Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001028.1 Hibiscus syriacus cultivar Beakdansim tig00002047_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: 78945
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3552 original size:16 final size:15
Alignment explanation
Indices: 3507--3553 Score: 71
Period size: 14 Copynumber: 3.2 Consensus size: 15
3497 TTTTAATATA
3507 AAATAAAATGT-TAG
1 AAATAAAATGTCTAG
3521 AAATAAAATG-CTAG
1 AAATAAAATGTCTAG
3535 AAATAAAATGCTCTAG
1 AAATAAAATG-TCTAG
3551 AAA
1 AAA
3554 GAAATGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 23 0.77
16 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.13, T:0.23
Consensus pattern (15 bp):
AAATAAAATGTCTAG
Found at i:10233 original size:13 final size:13
Alignment explanation
Indices: 10212--10251 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
10202 AGAAAACACA
10212 AAGAAAAGAGAGG
1 AAGAAAAGAGAGG
*
10225 AAGATAAGAGAGG
1 AAGAAAAGAGAGG
*
10238 AAGCAAAGGAGAGG
1 AAG-AAAAGAGAGG
10252 GAAGTGGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.55, C:0.03, G:0.40, T:0.03
Consensus pattern (13 bp):
AAGAAAAGAGAGG
Found at i:13244 original size:23 final size:23
Alignment explanation
Indices: 13209--13256 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
13199 ATCAAGTACA
*
13209 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
* *
13232 ATAATGTAATAGGTAGTGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
13255 AT
1 AT
13257 TGACATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:13562 original size:22 final size:23
Alignment explanation
Indices: 13517--13564 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
13507 ATATCCAATG
*
13517 TTATTATTTTGTTACTGTAAAGTTT
1 TTATTATTTTCTTACTG--AAGTTT
13542 TTATTATTTTCTTACTG-AGTTT
1 TTATTATTTTCTTACTGAAGTTT
13564 T
1 T
13565 GTTTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
25 16 0.73
ACGTcount: A:0.21, C:0.06, G:0.10, T:0.62
Consensus pattern (23 bp):
TTATTATTTTCTTACTGAAGTTT
Found at i:13955 original size:182 final size:182
Alignment explanation
Indices: 13645--14458 Score: 1278
Period size: 182 Copynumber: 4.5 Consensus size: 182
13635 TTTTTACTAT
* *
13645 CGGTTTTGTCATTTCGAGATCGATTTTATCATATTTTTACCTGTTATATTGTTATTGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * * *
13710 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTATTTTCTTTTAAATTCCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGT
*
13775 CGATACTTATAATAAAGTATCGACACTATCAACATAT-TCGGTAGCTCTTTAC
131 CGATACTTATAATAAAGTATCGACACTATCAACATATCT-GGTAGCGCTTTAC
13827 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
13892 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGT
** *
13957 CGATACTTATAATAAAGTATTAACACTATCAACATATCTGGTAGCTCTTTAC
131 CGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTAC
* *
14009 CGGTTTTGTCATTTCGAGACC-AGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATA
1 CGGTTTTGTCATTTCGAGACCGA-TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATA
*
14073 CATTTTTATAAAGTATCGACACTTTATTAGCGTTATAACTTCTTCTCTTTTAAATT-TCAAAAGT
65 CATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCT-AAAAGT
*
14137 GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
129 GTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTAC
* ** * * * *
14191 CTGTTTTGTCATTTATAGAACGGTTTTGTCAT-TTTTTACCTGTTTTATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* *
14255 ATTTTTATTAAGTATCGACACTTTATTAGCGCTATAACTTTTTTCTCTTTTAAATTCTAAAAGTG
66 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAAC-TTCTTCTCTTTTAAATTCTAAAAGTG
14320 TCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTAC
130 TCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTAC
* ** * * * * *
14373 CTGTTTTGTCATTTATAGATCGGTTTTGTCAT-TTTTTACCTGTTTTATTGTTATGGATTGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
14437 ATTTTTATAAAGTATCGACACT
66 ATTTTTATAAAGTATCGACACT
14459 ATCAACATAT
Statistics
Matches: 595, Mismatches: 31, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
181 67 0.11
182 526 0.88
183 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.44
Consensus pattern (182 bp):
CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGT
CGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTAC
Found at i:14587 original size:112 final size:111
Alignment explanation
Indices: 14332--14903 Score: 815
Period size: 112 Copynumber: 5.1 Consensus size: 111
14322 GATACTTATA
* * *
14332 ATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
14397 TTTGTCATTTTTTACCTGTTTTATTGTTATGGATTGATACATTTTT
66 TTTGTCATTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
* * * *
14443 ATAAAGTATCGACACTATCAACATATCTGGTAGTGATTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
14508 TTTGTCATTTTTTTACATATTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
* *
14555 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
14620 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTT
66 TTTGTCATTTTTTACATGTTATATTGTTATGGATCGATACA-TTTTT
* *
14667 ATAAAGTATCGTCACTTTCAATATATCTGGTAGCG-TGTTACCTGTTTTGTCATTTATACACCGG
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCT-TTACCTGTTTTGTCATTTATAGACCGG
* *
14731 TTTTGTCATTTTTTACATGTTATATT-TTTTGGATAGATACATTTTT
65 TTTTGTCATTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
* ** * * *
14777 ATAAAATATCGACACTTTCAATATATCCAGTAGTGCTTTACCTATTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
14842 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTC
66 TTTGTCA-TTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
*
14889 ATAAAGCATCGACAC
1 ATAAAGTATCGACAC
14904 AAACCGACAA
Statistics
Matches: 416, Mismatches: 39, Indels: 11
0.89 0.08 0.02
Matches are distributed among these distances:
110 68 0.16
111 130 0.31
112 218 0.52
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (111 bp):
ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
Found at i:14745 original size:223 final size:223
Alignment explanation
Indices: 14332--14903 Score: 855
Period size: 223 Copynumber: 2.6 Consensus size: 223
14322 GATACTTATA
* * * *
14332 ATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
14397 TTTGTCATTTTTTACCTGTTTTATTGTTATGGATTGATACA-TTTTTATAAAGTATCGACACTAT
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTTATAAAGTATCGACACTAT
* *
14461 CAACATATCTGGTAGTGATTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACAT
131 CAACATATCTGGTAGCGATTTACCTGTTTTGTCATTTATACACCGGTTTTGTCATTTTTTTACAT
* *
14526 ATTTTATTGTTATGGATCGATACATTTTT
196 ATTATATT-TTATGGATAGATACATTTTT
*
14555 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
14620 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTTATAAAGTATCGTCACTTT
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTTATAAAGTATCGACACTAT
*
14685 CAATATATCTGGTAGCG-TGTTACCTGTTTTGTCATTTATACACCGGTTTTGTCA-TTTTTTACA
131 CAACATATCTGGTAGCGAT-TTACCTGTTTTGTCATTTATACACCGGTTTTGTCATTTTTTTACA
* *
14748 TGTTATATTTTTTGGATAGATACATTTTT
195 TATTATATTTTATGGATAGATACATTTTT
* * * * *
14777 ATAAAATATCGACACTTTCAATATATCCAGTAGTGCTTTACCTATTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
14842 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATA-TTTTCATAAAGCATCGACAC
66 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTTATAAAGTATCGACAC
14904 AAACCGACAA
Statistics
Matches: 318, Mismatches: 28, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
222 101 0.32
223 147 0.46
224 70 0.22
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (223 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTTATAAAGTATCGACACTAT
CAACATATCTGGTAGCGATTTACCTGTTTTGTCATTTATACACCGGTTTTGTCATTTTTTTACAT
ATTATATTTTATGGATAGATACATTTTT
Found at i:23684 original size:31 final size:31
Alignment explanation
Indices: 23635--23710 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
23625 AGTTATAAAC
* * * *
23635 TAGTCACTAAATTTATTGAACAATTGCAAAA
1 TAGTCATTAAGTTTATTGAACAACTACAAAA
* *
23666 TTGTCATTAAGTTTATTGAACTACTACAAAA
1 TAGTCATTAAGTTTATTGAACAACTACAAAA
*
23697 TAATCATTAAGTTT
1 TAGTCATTAAGTTT
23711 TATTAAATTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (31 bp):
TAGTCATTAAGTTTATTGAACAACTACAAAA
Found at i:26606 original size:22 final size:20
Alignment explanation
Indices: 26561--26598 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26551 AAGGTCTAAG
26561 TTGATATTTACCCATATAAT
1 TTGATATTTACCCATATAAT
*
26581 TTGATATTTGCCCATATA
1 TTGATATTTACCCATATA
26599 TTTTTTGAAT
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:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (20 bp):
TTGATATTTACCCATATAAT
Found at i:28879 original size:20 final size:20
Alignment explanation
Indices: 28839--28879 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28829 TAAGGAGAGG
* *
28839 ATTGAAAGGTTAATACATTT
1 ATTGAAAGATTAAGACATTT
*
28859 ATTGAAAGATTAAGACCTTT
1 ATTGAAAGATTAAGACATTT
28879 A
1 A
28880 AATGAAATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (20 bp):
ATTGAAAGATTAAGACATTT
Found at i:33168 original size:23 final size:23
Alignment explanation
Indices: 33141--33191 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
33131 TATATACATT
33141 CATATCACAAAGGACAAAAATAA
1 CATATCACAAAGGACAAAAATAA
*
33164 CATATCACAAAGGACAAAAGTAA
1 CATATCACAAAGGACAAAAATAA
33187 CATAT
1 CATAT
33192 AATAAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.16
Consensus pattern (23 bp):
CATATCACAAAGGACAAAAATAA
Found at i:36615 original size:20 final size:20
Alignment explanation
Indices: 36590--36630 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
36580 TAGGGAGAGG
36590 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
36610 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
36630 A
1 A
36631 AATGAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
ATTGAAAGGTTAAGACCTTT
Found at i:37867 original size:18 final size:18
Alignment explanation
Indices: 37844--37889 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
37834 ACCGGTCACA
37844 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
37862 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
37880 ACTCGACCCG
1 ACCCGACCCG
37890 TTTACCGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.50, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:39256 original size:18 final size:18
Alignment explanation
Indices: 39230--39265 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39220 TCGAAAGGAC
*
39230 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
39248 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
39266 CGGATGGCAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:40445 original size:12 final size:12
Alignment explanation
Indices: 40430--40499 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
40420 GATACATTAC
40430 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
40442 CTGATTTCTGAT
1 CTGAATTCTGTT
*
40454 CTGGATTCTGTT
1 CTGAATTCTGTT
*
40466 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
*
40478 ATGAATTCTGTT
1 CTGAATTCTGTT
* *
40490 TTGATTTCTG
1 CTGAATTCTG
40500 ATATCTCCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:40449 original size:48 final size:48
Alignment explanation
Indices: 40393--40497 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
40383 AAATATTTTA
* *
40393 TCTGATTTCCGA-CTTGAATTCTGTTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTCCGATC-TGAATTCTGTTCTGATATC-TGACATGAATTCTGT
* * *
40441 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGTTCTGATATCTGACATGAATTCTGT
*
40489 TTTGATTTC
1 TCTGATTTC
40498 TGATATCTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 47 0.96
49 2 0.04
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTCTGTTCTGATATCTGACATGAATTCTGT
Found at i:40461 original size:24 final size:24
Alignment explanation
Indices: 40431--40503 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
40421 ATACATTACC
*
40431 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATA
* *
40455 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
*
40479 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
40503 T
1 T
40504 CTCCGTTTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:40671 original size:2 final size:2
Alignment explanation
Indices: 40664--40692 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40654 ACGGATGGGG
40664 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
40693 GTTTTAAAAA
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:42298 original size:27 final size:27
Alignment explanation
Indices: 42268--42327 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
42258 CTCTACCTCT
42268 ATCACCCCTACCTCCATAGCCTCCACG
1 ATCACCCCTACCTCCATAGCCTCCACG
*
42295 ATCACCTCTACCTCCATAGCCTCCACG
1 ATCACCCCTACCTCCATAGCCTCCACG
42322 ATCACC
1 ATCACC
42328 AACTCTACCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.23, C:0.50, G:0.07, T:0.20
Consensus pattern (27 bp):
ATCACCCCTACCTCCATAGCCTCCACG
Found at i:42348 original size:30 final size:27
Alignment explanation
Indices: 42268--42348 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
42258 CTCTACCTCT
* * * *
42268 ATCACCCCTACCTCCATAGCCTCCACG
1 ATCACCTCTACCACCAAAACCTCCACG
* * *
42295 ATCACCTCTACCTCCATAGCCTCCACG
1 ATCACCTCTACCACCAAAACCTCCACG
42322 ATCACCAACTCTACCACCAAAACCTCC
1 ATCA-C--CTCTACCACCAAAACCTCC
42349 TCTGTCAGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
27 30 0.64
28 1 0.02
30 16 0.34
ACGTcount: A:0.27, C:0.49, G:0.05, T:0.19
Consensus pattern (27 bp):
ATCACCTCTACCACCAAAACCTCCACG
Found at i:42404 original size:33 final size:33
Alignment explanation
Indices: 42367--42434 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
42357 ATCTGCCCCA
*
42367 TCCTCTATCTG-ATCTACCTCTACCCCGAAAGCC
1 TCCTCCATCTGAATC-ACCTCTACCCCGAAAGCC
* * *
42400 TCCTCCATCTGAATCCCCTCTACCTCTAAAGCC
1 TCCTCCATCTGAATCACCTCTACCCCGAAAGCC
42433 TC
1 TC
42435 TACCTGAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.21, C:0.44, G:0.07, T:0.28
Consensus pattern (33 bp):
TCCTCCATCTGAATCACCTCTACCCCGAAAGCC
Found at i:44214 original size:2 final size:2
Alignment explanation
Indices: 44201--44230 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
44191 TGTGAATGTT
*
44201 TG TG TT TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
44231 AGAGAGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:44235 original size:2 final size:2
Alignment explanation
Indices: 44230--44258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44220 GTGTGTGTGT
44230 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
44259 GGGGGGAGGG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52402 original size:38 final size:37
Alignment explanation
Indices: 52332--52424 Score: 134
Period size: 38 Copynumber: 2.5 Consensus size: 37
52322 ACTTTGCATG
* *
52332 ATATGTATATCT-TATATGGAAAAAAATTAAGAGATAT
1 ATATGTATAT-TGTATATGAAAAAAAATTAAGAGATAC
52369 ATATGTATATTGTATATGAAAAAAATATTAAGAGATAC
1 ATATGTATATTGTATATGAAAAAAA-ATTAAGAGATAC
*
52407 ATATGTATATCGTATATG
1 ATATGTATATTGTATATG
52425 GTTATAGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 1 0.02
37 22 0.43
38 28 0.55
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (37 bp):
ATATGTATATTGTATATGAAAAAAAATTAAGAGATAC
Found at i:70052 original size:11 final size:12
Alignment explanation
Indices: 70015--70064 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
70005 ATTCTTGACT
70015 ATATTTAAATCTA
1 ATATTTAAAT-TA
* * *
70028 AAAATTAAA-AA
1 ATATTTAAATTA
70039 ATATTT-AATTA
1 ATATTTAAATTA
70050 ATATTTAAATTA
1 ATATTTAAATTA
70062 ATA
1 ATA
70065 ATTACCTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
10 2 0.07
11 12 0.41
12 8 0.28
13 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATTTAAATTA
Found at i:70510 original size:12 final size:12
Alignment explanation
Indices: 70493--70543 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
70483 TTCAAAGAGG
70493 TTTTATATTTAA
1 TTTTATATTTAA
*
70505 TTTTATATTAAA
1 TTTTATATTTAA
* *
70517 TTTGAT-TTTGA
1 TTTTATATTTAA
70528 TTTTA-ATATTAA
1 TTTTATAT-TTAA
70540 TTTT
1 TTTT
70544 TTAAATAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 8 0.26
12 23 0.74
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:70559 original size:24 final size:26
Alignment explanation
Indices: 70532--70593 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
70522 TTTTGATTTT
70532 AATATTAATTTTTTAA-A-TAAATTA
1 AATATTAATTTTTTAATATTAAATTA
*
70556 AATATTAATTTTTTAATATTATATTA
1 AATATTAATTTTTTAATATTAAATTA
*
70582 GATATTAATTTT
1 AATATTAATTTT
70594 AATATTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 16 0.47
25 1 0.03
26 17 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
AATATTAATTTTTTAATATTAAATTA
Found at i:70594 original size:24 final size:25
Alignment explanation
Indices: 70532--70599 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 25
70522 TTTTGATTTT
*
70532 AATATTAATTTTTTAA-A-TAAATTA
1 AATATTAA-TTTTTAATATTATATTA
70556 AATATTAATTTTTTAATATTATATTA
1 AATATTAA-TTTTTAATATTATATTA
*
70582 GATATTAA-TTTTAATATT
1 AATATTAATTTTTAATATT
70600 GATTTTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 26 0.65
25 1 0.03
26 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
AATATTAATTTTTAATATTATATTA
Found at i:70596 original size:62 final size:62
Alignment explanation
Indices: 70505--70659 Score: 231
Period size: 62 Copynumber: 2.5 Consensus size: 62
70495 TTATATTTAA
* * * *
70505 TTTT-ATATTAAATTTGATTTTGATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
*
70566 TTTTAATATTATATTAGATATTAATTTTAATATTGATTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
70628 TTTTAATATTATATTATAGATATTTAATTTTA
1 TTTTAATATTATA-T-TAGATA-TTAATTTTA
70660 TATCATATAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
61 4 0.05
62 65 0.76
63 1 0.01
64 6 0.07
65 9 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (62 bp):
TTTTAATATTATATTAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
Found at i:70598 original size:38 final size:37
Alignment explanation
Indices: 70556--70638 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 37
70546 AAATAAATTA
* *
70556 AATATTAATTTTTTAATATTATATTAGATATTAA-TTTT
1 AATATTAATTTTTTAA-A-TAAATTAAATATTAATTTTT
*
70594 AATATTGATTTTTTAAATAAATTAAATATTAATTTTTT
1 AATATTAATTTTTTAAATAAATTAAATATTAA-TTTTT
70632 AATATTA
1 AATATTA
70639 TATTATAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 13 0.33
37 1 0.03
38 25 0.64
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (37 bp):
AATATTAATTTTTTAAATAAATTAAATATTAATTTTT
Found at i:70714 original size:20 final size:19
Alignment explanation
Indices: 70654--70715 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
70644 TAGATATTTA
*
70654 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
70673 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
70691 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
70711 ATTTT
1 ATTTT
70716 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:70947 original size:20 final size:22
Alignment explanation
Indices: 70922--70969 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
70912 AAATAATCAT
70922 AAAATAATTTGAT-AAATTA-A
1 AAAATAATTTGATAAAATTATA
**
70942 AAAAT-ATTTTCTAAAATTATA
1 AAAATAATTTGATAAAATTATA
70963 AAAATAA
1 AAAATAA
70970 ATTATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.22
20 11 0.48
21 6 0.26
22 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAATAATTTGATAAAATTATA
Found at i:71193 original size:31 final size:31
Alignment explanation
Indices: 71158--71217 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
71148 TAGTTGAATG
* *
71158 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
*
71189 AATTATTTAAATCTCCGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
71218 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:74094 original size:16 final size:16
Alignment explanation
Indices: 74053--74098 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
74043 CTCTAAAAAT
*
74053 TTTAAATTTTTATATAA
1 TTTATATTTTTA-ATAA
74070 TTTAT-TTTTTAATAA
1 TTTATATTTTTAATAA
*
74085 TTTTTATTTTTAAT
1 TTTATATTTTTAAT
74099 CACTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 8 0.31
16 14 0.54
17 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATATTTTTAATAA
Done.