC
* *
82108 AGACAAAACTTTGTTTTAAGGGAAATTGTCTCAAAAG
1 AGACAAAACTTTGTTTTGA-GTAAATTGTCTCAAAAG
**
82145 AGACAAAACTTTGTTTTGAGTAAATTAGTCTCAAGCG
1 AGACAAAACTTTGTTTTGAGTAAATT-GTCTCAAAAG
*
82182 AGAC-AACCTCTTGTTTTGAG
1 AGACAAAACT-TTGTTTTGAG
82202 AGAAACAATC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
36 10 0.20
37 40 0.80
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (36 bp):
AGACAAAACTTTGTTTTGAGTAAATTGTCTCAAAAG
Found at i:83846 original size:27 final size:27
Alignment explanation
Indices: 83822--83873 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
83812 TTTGTTTTCG
* *
83822 TTTTTTTCTTT-TTTATTTTCTTTTTAC
1 TTTTTTTATTTGTTT-TTCTCTTTTTAC
83849 TTTTTTTATTTGTTTTTCTCTTTTT
1 TTTTTTTATTTGTTTTTCTCTTTTT
83874 TCTTCTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.06, C:0.10, G:0.02, T:0.83
Consensus pattern (27 bp):
TTTTTTTATTTGTTTTTCTCTTTTTAC
Found at i:83880 original size:37 final size:37
Alignment explanation
Indices: 83792--83880 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 37
83782 TGTATTGTTT
* *
83792 TCTTTTTTCTTCATTTTTCCTTTGTTTTCGTTTTTTTC
1 TCTTTTTTCTTC-TTTTTACTTTGTTTTAGTTTTTTTC
* *
83830 T-TTTTTATTTTCTTTTTACTTT-TTTTATTTGTTTTTC
1 TCTTTTT-TCTTCTTTTTACTTTGTTTTAGTT-TTTTTC
83867 TCTTTTTTCTTCTT
1 TCTTTTTTCTTCTT
83881 CTCTTTTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
36 6 0.14
37 27 0.63
38 10 0.23
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.78
Consensus pattern (37 bp):
TCTTTTTTCTTCTTTTTACTTTGTTTTAGTTTTTTTC
Found at i:83893 original size:14 final size:15
Alignment explanation
Indices: 83857--83894 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
83847 ACTTTTTTTA
*
83857 TTTGTTTTTCTCTTT
1 TTTGTTCTTCTCTTT
*
83872 TTTCTTCTTCTC-TT
1 TTTGTTCTTCTCTTT
83886 TTTGTTCTT
1 TTTGTTCTT
83895 GATTGGATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTGTTCTTCTCTTT
Found at i:86952 original size:26 final size:27
Alignment explanation
Indices: 86918--86969 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
86908 AAAAGGACGA
* *
86918 AAATGTTAGAT-AGAAAAATAATAAAT
1 AAATATTAGATAAAAAAAATAATAAAT
86944 AAATATTAGATAAAAAAAATAATAAA
1 AAATATTAGATAAAAAAAATAATAAA
86970 ATAATAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (27 bp):
AAATATTAGATAAAAAAAATAATAAAT
Found at i:86972 original size:8 final size:8
Alignment explanation
Indices: 86959--87024 Score: 54
Period size: 7 Copynumber: 8.6 Consensus size: 8
86949 TTAGATAAAA
86959 AAAATAAT
1 AAAATAAT
86967 AAAATAAT
1 AAAATAAT
*
86975 -AAATCAAA
1 AAAAT-AAT
86983 ACAAATAAT
1 A-AAATAAT
86992 AAAA-AAGT
1 AAAATAA-T
87000 AAAA-AA-
1 AAAATAAT
87006 AAAATAA-
1 AAAATAAT
87013 AAAATAA-
1 AAAATAAT
87020 AAAAT
1 AAAAT
87025 TAAATTAGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
6 4 0.08
7 20 0.39
8 20 0.39
9 3 0.06
10 4 0.08
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAATAAT
Found at i:87038 original size:24 final size:22
Alignment explanation
Indices: 87011--87068 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 22
87001 AAAAAAAAAT
87011 AAAAAATAAA-AAATTAAATTAGA
1 AAAAAATAAATAAA-TAAATT-GA
*
87034 GAAAAATTAAATAAATAAATTGA
1 -AAAAAATAAATAAATAAATTGA
87057 AAAAAATAAATA
1 AAAAAATAAATA
87069 TAAAAGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 11 0.35
23 2 0.06
24 15 0.48
25 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (22 bp):
AAAAAATAAATAAATAAATTGA
Found at i:87065 original size:14 final size:13
Alignment explanation
Indices: 86956--87092 Score: 76
Period size: 14 Copynumber: 10.8 Consensus size: 13
86946 ATATTAGATA
86956 AAAAAAAT-AA-T
1 AAAAAAATAAATT
* *
86967 AAAATAATAAATC
1 AAAAAAATAAATT
86980 AAAACAAAT-AA-T
1 AAAA-AAATAAATT
*
86992 AAAAAAGTAAA--
1 AAAAAAATAAATT
*
87003 AAAAAAATAAAAAAT
1 AAAAAAAT--AAATT
*
87018 AAAAAATTAAATT
1 AAAAAAATAAATT
* *
87031 -AGAGAA-AAATT
1 AAAAAAATAAATT
*
87042 AAATAAATAAATT
1 AAAAAAATAAATT
87055 GAAAAAAATAAATAT
1 -AAAAAAATAAAT-T
*
87070 AAAAGAATAAA-T
1 AAAAAAATAAATT
87082 AAAAATAATAA
1 AAAAA-AATAA
87093 TAAAAATAAG
Statistics
Matches: 96, Mismatches: 17, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
11 22 0.23
12 19 0.20
13 23 0.24
14 24 0.25
15 8 0.08
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (13 bp):
AAAAAAATAAATT
Found at i:87087 original size:6 final size:6
Alignment explanation
Indices: 87058--87114 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
87048 ATAAATTGAA
* * *
87058 AAAAAT AAATAT AAAAGA- ATAAAT AAAAAT AATAAT AAAAAT AAGAGAAT
1 AAAAAT AAAAAT AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AA-A-AAT
87108 AAAAAT A
1 AAAAAT A
87115 TATATATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
5 1 0.02
6 32 0.78
7 3 0.07
8 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:87123 original size:14 final size:12
Alignment explanation
Indices: 86931--87126 Score: 59
Period size: 14 Copynumber: 15.4 Consensus size: 12
86921 TGTTAGATAG
86931 AAAAATAATAA-
1 AAAAATAATAAT
* *
86942 ATAAATATTAGAT
1 AAAAATAATA-AT
*
86955 AAAAAAAATAAT
1 AAAAATAATAAT
86967 -AAAATAATAAAT
1 AAAAATAAT-AAT
86979 CAAAACA-AATAAT
1 -AAAA-ATAATAAT
*
86992 AAAAAAGTAA-AAA
1 -AAAAA-TAATAAT
*
87005 AAAAATAAAAAAT
1 AAAAAT-AATAAT
*
87018 AAAAAATTAA-ATT
1 -AAAAA-TAATAAT
87031 AGAGAAA-AATTAA-
1 A-A-AAATAA-TAAT
* *
87044 ATAAATAA-ATT
1 AAAAATAATAAT
87055 GAAAAA-AATAAAT
1 -AAAAATAAT-AAT
*
87068 ATAAAAGAATAAAT
1 A-AAAATAAT-AAT
87082 AAAAATAATAAT
1 AAAAATAATAAT
*
87094 AAAAATAAGAGAAT
1 AAAAAT-A-ATAAT
87108 AAAAATATATATAT
1 AAAAATA-ATA-AT
87122 AAAAA
1 AAAAA
87127 ATTAAAAAAG
Statistics
Matches: 140, Mismatches: 19, Indels: 49
0.67 0.09 0.24
Matches are distributed among these distances:
10 1 0.01
11 21 0.15
12 33 0.24
13 39 0.28
14 44 0.31
15 2 0.01
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:87196 original size:8 final size:8
Alignment explanation
Indices: 87183--87221 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
87173 TTACATTTTG
87183 AAATAAAA
1 AAATAAAA
87191 AAAT---A
1 AAATAAAA
87196 AAATAAAA
1 AAATAAAA
87204 AAATAAAA
1 AAATAAAA
87212 AAATAAAA
1 AAATAAAA
87220 AA
1 AA
87222 GGAGTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
8 23 0.82
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATAAAA
Found at i:87219 original size:13 final size:13
Alignment explanation
Indices: 87183--87211 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
87173 TTACATTTTG
87183 AAATAAAAAAATA
1 AAATAAAAAAATA
87196 AAATAAAAAAATA
1 AAATAAAAAAATA
87209 AAA
1 AAA
87212 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:92458 original size:24 final size:24
Alignment explanation
Indices: 92431--92486 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
92421 CTATTCTTTT
92431 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
92455 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
92479 GCTTCAAT
1 GCTTCAAT
92487 CGAACTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:92723 original size:30 final size:30
Alignment explanation
Indices: 92687--92752 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
92677 AGTGAACCGG
*
92687 CGGTTCAAACCGGTTTTGCT-GGTTTTCAGA
1 CGGTTCAAACCGATTTT-CTCGGTTTTCAGA
** *
92717 CGGTTCACCCCGATTTTCTCGGTTTTCAGC
1 CGGTTCAAACCGATTTTCTCGGTTTTCAGA
92747 CGGTTC
1 CGGTTC
92753 TGTGCTAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.36
Consensus pattern (30 bp):
CGGTTCAAACCGATTTTCTCGGTTTTCAGA
Found at i:93202 original size:21 final size:21
Alignment explanation
Indices: 93178--93218 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
93168 ATTTTAAAAA
93178 TAAGATATTTTTAAAATTGTG
1 TAAGATATTTTTAAAATTGTG
*
93199 TAAGATATTTTTAAATTTGT
1 TAAGATATTTTTAAAATTGT
93219 TTTACTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (21 bp):
TAAGATATTTTTAAAATTGTG
Found at i:94613 original size:3 final size:3
Alignment explanation
Indices: 94605--94647 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
94595 ATTTAGTTCT
94605 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
94648 ATATATATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:94706 original size:4 final size:4
Alignment explanation
Indices: 94699--94736 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
94689 TAATCTAATA
94699 TATT TATT TA-T T-TT TATT TATT TATT TATT TA-T TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT T
94737 CCATTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 7 0.23
4 24 0.77
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:94716 original size:10 final size:10
Alignment explanation
Indices: 94701--94759 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
94691 ATCTAATATA
94701 TTTATTTATT
1 TTTATTTATT
94711 TTTATTTA--
1 TTTATTTATT
94719 TTTATTTATT
1 TTTATTTATT
94729 TATTATTTCCATT
1 T-TTATTT--ATT
94742 TATTA-TTATT
1 T-TTATTTATT
*
94752 TTTCTTTA
1 TTTATTTA
94760 AATAACATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
8 8 0.19
9 2 0.05
10 16 0.38
11 6 0.14
12 2 0.05
13 8 0.19
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATTTATT
Found at i:94801 original size:30 final size:30
Alignment explanation
Indices: 94767--94823 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
94757 TTAAATAACA
94767 TTTTTATATTATAT-TTTTTATTATTTTTTC
1 TTTTTAT-TTATATATTTTTATTATTTTTTC
* * *
94797 TTTTTGTTTCTATATTTTTATTGTTTT
1 TTTTTATTTATATATTTTTATTATTTT
94824 CTTTTCCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.77
Consensus pattern (30 bp):
TTTTTATTTATATATTTTTATTATTTTTTC
Found at i:94906 original size:5 final size:5
Alignment explanation
Indices: 94868--94930 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
94858 TATTATTTGC
* *
94868 ATTTT ATTCT -TTTT GTTTCT ATTTT A-TTT A-TTT ATTTT ATTTT ATTTTT
1 ATTTT ATTTT ATTTT ATTT-T ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT
* *
94917 ATTTC ATTTG ATTT
1 ATTTT ATTTT ATTT
94931 GTTTATTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
4 11 0.22
5 29 0.59
6 9 0.18
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:94910 original size:29 final size:30
Alignment explanation
Indices: 94870--94943 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 30
94860 TTATTTGCAT
* * *
94870 TTTATTCT-TTTTGTTTCTATTTTATTT-A
1 TTTATTTTATTTTATTTCTATTTCATTTGA
*
94898 TTTATTTTATTTTATTTTTATTTCATTTGA
1 TTTATTTTATTTTATTTCTATTTCATTTGA
* *
94928 TTT-GTTTATTTAATTT
1 TTTATTTTATTTTATTT
94944 AGTTAACTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 7 0.18
29 27 0.71
30 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (30 bp):
TTTATTTTATTTTATTTCTATTTCATTTGA
Found at i:94919 original size:20 final size:20
Alignment explanation
Indices: 94868--94930 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
94858 TATTATTTGC
* *
94868 ATTTTATTCTT-TTTGTTTCT
1 ATTTTATTTTTATTTATTT-T
94888 ATTTTA--TTTATTTATTTT
1 ATTTTATTTTTATTTATTTT
*
94906 ATTTTATTTTTATTTCATTTG
1 ATTTTATTTTTATTT-ATTTT
94927 ATTT
1 ATTT
94931 GTTTATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 9 0.25
19 6 0.17
20 13 0.36
21 8 0.22
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (20 bp):
ATTTTATTTTTATTTATTTT
Done.