Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000644.1 Hibiscus syriacus cultivar Beakdansim tig00001245_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: 53019
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7466 original size:27 final size:25
Alignment explanation
Indices: 7415--7466 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
7405 AGATTAAAAT
* * *
7415 TTTAATTTTTTTTTGAAGAGTTTAG
1 TTTAATTTTTTTTTCAAAAGATTAG
7440 TTTATATTTTTTTTTCAAAAGAATTAG
1 TTTA-ATTTTTTTTTCAAAAG-ATTAG
7467 AGATTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 4 0.18
26 14 0.64
27 4 0.18
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.58
Consensus pattern (25 bp):
TTTAATTTTTTTTTCAAAAGATTAG
Found at i:8615 original size:24 final size:25
Alignment explanation
Indices: 8583--8647 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
8573 ATATATACTC
8583 AACTTGTAGTAAGTCAGTT-AAAAA
1 AACTTGTAGTAAGTCAGTTAAAAAA
8607 AACTTGTAGTAAGTCAGTTAAAAAA
1 AACTTGTAGTAAGTCAGTTAAAAAA
8632 AACTTGTAGTAAGTCA
1 AACTTGTAGTAAGTCA
8648 ATAGTATACG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 19 0.47
25 21 0.52
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (25 bp):
AACTTGTAGTAAGTCAGTTAAAAAA
Found at i:10413 original size:2 final size:2
Alignment explanation
Indices: 10406--10436 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10396 TTTCTTTATT
10406 TA TA 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 TA TA T
10437 TCTCTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16702 original size:51 final size:51
Alignment explanation
Indices: 16626--16743 Score: 200
Period size: 51 Copynumber: 2.3 Consensus size: 51
16616 ATTTGACATC
* * * *
16626 AATTAACTTTATATACGTATATAGTTAGGATCCATTTATATTACGTAAAAA
1 AATTAATTTTACATATGTATATAGTTAAGATCCATTTATATTACGTAAAAA
16677 AATTAATTTTACATATGTATATAGTTAAGATCCATTTATATTACGTAAAAA
1 AATTAATTTTACATATGTATATAGTTAAGATCCATTTATATTACGTAAAAA
16728 AATTAATTTTACATAT
1 AATTAATTTTACATAT
16744 ATTTAAGATA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (51 bp):
AATTAATTTTACATATGTATATAGTTAAGATCCATTTATATTACGTAAAAA
Found at i:20215 original size:21 final size:21
Alignment explanation
Indices: 20164--20215 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
20154 ATTATAACTA
20164 TCGCAATGCGGTTTTCCAATT
1 TCGCAATGCGGTTTTCCAATT
** *
20185 TCGCGTTGCGTTTTTCACAA-T
1 TCGCAATGCGGTTTTC-CAATT
20206 TCGCAATGCG
1 TCGCAATGCG
20216 AATAAGTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGGTTTTCCAATT
Found at i:20231 original size:20 final size:21
Alignment explanation
Indices: 20206--20257 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20196 TTTTCACAAT
*
20206 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
20226 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
20247 TCGCAATGCGA
1 TCGCAATGCGA
20258 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:20332 original size:21 final size:20
Alignment explanation
Indices: 20280--20340 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
20270 CAATGCAATT
*
20280 TTTTCTAATTCGCATTGTGA
1 TTTTCTAATTCGCATTGCGA
* *
20300 TTTACGT-ATTCGCGTTGCGA
1 TTTTC-TAATTCGCATTGCGA
*
20320 TTTTCATAATTCGCAATGCGA
1 TTTTC-TAATTCGCATTGCGA
20341 ATACGTAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (20 bp):
TTTTCTAATTCGCATTGCGA
Found at i:20355 original size:20 final size:20
Alignment explanation
Indices: 20330--20423 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
20320 TTTTCATAAT
20330 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
20350 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
20370 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
20391 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
20411 TCGCAATGCGAAT
1 TCGCAATGCGAAT
20424 CTGACTATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:20361 original size:41 final size:41
Alignment explanation
Indices: 20191--20449 Score: 133
Period size: 41 Copynumber: 6.3 Consensus size: 41
20181 AATTTCGCGT
* * * *
20191 TGCGTTTTTCACAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAA
** *
20232 TGCGAATTTGGA-AAATCGCAATGCG-ATAC-TGACTATCGCAA
1 TGCG-ATTTTCATAAATCGCAATGCGAATACGT-A-AATCGCAA
* * * * * * **
20273 TGCAATTTTTTC-TAATTCGCATTGTGATTTACGT-ATTCGCGT
1 TGCGA--TTTTCATAAATCGCAATGCGA-ATACGTAAATCGCAA
*
20315 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAA
* * * *
20356 CGCGA--TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCA-TAAATCGCAATGCGAA-TACGTAAATCGCAA
* * * *
20397 TGCGA-ATACGTAAATCGCAATGCGAAT-C-TGACTATCGCAA
1 TGCGATTTTCATAAATCGCAATGCGAATACGT-A-AATCGCAA
*
20437 TGCGATTTACATA
1 TGCGATTTTCATA
20450 GCGCCATTCG
Statistics
Matches: 163, Mismatches: 38, Indels: 34
0.69 0.16 0.14
Matches are distributed among these distances:
39 5 0.03
40 43 0.26
41 85 0.52
42 26 0.16
44 3 0.02
45 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAA
Found at i:21009 original size:19 final size:20
Alignment explanation
Indices: 20967--21021 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
20957 TAGTTTCGAG
20967 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGCGGA
**
20987 AATGACTATCGCAACGC-GA
1 AATGAAAATCGCAACGCGGA
21006 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
21022 AGATAATCGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGGA
Found at i:21097 original size:33 final size:33
Alignment explanation
Indices: 21050--21178 Score: 177
Period size: 33 Copynumber: 3.9 Consensus size: 33
21040 ACCAAAATCG
*
21050 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATATTCATTTCGCGTTGCGATTCTCT
* * *
21083 CATTACGATTTTCATTTCGCGTTGTGATTCTCT
1 CATTGCGATATTCATTTCGCGTTGCGATTCTCT
* *
21116 CGTTGCGATAATCATTTCGCGTTGCGATTCTCT
1 CATTGCGATATTCATTTCGCGTTGCGATTCTCT
* *
21149 CGTTGCGATAGTCTATTTCGCGTTGCGATT
1 CATTGCGATATTC-ATTTCGCGTTGCGATT
21179 TTCATTATCT
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.82
34 16 0.18
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (33 bp):
CATTGCGATATTCATTTCGCGTTGCGATTCTCT
Found at i:21192 original size:20 final size:19
Alignment explanation
Indices: 21052--21206 Score: 70
Period size: 20 Copynumber: 8.8 Consensus size: 19
21042 CAAAATCGCA
*
21052 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
*
21071 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCTCG
* *
21085 TTACGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
*
21104 TTGTGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
** *
21118 TTGCGATAATCATTTCGCG
1 TTGCGATTTTCATTTCTCG
21137 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
** *
21151 TTGCGATAGTCTATTTCGCG
1 TTGCGATTTTC-ATTTCTCG
21171 TTGCGATTTTCATTATCTCG
1 TTGCGATTTTCATT-TCTCG
**
21191 TTGTAATTTTCATTTC
1 TTGCGATTTTCATTTC
21207 AACCAAAAGA
Statistics
Matches: 99, Mismatches: 20, Indels: 34
0.65 0.13 0.22
Matches are distributed among these distances:
14 27 0.27
16 7 0.07
17 8 0.08
19 28 0.28
20 29 0.29
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:23081 original size:94 final size:93
Alignment explanation
Indices: 22890--23265 Score: 571
Period size: 94 Copynumber: 4.1 Consensus size: 93
22880 TAGATTGCTT
* * *
22890 AGTAAATTTATTCGGTTACTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
22951 ATTTGTCTTTTGTTTTGTCTTCTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* *
22980 AGTAAATTTATTCGGTTGCTGCCAATTCTGGTAAACTGTGTATTCTTTAATACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
23045 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
23074 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
23139 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
23168 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
23233 ATTTGTCTTTGTTTTGTCTTTTAGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
23261 AGTAA
1 AGTAA
23266 TGCAATCCAT
Statistics
Matches: 265, Mismatches: 16, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
90 33 0.12
92 3 0.01
93 26 0.10
94 203 0.77
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:23354 original size:12 final size:12
Alignment explanation
Indices: 23337--23362 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23327 TTAGTAACAC
23337 TGTTTTGTCTTT
1 TGTTTTGTCTTT
23349 TGTTTTGTCTTT
1 TGTTTTGTCTTT
23361 TG
1 TG
23363 GTTTCGCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.19, T:0.73
Consensus pattern (12 bp):
TGTTTTGTCTTT
Found at i:23380 original size:19 final size:19
Alignment explanation
Indices: 23364--23453 Score: 91
Period size: 19 Copynumber: 4.9 Consensus size: 19
23354 TGTCTTTTGG
23364 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
23383 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
23399 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
**
23416 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
23435 TTTTTCACGTTGCGATTTT
1 --TTTCGCGTTGCGATTTT
23454 AAGTTCCAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 27 0.47
21 14 0.25
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:23930 original size:42 final size:42
Alignment explanation
Indices: 23854--23933 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
23844 GACTCGCCTG
* * *
23854 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
23896 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
23934 ACTGCCATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:25342 original size:14 final size:14
Alignment explanation
Indices: 25323--25358 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
25313 ATTGTTTAAT
25323 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
25337 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
25351 TGATTTGT
1 TGATTTGT
25359 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:25502 original size:14 final size:14
Alignment explanation
Indices: 25483--25539 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
25473 GCGAAATGAA
25483 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
25497 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
25516 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
25530 AATTGCAACG
1 AATCGCAACG
25540 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:25510 original size:33 final size:33
Alignment explanation
Indices: 25465--25577 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
25455 AAAAATGACT
*
25465 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
25498 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
25531 ATTGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
25564 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
25578 CTAAATTCGC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:25558 original size:19 final size:19
Alignment explanation
Indices: 25465--25558 Score: 82
Period size: 19 Copynumber: 5.5 Consensus size: 19
25455 AAAAATGACT
*
25465 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
25484 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
25498 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
25517 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
25531 ATTGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
25550 ATCGCAACG
1 ATCGCAACG
25559 ACAAAATCGC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 28 0.47
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:25605 original size:19 final size:19
Alignment explanation
Indices: 25583--25733 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
25573 CGAAACTAAA
25583 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
25602 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
25617 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
25635 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
25650 -TCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
* *
25668 TTCGCATTGCG--GTTC--
1 TTCGCGTTGCGATTTTCAT
* *
25683 -TCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
* **
25701 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
*
25720 TTCCGCGTTACGAT
1 TT-CGCGTTGCGAT
25734 AGACATTAAG
Statistics
Matches: 91, Mismatches: 25, Indels: 31
0.62 0.17 0.21
Matches are distributed among these distances:
14 25 0.27
16 7 0.08
17 8 0.09
19 42 0.46
20 9 0.10
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:25629 original size:33 final size:33
Alignment explanation
Indices: 25587--25713 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
25577 ACTAAATTCG
* *
25587 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
25620 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
25653 CGTTGCGATTTTTATTTCGCATTGCGGTTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
25686 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
25714 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:25779 original size:20 final size:20
Alignment explanation
Indices: 25707--25779 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
25697 TTATTTCGCA
**
25707 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCATG
* * ***
25727 TTACGATAGACATTAAGATG
1 TTGCGATAGTCATTTCCATG
25747 ATTGCGA-ACGTCATTTCCATG
1 -TTGCGATA-GTCATTTCCATG
25768 TTGCGATAGTCA
1 TTGCGATAGTCA
25780 AATGATTGCC
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCATG
Found at i:26621 original size:24 final size:24
Alignment explanation
Indices: 26566--26613 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
26556 TTCCAATGTT
26566 CCTGTAAATTTAAATAAATAATAC
1 CCTGTAAATTTAAATAAATAATAC
26590 CCTGTAAATTTAAATAAATAATAC
1 CCTGTAAATTTAAATAAATAATAC
26614 TTAGTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
CCTGTAAATTTAAATAAATAATAC
Found at i:28083 original size:12 final size:12
Alignment explanation
Indices: 28066--28090 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28056 TCTTCGGGGA
28066 CTTTTTCTTCTT
1 CTTTTTCTTCTT
28078 CTTTTTCTTCTT
1 CTTTTTCTTCTT
28090 C
1 C
28091 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:28299 original size:24 final size:24
Alignment explanation
Indices: 28265--28318 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
28255 CTGAAACATC
*
28265 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
28289 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
28313 ATCAAA
1 ATCAAA
28319 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:29196 original size:20 final size:20
Alignment explanation
Indices: 29042--29195 Score: 157
Period size: 20 Copynumber: 7.7 Consensus size: 20
29032 GATTCTGTAT
* *
29042 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
29062 AATCCCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
29082 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
29102 AATCACGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
29122 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * ** *
29142 TATCTCGTTACGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
29163 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
29183 TATCGCATTGCGA
1 TATCGCGTTGCGA
29196 TTTTCCAAAT
Statistics
Matches: 114, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
19 3 0.03
20 97 0.85
21 12 0.11
22 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:29278 original size:21 final size:22
Alignment explanation
Indices: 29230--29278 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
29220 ACTTATTCGT
29230 ATTGCG-AATTAGGAAAATCAC
1 ATTGCGAAATTAGGAAAATCAC
** *
29251 AACGCGAAATTA-GAAAATCGC
1 ATTGCGAAATTAGGAAAATCAC
29272 ATTGCGA
1 ATTGCGA
29279 TAGTCATAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (22 bp):
ATTGCGAAATTAGGAAAATCAC
Found at i:35007 original size:23 final size:23
Alignment explanation
Indices: 34977--35146 Score: 189
Period size: 23 Copynumber: 7.8 Consensus size: 23
34967 ATTGCGATAG
34977 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTAT
* *
35000 TCCAAGTT--CATTGCGA--TAG
1 TCCAAGTTCGCGTTGCGATTTAT
*
35019 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTAT
35042 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTAT
* * *
35065 TACAAATT--CGTTGCGA--TAG
1 TCCAAGTTCGCGTTGCGATTTAT
* *
35084 TCGAAGTTCGCGTTGCAATTTAT
1 TCCAAGTTCGCGTTGCGATTTAT
*
35107 TCCAAATTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTAT
35130 TCCAAGTT--CGTTGCGAT
1 TCCAAGTTCGCGTTGCGAT
35147 AGTCCAAAAT
Statistics
Matches: 121, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
19 16 0.13
21 38 0.31
23 67 0.55
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (23 bp):
TCCAAGTTCGCGTTGCGATTTAT
Found at i:35013 original size:42 final size:43
Alignment explanation
Indices: 34968--35159 Score: 189
Period size: 42 Copynumber: 4.5 Consensus size: 43
34958 GACTATCGCA
* *
34968 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT-CA
1 TTGCGATAGTCCAAATTCGCGTTGCGATTTATTCCAAGTTCCG
* *
35010 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGCG
1 TTGCGATAGTCCAAATTCGCGTTGCGATTTATTCCAAGTTC-CG
* * * *
35054 TTGCGATTTATTACAAATT--CGTTGCGA--TAGTCGAAGTTCGCG
1 TTGCGA--TAGTCCAAATTCGCGTTGCGATTTATTCCAAGTTC-CG
* *
35096 TTGCAATTTATTCCAAATTCGCGTTGCGATTTATTCCAAGTT-CG
1 TTGCGA--TAGTCCAAATTCGCGTTGCGATTTATTCCAAGTTCCG
*
35140 TTGCGATAGTCCAAAATCGC
1 TTGCGATAGTCCAAATTCGC
35160 AACGACGGTA
Statistics
Matches: 127, Mismatches: 15, Indels: 16
0.80 0.09 0.10
Matches are distributed among these distances:
42 81 0.64
44 30 0.24
46 16 0.13
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (43 bp):
TTGCGATAGTCCAAATTCGCGTTGCGATTTATTCCAAGTTCCG
Found at i:35051 original size:65 final size:65
Alignment explanation
Indices: 34977--35150 Score: 303
Period size: 65 Copynumber: 2.7 Consensus size: 65
34967 ATTGCGATAG
* *
34977 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTAT
* *
35042 TCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTAT
1 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTAT
*
35107 TCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
35151 CAAAATCGCA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 102 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (65 bp):
TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTAT
Found at i:35908 original size:21 final size:21
Alignment explanation
Indices: 35884--35954 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
35874 CACCAGTCGT
*
35884 TGCGATTTTGGACTATCGTAA
1 TGCGATTTTGGACTATCGCAA
** *
35905 TGCGATAGTCGACTATCGCAA
1 TGCGATTTTGGACTATCGCAA
** *
35926 TGCGAACTTGGACTATCGCAT
1 TGCGATTTTGGACTATCGCAA
35947 TGCGATTT
1 TGCGATTT
35955 ACATATTCGC
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (21 bp):
TGCGATTTTGGACTATCGCAA
Found at i:35966 original size:20 final size:20
Alignment explanation
Indices: 35941--36074 Score: 164
Period size: 20 Copynumber: 6.6 Consensus size: 20
35931 ACTTGGACTA
35941 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
35961 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
***
35981 TCGCATTGCGATAGCCGACTA-
1 TCGCATTGCGATTTAC-A-TAT
36002 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
***
36022 TCGCATTGCGATAGCCGACTA-
1 TCGCATTGCGATTTAC-A-TAT
36043 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
36063 TCGCATTGCGAT
1 TCGCATTGCGAT
36075 AGTCCAAGTT
Statistics
Matches: 96, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.04
20 60 0.62
21 28 0.29
22 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:36002 original size:82 final size:82
Alignment explanation
Indices: 35905--36076 Score: 226
Period size: 82 Copynumber: 2.1 Consensus size: 82
35895 ACTATCGTAA
* **
35905 TGCGATAGTCGACTATCGCAATGCGAACTTGGAC-TA-TCGCATTGCGATTTAC-A-TATTCGCA
1 TGCGATAGCCGACTATCGCAATGCG-A-TT-GACATATTCGCATTGCGATAGACGACTA-TCGCA
35966 TTGCGATTTACATATTCGCAT
62 TTGCGATTTACATATTCGCAT
* * *
35987 TGCGATAGCCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCCGACTATCGCATTGC
1 TGCGATAGCCGACTATCGCAATGCGATTGACATATTCGCATTGCGATAGACGACTATCGCATTGC
36052 GATTTACATATTCGCAT
66 GATTTACATATTCGCAT
36069 TGCGATAG
1 TGCGATAG
36077 TCCAAGTTCG
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
79 2 0.03
80 4 0.05
81 14 0.17
82 58 0.73
83 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (82 bp):
TGCGATAGCCGACTATCGCAATGCGATTGACATATTCGCATTGCGATAGACGACTATCGCATTGC
GATTTACATATTCGCAT
Found at i:36006 original size:41 final size:41
Alignment explanation
Indices: 35960--36179 Score: 277
Period size: 41 Copynumber: 5.3 Consensus size: 41
35950 GATTTACATA
* *
35960 TTCGCATTGCGATTTACATATTCGCATTGCGATAG-CCGAC
1 TTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
* *
36000 TATCGCATTGCGATTTACATATTCGCATTGCGATAG-CCGAC
1 T-TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
36041 TATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1 T-TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
* * *
36083 TTCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTTCAAG
1 TTCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAG
* *
36125 TTCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAG
36167 TTCGCATTGCGAT
1 TTCGCATTGCGAT
36180 AGTCCAAGTT
Statistics
Matches: 170, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
40 1 0.01
41 88 0.52
42 81 0.48
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (41 bp):
TTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
Found at i:36007 original size:21 final size:21
Alignment explanation
Indices: 35980--36199 Score: 272
Period size: 21 Copynumber: 10.6 Consensus size: 21
35970 GATTTACATA
* *
35980 TTCGCATTGCGATAG-CCGAC
1 TTCGCATTGCGATAGTCCAAG
* *
36000 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
* *
36021 TTCGCATTGCGATAG-CCGAC
1 TTCGCATTGCGATAGTCCAAG
* *
36041 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
36062 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
36083 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
36104 TTCGCATTGCGATAGTTCAAG
1 TTCGCATTGCGATAGTCCAAG
36125 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
36146 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
36167 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
36188 TTCGCGTTGCGA
1 TTCGCATTGCGA
36200 ATCTGGAAAC
Statistics
Matches: 176, Mismatches: 14, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.01
20 28 0.16
21 145 0.82
22 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:39516 original size:3 final size:3
Alignment explanation
Indices: 39508--39536 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39498 TTACCCATAT
39508 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39537 TTCATTTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40675 original size:20 final size:21
Alignment explanation
Indices: 40650--40694 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
40640 AATTTGTAAA
40650 TCGCAACACAGTTTC-CAAAT
1 TCGCAACACAGTTTCGCAAAT
* *
40670 TCGCAACTCAGTTTCGGAAAT
1 TCGCAACACAGTTTCGCAAAT
40691 TCGC
1 TCGC
40695 GTTGCCATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (21 bp):
TCGCAACACAGTTTCGCAAAT
Found at i:40782 original size:20 final size:20
Alignment explanation
Indices: 40753--40871 Score: 211
Period size: 20 Copynumber: 6.0 Consensus size: 20
40743 GAAAATCGCG
*
40753 TTGCGATAGTATTGTTTACA
1 TTGCGATAGTACTGTTTACA
*
40773 TTGTGATAGTACTGTTTACA
1 TTGCGATAGTACTGTTTACA
*
40793 TTACGATAGTACTGTTTACA
1 TTGCGATAGTACTGTTTACA
40813 TTGCGATAGTACTGTTTACA
1 TTGCGATAGTACTGTTTACA
40833 TTGCGATAGTACTGTTTACA
1 TTGCGATAGTACTGTTTACA
40853 TTGCGATAGTACTGTTTAC
1 TTGCGATAGTACTGTTTAC
40872 CTATATCGGT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 94 1.00
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTACTGTTTACA
Found at i:40928 original size:97 final size:97
Alignment explanation
Indices: 40813--41012 Score: 328
Period size: 97 Copynumber: 2.1 Consensus size: 97
40803 ACTGTTTACA
* *
40813 TTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATAT
1 TTGCGATAGTACTGTTTACATTGCGATACTACTGTTTACATTGCGATAATACTGTTTACCTATAT
* *
40878 CGGTAACTAGCATTGCGAATTTGAAAATCGTG
66 CGGTAACTAACATTGCGAATTTGAAAATCGCG
*
40910 TTGCGATAGTACTGTTTACATTGCGATACTATTGTTTACATTGCGATAATACTGTTTACCTATAT
1 TTGCGATAGTACTGTTTACATTGCGATACTACTGTTTACATTGCGATAATACTGTTTACCTATAT
* **
40975 CGGTAATTAATGTTGCGAATTTGAAAATCGCG
66 CGGTAACTAACATTGCGAATTTGAAAATCGCG
41007 TTGCGA
1 TTGCGA
41013 ATTTGAAAAT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (97 bp):
TTGCGATAGTACTGTTTACATTGCGATACTACTGTTTACATTGCGATAATACTGTTTACCTATAT
CGGTAACTAACATTGCGAATTTGAAAATCGCG
Found at i:40933 original size:20 final size:20
Alignment explanation
Indices: 40910--40968 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
40900 GAAAATCGTG
*
40910 TTGCGATAGTACTGTTTACA
1 TTGCGATAATACTGTTTACA
* *
40930 TTGCGATACTATTGTTTACA
1 TTGCGATAATACTGTTTACA
40950 TTGCGATAATACTGTTTAC
1 TTGCGATAATACTGTTTAC
40969 CTATATCGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (20 bp):
TTGCGATAATACTGTTTACA
Found at i:41011 original size:20 final size:20
Alignment explanation
Indices: 40987--41052 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
40977 GTAATTAATG
*
40987 TTGCGAATTTGAAAATCGCG
1 TTGCGAATTTGAAAATCGCA
41007 TTGCGAATTTGAAAATCGCA
1 TTGCGAATTTGAAAATCGCA
41027 TTGCGAATTTGAAAATCGCA
1 TTGCGAATTTGAAAATCGCA
41047 TTGCGA
1 TTGCGA
41053 TAGTACTGCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCGCA
Found at i:41011 original size:117 final size:115
Alignment explanation
Indices: 40796--41201 Score: 373
Period size: 117 Copynumber: 3.5 Consensus size: 115
40786 GTTTACATTA
40796 CGATAGTACTGTTTACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTA-C-AT-TGCG
1 CGATAGTACTGTTTACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATAT-CG
* * * * ** * * * *
40858 AT-AGT-ACTGTTTACCTATATCGGTAACTAGCATTGCGAATTTGAAAATCGTGTTG
65 GTAATTAAC-G-TT-GCGA-ATTTGAAAATCGC-TTGCGAATTTGAAAATCG-ATTG
* * *
40913 CGATAGTACTGTTTACATTGCGATACTATTGTTTACATTGCGATAATACTGTTTACCTATATCGG
1 CGATAGTACTGTTTACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATATCGG
*
40978 TAATTAATGTTGCGAATTTGAAAATCGCGTTGCGAATTTGAAAATCGCATTG
66 TAATTAACGTTGCGAATTTGAAAATCGC-TTGCGAATTTGAAAATCG-ATTG
* * ** * *
41030 CGA-A-T-TTGAAAATCGCATTGCGATAGTACTGCTTACATTGCGATAGTATTGTTTACCTATAT
1 CGATAGTACTG---TTTACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATAT
* * ***
41092 CGGTAATTAACGTTGCGAATTTGAAAATCGCATGCGATAGTACTGTTTA-C-ATTG
63 CGGTAATTAACGTTGCGAATTTGAAAATCGCTTGCGA-A-T-TTGAAAATCGATTG
*
41146 CGATAGTACTATTTACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTAC
1 CGATAGTACTGTTTACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTAC
41202 ATTGCGATAG
Statistics
Matches: 237, Mismatches: 38, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
114 2 0.01
115 1 0.00
116 53 0.22
117 159 0.67
118 6 0.03
119 11 0.05
120 4 0.02
121 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (115 bp):
CGATAGTACTGTTTACATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATATCGG
TAATTAACGTTGCGAATTTGAAAATCGCTTGCGAATTTGAAAATCGATTG
Found at i:41149 original size:20 final size:20
Alignment explanation
Indices: 41124--41241 Score: 227
Period size: 20 Copynumber: 5.9 Consensus size: 20
41114 GAAAATCGCA
41124 TGCGATAGTACTGTTTACAT
1 TGCGATAGTACTGTTTACAT
*
41144 TGCGATAGTACTATTTACAT
1 TGCGATAGTACTGTTTACAT
41164 TGCGATAGTACTGTTTACAT
1 TGCGATAGTACTGTTTACAT
41184 TGCGATAGTACTGTTTACAT
1 TGCGATAGTACTGTTTACAT
41204 TGCGATAGTACTGTTTACAT
1 TGCGATAGTACTGTTTACAT
41224 TGCGATAGTACTGTTTAC
1 TGCGATAGTACTGTTTAC
41242 CTATATCGGT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 96 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (20 bp):
TGCGATAGTACTGTTTACAT
Found at i:41453 original size:76 final size:77
Alignment explanation
Indices: 41279--41464 Score: 320
Period size: 77 Copynumber: 2.4 Consensus size: 77
41269 TGAAATTCAC
* *
41279 AACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATATGATTTTCAAATTCGCAACACGAT
1 AACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATACGATTTTCAAATTCACAACACGAT
*
41344 TTTCAAATTTGT
66 TTTCAAATTCGT
* *
41356 AACGCTAATTACCAATATAGGTAAACAGTACTATCGCAATACGATTTTTAAATTCAC-ACACGAT
1 AACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATACGATTTTCAAATTCACAACACGAT
41420 TTTCAAATTCGT
66 TTTCAAATTCGT
41432 AACGCTAATTACCGATATAGGTAAACAGTACTA
1 AACGCTAATTACCGATATAGGTAAACAGTACTA
41465 AAATCACGTT
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
76 50 0.49
77 53 0.51
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (77 bp):
AACGCTAATTACCGATATAGGTAAACAGTACTATCGCAATACGATTTTCAAATTCACAACACGAT
TTTCAAATTCGT
Found at i:43500 original size:26 final size:26
Alignment explanation
Indices: 43463--43522 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
43453 ACCGAAGTGC
* *
43463 TAATACATATAAGGTTGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
43489 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
43515 TAATACAC
1 TAATACAC
43523 TAAATGTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (26 bp):
TAATACACATAAGGTCGTGCCCACCA
Found at i:47987 original size:18 final size:17
Alignment explanation
Indices: 47954--47987 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
47944 GAATAATTAA
47954 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
47971 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
47988 ATACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Done.