Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000548.1 Hibiscus syriacus cultivar Beakdansim tig00001060_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: 76598
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4900 original size:16 final size:17
Alignment explanation
Indices: 4879--4911 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4869 AAGAAGTTGT
*
4879 CACCAAC-CTTCAATTC
1 CACCAACACATCAATTC
4895 CACCAACACATCAATTC
1 CACCAACACATCAATTC
4912 TCGAATCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.21
Consensus pattern (17 bp):
CACCAACACATCAATTC
Found at i:12017 original size:28 final size:28
Alignment explanation
Indices: 11977--12039 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
11967 ATTCATCCGC
11977 TTTACAATTGACAATTCTACTAACATGT
1 TTTACAATTGACAATTCTACTAACATGT
12005 TTTACAATTGACAATTCTACTAACATGT
1 TTTACAATTGACAATTCTACTAACATGT
12033 TTTACAA
1 TTTACAA
12040 CAACACTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (28 bp):
TTTACAATTGACAATTCTACTAACATGT
Found at i:14890 original size:13 final size:12
Alignment explanation
Indices: 14868--14898 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
14858 ACATTCCTTC
14868 TTTTTTTTATTT
1 TTTTTTTTATTT
14880 TTTTATTTTATTT
1 TTTT-TTTTATTT
14893 TTTTTT
1 TTTTTT
14899 AATATAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTATTT
Found at i:21490 original size:70 final size:69
Alignment explanation
Indices: 21378--21524 Score: 231
Period size: 70 Copynumber: 2.1 Consensus size: 69
21368 AAATTCGTGC
* * * * *
21378 TCTCTTCTCTGTTTTTCTTCCCCCTGTTCGAATGGATTTTCCTGAAATTGTCCTCTGTTTTGCTG
1 TCTCTCCTCTGTATTTCTTCCCCCTGTTCGAAGGGATTTTCCTGAAATTGCCCTCTATTTTGCTG
21443 ATGT
66 ATGT
*
21447 TCTCTCCTCTGGTATTTCTTTCCCCTGTTCGAAGGGATTTTCCTGAAATTGCCCTCTATTTTGCT
1 TCTCTCCTCT-GTATTTCTTCCCCCTGTTCGAAGGGATTTTCCTGAAATTGCCCTCTATTTTGCT
21512 GATGT
65 GATGT
21517 TCTCTCCT
1 TCTCTCCT
21525 TTACCTGTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
69 9 0.13
70 62 0.87
ACGTcount: A:0.11, C:0.27, G:0.16, T:0.47
Consensus pattern (69 bp):
TCTCTCCTCTGTATTTCTTCCCCCTGTTCGAAGGGATTTTCCTGAAATTGCCCTCTATTTTGCTG
ATGT
Found at i:22691 original size:36 final size:35
Alignment explanation
Indices: 22649--22764 Score: 90
Period size: 36 Copynumber: 3.2 Consensus size: 35
22639 AGGAAAATTG
22649 TCTCAAGCAAGACGAAGTAGGTTTTAAGAAAACCCA
1 TCTCAAGCAAGACGAAGTAGGTTTTAAGAAAA-CCA
** ** * ** * **
22685 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
1 TCTCAAGCAAGACGAAGTAGGTTT-TAA-GAAAACCA
22722 TCTCAAGCCAA-ACGAAGTAGGTTTTAAGAAAAACCA
1 TCTCAAG-CAAGACGAAGTAGGTTTTAAG-AAAACCA
22758 TCTCAAG
1 TCTCAAG
22765 TGAGATTCAT
Statistics
Matches: 56, Mismatches: 20, Indels: 8
0.67 0.24 0.10
Matches are distributed among these distances:
35 1 0.02
36 31 0.55
37 18 0.32
38 6 0.11
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (35 bp):
TCTCAAGCAAGACGAAGTAGGTTTTAAGAAAACCA
Found at i:22715 original size:73 final size:73
Alignment explanation
Indices: 22596--22858 Score: 325
Period size: 73 Copynumber: 3.6 Consensus size: 73
22586 TAAGAAACTT
* * *
22596 GTTTTAAGAGAAATA-C-TCTCAAGTGAGATAAATTTTGTTCCGAAGGAAAATTGTCTCAAGCAA
1 GTTTTAAGA-AAA-ACCATCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCAA
22659 GACGAAGTAG
64 GACGAAGTAG
*
22669 GTTTTAAGAAAACCCATCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCCAA-
1 GTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAG-CAAG
22733 ACGAAGTAG
65 ACGAAGTAG
** * * **
22742 GTTTTAAGAAAAACCATCTCAAGTGAGATTCATTTTGTTTCAAGGGAAAGCTGTCTCAAGTGAGA
1 GTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCAAGA
* * *
22807 TGAACTTG
66 CGAAGTAG
* * *
22815 GTTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTTGTTTCAA
1 GTTTTAAGAAAAACCATCTCAAGTGAGA-TAAATTTTGTTTCAA
22859 GATAAACTGT
Statistics
Matches: 166, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
72 5 0.03
73 147 0.89
74 14 0.08
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (73 bp):
GTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCAAGA
CGAAGTAG
Found at i:22727 original size:37 final size:37
Alignment explanation
Indices: 22612--22807 Score: 101
Period size: 37 Copynumber: 5.4 Consensus size: 37
22602 AGAGAAATAC
* * *
22612 TCTCAAGTGAGATAAATTTTGTTCCGAAGGAAAATTG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
** ** * ** * **
22649 TCTCAAGCAAGACGAAGTAGGTTT-TAA-GAAAACCCA
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAA-CTG
22685 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
** * ** * ** * * **
22722 TCTCAAGCCAAACGAAGTAGGTTT-TAAGAAAAACCA
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
** * *
22758 TCTCAAGTGAGATTCATTTTGTTTCAAGGGAAAGCTG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
22795 TCTCAAGTGAGAT
1 TCTCAAGTGAGAT
22808 GAACTTGGTT
Statistics
Matches: 106, Mismatches: 49, Indels: 8
0.65 0.30 0.05
Matches are distributed among these distances:
35 5 0.05
36 42 0.40
37 54 0.51
38 5 0.05
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (37 bp):
TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
Found at i:22901 original size:28 final size:29
Alignment explanation
Indices: 22844--22901 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
22834 CAAGGGAGAC
* *
22844 AAAACTTTGTTTCAAGATAAACTGTATCA
1 AAAACTTTGTTTCAAGAGAAACTATATCA
*
22873 AAAAC-TTGTTTCAAGAGAAACTATCTCA
1 AAAACTTTGTTTCAAGAGAAACTATATCA
22901 A
1 A
22902 GGGAGACAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (29 bp):
AAAACTTTGTTTCAAGAGAAACTATATCA
Found at i:22932 original size:15 final size:15
Alignment explanation
Indices: 22909--22940 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
22899 CAAGGGAGAC
*
22909 AGGGGAACTGTCTCA
1 AGGGAAACTGTCTCA
22924 AGGGAAACTGTCTCA
1 AGGGAAACTGTCTCA
22939 AG
1 AG
22941 AGAGACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (15 bp):
AGGGAAACTGTCTCA
Found at i:23023 original size:36 final size:36
Alignment explanation
Indices: 22921--23012 Score: 175
Period size: 36 Copynumber: 2.6 Consensus size: 36
22911 GGGAACTGTC
22921 TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
22957 TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
*
22993 TCAAGGGAAACTATCTCAAG
1 TCAAGGGAAACTGTCTCAAG
23013 CGATATAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (36 bp):
TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
Found at i:23061 original size:40 final size:40
Alignment explanation
Indices: 23017--23463 Score: 727
Period size: 40 Copynumber: 11.2 Consensus size: 40
23007 CTCAAGCGAT
* *
23017 ATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAGCGAG
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
*
23057 ATAAAATCTTCTGTTTCAAGGAAAAAACAATCTTGAGCGAG
1 ATAAAATCTTCTGTTTCAAGG-AAAAACAATCTTGAGTGAG
*
23098 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGCT-TG
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAG-TGAG
*
23138 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAATGAG
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
*
23178 ATAAAATCTTCTGTTTCAAGGAAAAATAATCTTGAGTGAG
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
* *
23218 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAATGGG
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
23258 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
*
23298 ATAAAATCTTCTGTTTCAAGGAAAAATAATCTTGAGTGAG
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
*
23338 ATAAAATCTTCTGTTTCAAGG-AAAATAATCTTGAGTGAG
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
* *
23377 ATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAATGAG
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
* * *
23417 ATAAAATCTTCTGTTTCAAGGAAAAATAATCTTGAGTCAA
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
23457 ATAAAAT
1 ATAAAAT
23464 GTCTTCTTTC
Statistics
Matches: 382, Mismatches: 21, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
39 39 0.10
40 303 0.79
41 40 0.10
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (40 bp):
ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAG
Found at i:23243 original size:20 final size:20
Alignment explanation
Indices: 23180--23243 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
23170 TGAATGAGAT
23180 AAAATCTTCTGTTTCAAGGA
1 AAAATCTTCTGTTTCAAGGA
** ** *
23200 AAAATAATCTTGAGT-GA-GA
1 AAAATCTTC-TGTTTCAAGGA
23219 TAAAATCTTCTGTTTCAAGGA
1 -AAAATCTTCTGTTTCAAGGA
23240 AAAA
1 AAAA
23244 CAATCTTGAA
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 5 0.17
20 20 0.67
21 5 0.17
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (20 bp):
AAAATCTTCTGTTTCAAGGA
Found at i:23343 original size:20 final size:20
Alignment explanation
Indices: 23320--23383 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
23310 GTTTCAAGGA
23320 AAAATAATCTTGAGTGAGAT
1 AAAATAATCTTGAGTGAGAT
** ** * *
23340 AAAATCTTC-TGTTTCA-AGG
1 AAAATAATCTTGAGTGAGA-T
23359 AAAATAATCTTGAGTGAGAT
1 AAAATAATCTTGAGTGAGAT
23379 AAAAT
1 AAAAT
23384 CTTTTGTTTC
Statistics
Matches: 29, Mismatches: 12, Indels: 6
0.62 0.26 0.13
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 16 0.55
21 1 0.03
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (20 bp):
AAAATAATCTTGAGTGAGAT
Found at i:28441 original size:55 final size:55
Alignment explanation
Indices: 28342--28488 Score: 197
Period size: 55 Copynumber: 2.7 Consensus size: 55
28332 AGCGGCCTTC
* * * * *
28342 TGTGGCGCTTGGAAAAATAATTCAGACACCCGAGA-TTATTTGACTAGTGGCCATG
1 TGTGGCG-TTCGAGAAACAATTCAGACACCCGAGATTTATTTGACTAGAGACCATG
* *
28397 TGTGGCGTTCGAGAAACAATTCGGACACCTGAGATTTATTTGACTAGAGACCATG
1 TGTGGCGTTCGAGAAACAATTCAGACACCCGAGATTTATTTGACTAGAGACCATG
* *
28452 TGTGGCGCTCGGGAAACAATTCAGACACCCGAGATTT
1 TGTGGCGTTCGAGAAACAATTCAGACACCCGAGATTT
28489 GTTAAATTAG
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 22 0.28
55 58 0.73
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (55 bp):
TGTGGCGTTCGAGAAACAATTCAGACACCCGAGATTTATTTGACTAGAGACCATG
Found at i:28506 original size:55 final size:53
Alignment explanation
Indices: 28331--28506 Score: 163
Period size: 55 Copynumber: 3.2 Consensus size: 53
28321 TTAACATAAT
* * * * * *
28331 TAGCGGCCTTCTGTGGCGCTTGGAAAAATAATTCAGACACCCGAGATTATTTGAC
1 TAGCGGCCATGTGTGGCGCTCGG-GAAACAATTCAGACACCCGAGATT-TTTAAC
* * * * * *
28386 TAGTGGCCATGTGTGGCGTTCGAGAAACAATTCGGACACCTGAGATTTATTTGAC
1 TAGCGGCCATGTGTGGCGCTCGGGAAACAATTCAGACACCCGAGA-TT-TTTAAC
* * *
28441 TAGAGACCATGTGTGGCGCTCGGGAAACAATTCAGACACCCGAGATTTGTTAAAT
1 TAGCGGCCATGTGTGGCGCTCGGGAAACAATTCAGACACCCGAGATTT-TT-AAC
28496 TAGCGGCCATG
1 TAGCGGCCATG
28507 AATGGCGCGG
Statistics
Matches: 98, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
53 1 0.01
54 22 0.22
55 75 0.77
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (53 bp):
TAGCGGCCATGTGTGGCGCTCGGGAAACAATTCAGACACCCGAGATTTTTAAC
Found at i:28590 original size:18 final size:18
Alignment explanation
Indices: 28559--28595 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28549 GTGTATCCTA
*
28559 ACAAGTTTGACCAATTTG
1 ACAAGCTTGACCAATTTG
*
28577 ACAAGCTTGGCCAATTTG
1 ACAAGCTTGACCAATTTG
28595 A
1 A
28596 TATGCAAGTG
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:0.19, G:0.19, T:0.30
Consensus pattern (18 bp):
ACAAGCTTGACCAATTTG
Found at i:38582 original size:21 final size:21
Alignment explanation
Indices: 38520--38575 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
38510 TTTTGGGTTG
38520 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
38541 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
38562 TGTGCATCGATGCA
1 TGTGCATCGATGCA
38576 CTCTCAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTGCATCGATGCATCTTCAA
Found at i:43713 original size:17 final size:17
Alignment explanation
Indices: 43691--43743 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
43681 TGAATAACGT
43691 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
43708 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
43725 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
43742 TA
1 TA
43744 ACTCTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:45017 original size:21 final size:19
Alignment explanation
Indices: 44979--45024 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
44969 AATTAATCCT
44979 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
44999 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
45020 A-TAAT
1 ACTAAT
45025 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:54784 original size:55 final size:55
Alignment explanation
Indices: 54695--54843 Score: 208
Period size: 55 Copynumber: 2.7 Consensus size: 55
54685 TATTTCACAC
* * *
54695 TTGGGGGTATCGATACACTCCTCAGTGTATTGATACACAAATAGAACTCGATGTT
1 TTGGGTGTATCGATACACTCCTCAGTGTACTGATACACAAATAGAACTCGAAGTT
* * * * * *
54750 TTGGGTGTATTGATATACTCCTCAGTGTACTGATACAGAAATGGCATTCGAAGTT
1 TTGGGTGTATCGATACACTCCTCAGTGTACTGATACACAAATAGAACTCGAAGTT
*
54805 TTGGGTGTATCGATACACTCCTCAGTGTACCGATACACA
1 TTGGGTGTATCGATACACTCCTCAGTGTACTGATACACA
54844 CTCATACAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 81 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.32
Consensus pattern (55 bp):
TTGGGTGTATCGATACACTCCTCAGTGTACTGATACACAAATAGAACTCGAAGTT
Found at i:60256 original size:12 final size:13
Alignment explanation
Indices: 60230--60259 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
60220 TGTAAATTGC
60230 ATAAAACATTAAA
1 ATAAAACATTAAA
60243 ATAAAACA-TAAA
1 ATAAAACATTAAA
60255 ATAAA
1 ATAAA
60260 TATAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAAACATTAAA
Found at i:60616 original size:55 final size:55
Alignment explanation
Indices: 60527--60669 Score: 214
Period size: 55 Copynumber: 2.6 Consensus size: 55
60517 CACACTTAGG
* *
60527 GTATCGATACACTCCTCATTGTACCGATACACAAATAGCACTCGATGTTTTGGGT
1 GTATCGATACACTCCTAAGTGTACCGATACACAAATAGCACTCGATGTTTTGGGT
* * * * *
60582 GTATTGATACACTCCTTAGTATACCGATACACAAATAGCATTCGATGTTTTTGGT
1 GTATCGATACACTCCTAAGTGTACCGATACACAAATAGCACTCGATGTTTTGGGT
*
60637 GTATCGATACACTCCTAAGTGTACTGATACACA
1 GTATCGATACACTCCTAAGTGTACCGATACACA
60670 CTCATATAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 78 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (55 bp):
GTATCGATACACTCCTAAGTGTACCGATACACAAATAGCACTCGATGTTTTGGGT
Found at i:65392 original size:17 final size:17
Alignment explanation
Indices: 65372--65474 Score: 66
Period size: 17 Copynumber: 5.9 Consensus size: 17
65362 AACTAAGTAG
65372 TTCATTAATTAAACTAA
1 TTCATTAATTAAACTAA
* * *
65389 TTCATTCATCAAACTAG
1 TTCATTAATTAAACTAA
* * *
65406 CTCATTCAAGTATAC-AA
1 TTCATT-AATTAAACTAA
*
65423 GTTCATTGAA-TAAAGTTAA
1 -TTCATT-AATTAAA-CTAA
* *
65442 TTTATTAATTAAACTAG
1 TTCATTAATTAAACTAA
*
65459 TTCATTTATTAAACTA
1 TTCATTAATTAAACTA
65475 TCTCTTAATT
Statistics
Matches: 63, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
17 41 0.65
18 20 0.32
19 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.40
Consensus pattern (17 bp):
TTCATTAATTAAACTAA
Found at i:66883 original size:18 final size:17
Alignment explanation
Indices: 66862--66897 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
66852 AAGTATTTTC
66862 AGAGTTCAAGGTATTGAG
1 AGAGTTCAAGGTA-TGAG
66880 AGAGTTCAAGGTATGAG
1 AGAGTTCAAGGTATGAG
66897 A
1 A
66898 TCGAGGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (17 bp):
AGAGTTCAAGGTATGAG
Done.