Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003017.1 Kokia drynarioides strain JFW-HI SEQ_115532, 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: 35923
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:335 original size:49 final size:49
Alignment explanation
Indices: 265--1257 Score: 508
Period size: 49 Copynumber: 20.4 Consensus size: 49
255 GAAGATATGG
* * * *
265 AGGGAAGGGTTTAAGTTGCAACGGCGAACCTTGTACCTCAAAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * ** * *
314 AGGGAAAGGTTTAAG-CTGCAACGGTGAATCCAT-TACGAC-GAAGACATGG
1 AGGGAAAGATTTAAGTC-GCAACGGCGAA-CCTTGTACCTCAAAAG-CATGA
* * * * * * *
363 AGGGAAAGGTTTAAGTCACAATGGCGAACCTTGTATCTCAGAAGCGTAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * *
412 AGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAAAAGCATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * * * * * *
461 AGGGAAAGATTTAAGTCGTAACAGCGAATCTAGTACCAC-GAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAG-CATGA
* * * *
510 AGGGAAAGATTTAAGTTGCAATGGTGAACCTTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * ** * * * *
559 AGGGAAAGATTTAA-ACTACAACGACGAATCC-AATACCAC-AAGGATATGG
1 AGGGAAAGATTTAAGTC-GCAACGGCGAA-CCTTGTACCTCAAAAG-CATGA
* * * * *
608 AGAGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAAGCATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * *
657 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * * * * *
706 AGAGAAAGATTTAA---G---C--CGAATCTAGTACCAC-GAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAG-CATGA
* * * *
747 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTAACTTAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * *
796 AGGGAAAGATTTAAG-CTGCAACGGCGAA--TTCAGTACCAC-AAGGATATGG
1 AGGGAAAGATTTAAGTC-GCAACGGCGAACCTT--GTACCTCAAAAG-CATGA
* * * * *
845 AGAGAAAGATTTAAGTCACAACGGTGAACCTTGTACCTCAGAAGCATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * * * *
894 AAGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTTAAAAGCATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * * * * ** * * * * * *
943 AAGAAAATATTTAAGCCACAAAGATGAATCTAGTACCAC-GAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAG-CATGA
* * *
992 AGGGAAATG-TTTAAGTCGCAACGGTGAATCTTGTACCTCAGAAGCATGA
1 AGGGAAA-GATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* ** * * * * *
1041 AAGGAAAGATTTAAACCGCAACGGCGAATCC-AGTACCAC-AAGGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCTCAAAAG-CATGA
* * * * ** *
1090 AGAGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCGCGGAAGCATTA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * ** * * * * *
1139 AGGGAAAAATTTAAGCCGCAATGGTAAATCTAGTACCAC-GAAGATATGGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAG-CAT-GA
* * * * *
1189 A-GGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACTTTAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* *
1237 AAGGAAAGATTTAAGCCGCAA
1 AGGGAAAGATTTAAGTCGCAA
1258 TGACGAATCC
Statistics
Matches: 708, Mismatches: 192, Indels: 88
0.72 0.19 0.09
Matches are distributed among these distances:
40 4 0.01
41 26 0.04
43 1 0.00
44 1 0.00
46 1 0.00
47 3 0.00
48 30 0.04
49 603 0.85
50 37 0.05
51 2 0.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (49 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
Found at i:790 original size:139 final size:143
Alignment explanation
Indices: 510--823 Score: 406
Period size: 139 Copynumber: 2.2 Consensus size: 143
500 GAAGATATGG
* * * * *
510 AGGGAAAGATTTAAGTTGCAATGGTGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAAC
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATAAAGAGAAAGATTT--A-
*
575 TACAACGACGAATCCAATACCACAAGGATATGGAGAGAAAGGTTTAAGTCGCAACGGTGAACCTT
63 TA-AACGACGAATCCAATACCACAAGGATATGGAGAGAAAGGTTTAAGTCGCAACGGCGAACCTT
*
640 GTACCTCAGAAGCATAA
127 GTAACTCAGAAGCATAA
*
657 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATAAAGAGAAAGA-TT-T-A
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATAAAGAGAAAGATTTATAA
* * * *
719 A-GCCGAATCTAGTACCACGAA-GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTA
66 ACGACGAATCCAATACCAC-AAGGATATGGAGAGAAAGGTTTAAGTCGCAACGGCGAACCTTGTA
* *
782 ACTTAGAAGCATGA
130 ACTCAGAAGCATAA
796 AGGGAAAGATTTAAG-CTGCAACGGCGAA
1 AGGGAAAGATTTAAGTC-GCAACGGCGAA
824 TTCAGTACCA
Statistics
Matches: 150, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
138 1 0.01
139 90 0.60
140 4 0.03
142 1 0.01
146 2 0.01
147 52 0.35
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (143 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATAAAGAGAAAGATTTATAA
ACGACGAATCCAATACCACAAGGATATGGAGAGAAAGGTTTAAGTCGCAACGGCGAACCTTGTAA
CTCAGAAGCATAA
Found at i:1244 original size:147 final size:144
Alignment explanation
Indices: 512--1345 Score: 555
Period size: 147 Copynumber: 5.7 Consensus size: 144
502 AGATATGGAG
* * * * * * **
512 GGAAAGATTTAAGTTGCAATGGTGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAACTA
1 GGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCAC-GAAGCATTAAGGGAAAGATTTAAGCCG
** * * *
577 CAACGACGAATCCAATACCAC-AAGGATATGG-AGAGAAAGGTTTAAGTCGCAACGGTGAACCTT
65 CAACGGTGAATCTAGTACCACGAA-GATATGGAAG-GAAAGGTTTAAGTCGCAACGGCGAACCTT
*
640 GTACCTCAGAAGCATAAA
128 GTA-CTTAGAAGCATAAA
* * * *
658 GGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATAAAGAGAAAGATTTAA---
1 -GGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCAC-GAAGCATTAAGGGAAAGATTTAAGCC
*
720 GC--C---GAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
64 GCAACGGTGAATCTAGTACCACGAAGATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
*
780 TAACTTAGAAGCATGAAG
129 T-ACTTAGAAGCAT-AAA
* * *
798 GGAAAGATTTAAG-CTGCAACGGCGAA--TTCAGTACCAC-AAGGATATGGAGAGAAAGATTTAA
1 GGAAAGATTTAAGTC-GCAACGGCGAACCTT--GTACCACGAAGCAT-T-AAGGGAAAGATTTAA
* * * * * * * *
859 GTCACAACGGTGAACCTTGTACCTCAGAAGCATA--AAAGGAAAGGTTTAAGTCGCAATGACGAA
61 GCCGCAACGGTGAATCTAGTACCAC-GAAG-ATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAA
*
922 CCTTGTACCTTAAAAGCATAAAA
124 CCTTGTA-CTTAGAAGCAT-AAA
* * * * * ** * * * *
945 GAAAATATTTAAGCCACAAAGATGAATCTAGTACCACGAAG-ATATGGAGGGAAATG-TTTAAGT
1 GGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACGAAGCAT-T-AAGGGAAA-GATTTAAGC
* * * * * **
1008 CGCAACGGTGAATCTTGTACCTCAGAAG-CATGAAAGGAAAGATTTAAACCGCAACGGCGAATCC
63 CGCAACGGTGAATCTAGTACCAC-GAAGATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAA-CC
* * * * *
1072 -AGTAC-CACAAGGATATGGA
126 TTGTACTTAGAAGCATA--AA
* * * *
1091 GAGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCGCGGAAGCATTAAGGGAAAAATTTAAGCC
1 G-GAAAGATTTAAGTCGCAACGGCGAACCTTGTACCAC-GAAGCATTAAGGGAAAGATTTAAGCC
* * *
1156 GCAATGGTAAATCTAGTACCACGAAGATATGGAAGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
64 GCAACGGTGAATCTAGTACCACGAAGATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
1221 TACTTTAGAAGCATGAAA
129 TAC-TTAGAAGCAT-AAA
* * * **
1239 GGAAAGATTTAAGCCGCAATGACGAATCC-AATACCACGAAG-ATATGAAGGGAAAGATTTAAGC
1 GGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCACGAAGCAT-T-AAGGGAAAGATTTAAGC
* * * * * *
1302 TGCAATGG-GAAATCCAGTACCACGACGATATGGAGGGAGAGGTT
63 CGCAACGGTG-AATCTAGTACCACGAAGATATGGAAGGAAAGGTT
1346 ACAACTGTAA
Statistics
Matches: 551, Mismatches: 93, Indels: 86
0.75 0.13 0.12
Matches are distributed among these distances:
137 7 0.01
138 1 0.00
139 102 0.19
140 6 0.01
142 2 0.00
144 3 0.01
145 9 0.02
146 15 0.03
147 373 0.68
148 20 0.04
149 12 0.02
150 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (144 bp):
GGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACGAAGCATTAAGGGAAAGATTTAAGCCGC
AACGGTGAATCTAGTACCACGAAGATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTA
CTTAGAAGCATAAA
Found at i:1286 original size:49 final size:49
Alignment explanation
Indices: 722--1333 Score: 262
Period size: 49 Copynumber: 12.5 Consensus size: 49
712 AGATTTAAGC
* * * * * *
722 CGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGG
1 CGAATCCAGTACCACGAAGATATGAAAGGAAAGATTTAAGCCGCAATGG
* * * * * *
771 CGAA-CCTTGTAACTTA-GAAG-CATGAAGGGAAAGATTTAAGCTGCAACGG
1 CGAATCC-AGT-AC-CACGAAGATATGAAAGGAAAGATTTAAGCCGCAATGG
* * * * *
820 CGAATTCAGTACCAC-AAGGATATG-GAGAGAAAGATTTAAGTCACAACGG
1 CGAATCCAGTACCACGAA-GATATGAAAG-GAAAGATTTAAGCCGCAATGG
* * * * * *
869 TGAA-CCTTGTACCTCAGAAGCATA--AAAGGAAAGGTTTAAGTCGCAATGA
1 CGAATCC-AGTACCAC-GAAG-ATATGAAAGGAAAGATTTAAGCCGCAATGG
* * * * * * *
918 CGAA-CCTTGTACCTTA-AAAGCATA--AAAGAAAATATTTAAGCCACAAAGA
1 CGAATCC-AGTACC--ACGAAG-ATATGAAAGGAAAGATTTAAGCCGCAATGG
* * * * * *
967 TGAATCTAGTACCACGAAGATATGGAGGGAAATG-TTTAAGTCGCAACGG
1 CGAATCCAGTACCACGAAGATATGAAAGGAAA-GATTTAAGCCGCAATGG
* ** * * * *
1016 TGAATCTTGTACCTCAGAAG-CATGAAAGGAAAGATTTAAACCGCAACGG
1 CGAATCCAGTACCAC-GAAGATATGAAAGGAAAGATTTAAGCCGCAATGG
* * * *
1065 CGAATCCAGTACCAC-AAGGATATG-GAGAGAAAGGTTTAAGTCGCAACGG
1 CGAATCCAGTACCACGAA-GATATGAAAG-GAAAGATTTAAGCCGCAATGG
* * * * *
1114 TGAA-CCTTGTACCGCGGAAGCAT-T-AAGGGAAAAATTTAAGCCGCAATGG
1 CGAATCC-AGTACCAC-GAAG-ATATGAAAGGAAAGATTTAAGCCGCAATGG
** * * * *
1163 TAAATCTAGTACCACGAAGATATGGAAGGAAAGGTTTAAGTCGCAATGG
1 CGAATCCAGTACCACGAAGATATGAAAGGAAAGATTTAAGCCGCAATGG
* * * *
1212 CGAA-CCTTGTACTTTA-GAAG-CATGAAAGGAAAGATTTAAGCCGCAATGA
1 CGAATCC-AGTAC--CACGAAGATATGAAAGGAAAGATTTAAGCCGCAATGG
* * *
1261 CGAATCCAATACCACGAAGATATGAAGGGAAAGATTTAAGCTGCAATGG
1 CGAATCCAGTACCACGAAGATATGAAAGGAAAGATTTAAGCCGCAATGG
*
1310 -GAAATCCAGTACCACGACGATATG
1 CG-AATCCAGTACCACGAAGATATG
1334 GAGGGAGAGG
Statistics
Matches: 423, Mismatches: 100, Indels: 80
0.70 0.17 0.13
Matches are distributed among these distances:
47 12 0.03
48 26 0.06
49 349 0.83
50 25 0.06
51 11 0.03
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.20
Consensus pattern (49 bp):
CGAATCCAGTACCACGAAGATATGAAAGGAAAGATTTAAGCCGCAATGG
Found at i:1307 original size:98 final size:98
Alignment explanation
Indices: 896--1309 Score: 465
Period size: 98 Copynumber: 4.2 Consensus size: 98
886 AAGCATAAAA
* * * * * * *
896 GGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTTAAAAGCATAAAAGAAAATATTTAAGCCA
1 GGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAAGGAAAGATTTAAGCCG
* * * *
961 CAAAGATGAATCTAGTACCACGAAGATATGGAG
66 CAATGACGAATCCAGTACCACGAAGATATGAAG
* * * * *
994 GGAAATGTTTAAGTCGCAACGGTGAATCTTGTACCTCAGAAGCATGAAAGGAAAGATTTAAACCG
1 GGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAAGGAAAGATTTAAGCCG
* * *
1059 CAACGGCGAATCCAGTACCAC-AAGGATATGGAG
66 CAATGACGAATCCAGTACCACGAA-GATATGAAG
* * * * * * * *
1092 AGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCGCGGAAGCATTAAGGGAAAAATTTAAGCCG
1 GGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAAGGAAAGATTTAAGCCG
*** *
1157 CAATGGTAAATCTAGTACCACGAAGATATGGAA-
66 CAATGACGAATCCAGTACCACGAAGATAT-GAAG
* *
1190 GGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACTTTAGAAGCATGAAAGGAAAGATTTAAGCCG
1 GGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAAGGAAAGATTTAAGCCG
*
1255 CAATGACGAATCCAATACCACGAAGATATGAAG
66 CAATGACGAATCCAGTACCACGAAGATATGAAG
*
1288 GGAAAGATTTAAG-CTGCAATGG
1 GGAAAGGTTTAAGTC-GCAATGG
1310 GAAATCCAGT
Statistics
Matches: 265, Mismatches: 46, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
97 6 0.02
98 255 0.96
99 4 0.02
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (98 bp):
GGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAAGGAAAGATTTAAGCCG
CAATGACGAATCCAGTACCACGAAGATATGAAG
Found at i:1358 original size:49 final size:49
Alignment explanation
Indices: 1138--1371 Score: 122
Period size: 49 Copynumber: 4.8 Consensus size: 49
1128 CGGAAGCATT
* * * * * *
1138 AAGGGAAAAATTTAAGCCGCAATGGTAAATCTAGTACCACGAAGATATGG
1 AAGGGAAAGAGTTAAACTGCAATGGCAAATCCAGTACCACGAAGATAT-G
* * * * * *
1188 AA-GGAAAG-GTTTAAGTCGCAATGGCGAA-CCTTGTACTTTA-GAAG-CATG
1 AAGGGAAAGAGTTAAACT-GCAATGGCAAATCC-AGTAC--CACGAAGATATG
* * * * * * *
1236 AAAGGAAAGATTTAAGCCGCAATGACGAATCCAATACCACGAAGATATG
1 AAGGGAAAGAGTTAAACTGCAATGGCAAATCCAGTACCACGAAGATATG
* * * *
1285 AAGGGAAAGATTTAAGCTGCAATGGGAAATCCAGTACCACGACGATATG
1 AAGGGAAAGAGTTAAACTGCAATGGCAAATCCAGTACCACGAAGATATG
* * *
1334 GAGGGAGAG-GTTACAACTGTAATGGCAAA-CTCAGTACC
1 AAGGGAAAGAGTTA-AACTGCAATGGCAAATC-CAGTACC
1372 TTAGAAACAT
Statistics
Matches: 138, Mismatches: 35, Indels: 23
0.70 0.18 0.12
Matches are distributed among these distances:
47 1 0.01
48 15 0.11
49 110 0.80
50 11 0.08
51 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (49 bp):
AAGGGAAAGAGTTAAACTGCAATGGCAAATCCAGTACCACGAAGATATG
Found at i:3097 original size:2 final size:2
Alignment explanation
Indices: 3090--3116 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3080 CTATTTTTCT
3090 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3117 GAAACCGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3949 original size:2 final size:2
Alignment explanation
Indices: 3942--3968 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3932 TATTTACTTT
3942 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3969 CTAATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11207 original size:17 final size:17
Alignment explanation
Indices: 11187--11221 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11177 TAAAATTAAA
11187 TTTTTATAA-ATGTTTAT
1 TTTTTA-AATATGTTTAT
11204 TTTTTAAATATGTTTAT
1 TTTTTAAATATGTTTAT
11221 T
1 T
11222 ACTTTATGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
TTTTTAAATATGTTTAT
Found at i:12520 original size:2 final size:2
Alignment explanation
Indices: 12513--12540 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12503 AATTTTTGTT
12513 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12541 AATTTAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13121 original size:33 final size:33
Alignment explanation
Indices: 13037--13122 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
13027 ATTTTAAATT
* *
13037 TCTTAAAAGTTAATAAAAATAATAAATTTGAGTC
1 TCTTAAAAATTAATAAAAA-AATAAATTTGAGAC
* *
13071 -CTTAAAAACTAA-AAAAAAAAAAATTTTGAGAC
1 TCTTAAAAATTAATAAAAAAATAAA-TTTGAGAC
*
13103 TCTTAAAAATTGATAAAAAA
1 TCTTAAAAATTAATAAAAAA
13123 TTTTTAACCT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
31 5 0.12
32 12 0.28
33 20 0.47
34 6 0.14
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (33 bp):
TCTTAAAAATTAATAAAAAAATAAATTTGAGAC
Found at i:13137 original size:28 final size:28
Alignment explanation
Indices: 13086--13173 Score: 94
Period size: 26 Copynumber: 3.2 Consensus size: 28
13076 AAACTAAAAA
13086 AAAAAAAATTTTGAGACTCTTAAAAATT
1 AAAAAAAATTTTGAGACTCTTAAAAATT
* *
13114 GATAAAAAATTTTTA-AC-CTATAAAAATT
1 -AAAAAAAATTTTGAGACTCT-TAAAAATT
* *
13142 AAAAAAAA-TTT-AAACCCTTAAAAATT
1 AAAAAAAATTTTGAGACTCTTAAAAATT
13168 AAAAAA
1 AAAAAA
13174 TAAAAATTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
25 1 0.02
26 19 0.36
27 11 0.21
28 10 0.19
29 12 0.23
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (28 bp):
AAAAAAAATTTTGAGACTCTTAAAAATT
Found at i:19026 original size:21 final size:21
Alignment explanation
Indices: 19000--19049 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
18990 TGGCAAGTTG
*
19000 TGTCTCGAGACAATGCTAATA
1 TGTCTCGAGACAAGGCTAATA
*
19021 TGTCTCGAGACAAGGCTAATG
1 TGTCTCGAGACAAGGCTAATA
19042 TGTCTCGA
1 TGTCTCGA
19050 TACATTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (21 bp):
TGTCTCGAGACAAGGCTAATA
Found at i:21031 original size:26 final size:26
Alignment explanation
Indices: 21002--21054 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
20992 GACTTAGACT
*
21002 TTTCGGTCATAGAAACCAATAAACAA
1 TTTCGGTCATAAAAACCAATAAACAA
*
21028 TTTCGGTCATAAAAACCAATAACCAA
1 TTTCGGTCATAAAAACCAATAAACAA
21054 T
1 T
21055 CTTCACCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (26 bp):
TTTCGGTCATAAAAACCAATAAACAA
Found at i:24610 original size:21 final size:22
Alignment explanation
Indices: 24569--24615 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
24559 CAAATATCTC
*
24569 AATTCGATTTTGTTTTCAATTA
1 AATTCGATTTTGATTTCAATTA
*
24591 AATT-GATTTTCGATTT-AATTT
1 AATTCGATTTT-GATTTCAATTA
24612 AATT
1 AATT
24616 TTATTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (22 bp):
AATTCGATTTTGATTTCAATTA
Found at i:25114 original size:53 final size:49
Alignment explanation
Indices: 25015--25124 Score: 112
Period size: 53 Copynumber: 2.2 Consensus size: 49
25005 TCAGATTTTG
* * *
25015 TTTAATTAATTTGTTTTTTTAGATTTGATGTTTTAAATAAATATAAATA
1 TTTATTTAATTTGTTTTTTTAGATCTGATGTTTTAAATAAACATAAATA
* * * *
25064 TTTATTTAATTTGTTTTTATTTAAGATCTGGTGTTTTTACATAAGCATAAATG
1 TTTATTTAATTTG-TTTT-TTT-AGATCTGATG-TTTTAAATAAACATAAATA
*
25117 TTTGTTTA
1 TTTATTTA
25125 TATTATTTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
49 12 0.24
50 4 0.08
51 3 0.06
52 8 0.16
53 22 0.45
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.55
Consensus pattern (49 bp):
TTTATTTAATTTGTTTTTTTAGATCTGATGTTTTAAATAAACATAAATA
Found at i:25502 original size:84 final size:82
Alignment explanation
Indices: 25317--25798 Score: 292
Period size: 84 Copynumber: 5.9 Consensus size: 82
25307 AAATTGGAAA
* * *
25317 AAATCTATTTCGGGATTTATTCCCACCGTTCAACAGATTTGCTTCTA-TTTTGATTTTTTTTCCA
1 AAATCTATTTCGGGATTTATTCCCACCGTTCAACAGATTTGATTCTATTTTTAATTTTATTTCCA
25381 AACAAGAATTAAGTGAAT
66 AACAAGAA-TAAGTGAAT
* ** * * * *
25399 AATTCTATTTCAAGATTTATTCTCACTGTTCAATAGATTTGATTTTATTTTTAATTTTATTTCCA
1 AAATCTATTTCGGGATTTATTCCCACCGTTCAACAGATTTGATTCTATTTTTAATTTTATTTCC-
25464 AAACAAGAATAAGTTGAAT
65 AAACAAGAATAAG-TGAAT
* * * * * * * *
25483 AAATCTGTTTTGGGATTTATTCCCGCCGTTCAACAAATTTTATTCTATTTTTTATTTTGTTTGCA
1 AAATCTATTTCGGGATTTATTCCCACCGTTCAACAGATTTGATTCTATTTTTAATTTTATTTCCA
25548 AACAAGAATTAA---AATT
66 AACAAGAA-TAAGTGAA-T
* * * * * * * * *
25564 AAATTTTTTTTTTTGAGATTTATTCCCGCCTTTCAACAAATTTGATT-TGA-TTTTGATTTTGTT
1 AAA---TCTATTTCGGGATTTATTCCCACCGTTCAACAGATTTGATTCT-ATTTTTAATTTTATT
* *
25627 TTCAAACAAGAATTAAAATTGAAT
62 TCCAAACAAGAA-T--AAGTGAAT
* * ** * ** * * * *
25651 AATTCTATTTCGAGATTTATTTTCGCTATTCAACA-A---AATT-GA-TTTTGATTTT-GTTCCA
1 AAATCTATTTCGGGATTTATTCCCACCGTTCAACAGATTTGATTCTATTTTTAATTTTATTTCCA
* *
25709 AATAAGAATTAATTGAAT
66 AACAAGAA-TAAGTGAAT
* * * * * * *
25727 AATTCTATTTCGGGATTTATTCCCGCCGTTCTATAGATTTGATT-TGA-TTTTGATTTTGTTTCA
1 AAATCTATTTCGGGATTTATTCCCACCGTTCAACAGATTTGATTCT-ATTTTTAATTTTATTTCC
25790 AAACAAGAA
65 AAACAAGAA
25799 ATAATTAAAT
Statistics
Matches: 323, Mismatches: 57, Indels: 40
0.77 0.14 0.10
Matches are distributed among these distances:
76 36 0.11
77 1 0.00
78 13 0.04
79 11 0.03
80 8 0.02
81 15 0.05
82 50 0.15
83 54 0.17
84 128 0.40
85 2 0.01
87 3 0.01
88 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (82 bp):
AAATCTATTTCGGGATTTATTCCCACCGTTCAACAGATTTGATTCTATTTTTAATTTTATTTCCA
AACAAGAATAAGTGAAT
Found at i:25769 original size:76 final size:78
Alignment explanation
Indices: 25531--25827 Score: 251
Period size: 82 Copynumber: 3.7 Consensus size: 78
25521 TTTATTCTAT
* * * * * * * *
25531 TTTTTATTTTGTTTGCAAACAAGAATTAAAATTAAAT-TTTTTTTTTTGAGATTTATTCCCGCCT
1 TTTTGATTTTGTTTCCAAACAAGAATT-AAATTGAATAATTCTATTTCGAGATTTATTCCCGCCA
25595 TTCAACAAATTTGATTTGA
65 TTCAAC--A---GATTTGA
* ** *
25614 TTTTGATTTTGTTTTCAAACAAGAATTAAAATTGAATAATTCTATTTCGAGATTTATTTTCGCTA
1 TTTTGATTTTGTTTCCAAACAAGAATT-AAATTGAATAATTCTATTTCGAGATTTATTCCCGCCA
* *
25679 TTCAACAAAATTGA
65 TTCAACAGATTTGA
* * *
25693 TTTTGATTTTG-TTCCAAATAAGAATT-AATTGAATAATTCTATTTCGGGATTTATTCCCGCCGT
1 TTTTGATTTTGTTTCCAAACAAGAATTAAATTGAATAATTCTATTTCGAGATTTATTCCCGCCAT
*
25756 TCTATAGATTTGATTTGA
66 TC-A-ACA---GATTTGA
* * * * *
25774 TTTTGATTTTGTTTCAAAACAAGAAAT-AATTAAATAATTCTGTTTCAAGATTTA
1 TTTTGATTTTGTTTCCAAACAAGAATTAAATTGAATAATTCTATTTCGAGATTTA
25828 ATCCTATCAT
Statistics
Matches: 177, Mismatches: 30, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
76 34 0.19
77 1 0.01
78 15 0.08
79 16 0.09
81 16 0.09
82 36 0.20
83 34 0.19
84 25 0.14
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.46
Consensus pattern (78 bp):
TTTTGATTTTGTTTCCAAACAAGAATTAAATTGAATAATTCTATTTCGAGATTTATTCCCGCCAT
TCAACAGATTTGA
Found at i:31034 original size:20 final size:17
Alignment explanation
Indices: 31000--31053 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 17
30990 AAACATATTA
*
31000 AATAAATACATAATAAAT
1 AATAAATA-TTAATAAAT
31018 AATTATAATATTAAATAAAT
1 AA-TA-AATATT-AATAAAT
31038 AATAAATATTAATAAA
1 AATAAATATTAATAAA
31054 AGAAAGTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.19
18 8 0.25
19 5 0.16
20 13 0.41
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAATATTAATAAAT
Found at i:32410 original size:57 final size:55
Alignment explanation
Indices: 32235--32466 Score: 182
Period size: 57 Copynumber: 4.1 Consensus size: 55
32225 AAAATTATAT
* * * *
32235 TTTTACCCCTAAACATTCAAGAATTACCATTTTGACCCC-AAACAACCAAAAATTACCA
1 TTTTACCCTTGAACATCCAA-AATTACCATTTT--CCCCTAAACATCC-AAAATTACCA
* ** * * * *
32293 TTTTTCCCTTGAACATCCAAAAATTA-CATTCTGACCGTCAAACATTCGAAATTACAA
1 TTTTACCCTTGAACATCC-AAAATTACCATT-TTCCCCT-AAACATCCAAAATTACCA
* *
32350 TTTTGCCCTTGAACATCCAAAATTTACCATTTTCCCCTGAACATCCAAAATTTACCA
1 TTTTACCCTTGAACATCCAAAA-TTACCATTTTCCCCTAAACATCCAAAA-TTACCA
* * * * *
32407 TTTTACCCTCGAACATCCATAAATTACCATTTTGCCCTTAAATATCAAAAATCA-CA
1 TTTTACCCTTGAACATCCA-AAATTACCATTTT-CCCCTAAACATCCAAAATTACCA
32463 TTTT
1 TTTT
32467 TCGACCTCAA
Statistics
Matches: 139, Mismatches: 26, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
56 21 0.15
57 70 0.50
58 46 0.33
59 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (55 bp):
TTTTACCCTTGAACATCCAAAATTACCATTTTCCCCTAAACATCCAAAATTACCA
Found at i:32444 original size:29 final size:28
Alignment explanation
Indices: 32246--32444 Score: 179
Period size: 29 Copynumber: 6.9 Consensus size: 28
32236 TTTACCCCTA
* *
32246 AACATTCAAGAATTACCATTTTGACCC-CA
1 AACATCCAA-AATTACCATTTTG-CCCTCG
* * *
32275 AACAACCAAAAATTACCATTTTTCCCTTG
1 AACATCC-AAAATTACCATTTTGCCCTCG
* * *
32304 AACATCCAAAAATTA-CATTCTGACCGTCA
1 AACATCC-AAAATTACCATTTTG-CCCTCG
* * * *
32333 AACATTCGAAATTACAATTTTGCCCTTG
1 AACATCCAAAATTACCATTTTGCCCTCG
*
32361 AACATCCAAAATTTACCATTTTCCCCT-G
1 AACATCCAAAA-TTACCATTTTGCCCTCG
*
32389 AACATCCAAAATTTACCATTTTACCCTCG
1 AACATCCAAAA-TTACCATTTTGCCCTCG
32418 AACATCCATAAATTACCATTTTGCCCT
1 AACATCCA-AAATTACCATTTTGCCCT
32445 TAAATATCAA
Statistics
Matches: 139, Mismatches: 24, Indels: 14
0.79 0.14 0.08
Matches are distributed among these distances:
28 53 0.38
29 81 0.58
30 5 0.04
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.31
Consensus pattern (28 bp):
AACATCCAAAATTACCATTTTGCCCTCG
Found at i:32536 original size:31 final size:30
Alignment explanation
Indices: 32475--32539 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
32465 TTTCGACCTC
* *
32475 AAATTTTCTAAAATTTCGATTTTAATCCCA
1 AAATTTCCAAAAATTTCGATTTTAATCCCA
* * *
32505 AAATTTCCAAAAATTTTGATTTTTATCCCC
1 AAATTTCCAAAAATTTCGATTTTAATCCCA
32535 AAATT
1 AAATT
32540 CCTCGAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTCCAAAAATTTCGATTTTAATCCCA
Found at i:32549 original size:31 final size:30
Alignment explanation
Indices: 32484--32550 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
32474 CAAATTTTCT
*
32484 AAAATTTCGATTTTAATCCCAAAATTTCCA
1 AAAATTTCGATTTTAATCCCAAAATTCCCA
* * * *
32514 AAAATTTTGATTTTTATCCCCAAATTCCTCG
1 AAAATTTCGATTTTAATCCCAAAATTCC-CA
32545 AAAATT
1 AAAATT
32551 ATGTTTTCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAATTTCGATTTTAATCCCAAAATTCCCA
Found at i:34152 original size:30 final size:30
Alignment explanation
Indices: 34118--34414 Score: 170
Period size: 29 Copynumber: 10.2 Consensus size: 30
34108 TTTTGACCTC
* *
34118 TAAACTTTTCAAAAATTACATTTTAACCAT
1 TAAACTTCTCAAAAATTACATTTTAACCCT
* *
34148 TAAACTT-TCCAAAAATTATATTTTCACCCT
1 TAAACTTCT-CAAAAATTACATTTTAACCCT
* * *
34178 CAAACTTCTCAAAATTTACATTTTTACCCCCT
1 TAAACTTCTCAAAAATTACA-TTTTA-ACCCT
* ** *
34210 TTAACTTCT-AAAAATTACATTTTTGCCCC
1 TAAACTTCTCAAAAATTACATTTTAACCCT
* * * *
34239 AAAACATCTC-AAAATTACATTTTTACCCC
1 TAAACTTCTCAAAAATTACATTTTAACCCT
* * *
34268 CAAACTTC-CAAAAATTACATTTTTA-TCT
1 TAAACTTCTCAAAAATTACATTTTAACCCT
* * *
34296 TCGAACTTC-C---AATCACATTTTTACCCT
1 T-AAACTTCTCAAAAATTACATTTTAACCCT
* * * *
34323 CAAACTTC-CAAAAATCACATTTTTACCCC
1 TAAACTTCTCAAAAATTACATTTTAACCCT
** * * *
34352 TAATTTTC-CTAAAATGACATTTTACCCCT
1 TAAACTTCTCAAAAATTACATTTTAACCCT
* * *
34381 AAAACTT-TCCAAAATTACGTTTTAACCC-
1 TAAACTTCTCAAAAATTACATTTTAACCCT
34409 TAAACT
1 TAAACT
34415 CTTTGAATCT
Statistics
Matches: 210, Mismatches: 45, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
26 19 0.09
27 2 0.01
28 7 0.03
29 113 0.54
30 44 0.21
31 14 0.07
32 11 0.05
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.37
Consensus pattern (30 bp):
TAAACTTCTCAAAAATTACATTTTAACCCT
Found at i:34197 original size:60 final size:59
Alignment explanation
Indices: 34114--34409 Score: 196
Period size: 58 Copynumber: 5.1 Consensus size: 59
34104 CATGTTTTGA
* * * *
34114 CCTCTAAACTTTTCAAAAATTACATTTTAACCATTAAACTTTCCAAAAATTATATTTTCAC
1 CCTCAAAACTTCTC-AAAATTACATTTTAACCCTTAAAC-TTCCAAAAATTACATTTTCAC
* * * **
34175 CCTC-AAACTTCTCAAAATTTACATTTTTACCCCCTTTAACTTCTAAAAATTACATTTTTGC
1 CCTCAAAACTTCTCAAAA-TTACA-TTTTA-ACCCTTAAACTTCCAAAAATTACATTTTCAC
* * ** * *
34236 CC-CAAAACATCTCAAAATTACATTTTTACCCCCAAACTTCCAAAAATTACATTTTTAT
1 CCTCAAAACTTCTCAAAATTACATTTTAACCCTTAAACTTCCAAAAATTACATTTTCAC
* * * * * * *
34294 CTTC-GAACTTC-C--AATCACATTTTTACCCTCAAACTTCCAAAAATCACATTTTTAC
1 CCTCAAAACTTCTCAAAATTACATTTTAACCCTTAAACTTCCAAAAATTACATTTTCAC
* ** * * * * *
34349 CC-CTAATTTTC-CTAAAATGACATTTTACCCCTAAAACTTTCC-AAAATTACGTTTTAAC
1 CCTCAAAACTTCTC-AAAATTACATTTTAACCCTTAAAC-TTCCAAAAATTACATTTTCAC
34407 CCT
1 CCT
34410 AAACTCTTTG
Statistics
Matches: 189, Mismatches: 35, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
54 1 0.01
55 45 0.24
57 1 0.01
58 63 0.33
59 13 0.07
60 19 0.10
61 40 0.21
62 7 0.04
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.37
Consensus pattern (59 bp):
CCTCAAAACTTCTCAAAATTACATTTTAACCCTTAAACTTCCAAAAATTACATTTTCAC
Found at i:34851 original size:97 final size:97
Alignment explanation
Indices: 34685--34878 Score: 289
Period size: 97 Copynumber: 2.0 Consensus size: 97
34675 AAAATATTTA
* * * * *
34685 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAAGTTGTGTCTTAACTTACTAGACGCGAT
1 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAAGTTGTGCCTAAACTTACTAGACACGAC
*
34750 TTTTCTTCAAACTGGGATAATCGAATACCCTT
66 TTTTCTTCAAACCGGGATAATCGAATACCCTT
* * * * *
34782 AAATCGAGGCAATGTTTCTTTATCTCTGGTTTTGAAAATTTGTGCCTAAACTTACTAGGCACGAC
1 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAAGTTGTGCCTAAACTTACTAGACACGAC
34847 TTTTCTTCAAACCGGGATAATCGAATACCCTT
66 TTTTCTTCAAACCGGGATAATCGAATACCCTT
34879 TTTCAAGGTT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 86 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAAGTTGTGCCTAAACTTACTAGACACGAC
TTTTCTTCAAACCGGGATAATCGAATACCCTT
Done.