Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000161.1 Hibiscus syriacus cultivar Beakdansim tig00000284_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: 58708
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:287 original size:24 final size:24
Alignment explanation
Indices: 236--287 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
226 ATCCAAGTAT
** *
236 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
260 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
284 TGAC
1 TGAC
288 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:1103 original size:20 final size:20
Alignment explanation
Indices: 1078--1207 Score: 172
Period size: 20 Copynumber: 6.5 Consensus size: 20
1068 TTGAAATTCA
*
1078 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
1098 GCGTTGCGTTAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
1118 GCGTTGCGATAGTCAGAATT
1 GCGTTGCGATAGTCAGAATC
*
1138 GAGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
**
1158 GCGTTGCGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
*
1179 ACGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
1199 GCGTTGCGA
1 GCGTTGCGA
1208 ATCTGGAAAC
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 76 0.81
21 14 0.15
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:1240 original size:81 final size:81
Alignment explanation
Indices: 1099--1249 Score: 191
Period size: 81 Copynumber: 1.9 Consensus size: 81
1089 GTCAGAATCG
* * *
1099 CGTTGCGTTAGTCAGAATCGCGTTGCGATAGTCAGAATTGAGTTGCGATAGTCAGAATCGCGTTG
1 CGTTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAACTGAGTTGCGATACTCAGAATCGCGTTG
1164 CGATTATGTATTATCA
66 CGATTATGTATTATCA
* * * *
1180 CGTTGCGATAGTCAGAATCGCGTTGCGA-A-TCTGGAAACTGATTTGTGATACT-GGAGATCGCG
1 CGTTGCGATAGTCAGAATCGCGTTGCGATAGTC-AG-AACTGAGTTGCGATACTCAGA-ATCGCG
1242 TTGCGATT
63 TTGCGATT
1250 TAGAGATTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
79 2 0.03
80 4 0.07
81 54 0.90
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (81 bp):
CGTTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAACTGAGTTGCGATACTCAGAATCGCGTTG
CGATTATGTATTATCA
Found at i:10953 original size:30 final size:30
Alignment explanation
Indices: 10912--11025 Score: 174
Period size: 30 Copynumber: 3.8 Consensus size: 30
10902 GCAGCTCCAT
* *
10912 AGGTCGACGTGTGCTCCTGGAGATCTATGG
1 AGGTCGCCGTGTGCTCCTGGAGACCTATGG
10942 AGGTCGCCGTGTGCTCCTGGAGACCTATGG
1 AGGTCGCCGTGTGCTCCTGGAGACCTATGG
* * *
10972 AGGTCGTCGTATGCTTCTGGAGACCTATGG
1 AGGTCGCCGTGTGCTCCTGGAGACCTATGG
*
11002 AGGTCGCCGTGTGTTCCTGGAGAC
1 AGGTCGCCGTGTGCTCCTGGAGAC
11026 TTATAGTGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.15, C:0.23, G:0.36, T:0.26
Consensus pattern (30 bp):
AGGTCGCCGTGTGCTCCTGGAGACCTATGG
Found at i:12204 original size:18 final size:18
Alignment explanation
Indices: 12160--12204 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
12150 ATGAAAATGG
12160 AAGATTAAAATAAGTTTA
1 AAGATTAAAATAAGTTTA
*
12178 GAGATTAAAATAAGTTTA
1 AAGATTAAAATAAGTTTA
*
12196 AAGACTAAA
1 AAGATTAAA
12205 TTAAAATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.29
Consensus pattern (18 bp):
AAGATTAAAATAAGTTTA
Found at i:14109 original size:12 final size:13
Alignment explanation
Indices: 14085--14114 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
14075 GTATAATTTC
14085 TAAAATGTACAAA
1 TAAAATGTACAAA
14098 TAAAAT-TACAAA
1 TAAAATGTACAAA
14110 TAAAA
1 TAAAA
14115 CTATACCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (13 bp):
TAAAATGTACAAA
Found at i:23953 original size:23 final size:23
Alignment explanation
Indices: 23927--23974 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
23917 ATAAAGTACA
*
23927 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
23950 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
23973 AT
1 AT
23975 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:24724 original size:18 final size:18
Alignment explanation
Indices: 24701--24737 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24691 CCGAATATAT
24701 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
24719 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
24737 A
1 A
24738 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:24967 original size:23 final size:23
Alignment explanation
Indices: 24941--25005 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
24931 ATGCGAGATA
24941 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
** **
24964 GATACCTATTTTATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
24987 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
25006 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:25388 original size:21 final size:22
Alignment explanation
Indices: 25363--25414 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
25353 ACACTTTACA
*
25363 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
25386 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
25409 ATATAA
1 ATATAA
25415 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:25399 original size:23 final size:23
Alignment explanation
Indices: 25373--25435 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
25363 ATATAACCAC
25373 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
25396 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
25419 TACCTATTACATCATAT
1 TACCTATTACATTATAT
25436 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:25789 original size:20 final size:21
Alignment explanation
Indices: 25750--25792 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
25740 TCCACAGTGA
* *
25750 AAAAAGTATGGACACTTTTAT
1 AAAAAGGATAGACACTTTTAT
25771 AAAAAGGATAGACAC-TTTAT
1 AAAAAGGATAGACACTTTTAT
25791 AA
1 AA
25793 TATAACCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (21 bp):
AAAAAGGATAGACACTTTTAT
Found at i:25819 original size:23 final size:23
Alignment explanation
Indices: 25792--25864 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
25782 ACACTTTATA
*
25792 ATATAACCACTACCTATTACATT
1 ATATAACGACTACCTATTACATT
25815 ATATAAACGA-TACCTATTACATT
1 ATAT-AACGACTACCTATTACATT
* * *
25838 ATATAAGGGCTACCTATTACATC
1 ATATAACGACTACCTATTACATT
25861 ATAT
1 ATAT
25865 GTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.07
23 37 0.84
24 4 0.09
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAACGACTACCTATTACATT
Found at i:25992 original size:428 final size:431
Alignment explanation
Indices: 24943--27248 Score: 4456
Period size: 429 Copynumber: 5.4 Consensus size: 431
24933 GCGAGATAGA
**
24943 TACCTATTACATTATATAAACGATACCTATTTTATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
25008 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
25073 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
25138 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
25203 AATTTAATAATAATATATACCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
25267 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
25332 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
25373 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
25438 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
25503 TGTAATTTATGTTTCAA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
*
25567 ATTTCATTTGCAC-AAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAAAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
25631 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
25696 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
*
25761 ACACTTTTATAAAAAGGATAGACACTTTATAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
25802 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
25867 TTACCTATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATAC-TTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
25930 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
25995 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAA-TTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
26059 --TTTAATAATAATATATACCGTAACGTAAAAAAT-AATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
26121 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAA-TATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
26185 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
26226 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
26291 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
26356 TGTAATTTATGTTTCAA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
*
26420 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
*
26485 AATTTAATAATAATATATATCGTAACGTAAAAAA-AAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
26549 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
26614 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
26655 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
26720 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTTAAAACTT
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTTAAAACTT
26785 ATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAAT
130 ATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAAT
26850 AATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTT
195 AATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTT
26915 TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
260 TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
26980 TAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATG
325 TAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATG
27045 GACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
390 GACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
27087 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
27152 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
27217 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
27249 ACTGCGAATT
Statistics
Matches: 1852, Mismatches: 11, Indels: 25
0.98 0.01 0.01
Matches are distributed among these distances:
424 145 0.08
425 208 0.11
426 68 0.04
427 31 0.02
428 275 0.15
429 507 0.27
430 177 0.10
431 191 0.10
432 250 0.13
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (431 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
Found at i:26241 original size:21 final size:22
Alignment explanation
Indices: 26216--26267 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
26206 ACACTTTACA
*
26216 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
26239 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
26262 ATATAA
1 ATATAA
26268 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:26252 original size:23 final size:23
Alignment explanation
Indices: 26226--26288 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
26216 ATATAACCAC
26226 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
26249 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
26272 TACCTATTACATCATAT
1 TACCTATTACATTATAT
26289 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:26344 original size:853 final size:859
Alignment explanation
Indices: 24943--27248 Score: 4448
Period size: 853 Copynumber: 2.7 Consensus size: 859
24933 GCGAGATAGA
**
24943 TACCTATTACATTATATAAACGATACCTATTTTATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
25008 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
25073 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
25138 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
25203 AATTTAATAATAATATATACCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 -ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
25267 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
325 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
25332 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGAT
390 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGAT
25397 ACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCC
455 ACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCC
25462 ATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTA
520 ATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTA
25527 ACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAC-AAAAATTATTT
585 ACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTT
*
25591 GATTGTTTTTATATTTTATAAAATATTATTTAAAATTTTTAATTTAATAATAATATATACCGTAA
650 GATTGTTTTGATATTTTATAAAATATTATTTAAAATTTTTAATTTAATAATAATATATACCGTAA
25656 CGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
715 CGTAAAAAA-AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
25721 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
779 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
*
25786 TTTATAATATAACCAC
844 TTTACAATATAACCAC
25802 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
25867 TTACCTATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATAC-TTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
25930 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
25995 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAA-TTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
26059 -TTTAATAATAATATATACCGTAACGTAAAAAAT-AATCATTAGACGCCTATAATTACTAAATTA
261 ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
26122 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAA-TATGGA
326 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
26186 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATA
391 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATA
26251 CCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCA
456 CCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCA
26316 TACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTAA
521 TACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTAA
26381 CAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTG
586 CAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTG
* *
26446 ATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAAC
651 ATTGTTTTGATATTTTATAAAATATTATTTAAAATTTTTAATTTAATAATAATATATACCGTAAC
26511 GTAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATA
716 GTAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATA
26576 ACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTT
781 ACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTT
26641 TACAATATAACCAC
846 TACAATATAACCAC
26655 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
26720 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTTAAAACTT
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTTAAAACTT
26785 ATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAAT
130 ATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAAT
26850 AATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTT
195 AATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTT
26915 TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
260 T-ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
26980 TAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATG
324 TAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATG
27045 GACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGA
389 GACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGA
*
27110 TACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTTTATTGAAAGTGTC
454 TACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTC
27175 CATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTT
519 CATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAA-TTTTT
27240 TAACAGTGT
583 TAACAGTGT
27249 ACTGCGAATT
Statistics
Matches: 1429, Mismatches: 7, Indels: 19
0.98 0.00 0.01
Matches are distributed among these distances:
853 488 0.34
854 210 0.15
855 6 0.00
856 143 0.10
857 143 0.10
858 14 0.01
859 131 0.09
860 88 0.06
861 192 0.13
862 14 0.01
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (859 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
CACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATA
CCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCA
TACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTAA
CAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTG
ATTGTTTTGATATTTTATAAAATATTATTTAAAATTTTTAATTTAATAATAATATATACCGTAAC
GTAAAAAAAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATA
ACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTT
TACAATATAACCAC
Found at i:26670 original size:21 final size:22
Alignment explanation
Indices: 26645--26696 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
26635 ACACTTTACA
*
26645 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
26668 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
26691 ATATAA
1 ATATAA
26697 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:26681 original size:23 final size:23
Alignment explanation
Indices: 26655--26717 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
26645 ATATAACCAC
26655 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
26678 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
26701 TACCTATTACATCATAT
1 TACCTATTACATTATAT
26718 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:27102 original size:21 final size:22
Alignment explanation
Indices: 27077--27128 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
27067 ACACTTTACA
*
27077 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
27100 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
27123 ATATAA
1 ATATAA
27129 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:27113 original size:23 final size:23
Alignment explanation
Indices: 27087--27149 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
27077 ATATAACCAC
27087 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
27110 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
27133 TACCTATTACATCATAT
1 TACCTATTACATTATAT
27150 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:28543 original size:199 final size:199
Alignment explanation
Indices: 28202--28721 Score: 979
Period size: 199 Copynumber: 2.6 Consensus size: 199
28192 ACAAAGATAA
28202 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCAC
1 TTTTGGGTTCGATGATTTTGGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCAC
28267 CTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATT
65 CTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATT
*
28332 TAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACAT
130 TAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTAAAAAATTACAGATTACAT
28397 TATAC
195 TATAC
* *
28402 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACC
1 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
28467 TTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTT
66 TTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTT
*
28532 AGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATT
131 AGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTAAAAAATTACAGATTACATT
28597 ATAC
196 ATAC
28601 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
1 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
*
28666 TTGTTTTTAATTCATTCTGG-AAAAAAATATCGACACAAACTATATTAGTATCGACA
66 TTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACA
28722 TGACCCTTAA
Statistics
Matches: 313, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
198 35 0.11
199 248 0.79
200 30 0.10
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (199 bp):
TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
TTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTT
AGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTAAAAAATTACAGATTACATT
ATAC
Found at i:28829 original size:19 final size:19
Alignment explanation
Indices: 28802--28846 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
28792 TATTCACATA
*
28802 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
28821 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
28840 AAAATTA
1 AAAATTA
28847 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:32838 original size:24 final size:24
Alignment explanation
Indices: 32801--32853 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
32791 CCGTTCTATC
32801 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
32825 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
32849 TATTT
1 TATTT
32854 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:33052 original size:20 final size:18
Alignment explanation
Indices: 32998--33043 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
32988 TCCGGTATCA
32998 TTTTACCGTTTTATCATT
1 TTTTACCGTTTTATCATT
*
33016 TTGATACCGGTTTTATCATAT
1 TT-TTACC-GTTTTATCAT-T
33037 TTTTACC
1 TTTTACC
33044 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 4 0.17
20 14 0.61
21 3 0.13
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (18 bp):
TTTTACCGTTTTATCATT
Found at i:33191 original size:20 final size:20
Alignment explanation
Indices: 33165--33210 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
33155 CACTTTTAAA
33165 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
33184 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
33205 TTTACC
1 TTTACC
33211 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:33677 original size:228 final size:226
Alignment explanation
Indices: 33276--33722 Score: 772
Period size: 228 Copynumber: 2.0 Consensus size: 226
33266 TTAAAACTGC
*
33276 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTCATGTTTTCCACCTACAATAT
1 TTTTAAAGTTATGTAATTTATGTTTCAAATTATTTAATAGTGTTCATGTTTTCCACCTACAATAT
**
33341 TAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATT
66 TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
* *
33406 TAGCATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGCATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAAG
*
33471 TATGGACACTTTTATAAAAATGATATATACTT
195 TATGGACACTTTTATAAAAAGGATATATACTT
33503 TTTTGAAAGTTATGTAATTTATGTTTCAAATT-TTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAAATTATTTAATAGTG-TTCATGTTTTCCACCTACAAT
*
33567 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
64 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
*
33632 TTTAG-ATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATA
129 TTTAGCA-TTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATA
33696 AGTATGGACACTTTTATAAAAAGGATA
193 AGTATGGACACTTTTATAAAAAGGATA
33723 GATAATTTAC
Statistics
Matches: 209, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
227 52 0.25
228 157 0.75
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (226 bp):
TTTTAAAGTTATGTAATTTATGTTTCAAATTATTTAATAGTGTTCATGTTTTCCACCTACAATAT
TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
TAGCATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAGT
ATGGACACTTTTATAAAAAGGATATATACTT
Found at i:34372 original size:29 final size:29
Alignment explanation
Indices: 34330--34406 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
34320 TTGTTGGAAT
*
34330 CCATGCAAACATAGACATCTGAATCTGAA
1 CCATGCAAACATAGACATCTGAATCCGAA
34359 CCATGCAAACATAGACATCTGAATCCGAA
1 CCATGCAAACATAGACATCTGAATCCGAA
*
34388 CCATGCAAACATAGGCATC
1 CCATGCAAACATAGACATC
34407 CGAACAAGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.40, C:0.27, G:0.14, T:0.18
Consensus pattern (29 bp):
CCATGCAAACATAGACATCTGAATCCGAA
Found at i:45222 original size:15 final size:15
Alignment explanation
Indices: 45186--45233 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
45176 ATCCGACCTG
* *
45186 ATCCGAATAACACAT
1 ATCCAAATAACATAT
45201 ATCCAAATAACATAT
1 ATCCAAATAACATAT
*
45216 A-CTCAAATATCATAT
1 ATC-CAAATAACATAT
45231 ATC
1 ATC
45234 TTAATTCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (15 bp):
ATCCAAATAACATAT
Found at i:46530 original size:44 final size:44
Alignment explanation
Indices: 46473--46567 Score: 181
Period size: 44 Copynumber: 2.2 Consensus size: 44
46463 TTAAGAGGGA
46473 AAAATTGATACGTTAGAGTTTAACATGTAATGCAAAGCGGAAAT
1 AAAATTGATACGTTAGAGTTTAACATGTAATGCAAAGCGGAAAT
*
46517 AAAATTGATACGTTAGAGTTTAACATGTAATGCGAAGCGGAAAT
1 AAAATTGATACGTTAGAGTTTAACATGTAATGCAAAGCGGAAAT
46561 AAAATTG
1 AAAATTG
46568 TTGAAGCCCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.27
Consensus pattern (44 bp):
AAAATTGATACGTTAGAGTTTAACATGTAATGCAAAGCGGAAAT
Found at i:53493 original size:6 final size:6
Alignment explanation
Indices: 53484--53508 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
53474 GGGATGATAA
53484 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
53509 AAATCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:53570 original size:13 final size:13
Alignment explanation
Indices: 53552--53581 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
53542 GTTGGTAATC
53552 CCCGCCCCGATTA
1 CCCGCCCCGATTA
53565 CCCGCCCCGATTA
1 CCCGCCCCGATTA
53578 CCCG
1 CCCG
53582 ACCGATACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.57, G:0.17, T:0.13
Consensus pattern (13 bp):
CCCGCCCCGATTA
Found at i:53623 original size:2 final size:2
Alignment explanation
Indices: 53616--53709 Score: 65
Period size: 2 Copynumber: 50.0 Consensus size: 2
53606 TAAAAATAAT
*
53616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA -A TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
53655 TT TA TT TA AA TA -A AA AA TA TA TA TT TA TA TT TA -A T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53694 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
53710 CCCGGCCCGA
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
1 6 0.08
2 66 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53679 original size:19 final size:21
Alignment explanation
Indices: 53633--53681 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
53623 ATATATATAT
*
53633 ATATATATATAAATAATAATA
1 ATATATATTTAAATAATAATA
53654 AT-T-TATTTAAATAA-AA-A
1 ATATATATTTAAATAATAATA
53671 ATATATATTTA
1 ATATATATTTA
53682 TATTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 3 0.12
19 16 0.64
20 1 0.04
21 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATATATTTAAATAATAATA
Done.