Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009268.1 Hibiscus syriacus cultivar Beakdansim tig00112926_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: 304330
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:202821 original size:40 final size:40
Alignment explanation
Indices: 202594--202828 Score: 190
Period size: 40 Copynumber: 5.8 Consensus size: 40
202584 GCTTTAAAAA
* *
202594 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT-TACGT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTATATGT
* * * ** *
202633 ATTGTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
1 -TCG-CGTTGCGATTTACAGATACGCGTTGCGATTTATATGT
* * ** *
202675 TCTCGTTGCGATTTACAGATACGTGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTATATGT
* * *
202715 TCTCGTTGCGATTTACGGATACGCGTTGCGATTT-TACGGAT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTATA-TG-T
* * *
202756 ACTCGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGT
1 TCGCGTTGCGAT-TTACAGATA-CGCGTTGCGATTTATATGT
* * *
202796 TCGCGTTGCGATTTTCATATCCGCGTTGCGATT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATT
202829 CTGGAAAATC
Statistics
Matches: 160, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
39 1 0.01
40 95 0.59
41 60 0.38
42 4 0.03
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACAGATACGCGTTGCGATTTATATGT
Found at i:202824 original size:121 final size:121
Alignment explanation
Indices: 202597--202828 Score: 306
Period size: 121 Copynumber: 1.9 Consensus size: 121
202587 TTAAAAATCG
* ** * *
202597 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGCATT
* * *
202662 GCGATTTACGTATTCTCGTTGCGATTTACAGATACGTGTTGCGATTTACGTATTCT
66 GCGATTTACATATTCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
*
202718 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAAT-CGCG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT--TCACGAATACGCA
* * * * *
202781 TTGCGATTTATATGTTCGCGTTGCGATTTTCATATCCGCGTTGCGATT
64 TTGCGATTTACATATTCGCGTTGCGATTTACAGATACGCGTTGCGATT
202829 CTGGAAAATC
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
121 90 0.95
122 3 0.03
123 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (121 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGCATT
GCGATTTACATATTCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
Found at i:202889 original size:42 final size:42
Alignment explanation
Indices: 202796--202889 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
202786 ATTTATATGT
* *
202796 TCGCGTTGCG-ATTTTCATATCCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATCCGCATTGCGATTCTGCAAAA
** * *
202837 TCGCAATGCGAATTTGT-ACTAT-CGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATCCGCATTGCGATTCTGCAAAA
202879 TCGCGTTGCGA
1 TCGCGTTGCGA
202890 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 30 0.71
43 4 0.10
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATCCGCATTGCGATTCTGCAAAA
Found at i:202927 original size:20 final size:19
Alignment explanation
Indices: 202878--202931 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
202868 ATTCTTCATA
202878 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
202897 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
202918 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
202932 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:203566 original size:50 final size:50
Alignment explanation
Indices: 203459--203587 Score: 145
Period size: 50 Copynumber: 2.5 Consensus size: 50
203449 CCCCTACGTG
** * *
203459 GCGTATAGCGCGGTGTAGGGCGCGCGCTATACCCCACGTGTAATCCAGTCA
1 GCGTATAGCGCGGTCAAGGG-GCGCGCTATACCCCACGTGTAAGCCAATCA
*
203510 GCGTATAGCGCGGTACAAGGGGCGCTCTATA-CCCACGTG-AAGCCAAATCA
1 GCGTATAGCGCGGT-CAAGGGGCGCGCTATACCCCACGTGTAAGCC-AATCA
* *
203560 GCGTATAACGCGGTTCAGGGGGCGCGCT
1 GCGTATAGCGCGG-TCAAGGGGCGCGCT
203588 TTATTGCTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
49 4 0.06
50 35 0.52
51 24 0.36
52 4 0.06
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.18
Consensus pattern (50 bp):
GCGTATAGCGCGGTCAAGGGGCGCGCTATACCCCACGTGTAAGCCAATCA
Found at i:207852 original size:42 final size:42
Alignment explanation
Indices: 207793--207908 Score: 214
Period size: 42 Copynumber: 2.8 Consensus size: 42
207783 CCCGAATTCA
*
207793 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTCC
*
207835 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTCC
207877 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
207909 TGTAATTCAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTCC
Found at i:208144 original size:22 final size:23
Alignment explanation
Indices: 208097--208157 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
208087 TAATTATTAA
* *
208097 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
208118 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
208141 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
208158 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:208204 original size:28 final size:27
Alignment explanation
Indices: 208123--208220 Score: 87
Period size: 28 Copynumber: 3.6 Consensus size: 27
208113 TTATTAATAT
208123 TTATAATAATAT-AATATTATATTTT-
1 TTATAATAATATAAATATTATATTTTA
* * * *
208148 TAAT-ATTATATAAA-ATAATCAATTATA
1 TTATAATAATATAAATATTAT--ATTTTA
208175 TTATAATAATATAAGATATTATATTTTA
1 TTATAATAATATAA-ATATTATATTTTA
*
208203 TTTTAATAATATATAATA
1 TTATAATAATATA-AATA
208221 ATTTTTTTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
24 10 0.18
25 5 0.09
26 4 0.07
27 3 0.05
28 28 0.50
29 2 0.04
30 4 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TTATAATAATATAAATATTATATTTTA
Found at i:208211 original size:23 final size:22
Alignment explanation
Indices: 208185--208229 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
208175 TTATAATAAT
* *
208185 ATAAGATATTATATTTTATTTTA
1 ATAAGATATAATAATTT-TTTTA
*
208208 ATAATATATAATAATTTTTTTA
1 ATAAGATATAATAATTTTTTTA
208230 TATATTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATAAGATATAATAATTTTTTTA
Found at i:208238 original size:30 final size:29
Alignment explanation
Indices: 208171--208273 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 29
208161 AATAATCAAT
208171 TATATTATAATAATATA-AGATATTATATTT-
1 TATATT-TAATAATATATA-ATATT-TATTTA
*
208201 TAT-TTTAATAATATATAATAATTTTTTTA
1 TATATTTAATAATATATAAT-ATTTATTTA
208230 TATATTTAATAATGA-ATAATA-TTATTTA
1 TATATTTAATAAT-ATATAATATTTATTTA
208258 TATATTTCAATAATAT
1 TATATTT-AATAATAT
208274 TTTAGTAAAG
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
28 30 0.47
29 16 0.25
30 17 0.27
31 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (29 bp):
TATATTTAATAATATATAATATTTATTTA
Found at i:208517 original size:20 final size:20
Alignment explanation
Indices: 208439--208508 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
208429 TTTCCAGATG
208439 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
208459 TTTTTCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
208479 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
208499 TTTTCCAGAA
1 TTTTCCAGAA
208509 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:208517 original size:40 final size:40
Alignment explanation
Indices: 208439--208517 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
208429 TTTCCAGATG
* * **
208439 TTTTCCAGAAATGTAATTCATTTTTCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
208479 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
208518 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:208527 original size:15 final size:15
Alignment explanation
Indices: 208491--208572 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
208481 TTACAGAAAT
**
208491 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
208506 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
208520 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
208535 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
208550 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
208565 GTAATTCA
1 GTAATTCA
208573 TTTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:208543 original size:30 final size:30
Alignment explanation
Indices: 208491--208572 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
208481 TTACAGAAAT
208491 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
208520 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
208550 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
208573 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:208565 original size:45 final size:44
Alignment explanation
Indices: 208491--208577 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
208481 TTACAGAAAT
**
208491 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
208535 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
208578 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:220660 original size:12 final size:12
Alignment explanation
Indices: 220643--220685 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
220633 ACGGCGGATC
220643 TCGATGAGCCGA
1 TCGATGAGCCGA
220655 TCGATGAG--GA
1 TCGATGAGCCGA
220665 TCTCGATGAGCCGA
1 --TCGATGAGCCGA
220679 TCGATGA
1 TCGATGA
220686 CGTGGTCGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.07
12 23 0.85
14 2 0.07
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.21
Consensus pattern (12 bp):
TCGATGAGCCGA
Found at i:220670 original size:24 final size:24
Alignment explanation
Indices: 220638--220685 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
220628 TAGTCACGGC
220638 GGATCTCGATGAGCCGATCGATGA
1 GGATCTCGATGAGCCGATCGATGA
220662 GGATCTCGATGAGCCGATCGATGA
1 GGATCTCGATGAGCCGATCGATGA
220686 CGTGGTCGAC
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:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (24 bp):
GGATCTCGATGAGCCGATCGATGA
Found at i:223985 original size:31 final size:32
Alignment explanation
Indices: 223943--224002 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
223933 AAAAAAAGGC
223943 AATAAATAATAA-AAAAAGTAAAAAAAGAATGA
1 AATAAATAATAATAAAAAG-AAAAAAAGAATGA
* *
223975 AATAAA-AATAATAATAAGAAATAAAGAA
1 AATAAATAATAATAAAAAGAAAAAAAGAA
224003 AACCAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (32 bp):
AATAAATAATAATAAAAAGAAAAAAAGAATGA
Found at i:224175 original size:2 final size:2
Alignment explanation
Indices: 224170--224221 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
224160 AAGGGTAAAA
224170 AT AT AT AT A- 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
224211 AT AT AT AT AT A
1 AT AT AT AT AT A
224222 AACAAAGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:224278 original size:17 final size:18
Alignment explanation
Indices: 224248--224283 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
224238 TAAGACATAT
*
224248 ACACAATGAAAAAAGTGA
1 ACACAATGAAAAAAATGA
224266 ACACAAT-AAAAAAATGA
1 ACACAATGAAAAAAATGA
224283 A
1 A
224284 ATGAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (18 bp):
ACACAATGAAAAAAATGA
Found at i:224540 original size:4 final size:4
Alignment explanation
Indices: 224531--224568 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
224521 GAAAAATTAA
*
224531 AAAT AAAT AAAT AAAT AAAT -AA- AAAT GAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
224569 TAAACTGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 4 0.13
4 26 0.87
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:229620 original size:16 final size:16
Alignment explanation
Indices: 229601--229669 Score: 74
Period size: 16 Copynumber: 4.6 Consensus size: 16
229591 ACCCCACCTG
229601 AAAGTAACTCGAACCA
1 AAAGTAACTCGAACCA
229617 AAAGTAACTCG-ACC-
1 AAAGTAACTCGAACCA
* * *
229631 --CGAAACCCGAACCA
1 AAAGTAACTCGAACCA
*
229645 AAAGTAACTCAAACCA
1 AAAGTAACTCGAACCA
229661 AAAGTAACT
1 AAAGTAACT
229670 TGAATCGAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
12 6 0.14
13 3 0.07
15 3 0.07
16 30 0.71
ACGTcount: A:0.49, C:0.28, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAGTAACTCGAACCA
Found at i:230324 original size:39 final size:39
Alignment explanation
Indices: 230281--230372 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
230271 TATTTCATTC
*
230281 TAACATTCTAAATTCCTAATTTTTTAAAAT-TTTCTACCA-
1 TAACATTCTAAATTCCTAATTTCTTAAAATATTTC-A-CAT
** *
230320 TAACATTCTAAATTTTTAATTTCTTAAATTATTTCACAT
1 TAACATTCTAAATTCCTAATTTCTTAAAATATTTCACAT
230359 TAACATTCTAAATT
1 TAACATTCTAAATT
230373 ATTTTTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 2 0.04
39 41 0.87
40 4 0.09
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (39 bp):
TAACATTCTAAATTCCTAATTTCTTAAAATATTTCACAT
Found at i:231546 original size:32 final size:31
Alignment explanation
Indices: 231497--231589 Score: 143
Period size: 32 Copynumber: 2.9 Consensus size: 31
231487 ATCATACATA
*
231497 ATGTTTACTTTTTGTTTCATTTTAGTACCCG
1 ATGTTTACTTTTTGTTTCATTTTAGTACCCC
231528 ATGTTTACTTTTTTGTTTCATTTTAGTACCCC
1 ATGTTTAC-TTTTTGTTTCATTTTAGTACCCC
231560 AT-TATTAACTTTTTGTTTCATTTTAGTACC
1 ATGT-TT-ACTTTTTGTTTCATTTTAGTACC
231590 TAATTTTTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
31 9 0.16
32 47 0.81
33 2 0.03
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (31 bp):
ATGTTTACTTTTTGTTTCATTTTAGTACCCC
Found at i:234921 original size:22 final size:23
Alignment explanation
Indices: 234895--234942 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
234885 GGGTTTCAAT
234895 AAAAT-AAGTAACTTAACAAAGA
1 AAAATCAAGTAACTTAACAAAGA
*
234917 AAAATCGAGTAACTTAACAAAGA
1 AAAATCAAGTAACTTAACAAAGA
234940 AAA
1 AAA
234943 TTCGAGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (23 bp):
AAAATCAAGTAACTTAACAAAGA
Found at i:234928 original size:23 final size:23
Alignment explanation
Indices: 234901--234949 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
234891 CAATAAAATA
234901 AGTAACTTAACAAAGAAAAATCG
1 AGTAACTTAACAAAGAAAAATCG
*
234924 AGTAACTTAACAAAGAAAATTCG
1 AGTAACTTAACAAAGAAAAATCG
234947 AGT
1 AGT
234950 TTTAGAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.20
Consensus pattern (23 bp):
AGTAACTTAACAAAGAAAAATCG
Found at i:235577 original size:30 final size:30
Alignment explanation
Indices: 235542--235599 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
235532 CGGGTGGAAG
235542 ATATATAAATTTTGGATCAGG-TCGGGTTGT
1 ATATATAAATTTTGGATC-GGATCGGGTTGT
* *
235572 ATATATAATTTTTGGGTCGGATCGGGTT
1 ATATATAAATTTTGGATCGGATCGGGTT
235600 CAGGTAGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (30 bp):
ATATATAAATTTTGGATCGGATCGGGTTGT
Found at i:237164 original size:22 final size:23
Alignment explanation
Indices: 237133--237176 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
237123 CCTTGTCCTG
*
237133 CGCCTTGCTCCCCGCTGCATGCT
1 CGCCTTGCTCCCCACTGCATGCT
*
237156 CGCC-TGCTCCCCATTGCATGC
1 CGCCTTGCTCCCCACTGCATGC
237177 AGGCAACCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.07, C:0.48, G:0.20, T:0.25
Consensus pattern (23 bp):
CGCCTTGCTCCCCACTGCATGCT
Found at i:237211 original size:22 final size:22
Alignment explanation
Indices: 237184--237225 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
237174 TGCAGGCAAC
237184 CTCTTCCGACGTGCATGGCGAA
1 CTCTTCCGACGTGCATGGCGAA
237206 CTCTTCCGACGTGCATGGCG
1 CTCTTCCGACGTGCATGGCG
237226 CATGCAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.33, G:0.29, T:0.24
Consensus pattern (22 bp):
CTCTTCCGACGTGCATGGCGAA
Found at i:237264 original size:31 final size:31
Alignment explanation
Indices: 237229--237290 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
237219 CATGGCGCAT
237229 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
**
237260 GCAAAGCTTCATCCTCTCGTCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
237291 TATAACACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Found at i:238646 original size:15 final size:14
Alignment explanation
Indices: 238624--238654 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
238614 AATTTTGTTA
238624 TTTAAAATTATAAT
1 TTTAAAATTATAAT
238638 TTTATAAATTATAAT
1 TTTA-AAATTATAAT
238653 TT
1 TT
238655 GTTTGACCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAAAATTATAAT
Found at i:243651 original size:22 final size:22
Alignment explanation
Indices: 243623--243686 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
243613 ACTGTTTCAT
243623 CTCTAGAGTAGAGATAGAGATA
1 CTCTAGAGTAGAGATAGAGATA
* * *
243645 CTCTAGAATAGAGATATAAATA
1 CTCTAGAGTAGAGATAGAGATA
243667 CTCTAGAGTAGAGATGAGAG
1 CTCTAGAGTAGAGAT-AGAG
243687 CTGAAGATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
22 33 0.94
23 2 0.06
ACGTcount: A:0.42, C:0.09, G:0.25, T:0.23
Consensus pattern (22 bp):
CTCTAGAGTAGAGATAGAGATA
Found at i:248814 original size:18 final size:18
Alignment explanation
Indices: 248780--248817 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
248770 TACATCCGCA
*
248780 AATAAATAAATATATTTT
1 AATAAATAAATAAATTTT
248798 AATAAA-AAATAAAATTTT
1 AATAAATAAAT-AAATTTT
248816 AA
1 AA
248818 GATGAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATAAATAAATTTT
Found at i:252134 original size:34 final size:36
Alignment explanation
Indices: 252094--252166 Score: 123
Period size: 37 Copynumber: 2.1 Consensus size: 36
252084 ATTTGTATTT
252094 AACCT-AAAAAA-ATAGTTATTAATCATTGTTATGA
1 AACCTAAAAAAAGATAGTTATTAATCATTGTTATGA
252128 AACCTAAAAAAAAGATAGTTATTAATCATTGTTATGA
1 AACCT-AAAAAAAGATAGTTATTAATCATTGTTATGA
252165 AA
1 AA
252167 TTATCAGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 5 0.14
36 6 0.17
37 25 0.69
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (36 bp):
AACCTAAAAAAAGATAGTTATTAATCATTGTTATGA
Found at i:253806 original size:45 final size:45
Alignment explanation
Indices: 253737--253884 Score: 183
Period size: 45 Copynumber: 3.3 Consensus size: 45
253727 GGGTAGACCA
* * **
253737 GGGTCACACAACATCAACTTCTCCCAAGTATCTCAGGTGAGGTCC
1 GGGTCACATAACATCGACACCTCCCAAGTATCTCAGGTGAGGTCC
* *
253782 GGGTCACATAACATCGGCACCTCCCAAGTATCTCAGGTGAGGTTC
1 GGGTCACATAACATCGACACCTCCCAAGTATCTCAGGTGAGGTCC
* * * *
253827 GGGTCACATAGCATCGACACCTCCCAA-TACCTTATGCT-AGGTCC
1 GGGTCACATAACATCGACACCTCCCAAGTATCTCA-GGTGAGGTCC
253871 GGGTCACATAACAT
1 GGGTCACATAACAT
253885 TGGTACCTTG
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
44 23 0.26
45 66 0.74
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.22
Consensus pattern (45 bp):
GGGTCACATAACATCGACACCTCCCAAGTATCTCAGGTGAGGTCC
Found at i:254930 original size:20 final size:20
Alignment explanation
Indices: 254907--254956 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
254897 AAATAAGGGA
*
254907 TCGATCCTTTTGAAAAGGAG
1 TCGATCCTTTTAAAAAGGAG
*
254927 TCGATCCTTTTAAAAAGGGG
1 TCGATCCTTTTAAAAAGGAG
*
254947 TCAATCCTTT
1 TCGATCCTTT
254957 ACTGGAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (20 bp):
TCGATCCTTTTAAAAAGGAG
Found at i:259984 original size:20 final size:20
Alignment explanation
Indices: 259961--260012 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
259951 AACGCGATCC
259961 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
259981 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
260001 CCAAAATCGCAA
1 CCAGAATCGCAA
260013 CGCGATTCTT
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:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:260093 original size:20 final size:20
Alignment explanation
Indices: 260068--260261 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
260058 GATTTTCCAT
* *
260068 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
260088 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
260108 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
260128 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
260148 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
260168 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
260188 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
260208 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
260229 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
260249 AATCGCAACGCGA
1 AATCGCAACGCGA
260262 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:260113 original size:40 final size:39
Alignment explanation
Indices: 260064--260261 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
260054 TTGCGATTTT
* ** *
260064 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
260102 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
260143 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
260183 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
260222 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
260262 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:260151 original size:60 final size:60
Alignment explanation
Indices: 260068--260260 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
260058 GATTTTCCAT
* ** * *
260068 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
260128 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
260188 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
260249 AATCGCAACGCG
1 AATCGCAACGCG
260261 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:260678 original size:33 final size:33
Alignment explanation
Indices: 260639--260709 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
260629 TTCACTTAGA
*
260639 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
260672 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
260705 TTTCA
1 TTTCA
260710 AGTTAGTATT
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:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:260849 original size:14 final size:14
Alignment explanation
Indices: 260830--260883 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
260820 AGAATGACTG
260830 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
260844 TCGCAACGCGAAATGAAA
1 TCGCAA--CGAGA-G-AA
260862 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
260876 TCGCAACG
1 TCGCAACG
260884 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 8 0.24
17 1 0.03
18 8 0.24
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:260865 original size:18 final size:16
Alignment explanation
Indices: 260840--260888 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
260830 TCGCAACGAG
260840 AGAATCGCAACGCGAA
1 AGAATCGCAACGCGAA
*
260856 ATGAAATCGCAA--CGAG
1 A-G-AATCGCAACGCGAA
260872 AGAATCGCAACGCGAA
1 AGAATCGCAACGCGAA
260888 A
1 A
260889 CCAAAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
15 1 0.04
16 9 0.33
17 1 0.04
18 8 0.30
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.08
Consensus pattern (16 bp):
AGAATCGCAACGCGAA
Found at i:260917 original size:19 final size:19
Alignment explanation
Indices: 260895--260992 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
260885 GAAACCAAAA
*
260895 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
260914 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
260928 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
260947 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
260961 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
260980 TCGCGTTGCGATT
1 TCGCGTTGCGATT
260993 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:260936 original size:14 final size:14
Alignment explanation
Indices: 260917--261006 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
260907 TTTCATTTCG
260917 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
260931 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
260950 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
260964 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
260981 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
260997 CGTTGCGATT
1 CGTTGCGATT
261007 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:260942 original size:33 final size:33
Alignment explanation
Indices: 260900--261014 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
260890 CAAAATCGCA
260900 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
260933 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
260966 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
260999 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
261015 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:262945 original size:88 final size:91
Alignment explanation
Indices: 262682--263128 Score: 691
Period size: 89 Copynumber: 5.1 Consensus size: 91
262672 TAGATTGCTT
* *
262682 AGTAAATTTATTCGGTTGCTG-CAATT-TGCTAAACTGTGTATT-TTAACAC---GAAATAGT-T
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTACACTGTGAAATAGTAT
262740 TTGTCTTTGTTTGTC-TTTGGTTGAA
66 TTGTCTTTGTTTGTCTTTTGGTTGAA
262765 AGTAAA-TTGTTCGGTTGCTG-CAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-ACACTGTGAAATAGTA
262826 TTTGTCTTTGTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTGTCTTTTGGTTGAA
262853 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA-ACTGTGAAATA-TAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTACACTGTGAAATAGTAT
262916 TTGTCTTTGTTTGTC-TTTGGTTGAA
66 TTGTCTTTGTTTGTCTTTTGGTTGAA
*
262941 AGTAAATTTGTTCGGTTGCTGCCAATT-TGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTACACTGTGAAATAGTAT
263005 TTGTC-TTGTTTTGTCTTTTGG-TGAA
66 TTGTCTTTG-TTTGTCTTTTGGTTGAA
263030 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAA-TGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-ACACTGTGAAATAGTA
263094 TTTGTCTTTGTTTTGTCTTTTGG-TGAA
65 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
263121 AGTAAATT
1 AGTAAATT
263129 ATCCATTCAA
Statistics
Matches: 342, Mismatches: 4, Indels: 28
0.91 0.01 0.07
Matches are distributed among these distances:
82 29 0.08
83 12 0.04
84 4 0.01
86 1 0.00
87 42 0.12
88 67 0.20
89 99 0.29
90 45 0.13
91 43 0.13
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (91 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTACACTGTGAAATAGTAT
TTGTCTTTGTTTGTCTTTTGGTTGAA
Found at i:263032 original size:177 final size:178
Alignment explanation
Indices: 262682--263128 Score: 697
Period size: 177 Copynumber: 2.5 Consensus size: 178
262672 TAGATTGCTT
* **
262682 AGTAAATTTATTCGGTTGCTG-CAATT-TGCTAAACTGTGTA-T-TTTAAC-ACGAAATAGT-TT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACTGTGAAATAGTATT
262741 TGTCTTTGTTTGTCTTTGGTTGAAAGTAAA-TTGTTCGGTTGCTGCAATTCTGCTAACTGTGTAT
66 TGTCTTTGTTTGTCTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCAATTCTGCTAACTGTGTAT
262805 TCTTTAACACTGTGAAATATATTTGTCTTTGTTTGTCTTTTGGTTGAA
131 TCTTTAACACTGTGAAATATATTTGTCTTTGTTTGTCTTTTGGTTGAA
262853 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACTGTGAAATA-TATT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACTGTGAAATAGTATT
262917 TGTCTTTGTTTGTCTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATT-TGCTAAACTGTGT
66 TGTCTTTGTTTGTCTTTGGTTGAAAGTAAATTTGTTCGGTTGCTG-CAATTCTGCT-AACTGTGT
262981 ATTC-TTAACACTGTGAAATAGTATTTGTC-TTGTTTTGTCTTTTGG-TGAA
129 ATTCTTTAACACTGTGAAATA-TATTTGTCTTTG-TTTGTCTTTTGGTTGAA
263030 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAA-TGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-A-ACTGTGAAATAGTA
263094 TTTGTCTTTGTTTTGTCTTTTGG-TGAAAGTAAATT
64 TTTGTCTTTG-TTTGTC-TTTGGTTGAAAGTAAATT
263129 ATCCATTCAA
Statistics
Matches: 257, Mismatches: 3, Indels: 23
0.91 0.01 0.08
Matches are distributed among these distances:
171 20 0.08
172 5 0.02
173 14 0.05
174 1 0.00
175 7 0.03
176 50 0.19
177 77 0.30
178 48 0.19
179 12 0.05
180 18 0.07
181 5 0.02
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (178 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACTGTGAAATAGTATT
TGTCTTTGTTTGTCTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCAATTCTGCTAACTGTGTAT
TCTTTAACACTGTGAAATATATTTGTCTTTGTTTGTCTTTTGGTTGAA
Found at i:263198 original size:19 final size:19
Alignment explanation
Indices: 263174--263301 Score: 87
Period size: 19 Copynumber: 7.3 Consensus size: 19
263164 TAGTTTACTT
**
263174 TCGCAACACGAAACTTAAA
1 TCGCAACACGAAACCAAAA
*
263193 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
* * **
263212 TCGCACCGCGAAATGAAAA
1 TCGCAACACGAAACCAAAA
*
263231 TCGC-A-ACG--A-CAGAA
1 TCGCAACACGAAACCAAAA
*
263245 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
*
263264 TCGC-A-ACG--A-CAAGA
1 TCGCAACACGAAACCAAAA
*
263278 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
263297 TCGCA
1 TCGCA
263302 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
14 15 0.18
15 4 0.05
16 4 0.05
17 4 0.05
18 3 0.04
19 53 0.64
ACGTcount: A:0.45, C:0.30, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACACGAAACCAAAA
Found at i:263255 original size:33 final size:32
Alignment explanation
Indices: 263209--263301 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
263199 CGCGAAACCA
* **
263209 AAATCGCACCGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
263241 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
263274 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
263302 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:263299 original size:52 final size:51
Alignment explanation
Indices: 263174--263301 Score: 127
Period size: 52 Copynumber: 2.5 Consensus size: 51
263164 TAGTTTACTT
** *
263174 TCGCAACACGAAACTTAAATCGCAACGCGAAACCAAAATCGCACCGCGAAA
1 TCGCAACACGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
263225 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC--CAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
263278 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACACGAAACCAAAATCGCA
263302 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
49 3 0.05
50 6 0.10
51 1 0.02
52 39 0.65
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.45, C:0.30, G:0.17, T:0.09
Consensus pattern (51 bp):
TCGCAACACGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:263338 original size:14 final size:14
Alignment explanation
Indices: 263319--263373 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
263309 TTTCATTTCG
263319 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
263333 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
263349 CGCATTGCGA-TCTGT
1 CG--TTGCGATTCTTT
263364 CGTTGCGATT
1 CGTTGCGATT
263374 TAATTTCGCG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 6 0.17
14 9 0.26
15 7 0.20
16 7 0.20
18 6 0.17
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:263349 original size:32 final size:32
Alignment explanation
Indices: 263302--263391 Score: 137
Period size: 31 Copynumber: 2.8 Consensus size: 32
263292 CAAAATCGCA
*
263302 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTCTGTCG
*
263335 TTGCGATTTCATTTCGCATTGCGA-TCTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
*
263366 TTGCGATTTAATTTCGCGTTGCGATT
1 TTGCGATTTCATTTCGCGTTGCGATT
263392 TGGTTTCGCG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 28 0.54
32 18 0.35
33 6 0.12
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
Found at i:263358 original size:18 final size:18
Alignment explanation
Indices: 263297--263410 Score: 102
Period size: 18 Copynumber: 6.8 Consensus size: 18
263287 GAAACCAAAA
*
263297 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
263316 TCGCGTTGCGA-TTC-TT
1 TCGCGTTGCGATTTCATT
263332 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
* *
263348 TCGCATTGCGA--TC-TG
1 TCGCGTTGCGATTTCATT
*
263363 T--CGTTGCGATTTAATT
1 TCGCGTTGCGATTTCATT
**
263379 TCGCGTTGCGATTTGGTT
1 TCGCGTTGCGATTTCATT
263397 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
263411 TAAGTTTCGT
Statistics
Matches: 78, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
13 7 0.09
14 8 0.10
15 6 0.08
16 10 0.13
17 3 0.04
18 34 0.44
19 10 0.13
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:265584 original size:19 final size:19
Alignment explanation
Indices: 265568--265666 Score: 133
Period size: 19 Copynumber: 5.6 Consensus size: 19
265558 CAAAATGACT
265568 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
265587 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
265606 ATCGCAA--CG-AA-G--A
1 ATCGCAATGCGAAATGAAA
265619 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
265638 ATCGCAATGCGGAAATG--A
1 ATCGCAATGC-GAAATGAAA
265656 ATCGCAATGCG
1 ATCGCAATGCG
265667 TTTATAATTT
Statistics
Matches: 73, Mismatches: 0, Indels: 16
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.11
15 3 0.04
16 4 0.05
17 4 0.05
18 11 0.15
19 37 0.51
20 6 0.08
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:265719 original size:19 final size:19
Alignment explanation
Indices: 265695--266001 Score: 367
Period size: 19 Copynumber: 17.4 Consensus size: 19
265685 GATTATCTCG
265695 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
265714 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
265733 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
265747 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
265766 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
265785 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
265804 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
265823 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
265837 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
265856 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
265875 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
265889 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
265908 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
265927 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
265941 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
265961 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
265975 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
265994 TTGCGATT
1 TTGCGATT
266002 GTATTTTCCG
Statistics
Matches: 250, Mismatches: 12, Indels: 52
0.80 0.04 0.17
Matches are distributed among these distances:
14 34 0.14
16 31 0.12
17 27 0.11
18 3 0.01
19 143 0.57
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:265770 original size:71 final size:71
Alignment explanation
Indices: 265695--265934 Score: 364
Period size: 71 Copynumber: 3.4 Consensus size: 71
265685 GATTATCTCG
265695 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
265760 TTCGCA
66 TTCGCA
*
265766 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
*
265829 TTC-TGTCG--
61 TTCATTTCGCA
* *
265837 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
265902 TTCGCA
66 TTCGCA
265908 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
265935 CTCTCGTTGC
Statistics
Matches: 153, Mismatches: 6, Indels: 20
0.85 0.03 0.11
Matches are distributed among these distances:
66 6 0.04
68 7 0.05
69 6 0.04
71 114 0.75
73 6 0.04
74 8 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:265827 original size:142 final size:139
Alignment explanation
Indices: 265657--266001 Score: 518
Period size: 142 Copynumber: 2.5 Consensus size: 139
265647 CGGAAATGAA
*
265657 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTT-TAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
*
265721 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
65 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
*
265786 TGCGATTTTCATT
130 TGCGA--TTC-TC
* *
265799 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
*
265864 TTCATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
66 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
265929 GCGATTCTC
131 GCGATTCTC
* * * *
265938 TCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGCGA
1 TCGCATTGCGATTTTAATTT-CGCATTGCGATTATC-TCGTTGCGATTTTCATTTCGCATTGCGA
266000 TT
64 TT
266002 GTATTTTCCG
Statistics
Matches: 189, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
137 14 0.07
138 39 0.21
139 5 0.03
140 3 0.02
142 125 0.66
143 3 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (139 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
GCGATTCTC
Found at i:265940 original size:52 final size:52
Alignment explanation
Indices: 265695--265973 Score: 379
Period size: 52 Copynumber: 5.2 Consensus size: 52
265685 GATTATCTCG
*
265695 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
*
265747 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
265804 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
265856 TTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
265908 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
265961 TTGCGATTTTCAT
1 TTGCGATTTTCAT
265974 GTTGGGATTT
Statistics
Matches: 215, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
52 159 0.74
53 17 0.08
54 7 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:268296 original size:12 final size:12
Alignment explanation
Indices: 268279--268303 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
268269 TCTTCGGGGA
268279 CTTTTTCTTCTT
1 CTTTTTCTTCTT
268291 CTTTTTCTTCTT
1 CTTTTTCTTCTT
268303 C
1 C
268304 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:268509 original size:22 final size:21
Alignment explanation
Indices: 268480--268521 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
268470 AAACATCATC
268480 AAAATCCGTG-TATTGACCAAT
1 AAAATCCG-GATATTGACCAAT
268501 AAAAGTCCGGATATTGACCAA
1 AAAA-TCCGGATATTGACCAA
268522 GACCAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (21 bp):
AAAATCCGGATATTGACCAAT
Found at i:269227 original size:20 final size:20
Alignment explanation
Indices: 269199--269586 Score: 453
Period size: 20 Copynumber: 19.4 Consensus size: 20
269189 AAATTTCAGT
* * * *
269199 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
269219 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
269239 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
269259 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
269279 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
269299 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
269319 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
269339 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
269359 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
269379 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
269399 GTTGCGGTTT-CGGATACGC
1 GTTGCGATTTACGGATACGC
269418 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
269438 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
269458 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
269478 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
269498 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
269518 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
269538 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
* ** *
269558 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
269578 GTTGCGATT
1 GTTGCGATT
269587 ATGGAAAATC
Statistics
Matches: 327, Mismatches: 32, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
19 22 0.07
20 300 0.92
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:275676 original size:24 final size:24
Alignment explanation
Indices: 275644--275695 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
275634 GGCAAAATAT
275644 GAAGACGAAGAAGAGCTTACATTG
1 GAAGACGAAGAAGAGCTTACATTG
275668 GAAGACGAAGAAGAGCTTACATTG
1 GAAGACGAAGAAGAGCTTACATTG
275692 GAAG
1 GAAG
275696 GTGAACCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.12, G:0.31, T:0.15
Consensus pattern (24 bp):
GAAGACGAAGAAGAGCTTACATTG
Found at i:295483 original size:35 final size:34
Alignment explanation
Indices: 295398--295484 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
295388 ATTTGATATT
*
295398 TAAATACAACAAACTTACAATAAGAATTAAATAG
1 TAAATACAACAAAATTACAATAAGAATTAAATAG
* * *
295432 TAAATGATAACCAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATAG
295470 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
295485 ACTAAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATAG
Found at i:296098 original size:18 final size:18
Alignment explanation
Indices: 296075--296112 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
296065 AGGCGATGGT
296075 GGCATCATATATGGCTGC
1 GGCATCATATATGGCTGC
296093 GGCATCATATATGGCTGC
1 GGCATCATATATGGCTGC
296111 GG
1 GG
296113 TGGCTGCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (18 bp):
GGCATCATATATGGCTGC
Found at i:298902 original size:25 final size:25
Alignment explanation
Indices: 298874--298928 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
298864 GATTTTAAAC
* *
298874 TTTTAGGGT-TTTTTTTAAATAATAA
1 TTTTA-GGTATTTTTTAAAATAAAAA
*
298899 TTTTATGTATTTTTTAAAATAAAAA
1 TTTTAGGTATTTTTTAAAATAAAAA
298924 TTTTA
1 TTTTA
298929 AAATTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (25 bp):
TTTTAGGTATTTTTTAAAATAAAAA
Found at i:298934 original size:24 final size:25
Alignment explanation
Indices: 298883--298935 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
298873 CTTTTAGGGT
* * **
298883 TTTTTTTAAATAATAATTTTATGTA
1 TTTTTTAAAATAAAAATTTTATAAA
298908 TTTTTTAAAATAAAAATTTTA-AAA
1 TTTTTTAAAATAAAAATTTTATAAA
298932 TTTT
1 TTTT
298936 AAGATAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTTTAAAATAAAAATTTTATAAA
Found at i:299215 original size:18 final size:17
Alignment explanation
Indices: 299192--299225 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
299182 TTAACAAGAA
299192 AATATAAAAATAATTTAG
1 AATAT-AAAATAATTTAG
*
299210 AATATATAATAATTTA
1 AATATAAAATAATTTA
299226 TTAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AATATAAAATAATTTAG
Found at i:299647 original size:2 final size:2
Alignment explanation
Indices: 299640--299664 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
299630 TACCGAAAAG
299640 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
299665 CACACAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:303102 original size:18 final size:19
Alignment explanation
Indices: 303067--303114 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
303057 GTTAGACCTT
*
303067 AGTGCATCG-TACACTAAA
1 AGTGCATCGATGCACTAAA
303085 AGTGCATCGATGCA-TAAA
1 AGTGCATCGATGCACTAAA
303103 A-TGCATTCGATG
1 AGTGCA-TCGATG
303115 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 4 0.15
18 20 0.74
19 3 0.11
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAA
Found at i:303163 original size:64 final size:61
Alignment explanation
Indices: 303086--303285 Score: 172
Period size: 64 Copynumber: 3.1 Consensus size: 61
303076 TACACTAAAA
303086 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTCAAAATA-CCTGAGTGCATCGATGCATGG-TG
* * * * *
303150 GTGCATCGATGCATCATTACATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGCATAGTAT
1 GTGCATCGATGCATAAATGCATTCGATG-TTTCA-AAATAC-CTGAGTGCATCGATGCATGGT-G
* * * * *
303214 GCGCATCGGTGCATGAAATGCATTTGATG-TTCAAATTATTCCATG-GTGCATTGATGCATGGAT
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTCAAA--ATACC-TGAGTGCATCGATGCATGG--
303277 TG
60 TG
303279 GTGCATC
1 GTGCATC
303286 AGTGCATCAC
Statistics
Matches: 109, Mismatches: 16, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
62 2 0.02
63 17 0.16
64 67 0.61
65 22 0.20
66 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (61 bp):
GTGCATCGATGCATAAATGCATTCGATGTTTCAAAATACCTGAGTGCATCGATGCATGGTG
Done.