Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004548.1 Hibiscus syriacus cultivar Beakdansim tig00010099_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: 65968
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:14497 original size:13 final size:13
Alignment explanation
Indices: 14479--14503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14469 AAAATACTTG
14479 AGACAAAATAACA
1 AGACAAAATAACA
14492 AGACAAAATAAC
1 AGACAAAATAAC
14504 CAACCTCGAC
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:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (13 bp):
AGACAAAATAACA
Found at i:24684 original size:21 final size:21
Alignment explanation
Indices: 24660--24738 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
24650 TTGTGCACGA
*
24660 GGTATCAATACCCCTGCAAAG
1 GGTACCAATACCCCTGCAAAG
* *
24681 GGTACCGATACCCCCTTTG-AATG
1 GGTACCAATA-CCCC--TGCAAAG
* * * **
24704 TGTATCGATACCCCCACAAAG
1 GGTACCAATACCCCTGCAAAG
24725 GGTACCAATACCCC
1 GGTACCAATACCCC
24739 CTTCGGGTTC
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
21 22 0.51
22 8 0.19
23 11 0.26
24 2 0.05
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (21 bp):
GGTACCAATACCCCTGCAAAG
Found at i:26668 original size:21 final size:20
Alignment explanation
Indices: 26642--26681 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
26632 TATGTTTTTG
26642 AATTTGATGTTTGAATGTTTA
1 AATTTG-TGTTTGAATGTTTA
* *
26663 AATTTGTTTTTGGATGTTT
1 AATTTGTGTTTGAATGTTT
26682 GAACTTACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (20 bp):
AATTTGTGTTTGAATGTTTA
Found at i:34091 original size:21 final size:20
Alignment explanation
Indices: 34058--34096 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
34048 CAGCCTGAAC
34058 ATGTAAAACAAATGTATATAA
1 ATGTAAAACAAAT-TATATAA
34079 ATGTAAATA-AAATTATAT
1 ATGTAAA-ACAAATTATAT
34097 TATATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 11 0.65
22 1 0.06
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (20 bp):
ATGTAAAACAAATTATATAA
Found at i:35329 original size:23 final size:23
Alignment explanation
Indices: 35285--35360 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
35275 AGGAATGTGC
35285 CACAAGAATAGAGAAAAAACGTGA
1 CACAAGAATAGAG-AAAAACGTGA
*
35309 CACAAGAATAGAGAAAAACGTGC
1 CACAAGAATAGAGAAAAACGTGA
*
35332 CACAAGAATAGAGAAAAACGTGT
1 CACAAGAATAGAGAAAAACGTGA
35355 CACAAG
1 CACAAG
35361 GACATAAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
23 37 0.74
24 13 0.26
ACGTcount: A:0.54, C:0.16, G:0.21, T:0.09
Consensus pattern (23 bp):
CACAAGAATAGAGAAAAACGTGA
Found at i:38634 original size:21 final size:22
Alignment explanation
Indices: 38596--38640 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
38586 TCATAAAAGG
38596 ATTTTATATTACATTTTTTAAT
1 ATTTTATATTACATTTTTTAAT
* *
38618 ATTTTCTATTA-ATTTTTTCAT
1 ATTTTATATTACATTTTTTAAT
38639 AT
1 AT
38641 AATTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTTATATTACATTTTTTAAT
Found at i:38828 original size:50 final size:51
Alignment explanation
Indices: 38705--38842 Score: 172
Period size: 50 Copynumber: 2.7 Consensus size: 51
38695 TGTAGCAATT
* * * *
38705 AACATATACTTACATCGGTGTAAGTATATATATCTCTCAAACCTAAAAATA
1 AACACATACTTACATCGGTGTAAGTATGTACATCTCTCAAACCGAAAAATA
* *
38756 AGCACATACTTACA-CTGGTGTAAGTATGTACATCTC-CCAACCGAAAAATA
1 AACACATACTTACATC-GGTGTAAGTATGTACATCTCTCAAACCGAAAAATA
* * *
38806 AACACATGCTTACATCGATGTAAGTATGTACGTCTCT
1 AACACATACTTACATCGGTGTAAGTATGTACATCTCT
38843 TATAAAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
50 43 0.58
51 31 0.42
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (51 bp):
AACACATACTTACATCGGTGTAAGTATGTACATCTCTCAAACCGAAAAATA
Found at i:44690 original size:39 final size:39
Alignment explanation
Indices: 44647--45110 Score: 598
Period size: 39 Copynumber: 12.0 Consensus size: 39
44637 TTAGTTTCTT
* * *
44647 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGGG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAG
*
44686 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAG
* * *
44725 ATAAAATCTTCTTTTTCGAGTGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAG
* *
44764 ATAAAATCTTCTATTTCGAGTGAAACTATCTCAAGAGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAG
* *
44803 ATAAAATCTTCTGTTTCGAGTGAAACTATCTGAAGAGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAG
* *
44842 ATAAAATCTTCTGTTTCGAGTGAAATTATCTCAAGAGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAG
* * *
44881 ATAAAATCTTCTGTTTCGAGTGAAAATATCTCATGAGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAG
* *
44920 ATAAAATCTTCTGTTTCTAGGGAAACTATCTCAAGCGA-
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAG
* * * * *
44958 A-AAAAACTATGTTGTTTCTAGGGAAACTATATCAAGTGAG
1 ATAAAATCT-T-CTGTTTCGAGGGAAACTATCTCAAGAGAG
* * *
44998 ACAAAATCATT-TGTTTCGAGAGAAACTATCTCAAGCGAG
1 ATAAAATC-TTCTGTTTCGAGGGAAACTATCTCAAGAGAG
* *
45037 AT-AAATCTTATGTTTCGAGGGAAACCATCTCAAGAGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAG
*
45075 ATAAAAT-TTCTATTTCGA-GGAAACTATCTCAAGAGA
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGA
45111 TACAAAATTC
Statistics
Matches: 385, Mismatches: 33, Indels: 16
0.89 0.08 0.04
Matches are distributed among these distances:
37 25 0.06
38 43 0.11
39 309 0.80
40 1 0.00
41 6 0.02
42 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (39 bp):
ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAG
Found at i:45199 original size:36 final size:36
Alignment explanation
Indices: 45149--45387 Score: 253
Period size: 36 Copynumber: 6.8 Consensus size: 36
45139 TCAAAGTTTA
* *
45149 TGTTTCAAGAGAAACTATCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * * *
45185 TGTTTTAAGGGAAACTGTCTCAAGAGATACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
*
45221 TGTTTCAAGAGAAAC-GTTCTCAA---AG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGGAGACAAAATT
*
45249 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* *
45286 TGTTTAAAGGGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * * *
45322 TGTTTCAAGTGAAACTGTCTTAAGGGATACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* *
45358 TGTTTCAAGGGAAATTGTCTCAAGGGAGAC
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAC
45388 TATCTTAAGG
Statistics
Matches: 168, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 20 0.12
30 1 0.01
32 2 0.01
33 1 0.01
35 1 0.01
36 139 0.83
37 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
Found at i:45226 original size:101 final size:101
Alignment explanation
Indices: 45044--45336 Score: 408
Period size: 101 Copynumber: 2.9 Consensus size: 101
45034 GAGATAAATC
* * * * * * * *
45044 TTATGTTTCGAGGGAAACCATCTCAAGAGAGATAAAATTTCTATTT-CGAGGAAACTATCTCAAG
1 TTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGT-TTTAAG-GGAAACTGTCTCAAG
* *
45108 AGATACAAAATTCGTTTCAAGAGAAATGTTCTCAAAGT
64 AGATACAAAATTTGTTTCAAGAGAAACGTTCTCAAAGT
*
45146 TTATGTTTCAAGAGAAACTATCTCAAGGGAGACGAAATTTGTTTTAAGGGAAACTGTCTCAAGAG
1 TTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACTGTCTCAAGAG
45211 ATACAAAATTTGTTTCAAGAGAAACGTTCTCAAAGT
66 ATACAAAATTTGTTTCAAGAGAAACGTTCTCAAAGT
* * * *
45247 TTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGGG
1 TTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACTGTCTCAAGAG
* *
45312 AGACAAAATTTGTTTCAAGTGAAAC
66 ATACAAAATTTGTTTCAAGAGAAAC
45337 TGTCTTAAGG
Statistics
Matches: 172, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
101 136 0.79
102 36 0.21
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (101 bp):
TTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACTGTCTCAAGAG
ATACAAAATTTGTTTCAAGAGAAACGTTCTCAAAGT
Found at i:45289 original size:65 final size:65
Alignment explanation
Indices: 45185--45308 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 65
45175 AGACGAAATT
* * * *
45185 TGTTTTAAGGGAAACTGTCTCAAGAGATACAAAATTTGTTTCAAGAGAAAC-GTTCTCAAAGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTG-TCTCAAAGTTT
45249 A
65 A
* * *
45250 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAA
45309 GGGAGACAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 50 0.98
66 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAAGTTTA
Found at i:45381 original size:51 final size:51
Alignment explanation
Indices: 45321--45435 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 51
45311 GAGACAAAAT
* * * *
45321 TTGTTTCAAGTGAAACTGTCTTAAGGGATACAAAACTTGTTTCAAGGGAAA
1 TTGTCTCAAGGGAAACTATCTTAAGGGAGACAAAACTTGTTTCAAGGGAAA
* * *
45372 TTGTCTCAAGGGAGACTATCTTAAGGGAGATAAAATTTGTTTCAAGGGAAA
1 TTGTCTCAAGGGAAACTATCTTAAGGGAGACAAAACTTGTTTCAAGGGAAA
*
45423 CTGTCTCAAGGGA
1 TTGTCTCAAGGGA
45436 GACAAAACTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (51 bp):
TTGTCTCAAGGGAAACTATCTTAAGGGAGACAAAACTTGTTTCAAGGGAAA
Found at i:45417 original size:36 final size:36
Alignment explanation
Indices: 45372--45815 Score: 587
Period size: 36 Copynumber: 12.4 Consensus size: 36
45362 TCAAGGGAAA
* * * * *
45372 TTGTCTCAAGGGAGACTATCTTAAGGGAGATAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
*
45408 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAC
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
* *
45444 TTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAGAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
*
45480 TTGTTTCAAGGGAAATTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
* *
45516 TTGTTTCAAGGGAAACTGTCTCAAGTGATA-AAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
*
45551 TTGTTTCAAGGGAAACTGTCTTAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
45587 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
*
45623 TTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
*
45659 TTGTTTCAAGGGAAATTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
* *
45695 TTGTTTCAAGGGAGACAAAATTTGTTTCAA-GG-G---AAA-
1 TTGTTTCAA-GG-G---AAA-CTGTCTCAAGGGAGACAAAAT
** * * *
45731 CCGTCTCAAGGGAGACTATCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
*
45767 TTGTTTCAAGGGAAACTGACTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
45803 TTGTTTCAAGGGA
1 TTGTTTCAAGGGA
45816 GACAAAATTT
Statistics
Matches: 359, Mismatches: 36, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
30 6 0.02
31 4 0.01
32 1 0.00
34 1 0.00
35 37 0.10
36 290 0.81
37 5 0.01
38 1 0.00
40 1 0.00
41 5 0.01
42 8 0.02
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.26
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
Found at i:45436 original size:51 final size:51
Alignment explanation
Indices: 45339--45438 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
45329 AGTGAAACTG
* *
45339 TCTTAAGGGATACAAAACTTGTTTCAAGGGAAATTGTCTCAAGGGAGACTA
1 TCTTAAGGGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGGGAGACTA
* *
45390 TCTTAAGGGAGATAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
1 TCTTAAGGGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
45439 AAAACTTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (51 bp):
TCTTAAGGGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGGGAGACTA
Found at i:45484 original size:123 final size:126
Alignment explanation
Indices: 45269--45872 Score: 506
Period size: 123 Copynumber: 4.5 Consensus size: 126
45259 AGAAATTGTC
* * *
45269 TCAAGGGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGTGA
1 TCAAGGGAGATAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
* * *
45334 AACTGTCTTAAGGGATACAAAACTTGTTTCAAGGGAAATTGTCTCAAGGGAGAC-TAT-CT
66 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAAGGGAGACATATGCT
*
45393 T-AAGGGAGATAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGA
1 TCAAGGGAGATAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
* * * *
45457 AACCGTCTCAAGGGAGACAAGATTTGTTTCAAGGGAAATTGTCTCAAGGGAGACAAAATTTGTT
66 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAAGGGAGAC---ATATGCT
*
45521 TCAAGGGAAACTGTCTCAAGTGATAAAAATTTGTTTCAAGGGAAACTGTCTTAAGGGAGACAAAA
1 TCAA-GG-----G-----A--GAT-AAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
**
45586 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGA
52 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAAGGGA
* *
45651 GACAAAATTTGTT
117 GAC---ATATGCT
* * *
45664 TCAA-GG-G---AAA-TTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAGACAAAATTTGTTTC
1 TCAAGGGAGATAAAATTTGTTTCAA-GG-G---AAA-CTGTCTCAAGGGAGACAAAATTTGTTTC
* *
45723 AAGGGAAACCGTCTCAAGGGAGACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGACT
60 AAGGGAAA----CT-------G----TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTGTCT
* *
45788 CAAGGGAGACAAAATTTGTT
110 CAAGGGAGAC---ATATGCT
* * * *
45808 TCAAGGGAGACAAAATTTATTTCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTTTTAAGGGA
1 TCAAGGGAGATAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
45873 GACAAAAAAA
Statistics
Matches: 404, Mismatches: 29, Indels: 74
0.80 0.06 0.15
Matches are distributed among these distances:
123 116 0.29
124 6 0.01
125 1 0.00
127 2 0.00
128 6 0.01
129 35 0.09
130 2 0.00
133 2 0.00
135 1 0.00
136 1 0.00
140 2 0.00
141 1 0.00
142 3 0.01
143 116 0.29
144 91 0.23
145 5 0.01
146 1 0.00
148 1 0.00
149 5 0.01
150 7 0.02
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.26
Consensus pattern (126 bp):
TCAAGGGAGATAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAAGGGAGACATATGCT
Found at i:45704 original size:57 final size:57
Alignment explanation
Indices: 45643--45879 Score: 360
Period size: 57 Copynumber: 4.3 Consensus size: 57
45633 GGAAACCGTC
**
45643 TCAAGGGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTT
* *
45700 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGAC------TATC
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTT
* *
45751 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGACTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTT
*
45808 TCAAGGGAGACAAAATTTATTTCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTT
*
45865 TTAAGGGAGACAAAA
1 TCAAGGGAGACAAAA
45880 AAAGTCAGGA
Statistics
Matches: 162, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
51 47 0.29
57 115 0.71
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.24
Consensus pattern (57 bp):
TCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTT
Found at i:45965 original size:36 final size:36
Alignment explanation
Indices: 45897--46009 Score: 111
Period size: 36 Copynumber: 3.1 Consensus size: 36
45887 GGAAAAACAA
* * * *
45897 TCTCAAGTGAGATTAATTTTG-TTTTAGGGAAAATTG
1 TCTCAAGTGAGATAAAATTTGTTTTTA-AGAAAACTG
* * *
45933 TCTCCAGTGAGATGAACTTTGTTTTTAAGAAAACTG
1 TCTCAAGTGAGATAAAATTTGTTTTTAAGAAAACTG
* * *
45969 TCTCAAGCGAGACAAAATTTGTTTTTACGAAAACTCG
1 TCTCAAGTGAGATAAAATTTGTTTTTAAGAAAACT-G
46006 TCTC
1 TCTC
46010 GAGCAAGACG
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
36 54 0.84
37 10 0.16
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (36 bp):
TCTCAAGTGAGATAAAATTTGTTTTTAAGAAAACTG
Found at i:47179 original size:13 final size:14
Alignment explanation
Indices: 47154--47183 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
47144 TTTGCATGTA
47154 TTTCTTGTTCTTTT
1 TTTCTTGTTCTTTT
47168 TTTCTT-TTCTTTT
1 TTTCTTGTTCTTTT
47181 TTT
1 TTT
47184 GCTCTTATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTCTTGTTCTTTT
Found at i:48448 original size:14 final size:14
Alignment explanation
Indices: 48424--48459 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
48414 TGAAATGCAT
*
48424 ATGCAAAATGCAAAG
1 ATGC-AAATGCAAAA
48439 ATGCAAATGCAAAA
1 ATGCAAATGCAAAA
48453 ATGCAAA
1 ATGCAAA
48460 AATGTTGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (14 bp):
ATGCAAATGCAAAA
Found at i:48448 original size:21 final size:22
Alignment explanation
Indices: 48418--48459 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
48408 TAAAAATGAA
*
48418 ATGCATATGC-AAAATGCAAAG
1 ATGCAAATGCAAAAATGCAAAG
48439 ATGCAAATGCAAAAATGCAAA
1 ATGCAAATGCAAAAATGCAAA
48460 AATGTTGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (22 bp):
ATGCAAATGCAAAAATGCAAAG
Found at i:48461 original size:8 final size:8
Alignment explanation
Indices: 48424--48463 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
48414 TGAAATGCAT
48424 ATGC-AAA
1 ATGCAAAA
*
48431 ATGCAAAG
1 ATGCAAAA
48439 ATGC--AA
1 ATGCAAAA
48445 ATGCAAAA
1 ATGCAAAA
48453 ATGCAAAA
1 ATGCAAAA
48461 ATG
1 ATG
48464 TTGATCCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
6 5 0.18
7 4 0.14
8 19 0.68
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.15
Consensus pattern (8 bp):
ATGCAAAA
Found at i:52577 original size:18 final size:18
Alignment explanation
Indices: 52554--52593 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
52544 TCAATAGTTT
52554 AAATAAAAATAATTTTAA
1 AAATAAAAATAATTTTAA
* *
52572 AAAT-AAAATCATTTTTA
1 AAATAAAAATAATTTTAA
52589 AAATA
1 AAATA
52594 TTTAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATAAAAATAATTTTAA
Found at i:57360 original size:17 final size:17
Alignment explanation
Indices: 57334--57370 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
57324 GTACATTAAT
*
57334 GAGAATAGAAGGTACGC
1 GAGAACAGAAGGTACGC
*
57351 GAGAACAGAAGGTACTC
1 GAGAACAGAAGGTACGC
57368 GAG
1 GAG
57371 TACATTGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.14, G:0.35, T:0.11
Consensus pattern (17 bp):
GAGAACAGAAGGTACGC
Found at i:59412 original size:2 final size:2
Alignment explanation
Indices: 59405--59439 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
59395 ATGTATCAAG
* *
59405 AC AC AC AC AC AC AC AC AC GC AC AC AT AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
59440 TATTTCATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.46, G:0.03, T:0.03
Consensus pattern (2 bp):
AC
Found at i:60220 original size:226 final size:226
Alignment explanation
Indices: 59858--60783 Score: 1450
Period size: 226 Copynumber: 4.1 Consensus size: 226
59848 TAACAAATCA
* *
59858 AGTAATTAACCGATTATGTTATCGT-TAGATTTCTAAGGCTCCATCAGCTGT--ACTTTGGTAAC
1 AGTAATTAACCGGTTATGTTATCGTCGA-ATTTCTAAGGCTCCATCAGCT-TAAACTTTGGTAAC
59920 ATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTT
64 ATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTT
* * *
59985 ATCGTCGGATTTCTAAGGCCCCATCAACTTTAAAAATGCGCTACCTATTACGTTACATAAGCTCT
129 ATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCT
*
60050 ACGTAATATGTTATTATGCTTGATAATGTTTCC
194 ACCTAATATGTTATTATGCTTGATAATGTTTCC
* * * *
60083 AGTAATTAATCGGTTATGTTATCGTCGAATTTTTAAAGCTCCATCAACTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
60148 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
*
60213 CGTCGGATTTCTTAA-GCCCAATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTA
131 CGTCGGATTTC-TAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTA
*
60277 CCTAATATGTTATTATGCTTGATAAAGTTTCC
195 CCTAATATGTTATTATGCTTGATAATGTTTCC
* * *
60309 AGTAATTAATCGGTTATGCTATCGTC-AAATTCTTAAGGCTCCATCAGCTTAAACTTTGGTAACA
1 AGTAATTAACCGGTTATGTTATCGTCGAATTTC-TAAGGCTCCATCAGCTTAAACTTTGGTAACA
* * * * * *
60373 TATTAGGTGTTAACTAATATGTTGATAATACTAATAACAAATTAAGTAATTAATCTATTTTGTTG
65 TTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTA
* * *
60438 TCGTCGGATTTCTAAAGCCCCATCAGCTTTAAAAAGGCGCTACGTATTACGTTACATAAGCGATA
130 TCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTA
* *
60503 CATAATATGTTATTACGCTTGATAATGTTTCC
195 CCTAATATGTTATTATGCTTGATAATGTTTCC
* *
60535 AGTAATTAACCAGTTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGCAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* *
60600 GTTAGGCGTTACCTAATATGTTGATAACACTGATAACAAATTAAAG-AATTAACCTATTTTGTTA
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATT-AAGTAATTAACCTATTTTGTTA
* * * *
60664 TCGTCAGATTTCTAAGGCCACATCATCTTTAAAAAAGACGCTACCTATTACGTTACATAAGCGCT
130 TCGTCGGATTTCTAAGGCCCCATCAGCTTT-AAAAAGGCGCTACCTATTACGTTACATAAGCGCT
60729 ACCTAATATGTTATTATGCTTGATAATGTTTCC
194 ACCTAATATGTTATTATGCTTGATAATGTTTCC
60762 AGTAATTAACCGGTTATGTTAT
1 AGTAATTAACCGGTTATGTTAT
60784 TGTCAATATT
Statistics
Matches: 641, Mismatches: 51, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
224 1 0.00
225 48 0.07
226 498 0.78
227 94 0.15
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (226 bp):
AGTAATTAACCGGTTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
CGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTAC
CTAATATGTTATTATGCTTGATAATGTTTCC
Found at i:61372 original size:3 final size:3
Alignment explanation
Indices: 61364--61431 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
61354 CAACCACTCC
61364 ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
61411 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
61432 TAACTAAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:65110 original size:20 final size:20
Alignment explanation
Indices: 65085--65160 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
65075 CAAGCCTTCA
* *
65085 GTATAGAGACTAATTTTTTG
1 GTATAGAGACCAATTTTTGG
65105 GTATAGAGACCAATTTTTGG
1 GTATAGAGACCAATTTTTGG
* *
65125 GTATGGACACCAATTTTTGG
1 GTATAGAGACCAATTTTTGG
65145 GTAT-GAAGACCAATTT
1 GTATAG-AGACCAATTT
65161 GGTCTCGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (20 bp):
GTATAGAGACCAATTTTTGG
Done.