Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004349.1 Hibiscus syriacus cultivar Beakdansim tig00009530_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: 72724
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Found at i:381 original size:88 final size:86
Alignment explanation
Indices: 274--576 Score: 262
Period size: 88 Copynumber: 3.5 Consensus size: 86
264 TACATTTTAA
* * *
274 AGTATAACATTTTCTGTTGATAATGCACTCATATGCATTTCAACTATTGTATACTTTTATTGATG
1 AGTAT-AC-TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTT-TTGATG
*
339 ACGTACCTATA-ACATCTCAACCAT
63 ACGTACCCATATACAT-TCAACCAT
* * * * *
363 AGTATACTTTTTCTGTTGAGAATGTACCCATATACATTTCAACTCTAGCATACTTTATGTTGATA
1 AGTATAC-TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTT-T-TTGATG
* *
428 ATC-CACCCATATGCATTCAA-C-T
63 A-CGTACCCATATACATTCAACCAT
* * * * * * * *
450 AGTATACTTTTATGTTGATGAT--AACCATATACATCTCAACCATAATATAC-TTTTTGTTGAAT
1 AGTATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTTTGATG-AC
*
512 GTACCCATATACATTTTAACCAT
65 GTACCCATATACA-TTCAACCAT
* *
535 ATTATACTTTTCTGTTGATAATGCACCCATA-GCATTTCAACT
1 AGTATACTTTTCTGTTGATAATGCACCCATATACATTTCAACT
577 CTGGCATCCT
Statistics
Matches: 169, Mismatches: 35, Indels: 23
0.74 0.15 0.10
Matches are distributed among these distances:
81 4 0.02
82 12 0.07
83 6 0.04
84 23 0.14
85 20 0.12
86 20 0.12
87 14 0.08
88 44 0.26
89 22 0.13
90 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (86 bp):
AGTATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTTTGATGACG
TACCCATATACATTCAACCAT
Found at i:437 original size:44 final size:43
Alignment explanation
Indices: 288--615 Score: 208
Period size: 42 Copynumber: 7.6 Consensus size: 43
278 TAACATTTTC
* *
288 TGTTGATAATGCACTCATATGCATTTCAA-CTATTGTATACTTT-
1 TGTTGATAATGCACCCATATACATTTCAACCTA--GTATACTTTA
* * * * * * *
331 TATTGATGACGTACCTATA-ACATCTCAACCATAGTATACTTTTTC
1 TGTTGATAATGCACCCATATACATTTCAACC-TAGTATAC--TTTA
* * *
376 TGTTGAGAATGTACCCATATACATTTCAACTCTAGCATACTTTA
1 TGTTGATAATGCACCCATATACATTTCAAC-CTAGTATACTTTA
* *
420 TGTTGATAATCCACCCATATGCA-TTCAA-CTAGTATACTTTTA
1 TGTTGATAATGCACCCATATACATTTCAACCTAGTATAC-TTTA
* * * * *
462 TGTTGATGAT--AACCATATACATCTCAACCATAATATACTTTT
1 TGTTGATAATGCACCCATATACATTTCAACC-TAGTATACTTTA
* * * *
504 TGTTG--AATGTACCCATATACATTTTAACCATATTATACTTTTC
1 TGTTGATAATGCACCCATATACATTTCAACC-TAGTATAC-TTTA
* * * *
547 TGTTGATAATGCACCCATA-GCATTTCAACTCTGGCATCCTTTCA
1 TGTTGATAATGCACCCATATACATTTCAAC-CTAGTATACTTT-A
** *
591 TGCCGATAATGCACCCATATGCATT
1 TGTTGATAATGCACCCATATACATT
616 GTTTTCTTTA
Statistics
Matches: 223, Mismatches: 43, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
40 11 0.05
41 12 0.05
42 59 0.26
43 37 0.17
44 56 0.25
45 31 0.14
46 16 0.07
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.38
Consensus pattern (43 bp):
TGTTGATAATGCACCCATATACATTTCAACCTAGTATACTTTA
Found at i:542 original size:126 final size:130
Alignment explanation
Indices: 283--576 Score: 374
Period size: 126 Copynumber: 2.3 Consensus size: 130
273 AAGTATAACA
* *
283 TTTTCTGTTGATAATGCACTCATATGCATTTCAACTATTGTATACTTTTATTGATGACGTACCTA
1 TTTTATGTTGATAATGCACCCATATGCATTTCAACTA-TGTATACTTTTATTGATGAC-TACCTA
*
348 TAACATCTCAACCATAGTATACTTTTTCTGTTGAGAATGTACCCATATACATTTCAACTCTAGCA
64 TAACATCTCAACCATAATATACTTTTTCTGTT-AGAATGTACCCATATACATTTCAACTCTAGCA
413 TAC
128 TAC
*
416 -TTTATGTTGATAATCCACCCATATGCA-TTCAACTA-GTATACTTTTATGTTGATGA-TAACC-
1 TTTTATGTTGATAATGCACCCATATGCATTTCAACTATGTATACTTTTA--TTGATGACT-ACCT
* *
476 ATATACATCTCAACCATAATATAC-TTTT-TGTT-GAATGTACCCATATACATTTTAAC-CATAT
63 ATA-ACATCTCAACCATAATATACTTTTTCTGTTAGAATGTACCCATATACATTTCAACTC-TAG
*
537 TATAC
126 CATAC
*
542 TTTTCTGTTGATAATGCACCCATA-GCATTTCAACT
1 TTTTATGTTGATAATGCACCCATATGCATTTCAACT
577 CTGGCATCCT
Statistics
Matches: 145, Mismatches: 9, Indels: 20
0.83 0.05 0.11
Matches are distributed among these distances:
125 1 0.01
126 32 0.22
127 28 0.19
128 4 0.03
129 19 0.13
130 22 0.15
131 15 0.10
132 24 0.17
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (130 bp):
TTTTATGTTGATAATGCACCCATATGCATTTCAACTATGTATACTTTTATTGATGACTACCTATA
ACATCTCAACCATAATATACTTTTTCTGTTAGAATGTACCCATATACATTTCAACTCTAGCATAC
Found at i:1128 original size:20 final size:22
Alignment explanation
Indices: 1103--1157 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1093 CGATATAGAC
1103 TGGTATCGATACCC-T-CACCA
1 TGGTATCGATACCCTTACACCA
* *
1123 TGGTATCGATACCCTTATACTA
1 TGGTATCGATACCCTTACACCA
1145 TGGTATCGATACC
1 TGGTATCGATACC
1158 TCCTCTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 16 0.52
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (22 bp):
TGGTATCGATACCCTTACACCA
Found at i:1185 original size:19 final size:19
Alignment explanation
Indices: 1148--1186 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1138 TATACTATGG
**
1148 TATCGATACCTCCTCTAGA
1 TATCGATACCTAATCTAGA
*
1167 TATCGATACCTAATTTAGA
1 TATCGATACCTAATCTAGA
1186 T
1 T
1187 TTGATATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (19 bp):
TATCGATACCTAATCTAGA
Found at i:1706 original size:24 final size:24
Alignment explanation
Indices: 1679--1734 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
1669 ACTTAGTTAA
*
1679 TCCCCTC-TAAACCTTTATTAAGCT
1 TCCCCTCAT-AACCTTTATTAAGAT
1703 T-CCCTCATAACCTTTATTAAGAT
1 TCCCCTCATAACCTTTATTAAGAT
1726 T-CCCTCATA
1 TCCCCTCATA
1735 GGAAAAGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.27, C:0.32, G:0.04, T:0.38
Consensus pattern (24 bp):
TCCCCTCATAACCTTTATTAAGAT
Found at i:1707 original size:23 final size:23
Alignment explanation
Indices: 1688--1734 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1678 ATCCCCTCTA
*
1688 AACCTTTATTAAGCTTCCCTCAT
1 AACCTTTATTAAGATTCCCTCAT
1711 AACCTTTATTAAGATTCCCTCAT
1 AACCTTTATTAAGATTCCCTCAT
1734 A
1 A
1735 GGAAAAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (23 bp):
AACCTTTATTAAGATTCCCTCAT
Found at i:6662 original size:21 final size:22
Alignment explanation
Indices: 6623--6664 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
6613 ACATAATGAT
* *
6623 AACATTATCATTATTAACATTC
1 AACATCATCATTAGTAACATTC
6645 AACATCATC-TTAGTAACATT
1 AACATCATCATTAGTAACATT
6665 ATCATCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (22 bp):
AACATCATCATTAGTAACATTC
Found at i:7352 original size:45 final size:44
Alignment explanation
Indices: 7303--7540 Score: 235
Period size: 45 Copynumber: 5.2 Consensus size: 44
7293 AGTATAACAT
* * * *
7303 CTTTTCTATTGATATTGCACCCATATGCATTTCAACTATTGTATA
1 CTTTTCTGTTGATA-TGTACCCATATACATTTCAACTATAGTATA
* * *
7348 CTTTTATGTTGATGATGTACCCATATACATCTCAACCATAGTATA
1 CTTTTCTGTTGAT-ATGTACCCATATACATTTCAACTATAGTATA
* * * * *
7393 CTTTTTCTATTGAGAATATACCCATATACATTTCAACTCTAGCATA
1 C-TTTTCTGTTGA-TATGTACCCATATACATTTCAACTATAGTATA
* * * *
7439 CTTTTCTGTTGATAATGCACCCATATGCATTTTAACTCTAGTATA
1 CTTTTCTGTTGAT-ATGTACCCATATACATTTCAACTATAGTATA
* *
7484 CTTTTATGTTGATGATGTACCCATATACATCTCAAGC-ATAGTATA
1 CTTTTCTGTTGAT-ATGTACCCATATACATTTCAA-CTATAGTATA
7529 CTTTTTCTGTTG
1 C-TTTTCTGTTG
7541 TGAATGTTCC
Statistics
Matches: 157, Mismatches: 30, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
45 110 0.70
46 47 0.30
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.42
Consensus pattern (44 bp):
CTTTTCTGTTGATATGTACCCATATACATTTCAACTATAGTATA
Found at i:7535 original size:91 final size:91
Alignment explanation
Indices: 7321--7540 Score: 250
Period size: 91 Copynumber: 2.4 Consensus size: 91
7311 TTGATATTGC
* * * * *
7321 ACCCATATGCATTTCAACTATTGTATACTTTTATGTTGATGATGTACCCATATACATCTCAACCA
1 ACCCATATACATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATACATCTCAACCA
*
7386 TAGTATACTTTTTCTATTGAGAATAT
66 TAGTATACTTTTTATATTGAGAATAT
* * * * *
7412 ACCCATATACATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTTAACTC
1 ACCCATATACATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATACATCTCAAC-C
* *
7477 -TAGTATAC-TTTTATGTTGATG-ATGT
65 ATAGTATACTTTTTATATTGA-GAATAT
*
7502 ACCCATATACATCTCAAGC-ATAGTATACTTTTTCTGTTG
1 ACCCATATACATTTCAA-CTATAGTATAC-TTTTCTGTTG
7541 TGAATGTTCC
Statistics
Matches: 109, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
90 35 0.32
91 73 0.67
92 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.40
Consensus pattern (91 bp):
ACCCATATACATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATACATCTCAACCA
TAGTATACTTTTTATATTGAGAATAT
Found at i:8224 original size:19 final size:21
Alignment explanation
Indices: 8173--8228 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
8163 TATCCTCACC
8173 ATGGTATCGATACCCCTATACT
1 ATGGTATCGATACCCC-ATACT
*
8195 ATGGTACCGATACCTCC-T-CT
1 ATGGTATCGATACC-CCATACT
8215 A-GGTATCGATACCC
1 ATGGTATCGATACCC
8229 AATTTAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 1 0.03
19 11 0.35
20 3 0.10
21 1 0.03
22 13 0.42
23 2 0.06
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (21 bp):
ATGGTATCGATACCCCATACT
Found at i:8224 original size:95 final size:95
Alignment explanation
Indices: 8125--8302 Score: 216
Period size: 95 Copynumber: 1.9 Consensus size: 95
8115 CCTTAATGCC
* * ** * *
8125 TCGATACCTAAATTA-ACTTCGATATAGGCTTGTATCGATATCCTCACCATGGTATCGATACCCC
1 TCGATACCCAAATTAGA-TTCGATATAGACGGGTATCGATACCCTCACCATGGTATCAATACCCC
8189 TATACTAT-GGTACCGATACCTCCTCTAGGTA
65 TATACT-TGGGTACCGATACCTCCTCTAGGTA
* ** *
8220 TCGATACCCAATTTAGATTCGATATTTACGGGTATCGATACCCTTACCATGGTATCAATACCCCT
1 TCGATACCCAAATTAGATTCGATATAGACGGGTATCGATACCCTCACCATGGTATCAATACCCCT
* *
8285 TTGCTTGGGTACCGATAC
66 ATACTTGGGTACCGATAC
8303 TTGTTGAATA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
94 1 0.01
95 67 0.97
96 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (95 bp):
TCGATACCCAAATTAGATTCGATATAGACGGGTATCGATACCCTCACCATGGTATCAATACCCCT
ATACTTGGGTACCGATACCTCCTCTAGGTA
Found at i:17324 original size:90 final size:90
Alignment explanation
Indices: 17168--17345 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
17158 CCTAACACAC
* *
17168 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCAAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
17233 ATTTAATTAATTGAAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* * * *
17258 CCTTTTATATCTATGTTACCCAAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATTTAT
1 CCTTTTATAGCCAAGTTACCCAAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
17323 ATTTGATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
17346 TTTGGGATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCAAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:17355 original size:24 final size:20
Alignment explanation
Indices: 17308--17349 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17298 ATTATTTCAA
*
17308 ATTAATTAAATTTATATTTG
1 ATTAATTAAATTAATATTTG
17328 ATTAATTGAAATTAAATATTTG
1 ATTAATT-AAATT-AATATTTG
17350 GGATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTAATTAAATTAATATTTG
Found at i:24207 original size:90 final size:90
Alignment explanation
Indices: 24054--24231 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
24044 CCTAACACAC
* * *
24054 CCTTTTATAGCTAAGTTACCCTAATCATATTAGGGGTTTTATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
24119 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATTAAAATTAAATAAT
* *
24144 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTATTTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
24209 ATTTAATTAATTAAAATTAAATA
66 ATTTAATTAATTAAAATTAAATA
24232 TTCGGGATTA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTAAAATTAAATAAT
Found at i:25593 original size:2 final size:2
Alignment explanation
Indices: 25588--25628 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
25578 ACACACACAC
25588 AT AT AT AT AT 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 AT AT AT AT AT A
25629 GTAGGATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27077 original size:25 final size:25
Alignment explanation
Indices: 27039--27104 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
27029 GGTGGCGTCA
* *
27039 TGGCAGCAGTGTCGGCAGTGATTTC
1 TGGCAGCAGCGTCGGCAATGATTTC
*
27064 TGGCAGCAGCGTCGACAATGATTTC
1 TGGCAGCAGCGTCGGCAATGATTTC
* *
27089 TGGAAGCAGCGACGGC
1 TGGCAGCAGCGTCGGC
27105 TGGGAGCTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.35, T:0.21
Consensus pattern (25 bp):
TGGCAGCAGCGTCGGCAATGATTTC
Found at i:27288 original size:3 final size:3
Alignment explanation
Indices: 27282--27323 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
27272 ATAATATATT
27282 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA GTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
27324 AAGTAGAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:28196 original size:16 final size:16
Alignment explanation
Indices: 28175--28206 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28165 TAATGTCATT
28175 AATGAAACTTGTTTAA
1 AATGAAACTTGTTTAA
28191 AATGAAACTTGTTTAA
1 AATGAAACTTGTTTAA
28207 CTGTTTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
AATGAAACTTGTTTAA
Found at i:29388 original size:37 final size:36
Alignment explanation
Indices: 29347--29432 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
29337 ATGCGCTCCT
29347 GGTCTGTAGCTCATTTGTTCGGAGAGAATACGCTACG
1 GGTCT-TAGCTCATTTGTTCGGAGAGAATACGCTACG
* * *
29384 GGTCTCTAGCTCATTTGTTCTGAGAGAATACTCTCCG
1 GGTCT-TAGCTCATTTGTTCGGAGAGAATACGCTACG
29421 GGTC-TAGCTCAT
1 GGTCTTAGCTCAT
29433 GTGTCATTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 8 0.18
37 37 0.82
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.33
Consensus pattern (36 bp):
GGTCTTAGCTCATTTGTTCGGAGAGAATACGCTACG
Found at i:36543 original size:15 final size:15
Alignment explanation
Indices: 36520--36554 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
36510 TTCAATTGCT
*
36520 CTATCCAAATATAAC
1 CTATGCAAATATAAC
36535 CTATGCAAATATAAC
1 CTATGCAAATATAAC
36550 CTATG
1 CTATG
36555 AGACTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (15 bp):
CTATGCAAATATAAC
Found at i:41010 original size:24 final size:24
Alignment explanation
Indices: 40981--41046 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
40971 GAGATATTAA
* *
40981 AAATCAAAACAGAATTCAGAACAT
1 AAATCATAACAGAATTCAGAACAG
* * *
41005 ATATCATAACAGAATCCAGATCAG
1 AAATCATAACAGAATTCAGAACAG
41029 AAATCATAACAGAATTCA
1 AAATCATAACAGAATTCA
41047 AGTCATGTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.53, C:0.18, G:0.09, T:0.20
Consensus pattern (24 bp):
AAATCATAACAGAATTCAGAACAG
Found at i:41058 original size:24 final size:25
Alignment explanation
Indices: 40983--41072 Score: 80
Period size: 24 Copynumber: 3.7 Consensus size: 25
40973 GATATTAAAA
* * *
40983 ATCAAAACAGAATTC-AGAACATAT
1 ATCATAACAGAATTCAAGATCATGT
* *
41007 ATCATAACAGAA-TCCAGATCA-GAA
1 ATCATAACAGAATTCAAGATCATG-T
41031 ATCATAACAGAATTCAAG-TCATGT
1 ATCATAACAGAATTCAAGATCATGT
* *
41055 ATCAGAACAAAATTCAAG
1 ATCATAACAGAATTCAAG
41073 TCTGTAATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
23 2 0.04
24 47 0.87
25 5 0.09
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (25 bp):
ATCATAACAGAATTCAAGATCATGT
Found at i:41082 original size:24 final size:24
Alignment explanation
Indices: 41030--41090 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
41020 CCAGATCAGA
*
41030 AATCATAACAGAATTCAAGTCATGT
1 AATCA-AACAAAATTCAAGTCATGT
41055 -ATCAGAACAAAATTCAAGTC-TGT
1 AATCA-AACAAAATTCAAGTCATGT
*
41078 AATCAAATAAAAT
1 AATCAAACAAAAT
41091 ATTTATATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (24 bp):
AATCAAACAAAATTCAAGTCATGT
Found at i:49945 original size:105 final size:105
Alignment explanation
Indices: 49751--49953 Score: 262
Period size: 105 Copynumber: 1.9 Consensus size: 105
49741 GACCATATAT
* * *
49751 AAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCAAAAGACCTCATACAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
49816 GCTCCAAAGAATACATATACGTCCCGAAAGACCACGTAGA
66 GCTCCAAAGAATACATATACGTCCCGAAAGACCACGTAGA
* *** * * *
49856 AAATTCCTTAAGAATCATATACATATGTTAAGGACCAAATATGTGTCGCAAAGGACCTCATAGAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
* * * * * *
49921 GTTCCATAGGATACCTATATGTCCCGAAGGACC
66 GCTCCAAAGAATACATATACGTCCCGAAAGACC
49954 GCATAGACCC
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
105 82 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (105 bp):
AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
GCTCCAAAGAATACATATACGTCCCGAAAGACCACGTAGA
Found at i:55201 original size:105 final size:105
Alignment explanation
Indices: 54992--55193 Score: 260
Period size: 105 Copynumber: 1.9 Consensus size: 105
54982 GACTATATAT
* * * *
54992 AAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCAAAAGACCTCATACAT
1 AAATTACTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
55057 GCTCCAAAGAATACATATACGTCCCAAAGGACCACGTAGA
66 GCTCCAAAGAATACATATACGTCCCAAAGGACCACGTAGA
* * * * * *
55097 AAATTACTTAAGAATCATATATATATACTAAGGACCAAATATGTGTCGCAAAGGACCTCATAGAT
1 AAATTACTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
* * * * * *
55162 GTTCCATAGGATACCTATATGTCCCGAAGGAC
66 GCTCCAAAGAATACATATACGTCCCAAAGGAC
55194 TGCGTAGACC
Statistics
Matches: 81, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
105 81 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (105 bp):
AAATTACTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
GCTCCAAAGAATACATATACGTCCCAAAGGACCACGTAGA
Found at i:58446 original size:30 final size:30
Alignment explanation
Indices: 58410--58527 Score: 85
Period size: 30 Copynumber: 3.7 Consensus size: 30
58400 TTTGTCTCGC
*
58410 TTGAGATAGTTTCTCTTGAAACATAAACCT
1 TTGAGATAGTTTCTCTCGAAACATAAACCT
* * *
58440 TTGAGATTGTTTCTCTCAAAACA-AAGTTTCGTCTCGT
1 TTGAGATAGTTTCTCTCGAAACATAA------AC-C-T
* *
58477 TTGAGATATTTTCTCTTGAAACATAAACCT
1 TTGAGATAGTTTCTCTCGAAACATAAACCT
* *
58507 TTGAGATTGTTTTTCTCGAAA
1 TTGAGATAGTTTCTCTCGAAA
58528 TAAAGTTTCG
Statistics
Matches: 66, Mismatches: 13, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
29 2 0.03
30 38 0.58
31 1 0.02
32 1 0.02
35 1 0.02
36 1 0.02
37 20 0.30
38 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (30 bp):
TTGAGATAGTTTCTCTCGAAACATAAACCT
Found at i:58492 original size:67 final size:67
Alignment explanation
Indices: 58382--58563 Score: 276
Period size: 67 Copynumber: 2.7 Consensus size: 67
58372 CCTTGAGACA
* * *
58382 GTTTCTCTTGAAACAAA-TTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGA
1 GTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGA
58446 TT
66 TT
* * *
58448 GTTTCTCTCAAAACAAAGTTTCGTCTCGTTTGAGATATTTTCTCTTGAAACATAAACCTTTGAGA
1 GTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGA
58513 TT
66 TT
* * *
58515 GTTTTTCTCGAAATAAAGTTTCGTCTCGCTTGAGACAATTTCTCTTGAA
1 GTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGATAATTTCTCTTGAA
58564 GCCCAAATTT
Statistics
Matches: 104, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
66 15 0.14
67 89 0.86
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (67 bp):
GTTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGA
TT
Found at i:60286 original size:12 final size:12
Alignment explanation
Indices: 60271--60306 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
60261 TTACATCATA
60271 TTATTTATATAT
1 TTATTTATATAT
*
60283 TTATGTATATAT
1 TTATTTATATAT
60295 TTATTTA-ATAT
1 TTATTTATATAT
60306 T
1 T
60307 CCCTTACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (12 bp):
TTATTTATATAT
Found at i:60388 original size:18 final size:18
Alignment explanation
Indices: 60352--60385 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
60342 TTTAATCTAT
60352 TTCATTTGATCTTATTTA
1 TTCATTTGATCTTATTTA
*
60370 TTCATTT-ATTTTATTT
1 TTCATTTGATCTTATTT
60386 TATAAAATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (18 bp):
TTCATTTGATCTTATTTA
Found at i:66446 original size:2 final size:2
Alignment explanation
Indices: 66441--66483 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
66431 TATAAATAAC
66441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66483 T
1 T
66484 TATTTACATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:67861 original size:20 final size:20
Alignment explanation
Indices: 67821--67861 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
67811 CTCAATCCTT
*
67821 TTATTTTTTATTTTTTCTTA
1 TTATTTTTTATTTTATCTTA
67841 TTATTTTTTGATTTTAT-TTA
1 TTATTTTTT-ATTTTATCTTA
67861 T
1 T
67862 ATGATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (20 bp):
TTATTTTTTATTTTATCTTA
Found at i:67908 original size:10 final size:10
Alignment explanation
Indices: 67893--67943 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
67883 CCTTTTATTA
67893 TTTATTTTTT
1 TTTATTTTTT
*
67903 TTTATTTATT
1 TTTATTTTTT
*
67913 TCTATTATATTT
1 TTTATT-T-TTT
*
67925 TTTATTTATT
1 TTTATTTTTT
67935 TTTATTTTT
1 TTTATTTTT
67944 ATCATTATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 24 0.73
11 2 0.06
12 7 0.21
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:67934 original size:40 final size:39
Alignment explanation
Indices: 67885--67973 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
67875 CTTTTAATCC
* *
67885 TTTTATTATTTATT-TTTTTTTATTTATTTCTATTA-TATT
1 TTTTATTATTT-TTATTTTTATA-TTATTCCTATTATTATT
67924 TTTTATTTATTTTTATTTTTATCATTATTCCTATTATTATT
1 TTTTA-TTATTTTTATTTTTAT-ATTATTCCTATTATTATT
67965 TTTT-TTATT
1 TTTTATTATT
67974 CTACTTATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
39 12 0.27
40 23 0.52
41 9 0.20
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.75
Consensus pattern (39 bp):
TTTTATTATTTTTATTTTTATATTATTCCTATTATTATT
Found at i:67938 original size:49 final size:49
Alignment explanation
Indices: 67822--67945 Score: 128
Period size: 49 Copynumber: 2.5 Consensus size: 49
67812 TCAATCCTTT
67822 TATTTTTTATTTTTTCTTATTATTT-TTTGATTTTATTTATATGATATTA
1 TATTTTTTATTTTTT-TTATTATTTATTTGATTTTATTTATATGATATTA
* * ** ** **
67871 TATACTTTTAATCCTTTTATTATTTATTTTTTTTTATTTAT-TTCTATTA
1 TAT-TTTTTATTTTTTTTATTATTTATTTGATTTTATTTATATGATATTA
67920 TATTTTTTATTTATTTTTATT-TTTAT
1 TATTTTTTATTT-TTTTTATTATTTAT
67946 CATTATTCCT
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
48 11 0.18
49 28 0.47
50 21 0.35
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (49 bp):
TATTTTTTATTTTTTTTATTATTTATTTGATTTTATTTATATGATATTA
Found at i:68191 original size:11 final size:11
Alignment explanation
Indices: 68156--68193 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
68146 TTTAATCCAC
*
68156 TTTTCTTTTCT
1 TTTTATTTTCT
68167 TTTT-TTTT-T
1 TTTTATTTTCT
68176 TTTTATTTTCT
1 TTTTATTTTCT
68187 TTTTATT
1 TTTTATT
68194 GTTATGTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 5 0.20
10 8 0.32
11 12 0.48
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTATTTTCT
Found at i:68334 original size:24 final size:24
Alignment explanation
Indices: 68306--68364 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
68296 GTTTTTTTTA
*
68306 TAATTT-ATTTATTTTTATCTATTT
1 TAATTTAATTTA-ATTTATCTATTT
*
68330 TAATTTAATTTAATTTATTTATTT
1 TAATTTAATTTAATTTATCTATTT
* *
68354 TATTTTCATTT
1 TAATTTAATTT
68365 TTACTTTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 25 0.83
25 5 0.17
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (24 bp):
TAATTTAATTTAATTTATCTATTT
Done.