Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001362.1 Hibiscus syriacus cultivar Beakdansim tig00002655_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: 681426
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 3 of 3
Found at i:639215 original size:54 final size:55
Alignment explanation
Indices: 639090--639309 Score: 329
Period size: 55 Copynumber: 4.0 Consensus size: 55
639080 CTTTTGAAAA
* **
639090 CGTGTCTGCTCCCTATTCCTTCAGAGAGTACGAGACTCGAACAATCTTCAACAAT
1 CGTGTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* * *
639145 CGTGTCTACTCCCTATTCTTTCAGAGAGTATGAGACTCGAA-TATCTTCAACAAT
1 CGTGTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
*
639199 CGTGTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAAACTTCAACAAT
1 CGTGTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* *
639254 CGCGTCTGCTCCCTATT-TCTTCAGAGAGTATAAGAC-CGAACAATCTTCAACGAT
1 CGTGTCTGCTCCCTATTCT-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
639308 CG
1 CG
639310 CTGGGAAACC
Statistics
Matches: 152, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
54 70 0.46
55 82 0.54
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (55 bp):
CGTGTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
Found at i:640311 original size:8 final size:8
Alignment explanation
Indices: 640298--640345 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
640288 TCTTGAACCC
640298 TCATTTTT
1 TCATTTTT
640306 TCATTTTT
1 TCATTTTT
640314 TCATTCATTT
1 TCATT--TTT
*
640324 T-TTTTTT
1 TCATTTTT
*
640331 TTATTTTT
1 TCATTTTT
640339 TCATTTT
1 TCATTTT
640346 CACTCATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 4 0.12
8 24 0.71
9 2 0.06
10 4 0.12
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.77
Consensus pattern (8 bp):
TCATTTTT
Found at i:640369 original size:31 final size:32
Alignment explanation
Indices: 640300--640369 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
640290 TTGAACCCTC
* * *
640300 ATTTTTTCATTTTTTCATTCATTTTTTTTTTTT
1 ATTTTTTCA-TTTTTCACTCATTTTTTCTTCTT
640333 ATTTTTTCA-TTTTCACTCATTTTTTCTTCTT
1 ATTTTTTCATTTTTCACTCATTTTTTCTTCTT
*
640364 CTTTTT
1 ATTTTT
640370 CTTCAAGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 24 0.73
33 9 0.27
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (32 bp):
ATTTTTTCATTTTTCACTCATTTTTTCTTCTT
Found at i:655441 original size:19 final size:19
Alignment explanation
Indices: 655413--655452 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
655403 ATTAGTATAT
*
655413 TAATAGAATCTCTT-TAAAA
1 TAATAAAATCT-TTCTAAAA
655432 TAATAAAATCTTTCTAAAA
1 TAATAAAATCTTTCTAAAA
655451 TA
1 TA
655453 TTCAAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (19 bp):
TAATAAAATCTTTCTAAAA
Found at i:656167 original size:99 final size:99
Alignment explanation
Indices: 655995--656571 Score: 904
Period size: 99 Copynumber: 5.8 Consensus size: 99
655985 AGAACGTGAG
* * *
655995 TCTTTTGTCAAGGATTTCGATCCAAACCGTCCTCAATTTCCTCTGGTGTATTACTCAAAAAAAGA
1 TCTTTTGTCAAGGATTTCGACCCAAACCGTCCTCAATTTCCCCTGGTGTATTACTCGAAAAAAGA
* *
656060 TGGCCAGTCTCAAGAGCAAGCAGAAAATGATAAA
66 TGGTCAGTCTCAAGAGCATGCAGAAAATGATAAA
* * * *
656094 TCTTTTATCAAGGATTTCAACCCAAACCGTCCTCAATTTCCCCTGGTATATTACTCAAAAAAAGA
1 TCTTTTGTCAAGGATTTCGACCCAAACCGTCCTCAATTTCCCCTGGTGTATTACTCGAAAAAAGA
*
656159 TGGTCAGTCTAAAGAGCATGCAGAAAATGATAAA
66 TGGTCAGTCTCAAGAGCATGCAGAAAATGATAAA
656193 TCTTTTGTCAAGGATTTCGACCCAAACCGTCCTCAATTTCCCCTGGTGTATTACTCGAAAAAAGA
1 TCTTTTGTCAAGGATTTCGACCCAAACCGTCCTCAATTTCCCCTGGTGTATTACTCGAAAAAAGA
*
656258 TGGTCAGTCTCAAGAGCATGAAGAAAATGATAAA
66 TGGTCAGTCTCAAGAGCATGCAGAAAATGATAAA
* * *
656292 TCTTTTGTCAAGGATTTCGACCCAAATCGTCCTCAATTCCCCCTAGTGTATTACTCGAAAAAAGA
1 TCTTTTGTCAAGGATTTCGACCCAAACCGTCCTCAATTTCCCCTGGTGTATTACTCGAAAAAAGA
* * *
656357 CGGCCAGTCTCAAGAGCATGCAAAAAATGATAAA
66 TGGTCAGTCTCAAGAGCATGCAGAAAATGATAAA
* * * * *
656391 TCTTTTGTTAAGGATTTCGATCCAAACCGTCCTCAATTCCCCCTAGTATATTACTCGAAAAAAGA
1 TCTTTTGTCAAGGATTTCGACCCAAACCGTCCTCAATTTCCCCTGGTGTATTACTCGAAAAAAGA
*
656456 TGG-CGAGTCTCGAGAGCATGCAGAAAATGATAAA
66 TGGTC-AGTCTCAAGAGCATGCAGAAAATGATAAA
** *
656490 TCTTTTGTCAAGGATTTCGACCCAAACCGTCCTCAATTTCCTTTGGTGTATTACTCCAAAAAAGA
1 TCTTTTGTCAAGGATTTCGACCCAAACCGTCCTCAATTTCCCCTGGTGTATTACTCGAAAAAAGA
656555 TGGTCAGTCTCAAGAGC
66 TGGTCAGTCTCAAGAGC
656572 CCACAAAAAC
Statistics
Matches: 439, Mismatches: 37, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
98 1 0.00
99 437 1.00
100 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (99 bp):
TCTTTTGTCAAGGATTTCGACCCAAACCGTCCTCAATTTCCCCTGGTGTATTACTCGAAAAAAGA
TGGTCAGTCTCAAGAGCATGCAGAAAATGATAAA
Found at i:661436 original size:19 final size:19
Alignment explanation
Indices: 661412--661450 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
661402 TTTGTAGAAG
661412 ATAAGCTACAAAGAAAAGA
1 ATAAGCTACAAAGAAAAGA
661431 ATAAGCTACAAAGAAAAGA
1 ATAAGCTACAAAGAAAAGA
661450 A
1 A
661451 GAAGATGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.10, G:0.15, T:0.10
Consensus pattern (19 bp):
ATAAGCTACAAAGAAAAGA
Found at i:666089 original size:362 final size:360
Alignment explanation
Indices: 665426--666131 Score: 1270
Period size: 362 Copynumber: 2.0 Consensus size: 360
665416 TTTAAAATAC
*
665426 AATATTTATAAAACATTAGTTTTTAGGGTAAATTATACTATTGACCACCTAATTATTTACCCTTT
1 AATATTTATAAAACATTAGTTTTTAGGGTAAAATATACTATTGACCACCTAATTATTTACCCTTT
*
665491 TAGTTTAACCACCGATTTTTGAATTTGTCAATCGAGTCACCTAATTTAAATATTGTCAATCAAGC
66 TAGTTTAACCACCGATTTTTCAATTTGTCAATCGAGTCACCTAATTTAAATATTGTCAATCAAGC
*
665556 CACATGTCATTAAATATTAACGGAGGAGATGATGGCAGTTAATAAAATTTGTATAATTACACATT
131 CACATGTCATTAAATATTAACGGAGGAGATGATGGCAGTTAATAAAATTTATATAATTACACATT
* **
665621 TAATCCCCATTACTTGCACATTCTATTAATTTGGTTTTAACTTTTATTTAATTAAATAAATTTAA
196 TAATCCCCATTACTTACACATTCTATTAATTTGGTCCTAACTTTTATTTAATTAAATAAATTTAA
*
665686 TCCTCAATCCGATTGTGACATGTGTCATTGTGTGATTGGATGTTTTTTATATTTTTATTTAATTT
261 TCCTCAATCCGATTGTGACATGTGTCATTATGTGATTGGATGTTTTTTATATTTTTATTTAATTT
665751 ATTTTCCATCCAATCAAATGGTGCCATATGTCAAT
326 ATTTTCCATCCAATCAAATGGTGCCATATGTCAAT
*
665786 AATATTTAT-AAATATTAGTTTTTAGGGTAAAATATACTATTGACCACCTAATTATTTACCCTTT
1 AATATTTATAAAACATTAGTTTTTAGGGTAAAATATACTATTGACCACCTAATTATTTACCCTTT
*
665850 TAGTTTAACCACCGATTTTTCAATTTTGTCAATCGAGTCACTTAATTTAAATATTGTCAATCAAG
66 TAGTTTAACCACCGATTTTTCAA-TTTGTCAATCGAGTCACCTAATTTAAATATTGTCAATCAAG
665915 CCACATGTCATTAAATATTAACGGAGGAGATGATGTGGCAGTTAATAAAATTTATATAATTACAC
130 CCACATGTCATTAAATATTAACGGAGGAGATGA--TGGCAGTTAATAAAATTTATATAATTACAC
* *
665980 ATTTAATCCTCATTACTTACACATTCTATTAATTTGGTCCTAACTTTTATTTAATTCAATAAATT
193 ATTTAATCCCCATTACTTACACATTCTATTAATTTGGTCCTAACTTTTATTTAATTAAATAAATT
*
666045 TAATCCTCAATCCGATTGTGACATGTGTCATTATGTGGTTGGATGTTTTTTATATTTTTATTTAA
258 TAATCCTCAATCCGATTGTGACATGTGTCATTATGTGATTGGATGTTTTTTATATTTTTATTTAA
666110 TTTATTTTCCATCCAATCAAAT
323 TTTATTTTCCATCCAATCAAAT
666132 AATGCCACGT
Statistics
Matches: 331, Mismatches: 12, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
359 75 0.23
360 82 0.25
362 174 0.53
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (360 bp):
AATATTTATAAAACATTAGTTTTTAGGGTAAAATATACTATTGACCACCTAATTATTTACCCTTT
TAGTTTAACCACCGATTTTTCAATTTGTCAATCGAGTCACCTAATTTAAATATTGTCAATCAAGC
CACATGTCATTAAATATTAACGGAGGAGATGATGGCAGTTAATAAAATTTATATAATTACACATT
TAATCCCCATTACTTACACATTCTATTAATTTGGTCCTAACTTTTATTTAATTAAATAAATTTAA
TCCTCAATCCGATTGTGACATGTGTCATTATGTGATTGGATGTTTTTTATATTTTTATTTAATTT
ATTTTCCATCCAATCAAATGGTGCCATATGTCAAT
Found at i:667493 original size:22 final size:22
Alignment explanation
Indices: 667467--667519 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
667457 TAAATATTGT
*
667467 ATTTTAATTAAATTATATTTAA
1 ATTTTAATTAAATTATAATTAA
* * *
667489 ATTTTAACTAATTTATAATTAT
1 ATTTTAATTAAATTATAATTAA
667511 ATATTTAAT
1 AT-TTTAAT
667520 ATTTTACAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTAATTAAATTATAATTAA
Found at i:669229 original size:159 final size:160
Alignment explanation
Indices: 668808--669543 Score: 773
Period size: 159 Copynumber: 4.6 Consensus size: 160
668798 TTATTTTAAG
* * * *
668808 CCGATACCGAGCGTCACGTCTTACGGCAG-AGATGAT-TTGGTCTT-AAGGAGAGCCGAAATCAT
1 CCGAGACCGAGCGTCACGTCTTACGGCAGCA-ATGATGTTGATCTTAAAGGAGTG--AAAATCAT
* * * * ** ** *
668870 TCACCATTGATTTTGAATCGAGACCGAGCGTCATTTCTTACAACGA-AATGAAGTTGATCTT-AA
63 TCACTAGTGATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGACAATGATGTTGATCTTAAA
*
668933 GGAGCT-AAGAAATCATTCACGAGTGACTTTGAA
128 GGAG-TGAAGAAATCATTCACTAGTGACTTTGAA
* * * *
668966 CCGATACCGAGCGTCACGTTTTACGGCGGCATTGATGTTGATCTTAAAGGAGTGAAGAAATCATT
1 CCGAGACCGAGCGTCACGTCTTACGGCAGCAATGATGTTGATCTTAAAGGAGTG-A-AAATCATT
* * *
669031 CACTAGAGACTTTGAACCGAGACCGAGCGTCACGTCTTACGGCGACAATGATGTTGATCTTAAAG
64 CACTAGTGATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGACAATGATGTTGATCTTAAAG
* *
669096 GAGTGAAGAAATCATTTACTAGTGA-TTTGAG
129 GAGTGAAGAAATCATTCACTAGTGACTTTGAA
* ** * *
669127 TCGAGA-CGAGCGTCACGTCTTACGGTGGCAATGATGTTGATCTTAAAGGAGTGCAAAAACCTTC
1 CCGAGACCGAGCGTCACGTCTTACGGCAGCAATGATGTTGATCTTAAAGGAGTG-AAAATCATTC
* * *
669191 ACTAGTGATTTTGAGCTGAGACCGAGTGTCACGTCTTACGGCGGCAATGATGTTGATCTTAAA-G
65 ACTAGTGATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGACAATGATGTTGATCTTAAAGG
* * *
669255 AGTGGAGAAATCATTCACTAGTGATTTTGAG
130 AGTGAAGAAATCATTCACTAGTGACTTTGAA
* * * * *
669286 CCGAGATCGAGTGTCACATCTTACGGCAGCAATGATGTGGATCTT-AAGGAGTGGAGAATCATTC
1 CCGAGACCGAGCGTCACGTCTTACGGCAGCAATGATGTTGATCTTAAAGGAGT-GAAAATCATTC
* * * * * * * *
669350 ACTAGTGATTTTGAACCAAGACCAAGTGTGA-GTCTTATGGTGACAATGATGGTGATCTCAAAGT
65 ACTAGTGATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGACAATGATGTTGATCTTAAAGG
* * **
669414 AGTGGAGAAATCATTCACTTGTGTTTTTGAA
130 AGTGAAGAAATCATTCACTAGTGACTTTGAA
* * * *
669445 CCGAGACCAAGTGTCACGTCTTACAGC-GCGAATGATGTTGATCTTAAAGGAGTGGAAATCATTC
1 CCGAGACCGAGCGTCACGTCTTACGGCAGC-AATGATGTTGATCTTAAAGGAGTGAAAATCATTC
* *
669509 ACTA-TG--TTTGAACGGAGACCGAGTGTCACTTCTTA
65 ACTAGTGATTTTGAACCGAGACCGAGTGTCACGTCTTA
669544 TCAAAAATCG
Statistics
Matches: 493, Mismatches: 71, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
156 18 0.04
157 5 0.01
158 84 0.17
159 201 0.41
160 137 0.28
161 24 0.05
162 24 0.05
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (160 bp):
CCGAGACCGAGCGTCACGTCTTACGGCAGCAATGATGTTGATCTTAAAGGAGTGAAAATCATTCA
CTAGTGATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGACAATGATGTTGATCTTAAAGGA
GTGAAGAAATCATTCACTAGTGACTTTGAA
Found at i:669244 original size:80 final size:79
Alignment explanation
Indices: 668800--669543 Score: 708
Period size: 79 Copynumber: 9.4 Consensus size: 79
668790 ATTTTCTATT
* * * * *
668800 ATTTT-AAGCCGATACCGAGCGTCACGTCTTACGGCAG-AGATGAT-TTGGTCTT-AAGGAGAGC
1 ATTTTGAA-CCGAGACCGAGTGTCACGTCTTACGGCGGCA-ATGATGTTGATCTTAAAGGAGTG-
* * *
668861 CGAAATCATTCACCATTG
63 -AAAATCATTCACTAGTG
* * ** ** * * *
668879 ATTTTGAATCGAGACCGAGCGTCATTTCTTACAAC-GAAATGAAGTTGATCTT-AAGGAGCTAAG
1 ATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAATGATGTTGATCTTAAAGGAG-TGA-
*
668942 AAATCATTCACGAGTG
64 AAATCATTCACTAGTG
* * * * *
668958 ACTTTGAACCGATACCGAGCGTCACGTTTTACGGCGGCATTGATGTTGATCTTAAAGGAGTGAAG
1 ATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAATGATGTTGATCTTAAAGGAGTG-A-
*
669023 AAATCATTCACTAGAG
64 AAATCATTCACTAGTG
* * *
669039 ACTTTGAACCGAGACCGAGCGTCACGTCTTACGGCGACAATGATGTTGATCTTAAAGGAGTGAAG
1 ATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAATGATGTTGATCTTAAAGGAGTG-A-
*
669104 AAATCATTTACTAGTG
64 AAATCATTCACTAGTG
** * *
669120 A-TTTGAGTCGAGA-CGAGCGTCACGTCTTACGGTGGCAATGATGTTGATCTTAAAGGAGTGCAA
1 ATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAATGATGTTGATCTTAAAGGAGTG-AA
* *
669183 AAACCTTCACTAGTG
65 AATCATTCACTAGTG
* *
669198 ATTTTGAGCTGAGACCGAGTGTCACGTCTTACGGCGGCAATGATGTTGATCTTAAA-GAGTGGAG
1 ATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAATGATGTTGATCTTAAAGGAGT-GA-
669262 AAATCATTCACTAGTG
64 AAATCATTCACTAGTG
* * * * * *
669278 ATTTTGAGCCGAGATCGAGTGTCACATCTTACGGCAGCAATGATGTGGATCTT-AAGGAGTGGAG
1 ATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAATGATGTTGATCTTAAAGGAGT-GAA
669342 AATCATTCACTAGTG
65 AATCATTCACTAGTG
* * * * * * * * *
669357 ATTTTGAACCAAGACCAAGTGTGA-GTCTTATGGTGACAATGATGGTGATCTCAAAGTAGTGGAG
1 ATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAATGATGTTGATCTTAAAGGAGT-GA-
*
669421 AAATCATTCACTTGTG
64 AAATCATTCACTAGTG
* * * *
669437 TTTTTGAACCGAGACCAAGTGTCACGTCTTACAGC-GCGAATGATGTTGATCTTAAAGGAGTGGA
1 ATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGC-AATGATGTTGATCTTAAAGGAGTGAA
669501 AATCATTCACTA-TG
65 AATCATTCACTAGTG
* *
669515 --TTTGAACGGAGACCGAGTGTCACTTCTTA
1 ATTTTGAACCGAGACCGAGTGTCACGTCTTA
669544 TCAAAAATCG
Statistics
Matches: 564, Mismatches: 84, Indels: 37
0.82 0.12 0.05
Matches are distributed among these distances:
76 26 0.05
78 41 0.07
79 199 0.35
80 173 0.31
81 125 0.22
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (79 bp):
ATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAATGATGTTGATCTTAAAGGAGTGAAA
ATCATTCACTAGTG
Found at i:669310 original size:239 final size:239
Alignment explanation
Indices: 668808--669543 Score: 746
Period size: 239 Copynumber: 3.1 Consensus size: 239
668798 TTATTTTAAG
* * * * * **
668808 CCGATACCGAGCGTCACGTCTTACGGCAG-AGATGATTTGG-TCTTAAGGAGAGCCGAAATCATT
1 CCGAGACCGAGTGTCACATCTTACGGCAGCA-ATGATGTGGATCTTAAGGAGTGAAG-AATCATT
* * * * * * *** * * *
668871 CACCATTGATTTTGAATCGAGACCGAGCGTCATTTCTTACAACGA-AATGAAGTTGATCT-TAAG
64 CACTAGTGATTTTGAACCAAGACCAAGCGTCA-GTCTTACGGTGACAATGATGGTGATCTCAAAG
* * * * * * * *
668934 GAGCT-AAGAAATCATTCACGAGTGACTTTGAACCGATACCGAGCGTCACGTTTTACGGCGGCAT
128 GAG-TGCAGAAAACATTCACTAGTGATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAA
* *
668998 TGATGTTGATCTTAAAGGAGTGAAGAAATCATTCACTAGAGACTTTGAA
192 TGATGTTGATCTTAAAGGAGTGGAGAAATCATTCACTAGTGA-TTTGAA
* * *
669047 CCGAGACCGAGCGTCACGTCTTACGGC-GACAATGATGTTGATCTTAAAGGAGTGAAGAAATCAT
1 CCGAGACCGAGTGTCACATCTTACGGCAG-CAATGATGTGGATCTT-AAGGAGTGAAG-AATCAT
* ** * * * * *
669111 TTACTAGTGA-TTTGAGTCGAGA-CGAGCGTCACGTCTTACGGTGGCAATGATGTTGATCTTAAA
63 TCACTAGTGATTTTGAACCAAGACCAAGCGTCA-GTCTTACGGTGACAATGATGGTGATCTCAAA
* * *
669174 GGAGTGCA-AAAACCTTCACTAGTGATTTTGAGCTGAGACCGAGTGTCACGTCTTACGGCGGCAA
127 GGAGTGCAGAAAACATTCACTAGTGATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAA
*
669238 TGATGTTGATCTTAAA-GAGTGGAGAAATCATTCACTAGTGATTTTGAG
192 TGATGTTGATCTTAAAGGAGTGGAGAAATCATTCACTAGTGA-TTTGAA
* *
669286 CCGAGATCGAGTGTCACATCTTACGGCAGCAATGATGTGGATCTTAAGGAGTGGAGAATCATTCA
1 CCGAGACCGAGTGTCACATCTTACGGCAGCAATGATGTGGATCTTAAGGAGTGAAGAATCATTCA
* * * *
669351 CTAGTGATTTTGAACCAAGACCAAGTGTGAGTCTTATGGTGACAATGATGGTGATCTCAAAGTAG
66 CTAGTGATTTTGAACCAAGACCAAGCGTCAGTCTTACGGTGACAATGATGGTGATCTCAAAGGAG
* * * * * *
669416 TGGAGAAATCATTCACTTGTGTTTTTGAACCGAGACCAAGTGTCACGTCTTACAGC-GCGAATGA
131 TGCAGAAAACATTCACTAGTGATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGC-AATGA
669480 TGTTGATCTTAAAGGAGT-G-GAAATCATTCACTA-TG-TTTGAA
195 TGTTGATCTTAAAGGAGTGGAGAAATCATTCACTAGTGATTTGAA
* *
669521 CGGAGACCGAGTGTCACTTCTTA
1 CCGAGACCGAGTGTCACATCTTA
669544 TCAAAAATCG
Statistics
Matches: 421, Mismatches: 63, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
235 25 0.06
237 17 0.04
238 69 0.16
239 184 0.44
240 97 0.23
241 29 0.07
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (239 bp):
CCGAGACCGAGTGTCACATCTTACGGCAGCAATGATGTGGATCTTAAGGAGTGAAGAATCATTCA
CTAGTGATTTTGAACCAAGACCAAGCGTCAGTCTTACGGTGACAATGATGGTGATCTCAAAGGAG
TGCAGAAAACATTCACTAGTGATTTTGAACCGAGACCGAGTGTCACGTCTTACGGCGGCAATGAT
GTTGATCTTAAAGGAGTGGAGAAATCATTCACTAGTGATTTGAA
Found at i:669623 original size:54 final size:50
Alignment explanation
Indices: 669499--669698 Score: 176
Period size: 54 Copynumber: 4.0 Consensus size: 50
669489 TAAAGGAGTG
** *
669499 GAAATCATTCACTA-TG--TTTGAACGGAGACCGAGTGTCACTTCTTATCA
1 GAAATCATTCACTAGTGATTTTGAAC-GAGACCGAGTACCACATCTTATCA
* *
669547 AAAATCGTTCACTAGTGATTTTGAACTGAGACCGAGTACCACATCTTATGGCCA
1 GAAATCATTCACTAGTGATTTTGAAC-GAGACCGAGTACCACATCTTAT---CA
* * **
669601 GAAATCGTTCACTAGTGATTTTGAAACGAGACC-AATATTACATCTTAT-A
1 GAAATCATTCACTAGTGATTTTG-AACGAGACCGAGTACCACATCTTATCA
* * * * *
669650 GCAATCATTCACTAGTGATTTTGAACCAAGTCTGAGTACCACATTTTAT
1 GAAATCATTCACTAGTGATTTTGAA-CGAGACCGAGTACCACATCTTAT
669699 GGCTAGAAAC
Statistics
Matches: 124, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
48 14 0.11
49 28 0.23
50 11 0.09
51 26 0.21
53 12 0.10
54 30 0.24
55 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (50 bp):
GAAATCATTCACTAGTGATTTTGAACGAGACCGAGTACCACATCTTATCA
Found at i:675475 original size:26 final size:26
Alignment explanation
Indices: 675446--675500 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
675436 ACATTACCTT
*
675446 ATTGTTACAATTAATTAAGTGACTTG
1 ATTGTTACAATAAATTAAGTGACTTG
*
675472 ATTGTTACAATAAATTGAGTGACTTG
1 ATTGTTACAATAAATTAAGTGACTTG
675498 ATT
1 ATT
675501 ATAACTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (26 bp):
ATTGTTACAATAAATTAAGTGACTTG
Done.