Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005691.1 Hibiscus syriacus cultivar Beakdansim tig00013312_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: 71358
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:228 original size:19 final size:19
Alignment explanation
Indices: 184--227 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
174 AATGTCGAGT
184 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
203 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
222 T-ATTTT
1 TAATTTT
228 TTTATGTGAT
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:1098 original size:196 final size:199
Alignment explanation
Indices: 309--1904 Score: 2738
Period size: 196 Copynumber: 8.1 Consensus size: 199
299 TTAAGGGTCA
* *
309 TGTCGATACTAATATAGTTT-TGTCGA-AATTTTTTTCCAGAATGAATT-AAAACAAGGTGCACG
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT----G
371 CACCCAT-AAGTGTCGATCCATATATAAAAAGTGTCGAT-CCAAAATCATCGAACCC-AAAGTAT
62 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
433 AATGTAATATGTAA-TTTTTAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCT
127 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
496 AAATAATG
192 AAATAATG
*
504 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
*
568 AATAAAGTGTCGATCCATATAT--AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT-
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
630 TAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
695 AATG
196 AATG
699 TGTCGACACTAATA-AGTTTGTGTCGATATTTTTTTTTCCAGAATGAATTAAAAACAAGGTGCA-
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGAATTAAAAACAAGGTGCAC
762 CC----A-TGTCG-TCCATATTAATAAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTAT
65 CCATAAAGTGTCGATCCATA-T-AT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
*
820 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGATTTTATGAGAGAAT-AGTCT
127 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
884 AAATAATG
192 AAATAATG
892 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
957 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1021 T-ATATGTAATTTTTTAATCTAA-CGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1084 AATG
196 AATG
1088 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCA-C
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1152 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1217 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1282 AATG
196 AATG
1286 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
*
1350 CATAAAGTGTCGATCCTATATAAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCC-ATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1415 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1480 TAATG
195 TAATG
*
1485 TGTCGACACTAA-ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCA-C
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1548 CATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
1612 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1677 AATG
196 AATG
*
1681 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1745 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
1810 TAATATGTAA-TTTTCAA--TAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1872 AATG
196 AATG
*
1876 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1905 CTAATTTAAA
Statistics
Matches: 1350, Mismatches: 16, Indels: 70
0.94 0.01 0.05
Matches are distributed among these distances:
189 6 0.00
190 6 0.00
191 3 0.00
192 11 0.01
193 103 0.08
194 164 0.12
195 211 0.16
196 350 0.26
197 144 0.11
198 179 0.13
199 167 0.12
200 6 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:1649 original size:395 final size:395
Alignment explanation
Indices: 309--1904 Score: 2765
Period size: 395 Copynumber: 4.1 Consensus size: 395
299 TTAAGGGTCA
* *
309 TGTCGATACTAATATAGTTT-TGTCGA-AATTTTTTTCCAGAATGAATT-AAAACAAGGTGCACG
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCAC-
*
371 CACCCATAAGTGTCGATCCATATATAAAAAGTGTCGAT-CCAAAATCATCGAACCCAAAGTATAA
65 CA--TA-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAGTATAA
435 TGTAATATGTAA-TTTTTAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAA
127 TGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
498 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGT
192 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGT
* *
563 GCATCAATAAAGTGTCGATCCATATAT--AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
257 GCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
*
626 TAAT-TAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
322 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
690 TAAATAATG
387 TAAATAATG
699 TGTCGACACTAATA-AGTTTGTGTCGATATTTTTTTTTCCAGAATGAATTAAAAACAAGGTGCAC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGAATTAAAAACAAGGTGCAC
763 C----A-TGTCG-TCCATATTAATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAGTATAA
65 CATAAAGTGTCGATCCATA-T-AT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAGTATAA
*
822 TGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGATTTTATGAGAGAAT-AGTCTAA
127 TGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
886 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGG
192 ATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGG
951 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGT
256 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
*
1015 ATAATGT-ATATGTAATTTTTTAATCTAA-CGGTACAATTATACCGGTTTTATGAGAGAATAAGT
321 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
1078 CTAAATAATG
386 CTAAATAATG
1088 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1153 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATGT
1218 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
130 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
1283 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCA
195 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCA
*
1348 CCCATAAAGTGTCGATCCTATATAAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
260 CCCATAAAGTGTCGATCC-ATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
*
1413 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
324 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
1478 AATAATG
389 AATAATG
*
1485 TGTCGACACTAA-ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1549 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATGT
* *
1613 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
130 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
*
1678 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGAATGAATTAAAAACAAGGTGCA
195 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCA
1743 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
260 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
*
1808 TGTAATATGTAA-TTTTCAA--TAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
325 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
1870 ATAATG
390 ATAATG
*
1876 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1905 CTAATTTAAA
Statistics
Matches: 1161, Mismatches: 17, Indels: 54
0.94 0.01 0.04
Matches are distributed among these distances:
383 6 0.01
384 6 0.01
385 3 0.00
386 13 0.01
387 38 0.03
388 68 0.06
389 171 0.15
390 77 0.07
391 76 0.07
392 66 0.06
393 139 0.12
394 127 0.11
395 221 0.19
396 93 0.08
397 57 0.05
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (395 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAGTATAATGTA
ATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAA
TGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCAC
CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATG
Found at i:3389 original size:3 final size:3
Alignment explanation
Indices: 3368--3451 Score: 60
Period size: 3 Copynumber: 28.0 Consensus size: 3
3358 TGAAGCTGAC
* * * * * * ** *
3368 GAT GAA GAT GAC GAC GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * *
3416 GAT GCT GAC GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3452 CCAAACAAGT
Statistics
Matches: 60, Mismatches: 21, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:3403 original size:42 final size:42
Alignment explanation
Indices: 3356--3438 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
3346 GGTCGCAGAA
3356 GATGAAGCTGACGATGAAGATGAC-GACGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATG-CTGACGATGATGATGATGAC
*
3398 GATGAAGCTGGCGATGAAGATGCTGACGATGATGATGATGA
1 GATGAAGCTGACGATGAAGATGCTGACGATGATGATGATGA
3439 TGAAGATGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.34, C:0.11, G:0.35, T:0.20
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGCTGACGATGATGATGATGAC
Found at i:3451 original size:12 final size:12
Alignment explanation
Indices: 3356--3447 Score: 58
Period size: 12 Copynumber: 6.9 Consensus size: 12
3346 GGTCGCAGAA
*
3356 GATGAAGCTGAC
1 GATGAAGATGAC
3368 GATGAAGATGACGAC
1 GATGAAGAT---GAC
3383 GATGATGATGATGAC
1 GATGA--A-GATGAC
* *
3398 GATGAAGCTGGC
1 GATGAAGATGAC
3410 GATGAAGATGCTGAC
1 GATGAAGA---TGAC
* *
3425 GATGATGATGAT
1 GATGAAGATGAC
3437 GATGAAGATGA
1 GATGAAGATGA
3448 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
12 32 0.51
13 1 0.02
15 26 0.41
17 1 0.02
18 3 0.05
ACGTcount: A:0.35, C:0.10, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:3451 original size:15 final size:15
Alignment explanation
Indices: 3364--3450 Score: 87
Period size: 15 Copynumber: 6.2 Consensus size: 15
3354 AAGATGAAGC
3364 TGACGATGAAGATGA
1 TGACGATGAAGATGA
* *
3379 CGACGATGATGATGA
1 TGACGATGAAGATGA
*
3394 TGACGATGAAGCTG-
1 TGACGATGAAGATGA
*
3408 -G-CGATGAAGATGC
1 TGACGATGAAGATGA
3421 TGACGAT---GATGA
1 TGACGATGAAGATGA
*
3433 TGATGATGAAGATGA
1 TGACGATGAAGATGA
3448 TGA
1 TGA
3451 TCCAAACAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
12 20 0.34
13 1 0.02
14 1 0.02
15 36 0.62
ACGTcount: A:0.34, C:0.09, G:0.34, T:0.22
Consensus pattern (15 bp):
TGACGATGAAGATGA
Found at i:5460 original size:184 final size:184
Alignment explanation
Indices: 4912--5560 Score: 1175
Period size: 184 Copynumber: 3.6 Consensus size: 184
4902 CTTTCAACAT
** * *
4912 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATA
4977 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
5042 AA--TGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAA-CCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
5093 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCCAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATA
5158 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
5222 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
5276 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCCAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATA
5341 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
5406 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
5460 ATTATAATGTAATAGATAATTTTGTAATATAACCGG--TAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATA
5523 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTC
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTC
5561 AGAAACGTTT
Statistics
Matches: 455, Mismatches: 9, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
180 44 0.10
181 82 0.18
182 106 0.23
183 92 0.20
184 131 0.29
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:13298 original size:19 final size:20
Alignment explanation
Indices: 13274--13317 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
13264 GTCATCCAAT
*
13274 TTTTTAAA-CCCATACCGGA
1 TTTTTAAACCCCAAACCGGA
*
13293 TTTTTAAACCCCAAATCGGA
1 TTTTTAAACCCCAAACCGGA
13313 TTTTT
1 TTTTT
13318 TTCGGGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (20 bp):
TTTTTAAACCCCAAACCGGA
Found at i:16567 original size:16 final size:16
Alignment explanation
Indices: 16546--16580 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
16536 ACACTTTACG
16546 TCATTCACCTATTAAC
1 TCATTCACCTATTAAC
16562 TCATTCACCTATTAAC
1 TCATTCACCTATTAAC
16578 TCA
1 TCA
16581 CTTTAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (16 bp):
TCATTCACCTATTAAC
Found at i:20364 original size:2 final size:2
Alignment explanation
Indices: 20357--20387 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20347 GATCATGCCC
20357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20388 AAGAAAGCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27990 original size:11 final size:10
Alignment explanation
Indices: 27974--28019 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
27964 TTGTTATGGT
27974 TTGTTATTAG
1 TTGTTATTAG
27984 CTTGTTATTAG
1 -TTGTTATTAG
*
27995 TTGTTATTATT
1 TTGTTATTA-G
28006 TTGTTA-TAG
1 TTGTTATTAG
28015 TTGTT
1 TTGTT
28020 GGTTACTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 5 0.16
10 11 0.34
11 16 0.50
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.63
Consensus pattern (10 bp):
TTGTTATTAG
Found at i:27998 original size:21 final size:20
Alignment explanation
Indices: 27964--28019 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
27954 ATGTTAGAGT
*
27964 TTGTTATGGTTTGTTATTAGC
1 TTGTTATAG-TTGTTATTAGC
**
27985 TTGTTATTAGTTGTTATTATT
1 TTGTTA-TAGTTGTTATTAGC
28006 TTGTTATAGTTGTT
1 TTGTTATAGTTGTT
28020 GGTTACTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.26
21 21 0.68
22 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.20, T:0.62
Consensus pattern (20 bp):
TTGTTATAGTTGTTATTAGC
Found at i:29338 original size:14 final size:14
Alignment explanation
Indices: 29319--29367 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
29309 TTATGTTTGT
29319 TTATGTTCGTTCGG
1 TTATGTTCGTTCGG
29333 TTATGTTCG-T---
1 TTATGTTCGTTCGG
29343 TTATGTTCGTTCGG
1 TTATGTTCGTTCGG
29357 TTATGTTCGTT
1 TTATGTTCGTT
29368 TATGTTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.29
11 1 0.03
13 1 0.03
14 20 0.65
ACGTcount: A:0.08, C:0.12, G:0.24, T:0.55
Consensus pattern (14 bp):
TTATGTTCGTTCGG
Found at i:29387 original size:24 final size:24
Alignment explanation
Indices: 29302--29374 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
29292 CGTTCGTGAA
*
29302 CGTTCGGTTATGTTTGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
29326 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
29350 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
29374 C
1 C
29375 ATTCATTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.55
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:30484 original size:16 final size:15
Alignment explanation
Indices: 30463--30513 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
30453 GTCTCCAACG
30463 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTT-A
*
30479 TTTATGTTCGTGTTTG
1 TTTATGTTCGTG-TTA
30495 TTTATGTTCGT-TTA
1 TTTATGTTCGTGTTA
30509 TTTAT
1 TTTAT
30514 TAAATGAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 7 0.22
16 23 0.72
17 2 0.06
ACGTcount: A:0.12, C:0.08, G:0.18, T:0.63
Consensus pattern (15 bp):
TTTATGTTCGTGTTA
Found at i:34231 original size:21 final size:21
Alignment explanation
Indices: 34207--34249 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
34197 AAAAGATTAA
*
34207 TATTGTGTTAGTTCACGATAC
1 TATTGTGTCAGTTCACGATAC
*
34228 TATTGTGTCAGTTCATGATAC
1 TATTGTGTCAGTTCACGATAC
34249 T
1 T
34250 GACGTGGCGA
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:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (21 bp):
TATTGTGTCAGTTCACGATAC
Found at i:34263 original size:21 final size:21
Alignment explanation
Indices: 34239--34285 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
34229 ATTGTGTCAG
* *
34239 TTCATGATACTGACGTGGCGA
1 TTCATGATACTGACGTGACAA
* *
34260 TTCACGATGCTGACGTGACAA
1 TTCATGATACTGACGTGACAA
34281 TTCAT
1 TTCAT
34286 CTGTCATGTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (21 bp):
TTCATGATACTGACGTGACAA
Done.