Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004546.1 Hibiscus syriacus cultivar Beakdansim tig00010089_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: 50731
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:3386 original size:2 final size:2
Alignment explanation
Indices: 3379--3427 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
3369 TTAATAAATA
3379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3420 AT AT AT AT
1 AT AT AT AT
3428 TTATTAATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3713 original size:2 final size:2
Alignment explanation
Indices: 3706--3739 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3696 TGAAAAATAC
3706 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3740 AGACTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4442 original size:34 final size:34
Alignment explanation
Indices: 4394--4459 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
4384 TGATAACGAT
*
4394 GGTGGCTCGACGACGACTGGAACGTTGGCTCGTC
1 GGTGGCTCGACGACGACTGGAACGTGGGCTCGTC
*
4428 GGTGGCTCGGCGACGACTGGAACGTGGGCTCG
1 GGTGGCTCGACGACGACTGGAACGTGGGCTCG
4460 GGTGGAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.14, C:0.26, G:0.42, T:0.18
Consensus pattern (34 bp):
GGTGGCTCGACGACGACTGGAACGTGGGCTCGTC
Found at i:4609 original size:3 final size:3
Alignment explanation
Indices: 4595--4640 Score: 74
Period size: 3 Copynumber: 14.7 Consensus size: 3
4585 TGTAAAACAC
4595 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA
4641 GAATTTTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:7265 original size:22 final size:22
Alignment explanation
Indices: 7221--7265 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
7211 CTTCTACACC
** *
7221 AGTATCGATACTCCCATGCCAT
1 AGTATCGATACTCAAATGACAT
*
7243 AGTATCGATACTGAAATGACAT
1 AGTATCGATACTCAAATGACAT
7265 A
1 A
7266 TTAGAATCTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (22 bp):
AGTATCGATACTCAAATGACAT
Found at i:7313 original size:20 final size:20
Alignment explanation
Indices: 7288--7341 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
7278 ATGTTATCTT
* * *
7288 GGTATCGATACCACCCCATG
1 GGTATCGATACCAACACATA
7308 GGTATCGATACCAACACATA
1 GGTATCGATACCAACACATA
*
7328 TGTATCGATACCAA
1 GGTATCGATACCAA
7342 ACCTATAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (20 bp):
GGTATCGATACCAACACATA
Found at i:7745 original size:18 final size:18
Alignment explanation
Indices: 7719--7754 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
7709 TTTAACTACT
7719 CAAAACTCTCTTGCATTC
1 CAAAACTCTCTTGCATTC
*
7737 CAAAGCTCTCTTGCATTC
1 CAAAACTCTCTTGCATTC
7755 TTTAACTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.33, G:0.08, T:0.33
Consensus pattern (18 bp):
CAAAACTCTCTTGCATTC
Found at i:10118 original size:30 final size:30
Alignment explanation
Indices: 10038--10121 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 30
10028 ATAAGGAATG
*
10038 ATATGAACATGTGATATGTGAACATAAGAGA
1 ATATG-ACATGAGATATGTGAACATAAGAGA
* * * * *
10069 TTAAGTGATATGAGCTATGTGAACATATGGGA
1 AT-A-TGACATGAGATATGTGAACATAAGAGA
10101 ATATGACATGAGATATGTGAA
1 ATATGACATGAGATATGTGAA
10122 TTATATAGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
30 16 0.38
31 2 0.05
32 22 0.52
33 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (30 bp):
ATATGACATGAGATATGTGAACATAAGAGA
Found at i:10659 original size:12 final size:12
Alignment explanation
Indices: 10644--10675 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10634 TAATAATGTT
10644 AATAATGATAAG
1 AATAATGATAAG
*
10656 AATAATAATAAG
1 AATAATGATAAG
10668 AATAATGA
1 AATAATGA
10676 ATTGATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (12 bp):
AATAATGATAAG
Found at i:14655 original size:23 final size:21
Alignment explanation
Indices: 14620--14667 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
14610 AAGTATTTAC
14620 TTTTTTTTTAAATCAA-ATTAT
1 TTTTTTTTTAAAT-AATATTAT
14641 TTTTTTATTTGAAATAATATTAT
1 TTTTTT-TTT-AAATAATATTAT
14664 TTTT
1 TTTT
14668 AAATTTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.25
22 5 0.21
23 13 0.54
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTTTTTAAATAATATTAT
Found at i:14812 original size:23 final size:23
Alignment explanation
Indices: 14775--14853 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 23
14765 GATAATTTAA
*
14775 AAATAAAATTATTTCAAATAAAT
1 AAATAATATTATTTCAAATAAAT
14798 -AATGAATATTATTTCAAATAAAT
1 AAAT-AATATTATTTCAAATAAAT
* *
14821 AAATAATATGATTTCAAA-AATT
1 AAATAATATTATTTCAAATAAAT
14843 AAATAAATATT
1 AAAT-AATATT
14854 TTAAAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.20
23 36 0.73
24 3 0.06
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.37
Consensus pattern (23 bp):
AAATAATATTATTTCAAATAAAT
Found at i:14875 original size:22 final size:22
Alignment explanation
Indices: 14848--14901 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
14838 AAATTAAATA
*
14848 AATATTTTAAAAATATTTTTAT
1 AATATTTTAAAAATATTTTTAG
* *
14870 AATATTATAAATATATTTTTAG
1 AATATTTTAAAAATATTTTTAG
*
14892 AATAATTTAA
1 AATATTTTAA
14902 TATGAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AATATTTTAAAAATATTTTTAG
Found at i:17260 original size:45 final size:45
Alignment explanation
Indices: 17211--17302 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
17201 GAAAAAGAGA
* *
17211 AGGCTGAAGATGAATTGGAAGGAGAAGATGGAGAGGAACAAGAAG
1 AGGCTGAAGATGAATTGAAAGGAGAAGATGAAGAGGAACAAGAAG
17256 AGGCTGAAGATGAATTGAAAGGAGAAGATGAAGAGGAACAAGAAG
1 AGGCTGAAGATGAATTGAAAGGAGAAGATGAAGAGGAACAAGAAG
17301 AG
1 AG
17303 AACTCTGAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.47, C:0.04, G:0.38, T:0.11
Consensus pattern (45 bp):
AGGCTGAAGATGAATTGAAAGGAGAAGATGAAGAGGAACAAGAAG
Found at i:19933 original size:18 final size:18
Alignment explanation
Indices: 19912--19947 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19902 GGATGAGTCT
* *
19912 GAAGAAGAGGAGGAGGAA
1 GAAGAAAAGGAAGAGGAA
19930 GAAGAAAAGGAAGAGGAA
1 GAAGAAAAGGAAGAGGAA
19948 CAGAATGTAG
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:0.00, G:0.44, T:0.00
Consensus pattern (18 bp):
GAAGAAAAGGAAGAGGAA
Found at i:24384 original size:13 final size:13
Alignment explanation
Indices: 24366--24393 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
24356 CCATTCCTGC
24366 TGTACTTGCTTTT
1 TGTACTTGCTTTT
24379 TGTACTTGCTTTT
1 TGTACTTGCTTTT
24392 TG
1 TG
24394 AAACACACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.18, T:0.61
Consensus pattern (13 bp):
TGTACTTGCTTTT
Found at i:26667 original size:32 final size:32
Alignment explanation
Indices: 26623--26687 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
26613 CATATATTTT
*
26623 AAAAATTTAATTTAATTAATATTATTTTAACC
1 AAAAATTTAATTTAATAAATATTATTTTAACC
*
26655 AAAATTTTAATTTAATAAATATTATTTTAACC
1 AAAAATTTAATTTAATAAATATTATTTTAACC
26687 A
1 A
26688 TATATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (32 bp):
AAAAATTTAATTTAATAAATATTATTTTAACC
Found at i:26683 original size:15 final size:15
Alignment explanation
Indices: 26617--26684 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
26607 GATTTACATA
26617 TATTTTAA-AAAT-T
1 TATTTTAATAAATAT
* *
26630 TAATTTAATTAATAT
1 TATTTTAATAAATAT
* *
26645 TATTTTAACCAAAATTT
1 TATTTTAA--TAAATAT
*
26662 TAATTTAATAAATAT
1 TATTTTAATAAATAT
26677 TATTTTAA
1 TATTTTAA
26685 CCATATATTA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
13 7 0.17
14 3 0.07
15 20 0.49
17 11 0.27
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTTTAATAAATAT
Found at i:26703 original size:31 final size:32
Alignment explanation
Indices: 26640--26703 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
26630 TAATTTAATT
* **
26640 AATATTATTTTAACCAAAATTTTAATTTAATA
1 AATATTATTTTAACCAAAATATTAATAAAATA
*
26672 AATATTATTTTAACC-ATATATTAATAAAATA
1 AATATTATTTTAACCAAAATATTAATAAAATA
26703 A
1 A
26704 TAATAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (32 bp):
AATATTATTTTAACCAAAATATTAATAAAATA
Found at i:26707 original size:3 final size:3
Alignment explanation
Indices: 26693--26762 Score: 67
Period size: 3 Copynumber: 24.0 Consensus size: 3
26683 AACCATATAT
* * *
26693 TAA TAA -AA TAA TAA TAA TAA -ATG TCA T-A TTA TACA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA
26737 TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
26763 GATATGACGA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
2 7 0.12
3 47 0.82
4 3 0.05
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31043 original size:2 final size:2
Alignment explanation
Indices: 31036--31064 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31026 AAGTCACCAT
31036 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31065 TAGGTATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36597 original size:21 final size:21
Alignment explanation
Indices: 36545--36603 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
36535 TTTAATGCAT
* *
36545 AAGGGATCAATCCTTTGGTAA
1 AAGGGATCGATCTTTTGGTAA
* *
36566 AAGGGACCGATCTTTTGGTGA
1 AAGGGATCGATCTTTTGGTAA
36587 AAGGGATCGATCATTTT
1 AAGGGATCGATC-TTTT
36604 TCAAATAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.31
Consensus pattern (21 bp):
AAGGGATCGATCTTTTGGTAA
Found at i:45121 original size:19 final size:22
Alignment explanation
Indices: 45073--45127 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
45063 CGTTTTTGTT
45073 TTTTATATAAAATGATAGTATAA
1 TTTTATATAAAAT-ATAGTATAA
45096 TTATTATATAAAAT-TA-TA-AA
1 TT-TTATATAAAATATAGTATAA
45116 TTTTATTATAAA
1 TTTTA-TATAAA
45128 TGCAGGTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.10
20 10 0.33
21 2 0.07
22 2 0.07
23 2 0.07
24 11 0.37
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTTATATAAAATATAGTATAA
Found at i:45544 original size:21 final size:21
Alignment explanation
Indices: 45519--45562 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
45509 AAGACAATCA
45519 AGAGTCGAAGAGAAACTTAAG
1 AGAGTCGAAGAGAAACTTAAG
* *
45540 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTAAG
45561 AG
1 AG
45563 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.32, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTAAG
Found at i:45638 original size:33 final size:33
Alignment explanation
Indices: 45596--45695 Score: 191
Period size: 33 Copynumber: 3.0 Consensus size: 33
45586 AAATAGATGG
45596 AGTGGTGAAAGAAGTTGGGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGGGGTGTTGAGGGGTGA
45629 AGTGGTGAAAGAAGTTGGGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGGGGTGTTGAGGGGTGA
*
45662 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGGGGTGTTGAGGGGTGA
45695 A
1 A
45696 AAAATTGATA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.26, C:0.00, G:0.50, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGGGGTGTTGAGGGGTGA
Found at i:48535 original size:200 final size:201
Alignment explanation
Indices: 47811--48971 Score: 1428
Period size: 200 Copynumber: 5.8 Consensus size: 201
47801 GTAAGCATAT
*
47811 GTGTCGATACATTTATAAAAAGCGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * *
47876 GGTAATTTTATAATATAACTGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * ** * * *
47941 ATCAACACTT-T-TCATAATGTGTCGATACTTTTTGTCCAGAATTAATGTCC-AAAATGATGAAC
131 ATCGACACTTGTGTAAT-TTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAAGGGTGAAC
48003 GCATAAA
195 GCATAAA
** * *
48010 GTGTCGATACATTTATTGAAAGTGTCGATCCCAGAAACATCGAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * ** *
48075 GGTAAATTTACAATGTAACCAGTATAACTAAACCGGTTTTATGAGAGAATATATGTACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* *
48140 ATCGACACTTCTAG-AATTTGTGTCGATA-TTGTTTGTCCAGAAGGAATGCCCAAAAAGGGTGCA
131 ATCGACACTTGT-GTAATTTGTGTCGATACTT-TTTGTCCAGAAGGAATGCCCAAAAAGGGTGAA
*
48203 CGCAAAAA
194 CGCATAAA
* * *
48211 GTGTCGATACATTTATAAACAAGTATCGATCCCAAAAACATTGAAACCCATAATTATAATTTAAT
1 GTGTCGATACATTTATAAA-AAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * * * *
48276 AGGTAATTTTTCAATGTAATCGGTATATATATACCGGTTTTATGAGAGAATATGTCTACA-ATAT
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATA-AT
* *
48340 GTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAAGGAATGCCCAAAAAGGGTGCA
129 GTATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAAGGGTGAA
*
48405 C-CATTAA
194 CGCATAAA
* * *
48412 GTGTCGATACATTTATAAAAACTGTCGATCCCAAAAACAACGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* ** * * *
48477 GGTAATTTTTTAATATAACCGGTATAAATATACTGGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * * * * *
48542 ATCGACACTTTTTTATTTTGTGTCGATACCTTTTGTCCAGAATGAATGCCC-AAAATGATGAACG
131 ATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAAGGGTGAACG
*
48606 CATACA
196 CATAAA
** * * *
48612 GTGTCGATACATTTATTGAAAGTGTCGATACCAGAAACATCGAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
** * * *
48677 CATAAATTTACAATGTAACCGATATAACTATACCGGTTTTATAAGAGAATAGGTCTACA-ACATG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATA-ATG
* * * *
48741 TATCAACACTTGTGGAATTTGTGTCGATACTTTTTATCCAGAAGGAATG-CCAAAAAGGGTTGTA
130 TATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAAGGG-TGAA
48805 CGCATAAA
194 CGCATAAA
* * * *
48813 GTGTCGATACATTTTTAAAAAGTGTCGATCTCAAAAACATCGAAACCGATAATTATAATGCAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
48878 GGTAAATTTTCAATGTGACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ATTATAAAG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CATAATG
* *
48942 TATCGACAATTAT-TAAATTTGTGTCGATAC
130 TATCGACACTTGTGT-AATTTGTGTCGATAC
48972 CATTTTAAAT
Statistics
Matches: 820, Mismatches: 125, Indels: 32
0.84 0.13 0.03
Matches are distributed among these distances:
199 136 0.17
200 328 0.40
201 201 0.25
202 153 0.19
203 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (201 bp):
GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAAGGGTGAACG
CATAAA
Found at i:48931 original size:401 final size:399
Alignment explanation
Indices: 47811--48977 Score: 1463
Period size: 401 Copynumber: 2.9 Consensus size: 399
47801 GTAAGCATAT
*
47811 GTGTCGATACATTTATAAAAAGCGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
47876 GGTAATTTTATAATATAACTGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTACAATGTAACCGGTAT-AATATACCGGTTTTATGAGAGAATAGGTCTACA-AATGT
* * ** * * *
47941 ATCAACACTT-T-TCATAATGTGTCGATACTTTTTGTCCAGAATTAATGTCC-AAAATGATGAAC
129 ATCAACACTTGTGTAAT-TTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAAGGGTGAAC
* * *
48003 GCATAAAGTGTCGATACATTTATT-GAAAGTGTCGATCCCAGAAACATCGAAACCCATAAATATA
193 GCATAAAGTGTCGATACATTT-TTAAAAAGTGTCGATCCCAAAAACATCGAAA-CCATAATTATA
* * * * ** *
48067 ATGTAATAGGTAAATTTACAATGTAACCAGTATAACTAAACCGGTTTTATGAGAGAATATATGTA
256 ATGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA
* *
48132 CATAATGTATCGACACTT-CTAGAATTTGTGTCGATA-TTGTTTGTCCAGAAGGAATGCCCAAAA
321 CATAATGTATCGACACTTATTA-AATTTGTGTCGATACCT-TTTGTCCAGAAGGAATGCCCAAAA
* *
48195 AGGGTGCACGCAAAAA
384 AGGATGAACGCAAAAA
* * *
48211 GTGTCGATACATTTATAAACAAGTATCGATCCCAAAAACATTGAAACCCATAATTATAATTTAAT
1 GTGTCGATACATTTATAAA-AAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * *
48276 AGGTAATTTTTCAATGTAATCGGTATATATATACCGGTTTTATGAGAGAATATGTCTACAATATG
65 AGGTAATTTTACAATGTAACCGGTATA-ATATACCGGTTTTATGAGAGAATAGGTCTACAA-ATG
* * *
48341 TATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAAGGAATGCCCAAAAAGGGTGCAC
128 TATCAACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAAGGGTGAAC
* * * *
48406 -CATTAAGTGTCGATACATTTATAAAAACTGTCGATCCCAAAAACAACGAAACTCATAATTATAA
193 GCATAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAAC-CATAATTATAA
* * * * *
48470 TGTAATAGGTAATTTTTTAATATAACCGGTATAAATATACTGGTTTTATGTGAGAATAGGTCTAC
257 TGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAC
* * * * *
48535 ATAATGTATCGACACTTTTTTATTTTGTGTCGATACCTTTTGTCCAGAATGAATGCCC-AAAATG
322 ATAATGTATCGACACTTATTAAATTTGTGTCGATACCTTTTGTCCAGAAGGAATGCCCAAAAAGG
* *
48599 ATGAACGCATACA
387 ATGAACGCAAAAA
** * * *
48612 GTGTCGATACATTTATTGAAAGTGTCGATACCAGAAACATCGAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
** * * *
48677 CATAAATTTACAATGTAACCGATATAACTATACCGGTTTTATAAGAGAATAGGTCTACAACATGT
66 GGTAATTTTACAATGTAACCGGTATAA-TATACCGGTTTTATGAGAGAATAGGTCTACAA-ATGT
* * *
48742 ATCAACACTTGTGGAATTTGTGTCGATACTTTTTATCCAGAAGGAATG-CCAAAAAGGGTTGTAC
129 ATCAACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAAGGG-TGAAC
*
48806 GCATAAAGTGTCGATACATTTTTAAAAAGTGTCGATCTCAAAAACATCGAAACCGATAATTATAA
193 GCATAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACC-ATAATTATAA
* * *
48871 TGCAATAGGTAAATTTTCAATGTGACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-AT
257 TGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-
* * *
48935 TATAAAGTATCGACAATTATTAAATTTGTGTCGATACCATTTT
321 CATAATGTATCGACACTTATTAAATTTGTGTCGATACC-TTTT
48978 AAATATCGCG
Statistics
Matches: 659, Mismatches: 92, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
399 11 0.02
400 165 0.25
401 280 0.42
402 189 0.29
403 14 0.02
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (399 bp):
GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTACAATGTAACCGGTATAATATACCGGTTTTATGAGAGAATAGGTCTACAAATGTAT
CAACACTTGTGTAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAAGGGTGAACGCA
TAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCATAATTATAATGTA
ATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAA
TGTATCGACACTTATTAAATTTGTGTCGATACCTTTTGTCCAGAAGGAATGCCCAAAAAGGATGA
ACGCAAAAA
Found at i:48947 original size:601 final size:601
Alignment explanation
Indices: 47811--48971 Score: 1782
Period size: 601 Copynumber: 1.9 Consensus size: 601
47801 GTAAGCATAT
*
47811 GTGTCGATACATTTATAAAAAGCGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGCGTCGATCCCAAAAACAACGAAACCCATAATTATAATGTAATA
*
47876 GGTAATTTTATAATATAACTGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTATAATATAACCGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAATGT
* * *
47941 ATCAACACTTTTCATAATGTGTCGATACTTTTTGTCCAGAATTAATGTCCAAAATGATGAACGCA
131 ATCAACACTTTTCATAATGTGTCGATACCTTTTGTCCAGAATGAATGCCCAAAATGATGAACGCA
*
48006 TAAAGTGTCGATACATTTATTGAAAGTGTCGATCCCAGAAACATCGAAACCCATAAATATAATGT
196 TAAAGTGTCGATACATTTATTGAAAGTGTCGATACCAGAAACATCGAAACCCATAAATATAATGT
** * * *
48071 AATAGGTAAATTTACAATGTAACCAGTATAACTAAACCGGTTTTATGAGAGAATATATGTACATA
261 AATACATAAATTTACAATGTAACCAGTATAACTAAACCGGTTTTATAAGAGAATAGATCTACATA
* *
48136 ATGTATCGACACTTCTAGAATTTGTGTCGATATTGTTTGTCCAGAAGGAATGCCCAAAAAGGGTG
326 ATGTATCAACACTTCTAGAATTTGTGTCGATATTGTTTATCCAGAAGGAATGCCCAAAAAGGGTG
*
48201 CACGCAAAAAGTGTCGATACATTTATAAACAAGTATCGATCCCAAAAACATTGAAACCCATAATT
391 CACGCAAAAAGTGTCGATACATTTATAAACAAGTATCGATCCCAAAAACATCGAAACCCATAATT
** * * * * *
48266 ATAATTTAATAGGTAATTTTTCAATGTAATCGGTATATATATACCGGTTTTATGAGAGAATATGT
456 ATAATGCAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGT
* *
48331 CTACAATATGTATCGACACTTGTGT-AATTTGTGTCGATACTTTTGGTCCAGAAGGAATGCCCAA
521 CTACAATATGTATCGACAATTAT-TAAATTTGTGTCGATACTTTTGGTCCAGAAGGAATGCCCAA
48395 AAAGGGTGCACCATTAA
585 AAAGGGTGCACCATTAA
*
48412 GTGTCGATACATTTATAAAAA-CTGTCGATCCCAAAAACAACGAAACTCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGC-GTCGATCCCAAAAACAACGAAACCCATAATTATAATGTAAT
* **
48476 AGGTAATTTTTTAATATAACCGGTATAAATATACTGGTTTTATGTGAGAATAGGTCTACATAATG
65 AGGTAATTTTATAATATAACCGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAATG
* * **
48541 TATCGACACTTTTTTATTTTGTGTCGATACCTTTTGTCCAGAATGAATGCCCAAAATGATGAACG
130 TATCAACAC-TTTTCATAATGTGTCGATACCTTTTGTCCAGAATGAATGCCCAAAATGATGAACG
*
48606 CATACAGTGTCGATACATTTATTGAAAGTGTCGATACCAGAAACATCGAAACCCATAAATATAAT
194 CATAAAGTGTCGATACATTTATTGAAAGTGTCGATACCAGAAACATCGAAACCCATAAATATAAT
* *
48671 GTAATACATAAATTTACAATGTAACC-GATATAACTATACCGGTTTTATAAGAGAATAGGTCTAC
259 GTAATACATAAATTTACAATGTAACCAG-TATAACTAAACCGGTTTTATAAGAGAATAGATCTAC
* *
48735 A-ACATGTATCAACACTTGTGGAATTTGTGTCGATACTT-TTTATCCAGAAGGAATG-CCAAAAA
323 ATA-ATGTATCAACACTTCTAGAATTTGTGTCGATA-TTGTTTATCCAGAAGGAATGCCCAAAAA
* * * * * *
48797 GGGTTGTACGCATAAAGTGTCGATACATTTTTAAA-AAGTGTCGATCTCAAAAACATCGAAACCG
386 GGG-TGCACGCAAAAAGTGTCGATACATTTATAAACAAGTATCGATCCCAAAAACATCGAAACCC
*
48861 ATAATTATAATGCAATAGGTAAATTTTCAATGTGACCGGTATAAATATACCGGTTTTATGAGAAA
450 ATAATTATAATGCAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAAA
*
48926 ATAGGTCATTATAA-A-GTATCGACAATTATTAAATTTGTGTCGATAC
515 ATAGGTC--TACAATATGTATCGACAATTATTAAATTTGTGTCGATAC
48972 CATTTTAAAT
Statistics
Matches: 507, Mismatches: 44, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
600 2 0.00
601 257 0.51
602 242 0.48
603 6 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (601 bp):
GTGTCGATACATTTATAAAAAGCGTCGATCCCAAAAACAACGAAACCCATAATTATAATGTAATA
GGTAATTTTATAATATAACCGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAATGT
ATCAACACTTTTCATAATGTGTCGATACCTTTTGTCCAGAATGAATGCCCAAAATGATGAACGCA
TAAAGTGTCGATACATTTATTGAAAGTGTCGATACCAGAAACATCGAAACCCATAAATATAATGT
AATACATAAATTTACAATGTAACCAGTATAACTAAACCGGTTTTATAAGAGAATAGATCTACATA
ATGTATCAACACTTCTAGAATTTGTGTCGATATTGTTTATCCAGAAGGAATGCCCAAAAAGGGTG
CACGCAAAAAGTGTCGATACATTTATAAACAAGTATCGATCCCAAAAACATCGAAACCCATAATT
ATAATGCAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGT
CTACAATATGTATCGACAATTATTAAATTTGTGTCGATACTTTTGGTCCAGAAGGAATGCCCAAA
AAGGGTGCACCATTAA
Found at i:49635 original size:2 final size:2
Alignment explanation
Indices: 49628--49655 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
49618 ATGGGGAAGG
49628 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
49656 CTCCGGAAAC
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:50508 original size:9 final size:9
Alignment explanation
Indices: 50469--50528 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
50459 GGTCAATAAA
*
50469 GATGAAGAT
1 GATGATGAT
* *
50478 GACGATGAA
1 GATGATGAT
* *
50487 CATGATGAA
1 GATGATGAT
50496 GATGATGAT
1 GATGATGAT
50505 GATGATGAT
1 GATGATGAT
*
50514 GATGATTAT
1 GATGATGAT
50523 GATGAT
1 GATGAT
50529 CTAAACAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.38, C:0.03, G:0.30, T:0.28
Consensus pattern (9 bp):
GATGATGAT
Found at i:50519 original size:6 final size:6
Alignment explanation
Indices: 50469--50528 Score: 66
Period size: 6 Copynumber: 10.0 Consensus size: 6
50459 GGTCAATAAA
* * * * *
50469 GATGAA GATGAC GATGAA CATGAT GAAGAT GATGAT GATGAT GATGAT
1 GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT
*
50517 GATTAT GATGAT
1 GATGAT GATGAT
50529 CTAAACAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.38, C:0.03, G:0.30, T:0.28
Consensus pattern (6 bp):
GATGAT
Done.