Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003655.1 Hibiscus syriacus cultivar Beakdansim tig00007773_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: 78763
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:5718 original size:53 final size:53
Alignment explanation
Indices: 5537--5836 Score: 312
Period size: 53 Copynumber: 5.8 Consensus size: 53
5527 TTCGATCAGT
* * ** * * *
5537 GGTTCACTCCCTCTTACTTCAGGGAGTAGAACTTGAACAAT-TCAT-CTTACA
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTATGCCTACG
* * * *
5588 GGTTCACT-CCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTG-C-A--
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTATGCCTACG
* * * *
5636 --TACGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACATTCTTTTGCCTACG
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTATGCCTACG
* * * *
5687 GGTTCGCTCCTTATTGCTTCAAGGAGTAGAACTCAAACAATCTTCTGCCTACG
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTATGCCTACG
* * * * *
5740 GGTTTGCTCCTTCTTACTTCAGGGAGTAGAACTCAAACAATCTTATGCATATG
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTATGCCTACG
*
5793 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTT
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTT
5837 CTGGTGTGAA
Statistics
Matches: 211, Mismatches: 29, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
46 4 0.02
47 35 0.17
48 1 0.00
49 1 0.00
50 30 0.14
51 10 0.05
53 130 0.62
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (53 bp):
GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTATGCCTACG
Found at i:5798 original size:106 final size:99
Alignment explanation
Indices: 5543--5839 Score: 355
Period size: 106 Copynumber: 2.9 Consensus size: 99
5533 CAGTGGTTCA
* * * * *
5543 CTCCCTCTTACTTCAGGGAGTAGAACTTGAACAAT-TCAT-CTTACAGGTTCACTCCTCTTGCTT
1 CTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTATGCATACGGGTTCGCTCCTCTTGCTT
*
5606 CAGGGAGTAGAACTCGAATAATCTTCTGCATACG
66 CAGGGAGTAGAACTCGAACAATCTTCTGCATACG
* * * * *
5640 CTCCCTCTTGCTTCAGGGAGTAGAACTCGAACATTCTTTTGCCTACGGGTTCGCTCCTTATTGCT
1 CTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTATGCATACGGGTTCGCTCC-TCTTGCT
* * *
5705 TCAAGGAGTAGAACTCAAACAATCTTCTGCCTACGGGTTTG
65 TCAGGGAGTAGAACTCGAACAATCTTCTGCATAC------G
* * *
5746 CTCCTTCTTACTTCAGGGAGTAGAACTCAAACAATCTTATGCATATGGGTTCGCTCCCTCTTGCT
1 CTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTATGCATACGGGTTCGCT-CCTCTTGCT
5811 TCAGGGAGTAGAACTCGAACAATCTTCTG
65 TCAGGGAGTAGAACTCGAACAATCTTCTG
5840 GTGTGAATCT
Statistics
Matches: 167, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
97 32 0.19
98 2 0.01
99 13 0.08
100 36 0.22
106 82 0.49
107 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (99 bp):
CTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTATGCATACGGGTTCGCTCCTCTTGCTT
CAGGGAGTAGAACTCGAACAATCTTCTGCATACG
Found at i:6386 original size:42 final size:42
Alignment explanation
Indices: 6271--6510 Score: 168
Period size: 42 Copynumber: 5.8 Consensus size: 42
6261 TCTTATGGAT
* * * * * *
6271 CCGAAGGATTT-ATCATCTTACTCGAGAGACTCACAAATGAC
1 CCGAAGGATTTCATCATCATGCTCGAAAGACTTACTAATGGC
* *
6312 CCGAAGGATTTAATCATCATGCTCAAAAGACTTACTAATGGC
1 CCGAAGGATTTCATCATCATGCTCGAAAGACTTACTAATGGC
* *
6354 CCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGAT
1 CCGAAGGATTTCATCATCATGCTCGAAAGACTTACTAATGG-C
** **** * * * * * **
6397 TTGCTTAACTAC-TCTTCA-G-T-G-AAGGCTTACCAATTAC
1 CCGAAGGATTTCATCATCATGCTCGAAAGACTTACTAATGGC
* * * * *
6434 CCGAAGGATTTAACCATCATGCTTGAAAGACTTACTGATGGT
1 CCGAAGGATTTCATCATCATGCTCGAAAGACTTACTAATGGC
*
6476 CCGAAGGATTTCATCATCATGCTCAAAAGACTTAC
1 CCGAAGGATTTCATCATCATGCTCGAAAGACTTAC
6511 AGATAAAACT
Statistics
Matches: 145, Mismatches: 47, Indels: 13
0.71 0.23 0.06
Matches are distributed among these distances:
37 3 0.02
38 14 0.10
39 2 0.01
40 2 0.01
41 13 0.09
42 107 0.74
43 4 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (42 bp):
CCGAAGGATTTCATCATCATGCTCGAAAGACTTACTAATGGC
Found at i:14964 original size:28 final size:28
Alignment explanation
Indices: 14911--14964 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
14901 TAGTTTAATA
* * *
14911 TAAAAATTATATACATACTTTTTATAAC
1 TAAAAATTATAAACATACTATATATAAC
14939 TAAAAATTATAAACTATA-TATATATA
1 TAAAAATTATAAAC-ATACTATATATA
14965 GTAAGATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 19 0.86
29 3 0.14
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAAAATTATAAACATACTATATATAAC
Found at i:16450 original size:22 final size:22
Alignment explanation
Indices: 16422--16498 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
16412 ACATGGCTGC
16422 TGCAACCGGGTTCGGGTCTGGT
1 TGCAACCGGGTTCGGGTCTGGT
*
16444 TGCAACCGGGTTCGGGTCTAGT
1 TGCAACCGGGTTCGGGTCTGGT
* *
16466 TGCAACCGAGTTCGGATCTGGT
1 TGCAACCGGGTTCGGGTCTGGT
*
16488 TGTAACCGGGT
1 TGCAACCGGGT
16499 CTGGGTCGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.14, C:0.22, G:0.36, T:0.27
Consensus pattern (22 bp):
TGCAACCGGGTTCGGGTCTGGT
Found at i:16517 original size:44 final size:44
Alignment explanation
Indices: 16423--16520 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
16413 CATGGCTGCT
* * * *
16423 GCAACCGGGTTCGGGTCTGGTTGCAACCGGGTTCGGGTCTAGTT
1 GCAACCGAGTTCGGATCTGGTTGCAACCGGGTTCGGGTCGAGTC
* *
16467 GCAACCGAGTTCGGATCTGGTTGTAACCGGG-TCTGGGTCGGGTC
1 GCAACCGAGTTCGGATCTGGTTGCAACCGGGTTC-GGGTCGAGTC
*
16511 GTAACCGAGT
1 GCAACCGAGT
16521 CTCACTTGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
43 2 0.04
44 44 0.96
ACGTcount: A:0.14, C:0.22, G:0.38, T:0.26
Consensus pattern (44 bp):
GCAACCGAGTTCGGATCTGGTTGCAACCGGGTTCGGGTCGAGTC
Found at i:18889 original size:20 final size:20
Alignment explanation
Indices: 18860--18912 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
18850 TGATTCAATC
* *
18860 AGTATTGATACCAAAAGGGG
1 AGTATCGATACCAAAAGGGA
*
18880 AGTATCGATACC-GAAGGGA
1 AGTATCGATACCAAAAGGGA
18899 AGGTATCGATACCA
1 A-GTATCGATACCA
18913 TTTCGAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (20 bp):
AGTATCGATACCAAAAGGGA
Found at i:19002 original size:20 final size:22
Alignment explanation
Indices: 18962--19006 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
18952 ATAATATATG
18962 TACCATAGTATGGTAGTATCGA
1 TACCATAGTATGGTAGTATCGA
*
18984 TACCATGGTAT-GT-GTATCGA
1 TACCATAGTATGGTAGTATCGA
19004 TAC
1 TAC
19007 TGAGGAGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
21 2 0.09
22 10 0.45
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (22 bp):
TACCATAGTATGGTAGTATCGA
Found at i:24699 original size:19 final size:19
Alignment explanation
Indices: 24671--24713 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
24661 CATTTCCCCT
*
24671 TATACGTATAGTGAGCTTC
1 TATACATATAGTGAGCTTC
*
24690 TATACATATAGTGAGTTTC
1 TATACATATAGTGAGCTTC
24709 TATAC
1 TATAC
24714 GTACTTCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (19 bp):
TATACATATAGTGAGCTTC
Found at i:25200 original size:17 final size:16
Alignment explanation
Indices: 25184--25225 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
25174 AAAGGAAAAG
25184 GAAATAAAAAAATAAA
1 GAAATAAAAAAATAAA
*
25200 GAAATAAAGAAAATGAA
1 GAAATAAA-AAAATAAA
25217 GAAATAAAA
1 GAAATAAAA
25226 GAAAGGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
GAAATAAAAAAATAAA
Found at i:25218 original size:9 final size:9
Alignment explanation
Indices: 25180--25229 Score: 52
Period size: 8 Copynumber: 5.8 Consensus size: 9
25170 TCAAAAAGGA
*
25180 AAAGGAAAT
1 AAAGAAAAT
25189 AAA-AAAAT
1 AAAGAAAAT
25197 AAAG-AAAT
1 AAAGAAAAT
25205 AAAGAAAAT
1 AAAGAAAAT
*
25214 GAAG-AAAT
1 AAAGAAAAT
25222 AAAAGAAA
1 -AAAGAAA
25230 GGGGTTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
8 19 0.56
9 13 0.38
10 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (9 bp):
AAAGAAAAT
Found at i:27299 original size:83 final size:82
Alignment explanation
Indices: 27195--27476 Score: 343
Period size: 83 Copynumber: 3.4 Consensus size: 82
27185 GGCGACCTTG
*
27195 AATCCGAAGAAGCAAGATCATTCCAAAATTTGACATCCTCAAACAAATGAGCAAATCATTTTAAC
1 AATCCGAAGGAGCAAGATCATTCCAAAATTTGACATCCTCAAACAAATGAGCAAATCATTTTAAC
* *
27260 AGTTACTTGGAGTCCTCG
66 A-TGACTTGGAGTCCTCA
* * * * * *
27278 AATCCGAAGGAGCAAGATCATTCCCAGATTTGGCATCCTGAAACAAAGGTGCAAATCATTTTAAC
1 AATCCGAAGGAGCAAGATCATTCCAAAATTTGACATCCTCAAACAAATGAGCAAATCATTTTAAC
27343 AATGACTTGGCA-TCCTCA
66 -ATGACTTGG-AGTCCTCA
* * *
27361 AATTCGAAGGAGCAAGATCATTCCCATATTTGGA-ATCCTCAAACAAATGAGCAAATCATTTTAA
1 AATCCGAAGGAGCAAGATCATTCCAAAATTT-GACATCCTCAAACAAATGAGCAAATCATTTTAA
*
27425 CTATGACTTGGCGTCCTCA
65 C-ATGACTTGGAGTCCTCA
** * *
27444 AATTTGAATGAGCAAGATCGTTCTCAAAATTTG
1 AATCCGAAGGAGCAAGATCATTC-CAAAATTTG
27477 GCGTCCCTAG
Statistics
Matches: 172, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
83 163 0.95
84 9 0.05
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (82 bp):
AATCCGAAGGAGCAAGATCATTCCAAAATTTGACATCCTCAAACAAATGAGCAAATCATTTTAAC
ATGACTTGGAGTCCTCA
Found at i:27354 original size:42 final size:42
Alignment explanation
Indices: 27228--27445 Score: 148
Period size: 42 Copynumber: 5.2 Consensus size: 42
27218 CAAAATTTGA
* * *
27228 CATCCTCAAACAAATGAGCAAATCATTTTAACAGTTACTTGG
1 CATCCTCAAACAAAGGAGCAAATCATTTTAACAATGACTTGG
* * * * *
27270 -AGTCCTCGAATCCGAAGGAGCAAGATCA--TT-CCCA-GATTTGG
1 CA-TCCTC-AA-ACAAAGGAGCAA-ATCATTTTAACAATGACTTGG
* *
27311 CATCCTGAAACAAAGGTGCAAATCATTTTAACAATGACTTGG
1 CATCCTCAAACAAAGGAGCAAATCATTTTAACAATGACTTGG
* * * *
27353 CATCCTCAAATTCGAAGGAGCAAGATCA--TT-CCCAT-ATTTGG
1 CATCCTCAAA--CAAAGGAGCAA-ATCATTTTAACAATGACTTGG
* * *
27394 AATCCTCAAACAAATGAGCAAATCATTTTAACTATGACTTGG
1 CATCCTCAAACAAAGGAGCAAATCATTTTAACAATGACTTGG
*
27436 CGTCCTCAAA
1 CATCCTCAAA
27446 TTTGAATGAG
Statistics
Matches: 131, Mismatches: 29, Indels: 32
0.68 0.15 0.17
Matches are distributed among these distances:
38 8 0.06
39 18 0.14
40 6 0.05
41 29 0.22
42 38 0.29
43 6 0.05
44 18 0.14
45 8 0.06
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (42 bp):
CATCCTCAAACAAAGGAGCAAATCATTTTAACAATGACTTGG
Found at i:27400 original size:41 final size:40
Alignment explanation
Indices: 27266--27420 Score: 111
Period size: 41 Copynumber: 3.8 Consensus size: 40
27256 TAACAGTTAC
* * *
27266 TTGGAGTCCTCGAATCCGAAGGAGCAAGATCATTCCCAGAT
1 TTGGAATCCTCAAAT-CGAAGGAGCAAGATCATTCCCATAT
* * * * * * *
27307 TTGGCATCCTGAAA-CAAAGGTGCAA-ATCATTTTAACAATGAC
1 TTGGAATCCTCAAATCGAAGGAGCAAGATCA--TT-CCCAT-AT
*
27349 TTGGCATCCTCAAATTCGAAGGAGCAAGATCATTCCCATAT
1 TTGGAATCCTCAAA-TCGAAGGAGCAAGATCATTCCCATAT
* *
27390 TTGGAATCCTCAAA-CAAATGAGCAA-ATCATT
1 TTGGAATCCTCAAATCGAAGGAGCAAGATCATT
27421 TTAACTATGA
Statistics
Matches: 88, Mismatches: 19, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
38 10 0.11
39 18 0.20
40 2 0.02
41 26 0.30
42 17 0.19
43 2 0.02
44 9 0.10
45 4 0.05
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (40 bp):
TTGGAATCCTCAAATCGAAGGAGCAAGATCATTCCCATAT
Found at i:34402 original size:24 final size:24
Alignment explanation
Indices: 34370--34415 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
34360 TGTTCCTCAC
*
34370 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCCCTCTTCTTCGA
*
34394 TGCTTCCTCTTCCCTCTTCTTC
1 TGCTTCCTCGTCCCTCTTCTTC
34416 TCCAACCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.02, C:0.41, G:0.09, T:0.48
Consensus pattern (24 bp):
TGCTTCCTCGTCCCTCTTCTTCGA
Found at i:39531 original size:24 final size:24
Alignment explanation
Indices: 39499--39544 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
39489 TGTTCCTCAC
*
39499 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCCCTCTTCTTCGA
*
39523 TGCTTCCTCTTCCCTCTTCTTC
1 TGCTTCCTCGTCCCTCTTCTTC
39545 TCCAACCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.02, C:0.41, G:0.09, T:0.48
Consensus pattern (24 bp):
TGCTTCCTCGTCCCTCTTCTTCGA
Found at i:41789 original size:60 final size:60
Alignment explanation
Indices: 41647--41811 Score: 170
Period size: 60 Copynumber: 2.8 Consensus size: 60
41637 ACTTTAATTT
* * * * *
41647 TAAATTGGTCTTCAAACTTTTAAAGATTCCAATTTCATCCTCAAACTATGAATCTCATTC
1 TAAATTGGTCCTCAAACTTTTGAACATTCTAATTTCATCCTCAAACTATGAACCTCATTC
*** * * *
41707 TAAATCAATCCTTAAACTTTTGAACATTCTAATTTCATACCT-AAACTATGACCCTCTTTC
1 TAAATTGGTCCTCAAACTTTTGAACATTCTAATTTCAT-CCTCAAACTATGAACCTCATTC
* * * * *
41767 TAAATTGGTCCCCAAACATTTGAATATTTTAATTTCATCCCCAAA
1 TAAATTGGTCCTCAAACTTTTGAACATTCTAATTTCATCCTCAAA
41812 TTCATGTAAA
Statistics
Matches: 83, Mismatches: 20, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
59 2 0.02
60 78 0.94
61 3 0.04
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (60 bp):
TAAATTGGTCCTCAAACTTTTGAACATTCTAATTTCATCCTCAAACTATGAACCTCATTC
Found at i:46509 original size:31 final size:30
Alignment explanation
Indices: 46473--46530 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
46463 CTTTTTCCTT
* *
46473 GTAGGATATTCAAAGAGACATATCTTTTCAA
1 GTAGGAAATTC-AAGAAACATATCTTTTCAA
*
46504 GTAGGAAATTCAAGAAACATGTCTTTT
1 GTAGGAAATTCAAGAAACATATCTTTT
46531 GAAGAACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (30 bp):
GTAGGAAATTCAAGAAACATATCTTTTCAA
Found at i:51543 original size:46 final size:45
Alignment explanation
Indices: 51413--51545 Score: 194
Period size: 45 Copynumber: 2.9 Consensus size: 45
51403 TTTTTCTTAT
* *
51413 CAATATATTTACCATTTATCCCATAAGCTCGTAAGCTTATTATAC
1 CAATATAATTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* * *
51458 CAATATAATTACCATTTATTCTATAAGCTCGTAAGCTTATTTTTC
1 CAATATAATTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
51503 CAATATACTTACAATTTAATCCCATAAGCTCGTAAGCTTATTT
1 CAATATAATTACCATTT-ATCCCATAAGCTCGTAAGCTTATTT
51546 GCATGGTTAC
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 55 0.71
46 23 0.29
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (45 bp):
CAATATAATTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:51753 original size:59 final size:59
Alignment explanation
Indices: 51659--51780 Score: 165
Period size: 59 Copynumber: 2.1 Consensus size: 59
51649 CTAACCTGAG
** *
51659 TATGACACATAAGGTCGTGCCCACCAACTGTACTAGGTATTCTTAAGTGCAGTCCCAAA
1 TATGACACATAAGGTCGTGCCCACCAACTACACTAGGTATCCTTAAGTGCAGTCCCAAA
* * * *
51718 TATGACACATAAGGTCGTGCCCACCATA-TACACTAGGTATCCTTTAGTGTATTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCA-ACTACACTAGGTATCCTTAAGTGCAGTCCCAAA
51777 TATG
1 TATG
51781 CAGCCTGCTG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 54 0.98
60 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCAACTACACTAGGTATCCTTAAGTGCAGTCCCAAA
Found at i:53554 original size:45 final size:44
Alignment explanation
Indices: 53490--53586 Score: 176
Period size: 45 Copynumber: 2.2 Consensus size: 44
53480 ACCATTAATA
*
53490 TTATTTTCCAACATTTAAAAATGTGAAAATAATATTTTTTTTTTC
1 TTATTTTCCAACATTTAAAAATGTGAAAATAATA-TTTTATTTTC
53535 TTATTTTCCAACATTTAAAAATGTGAAAATAATATTTTATTTTC
1 TTATTTTCCAACATTTAAAAATGTGAAAATAATATTTTATTTTC
53579 TTATTTTC
1 TTATTTTC
53587 GTGACCCATT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 17 0.33
45 34 0.67
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (44 bp):
TTATTTTCCAACATTTAAAAATGTGAAAATAATATTTTATTTTC
Found at i:55439 original size:5 final size:5
Alignment explanation
Indices: 55429--55487 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
55419 ATTTTTTTTC
* * *
55429 TTCTT TTCTT TTCTT TTCTTT TTCTA TT-TT CTGTT TTCTTT TTCCTT
1 TTCTT TTCTT TTCTT TTC-TT TTCTT TTCTT TTCTT TTC-TT TT-CTT
55476 TTCTT TT-TT TTC
1 TTCTT TTCTT TTC
55488 ATATATATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
4 6 0.14
5 24 0.55
6 13 0.30
7 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:55460 original size:7 final size:6
Alignment explanation
Indices: 55420--55483 Score: 64
Period size: 6 Copynumber: 10.8 Consensus size: 6
55410 GCATCTCTCA
55420 TTTTT- TTTCTTC -TTTTC -TTTTC -TTTTC TTTTTC TATTTTC TGTTTTC
1 TTTTTC TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC T-TTTTC
*
55467 TTTTTC CTTTTC TTTTT
1 TTTTTC TTTTTC TTTTT
55484 TTTCATATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
5 16 0.31
6 24 0.46
7 12 0.23
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:58620 original size:2 final size:2
Alignment explanation
Indices: 58613--58670 Score: 77
Period size: 2 Copynumber: 30.5 Consensus size: 2
58603 AAATTAAGTA
58613 AT AT AT AT AT AT AT AT -T AT AT -T AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
58652 AT AT GT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
58671 GGTTATAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:58677 original size:25 final size:24
Alignment explanation
Indices: 58633--58681 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
58623 ATATATTATA
*
58633 TTATATATATATATAATATATATGT
1 TTATATATATATAGAATATA-ATGT
**
58658 TTATATATATATAGGTTATAATGT
1 TTATATATATATAGAATATAATGT
58682 AAGTGCATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (24 bp):
TTATATATATATAGAATATAATGT
Found at i:59417 original size:23 final size:23
Alignment explanation
Indices: 59385--59474 Score: 126
Period size: 23 Copynumber: 3.9 Consensus size: 23
59375 ATCTTATATG
59385 GCACTACGGTGCATTTCTACACT
1 GCACTACGGTGCATTTCTACACT
*
59408 GCACTTCGGTGCATTTCTACACT
1 GCACTACGGTGCATTTCTACACT
* *
59431 GCACTTCGGTGCAATTCTACACT
1 GCACTACGGTGCATTTCTACACT
* **
59454 ACACTACACTGCATTTCTACA
1 GCACTACGGTGCATTTCTACA
59475 ATGGATTAGT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (23 bp):
GCACTACGGTGCATTTCTACACT
Found at i:60256 original size:19 final size:19
Alignment explanation
Indices: 60232--60278 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
60222 CATTTAATGC
60232 ATCGATGCATAAGGAGTGA
1 ATCGATGCATAAGGAGTGA
*
60251 ATCGATGCATAAGGAGTGC
1 ATCGATGCATAAGGAGTGA
60270 ATCGATGCA
1 ATCGATGCA
60279 CATGTTAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (19 bp):
ATCGATGCATAAGGAGTGA
Found at i:62319 original size:12 final size:12
Alignment explanation
Indices: 62302--62340 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
62292 CGTAGGTTAC
62302 AGAAGCGAGAAG
1 AGAAGCGAGAAG
62314 AGAAGCGAGAAG
1 AGAAGCGAGAAG
62326 AGAAGCGAAGAAG
1 AGAAGCG-AGAAG
62339 AG
1 AG
62341 CAAGACAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.51, C:0.08, G:0.41, T:0.00
Consensus pattern (12 bp):
AGAAGCGAGAAG
Found at i:63437 original size:21 final size:21
Alignment explanation
Indices: 63412--63451 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
63402 TTTAAAATGT
63412 GTATCGATGCACAGCTACAGA
1 GTATCGATGCACAGCTACAGA
*
63433 GTATCGATGCACTGCTACA
1 GTATCGATGCACAGCTACA
63452 ATAACTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
GTATCGATGCACAGCTACAGA
Found at i:63967 original size:46 final size:45
Alignment explanation
Indices: 63835--63967 Score: 203
Period size: 45 Copynumber: 2.9 Consensus size: 45
63825 AATTTCTTAT
*
63835 CAATATATTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATAATTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* * *
63880 TAATATAATAACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATAATTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
63925 CAATATACTTACCATTTAATCCCATAAGCTCATAAGCTTATTT
1 CAATATAATTACCATTT-ATCCCATAAGCTCGTAAGCTTATTT
63968 GCACGATTAC
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 55 0.71
46 23 0.29
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (45 bp):
CAATATAATTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:64202 original size:59 final size:59
Alignment explanation
Indices: 64083--64204 Score: 154
Period size: 59 Copynumber: 2.1 Consensus size: 59
64073 CTAACCCGAG
* ** * *
64083 TATGACACATAAGGTCGTGCCCACCATCTGTACTAGGTATCCTTAAGTACAGTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAGTCCAGAA
* * ** *
64142 TATGACATATAAGGTCGTGCCCACCATATACAATAGGTATCCTTTAGTGTATTCCAGAA
1 TATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAGTCCAGAA
64201 TATG
1 TATG
64205 CAGCCTACTG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAGTCCAGAA
Found at i:64532 original size:23 final size:24
Alignment explanation
Indices: 64492--64539 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
64482 AGTCTTCCCG
64492 ATGATGTATAAAAAATCTATGTAC
1 ATGATGTATAAAAAATCTATGTAC
64516 ATGATGTAT-AAAAATCTATGTAC
1 ATGATGTATAAAAAATCTATGTAC
64539 A
1 A
64540 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAAAATCTATGTAC
Found at i:66062 original size:30 final size:30
Alignment explanation
Indices: 66036--66094 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
66026 TTTGGTCCTT
* *
66036 AAACTTT-TCAAAGTTTATACTTTGGTCACC
1 AAACTTTACCAAA-TTTATAATTTGGTCACC
66066 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATTTATAATTTGGTCAC
66095 TAATTAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTTGGTCACC
Found at i:66982 original size:46 final size:45
Alignment explanation
Indices: 66852--66983 Score: 203
Period size: 44 Copynumber: 2.9 Consensus size: 45
66842 AATTTCTTAT
* *
66852 CAATATATTTACCATTTATCCTATAAGCTCATAAGCTTATTTTAC
1 CAATATAATTACCATTTATCCCATAAGCTCATAAGCTTATTTTAC
* *
66897 CAATATAATTACCA-TTATTCCATAAGCTCATAAGCTTATTTTTC
1 CAATATAATTACCATTTATCCCATAAGCTCATAAGCTTATTTTAC
*
66941 CAATATACTTACCATTTAATCCCATAAGCTCATAAGCTTATTT
1 CAATATAATTACCATTT-ATCCCATAAGCTCATAAGCTTATTT
66984 GTATGGTTAC
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
44 40 0.51
45 15 0.19
46 24 0.30
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (45 bp):
CAATATAATTACCATTTATCCCATAAGCTCATAAGCTTATTTTAC
Found at i:69083 original size:22 final size:23
Alignment explanation
Indices: 69040--69085 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
69030 AGTCTTCCCG
*
69040 ATGATGTATAAACATCTATGTAC
1 ATGATGTATAAACACCTATGTAC
69063 ATGATGTATAAA-ACCTATGTAC
1 ATGATGTATAAACACCTATGTAC
69085 A
1 A
69086 ATGTTATGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (23 bp):
ATGATGTATAAACACCTATGTAC
Found at i:70695 original size:30 final size:29
Alignment explanation
Indices: 70627--70702 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
70617 TTAATTTTTT
* *
70627 AAAATTATATTTTGGTCCCTAAACTTTTC
1 AAAATTATAATTTGGTCCCTAAACTTTCC
* *
70656 AAAGTTTATACTTTGGTCACC-AAACTTTACC
1 AAA-ATTATAATTTGGTC-CCTAAACTTT-CC
70687 AAAATTATAATTTGGT
1 AAAATTATAATTTGGT
70703 TACTAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 3 0.08
30 30 0.77
31 6 0.15
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (29 bp):
AAAATTATAATTTGGTCCCTAAACTTTCC
Found at i:76998 original size:17 final size:18
Alignment explanation
Indices: 76976--77009 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
76966 TATGTTATTT
76976 AATTATTA-AAAATATAA
1 AATTATTATAAAATATAA
76993 AATTATTATAAAATATA
1 AATTATTATAAAATATA
77010 TTATTTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTATTATAAAATATAA
Found at i:77018 original size:41 final size:42
Alignment explanation
Indices: 76955--77056 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
76945 TTTAGTTTTA
*
76955 TATTATTAAAATATGTTA-TTTAA-TTATTAAAA-AT-ATAAAAT
1 TATTA-TAAAATATATTATTTTAACTT-TTAAAATATAAT-AAAT
76996 TATTATAAAATATATTATTTTAACCTTTTAAAATATAATAAAT
1 TATTATAAAATATATTATTTTAA-CTTTTAAAATATAATAAAT
*
77039 AATTAT-AAATATATTATT
1 TATTATAAAATATATTATT
77057 ATAAAATATT
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
40 11 0.20
41 10 0.19
42 18 0.33
43 13 0.24
44 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (42 bp):
TATTATAAAATATATTATTTTAACTTTTAAAATATAATAAAT
Found at i:77057 original size:14 final size:13
Alignment explanation
Indices: 77040--77095 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
77030 ATAATAAATA
77040 ATTATAAATATATT
1 ATTATAAA-ATATT
77054 ATTATAAAATATT
1 ATTATAAAATATT
* *
77067 ATT-TTAATTATT
1 ATTATAAAATATT
77079 -TT-TAAAATATT
1 ATTATAAAATATT
*
77090 AATATA
1 ATTATA
77096 TTCGGATCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 9 0.26
12 8 0.23
13 10 0.29
14 8 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTATAAAATATT
Found at i:77943 original size:21 final size:22
Alignment explanation
Indices: 77899--77943 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
77889 CACCGAAGTG
*
77899 CCACATAGAATGTCCCCAAGGA
1 CCACATAGAATGTCCCCAAAGA
*
77921 CCACATAG-ATGTCCCGAAAGA
1 CCACATAGAATGTCCCCAAAGA
77942 CC
1 CC
77944 GCGTAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.36, C:0.33, G:0.18, T:0.13
Consensus pattern (22 bp):
CCACATAGAATGTCCCCAAAGA
Found at i:77950 original size:21 final size:22
Alignment explanation
Indices: 77891--77996 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
77881 TAAAATTGCA
*
77891 CCGAAGTG-CCACATAGAATGTC
1 CCGAAG-GACCACGTAGAATGTC
* *
77913 CCCAAGGACCACATAG-ATGTC
1 CCGAAGGACCACGTAGAATGTC
* * **
77934 CCGAAAGACCGCGTAGAAAATC
1 CCGAAGGACCACGTAGAATGTC
* *
77956 CTGAATGACCACGTAGAATTGTC
1 CCGAAGGACCACGTAGAA-TGTC
*
77979 CCGAAGGACCGCGTAGAA
1 CCGAAGGACCACGTAGAA
77997 CCCTCGACCC
Statistics
Matches: 66, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
21 18 0.27
22 31 0.47
23 17 0.26
ACGTcount: A:0.34, C:0.27, G:0.24, T:0.15
Consensus pattern (22 bp):
CCGAAGGACCACGTAGAATGTC
Found at i:77951 original size:43 final size:45
Alignment explanation
Indices: 77911--77996 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
77901 ACATAGAATG
77911 TCCCCAAGGACCACATAG-A-TGTCCCGAAAGACCGCGTAGAAAA
1 TCCCCAAGGACCACATAGAATTGTCCCGAAAGACCGCGTAGAAAA
** * * *
77954 TCCTGAATGACCACGTAGAATTGTCCCGAAGGACCGCGTAGAA
1 TCCCCAAGGACCACATAGAATTGTCCCGAAAGACCGCGTAGAA
77997 CCCTCGACCC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 14 0.39
44 1 0.03
45 21 0.58
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (45 bp):
TCCCCAAGGACCACATAGAATTGTCCCGAAAGACCGCGTAGAAAA
Done.