Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold51
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: 3712191
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.32
Warning! 131352 characters in sequence are not A, C, G, or T
File 20 of 23
Found at i:3219640 original size:52 final size:52
Alignment explanation
Indices: 3219492--3219620 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
3219482 CGAAATATGA
3219492 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
*
3219544 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
3219596 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3219621 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
Found at i:3219720 original size:19 final size:19
Alignment explanation
Indices: 3219696--3219767 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
3219686 TAGCTTACAT
3219696 TGTATCGATACAAAACGTA
1 TGTATCGATACAAAACGTA
*
3219715 TGTATCGATAC--AATGTA
1 TGTATCGATACAAAACGTA
* *
3219732 TCGATATCGATACAACACTTTA
1 T-G-TATCGATACAAAAC-GTA
3219754 TGTATCGATACAAA
1 TGTATCGATACAAA
3219768 TCGTTGAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 6 0.14
18 1 0.02
19 20 0.47
20 11 0.26
21 2 0.05
22 3 0.07
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACGTA
Found at i:3222258 original size:20 final size:20
Alignment explanation
Indices: 3222233--3222307 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
3222223 AAAACCCCAG
*
3222233 AATGTATCAATACAATGAGA
1 AATGTATCAATACAATTAGA
** *
3222253 AATGTATTGATACAATTATA
1 AATGTATCAATACAATTAGA
* *
3222273 AGCATGTATCAATACATTTAGT
1 A--ATGTATCAATACAATTAGA
*
3222295 AATGTATCGATAC
1 AATGTATCAATAC
3222308 CTTTTCTTGG
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 28 0.65
22 15 0.35
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCAATACAATTAGA
Found at i:3222353 original size:13 final size:13
Alignment explanation
Indices: 3222335--3222417 Score: 62
Period size: 13 Copynumber: 6.0 Consensus size: 13
3222325 CAGGGTGGTT
*
3222335 TTGTATTGATACA
1 TTGTATCGATACA
3222348 TTGTATCGATACATAA
1 TTGTATCGATAC---A
3222364 GTTTTGTATCGATACA
1 ---TTGTATCGATACA
*
3222380 ATGTATCGATACA
1 TTGTATCGATACA
*
3222393 -T-AAGTCGATACA
1 TTGTA-TCGATACA
3222405 TTGTATCGATACA
1 TTGTATCGATACA
3222418 AAACTTATGT
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
11 1 0.02
12 9 0.16
13 32 0.56
14 1 0.02
16 2 0.04
19 12 0.21
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3222378 original size:32 final size:32
Alignment explanation
Indices: 3222332--3222436 Score: 116
Period size: 32 Copynumber: 3.5 Consensus size: 32
3222322 ATGCAGGGTG
*
3222332 GTTTTGTATTGATACATTGTATCGATACATAA
1 GTTTTGTATCGATACATTGTATCGATACATAA
*
3222364 GTTTTGTATCGATACAATGTATCGATACATAA
1 GTTTTGTATCGATACATTGTATCGATACATAA
*
3222396 -----G--TCGATACATTGTATCGATACAAAA
1 GTTTTGTATCGATACATTGTATCGATACATAA
* *
3222421 CTTATGTATCGATACA
1 GTTTTGTATCGATACA
3222437 AAACTTATGT
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
25 22 0.35
27 1 0.02
30 1 0.02
32 38 0.61
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (32 bp):
GTTTTGTATCGATACATTGTATCGATACATAA
Found at i:3222430 original size:19 final size:19
Alignment explanation
Indices: 3222406--3222495 Score: 135
Period size: 19 Copynumber: 4.6 Consensus size: 19
3222396 GTCGATACAT
3222406 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
3222425 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
** *
3222444 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-AAACT-TA
3222465 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
3222484 TGTATCGATACA
1 TGTATCGATACA
3222496 TTTACTGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
19 44 0.70
20 6 0.10
21 13 0.21
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:3222470 original size:21 final size:21
Alignment explanation
Indices: 3222444--3222516 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
3222434 ACAAAACTTA
3222444 TGTATCGATACATTTACTGTT
1 TGTATCGATACATTTACTGTT
** *
3222465 TGTATCGATACA-AAACT-TA
1 TGTATCGATACATTTACTGTT
3222484 TGTATCGATACATTTACTGTT
1 TGTATCGATACATTTACTGTT
*
3222505 TTTATCGATACA
1 TGTATCGATACA
3222517 AATTGTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 13 0.30
20 6 0.14
21 24 0.56
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTTACTGTT
Found at i:3222477 original size:40 final size:40
Alignment explanation
Indices: 3222425--3222518 Score: 179
Period size: 40 Copynumber: 2.4 Consensus size: 40
3222415 ACAAAACTTA
3222425 TGTATCGATACAAAACTTATGTATCGATACATTTACTGTT
1 TGTATCGATACAAAACTTATGTATCGATACATTTACTGTT
3222465 TGTATCGATACAAAACTTATGTATCGATACATTTACTGTT
1 TGTATCGATACAAAACTTATGTATCGATACATTTACTGTT
*
3222505 TTTATCGATACAAA
1 TGTATCGATACAAA
3222519 TTGTAAAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (40 bp):
TGTATCGATACAAAACTTATGTATCGATACATTTACTGTT
Found at i:3223792 original size:19 final size:21
Alignment explanation
Indices: 3223744--3223799 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
3223734 AATTTCAACA
3223744 ATTTGTATCGATACAAACAGT
1 ATTTGTATCGATACAAACAGT
** *
3223765 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAACAGT
3223785 -TTTGTATCGATACAA
1 ATTTGTATCGATACAA
3223800 TGTATCTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 12 0.41
20 3 0.10
21 14 0.48
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (21 bp):
ATTTGTATCGATACAAACAGT
Found at i:3223805 original size:13 final size:13
Alignment explanation
Indices: 3223787--3223876 Score: 54
Period size: 13 Copynumber: 6.0 Consensus size: 13
3223777 ACATAAGTTT
3223787 TGTATCGATACAA
1 TGTATCGATACAA
*
3223800 TGTATCTATACGTAA
1 TGTATCGATAC--AA
3223815 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
3223832 TGTATCGATACGTAA
1 TGTATCGATAC--AA
3223847 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
3223864 TGTATCGCTACAA
1 TGTATCGATACAA
3223877 AGCTATTGCC
Statistics
Matches: 62, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
13 33 0.53
15 4 0.06
17 4 0.06
19 21 0.34
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3223816 original size:32 final size:32
Alignment explanation
Indices: 3223766--3223870 Score: 183
Period size: 32 Copynumber: 3.3 Consensus size: 32
3223756 ACAAACAGTA
* *
3223766 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACGTAAGTGTTGTATCGATAC
*
3223798 AATGTATCTATACGTAAGTGTTGTATCGATAC
1 AATGTATCGATACGTAAGTGTTGTATCGATAC
3223830 AATGTATCGATACGTAAGTGTTGTATCGATAC
1 AATGTATCGATACGTAAGTGTTGTATCGATAC
3223862 AATGTATCG
1 AATGTATCG
3223871 CTACAAAGCT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACGTAAGTGTTGTATCGATAC
Found at i:3223824 original size:19 final size:19
Alignment explanation
Indices: 3223768--3223861 Score: 77
Period size: 19 Copynumber: 5.6 Consensus size: 19
3223758 AAACAGTAAA
* *
3223768 TGTATCGATACATAAGTTT
1 TGTATCGATACGTAAGTGT
3223787 TGTATCGATAC--AA----
1 TGTATCGATACGTAAGTGT
*
3223800 TGTATCTATACGTAAGTGT
1 TGTATCGATACGTAAGTGT
3223819 TGTATCGATAC--AA----
1 TGTATCGATACGTAAGTGT
3223832 TGTATCGATACGTAAGTGT
1 TGTATCGATACGTAAGTGT
3223851 TGTATCGATAC
1 TGTATCGATAC
3223862 AATGTATCGC
Statistics
Matches: 61, Mismatches: 2, Indels: 24
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.34
15 4 0.07
17 4 0.07
19 32 0.52
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (19 bp):
TGTATCGATACGTAAGTGT
Found at i:3224842 original size:29 final size:29
Alignment explanation
Indices: 3224809--3224865 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
3224799 TACTATGCTT
3224809 CATGCATTTATAG-CATGTTCTTGCATGAC
1 CATGCATTTAT-GTCATGTTCTTGCATGAC
3224838 CATGCATTTATGTCATGTTCTTGCATGA
1 CATGCATTTATGTCATGTTCTTGCATGA
3224866 TCATCACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (29 bp):
CATGCATTTATGTCATGTTCTTGCATGAC
Found at i:3230601 original size:21 final size:21
Alignment explanation
Indices: 3230575--3230632 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
3230565 TAAAATTTCC
3230575 CAAATGTATCGATACA-AAGTT
1 CAAATGTATCGATACATAAG-T
3230596 CAAATGTATCGATACATTAAGT
1 CAAATGTATCGATACA-TAAGT
3230618 --AATGTATCGATACAT
1 CAAATGTATCGATACAT
3230633 TTCCTTGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.03
20 14 0.40
21 16 0.46
22 1 0.03
23 3 0.09
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (21 bp):
CAAATGTATCGATACATAAGT
Found at i:3230623 original size:20 final size:22
Alignment explanation
Indices: 3230576--3230633 Score: 79
Period size: 20 Copynumber: 2.8 Consensus size: 22
3230566 AAAATTTCCC
3230576 AAATGTATCGATACA--AAGTT
1 AAATGTATCGATACATTAAGTT
3230596 CAAATGTATCGATACATTAAG-T
1 -AAATGTATCGATACATTAAGTT
3230618 -AATGTATCGATACATT
1 AAATGTATCGATACATT
3230634 TCCTTGGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 16 0.46
21 15 0.43
22 1 0.03
23 3 0.09
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
AAATGTATCGATACATTAAGTT
Found at i:3230673 original size:13 final size:13
Alignment explanation
Indices: 3230655--3230719 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 13
3230645 AGCTTCGTAG
3230655 CGATACATTGTAT
1 CGATACATTGTAT
*
3230668 CGATACATTTTAT
1 CGATACATTGTAT
3230681 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
*
3230700 TGATACATTGTAT
1 CGATACATTGTAT
3230713 CGATACA
1 CGATACA
3230720 AATTGTTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
13 27 0.64
14 1 0.02
16 6 0.14
18 1 0.02
19 7 0.17
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:3234514 original size:3 final size:3
Alignment explanation
Indices: 3234506--3234534 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3234496 ATAATTTTTT
3234506 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3234535 GGTACTAGTA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3238404 original size:34 final size:35
Alignment explanation
Indices: 3238356--3238425 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
3238346 CGATCAAAGG
* *
3238356 AAAGAAATCTC-TTTTTTGTA-TCAGAAGAAGTCA
1 AAAGAAAGCTCTTTTTTTGTAGGCAGAAGAAGTCA
3238389 AAAGAAAAGCTCTTTTTTTGTAGGCAGAAGAAGTCA
1 AAAG-AAAGCTCTTTTTTTGTAGGCAGAAGAAGTCA
3238425 A
1 A
3238426 CACTAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 4 0.12
34 6 0.19
35 9 0.28
36 13 0.41
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (35 bp):
AAAGAAAGCTCTTTTTTTGTAGGCAGAAGAAGTCA
Found at i:3239496 original size:19 final size:19
Alignment explanation
Indices: 3239472--3239534 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
3239462 TAGCCAAACT
3239472 TGTATCGATACACAAAGTA
1 TGTATCGATACACAAAGTA
3239491 TGTATCGAT--AC--A--A
1 TGTATCGATACACAAAGTA
3239504 TGTATCGATACACAAAGTA
1 TGTATCGATACACAAAGTA
3239523 TGTATCGATACA
1 TGTATCGATACA
3239535 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
15 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACAAAGTA
Found at i:3239508 original size:13 final size:13
Alignment explanation
Indices: 3239490--3239547 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
3239480 TACACAAAGT
3239490 ATGTATCGATACA
1 ATGTATCGATACA
3239503 ATGTATCGATACACAAA
1 ATGTATCGAT--AC--A
3239520 GTATGTATCGATACA
1 --ATGTATCGATACA
3239535 ATGTATCGATACA
1 ATGTATCGATACA
3239548 CAAAAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.59
15 3 0.08
17 3 0.08
19 10 0.26
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3239513 original size:32 final size:32
Alignment explanation
Indices: 3239472--3239567 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
3239462 TAGCCAAACT
3239472 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAGTATGTATCGATACAA
3239504 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAGTATGTATCGATACAA
**
3239536 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAGTA-TGTATCGATACA
3239568 TTGGCTTGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 49 0.80
33 12 0.20
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAGTATGTATCGATACAA
Found at i:3245790 original size:20 final size:20
Alignment explanation
Indices: 3245747--3245792 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3245737 AAATCTTTTG
3245747 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3245768 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3245788 CAAAA
1 CAAAA
3245793 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:3246092 original size:18 final size:17
Alignment explanation
Indices: 3246065--3246099 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3246055 TAGGCAGCAC
*
3246065 CACCAGGTCGCGACCGG
1 CACCAGGTCGCAACCGG
3246082 CACCTAGGTCGCAACCGG
1 CACC-AGGTCGCAACCGG
3246100 GCAGTCCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.40, G:0.31, T:0.09
Consensus pattern (17 bp):
CACCAGGTCGCAACCGG
Found at i:3248202 original size:13 final size:13
Alignment explanation
Indices: 3248184--3248209 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3248174 TACACAAAGT
3248184 ATGTATCGATACA
1 ATGTATCGATACA
3248197 ATGTATCGATACA
1 ATGTATCGATACA
3248210 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3248207 original size:32 final size:33
Alignment explanation
Indices: 3248166--3248229 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3248156 TAGCCAAACT
**
3248166 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3248198 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3248230 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3250670 original size:37 final size:37
Alignment explanation
Indices: 3250573--3250674 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 37
3250563 CAACCGTGCT
* *
3250573 ACCAATTAAGAATAGTGATTTTTGTTTCGAACTTTGTC
1 ACCAGTTAAGAATAGTGATTTTTG-TTCCAACTTTGTC
** * *
3250611 ACTGGTTTAGAATAGTGGTTTTTGTTCCAA-TTTGTGCC
1 ACCAGTTAAGAATAGTGATTTTTGTTCCAACTTTGT--C
3250649 ACCAG-TAAGAATAGTGATTTTTGTTC
1 ACCAGTTAAGAATAGTGATTTTTGTTC
3250675 TGAACAGTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
36 5 0.10
37 24 0.46
38 23 0.44
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (37 bp):
ACCAGTTAAGAATAGTGATTTTTGTTCCAACTTTGTC
Found at i:3254267 original size:20 final size:20
Alignment explanation
Indices: 3254242--3254279 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3254232 TCAAAAACCC
*
3254242 ATAATGTATTGATCCAATGA
1 ATAATGTATTGATACAATGA
3254262 ATAATGTATTGATACAAT
1 ATAATGTATTGATACAAT
3254280 TTAAGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
ATAATGTATTGATACAATGA
Found at i:3255098 original size:13 final size:13
Alignment explanation
Indices: 3255080--3255104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3255070 CATAAAGTGT
3255080 TGTATCGATACAA
1 TGTATCGATACAA
3255093 TGTATCGATACA
1 TGTATCGATACA
3255105 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3255120 original size:32 final size:33
Alignment explanation
Indices: 3255060--3255128 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
3255050 TTCAACAATT
3255060 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
3255093 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
3255125 TGTA
1 TGTA
3255129 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:3255163 original size:13 final size:13
Alignment explanation
Indices: 3255145--3255169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3255135 TGCCAAAAAA
3255145 TGTATCGATACAT
1 TGTATCGATACAT
3255158 TGTATCGATACA
1 TGTATCGATACA
3255170 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3255236 original size:52 final size:52
Alignment explanation
Indices: 3255178--3255306 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
3255168 CACTGATCTT
3255178 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
3255230 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATCCACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3255282 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3255307 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3258407 original size:21 final size:19
Alignment explanation
Indices: 3258360--3258417 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
3258350 TACGACAGAT
*
3258360 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
3258379 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
3258398 ACAAATTGTATTGATACATG
1 AC--ATTGTATCGATACATG
3258418 AAACTGACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 18 0.55
21 15 0.45
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:3266083 original size:28 final size:29
Alignment explanation
Indices: 3266023--3266104 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 29
3266013 TTTTGGAGAT
*
3266023 AATAACGGGGTTGGAGTGTCCCC--TCGA
1 AATAACGGGGTTGGAGTATCCCCGATCGA
3266050 AGATAACGGGGTTGGAGTATCCCCGAT-GA
1 A-ATAACGGGGTTGGAGTATCCCCGATCGA
* * *
3266079 AATAATGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
3266105 TGTGAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 1 0.02
28 43 0.90
29 3 0.06
30 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (29 bp):
AATAACGGGGTTGGAGTATCCCCGATCGA
Found at i:3266223 original size:51 final size:50
Alignment explanation
Indices: 3266112--3266456 Score: 216
Period size: 51 Copynumber: 6.6 Consensus size: 50
3266102 GATTGTGAAA
* * ** * *
3266112 AAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATT-GTGAAAAATTAGTGTTTTG
3266163 AAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAG
1 -AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTT-G
* * * * * *
3266215 AAATAAAACCGGGGTTAGAGTATCCCCGATCGTGAGAAATCAATATTTTGG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTT-G
* * * *** * **
3266266 AAATAAAGCCGGGGTTGGGGTATCCCCTCGGA-GGT-AACGGGGTTGGAGTATCCCTG
1 AAATAAAACCGGGGTTGGAGTAT-CCC-C-GATTGTGAA--AAATT--AGTGT-TTTG
* * *
3266322 ATGAT-TAA-CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTGG
1 A-AATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTG--TTTT-G
* * *
3266374 AAATAAAATCGGAGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGA-AAAATTAGTGTTTTG
* *
3266424 AAAATAAAATCGGAGTTGG-GATATCCCCGATTG
1 -AAATAAAACCGGGGTTGGAG-TATCCCCGATTG
3266457 CAAAGAATTG
Statistics
Matches: 230, Mismatches: 43, Indels: 41
0.73 0.14 0.13
Matches are distributed among these distances:
50 4 0.02
51 114 0.50
52 44 0.19
53 37 0.16
54 8 0.03
55 13 0.06
56 7 0.03
57 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (50 bp):
AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTG
Found at i:3266316 original size:28 final size:28
Alignment explanation
Indices: 3266275--3266347 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
3266265 GAAATAAAGC
*
3266275 CGGGGTTGGGGTATCCCCTCG--GAGGTAA
1 CGGGGTTGGAGTATCCCCT-GATGA-GTAA
*
3266303 CGGGGTTGGAGTAT-CCCTGATGATTAA
1 CGGGGTTGGAGTATCCCCTGATGAGTAA
3266330 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
3266348 GATTGTGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.16, C:0.21, G:0.38, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTGATGAGTAA
Found at i:3268809 original size:13 final size:13
Alignment explanation
Indices: 3268791--3268816 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3268781 CAAAGAATAG
3268791 ATGTATCGATACA
1 ATGTATCGATACA
3268804 ATGTATCGATACA
1 ATGTATCGATACA
3268817 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3268813 original size:34 final size:33
Alignment explanation
Indices: 3268770--3268836 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
3268760 AACTTCCTAG
*
3268770 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
*
3268804 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
3268837 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:3268918 original size:32 final size:32
Alignment explanation
Indices: 3268860--3268932 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
3268850 AGCTTCCTAG
* * *
3268860 CGATACATTGTATTGATATAAAACTTATGTAT
1 CGATACATTATATCGATACAAAACTTATGTAT
*
3268892 CGATACATTATATCGATACAACACTTATGTAT
1 CGATACATTATATCGATACAAAACTTATGTAT
3268924 CGATACATT
1 CGATACATT
3268933 TACAGAATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (32 bp):
CGATACATTATATCGATACAAAACTTATGTAT
Found at i:3269013 original size:21 final size:22
Alignment explanation
Indices: 3268989--3269046 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
3268979 ATTGGGACCT
* *
3268989 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
*
3269010 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTGCACAAA
3269031 TGTATCGATACATTTG
1 TGTATCGATACATTTG
3269047 GATAAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:3269674 original size:40 final size:42
Alignment explanation
Indices: 3269630--3269726 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
3269620 CCACTTTTCA
* *
3269630 AGGACAAAGGAAAAG-AG-AATGAAATAG-GTCTTGCTCCTTG
1 AGGACAAAGGAAAAGAAGAAAAGAAA-AGTGTCCTGCTCCTTG
* * * *
3269670 AGGACCAAGGAAGAGAAGAAAAGGAAAGTGTCCTGCTTCTTG
1 AGGACAAAGGAAAAGAAGAAAAGAAAAGTGTCCTGCTCCTTG
3269712 AGGACAAAGTGAAAA
1 AGGACAAAG-GAAAA
3269727 AGAGTACGTC
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
40 13 0.29
41 4 0.09
42 24 0.53
43 4 0.09
ACGTcount: A:0.42, C:0.12, G:0.29, T:0.16
Consensus pattern (42 bp):
AGGACAAAGGAAAAGAAGAAAAGAAAAGTGTCCTGCTCCTTG
Found at i:3269986 original size:55 final size:55
Alignment explanation
Indices: 3269819--3270851 Score: 873
Period size: 55 Copynumber: 17.9 Consensus size: 55
3269809 ATAAAGTGTA
* * * *
3269819 TCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* ** *
3269874 TCCTGCTCTTTGAGGAGTGAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* * *
3269928 TCCTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* *
3269983 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* ** * *
3270038 TCCTGCTCTTTGGGGACTGAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTT--AAAG---AGGCG
* * *
3270099 TCCTGCTCTTTGAGGACTGAAAGGTTCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* * * * *
3270154 TCCTGCTCTTTTAGGACTAGAAAATGCCACTAACTTGTGTGGGTTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* * * * * *
3270209 TCATGCTCTTTGGGGACTGAAAGAAGCATCCCCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-ATGC--CACCAACTTGTGTGGGCTTT--AAAG---AGGCG
* * * * * *
3270272 TCC-CCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCCCAACTTGTGTGGGCTTTGAAAAGAA
1 TCCTGC-TCTT-TGAGGAC--T-----GAAAATGC--CACCAACTTGTGTGGGCTTT--AAAG--
* *
3270336 AAAGCA
51 -AGGCG
*
3270342 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* *
3270397 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* * * *
3270452 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTT--AAAG---AGGCG
* * *
3270513 TCCTGCTCTTTGAGGACTAGAAAATGGCACCAACTTGTGTGGGCTTTGAA-AGGCA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* *
3270568 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
*
3270623 TCCTGCTCTTTGAGGACTAGAAAATGTCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT--AA--AG-AGGCG
** * * *
3270684 TCCTGCTCTTTGAGGACTGAAGGTGCCACTAACTTGTGTGGGCTTTAAAAAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT---AAAGAGGCG
* * *
3270742 TCCTGCTCTTTGGGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT--AAAG---AGGCG
* **
3270803 TCCTGCTCTTTGAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTTAAA
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAA
3270852 AGGAAAAGGC
Statistics
Matches: 833, Mismatches: 92, Indels: 103
0.81 0.09 0.10
Matches are distributed among these distances:
54 64 0.08
55 387 0.46
56 14 0.02
57 22 0.03
58 34 0.04
59 31 0.04
60 50 0.06
61 148 0.18
62 5 0.01
63 15 0.02
64 5 0.01
66 1 0.00
67 1 0.00
69 5 0.01
70 46 0.06
71 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
Found at i:3270154 original size:171 final size:167
Alignment explanation
Indices: 3269819--3270885 Score: 1073
Period size: 171 Copynumber: 6.1 Consensus size: 167
3269809 ATAAAGTGTA
* *
3269819 TCCTACTCTTTGAGGACTA-AAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCT
* ** * *
3269883 TTGAGGAGT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTTTTTGAGGACTG
65 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTG
*
3269947 AAAGGTGCCACCAACTTGTGTGGGCTTT-AAG-AGGTG
130 AAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAGGCG
* *
3269983 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
* **
3270048 TGGGGACT-GAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGA
66 TGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCATCCTGCTCTTTGA
* *
3270112 GGACTGAAAGGTTCCACCAACTTGTGTGGGCTTT-AAG-AGGTG
124 GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAGGCG
* * * * *
3270154 TCCTGCTCTTTTAGGACTAGAAAATGCCACTAACTTGTGTGGGTTTTGAAAGGTGTCATGCTCTT
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
* * * * *
3270219 TGGGGACT-GAAAGAAGCATCCCCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC-CCAACTT
66 TGAGGACTGGAAA-ATGC--CACCAACTTGTGTGGGCTTTG-AAAG-----GCATCCTGC-TCTT
* * ** * * *
3270282 GTGTGGGCTTTGAAAAGAAAAAGCATCCCCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
121 -TGAGGAC--TG-AAAG---GTGC--CACCAACTTGTGTGGGCTTT--AAAG--AAGGCG
*
3270342 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCGTCCTGCTCT
* ** *
3270406 TTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTG
65 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTG
* *
3270471 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
130 AAAGGTGCCACCAACTTGTGTGGGCTTT--AAAG--AAGGCG
* *
3270513 TCCTGCTCTTTGAGGACTAGAAAATGGCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTT
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
3270578 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTAG
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACT-G
* *
3270643 AAA-ATGTCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCG
130 AAAGGTGCCACCAACTTGTGTGGGCTTT--AA--AGAAGGCG
** * * *
3270684 TCCTGCTCTTTGAGGACT-GAAGGTGCCACTAACTTGTGTGGGCTTTAAAAAAAAGGCATCCTGC
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT----GAAAGGCGTCCTGC
*
3270748 TCTTTGGGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTT
62 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCATCCTGCTCTT
* *
3270813 TGAGGATTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
121 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-G--AAGGCG
*
3270863 TCATGCTCTTTGAGGACTA-AAAA
1 TCCTGCTCTTTGAGGACTAGAAAA
3270886 GCGGAAGGAG
Statistics
Matches: 781, Mismatches: 73, Indels: 83
0.83 0.08 0.09
Matches are distributed among these distances:
164 65 0.08
165 26 0.03
166 4 0.01
170 24 0.03
171 328 0.42
172 8 0.01
173 41 0.05
174 59 0.08
175 4 0.01
176 7 0.01
177 7 0.01
178 5 0.01
179 52 0.07
180 28 0.04
181 1 0.00
182 19 0.02
185 7 0.01
186 20 0.03
187 2 0.00
188 70 0.09
189 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (167 bp):
TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTGA
AAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAGGCG
Found at i:3270272 original size:35 final size:35
Alignment explanation
Indices: 3270227--3270344 Score: 227
Period size: 35 Copynumber: 3.3 Consensus size: 35
3270217 TTTGGGGACT
3270227 GAAAGAAGCATCCCCAACTTGTGTGGGCTTTGAAAA
1 GAAA-AAGCATCCCCAACTTGTGTGGGCTTTGAAAA
3270263 GAAAAAGCATCCCCAACTTGTGTGGGCTTTGAAAA
1 GAAAAAGCATCCCCAACTTGTGTGGGCTTTGAAAA
3270298 GAAAAAGCATCCCCAACTTGTGTGGGCTTTGAAAA
1 GAAAAAGCATCCCCAACTTGTGTGGGCTTTGAAAA
3270333 GAAAAAGCATCC
1 GAAAAAGCATCC
3270345 TGCTCTTTGA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
35 78 0.95
36 4 0.05
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (35 bp):
GAAAAAGCATCCCCAACTTGTGTGGGCTTTGAAAA
Found at i:3270502 original size:29 final size:29
Alignment explanation
Indices: 3270421--3270502 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 29
3270411 GACTAGAAAA
3270421 TGCCACCAACTTGTGTGGGCTTTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGG
** *
3270450 TGTCCTGC-TCTT-TG-GGGAC--TGAAAGG
1 TG-CCACCAACTTGTGTGGG-CTTTGAAAGG
3270476 TGCCACCAACTTGTGTGGGCTTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAA
3270503 AGAAAAAGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
25 3 0.08
26 12 0.30
27 6 0.15
28 6 0.15
29 10 0.25
30 3 0.08
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGG
Found at i:3270563 original size:28 final size:28
Alignment explanation
Indices: 3270532--3270673 Score: 80
Period size: 28 Copynumber: 5.1 Consensus size: 28
3270522 TTGAGGACTA
3270532 GAAAATGGCACCAACTTGTGTGGGCTTT
1 GAAAATGGCACCAACTTGTGTGGGCTTT
** * * * *
3270560 G-AAA-GGCATCCTGCTCTTTGAGGAC-TG
1 GAAAATGGCA-CCAACT-TGTGTGGGCTTT
*
3270587 GAAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAATGGCACCAACTTGTGTGGGCTTT
** * * * *
3270615 G-AAA-GGCATCCTGCTCTTTGAGGAC-TA
1 GAAAATGGCA-CCAACT-TGTGTGGGCTTT
*
3270642 GAAAATGTCACCAACTTGTGTGGGCTTT
1 GAAAATGGCACCAACTTGTGTGGGCTTT
3270670 GAAA
1 GAAA
3270674 GGAGAAGGCG
Statistics
Matches: 77, Mismatches: 27, Indels: 20
0.62 0.22 0.16
Matches are distributed among these distances:
26 7 0.09
27 30 0.39
28 34 0.44
29 6 0.08
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (28 bp):
GAAAATGGCACCAACTTGTGTGGGCTTT
Found at i:3270645 original size:27 final size:28
Alignment explanation
Indices: 3270510--3270645 Score: 68
Period size: 27 Copynumber: 4.9 Consensus size: 28
3270500 AAAAGAAAAA
3270510 GCATCCTGCTCTTTGAGGACTAGAAAATG
1 GCATCCTGCTCTTTGAGGACTAG-AAATG
** * * * *
3270539 GCA-CCAACT-TGTGTGGGCTTTGAAA-G
1 GCATCCTGCTCTTTGAGGAC-TAGAAATG
*
3270565 GCATCCTGCTCTTTGAGGACTGGAAAATG
1 GCATCCTGCTCTTTGAGGACTAG-AAATG
* ** * * * *
3270594 CCA-CCAACT-TGTGTGGGCTTTGAAA-G
1 GCATCCTGCTCTTTGAGGAC-TAGAAATG
3270620 GCATCCTGCTCTTTGAGGACTAGAAA
1 GCATCCTGCTCTTTGAGGACTAGAAA
3270646 ATGTCACCAA
Statistics
Matches: 73, Mismatches: 26, Indels: 18
0.62 0.22 0.15
Matches are distributed among these distances:
26 7 0.10
27 33 0.45
28 27 0.37
29 6 0.08
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (28 bp):
GCATCCTGCTCTTTGAGGACTAGAAATG
Found at i:3271871 original size:14 final size:13
Alignment explanation
Indices: 3271852--3271884 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3271842 CAGATTCTTC
3271852 TTTTTTTTTT-GT
1 TTTTTTTTTTGGT
3271864 TGTTTTTTTTTGGT
1 T-TTTTTTTTTGGT
3271878 TTTTTTT
1 TTTTTTT
3271885 GAAAAAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 15 0.79
14 3 0.16
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTGGT
Found at i:3284799 original size:52 final size:52
Alignment explanation
Indices: 3284721--3284849 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
3284711 CGAAATATGA
3284721 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
** *
3284773 AAATTTGCCTATATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
3284825 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3284850 AAGATTAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:3284859 original size:52 final size:52
Alignment explanation
Indices: 3284721--3284869 Score: 203
Period size: 52 Copynumber: 2.9 Consensus size: 52
3284711 CGAAATATGA
*
3284721 AAATTTGCCTGCATGTATCGATACATTTCA-TAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-ATCATTAGTGTATCGATACATCTGGGC
** **
3284773 AAATTTGCCTATATGTATCGATAC-ATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACAATCAT-TAGTGTATCGATACATCTGGGC
**
3284825 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAATCATTAGTGTATCGATACA
3284870 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.01
52 81 0.96
53 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACAATCATTAGTGTATCGATACATCTGGGC
Found at i:3284876 original size:13 final size:13
Alignment explanation
Indices: 3284858--3284882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3284848 CAAAGATTAG
3284858 TGTATCGATACAA
1 TGTATCGATACAA
3284871 TGTATCGATACA
1 TGTATCGATACA
3284883 TTTCAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3284949 original size:19 final size:18
Alignment explanation
Indices: 3284925--3285022 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
3284915 TAGCTTAAAT
3284925 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
3284944 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
3284957 TGTATTGATACAACACTTA
1 TGTATCGATACAA-ACTTA
3284976 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
3284989 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
3285009 TGTATCGATACAAA
1 TGTATCGATACAAA
3285023 TCATTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:3284966 original size:13 final size:13
Alignment explanation
Indices: 3284944--3285000 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
3284934 ACAAAACTTA
3284944 TGTATCGATACAT
1 TGTATCGATACAT
*
3284957 TGTATTGATACAACACTT
1 TGTATCGAT---ACA--T
3284975 ATGTATCGATACAT
1 -TGTATCGATACAT
3284989 TGTATCGATACA
1 TGTATCGATACA
3285001 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 6 0.17
18 1 0.03
19 8 0.22
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3284967 original size:32 final size:32
Alignment explanation
Indices: 3284923--3285020 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
3284913 AGTAGCTTAA
*
3284923 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
3284955 ATTGTATTGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
3284987 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
3285020 A
1 A
3285021 AATCATTGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 47 0.76
33 15 0.24
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:3285667 original size:52 final size:52
Alignment explanation
Indices: 3285541--3286566 Score: 300
Period size: 49 Copynumber: 20.2 Consensus size: 52
3285531 CCACTATGCA
* * * * *
3285541 GATTCAAGGCCTACCACACTAGAGTTAAAGATGAGAAAAAGGATGTCAATGTGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAG-AAAA--ATGCCAATGTGCT
* * * * *
3285596 GATTCACGGTCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
* * ** ** *
3285648 GATTCAAGGCCAAAAACATTGGGTTTTAAAGATGATG-AAGGTGCCAATATGCT
1 GATTCAAGGCCAACAACATT-AGACTTAAAGATGA-GAAAAATGCCAATGTGCT
* * * *
3285701 GATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTGAGAAAAGTGATAAAGATGCCAATATG
1 GATTCAAGGCCAACAACATTAGACTT-AA-A-G-A--T--G---A--GA-AAA-ATGCCAATGTG
*
3285766 TT
51 CT
* * * * * * *
3285768 GATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAGGGATGTCAACGTGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAA---ATGCCAATGTGCT
* * * * * *
3285823 AATTCAAGACCAGCTACATT-GAGCTTAAAGATG-GAAAAGGTGCCAATATGCT
1 GATTCAAGGCCAACAACATTAGA-CTTAAAGATGAGAAAA-ATGCCAATGTGCT
* * * *
3285875 GATTCAAGGCCATCTATATTGGACTT-AA-A-G-G-----TGCCAATGTGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
* * * ** *
3285918 GATTCAAGGCCAGCTACATTGGACTTAAAGA--AG-AAGGTGCCAATATGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
* * * * *
3285967 GATTCAAGGCTAGCTATATTGGACTT-AA-A-G-G-----TGCCAATGTGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
* * * ** *
3286010 GATTCAAGGCCAGCTACATTGGACTTAAAGAT--G-AAGGTGCCAATATGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
* * * * * * *
3286059 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGAGAAAAAGGATGTCAATGTGTT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAG-AAAA--ATGCCAATGTGCT
* * * * * * *
3286114 GATTCACGGTCAGCGACATTAGACTTGAAGATGAGAAAAATGACAATGTGTT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
* ** ***
3286166 GATTCAAGGCCAACAACATTGGGTTTTAAAGATGATG-AAGGCGCCAATGTGCT
1 GATTCAAGGCCAACAACATT-AGACTTAAAGATGA-GAAAAATGCCAATGTGCT
* ** ** *
3286219 GATTCAAGGCCAACAACATTGGGTTTTAAAGATGATG-AAGGTGCCAATATGCT
1 GATTCAAGGCCAACAACATT-AGACTTAAAGATGA-GAAAAATGCCAATGTGCT
* * * * * *
3286272 GATTCAAGGCCAGCAATATTGGACTT-AA-A-GACAAAGATGCCAATATGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
* * * * ** *
3286321 GATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAG---GGTGCCAATATGCT
1 GATTCAAGGCCAACAACATTAGACTT-AAAGATGAGAAAAATGCCAATGTGCT
* * * * *
3286371 GATTTAAGGCCAGCGATATTAGACTT---G--GAG----GTGCCAATGTGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
* * * * *
3286414 GATTCAAGGCCAGCTACATTGGACTTAAAGATGATG----GTGCCAATATGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGA-GAAAAATGCCAATGTGCT
* * *
3286463 GATTCAAGGCCAACGATATTGGACTT-AA-A-G-G-----TGCCAATGTGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
* * * ** *
3286506 GATTCAAGGCCAGCTACATTGGACTTAAAGAT--G-AAGGTGCCAATATGCT
1 GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
3286555 GATTCAAGGCCA
1 GATTCAAGGCCA
3286567 GCGATATTGG
Statistics
Matches: 788, Mismatches: 121, Indels: 130
0.76 0.12 0.13
Matches are distributed among these distances:
43 138 0.18
44 10 0.01
45 6 0.01
46 3 0.00
47 3 0.00
48 6 0.01
49 177 0.22
50 37 0.05
51 7 0.01
52 93 0.12
53 141 0.18
54 19 0.02
55 99 0.13
56 2 0.00
58 1 0.00
59 1 0.00
60 1 0.00
61 1 0.00
63 2 0.00
64 3 0.00
65 1 0.00
66 4 0.01
67 33 0.04
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (52 bp):
GATTCAAGGCCAACAACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCT
Found at i:3285797 original size:67 final size:68
Alignment explanation
Indices: 3285675--3285801 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
3285665 ATTGGGTTTT
* * *
3285675 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGGTG
3285740 AGA
66 AGA
* * * *
3285743 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
3285802 GAAAAGGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGGTG
AGA
Found at i:3285919 original size:43 final size:43
Alignment explanation
Indices: 3285858--3286091 Score: 306
Period size: 43 Copynumber: 5.2 Consensus size: 43
3285848 TAAAGATGGA
*
3285858 AAAGGTGCCAATATGCTGATTCAAGGCCATCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3285901 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
3285944 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
3285993 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
3286036 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
3286085 AAAGGTG
1 AAAGGTG
3286092 AGAAAAAGGA
Statistics
Matches: 168, Mismatches: 11, Indels: 24
0.83 0.05 0.12
Matches are distributed among these distances:
43 85 0.51
44 1 0.01
45 1 0.01
47 1 0.01
48 1 0.01
49 79 0.47
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:3285985 original size:92 final size:92
Alignment explanation
Indices: 3285818--3286586 Score: 757
Period size: 92 Copynumber: 7.9 Consensus size: 92
3285808 GGATGTCAAC
* * *
3285818 GTGCTAATTCAAGACCAGCTACATT-GAGCTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAA
1 GTGCTGATTCAAGGCCAGCTACATTGGA-CTTAAAGA---AGAAGGTGCCAATATGCTGATTCAA
* *
3285882 GGCCATCTATATTGGACTTAAAGGTGCCAAT
62 GGCCAGCGATATTGGACTTAAAGGTGCCAAT
*
3285913 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
*
3285978 AGCTATATTGGACTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
*
3286005 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
* *
3286070 AGCTATATTGGACTTAAAGGTGAGAAAAAGGATGTCAAT
66 AGCGATATTGGAC-T-----T-----AAAGG-TGCCAAT
* * * * * * ** * * *
3286109 GTGTTGATTCACGGTCAGCGACATTAGACTTGAAGATGAGAAAAATGACAATGTGTTGATTCAAG
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--AG-AAGGTGCCAATATGCTGATTCAAG
* * * **
3286174 GCCAACAACATTGGGTTTTAAAGATGATGAAGGCGCCAAT
63 GCCAGCGATATT-GGACTTAAAG--G-T------GCCAAT
* * **
3286214 GTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATGAAGGTGCCAATATGCTGATTCAA
1 GTGCTGATTCAAGGCCAGCTACATT-GGACTTAAAGA--A-GAAGGTGCCAATATGCTGATTCAA
*
3286279 GGCCAGCAATATTGGACTTAAAGACAAAGATGCCAAT
62 GGCCAGCGATATTGGACTTAAAG-----G-TGCCAAT
* * * * * *
3286316 ATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAGGGTGCCAATATGCTGATTTAAGGC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGAAGAAGGTGCCAATATGCTGATTCAAGGC
* **
3286381 CAGCGATATTAGACTTGGAGGTGCCAAT
65 CAGCGATATTGGACTTAAAGGTGCCAAT
* *
3286409 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
*
3286474 AACGATATTGGACTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
*
3286501 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
*
3286566 AGCGATATTGGGCTTAGAAGG
66 AGCGATATTGGACTTA-AAGG
3286587 GTTGCCACCG
Statistics
Matches: 573, Mismatches: 69, Indels: 66
0.81 0.10 0.09
Matches are distributed among these distances:
92 262 0.46
93 40 0.07
94 1 0.00
95 31 0.05
96 2 0.00
97 4 0.01
98 1 0.00
99 44 0.08
101 4 0.01
102 34 0.06
103 5 0.01
104 36 0.06
105 33 0.06
106 40 0.07
107 30 0.05
108 6 0.01
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (92 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAAGGTGCCAAT
Found at i:3286018 original size:21 final size:20
Alignment explanation
Indices: 3285951--3286018 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
3285941 CTTAAAGAAG
3285951 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
* *
3285972 AAGGCTAGCTATATTG--GACTTA
1 AAGG-T-GCCA-ATTGCTGA-TTC
3285994 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
3286015 AAGG
1 AAGG
3286019 CCAGCTACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (20 bp):
AAGGTGCCAATTGCTGATTC
Found at i:3286576 original size:49 final size:49
Alignment explanation
Indices: 3285819--3286568 Score: 659
Period size: 49 Copynumber: 15.4 Consensus size: 49
3285809 GATGTCAACG
* *
3285819 TGCTAATTCAAGACCAGCTACATT-GAGCTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGA-CTTAAAGAT-G--AAGGTGCCAATA
* * *
3285871 TGCTGATTCAAGGCCATCTATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
*
3285914 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
3285963 TGCTGATTCAAGGCTAGCTATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
3286006 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
3286055 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAGAAAAAGGATGTCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT--G---AAGG-TGCCAATA
* * * * * * ** * *
3286110 TGTTGATTCACGGTCAGCGACATTAGACTTGAAGATGAGAAAAATGACAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT--G-AAGGTGCCAATA
* * * ** * *
3286162 TGTTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATGAAGGCGCCAATG
1 TGCTGATTCAAGGCCAGCTACATT-GGACTT-AA-A-GATGAAGGTGCCAATA
* * **
3286215 TGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATGAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATT-GGACTT-AA-A-GATGAAGGTGCCAATA
* * ** *
3286268 TGCTGATTCAAGGCCAGCAATATTGGACTTAAAGACAAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
3286317 TGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAGGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGATGAAGGTGCCAATA
* * * * *
3286367 TGCTGATTTAAGGCCAGCGATATTAGACTT---G--G-AGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
*
3286410 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
3286459 TGCTGATTCAAGGCCAACGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
3286502 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
3286551 TGCTGATTCAAGGCCAGC
1 TGCTGATTCAAGGCCAGC
3286569 GATATTGGGC
Statistics
Matches: 583, Mismatches: 79, Indels: 75
0.79 0.11 0.10
Matches are distributed among these distances:
43 150 0.26
44 1 0.00
45 2 0.00
46 2 0.00
47 3 0.01
48 2 0.00
49 189 0.32
50 42 0.07
51 3 0.01
52 54 0.09
53 88 0.15
54 6 0.01
55 38 0.07
56 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
Found at i:3286688 original size:32 final size:32
Alignment explanation
Indices: 3286583--3286718 Score: 193
Period size: 33 Copynumber: 4.2 Consensus size: 32
3286573 TTGGGCTTAG
*
3286583 AAGGGTTGCCACCGACTTGTGTGGGCTTTAGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTT-GAA
* *
3286616 AATGGTTGCCACCAACTTGTGTGGGCTTTTGAA
1 AAGGGTTGCCACCGACTTGTGTGGGC-TTTGAA
3286649 GAA-GGTTGCCACCGACTTGTGTGGGCTTTGAA
1 -AAGGGTTGCCACCGACTTGTGTGGGCTTTGAA
* *
3286681 AAGGGTTGCCACCGACTTGTGTGAGCTTTAAA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAA
3286713 AAGGGT
1 AAGGGT
3286719 GAAAGATGCC
Statistics
Matches: 94, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
31 2 0.02
32 39 0.41
33 48 0.51
34 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (32 bp):
AAGGGTTGCCACCGACTTGTGTGGGCTTTGAA
Found at i:3286781 original size:34 final size:34
Alignment explanation
Indices: 3286733--3287284 Score: 507
Period size: 34 Copynumber: 16.4 Consensus size: 34
3286723 GATGCCATAA
**
3286733 AGTTGTGGAC-TTAAAAGGAGCAAGGTGCCACGG
1 AGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGG
* **
3286766 AGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACAA
1 AGTTGTGGACTTTAAAA-GGAAAAAG-GTGCCACGG
* **
3286802 AGTTGTGGGCTTTGAAAA-GAGCAAGGTGCCACGG
1 AGTTGTGGACTTT-AAAAGGAAAAAGGTGCCACGG
*
3286836 GGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACGG
1 AGTTGTGGACTTT-AAAAGGAAAAAG-GTGCCACGG
*
3286872 AGTTGTGGGCTTTGAAAA-G---AAGGTGCCACGG
1 AGTTGTGGACTTT-AAAAGGAAAAAGGTGCCACGG
* * * **
3286903 AGTCGTGGAC-TTAAAAAGAACAAGGTGCCATAG
1 AGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGG
3286936 AGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGG
1 AGTTGTGGACTTTAAAA-GGAAAAAG-GTGCCACGG
*
3286972 AGTTGTGGGCTTTGAAAA-G---AAGGTGCCACGG
1 AGTTGTGGACTTT-AAAAGGAAAAAGGTGCCACGG
* * **
3287003 AGTCGTGGACTTTGAAAGGAAGGAGGTGCCACGG
1 AGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGG
3287037 AGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGG
1 AGTTGTGGACTTTAAAA-GGAAAAAG-GTGCCACGG
* * *
3287073 AGTTATGGGCTTT-GAA--AAAAAGGTGCCACGG
1 AGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGG
*
3287104 AGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCACGG
1 AGTTGTGGACTTTAAAAGGAAAAAG-GTGCCACGG
* * *
3287138 AGTTATGGGC-TTAGAAGGAAAAAGAGTGCCACGG
1 AGTTGTGGACTTTAAAAGGAAAAAG-GTGCCACGG
* ** *
3287172 AGTTGTGGGCTTTAAAAAGGAAAAATATGCCACAG
1 AGTTGTGGACTTT-AAAAGGAAAAAGGTGCCACGG
*
3287207 AGTTGTGGGCTTT----GGAAAGAAGGTGCCACGG
1 AGTTGTGGACTTTAAAAGGAAA-AAGGTGCCACGG
*
3287238 AGTCGTGGACTTTGAAAA-GAAAAAGGTGCCACGG
1 AGTTGTGGACTTT-AAAAGGAAAAAGGTGCCACGG
*
3287272 AGTCGTGGACTTT
1 AGTTGTGGACTTT
3287285 GATGCCACTG
Statistics
Matches: 435, Mismatches: 52, Indels: 63
0.79 0.09 0.11
Matches are distributed among these distances:
29 4 0.01
30 13 0.03
31 78 0.18
32 12 0.03
33 34 0.08
34 135 0.31
35 58 0.13
36 93 0.21
37 8 0.02
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
AGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGG
Found at i:3286941 original size:100 final size:101
Alignment explanation
Indices: 3286733--3287286 Score: 576
Period size: 100 Copynumber: 5.5 Consensus size: 101
3286723 GATGCCATAA
**
3286733 AGTTGTGGAC-TT-AAAAGGAGCAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAG
1 AGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA--G---AAG-G
** * * * *
3286794 TGCCACAAAGTTGTGGGCTTTGAAAAGAGCAAGGTGCCACGG
60 TGCCACGGAGTCGTGGACTTTAAAAAGAACAAGGTGCCACGG
*
3286836 GGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
1 AGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
**
3286901 GGAGTCGTGGAC-TTAAAAAGAACAAGGTGCCATAG
66 GGAGTCGTGGACTTTAAAAAGAACAAGGTGCCACGG
*
3286936 AGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
1 AGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
* * **
3287001 GGAGTCGTGGACTTTGAAAGGAAGGAGGTGCCACGG
66 GGAGTCGTGGACTTTAAAAAGAACAAGGTGCCACGG
* * *
3287037 AGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTATGGGCTTTGAAAAAAAGGTGCCAC
1 AGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
* * * *
3287102 GGAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCACGG
66 GGAGTCGTGGACTTTAAAAAGAACAAG-GTGCCACGG
* * * * **
3287138 AGTTATGGGC-TT-AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAATATG
1 AGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA-G---AAGGTG
* * * **
3287201 CCACAGAGTTGTGGGCTTTGGAAAG---AAGGTGCCACGG
62 CCACGGAGTCGTGGACTTTAAAAAGAACAAGGTGCCACGG
* * * *
3287238 AGTCGTGGACTTTGAAAA-GAAAAAG-GTGCCACGGAGTCGTGGACTTTGA
1 AGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
3287287 TGCCACTGAG
Statistics
Matches: 392, Mismatches: 46, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
99 36 0.09
100 143 0.36
101 135 0.34
102 6 0.02
103 27 0.07
104 8 0.02
105 11 0.03
106 22 0.06
107 4 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.20
Consensus pattern (101 bp):
AGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
GGAGTCGTGGACTTTAAAAAGAACAAGGTGCCACGG
Found at i:3287032 original size:201 final size:198
Alignment explanation
Indices: 3286720--3287286 Score: 691
Period size: 201 Copynumber: 2.8 Consensus size: 198
3286710 AAAAAGGGTG
* **
3286720 AAAGA-TGCCATAAAGTTGTGGACTTAAAAGGAGCAAG-GTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGAGTGCCATAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
* *
3286783 GGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTGAAAAGAGCAAGGTGCCACGGGGTTGTGGACTT
66 -GG--AAAG-GTGCCACAGAGTTGTGGGCTTTG-AAAGAG--AGGTGCCACGGAGTTGTGGACTT
*
3286848 TAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGAC
124 TAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAAAAGGTGCCACGGAGTCGTGGAC
3286913 TTAAAAAGAA
189 TTAAAAAGAA
*
3286923 CAAG-GTGCCATAGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAGAGTGCCATAGAGTTGTGGAC-TTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A
* * *
3286987 AAA-G-AAGGTGCCACGGAGTCGTGGACTTTGAAAGGAAGGAGGTGCCACGGAGTTGTGGACTTT
63 AAAGGAAAGGTGCCACAGAGTTGTGGGCTTTGAAA-G-A-GAGGTGCCACGGAGTTGTGGACTTT
* * *
3287050 AAAAGGGAAAAAGAGTGCCACGGAGTTATGGGCTTTGAAAAAAAGGTGCCACGGAGTTGTGGACT
125 AAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAAAAGGTGCCACGGAGTCGTGGACT
* *
3287115 TAGAAGGAA
190 TAAAAAGAA
** * * *
3287124 AAAGAGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGAGTGCCATAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAA
** * *
3287189 AGGAAAAATATGCCACAGAGTTGTGGGCTTTGGAAAGA-AGGTGCCACGGAGTCGTGGACTTTGA
65 AGG--AAAGGTGCCACAGAGTTGTGGGCTTT-GAAAGAGAGGTGCCACGGAGTTGTGGACTTTAA
* *
3287253 AAA-GAAAAAG-GTGCCACGGAGTCGTGGACTTTGA
127 AAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
3287287 TGCCACTGAG
Statistics
Matches: 317, Mismatches: 33, Indels: 32
0.83 0.09 0.08
Matches are distributed among these distances:
199 21 0.07
200 45 0.14
201 146 0.46
202 19 0.06
203 22 0.07
204 27 0.09
205 11 0.03
206 22 0.07
207 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (198 bp):
AAAGAGTGCCATAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
GGAAAGGTGCCACAGAGTTGTGGGCTTTGAAAGAGAGGTGCCACGGAGTTGTGGACTTTAAAAAG
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAAAAGGTGCCACGGAGTCGTGGACTTAAAAA
GAA
Found at i:3287089 original size:101 final size:100
Alignment explanation
Indices: 3286733--3287286 Score: 601
Period size: 101 Copynumber: 5.5 Consensus size: 100
3286723 GATGCCATAA
**
3286733 AGTTGTGGAC-TTAAAAGGAGCAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGT
1 AGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA--G---AAG-GT
** *
3286795 GCCACAAAGTTGTGGGCTTTGAAAAG-AGCAAGGTGCCACGG
60 GCCACGGAGTTGTGGACTTTGAAAAGAAG-AAGGTGCCACGG
*
3286836 GGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
1 AGTTGTGGACTTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
* * * **
3286901 GGAGTCGTGGAC-TTAAAAAGAACAAGGTGCCATAG
65 GGAGTTGTGGACTTTGAAAAGAAGAAGGTGCCACGG
3286936 AGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
1 AGTTGTGGACTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
* * *
3287001 GGAGTCGTGGACTTTGAAAGGAAGGAGGTGCCACGG
65 GGAGTTGTGGACTTTGAAAAGAAGAAGGTGCCACGG
* *
3287037 AGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTATGGGCTTTGAAAAAAAGGTGCCAC
1 AGTTGTGGACTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
* * *
3287102 GGAGTTGTGGACTTAG-AAGGAAAAAGAGTGCCACGG
65 GGAGTTGTGGACTTTGAAAAGAAGAAG-GTGCCACGG
* * * * **
3287138 AGTTATGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAATATGC
1 AGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA-G---AAGGTGC
* * *
3287202 CACAGAGTTGTGGGCTTTG--GA-AAGAAGGTGCCACGG
62 CACGGAGTTGTGGACTTTGAAAAGAAGAAGGTGCCACGG
* * *
3287238 AGTCGTGGACTTTGAAAA-GAAAAAG-GTGCCACGGAGTCGTGGACTTTGA
1 AGTTGTGGACTTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
3287287 TGCCACTGAG
Statistics
Matches: 392, Mismatches: 45, Indels: 31
0.84 0.10 0.07
Matches are distributed among these distances:
99 38 0.10
100 138 0.35
101 141 0.36
102 6 0.02
103 30 0.08
104 2 0.01
105 11 0.03
106 22 0.06
107 4 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.20
Consensus pattern (100 bp):
AGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACG
GAGTTGTGGACTTTGAAAAGAAGAAGGTGCCACGG
Found at i:3287297 original size:23 final size:23
Alignment explanation
Indices: 3287264--3287309 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3287254 AAGAAAAAGG
3287264 TGCCACGGAGTCGTGGACTTTGA
1 TGCCACGGAGTCGTGGACTTTGA
*
3287287 TGCCACTGAGTCGTGGACTTTGA
1 TGCCACGGAGTCGTGGACTTTGA
3287310 GACAAGATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (23 bp):
TGCCACGGAGTCGTGGACTTTGA
Found at i:3287366 original size:32 final size:31
Alignment explanation
Indices: 3287285--3287431 Score: 142
Period size: 32 Copynumber: 4.7 Consensus size: 31
3287275 CGTGGACTTT
**
3287285 GATGCCACTGAGTCGTGGACTTTGA-GACAA-
1 GATGCCACTGAGTCGTGGACTTAAAGGA-AAG
*
3287315 GATGCCACTAAGTCGTGGACTTAAAAGGAAAG
1 GATGCCACTGAGTCGTGGACTT-AAAGGAAAG
* * *
3287347 GATGCCACTGAGTCATGGACTTTGAAGAAAAG
1 GATGCCACTGAGTCGTGGAC-TTAAAGGAAAG
3287379 GATGCCACTGAGTCGTGGACTTTGAGAA-GAAA-
1 GATGCCACTGAGTCGTGGAC-TT-A-AAGGAAAG
*
3287411 -TTGCCACTGAGTCGTGGACTT
1 GATGCCACTGAGTCGTGGACTT
3287432 TGAGAAGAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
30 23 0.23
31 21 0.21
32 49 0.49
33 5 0.05
34 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (31 bp):
GATGCCACTGAGTCGTGGACTTAAAGGAAAG
Found at i:3287419 original size:31 final size:30
Alignment explanation
Indices: 3287286--3287463 Score: 193
Period size: 31 Copynumber: 5.7 Consensus size: 30
3287276 GTGGACTTTG
*
3287286 ATGCCACTGAGTCGTGGACTTTGAGACA-AG
1 ATGCCACTGAGTCGTGGACTTTGAGA-AGAA
* *
3287316 ATGCCACTAAGTCGTGGAC-TT-AAAAGGAAA
1 ATGCCACTGAGTCGTGGACTTTGAGAA-G-AA
*
3287346 GGATGCCACTGAGTCATGGACTTTGAAGAA-AA
1 --ATGCCACTGAGTCGTGGACTTTG-AGAAGAA
3287378 GGATGCCACTGAGTCGTGGACTTTGAGAAGAA
1 --ATGCCACTGAGTCGTGGACTTTGAGAAGAA
3287410 ATTGCCACTGAGTCGTGGACTTTGAGAAGAA
1 A-TGCCACTGAGTCGTGGACTTTGAGAAGAA
*
3287441 ATTGCCACTGATTCGTGGACTTT
1 A-TGCCACTGAGTCGTGGACTTT
3287464 AAAATGGTAT
Statistics
Matches: 130, Mismatches: 8, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
27 1 0.01
28 2 0.02
29 2 0.02
30 20 0.15
31 55 0.42
32 45 0.35
33 2 0.02
35 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (30 bp):
ATGCCACTGAGTCGTGGACTTTGAGAAGAA
Found at i:3288446 original size:14 final size:14
Alignment explanation
Indices: 3288423--3288463 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3288413 TCCCTTCTTC
*
3288423 TTCTTTTTTTTTGT
1 TTCTTCTTTTTTGT
3288437 TTCTTCTTTTTT-T
1 TTCTTCTTTTTTGT
3288450 TTC--CTTTTTTGT
1 TTCTTCTTTTTTGT
3288462 TT
1 TT
3288464 TGTTTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 7 0.28
12 3 0.12
13 4 0.16
14 11 0.44
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (14 bp):
TTCTTCTTTTTTGT
Found at i:3288464 original size:17 final size:17
Alignment explanation
Indices: 3288426--3288477 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
3288416 CTTCTTCTTC
3288426 TTTTT-TTTTGTTT-C-
1 TTTTTGTTTTGTTTCCT
*
3288440 TTCTT-TTTT-TTTCCT
1 TTTTTGTTTTGTTTCCT
*
3288455 TTTTTGTTTTGTTTCTT
1 TTTTTGTTTTGTTTCCT
3288472 TTTTTG
1 TTTTTG
3288478 GAAAAAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 3 0.10
14 9 0.29
15 4 0.13
16 4 0.13
17 11 0.35
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.83
Consensus pattern (17 bp):
TTTTTGTTTTGTTTCCT
Found at i:3291846 original size:20 final size:20
Alignment explanation
Indices: 3291823--3291895 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3291813 ACAATTCAAA
3291823 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3291843 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3291864 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3291884 GTATCGATACAT
1 GTATCGATACAT
3291896 AAACAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3291867 original size:21 final size:21
Alignment explanation
Indices: 3291841--3291916 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
3291831 ACATGTTGCA
3291841 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3291862 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
3291882 ATGTATCGATACAT-AAACAAG
1 ATGTATCGATACATGAAA-AAG
*
3291903 TTGTATCGATACAT
1 ATGTATCGATACAT
3291917 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3291874 original size:41 final size:41
Alignment explanation
Indices: 3291823--3291916 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
3291813 ACAATTCAAA
3291823 GTATCGATACATGTTGCAATGTATCGATACATGAAA-AAGAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAACAAGAT
*
3291864 GTATCGATACATGTTGCAATGTATCGATACATAAACAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAACAAGAT
3291905 GTATCGATACAT
1 GTATCGATACAT
3291917 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 3 0.06
41 48 0.94
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAACAAGAT
Found at i:3291973 original size:13 final size:13
Alignment explanation
Indices: 3291955--3291980 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3291945 TACAGCAAGT
3291955 ATGTATCGATACA
1 ATGTATCGATACA
3291968 ATGTATCGATACA
1 ATGTATCGATACA
3291981 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3298090 original size:20 final size:20
Alignment explanation
Indices: 3298064--3298141 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
3298054 AATGTCCAAA
3298064 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
3298084 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T-G--TTTCT
*
3298109 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
3298129 TTGTATCGATACA
1 ATGTATCGATACA
3298142 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 28 0.60
22 1 0.02
23 2 0.04
25 16 0.34
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:3298148 original size:13 final size:13
Alignment explanation
Indices: 3298130--3298167 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3298120 CATTTTTCTT
3298130 TGTATCGATACAA
1 TGTATCGATACAA
*
3298143 TGTATCGATACAC
1 TGTATCGATACAA
3298156 TGTATCGATACA
1 TGTATCGATACA
3298168 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3299981 original size:21 final size:21
Alignment explanation
Indices: 3299955--3299996 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3299945 AAATAAATTT
3299955 TTGTTGTGAATTACTTGATTA
1 TTGTTGTGAATTACTTGATTA
3299976 TTGTTGTGAATTACTTGATTA
1 TTGTTGTGAATTACTTGATTA
3299997 AGAGGGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.52
Consensus pattern (21 bp):
TTGTTGTGAATTACTTGATTA
Found at i:3300654 original size:20 final size:20
Alignment explanation
Indices: 3300631--3300703 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3300621 ACAATTCAAA
3300631 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3300651 GTATCGATACATGAAAAACAT
1 GTATCGATACATGTTGCA-AT
3300672 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3300692 GTATCGATACAT
1 GTATCGATACAT
3300704 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3300675 original size:21 final size:20
Alignment explanation
Indices: 3300648--3300724 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 20
3300638 TACATGTTGC
3300648 AATGTATCGATACATGAAAA
1 AATGTATCGATACATGAAAA
****
3300668 ACATGTATCGATACATGTTGC
1 A-ATGTATCGATACATGAAAA
3300689 AATGTATCGATACAT-AAAA
1 AATGTATCGATACATGAAAA
3300708 AAGTTGTATCGATACAT
1 AA--TGTATCGATACAT
3300725 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
21 29 0.63
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:3300682 original size:41 final size:41
Alignment explanation
Indices: 3300631--3300724 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
3300621 ACAATTCAAA
*
3300631 GTATCGATACATGTTGCAATGTATCGATACATGAAAAACAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAACAT
**
3300672 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAACAT
3300713 GTATCGATACAT
1 GTATCGATACAT
3300725 TTCTTGGCAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAACAT
Found at i:3300781 original size:13 final size:13
Alignment explanation
Indices: 3300763--3300788 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3300753 TACAGCAAGT
3300763 ATGTATCGATACA
1 ATGTATCGATACA
3300776 ATGTATCGATACA
1 ATGTATCGATACA
3300789 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3305596 original size:52 final size:52
Alignment explanation
Indices: 3305518--3305646 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
3305508 CGAAATATGA
* *
3305518 AAATTTGCCTGCATGTATCTATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
** *
3305570 AAATTTGCCTATATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
3305622 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3305647 AAGATTAGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:3305656 original size:52 final size:52
Alignment explanation
Indices: 3305518--3305666 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 52
3305508 CGAAATATGA
* * *
3305518 AAATTTGCCTGCATGTATCTATACATTTCA-TAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACA-ATCATTAGTGTATCGATACATCTGGGC
** **
3305570 AAATTTGCCTATATGTATCGATAC-ATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACAATCAT-TAGTGTATCGATACATCTGGGC
**
3305622 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAATCATTAGTGTATCGATACA
3305667 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.01
52 79 0.96
53 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACAATCATTAGTGTATCGATACATCTGGGC
Found at i:3305673 original size:13 final size:13
Alignment explanation
Indices: 3305655--3305679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3305645 CAAAGATTAG
3305655 TGTATCGATACAA
1 TGTATCGATACAA
3305668 TGTATCGATACA
1 TGTATCGATACA
3305680 TTTCAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3305759 original size:13 final size:13
Alignment explanation
Indices: 3305741--3305765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3305731 ACAAAACTTA
3305741 TGTATCGATACAT
1 TGTATCGATACAT
3305754 TGTATCGATACA
1 TGTATCGATACA
3305766 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3305761 original size:32 final size:32
Alignment explanation
Indices: 3305720--3305784 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
3305710 AGTAGCTTAA
3305720 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
3305752 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
3305784 A
1 A
3305785 ACACTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAC
Found at i:3305795 original size:20 final size:19
Alignment explanation
Indices: 3305722--3305805 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
3305712 TAGCTTAAAT
*
3305722 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
3305741 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
3305754 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
3305773 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
3305793 TGTATCGATACAA
1 TGTATCGATACAA
3305806 ATCATTGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 5 0.09
18 1 0.02
19 25 0.44
20 16 0.28
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:3308231 original size:28 final size:27
Alignment explanation
Indices: 3308171--3308243 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
3308161 TTTTGGAGAT
*
3308171 AATAACGGGGTTGGAGTGTTCCCTTAA
1 AATAACGGGGTTGGAGTGTTCCCATAA
*
3308198 AGATAACGGGGTTGGAGTG-TCACCGATGA
1 A-ATAACGGGGTTGGAGTGTTC-CC-ATAA
* *
3308227 AATAATGAGGTTGGAGT
1 AATAACGGGGTTGGAGT
3308244 ATCCTCGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
27 3 0.08
28 33 0.85
29 3 0.08
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (27 bp):
AATAACGGGGTTGGAGTGTTCCCATAA
Found at i:3308335 original size:52 final size:50
Alignment explanation
Indices: 3308259--3308388 Score: 152
Period size: 51 Copynumber: 2.5 Consensus size: 50
3308249 CGATTGTGAA
** * * *
3308259 AAAATAAAATTGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTT
1 AAAATAAAACCGGGGTTGGAGTATCCCCGATT-AAGAAAAATTAGTGTTTT
* **
3308310 GAAAATAAAACCGGGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTT
1 -AAAATAAAACCGGGGTTGGAGTATCCCCGATTAAGAAAAATTAGTGTTTT
*
3308361 AGAAATAAAACCGGGGTTAGAGTATCCC
1 A-AAATAAAACCGGGGTTGGAGTATCCC
3308389 TGATCGTGAG
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 1 0.01
51 39 0.57
52 28 0.41
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (50 bp):
AAAATAAAACCGGGGTTGGAGTATCCCCGATTAAGAAAAATTAGTGTTTT
Found at i:3308371 original size:51 final size:50
Alignment explanation
Indices: 3308273--3308439 Score: 181
Period size: 51 Copynumber: 3.3 Consensus size: 50
3308263 TAAAATTGGA
* ** * *
3308273 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCTGATT-GTGAAAAATTAGTGTTTTG-AAATAAAACCGGG
3308325 GTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTT-GAAATAAAACCGGG
* * * * * * *
3308376 GTTAGAGTATCCCTGATCGTGAGAAATCAATATTTTGGAAATAAAGCCGGG
1 GTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTT-GAAATAAAACCGGG
*
3308427 GTTGGGGTATCCC
1 GTTGGAGTATCCC
3308440 CTCGGAGGTA
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
51 81 0.82
52 18 0.18
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTGAAATAAAACCGGG
Found at i:3308466 original size:28 final size:27
Alignment explanation
Indices: 3308426--3308497 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
3308416 ATAAAGCCGG
* **
3308426 GGTTGGGGTATCCCCTCGGAGGTAACGA
1 GGTTGGAGTATCCCCGAGGA-GTAACGA
* *
3308454 GGTTGGAGTATCCCCGATGATTAACGA
1 GGTTGGAGTATCCCCGAGGAGTAACGA
3308481 GGTTGGAGTATCCCCGA
1 GGTTGGAGTATCCCCGA
3308498 TTATGAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.24
Consensus pattern (27 bp):
GGTTGGAGTATCCCCGAGGAGTAACGA
Found at i:3308597 original size:51 final size:52
Alignment explanation
Indices: 3308482--3308603 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 52
3308472 GATTAACGAG
* *
3308482 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTTGAAAATAAAATCGGA
*
3308535 GTTGTAGTATCCCCGATTAT-AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTTGAAAATAAAATCGGA
*
3308586 GTTAGGA-TATCCCTGATT
1 GTT-GGAGTATCCCCGATT
3308604 GCGGAGAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
51 31 0.50
52 3 0.05
53 28 0.45
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:3310990 original size:34 final size:33
Alignment explanation
Indices: 3310947--3311010 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
3310937 AACTTCCTAG
*
3310947 ATGTATCGATACAAAGAATAGATGTATCGATGCA
1 ATGTATCGATACAAAGAA-AAATGTATCGATGCA
*
3310981 ATGTATCGATACACAGAAAAATGTATCGAT
1 ATGTATCGATACAAAGAAAAATGTATCGAT
3311011 ACATTTCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 11 0.39
34 17 0.61
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATGCA
Found at i:3311055 original size:13 final size:13
Alignment explanation
Indices: 3311037--3311088 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
3311027 AGCTTCCTAG
3311037 CGATACATTGTAT
1 CGATACATTGTAT
3311050 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
3311069 CGATACATTGTAT
1 CGATACATTGTAT
3311082 CGATACA
1 CGATACA
3311089 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:3311069 original size:19 final size:18
Alignment explanation
Indices: 3311045--3311107 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
3311035 AGCGATACAT
3311045 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
3311064 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
3311077 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
3311096 TGTATCGATACA
1 TGTATCGATACA
3311108 TTTACTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:3311078 original size:32 final size:32
Alignment explanation
Indices: 3311037--3311109 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
3311027 AGCTTCCTAG
3311037 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
3311069 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
3311101 CGATACATT
1 CGATACATT
3311110 TACTGAATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:3313376 original size:19 final size:19
Alignment explanation
Indices: 3313347--3313404 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
3313337 ATGTATCGAT
* *
3313347 ACATTGCATCGATACATGT
1 ACATTGTATCGATACATGG
*
3313366 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
3313385 ACAAATTGTATCGATACATG
1 AC--ATTGTATCGATACATG
3313405 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:3313470 original size:13 final size:13
Alignment explanation
Indices: 3313449--3313479 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3313439 CGATACATGG
*
3313449 TACAATGTATCGA
1 TACATTGTATCGA
3313462 TACATTGTATCGA
1 TACATTGTATCGA
3313475 TACAT
1 TACAT
3313480 GAAGGAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:3313478 original size:33 final size:31
Alignment explanation
Indices: 3313436--3313532 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 31
3313426 TCACTATTTA
3313436 TATCGATACATGGTACAATGTATCGATACATTG
1 TATCGATACATGG-A-AATGTATCGATACATTG
*
3313469 TATCGATACATGAAGGAATGTATCGATACATTG
1 TATCGATACATG--GAAATGTATCGATACATTG
*
3313502 AATCGATACATGAAGAAATGTATCGATACAT
1 TATCGATACATG--GAAATGTATCGATACAT
3313533 AGCTTGTAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 58 0.98
35 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (31 bp):
TATCGATACATGGAAATGTATCGATACATTG
Found at i:3314889 original size:87 final size:87
Alignment explanation
Indices: 3314743--3314902 Score: 241
Period size: 87 Copynumber: 1.8 Consensus size: 87
3314733 TTTGGTTTTC
*
3314743 TAAGGCTTGACCTCCTTAGACTAGTGCCAACTAATATGGACTTAACTCGAACTTAGGTGCCACCA
1 TAAGGCTTAACCTCCTTAGACTAGTGCCAACTAATATGGACTTAACTCGAACTTAGGTGCCACCA
3314808 ACTTGTGTGAGCTTTGACATCT
66 ACTTGTGTGAGCTTTGACATCT
** * * *
3314830 TAAGGCTTAACCTTTTTAGAC-AGGTGCCAACTAATTTGGACTTGACTCGAACTTAGGTGCCACT
1 TAAGGCTTAACCTCCTTAGACTA-GTGCCAACTAATATGGACTTAACTCGAACTTAGGTGCCACC
*
3314894 AGCTTGTGT
65 AACTTGTGT
3314903 AGGCTTCGAC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
86 1 0.02
87 64 0.98
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (87 bp):
TAAGGCTTAACCTCCTTAGACTAGTGCCAACTAATATGGACTTAACTCGAACTTAGGTGCCACCA
ACTTGTGTGAGCTTTGACATCT
Found at i:3314982 original size:31 final size:31
Alignment explanation
Indices: 3314884--3314982 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 31
3314874 ACTCGAACTT
*
3314884 AGGTGCCACTAGCTTGTGTA-GGCTTCGACTC
1 AGGTGCCACTAGCTTGTG-AGGGCTTAGACTC
** * * *
3314915 AGGTGCTGCTAACTCGTGAGGGCTTAAACTC
1 AGGTGCCACTAGCTTGTGAGGGCTTAGACTC
* * * *
3314946 GGGTGCCACTAGCTTGTGCGGGCTTTGACTA
1 AGGTGCCACTAGCTTGTGAGGGCTTAGACTC
3314977 AGGTGC
1 AGGTGC
3314983 TATCAACTCA
Statistics
Matches: 51, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
30 1 0.02
31 50 0.98
ACGTcount: A:0.17, C:0.23, G:0.32, T:0.27
Consensus pattern (31 bp):
AGGTGCCACTAGCTTGTGAGGGCTTAGACTC
Found at i:3314991 original size:62 final size:62
Alignment explanation
Indices: 3314885--3315001 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 62
3314875 CTCGAACTTA
* * *
3314885 GGTGCCACTAGCTTGTGTAGGCTTCGACTCAGGTGCTGCTAACTCGTGAGGGCTTAAACTCG
1 GGTGCCACTAGCTTGTGCAGGCTTCGACTAAGGTGCTGCTAACTCATGAGGGCTTAAACTCG
* * * *
3314947 GGTGCCACTAGCTTGTGCGGGCTTTGACTAAGGTGCT-ATCAACTCATGTGGGCTT
1 GGTGCCACTAGCTTGTGCAGGCTTCGACTAAGGTGCTGCT-AACTCATGAGGGCTT
3315002 TGACATTCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 1 0.02
62 46 0.98
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (62 bp):
GGTGCCACTAGCTTGTGCAGGCTTCGACTAAGGTGCTGCTAACTCATGAGGGCTTAAACTCG
Found at i:3315314 original size:180 final size:175
Alignment explanation
Indices: 3314813--3315361 Score: 578
Period size: 180 Copynumber: 3.1 Consensus size: 175
3314803 CACCAACTTG
* **
3314813 TGTGAGCTTTGACA-TCTTAAGGCTTAACCTTTTTAGACAGGTGCCAACTAATTTGGACTTGACT
1 TGTGGGCTTTGACATTC-TAAGGCTTAACCTCCTTAGACAGGTGCCAACTAATTTGGACTTGACT
* * * *
3314877 CGAACTTAGGTGCCACTAGCTTGTGTAGGCTTCGACTCAGGTGCTGCTAACTCGTGAGGGCTTAA
65 CGAACTTAAGTGCCACCAGCTTGTG-A-GCTTCGACTCAGGTTC-GCCAACTCGTGAGGGCTT-A
* * * * * * *
3314942 ACTCGGGTGCCACTAGCTTGTGCGGGCTTTGACTAAGGTGCTATCAACTCA
126 ACTC-GGTGCCACCAACTTGTACGGGCTTTAACTAGGGTGCTACCAATTCA
*
3314993 TGTGGGCTTTGACATTCTAAGGCTTAACCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTC
1 TGTGGGCTTTGACATTCTAAGGCTTAACCTCCTTAGACAGGTGCCAACTAATTTGGACTTGACTC
* * * * ** * *
3315058 GAACTTAAGTGCCACCAGTTTGTGTGGGCTTCGACTCAGGTGTCGTCAGCTTATGCGGGTTGTAA
66 GAACTTAAGTGCCACCAG-CT-TGTGAGCTTCGACTCAGGT-TCGCCAACTCGTGAGGGCT-TAA
* * * *
3315123 CTATGGTGCCACCAACTTGTACGAGCTTTAACTGGGGTACTACCAATTCA
127 CT-CGGTGCCACCAACTTGTACGGGCTTTAACTAGGGTGCTACCAATTCA
* *
3315173 TGTGGGCTTTGACATTCTAAGGCTTGACCTCCTTAGACAGGTGCCAACTAATTTAGACTTGACTC
1 TGTGGGCTTTGACATTCTAAGGCTTAACCTCCTTAGACAGGTGCCAACTAATTTGGACTTGACTC
* * * * * * **
3315238 AAACTTATGTACCACCAACTTCCATGAGCTTTGACTCAGGTATCGCCAACTCGTGTTGGCTTAGA
66 GAACTTAAGTGCCACCAGCTT--GTGAGCTTCGACTCAGGT-TCGCCAACTCGTGAGGGCTTA-A
* * * *
3315303 CTCGAGTGCCACCAACTTATACGGGCTTTAACTAGGGTGCCACTAATTCG
127 CTCG-GTGCCACCAACTTGTACGGGCTTTAACTAGGGTGCTACCAATTCA
3315353 TGTGGGCTT
1 TGTGGGCTT
3315362 ATAAAAGAGG
Statistics
Matches: 305, Mismatches: 54, Indels: 20
0.80 0.14 0.05
Matches are distributed among these distances:
178 1 0.00
179 4 0.01
180 291 0.95
181 5 0.02
182 4 0.01
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (175 bp):
TGTGGGCTTTGACATTCTAAGGCTTAACCTCCTTAGACAGGTGCCAACTAATTTGGACTTGACTC
GAACTTAAGTGCCACCAGCTTGTGAGCTTCGACTCAGGTTCGCCAACTCGTGAGGGCTTAACTCG
GTGCCACCAACTTGTACGGGCTTTAACTAGGGTGCTACCAATTCA
Found at i:3315542 original size:43 final size:43
Alignment explanation
Indices: 3315452--3315585 Score: 182
Period size: 43 Copynumber: 3.1 Consensus size: 43
3315442 AAAAAAGAAA
* **
3315452 GAAAAAA-AGAAAAA-AATGTGTCTTGCTCCTTGATCACAAAG
1 GAAAAAAGAAAAAAAGAATGTGTCTTGCTCCTTGAGGACAAAG
3315493 GAAAAAAAGAAAAAAAGAATGTGTCTTGCTCCTTGAGGACAAAG
1 G-AAAAAAGAAAAAAAGAATGTGTCTTGCTCCTTGAGGACAAAG
* * *
3315537 GAAAAAAGAAAAAAGGAATGTGTCCTGCTCCTTGAGGATAAAAG
1 GAAAAAAGAAAAAAAGAATGTGTCTTGCTCCTTGAGGA-CAAAG
3315581 GAAAA
1 GAAAA
3315586 GAAGTATGCA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
41 1 0.01
42 6 0.07
43 41 0.49
44 35 0.42
ACGTcount: A:0.48, C:0.12, G:0.22, T:0.19
Consensus pattern (43 bp):
GAAAAAAGAAAAAAAGAATGTGTCTTGCTCCTTGAGGACAAAG
Found at i:3315581 original size:44 final size:42
Alignment explanation
Indices: 3315449--3315585 Score: 179
Period size: 44 Copynumber: 3.2 Consensus size: 42
3315439 AGGAAAAAAG
* **
3315449 AAAGAAAAAAAG-AAAAA-AATGTGTCTTGCTCCTTGATCAC
1 AAAGGAAAAAAGAAAAAAGAATGTGTCTTGCTCCTTGAGGAC
3315489 AAAGGAAAAAAAGAAAAAAAGAATGTGTCTTGCTCCTTGAGGAC
1 AAAGG-AAAAAAG-AAAAAAGAATGTGTCTTGCTCCTTGAGGAC
* *
3315533 AAAGGAAAAAAGAAAAAAGGAATGTGTCCTGCTCCTTGAGGATA
1 AAAGGAAAAAAGAAAAAA-GAATGTGTCTTGCTCCTTGAGGA-C
3315577 AAAGGAAAA
1 AAAGGAAAA
3315586 GAAGTATGCA
Statistics
Matches: 86, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
40 4 0.05
41 7 0.08
42 6 0.07
43 34 0.40
44 35 0.41
ACGTcount: A:0.49, C:0.12, G:0.21, T:0.18
Consensus pattern (42 bp):
AAAGGAAAAAAGAAAAAAGAATGTGTCTTGCTCCTTGAGGAC
Found at i:3315742 original size:41 final size:40
Alignment explanation
Indices: 3315519--3315827 Score: 133
Period size: 41 Copynumber: 7.7 Consensus size: 40
3315509 GAATGTGTCT
* * **
3315519 TGCTCCTTGAGGACAAAGGAAAAAAGAAAAAAGGAATGTGTCC
1 TGCTCCTTGAGGACAAA-GAGAAAAG--AAAATGAATGCATCC
* *
3315562 TGCTCCTTGAGGATAAA-AGGAAAAG--AA-GTATGCATCC
1 TGCTCCTTGAGGACAAAGA-GAAAAGAAAATGAATGCATCC
* *
3315599 TACTCTTTGAGGACAAA-AGAAAAGGAGAAAAAT-AATGTC-TCC
1 TGCTCCTTGAGGACAAAGAG-AAA--AG-AAAATGAATG-CATCC
** * * **
3315641 TATTCCTTGAGGACAAAG-GGAAA-AAAA-G-ATACATTG
1 TGCTCCTTGAGGACAAAGAGAAAAGAAAATGAATGCATCC
* *
3315677 TGCT-CTTCGAAGATAAAG-GAAAAAGAAAATGAAGTGCATCC
1 TGCTCCTT-GAGGACAAAGAG-AAAAGAAAATGAA-TGCATCC
* *** **
3315718 TGCTCTTTGAGGACAAAGAGAAAAGGGGATGAAATGGGTCC
1 TGCTCCTTGAGGACAAAGAGAAAAGAAAATG-AATGCATCC
* * * *
3315759 TGCTCCTTGAAGACAAAAGAAAAAGGAGAAAAAGAATTCATCC
1 TGCTCCTTGAGGAC-AAAGAGAAA--AGAAAATGAATGCATCC
*
3315802 TGATCCTTGAGGACAAAG-GAAAAGAA
1 TGCTCCTTGAGGACAAAGAGAAAAGAA
3315828 GTGTATCCTG
Statistics
Matches: 198, Mismatches: 44, Indels: 52
0.67 0.15 0.18
Matches are distributed among these distances:
35 4 0.02
36 15 0.08
37 32 0.16
38 6 0.03
39 8 0.04
40 1 0.01
41 47 0.24
42 46 0.23
43 35 0.18
44 4 0.02
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (40 bp):
TGCTCCTTGAGGACAAAGAGAAAAGAAAATGAATGCATCC
Found at i:3317000 original size:10 final size:9
Alignment explanation
Indices: 3316983--3317035 Score: 52
Period size: 9 Copynumber: 5.3 Consensus size: 9
3316973 AATACCTTTC
3316983 TTTTTTTTG
1 TTTTTTTTG
3316992 TTATTTTTTG
1 TT-TTTTTTG
3317002 TTTTCGTTTTG
1 TTTT--TTTTG
*
3317013 TTTTGTTTTTT
1 -TTT-TTTTTG
3317024 TTTTTTTTG
1 TTTTTTTTG
3317033 TTT
1 TTT
3317036 AGGCATAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 12 0.32
10 12 0.32
11 9 0.24
12 3 0.08
13 1 0.03
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:3317000 original size:11 final size:10
Alignment explanation
Indices: 3316983--3317035 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
3316973 AATACCTTTC
3316983 TTTTTTTTGT
1 TTTTTTTTGT
*
3316993 TATTTTTTGT
1 TTTTTTTTGT
*
3317003 TTTCGTTTTGT
1 TTT-TTTTTGT
3317014 TTTGTTTTT-T
1 TTT-TTTTTGT
3317024 TTTTTTTTGT
1 TTTTTTTTGT
3317034 TT
1 TT
3317036 AGGCATAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 5 0.14
10 18 0.50
11 13 0.36
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:3317015 original size:5 final size:5
Alignment explanation
Indices: 3316983--3317035 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
3316973 AATACCTTTC
* *
3316983 TTTT- TTTTG TTATT- TTTTG TTTTCG TTTTG TTTTG TTTTT TTTTT TTTTG
1 TTTTG TTTTG TT-TTG TTTTG TTTT-G TTTTG TTTTG TTTTG TTTTG TTTTG
3317033 TTT
1 TTT
3317036 AGGCATAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
4 6 0.14
5 30 0.70
6 7 0.16
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (5 bp):
TTTTG
Found at i:3321087 original size:13 final size:13
Alignment explanation
Indices: 3321069--3321096 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3321059 ATACAAAGAT
3321069 CAATGTATCGATA
1 CAATGTATCGATA
3321082 CAATGTATCGATA
1 CAATGTATCGATA
3321095 CA
1 CA
3321097 TTGAATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3321174 original size:19 final size:19
Alignment explanation
Indices: 3321148--3321210 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
3321138 AGTGATACAT
3321148 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
3321167 TTTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
3321180 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
3321199 TGTATCGATACA
1 TGTATCGATACA
3321211 TTTACTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
16 6 0.17
18 1 0.03
19 20 0.56
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:3321182 original size:32 final size:32
Alignment explanation
Indices: 3321141--3321212 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
3321131 GCTTTGTAGT
*
3321141 GATACATTGTATCGATACAACACTTATTTATC
1 GATACATTGTATCGATACAACACTTATGTATC
3321173 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
3321205 GATACATT
1 GATACATT
3321213 TACTGTTTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (32 bp):
GATACATTGTATCGATACAACACTTATGTATC
Found at i:3322044 original size:52 final size:49
Alignment explanation
Indices: 3321971--3322106 Score: 137
Period size: 52 Copynumber: 2.7 Consensus size: 49
3321961 TTGAAGGAAA
** *
3321971 ATGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGGCTCAAAAATGTTAAAG
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTCAAAAATG---AAG
* * * * * * *
3322023 ATGCCAATATGCTGATTCAAGGCTAACGATATCGGACTTAAAGATGAAG
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTCAAAAATGAAG
* *
3322072 GTGCCAATGTGCTGATTCAAGGACAGCGACATTGG
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
3322107 TCTTAAAGAC
Statistics
Matches: 67, Mismatches: 17, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
49 31 0.46
52 36 0.54
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.22
Consensus pattern (49 bp):
ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTCAAAAATGAAG
Found at i:3322112 original size:49 final size:49
Alignment explanation
Indices: 3321972--3322345 Score: 206
Period size: 49 Copynumber: 7.9 Consensus size: 49
3321962 TGAAGGAAAA
* ** * * *
3321972 TGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGGCTCAAAAATGTTAAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATG---AAGG
* * * * *
3322024 TGCCAATATGCTGATTCAAGGCTAACGATATCGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
* * * *
3322073 TGCCAATGTGCTGATTCAAGGACAGCGACATTGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
* * * * *
3322121 TGTCAACATGCCGATTCAAAGCCAGCGATATTGGGC-T-----T--A--
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
* * * ** **
3322160 TGCCAATGTGCTGATTCAGGGCCAGCAACATTGGTTTTAAAGATGCCGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
* * * * * **
3322209 TACCAATATGTTGATTCAAGGCCAACGATATCGAACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
* * * * *
3322252 TGTCGATATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGG-CTTAAAGATGAAGG
* * *
3322302 TGCCAATATGCTGGTTCAAGGCCAGCGATATTGGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTA-AAGA
3322346 AGATGCCACC
Statistics
Matches: 238, Mismatches: 65, Indels: 40
0.69 0.19 0.12
Matches are distributed among these distances:
39 26 0.11
40 1 0.00
41 1 0.00
43 29 0.12
44 2 0.01
45 2 0.01
47 1 0.00
48 33 0.14
49 69 0.29
50 39 0.16
52 35 0.15
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
Found at i:3322427 original size:28 final size:28
Alignment explanation
Indices: 3322362--3322434 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
3322352 CACCAACTTG
3322362 TGTGGGCTTTTGAAAAGGTTGCATCAACT
1 TGTGGGCTTTTG-AAAGGTTGCATCAACT
* **
3322391 TGTGTGCTTTTG-AAGGTTGCCATTGACT
1 TGTGGGCTTTTGAAAGGTTG-CATCAACT
3322419 TGTGGGC-TTTGAAAGG
1 TGTGGGCTTTTGAAAGG
3322435 GGTGCTACCG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 11 0.29
28 16 0.42
29 11 0.29
ACGTcount: A:0.19, C:0.12, G:0.32, T:0.37
Consensus pattern (28 bp):
TGTGGGCTTTTGAAAGGTTGCATCAACT
Found at i:3322477 original size:27 final size:27
Alignment explanation
Indices: 3322415--3322489 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
3322405 GGTTGCCATT
*
3322415 GACTTGTGGGCTTTGAAAGGGGTGCTACC
1 GACTTGTGGGC-TT-AAAAGGGTGCTACC
3322444 GACTTGTGGGCTTAAAAGGGTGCTA-C
1 GACTTGTGGGCTTAAAAGGGTGCTACC
* *
3322470 GAAGTTGTGGACTTAAAAGG
1 G-ACTTGTGGGCTTAAAAGG
3322490 AAAAAGAGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 2 0.05
27 27 0.64
28 2 0.05
29 11 0.26
ACGTcount: A:0.24, C:0.13, G:0.36, T:0.27
Consensus pattern (27 bp):
GACTTGTGGGCTTAAAAGGGTGCTACC
Found at i:3322495 original size:34 final size:34
Alignment explanation
Indices: 3322457--3322790 Score: 442
Period size: 34 Copynumber: 9.8 Consensus size: 34
3322447 TTGTGGGCTT
* * *
3322457 AAAAGGGTGCTACGAAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGA
* *
3322491 AAAAGAGTGTCACGGAGTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGA
3322525 AAAAGAGTGCCAC-AGAGTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACGA-AGTTGTGGGCTTAAAAGGA
*
3322559 AAAAAAGTGCCACGAAGTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGA
*
3322593 AAAAGAGTGCCAC-AGAGTTGTGGGTTTAAAAGGA
1 AAAAGAGTGCCACGA-AGTTGTGGGCTTAAAAGGA
*
3322627 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGA
3322661 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGA
* * *
3322695 AAAAGAATGCCAC-AGAGTTGTGAGCTTTAAAAAGA
1 AAAAGAGTGCCACGA-AGTTGTGGGC-TTAAAAGGA
* * * * *
3322730 AAAA-AGGTGCCACGGACTTATGGACTTAGAAGGA
1 AAAAGA-GTGCCACGAAGTTGTGGGCTTAAAAGGA
*
3322764 AAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGAGTGCCACGAAGTTGTGGGCTT
3322791 TTGACAGGGT
Statistics
Matches: 264, Mismatches: 27, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.01
34 236 0.89
35 26 0.10
ACGTcount: A:0.38, C:0.11, G:0.32, T:0.19
Consensus pattern (34 bp):
AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGA
Found at i:3322616 original size:102 final size:102
Alignment explanation
Indices: 3322457--3322790 Score: 499
Period size: 102 Copynumber: 3.3 Consensus size: 102
3322447 TTGTGGGCTT
* * * * *
3322457 AAAAGGGTGCTACGAAGTTGTGGACTTAAAAGGAAAAAGAGTGTCACGGAGTTGTGGGCTTAAAA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAA
*
3322522 GGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGA
66 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
* *
3322559 AAAAAAGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGTTTAAAA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAA
3322624 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
66 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
* *
3322661 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAAGAATGCCACAGAGTTGTGAGCTTTAAA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TTAAA
* * * * *
3322726 AAGAAAAA-AGGTGCCACGGACTTATGGACTTAGAAGGA
65 AGGAAAAAGA-GTGCCACGGAGTTGTGGGCTTAAAAGGA
*
3322764 AAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGAGTGCCACGAAGTTGTGGGCTT
3322791 TTGACAGGGT
Statistics
Matches: 212, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
102 150 0.71
103 62 0.29
ACGTcount: A:0.38, C:0.11, G:0.32, T:0.19
Consensus pattern (102 bp):
AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAA
GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
Found at i:3324225 original size:1 final size:1
Alignment explanation
Indices: 3324221--3324278 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
3324211 TTTGTCGTTG
* * * * * * *
3324221 TTTTTTTTTCTTTTTTTTGTTTTTTTCTTCTTTTTTTTTGTTTGTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3324279 GTATGGAGGA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:3324242 original size:19 final size:19
Alignment explanation
Indices: 3324218--3324280 Score: 83
Period size: 19 Copynumber: 3.2 Consensus size: 19
3324208 CTTTTTGTCG
3324218 TTGTTTTTTTTTCTTTTTT
1 TTGTTTTTTTTTCTTTTTT
3324237 TTGTTTTTTTCTTCTTTTTTT
1 TTGTTTTTTT-TTC-TTTTTT
*
3324258 TTGTTTGTTTTGT-TTTTTT
1 TTGTTT-TTTTTTCTTTTTT
3324277 TTGT
1 TTGT
3324281 ATGGAGGATG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 20 0.50
20 3 0.08
21 13 0.32
22 4 0.10
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.86
Consensus pattern (19 bp):
TTGTTTTTTTTTCTTTTTT
Found at i:3324246 original size:20 final size:20
Alignment explanation
Indices: 3324221--3324280 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
3324211 TTTGTCGTTG
3324221 TTTTTTTTTCTTTTTTTTGT
1 TTTTTTTTTCTTTTTTTTGT
*
3324241 TTTTTTCTTCTTTTTTTTTGT
1 TTTTTTTTTC-TTTTTTTTGT
* *
3324262 TTGTTTTGT-TTTTTTTTGT
1 TTTTTTTTTCTTTTTTTTGT
3324281 ATGGAGGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.29
20 9 0.26
21 16 0.46
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (20 bp):
TTTTTTTTTCTTTTTTTTGT
Done.