Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008068.1 Hibiscus syriacus cultivar Beakdansim tig00110566_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: 71683
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1545 original size:19 final size:18
Alignment explanation
Indices: 1519--1618 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
1509 ATCGCAACGA
1519 GAAATCGCAACGCGAGAT
1 GAAATCGCAACGCGAGAT
1537 GACAATCGCAA--CGAGA-
1 GA-AATCGCAACGCGAGAT
*
1553 G-AATCGCAACGCGAAAT
1 GAAATCGCAACGCGAGAT
1570 GAAAATCGCAA--CGAGA-
1 G-AAATCGCAACGCGAGAT
*
1586 G-AATCGCAACGCGAAAT
1 GAAATCGCAACGCGAGAT
*
1603 GAAAATCGCAATGCGA
1 G-AAATCGCAACGCGA
1619 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
14 16 0.24
16 10 0.15
17 11 0.16
18 2 0.03
19 28 0.42
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
GAAATCGCAACGCGAGAT
Found at i:1559 original size:14 final size:14
Alignment explanation
Indices: 1508--1596 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1498 TTGAAATGAA
1508 AATCGCAACGAGA-
1 AATCGCAACGAGAG
1521 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1538 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1554 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1573 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1587 AATCGCAACG
1 AATCGCAACG
1597 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 21
0.73 0.02 0.24
Matches are distributed among these distances:
13 8 0.13
14 20 0.32
15 6 0.10
16 3 0.05
17 7 0.11
18 1 0.02
19 18 0.29
ACGTcount: A:0.43, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1563 original size:33 final size:33
Alignment explanation
Indices: 1500--1613 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
1490 TCTTTTGGTT
1500 GAAATGAAAATCGCAACGAGA-AATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1532 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1565 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1598 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1614 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 19 0.25
33 58 0.75
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1649 original size:14 final size:14
Alignment explanation
Indices: 1630--1684 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1620 TTTGGTTTCG
1630 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1644 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
1663 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1677 CGTTGCGA
1 CGTTGCGA
1685 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1847 original size:33 final size:33
Alignment explanation
Indices: 1805--1875 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1795 AATACTAACT
*
1805 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1838 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1871 TGAAA
1 TGAAA
1876 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2109 original size:22 final size:22
Alignment explanation
Indices: 2057--2111 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2047 TGGTTGTGAG
**
2057 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2079 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2101 GGATTTCTTCG
1 GGATTTCTTCG
2112 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2278 original size:20 final size:20
Alignment explanation
Indices: 2253--2445 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
2243 CTTTAAATAT
2253 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2273 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2295 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2314 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2334 CGCATTGCGATTTAC-CATA
1 CGCGTTGCGATTTACGGATA
2353 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2373 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2393 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2413 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2433 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2446 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
19 19 0.13
20 111 0.76
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2389 original size:59 final size:60
Alignment explanation
Indices: 2255--2425 Score: 220
Period size: 59 Copynumber: 2.9 Consensus size: 60
2245 TTAAATATCG
** * *
2255 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATCCATTAGCGTTGCGATTTACGGATACA
* *
2316 CGTTGCGATATACGGATACGCATTGCGATTTA-CCA-TACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATCCATTA-GCGTTGCGATTTACGGATACA
*** *
2375 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATCCATTAGCGTTGCGATTT
2426 TCATATTCGC
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
58 2 0.02
59 50 0.53
60 16 0.17
61 27 0.28
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATCCATTAGCGTTGCGATTTACGGATACA
Found at i:2462 original size:21 final size:20
Alignment explanation
Indices: 2438--2514 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
2428 ATATTCGCGT
2438 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
2459 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
2479 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
2501 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
2515 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:2525 original size:20 final size:20
Alignment explanation
Indices: 2500--2551 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2490 AAGAATCGCG
*
2500 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2520 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2540 TTGCGATTCTGG
1 TTGCGATTCTGG
2552 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:6830 original size:2 final size:2
Alignment explanation
Indices: 6823--6854 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6813 ACCCTAGATT
6823 TA TA 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 TA TA
6855 AAAGTTTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8341 original size:3 final size:3
Alignment explanation
Indices: 8333--8361 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
8323 ACACTTGATT
8333 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
8362 TTGTATAATC
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:9133 original size:22 final size:22
Alignment explanation
Indices: 9121--9179 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
9111 TTTTACTAAC
9121 TTTTATTTATATTTGTTATCTA
1 TTTTATTTATATTTGTTATCTA
*
9143 TTTTATTTAT-TTTATTAT-TA
1 TTTTATTTATATTTGTTATCTA
9163 TTATTATATTAATATTT
1 TT-TTAT-TT-ATATTT
9180 TTTCTTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.12
21 11 0.34
22 12 0.38
23 2 0.06
24 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTATTTATATTTGTTATCTA
Found at i:9211 original size:17 final size:17
Alignment explanation
Indices: 9148--9212 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
9138 ATCTATTTTA
9148 TTTATTTTAT-TATTATT
1 TTTATTTTATAT-TTATT
* *
9165 ATTATATTAATATTT-TT
1 TTTAT-TTTATATTTATT
* *
9182 TCTTGTTTCATATTTATT
1 T-TTATTTTATATTTATT
9200 TTTATTTTATATT
1 TTTATTTTATATT
9213 CTAACATCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 24 0.65
18 12 0.32
19 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTATTTTATATTTATT
Found at i:12918 original size:43 final size:43
Alignment explanation
Indices: 12861--12943 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
12851 AACTCACTGC
* *
12861 TTGTGCTAGTATTGCTCTTAAATTGC-GTAGGTGATATTGTGCT
1 TTGTGCCAGTATTGCTCTTAAATTGCAAT-GGTGATATTGTGCT
*
12904 TTGTGCCAGTATTGCTCTTGAATTGCAATGGTGATATTGT
1 TTGTGCCAGTATTGCTCTTAAATTGCAATGGTGATATTGT
12944 TGAAAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.43
Consensus pattern (43 bp):
TTGTGCCAGTATTGCTCTTAAATTGCAATGGTGATATTGTGCT
Found at i:14365 original size:12 final size:12
Alignment explanation
Indices: 14332--14366 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
14322 CCGTTTCAAG
14332 TCCCCGTATCCA
1 TCCCCGTATCCA
*
14344 TCCCCATATCCA
1 TCCCCGTATCCA
*
14356 TCCCTGTATCC
1 TCCCCGTATCC
14367 GTATCAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.49, G:0.06, T:0.29
Consensus pattern (12 bp):
TCCCCGTATCCA
Found at i:15408 original size:2 final size:2
Alignment explanation
Indices: 15401--15438 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15391 AAATAACTGA
15401 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
15439 CTTTTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15924 original size:32 final size:32
Alignment explanation
Indices: 15888--15951 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
15878 CTTTATCTCC
*
15888 TCAACTATAAATCATTGTCCCGTTTATTCCAA
1 TCAACTATAAATCATTGTCCCATTTATTCCAA
* *
15920 TCAACTATAAATCATTGTTCTATTTATTCCAA
1 TCAACTATAAATCATTGTCCCATTTATTCCAA
15952 ATCGTTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (32 bp):
TCAACTATAAATCATTGTCCCATTTATTCCAA
Found at i:19569 original size:21 final size:21
Alignment explanation
Indices: 19543--19587 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 21
19533 ATAAAAATAT
19543 TTTTTTTATTATTTCGGGTCGGG
1 TTTTTTTA-TA-TTCGGGTCGGG
19566 TTTTTTTATATTCGGGTCGGG
1 TTTTTTTATATTCGGGTCGGG
19587 T
1 T
19588 CGGGTCCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.55
22 2 0.09
23 8 0.36
ACGTcount: A:0.09, C:0.09, G:0.27, T:0.56
Consensus pattern (21 bp):
TTTTTTTATATTCGGGTCGGG
Found at i:20044 original size:268 final size:262
Alignment explanation
Indices: 19572--20081 Score: 765
Period size: 268 Copynumber: 1.9 Consensus size: 262
19562 CGGGTTTTTT
*
19572 TATATTCGGGTCGGGTCGGGTCCGGTGAAACTTTATTTTGGTCGGGTCAGTTTTTTTAAGTGTGA
1 TATATTCGGGTCGGGTCGAGTCCGGTGAAACTTTATTTTGGTCGGGTCAGTTTTTTTAAGTGTGA
** * *
19637 TATTCGGGTCGGGTCGAGTTCGGGTTTATGGTGAAAAATACCCGACCCGAAAATATATATAATTT
66 TATTCAAGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTT
* * * * *
19702 TACCTTATATATTTAGGAATAATTATAATAATATCCCTCTATATATAATTTTTTTCAATTAAGTC
131 TACCTTATATATTTAGGAATAATTACAATAATATCCATATATATATAATTATTTCCAATTAAGTC
*
19767 ACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTTGGGTCGGGTCAGGTCAGATTTTTAAT
196 ACTGTTTTTATTGAATAAAAAT-ATTTTTTTATTATTTCGGGTCGGGTCAGGTCAGATTTTTAAT
19832 TCA
260 TCA
* * *
19835 TATATTCGGGTTGGGTCGAGT-CGAGTGAAATTTTATTTTGGTCGGGTCGATTTTTTTTAAGTGT
1 TATATTCGGGTCGGGTCGAGTCCG-GTGAAACTTTATTTTGGTCGGGTC-AGTTTTTTTAAGTGT
* *
19899 GATATTCAAGTCGGGTCGGGTTCTGGTTTAGGGTGAAAAATACCTGACTCGACCC-AAAAAATAT
64 GATATTCAAGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATA-C---C-CGACCCGAAAAAATAT
*
19963 ATAATTTTACCTTATATATTTAGGATTAATTACAATAATATCCATATATATAT-ATATATTTCCA
124 ATAATTTTACCTTATATATTTAGGAATAATTACAATAATATCCATATATATATAAT-TATTTCCA
20027 ATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGT
188 ATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGT
20082 TTATAATTCA
Statistics
Matches: 222, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
262 2 0.01
263 42 0.19
264 51 0.23
265 1 0.00
267 26 0.12
268 94 0.42
269 6 0.03
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.41
Consensus pattern (262 bp):
TATATTCGGGTCGGGTCGAGTCCGGTGAAACTTTATTTTGGTCGGGTCAGTTTTTTTAAGTGTGA
TATTCAAGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTT
TACCTTATATATTTAGGAATAATTACAATAATATCCATATATATATAATTATTTCCAATTAAGTC
ACTGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCAGGTCAGATTTTTAATT
CA
Found at i:20520 original size:17 final size:18
Alignment explanation
Indices: 20498--20545 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
20488 ATATGAAATT
*
20498 GGATTCCAATTCC-TGAC
1 GGATTCCAATTCCTTCAC
20515 GGATTCCAATTCCTTCAC
1 GGATTCCAATTCCTTCAC
*
20533 AGATTCCAATTCC
1 GGATTCCAATTCC
20546 CTCAGAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.31
Consensus pattern (18 bp):
GGATTCCAATTCCTTCAC
Found at i:24084 original size:19 final size:19
Alignment explanation
Indices: 24033--24089 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
24023 TATTTTAGCA
* *
24033 TAAATAATTTATTAATAGT
1 TAAATATTTTATTTATAGT
*
24052 CAAATATTTTATTTATAGT
1 TAAATATTTTATTTATAGT
*
24071 TAAATATTTTATTTTTAGT
1 TAAATATTTTATTTATAGT
24090 GTTTAGTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (19 bp):
TAAATATTTTATTTATAGT
Found at i:25433 original size:35 final size:35
Alignment explanation
Indices: 25387--25498 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
25377 AAAACATTCC
*
25387 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
25422 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
25457 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
25492 TCAATTT
1 TCAATTT
25499 AAGGAGGAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:26603 original size:35 final size:34
Alignment explanation
Indices: 26554--26666 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
26544 AAAAAAGGCA
*
26554 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTGGG-TTTAGAAT
*
26589 GTAATTGAATTATTTTAGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTAGAATTT-GGGTTTAGAAT
* *
26624 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTG-GGTTTAGAAT
26659 GAAATTGA
1 GAAATTGA
26667 GGATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTAGAATTTGGGTTTAGAAT
Found at i:27438 original size:20 final size:20
Alignment explanation
Indices: 27413--27463 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
27403 TTTTCCCAAT
*
27413 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
27433 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
27453 TCGCAATGCGA
1 TCGCAATGCGA
27464 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:27475 original size:20 final size:20
Alignment explanation
Indices: 27452--27586 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
27442 GAATTGGGAA
27452 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
27472 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
27492 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
27513 ATCGCAACGAGATATTGACT
1 ATCGCAATGCGATACTGACT
* * *
27533 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
27553 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
27573 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
27587 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 65 0.68
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:27515 original size:81 final size:82
Alignment explanation
Indices: 27430--27586 Score: 187
Period size: 81 Copynumber: 1.9 Consensus size: 82
27420 GCGAATAAGT
* * * *
27430 AAATCGCAACGCGA-ATTGGGA-AATCGCAATGCGATACTGACTATCGCAATGCGATACTTAC-T
1 AAATCGCAACGAGATATT--GACAATCGCAACGCGATACTGACTATCGCAACGCGATA-ATACAT
27492 -ATCGCAATGCGATAATACA
63 AATCGCAATGCGATAATACA
** * *
27511 AAATCGCAACGAGATATTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATAAT
1 AAATCGCAACGAGATATTGACAATCGCAACGCGATACTGACTATCGCAACGCGATAATACATAAT
27576 CGCAATGCGAT
66 CGCAATGCGAT
27587 TTTCAAAGCG
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
80 5 0.08
81 43 0.67
82 16 0.25
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (82 bp):
AAATCGCAACGAGATATTGACAATCGCAACGCGATACTGACTATCGCAACGCGATAATACATAAT
CGCAATGCGATAATACA
Found at i:27538 original size:61 final size:61
Alignment explanation
Indices: 27450--27580 Score: 172
Period size: 61 Copynumber: 2.1 Consensus size: 61
27440 GCGAATTGGG
* * * * *
27450 AAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATACA
1 AAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
* * * *
27511 AAATCGCAACGAGATATTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACA
1 AAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
*
27572 TAATCGCAA
1 AAATCGCAA
27581 TGCGATTTTC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (61 bp):
AAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
Found at i:28071 original size:20 final size:20
Alignment explanation
Indices: 28022--28085 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
28012 GCGATTTTAG
*
28022 TTTCGCGTTGCGATAGTCAAA
1 TTTCGCGTTGCGATAGTC-AT
28043 TTT-GCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
28062 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
28082 TTTC
1 TTTC
28086 AGAAACTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 4 0.11
20 31 0.82
21 3 0.08
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:29426 original size:18 final size:18
Alignment explanation
Indices: 29405--29449 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
29395 TCCACTTCGG
*
29405 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
29423 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
29441 GAGCCATCA
1 GAGCCATCA
29450 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:29965 original size:20 final size:19
Alignment explanation
Indices: 29942--30051 Score: 72
Period size: 19 Copynumber: 6.1 Consensus size: 19
29932 AGCAACACGA
29942 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGC-G
* *
29962 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAACGCG
**
29981 AAATGAAAATCGCAA--CG
1 AAATGACTATCGCAACGCG
*
29998 ACAA--A--ATCGCAATGCG
1 A-AATGACTATCGCAACGCG
*
30014 AAATGA-AATCGCAACGCG
1 AAATGACTATCGCAACGCG
** *
30032 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAACGCG
30051 A
1 A
30052 TTTGTGTTTC
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.09
15 2 0.03
16 4 0.05
17 4 0.05
18 18 0.24
19 25 0.33
20 16 0.21
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.15
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:29985 original size:19 final size:20
Alignment explanation
Indices: 29942--29997 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
29932 AGCAACACGA
29942 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
29962 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
29981 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
29998 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:30043 original size:19 final size:19
Alignment explanation
Indices: 29970--30051 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
29960 GGAAATGGCT
29970 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
29989 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
30003 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
30021 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
30040 ATCGCAATGCGA
1 ATCGCAATGCGA
30052 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 18 0.34
19 20 0.38
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:30131 original size:20 final size:19
Alignment explanation
Indices: 30088--30144 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
30078 GTTGCGCTTT
*
30088 TCATTTCGCATTGTGATAG
1 TCATTTCGCATTGCGATAG
* *
30107 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
30127 TCATTTTCGCATTGCGAT
1 TCA-TTTCGCATTGCGAT
30145 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.39
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:30241 original size:27 final size:25
Alignment explanation
Indices: 30183--30243 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
30173 ATTCTTCTTC
30183 TGGAATGTTTATATATGTTATCCTTT
1 TGGAATGTTTATATATGTTA-CCTTT
*
30209 T-AAATGTTTATATAAGTGCTTA-CTTT
1 TGGAATGTTTATAT-A-TG-TTACCTTT
30235 TGGAATGTT
1 TGGAATGTT
30244 ATCTAAGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
25 11 0.38
26 7 0.24
27 8 0.28
28 3 0.10
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (25 bp):
TGGAATGTTTATATATGTTACCTTT
Found at i:30607 original size:41 final size:42
Alignment explanation
Indices: 30511--30598 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
30501 GACTCACCTG
* *
30511 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
30553 TCCTCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
30594 TCATC
1 TCATC
30599 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:32047 original size:14 final size:14
Alignment explanation
Indices: 32015--32049 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
32005 GATTGTTTAA
32015 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
32029 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
32043 TTGATTT
1 TTGATTT
32050 ATTTAATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:32197 original size:14 final size:16
Alignment explanation
Indices: 32178--32252 Score: 59
Period size: 19 Copynumber: 4.6 Consensus size: 16
32168 GAAACTGACT
32178 ATCGCAATG-A-GAAA
1 ATCGCAATGAATGAAA
32192 ATCGCAATGCGAAATGAAA
1 ATCGCAAT--G-AATGAAA
32211 ATCGCAATGCAAAATGAAA
1 ATCGCAATG---AATGAAA
*
32230 ATCGCAACG-A-GAAA
1 ATCGCAATGAATGAAA
32244 ATCGCAATG
1 ATCGCAATG
32253 TGATTTTCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
14 20 0.38
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 28 0.54
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (16 bp):
ATCGCAATGAATGAAA
Found at i:32212 original size:19 final size:19
Alignment explanation
Indices: 32188--32236 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
32178 ATCGCAATGA
*
32188 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCAAAAT
32207 GAAAATCGCAATGCAAAAT
1 GAAAATCGCAATGCAAAAT
32226 GAAAATCGCAA
1 GAAAATCGCAA
32237 CGAGAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCAAAAT
Found at i:32299 original size:20 final size:20
Alignment explanation
Indices: 32274--32369 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
32264 TCGCATTGCG
*
32274 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
32294 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
32315 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
32334 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
32354 ATTTTCGCA-TTGCGAT
1 ATTTTCG-AGTTGCGAT
32370 TTCCCCGTTC
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.05
20 54 0.90
21 3 0.05
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:32307 original size:34 final size:36
Alignment explanation
Indices: 32262--32349 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
32252 GTGATTTTCA
* *
32262 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
32296 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
32336 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
32350 AGCCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 1 0.02
39 1 0.02
40 27 0.59
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:32360 original size:40 final size:41
Alignment explanation
Indices: 32274--32369 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 41
32264 TCGCATTGCG
* * ***
32274 ATTTTCTAGTTGCGATAGCCATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAATTGCGATAGCCATTTTCGCGTTGCGATTAGCC
32315 A-TTTCGAATTGCGATAGCCATTTTCGCGTTGCGA-TAGCC
1 ATTTTCGAATTGCGATAGCCATTTTCGCGTTGCGATTAGCC
*
32354 ATTTTCGCATTGCGAT
1 ATTTTCGAATTGCGAT
32370 TTCCCCGTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.06
40 44 0.92
41 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (41 bp):
ATTTTCGAATTGCGATAGCCATTTTCGCGTTGCGATTAGCC
Found at i:32608 original size:20 final size:20
Alignment explanation
Indices: 32583--32632 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
32573 TTGAAGATGA
32583 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
32603 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
32623 TTGCGATTTT
1 TTGCGATTTT
32633 GTGTATTATC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:32661 original size:23 final size:22
Alignment explanation
Indices: 32597--32661 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
32587 GATTTTCAGA
*
32597 ATCTCGTTGCGAAAGTCAG-A-
1 ATCTCGTTGCGATAGTCAGTAT
** **
32617 ATCTCGTTGCGATTTTGTGTATT
1 ATCTCGTTGCGATAGTCAGTA-T
32640 ATCTCGTTGCGATAGTCAGTAT
1 ATCTCGTTGCGATAGTCAGTAT
32662 CGCATTGCGA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
20 14 0.42
21 1 0.03
22 1 0.03
23 17 0.52
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (22 bp):
ATCTCGTTGCGATAGTCAGTAT
Found at i:32705 original size:20 final size:21
Alignment explanation
Indices: 32661--32712 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
32651 ATAGTCAGTA
*
32661 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
32682 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
*
32702 TCGCTTTGCGA
1 TCGCATTGCGA
32713 ATTAGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:32928 original size:12 final size:12
Alignment explanation
Indices: 32909--32942 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
32899 CTCTCCGGTG
32909 ACATCCGTTCCT
1 ACATCCGTTCCT
*
32921 ATATCCGTTCCT
1 ACATCCGTTCCT
32933 ACATCC-TTCC
1 ACATCCGTTCC
32943 CCATCCAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:33525 original size:24 final size:24
Alignment explanation
Indices: 33498--33551 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
33488 GTATTCGAAA
*
33498 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
33522 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
33546 TTTGAT
1 TTTGAT
33552 GATGTTTCAG
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:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:33743 original size:12 final size:12
Alignment explanation
Indices: 33726--33750 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33716 ATATAATCCT
33726 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33738 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33750 G
1 G
33751 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:36084 original size:33 final size:33
Alignment explanation
Indices: 36042--36168 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
36032 GGAAATTACT
36042 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * **
36075 ATCGCAATGCAAAATGAAAATCACAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
36107 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
36141 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
36169 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:36149 original size:66 final size:66
Alignment explanation
Indices: 36043--36175 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
36033 GAAATTACTA
*
36043 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCACAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCACAACGCGAAT
36108 T
66 T
* * *
36109 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCACAACGCGAAT
36174 T
66 T
36175 T
1 T
36176 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCACAACGCGAAT
T
Found at i:36200 original size:14 final size:14
Alignment explanation
Indices: 36183--36239 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
36173 TTTAATTTCG
36183 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
36197 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
36216 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
36230 CGTTGCGATT
1 CGTTGCGATT
36240 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36219 original size:33 final size:33
Alignment explanation
Indices: 36168--36257 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
36158 AAATCGCAAC
* *
36168 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
36201 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
36234 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
36258 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:36221 original size:19 final size:19
Alignment explanation
Indices: 36197--36257 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
36187 GCGATTCTCT
36197 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
36216 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
36230 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
36249 CATTGCGAT
1 CGTTGCGAT
36258 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:36386 original size:14 final size:14
Alignment explanation
Indices: 36367--36400 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
36357 CATCAATTAA
36367 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
36381 ACAAATCACCTTTT
1 ACAAATCAACTTTT
36395 ACAAAT
1 ACAAAT
36401 AAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:37636 original size:21 final size:21
Alignment explanation
Indices: 37612--37727 Score: 56
Period size: 21 Copynumber: 5.5 Consensus size: 21
37602 GTGGGAGGGA
37612 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
* * ** *
37633 CCTCTTGAACGGTGGGAGAGG
1 CCTCTTCAACGATGACAGTGG
* * * * *
37654 ACTC-TCGAGGAATGATAGGGG
1 CCTCTTCAACG-ATGACAGTGG
*
37675 CCTCTTCAACGAT-AGGAGTGG
1 CCTCTTCAACGATGA-CAGTGG
* * **
37696 ACTCTTGAGGGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
*
37717 CCTCTTGAACG
1 CCTCTTCAACG
37728 GTGGGAGGGG
Statistics
Matches: 65, Mismatches: 26, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
20 4 0.06
21 56 0.86
22 5 0.08
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.22
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGTGG
Found at i:37677 original size:42 final size:42
Alignment explanation
Indices: 37592--37796 Score: 198
Period size: 42 Copynumber: 4.9 Consensus size: 42
37582 GTGAATCGGG
* * * *
37592 CTCTTGAATGGTGGGAG-GGACCTCTTCAACG-ATGACAGTGGC
1 CTCTTGAACGGTGGGAGTGGA-CTC-TCGAGGAATGACAGGGGC
* *
37634 CTCTTGAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGTGGACTCTCGAGGAATGACAGGGGC
* * * * * *
37676 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAGTGGACTCTCGAGGAATGACAGGGGC
* * *
37718 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGA
1 CTCTTGAACGGTGGGAGTGGACTCTCGAGGAATGACAGGGGC
* * * * *
37760 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACA
1 CTCTTGAACGGTGGGAGTGGACTCTCGAGGAATGACA
37797 ATCGAGTCGG
Statistics
Matches: 132, Mismatches: 29, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
41 4 0.03
42 125 0.95
43 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGTGGACTCTCGAGGAATGACAGGGGC
Found at i:37733 original size:84 final size:84
Alignment explanation
Indices: 37622--37796 Score: 332
Period size: 84 Copynumber: 2.1 Consensus size: 84
37612 CCTCTTCAAC
*
37622 GATGACAGTGGCCTCTTGAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGACTCTTCAACGA
37687 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
37706 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGACTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGACTCTTCAACGA
37771 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
37790 GATGACA
1 GATGACA
37797 ATCGAGTCGG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.25, C:0.17, G:0.37, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGACTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:38192 original size:91 final size:90
Alignment explanation
Indices: 38016--38200 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
38006 ATTTCAAACT
*
38016 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
38081 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
38109 TTCAACCAAAAGACAAAACAAAAAGATAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
38173 GTATTGGCAGCAACTGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
38200 T
1 T
38201 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:39918 original size:20 final size:19
Alignment explanation
Indices: 39887--39975 Score: 80
Period size: 20 Copynumber: 4.8 Consensus size: 19
39877 TCTTTTGGTT
39887 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
39906 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
39927 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
39946 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
39960 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
39976 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 2 0.04
19 11 0.20
20 29 0.52
21 2 0.04
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:39973 original size:33 final size:34
Alignment explanation
Indices: 39912--39975 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
39902 ACGAGATAAT
**
39912 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGGAAATGAAAATCGCAACGA
39946 GAGAATCGCAACGC-GAAATGAAAATCGCAA
1 GAGAATCGCAACGCGGAAATGAAAATCGCAA
39976 TGCGATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (34 bp):
GAGAATCGCAACGCGGAAATGAAAATCGCAACGA
Found at i:39992 original size:19 final size:19
Alignment explanation
Indices: 39970--40042 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
39960 GAAATGAAAA
* *
39970 TCGCAATGCGATTTTGGTT
1 TCGCATTGCGATTTTGATT
* *
39989 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTGATT
*
40008 TCGCATTGCGATAGTT-ATT
1 TCGCATTGCGAT-TTTGATT
*
40027 TCCGCGTTGCGATTTT
1 T-CGCATTGCGATTTT
40043 CATTCTCGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 32 0.73
20 12 0.27
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTGATT
Found at i:40038 original size:20 final size:19
Alignment explanation
Indices: 39987--40039 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
39977 GCGATTTTGG
**
39987 TTTCGCGTTGCGATTTTTA
1 TTTCGCGTTGCGATAGTTA
*
40006 TTTCGCATTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
40025 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
40040 TTTCATTCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:40585 original size:20 final size:20
Alignment explanation
Indices: 40560--40612 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
40550 GCATTATGTA
40560 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
40580 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
40600 TATCTCGTTGCGA
1 AATCGCGTTGCGA
40613 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:40646 original size:20 final size:20
Alignment explanation
Indices: 40621--40674 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
40611 GATTTTGTAT
40621 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
40641 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
40661 TATCGCATTGCGAT
1 TATCGCATTGCGAT
40675 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:40659 original size:61 final size:61
Alignment explanation
Indices: 40561--40677 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
40551 CATTATGTAA
* * * * *
40561 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
40622 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
40678 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:40693 original size:61 final size:61
Alignment explanation
Indices: 40561--40695 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
40551 CATTATGTAA
* * * * * ** *
40561 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
40622 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
40684 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
40696 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:40785 original size:21 final size:21
Alignment explanation
Indices: 40745--40785 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40735 ACTGTAGACC
**
40745 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
40766 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
40786 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:43189 original size:21 final size:21
Alignment explanation
Indices: 43137--43200 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
43127 TCAAGCGCAC
*
43137 TAGTATCGATACTT-CTCCTA
1 TAGTATCGATACTTCCTTCTA
* *
43157 AAGTACCGATACTTCCTTCTA
1 TAGTATCGATACTTCCTTCTA
*
43178 TGGTATCGATAC-TCACTTCTA
1 TAGTATCGATACTTC-CTTCTA
43199 TA
1 TA
43201 CCGATACCAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (21 bp):
TAGTATCGATACTTCCTTCTA
Found at i:44598 original size:22 final size:22
Alignment explanation
Indices: 44565--44617 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
44555 GGTGAGAAGT
44565 AAAAAAAAGAAG-G-GAAAACC
1 AAAAAAAAGAAGAGAGAAAACC
*
44585 AAAAATAATAGAAGAGAGAAAAGC
1 AAAAA-AA-AGAAGAGAGAAAACC
*
44609 AAAAGAAAG
1 AAAAAAAAG
44618 CAAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.19
21 2 0.07
22 7 0.26
23 3 0.11
24 10 0.37
ACGTcount: A:0.70, C:0.06, G:0.21, T:0.04
Consensus pattern (22 bp):
AAAAAAAAGAAGAGAGAAAACC
Found at i:44703 original size:22 final size:23
Alignment explanation
Indices: 44666--44712 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
44656 CAACGGTGAA
*
44666 GGGAGAAGAGAAATGGGGTAAAT
1 GGGAGAAGAGAAATGGGATAAAT
*
44689 GGGAGGAGA-AAATGGGATAAAT
1 GGGAGAAGAGAAATGGGATAAAT
44711 GG
1 GG
44713 TGTGATTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.45, T:0.13
Consensus pattern (23 bp):
GGGAGAAGAGAAATGGGATAAAT
Found at i:47969 original size:4 final size:4
Alignment explanation
Indices: 47953--48002 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
47943 GAGCTTTACT
* * * * *
47953 TATA TAAA TATA TATA TATA TATA TATA TACA TATA CATA CATA CATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
48001 TA
1 TA
48003 ATAATTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (4 bp):
TATA
Found at i:47969 original size:6 final size:6
Alignment explanation
Indices: 47953--48002 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
47943 GAGCTTTACT
* * * * *
47953 TATATA AATATA TATATA TATATA TATATA CATATA CATACA TACATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
48001 TA
1 TA
48003 ATAATTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (6 bp):
TATATA
Found at i:47993 original size:10 final size:10
Alignment explanation
Indices: 47954--48002 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
47944 AGCTTTACTT
* *
47954 ATATAAATAT
1 ATATATATAC
*
47964 ATATATATAT
1 ATATATATAC
47974 ATATATATAC
1 ATATATATAC
*
47984 ATATACATAC
1 ATATATATAC
*
47994 ATACATATA
1 ATATATATA
48003 ATAATTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATATATAC
Found at i:51537 original size:17 final size:17
Alignment explanation
Indices: 51482--51537 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 17
51472 ATATGAATGA
*
51482 TTTTTTTAATTTAAT-T
1 TTTTTTTAATTAAATAT
** * *
51498 TAATTTTAAATAAAAAT
1 TTTTTTTAATTAAATAT
51515 TATTTTTTAATTAAATAT
1 T-TTTTTTAATTAAATAT
51533 TTTTT
1 TTTTT
51538 ATTTTTTTAC
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
16 10 0.34
17 6 0.21
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTTTAATTAAATAT
Found at i:54747 original size:22 final size:22
Alignment explanation
Indices: 54722--54766 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
54712 ATATGTTACT
54722 TAAGATAATTATTGACCTGATA
1 TAAGATAATTATTGACCTGATA
54744 TAAGATAATTATTGACCTGATA
1 TAAGATAATTATTGACCTGATA
54766 T
1 T
54767 TTTTTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (22 bp):
TAAGATAATTATTGACCTGATA
Found at i:57885 original size:21 final size:21
Alignment explanation
Indices: 57859--57900 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
57849 AAGTGTTTGT
57859 GGTGCTTTATTCTATAATTGC
1 GGTGCTTTATTCTATAATTGC
*
57880 GGTGCTTTATTCTATGATTGC
1 GGTGCTTTATTCTATAATTGC
57901 ATCATCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (21 bp):
GGTGCTTTATTCTATAATTGC
Done.