Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008978.1 Hibiscus syriacus cultivar Beakdansim tig00112335_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: 38115
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5561 original size:97 final size:92
Alignment explanation
Indices: 5311--5563 Score: 285
Period size: 93 Copynumber: 2.7 Consensus size: 92
5301 TAATATTAAT
*
5311 ATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACTCCCCGACTTTATGGATAA
1 ATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACACCCCG-CTTTATGGATAA
* *
5376 GATTCAGCTAGCCTGATAAAGGTGATTA
65 GATTCAGCTAACCTGATAAAGATGATTA
* * * * *
5404 ATGTACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTATGGATAA
1 ATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACACC-CCGCTTTATGGATAA
*
5469 TATTCAGCTAACCTGAT-AAGATGATT-
65 GATTCAGCTAACCTGATAAAGATGATTA
* * * * *
5495 ATAATATCTATACAATGATGCTGAGCTATCCCTCTAAAGCATTTGGTTAAACACCCCAGCTCTAT
1 AT-ATA-CAATA-AA-GCT--TGAGCTGTCCCTCTAAAGCAATTGGTTAAACACCCC-GCTTTAT
5560 GGAT
59 GGAT
5564 CCAGCTAGCC
Statistics
Matches: 134, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
91 2 0.01
92 10 0.07
93 76 0.57
94 4 0.03
95 2 0.01
96 1 0.01
97 39 0.29
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (92 bp):
ATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACACCCCGCTTTATGGATAAG
ATTCAGCTAACCTGATAAAGATGATTA
Found at i:6710 original size:85 final size:84
Alignment explanation
Indices: 6366--7297 Score: 1013
Period size: 85 Copynumber: 11.1 Consensus size: 84
6356 AAAAGTACCT
* * * * **
6366 TCAACAAAAGGCCTTCGAGTTCGATTACACTCAGCTCAAAGGCGCATCAAATTTGCAACATGGCT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-AATTTACAGCATAACT
* *
6431 CAA-GTGAGAAGGGCTATCT-
64 CAAGGCGAGAAGGGTTATCTG
* * * * * ** *
6450 ACCACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGTACATC-TTTTGTAGCATAGCTC
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTACAGCATAACTC
* *
6514 AAGTCGAGAAGGGTTATCTA
65 AAGGCGAGAAGGGTTATCTG
* * * * **
6534 CCAATAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG--TATC-ATTTATAGCATGGCTCA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTACAGCATAACTCA
*
6596 AGGCGAGAAGGGCTATC-G
66 AGGCGAGAAGGGTTATCTG
* * *
6614 ACCAACAAAGACCTTCAAGTTTGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
1 -TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CAATTTACAGCATAACT
6679 CAAGGCGAGAAGGGTTATCTG
64 CAAGGCGAGAAGGGTTATCTG
* * * * * *
6700 TCAACCAAGACCTTTGAGTTTGATTACACTCAGCTCAAAGGCACATC-ATTTGCATCATAGCTCA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTACAGCATAACTCA
* * *
6764 AGGCGAAAAGGGCTATCGG
66 AGGCGAGAAGGGTTATCTG
* * *
6783 CCAACAAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGTATAACT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CAATTTACAGCATAACT
*
6848 CAAGGTGAGAAGGGTTATCTG
64 CAAGGCGAGAAGGGTTATCTG
* * *
6869 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-ATTTGCAGTATAACTCA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTACAGCATAACTCA
6933 AGGCGAGAAGGGTTATCTG
66 AGGCGAGAAGGGTTATCTG
* * * *
6952 TCAACAAA-AGCCTTCGAGTTCAATTACACTCAGCTCAAAGGCACATCAAATTTGCAACATAGCT
1 TCAACAAAGA-CCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-AATTTACAGCATAACT
* *
7016 CAAGGTGAGAAGGGCTATCTG
64 CAAGGCGAGAAGGGTTATCTG
* * * *
7037 CCAACAAAGACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAATTTACAGCATAACTCA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTACAGCATAACTCA
** *
7102 ATACGGGAAGGGTTATCTG
66 AGGCGAGAAGGGTTATCTG
* * * * *
7121 TCAACCAAGACCTTCGAGTTCGATTACATTCATCTCAGAGGCAAATCCAATTTACAGCATAACTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CAATTTACAGCATAACTC
7186 AAGGCGAGAAGGGTTATCTG
65 AAGGCGAGAAGGGTTATCTG
* * * * * ** * *
7206 TCAA-GAATACCTTCGAGTTCGATTCCATTCAGCTCAAGGGCATGTCAACTTTACAGTATAACTT
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAA-TTTACAGCATAACTC
* ** *
7270 AAGTCGAGAAAAGATATCTG
65 AAGGCGAGAAGGGTTATCTG
7290 TCAACAAA
1 TCAACAAA
7298 AAAACTGTCA
Statistics
Matches: 727, Mismatches: 103, Indels: 35
0.84 0.12 0.04
Matches are distributed among these distances:
81 70 0.10
82 15 0.02
83 164 0.23
84 220 0.30
85 224 0.31
86 34 0.05
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (84 bp):
TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTACAGCATAACTCA
AGGCGAGAAGGGTTATCTG
Found at i:6832 original size:169 final size:169
Alignment explanation
Indices: 6366--7247 Score: 1066
Period size: 169 Copynumber: 5.3 Consensus size: 169
6356 AAAAGTACCT
* * * *
6366 TCAACAAAAGGCCTTCGAGTTCGATTACACTCAGCTCAAAGGCGCATCAAATTTGCAACATGGCT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCT
* * * *
6431 CAA-GTGAGAAGGGCTATCTACC-ACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGTA
63 CAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
* ** * * *
6494 CAT-C-TTTTGTAGCATAGCTCAAGTCGAGAAGGGTTATCTA
128 CATCCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * * ** *
6534 CCAATAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG--TATCATTTATAGCATGGCTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
6597 GGCGAGAAGGGCTATC-GACCAAC-AAAGACCTTCAAGTTTGATTACACTCAGCTCAAAGGCACA
66 GGCGAGAAGGGCTATCTG-CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACA
6660 TCCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
130 TCCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * * *
6700 TCAACCAAGACCTTTGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCATCATAGCTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * *
6765 GGCGAAAAGGGCTATCGGCCAACAAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACAT
66 GGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* *
6830 CCAATTTACAGTATAACTCAAGGTGAGAAGGGTTATCTG
131 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * *
6869 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATAACTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * *
6934 GGCGAGAAGGGTTATCTGTCAACAAAAG-CCTTCGAGTTCAATTACACTCAGCTCAAAGGCACAT
66 GGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* * * * * *
6998 CAAATTTGCAACATAGCTCAAGGTGAGAAGGGCTATCTG
131 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * * * * *
7037 CCAACAAAGACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAATTTACAGCATAACTCA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-ATTTGCAGCATAGCTCA
** * * * * * * * *
7102 ATACGGGAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACATTCATCTCAGAGGCAAA
65 AGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACA
7166 TCCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
130 TCCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * * * *
7206 TCAA-GAATACCTTCGAGTTCGATTCCATTCAGCTCAAGGGCA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
7248 TGTCAACTTT
Statistics
Matches: 627, Mismatches: 76, Indels: 22
0.86 0.10 0.03
Matches are distributed among these distances:
163 15 0.02
164 55 0.09
165 6 0.01
166 66 0.11
167 35 0.06
168 185 0.30
169 265 0.42
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (169 bp):
TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
GGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
Found at i:7020 original size:337 final size:337
Alignment explanation
Indices: 6367--7298 Score: 1094
Period size: 337 Copynumber: 2.8 Consensus size: 337
6357 AAAGTACCTT
* * *
6367 CAACAAAAGGCCTTCGAGTTCGATTACACTCAGCTCAAAGGCGCATCAAATTTGCAACATGGCTC
1 CAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-AATTTGCAACATAGCTC
* * * *
6432 AAGTGAGAAGGGCTATCTACC-ACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGTACA
64 AAGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACA
* ** * **
6496 T-C-TTTTGTAGCATAGCTCAA-GTCGAGAAGGGTTATCTACCAATAAAGACCTTCGAGTTCGAT
129 TCCAATTTACAGCATAACTCAAGGT-GAGAAGGGTTATCTGTCAA-AAAGACCTTCGAGTTCGAT
* * ** * *
6558 TACACTCAGCTCAAAGG--TATCATTTATAGCATGGCTCAAGGCGAGAAGGGCTATC-GACCAAC
192 TACACTCAGCTCAAAGGCATATCATTTACAGTATAACTCAAGGCGAGAAGGGATATCTG-TCAAC
** * *
6620 -AAAGACCTTCAAGTTTGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTCAAGG
256 AAAAGACCTTCAAGTTCAATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAACTCAAGG
* *
6684 CGAGAAGGGTTATCTGT
321 CGAGAAGGGCTATCTGC
* * * *
6701 CAACCAAGACCTTTGAGTTTGATTACACTCAGCTCAAAGGCACATC-ATTTGCATCATAGCTCAA
1 CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTGCAACATAGCTCAA
* * *
6765 GGCGAAAAGGGCTATCGGCCAACAAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACAT
66 -GCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* *
6830 CCAATTTACAGTATAACTCAAGGTGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTA
130 CCAATTTACAGCATAACTCAAGGTGAGAAGGGTTATCTGTCAA-AAAGACCTTCGAGTTCGATTA
* * *
6895 CACTCAGCTCAAAGGCACATCATTTGCAGTATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAA
194 CACTCAGCTCAAAGGCATATCATTTACAGTATAACTCAAGGCGAGAAGGGATATCTGTCAACAAA
* * * *
6960 AG-CCTTCGAGTTCAATTACACTCAGCTCAAAGGCACATCAAATTTGCAACATAGCTCAAGGTGA
259 AGACCTTCAAGTTCAATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAACTCAAGGCGA
7024 GAAGGGCTATCTGC
324 GAAGGGCTATCTGC
* * * * * *
7038 CAACAAAGACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAATTTACAGCATAACTCAA
1 CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTGCAACATAGCTCAA
* * * * * * * * *
7103 TACGGGAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACATTCATCTCAGAGGCAAAT
66 -GCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* * * *
7167 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAGAATACCTTCGAGTTCGATTCC
130 CCAATTTACAGCATAACTCAAGGTGAGAAGGGTTATCTGTCAAAAAGACCTTCGAGTTCGATTAC
* * * * * **
7232 ATTCAGCTCAAGGGCATGTCAACTTTACAGTATAACTTAAGTCGAGAAAAGATATCTGTCAACAA
195 ACTCAGCTCAAAGGCATATC-A-TTTACAGTATAACTCAAGGCGAGAAGGGATATCTGTCAACAA
7297 AA
258 AA
7299 AAACTGTCAA
Statistics
Matches: 508, Mismatches: 78, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
331 16 0.03
332 15 0.03
333 78 0.15
334 5 0.01
335 65 0.13
336 37 0.07
337 218 0.43
338 74 0.15
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (337 bp):
CAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTGCAACATAGCTCAA
GCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC
CAATTTACAGCATAACTCAAGGTGAGAAGGGTTATCTGTCAAAAAGACCTTCGAGTTCGATTACA
CTCAGCTCAAAGGCATATCATTTACAGTATAACTCAAGGCGAGAAGGGATATCTGTCAACAAAAG
ACCTTCAAGTTCAATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAACTCAAGGCGAGA
AGGGCTATCTGC
Found at i:8696 original size:14 final size:15
Alignment explanation
Indices: 8677--8767 Score: 67
Period size: 14 Copynumber: 6.7 Consensus size: 15
8667 TTTGTCCTGG
8677 TTATAAATATTA-TA
1 TTATAAATATTATTA
8691 TTAT--A-ATTATTA
1 TTATAAATATTATTA
* *
8703 CTAT-TATATTATTA
1 TTATAAATATTATTA
*
8717 TTAT-ATTA-TATTA
1 TTATAAATATTATTA
8730 TTATAACA-ATTA-TA
1 TTATAA-ATATTATTA
8744 TTATAAA-ATTATTA
1 TTATAAATATTATTA
*
8758 TTATTAATAT
1 TTATAAATAT
8768 CATGTAGTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
11 4 0.06
12 6 0.10
13 15 0.24
14 34 0.54
15 4 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATAAATATTATTA
Found at i:8715 original size:3 final size:3
Alignment explanation
Indices: 8684--8763 Score: 55
Period size: 3 Copynumber: 28.7 Consensus size: 3
8674 TGGTTATAAA
* *
8684 TAT TA- TAT TAT AAT TAT TAC TAT TA- TAT TAT TAT TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
8728 TAT TAT AAC AAT TA- TAT TA- TAA AAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
8764 ATATCATGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
2 12 0.20
3 48 0.80
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:8742 original size:33 final size:31
Alignment explanation
Indices: 8684--8747 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
8674 TGGTTATAAA
* *
8684 TATTATATTATAATTATTACTATTATATTAT
1 TATTATATTATAATTATAACAATTATATTAT
8715 TATTATATTATATTATTATAACAATTATATTAT
1 TATTATATTATA--ATTATAACAATTATATTAT
8748 AAAATTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 12 0.41
33 17 0.59
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (31 bp):
TATTATATTATAATTATAACAATTATATTAT
Found at i:8748 original size:5 final size:5
Alignment explanation
Indices: 8683--8730 Score: 62
Period size: 5 Copynumber: 9.4 Consensus size: 5
8673 CTGGTTATAA
*
8683 ATATT ATATT ATAAT -TATT ACTATT ATATT ATTATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT A-TATT ATATT A-TATT ATATT ATATT AT
8731 TATAACAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 3 0.08
5 25 0.66
6 10 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:8763 original size:22 final size:22
Alignment explanation
Indices: 8709--8763 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
8699 ATTACTATTA
**
8709 TATTATTATTATATTATATTAT
1 TATTATTATTATATTATAAAAT
* **
8731 TATAACAATTATATTATAAAAT
1 TATTATTATTATATTATAAAAT
8753 TATTATTATTA
1 TATTATTATTA
8764 ATATCATGTA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTATTATTATATTATAAAAT
Found at i:17086 original size:13 final size:12
Alignment explanation
Indices: 17001--17109 Score: 57
Period size: 12 Copynumber: 9.3 Consensus size: 12
16991 GGTTTTGCTT
*
17001 AAAGATAAAAAA
1 AAAGAAAAAAAA
*
17013 AATGAAAAAAAA
1 AAAGAAAAAAAA
17025 TAAA-AAATAAAAA
1 -AAAGAAA-AAAAA
* * *
17038 AATGAAATAGAA
1 AAAGAAAAAAAA
* *
17050 AAA-TAGAAAAA
1 AAAGAAAAAAAA
**
17061 ATGGAAAAAAAA
1 AAAGAAAAAAAA
*
17073 GAAG--AAAAAA
1 AAAGAAAAAAAA
17083 AAAGAAAAAAAA
1 AAAGAAAAAAAA
* *
17095 CAA-AAAAAATA
1 AAAGAAAAAAAA
17106 AAAG
1 AAAG
17110 GGGGTTCAAG
Statistics
Matches: 68, Mismatches: 22, Indels: 14
0.65 0.21 0.13
Matches are distributed among these distances:
10 9 0.13
11 14 0.21
12 35 0.51
13 10 0.15
ACGTcount: A:0.81, C:0.01, G:0.10, T:0.08
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:18449 original size:55 final size:55
Alignment explanation
Indices: 18366--18752 Score: 549
Period size: 55 Copynumber: 7.2 Consensus size: 55
18356 GTGAAGCAAA
*
18366 GAAGATTGTTCGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
18420 GAAGATTATTCTAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGAT-GAT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
18474 GAAGATT-GTGGA-TCTTATACTCTCTGAAGAAATAGGGGGGCAGATGCGATCGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATA-GGGGGCAGACGCGATCGTT
* * * *
18528 GAAGATTATTCGAGTCTTATACTCTCTAAAG-AATAGGGGGCAGACACGATTGAT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
18582 AAAGATT-GTGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
18635 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
18690 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
18745 G--GATTATT
1 GAAGATTATT
18753 GTTCGAGTTC
Statistics
Matches: 295, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
52 38 0.13
53 51 0.17
54 53 0.18
55 137 0.46
56 16 0.05
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:18560 original size:108 final size:109
Alignment explanation
Indices: 18366--18752 Score: 624
Period size: 108 Copynumber: 3.6 Consensus size: 109
18356 GTGAAGCAAA
18366 GAAGATTGTTCGATCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTC
1 GAAGATTGTTCGATCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTC
*
18431 TAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA-TGAT
66 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
18474 GAAGATTG-TGGATCTTATACTCTCTGAAGAAATAGGGGGGCAGATGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGATCTTATACTCTCTGAAGAAATA-GGGGGCAGACGCGATCGTTGAAGATTATT
* *
18538 CGAGTCTTATACTCTCTAAAG-AATAGGGGGCAGACACGATTGAT
65 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* * *
18582 AAAGATTG-TGGATCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTC
1 GAAGATTGTTCGATCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTC
* *
18646 GAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
66 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
18690 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG--GATTATT
1 GAAGATTGTTCGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
18753 GTTCGAGTTC
Statistics
Matches: 259, Mismatches: 15, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
107 88 0.34
108 126 0.49
109 3 0.01
110 42 0.16
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (109 bp):
GAAGATTGTTCGATCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTC
GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
Found at i:18808 original size:52 final size:52
Alignment explanation
Indices: 18746--19290 Score: 863
Period size: 52 Copynumber: 10.6 Consensus size: 52
18736 GCGATCGTTG
*
18746 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACTCGTAGGAA
* **
18798 GATTATTGTTCGAGTTCTAGTCCCTGGAGAAAATTGGGCATTCTCGTAGGAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACTCGTAGGAA
*
18850 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTA-GAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACTCGTAGGAA
* *
18901 GATTATTGTTCGAGTTCTAGTCCCTGAAG-AAATTGGAC-GACCCGTAGGAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACTCGTAGGAA
*
18951 GATTATTGTTCGAGTTCTAGT-CCTG-AGAAAATTGGGCAGACCCGTAGGAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACTCGTAGGAA
* * *
19001 GATTTTTATTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACTCGTAGGAA
*
19053 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACTCGTAGGAA
*
19105 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACTCGTAGGAA
* *
19157 GATTATTGTTCGAGTTCTAGTCCCT-AAGAAAATTGGACA-ATATCGTAGGAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGA-CTCGTAGGAA
*
19208 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTA-GAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACTCGTAGGAA
* *
19259 GATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 GATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
19291 TAGAGCGAAC
Statistics
Matches: 457, Mismatches: 28, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
48 2 0.00
49 18 0.04
50 63 0.14
51 116 0.25
52 258 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (52 bp):
GATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACTCGTAGGAA
Found at i:23781 original size:3 final size:3
Alignment explanation
Indices: 23775--23835 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
23765 AAAAAATATG
* **
23775 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23819 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
23836 CGATAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:23812 original size:29 final size:30
Alignment explanation
Indices: 23780--23842 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
23770 ATATGTAATA
*
23780 ATAAATAATAATAA-AATAATAAGATAACG
1 ATAAATAATAATAATAATAATAAAATAACG
23809 AT-AATAATAATAATAATAATAAAATAACG
1 ATAAATAATAATAATAATAATAAAATAACG
23838 ATAAA
1 ATAAA
23843 AAAACCCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 11 0.35
29 18 0.58
30 2 0.06
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (30 bp):
ATAAATAATAATAATAATAATAAAATAACG
Found at i:26961 original size:31 final size:32
Alignment explanation
Indices: 26920--26979 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
26910 AAGGTTAAAT
* *
26920 TATGTGTTTAGTACTTAAATTATCAATTTCAG
1 TATGTGTTTAGTACCTAAACTATCAATTTCAG
26952 TATGT-TTTAGTACCTAAACTATCAATTT
1 TATGTGTTTAGTACCTAAACTATCAATTT
26980 TTTCAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.47
Consensus pattern (32 bp):
TATGTGTTTAGTACCTAAACTATCAATTTCAG
Found at i:27193 original size:22 final size:21
Alignment explanation
Indices: 27168--27213 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
27158 ATGATTTTAA
27168 AAAATTTAAAAGTTTAGGTACT
1 AAAA-TTAAAAGTTTAGGTACT
* *
27190 AAAATTGATAGTTTAGGTACT
1 AAAATTAAAAGTTTAGGTACT
27211 AAA
1 AAA
27214 CTATCAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (21 bp):
AAAATTAAAAGTTTAGGTACT
Found at i:35579 original size:2 final size:2
Alignment explanation
Indices: 35572--35633 Score: 101
Period size: 2 Copynumber: 31.5 Consensus size: 2
35562 TTGACCTCTA
35572 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
35614 AT A- AT AT AT A- AT AT GAT AT A
1 AT AT AT AT AT AT AT AT -AT AT A
35634 ATAACTTTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.04
2 53 0.93
3 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Done.