Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002180.1 Hibiscus syriacus cultivar Beakdansim tig00004441_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: 140157
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4803 original size:36 final size:36
Alignment explanation
Indices: 4763--4833 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
4753 AGACCTCAAA
4763 TATACATTGTTGAGTTTTACCCTCCATTGCCAATCC
1 TATACATTGTTGAGTTTTACCCTCCATTGCCAATCC
*
4799 TATACATTGTTGAGTTTTACTCTCCATTGCCAATC
1 TATACATTGTTGAGTTTTACCCTCCATTGCCAATC
4834 ATTTCAATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (36 bp):
TATACATTGTTGAGTTTTACCCTCCATTGCCAATCC
Found at i:26474 original size:229 final size:228
Alignment explanation
Indices: 26063--26512 Score: 785
Period size: 229 Copynumber: 2.0 Consensus size: 228
26053 GTAAATTATC
* * *
26063 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTTATTATTATCTTTAG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTTATTATTATATTTAG
**
26128 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
66 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
*
26193 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
131 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
26258 GAAACATAAATTACATAACTTTCAAAAAAGTATA
196 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
26292 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATA-TTTATTATTATATTTG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTTATTATTATATTTA
*
26356 GTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
65 GTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
* *
26421 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAAT
130 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAAT
26486 TGAAACATAAATTACATAACTTTAAAA
195 TGAAACATAAATTACATAACTTTAAAA
26513 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
228 4 0.02
229 197 0.94
230 9 0.04
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTTATTATTATATTTAG
TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
GAAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:26601 original size:20 final size:19
Alignment explanation
Indices: 26578--26624 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
26568 CGATATACCA
26578 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
26598 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
26618 GGTAAAA
1 GGTAAAA
26625 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:26768 original size:20 final size:19
Alignment explanation
Indices: 26745--26791 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
26735 CGATATAACA
*
26745 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
26765 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
26785 GGTAAAA
1 GGTAAAA
26792 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:29133 original size:33 final size:33
Alignment explanation
Indices: 29091--29156 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
29081 AAATAGATGG
*
29091 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
29124 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
29157 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:30991 original size:19 final size:19
Alignment explanation
Indices: 30947--30990 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
30937 AATGTCGAGT
30947 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
30966 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
30985 T-ATTTT
1 TAATTTT
30991 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:31442 original size:199 final size:199
Alignment explanation
Indices: 31073--32490 Score: 2639
Period size: 199 Copynumber: 7.1 Consensus size: 199
31063 TTAAGGGTCA
*
31073 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
31138 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
31202 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
31267 AATG
196 AATG
31271 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
31336 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
31401 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
31466 AATG
196 AATG
* *
31470 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
*
31535 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
31599 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
31664 TAATG
195 TAATG
31669 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
31734 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
31799 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
31864 AATG
196 AATG
31868 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
31933 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
31998 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
32063 AATG
196 AATG
*
32067 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCA-C
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
*
32131 CATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
32195 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
32260 AATG
196 AATG
* *
32264 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
* *
32328 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
32393 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
32458 AATG
196 AATG
*
32462 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
32491 CTAATTTAAA
Statistics
Matches: 1199, Mismatches: 16, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
196 33 0.03
197 162 0.14
198 292 0.24
199 696 0.58
200 16 0.01
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:33969 original size:12 final size:12
Alignment explanation
Indices: 33942--34032 Score: 67
Period size: 12 Copynumber: 7.4 Consensus size: 12
33932 GGTCGCAGAA
*
33942 GATGAAGCTG-C
1 GATGAAGATGAC
33953 GATGAAGATGAC
1 GATGAAGATGAC
33965 GATGATGATGATGAC
1 GATGA--A-GATGAC
* *
33980 GATGAAGCTGGC
1 GATGAAGATGAC
*
33992 GATGAAGATGAT
1 GATGAAGATGAC
* * *
34004 GACGATGATGAT
1 GATGAAGATGAC
* *
34016 GATGATGATGAA
1 GATGAAGATGAC
34028 GATGA
1 GATGA
34033 TGATCCAAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
11 9 0.14
12 44 0.67
13 1 0.02
14 1 0.02
15 11 0.17
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:33977 original size:15 final size:15
Alignment explanation
Indices: 33953--34035 Score: 91
Period size: 15 Copynumber: 5.7 Consensus size: 15
33943 ATGAAGCTGC
*
33953 GATGAAGATGACGAT
1 GATGATGATGACGAT
33968 GATGATGATGACGAT
1 GATGATGATGACGAT
* *
33983 GA--A-GCTGGCGAT
1 GATGATGATGACGAT
*
33995 GAAGATGATGACGAT
1 GATGATGATGACGAT
*
34010 GATGATGATGATGAT
1 GATGATGATGACGAT
*
34025 GAAGATGATGA
1 GATGATGATGA
34036 TCCAAACAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
12 9 0.16
13 1 0.02
14 1 0.02
15 46 0.81
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (15 bp):
GATGATGATGACGAT
Found at i:36031 original size:181 final size:183
Alignment explanation
Indices: 35396--36242 Score: 1555
Period size: 183 Copynumber: 4.7 Consensus size: 183
35386 ACTTTCACAT
**
35396 ATTATAATAAAATAGAT-ATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
35460 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
35525 AATGTGTCGATACGATTTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATAC-AATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
35579 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAA-ATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
35643 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
35708 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATA
35762 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
35826 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
**
35890 AATGTGTCGATACAATTTAAAAAGTGTCGACATTTTACACATCATAACCC-TA
131 AATGTGTCGATACAATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
35942 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
36007 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
36072 AATGTGTCGATACGATTTAAAAAGTGTCGACATTTT-CACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
36124 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGT-TTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
36188 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
36243 CCATTTAAAA
Statistics
Matches: 648, Mismatches: 10, Indels: 14
0.96 0.01 0.02
Matches are distributed among these distances:
180 41 0.06
181 194 0.30
182 116 0.18
183 273 0.42
184 24 0.04
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:36067 original size:364 final size:365
Alignment explanation
Indices: 35396--36242 Score: 1553
Period size: 364 Copynumber: 2.3 Consensus size: 365
35386 ACTTTCACAT
**
35396 ATTATAATAAAATAGAT-ATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
35460 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
35525 AATGTGTCGATACGATTTTAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
131 AATGTGTCGATACGAATTTAAAAAGTGTCGACATTTTACACATCAGAACCCATAATTATAATGTA
35590 ATAGATAATTTTGTAATATAACCGGTATAAAATACCGGTCTTATGCGCGAATAGGTCTACAACCT
196 ATAGATAATTTTGTAATATAACCGGTATAAAATACCGGTCTTATGCGCGAATAGGTCTACAACCT
35655 ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA
261 ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA
35720 CAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
326 CAATTT-AAAAAGTGTCGACATTTT-CACATCGGAACCCATA
35762 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
35826 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
35890 AATGTGTCGATAC-AATTTAAAAAGTGTCGACATTTTACACATCATAACCC-TAATTATAATGTA
131 AATGTGTCGATACGAATTTAAAAAGTGTCGACATTTTACACATCAGAACCCATAATTATAATGTA
35953 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAA-ATACCGGTCTTATGCGCGAATAGGTCTACAACC
36018 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
260 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
*
36083 ACGATTTAAAAAGTGTCGACATTTTCACATCGGAACCCATA
325 ACAATTTAAAAAGTGTCGACATTTTCACATCGGAACCCATA
*
36124 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGT-TTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
36188 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
36243 CCATTTAAAA
Statistics
Matches: 470, Mismatches: 8, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
362 121 0.26
363 73 0.16
364 138 0.29
365 15 0.03
366 102 0.22
367 21 0.04
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (365 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGAATTTAAAAAGTGTCGACATTTTACACATCAGAACCCATAATTATAATGTA
ATAGATAATTTTGTAATATAACCGGTATAAAATACCGGTCTTATGCGCGAATAGGTCTACAACCT
ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA
CAATTTAAAAAGTGTCGACATTTTCACATCGGAACCCATA
Found at i:38814 original size:23 final size:23
Alignment explanation
Indices: 38783--38845 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
38773 ATAGGTAAAC
*
38783 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
38806 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
38829 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
38846 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:38853 original size:23 final size:23
Alignment explanation
Indices: 38783--38855 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
38773 ATAGGTAAAC
* * **
38783 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
38806 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
38829 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
38852 ATAT
1 ATAT
38856 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:39273 original size:23 final size:23
Alignment explanation
Indices: 39210--39274 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
39200 ATAGGTAAAC
* *
39210 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
39233 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
39256 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
39275 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:39498 original size:18 final size:18
Alignment explanation
Indices: 39477--39513 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39467 GTAATTGGAG
39477 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
39495 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
39513 T
1 T
39514 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:39521 original size:24 final size:24
Alignment explanation
Indices: 39469--39515 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
39459 TTTCATATGT
* *
39469 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
39493 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
39516 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:39883 original size:20 final size:20
Alignment explanation
Indices: 39858--39896 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39848 GGTTATATTG
* *
39858 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
39878 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
39897 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:47267 original size:12 final size:12
Alignment explanation
Indices: 47250--47274 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47240 TTTGACTGAG
47250 TCAAGTAAAAAT
1 TCAAGTAAAAAT
47262 TCAAGTAAAAAT
1 TCAAGTAAAAAT
47274 T
1 T
47275 TGAGTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (12 bp):
TCAAGTAAAAAT
Found at i:56381 original size:40 final size:39
Alignment explanation
Indices: 56299--56386 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 39
56289 TCAGGTCAGG
* * **
56299 TTTTTTTAAGTTTGATATTCGGGTCGGATCGGGTTGGGT
1 TTTTTTTAAGTGTGATATTCGGGTCGGATCGGGTCGAAT
*
56338 TTTTATTTAAGTGTGATATTCGGGTCGGGTTC-GGTCGAAT
1 TTTT-TTTAAGTGTGATATTCGGGTC-GGATCGGGTCGAAT
56378 TTTTTTTAA
1 TTTTTTTAA
56387 AAAAAAATCG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 9 0.21
40 29 0.69
41 4 0.10
ACGTcount: A:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (39 bp):
TTTTTTTAAGTGTGATATTCGGGTCGGATCGGGTCGAAT
Found at i:56476 original size:27 final size:27
Alignment explanation
Indices: 56411--56469 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
56401 CGGGTCGGGC
*
56411 CGGGTCGAGTTTTTTAAGTTTGATATT
1 CGGGTCGAGTTTTTTAAGTGTGATATT
56438 CGGGTCGAGTTTTTTAAGTGTGATATT
1 CGGGTCGAGTTTTTTAAGTGTGATATT
56465 CGGGT
1 CGGGT
56470 TGGGTTTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.08, G:0.31, T:0.44
Consensus pattern (27 bp):
CGGGTCGAGTTTTTTAAGTGTGATATT
Found at i:62656 original size:2 final size:2
Alignment explanation
Indices: 62649--62674 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62639 AGTGAAAATA
62649 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
62675 TGGCTAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68690 original size:22 final size:22
Alignment explanation
Indices: 68665--68706 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
68655 ACTAACTAGT
68665 AAAAAACAAAGAAGTTAAACTG
1 AAAAAACAAAGAAGTTAAACTG
* * *
68687 AAAACACAAAGGATTTAAAC
1 AAAAAACAAAGAAGTTAAAC
68707 CCCAAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.14
Consensus pattern (22 bp):
AAAAAACAAAGAAGTTAAACTG
Found at i:72306 original size:33 final size:33
Alignment explanation
Indices: 72264--72334 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
72254 AGGAATGAAG
72264 AATGAAACTAAGTGATATTTTATTTGATTATAC
1 AATGAAACTAAGTGATATTTTATTTGATTATAC
*
72297 AATGAAACTAAGTGATGTTTTATTTGATTATAC
1 AATGAAACTAAGTGATATTTTATTTGATTATAC
72330 AATGA
1 AATGA
72335 CACTGATGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (33 bp):
AATGAAACTAAGTGATATTTTATTTGATTATAC
Found at i:72351 original size:29 final size:31
Alignment explanation
Indices: 72276--72354 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 31
72266 TGAAACTAAG
* *
72276 TGATATTTTATTTGATTATACAATGAAACTAAG
1 TGATGTTTTATTTGATTATACAATG-AAC-AAC
72309 TGATGTTTTATTTGATTATACAATG-AC-AC
1 TGATGTTTTATTTGATTATACAATGAACAAC
72338 TGATGTTTTATTTGATT
1 TGATGTTTTATTTGATT
72355 TTCTGGCTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 18 0.41
31 2 0.05
33 24 0.55
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (31 bp):
TGATGTTTTATTTGATTATACAATGAACAAC
Found at i:85481 original size:21 final size:21
Alignment explanation
Indices: 85452--85497 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
85442 CCGGAAATAA
*
85452 TATTATTTCTATCGATTTTGT
1 TATTATTTCTATCGATTTTAT
*
85473 TATTTTTTCTATCGATTTTAT
1 TATTATTTCTATCGATTTTAT
85494 TATT
1 TATT
85498 GTTGGACACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.65
Consensus pattern (21 bp):
TATTATTTCTATCGATTTTAT
Found at i:85548 original size:21 final size:21
Alignment explanation
Indices: 85523--85565 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
85513 AAAAATGTTA
* *
85523 AAAAATATTGATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
85544 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
85565 A
1 A
85566 TTTTTTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:90464 original size:17 final size:16
Alignment explanation
Indices: 90442--90496 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
90432 GGAAAAAAAT
90442 AAAATAAAAATAAGTAA
1 AAAATAAAAATAA-TAA
*
90459 AAAATAATAATAATAA
1 AAAATAAAAATAATAA
*
90475 ATAATGATAATAATAATAA
1 A-AA--ATAAAAATAATAA
90494 AAA
1 AAA
90497 CTATATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
16 4 0.12
17 14 0.41
18 2 0.06
19 14 0.41
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (16 bp):
AAAATAAAAATAATAA
Found at i:90469 original size:3 final size:3
Alignment explanation
Indices: 90439--90493 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
90429 ACGGGAAAAA
* *
90439 AAT AA- AAT AAA AAT AAGT AA- AA- AAT AAT AAT AAT AAAT AAT GAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT AAT
90483 AAT AAT AAT AA
1 AAT AAT AAT AA
90494 AAACTATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 6 0.14
3 32 0.73
4 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:90664 original size:36 final size:36
Alignment explanation
Indices: 90619--90880 Score: 179
Period size: 37 Copynumber: 6.9 Consensus size: 36
90609 ACCATATAAT
* * *
90619 TTTTAAAAATGTTTTAAAAATTACATATTATATATG
1 TTTTCAAAATGTTTTAAAAATTATATATTATATATA
*
90655 CTTTCAAAATGTTTTTCAAAAAATTATATATTATATATTATATATTTA
1 TTTTCAAAATG-TTTT-----AA--A-A-ATTATATATTATATA--TA
* * * *
90703 TTTTCAAAACGTTTTAAAAACTATATAATATGTATA
1 TTTTCAAAATGTTTTAAAAATTATATATTATATATA
* * * *
90739 TTTTCAAAAATGTTTTGAAAACTATATATTATATTTC
1 TTTTC-AAAATGTTTTAAAAATTATATATTATATATA
* * * *
90776 TTTTCAAAAACGTTTT-AAAACTATATAATATATAAATG
1 TTTTC-AAAATGTTTTAAAAATTATAT-AT-TATATATA
* *
90814 TTTTTAAAATGTTTTAAAAATTATATA-T-CATATA
1 TTTTCAAAATGTTTTAAAAATTATATATTATATATA
* *
90848 TTTTCAAAATGTTTTTAAAATTATATAATATAT
1 TTTTCAAAATGTTTTAAAAATTATATATTATAT
90881 TAAATAAAAA
Statistics
Matches: 180, Mismatches: 28, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
34 28 0.16
35 2 0.01
36 28 0.16
37 56 0.31
38 30 0.17
39 1 0.01
40 1 0.01
42 4 0.02
44 1 0.01
45 1 0.01
46 14 0.08
47 4 0.02
48 10 0.06
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTTCAAAATGTTTTAAAAATTATATATTATATATA
Found at i:90763 original size:37 final size:35
Alignment explanation
Indices: 90688--90880 Score: 192
Period size: 37 Copynumber: 5.3 Consensus size: 35
90678 TTATATATTA
* * *
90688 TATATTATATATTTATTTTCAAAACGTTTTAAAAAC
1 TATATAATATATATATTTTCAAAATGTTTT-AAAAC
*
90724 TATATAATATGTATATTTTCAAAAATGTTTTGAAAAC
1 TATATAATATATATATTTTC-AAAATGTTTT-AAAAC
* * * *
90761 TATATATTATATTTCTTTTCAAAAACGTTTTAAAAC
1 TATATAATATATATATTTTC-AAAATGTTTTAAAAC
* * *
90797 TATATAATATATAAATGTTTTTAAAATGTTTTAAAAA
1 TATATAATATAT--ATATTTTCAAAATGTTTTAAAAC
*
90834 T-TAT-ATATCATATATTTTCAAAATGTTTTTAAAAT
1 TATATAATAT-ATATATTTTCAAAATG-TTTTAAAAC
90869 TATATAATATAT
1 TATATAATATAT
90881 TAAATAAAAA
Statistics
Matches: 131, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
34 12 0.09
35 13 0.10
36 43 0.33
37 58 0.44
38 5 0.04
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (35 bp):
TATATAATATATATATTTTCAAAATGTTTTAAAAC
Found at i:90780 original size:73 final size:73
Alignment explanation
Indices: 90686--90885 Score: 235
Period size: 74 Copynumber: 2.7 Consensus size: 73
90676 AATTATATAT
* *
90686 TATATATTATATATTTATTTTCAAAACGTTTTAAAAACTATATAATATGTATAT-TTTCAAAAAT
1 TATATA-T-TATATTTATTTTCAAAACGTTTT-AAAACTATATAATATATAAATGTTTCAAAAAT
*
90750 GTTTTGAAAAC
63 GTTTTAAAAAC
* **
90761 TATATATTATATTTCTTTTCAAAAACGTTTTAAAACTATATAATATATAAATGTTTTTAAAATGT
1 TATATATTATATTTATTTTC-AAAACGTTTTAAAACTATATAATATATAAATGTTTCAAAAATGT
*
90826 TTTAAAAAT
65 TTTAAAAAC
* * *
90835 TATATATCATA--TATTTTCAAAATGTTTTTAAAATTATATAATATATTAAAT
1 TATATATTATATTTATTTTCAAAACG-TTTTAAAACTATATAATATA-TAAAT
90886 AAAAAACAAA
Statistics
Matches: 110, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
71 5 0.05
72 25 0.23
73 36 0.33
74 38 0.35
75 6 0.05
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (73 bp):
TATATATTATATTTATTTTCAAAACGTTTTAAAACTATATAATATATAAATGTTTCAAAAATGTT
TTAAAAAC
Found at i:101760 original size:60 final size:60
Alignment explanation
Indices: 101707--101849 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 60
101697 ATTTTAAGTG
* *
101707 TTTAAATTTTATCCCTAAACTATGA-CTATCACTCTAAATTGATCCTCAAAATTTTGAACA
1 TTTAAATTTCATCCCCAAACTATGACCT-TCACTCTAAATTGATCCTCAAAATTTTGAACA
* * * ** *
101767 TTTCAATTTCATCCCCAAACTATGACCTTCATTCTAAATT-AGTCTCTGAACTTTTTGAATA
1 TTTAAATTTCATCCCCAAACTATGACCTTCACTCTAAATTGA-TC-CTCAAAATTTTGAACA
*
101828 TTTCAATTTCA-CCCCAAACTAT
1 TTTAAATTTCATCCCCAAACTAT
101850 TCATATATAC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.01
60 46 0.64
61 25 0.35
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (60 bp):
TTTAAATTTCATCCCCAAACTATGACCTTCACTCTAAATTGATCCTCAAAATTTTGAACA
Found at i:112690 original size:183 final size:182
Alignment explanation
Indices: 112328--112697 Score: 449
Period size: 183 Copynumber: 2.0 Consensus size: 182
112318 CTTCATTTGT
* * * *
112328 GAACCAAAAGATTCACTTGATCCATTGCCATATCCTTCATGTGCGACATTACTATGAGCTCTCTC
1 GAACCAAAAGATTCACTTGATCCATTGCCAAATCCTTCATATGCGACATTACGATGAACTCTCTC
* * *
112393 TCTCATTCTGCCTGATCTCGAACGTGGAGGAATCAGGGAACCTAAAACATCACTCTCATCAAATT
66 TCTCATTCTGCCAGATCTCGAACGTGCAGGAATCAGGGAACCTAAAACATCACTCTCATCAAACT
* * * **
112458 TCTCCAAATTTTCAGAATATAAATCACCAAATGCCCTACCTTTACTCTTATTA
131 TCTCCAAATTTTCAGAACACAAATCACCAAA-GCCCTACATGCACTCTTATTA
* *
112511 GAACCAGAAGATTCACTTGATCCATTGCCAAATCCTTCATATGTGACATTACGATGAACTCTCT-
1 GAACCAAAAGATTCACTTGATCCATTGCCAAATCCTTCATATGCGACATTACGATGAACTCTCTC
* * * * * * *
112575 TCTTCATTCTTCCAGATCTCGAATGTTCAGGGAT-TGAGGAACCTACAACATCACTCTCATTAAA
66 TC-TCATTCTGCCAGATCTCGAACGTGCAGGAATCAG-GGAACCTAAAACATCACTCTCATCAAA
* * * *
112639 CTTCTCCAAATTTTCCGAACCCAAATCCCCAAA-CCCTATACATGCACTCTTATTG
129 CTTCTCCAAATTTTCAGAACACAAATCACCAAAGCCC--TACATGCACTCTTATTA
112694 GAAC
1 GAAC
112698 TATCCGGCGA
Statistics
Matches: 158, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
181 3 0.02
182 3 0.02
183 152 0.96
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.30
Consensus pattern (182 bp):
GAACCAAAAGATTCACTTGATCCATTGCCAAATCCTTCATATGCGACATTACGATGAACTCTCTC
TCTCATTCTGCCAGATCTCGAACGTGCAGGAATCAGGGAACCTAAAACATCACTCTCATCAAACT
TCTCCAAATTTTCAGAACACAAATCACCAAAGCCCTACATGCACTCTTATTA
Found at i:112899 original size:393 final size:396
Alignment explanation
Indices: 112157--112907 Score: 962
Period size: 393 Copynumber: 1.9 Consensus size: 396
112147 AGACGGGCGA
* * *
112157 GTGACATTACAATGAACTCTCTCTCTCATTCTTCCGGATTTCAAAAGCCAAGGAATCGGGGAACC
1 GTGACATTACAATGAACTCTCTCTCTCATTCTTCCAGATCTCAAAAGCCAAGGAATCGAGGAACC
* * * *
112222 TAAAACATCACTCTTATTAGACTCCCCCTCAGAATTTTCAGAACCAAAATCACCAAATCCTCTAC
66 TAAAACATCACTCTCATTAAACTCCCCCTCAGAATTTTCAGAACCAAAATCACCAAACCCTATAC
* * * *
112287 CTATATTCTTATTAGAACTATCCGGCTAATCCTTCATTTGTGAACCAAAAGATTCACTTGATCCA
131 ATACACTCTTATTAGAACTATCCGGCGAATCCTTCATTTGTGAACCAAAAGATTCACTTGATCCA
* * * *
112352 TTGCCATATCCTTCATGTGCGACATTACTATGAGCTCTCTCTCTCATTCTGCCTGATCTCGAACG
196 TTGCCATATCCTTCATATGCGACATTACTATGAACTCTCACTCTCATTCTGCCAGATCTCGAACG
* * * * *
112417 TGGAGGAATCAGGGAACCTAAAACATCACTCTCATCAAATTTCTCCAAATTTTCAGAATATAAAT
261 TGGAGAAATCAGGGAACCTAAAACATCAATATCATCAAATTTCTCCAAATTTTCAGAACACAAAT
*
112482 CACCAAATGCCCTACCTTTACTCTTATTAGAACCAGAAGATTCACTTGATCCATTGCCAAATCCT
326 CACAAAATGCCCTACCTTTACTCTTATTAGAACCAGAAGATTCACTTGATCCATTGCCAAATCCT
112547 TCATAT
391 TCATAT
* * * * * *
112553 GTGACATTACGATGAACTCTCT-TCTTCATTCTTCCAGATCTCGAATGTTC-AGGGATTGAGGAA
1 GTGACATTACAATGAACTCTCTCTC-TCATTCTTCCAGATCTCAAAAG-CCAAGGAATCGAGGAA
* * * * * *
112616 CCTACAACATCACTCTCATTAAACT-TCTC-CA-AATTTTCCGAACCCAAATCCCCAAACCCTAT
64 CCTAAAACATCACTCTCATTAAACTCCCCCTCAGAATTTTCAGAACCAAAATCACCAAACCCTAT
* * ** *
112678 ACATGCACTCTTATTGGAACTATCCGGCGAATCCTTCATTTGTGAACCTGAAGATTCTCTTGATC
129 ACATACACTCTTATTAGAACTATCCGGCGAATCCTTCATTTGTGAACCAAAAGATTCACTTGATC
* * * *
112743 CATTGCTATATCCTTCATATGTGACATTACTATGAACTCTCACTCTCGTTCTTCCAGATCTCGAA
194 CATTGCCATATCCTTCATATGCGACATTACTATGAACTCTCACTCTCATTCTGCCAGATCTCGAA
* * * * *
112808 CGCT-GAGAAAT-TGAGGAACCTAAAACATTAATATCATTAGATTTCTCCAAATTTTCAGAACCC
259 CG-TGGAGAAATCAG-GGAACCTAAAACATCAATATCATCAAATTTCTCCAAATTTTCAGAACAC
112871 AAATCACAAAAT-CCCTTA-CTTCTACTCTTATTAGAAC
322 AAATCACAAAATGCCC-TACCTT-TACTCTTATTAGAAC
112908 TACCATACGA
Statistics
Matches: 302, Mismatches: 47, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
392 7 0.02
393 216 0.72
394 3 0.01
395 4 0.01
396 71 0.24
397 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (396 bp):
GTGACATTACAATGAACTCTCTCTCTCATTCTTCCAGATCTCAAAAGCCAAGGAATCGAGGAACC
TAAAACATCACTCTCATTAAACTCCCCCTCAGAATTTTCAGAACCAAAATCACCAAACCCTATAC
ATACACTCTTATTAGAACTATCCGGCGAATCCTTCATTTGTGAACCAAAAGATTCACTTGATCCA
TTGCCATATCCTTCATATGCGACATTACTATGAACTCTCACTCTCATTCTGCCAGATCTCGAACG
TGGAGAAATCAGGGAACCTAAAACATCAATATCATCAAATTTCTCCAAATTTTCAGAACACAAAT
CACAAAATGCCCTACCTTTACTCTTATTAGAACCAGAAGATTCACTTGATCCATTGCCAAATCCT
TCATAT
Found at i:112900 original size:210 final size:210
Alignment explanation
Indices: 112510--112992 Score: 598
Period size: 210 Copynumber: 2.3 Consensus size: 210
112500 TACTCTTATT
* * *
112510 AGAACCAGAAGATTCACTTGATCCATTGCCAAATCCTTCATATGTGACATTACGATGAACTCTCT
1 AGAACCAGAAGATTCACTTGATCCATTGCTAAATCCTTCATATGTGACATTACTATGAACTCTCC
* * ** * * *
112575 TCTTCATTCTTCCAGATCTCGAATGTTCAGGGATTGAGGAACCTACAACATCACTCTCATTAAAC
66 TCTTCATTCTTCCAGATCTCGAACGCTCAGAAATTGAGGAACCTAAAACATCAATATCATTAAAC
* * * *
112640 TTCTCCAAATTTTCCGAACCCAAATCCCCAAACCCTATACATGCACTCTTATTGGAACTATCC-G
131 TTCTCCAAATTTTCAGAACCCAAATCACAAAACCCTATACATGCACTCTTATTAGAACTA-CCAG
* *
112704 GCGAATCCTTCATTTG
195 ACGAATCATTCATTTG
* * * *
112720 TGAACCTGAAGATTCTCTTGATCCATTGCTATATCCTTCATATGTGACATTACTATGAACTCTCA
1 AGAACCAGAAGATTCACTTGATCCATTGCTAAATCCTTCATATGTGACATTACTATGAACTCTC-
* * * *
112785 CTC-TCGTTCTTCCAGATCTCGAACGCTGAGAAATTGAGGAACCTAAAACATTAATATCATTAGA
65 CTCTTCATTCTTCCAGATCTCGAACGCTCAGAAATTGAGGAACCTAAAACATCAATATCATTAAA
* *
112849 TTTCTCCAAATTTTCAGAACCCAAATCACAAAATCCCT-TAC-TTCTACTCTTATTAGAACTACC
130 CTTCTCCAAATTTTCAGAACCCAAATCACAAAA-CCCTATACATGC-ACTCTTATTAGAACTACC
* *
112912 ATACGAATCATTTATTTG
193 AGACGAATCATTCATTTG
* * **
112930 AGAACCAGAAGATTCACTTGAGCCATTG-TCAGATCCTTGGTATGTGACATTACTATGAACTCT
1 AGAACCAGAAGATTCACTTGATCCATTGCT-AAATCCTTCATATGTGACATTACTATGAACTCT
112993 GTCTCCCCAC
Statistics
Matches: 233, Mismatches: 35, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
209 5 0.02
210 222 0.95
211 6 0.03
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (210 bp):
AGAACCAGAAGATTCACTTGATCCATTGCTAAATCCTTCATATGTGACATTACTATGAACTCTCC
TCTTCATTCTTCCAGATCTCGAACGCTCAGAAATTGAGGAACCTAAAACATCAATATCATTAAAC
TTCTCCAAATTTTCAGAACCCAAATCACAAAACCCTATACATGCACTCTTATTAGAACTACCAGA
CGAATCATTCATTTG
Found at i:113068 original size:210 final size:208
Alignment explanation
Indices: 112510--113168 Score: 566
Period size: 210 Copynumber: 3.1 Consensus size: 208
112500 TACTCTTATT
* * * *
112510 AGAACCAGAAGATTCACTTGATCCATTGCCAAATCCTTCATATGTGACATTACGATGAACTCT-C
1 AGAACCAGAAGATTCACTTGAGCCATTGCTAGATCCTTCATATGTGACATTACTATGAACTCTAC
** ** * * ** * * *
112574 TTCTTCATTCTTCCAGATCTCGAATGTTC-AGGGATTGAGGAACCTACAACATCACTCTCATTAA
66 -TC-TC-GCCCACCAGATCTCGAACG-CCGAGAAATCGAGGAACCTAAAACATCACTCTCATTTA
* * * *
112638 ACTTCTCCAAATTTTCCGAACCCAAATCCCCAAA-CCCTATACATGC-ACTCTTATTGGAACTAT
127 ACTTCTCCAAATTTTCAGAACCCAAATCACCAAATCCCT-TAC-TTCTACTCTTATTAGAACTAT
* *
112701 CCGGCGAATCCTTCATTTG
190 CCGACGAATCATTCATTTG
* * * * *
112720 TGAACCTGAAGATTCTCTTGATCCATTGCTATATCCTTCATATGTGACATTACTATGAACTCTCA
1 AGAACCAGAAGATTCACTTGAGCCATTGCTAGATCCTTCATATGTGACATTACTATGAACTCT-A
* ** * * * * *
112785 CTCTCGTTCTTCCAGATCTCGAACGCTGAGAAATTGAGGAACCTAAAACATTAATATCA-TTAGA
65 CTCTCG-CCCACCAGATCTCGAACGCCGAGAAATCGAGGAACCTAAAACATCACTCTCATTTA-A
* *
112849 TTTCTCCAAATTTTCAGAACCCAAATCACAAAATCCCTTACTTCTACTCTTATTAGAACTA-CCA
128 CTTCTCCAAATTTTCAGAACCCAAATCACCAAATCCCTTACTTCTACTCTTATTAGAACTATCC-
* *
112913 TACGAATCATTTATTTG
192 GACGAATCATTCATTTG
**
112930 AGAACCAGAAGATTCACTTGAGCCATTG-TCAGATCCTTGGTATGTGACATTACTATGAACTCT-
1 AGAACCAGAAGATTCACTTGAGCCATTGCT-AGATCCTTCATATGTGACATTACTATGAACTCTA
* * * * **
112993 GTCTC-CCCACCTAGATCTCGAAGGCCGAGTAATCGGGGAATGTAAAACATCACTCTCATTTAAC
65 CTCTCGCCCACC-AGATCTCGAACGCCGAGAAATCGAGGAACCTAAAACATCACTCTCATTTAAC
* * * * *
113057 TTCCCCTCCAAATTTTCAGAAGCAAAACCACCAAATCCCCTA-TCTCTACTCTCATTAGAACCT-
129 TT---CTCCAAATTTTCAGAACCCAAATCACCAAATCCCTTACT-TCTACTCTTATTAGAA-CTA
** * *
113120 TGTGACGAATCCTTCATATG
189 TCCGACGAATCATTCATTTG
* * *
113140 TGAACCAGAAGGTTCACTTGATCCATTGC
1 AGAACCAGAAGATTCACTTGAGCCATTGC
113169 CAAATTCAGG
Statistics
Matches: 367, Mismatches: 64, Indels: 35
0.79 0.14 0.08
Matches are distributed among these distances:
206 3 0.01
207 39 0.11
208 7 0.02
209 8 0.02
210 301 0.82
211 8 0.02
212 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (208 bp):
AGAACCAGAAGATTCACTTGAGCCATTGCTAGATCCTTCATATGTGACATTACTATGAACTCTAC
TCTCGCCCACCAGATCTCGAACGCCGAGAAATCGAGGAACCTAAAACATCACTCTCATTTAACTT
CTCCAAATTTTCAGAACCCAAATCACCAAATCCCTTACTTCTACTCTTATTAGAACTATCCGACG
AATCATTCATTTG
Found at i:114232 original size:14 final size:14
Alignment explanation
Indices: 114215--114263 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
114205 GAACGTTCTG
* *
114215 TTATGTTCGTTCGT
1 TTATGTTCATTCAT
114229 TTATGTTCATTCAT
1 TTATGTTCATTCAT
*
114243 TTATATTCATTCAT
1 TTATGTTCATTCAT
114257 TTATGTT
1 TTATGTT
114264 TAACCCAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.18, C:0.12, G:0.10, T:0.59
Consensus pattern (14 bp):
TTATGTTCATTCAT
Found at i:115195 original size:16 final size:16
Alignment explanation
Indices: 115174--115210 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
115164 ACTCCAACGT
*
115174 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCC
115190 TTTATGTTCGTGTTCC
1 TTTATGTTCGTGTTCC
115206 TTTAT
1 TTTAT
115211 TTATTAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.14, G:0.19, T:0.59
Consensus pattern (16 bp):
TTTATGTTCGTGTTCC
Found at i:115298 original size:16 final size:16
Alignment explanation
Indices: 115277--115307 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
115267 AAAAAAATTG
115277 TTCGTTTATGTTCGTA
1 TTCGTTTATGTTCGTA
115293 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
115308 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTA
Found at i:115707 original size:20 final size:20
Alignment explanation
Indices: 115647--115707 Score: 54
Period size: 23 Copynumber: 2.9 Consensus size: 20
115637 ACGTGGTATT
*
115647 TTTTTAATT-ATTTTCTTAA
1 TTTTTAATTAATTTTATTAA
115666 TTTTTAAATTATTATTTATATT-A
1 TTTTT-AATTA--ATTT-TATTAA
115689 TTATTTAATTAATTTTATT
1 TT-TTTAATTAATTTTATT
115708 CAACTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
19 5 0.14
20 8 0.23
21 4 0.11
23 12 0.34
24 6 0.17
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAATTAATTTTATTAA
Found at i:116077 original size:22 final size:21
Alignment explanation
Indices: 116030--116081 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
116020 AAATAATTAG
*
116030 AAATTTAAATTTATTTTCTAA
1 AAATTTAAATTTAATTTCTAA
*
116051 AAATTTTAATTTCAATTT-TAA
1 AAATTTAAATTT-AATTTCTAA
116072 ATAA-TTAAAT
1 A-AATTTAAAT
116082 ACATACAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATTTAAATTTAATTTCTAA
Found at i:123848 original size:121 final size:122
Alignment explanation
Indices: 123633--123875 Score: 398
Period size: 121 Copynumber: 2.0 Consensus size: 122
123623 CGCAACTACT
* * *
123633 AGTCTAAAATTTCAAAAGAGAACAATATTCTACTTAATTATTGAAACCACTTAATGAATTATTAT
1 AGTCTAAAATCTAAAAAGAGAACAATATTCTACTTAATTATTGAAACCACTCAATGAATTATTAT
* *
123698 GAAGTCTTTAAAGACAATAGATAGTATTGTGTTAGCCGTTAAATAATGAAATCTTTA
66 GAAGTCTTTAAACACAATAGATAGTATTGTGTTAACCGTTAAATAATGAAATCTTTA
*
123755 AGTCTAAAATCTAAAAAGTGAACAATATTCTAC-TAATTATTGAAACCACTCAATGAATTATTAT
1 AGTCTAAAATCTAAAAAGAGAACAATATTCTACTTAATTATTGAAACCACTCAATGAATTATTAT
* * *
123819 GAAGTCTTTAAACACAGTAGTTAGTATTGTGTTAACCGTTGAATAATGAAATCTTTA
66 GAAGTCTTTAAACACAATAGATAGTATTGTGTTAACCGTTAAATAATGAAATCTTTA
123876 TTACATGATT
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
121 82 0.73
122 30 0.27
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (122 bp):
AGTCTAAAATCTAAAAAGAGAACAATATTCTACTTAATTATTGAAACCACTCAATGAATTATTAT
GAAGTCTTTAAACACAATAGATAGTATTGTGTTAACCGTTAAATAATGAAATCTTTA
Found at i:125138 original size:14 final size:16
Alignment explanation
Indices: 125119--125151 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
125109 AGATTAAGGT
125119 AGATAT-GAGATTG-G
1 AGATATGGAGATTGTG
125133 AGATATGGAGATTGTG
1 AGATATGGAGATTGTG
125149 AGA
1 AGA
125152 ACAATGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 7 0.41
16 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.27
Consensus pattern (16 bp):
AGATATGGAGATTGTG
Found at i:128792 original size:23 final size:21
Alignment explanation
Indices: 128748--128806 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
128738 CTAAATAATA
* *
128748 TATTTATTAAAATATATTATTTT
1 TATTTAATAAAA-ATATGA-TTT
128771 TATTTAATAAAAATATGGATTT
1 TATTTAATAAAAATAT-GATTT
*
128793 TATTGAA-AAAAATA
1 TATTTAATAAAAATA
128807 ATATAGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 7 0.22
22 13 0.41
23 12 0.38
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
TATTTAATAAAAATATGATTT
Found at i:134179 original size:17 final size:16
Alignment explanation
Indices: 134154--134211 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
134144 TGTCCGGGTC
134154 TTTTTTATTATTATTA
1 TTTTTTATTATTATTA
134170 TTTTTATATT-TATATTA
1 TTTTT-TATTAT-TATTA
*
134187 TTATTTTATTAATATTA
1 TT-TTTTATTATTATTA
134204 TATTTTTA
1 T-TTTTTA
134212 CATATTTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 6 0.17
17 26 0.72
18 4 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTATTATTATTA
Found at i:135794 original size:30 final size:30
Alignment explanation
Indices: 135733--135794 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
135723 GTAATTACTG
*
135733 TTTAGTCCTTTAAATTTATGTTTTTCTTAT
1 TTTAGTCCTTTAAATTTATGTTTTGCTTAT
*
135763 TTTAGTCCTTTAAGTTTATGTTTGTGC-TAT
1 TTTAGTCCTTTAAATTTATGTTT-TGCTTAT
135793 TT
1 TT
135795 ACATCCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.18, C:0.10, G:0.11, T:0.61
Consensus pattern (30 bp):
TTTAGTCCTTTAAATTTATGTTTTGCTTAT
Found at i:136040 original size:19 final size:19
Alignment explanation
Indices: 135999--136041 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
135989 ATTCCTTTTG
* **
135999 TATGTACTTATTTTTATGT
1 TATGTACTTATTTATATCA
*
136018 TATGTATTTATTTATATCA
1 TATGTACTTATTTATATCA
136037 TATGT
1 TATGT
136042 GAATTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (19 bp):
TATGTACTTATTTATATCA
Done.