Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007282.1 Kokia drynarioides strain JFW-HI SEQ_121898, 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: 3439
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Found at i:302 original size:43 final size:42
Alignment explanation
Indices: 255--388 Score: 130
Period size: 43 Copynumber: 3.1 Consensus size: 42
245 CATCGGGAAG
*
255 CATCGGTACCTTGGTGCTTTAGATGTACAAGAGCATCGGACAC
1 CATCGGTACCTTGGTGC-TTAGATGTACGAGAGCATCGGACAC
* * ** *
298 CATCGGTAACTTAG-GCCGATGGTGGTACGAGA-CAATCGAGA-AC
1 CATCGGTACCTTGGTGCTTA-GAT-GTACGAGAGC-ATCG-GACAC
*
341 CATCGGTACCTTGGTGACTTAGATGTGCGAGAGCATCGGACAC
1 CATCGGTACCTTGGTG-CTTAGATGTACGAGAGCATCGGACAC
384 CATCG
1 CATCG
389 CCAACTTATG
Statistics
Matches: 71, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
41 1 0.01
42 7 0.10
43 55 0.77
44 6 0.08
45 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.22
Consensus pattern (42 bp):
CATCGGTACCTTGGTGCTTAGATGTACGAGAGCATCGGACAC
Found at i:305 original size:86 final size:84
Alignment explanation
Indices: 203--485 Score: 368
Period size: 86 Copynumber: 3.3 Consensus size: 84
193 CTCGAACACA
* * *
203 ATCGGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGGGAAGCATCGGTACCTTG
1 ATCGGACACCATCGGCAACTTAGG-CGATGGTGGTGCGAGACAATCGGGAACCATCGGTACCTTG
*
268 GTGCTTTAGATGTACAAGAGC
65 GTGC-TTAGATGTACGAGAGC
* * *
289 ATCGGACACCATCGGTAACTTAGGCCGATGGTGGTACGAGACAATCGAGAACCATCGGTACCTTG
1 ATCGGACACCATCGGCAACTTAGG-CGATGGTGGTGCGAGACAATCGGGAACCATCGGTACCTTG
*
354 GTGACTTAGATGTGCGAGAGC
65 GTG-CTTAGATGTACGAGAGC
* * * **
375 ATCGGACACCATCGCCAACTTATGCTGATGGTGGTGCGGGACAATCGGGAACCATTAGTACCTTG
1 ATCGGACACCATCGGCAACTTAGGC-GATGGTGGTGCGAGACAATCGGGAACCATCGGTACCTTG
* *
440 GTGCCCTGGATGTACGAGAGC
65 GTG-CTTAGATGTACGAGAGC
*
461 ATTGGACACCATCGGCAACTTAGGC
1 ATCGGACACCATCGGCAACTTAGGC
486 TTATGATAGT
Statistics
Matches: 173, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
85 1 0.01
86 171 0.99
87 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.22
Consensus pattern (84 bp):
ATCGGACACCATCGGCAACTTAGGCGATGGTGGTGCGAGACAATCGGGAACCATCGGTACCTTGG
TGCTTAGATGTACGAGAGC
Found at i:750 original size:86 final size:86
Alignment explanation
Indices: 508--999 Score: 443
Period size: 86 Copynumber: 5.7 Consensus size: 86
498 CTAACCACCG
* * * * * * * *
508 GGAAGCATCAAACACCATTGACAACTAAGGCCGATGGTGGTCCG-GACCATCAGGAAGTATTGGC
1 GGAAGCATCGAACACCATCGATAACTTAGGCCGATGGTGGTGCGAGACCATCGGGAAGCATCGGC
* * * *
572 ACCATGGTGCCTTCGATATGC
66 ACCTTGGTGCCTTGGATGTAC
* * * * * * ** * *
593 GGGAGCATCGGACACCATCGATAACTAAGGTCGATGGTGGTACGGGACCATCAAGAAGTATCGGT
1 GGAAGCATCGAACACCATCGATAACTTAGGCCGATGGTGGTGCGAGACCATCGGGAAGCATCGGC
* * * *
658 AACTTGGTGTCTTCGATGTGC
66 ACCTTGGTGCCTTGGATGTAC
* * * **
679 GGAAGCATCGAACACCATCGATAACTTAGGCCGATGGTGGTGCGGGACCATTGGGAAGCAACAAC
1 GGAAGCATCGAACACCATCGATAACTTAGGCCGATGGTGGTGCGAGACCATCGGGAAGCATCGGC
*
744 ACCTTGGTACCTTGGATGTA-
66 ACCTTGGTGCCTTGGATGTAC
* * * * * *
764 AGAGAGCATTGAACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACAATCGGGAACCATCGG
1 GGA-AGCATCGAACACCATCGATAACTTAGGCCGATGGTGGTGCGAGACCATCGGGAAGCATCGG
*
829 TACCTTGGTGCCTTGGATGTAC
65 CACCTTGGTGCCTTGGATGTAC
* * * * * *
851 -GAGGGCATGGGAA-ACCATCGATAACTTAGACCGATGGTGGTGCAAGACAATCGGGAACCATCG
1 GGA-AGCAT-CGAACACCATCGATAACTTAGGCCGATGGTGGTGCGAGACCATCGGGAAGCATCG
* *
914 GCACCTTAGTACCTTGGATGTAC
64 GCACCTTGGTGCCTTGGATGTAC
* * * * * * *
937 GAAAGCATCGGATACCATCGGTAACTTAGGTCGATGGTGGTGTGAGACCATCGAGAAGCATCG
1 GGAAGCATCGAACACCATCGATAACTTAGGCCGATGGTGGTGCGAGACCATCGGGAAGCATCG
1000 AACACCATCG
Statistics
Matches: 335, Mismatches: 66, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
85 41 0.12
86 290 0.87
87 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (86 bp):
GGAAGCATCGAACACCATCGATAACTTAGGCCGATGGTGGTGCGAGACCATCGGGAAGCATCGGC
ACCTTGGTGCCTTGGATGTAC
Found at i:830 original size:172 final size:172
Alignment explanation
Indices: 595--999 Score: 499
Period size: 172 Copynumber: 2.4 Consensus size: 172
585 CGATATGCGG
* * * * * *
595 GAGCATCGGACACCATCGATAACTAAGGTCGATGGTGGTACGGGACCATCAAGAAGTATCGGTAA
1 GAGCATCGGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATCGGTAA
* * * *
660 CTTGGTGTCTTCGATGTGCG-GAAGCAT-CGAACACCATCGATAACTTAGGCCGATGGTGGTGCG
66 CTTGGTGCCTTCGATGTACGAG-AGCATGCGAA-ACCATCGATAACTTAGACCGATGGTGGTGCA
* * * * *
723 GGACCATTGGGAAGCAACAACACCTTGGTACCTTGGATGTAAGA
129 AGACAATCGGGAACCAACAACACCTTAGTACCTTGGATGTAAGA
* * * * * *
767 GAGCATTGAACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACAATCGGGAACCATCGGTAC
1 GAGCATCGGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATCGGTAA
* * *
832 CTTGGTGCCTTGGATGTACGAGGGCATGGGAAACCATCGATAACTTAGACCGATGGTGGTGCAAG
66 CTTGGTGCCTTCGATGTACGAGAGCATGCGAAACCATCGATAACTTAGACCGATGGTGGTGCAAG
* ** *
897 ACAATCGGGAACCATCGGCACCTTAGTACCTTGGATGTACGA
131 ACAATCGGGAACCAACAACACCTTAGTACCTTGGATGTAAGA
* * *
939 AAGCATCGGATACCATCGGTAACTTAGGTCGATGGTGGTGTGAGACCATCGAGAAGCATCG
1 GAGCATCGGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATCG
1000 AACACCATCG
Statistics
Matches: 195, Mismatches: 36, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
172 191 0.98
173 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.21
Consensus pattern (172 bp):
GAGCATCGGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATCGGTAA
CTTGGTGCCTTCGATGTACGAGAGCATGCGAAACCATCGATAACTTAGACCGATGGTGGTGCAAG
ACAATCGGGAACCAACAACACCTTAGTACCTTGGATGTAAGA
Found at i:989 original size:43 final size:42
Alignment explanation
Indices: 778--999 Score: 137
Period size: 43 Copynumber: 5.2 Consensus size: 42
768 AGCATTGAAC
*
778 ACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACAATCGGGA
1 ACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATC-GGA
* ** * ** *
821 ACCATCGGTACCTT-GGTGCCTTGGAT-GTACGAGGGCATGGGAA
1 ACCATCGGTAACTTAGGT-CGATGG-TGGTGCGAGACCATCGG-A
* ** * *
864 ACCATCGATAACTTAGACCGATGGTGGTGCAAGACAATCGGGA
1 ACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATC-GGA
* * ** * * *
907 ACCATCGGCACCTTA-GTACCTTGGAT-GTACGAAAGCATCGGA
1 ACCATCGGTAACTTAGGT-CGATGG-TGGTGCGAGACCATCGGA
*
949 TACCATCGGTAACTTAGGTCGATGGTGGTGTGAGACCATCGAGA
1 -ACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCG-GA
*
993 AGCATCG
1 ACCATCG
1000 AACACCATCG
Statistics
Matches: 126, Mismatches: 41, Indels: 24
0.66 0.21 0.13
Matches are distributed among these distances:
42 10 0.08
43 107 0.85
44 9 0.07
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (42 bp):
ACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGGA
Found at i:1007 original size:53 final size:52
Alignment explanation
Indices: 939--1059 Score: 170
Period size: 53 Copynumber: 2.3 Consensus size: 52
929 GGATGTACGA
* * * **
939 AAGCATCGGATACCATCGGTAACTTAGGTCGATGGTGGTGTGAGACCATCGAG
1 AAGCATC-GACACCATCGATAACTAAGGTCGATGGTGGTACGAGACCATCGAG
992 AAGCATCGAACACCATCGATAACTAAGGTCGATGGTGGTACGAGACCATCGAG
1 AAGCATCG-ACACCATCGATAACTAAGGTCGATGGTGGTACGAGACCATCGAG
*
1045 AAGTATCGACACCAT
1 AAGCATCGACACCAT
1060 GGTGCCTTCG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
52 8 0.13
53 53 0.87
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.20
Consensus pattern (52 bp):
AAGCATCGACACCATCGATAACTAAGGTCGATGGTGGTACGAGACCATCGAG
Found at i:1095 original size:139 final size:138
Alignment explanation
Indices: 864--1143 Score: 335
Period size: 139 Copynumber: 2.0 Consensus size: 138
854 GGCATGGGAA
* * * * *
864 ACCATCGATAACTTAGACCGATGGTGGTGCAAGACAATCGGGAACCATCGGCACCTTAGTACCTT
1 ACCATCGATAACTAAGACCGATGGTGGTACAAGACAATCGAGAACCATCGACACCATAGTACCTT
* * * * * * *
929 GGATGTACGAAAGCATCGGATACCATCGGTAACTTAGGTCGATGGTGGTGTGAGACCATCGAGAA
66 CGATGTACGAAAGCATCAGACACCATCGGTAACTTAGGTCGATGATGATGCGAGACCATCAAGAA
994 GCATCGAAC
131 GCATCG-AC
** * * ** * *
1003 ACCATCGATAACTAAGGTCGATGGTGGTACGAGACCATCGAGAAGTATCGACACCATGGTGCCTT
1 ACCATCGATAACTAAGACCGATGGTGGTACAAGACAATCGAGAACCATCGACACCATAGTACCTT
** *
1068 CGATGTACGGGAGTATCAGACACCATCGGTAACTTAGGTCGATGATGATGCGAGACCATCAAGAA
66 CGATGTACGAAAGCATCAGACACCATCGGTAACTTAGGTCGATGATGATGCGAGACCATCAAGAA
*
1133 GTATCGAC
131 GCATCGAC
1141 ACC
1 ACC
1144 TTGGTGCCTT
Statistics
Matches: 117, Mismatches: 24, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
138 5 0.04
139 112 0.96
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.21
Consensus pattern (138 bp):
ACCATCGATAACTAAGACCGATGGTGGTACAAGACAATCGAGAACCATCGACACCATAGTACCTT
CGATGTACGAAAGCATCAGACACCATCGGTAACTTAGGTCGATGATGATGCGAGACCATCAAGAA
GCATCGAC
Found at i:1101 original size:86 final size:86
Alignment explanation
Indices: 988--1698 Score: 543
Period size: 86 Copynumber: 8.3 Consensus size: 86
978 GTGAGACCAT
* * * *
988 CGAGAAGCATC-GAACACCATCGATAACTAAGGTCGATGGTGGTACGAGACCATCGAGAAGTATC
1 CGAG-AGCATCAG-ACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATC
*
1052 GACACCATGGTGCCTTCGATGTA
64 GACACCTTGGTGCCTTCGATGTA
* * * * * *
1075 CGGGAGTATCAGACACCATCGGTAACTTAGGTCGATGATGATGCGAGACCATCAAGAAGTATCGA
1 CGAGAGCATCAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATCGA
* *
1140 CACCTTGGTGCCTTCGTTGTG
66 CACCTTGGTGCCTTCGATGTA
* * ** * * * * * * * *
1161 CGGGAGTATCAGACATTATCGGAAACTTAGGCCAATGGTGGTGCGGGACCATCAAGAAGTATTGG
1 CGAGAGCATCAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATCGA
* *
1226 CACCTTGGTGCCTTGGATGTG
66 CACCTTGGTGCCTTCGATGTA
* * * * * * * ** * * *
1247 CGAGAGCATCAGACACCATCGGTAAGTTAGGCCAATAGTGCTACGGGATAATCGGGAACCATTTG
1 CGAGAGCATCAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCA-TCG
*
1312 -CACCTTGGTGCCTTGGATGTA
65 ACACCTTGGTGCCTTCGATGTA
* * ** * * * * *
1333 CGAGAGCATCAAACCCCATCGGTAACTTAGACCGATGGTAGTGCGAGACCATTGGGAACCATCGG
1 CGAGAGCATCAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATCGA
* * *
1398 CACCTTGGTACCTTGGATGTG
66 CACCTTGGTGCCTTCGATGTA
* ** * * * * *
1419 CGAAAGCATTGGACACCATCGATAACTTAGG-CTAATGGTGGTGCGGGACCATTGGGAAGCATCG
1 CGAGAGCATCAGACACCATCGGTAACTTAGGTC-GATGGTGGTGCGAGACCATCGAGAAGCATCG
* *
1483 ACACCTTAGTGCC-TCAGATATA
65 ACACCTTGGTGCCTTC-GATGTA
* * * * * * * *
1505 CGGGAGCATCGGATACCATCGGTAACTAAGGTCGATGGTAGTGCGAGACCATTGGGAAGTATCGA
1 CGAGAGCATCAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATCGA
* * * * *
1570 TATCATGGTGCCTTCAATGTG
66 CACCTTGGTGCCTTCGATGTA
* ** * * * *
1591 CG-GCATCATTGGACACCGTCAGCAACTTAGGTCGATGGTGGTGCGGGACCATCGAGAAGCATCG
1 CGAG-AGCATCAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATCG
**
1655 GTACCTTGGTGCCTT-GCATGTA
65 ACACCTTGGTGCCTTCG-ATGTA
**
1677 CGAGAGCATGGGACACCATCGG
1 CGAGAGCATCAGACACCATCGG
1699 CCCAAAAAAA
Statistics
Matches: 504, Mismatches: 110, Indels: 21
0.79 0.17 0.03
Matches are distributed among these distances:
85 5 0.01
86 488 0.97
87 11 0.02
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (86 bp):
CGAGAGCATCAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGAGACCATCGAGAAGCATCGA
CACCTTGGTGCCTTCGATGTA
Found at i:1146 original size:397 final size:397
Alignment explanation
Indices: 596--1384 Score: 907
Period size: 397 Copynumber: 2.0 Consensus size: 397
586 GATATGCGGG
* * **
596 AGCATCGGACACCATCGATAACTAAGGTCGATGGTGGTACGGGACCATCAAGAAGTATCGGTAAC
1 AGCATCGAACACCATCGATAACTAAGGTCGATGGTGGTACGAGACCATCAAGAAGTATCGACAAC
* * * * * *
661 TTGGTGTCTTCGATGTGCGGAAGCATCGAACACCATCGATAACTTAGGCCGATGGTGGTGCGGGA
66 ATGGTGCCTTCGATGTACGGAAGCATCGAACACCATCGATAACTTAGGCCGATGATGATGCGAGA
*** * * *
726 CCATTGGGAAGCAACAACACCTTGGTACCTTGGATGTAAGAGAGCAT-TGAACACCATCGGTAAC
131 CCATCAAGAAGCAACAACACCTTGGTACCTTCGATGTAAGAGAGCATCAG-ACACCATCGGAAAC
* * ** * *
790 TTAGGTCGATGGTGGTGCGAGACAATCGGGAACCATCGGTACCTTGGTGCCTTGGATGTACGAGG
195 TTAGGCCAATGGTGGTGCGAGACAATCAAGAACCATCGGCACCTTGGTGCCTTGGATGTACGAGA
** * * * *
855 GCATGGGAAACCATCGATAACTTAGACCGATGGTGGTGCAAGACAATCGGGAACCATCGGCACCT
260 GCATCAGAAACCATCGATAACTTAGACCAATAGTGCTACAAGACAATCGGGAACCATCGGCACCT
** * ** * *
920 TAGTACCTTGGATGTACGAAAGCATCGGATACCATCGGTAACTTAGGTCGATGGTGGTGTGAGAC
325 TAGTACCTTGGATGTACGAAAGCATCAAACACCATCGGTAACTTAGACCGATGGTAGTGCGAGAC
985 CATCGAGA
390 CATCGAGA
* *
993 AGCATCGAACACCATCGATAACTAAGGTCGATGGTGGTACGAGACCATCGAGAAGTATCGACACC
1 AGCATCGAACACCATCGATAACTAAGGTCGATGGTGGTACGAGACCATCAAGAAGTATCGACAAC
* * * *
1058 ATGGTGCCTTCGATGTACGGGAGTATC-AGACACCATCGGTAACTTAGGTCGATGATGATGCGAG
66 ATGGTGCCTTCGATGTACGGAAGCATCGA-ACACCATCGATAACTTAGGCCGATGATGATGCGAG
* * * * * ** * * **
1122 ACCATCAAGAAGTATCGACACCTTGGTGCCTTCGTTGTGCGGGAGTATCAGACATTATCGGAAAC
130 ACCATCAAGAAGCAACAACACCTTGGTACCTTCGATGTAAGAGAGCATCAGACACCATCGGAAAC
* * ** * *
1187 TTAGGCCAATGGTGGTGCGGGACCATCAAGAAGTATTGGCACCTTGGTGCCTTGGATGTGCGAGA
195 TTAGGCCAATGGTGGTGCGAGACAATCAAGAACCATCGGCACCTTGGTGCCTTGGATGTACGAGA
* * * * ** * **
1252 GCATCAGACACCATCGGTAAGTTAGGCCAATAGTGCTACGGGATAATCGGGAACCATTTGCACCT
260 GCATCAGAAACCATCGATAACTTAGACCAATAGTGCTACAAGACAATCGGGAACCATCGGCACCT
* * * *
1317 TGGTGCCTTGGATGTACGAGAGCATCAAACCCCATCGGTAACTTAGACCGATGGTAGTGCGAGAC
325 TAGTACCTTGGATGTACGAAAGCATCAAACACCATCGGTAACTTAGACCGATGGTAGTGCGAGAC
1382 CAT
390 CAT
1385 TGGGAACCAT
Statistics
Matches: 319, Mismatches: 71, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
396 1 0.00
397 317 0.99
398 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (397 bp):
AGCATCGAACACCATCGATAACTAAGGTCGATGGTGGTACGAGACCATCAAGAAGTATCGACAAC
ATGGTGCCTTCGATGTACGGAAGCATCGAACACCATCGATAACTTAGGCCGATGATGATGCGAGA
CCATCAAGAAGCAACAACACCTTGGTACCTTCGATGTAAGAGAGCATCAGACACCATCGGAAACT
TAGGCCAATGGTGGTGCGAGACAATCAAGAACCATCGGCACCTTGGTGCCTTGGATGTACGAGAG
CATCAGAAACCATCGATAACTTAGACCAATAGTGCTACAAGACAATCGGGAACCATCGGCACCTT
AGTACCTTGGATGTACGAAAGCATCAAACACCATCGGTAACTTAGACCGATGGTAGTGCGAGACC
ATCGAGA
Found at i:1248 original size:43 final size:43
Alignment explanation
Indices: 1111--1257 Score: 111
Period size: 43 Copynumber: 3.4 Consensus size: 43
1101 TTAGGTCGAT
* *
1111 GATGATGCGAGACCATCAAGAAGTATCGACACCTTGGTGCCTTC
1 GATG-TGCGAGACCATCAAGAAGTATCGGCACCTTGGTGCCTTG
* * ** * * * * *
1155 GTTGTGCGGGAGTATC-AGACATTATCGGAAACTTAG-GCCAATG
1 GATGTGCGAGACCATCAAGA-AGTATCGGCACCTTGGTGCC-TTG
* *
1198 G-TGGTGCGGGACCATCAAGAAGTATTGGCACCTTGGTGCCTTG
1 GAT-GTGCGAGACCATCAAGAAGTATCGGCACCTTGGTGCCTTG
*
1241 GATGTGCGAGAGCATCA
1 GATGTGCGAGACCATCA
1258 GACACCATCG
Statistics
Matches: 76, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
42 7 0.09
43 59 0.78
44 10 0.13
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (43 bp):
GATGTGCGAGACCATCAAGAAGTATCGGCACCTTGGTGCCTTG
Found at i:1396 original size:43 final size:42
Alignment explanation
Indices: 1348--1482 Score: 103
Period size: 43 Copynumber: 3.1 Consensus size: 42
1338 GCATCAAACC
1348 CCATCGGTAACTTAGACCGATGGTAGTGCGAGACCATTGGGAA
1 CCATCGGTAACTTAGACC-ATGGTAGTGCGAGACCATTGGGAA
* * * * * *
1391 CCATCGGCACCTTGGTACCTTGG-ATGTGCGAAAGCATT-GGACA
1 CCATCGGTAACTTAG-ACCATGGTA-GTGCGAGACCATTGGGA-A
* * * * *
1434 CCATCGATAACTTAGGCTAATGGTGGTGCGGGACCATTGGGAA
1 CCATCGGTAACTTAGAC-CATGGTAGTGCGAGACCATTGGGAA
*
1477 GCATCG
1 CCATCG
1483 ACACCTTAGT
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
42 5 0.07
43 57 0.84
44 6 0.09
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.22
Consensus pattern (42 bp):
CCATCGGTAACTTAGACCATGGTAGTGCGAGACCATTGGGAA
Found at i:2434 original size:43 final size:43
Alignment explanation
Indices: 2341--2760 Score: 304
Period size: 43 Copynumber: 9.8 Consensus size: 43
2331 CAACAGACAT
* * * * * * *
2341 CATCGACACCTTGGTGCCTTGGATGTACGGGATCATTGGACAC
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCCTCGAACAC
* * * *
2384 TACCGGCACCTTGGTGCCTCGGATGTACGGGTGCCTCGAACAC
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCCTCGAACAC
* * * *
2427 CATCGGCACTTTGGTGCCTCGGATGTGCTGGAGCATCAAACAC
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCCTCGAACAC
** * * * *
2470 TGTTGGTACCTTGGTGCCTCGGATGTGTGGGTGCCTCGAACAC
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCCTCGAACAC
* * * * * ** * * *
2513 CGTCGGTACCTTGGTACCTTGGTTGTGCGACAGCATTGGACAC
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCCTCGAACAC
* * *
2556 TATTGGCACCTTGGTGCCTTGGATGTGCGGGAGCCTC-AGACAC
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCCTCGA-ACAC
* * * *
2599 CATTGGCACCTTGGTGCCTCGGATATGCGGGAGTCTCGAACTC
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCCTCGAACAC
* * * *
2642 CATCGGCACCTTGGTGCCTCGGATGTGTGAGAGCATCGGACAC
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCCTCGAACAC
* ** * * * * ** *
2685 CACCGATATCTTAGTGCCTTGGATGTGCCGGAGTATCGGACAC
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCCTCGAACAC
* * * * *
2728 C-TCAGAACATTGGTGCCTTGGATGTCCGGGAGC
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGC
2761 ATCGGGCTAA
Statistics
Matches: 292, Mismatches: 83, Indels: 5
0.77 0.22 0.01
Matches are distributed among these distances:
42 22 0.08
43 269 0.92
44 1 0.00
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.25
Consensus pattern (43 bp):
CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCCTCGAACAC
Found at i:2684 original size:86 final size:86
Alignment explanation
Indices: 2341--2760 Score: 342
Period size: 86 Copynumber: 4.9 Consensus size: 86
2331 CAACAGACAT
* * * * * * *
2341 CATCGACACCTTGGTGCCTTGGATGTACGGGATCATTGGACACTACCGGCACCTTGGTGCCTCGG
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCATCGAACACTATCGGCACCTTGGTGCCTCGG
* *
2406 ATGTACGGGTGCCTCGAACAC
66 ATGTGCGGGAGCCTCGAACAC
* * * * * *
2427 CATCGGCACTTTGGTGCCTCGGATGTGCTGGAGCATCAAACACTGTTGGTACCTTGGTGCCTCGG
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCATCGAACACTATCGGCACCTTGGTGCCTCGG
* *
2492 ATGTGTGGGTGCCTCGAACAC
66 ATGTGCGGGAGCCTCGAACAC
* * * * * ** * * * *
2513 CGTCGGTACCTTGGTACCTTGGTTGTGCGACAGCATTGGACACTATTGGCACCTTGGTGCCTTGG
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCATCGAACACTATCGGCACCTTGGTGCCTCGG
2578 ATGTGCGGGAGCCTC-AGACAC
66 ATGTGCGGGAGCCTCGA-ACAC
* * * *
2599 CATTGGCACCTTGGTGCCTCGGATATGCGGGAGTC-TCGAACTCCATCGGCACCTTGGTGCCTCG
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAG-CATCGAACACTATCGGCACCTTGGTGCCTCG
* * * *
2663 GATGTGTGAGAGCATCGGACAC
65 GATGTGCGGGAGCCTCGAACAC
* ** * * * * * * * * * * *
2685 CACCGATATCTTAGTGCCTTGGATGTGCCGGAGTATCGGACAC-CTCAGAACATTGGTGCCTTGG
1 CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCATCGAACACTATCGGCACCTTGGTGCCTCGG
*
2749 ATGTCCGGGAGC
66 ATGTGCGGGAGC
2761 ATCGGGCTAA
Statistics
Matches: 259, Mismatches: 71, Indels: 9
0.76 0.21 0.03
Matches are distributed among these distances:
85 26 0.10
86 232 0.90
87 1 0.00
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.25
Consensus pattern (86 bp):
CATCGGCACCTTGGTGCCTCGGATGTGCGGGAGCATCGAACACTATCGGCACCTTGGTGCCTCGG
ATGTGCGGGAGCCTCGAACAC
Found at i:2727 original size:129 final size:128
Alignment explanation
Indices: 2328--2728 Score: 352
Period size: 129 Copynumber: 3.1 Consensus size: 128
2318 ACATGTACGA
* * * * * * * * * * * * *
2328 GAGCAACAGACATCATCGACACCTTGGTGCCTTGGATGTACGGGATCATTGGACACTACCGGCAC
1 GAGCATCAGACACCATTGGCACCTTGGTGCCTCGGATATGCGGGAGCCTCGAACACCATCGGCAC
* * * * * * *
2393 CTTGGTGCCTCGGATGTACGGGTGCCTCGAACACCATCGGCACTTTGGTGCCTCGGATGTGCTG
66 CTTGGTGCCTCGGATGTGCGAGAGCATCGGACACCATCGGCAC-TTGGTGCCTTGGATGTGCCG
* ** * * * * * *
2457 GAGCATCAAACACTGTTGGTACCTTGGTGCCTCGGATGTGTGGGTGCCTCGAACACCGTCGGTAC
1 GAGCATCAGACACCATTGGCACCTTGGTGCCTCGGATATGCGGGAGCCTCGAACACCATCGGCAC
* * * * * * * *
2522 CTTGGTACCTTGGTTGTGCGACAGCATTGGACACTATTGGCACCTTGGTGCCTTGGATGTGCGG
66 CTTGGTGCCTCGGATGTGCGAGAGCATCGGACACCATCGGCA-CTTGGTGCCTTGGATGTGCCG
* * *
2586 GAGCCTCAGACACCATTGGCACCTTGGTGCCTCGGATATGCGGGAGTCTCGAACTCCATCGGCAC
1 GAGCATCAGACACCATTGGCACCTTGGTGCCTCGGATATGCGGGAGCCTCGAACACCATCGGCAC
* * ** *
2651 CTTGGTGCCTCGGATGTGTGAGAGCATCGGACACCACCGATATCTTAGTGCCTTGGATGTGCCG
66 CTTGGTGCCTCGGATGTGCGAGAGCATCGGACACCATCGGCA-CTTGGTGCCTTGGATGTGCCG
* *
2715 GAGTATCGGACACC
1 GAGCATCAGACACC
2729 TCAGAACATT
Statistics
Matches: 208, Mismatches: 63, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
129 207 1.00
130 1 0.00
ACGTcount: A:0.18, C:0.27, G:0.30, T:0.24
Consensus pattern (128 bp):
GAGCATCAGACACCATTGGCACCTTGGTGCCTCGGATATGCGGGAGCCTCGAACACCATCGGCAC
CTTGGTGCCTCGGATGTGCGAGAGCATCGGACACCATCGGCACTTGGTGCCTTGGATGTGCCG
Done.