Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001335.1 Hibiscus syriacus cultivar Beakdansim tig00002608_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: 78298
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1323 original size:14 final size:17
Alignment explanation
Indices: 1289--1324 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
1279 TTTCATAGAA
1289 CCTTTATCACATTTGAT
1 CCTTTATCACATTTGAT
1306 CCTTTAT-A-ATTT-AT
1 CCTTTATCACATTTGAT
1320 CCTTT
1 CCTTT
1325 CCTTTCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.37
15 4 0.21
16 1 0.05
17 7 0.37
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (17 bp):
CCTTTATCACATTTGAT
Found at i:5349 original size:24 final size:24
Alignment explanation
Indices: 5322--5402 Score: 89
Period size: 23 Copynumber: 3.5 Consensus size: 24
5312 CAGCTCGTAT
5322 AAATTGCACCGAAGTGCCACATAG
1 AAATTGCACCGAAGTGCCACATAG
* * *
5346 AAATTATC-CCGAAG-GACCGCGTAG
1 AAATT-GCACCGAAGTG-CCACATAG
5370 AAA-TGCACCGAAGTGCCACATAG
1 AAATTGCACCGAAGTGCCACATAG
5393 -AATTGCACCG
1 AAATTGCACCG
5403 TAGGGCCATA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
22 3 0.07
23 21 0.46
24 21 0.46
25 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCCACATAG
Found at i:5864 original size:27 final size:28
Alignment explanation
Indices: 5820--5878 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
5810 TTATTCTTAT
5820 ATCATCATATATATTTCATCTATGTATC
1 ATCATCATATATATTTCATCTATGTATC
*
5848 ATCAT-ATATATATTTCATCTATGTTTC
1 ATCATCATATATATTTCATCTATGTATC
5875 ATCA
1 ATCA
5879 CCTAACCTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.32, C:0.17, G:0.03, T:0.47
Consensus pattern (28 bp):
ATCATCATATATATTTCATCTATGTATC
Found at i:6507 original size:20 final size:20
Alignment explanation
Indices: 6482--6519 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6472 TTTCATTTAG
6482 GGGGGAATC-GATACCCCCCA
1 GGGGGAATCTG-TACCCCCCA
6502 GGGGGAATCTGTACCCCC
1 GGGGGAATCTGTACCCCC
6520 TGCACAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.21, C:0.34, G:0.32, T:0.13
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCCA
Found at i:9835 original size:28 final size:28
Alignment explanation
Indices: 9795--9849 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
9785 TTACATCATC
9795 ATGTTGAATCATTGAGAATCAAATGATG
1 ATGTTGAATCATTGAGAATCAAATGATG
9823 ATGTTGAATCATTGAGAATCAAATGAT
1 ATGTTGAATCATTGAGAATCAAATGAT
9850 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (28 bp):
ATGTTGAATCATTGAGAATCAAATGATG
Found at i:15712 original size:30 final size:28
Alignment explanation
Indices: 15689--15743 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
15679 CGGTGATCGG
15689 TATATTTACCGATCTAACACCGGTCAGAT
1 TATATTTACCGATCTAACACCGGT-AGAT
* *
15718 TATATTTCCCGATCTAACACCCGTAG
1 TATATTTACCGATCTAACACCGGTAG
15744 CAGTAAAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (28 bp):
TATATTTACCGATCTAACACCGGTAGAT
Found at i:17282 original size:35 final size:34
Alignment explanation
Indices: 17197--17283 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
17187 ATTTGGTATT
*
17197 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
17231 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
17269 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
17284 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:17511 original size:6 final size:6
Alignment explanation
Indices: 17495--17557 Score: 54
Period size: 6 Copynumber: 10.5 Consensus size: 6
17485 ACTCCTCGCT
* * * * **
17495 GTCATC ATCATC GTCATC GTCGTC GTCATC GTCGTC ATCGCC GTCATC
1 GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC
**
17543 ACCATC GTCATC GTC
1 GTCATC GTCATC GTC
17558 GTCCTAAGTA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.16, C:0.37, G:0.17, T:0.30
Consensus pattern (6 bp):
GTCATC
Found at i:17524 original size:21 final size:21
Alignment explanation
Indices: 17495--17560 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
17485 ACTCCTCGCT
17495 GTCATCATCATCGTCATCGTC
1 GTCATCATCATCGTCATCGTC
* * *
17516 GTCGTCATCGTCGTCATCGCC
1 GTCATCATCATCGTCATCGTC
*
17537 GTCATCACCATCGTCATCGTC
1 GTCATCATCATCGTCATCGTC
17558 GTC
1 GTC
17561 CTAAGTAGGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.15, C:0.36, G:0.18, T:0.30
Consensus pattern (21 bp):
GTCATCATCATCGTCATCGTC
Found at i:17560 original size:9 final size:9
Alignment explanation
Indices: 17502--17542 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
17492 GCTGTCATCA
*
17502 TCATCGTCA
1 TCATCGTCG
*
17511 TCGTCGTCG
1 TCATCGTCG
17520 TCATCGTCG
1 TCATCGTCG
*
17529 TCATCGCCG
1 TCATCGTCG
17538 TCATC
1 TCATC
17543 ACCATCGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.12, C:0.37, G:0.20, T:0.32
Consensus pattern (9 bp):
TCATCGTCG
Found at i:20629 original size:111 final size:111
Alignment explanation
Indices: 20487--20819 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
20477 ATTACAAAAA
20487 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
20552 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTCGAGATGT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
20598 TTAATTCTTAATCTAATAATCATGGATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
20663 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATATCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* *
20709 TTAATTCTTCATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
20774 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
20820 ATGATTTTCA
Statistics
Matches: 211, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 211 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:20981 original size:10 final size:10
Alignment explanation
Indices: 20945--20986 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
20935 CTTAAAAAGA
*
20945 GAGAGTATTT
1 GAGAGAATTT
*
20955 GAGATAAATTT
1 GAGA-GAATTT
20966 -AGAGAATTT
1 GAGAGAATTT
20975 GAGAGAATTT
1 GAGAGAATTT
20985 GA
1 GA
20987 TGTGATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 5 0.19
10 18 0.67
11 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.33
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:25869 original size:235 final size:234
Alignment explanation
Indices: 25450--25921 Score: 766
Period size: 235 Copynumber: 2.0 Consensus size: 234
25440 AATATTTAAA
* *
25450 AATAGAAAAGGTCATAAATATACCAATGATGTTTAATTTGCGGCAATATTTCAAAAATGGGTTGG
1 AATAAAAAAGGTCATAAATATACCAATGATGATTAATTTGCGGCAATATTTCAAAAATGGGTTGG
* * *
25515 CCAATTGTACGAAAGTTCAACTTTTGCACGAAATCTAGTTTATTCCACTTGTGTTCTTAGTTATC
66 CCAATTGTACGAAAGTTCAACTTTTGCACCAAATCTAGCTTATTCCACATGTGTTCTTAGTTATC
** *
25580 CAACACCCTTGAACTAATCTAGCTTTTATATTAAACACTTTATTTTCGTATCTTCCTAAGCCCTC
131 CAACACCCTTGAACTAATCTAGCTTTTATATTAAACACTTTATTGCCATATCTTCCTAAGCCCTC
* *
25645 CGTCCAATCTCTTACTCTTTTTTTTCATTAGTTAAAATAG
196 CATCCAATCCCTTAC-CTTTTTTTTCATTAGTTAAAATAG
25685 AATAAAAAAGGTCATAAATATACCAATGATGATTAATTTGCGGCAATATTGT-AAAAATGGGTTG
1 AATAAAAAAGGTCATAAATATACCAATGATGATTAATTTGCGGCAATATT-TCAAAAATGGGTTG
* * * *
25749 TCCAATTGTACGAAAGTTCAACTTTTGCACCAAGTCTTGCTTCTTCCACATGTGTTCTTAGTTAT
65 GCCAATTGTACGAAAGTTCAACTTTTGCACCAAATCTAGCTTATTCCACATGTGTTCTTAGTTAT
* *
25814 CCAACACCCTTGAACTAATCTTGCTTTTATATTAAACACTTTATTGCCATATCTTCCTATGCCCT
130 CCAACACCCTTGAACTAATCTAGCTTTTATATTAAACACTTTATTGCCATATCTTCCTAAGCCCT
*
25879 CCATCCAATCCCTTACGTTTTTTTTCATTAGTTAAAATAG
195 CCATCCAATCCCTTACCTTTTTTTTCATTAGTTAAAATAG
25919 AAT
1 AAT
25922 TGTTACCCCA
Statistics
Matches: 219, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
234 26 0.12
235 192 0.88
236 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (234 bp):
AATAAAAAAGGTCATAAATATACCAATGATGATTAATTTGCGGCAATATTTCAAAAATGGGTTGG
CCAATTGTACGAAAGTTCAACTTTTGCACCAAATCTAGCTTATTCCACATGTGTTCTTAGTTATC
CAACACCCTTGAACTAATCTAGCTTTTATATTAAACACTTTATTGCCATATCTTCCTAAGCCCTC
CATCCAATCCCTTACCTTTTTTTTCATTAGTTAAAATAG
Found at i:26551 original size:39 final size:39
Alignment explanation
Indices: 26491--26590 Score: 168
Period size: 39 Copynumber: 2.6 Consensus size: 39
26481 ACATAGCATA
26491 AGGA-CCTGCGGTAAGGACTTACCCTGAGCACAAAG-CTG
1 AGGAGCCTGCGGTAAGGACTTACCCTGAGCACAAAGTC-G
*
26529 AGGAGCTTGCGGTAAGGACTTACCCTGAGCACAAAGTCG
1 AGGAGCCTGCGGTAAGGACTTACCCTGAGCACAAAGTCG
26568 AGGAGCCTGCGGTAAGGACTTAC
1 AGGAGCCTGCGGTAAGGACTTAC
26591 AAGTCATAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
38 4 0.07
39 53 0.91
40 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.31, T:0.17
Consensus pattern (39 bp):
AGGAGCCTGCGGTAAGGACTTACCCTGAGCACAAAGTCG
Found at i:28406 original size:226 final size:227
Alignment explanation
Indices: 27996--28474 Score: 670
Period size: 226 Copynumber: 2.1 Consensus size: 227
27986 GTGTGACAAG
27996 AATAGAAAAAAAA-TCATAAATATACCAATGATGATTAATTTGCGGCAATATTGTAAAAATGGGT
1 AATAGAAAAAAAAGTCATAAATATACCAATGATGATTAATTTGCGGCAATATTGTAAAAATGGGT
28060 TGGCCAATTGTACGAAGTTCAACTTTTGCACCAAATCCTGCTTCTTCCACTTGTGTTCTTAGTTA
66 TGGCCAATTGTACGAAGTTCAACTTTTGCACCAAATCCTGCTTCTTCCACTTGTGTTCTTAGTTA
** * * * * * *
28125 TTGAACACCCTTGGACTAATCTAGCTTTTATATTAAACCCTTTATTTTTGTATCTTCCTAAGTCC
131 TCCAACACCCTTGAACTAATATAACTTGTATATTAAACCCTTTATTTTCGTATCTTCCTAAGCCC
28190 TCCGA-CCAATC-C-C-TTTTTTCATTACTTAA
196 TCC-ATCCAATCACTCTTTTTTTCATTACTTAA
* *
28219 AATAGAATAAAAAAGGTCATAAATATACGAATGATGTTTAATTTGCGGCAATATT-TAAAAAATG
1 AATAGAA-AAAAAA-GTCATAAATATACCAATGATGATTAATTTGCGGCAATATTGT-AAAAATG
* *
28283 GGTTGGCCAATTGTACGGAAGTTTAACTTTTGCACCAAATCTTGCTTCTTCCACTTGTGTTCTTA
63 GGTTGGCCAATTGTAC-GAAGTTCAACTTTTGCACCAAATCCTGCTTCTTCCACTTGTGTTCTTA
* *
28348 GTTATCCAACACCCTTGAACTAATATAACTTGTATATT-AACACC-TTCTTTTCGTATCTTCCTG
127 GTTATCCAACACCCTTGAACTAATATAACTTGTATATTAAAC-CCTTTATTTTCGTATCTTCCTA
28411 AGCCCTCCATCCAATCACTTACTTTTTTTTTCATTACTTAA
191 AGCCCTCCATCCAATCAC-T-C--TTTTTTTCATTACTTAA
*
28452 AATAGAAAAAGAAG-CATAAATAT
1 AATAGAAAAAAAAGTCATAAATAT
28475 TGCTGAATTG
Statistics
Matches: 227, Mismatches: 15, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
223 7 0.03
224 6 0.03
225 2 0.01
226 92 0.41
227 81 0.36
230 10 0.04
231 1 0.00
232 5 0.02
233 23 0.10
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (227 bp):
AATAGAAAAAAAAGTCATAAATATACCAATGATGATTAATTTGCGGCAATATTGTAAAAATGGGT
TGGCCAATTGTACGAAGTTCAACTTTTGCACCAAATCCTGCTTCTTCCACTTGTGTTCTTAGTTA
TCCAACACCCTTGAACTAATATAACTTGTATATTAAACCCTTTATTTTCGTATCTTCCTAAGCCC
TCCATCCAATCACTCTTTTTTTCATTACTTAA
Found at i:29896 original size:80 final size:80
Alignment explanation
Indices: 29758--29910 Score: 243
Period size: 80 Copynumber: 1.9 Consensus size: 80
29748 CGGCTAGTGG
*
29758 TATTGACGATGATGGAAAACAAGCACAGTGGAAGACATAAAAGAAGATGAAGATGATAATTGGAA
1 TATTGACGATGATGGAAAACAAGCACAGTGGAAGACATAAAAGAAGATGAAGAAGATAATTGGAA
29823 GAAGATAAATACAAT
66 GAAGATAAATACAAT
* * ** * *
29838 TATTGACGATGATGGACAAGAAGGTCAGTGGGAGATATAAAAGAAGATGAAGAAGATAATTGGAA
1 TATTGACGATGATGGAAAACAAGCACAGTGGAAGACATAAAAGAAGATGAAGAAGATAATTGGAA
29903 GAAGATAA
66 GAAGATAA
29911 CTGCAATACA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.48, C:0.06, G:0.27, T:0.19
Consensus pattern (80 bp):
TATTGACGATGATGGAAAACAAGCACAGTGGAAGACATAAAAGAAGATGAAGAAGATAATTGGAA
GAAGATAAATACAAT
Found at i:37611 original size:31 final size:31
Alignment explanation
Indices: 37573--37648 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
37563 TAAGACGACC
*
37573 CTTGGGTAGGCTCTGAGGTCCCGAGGACTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGGACTTT
* * *
37604 CTTGGGTAGGCCCCGATGCCCCGAGGACTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGGACTTT
*
37635 CTCGGGTAGGCTCT
1 CTTGGGTAGGCTCT
37649 CAGACCCCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.12, C:0.28, G:0.34, T:0.26
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGAGGCCCCGAGGACTTT
Found at i:39401 original size:2 final size:2
Alignment explanation
Indices: 39394--39445 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
39384 CACGTATTGC
39394 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
39436 AT AT AT AT AT
1 AT AT AT AT AT
39446 TAAAATTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42374 original size:15 final size:15
Alignment explanation
Indices: 42354--42395 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
42344 GTTGTTGGGT
42354 TTTTTTAATAATTTA
1 TTTTTTAATAATTTA
* **
42369 TTTTTTATTTTTTTA
1 TTTTTTAATAATTTA
42384 TTTTTTAA-AATT
1 TTTTTTAATAATT
42396 CTCAAAATTA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTAATAATTTA
Found at i:48343 original size:21 final size:21
Alignment explanation
Indices: 48317--48358 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48307 AATTCGAAAA
*
48317 TGCTTAGTTATTTTAGCATTT
1 TGCTTAATTATTTTAGCATTT
* *
48338 TGCTTAATTTTTTTAGGATTT
1 TGCTTAATTATTTTAGCATTT
48359 GATTATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.07, G:0.14, T:0.60
Consensus pattern (21 bp):
TGCTTAATTATTTTAGCATTT
Found at i:49019 original size:39 final size:39
Alignment explanation
Indices: 48963--49041 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
48953 TTACCGCTTT
* *
48963 CCACAAACTCCTTTGCTTTGTGCGC-AGGATAAGACCTTA
1 CCACAAACTCCTATGCTTTGTGCACAAGG-TAAGACCTTA
* *
49002 CCACAGACTCCTATGCTTTGTGCACAAGGTAAGCCCTTA
1 CCACAAACTCCTATGCTTTGTGCACAAGGTAAGACCTTA
49041 C
1 C
49042 TGGGTGTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.91
40 3 0.09
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (39 bp):
CCACAAACTCCTATGCTTTGTGCACAAGGTAAGACCTTA
Found at i:54598 original size:16 final size:16
Alignment explanation
Indices: 54579--54612 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54569 CAATATACGA
54579 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
54595 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
54611 AT
1 AT
54613 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:54685 original size:16 final size:18
Alignment explanation
Indices: 54653--54686 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
54643 TATTAATGTA
54653 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
54671 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
54687 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:55358 original size:130 final size:130
Alignment explanation
Indices: 55154--55401 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
55144 AATTTTCTTC
* *
55154 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** * *
55219 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGAACAAATTGATAGCATATATAAA
* *
55284 TAATTAGGTGGTGACATGTGTCACCAATGACACATGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
55349 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGAACAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGAACAAATTGAT
55402 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGAACAAATTGATAGCATATATAAA
Found at i:55857 original size:35 final size:35
Alignment explanation
Indices: 55796--55869 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
55786 AATTGAATTT
* * *
55796 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGAAAATTAGGGTTTAGAATGA
*
55831 AATTGAATTACTTTGAAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGAAAATTAGGGTTTAGAATGA
55866 AATT
1 AATT
55870 AAGGACTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AATTGAATTACTTTGAAAATTAGGGTTTAGAATGA
Found at i:57855 original size:78 final size:77
Alignment explanation
Indices: 57699--58039 Score: 248
Period size: 78 Copynumber: 4.3 Consensus size: 77
57689 CGTGATGTTA
* * *
57699 ATCCAACTC-TTTATGTGATGGA-CGAGCAAAGGTTGAACAAGTTCATCTCATTATGAACTTCTT
1 ATCCAACTCATTT-TGTGATGAATCGAGC-AAGGTTGAACAAGTTCTTCTCATTATGAACTTGTT
**
57762 CT-TTGGAAATATTG
64 -TATCAGAAATATTG
* * *
57776 ATTCATCTCATTTTGTGATGAATCGAGCAAGGGTTGAACAAGTTCTTCTCATTATGAACCTGTTT
1 ATCCAACTCATTTTGTGATGAATCGAGCAA-GGTTGAACAAGTTCTTCTCATTATGAACTTGTTT
* *
57841 ATCAGAATTGTTG
65 ATCAGAAATATTG
* * * ** * *
57854 ATCCAACTCTTTTTGTGATGGACTAGAGCAAAATAGTGAACAAGTTTTTTTCATTATGAACTTGT
1 ATCCAACTCATTTTGTGAT-GAATCGAGCAAGGT--TGAACAAGTTCTTCTCATTATGAACTTG-
*
57919 TTTATCAGAAATACTG
62 TTTATCAGAAATATTG
* * * * * *
57935 ATCCAACTCCTTCTT-TGATAGACTCGAGGAAAATGG-TGAATAAGTTTTTCTCATTATGAATTT
1 ATCCAACTCATT-TTGTGAT-GAATCGA-G-CAA-GGTTGAACAAGTTCTTCTCATTATGAACTT
* *
57998 CTTCT-TCAGAAAGATTG
61 GTT-TATCAGAAATATTG
*
58015 ATCC-ACTC-TTCTGTGATAGAATCGA
1 ATCCAACTCATTTTGTGAT-GAATCGA
58040 ACGAATTGAT
Statistics
Matches: 213, Mismatches: 37, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
77 19 0.09
78 76 0.36
79 13 0.06
80 41 0.19
81 59 0.28
82 3 0.01
83 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (77 bp):
ATCCAACTCATTTTGTGATGAATCGAGCAAGGTTGAACAAGTTCTTCTCATTATGAACTTGTTTA
TCAGAAATATTG
Found at i:57968 original size:81 final size:80
Alignment explanation
Indices: 57810--58039 Score: 259
Period size: 81 Copynumber: 2.9 Consensus size: 80
57800 GAGCAAGGGT
* * * * * *
57810 TGAACAAGTTCTTCTCATTATGAACCTG-TTTATCAGAATTGTTGATCCAACTCTTTTTGTGATG
1 TGAACAAGTTTTTCTCATTATGAACTTGTTTTATCAGAAATATTGATCCAACTCTTCTT-TGATA
*
57874 GACTAGAGCAAAATAG
65 GACTCGAGCAAAATAG
* *
57890 TGAACAAGTTTTTTTCATTATGAACTTGTTTTATCAGAAATACTGATCCAACTCCTTCTTTGATA
1 TGAACAAGTTTTTCTCATTATGAACTTGTTTTATCAGAAATATTGATCCAACT-CTTCTTTGATA
* *
57955 GACTCGAGGAAAATGG
65 GACTCGAGCAAAATAG
* * * * * *
57971 TGAATAAGTTTTTCTCATTATGAATTTCTTCT-TCAGAAAGATTGATCC-ACTCTTCTGTGATAG
1 TGAACAAGTTTTTCTCATTATGAACTTGTTTTATCAGAAATATTGATCCAACTCTTCTTTGATAG
*
58034 AATCGA
66 ACTCGA
58040 ACGAATTGAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
78 16 0.12
79 3 0.02
80 39 0.30
81 65 0.51
82 5 0.04
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (80 bp):
TGAACAAGTTTTTCTCATTATGAACTTGTTTTATCAGAAATATTGATCCAACTCTTCTTTGATAG
ACTCGAGCAAAATAG
Found at i:59955 original size:29 final size:29
Alignment explanation
Indices: 59917--59988 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
59907 TTTTCTTCCC
*
59917 TCTTTATTTTT-TTTGCTCTTTGTCTCT-TTT
1 TCTTT-TTTTTCTTT-CTCTTT-TCTCTATAT
*
59947 TCTTTTTTTTCTTTTTCTTTTCTCTATAT
1 TCTTTTTTTTCTTTCTCTTTTCTCTATAT
*
59976 TCTTTTCTTTCTT
1 TCTTTTTTTTCTT
59989 GTTATTTTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.14
29 24 0.65
30 8 0.22
ACGTcount: A:0.04, C:0.18, G:0.03, T:0.75
Consensus pattern (29 bp):
TCTTTTTTTTCTTTCTCTTTTCTCTATAT
Found at i:59969 original size:20 final size:20
Alignment explanation
Indices: 59944--59999 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
59934 CTTTGTCTCT
59944 TTTTCTTTTTTTTCTTTTTC
1 TTTTCTTTTTTTTCTTTTTC
* * *
59964 TTTTCTCTATATTC-TTTTC
1 TTTTCTTTTTTTTCTTTTTC
59983 -TTTCTTGTTATTTTCTT
1 TTTTCTT-TT-TTTTCTT
60000 CAAGCATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
18 5 0.19
19 6 0.22
20 15 0.56
21 1 0.04
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTTTTTCTTTTTC
Found at i:62546 original size:22 final size:22
Alignment explanation
Indices: 62501--62562 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
62491 CCGTTGACTT
*
62501 GGTCAGA--GTTGACTGTTGATC
1 GGTCAGACCGTTGACT-TTGACC
*
62522 GGTCAGTCCGTTGACTTTGACC
1 GGTCAGACCGTTGACTTTGACC
*
62544 GGTCTGACCGTTGACTTTG
1 GGTCAGACCGTTGACTTTG
62563 TCCAAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.17
22 22 0.63
23 7 0.20
ACGTcount: A:0.15, C:0.21, G:0.31, T:0.34
Consensus pattern (22 bp):
GGTCAGACCGTTGACTTTGACC
Found at i:63549 original size:27 final size:28
Alignment explanation
Indices: 63511--63569 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
63501 ATTATAGAAC
* *
63511 TACCCTTGAAGTGTAAAATGA-CTAAAA
1 TACCCCTGAAGTGAAAAATGACCTAAAA
*
63538 TACCCCTGAAGTGAAAAATGACCTAAAG
1 TACCCCTGAAGTGAAAAATGACCTAAAA
63566 TACC
1 TACC
63570 TCTAAACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.22
Consensus pattern (28 bp):
TACCCCTGAAGTGAAAAATGACCTAAAA
Found at i:64279 original size:57 final size:57
Alignment explanation
Indices: 64191--64318 Score: 229
Period size: 57 Copynumber: 2.2 Consensus size: 57
64181 TATGCAAAAG
*
64191 ATCCTTAATACCTCATTTGGTTCAATTGGACTTAAAATCCTAATAATTCAATTCATA
1 ATCCTGAATACCTCATTTGGTTCAATTGGACTTAAAATCCTAATAATTCAATTCATA
*
64248 ATCCTGAATACCTCATTTGGTTCAATTGGACTTAAAATCCTAATAATTTAATTCATA
1 ATCCTGAATACCTCATTTGGTTCAATTGGACTTAAAATCCTAATAATTCAATTCATA
*
64305 ATCTTGAATACCTC
1 ATCCTGAATACCTC
64319 TTATTGTTGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 68 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (57 bp):
ATCCTGAATACCTCATTTGGTTCAATTGGACTTAAAATCCTAATAATTCAATTCATA
Found at i:65187 original size:30 final size:31
Alignment explanation
Indices: 65151--65226 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
65141 TAAGGTGACC
* *
65151 CTTGGGTAGGCTCTA-GATCCCGAGAT-CTTT
1 CTTGGGTAGGCTCTATGA-CCCCAAATACTTT
* *
65181 CTTGGGTAGGCCCCATGACCCCAAATAACTTT
1 CTTGGGTAGGCTCTATGACCCCAAAT-ACTTT
65213 CTTGGGTAGGCTCT
1 CTTGGGTAGGCTCT
65227 CGGGCCCCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 19 0.51
31 2 0.05
32 16 0.43
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.30
Consensus pattern (31 bp):
CTTGGGTAGGCTCTATGACCCCAAATACTTT
Found at i:67279 original size:17 final size:17
Alignment explanation
Indices: 67259--67293 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
67249 CCCGTTGAGC
67259 TGACCAAATCATTGACT
1 TGACCAAATCATTGACT
67276 TGACCAAATCATTGACT
1 TGACCAAATCATTGACT
67293 T
1 T
67294 TGATCAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (17 bp):
TGACCAAATCATTGACT
Found at i:69173 original size:24 final size:23
Alignment explanation
Indices: 69109--69176 Score: 100
Period size: 24 Copynumber: 2.9 Consensus size: 23
69099 CATAATTTAG
*
69109 GTCAGATATCATAACAAAATCCA
1 GTCAGATATCATAACAGAATCCA
69132 GTTCAGATATCATAACAGAATCCA
1 G-TCAGATATCATAACAGAATCCA
*
69156 TGTCAGGTATCATAACAGAAT
1 -GTCAGATATCATAACAGAAT
69177 TCAAATCGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.02
24 39 0.95
25 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (23 bp):
GTCAGATATCATAACAGAATCCA
Found at i:73614 original size:157 final size:155
Alignment explanation
Indices: 73328--73634 Score: 501
Period size: 157 Copynumber: 2.0 Consensus size: 155
73318 TAAAATTCAG
*
73328 AAACCATAGTAATCCCTCCAGCTCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
1 AAACCATAGTAATCCCTCCAACTCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
* *
73393 CTATCACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTATAGTTCCTCCAACAA
66 CTATCACATCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTACAAGTATAGTTCCTCCAACAA
73458 TAGCCCCCCAAATAAAACATTTATCAA
131 TA--CCCCCAAATAAAACATTTATCAA
* *
73485 AAACCATAGTAATCCCTCCAAC-CAAACACGTCATAATGTGTAGGTTCCCCATAACCATACACCC
1 AAACCATAGTAATCCCTCCAACTC-AACACATCATAATGTGTAGGTTCCCCAGAACCATACACCC
* *
73549 ACTCTCACATCCAGTAAGGCCCTGAGCACAAAGTCGAGGAGCCTACAAGTATTA-TTCCTCCAAC
65 ACTATCACATCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTACAAGTA-TAGTTCCTCCAAC
73613 AATACCCCCAAATAAAACATTT
129 AATACCCCCAAATAAAACATTT
73635 TCCATCCGTA
Statistics
Matches: 141, Mismatches: 7, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
155 18 0.13
156 1 0.01
157 120 0.85
158 2 0.01
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.20
Consensus pattern (155 bp):
AAACCATAGTAATCCCTCCAACTCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
CTATCACATCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTACAAGTATAGTTCCTCCAACAA
TACCCCCAAATAAAACATTTATCAA
Found at i:73693 original size:24 final size:24
Alignment explanation
Indices: 73661--73748 Score: 77
Period size: 24 Copynumber: 3.7 Consensus size: 24
73651 TATATCAAAA
* * *
73661 ATCAAAACATAATTCAGGTCATAT
1 ATCATAACATAATTCAGATCAGAT
* *
73685 ATCATAACAAAATCCAGATCAGAT
1 ATCATAACATAATTCAGATCAGAT
* * * ** *
73709 ATCAGAACAGAATACATTTCAGGT
1 ATCATAACATAATTCAGATCAGAT
73733 ATCATAACATAATTCA
1 ATCATAACATAATTCA
73749 AATCGGAACA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.26
Consensus pattern (24 bp):
ATCATAACATAATTCAGATCAGAT
Found at i:75388 original size:22 final size:22
Alignment explanation
Indices: 75360--75404 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
75350 GGTATTTTTA
75360 TAATTTCACCTAACTGAAGTAT
1 TAATTTCACCTAACTGAAGTAT
75382 TAATTTCACCTAACTGAAGTAT
1 TAATTTCACCTAACTGAAGTAT
75404 T
1 T
75405 CTCTTAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (22 bp):
TAATTTCACCTAACTGAAGTAT
Found at i:77264 original size:17 final size:17
Alignment explanation
Indices: 77242--77282 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
77232 TAAGCATATC
77242 TTAAAAA-ATGAAAAAAA
1 TTAAAAAGA-GAAAAAAA
*
77259 TTAAAAAGAGAAATAAA
1 TTAAAAAGAGAAAAAAA
77276 TTAAAAA
1 TTAAAAA
77283 TAATACATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (17 bp):
TTAAAAAGAGAAAAAAA
Done.