Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001691.1 Hibiscus syriacus cultivar Beakdansim tig00003379_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: 59364
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7327 original size:14 final size:14
Alignment explanation
Indices: 7290--7342 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
7280 TTTTAAACGA
7290 TTTATTTTTAATTA-
1 TTTATTTTT-ATTAT
7304 TTTA-TTTTATTAT
1 TTTATTTTTATTAT
7317 TTTATTTTTATCT-T
1 TTTATTTTTAT-TAT
*
7331 TTTATCTTTATT
1 TTTATTTTTATT
7343 TGAAATTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
12 4 0.11
13 9 0.26
14 21 0.60
15 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTATTTTTATTAT
Found at i:7334 original size:27 final size:28
Alignment explanation
Indices: 7290--7342 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
7280 TTTTAAACGA
7290 TTTATTTTTAATTATTTAT-TTTATTAT
1 TTTATTTTTAATTATTTATCTTTATTAT
*
7317 TTTATTTTT-ATCTTTTTATCTTTATT
1 TTTATTTTTAAT-TATTTATCTTTATT
7343 TGAAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.09
27 15 0.65
28 6 0.26
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTATTTTTAATTATTTATCTTTATTAT
Found at i:7335 original size:19 final size:18
Alignment explanation
Indices: 7290--7343 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 18
7280 TTTTAAACGA
7290 TTTATTTTTAATTATTTATTT
1 TTTA-TTTT-ATT-TTTATTT
7311 TATTATTTTATTTTTATCTT
1 T-TTATTTTATTTTTAT-TT
7331 TTTATCTTTATTT
1 TTTAT-TTTATTT
7344 GAAATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 9 0.30
20 13 0.43
21 5 0.17
22 3 0.10
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTATTTTTATTT
Found at i:8345 original size:81 final size:81
Alignment explanation
Indices: 8175--8400 Score: 229
Period size: 81 Copynumber: 2.8 Consensus size: 81
8165 AGTCCTAGAC
* * * * * *
8175 TCGATCATGGTAGCATGCAGTAGATCATCATTCAACTTGATTCAATCATGGTAACATGCAGTACA
1 TCGATCATGGTAGCATGCAATAGATCATCA-TCAACTTAATTCAATCAAGATAACATACAATACA
8240 TCATAATTCAACTTGAT
65 TCATAATTCAACTTGAT
* * * * **
8257 TCAATCATGGTAACATGCAATAGATCATCATCGA-TTCAATTCAATCAAGATAACATATAATAGT
1 TCGATCATGGTAGCATGCAATAGATCATCATCAACTT-AATTCAATCAAGATAACATACAATACA
* * *
8321 TCATCATTTAATTTGAT
65 TCATAATTCAACTTGAT
* * * * * *
8338 TCGATCATGGTAGCATGCAATAGATAATCATTCAAATTGATTCAATCATGGTAACATGCAATA
1 TCGATCATGGTAGCATGCAATAGATCATCA-TCAACTTAATTCAATCAAGATAACATACAATA
8401 ATTCAACATT
Statistics
Matches: 117, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
80 2 0.02
81 63 0.54
82 50 0.43
83 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (81 bp):
TCGATCATGGTAGCATGCAATAGATCATCATCAACTTAATTCAATCAAGATAACATACAATACAT
CATAATTCAACTTGAT
Found at i:8432 original size:82 final size:82
Alignment explanation
Indices: 8199--8972 Score: 762
Period size: 82 Copynumber: 9.5 Consensus size: 82
8189 ATGCAGTAGA
* * * * *
8199 TCATCATTCAACTTGATTCAATCATGGTAACATGCAGTACA-TCATA-ATTCAACTT-GATTCAA
1 TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATA-ATTCA-ACATTCGA-TTCAATTCAA
* * ** *
8261 TCATGGTAACATGCAATAGA
63 TCAAGGTAGCATATAATAGT
* ** * * * ** * * ** ** *
8281 TCATCA-TCGATTCAATTCAATCAAGATAACATATAATAGTTCATCATTTAATTTGATTCGATCA
1 TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATTCAACATTCGATTCAATTCAATCA
* ** *
8345 TGGTAGCATGCAATAGA
66 AGGTAGCATATAATAGT
* * *
8362 TAATCATTCAAATTGATTCAATCATGGTAACATGCAATAATTCAACATTCGATTCAATTCAATCA
1 TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATTCAACATTCGATTCAATTCAATCA
8427 AGGTAGCATATAATAGT
66 AGGTAGCATATAATAGT
* * * * *
8444 TTATCCTTCAATTTGATTCGATCATGGTAGCATGCAATAATTCAACATTCGATTTAATTCAATAA
1 TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATTCAACATTCGATTCAATTCAATCA
*
8509 AGTTAGCATATAATAGT
66 AGGTAGCATATAATAGT
* * * * * *
8526 TTATCCTTCAATTTGATTCGATCATGGTAGCATTCAATAGA-TCATCATTTGATTCAATTCAATC
1 TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATA-ATTCAACATTCGATTCAATTCAATC
* **
8590 AAGGCATAATATAATAGT
65 AAGGTAGCATATAATAGT
* *
8608 TCATCATTCAATTTGATCCAATCATGGTAGCATGCAATAATT-AGACATTTGATTCAATTCAATC
1 TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATTCA-ACATTCGATTCAATTCAATC
*
8672 AAGGTATCATATAATAGT
65 AAGGTAGCATATAATAGT
* * * * * *
8690 TTATCCTTCAATTTGATTCAATCATGGTAACATGCAATAGA-TCATCATTCAATTCAAATCAATC
1 TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATA-ATTCAACATTCGATTCAATTCAATC
* *
8754 AAGGCATCATATAATAGT
65 AAGGTAGCATATAATAGT
* *
8772 TCATCATTCAATTTGTTTCAATCATGGTAGCATGCAATAATT---CATTTGATTCAATTCAATCA
1 TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATTCAACATTCGATTCAATTCAATCA
8834 AGGTAGCATATAATAGT
66 AGGTAGCATATAATAGT
* * * * * *
8851 TTATCCTTCAATTTAATTCGATCATGGTATCATGCAATAGA-TCATCATTCGATTCAATTCAATC
1 TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATA-ATTCAACATTCGATTCAATTCAATC
* *
8915 AA-GTCATCATATAATAAT
65 AAGGT-AGCATATAATAGT
* *
8933 TCATCATCCAATTGGATTCAATCATGGTAGCATGCAATAA
1 TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAA
8973 CCAATTTATC
Statistics
Matches: 584, Mismatches: 93, Indels: 31
0.82 0.13 0.04
Matches are distributed among these distances:
79 66 0.11
80 3 0.01
81 67 0.11
82 445 0.76
83 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (82 bp):
TCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATTCAACATTCGATTCAATTCAATCA
AGGTAGCATATAATAGT
Found at i:8582 original size:164 final size:163
Alignment explanation
Indices: 8205--8972 Score: 916
Period size: 164 Copynumber: 4.7 Consensus size: 163
8195 TAGATCATCA
* * * * * * * *
8205 TTCAACTTGATTCAATCATGGTAACATGCAGTACATCATAATTCAACTT-GATTCAATCATGGTA
1 TTCAATTTGATTCAATCATGGTAACATGCAATAGATCATCATTCGA-TTCAATTCAATCAAGGCA
* ** * * ** * * * ** * * *
8269 ACATGCAATAGATCATCA-TCGATTCAATTCAATCAAGATAACATATAATAGTTCATCATTTAAT
65 TCATATAATAGTTCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATT-AACATTTGAT
** * * ** * * *
8333 TTGATTCGATCATGGTAGCATGCAATAGATAATCA
129 TCAATTCAATCAAGGTAGCATATAATAGTTTATCC
* * *
8368 TTCAAATTGATTCAATCATGGTAACATGCAATA-ATTCAACATTCGATTCAATTCAATCAAGGTA
1 TTCAATTTGATTCAATCATGGTAACATGCAATAGA-TCATCATTCGATTCAATTCAATCAAGGCA
* * * * *
8432 GCATATAATAGTTTATCCTTCAATTTGATTCGATCATGGTAGCATGCAATAATTCAACATTCGAT
65 TCATATAATAGTTCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATT-AACATTTGAT
* * *
8497 TTAATTCAATAAAGTTAGCATATAATAGTTTATCC
129 TCAATTCAATCAAGGTAGCATATAATAGTTTATCC
* * * *
8532 TTCAATTTGATTCGATCATGGTAGCATTCAATAGATCATCATTTGATTCAATTCAATCAAGGCAT
1 TTCAATTTGATTCAATCATGGTAACATGCAATAGATCATCATTCGATTCAATTCAATCAAGGCAT
* *
8597 AATATAATAGTTCATCATTCAATTTGATCCAATCATGGTAGCATGCAATAATTAGACATTTGATT
66 CATATAATAGTTCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATTA-ACATTTGATT
*
8662 CAATTCAATCAAGGTATCATATAATAGTTTATCC
130 CAATTCAATCAAGGTAGCATATAATAGTTTATCC
* *
8696 TTCAATTTGATTCAATCATGGTAACATGCAATAGATCATCATTCAATTCAAATCAATCAAGGCAT
1 TTCAATTTGATTCAATCATGGTAACATGCAATAGATCATCATTCGATTCAATTCAATCAAGGCAT
*
8761 CATATAATAGTTCATCATTCAATTTGTTTCAATCATGGTAGCATGCAATAATT--CATTTGATTC
66 CATATAATAGTTCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATTAACATTTGATTC
8824 AATTCAATCAAGGTAGCATATAATAGTTTATCC
131 AATTCAATCAAGGTAGCATATAATAGTTTATCC
* * * *
8857 TTCAATTTAATTCGATCATGGTATCATGCAATAGATCATCATTCGATTCAATTCAATCAAGTCAT
1 TTCAATTTGATTCAATCATGGTAACATGCAATAGATCATCATTCGATTCAATTCAATCAAGGCAT
* * *
8922 CATATAATAATTCATCATCCAATTGGATTCAATCATGGTAGCATGCAATAA
66 CATATAATAGTTCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAA
8973 CCAATTTATC
Statistics
Matches: 526, Mismatches: 74, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
161 148 0.28
162 3 0.01
163 65 0.12
164 309 0.59
165 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (163 bp):
TTCAATTTGATTCAATCATGGTAACATGCAATAGATCATCATTCGATTCAATTCAATCAAGGCAT
CATATAATAGTTCATCATTCAATTTGATTCAATCATGGTAGCATGCAATAATTAACATTTGATTC
AATTCAATCAAGGTAGCATATAATAGTTTATCC
Found at i:8972 original size:41 final size:41
Alignment explanation
Indices: 8178--8972 Score: 509
Period size: 41 Copynumber: 19.5 Consensus size: 41
8168 CCTAGACTCG
* *
8178 ATCATGGTAGCATGCAGTAGA-TCATCATTCAACTTGATTCA
1 ATCATGGTAGCATGCAATA-ATTCATCATTCAATTTGATTCA
* * * *
8219 ATCATGGTAACATGCAGTACA-TCATAATTCAACTTGATTCA
1 ATCATGGTAGCATGCAATA-ATTCATCATTCAATTTGATTCA
* * **
8260 ATCATGGTAACATGCAATAGA-TCATCA-TCGATTCAATTCA
1 ATCATGGTAGCATGCAATA-ATTCATCATTCAATTTGATTCA
* * * ** * * *
8300 ATCAAGATAACATATAATAGTTCATCATTTAATTTGATTCG
1 ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
* *
8341 ATCATGGTAGCATGCAATAGA-TAATCATTCAAATTGATTCA
1 ATCATGGTAGCATGCAATA-ATTCATCATTCAATTTGATTCA
* * * **
8382 ATCATGGTAACATGCAATAATTCAACATTCGATTCAATTCA
1 ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
* ** * * * *
8423 ATCAAGGTAGCATATAATAGTTTATCCTTCAATTTGATTCG
1 ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
* * *
8464 ATCATGGTAGCATGCAATAATTCAACATTCGATTTAATTCA
1 ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
* * * ** * * * *
8505 ATAAAGTTAGCATATAATAGTTTATCCTTCAATTTGATTCG
1 ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
* ** **
8546 ATCATGGTAGCATTCAATAGA-TCATCATTTGATTCAATTCA
1 ATCATGGTAGCATGCAATA-ATTCATCATTCAATTTGATTCA
* * ** ** * *
8587 ATCAAGGCATAATATAATAGTTCATCATTCAATTTGATCCA
1 ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
* ** **
8628 ATCATGGTAGCATGCAATAATT-AGACATTTGATTCAATTCA
1 ATCATGGTAGCATGCAATAATTCA-TCATTCAATTTGATTCA
* * ** * * *
8669 ATCAAGGTATCATATAATAGTTTATCCTTCAATTTGATTCA
1 ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
* ** *
8710 ATCATGGTAACATGCAATAGA-TCATCATTCAATTCAAATCA
1 ATCATGGTAGCATGCAATA-ATTCATCATTCAATTTGATTCA
* * * ** * *
8751 ATCAAGGCATCATATAATAGTTCATCATTCAATTTGTTTCA
1 ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
* **
8792 ATCATGGTAGCATGCAATAATTCAT--TT-GATTCAATTCA
1 ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
* ** * * * * *
8830 ATCAAGGTAGCATATAATAGTTTATCCTTCAATTTAATTCG
1 ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
* * **
8871 ATCATGGTATCATGCAATAGA-TCATCATTCGATTCAATTCA
1 ATCATGGTAGCATGCAATA-ATTCATCATTCAATTTGATTCA
* * ** * *
8912 ATCA-AGTCATCATATAATAATTCATCATCCAATTGGATTCA
1 ATCATGGT-AGCATGCAATAATTCATCATTCAATTTGATTCA
8953 ATCATGGTAGCATGCAATAA
1 ATCATGGTAGCATGCAATAA
8973 CCAATTTATC
Statistics
Matches: 558, Mismatches: 179, Indels: 34
0.72 0.23 0.04
Matches are distributed among these distances:
38 27 0.05
39 2 0.00
40 37 0.07
41 489 0.88
42 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (41 bp):
ATCATGGTAGCATGCAATAATTCATCATTCAATTTGATTCA
Found at i:9078 original size:20 final size:20
Alignment explanation
Indices: 9053--9098 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
9043 TTTTAAGACT
9053 TAATTTCATTATTAACATAC
1 TAATTTCATTATTAACATAC
9073 TAATTTCATTATTAACATAC
1 TAATTTCATTATTAACATAC
9093 TAATTT
1 TAATTT
9099 AATAAGCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATTTCATTATTAACATAC
Found at i:10720 original size:68 final size:68
Alignment explanation
Indices: 10637--10823 Score: 295
Period size: 68 Copynumber: 2.8 Consensus size: 68
10627 CTTTCTATTA
* *
10637 AGTCATTATCTAATTCAATTAGTTTAAATTTTAATTCAACTTGGTTTTTATCTTAGGCAATTCAA
1 AGTCCTTATCTAATTCAATTAATTTAAATTTTAATTCAACTTGGTTTTTATCTTAGGCAATTCAA
10702 TTG
66 TTG
* *
10705 AGTCCTTATCTAATTCAATTAATTTAAATTTTAATTCAACCTGGTTTTTATCTTAGGCAATTCGA
1 AGTCCTTATCTAATTCAATTAATTTAAATTTTAATTCAACTTGGTTTTTATCTTAGGCAATTCAA
10770 TTG
66 TTG
* * *
10773 -GATCCTTATCTAATTCAATTAATTTAAATCTCAATTCAATTTGGTTTTTAT
1 AG-TCCTTATCTAATTCAATTAATTTAAATTTTAATTCAACTTGGTTTTTAT
10824 ATCCTAGGAA
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
67 1 0.01
68 109 0.99
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.47
Consensus pattern (68 bp):
AGTCCTTATCTAATTCAATTAATTTAAATTTTAATTCAACTTGGTTTTTATCTTAGGCAATTCAA
TTG
Found at i:12874 original size:4 final size:4
Alignment explanation
Indices: 12865--12898 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
12855 GTCCACGTGA
12865 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
12899 GACAAATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:17393 original size:25 final size:25
Alignment explanation
Indices: 17362--17412 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
17352 AAACCAACCC
17362 TATGCTCCATTTTAATATAAAACTA
1 TATGCTCCATTTTAATATAAAACTA
17387 TATGCTCCATTTTAATATAAAACTA
1 TATGCTCCATTTTAATATAAAACTA
17412 T
1 T
17413 CCTTTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TATGCTCCATTTTAATATAAAACTA
Found at i:17616 original size:2 final size:2
Alignment explanation
Indices: 17609--17640 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17599 TTAATAAGAA
17609 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
17641 TGCTATTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24195 original size:111 final size:111
Alignment explanation
Indices: 24001--24219 Score: 411
Period size: 111 Copynumber: 2.0 Consensus size: 111
23991 ATCGAGCCTA
24001 AAAATTGGTATCAGAGCGGGTCACAATCGACGGTTTAACAACCTTGTGAAGATCCTTGAAGATCT
1 AAAATTGGTATCAGAGCGGGTCACAATCGACGGTTTAACAACCTTGTGAAGATCCTTGAAGATCT
24066 CTATCAATTTTTAGCTCGAGAATATGGTTTTTTCTCCGAAGCTCCT
66 CTATCAATTTTTAGCTCGAGAATATGGTTTTTTCTCCGAAGCTCCT
24112 AAAATTGGTATCAGAGCGGGTCACAATCGACGGTTTAACAACCTTGTGAAGATCCTTGAAGATCT
1 AAAATTGGTATCAGAGCGGGTCACAATCGACGGTTTAACAACCTTGTGAAGATCCTTGAAGATCT
* * *
24177 CTATCAATTTTTGGCTCGAGAATATGTTTTTTTCTCCGGAGCT
66 CTATCAATTTTTAGCTCGAGAATATGGTTTTTTCTCCGAAGCT
24220 TACTACATCG
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (111 bp):
AAAATTGGTATCAGAGCGGGTCACAATCGACGGTTTAACAACCTTGTGAAGATCCTTGAAGATCT
CTATCAATTTTTAGCTCGAGAATATGGTTTTTTCTCCGAAGCTCCT
Found at i:24980 original size:312 final size:312
Alignment explanation
Indices: 24415--25039 Score: 1214
Period size: 312 Copynumber: 2.0 Consensus size: 312
24405 AGAGTTCCAA
*
24415 TTCAGTGCTAAGGTCATGCATATTTTATTTTGTGCATTAGGCCCGGATTAATATGGAAGAGTCTC
1 TTCAGTGCTAAGGTCATGCATATTTTATTTTGTGCATTAGGCCCAGATTAATATGGAAGAGTCTC
*
24480 TTCTTGTTCAAATGCCAAGGAGATTTGGGACAAGCTCCAAGTCACTCATGAAAGAACCGATGAAG
66 TTCTTGTTCAAATGCCAAGGAGATTTGGGACAAGCTCCAAGTCACACATGAAAGAACCGATGAAG
*
24545 TGAGGGAAACAAAAACGAATATTTTTAACCATAGCTATAATAATTTCAAGATGAAACCGGATGAA
131 TGAGGGAAACAAAAACGAATATTTTTAACCATAGCTACAATAATTTCAAGATGAAACCGGATGAA
24610 GACATCAAAGCTCTAATGAATAGATTTTTTCATGATTATCAATTGTCTCAAGGATACAGAGAGAT
196 GACATCAAAGCTCTAATGAATAGATTTTTTCATGATTATCAATTGTCTCAAGGATACAGAGAGAT
24675 TATCCCTAATGAGAAGCTTGCTAGGAAGATGATATATTCTCTTCCAAAATCT
261 TATCCCTAATGAGAAGCTTGCTAGGAAGATGATATATTCTCTTCCAAAATCT
24727 TTCAGTGCTAAGGTCATGCATATTTTATTTTGTGCATTAGGCCCAGATTAATATGGAAGAGTCTC
1 TTCAGTGCTAAGGTCATGCATATTTTATTTTGTGCATTAGGCCCAGATTAATATGGAAGAGTCTC
24792 TTCTTGTTCAAATGCCAAGGAGATTTGGGACAAGCTCCAAGTCACACATGAAAGAACCGATGAAG
66 TTCTTGTTCAAATGCCAAGGAGATTTGGGACAAGCTCCAAGTCACACATGAAAGAACCGATGAAG
24857 TGAGGGAAACAAAAACGAATATTTTTAACCATAGCTACAATAATTTCAAGATGAAACCGGATGAA
131 TGAGGGAAACAAAAACGAATATTTTTAACCATAGCTACAATAATTTCAAGATGAAACCGGATGAA
*
24922 GACATCAAAGCTCTAATGAATAGATTTTTTCGTGATTATCAATTGTCTCAAGGATACAGAGAGAT
196 GACATCAAAGCTCTAATGAATAGATTTTTTCATGATTATCAATTGTCTCAAGGATACAGAGAGAT
24987 TATCCCTAATGAGAAGCTTGCTAGGAAGATGATATATTCTCTTCCAAAATCT
261 TATCCCTAATGAGAAGCTTGCTAGGAAGATGATATATTCTCTTCCAAAATCT
25039 T
1 T
25040 GGTAATCGAA
Statistics
Matches: 309, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
312 309 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (312 bp):
TTCAGTGCTAAGGTCATGCATATTTTATTTTGTGCATTAGGCCCAGATTAATATGGAAGAGTCTC
TTCTTGTTCAAATGCCAAGGAGATTTGGGACAAGCTCCAAGTCACACATGAAAGAACCGATGAAG
TGAGGGAAACAAAAACGAATATTTTTAACCATAGCTACAATAATTTCAAGATGAAACCGGATGAA
GACATCAAAGCTCTAATGAATAGATTTTTTCATGATTATCAATTGTCTCAAGGATACAGAGAGAT
TATCCCTAATGAGAAGCTTGCTAGGAAGATGATATATTCTCTTCCAAAATCT
Found at i:29755 original size:15 final size:15
Alignment explanation
Indices: 29731--29783 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
29721 TTTTTTTTTC
29731 TTTTTCTTTCGAACAG
1 TTTTT-TTTCGAACAG
*
29747 TTTTTTTTCGAACTG
1 TTTTTTTTCGAACAG
29762 CTATTTTTTTC-AACA-
1 -T-TTTTTTTCGAACAG
29777 TTTTTTT
1 TTTTTTT
29784 GTGATGGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 6 0.18
14 1 0.03
15 9 0.27
16 9 0.27
17 8 0.24
ACGTcount: A:0.17, C:0.15, G:0.08, T:0.60
Consensus pattern (15 bp):
TTTTTTTTCGAACAG
Found at i:39400 original size:31 final size:29
Alignment explanation
Indices: 39360--39417 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
39350 TTAAATTGAA
*
39360 ATTTTATCTAAAATTCAAGAGTCAAATTAGT
1 ATTTCATCTAAAATT-AA-AGTCAAATTAGT
*
39391 ATTTCATCTAAAATTTAAGTCAAATTA
1 ATTTCATCTAAAATTAAAGTCAAATTA
39418 ATTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 1 0.04
31 14 0.56
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (29 bp):
ATTTCATCTAAAATTAAAGTCAAATTAGT
Found at i:41278 original size:22 final size:22
Alignment explanation
Indices: 41237--41279 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41227 CACGATAACA
***
41237 ATATTTTAAAATTTTTATTAAG
1 ATATTTTAAAATTAAGATTAAG
41259 ATATTTTAAAATTAAGATTAA
1 ATATTTTAAAATTAAGATTAA
41280 TTTAAGATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
ATATTTTAAAATTAAGATTAAG
Found at i:46248 original size:29 final size:28
Alignment explanation
Indices: 46215--46271 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
46205 TTTGGGTTTG
*
46215 AATTTAGTAAAAATTCAATTTAGTTCCCA
1 AATTTAATAAAAATTCAATTTAG-TCCCA
*
46244 AATTTAATATAAATTCAATTTAGTCCCA
1 AATTTAATAAAAATTCAATTTAGTCCCA
46272 GAATAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (28 bp):
AATTTAATAAAAATTCAATTTAGTCCCA
Found at i:49231 original size:32 final size:32
Alignment explanation
Indices: 49186--49307 Score: 165
Period size: 32 Copynumber: 3.8 Consensus size: 32
49176 ACCAGATACT
**
49186 AGTCAAGT-TTACATTCAGATAATGCACAACAG
1 AGTC-AGTGTTACATTCAGATAATGCACAGTAG
* * *
49218 AGTTAGTGTTACATTCAAATAATGCACAGTAT
1 AGTCAGTGTTACATTCAGATAATGCACAGTAG
*
49250 AGTCAGTGTTGCATTCAGATAATGCACAGTAG
1 AGTCAGTGTTACATTCAGATAATGCACAGTAG
*
49282 AGTCAGTGTTGCATTCAGATAATGCA
1 AGTCAGTGTTACATTCAGATAATGCA
49308 TAAGAGTTTC
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 3 0.04
32 77 0.96
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (32 bp):
AGTCAGTGTTACATTCAGATAATGCACAGTAG
Found at i:49320 original size:32 final size:31
Alignment explanation
Indices: 49197--49328 Score: 112
Period size: 32 Copynumber: 4.1 Consensus size: 31
49187 GTCAAGTTTA
*
49197 CATTCAGATAATGCACAACAGAGTT-AGTGTTA
1 CATTCAGATAATG--CAACAGAGTTCAGTGTTG
*
49229 CATTCAAATAATGC-ACAGTA-TAGTCAGTGTTG
1 CATTCAGATAATGCAACAG-AGT--TCAGTGTTG
*
49261 CATTCAGATAATGC-ACAGTAGAGTCAGTGTTG
1 CATTCAGATAATGCAACAG-AG-TTCAGTGTTG
*
49293 CATTCAGATAATGCATA-AGAGTTTCAGTGTCG
1 CATTCAGATAATGCA-ACAGAG-TTCAGTGTTG
49325 CATT
1 CATT
49329 TAAAGAATCC
Statistics
Matches: 85, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
29 5 0.06
30 2 0.02
31 1 0.01
32 74 0.87
33 2 0.02
34 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (31 bp):
CATTCAGATAATGCAACAGAGTTCAGTGTTG
Found at i:49320 original size:64 final size:64
Alignment explanation
Indices: 49197--49328 Score: 160
Period size: 64 Copynumber: 2.1 Consensus size: 64
49187 GTCAAGTTTA
* * *
49197 CATTCAGATAATGCACAACAGAGTTAGTGTTACATTCAAATAATGCACAGTATAGTCAGTGTTG
1 CATTCAGATAATGCACAACAGAGTCAGTGTTACATTCAAATAATGCAAAGTATAGTCAGTGTCG
** * * *
49261 CATTCAGATAATGCACAGTAGAGTCAGTGTTGCATTCAGATAATGCATAAG-AGT-TTCAGTGTC
1 CATTCAGATAATGCACAACAGAGTCAGTGTTACATTCAAATAATGCA-AAGTA-TAGTCAGTGTC
49324 G
64 G
49325 CATT
1 CATT
49329 TAAAGAATCC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 55 0.95
65 3 0.05
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (64 bp):
CATTCAGATAATGCACAACAGAGTCAGTGTTACATTCAAATAATGCAAAGTATAGTCAGTGTCG
Done.