Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004103.1 Hibiscus syriacus cultivar Beakdansim tig00008972_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: 67719
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:1181 original size:19 final size:18
Alignment explanation
Indices: 1144--1186 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1134 AAATTCTTAA
* * *
1144 TATTTTATATCTTATCAT
1 TATTTTACATCTAAACAT
1162 TAATTTTACATCTAAACAT
1 T-ATTTTACATCTAAACAT
1181 TATTTT
1 TATTTT
1187 TTTTATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTACATCTAAACAT
Found at i:1271 original size:28 final size:29
Alignment explanation
Indices: 1203--1311 Score: 105
Period size: 29 Copynumber: 3.8 Consensus size: 29
1193 TTAACTTATT
* **
1203 AAATATATTTTATTCTT-TTCATAACCTAA
1 AAATATATTTTATTCTTATTTA-AATTTAA
* *
1232 AAATATATTTTATTCTTATTTTAGTTTAA
1 AAATATATTTTATTCTTATTTAAATTTAA
* *
1261 AAAT-TATTTTAATCTTATATTAAATTAAA
1 AAATATATTTTATTCTTAT-TTAAATTTAA
* *
1290 AAATACAATTTATTCTTATTTA
1 AAATATATTTTATTCTTATTTA
1312 TTTATATTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
28 13 0.20
29 39 0.60
30 13 0.20
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.51
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTAAATTTAA
Found at i:1372 original size:29 final size:28
Alignment explanation
Indices: 1340--1412 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
1330 AAATTTAAAT
1340 TTAAGATAAAAAATATAATAATTTTGTAG
1 TTAAGATAAAAAATATAA-AATTTTGTAG
*
1369 TTAAGATAAAATAA-A-AACATTTTGTAG
1 TTAAGATAAAA-AATATAAAATTTTGTAG
*
1396 TTAAAATAAAAATATAT
1 TTAAGATAAAAA-ATAT
1413 TTTTAAGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 3 0.08
29 12 0.32
30 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (28 bp):
TTAAGATAAAAAATATAAAATTTTGTAG
Found at i:1381 original size:22 final size:23
Alignment explanation
Indices: 1356--1428 Score: 60
Period size: 27 Copynumber: 3.0 Consensus size: 23
1346 TAAAAAATAT
1356 AATA-ATTTTGTAGTTAAGATAA
1 AATACATTTTGTAGTTAAGATAA
*
1378 AATAAAAACATTTTGTAGTTAAAATAAA
1 AAT----ACATTTTGTAGTTAAGAT-AA
*
1406 AATATATTTT-TAAGTTAAGATAA
1 AATACATTTTGT-AGTTAAGATAA
1429 GAAAAAGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
22 3 0.07
23 3 0.07
24 14 0.34
26 1 0.02
27 15 0.37
28 5 0.12
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (23 bp):
AATACATTTTGTAGTTAAGATAA
Found at i:1580 original size:29 final size:29
Alignment explanation
Indices: 1531--1641 Score: 88
Period size: 27 Copynumber: 4.0 Consensus size: 29
1521 AATTTTGTAA
*
1531 TAAGTTAAGA-AAAGAATAAAACATTTTT
1 TAAGTTAAGATAAAGAATAAAACATATTT
* * *
1559 TAAGTTAAGATAAATATTAAAATATATTT
1 TAAGTTAAGATAAAGAATAAAACATATTT
* * * *
1588 TAAGCTAAAAT-AAGAAT-AAATATACTT
1 TAAGTTAAGATAAAGAATAAAACATATTT
* * *
1615 TAGGTTAAG--ACAGAATAAAATATATTT
1 TAAGTTAAGATAAAGAATAAAACATATTT
1642 AATAATTTAA
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
26 5 0.08
27 24 0.36
28 14 0.21
29 23 0.35
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (29 bp):
TAAGTTAAGATAAAGAATAAAACATATTT
Found at i:2214 original size:22 final size:21
Alignment explanation
Indices: 2164--2202 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2154 GGTCACTGGT
*
2164 ATAATTTATCCTTTAATTTAA
1 ATAATTTATCCTTAAATTTAA
2185 ATAATTTA-CCTTAAATTT
1 ATAATTTATCCTTAAATTT
2203 CTAACTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAATTTATCCTTAAATTTAA
Found at i:6649 original size:14 final size:14
Alignment explanation
Indices: 6632--6662 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6622 CATAAAACTG
6632 ATTCCGAAAAATGA
1 ATTCCGAAAAATGA
*
6646 ATTCCGTAAAATGA
1 ATTCCGAAAAATGA
6660 ATT
1 ATT
6663 ACATTTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (14 bp):
ATTCCGAAAAATGA
Found at i:9264 original size:5 final size:5
Alignment explanation
Indices: 9254--9278 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9244 AATGTTTAAA
9254 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
9279 TAAAACCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:9607 original size:62 final size:63
Alignment explanation
Indices: 9478--9597 Score: 190
Period size: 62 Copynumber: 1.9 Consensus size: 63
9468 AATCCTAATT
* * *
9478 TACTATTATAGACCGTTTAAATAAAACTGAATAGCAGACTGATAACATAAATATACATACAAA
1 TACTATTATAGACCATTTAAATAAAACTGAATAGCAAACTGATAACATAAATACACATACAAA
9541 TACTA-TATAGACCATTTAAATAAAACTGACA-AGCAAACTGATAACATAAATACACAT
1 TACTATTATAGACCATTTAAATAAAACTGA-ATAGCAAACTGATAACATAAATACACAT
9598 GCCACTACTA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
62 47 0.89
63 6 0.11
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (63 bp):
TACTATTATAGACCATTTAAATAAAACTGAATAGCAAACTGATAACATAAATACACATACAAA
Found at i:13967 original size:24 final size:24
Alignment explanation
Indices: 13936--13990 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
13926 ATCAATCACA
*
13936 TTTT-CCAAGAAAGCTGTGCAACC
1 TTTTGCCAAGAAAGCTATGCAACC
13959 TTTTGCCAAGAAAGCTATGCAACC
1 TTTTGCCAAGAAAGCTATGCAACC
13983 TTTTGCCA
1 TTTTGCCA
13991 TCATTTTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (24 bp):
TTTTGCCAAGAAAGCTATGCAACC
Found at i:16425 original size:9 final size:10
Alignment explanation
Indices: 16385--16429 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 10
16375 AAGGTGAGAC
16385 AAAATATATAT
1 AAAATATAT-T
16396 AAAATATCA-T
1 AAAATAT-ATT
16406 -AAATATATT
1 AAAATATATT
16415 AAAATAT-TT
1 AAAATATATT
16424 AAAATA
1 AAAATA
16430 ATTCAAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 1 0.03
9 15 0.48
10 7 0.23
11 7 0.23
12 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATATATT
Found at i:16429 original size:19 final size:19
Alignment explanation
Indices: 16384--16421 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
16374 AAAGGTGAGA
16384 CAAAATATATATAAAATAT
1 CAAAATATATATAAAATAT
16403 CATAAATATAT-TAAAATAT
1 CA-AAATATATATAAAATAT
16422 TTAAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
CAAAATATATATAAAATAT
Found at i:20274 original size:19 final size:19
Alignment explanation
Indices: 20219--20275 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 19
20209 GATATCAAAC
20219 TTTT-CAAATTCGTTGCGA
1 TTTTCCAAATTCGTTGCGA
** * *
20237 TAGTCGAAGTTCGCGTTGCGA
1 TTTTCCAAATT--CGTTGCGA
20258 TTTTCCAAATTCGTTGCG
1 TTTTCCAAATTCGTTGCG
20276 TATTGCATTT
Statistics
Matches: 28, Mismatches: 8, Indels: 5
0.68 0.20 0.12
Matches are distributed among these distances:
18 2 0.07
19 11 0.39
21 15 0.54
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (19 bp):
TTTTCCAAATTCGTTGCGA
Found at i:20392 original size:5 final size:6
Alignment explanation
Indices: 20347--20389 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
20337 GACACGTATT
*
20347 ACCACG ACCACG ACCACG ACCACG ACCTCG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
20390 CGAGACGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.28, C:0.53, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:20938 original size:6 final size:6
Alignment explanation
Indices: 20895--20937 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
20885 CCGTCTCGGT
* *
20895 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TAGTGG TAGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
20938 AATACGTGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.05, C:0.12, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:21094 original size:42 final size:42
Alignment explanation
Indices: 21030--21151 Score: 190
Period size: 42 Copynumber: 2.9 Consensus size: 42
21020 TGCGATTTTG
*
21030 GACTATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
21072 GACTCTCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * * *
21114 GACTATCACAACGAACTTAGATTAAATCGCAACGCGAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAA
21152 TTTGGAATAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:21168 original size:65 final size:63
Alignment explanation
Indices: 21083--21246 Score: 215
Period size: 65 Copynumber: 2.6 Consensus size: 63
21073 ACTCTCGCAA
21083 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTAGATTAAATCGCAACG
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTAGA--AAATCGCAACG
* * *
21148 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACG
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTAGAAAATCGCAACG
* * * * * *
21211 CAAACTTCGACT--ATTGCAACGCGAACTTGGACTATC
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
21247 GCAATGCGAA
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
61 22 0.24
63 19 0.21
65 49 0.54
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (63 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTAGAAAATCGCAACG
Found at i:21217 original size:40 final size:42
Alignment explanation
Indices: 21139--21231 Score: 136
Period size: 40 Copynumber: 2.2 Consensus size: 42
21129 CTTAGATTAA
*
21139 ATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAATTTGGAATAAATCGCAACGCAAACTTCGACT
21183 ATCGCAACGAATTTGG-A-AAATCGCAACGCAAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTCGACT
*
21223 ATTGCAACG
1 ATCGCAACG
21232 CGAACTTGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
40 30 0.64
41 1 0.02
42 9 0.19
44 7 0.15
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTCGACT
Found at i:21230 original size:21 final size:21
Alignment explanation
Indices: 21055--21256 Score: 137
Period size: 21 Copynumber: 9.6 Consensus size: 21
21045 TTTGGAATAA
*
21055 ATCGCAACGTGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * * *
21076 CTCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
21095 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * *
21118 ATCACAA--CGAACTTAGATT
1 ATCGCAACGCGAACTTCGACT
* * *
21137 AAATCGCAACGCGAATTTGGAAT
1 --ATCGCAACGCGAACTTCGACT
21160 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * **
21183 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
21202 ATCGCAACGCAAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
21223 ATTGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
21244 ATCGCAATGCGAA
1 ATCGCAACGCGAA
21257 TATGTAAATC
Statistics
Matches: 138, Mismatches: 33, Indels: 20
0.72 0.17 0.10
Matches are distributed among these distances:
19 33 0.24
21 67 0.49
23 38 0.28
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:21238 original size:107 final size:105
Alignment explanation
Indices: 21034--21224 Score: 323
Period size: 107 Copynumber: 1.8 Consensus size: 105
21024 ATTTTGGACT
* *
21034 ATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACTCTCGCAACGAATTTGGAATAAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
*
21099 CGCAACGCGAACTTCGACTATCACAACGAACTTAGATTAA
66 CGCAACGCAAACTTCGACTATCACAACGAACTTAGATTAA
21139 ATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG-A-AA
1 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
21202 ATCGCAACGCAAACTTCGACTAT
64 ATCGCAACGCAAACTTCGACTAT
21225 TGCAACGCGA
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
105 31 0.38
106 1 0.01
107 49 0.60
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (105 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
CGCAACGCAAACTTCGACTATCACAACGAACTTAGATTAA
Found at i:23696 original size:14 final size:14
Alignment explanation
Indices: 23679--23705 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23669 ATTAAAATAA
23679 GAATATATTTTAAG
1 GAATATATTTTAAG
23693 GAATATATTTTAA
1 GAATATATTTTAA
23706 ATATTTAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
GAATATATTTTAAG
Found at i:31984 original size:2 final size:2
Alignment explanation
Indices: 31977--32018 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
31967 AATCAACCCA
31977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32019 CTTCAATTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32360 original size:24 final size:24
Alignment explanation
Indices: 32328--32386 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
32318 TATGGCTGAG
32328 TTAAATTTTTATAATTTTATATGC
1 TTAAATTTTTATAATTTTATATGC
32352 TTAAATTTTTATAATTTTATATGC
1 TTAAATTTTTATAATTTTATATGC
32376 TTAAATTTTTA
1 TTAAATTTTTA
32387 ATTTATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (24 bp):
TTAAATTTTTATAATTTTATATGC
Found at i:34378 original size:15 final size:15
Alignment explanation
Indices: 34360--34425 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
34350 AAAAGGACTG
34360 AAATAAAATGCTGAA
1 AAATAAAATGCTGAA
*
34375 AAATTAAAAAG-TAGAA
1 AAA-TAAAATGCT-GAA
*
34391 AAATAAAGTGCTGAA
1 AAATAAAATGCTGAA
** * *
34406 ATTTAAAGTACTGAA
1 AAATAAAATGCTGAA
34421 AAATA
1 AAATA
34426 GATAAAATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 27 0.68
16 13 0.32
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.23
Consensus pattern (15 bp):
AAATAAAATGCTGAA
Found at i:35750 original size:104 final size:104
Alignment explanation
Indices: 35570--35760 Score: 253
Period size: 104 Copynumber: 1.8 Consensus size: 104
35560 AAGACTATAG
* * *
35570 TGTTCCTTCATGTTGAGGACTTCGAGTAAATCTGGGTATAATTTAGTGTTAAAGATGACACTGTT
1 TGTTCCTTCATGTTGAGGACATCAAGTAAATCTGGGTATAATTTAGTGTTAAAGATGACACTGCT
*
35635 CATCCATGTTGAAGAGGTCTGGCCTTTTGAAGATGTCGT
66 CATCCATGTTGAAGAGATCTGGCCTTTTGAAGATGTCGT
* * * *
35674 TGTTCCTTCTTGTTGAGGGA-ATCAAGTCAATCTGGAG-ATAATTTGGTGTTGAAGATGACTA-T
1 TGTTCCTTCATGTTGA-GGACATCAAGTAAATCTGG-GTATAATTTAGTGTTAAAGATGAC-ACT
*
35736 GCTCATCCGTGTTGAAGAGATCTGG
63 GCTCATCCATGTTGAAGAGATCTGG
35761 TCACTTTCAA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
104 70 0.93
105 5 0.07
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (104 bp):
TGTTCCTTCATGTTGAGGACATCAAGTAAATCTGGGTATAATTTAGTGTTAAAGATGACACTGCT
CATCCATGTTGAAGAGATCTGGCCTTTTGAAGATGTCGT
Found at i:36067 original size:220 final size:220
Alignment explanation
Indices: 35699--36118 Score: 556
Period size: 220 Copynumber: 1.9 Consensus size: 220
35689 AGGGAATCAA
* * * * * * *
35699 GTCAATCTGGAGATAATTTGGTGTTGAAGATGACTATGCTCATCCGTGTTGAAGAGATCTGGTCA
1 GTCAATCTAGAGATAATTTGATGTTGAAGACGACGATACTCATCCGTGTTAAAAAGATCTGGTCA
* * * * * *
35764 CTTTCAAATAAATTGTTTATTGAAGATGATGTTGTTCATTCTCGTTAAGGAAGTCGGGTTAATCT
66 CTTTCAAATAAATTATTTATTGAAGATGACGATGTTCATTCGCGTTAAGGAAATCGGGTCAATCT
*
35829 GGAGATAATTTAGAGACAACACGGTTCCTTAGCT-TTGAGGAAGTCTGATTGTCTGT-GGATGAC
131 GGAGATAATTTAGAGACAACACGGTTCCTTAG-TATTGAGAAAGTCTGATTGTCT-TAGGATGAC
35892 ACTACTCCTTCGCGTTGAGGAGATTGG
194 ACTACTCCTTCGCGTTGAGGAGATTGG
* *
35919 GTCAATCTAGAGATAATTTGATGTTGAAGACGACGCTACTTATCCGTGTTAAAAAGATCTGGTCA
1 GTCAATCTAGAGATAATTTGATGTTGAAGACGACGATACTCATCCGTGTTAAAAAGATCTGGTCA
* ** * * *
35984 TTTTCAGGTAAATTATTTGTTGAAGATGACGATGTTCCTTCGCGTTGAGGAAATCGGGTCAATCT
66 CTTTCAAATAAATTATTTATTGAAGATGACGATGTTCATTCGCGTTAAGGAAATCGGGTCAATCT
* * * * * *
36049 GGAGATAATTTGGAGACAATATGGTTCCTTCGTATTGAGAAAGTTTGATTGTCTTAGGATGACGC
131 GGAGATAATTTAGAGACAACACGGTTCCTTAGTATTGAGAAAGTCTGATTGTCTTAGGATGACAC
36114 TACTC
196 TACTC
36119 ATCCGTGTTG
Statistics
Matches: 170, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
219 2 0.01
220 168 0.99
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (220 bp):
GTCAATCTAGAGATAATTTGATGTTGAAGACGACGATACTCATCCGTGTTAAAAAGATCTGGTCA
CTTTCAAATAAATTATTTATTGAAGATGACGATGTTCATTCGCGTTAAGGAAATCGGGTCAATCT
GGAGATAATTTAGAGACAACACGGTTCCTTAGTATTGAGAAAGTCTGATTGTCTTAGGATGACAC
TACTCCTTCGCGTTGAGGAGATTGG
Found at i:36240 original size:159 final size:159
Alignment explanation
Indices: 35950--36295 Score: 523
Period size: 159 Copynumber: 2.2 Consensus size: 159
35940 TGTTGAAGAC
* * *
35950 GACGCTACTTATCCGTGTTAAAAAGATCTGGTCATTTTCAGGTAAATTATTTGTTGAAGATGACG
1 GACGCTACTCATCCGTGTTGAAGAGATCTGGTCATTTTCAGGTAAATTATTTGTTGAAGATGACG
* * * *
36015 ATGTTCCTTCGCGTTGAGGAAATCGGGTCAATCTGGAGATAATTTGGAGACAATATGGTTCCTTC
66 ATGTTCCTCCGCGTTGAGGAAATCGGGTCAATCTGGAGATAATTTGGAGACAATACGATTCATTC
*
36080 GTATTGAGAAAGTTTGATTGTCTTAGGAT
131 GTATTGAGAAAGTCTGATTGTCTTAGGAT
* *
36109 GACGCTACTCATCCGTGTTGAAGAGATCTGGTCATTTTCCGGTAAATTGTTTGTTGAAGATGACG
1 GACGCTACTCATCCGTGTTGAAGAGATCTGGTCATTTTCAGGTAAATTATTTGTTGAAGATGACG
*
36174 ATGTTCCTCCGCGTTGAGGAAATCGGGTCAATTTGGAGATAATTTGGAGACAATACGATTCATTC
66 ATGTTCCTCCGCGTTGAGGAAATCGGGTCAATCTGGAGATAATTTGGAGACAATACGATTCATTC
* *
36239 GTGTTGAGGAAGTCTGATTGTCTTAGGAT
131 GTATTGAGAAAGTCTGATTGTCTTAGGAT
* * * *
36268 GATGCTGATTC-TTCGTGTTGAGGAGATC
1 GACGCT-ACTCATCCGTGTTGAAGAGATC
36296 GAGTCAATCT
Statistics
Matches: 169, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
159 166 0.98
160 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.34
Consensus pattern (159 bp):
GACGCTACTCATCCGTGTTGAAGAGATCTGGTCATTTTCAGGTAAATTATTTGTTGAAGATGACG
ATGTTCCTCCGCGTTGAGGAAATCGGGTCAATCTGGAGATAATTTGGAGACAATACGATTCATTC
GTATTGAGAAAGTCTGATTGTCTTAGGAT
Found at i:36349 original size:159 final size:159
Alignment explanation
Indices: 35950--36342 Score: 434
Period size: 159 Copynumber: 2.5 Consensus size: 159
35940 TGTTGAAGAC
* * * * * * * *
35950 GACGCTACTTATCCGTGTTAAAAAGATCTGGTCATTTTCAGGTAAATTATTTGTTGAAGATGACG
1 GACGCTACTCATCCGTGTTGAAGAGATCTGGTCAATCTCAGGTAAATTGTATGTTGAAGACGACG
* * * * * *
36015 ATGTTCCTTCGCGTTGAGGAAATCGGGTCAATCTGGAGATAATTTGGAGACAATATGGTTCCTTC
66 ATGCTCATCCGCGTTGAGGAAATCGGGTCAATCTGGAGATAATTTGGAGACAATACGATTCATTC
*
36080 GTATTGAGAAAGTTTGATTGTCTTAGGAT
131 GTATTGAGAAAGTCTGATTGTCTTAGGAT
* * * * *
36109 GACGCTACTCATCCGTGTTGAAGAGATCTGGTCATTTTCCGGTAAATTGTTTGTTGAAGATGACG
1 GACGCTACTCATCCGTGTTGAAGAGATCTGGTCAATCTCAGGTAAATTGTATGTTGAAGACGACG
* * *
36174 ATGTTCCTCCGCGTTGAGGAAATCGGGTCAATTTGGAGATAATTTGGAGACAATACGATTCATTC
66 ATGCTCATCCGCGTTGAGGAAATCGGGTCAATCTGGAGATAATTTGGAGACAATACGATTCATTC
* *
36239 GTGTTGAGGAAGTCTGATTGTCTTAGGAT
131 GTATTGAGAAAGTCTGATTGTCTTAGGAT
* * * * * *
36268 GATGCTGATTC-TTCGTGTTGAGGAGATC-GAGTCAATCT-AGAGATGATTTG-ATGTTGAAGAC
1 GACGCT-ACTCATCCGTGTTGAAGAGATCTG-GTCAATCTCAG-G-TAAATTGTATGTTGAAGAC
*
36329 GATGATGCTCATCC
62 GACGATGCTCATCC
36343 TTGTTGAAGA
Statistics
Matches: 203, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
158 2 0.01
159 193 0.95
160 8 0.04
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (159 bp):
GACGCTACTCATCCGTGTTGAAGAGATCTGGTCAATCTCAGGTAAATTGTATGTTGAAGACGACG
ATGCTCATCCGCGTTGAGGAAATCGGGTCAATCTGGAGATAATTTGGAGACAATACGATTCATTC
GTATTGAGAAAGTCTGATTGTCTTAGGAT
Found at i:37175 original size:83 final size:84
Alignment explanation
Indices: 37035--37262 Score: 282
Period size: 83 Copynumber: 2.7 Consensus size: 84
37025 GTCATCGAGT
* * * * *
37035 TGAATGGAATCAAACTCGAAGGTATTTGTTAACAGATAACCCTTCTCGTCTTGAGTTATGCTGTA
1 TGAATGTAATCAAACTCGAAGG-ATTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTA
37100 AATTTGACATGTCC-TTGAGC
65 AATTTGACATG-CCTTTGAGC
37120 TGAATGTAATCAAACTCGAAGGA-TGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTAA
1 TGAATGTAATCAAACTCGAAGGATTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTAA
*
37184 ATTTGATATGCCTTTGAGC
66 ATTTGACATGCCTTTGAGC
* * * * * * *
37203 TGAGTGTAGTCGAACTCGAA-GATCTTGGTTGGCAGATAGCCTTTCTCGCCTTGAGGTATG
1 TGAATGTAATCAAACTCGAAGGA--TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
37263 TGTGAATAGT
Statistics
Matches: 126, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
82 4 0.03
83 69 0.55
84 1 0.01
85 52 0.41
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (84 bp):
TGAATGTAATCAAACTCGAAGGATTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTAA
ATTTGACATGCCTTTGAGC
Found at i:37656 original size:24 final size:22
Alignment explanation
Indices: 37619--37685 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 22
37609 TTTTTTATTT
*
37619 TCAAAAGTTATGAAAATATCAA
1 TCAAAAGTTTTGAAAATATCAA
* *
37641 TTAGAAGAGTTTTGAAAAATATTTAA
1 TCA-AA-AGTTTTG-AAAATA-TCAA
37667 TCAAAAGTTTTGAAAATAT
1 TCAAAAGTTTTGAAAATAT
37686 TGCCTCTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.08
23 8 0.22
24 13 0.35
25 8 0.22
26 5 0.14
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.34
Consensus pattern (22 bp):
TCAAAAGTTTTGAAAATATCAA
Found at i:38990 original size:40 final size:40
Alignment explanation
Indices: 38946--39027 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
38936 ACCGTAGTGC
38946 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
38986 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
39026 TA
1 TA
39028 TAAACCTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:44089 original size:6 final size:6
Alignment explanation
Indices: 44072--44108 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
44062 ACACTTGTAT
*
44072 CATGAC CGTGAC CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC CATGAC C
44109 TATGGGTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:46081 original size:40 final size:40
Alignment explanation
Indices: 46037--46198 Score: 306
Period size: 40 Copynumber: 4.0 Consensus size: 40
46027 ACCGTAGTGC
46037 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
46077 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
46117 TACACATAAGGTCGAGCCCACCATATACACGGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
46157 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
46197 TA
1 TA
46199 TAAACCTGCA
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 118 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:50884 original size:2 final size:2
Alignment explanation
Indices: 50877--50924 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
50867 GGACAACAAG
50877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50919 AT AT AT
1 AT AT AT
50925 GTTTGTTCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57586 original size:20 final size:21
Alignment explanation
Indices: 57544--57599 Score: 96
Period size: 20 Copynumber: 2.7 Consensus size: 21
57534 CTTTGAAGGA
*
57544 GAATCGATTCCCCCCACAGGG
1 GAATCGATACCCCCCACAGGG
57565 GAATCGATACCCCCCACA-GG
1 GAATCGATACCCCCCACAGGG
57585 GAATCGATACCCCCC
1 GAATCGATACCCCCC
57600 TGGGGTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.27, C:0.41, G:0.20, T:0.12
Consensus pattern (21 bp):
GAATCGATACCCCCCACAGGG
Found at i:66009 original size:10 final size:10
Alignment explanation
Indices: 65994--66020 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
65984 TACATAAATT
65994 TTTTAATAAA
1 TTTTAATAAA
66004 TTTTAATAAA
1 TTTTAATAAA
66014 TTTTAAT
1 TTTTAAT
66021 TTGTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAATAAA
Done.