Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003776.1 Hibiscus syriacus cultivar Beakdansim tig00008085_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: 72698
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3134 original size:3 final size:3
Alignment explanation
Indices: 3126--3153 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3116 TTTTGACAAG
3126 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
3154 AACCCTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:35443 original size:201 final size:192
Alignment explanation
Indices: 35088--35483 Score: 540
Period size: 201 Copynumber: 2.0 Consensus size: 192
35078 ATTTGGAAAA
* **
35088 GCTCGTGAAAGATATCATTGGTGATTTTCTTCACACTCTGCATCCAGCATTTTATATTAGCTAGC
1 GCTCATGAAAGATATCATTGGTGATTTTCTTCACACAATGCATCCAGCATTTTATATTAGCTAGC
* * ** * * ** *
35153 TCGTTAATTTTGTTTTTTTTTTCCATCCATGGTTTATTTATATGCTTTTACATTTGAATCCAATC
66 CCGTTAACTTTGGGTTTTTTTCCCATCCATGATTTATGCATATGCTTTTACATTTGAATCCAATA
** *
35218 GCTGTTCTATCAACTTCTTTCCGGGAAAGAAGTTGATGCAGGTTTTGGTTCTTTATTAGAAGT
131 GCTGTTCTATCAACTTCTTTCCGGGAAAGAAGAAGATGCAGGTTTTGGTTCTCTATT-GAAGT
* *
35281 GCTCATGAAAGATATCATTGGTGATTTTCTTCACACAATGCATTCAGTATTTTATATTATTAGCT
1 GCTCATGAAAGATATCATTGGTGATTTTCTTCACACAATGCATCCAGCA-TTT-TA-TATTAGCT
*
35346 AGCCCGTTAACTTTGGGTTTTTTTCCCATCCATATATGATTTATGCATATTCTTTTTACATTTGA
63 AGCCCGTTAACTTTGGGTTTTTTTCCCATCC----ATGATTTATGCATATGC-TTTTACATTTGA
*
35411 ATCCAATAGTTGTTCTATCAACTTCTTTCCGGGAAAGAAGAAGATGCAGGTTTTGGTTCTCTATT
123 ATCCAATAGCTGTTCTATCAACTTCTTTCCGGGAAAGAAGAAGATGCAGGTTTTGGTTCTCTATT
35476 GAAGT
188 GAAGT
35481 GCT
1 GCT
35484 GCTCAAATGC
Statistics
Matches: 176, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
193 44 0.25
194 3 0.02
195 2 0.01
196 34 0.19
200 21 0.12
201 72 0.41
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (192 bp):
GCTCATGAAAGATATCATTGGTGATTTTCTTCACACAATGCATCCAGCATTTTATATTAGCTAGC
CCGTTAACTTTGGGTTTTTTTCCCATCCATGATTTATGCATATGCTTTTACATTTGAATCCAATA
GCTGTTCTATCAACTTCTTTCCGGGAAAGAAGAAGATGCAGGTTTTGGTTCTCTATTGAAGT
Found at i:41810 original size:3 final size:3
Alignment explanation
Indices: 41797--41827 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
41787 ATAAATAAGC
41797 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
41828 TACAATTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:42178 original size:43 final size:43
Alignment explanation
Indices: 41993--42327 Score: 209
Period size: 43 Copynumber: 7.7 Consensus size: 43
41983 TGTTGGGGAC
* * * * * ** * *
41993 GACACTGCTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGGT
1 GACACGGCTCCTACGTGATGAGGAGATCTGGTTATCTATGGTT
* * * * *
42036 GACATGGTTCCTACGTGATGAGGAAATCTGG---TCGAGGGTT
1 GACACGGCTCCTACGTGATGAGGAGATCTGGTTATCTATGGTT
* * * * ** *
42076 GACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGAT
1 GACACGGCTCCTACGTGATGAGGAGATC-TGGTTATC-TATGGT--T
* * *
42123 AACACGGTTCCTACGTGATGAGGACGGT-TGGTTATCTATGGTT
1 GACACGGCTCCTACGTGATGAGGA-GATCTGGTTATCTATGGTT
** *
42166 GACACGGCTCCTACGTGATGAGGAGATCTGG---TCTGGGGAAT
1 GACACGGCTCCTACGTGATGAGGAGATCTGGTTATCTATGG-TT
* * * ** *
42207 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGAT
1 GACACGGCTCCTACGTGATGAGGAGATCTGGTTATCT-ATGGT--T
* *
42253 AACACGGTTCCTACGTGATGAGGACGA-CTGGTTATCTATGGTT
1 GACACGGCTCCTACGTGATGAGGA-GATCTGGTTATCTATGGTT
42296 GACACGGCTCCTACGTGATGAGGAGATCTGGT
1 GACACGGCTCCTACGTGATGAGGAGATCTGGT
42328 CTGGGGATGA
Statistics
Matches: 223, Mismatches: 51, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
40 32 0.14
41 32 0.14
42 4 0.02
43 77 0.35
44 5 0.02
45 15 0.07
46 35 0.16
47 21 0.09
48 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.27
Consensus pattern (43 bp):
GACACGGCTCCTACGTGATGAGGAGATCTGGTTATCTATGGTT
Found at i:42239 original size:130 final size:129
Alignment explanation
Indices: 42035--42373 Score: 511
Period size: 130 Copynumber: 2.6 Consensus size: 129
42025 CGTCTAAGGG
* * * * *
42035 TGACATGGTTCCTACGTGATGAGGAAATCTGGTC-GAGGGTTGACACTGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTG-GGGATGACACGGCTCATACGTGATGAAG
**
42099 AGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCTATGG
65 AGTTC-TGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTATGG
42164 T
129 T
42165 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAG
*
42230 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTATGGT
65 AGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTATGGT
* * * *
42295 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
*
42360 CG-GCTGGCCATCTT
66 -GTTCTGGCCATCTT
42374 TAGGAGTTAT
Statistics
Matches: 192, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
129 32 0.17
130 131 0.68
131 29 0.15
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (129 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTATGGT
Found at i:42425 original size:28 final size:28
Alignment explanation
Indices: 42405--42466 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
42395 AAACCAAATT
42405 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
42433 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
42461 AAAGAT
1 AAAGAT
42467 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:43528 original size:30 final size:30
Alignment explanation
Indices: 43494--43651 Score: 130
Period size: 30 Copynumber: 5.1 Consensus size: 30
43484 AGAGACAAAA
* *
43494 TTTTGTTTCCAAAGAAACAGACCCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
**
43524 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAA-A-
1 TTTTGTTTCAAAAG-AA--A-C-----AGACTCAAAGAT
*
43561 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
*
43591 TTTTGTTTCAAAAGAAATAGACTCAAAGA-
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
43620 -TTT-TTTCAAAAGAAACA-ATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGA-CTCAAAGAT
43648 TTTT
1 TTTT
43652 TCACAAAATT
Statistics
Matches: 105, Mismatches: 9, Indels: 29
0.73 0.06 0.20
Matches are distributed among these distances:
26 1 0.01
27 21 0.20
28 10 0.10
29 4 0.04
30 40 0.38
31 2 0.02
33 2 0.02
34 2 0.02
36 2 0.02
37 13 0.12
38 1 0.01
39 7 0.07
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:43608 original size:67 final size:67
Alignment explanation
Indices: 43438--43608 Score: 288
Period size: 67 Copynumber: 2.5 Consensus size: 67
43428 TCATTTTAAG
* * * *
43438 AGAAACAGATTCAAAGATTTTTTTTTTCAAATGAAAATATCTTAAGAGAGACAAAATTTTGTTTC
1 AGAAACAGACTCAAAGA-TTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTC
43503 CAA
65 CAA
*
43506 AGAAACAGACCCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
43571 AA
66 AA
43573 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAAT
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAAT
43609 AGACTCAAAG
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
67 82 0.85
68 15 0.15
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.32
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:43634 original size:27 final size:27
Alignment explanation
Indices: 43566--43654 Score: 117
Period size: 27 Copynumber: 3.2 Consensus size: 27
43556 CAAAATTTTG
*
43566 TTTCCAAAGAAACAGACTCAAAGATTTTT
1 TTTCAAAAGAAACAGACTCAAAGA--TTT
*
43595 GTTTCAAAAGAAATAGACTCAAAGATTT
1 -TTTCAAAAGAAACAGACTCAAAGATTT
43623 TTTCAAAAGAAACA-ATCTCAAAGATTT
1 TTTCAAAAGAAACAGA-CTCAAAGATTT
43650 TTTCA
1 TTTCA
43655 CAAAATTGTC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
26 1 0.02
27 29 0.53
28 3 0.05
30 22 0.40
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (27 bp):
TTTCAAAAGAAACAGACTCAAAGATTT
Found at i:43985 original size:36 final size:36
Alignment explanation
Indices: 43901--44004 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
43891 GAGAAAATGA
* *
43901 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
43935 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
43971 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
44005 ACGATCTCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 20 0.34
35 10 0.17
36 29 0.49
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:44032 original size:36 final size:36
Alignment explanation
Indices: 43902--44020 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
43892 AGAAAATGAT
* * *
43902 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
43936 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
43972 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
44007 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
44021 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 20 0.29
35 12 0.17
36 38 0.54
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:44151 original size:105 final size:101
Alignment explanation
Indices: 43972--44208 Score: 268
Period size: 105 Copynumber: 2.3 Consensus size: 101
43962 TAGAGAAATT
*
43972 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
*
44036 GTGAAACAAATTCGAAATTTGGATCTAAAAGGGAAA-AG
64 GTGAAACAAATTCAAAATTTGGATCTAAAA-GGAAATAG
* *
44074 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTGTTT
* * * * *
44138 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAATAT
61 AAT-GTGAAACAAATTCAAAATTTGGATCTAAAAGGAAATAG
*
44179 GTCTCAAGCGAGACGCAATTTGTTTT-AGAA
1 GTCTCAAGCGAGACGAAATTTGTTTTGAGAA
44209 TTCTCAAAAT
Statistics
Matches: 117, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
101 7 0.06
102 20 0.17
103 5 0.04
104 10 0.09
105 75 0.64
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTAAAAGGAAATAG
Found at i:44682 original size:4 final size:4
Alignment explanation
Indices: 44673--44718 Score: 78
Period size: 4 Copynumber: 12.0 Consensus size: 4
44663 TTTATGTATC
44673 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44719 GTATACTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
4 38 0.95
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:45946 original size:11 final size:11
Alignment explanation
Indices: 45930--45969 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
45920 TTCTTTGCTC
45930 TTTTTCTTTGA
1 TTTTTCTTTGA
45941 TTTTTCTTTG-
1 TTTTTCTTTGA
45951 TTTTTGCTTTGA
1 TTTTT-CTTTGA
45963 TTTTTCT
1 TTTTTCT
45970 CTCTGCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.19
11 17 0.63
12 5 0.19
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.75
Consensus pattern (11 bp):
TTTTTCTTTGA
Found at i:45960 original size:22 final size:24
Alignment explanation
Indices: 45918--45999 Score: 86
Period size: 22 Copynumber: 3.7 Consensus size: 24
45908 TGTTCTTTGC
*
45918 TTTTCTTTGCTCTTTTTCTTTGAT
1 TTTTCTTTGCTCTTTTGCTTTGAT
45942 TTTTCTTTG-T-TTTTGCTTTGAT
1 TTTTCTTTGCTCTTTTGCTTTGAT
** *
45964 TTTTC--T-CTCTGCT-CTTTGTT
1 TTTTCTTTGCTCTTTTGCTTTGAT
45984 TTTTCTTTGCTCTTTT
1 TTTTCTTTGCTCTTTT
46000 CTCTTTGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
20 13 0.28
21 2 0.04
22 17 0.36
23 6 0.13
24 9 0.19
ACGTcount: A:0.02, C:0.17, G:0.10, T:0.71
Consensus pattern (24 bp):
TTTTCTTTGCTCTTTTGCTTTGAT
Found at i:45985 original size:18 final size:18
Alignment explanation
Indices: 45964--45998 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45954 TTGCTTTGAT
45964 TTTTCTCTCTGCTCTTTG
1 TTTTCTCTCTGCTCTTTG
* *
45982 TTTTTTCTTTGCTCTTT
1 TTTTCTCTCTGCTCTTT
45999 TCTCTTTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.69
Consensus pattern (18 bp):
TTTTCTCTCTGCTCTTTG
Found at i:46693 original size:46 final size:45
Alignment explanation
Indices: 46604--46693 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 45
46594 AATACAGTGT
* * *
46604 TTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAATGC
1 TTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAATGC
*
46649 TTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAATG
1 TTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAATG
46694 TCAAAAATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 8 0.20
46 32 0.80
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (45 bp):
TTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAATGC
Found at i:56021 original size:3 final size:3
Alignment explanation
Indices: 56015--56058 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
56005 ATCTACTTTA
*
56015 AAT AAT AAT AAT AAA AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56059 CGAAATATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:56039 original size:20 final size:20
Alignment explanation
Indices: 56014--56054 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
56004 CATCTACTTT
56014 AAATAATAATAATAAAAATA
1 AAATAATAATAATAAAAATA
*
56034 AAATAATAATAATAATAATA
1 AAATAATAATAATAAAAATA
56054 A
1 A
56055 TAATCGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATAATAATAATAAAAATA
Found at i:56147 original size:16 final size:17
Alignment explanation
Indices: 56115--56147 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56105 GTCCGATCCA
*
56115 ATGAACTTTAGTGGACT
1 ATGAACTATAGTGGACT
56132 ATGAACTATA-TGGACT
1 ATGAACTATAGTGGACT
56148 TAAGTAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (17 bp):
ATGAACTATAGTGGACT
Found at i:63849 original size:33 final size:32
Alignment explanation
Indices: 63796--63865 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
63786 ATATTCAACG
* *
63796 TAATAAAAATATACTTTAATTTATAATTAAGA
1 TAATAAAAATATACTTTAATTTATAAATAAAA
63828 TAATAAAATATATA-TTCTAATTTATAAATAAAA
1 TAATAAAA-ATATACTT-TAATTTATAAATAAAA
63861 TAATA
1 TAATA
63866 TTCAAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 10 0.29
33 24 0.71
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (32 bp):
TAATAAAAATATACTTTAATTTATAAATAAAA
Found at i:64344 original size:19 final size:19
Alignment explanation
Indices: 64312--64357 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
64302 AAATTAATAT
*
64312 GAAAAT-AT-GATAAAGAC
1 GAAAATGATAGATAAAGAA
64329 GAAAATGATAGATAAAGAA
1 GAAAATGATAGATAAAGAA
*
64348 AAAAATGATA
1 GAAAATGATA
64358 AATTGAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.24
18 2 0.08
19 17 0.68
ACGTcount: A:0.63, C:0.02, G:0.17, T:0.17
Consensus pattern (19 bp):
GAAAATGATAGATAAAGAA
Found at i:66609 original size:92 final size:89
Alignment explanation
Indices: 66400--66578 Score: 277
Period size: 92 Copynumber: 1.9 Consensus size: 89
66390 TTCTTGCCTT
*
66400 GATAACTTTGCAAGTGTCCATTAACACGAACATAAGTTCTCTCTCTGTTGCACAAAAAAATTCAA
1 GATAAC-TAGCAAGTGT-CATTAACACGAACATAAGTTCTCTCTCTGTTGCACAAAAAAATTCAA
*
66465 GTATGTAACCAAATATAATAACGCCTT
64 GTATGTAACCAAATATAATAACG-CTA
*
66492 GATAACTTTGCAAGTGTCCATTAACACGAACATAAGTTCTCTCTCTGTTGCACCAAAAAAATTCA
1 GATAAC-TAGCAAGTGT-CATTAACACGAACATAAGTTCTCTCTCTGTTGCA-CAAAAAAATTCA
66557 AGTATGTAACCAAATATAATAA
63 AGTATGTAACCAAATATAATAA
66579 TGTAGAACTA
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 52 0.60
93 34 0.40
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (89 bp):
GATAACTAGCAAGTGTCATTAACACGAACATAAGTTCTCTCTCTGTTGCACAAAAAAATTCAAGT
ATGTAACCAAATATAATAACGCTA
Done.