Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008387.1 Hibiscus syriacus cultivar Beakdansim tig00111151_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2491990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2312841 original size:2 final size:2
Alignment explanation
Indices: 2312783--2312832 Score: 50
Period size: 2 Copynumber: 25.0 Consensus size: 2
2312773 TTAAGTAAAC
* *
2312783 TA TA TA GTA TA TA TA TA -A TA TA TA GTT TA TC TA TA TA TA T- TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
2312825 TA TA TA TA
1 TA TA TA TA
2312833 GTTTATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
1 2 0.05
2 35 0.88
3 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2312841 original size:9 final size:8
Alignment explanation
Indices: 2312783--2312832 Score: 50
Period size: 7 Copynumber: 6.2 Consensus size: 8
2312773 TTAAGTAAAC
2312783 TATATAGTA
1 TATATA-TA
2312792 TATATATA
1 TATATATA
2312800 -ATATATA
1 TATATATA
* *
2312807 GTTTATCTA
1 -TATATATA
2312816 TATATAT-
1 TATATATA
2312823 TATATATA
1 TATATATA
2312831 TA
1 TA
2312833 GTTTATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
7 14 0.41
8 9 0.26
9 11 0.32
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (8 bp):
TATATATA
Found at i:2317487 original size:29 final size:26
Alignment explanation
Indices: 2317418--2317615 Score: 133
Period size: 22 Copynumber: 8.0 Consensus size: 26
2317408 AAATTTAACA
2317418 ATATAGTTTATACCTATATAGTTTATAT
1 ATATAGTTTATA-C-ATATAGTTTATAT
* *
2317446 ATATTGCTTATACATATAGTTTATAATTT
1 ATATAGTTTATACATATAGTTTAT-A--T
*
2317475 ATATAGTTTATACATATAGTTTATCT
1 ATATAGTTTATACATATAGTTTATAT
*
2317501 ATATAGATTAT--ATATAGTTTATAT
1 ATATAGTTTATACATATAGTTTATAT
*
2317525 AAATAG-TT-TAC--ATAGTTTATAGT
1 ATATAGTTTATACATATAGTTTATA-T
*
2317548 A-ATAG---AT-TATATAG-TT-TAT
1 ATATAGTTTATACATATAGTTTATAT
* *
2317567 ATATAGTTTAT--ATATA-ATT-CAT
1 ATATAGTTTATACATATAGTTTATAT
* *
2317589 ATATAGTTTATATATATAGTATATAT
1 ATATAGTTTATACATATAGTTTATAT
2317615 A
1 A
2317616 GTTTATATAT
Statistics
Matches: 139, Mismatches: 13, Indels: 38
0.73 0.07 0.20
Matches are distributed among these distances:
19 2 0.01
20 6 0.04
21 3 0.02
22 39 0.28
23 6 0.04
24 22 0.16
25 1 0.01
26 25 0.18
27 2 0.01
28 10 0.07
29 23 0.17
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (26 bp):
ATATAGTTTATACATATAGTTTATAT
Found at i:2317505 original size:42 final size:42
Alignment explanation
Indices: 2317418--2317512 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
2317408 AAATTTAACA
* *
2317418 ATATAGTTTAT-ACCTATATAGTTTATATATATTGCTTATAC
1 ATATAGTTTATAACCTATATAGTTTATACATATAGCTTATAC
** *
2317459 ATATAGTTTATAATTTATATAGTTTATACATATAGTTTAT-C
1 ATATAGTTTATAACCTATATAGTTTATACATATAGCTTATAC
*
2317500 TATATAGATTATA
1 -ATATAGTTTATA
2317513 TATAGTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 12 0.26
42 34 0.74
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.49
Consensus pattern (42 bp):
ATATAGTTTATAACCTATATAGTTTATACATATAGCTTATAC
Found at i:2317526 original size:55 final size:54
Alignment explanation
Indices: 2317418--2317625 Score: 155
Period size: 55 Copynumber: 3.7 Consensus size: 54
2317408 AAATTTAACA
* *
2317418 ATATAGTTTATACCTATATAGTTTATATATATTGCTTATACATATAG-TT-TATAATTT
1 ATATAGTTTATA-C-ATATAGTTTAT-TATATAGATTAT--ATATAGTTTATATAATTT
2317475 ATATAGTTTATACATATAGTTTATCTATATAGATTATATATAGTTTATATAAATAGTTT
1 ATATAGTTTATACATATAGTTTAT-TATATAGATTATATATAGTTTATAT--A-A-TTT
* * *
2317534 ACATAGTTTATA-GTAATAG---ATTATATAGTTTATATATAGTTTATATATAATTCAT
1 ATATAGTTTATACAT-ATAGTTTATTATATAGATTATATATAG-TT-TATATAATT--T
* *
2317589 ATATAGTTTATATATATAG--TA-TATATAGTTTATATAT
1 ATATAGTTTATACATATAGTTTATTATATAGATTATATAT
2317626 GTCACACCTC
Statistics
Matches: 130, Mismatches: 8, Indels: 28
0.78 0.05 0.17
Matches are distributed among these distances:
53 8 0.06
54 3 0.02
55 74 0.57
56 7 0.05
57 18 0.14
58 2 0.02
59 18 0.14
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (54 bp):
ATATAGTTTATACATATAGTTTATTATATAGATTATATATAGTTTATATAATTT
Found at i:2317571 original size:13 final size:13
Alignment explanation
Indices: 2317418--2317625 Score: 143
Period size: 13 Copynumber: 16.2 Consensus size: 13
2317408 AAATTTAACA
2317418 ATATAGTTTATACCT
1 ATATAGTTTATA--T
2317433 ATATAGTTTATAT
1 ATATAGTTTATAT
* * *
2317446 ATATTGCTTATAC
1 ATATAGTTTATAT
2317459 ATATAGTTTATAATTT
1 ATATAGTTTAT-A--T
*
2317475 ATATAGTTTATAC
1 ATATAGTTTATAT
*
2317488 ATATAGTTTATCT
1 ATATAGTTTATAT
*
2317501 ATATAG-AT-TAT
1 ATATAGTTTATAT
2317512 ATATAGTTTATAT
1 ATATAGTTTATAT
*
2317525 AAATAGTTTACATAGT
1 ATATAGTTT--ATA-T
* * *
2317541 TTATAGTAATAGATT
1 ATATAGT-TTATA-T
2317556 ATATAG-TT-TAT
1 ATATAGTTTATAT
2317567 ATATAGTTTATAT
1 ATATAGTTTATAT
*
2317580 ATA-A--TT-CAT
1 ATATAGTTTATAT
2317589 ATATAGTTTATAT
1 ATATAGTTTATAT
2317602 ATATAG----TAT
1 ATATAGTTTATAT
2317611 ATATAGTTTATAT
1 ATATAGTTTATAT
2317624 AT
1 AT
2317626 GTCACACCTC
Statistics
Matches: 151, Mismatches: 23, Indels: 40
0.71 0.11 0.19
Matches are distributed among these distances:
9 14 0.09
10 3 0.02
11 15 0.10
12 8 0.05
13 68 0.45
14 1 0.01
15 24 0.16
16 17 0.11
17 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (13 bp):
ATATAGTTTATAT
Found at i:2317581 original size:22 final size:22
Alignment explanation
Indices: 2317474--2317625 Score: 134
Period size: 22 Copynumber: 6.7 Consensus size: 22
2317464 GTTTATAATT
2317474 TATATAGTTTATACATATAGTTTA
1 TATATAGTTTAT--ATATAGTTTA
*
2317498 TCTATATAGATTATATATAGTTTA
1 --TATATAGTTTATATATAGTTTA
*
2317522 TATAAATAG-TT-TACATAGTTTA
1 TAT--ATAGTTTATATATAGTTTA
*
2317544 TAGTAATAG-AT-TATATAGTTTA
1 TA-T-ATAGTTTATATATAGTTTA
* *
2317566 TATATAGTTTATATATAATTCA
1 TATATAGTTTATATATAGTTTA
*
2317588 TATATAGTTTATATATA-TAGTA
1 TATATAGTTTATATATAGT-TTA
2317610 TATATAGTTTATATAT
1 TATATAGTTTATATAT
2317626 GTCACACCTC
Statistics
Matches: 111, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
20 4 0.04
21 3 0.03
22 76 0.68
23 3 0.03
24 14 0.13
26 11 0.10
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (22 bp):
TATATAGTTTATATATAGTTTA
Found at i:2320441 original size:24 final size:24
Alignment explanation
Indices: 2320414--2320494 Score: 162
Period size: 24 Copynumber: 3.4 Consensus size: 24
2320404 GCATGGGTAG
2320414 TGCATCGATGCACATGTTAAAGGA
1 TGCATCGATGCACATGTTAAAGGA
2320438 TGCATCGATGCACATGTTAAAGGA
1 TGCATCGATGCACATGTTAAAGGA
2320462 TGCATCGATGCACATGTTAAAGGA
1 TGCATCGATGCACATGTTAAAGGA
2320486 TGCATCGAT
1 TGCATCGAT
2320495 ACACTATAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAAGGA
Found at i:2321269 original size:13 final size:14
Alignment explanation
Indices: 2321240--2321286 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
2321230 ATCATATGAA
*
2321240 ATGTGATAAAGAGCT
1 ATGTGAT-AAGAACT
2321255 ATGTG-TAAGAACT
1 ATGTGATAAGAACT
*
2321268 ATGTGATATGAA-T
1 ATGTGATAAGAACT
2321281 ATGTGA
1 ATGTGA
2321287 ATGTGTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 18 0.62
14 6 0.21
15 5 0.17
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (14 bp):
ATGTGATAAGAACT
Found at i:2321662 original size:7 final size:7
Alignment explanation
Indices: 2321595--2321659 Score: 114
Period size: 7 Copynumber: 9.4 Consensus size: 7
2321585 GCGAAATGAT
2321595 ATATGTG
1 ATATGTG
2321602 ATATGTG
1 ATATGTG
2321609 ATATGTG
1 ATATGTG
2321616 ATATGTG
1 ATATGTG
2321623 ATATGTG
1 ATATGTG
2321630 ATATGTG
1 ATATGTG
2321637 ATATGTG
1 ATATGTG
2321644 ATATGT-
1 ATATGTG
*
2321650 ATAAGTG
1 ATATGTG
2321657 ATA
1 ATA
2321660 AGTTAGAATC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
6 5 0.09
7 51 0.91
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (7 bp):
ATATGTG
Found at i:2324145 original size:64 final size:64
Alignment explanation
Indices: 2324066--2324201 Score: 177
Period size: 64 Copynumber: 2.1 Consensus size: 64
2324056 CATGTGTATT
* *
2324066 GATGCACTACCTATGCATCGATACACAAAACACCTTCGATGTTTTCA-TTTTAAGGGGGTGCATC
1 GATGCACTACCTATGCATCGATACACAAAACACATTCGATGTTTCCATTTTTAA-GGGGTGCATC
* * ** *
2324130 GATGCACT-CCTTATGCATCGATGCACTAATTACATTCGATGTTTCCATTTTTAATGGGTGCATC
1 GATGCACTACC-TATGCATCGATACACAAAACACATTCGATGTTTCCATTTTTAAGGGGTGCATC
2324194 GATGCACT
1 GATGCACT
2324202 TATTGTGCAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
63 2 0.03
64 55 0.87
65 6 0.10
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (64 bp):
GATGCACTACCTATGCATCGATACACAAAACACATTCGATGTTTCCATTTTTAAGGGGTGCATC
Found at i:2326202 original size:20 final size:21
Alignment explanation
Indices: 2326161--2326203 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2326151 AATATGTAAA
*
2326161 TCGCGATGCGATTTTCCAAAT
1 TCGCAATGCGATTTTCCAAAT
2326182 TCGCAATGCGATTTT-CAAAT
1 TCGCAATGCGATTTTCCAAAT
2326202 TC
1 TC
2326204 ATAATGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAAAT
Found at i:2326209 original size:20 final size:21
Alignment explanation
Indices: 2326166--2326210 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2326156 GTAAATCGCG
*
2326166 ATGCGATTTTCCAAATTCGCA
1 ATGCGATTTTCCAAATTCACA
*
2326187 ATGCGATTTT-CAAATTCATA
1 ATGCGATTTTCCAAATTCACA
2326207 ATGC
1 ATGC
2326211 TAATTATCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (21 bp):
ATGCGATTTTCCAAATTCACA
Found at i:2326271 original size:57 final size:57
Alignment explanation
Indices: 2326182--2326295 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
2326172 TTTTCCAAAT
* *
2326182 TCGCAATGCGATTTTCAAATTCATAATGCTAATTATCGATATAGGTAAACAGTACTA
1 TCGCAATGCGATTTTCAAATTCACAATGCTAATTACCGATATAGGTAAACAGTACTA
* * *
2326239 TCGCAATGTGATTTTCAAATTCGCAACT-CTAATTACCGATATAGGTAAACTGTACTA
1 TCGCAATGCGATTTTCAAATTCACAA-TGCTAATTACCGATATAGGTAAACAGTACTA
2326296 AAATTTGCGT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 50 0.98
58 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (57 bp):
TCGCAATGCGATTTTCAAATTCACAATGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:2326338 original size:20 final size:20
Alignment explanation
Indices: 2326302--2326353 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2326292 ACTAAAATTT
*
2326302 GCGTTGCGATTTTGAAAATC
1 GCGTTGCGATTTGGAAAATC
2326322 -CGTTGCGGATTTGGAAAATC
1 GCGTTGC-GATTTGGAAAATC
2326342 GCGTTGCGATTT
1 GCGTTGCGATTT
2326354 CGCAACGCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.21
20 17 0.59
21 6 0.21
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (20 bp):
GCGTTGCGATTTGGAAAATC
Found at i:2326380 original size:20 final size:20
Alignment explanation
Indices: 2326353--2326398 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2326343 CGTTGCGATT
*
2326353 TCGCAACGCGAATAGGTAAA
1 TCGCAACGAGAATAGGTAAA
* *
2326373 TTGCAACGATAATAGGTAAA
1 TCGCAACGAGAATAGGTAAA
2326393 TCGCAA
1 TCGCAA
2326399 TGCAATTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (20 bp):
TCGCAACGAGAATAGGTAAA
Found at i:2326487 original size:57 final size:58
Alignment explanation
Indices: 2326392--2326507 Score: 198
Period size: 57 Copynumber: 2.0 Consensus size: 58
2326382 TAATAGGTAA
*
2326392 ATCGCAATGCAATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACT
1 ATCGCAATGCAATTTTCCAAAATCGCAACGCGAATTACCGATATAGGTAAACAGTACT
* *
2326450 ATCGCAATGCGATTTT-CAAATTCGCAACGCGAATTACCGATATAGGTAAACAGTACT
1 ATCGCAATGCAATTTTCCAAAATCGCAACGCGAATTACCGATATAGGTAAACAGTACT
2326507 A
1 A
2326508 AAATTCGCGT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 40 0.73
58 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.26
Consensus pattern (58 bp):
ATCGCAATGCAATTTTCCAAAATCGCAACGCGAATTACCGATATAGGTAAACAGTACT
Found at i:2327405 original size:134 final size:131
Alignment explanation
Indices: 2327012--2327424 Score: 483
Period size: 134 Copynumber: 3.1 Consensus size: 131
2327002 GGCGACGGTG
* * * * *
2327012 GAATGAATCAACGTCCTCATATCTGA-TTTTCACTAAAGAAGAAGCGGAATAAATCCCTCTCTTT
1 GAATGAATCAACATCCTCATATATGATTTTTC-CTCAAGAAGAAGC-GAACAAATCCCTCACTTT
* * *
2327076 CAAGATTTGATATTCCC-AGAGTAACAGTGGAACAAGTTTGCCTCGATTCAATCGTCCCTAAAGA
64 CAAGATTTGATATTCCCTA-AGTAACAGTGGAACAAGTTTGCCTCGATTCAATCTTCCCTGAGGA
*
2327140 ATATT
128 A-GTT
* * * *
2327145 AGAATAAATCAACATCCCCAAATATGATTTTCCCTCAAGAAGAAGCGAAACAAATCCCT-ACCTT
1 -GAATGAATCAACATCCTCATATATGATTTTTCCTCAAGAAGAAGCG-AACAAATCCCTCA-CTT
* * * * * *
2327209 TCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTACATTGATTCAATCTTCCCTGAGTG
63 TCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTTTGCCTCGATTCAATCTTCCCTGAG-G
2327274 ACAGTT
127 A-AGTT
* *
2327280 GAATGAATCAACATCCTCATATATGATTTTTCCTCACCG-AGAAGCAGAACAGATCCCTCACTTT
1 GAATGAATCAACATCCTCATATATGATTTTTCCTCA-AGAAGAAGC-GAACAAATCCCTCACTTT
2327344 CAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTTTGCCTCGATTCAATCTTCCCTGAGGAA
64 CAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTTTGCCTCGATTCAATCTTCCCTGAGG-A
*
2327409 TAGTG
128 -AGTT
2327414 GAATGAATCAA
1 GAATGAATCAA
2327425 TGTTTCTCAA
Statistics
Matches: 236, Mismatches: 33, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
133 2 0.01
134 222 0.94
135 11 0.05
136 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (131 bp):
GAATGAATCAACATCCTCATATATGATTTTTCCTCAAGAAGAAGCGAACAAATCCCTCACTTTCA
AGATTTGATATTCCCTAAGTAACAGTGGAACAAGTTTGCCTCGATTCAATCTTCCCTGAGGAAGT
T
Found at i:2328258 original size:13 final size:13
Alignment explanation
Indices: 2328232--2328299 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 13
2328222 TGAGATGATT
*
2328232 GAAAAA-AAACAA
1 GAAAAAGAAAAAA
2328244 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
2328257 G-AAAAGAAAGAAA
1 GAAAAAGAAA-AAA
2328270 TGAATAAAAGAATAAAA
1 -G-A-AAAAGAA-AAAA
2328287 GAATAAAAGAAAA
1 G-A-AAAAGAAAA
2328300 GAGTGTAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
12 14 0.29
13 9 0.19
14 1 0.02
15 2 0.04
16 11 0.23
17 10 0.21
18 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.15, T:0.06
Consensus pattern (13 bp):
GAAAAAGAAAAAA
Found at i:2328292 original size:16 final size:15
Alignment explanation
Indices: 2328246--2328299 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
2328236 AAAAACAAGA
2328246 AAAAGAAAAAAG---
1 AAAAGAAAAAAGAAT
2328258 AAAAGAAAGAAATGAAT
1 AAAAGAAA-AAA-GAAT
2328275 AAAAGAATAAAAGAAT
1 AAAAGAA-AAAAGAAT
2328291 AAAAGAAAA
1 AAAAGAAAA
2328300 GAGTGTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
14 1 0.03
15 2 0.06
16 11 0.31
17 10 0.28
18 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAAGAAT
Found at i:2330265 original size:130 final size:131
Alignment explanation
Indices: 2329956--2330304 Score: 407
Period size: 130 Copynumber: 2.7 Consensus size: 131
2329946 GAGAATAGTA
* * * *
2329956 ATATCTTTTCATTTCGGTTGGAGTAATAAATGACTGCTCTAAGGCATGAGAGATCATTTATTCTC
1 ATATCTTTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTC
* * * ** * * * *
2330021 GAATGGAAATAATTCA-ATATTATCATTCTCTCTCGAATTAATGTCGATTTTTAAGATGGAATAG
66 GATTGGAAATAATT-AGATATTATCATTCTCGCTCAAACCAATATCGAATTTTAAGAAGGAATAA
2330085 TG
130 TG
* * * * *
2330087 ATTTTTTTTCATTTCGATTGGAGCAATAAATGACTGCTTTGAGATATGAGAGGTCATTTATTCTC
1 ATATCTTTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTC
* * * *
2330152 GATTGGAAATCATTAGATATTATCGTT-TCGCTCAAACCGATATTGAATTTTAAGAAGGAATAAT
66 GATTGGAAATAATTAGATATTATCATTCTCGCTCAAACCAATATCGAATTTTAAGAAGGAATAAT
2330216 G
131 G
* * * * * *
2330217 ATATCTCTTCATTTCGATTGGAGTAATAAATTATTGTTTTAAGGTATGAAATGTCATTTATTCTC
1 ATATCTTTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTC
2330282 GATTGGAAATAATT-GTATATTAT
66 GATTGGAAATAATTAG-ATATTAT
2330305 TATTTTCTCT
Statistics
Matches: 182, Mismatches: 34, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
129 1 0.01
130 103 0.57
131 78 0.43
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (131 bp):
ATATCTTTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTC
GATTGGAAATAATTAGATATTATCATTCTCGCTCAAACCAATATCGAATTTTAAGAAGGAATAAT
G
Found at i:2330841 original size:2 final size:2
Alignment explanation
Indices: 2330834--2330894 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
2330824 AACCGTTTCG
2330834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2330876 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2330895 GAGAGAGAGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2332860 original size:15 final size:17
Alignment explanation
Indices: 2332842--2332873 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2332832 AAAAATATTC
2332842 AATTTAA-C-CATAAAT
1 AATTTAATCACATAAAT
2332857 AATTTAATCACATAAAT
1 AATTTAATCACATAAAT
2332874 CCAAAATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTTAATCACATAAAT
Found at i:2335467 original size:7 final size:7
Alignment explanation
Indices: 2335441--2335498 Score: 91
Period size: 7 Copynumber: 8.4 Consensus size: 7
2335431 GTCAAAGGAA
2335441 GTCAACG
1 GTCAACG
2335448 GTC-ACG
1 GTCAACG
*
2335454 ATCAACG
1 GTCAACG
*
2335461 GTAAACG
1 GTCAACG
2335468 GTCAACG
1 GTCAACG
2335475 GTCAACG
1 GTCAACG
2335482 GTCAACG
1 GTCAACG
2335489 GTCAACG
1 GTCAACG
2335496 GTC
1 GTC
2335499 GGGTCGGGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
6 5 0.11
7 41 0.89
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:2335513 original size:14 final size:14
Alignment explanation
Indices: 2335496--2335524 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2335486 ACGGTCAACG
2335496 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
2335510 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
2335524 G
1 G
2335525 ACCGATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:2342735 original size:13 final size:14
Alignment explanation
Indices: 2342702--2342739 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2342692 GATCAAAGAA
*
2342702 AGTCAACAGTCAAC
1 AGTCAACGGTCAAC
*
2342716 GGTCAACGGTC-AC
1 AGTCAACGGTCAAC
2342729 AGTCAACGGTC
1 AGTCAACGGTC
2342740 GGGTCGGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.16
Consensus pattern (14 bp):
AGTCAACGGTCAAC
Found at i:2342752 original size:17 final size:17
Alignment explanation
Indices: 2342730--2342767 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2342720 AACGGTCACA
2342730 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
2342747 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
2342764 GTCA
1 GTCA
2342768 GTCGAGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:2342793 original size:9 final size:9
Alignment explanation
Indices: 2342779--2342844 Score: 69
Period size: 9 Copynumber: 7.0 Consensus size: 9
2342769 TCGAGTTAGG
2342779 CAAACCGGT
1 CAAACCGGT
*
2342788 CAAACCGATT
1 CAAACCG-GT
*
2342798 CAGACCGGT
1 CAAACCGGT
2342807 CAAACCGGTT
1 CAAACCGG-T
* *
2342817 CGAACCAGT
1 CAAACCGGT
2342826 CGAAACCGGT
1 C-AAACCGGT
2342836 CAAACCGGT
1 CAAACCGGT
2342845 TTCCAGCCCT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
9 25 0.54
10 21 0.46
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.14
Consensus pattern (9 bp):
CAAACCGGT
Found at i:2349954 original size:2 final size:2
Alignment explanation
Indices: 2349947--2349974 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2349937 ACTCTACCTT
2349947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2349975 ATGTACATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2350869 original size:27 final size:28
Alignment explanation
Indices: 2350819--2350874 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
2350809 TAAAATAGTA
* * *
2350819 ATTAAAAATTATTAATATATAAAATTAT
1 ATTAAAAATTATAAAAATACAAAATTAT
2350847 ATTAAAAATT-TAAAAATACAAAATTAT
1 ATTAAAAATTATAAAAATACAAAATTAT
2350874 A
1 A
2350875 AAATTTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
ATTAAAAATTATAAAAATACAAAATTAT
Found at i:2351984 original size:17 final size:17
Alignment explanation
Indices: 2351962--2351996 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2351952 TAGAAGTAAC
2351962 ATTTCTTAGTTATTAAT
1 ATTTCTTAGTTATTAAT
2351979 ATTTCTTAGTTATTAAT
1 ATTTCTTAGTTATTAAT
2351996 A
1 A
2351997 ACTCGTACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (17 bp):
ATTTCTTAGTTATTAAT
Found at i:2353269 original size:69 final size:72
Alignment explanation
Indices: 2353187--2353373 Score: 229
Period size: 69 Copynumber: 2.6 Consensus size: 72
2353177 TAAAACATCT
* * *
2353187 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCT-A-AAA-ATAATAT-TTAAA
1 TAAAT-CTAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAACAAAGATAAAATATAAAA
2353248 ATAATATTC
64 ATAATATTC
* *
2353257 TAAATCTAATTAAAATACTAACACCTATTTAAACTAAAATATCTAAAACAAAGATAAAATATAAA
1 TAAATCTAATTAAAATACTAA-AACTATTTAAACTAAAATACCT--AACAAAGATAAAATATAAA
2353322 AATAATATTC
63 AATAATATTC
*
2353332 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA
1 TAAATC-TAATTAAAATACTAAAA-CTATTTAAACTAAAATA
2353374 AAAAGATAAA
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
68 3 0.03
69 32 0.32
70 5 0.05
72 1 0.01
73 3 0.03
74 6 0.06
75 19 0.19
76 32 0.32
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (72 bp):
TAAATCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAACAAAGATAAAATATAAAAAT
AATATTC
Found at i:2353359 original size:76 final size:69
Alignment explanation
Indices: 2353193--2353373 Score: 229
Period size: 76 Copynumber: 2.5 Consensus size: 69
2353183 ATCTTAAATC
* * *
2353193 CTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAATAATATTTAAAATAATATTC
1 CTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAATAAAATTAAAAATAATATTC
*
2353257 TAAAT
65 TAAAA
* *
2353262 CTAATTAAAATACTAACACCTATTTAAACTAAAATATCTAAAACAAAGATAAAATATAAAAATAA
1 CTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT---A-AAA-ATAAAAT-TAAAAATAA
2353327 TATTCTAAAA
60 TATTCTAAAA
2353337 CTTAATTAAAATACTAAAACCTATTTAAACTAAAATA
1 C-TAATTAAAATACTAAAACCTATTTAAACTAAAATA
2353374 AAAAGATAAA
Statistics
Matches: 97, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
68 4 0.04
69 31 0.32
72 1 0.01
73 3 0.03
74 6 0.06
75 18 0.19
76 34 0.35
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (69 bp):
CTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAATAAAATTAAAAATAATATTCT
AAAA
Found at i:2353398 original size:76 final size:75
Alignment explanation
Indices: 2353193--2353398 Score: 225
Period size: 76 Copynumber: 2.8 Consensus size: 75
2353183 ATCTTAAATC
* *
2353193 CTAATTAAAACACTTAAAA-CTATTTAAACTAAAAT----ACCTAAAA-ATAATATTT-AAAATA
1 CTAATTAAAATAC-TAAAACCTATTTAAACTAAAATAAAAACATAAAATATAATATTTAAAAATA
*
2353251 ATATTCTAAAT
65 ATATTCTAAAA
* * *
2353262 CTAATTAAAATACTAACACCTATTTAAACTAAAATATCTAAAACA-AAGATA-AA-ATATAAAAA
1 CTAATTAAAATACTAAAACCTATTTAAACTAAAATA---AAAACATAAAATATAATATTTAAAAA
2353324 TAATATTCTAAAA
63 TAATATTCTAAAA
* *
2353337 CTTAATTAAAATACTAAAACCTATTTAAACTAAAATAAAAAGATAAAATATAATGTTTAAAA
1 C-TAATTAAAATACTAAAACCTATTTAAACTAAAATAAAAACATAAAATATAATATTTAAAA
2353399 TATTATCCTA
Statistics
Matches: 112, Mismatches: 11, Indels: 21
0.78 0.08 0.15
Matches are distributed among these distances:
68 4 0.04
69 28 0.25
73 5 0.04
74 8 0.07
75 24 0.21
76 43 0.38
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.31
Consensus pattern (75 bp):
CTAATTAAAATACTAAAACCTATTTAAACTAAAATAAAAACATAAAATATAATATTTAAAAATAA
TATTCTAAAA
Found at i:2358922 original size:19 final size:19
Alignment explanation
Indices: 2358898--2358935 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2358888 AAATAATATC
*
2358898 CTAAAACTTAATTAAAATA
1 CTAAAACATAATTAAAATA
*
2358917 CTAAAACATATTTAAAATA
1 CTAAAACATAATTAAAATA
2358936 AAATACAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
CTAAAACATAATTAAAATA
Found at i:2362443 original size:20 final size:21
Alignment explanation
Indices: 2362418--2362469 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2362408 AAATAAAGGG
*
2362418 TAGTATCGATACTCTC-A-AGT
1 TAGTATCGATACT-TCAACACT
2362438 TAGTATCGATA-TTCAACACT
1 TAGTATCGATACTTCAACACT
2362458 TAGTATCGATAC
1 TAGTATCGATAC
2362470 CAAAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 2 0.07
20 24 0.86
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (21 bp):
TAGTATCGATACTTCAACACT
Found at i:2365617 original size:23 final size:23
Alignment explanation
Indices: 2365588--2365634 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
2365578 AATAAAAAAG
2365588 TCACTTCATTTTTGTAATTTATT
1 TCACTTCATTTTTGTAATTTATT
*
2365611 TCACTTCATTTTTGTGATTTATT
1 TCACTTCATTTTTGTAATTTATT
2365634 T
1 T
2365635 TTTAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.62
Consensus pattern (23 bp):
TCACTTCATTTTTGTAATTTATT
Found at i:2372040 original size:29 final size:29
Alignment explanation
Indices: 2372007--2372105 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 29
2371997 AGAGGGTCAT
2372007 AGTTTAAGGATGAAATTAGAATATTCAAA
1 AGTTTAAGGATGAAATTAGAATATTCAAA
* * * *
2372036 AGTTTAAGGACT-TAGTTAGAATGAGAGTC-AT
1 AGTTTAAGGA-TGAAATTAGAAT---ATTCAAA
* * *
2372067 A-TTTAAAGATGAAATTGGAATATACAAA
1 AGTTTAAGGATGAAATTAGAATATTCAAA
2372095 AGTTTAAGGAT
1 AGTTTAAGGAT
2372106 CAATTTGAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
27 2 0.04
28 2 0.04
29 27 0.53
30 15 0.29
31 2 0.04
32 3 0.06
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.31
Consensus pattern (29 bp):
AGTTTAAGGATGAAATTAGAATATTCAAA
Found at i:2378625 original size:16 final size:15
Alignment explanation
Indices: 2378602--2378634 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
2378592 GATAATTTAA
2378602 ATATTATATAAAAAT
1 ATATTATATAAAAAT
2378617 ATATATATATAAAAAT
1 ATAT-TATATAAAAAT
2378633 AT
1 AT
2378635 TTTCCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATTATATAAAAAT
Found at i:2382944 original size:20 final size:19
Alignment explanation
Indices: 2382919--2382975 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
2382909 ATTAGAACAT
2382919 GGGGTTTTGAAACTAGGAA
1 GGGGTTTTGAAACTAGGAA
* * *
2382938 GGGGGTTTAGAAACCAGTCAA
1 -GGGGTTTTGAAACTAG-GAA
2382959 GGGGTTTTGAAACTAGG
1 GGGGTTTTGAAACTAGG
2382976 TACAAGGGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.30, C:0.09, G:0.37, T:0.25
Consensus pattern (19 bp):
GGGGTTTTGAAACTAGGAA
Found at i:2385393 original size:39 final size:38
Alignment explanation
Indices: 2385281--2385432 Score: 144
Period size: 39 Copynumber: 3.9 Consensus size: 38
2385271 CGCTTTCCGC
* *
2385281 AGGCTCCTCTGCTTTATGCACAGGATAAGACCTTACCGT
1 AGGCTCTTC-GCTTTGTGCACAGGATAAGACCTTACCGT
* ** * * *
2385320 AGGCTCCTCGACTTTGTGCTTAGGGTAAGTCCTTACTGT
1 AGGCTCTTCG-CTTTGTGCACAGGATAAGACCTTACCGT
* *
2385359 AGGCTCATTCGCTTTGTGCACATGATAAGACCTTACCGC
1 AGGCTC-TTCGCTTTGTGCACAGGATAAGACCTTACCGT
* *
2385398 ATGCTCTTCTGCTTTGTGCACATGG-TAAGCCCTTA
1 AGGCTCTTC-GCTTTGTGCACA-GGATAAGACCTTA
2385433 TTGGGTGTAC
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
38 4 0.04
39 84 0.91
40 4 0.04
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (38 bp):
AGGCTCTTCGCTTTGTGCACAGGATAAGACCTTACCGT
Found at i:2385792 original size:2 final size:2
Alignment explanation
Indices: 2385787--2385841 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
2385777 CTTTTTTTCT
* *
2385787 TA TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2385829 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
2385842 CGTATGAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2396797 original size:43 final size:43
Alignment explanation
Indices: 2396740--2396822 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
2396730 GTATCATACA
* * *
2396740 TTTAGCGGAATTTGTAT-TTAAAAAACGCCACTATATACCAACC
1 TTTAACGGAATTTGTATCCT-AAAAACGCCACTAAATACCAACC
* *
2396783 TTTAACGGCATTTGTATCCTAAAAACGCCGCTAAATACCA
1 TTTAACGGAATTTGTATCCTAAAAACGCCACTAAATACCA
2396823 TAATTTTAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 33 0.97
44 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (43 bp):
TTTAACGGAATTTGTATCCTAAAAACGCCACTAAATACCAACC
Found at i:2396862 original size:44 final size:43
Alignment explanation
Indices: 2396759--2396862 Score: 109
Period size: 44 Copynumber: 2.4 Consensus size: 43
2396749 ATTTGTATTT
* * * *
2396759 AAAAAACGCCACTATATACCAACCTTTAACGGCATTTGTATCC
1 AAAAAACGCCACTAAATACCAAACTTTAACGGCATTTGCATCA
* * * * *
2396802 TAAAAACGCCGCTAAATACCATAATTTTAGCGGCGTTTGCATCA
1 AAAAAACGCCACTAAATACCA-AACTTTAACGGCATTTGCATCA
*
2396846 AAAAAATGCCACTAAAT
1 AAAAAACGCCACTAAAT
2396863 CTCAAAACTT
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
43 18 0.38
44 30 0.62
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (43 bp):
AAAAAACGCCACTAAATACCAAACTTTAACGGCATTTGCATCA
Found at i:2396939 original size:43 final size:44
Alignment explanation
Indices: 2396892--2396975 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
2396882 CTTGTGATAA
* *
2396892 AAACGTCGCTAAATCTCAACACCTATTGCGGCATTT-TTAAGAC
1 AAACGACGCTAAATATCAACACCTATTGCGGCATTTGTTAAGAC
** *
2396935 AAACGACGCTAAATATCAGTACCTATTGCGGCGTTTGTTAA
1 AAACGACGCTAAATATCAACACCTATTGCGGCATTTGTTAA
2396976 ACGCCGCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 31 0.89
44 4 0.11
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (44 bp):
AAACGACGCTAAATATCAACACCTATTGCGGCATTTGTTAAGAC
Found at i:2396990 original size:39 final size:39
Alignment explanation
Indices: 2396935--2397009 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
2396925 TTTTTAAGAC
2396935 AAACGACGCTAAATATCAG-TACCTATTGCGGCGTTTGTT
1 AAACGACGCTAAATATC-GTTACCTATTGCGGCGTTTGTT
* * *
2396974 AAACGCCGCTATATATCGTTACCTATTGCGGTGTTT
1 AAACGACGCTAAATATCGTTACCTATTGCGGCGTTT
2397010 TTGTTAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (39 bp):
AAACGACGCTAAATATCGTTACCTATTGCGGCGTTTGTT
Found at i:2405538 original size:21 final size:21
Alignment explanation
Indices: 2405488--2405552 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
2405478 GGCTAAACAC
*
2405488 TCAAAAGGGATGTATCCCTTTT
1 TCAAAAGGGATGGAT-CCTTTT
* *
2405510 T--TAAGGGATTGAT-CTATTT
1 TCAAAAGGGATGGATCCT-TTT
2405529 TCAAAAGGGATGGATCCTTTT
1 TCAAAAGGGATGGATCCTTTT
2405550 TCA
1 TCA
2405553 TAAGAGATCG
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 9 0.26
21 16 0.47
22 3 0.09
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (21 bp):
TCAAAAGGGATGGATCCTTTT
Found at i:2405570 original size:41 final size:41
Alignment explanation
Indices: 2405488--2405570 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
2405478 GGCTAAACAC
* * * *
2405488 TCAAAAGGGATGTATCCCTTTTTTAAGGGATTGATCTATTT
1 TCAAAAGGGATGGATCCCTTTTTTAAGAGATCGATCAATTT
2405529 TCAAAAGGGATGGAT-CCTTTTTCATAAGAGATCGAT-AATTT
1 TCAAAAGGGATGGATCCCTTTTT--TAAGAGATCGATCAATTT
2405570 T
1 T
2405571 TCATGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 7 0.19
41 19 0.53
42 10 0.28
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (41 bp):
TCAAAAGGGATGGATCCCTTTTTTAAGAGATCGATCAATTT
Found at i:2406940 original size:19 final size:19
Alignment explanation
Indices: 2406919--2406954 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2406909 AATATATTTA
2406919 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
2406937 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
2406955 GACTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:2407811 original size:18 final size:18
Alignment explanation
Indices: 2407790--2407844 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
2407780 TCTCTGTTTT
2407790 TTTTTCTTTCTGTCTCTC
1 TTTTTCTTTCTGTCTCTC
* *
2407808 TTTTTTTTTTTGTCTCTC
1 TTTTTCTTTCTGTCTCTC
*
2407826 TGTTTCGTTCTCTGTCTCT
1 TTTTTC-TT-TCTGTCTCT
2407845 GTTCCTTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 20 0.67
19 2 0.07
20 8 0.27
ACGTcount: A:0.00, C:0.24, G:0.09, T:0.67
Consensus pattern (18 bp):
TTTTTCTTTCTGTCTCTC
Found at i:2408325 original size:3 final size:3
Alignment explanation
Indices: 2408317--2408411 Score: 154
Period size: 3 Copynumber: 31.7 Consensus size: 3
2408307 TTAATATATT
* *
2408317 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2408365 TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2408412 TGGATAAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2408976 original size:113 final size:113
Alignment explanation
Indices: 2408729--2409618 Score: 1396
Period size: 113 Copynumber: 7.9 Consensus size: 113
2408719 GAATTATGCC
* * *
2408729 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
2408793 TATGAACT---TCTCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTCGAACT-GGAAAAGATGATCCATCAAATGATGGATTCAGGT
2408839 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** * * **
2408904 TATGAACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTCGAACTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
2408952 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
2409017 TATGAACTCGAACTGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTCGAACTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
*
2409065 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * * **
2409130 TATGAACT--TTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTCGAACTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
2409176 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2409241 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
66 TATGAACTCGAACTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
2409289 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** * * **
2409354 TATGAACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTCGAACTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
2409402 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 -AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
2409467 TTATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
65 TTATGAACTCGAACTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
2409516 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* **
2409581 TATGAACTCGAACTGGAAAAGCTGATCTTTCAAATGAT
66 TATGAACTCGAACTGGAAAAGATGATCCATCAAATGAT
2409619 AAATTTGAAT
Statistics
Matches: 715, Mismatches: 58, Indels: 11
0.91 0.07 0.01
Matches are distributed among these distances:
110 4 0.01
111 167 0.23
113 437 0.61
114 107 0.15
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCGAACTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
Found at i:2408990 original size:224 final size:225
Alignment explanation
Indices: 2408729--2409607 Score: 1543
Period size: 224 Copynumber: 3.9 Consensus size: 225
2408719 GAATTATGCC
* * *
2408729 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
2408793 TATGAACT--TCTCGGAAAAGATAATCCATCAATTGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTCAACT-GGAAAAGATAATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
2408856 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
2408921 AAAGCTGATCCATTAAATGATGGATTCATAT
195 AAAGCTGATCCATTAAATGATGGATTCATAT
2408952 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
2409017 TATGAACTCGAACTGGAAAAGATAATCCATCAATTGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTC-AACTGGAAAAGATAATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
*
2409082 CTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAC-TT-TCTGGA
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
2409145 AAAGCTGATCCATTAAATGATGGATTCATAT
195 AAAGCTGATCCATTAAATGATGGATTCATAT
2409176 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2409241 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTC-AACTGGAAAAGATAATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
2409306 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
2409371 AAAGCTGATCCATTAAATGATGGATTCATAT
195 AAAGCTGATCCATTAAATGATGGATTCATAT
2409402 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 -AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
2409467 TTATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAAT
65 TTATGAACTC-AACTGGAAAAGATAATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAAT
****
2409532 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
129 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
2409597 AAAAGCTGATC
194 AAAAGCTGATC
2409608 TTTCAAATGA
Statistics
Matches: 636, Mismatches: 13, Indels: 10
0.97 0.02 0.02
Matches are distributed among these distances:
223 4 0.01
224 283 0.44
225 4 0.01
226 142 0.22
227 203 0.32
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (225 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCAACTGGAAAAGATAATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
AAGCTGATCCATTAAATGATGGATTCATAT
Found at i:2409170 original size:337 final size:337
Alignment explanation
Indices: 2408729--2409607 Score: 1413
Period size: 337 Copynumber: 2.6 Consensus size: 337
2408719 GAATTATGCC
* *
2408729 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCAT
* *
2408793 TATGAAC-TTCTCGGAAAAGATAATCCATCAATTGATGGATTCAGGTAAAAGGTTGAACAAATTC
65 TATGAACTTTCT-GGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
****
2408857 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
129 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAA
** *
2408922 AAGCTGATCCATTAAATGATGGATTCATATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
194 AAGCTGATCCACCAAATGATGGATTCAGATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
*
2408987 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAATT
259 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAAT
*
2409052 GATGGATTCAGGT-
324 GATGGATTCAGATA
2409065 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCAT
* * **
2409130 TATGAACTTTCTGGAAAAGCTGATCCATTAAATGATGGATTCATATAAAAGGTTGAACAAATTCT
65 TATGAACTTTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCT
2409195 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAA
130 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAA
* *
2409260 AGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
195 AGCTGATCCACCAAATGATGGATTCAGATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
**** * * *
2409325 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATTAAATG
260 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAATG
*
2409390 ATGGATTCATATA
325 ATGGATTCAGATA
2409403 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
** *
2409468 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
65 TATGAACT--TTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
2409533 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
128 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
2409598 AAAGCTGATC
193 AAAGCTGATC
2409608 TTTCAAATGA
Statistics
Matches: 501, Mismatches: 35, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
336 7 0.01
337 296 0.59
338 75 0.15
339 1 0.00
340 122 0.24
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (337 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTT
CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAA
GCTGATCCACCAAATGATGGATTCAGATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAATGA
TGGATTCAGATA
Found at i:2410544 original size:83 final size:83
Alignment explanation
Indices: 2410341--2410803 Score: 804
Period size: 83 Copynumber: 5.6 Consensus size: 83
2410331 CCTACTGAAT
* ** *
2410341 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTTTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
* *
2410405 ATGATT-GTTCTGTCAAAT
65 ATGATTGGTTTTGTCAAAC
2410423 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
2410488 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
2410506 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
2410571 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
2410589 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
2410654 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
*
2410672 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
* *
2410737 TGATTGGTTCTGTCTAAC
66 TGATTGGTTTTGTCAAAC
*
2410755 CAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACAT
2410804 ATAAAAGGTT
Statistics
Matches: 368, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
82 63 0.17
83 299 0.81
84 6 0.02
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
TGATTGGTTTTGTCAAAC
Found at i:2411374 original size:22 final size:21
Alignment explanation
Indices: 2411349--2411402 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 21
2411339 AAATTATGTT
2411349 AATTCAATAAAAGAATAAATTG
1 AATTCAATAAAA-AATAAATTG
2411371 AATTTC--T-AAAAATAAATTG
1 AA-TTCAATAAAAAATAAATTG
2411390 AATCTCAAATAAA
1 AAT-TC-AATAAA
2411403 TTGAACTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 11
0.70 0.00 0.30
Matches are distributed among these distances:
18 1 0.04
19 13 0.50
20 3 0.12
21 1 0.04
22 3 0.12
23 5 0.19
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.30
Consensus pattern (21 bp):
AATTCAATAAAAAATAAATTG
Found at i:2411759 original size:19 final size:18
Alignment explanation
Indices: 2411737--2411783 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 18
2411727 TTGACCCACC
2411737 TTTTTTCTTTTTTTCTCTT
1 TTTTTTCTTTTTTT-TCTT
2411756 TTTTTTCTTTTTTTTCTT
1 TTTTTTCTTTTTTTTCTT
2411774 TCTTTTTCTT
1 T-TTTTTCTT
2411784 CAAGCATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTCTTTTTTTTCTT
Found at i:2411779 original size:9 final size:9
Alignment explanation
Indices: 2411737--2411783 Score: 76
Period size: 9 Copynumber: 5.0 Consensus size: 9
2411727 TTGACCCACC
2411737 TTTTTTCTT
1 TTTTTTCTT
2411746 TTTTTCTCTT
1 TTTTT-TCTT
2411756 TTTTTTCTT
1 TTTTTTCTT
2411765 TTTTTTCTT
1 TTTTTTCTT
2411774 TCTTTTTCTT
1 T-TTTTTCTT
2411784 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
9 19 0.53
10 17 0.47
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:2413687 original size:16 final size:16
Alignment explanation
Indices: 2413666--2413705 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
2413656 TGGTTGACAT
2413666 AGATAATATCAAACTC
1 AGATAATATCAAACTC
2413682 AGATAATATCAAACTC
1 AGATAATATCAAACTC
2413698 AGATAATA
1 AGATAATA
2413706 ACATCTGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (16 bp):
AGATAATATCAAACTC
Found at i:2423241 original size:19 final size:19
Alignment explanation
Indices: 2423220--2423255 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2423210 AATATATTTA
2423220 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
2423238 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
2423256 GACTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:2424638 original size:3 final size:3
Alignment explanation
Indices: 2424625--2424728 Score: 174
Period size: 3 Copynumber: 34.7 Consensus size: 3
2424615 TTAATATATT
*
2424625 TAA TAA T-A TAA TAA TGAA TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2424670 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2424718 TAA TAA TAA TA
1 TAA TAA TAA TA
2424729 TGGATAAAAA
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.02
3 90 0.95
4 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2425452 original size:79 final size:78
Alignment explanation
Indices: 2425317--2425464 Score: 233
Period size: 79 Copynumber: 1.9 Consensus size: 78
2425307 ATTCATTTTG
* ** *
2425317 AAACACAATCACAATTGGTTGTCATAACTTCACACATATGGACAGCGAGAAGATCGACTCGTCCA
1 AAACACAATCACAAATGGTTGTCATAACAACACACATATGGACAACGAGAAGATCGACTCGTCCA
2425382 AGCATACATTCTA
66 AGCATACATTCTA
* *
2425395 AAACACAATCACAAATGGTTGTCATTATCAACCCACATATGGACAACGAGAAGATCGACTCGTCC
1 AAACACAATCACAAATGGTTGTCA-TAACAACACACATATGGACAACGAGAAGATCGACTCGTCC
2425460 AAGCA
65 AAGCA
2425465 CACTTTCACA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 23 0.37
79 40 0.63
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.21
Consensus pattern (78 bp):
AAACACAATCACAAATGGTTGTCATAACAACACACATATGGACAACGAGAAGATCGACTCGTCCA
AGCATACATTCTA
Found at i:2427170 original size:22 final size:24
Alignment explanation
Indices: 2427120--2427172 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2427110 TTCACTCCAT
* *
2427120 AAAAT-ATATTTTTATATTAATTA
1 AAAATCATATTTTAATATTAATCA
2427143 AAAATCATATTTTAATATT-A-CA
1 AAAATCATATTTTAATATTAATCA
2427165 AAAATCAT
1 AAAATCAT
2427173 TTAAACACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 9 0.33
23 6 0.22
24 12 0.44
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATCATATTTTAATATTAATCA
Found at i:2432880 original size:3 final size:3
Alignment explanation
Indices: 2432872--2432919 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
2432862 CTGCAAACAA
*
2432872 AAT AAT AAT AAT AAT AAT AAAT AAT AAT GAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
2432918 AA
1 AA
2432920 AATTAAAACG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2434296 original size:77 final size:78
Alignment explanation
Indices: 2434156--2434308 Score: 197
Period size: 77 Copynumber: 2.0 Consensus size: 78
2434146 ATATAGTAAG
*
2434156 TAAACATTAAAATAATGTAATTTTGATTACAACTCTTTTAATTGATATTTAATTCGGAATAATTA
1 TAAACATTAAAAT-ATGTAATTCTGATTACAACTCTTTTAATTGATATTTAATTCGGAATAATTA
2434221 AATAAGATTTTAAA
65 AATAAGATTTTAAA
* * *
2434235 TAAACATTAAAGAT-TGTAATTCTGATTATAAGTC-TTTAA-TGTATATTTAATT-TGAATTAAT
1 TAAACATTAAA-ATATGTAATTCTGATTACAACTCTTTTAATTG-ATATTTAATTCGGAA-TAAT
*
2434296 TAAATAAGTTTTT
63 TAAATAAGATTTT
2434309 TTAATTCGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
76 5 0.08
77 31 0.47
78 17 0.26
79 11 0.17
80 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (78 bp):
TAAACATTAAAATATGTAATTCTGATTACAACTCTTTTAATTGATATTTAATTCGGAATAATTAA
ATAAGATTTTAAA
Found at i:2449968 original size:205 final size:205
Alignment explanation
Indices: 2449718--2450092 Score: 531
Period size: 205 Copynumber: 1.8 Consensus size: 205
2449708 TTCAGTAAAC
* * * *
2449718 GTAAACGTTTTTAAACGTTAATGGTTGAGTGATTAATAATTATTTGAACAAATATTATTT-TA-T
1 GTAAACGTTTTCAAACGTTAATGATCGACTGATTAATAATTATTTGAACAAATATTATTTATACT
* * * * * *
2449781 ATTTTTATATTTAAAAATTAAATTATTAATAAAGATTCAATTAAATCAGTTTTATTCATCGACT-
66 A-TTTCATATTAAAAAATTAAATTAATAATAAA-AAT-AATTAAATCAGTCTAATTCATCGACTA
2449845 TTTGTTTTACCATTACATCAGCATCTCTATTGACTATATTCCGTCATCTCCAAAGATTTTAGGTT
128 TTTGTTTTACCATTACATCAGCATCTCTATTGACTATATTCCGTCATCTCCAAAGATTTTAGGTT
2449910 CAAGCATACTTCA
193 CAAGCATACTTCA
* *
2449923 GTAAACGTTTTCAAACGTTAATTATCGACTGATTAATAATTATTTGAATAAATATTATTTATACT
1 GTAAACGTTTTCAAACGTTAATGATCGACTGATTAATAATTATTTGAACAAATATTATTTATACT
* * *
2449988 CATTTCATATTAAAAAATTAATTTAATAATAAAAATAATTAAATCGGTCTAATTCATCGATTATT
66 -ATTTCATATTAAAAAATTAAATTAATAATAAAAATAATTAAATCAGTCTAATTCATCGACTATT
* **
2450053 TGTTTTACCATTACGTCAGCATCTCTATTGTTTATATTCC
130 TGTTTTACCATTACATCAGCATCTCTATTGACTATATTCC
2450093 TCTGTAAGTG
Statistics
Matches: 148, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
205 76 0.51
206 43 0.29
207 28 0.19
208 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (205 bp):
GTAAACGTTTTCAAACGTTAATGATCGACTGATTAATAATTATTTGAACAAATATTATTTATACT
ATTTCATATTAAAAAATTAAATTAATAATAAAAATAATTAAATCAGTCTAATTCATCGACTATTT
GTTTTACCATTACATCAGCATCTCTATTGACTATATTCCGTCATCTCCAAAGATTTTAGGTTCAA
GCATACTTCA
Found at i:2450573 original size:97 final size:97
Alignment explanation
Indices: 2450407--2450604 Score: 288
Period size: 97 Copynumber: 2.0 Consensus size: 97
2450397 TCCTTGTTTC
* * * *
2450407 TTTGTTCTCTTGGTATTCATCATGGGTTATCGTAATGATTAATTTGATAATGATACAATCTTTAC
1 TTTGTTCTCTTGGTATTCATCATGGGTGATCCTAATAATTAATTTGATAATGATACAATCCTTAC
* * *
2450472 TATCTTCATCAGTCTGATAATCCAGGAATTAT
66 TATCTTCATCAGCCAGATAATCCAGGAATGAT
* * *
2450504 TTTGTTCTCTTGGTATTCATCATGGGTGATCCTAGTAATTAATTTGATAATGATGCAATCCTTAT
1 TTTGTTCTCTTGGTATTCATCATGGGTGATCCTAATAATTAATTTGATAATGATACAATCCTTAC
* *
2450569 TATCTTCATCAGCCAGGTAATCCAGGTATGAT
66 TATCTTCATCAGCCAGATAATCCAGGAATGAT
2450601 TTTG
1 TTTG
2450605 GTTACTTCGC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.42
Consensus pattern (97 bp):
TTTGTTCTCTTGGTATTCATCATGGGTGATCCTAATAATTAATTTGATAATGATACAATCCTTAC
TATCTTCATCAGCCAGATAATCCAGGAATGAT
Found at i:2460967 original size:22 final size:22
Alignment explanation
Indices: 2460935--2460993 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
2460925 CCTCAAACGG
2460935 TGGCTTGAATGACTCGACTTAA
1 TGGCTTGAATGACTCGACTTAA
*
2460957 TGGTTTGAATGACTCGACTTAA
1 TGGCTTGAATGACTCGACTTAA
2460979 TGGCTTGAATGACTC
1 TGGCTTGAATGACTC
2460994 AGATGATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (22 bp):
TGGCTTGAATGACTCGACTTAA
Found at i:2469354 original size:21 final size:21
Alignment explanation
Indices: 2469328--2469367 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2469318 AGAACCCCCA
*
2469328 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2469349 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2469368 TCAAAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2486601 original size:19 final size:20
Alignment explanation
Indices: 2486560--2486604 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2486550 CGAGGAGTAT
2486560 GATACTGAAAGACCGGCATC
1 GATACTGAAAGACCGGCATC
*
2486580 GATACTGAAAGGCCGG-ATC
1 GATACTGAAAGACCGGCATC
2486599 GATACT
1 GATACT
2486605 CACAGGATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (20 bp):
GATACTGAAAGACCGGCATC
Done.