Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006880.1 Hibiscus syriacus cultivar Beakdansim tig00017531_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: 83635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:58 original size:26 final size:27
Alignment explanation
Indices: 2--59 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
1 T
*
2 ATATAGTAATATAATTTATAATTATAC
1 ATATAGTAATATAATTTATAATTATAA
* *
29 ATATA-TAATAT-ATTTGTATATTTTAA
1 ATATAGTAATATAATTTATA-ATTATAA
55 ATATA
1 ATATA
60 ATTCATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.22
26 16 0.59
27 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
ATATAGTAATATAATTTATAATTATAA
Found at i:77 original size:19 final size:20
Alignment explanation
Indices: 65--119 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 20
55 ATATAATTCA
65 TATATATTTATAT-ATAAAC
1 TATATATTTATATAATAAAC
84 TATATATTTATATTAATAAAC
1 TATATATTTATA-TAATAAAC
105 TATATAGTTTATATA
1 TATATA-TTTATATA
120 TAGTTTAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.36
20 1 0.03
21 14 0.42
22 6 0.18
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
TATATATTTATATAATAAAC
Found at i:79 original size:21 final size:21
Alignment explanation
Indices: 45--121 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
35 AATATATTTG
* *
45 TATAT-TTTAAATATAATTCA
1 TATATATTTATATATAATACA
65 TATATATTTATATATAA-AC-
1 TATATATTTATATATAATACA
*
84 TATATATTTATAT-TAATAAA
1 TATATATTTATATATAATACA
104 CTATATAGTTTATATATA
1 -TATATA-TTTATATATA
122 GTTTAGTTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.06
19 14 0.29
20 6 0.12
21 16 0.33
22 7 0.15
23 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (21 bp):
TATATATTTATATATAATACA
Found at i:178 original size:2 final size:2
Alignment explanation
Indices: 156--396 Score: 124
Period size: 2 Copynumber: 119.5 Consensus size: 2
146 TTATACATGG
* * *
156 TA TA TA T- TT TA TA CA TA -A TA TA TA TA T- TA TA GTT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
196 TA GTA TA TA -A TA TA TA AA TA TA AA CTA TA TA TT TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
239 TA TA TA CT- TA TA TA CA CTA TA TA GTT TA TA TA TA T- TT TA T-
1 TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * * *
279 TA AA AA CTA TA TA GTT TC T- TA TC TA GTT TA TA TA -A TA TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * *
320 TA CTT TA TA AA AA CCA TA TA GTT TA TA TA TA TA TA TA TA TA TA
1 TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
397 TGTTTCAATT
Statistics
Matches: 186, Mismatches: 31, Indels: 44
0.71 0.12 0.17
Matches are distributed among these distances:
1 10 0.05
2 163 0.88
3 13 0.07
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:763 original size:27 final size:27
Alignment explanation
Indices: 728--780 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
718 TATTTAAATT
728 TTTACTTC-TAAATATATATTTGTTCAA
1 TTTACTTCTTAAATATATATTT-TTCAA
* *
755 TTTAGTTCTTAAATTTATATTTTTCA
1 TTTACTTCTTAAATATATATTTTTCA
781 TAAAATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (27 bp):
TTTACTTCTTAAATATATATTTTTCAA
Found at i:6882 original size:27 final size:28
Alignment explanation
Indices: 6843--6909 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
6833 CACAAATATT
* *
6843 AATATTATAAAAAATTT-ATATGAA-ATA
1 AATATAATTAAAAATTTAATATGAACA-A
*
6870 AATATAATTAAAATTTTCAATATGAACAA
1 AATATAATTAAAAATTT-AATATGAACAA
*
6899 AATAAAATTAA
1 AATATAATTAA
6910 TTAATTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 14 0.42
29 18 0.55
30 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
AATATAATTAAAAATTTAATATGAACAA
Found at i:15159 original size:19 final size:19
Alignment explanation
Indices: 15135--15173 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
15125 TATGTGGTTG
*
15135 TTTTTTT-TTTGTTTTTGAA
1 TTTTTTTATTT-TTTTAGAA
15154 TTTTTTTATTTTTTTAGAA
1 TTTTTTTATTTTTTTAGAA
15173 T
1 T
15174 GGTAGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (19 bp):
TTTTTTTATTTTTTTAGAA
Found at i:20550 original size:146 final size:146
Alignment explanation
Indices: 20271--20572 Score: 545
Period size: 146 Copynumber: 2.1 Consensus size: 146
20261 GCACGAAGTG
*
20271 CCGCGTAGAATGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATCCTTAAGAA
1 CCGCGTAGAATGCACCGTAGTGCCATATAATGATGTACATAAGGACCACATAGAATCCTTAAGAA
*
20336 TCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATAT
66 TCATATACATATGCTAGAGATCATATA-GTGTCTTTCCAGACTTCACACATGTTCCAAAGAATAT
20401 ACATATGTCCCGAAGGA
130 ACATATGTCCCGAAGGA
20418 -CGCGTAGAATTGCACCGTAGTGCCATATAATGATGTACATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAA-TGCACCGTAGTGCCATATAATGATGTACATAAGGACCACATAGAA-TCCTTAAG
20482 AATCATATACATATGCTAGAGATCATATA-TGTCTTTCCAGACTTCACACATGTTCCAAAGAATA
64 AATCATATACATATGCTAGAGATCATATAGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATA
20546 TACATATGTCCCGAAGGA
129 TACATATGTCCCGAAGGA
20564 CCGCGTAGA
1 CCGCGTAGA
20573 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
146 62 0.41
147 52 0.35
148 36 0.24
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (146 bp):
CCGCGTAGAATGCACCGTAGTGCCATATAATGATGTACATAAGGACCACATAGAATCCTTAAGAA
TCATATACATATGCTAGAGATCATATAGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGGA
Found at i:21234 original size:13 final size:13
Alignment explanation
Indices: 21216--21257 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
21206 TATATATATA
21216 TATCCTCAAGATT
1 TATCCTCAAGATT
*
21229 TATCCT--A-ATA
1 TATCCTCAAGATT
21239 TATCCTCAAGATT
1 TATCCTCAAGATT
21252 TATCCT
1 TATCCT
21258 AATATAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 8 0.33
11 1 0.04
12 1 0.04
13 14 0.58
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (13 bp):
TATCCTCAAGATT
Found at i:21243 original size:23 final size:23
Alignment explanation
Indices: 21213--21263 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
21203 ATCTATATAT
21213 ATATATCCTCAAGATTTATCCTA
1 ATATATCCTCAAGATTTATCCTA
21236 ATATATCCTCAAGATTTATCCTA
1 ATATATCCTCAAGATTTATCCTA
21259 ATATA
1 ATATA
21264 AATCATATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (23 bp):
ATATATCCTCAAGATTTATCCTA
Found at i:21501 original size:18 final size:18
Alignment explanation
Indices: 21480--21514 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21470 TTCCATCTAG
21480 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
21498 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
21515 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:22119 original size:21 final size:21
Alignment explanation
Indices: 22095--22139 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
22085 TGTTGTTCGT
* *
22095 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
22116 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
22137 TTG
1 TTG
22140 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:25591 original size:25 final size:24
Alignment explanation
Indices: 25563--25609 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
25553 TAACTTTAAC
25563 TATTTGATAGAAATTTTGTTAACAA
1 TATTTGATA-AAATTTTGTTAACAA
* * *
25588 TATTTTATAAGATTTTTTTAAC
1 TATTTGATAAAATTTTGTTAAC
25610 TGAGAGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (24 bp):
TATTTGATAAAATTTTGTTAACAA
Found at i:27252 original size:128 final size:126
Alignment explanation
Indices: 27092--27346 Score: 476
Period size: 128 Copynumber: 2.0 Consensus size: 126
27082 CAATCAATTT
27092 CCCCACACATTAAGTAAGTCTCTCTCTCTCTATCCCCTAAAA-ATTGTATAGGGTGAGCCATTGG
1 CCCCACACATTAAGTAAGTCTCTCTCTCTCTAT-CCCTAAAATATTGTATAGGGTGAGCCATTGG
27156 CACTTGCAGACATTGCTATAATTACATCATAAATGTAAAGACAAACTTGGAGGAGTTAGAAA
65 CACTTGCAGACATTGCTATAATTACATCATAAATGTAAAGACAAACTTGGAGGAGTTAGAAA
27218 CCCCACACATTATAAGTAAGTCTCTCTCTCTCTATCCCTAAAATATTGTATAGGGTGAGCCATTG
1 CCCCACACA-T-TAAGTAAGTCTCTCTCTCTCTATCCCTAAAATATTGTATAGGGTGAGCCATTG
27283 GCACTTGCAGACATTGCTATAATTACATCATAAATGTAAAGACAAACTTGGAGGAGTTAGAAA
64 GCACTTGCAGACATTGCTATAATTACATCATAAATGTAAAGACAAACTTGGAGGAGTTAGAAA
27346 C
1 C
27347 AATTCACTTT
Statistics
Matches: 126, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
126 9 0.07
127 9 0.07
128 108 0.86
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (126 bp):
CCCCACACATTAAGTAAGTCTCTCTCTCTCTATCCCTAAAATATTGTATAGGGTGAGCCATTGGC
ACTTGCAGACATTGCTATAATTACATCATAAATGTAAAGACAAACTTGGAGGAGTTAGAAA
Found at i:34499 original size:36 final size:36
Alignment explanation
Indices: 34452--34531 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
34442 CATTCTTCAA
34452 TCTATACAAAGATTAACATTGATCCTATCTTTCATG
1 TCTATACAAAGATTAACATTGATCCTATCTTTCATG
34488 TCTATACAAAGATTAACATTGATCCTATCTTTCATG
1 TCTATACAAAGATTAACATTGATCCTATCTTTCATG
*
34524 TCTCTACA
1 TCTATACA
34532 TCAACCAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (36 bp):
TCTATACAAAGATTAACATTGATCCTATCTTTCATG
Found at i:34902 original size:56 final size:55
Alignment explanation
Indices: 34799--34916 Score: 152
Period size: 56 Copynumber: 2.1 Consensus size: 55
34789 GCGTTTGAGA
34799 ACTAAAAACGCCGCAATAGGTCAAGATCTACTGCGGCGCTTTTGGAACAAACGCC
1 ACTAAAAACGCCGCAATAGGTCAAGATCTACTGCGGCGCTTTTGGAACAAACGCC
* *
34854 ACTATAAACGCCGCTAA-AGGTCAAATATCTA-TAGCGGCG-TTTTAGGAACAAACGCC
1 ACTAAAAACGCCGC-AATAGGTC-AAGATCTACT-GCGGCGCTTTT-GGAACAAACGCC
*
34910 GCTAAAA
1 ACTAAAA
34917 GTTGATGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
55 23 0.42
56 32 0.58
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (55 bp):
ACTAAAAACGCCGCAATAGGTCAAGATCTACTGCGGCGCTTTTGGAACAAACGCC
Found at i:34982 original size:42 final size:42
Alignment explanation
Indices: 34880--35032 Score: 186
Period size: 42 Copynumber: 3.6 Consensus size: 42
34870 AAGGTCAAAT
*
34880 ATCTATAGCGGCGTTTT-AGGAACAAACGCCGCTAAAA-GT-TG
1 ATCTATAGCGGCGTTTTCA-GAACAAACGCCGC-AAAATGTCAG
* * *
34921 ATGTATATAGCGGCGTTTTCGGAACAAACGCCACAAAATGTCAG
1 A--TCTATAGCGGCGTTTTCAGAACAAACGCCGCAAAATGTCAG
* *
34965 ATCTATAGCGGCGTTTTCATAACAAACGCCGCAAAATGTCAA
1 ATCTATAGCGGCGTTTTCAGAACAAACGCCGCAAAATGTCAG
*
35007 ATCTATAGCGGCGTTTTTAGAACAAA
1 ATCTATAGCGGCGTTTTCAGAACAAA
35033 AGGTCGTTCT
Statistics
Matches: 96, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
41 1 0.01
42 64 0.67
43 29 0.30
44 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
ATCTATAGCGGCGTTTTCAGAACAAACGCCGCAAAATGTCAG
Found at i:35253 original size:42 final size:42
Alignment explanation
Indices: 35084--35387 Score: 309
Period size: 42 Copynumber: 7.2 Consensus size: 42
35074 AGAACAACAT
* * *
35084 CAAAAGCCGCTAAAGGTCGATATCTATAGCGGCG-TTTTAGGAA
1 CAAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTA-GAA
* * * **
35127 CAAACGCCACTAAAA-GTC-GATATATAGCGGCATTTTCGGAA
1 CAAACGCCGC-AAAAGGTCAGATCTATAGCGGCGTTTTTAGAA
* * * *
35168 CAAACGCCACAAAAGGTAGAGATATATAGCGGCGTTTTCAGAA
1 CAAACGCCGCAAAAGGT-CAGATCTATAGCGGCGTTTTTAGAA
*
35211 CAAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTAGAA
1 CAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTAGAA
* * * *
35253 CAAAACGCCGTAAAAGGTC-GTTCTAT-GACAGC-ATTTT-GATA
1 C-AAACGCCGCAAAAGGTCAGATCTATAG-CGGCGTTTTTAGA-A
* *
35294 CAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTTGAA
1 CAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTAGAA
35336 CAAACGCCGCAAAAGGTCA-ATTCTATAGCGGCGTTTTTAGAA
1 CAAACGCCGCAAAAGGTCAGA-TCTATAGCGGCGTTTTTAGAA
35378 CAAACGCCGC
1 CAAACGCCGC
35388 TAATTGAAAC
Statistics
Matches: 221, Mismatches: 27, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
40 22 0.10
41 43 0.19
42 89 0.40
43 64 0.29
44 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (42 bp):
CAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTAGAA
Found at i:35373 original size:125 final size:124
Alignment explanation
Indices: 35084--35386 Score: 364
Period size: 125 Copynumber: 2.4 Consensus size: 124
35074 AGAACAACAT
* * * *
35084 CAAAAGCCGCTAAAGGTCGATATCTATAGCGGCG-TTTTAGGAACAAACGCCACTAAAAGTCGAT
1 CAAACGCCGCAAAAGGTCAAT-TCTATAGCGGCGTTTTTA-GAACAAACGCC-GTAAAAGTCGAT
* * *
35148 ATATAGCGGCATTTTCGGAACAAACGCCACAAAAGGTAGAGATATATAGCGGCGTTTTCAGAA
63 ATATAGCAGCATTTTC-GAACAAACGCCACAAAAGGTACAGATATATAGCGGCATTTTCAGAA
* *
35211 CAAACGCCGCAAAATGTCAGA-TCTATAGCGGCGTTTTTAGAACAAAACGCCGTAAAAGGTCGTT
1 CAAACGCCGCAAAAGGTCA-ATTCTATAGCGGCGTTTTTAGAAC-AAACGCCGTAAAA-GTCGAT
* * * **
35275 CTAT-GACAGCATTTT-GATACAAACGCCGCAAAAGGT-CAGATCTATAGCGGCATTTTTTGAA
63 ATATAG-CAGCATTTTCGA-ACAAACGCCACAAAAGGTACAGATATATAGCGGCATTTTCAGAA
35336 CAAACGCCGCAAAAGGTCAATTCTATAGCGGCGTTTTTAGAACAAACGCCG
1 CAAACGCCGCAAAAGGTCAATTCTATAGCGGCGTTTTTAGAACAAACGCCG
35387 CTAATTGAAA
Statistics
Matches: 154, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
124 9 0.06
125 62 0.40
126 39 0.25
127 43 0.28
128 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (124 bp):
CAAACGCCGCAAAAGGTCAATTCTATAGCGGCGTTTTTAGAACAAACGCCGTAAAAGTCGATATA
TAGCAGCATTTTCGAACAAACGCCACAAAAGGTACAGATATATAGCGGCATTTTCAGAA
Found at i:35935 original size:20 final size:20
Alignment explanation
Indices: 35888--35942 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
35878 ATACTAAGCT
*
35888 AAAATGAGGAAATTCATTTA
1 AAAATGATGAAATTCATTTA
35908 AAAATGATGAAATTCATTTA
1 AAAATGATGAAATTCATTTA
*
35928 AAAATGATAAAATTC
1 AAAATGATGAAATTC
35943 CAAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.31
Consensus pattern (20 bp):
AAAATGATGAAATTCATTTA
Found at i:38958 original size:41 final size:41
Alignment explanation
Indices: 38906--39127 Score: 286
Period size: 41 Copynumber: 5.4 Consensus size: 41
38896 TTATAAATAC
* * * *
38906 AAACGCCACTAAAGTACTAGTGAATAACAGTGTTTGTATAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
38947 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
* * * * * *
38988 AAACGCCACTAAAGTACAAGTCTTTCGCGGCGTTTATAAACAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGT--ATAA
*
39031 AAACGCCACTAAAGTACAATTGTATAG-GGTGTTTGTATAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
* * *
39071 AAATGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
39112 AAACGCCAC-AAAGTAC
1 AAACGCCACTAAAGTAC
39128 TACTCTGTTG
Statistics
Matches: 156, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
40 34 0.22
41 89 0.57
42 7 0.04
43 26 0.17
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (41 bp):
AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
Found at i:39086 original size:83 final size:82
Alignment explanation
Indices: 38906--39127 Score: 286
Period size: 83 Copynumber: 2.7 Consensus size: 82
38896 TTATAAATAC
* ** * * * * *
38906 AAACGCCACTAAAGTACTAGTGAATAACAGTGTTTGTATAAAAACGCCACTAAAGTACAAGTGTA
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTATACAAAAACGCCACTAAAGTACAAGTGTA
38971 TAGCGGTGTTTGTATAA
66 TAGCGGTGTTTGTATAA
* * *
38988 AAACGCCACTAAAGTACAAGTCTTTCGCGGCGTTTATAAACAAAAACGCCACTAAAGTACAATTG
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTAT--ACAAAAACGCCACTAAAGTACAAGTG
39053 TATAG-GGTGTTTGTATAA
64 TATAGCGGTGTTTGTATAA
* * *
39071 AAATGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCAC-AAAGTAC
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTATACAAAAACGCCACTAAAGTAC
39128 TACTCTGTTG
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
80 7 0.06
81 12 0.10
82 28 0.23
83 46 0.38
84 29 0.24
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (82 bp):
AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTATACAAAAACGCCACTAAAGTACAAGTGTA
TAGCGGTGTTTGTATAA
Found at i:39110 original size:124 final size:124
Alignment explanation
Indices: 38889--39127 Score: 372
Period size: 124 Copynumber: 1.9 Consensus size: 124
38879 TTATAAATTT
* * *
38889 GCGGCGTTTATAAATACAAACGCCACTAAAGTACTAGTGAATAACAGTGTTTGTATAAAAACGCC
1 GCGGCGTTTATAAACAAAAACGCCACTAAAGTACAAGTGAATAACAGTGTTTGTATAAAAACGCC
* *
38954 ACTAAAGTACAAGTGTATAGCGGTGTTTGTATAAAAACGCCACTAAAGTACAAGTCTTTC
66 ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCAC-AAAGTACAAGTCTTTC
* * ** *
39014 GCGGCGTTTATAAACAAAAACGCCACTAAAGTACAATTGTAT-AGGGTGTTTGTATAAAAATGCC
1 GCGGCGTTTATAAACAAAAACGCCACTAAAGTACAAGTGAATAACAGTGTTTGTATAAAAACGCC
39078 ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACAAAGTAC
66 ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACAAAGTAC
39128 TACTCTGTTG
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
123 7 0.07
124 60 0.58
125 37 0.36
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.26
Consensus pattern (124 bp):
GCGGCGTTTATAAACAAAAACGCCACTAAAGTACAAGTGAATAACAGTGTTTGTATAAAAACGCC
ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACAAAGTACAAGTCTTTC
Found at i:39145 original size:40 final size:41
Alignment explanation
Indices: 38937--39186 Score: 258
Period size: 41 Copynumber: 6.1 Consensus size: 41
38927 GAATAACAGT
* * * *
38937 GTTTGTATAAAAACGCCACTAAAGTACAAGTGTATAGCGGT
1 GTTTGTATAAAAACGCCACTAAAGTACAAGTCTGTTGCGGC
38978 GTTTGTATAAAAACGCCACTAAAGTACAAGTCT-TTCGCGGC
1 GTTTGTATAAAAACGCCACTAAAGTACAAGTCTGTT-GCGGC
* * *
39019 GTTTATAAACAAAAACGCCACTAAAGTACAA-T-TGTATAG-GGT
1 GTTTGT--ATAAAAACGCCACTAAAGTACAAGTCTGT-T-GCGGC
* * *
39061 GTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAGCGGC
1 GTTTGTATAAAAACGCCACTAAAGTACAAGTCTGTTGCGGC
* * *
39102 GTTTGTATAAAAACGCCAC-AAAGTACTACTCTGTTGCGAC
1 GTTTGTATAAAAACGCCACTAAAGTACAAGTCTGTTGCGGC
* * * * *
39142 GTTTTTCTAGAAACGCCACTAAAGTACTACTCTGTTGCGGC
1 GTTTGTATAAAAACGCCACTAAAGTACAAGTCTGTTGCGGC
39183 GTTT
1 GTTT
39187 ATTGAAAAAA
Statistics
Matches: 177, Mismatches: 23, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
40 55 0.31
41 87 0.49
42 11 0.06
43 24 0.14
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
GTTTGTATAAAAACGCCACTAAAGTACAAGTCTGTTGCGGC
Found at i:47311 original size:12 final size:12
Alignment explanation
Indices: 47286--47319 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
47276 TCGTAACTAT
*
47286 TATATATATATA
1 TATATATGTATA
*
47298 TATGTATGTATA
1 TATATATGTATA
47310 TATATATGTA
1 TATATATGTA
47320 GCTCAAGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
TATATATGTATA
Found at i:51737 original size:36 final size:36
Alignment explanation
Indices: 51663--51737 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
51653 TTTTTATATT
*
51663 TTTAATTTTGTAAAAAAAATATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATATATAAATATTATCAA
* * *
51699 TTTAATTTTTTAAAGAAAATATAT-AATATTTTACAA
1 TTTAATTTTGTAAAAAAAATATATAAATATTAT-CAA
51735 TTT
1 TTT
51738 GTAATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
36 27 0.79
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAAATATATAAATATTATCAA
Found at i:51916 original size:20 final size:20
Alignment explanation
Indices: 51877--51916 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
51867 GTAATCCTAT
**
51877 TCACTGGTAATCTTTTATTC
1 TCACTGGTAATCTTACATTC
51897 TCACTGGTAATCTTACATTC
1 TCACTGGTAATCTTACATTC
51917 CGTGAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (20 bp):
TCACTGGTAATCTTACATTC
Found at i:56199 original size:35 final size:36
Alignment explanation
Indices: 56120--56205 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 36
56110 TTGGATGTAT
* * *
56120 CTTAAAATGTTATTTTTTTTCTAACATTTTTAGTTTAA
1 CTTAAAATGTTA--TTTTTTCTAACATTTTCACTTGAA
*
56158 CCTAAAATGTTATTTTTT-TAACATTTTCACTTGAA
1 CTTAAAATGTTATTTTTTCTAACATTTTCACTTGAA
*
56193 CTTAAAATTTTAT
1 CTTAAAATGTTAT
56206 CTTATTCATG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 25 0.60
36 6 0.14
38 11 0.26
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.53
Consensus pattern (36 bp):
CTTAAAATGTTATTTTTTCTAACATTTTCACTTGAA
Found at i:57451 original size:11 final size:11
Alignment explanation
Indices: 57429--57493 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
57419 TTCATTTTTT
57429 TAAAAATA-AA
1 TAAAAATATAA
57439 TAAAAATATAA
1 TAAAAATATAA
*
57450 TAAAAA-AGAA
1 TAAAAATATAA
* *
57460 TTAAAAGT-GAA
1 -TAAAAATATAA
57471 T-AAAAT-TCAA
1 TAAAAATAT-AA
57481 TAAAAATATAA
1 TAAAAATATAA
57492 TA
1 TA
57494 TAAAGCTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
9 4 0.09
10 15 0.33
11 25 0.56
12 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (11 bp):
TAAAAATATAA
Found at i:57455 original size:12 final size:10
Alignment explanation
Indices: 57429--57493 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
57419 TTCATTTTTT
57429 TAAAAATAAA
1 TAAAAATAAA
57439 TAAAAATATAA
1 TAAAAATA-AA
57450 TAAAAA-AGAA
1 TAAAAATA-AA
* *
57460 TTAAAAGTGAA
1 -TAAAAATAAA
* *
57471 TAAAATTCAA
1 TAAAAATAAA
57481 TAAAAATATAA
1 TAAAAATA-AA
57492 TA
1 TA
57494 TAAAGCTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
10 25 0.57
11 19 0.43
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:57455 original size:21 final size:21
Alignment explanation
Indices: 57429--57493 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
57419 TTCATTTTTT
57429 TAAAAATAAATAAAAATATAA
1 TAAAAATAAATAAAAATATAA
* *
57450 TAAAAA-AGAATTAAAAGT-GAA
1 TAAAAATA-AA-TAAAAATATAA
* *
57471 TAAAATTCAATAAAAATATAA
1 TAAAAATAAATAAAAATATAA
57492 TA
1 TA
57494 TAAAGCTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
20 7 0.21
21 21 0.62
22 6 0.18
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (21 bp):
TAAAAATAAATAAAAATATAA
Found at i:58932 original size:18 final size:18
Alignment explanation
Indices: 58906--58954 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
58896 TCACGTAATG
58906 TAAGATTACTAAAGGGAA
1 TAAGATTACTAAAGGGAA
* ***
58924 TAGGATTACTGGCGGGAA
1 TAAGATTACTAAAGGGAA
58942 TAAGATTACTAAA
1 TAAGATTACTAAA
58955 AATGTTGCAT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.24
Consensus pattern (18 bp):
TAAGATTACTAAAGGGAA
Found at i:59145 original size:28 final size:27
Alignment explanation
Indices: 59113--59169 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
59103 TACTATAACT
59113 AATTTATAT-ATTTTCTTTAAAAAATGTA
1 AATTTATATAATTTT-TTTAAAAAAT-TA
*
59141 AATTTATATAATTTTTTTACAAAATTA
1 AATTTATATAATTTTTTTAAAAAATTA
59168 AA
1 AA
59170 AAGATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 18 0.67
29 5 0.19
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (27 bp):
AATTTATATAATTTTTTTAAAAAATTA
Found at i:68316 original size:21 final size:22
Alignment explanation
Indices: 68280--68320 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
68270 TTAGAAATTA
68280 TAAAGGAAGTACCGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
*
68302 TAAAGG-AGTATCGATACTC
1 TAAAGGAAGTACCGATACTC
68321 CTTGTCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:68537 original size:34 final size:34
Alignment explanation
Indices: 68489--68557 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
68479 AGAGAAGAGC
*
68489 TTTGCAATCTTATTTTCCTTTCTCTTGTAAATAT
1 TTTGAAATCTTATTTTCCTTTCTCTTGTAAATAT
68523 TTTGAAATCTTATTTTCCTTTCTCTTGTAAATAT
1 TTTGAAATCTTATTTTCCTTTCTCTTGTAAATAT
68557 T
1 T
68558 AGTGTGTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.57
Consensus pattern (34 bp):
TTTGAAATCTTATTTTCCTTTCTCTTGTAAATAT
Found at i:69846 original size:15 final size:15
Alignment explanation
Indices: 69818--69856 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
69808 TGGCCCCAAA
*
69818 AGCCGAGAAGAAGCC
1 AGCCGAGAAAAAGCC
*
69833 AGCTGAGAAAAAGCC
1 AGCCGAGAAAAAGCC
69848 AGCCGAGAA
1 AGCCGAGAA
69857 GGCCCCAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.23, G:0.31, T:0.03
Consensus pattern (15 bp):
AGCCGAGAAAAAGCC
Found at i:69854 original size:30 final size:31
Alignment explanation
Indices: 69817--69894 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
69807 ATGGCCCCAA
69817 AAGCCGAGAAGAAGCCAGCTGAGAAAAAGCC
1 AAGCCGAGAAGAAGCCAGCTGAGAAAAAGCC
*** *
69848 -AGCCGAGAAGGCCCCAGCTGAGAAGAAGCC
1 AAGCCGAGAAGAAGCCAGCTGAGAAAAAGCC
69878 AAGAGCCGAGAAGAAGC
1 -A-AGCCGAGAAGAAGC
69895 TGCCCAAAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 26 0.70
33 11 0.30
ACGTcount: A:0.41, C:0.24, G:0.32, T:0.03
Consensus pattern (31 bp):
AAGCCGAGAAGAAGCCAGCTGAGAAAAAGCC
Found at i:70763 original size:16 final size:16
Alignment explanation
Indices: 70738--70780 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
70728 AACGTCTTTT
70738 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
70754 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
70771 ACAAAAATTT
1 AAAAAAATTT
70781 GGTCTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:71768 original size:20 final size:18
Alignment explanation
Indices: 71712--71769 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 18
71702 TCTTCTCTCA
71712 TTTTTTCTGTTTTTTTCCT
1 TTTTTTCTGTTTTTTT-CT
71731 TTTTTT-T-TTGTTTTTCT
1 TTTTTTCTGTT-TTTTTCT
71748 TTTTTTCTGTTCTTTTATCT
1 TTTTTTCTGTT-TTTT-TCT
71768 TT
1 TT
71770 GCTTGCCCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 10 0.29
18 7 0.21
19 12 0.35
20 5 0.15
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTTTCTGTTTTTTTCT
Found at i:72194 original size:3 final size:3
Alignment explanation
Indices: 72186--72239 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
72176 TATGTAAAAT
72186 TAA TAA TAA TAA TAA TAA TTAA TAA TAA TAA -AA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
72229 -AA TAA AAA TAA
1 TAA TAA TAA TAA
72240 ACATAAAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 34 0.76
4 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:72222 original size:10 final size:11
Alignment explanation
Indices: 72180--72245 Score: 64
Period size: 13 Copynumber: 5.7 Consensus size: 11
72170 ATGTAATATG
72180 TAAAATTAATAA
1 TAAAA-TAATAA
72192 TAATAATAATAA
1 TAA-AATAATAA
72204 TTAATAATAATAA
1 -TAA-AATAATAA
72217 -AAAATAA-AA
1 TAAAATAATAA
*
72226 TAAAATAAAAA
1 TAAAATAATAA
72237 TAAACATAA
1 TAAA-ATAA
72246 AAGACCCGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
9 2 0.04
10 12 0.24
11 8 0.16
12 13 0.27
13 14 0.29
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:72235 original size:16 final size:17
Alignment explanation
Indices: 72187--72245 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 17
72177 ATGTAAAATT
*
72187 AATAATAATAATAATAA
1 AATAATAATAAAAATAA
72204 TTAATAATAATAAAAAATAA
1 --AATAATAAT-AAAAATAA
72224 AATAA-AATAAAAATAA
1 AATAATAATAAAAATAA
72240 ACATAA
1 A-ATAA
72246 AAGACCCGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 9 0.24
17 7 0.19
18 5 0.14
19 9 0.24
20 7 0.19
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AATAATAATAAAAATAA
Found at i:73701 original size:16 final size:16
Alignment explanation
Indices: 73680--73715 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
73670 TCCTTTATTT
73680 ATTTTTC-TTCTTTTTC
1 ATTTTTCATT-TTTTTC
73696 ATTTTTCATTTTTTTC
1 ATTTTTCATTTTTTTC
73712 ATTT
1 ATTT
73716 CCTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTCATTTTTTTC
Done.