Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, 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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 53 of 117
Found at i:12024298 original size:24 final size:25
Alignment explanation
Indices: 12024256--12024304 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
12024246 TTGTTACGTG
**
12024256 TATTATTTAAATATTTAAAA-TTAT
1 TATTATTTAAATAAATAAAACTTAT
*
12024280 TATTTTTTAAATAAATAAAACTTAT
1 TATTATTTAAATAAATAAAACTTAT
12024305 CTTAAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TATTATTTAAATAAATAAAACTTAT
Found at i:12024633 original size:11 final size:12
Alignment explanation
Indices: 12024608--12024638 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12024598 TTTAATAATA
12024608 TTAATTTTTATT
1 TTAATTTTTATT
12024620 TTAATTTTTATT
1 TTAATTTTTATT
*
12024632 TAAATTT
1 TTAATTT
12024639 AAATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTAATTTTTATT
Found at i:12025531 original size:16 final size:16
Alignment explanation
Indices: 12025499--12025537 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
12025489 AATGCCAAAA
12025499 TTATTTTTTATTATAT
1 TTATTTTTTATTATAT
12025515 TTATTCTTTTATT-TAT
1 TTATT-TTTTATTATAT
12025531 TT-TTTTT
1 TTATTTTT
12025538 CTAACAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 2 0.09
16 10 0.45
17 7 0.32
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTTTATTATAT
Found at i:12031390 original size:13 final size:13
Alignment explanation
Indices: 12031372--12031396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12031362 ATATATTTTT
12031372 TAAAAATAAAATA
1 TAAAAATAAAATA
12031385 TAAAAATAAAAT
1 TAAAAATAAAAT
12031397 TTTCACATTC
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAATAAAATA
Found at i:12037635 original size:23 final size:23
Alignment explanation
Indices: 12037605--12037655 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
12037595 AATTAATTCA
12037605 TTTTTCCTTTTCTAT-TTTTTTTC
1 TTTTTCC-TTTCTATCTTTTTTTC
* *
12037628 TTTTTCCTTTCTTTCTTTTTTTT
1 TTTTTCCTTTCTATCTTTTTTTC
12037651 TTTTT
1 TTTTT
12037656 ACAAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTCCTTTCTATCTTTTTTTC
Found at i:12038159 original size:7 final size:7
Alignment explanation
Indices: 12038140--12038273 Score: 84
Period size: 7 Copynumber: 19.6 Consensus size: 7
12038130 TTGAGATCTA
12038140 GTTTAGG
1 GTTTAGG
12038147 GTTTTAGG
1 G-TTTAGG
*
12038155 GTTTAAG
1 GTTTAGG
*
12038162 G-TTAGT
1 GTTTAGG
12038168 GTTTAGG
1 GTTTAGG
*
12038175 GTTTTAAG
1 G-TTTAGG
12038183 G-TTAGG
1 GTTTAGG
12038189 GTTTAGG
1 GTTTAGG
* *
12038196 CTTTAGT
1 GTTTAGG
*
12038203 GTTTAAG
1 GTTTAGG
*
12038210 ATTTA-G
1 GTTTAGG
12038216 GTTTAGG
1 GTTTAGG
*
12038223 G-TTGGG
1 GTTTAGG
12038229 GTTTAAGG
1 GTTT-AGG
*
12038237 G-TTAGA
1 GTTTAGG
12038243 GTTTA--
1 GTTTAGG
*
12038248 GCTTAGG
1 GTTTAGG
*
12038255 GTTTTAAG
1 G-TTTAGG
12038263 GTTTAGG
1 GTTTAGG
12038270 GTTT
1 GTTT
12038274 GATGGGAGAT
Statistics
Matches: 96, Mismatches: 20, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
5 4 0.04
6 22 0.23
7 49 0.51
8 21 0.22
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:12038207 original size:27 final size:26
Alignment explanation
Indices: 12038170--12038273 Score: 95
Period size: 27 Copynumber: 3.8 Consensus size: 26
12038160 AGGTTAGTGT
12038170 TTAGGGTTTTAAGGTTAGGGTTTAGGC
1 TTAGGG-TTTAAGGTTAGGGTTTAGGC
* * *
12038197 TTTAGTGTTTAAGATTTA-GGTTTAGGG
1 -TTAGGGTTTAAG-GTTAGGGTTTAGGC
* *
12038224 TTGGGGTTTAAGGGTTAGAGTTTA-GC
1 TTAGGGTTTAA-GGTTAGGGTTTAGGC
12038250 TTAGGGTTTTAAGGTTTAGGGTTT
1 TTAGGG-TTTAAGG-TTAGGGTTT
12038274 GATGGGAGAT
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
26 20 0.33
27 33 0.54
28 8 0.13
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.44
Consensus pattern (26 bp):
TTAGGGTTTAAGGTTAGGGTTTAGGC
Found at i:12039207 original size:22 final size:22
Alignment explanation
Indices: 12039178--12039227 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
12039168 TAAAAGAAAT
12039178 TTTC-AAAAAAAATTTAAAAAA
1 TTTCTAAAAAAAATTTAAAAAA
***
12039199 TTTCTAAAAATTCTTTAAAAAA
1 TTTCTAAAAAAAATTTAAAAAA
12039221 -TTCTAAA
1 TTTCTAAA
12039228 TTTTTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTCTAAAAAAAATTTAAAAAA
Found at i:12039353 original size:30 final size:31
Alignment explanation
Indices: 12039303--12039363 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
12039293 TTAACAACTA
*
12039303 AAAAATAATTCTAAAATTTTTTATAATTTTT
1 AAAAATAATTCTAAAATTTTTTAGAATTTTT
* * *
12039334 AAAAA-AATTTTAAATTTTTTTGGAATTTTT
1 AAAAATAATTCTAAAATTTTTTAGAATTTTT
12039364 TTTTGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (31 bp):
AAAAATAATTCTAAAATTTTTTAGAATTTTT
Found at i:12039373 original size:42 final size:41
Alignment explanation
Indices: 12039305--12039413 Score: 107
Period size: 42 Copynumber: 2.7 Consensus size: 41
12039295 AACAACTAAA
* * *
12039305 AAATAATTCTAAAA-TTTTTTATAATTTTTAAAAAAATTTT
1 AAATTATTTTAAAATTTTTTTATAATTTTCAAAAAAATTTT
* ** * *
12039345 AAATTTTTTTGGAATTTTTTTTTGAATTTTCAAAACAATTTT
1 AAATTATTTTAAAATTTTTTTAT-AATTTTCAAAAAAATTTT
*
12039387 TAATTATTTTAAAA--TTTTTATAATTTT
1 AAATTATTTTAAAATTTTTTTATAATTTT
12039414 ATGACATTTT
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
39 6 0.11
40 15 0.28
41 7 0.13
42 26 0.48
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (41 bp):
AAATTATTTTAAAATTTTTTTATAATTTTCAAAAAAATTTT
Found at i:12039405 original size:9 final size:9
Alignment explanation
Indices: 12039393--12039474 Score: 51
Period size: 9 Copynumber: 9.1 Consensus size: 9
12039383 TTTTTAATTA
12039393 TTTTAAAAT
1 TTTTAAAAT
*
12039402 TTTTATAAT
1 TTTTAAAAT
* *
12039411 TTTATGACA-
1 TTT-TAAAAT
*
12039420 TTTTAAAAA
1 TTTTAAAAT
*
12039429 TTTTAGAAT
1 TTTTAAAAT
*
12039438 TTTT-TAAT
1 TTTTAAAAT
* *
12039446 TTTTTAGAT
1 TTTTAAAAT
*
12039455 TTTTATAACT
1 TTTTA-AAAT
12039465 TTTTAAAAT
1 TTTTAAAAT
12039474 T
1 T
12039475 GTTTTGAATT
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
8 10 0.19
9 35 0.65
10 9 0.17
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:12039413 original size:27 final size:28
Alignment explanation
Indices: 12039383--12039470 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
12039373 TTCAAAACAA
12039383 TTTTTAATTATTTTAAAATTTTTATAA-
1 TTTTTAATTATTTTAAAATTTTTATAAC
* * * * *
12039410 TTTTATGA-CATTTTAAAAATTTTAGAAT
1 TTTT-TAATTATTTTAAAATTTTTATAAC
*
12039438 TTTTTAATT-TTTT-AGATTTTTATAAC
1 TTTTTAATTATTTTAAAATTTTTATAAC
12039464 TTTTTAA
1 TTTTTAA
12039471 AATTGTTTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
26 16 0.33
27 26 0.54
28 6 0.12
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTTAATTATTTTAAAATTTTTATAAC
Found at i:12040843 original size:20 final size:20
Alignment explanation
Indices: 12040820--12040859 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12040810 CGTTTTTATC
12040820 AAGTTTAAATAATTTTGACT
1 AAGTTTAAATAATTTTGACT
* *
12040840 AAGTTTGACTAATTTTGACT
1 AAGTTTAAATAATTTTGACT
12040860 TTGCTTATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (20 bp):
AAGTTTAAATAATTTTGACT
Found at i:12041189 original size:48 final size:49
Alignment explanation
Indices: 12041093--12041223 Score: 124
Period size: 48 Copynumber: 2.7 Consensus size: 49
12041083 TAAGAGTTTT
* * * * * **
12041093 TATAAACATAGGCAAGTAACTTT-AAAAATCAATTTTGAAAATGGCTCC
1 TATAAAAATAGGCAAATAACTTTAAAAAATCTATCTAGAAAATAACTCC
* *
12041141 TATAAATATAGGCAAATGACTTTAAAAAATCTATCTAG-AAATAACTCC
1 TATAAAAATAGGCAAATAACTTTAAAAAATCTATCTAGAAAATAACTCC
* *
12041189 TACAAAAACAGGC-AATAAACTTTAGAAAAATCTAT
1 TATAAAAATAGGCAAAT-AACTTTA-AAAAATCTAT
12041224 TTGAAAAGGG
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
47 3 0.04
48 44 0.65
49 21 0.31
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (49 bp):
TATAAAAATAGGCAAATAACTTTAAAAAATCTATCTAGAAAATAACTCC
Found at i:12041298 original size:2 final size:2
Alignment explanation
Indices: 12041291--12041315 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12041281 TTTTCTTCTT
12041291 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
12041316 TCTTTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12041745 original size:24 final size:24
Alignment explanation
Indices: 12041693--12041775 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
12041683 AAGACTTTAA
* *
12041693 ATATCACCACCAAA-AAAGACTCGG
1 ATATCACCACCAAAGAGA-ATTCGG
**
12041717 ATATCACCACTGAAGAGAATTC-G
1 ATATCACCACCAAAGAGAATTCGG
12041740 ATTATCACCACCAAAGAGAATTCGG
1 A-TATCACCACCAAAGAGAATTCGG
12041765 ATATCACCACC
1 ATATCACCACC
12041776 GAGTGAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.04
24 44 0.88
25 4 0.08
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18
Consensus pattern (24 bp):
ATATCACCACCAAAGAGAATTCGG
Found at i:12041859 original size:24 final size:23
Alignment explanation
Indices: 12041832--12041879 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12041822 ATGACTTTGG
*
12041832 ATATCACCAACGAAGAAAACTTAA
1 ATATCA-CAACCAAGAAAACTTAA
* *
12041856 ATATCACTACCAAGAAAATTTAA
1 ATATCACAACCAAGAAAACTTAA
12041879 A
1 A
12041880 AAAAAGTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.54, C:0.19, G:0.06, T:0.21
Consensus pattern (23 bp):
ATATCACAACCAAGAAAACTTAA
Found at i:12044178 original size:9 final size:9
Alignment explanation
Indices: 12044166--12044236 Score: 61
Period size: 9 Copynumber: 7.6 Consensus size: 9
12044156 CATTTATTCT
12044166 TTTTTTTTC
1 TTTTTTTTC
12044175 TTTTTTTTC
1 TTTTTTTTC
* *
12044184 TTTTAAATTTG
1 TTTT--TTTTC
*
12044195 TTATTTTTC
1 TTTTTTTTC
*
12044204 TTTATTTTC
1 TTTTTTTTC
*
12044213 TCCTTTTTTC
1 T-TTTTTTTC
*
12044223 ATTTTTTTC
1 TTTTTTTTC
12044232 TTTTT
1 TTTTT
12044237 CATTTTTTTC
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
9 35 0.74
10 6 0.13
11 6 0.13
ACGTcount: A:0.08, C:0.11, G:0.01, T:0.79
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:12044250 original size:16 final size:16
Alignment explanation
Indices: 12044198--12044250 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
12044188 AAATTTGTTA
*
12044198 TTTTTCTTTATTTTCTCC
1 TTTTTCATT-TTTT-TCC
12044216 TTTTTTCATTTTTTT-C
1 -TTTTTCATTTTTTTCC
12044232 TTTTTCATTTTTTTCC
1 TTTTTCATTTTTTTCC
12044248 TTT
1 TTT
12044251 AAGTGGATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
15 14 0.44
16 5 0.16
17 1 0.03
18 4 0.12
19 8 0.25
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTCATTTTTTTCC
Found at i:12051067 original size:36 final size:36
Alignment explanation
Indices: 12051025--12051096 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
12051015 TGCAATGAGG
* *
12051025 TGAAATGCATATGCTACTTATTAAAATGTGCATGAA
1 TGAAATGCATATACCACTTATTAAAATGTGCATGAA
* * *
12051061 TGAAATGTATATACCATTTATTAACATGTGCATGAA
1 TGAAATGCATATACCACTTATTAAAATGTGCATGAA
12051097 ATGGAATCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (36 bp):
TGAAATGCATATACCACTTATTAAAATGTGCATGAA
Found at i:12052334 original size:8 final size:8
Alignment explanation
Indices: 12052321--12052354 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
12052311 AAATCACAAC
12052321 ATTTTTTT
1 ATTTTTTT
12052329 ATTTTTTT
1 ATTTTTTT
12052337 ATTTTTGTT
1 ATTTTT-TT
12052346 ATTTTTTT
1 ATTTTTTT
12052354 A
1 A
12052355 AAATTTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (8 bp):
ATTTTTTT
Found at i:12052347 original size:17 final size:16
Alignment explanation
Indices: 12052321--12052354 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
12052311 AAATCACAAC
12052321 ATTTTTTTATTTTTTT
1 ATTTTTTTATTTTTTT
12052337 ATTTTTGTTATTTTTTT
1 ATTTTT-TTATTTTTTT
12052354 A
1 A
12052355 AAATTTTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
ATTTTTTTATTTTTTT
Found at i:12057326 original size:6 final size:6
Alignment explanation
Indices: 12057316--12057361 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
12057306 AATTAATTCT
12057316 TTTTTCC TTTTCTC TTTTT- TTTTTC TTTTTC TTTTTC TTTTTC TTT
1 TTTTT-C TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT
12057362 CTATTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.14
6 22 0.59
7 9 0.24
8 1 0.03
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:12057338 original size:18 final size:18
Alignment explanation
Indices: 12057315--12057370 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
12057305 AAATTAATTC
*
12057315 TTTTTTCCTTTTCTCTTT
1 TTTTTTTCTTTTCTCTTT
12057333 TTTTTTTCTTTT-TCTTT
1 TTTTTTTCTTTTCTCTTT
*
12057350 TTCTTTTTC-TTTCTATTT
1 TT-TTTTTCTTTTCTCTTT
12057368 TTT
1 TTT
12057371 AGAAAGCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 11 0.32
18 23 0.68
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTCTTTTCTCTTT
Found at i:12057826 original size:19 final size:19
Alignment explanation
Indices: 12057802--12057866 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 19
12057792 GCACAATTGA
12057802 TTTAGGGTTTAAGATAGGT
1 TTTAGGGTTTAAGATAGGT
* * *
12057821 TTTAGGCTTT-AGGTTGGT
1 TTTAGGGTTTAAGATAGGT
* * *
12057839 TTT-GGGTATAAGTTAGGG
1 TTTAGGGTTTAAGATAGGT
12057857 TTTAGGGTTT
1 TTTAGGGTTT
12057867 TAGGGTTAAG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
17 4 0.11
18 17 0.49
19 14 0.40
ACGTcount: A:0.18, C:0.02, G:0.34, T:0.46
Consensus pattern (19 bp):
TTTAGGGTTTAAGATAGGT
Found at i:12060460 original size:15 final size:15
Alignment explanation
Indices: 12060442--12060491 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12060432 TTGAAATTTT
*
12060442 TTTTATGGAATTTAA
1 TTTTATGTAATTTAA
* *
12060457 TTTTATATAATTTAC
1 TTTTATGTAATTTAA
*
12060472 TTTCATGTAACTTTAA
1 TTTTATGTAA-TTTAA
12060488 TTTT
1 TTTT
12060492 CTTTGCACTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (15 bp):
TTTTATGTAATTTAA
Found at i:12066062 original size:2 final size:2
Alignment explanation
Indices: 12066055--12066081 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12066045 TGAAGTTTAA
12066055 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12066082 AATGAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12066107 original size:21 final size:20
Alignment explanation
Indices: 12066081--12066121 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
12066071 ATATATATAT
*
12066081 AAATGAATGAATGAAAAAAAA
1 AAATGAAAGAAT-AAAAAAAA
*
12066102 AAATGAAAGGATAAAAAAAA
1 AAATGAAAGAATAAAAAAAA
12066122 GAGTAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (20 bp):
AAATGAAAGAATAAAAAAAA
Found at i:12069486 original size:37 final size:36
Alignment explanation
Indices: 12069445--12069526 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
12069435 TACCAAAAAA
* * *
12069445 AAAAATTCTAGGTCTTTATGGAGCTCGAGCAATTGGC
1 AAAAATTCTAGGTC-ATATAGAGCTCAAGCAATTGGC
*
12069482 AAAAACTCTAGGTCATATAGAGCTCAAGCAATTGGC
1 AAAAATTCTAGGTCATATAGAGCTCAAGCAATTGGC
12069518 -AAAATTCTA
1 AAAAATTCTA
12069527 TTAAAGGGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 8 0.20
36 19 0.47
37 13 0.32
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (36 bp):
AAAAATTCTAGGTCATATAGAGCTCAAGCAATTGGC
Found at i:12072963 original size:21 final size:23
Alignment explanation
Indices: 12072937--12072992 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 23
12072927 TTCATTATTT
12072937 TTATTTTATATTT-AAATTTT-A
1 TTATTTTATATTTAAAATTTTGA
*
12072958 TTATTTTTTATTTAAAATTTTGA
1 TTATTTTATATTTAAAATTTTGA
*
12072981 TTAATTTA-ATTT
1 TTATTTTATATTT
12072993 TTGAATCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.40
22 11 0.37
23 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTATTTTATATTTAAAATTTTGA
Found at i:12072992 original size:22 final size:21
Alignment explanation
Indices: 12072937--12072992 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
12072927 TTCATTATTT
12072937 TTAT-TTTATATTTAAATTTTA
1 TTATATTTA-ATTTAAATTTTA
* *
12072958 TTATTTTTTATTTAAAATTTTGA
1 TTATATTTAATTT-AAATTTT-A
12072981 TTA-ATTTAATTT
1 TTATATTTAATTT
12072993 TTGAATCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 8 0.28
22 17 0.59
23 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATATTTAATTTAAATTTTA
Found at i:12076460 original size:2 final size:2
Alignment explanation
Indices: 12076449--12076484 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
12076439 TGTATGTTGT
12076449 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12076485 GATTAGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12083752 original size:2 final size:2
Alignment explanation
Indices: 12083745--12083778 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
12083735 TTTTGTCCAG
*
12083745 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12083779 ATTATTCTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12084886 original size:18 final size:17
Alignment explanation
Indices: 12084846--12084879 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12084836 TAAATGAGTA
12084846 AATAAAAAATATAAATG
1 AATAAAAAATATAAATG
*
12084863 AGTAAAAAATTATAAAT
1 AATAAAAAA-TATAAAT
12084880 ATATAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
AATAAAAAATATAAATG
Found at i:12086727 original size:2 final size:2
Alignment explanation
Indices: 12086720--12086747 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12086710 TGCAAAAATC
12086720 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
12086748 GAGATTCGAG
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):
AT
Found at i:12087755 original size:5 final size:5
Alignment explanation
Indices: 12087745--12087787 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
12087735 AATGGGTTAG
* *
12087745 AAATA AAATA AAATC AAATA AAAT- CAA-A AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
12087788 GAAAAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:12088616 original size:3 final size:3
Alignment explanation
Indices: 12088591--12088633 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
12088581 AGGAAACAAA
*
12088591 AAT AA- AAT AA- AATT AAA AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12088634 AAGCATCTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.83
4 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:12089229 original size:147 final size:147
Alignment explanation
Indices: 12088959--12089238 Score: 346
Period size: 147 Copynumber: 1.9 Consensus size: 147
12088949 ACGGAGCCAT
** * *
12088959 GAATCATAAGAAATGATCTGGACTGAACCAAGATCAAGTGATCAGGATGAAACCACAAGTTAAAA
1 GAATCATAAGAAATGATCTAAACTGAACCAAGATCAAGTGATCAGGATAAAACCACAAGTAAAAA
* * * * * *
12089024 TAAAACAACCAGGATCGAGTTGAGGTTAAAAATGAATGATTGGGACGAATCAATGAATCATAAGA
66 TAAAACAACCAGGATCGAGCTGAGGTTAAAAATAAATGACTAGGACGAAACAACGAATCATAAGA
12089089 AATTATATAGAACTCAC
131 AATTATATAGAACTCAC
* * * * * *
12089106 GAATCATAAGAGATGATCTAAACTGAGCCAATATTAGGTGATC-GAGATAAAACCATAAGTAAAA
1 GAATCATAAGAAATGATCTAAACTGAACCAAGATCAAGTGATCAG-GATAAAACCACAAGTAAAA
* * * * * *
12089170 ATAAAGCGACTAGGATCGAGCTGAGGTTGAAAATAAATGACTAGGATGAAACCACGAATCATAAG
65 ATAAAACAACCAGGATCGAGCTGAGGTTAAAAATAAATGACTAGGACGAAACAACGAATCATAAG
12089235 AAAT
130 AAAT
12089239 AATCTAAACT
Statistics
Matches: 110, Mismatches: 22, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
146 1 0.01
147 109 0.99
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (147 bp):
GAATCATAAGAAATGATCTAAACTGAACCAAGATCAAGTGATCAGGATAAAACCACAAGTAAAAA
TAAAACAACCAGGATCGAGCTGAGGTTAAAAATAAATGACTAGGACGAAACAACGAATCATAAGA
AATTATATAGAACTCAC
Found at i:12089681 original size:118 final size:120
Alignment explanation
Indices: 12089127--12089713 Score: 543
Period size: 119 Copynumber: 4.9 Consensus size: 120
12089117 GATGATCTAA
* * * * * *
12089127 ACTGAGCCAATATTAGGTGA-TCGAGATAAAACCATAAGTAAAAAT-AAAGCGACTAGGATCGAG
1 ACTGAGCCAAGATCAGGTGACT-GGGATGAAACCATAAGTCAAAATAAAAGCGACCAGGATCGAG
* * * * * * * **
12089190 CTGAGGTTGAAAATAAATGA-CTAGGA-TGAAACCACGAATCATAAGAAATAATCTAA
65 TTAAGGTTGAAAATGAATGATCGA-GACAG-AACCACGAATCATAAAAAATAATATGG
* * * *
12089246 ACTAAGCCAAGATCAGGTGACTGGGATGAAACCATAAGTCAAAATAAAA-TGATCAGGTTCGAGT
1 ACTGAGCCAAGATCAGGTGACTGGGATGAAACCATAAGTCAAAATAAAAGCGACCAGGATCGAGT
* * * * * *
12089310 AAAGATTAAAAATGAATAATCGAGACAGAACCACGAATCATAAAAAATGATTTGG
66 TAAGGTTGAAAATGAATGATCGAGACAGAACCACGAATCATAAAAAATAATATGG
* * * * *
12089365 ACTGAGCCAAGATCAAGTGACCT-GGATGAAACCATAAGTTAAAATAAAA-TGACCAGGACCAAG
1 ACTGAGCCAAGATCAGGTGA-CTGGGATGAAACCATAAGTCAAAATAAAAGCGACCAGGATCGAG
* * * * * * *
12089428 TTGAGATCGAAAATGAATGATC-ATGACAAAACTAAGAATCATAAAAAATGATATGG
65 TTAAGGTTGAAAATGAATGATCGA-GACAGAACCACGAATCATAAAAAATAATATGG
* * * *
12089484 ACTGAGCCAAGATCAGGTGACTGGGATGAAACTACAAGTCAAAAT-AAAGCGACCAAGATTGAGT
1 ACTGAGCCAAGATCAGGTGACTGGGATGAAACCATAAGTCAAAATAAAAGCGACCAGGATCGAGT
* * *
12089548 TAAGGTCGAAAATGAATGATCGAGACAGAACCATGAATCATAAGAAATAATATGG
66 TAAGGTTGAAAATGAATGATCGAGACAGAACCACGAATCATAAAAAATAATATGG
* * * * *
12089603 A-TGAGCCAAGATCAGGT-AATCGGGACGAAACCACAAGTCAAAATAAAAGCGATCAAGATCGAG
1 ACTGAGCCAAGATCAGGTGACT-GGGATGAAACCATAAGTCAAAATAAAAGCGACCAGGATCGAG
* * **
12089666 -TCAGGTTGAAAATGAATGATCAAGAC-GAAACCGTGAATCATAAAAAAT
65 TTAAGGTTGAAAATGAATGATCGAGACAG-AACCACGAATCATAAAAAAT
12089714 GATCTAGACT
Statistics
Matches: 390, Mismatches: 66, Indels: 25
0.81 0.14 0.05
Matches are distributed among these distances:
117 3 0.01
118 84 0.22
119 293 0.75
120 10 0.03
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (120 bp):
ACTGAGCCAAGATCAGGTGACTGGGATGAAACCATAAGTCAAAATAAAAGCGACCAGGATCGAGT
TAAGGTTGAAAATGAATGATCGAGACAGAACCACGAATCATAAAAAATAATATGG
Found at i:12100911 original size:15 final size:14
Alignment explanation
Indices: 12100891--12100920 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
12100881 TTTTTTAACC
12100891 AAAAAATAATAAAAT
1 AAAAAATAA-AAAAT
12100906 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
12100920 A
1 A
12100921 GGTTAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAATAAAAAAT
Found at i:12100916 original size:6 final size:7
Alignment explanation
Indices: 12100891--12100920 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
12100881 TTTTTTAACC
12100891 AAAAAAT
1 AAAAAAT
12100898 AATAAAAT
1 AA-AAAAT
12100906 AAAAAAT
1 AAAAAAT
12100913 AAAAAAT
1 AAAAAAT
12100920 A
1 A
12100921 GGTTAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAAAAT
Found at i:12101213 original size:51 final size:51
Alignment explanation
Indices: 12101127--12101226 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
12101117 CTCTGACCTC
* * * * *
12101127 TTTCTAGAAAACTCACTGAAAAGTTCAACTGAAAATTGAAAATCCCACCAG
1 TTTCTAGAAAACTCACCGAAAAATTCAACTAAAAATTAAAAAACCCACCAG
12101178 TTTCT-GAAAACTTCACCGAAAAATTCAA-TCAAAAATTAAAAAACCCACC
1 TTTCTAGAAAAC-TCACCGAAAAATTCAACT-AAAAATTAAAAAACCCACC
12101227 GATTTATGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 7 0.17
51 35 0.83
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (51 bp):
TTTCTAGAAAACTCACCGAAAAATTCAACTAAAAATTAAAAAACCCACCAG
Found at i:12101237 original size:51 final size:50
Alignment explanation
Indices: 12101133--12101238 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 50
12101123 CCTCTTTCTA
* * * * * *
12101133 GAAAACTCACTGAAAAGTTCAACTGAAAATTGAAAATCCCACCAGTTTCT
1 GAAAACTCACCGAAAAATTCAACTAAAAATTAAAAAACCCACCAGTTTAT
12101183 GAAAACTTCACCGAAAAATTCAA-TCAAAAATTAAAAAACCCACC-GATTTAT
1 GAAAAC-TCACCGAAAAATTCAACT-AAAAATTAAAAAACCCACCAG-TTTAT
12101234 GAAAA
1 GAAAA
12101239 ACCTGTCGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
50 8 0.17
51 39 0.83
ACGTcount: A:0.48, C:0.21, G:0.09, T:0.22
Consensus pattern (50 bp):
GAAAACTCACCGAAAAATTCAACTAAAAATTAAAAAACCCACCAGTTTAT
Found at i:12101416 original size:21 final size:20
Alignment explanation
Indices: 12101391--12101433 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12101381 CCTTCCCTGA
*
12101391 ACCTTCTACAACCCTAAATTC
1 ACCTT-TACAAACCTAAATTC
* *
12101412 ACCTTTAGAAACCTGAATTC
1 ACCTTTACAAACCTAAATTC
12101432 AC
1 AC
12101434 TCCCAAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.28
Consensus pattern (20 bp):
ACCTTTACAAACCTAAATTC
Found at i:12101786 original size:20 final size:21
Alignment explanation
Indices: 12101761--12101827 Score: 82
Period size: 23 Copynumber: 3.1 Consensus size: 21
12101751 AAAGGAAACA
12101761 AAAATAAAATAAAATAA-AAT
1 AAAATAAAATAAAATAATAAT
* *
12101781 AAAATAATAATAATATAATAAA
1 AAAATAA-AATAAAATAATAAT
12101803 AATAATAAAATAATAATAATAAT
1 AA-AATAAAATAA-AATAATAAT
12101826 AA
1 AA
12101828 TAAAAGCATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 7 0.18
21 9 0.23
22 9 0.23
23 14 0.36
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAATAAAATAAAATAATAAT
Found at i:12101791 original size:3 final size:3
Alignment explanation
Indices: 12101763--12101830 Score: 85
Period size: 3 Copynumber: 24.7 Consensus size: 3
12101753 AGGAAACAAA
*
12101763 AAT AA- AAT AA- AAT AA- AAT AA- AAT AAT AAT AAT -AT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12101806 AAT AA- AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
12101831 AAGCATATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
2 12 0.21
3 45 0.79
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:12101800 original size:14 final size:14
Alignment explanation
Indices: 12101763--12101830 Score: 77
Period size: 14 Copynumber: 4.9 Consensus size: 14
12101753 AGGAAACAAA
*
12101763 AATAAAATAA-AAT
1 AATAATATAATAAT
*
12101776 AA-AATAAAATAAT
1 AATAATATAATAAT
*
12101789 AATAATATAATAAA
1 AATAATATAATAAT
*
12101803 AATAATAAAATAAT
1 AATAATATAATAAT
12101817 AATAATAATAATAA
1 AATAAT-ATAATAA
12101831 AAGCATATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
12 5 0.11
13 7 0.16
14 27 0.60
15 6 0.13
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAATATAATAAT
Found at i:12101828 original size:20 final size:20
Alignment explanation
Indices: 12101763--12101832 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
12101753 AGGAAACAAA
12101763 AATAA-AATAAAATAA-AAT
1 AATAATAATAAAATAATAAT
12101781 AA-AATAATAATAAT-ATAAT
1 AATAATAATAA-AATAATAAT
*
12101800 AAAAATAATAAAATAATAAT
1 AATAATAATAAAATAATAAT
12101820 AATAATAATAAAA
1 AATAATAATAAAA
12101833 GCATATTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
17 2 0.04
18 8 0.17
19 11 0.24
20 25 0.54
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAATAATAAAATAATAAT
Found at i:12112508 original size:99 final size:98
Alignment explanation
Indices: 12112331--12112519 Score: 279
Period size: 99 Copynumber: 1.9 Consensus size: 98
12112321 CACCAAAGTT
* * * *
12112331 TTCCATTTTGGTGAGAAAAAAATTGTATTAGGACCTGGGGGAATCCATCCTGATCCAACGATTCA
1 TTCCATTTTGGTGAGAAAAAAATTGAACTAGGACCTGGGGGAATCCATCCTGATCCAACCATACA
* *
12112396 GCGGGATTCGATCCGTTATTCGGTTAAAAAAAC
66 GCGCGATTCGATCCATTATTCGGTTAAAAAAAC
* * *
12112429 TTCCATTTTGGTGAGAAAAAAGTTGAACTGGGACCTGGGGGTAATCCGTCCTGATCCAACCATAC
1 TTCCATTTTGGTGAGAAAAAAATTGAACTAGGACCTGGGGG-AATCCATCCTGATCCAACCATAC
*
12112494 AGTGCGATTCGATCCATTATTCGGTT
65 AGCGCGATTCGATCCATTATTCGGTT
12112520 TTTTTTTTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
98 37 0.46
99 43 0.54
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (98 bp):
TTCCATTTTGGTGAGAAAAAAATTGAACTAGGACCTGGGGGAATCCATCCTGATCCAACCATACA
GCGCGATTCGATCCATTATTCGGTTAAAAAAAC
Found at i:12119435 original size:24 final size:24
Alignment explanation
Indices: 12119408--12119457 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12119398 TTTTTGCTAT
12119408 AATTGTG-GAAAAACTAAAAAATAA
1 AATTGTGTGAAAAACT-AAAAATAA
* *
12119432 AATTGTGTGGAAAACTAAGAATAA
1 AATTGTGTGAAAAACTAAAAATAA
12119456 AA
1 AA
12119458 CTGAATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (24 bp):
AATTGTGTGAAAAACTAAAAATAA
Found at i:12120784 original size:33 final size:33
Alignment explanation
Indices: 12120742--12120842 Score: 193
Period size: 33 Copynumber: 3.1 Consensus size: 33
12120732 TTATTTTTGC
12120742 AAATCTCTCGAATTAAGCCCTAGGAGATTGTTT
1 AAATCTCTCGAATTAAGCCCTAGGAGATTGTTT
12120775 AAATCTCTCGAATTAAGCCCTAGGAGATTGTTT
1 AAATCTCTCGAATTAAGCCCTAGGAGATTGTTT
*
12120808 AAATCTCTCGAATTAAGCCCTAGGAGATTGATT
1 AAATCTCTCGAATTAAGCCCTAGGAGATTGTTT
12120841 AA
1 AA
12120843 GGCCATATGA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (33 bp):
AAATCTCTCGAATTAAGCCCTAGGAGATTGTTT
Found at i:12123749 original size:22 final size:22
Alignment explanation
Indices: 12123721--12123763 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12123711 TTTTCTGTCA
* *
12123721 TTAATTCTAGGGATGCAAATAC
1 TTAATTCTAGAGATACAAATAC
12123743 TTAATTCTAGAGATACAAATA
1 TTAATTCTAGAGATACAAATA
12123764 TAAATATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
TTAATTCTAGAGATACAAATAC
Found at i:12125320 original size:3 final size:3
Alignment explanation
Indices: 12125312--12125340 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12125302 TCATGGTTTA
12125312 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12125341 GCAGTTCTAG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12130733 original size:8 final size:8
Alignment explanation
Indices: 12130713--12130765 Score: 81
Period size: 8 Copynumber: 6.8 Consensus size: 8
12130703 ATATTATTTT
12130713 TAAA-ATA
1 TAAATATA
*
12130720 TAAATATT
1 TAAATATA
12130728 TAAATATA
1 TAAATATA
*
12130736 TAATTATA
1 TAAATATA
12130744 TAAATATA
1 TAAATATA
12130752 TAAATATA
1 TAAATATA
12130760 TAAATA
1 TAAATA
12130766 AAAAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
7 4 0.10
8 37 0.90
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAAATATA
Found at i:12135907 original size:3 final size:3
Alignment explanation
Indices: 12135899--12135928 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12135889 CAACAAAATA
12135899 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12135929 AGCTGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12139182 original size:40 final size:39
Alignment explanation
Indices: 12139116--12139208 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 39
12139106 TATTTAATTG
* * *
12139116 TTGATTACATCAAAAATGGCTAGAAAAACTATCAT-ATTC
1 TTGATTATATCCAAAATGGCAAGAAAAACTATCATCA-TC
* *
12139155 TTGATTATATCCAAAATGTCAATGAAAAGCTATCATCATC
1 TTGATTATATCCAAAATGGCAA-GAAAAACTATCATCATC
12139195 TTGATTATATCCAA
1 TTGATTATATCCAA
12139209 TGTTAAAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
39 18 0.38
40 28 0.60
41 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (39 bp):
TTGATTATATCCAAAATGGCAAGAAAAACTATCATCATC
Found at i:12146315 original size:28 final size:28
Alignment explanation
Indices: 12146259--12146316 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
12146249 TTAAAAAGAA
*
12146259 ATTCTTTAATTTTAGGTATAAAAACCTC
1 ATTCTTTAATTTTAGATATAAAAACCTC
*
12146287 ATTCTTTAATTTTAGATATAAAAATCTC
1 ATTCTTTAATTTTAGATATAAAAACCTC
12146315 AT
1 AT
12146317 ACTCCACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (28 bp):
ATTCTTTAATTTTAGATATAAAAACCTC
Found at i:12147843 original size:27 final size:27
Alignment explanation
Indices: 12147795--12147858 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
12147785 ATTTTAAATG
* * *
12147795 TTAAATATATATATATACAAATATTTT
1 TTAAATATATATATACAAAAATATTAT
* *
12147822 TTAAATATTTATTTACAAAAATATTAT
1 TTAAATATATATATACAAAAATATTAT
12147849 TTAACATATA
1 TTAA-ATATA
12147859 AAAATAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAATATATATATACAAAAATATTAT
Found at i:12148688 original size:2 final size:2
Alignment explanation
Indices: 12148681--12148710 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12148671 AAAACAAACC
12148681 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12148711 GGAAGATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12156691 original size:3 final size:3
Alignment explanation
Indices: 12156683--12156709 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12156673 TATATTTTTA
12156683 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
12156710 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12157018 original size:7 final size:7
Alignment explanation
Indices: 12157006--12157032 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12156996 TTAATTCTGT
12157006 ATTTAAA
1 ATTTAAA
12157013 ATTTAAA
1 ATTTAAA
12157020 ATTTAAA
1 ATTTAAA
12157027 ATTTAA
1 ATTTAA
12157033 TGGTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTAAA
Found at i:12157172 original size:15 final size:16
Alignment explanation
Indices: 12157146--12157178 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
12157136 TACATTTTTA
12157146 ACATTATTTAACTAAT
1 ACATTATTTAACTAAT
12157162 ACATT-TTTAACTAAT
1 ACATTATTTAACTAAT
12157177 AC
1 AC
12157179 TATCTAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
ACATTATTTAACTAAT
Found at i:12164754 original size:30 final size:30
Alignment explanation
Indices: 12164696--12164757 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
12164686 TTTGGGTTGA
* * * * *
12164696 GTTTTGAGGGTTTTAGGGTTTGGTTTTAAG
1 GTTTAGAGGGTCTTAAGGCTTGGATTTAAG
12164726 GTTTAGAGGGTCTTAAGGCTTGGATTTAAG
1 GTTTAGAGGGTCTTAAGGCTTGGATTTAAG
12164756 GT
1 GT
12164758 ATGGAAGGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.18, C:0.03, G:0.35, T:0.44
Consensus pattern (30 bp):
GTTTAGAGGGTCTTAAGGCTTGGATTTAAG
Found at i:12164811 original size:22 final size:20
Alignment explanation
Indices: 12164763--12164811 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
12164753 AAGGTATGGA
12164763 AGGTTTAGGATTTTGATTTT
1 AGGTTTAGGATTTTGATTTT
12164783 AGAGTTTAGAGATTTTAGGATTTT
1 AG-GTTTAG-GATTTT--GATTTT
12164807 -GGTTT
1 AGGTTT
12164812 TAAAATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.08
21 6 0.24
22 10 0.40
23 1 0.04
24 6 0.24
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (20 bp):
AGGTTTAGGATTTTGATTTT
Found at i:12165178 original size:3 final size:3
Alignment explanation
Indices: 12165170--12165208 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
12165160 ATTTATTTAT
*
12165170 TTA TTA TTA TTA TTA TTA TTA TAGA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TT
12165209 TAAAGCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:12166306 original size:3 final size:3
Alignment explanation
Indices: 12166300--12166376 Score: 61
Period size: 3 Copynumber: 26.3 Consensus size: 3
12166290 TTTATCTCTT
* * * *
12166300 TTA TTA TTA TTA -TA TTA TTA ATA ATA TTT TTA -AA TATA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
** *
12166343 TTA TTA TTA TTA TTA AAA TTA TTA TTG TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12166377 ATTGAAAATA
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
2 5 0.09
3 51 0.88
4 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:12166939 original size:171 final size:170
Alignment explanation
Indices: 12166654--12167664 Score: 1246
Period size: 171 Copynumber: 5.9 Consensus size: 170
12166644 ATTAGGATTA
* ** * * *
12166654 AACTTGGATTGAATCACAAGTCAGAAAATAAGGAGATCGAGAATAAACCACGAGTCAGAGGATAA
1 AACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGATTAAACCACGAGTCAGGGGATAA
* * *
12166719 CAACAA-CTGAGATTAAACTATGATTTTGAATTAAAGAGATCGGGATTGAATCGTAAATAAAAGA
66 CAACAATC-GAGATTAAACTATGATTTTGAATTAAAGAGATCGGGATTGAATCATGAATCAAAGA
* * *
12166783 ATAAAGAGACAGGGATTAAATTGTGAGTTAGAAAATGACGTT
130 ATAAAGAGACA-GGATTAAATCGTGAGTCAGAAAATGATGTT
* *
12166825 AACTTGGATTGAATCACAAGTCAAAAAATAAGAAGACCGGGATTAAACCACGAGTCAGGGGATAA
1 AACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGATTAAACCACGAGTCAGGGGATAA
* *
12166890 CAACAA-CTGAGATTAAACTATGATTTTAAATTAAAGAGATCGGGATTGAATCATGAATCGAAGA
66 CAACAATC-GAGATTAAACTATGATTTTGAATTAAAGAGATCGGGATTGAATCATGAATCAAAGA
* * *
12166954 ATAAAGAAACCAGGATTAAACCGAGAGTCAGAAAATGATGTT
130 ATAAAGAGA-CAGGATTAAATCGTGAGTCAGAAAATGATGTT
* * ** *
12166996 AACTTAGATTGAATCACAAGTCAAAAAATAAAAAAATTGAGATTAAACCACGAGTCAGGAGATAA
1 AACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGATTAAACCACGAGTCAGGGGATAA
* * **
12167061 TAACAATCGAGATTAAACTGTGATTTTGAATTAAAGAGATCGGGATTGAATCATGAATTGAAGAA
66 CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCGGGATTGAATCATGAATCAAAGAA
* *
12167126 TAAAGAGACCAGGATTAAATCGCGAGTCAAAAAATGATGTT
131 TAAAGAGA-CAGGATTAAATCGTGAGTCAGAAAATGATGTT
* * * *
12167167 AACTTGGATTGAATCACAAGTAAAAAAATAAAAAGATC-AGGATTAAACCACGAGTCAAGAGATA
1 AACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGA-GATTAAACCACGAGTCAGGGGATA
* * * * * *
12167231 ACAACAATCGAGATTAAACTACGATTTTGAATTAAAGAGATCGAGATTGAACCGTGAATTAGAGA
65 ACAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCGGGATTGAATCATGAATCAAAGA
* * * *
12167296 ATAAAGAGACCGAGATTAAATTGTGAGTTAGAAAATAATGTT
130 ATAAAGAGACAG-GATTAAATCGTGAGTCAGAAAATGATGTT
* * *
12167338 AACTTGGATTGAATCACAAGTCAGAAAATAAGAAGACC-ATGATTAAACCATGAGTCAGGGGATA
1 AACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGA-GATTAAACCACGAGTCAGGGGATA
* ** * * **
12167402 ATAACAA-CTGAGATTAAACTGCGATTTTGAATTAAAGAGATCGGGATTCAACCACAAATCAAAG
65 ACAACAATC-GAGATTAAACTATGATTTTGAATTAAAGAGATCGGGATTGAATCATGAATCAAAG
** * *
12167466 AATAAAGAGACTAAAATTAAA-C-TGAGTCAAAAAAATAATGTT
129 AATAAAGAGAC-AGGATTAAATCGTGAGTC-AGAAAATGATGTT
* **
12167508 AACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGATTAAATCATAAGTCAGGGGATAA
1 AACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGATTAAACCACGAGTCAGGGGATAA
* * **
12167573 CAACAATCGAGATTAAAACTATGATTTTGAATTAAAAAGATCGGGATTGAATCACGAAT-TGAGA
66 CAACAATCGAGATT-AAACTATGATTTTGAATTAAAGAGATCGGGATTGAATCATGAATCAAAGA
* *
12167637 ATAAAGAGACTGGGATTAAATCGCGAGT
130 ATAAAGAGAC-AGGATTAAATCGTGAGT
12167665 AAAAAAAATA
Statistics
Matches: 737, Mismatches: 91, Indels: 23
0.87 0.11 0.03
Matches are distributed among these distances:
169 5 0.01
170 106 0.14
171 619 0.84
172 7 0.01
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (170 bp):
AACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGATTAAACCACGAGTCAGGGGATAA
CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCGGGATTGAATCATGAATCAAAGAA
TAAAGAGACAGGATTAAATCGTGAGTCAGAAAATGATGTT
Found at i:12167327 original size:34 final size:34
Alignment explanation
Indices: 12167263--12167333 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
12167253 GATTTTGAAT
* * *
12167263 TAAAGAGATCGAGATTGAACCGTGAATTAGAGAA
1 TAAAGAGACCGAGATTAAACCGTGAATTAGAAAA
** *
12167297 TAAAGAGACCGAGATTAAATTGTGAGTTAGAAAA
1 TAAAGAGACCGAGATTAAACCGTGAATTAGAAAA
12167331 TAA
1 TAA
12167334 TGTTAACTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.23
Consensus pattern (34 bp):
TAAAGAGACCGAGATTAAACCGTGAATTAGAAAA
Found at i:12167673 original size:513 final size:513
Alignment explanation
Indices: 12166654--12167671 Score: 1499
Period size: 513 Copynumber: 2.0 Consensus size: 513
12166644 ATTAGGATTA
* * **
12166654 AACTTGGATTGAATCACAAGTCAGAAAATAAGGAGATCGAGAATAAACCACGAGTCAGAGGATAA
1 AACTTGGATTGAATCACAAGTAAAAAAATAAAAAGATCGAGAATAAACCACGAGTCAGAGGATAA
* * *
12166719 CAACAACTGAGATTAAACTATGATTTTGAATTAAAGAGATCGGGATTGAATCGTAAATAAAAGAA
66 CAACAACTGAGATTAAACTACGATTTTGAATTAAAGAGATCGAGATTGAACCGTAAATAAAAGAA
* *
12166784 TAAAGAGACAGGGATTAAATTGTGAGTTAGAAAATGACGTTAACTTGGATTGAATCACAAGTCAA
131 TAAAGAGACAGAGATTAAATTGTGAGTTAGAAAATAACGTTAACTTGGATTGAATCACAAGTCAA
* *
12166849 AAAATAAGAAGACCGGGATTAAACCACGAGTCAGGGGATAACAACAACTGAGATTAAACTATGAT
196 AAAATAAGAAGACCAGGATTAAACCACGAGTCAGGGGATAACAACAACTGAGATTAAACTACGAT
* * ** * **
12166914 TTTAAATTAAAGAGATCGGGATTGAATCATGAATCGAAGAATAAAGAAACCAGGATTAAACCGAG
261 TTTAAATTAAAGAGATCGGGATTCAACCACAAATCAAAGAATAAAGAAACCAAAATTAAACCGAG
* * **
12166979 AGTCAGAAAATGATGTTAACTTAGATTGAATCACAAGTCAAAAAATAAAAAAATTGAGATTAAAC
326 AGTCAAAAAATAATGTTAACTTAGATTGAATCACAAGTCAAAAAATAAAAAAACCGAGATTAAAC
* * * *
12167044 CACGAGTCAGGAGATAATAACAATCGAGATTAAACTGTGATTTTGAATTAAAGAGATCGGGATTG
391 CACAAGTCAGGAGATAACAACAATCGAGATTAAACTATGATTTTGAATTAAAAAGATCGGGATTG
* *
12167109 AATCATGAATTGAAGAATAAAGAGACCAGGATTAAATCGCGAGTCAAAAAATGATGTT
456 AATCACGAATTGAAGAATAAAGAGACCAGGATTAAATCGCGAGTAAAAAAATGATGTT
*
12167167 AACTTGGATTGAATCACAAGTAAAAAAATAAAAAGATC-AGGATTAAACCACGAGTCA-AGAGAT
1 AACTTGGATTGAATCACAAGTAAAAAAATAAAAAGATCGA-GAATAAACCACGAGTCAGAG-GAT
* * *
12167230 AACAACAA-TCGAGATTAAACTACGATTTTGAATTAAAGAGATCGAGATTGAACCGTGAATTAGA
64 AACAACAACT-GAGATTAAACTACGATTTTGAATTAAAGAGATCGAGATTGAACCGTAAATAAAA
* *
12167294 GAATAAAGAGACCGAGATTAAATTGTGAGTTAGAAAATAATGTTAACTTGGATTGAATCACAAGT
128 GAATAAAGAGACAGAGATTAAATTGTGAGTTAGAAAATAACGTTAACTTGGATTGAATCACAAGT
* * * * *
12167359 CAGAAAATAAGAAGACCATGATTAAACCATGAGTCAGGGGATAATAACAACTGAGATTAAACTGC
193 CAAAAAATAAGAAGACCAGGATTAAACCACGAGTCAGGGGATAACAACAACTGAGATTAAACTAC
* * *
12167424 GATTTTGAATTAAAGAGATCGGGATTCAACCACAAATCAAAGAATAAAGAGACTAAAATTAAA-C
258 GATTTTAAATTAAAGAGATCGGGATTCAACCACAAATCAAAGAATAAAGAAACCAAAATTAAACC
* * *
12167488 -TGAGTCAAAAAAATAATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGATT
323 GAGAGTC-AAAAAATAATGTTAACTTAGATTGAATCACAAGTCAAAAAATAAAAAAACCGAGATT
* * *
12167552 AAATCATAAGTCAGGGGATAACAACAATCGAGATTAAAACTATGATTTTGAATTAAAAAGATCGG
387 AAACCACAAGTCAGGAGATAACAACAATCGAGATT-AAACTATGATTTTGAATTAAAAAGATCGG
**
12167617 GATTGAATCACGAATTG-AGAATAAAGAGACTGGGATTAAATCGCGAGTAAAAAAA
451 GATTGAATCACGAATTGAAGAATAAAGAGACCAGGATTAAATCGCGAGTAAAAAAA
12167672 ATAAAAACGA
Statistics
Matches: 450, Mismatches: 50, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
511 5 0.01
512 121 0.27
513 324 0.72
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (513 bp):
AACTTGGATTGAATCACAAGTAAAAAAATAAAAAGATCGAGAATAAACCACGAGTCAGAGGATAA
CAACAACTGAGATTAAACTACGATTTTGAATTAAAGAGATCGAGATTGAACCGTAAATAAAAGAA
TAAAGAGACAGAGATTAAATTGTGAGTTAGAAAATAACGTTAACTTGGATTGAATCACAAGTCAA
AAAATAAGAAGACCAGGATTAAACCACGAGTCAGGGGATAACAACAACTGAGATTAAACTACGAT
TTTAAATTAAAGAGATCGGGATTCAACCACAAATCAAAGAATAAAGAAACCAAAATTAAACCGAG
AGTCAAAAAATAATGTTAACTTAGATTGAATCACAAGTCAAAAAATAAAAAAACCGAGATTAAAC
CACAAGTCAGGAGATAACAACAATCGAGATTAAACTATGATTTTGAATTAAAAAGATCGGGATTG
AATCACGAATTGAAGAATAAAGAGACCAGGATTAAATCGCGAGTAAAAAAATGATGTT
Found at i:12167923 original size:109 final size:107
Alignment explanation
Indices: 12167697--12168092 Score: 382
Period size: 109 Copynumber: 3.6 Consensus size: 107
12167687 ATTAAATCGT
* * * * *
12167697 AAGTCAAAAAATCAA-GAATCAATCGAGAACATCGTGAATCAAATTTATGCCCGAAGGTCTTAGG
1 AAGTCAAAAAAT-AATGAATCGATCGATAACACCGTGAATCAAATTTATGCCCGAAAGTCTTAGA
* * * * *
12167761 AATCATGTCTGGAGGTCTTACAAAATTGACTTGGACAACACCAC
65 AATCATGTCTGGAGGTCTTACAGAA-TCAATGGGACAACACCGC
* * ** **
12167805 AAGTCAAAAATTAA-GAATCGATCGGAATAACACCATGAATTGAATTTATGCTTGAAAGTCTTAG
1 AAGTCAAAAAATAATGAATCGATC-G-ATAACACCGTGAATCAAATTTATGCCCGAAAGTCTTAG
* * * * *
12167869 GAATCATGCCTGAAGGTCTTACAGAATCAATGGGACAATACCGT
64 AAATCATGTCTGGAGGTCTTACAGAATCAATGGGACAACACCGC
* * * ** * *
12167913 AAGTCAAAAAATAATGAATTGATCGAGATAACACCGTAAATTAAATTTATGCTAGAAGGTCTTAA
1 AAGTCAAAAAATAATGAATCGATC--GATAACACCGTGAATCAAATTTATGCCCGAAAGTCTTAG
* *
12167978 AAATCATGTCTGGAGGTCTTACAGAATCGACGGGACAACACCGC
64 AAATCATGTCTGGAGGTCTTACAGAATCAATGGGACAACACCGC
* * * * * *
12168022 AAGTTAAAAAATAATGAATTGATCAGGATTATACCGTGAATCGAATTTATGCCCGGAAGTCTTAG
1 AAGTCAAAAAATAATGAATCGATC--GATAACACCGTGAATCAAATTTATGCCCGAAAGTCTTAG
12168087 AAATCA
64 AAATCA
12168093 ACATCTTTGG
Statistics
Matches: 236, Mismatches: 48, Indels: 7
0.81 0.16 0.02
Matches are distributed among these distances:
107 10 0.04
108 37 0.16
109 188 0.80
110 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (107 bp):
AAGTCAAAAAATAATGAATCGATCGATAACACCGTGAATCAAATTTATGCCCGAAAGTCTTAGAA
ATCATGTCTGGAGGTCTTACAGAATCAATGGGACAACACCGC
Found at i:12168070 original size:218 final size:216
Alignment explanation
Indices: 12167694--12168092 Score: 516
Period size: 218 Copynumber: 1.8 Consensus size: 216
12167684 GGGATTAAAT
* * *
12167694 CGTAAGTCAAAAAATCAAGAATCAATCGAGAACATCGTGAATCAAATTTATGCCCGAAGGTCTTA
1 CGTAAGTCAAAAAATCAAGAATCAATCGAGAACACCGTAAATCAAATTTATGCCAGAAGGTCTTA
** * * *
12167759 GGAATCATGTCTGGAGGTCTTACAAAATTGACTTGGACAACACCACAAGTCAAAAATTAAGAATC
66 AAAATCATGTCTGGAGGTCTTACAAAATCGACTGGGACAACACCACAAGTCAAAAAATAAGAATC
* ** *
12167824 GATCGGAATAACACCATGAATTGAATTTATGCTTGAAAGTCTTAGGAATCATGCCTGAAGGTCTT
131 GATCGGAATAACACCATGAATCGAATTTATGCCCGAAAGTCTTAGAAATCATGCCTGAAGGTCTT
12167889 ACAGAATCAATGGGACAATAC
196 ACAGAATCAATGGGACAATAC
** * *
12167910 CGTAAGTCAAAAAAT-AATGAATTGATCGAGATAACACCGTAAATTAAATTTATGCTAGAAGGTC
1 CGTAAGTCAAAAAATCAA-GAATCAATCGAG--AACACCGTAAATCAAATTTATGCCAGAAGGTC
* * *
12167974 TTAAAAATCATGTCTGGAGGTCTTACAGAATCGAC-GGGACAACACCGCAAGTTAAAAAATAATG
63 TTAAAAATCATGTCTGGAGGTCTTACAAAATCGACTGGGACAACACCACAAGTCAAAAAATAA-G
* * * * *
12168038 AATTGATCAGG-ATTATACCGTGAATCGAATTTATGCCCGGAAGTCTTAGAAATCA
127 AATCGATC-GGAATAACACCATGAATCGAATTTATGCCCGAAAGTCTTAGAAATCA
12168093 ACATCTTTGG
Statistics
Matches: 154, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
215 2 0.01
216 25 0.16
217 23 0.15
218 102 0.66
219 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (216 bp):
CGTAAGTCAAAAAATCAAGAATCAATCGAGAACACCGTAAATCAAATTTATGCCAGAAGGTCTTA
AAAATCATGTCTGGAGGTCTTACAAAATCGACTGGGACAACACCACAAGTCAAAAAATAAGAATC
GATCGGAATAACACCATGAATCGAATTTATGCCCGAAAGTCTTAGAAATCATGCCTGAAGGTCTT
ACAGAATCAATGGGACAATAC
Found at i:12176823 original size:29 final size:30
Alignment explanation
Indices: 12176776--12176835 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
12176766 AAGATTCGGA
*
12176776 TTTTAGGATTTTGGGTTAA-GTTTTGAGGG
1 TTTTAGGATTTTGGGTTAAGGTTTAGAGGG
*
12176805 TTTTAGGA-TTTGGTTTTAAGGTTTAGAGGG
1 TTTTAGGATTTTGG-GTTAAGGTTTAGAGGG
12176835 T
1 T
12176836 CTTAAGGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 5 0.19
29 12 0.44
30 10 0.37
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.48
Consensus pattern (30 bp):
TTTTAGGATTTTGGGTTAAGGTTTAGAGGG
Found at i:12177265 original size:3 final size:3
Alignment explanation
Indices: 12177259--12177288 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
12177249 TAATAAAATT
12177259 TTA TTA TTA TTA TTA TTA TATA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TT
12177289 TTTTAAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12187106 original size:41 final size:42
Alignment explanation
Indices: 12187057--12187139 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
12187047 AAAAAAAGAT
12187057 AGATTATTTGGGTA-CCTTTGGCTCTATTTCAACAAAGAAAA
1 AGATTATTTGGGTACCCTTTGGCTCTATTTCAACAAAGAAAA
12187098 AGATTATTTGGGTACCCTTTGGCTCTATTTCAACAAAGAAAA
1 AGATTATTTGGGTACCCTTTGGCTCTATTTCAACAAAGAAAA
12187140 TTTAAGGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 14 0.34
42 27 0.66
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (42 bp):
AGATTATTTGGGTACCCTTTGGCTCTATTTCAACAAAGAAAA
Found at i:12191079 original size:4 final size:4
Alignment explanation
Indices: 12191070--12191105 Score: 54
Period size: 4 Copynumber: 8.5 Consensus size: 4
12191060 TTATAAATTA
12191070 TTAT TTAT TTAT TTAT TTAT TTATT TTCAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTA-T TT-AT TTAT TT
12191106 TGTTCCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 23 0.77
5 6 0.20
6 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:12191526 original size:10 final size:10
Alignment explanation
Indices: 12191506--12191535 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
12191496 TAGAGCTTTC
12191506 TGAGA-TTTT
1 TGAGATTTTT
12191515 TGAGATTTTT
1 TGAGATTTTT
12191525 TGAGATTTTT
1 TGAGATTTTT
12191535 T
1 T
12191536 TGTGTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.25
10 15 0.75
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (10 bp):
TGAGATTTTT
Found at i:12195854 original size:10 final size:11
Alignment explanation
Indices: 12195834--12195859 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12195824 ATGCTCTACC
12195834 AAAAAGAAAAA
1 AAAAAGAAAAA
12195845 AAAAAGAAAAA
1 AAAAAGAAAAA
12195856 AAAA
1 AAAA
12195860 TTTGATGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:12195866 original size:58 final size:55
Alignment explanation
Indices: 12195728--12195881 Score: 168
Period size: 59 Copynumber: 2.7 Consensus size: 55
12195718 TTGATAAATG
* * * * *
12195728 AAAAAATAAAAAAAAA-TTGATGGGATAAAATACTAATGTGCTTCACCAAAAAAAA
1 AAAAAAGAAAAAAAAATTTGATGGG-CAAAATGCCAATATGCTTCACCAAAAAAAA
12195783 AAAAAAGAAAAAGAAAAATTTTGATGAGGCAAAATGCCAATATGC-TCTACCAAAAAGAAAA
1 AAAAAAG-AAAA-AAAAA-TTTGATG-GGCAAAATGCCAATATGCTTC-ACC-AAAA-AAAA
12195844 AAAAAAGAAAAAAAAATTTGATGGGGCAAAATGCCAAT
1 AAAAAAGAAAAAAAAATTTGAT-GGGCAAAATGCCAAT
12195882 TTATTTATTC
Statistics
Matches: 85, Mismatches: 5, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
55 6 0.07
56 4 0.05
57 5 0.06
58 22 0.26
59 27 0.32
60 10 0.12
61 11 0.13
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.18
Consensus pattern (55 bp):
AAAAAAGAAAAAAAAATTTGATGGGCAAAATGCCAATATGCTTCACCAAAAAAAA
Found at i:12196816 original size:22 final size:21
Alignment explanation
Indices: 12196761--12196824 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 21
12196751 AAATAAGAAG
12196761 TTTT-GAAATTTTGGATGTGAA
1 TTTTAGAAATTTT-GATGTGAA
*
12196782 --ATAGTAAAGTTTTGAATGTGAA
1 TTTTAG-AAA-TTTTG-ATGTGAA
12196804 TTTTAGAAATTTT-ATGTGAA
1 TTTTAGAAATTTTGATGTGAA
12196824 T
1 T
12196825 CCATTAGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 13
0.70 0.04 0.26
Matches are distributed among these distances:
19 1 0.03
20 9 0.26
21 4 0.11
22 15 0.43
23 3 0.09
24 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.45
Consensus pattern (21 bp):
TTTTAGAAATTTTGATGTGAA
Found at i:12197079 original size:17 final size:17
Alignment explanation
Indices: 12197059--12197154 Score: 57
Period size: 17 Copynumber: 5.6 Consensus size: 17
12197049 ATGACGAAGT
12197059 TGAAATTCTTGCGAATC
1 TGAAATTCTTGCGAATC
** *
12197076 TGAAAACCTTGCAAATC
1 TGAAATTCTTGCGAATC
* * *
12197093 ATTAAATTTTTGTGAATC
1 -TGAAATTCTTGCGAATC
* * **
12197111 TAAAATTTTTTTGAATC
1 TGAAATTCTTGCGAATC
** * *
12197128 TTCAATTCTTACGAATA
1 TGAAATTCTTGCGAATC
12197145 TGAAATTCTT
1 TGAAATTCTT
12197155 ACAAATTTTT
Statistics
Matches: 59, Mismatches: 19, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
17 48 0.81
18 11 0.19
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (17 bp):
TGAAATTCTTGCGAATC
Found at i:12197477 original size:18 final size:18
Alignment explanation
Indices: 12197425--12197479 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
12197415 TTTTTAGTTT
12197425 TTGCCAATCTAAAAATTC
1 TTGCCAATCTAAAAATTC
* ** **
12197443 ATGTGAAT-TTGAAATTC
1 TTGCCAATCTAAAAATTC
12197460 TTGCCAATCTAAAAATTC
1 TTGCCAATCTAAAAATTC
12197478 TT
1 TT
12197480 ACAAAACTGA
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (18 bp):
TTGCCAATCTAAAAATTC
Found at i:12197491 original size:35 final size:35
Alignment explanation
Indices: 12197425--12197529 Score: 102
Period size: 35 Copynumber: 3.0 Consensus size: 35
12197415 TTTTTAGTTT
* ** *
12197425 TTGCCAATCTAAAAATTCATGTGAATTTGAAATTC
1 TTGCCAATCTAAAAATTCTTACGAAATTGAAATTC
* *
12197460 TTGCCAATCTAAAAATTCTTACAAAACTGAAAATTC
1 TTGCCAATCTAAAAATTCTTACGAAATTG-AAATTC
*** **
12197496 TTAAAAATCTTTAAATTCTTACGAAATTGAAATT
1 TTGCCAATCTAAAAATTCTTACGAAATTGAAATT
12197530 TTGTGCATAT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
35 28 0.50
36 28 0.50
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (35 bp):
TTGCCAATCTAAAAATTCTTACGAAATTGAAATTC
Found at i:12197492 original size:18 final size:18
Alignment explanation
Indices: 12197471--12197527 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
12197461 TGCCAATCTA
12197471 AAAATTCTTACAAAACTG
1 AAAATTCTTACAAAACTG
*
12197489 AAAATTCTTA-AAAATCTT
1 AAAATTCTTACAAAA-CTG
* * *
12197507 TAAATTCTTACGAAATTG
1 AAAATTCTTACAAAACTG
12197525 AAA
1 AAA
12197528 TTTTGTGCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 4 0.13
18 24 0.77
19 3 0.10
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.33
Consensus pattern (18 bp):
AAAATTCTTACAAAACTG
Found at i:12197961 original size:6 final size:6
Alignment explanation
Indices: 12197950--12198032 Score: 76
Period size: 6 Copynumber: 13.7 Consensus size: 6
12197940 AAAGCCTAAA
* * **
12197950 AATTTT AATTTT AATTTT GATTTT AGTTTT AATTTT GGGTTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT -AATTTT AATTTT
* * ** *
12197999 AGTTTT AATTTT GATTTT GGTTTT AGTTTT AATT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATT
12198033 ATTTTGTCAA
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
6 58 0.94
7 4 0.06
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:12197967 original size:12 final size:12
Alignment explanation
Indices: 12197952--12198032 Score: 92
Period size: 12 Copynumber: 6.7 Consensus size: 12
12197942 AGCCTAAAAA
*
12197952 TTTTAATTTTAA
1 TTTTAATTTTAG
*
12197964 TTTTGATTTTAG
1 TTTTAATTTTAG
*
12197976 TTTTAATTTTGGG
1 TTTTAATTTT-AG
12197989 TTTTAATTTTAG
1 TTTTAATTTTAG
12198001 TTTTAATTTT-G
1 TTTTAATTTTAG
**
12198012 ATTTTGGTTTTAG
1 -TTTTAATTTTAG
12198025 TTTTAATT
1 TTTTAATT
12198033 ATTTTGTCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
11 1 0.02
12 44 0.77
13 12 0.21
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (12 bp):
TTTTAATTTTAG
Found at i:12197998 original size:25 final size:24
Alignment explanation
Indices: 12197952--12198032 Score: 117
Period size: 24 Copynumber: 3.3 Consensus size: 24
12197942 AGCCTAAAAA
*
12197952 TTTTAATTTTAATTTTGATTTTAG
1 TTTTAATTTTGATTTTGATTTTAG
* *
12197976 TTTTAATTTTGGGTTTTAATTTTAG
1 TTTTAATTTT-GATTTTGATTTTAG
*
12198001 TTTTAATTTTGATTTTGGTTTTAG
1 TTTTAATTTTGATTTTGATTTTAG
12198025 TTTTAATT
1 TTTTAATT
12198033 ATTTTGTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
24 29 0.58
25 21 0.42
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (24 bp):
TTTTAATTTTGATTTTGATTTTAG
Found at i:12199199 original size:20 final size:20
Alignment explanation
Indices: 12199163--12199200 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12199153 TTTGGTAAGA
*
12199163 TTATTTATGATTGTTTTTAT
1 TTATTTATGATTATTTTTAT
12199183 TTATTTAT-ATATATTTTT
1 TTATTTATGAT-TATTTTT
12199201 TGCATGATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
TTATTTATGATTATTTTTAT
Found at i:12199242 original size:21 final size:19
Alignment explanation
Indices: 12199216--12199296 Score: 74
Period size: 21 Copynumber: 4.1 Consensus size: 19
12199206 GATTGTTAAT
12199216 TAATTGCATGATACTTTATTA
1 TAATTGCATGATA-TTTA-TA
* *
12199237 TAATTGTATAATAATTTATA
1 TAATTGCATGAT-ATTTATA
12199257 TTAATTGCATGATATATTATA
1 -TAATTGCATGATAT-TTATA
* *
12199278 TTATTACATGATA-TTATA
1 TAATTGCATGATATTTATA
12199296 T
1 T
12199297 TATTTGAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.12
20 15 0.29
21 29 0.57
22 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (19 bp):
TAATTGCATGATATTTATA
Found at i:12199300 original size:21 final size:21
Alignment explanation
Indices: 12199252--12199300 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
12199242 GTATAATAAT
*
12199252 TTATATTA--ATTGCATGATA
1 TTATATTATTATTACATGATA
12199271 -TAT-TATATTATTACATGATA
1 TTATAT-TATTATTACATGATA
12199291 TTATATTATT
1 TTATATTATT
12199301 TGAATGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
17 1 0.04
18 5 0.21
20 10 0.42
21 7 0.29
22 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (21 bp):
TTATATTATTATTACATGATA
Found at i:12202327 original size:3 final size:3
Alignment explanation
Indices: 12202313--12202362 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
12202303 CTGATTGGGT
*
12202313 TAC TACC TAC TAC TAC TAT TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TA-C TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
12202359 TAC T
1 TAC T
12202363 TGACCATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TAC
Found at i:12202396 original size:15 final size:15
Alignment explanation
Indices: 12202372--12202409 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12202362 TTGACCATTT
*
12202372 TTTTTATTTATTTTA
1 TTTTTATTTATTTGA
*
12202387 TTTTTCTTTATTTGA
1 TTTTTATTTATTTGA
12202402 TTTTTATT
1 TTTTTATT
12202410 ATGATTTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTATTTATTTGA
Found at i:12203610 original size:57 final size:55
Alignment explanation
Indices: 12203489--12203688 Score: 187
Period size: 58 Copynumber: 3.5 Consensus size: 55
12203479 ATGAAAATTT
* *
12203489 TAAAATA-CAAATTTTTCTTTAAATAAAAAAATATTTC-AAGAAAAGTTTGACGAAAAGT
1 TAAAATATCAAATTTTTC-TTAAAT-AAAAAA-ATTTCAAAAAAAAGTTTGA-GAAAA-A
*
12203547 TGAAATATC-AATTTTTCTTAAATAAAAAAATTTCAAAAAAAAGGGTTTGAGGAAAAA
1 TAAAATATCAAATTTTTCTTAAATAAAAAAATTTCAAAAAAAA--GTTTGA-GAAAAA
* * *
12203604 TAAAATATC-AA-TTTTCTTGAAATAGAAAATATTTCAAAAAATATTTTGAGAAAAA
1 TAAAATATCAAATTTTTCTT-AAATA-AAAAAATTTCAAAAAAAAGTTTGAGAAAAA
*
12203659 GTTGAAATATCAAATTTTT-TTAAATAAAAA
1 --TAAAATATCAAATTTTTCTTAAATAAAAA
12203689 GTAATTTAAA
Statistics
Matches: 123, Mismatches: 9, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
55 11 0.09
56 28 0.23
57 34 0.28
58 45 0.37
59 5 0.04
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.34
Consensus pattern (55 bp):
TAAAATATCAAATTTTTCTTAAATAAAAAAATTTCAAAAAAAAGTTTGAGAAAAA
Found at i:12203700 original size:57 final size:55
Alignment explanation
Indices: 12203454--12203878 Score: 285
Period size: 57 Copynumber: 7.7 Consensus size: 55
12203444 TTAGAAAAAA
* * * * ** *
12203454 TAAATAAAAATATTTTCCAAAA-TTAATGAAAATTTTAAAATA-CAAATTTTTCTT
1 TAAATAAAAATAATTTCAAAAATTTGAGGAAAAAGTTGAAATATCAAA-TTTTCTT
* * *
12203508 TAAATAAAAAAATATTTCAAGAAAAGTTTGACG-AAAAGTTGAAATATCAATTTTTC-T
1 TAAATAAAAATA-ATTTC-A-AAAA-TTTGAGGAAAAAGTTGAAATATCAAATTTTCTT
*
12203565 TAAATAAAAA-AATTTCAAAAAAAAGGGTTTGAGGAAAAA--TAAAATATC-AATTTTCTT
1 TAAATAAAAATAATTTC---AAAAA---TTTGAGGAAAAAGTTGAAATATCAAATTTTCTT
*
12203622 GAAATAGAAAAT-ATTTCAAAAAATATTTTGA-GAAAAAGTTGAAATATCAAATTTT-TT
1 TAAATA-AAAATAATTTC--AAAA-A-TTTGAGGAAAAAGTTGAAATATCAAATTTTCTT
* * * **
12203679 TAAATAAAAAGTAATTT-AAAAATTT-AAGAAAAGGTTGAAGTATCAAATTTTCCG
1 TAAATAAAAA-TAATTTCAAAAATTTGAGGAAAAAGTTGAAATATCAAATTTTCTT
** * * * *
12203733 TAAATAAAAATTAATTT-TGAAATTTGAGGAAAAAATTGAAATATTAATTTTTCCT
1 TAAATAAAAA-TAATTTCAAAAATTTGAGGAAAAAGTTGAAATATCAAATTTTCTT
* *
12203788 T-AA-AACAATAATTTC-AAAATTTGA-GAAAAAGTTGAAGTATCAAATTTTCCTT
1 TAAATAAAAATAATTTCAAAAATTTGAGGAAAAAGTTGAAATATCAAATTTT-CTT
*
12203840 TAAATAAAAAGAATAATTTC-AAAATTTAAGGAAAAAGTT
1 TAAAT--AAA-AATAATTTCAAAAATTTGAGGAAAAAGTT
12203879 AAAGTATTAG
Statistics
Matches: 301, Mismatches: 39, Indels: 58
0.76 0.10 0.15
Matches are distributed among these distances:
51 20 0.07
52 18 0.06
53 31 0.10
54 36 0.12
55 42 0.14
56 22 0.07
57 70 0.23
58 51 0.17
59 11 0.04
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (55 bp):
TAAATAAAAATAATTTCAAAAATTTGAGGAAAAAGTTGAAATATCAAATTTTCTT
Found at i:12203815 original size:106 final size:109
Alignment explanation
Indices: 12203648--12203905 Score: 296
Period size: 106 Copynumber: 2.4 Consensus size: 109
12203638 CAAAAAATAT
*
12203648 TTTGA-GAAAAAGTTGAAATATCAAATTTTT-TTAAATAAAAAGTAATTTAAAAATTTAAGAAAA
1 TTTGAGGAAAAAGTTGAAATAT-TAATTTTTCTT-AA-AAAAAGTAATTTAAAAATTTAAGAAAA
* * **
12203711 GGTTGAAGTATCAAATTTTCC-GTAAAT-AAAA-ATTAATTTTGAAA
63 AGTTGAAGTATCAAATTTTCCTGTAAATAAAAAGAATAATTTCAAAA
* * * *
12203755 TTTGAGGAAAAAATTGAAATATTAATTTTTCCTTAAAACAA-TAATTTCAAAATTTGAGAAAAAG
1 TTTGAGGAAAAAGTTGAAATATTAATTTTT-CTTAAAAAAAGTAATTTAAAAATTTAAGAAAAAG
*
12203819 TTGAAGTATCAAATTTTCCTTTAAATAAAAAGAATAATTTCAAAA
65 TTGAAGTATCAAATTTTCCTGTAAATAAAAAGAATAATTTCAAAA
* *
12203864 TTTAAGGAAAAAGTT-AAAGTATTAGTTTTTTCTTAAATAAAA
1 TTTGAGGAAAAAGTTGAAA-TATTA-ATTTTTCTTAAA-AAAA
12203906 AATAACGATT
Statistics
Matches: 128, Mismatches: 14, Indels: 15
0.82 0.09 0.10
Matches are distributed among these distances:
106 39 0.30
107 21 0.16
108 24 0.19
109 36 0.28
110 8 0.06
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.36
Consensus pattern (109 bp):
TTTGAGGAAAAAGTTGAAATATTAATTTTTCTTAAAAAAAGTAATTTAAAAATTTAAGAAAAAGT
TGAAGTATCAAATTTTCCTGTAAATAAAAAGAATAATTTCAAAA
Found at i:12203907 original size:58 final size:56
Alignment explanation
Indices: 12203652--12203975 Score: 194
Period size: 58 Copynumber: 5.8 Consensus size: 56
12203642 AAATATTTTG
* *
12203652 AGAAAAAGTTGAAA-TATCAAATTTTT-TTAAAT---AAAAAGTAATTTAAAAATTTA
1 AGAAAAAGTT-AAAGTATC-AATTTTTCTTAAATAAAAAAAAATAATTTCAAAATTTA
* * * * * **
12203705 AGAAAAGGTTGAAGTATCAAATTTTCCGTAAAT---AAAAATTAATTTTGAAATTTGA
1 AGAAAAAGTTAAAGTATC-AATTTTTCTTAAATAAAAAAAAATAATTTCAAAATTT-A
* * * * * *
12203760 GGAAAAAATTGAAA-TATTAATTTTTCCT---T--AAAACAATAATTTCAAAATTTG
1 AGAAAAAGTT-AAAGTATCAATTTTTCTTAAATAAAAAAAAATAATTTCAAAATTTA
* * *
12203811 AGAAAAAGTTGAAGTATCAAATTTTCCTTTAAAT-AAAAAGAATAATTTCAAAATTTA
1 AGAAAAAGTTAAAGTATC-AATTTTTC-TTAAATAAAAAAAAATAATTTCAAAATTTA
* * * ** *
12203868 AGGAAAAAGTTAAAGTATTAGTTTTTTCTTAAATAAAAAATAACGATTTCAAATGTTTTA
1 A-GAAAAAGTTAAAGTATCA-ATTTTTCTTAAATAAAAAAAAATAATTTCAAA--ATTTA
*
12203928 A-AGAAAAGTTAAAGTATCAATTTTTCTAAAATAAATAAAAAATAATTT
1 AGA-AAAAGTTAAAGTATCAATTTTTCTTAAATAAA-AAAAAATAATTT
12203976 TAAATTTTCC
Statistics
Matches: 211, Mismatches: 41, Indels: 32
0.74 0.14 0.11
Matches are distributed among these distances:
50 2 0.01
51 12 0.06
52 25 0.12
53 21 0.10
54 30 0.14
55 11 0.05
56 3 0.01
57 28 0.13
58 50 0.24
59 24 0.11
60 5 0.02
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (56 bp):
AGAAAAAGTTAAAGTATCAATTTTTCTTAAATAAAAAAAAATAATTTCAAAATTTA
Found at i:12209077 original size:12 final size:11
Alignment explanation
Indices: 12209045--12209081 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
12209035 GGAATAAAGC
12209045 AAAAAAAA-AA
1 AAAAAAAAGAA
12209055 AAAAAAAAGAA
1 AAAAAAAAGAA
12209066 AAAAAAAGAGAA
1 AAAAAAA-AGAA
12209078 AAAA
1 AAAA
12209082 TGAATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 8 0.32
11 9 0.36
12 8 0.32
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:12210155 original size:37 final size:37
Alignment explanation
Indices: 12210105--12210382 Score: 230
Period size: 37 Copynumber: 7.9 Consensus size: 37
12210095 TATTTTGATT
* *
12210105 TCTT-ATTTCGACTTATAGGTTCAAACCAAGTAATCA
1 TCTTCATTTTGACTTATAGGTTCAGACCAAGTAATCA
* * *
12210141 TCTTCATTTTGACTTATAAGCTCAGACCAAGTTATCA
1 TCTTCATTTTGACTTATAGGTTCAGACCAAGTAATCA
* **
12210178 TC-TCAATTTTGAATTATAGACTCAGACCAAGTAATCA
1 TCTTC-ATTTTGACTTATAGGTTCAGACCAAGTAATCA
* * * *
12210215 TCTTTATTTTAACTTATAGGCTCAGACTAAG---TCA
1 TCTTCATTTTGACTTATAGGTTCAGACCAAGTAATCA
*
12210249 TCTTCATTTTGACTTATAGGCTT-AGACCAAGTCATCA
1 TCTTCATTTTGACTTATAGG-TTCAGACCAAGTAATCA
*
12210286 --TT--TTTT-ACTTATAAGG-TCAAACC-A--AATCA
1 TCTTCATTTTGACTTAT-AGGTTCAGACCAAGTAATCA
* * *
12210315 TCAT--TTTTGACTTATAGATTCAGACCAAGTCATCA
1 TCTTCATTTTGACTTATAGGTTCAGACCAAGTAATCA
* *
12210350 TCATCATTTTCGACTTATAGATTCAGACCAAGT
1 TCTTCATTTT-GACTTATAGGTTCAGACCAAGT
12210383 CCTTATTTTT
Statistics
Matches: 199, Mismatches: 24, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
29 4 0.02
31 9 0.05
32 22 0.11
33 8 0.04
34 28 0.14
35 11 0.06
36 6 0.03
37 88 0.44
38 23 0.12
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (37 bp):
TCTTCATTTTGACTTATAGGTTCAGACCAAGTAATCA
Found at i:12210310 original size:32 final size:32
Alignment explanation
Indices: 12210255--12210350 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
12210245 GTCATCTTCA
* *
12210255 TTTTGACTTATAG-GCTTAGACCAAGTCATCAT
1 TTTTGACTTATAGAG-TCAAACCAAGTCATCAT
* *
12210287 TTTTTACTTATA-AGGTCAAACCAAATCATCAT
1 TTTTGACTTATAGA-GTCAAACCAAGTCATCAT
* *
12210319 TTTTGACTTATAGATTCAGACCAAGTCATCAT
1 TTTTGACTTATAGAGTCAAACCAAGTCATCAT
12210351 CATCATTTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
32 51 0.96
33 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (32 bp):
TTTTGACTTATAGAGTCAAACCAAGTCATCAT
Found at i:12210772 original size:32 final size:32
Alignment explanation
Indices: 12210690--12210823 Score: 132
Period size: 33 Copynumber: 4.1 Consensus size: 32
12210680 TATATTTCTC
12210690 TTTTTTACTTCGACTAA-ATCCAAGTCATCTTA
1 TTTTTTACTTCGACTAAGA-CCAAGTCATCTTA
* * * *
12210722 TTTTCTAACTTCAACTAAGACCAAGTTATTTTA
1 TTTT-TTACTTCGACTAAGACCAAGTCATCTTA
*
12210755 TTTTTTACTTCGGCTAAGACCAAGTCATCTTA
1 TTTTTTACTTCGACTAAGACCAAGTCATCTTA
*
12210787 GTTTTTGACTAT-GACTAA-ACCCAAGTCAT-TTCA
1 -TTTTTTACT-TCGACTAAGA-CCAAGTCATCTT-A
12210820 TTTT
1 TTTT
12210824 GACCTTCGAC
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
32 34 0.40
33 49 0.58
34 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (32 bp):
TTTTTTACTTCGACTAAGACCAAGTCATCTTA
Found at i:12210804 original size:65 final size:65
Alignment explanation
Indices: 12210690--12210823 Score: 159
Period size: 65 Copynumber: 2.1 Consensus size: 65
12210680 TATATTTCTC
* *
12210690 TTTTTTACTTCGACTAAATCCAAGTCATCTTATTTTCTAACTTCAACTAAGA-CCAAGTTATTTT
1 TTTTTTACTTCGACTAAATCCAAGTCATCTTATTTTCTAACTTCAACTAA-ACCCAAGTCATTTC
12210754 A
65 A
* * *
12210755 TTTTTTACTTCGGCTAAGA-CCAAGTCATCTTAGTTTT-TGACTAT-GACTAAACCCAAGTCATT
1 TTTTTTACTTCGACTAA-ATCCAAGTCATCTTA-TTTTCTAACT-TCAACTAAACCCAAGTCATT
12210817 TCA
63 TCA
12210820 TTTT
1 TTTT
12210824 GACCTTCGAC
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
64 1 0.02
65 53 0.88
66 6 0.10
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (65 bp):
TTTTTTACTTCGACTAAATCCAAGTCATCTTATTTTCTAACTTCAACTAAACCCAAGTCATTTCA
Found at i:12212553 original size:56 final size:56
Alignment explanation
Indices: 12212277--12212761 Score: 410
Period size: 57 Copynumber: 8.6 Consensus size: 56
12212267 GAATACCAAT
* * * * *
12212277 TTTTCTTTAAATAAAATAAT-ATTTCAAGAAATGTTTAAGGAAAAA-TTGAAATATCAA
1 TTTTCCTTAAATAAAAAAATAATTT--TGAAAT-TTTGAGGAAAAAGTTGAAGTATCAA
* *
12212334 TTTTCCTTAAATAAAAAAAT-ATTTCAAGAAATGTTTGAGG-AAAAGTTGAAATATCAA
1 TTTTCCTTAAATAAAAAAATAATTT--TGAAAT-TTTGAGGAAAAAGTTGAAGTATCAA
**
12212391 TTTTCCTTAAAT-AAAAAAT-ATTTCAAAAAATATTTTGA-GAAAAAGTTGAAGTATCAA
1 TTTTCCTTAAATAAAAAAATAATTT---TGAA-ATTTTGAGGAAAAAGTTGAAGTATCAA
* * * *
12212448 TTTTCTTTAAAT-AAAAAATAA-TTTAAAATTTTGAGAAAAAAGTTAAAGTATCAA
1 TTTTCCTTAAATAAAAAAATAATTTTGAAATTTTGAGGAAAAAGTTGAAGTATCAA
**
12212502 TTTTCCCTTAAATAAAAAAATAATTTTGAAA-TTTGAGGAAAATTTTGAAGTATCAA
1 TTTT-CCTTAAATAAAAAAATAATTTTGAAATTTTGAGGAAAAAGTTGAAGTATCAA
* * *
12212558 TTTTACTTTAAATAAAAAAATAATTTT-AAAATTTGAGGAAAAAGTTGAAGTATTAA
1 TTTT-CCTTAAATAAAAAAATAATTTTGAAATTTTGAGGAAAAAGTTGAAGTATCAA
* * * * *
12212614 TTTTTCTT--A-AAAAGAATAATTTTGAAA-TTTGAGGAAAAAAATTAAAGTATTAAA
1 TTTTCCTTAAATAAAAAAATAATTTTGAAATTTTGAGG-AAAAAGTTGAAGTA-TCAA
* * * *
12212668 TTTTCCTTAAAT-AAAAAATAATGATTTCAAATGTTTAAAAGAAAAAATTGAAGTATCAA
1 TTTTCCTTAAATAAAAAAATAAT--TTTGAAAT-TTT-GAGGAAAAAGTTGAAGTATCAA
* *
12212727 TTTTCCTAAAATAAATAAAAATAA-TTTCAAATTTT
1 TTTTCCTTAAAT-AA-AAAAATAATTTTGAAATTTT
12212762 CCCTTAAAAC
Statistics
Matches: 369, Mismatches: 35, Indels: 47
0.82 0.08 0.10
Matches are distributed among these distances:
52 20 0.05
53 23 0.06
54 34 0.09
55 12 0.03
56 107 0.29
57 112 0.30
58 12 0.03
59 22 0.06
60 16 0.04
61 3 0.01
62 8 0.02
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.36
Consensus pattern (56 bp):
TTTTCCTTAAATAAAAAAATAATTTTGAAATTTTGAGGAAAAAGTTGAAGTATCAA
Found at i:12212740 original size:108 final size:105
Alignment explanation
Indices: 12212424--12212737 Score: 246
Period size: 110 Copynumber: 2.9 Consensus size: 105
12212414 CAAAAAATAT
* * * * **
12212424 TTTGA-GAAAAAGTTGAAGTATCAATTTT-CTTTAAAT-AAAAAATAA-TTTAAAATTTTGAGAA
1 TTTGAGGAAAAAATTAAAGTATAAATTTTACCTTAAATAAAAAAATAATTTTAAAATTTAAAGAA
* *
12212485 AAAAGTTAAAGTATCAATTTTCCCTTAAATAAAAAAATAATTTTGAAA
66 AAAA-TTGAAGTATCAATTTTTCC-----T--AAAAATAATTTTGAAA
** * * * * *
12212533 TTTGAGGAAAATTTTGAAGTATCAATTTTACTTTAAATAAAAAAATAATTTTAAAATTTGAGGAA
1 TTTGAGGAAAAAATTAAAGTATAAATTTTACCTTAAATAAAAAAATAATTTTAAAATTTAAAGAA
* * *
12212598 AAAGTTGAAGTATTAATTTTTCTTAAAAAGAATAATTTTGAAA
66 AAAATTGAAGTATCAATTTTTCCT--AAA-AATAATTTTGAAA
*
12212641 TTTGAGGAAAAAAATTAAAGTATTAAATTTT-CCTTAAAT-AAAAAATAATGATTTCAAATGTTT
1 TTTGAGG-AAAAAATTAAAGTA-TAAATTTTACCTTAAATAAAAAAATAAT--TTT-AAA-ATTT
12212704 AAAAGAAAAAATTGAAGTATCAA-TTTTCCTAAAA
60 -AAAGAAAAAATTGAAGTATCAATTTTTCCTAAAA
12212738 TAAATAAAAA
Statistics
Matches: 172, Mismatches: 21, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
107 6 0.03
108 30 0.17
109 24 0.14
110 34 0.20
111 11 0.06
112 33 0.19
113 34 0.20
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (105 bp):
TTTGAGGAAAAAATTAAAGTATAAATTTTACCTTAAATAAAAAAATAATTTTAAAATTTAAAGAA
AAAATTGAAGTATCAATTTTTCCTAAAAATAATTTTGAAA
Found at i:12213964 original size:18 final size:18
Alignment explanation
Indices: 12213941--12214028 Score: 70
Period size: 18 Copynumber: 4.8 Consensus size: 18
12213931 GACCCTAAAA
12213941 CCTAACCCTAAACCAAAC
1 CCTAACCCTAAACCAAAC
* ** *
12213959 CCTAACCATAAGTCAAAG
1 CCTAACCCTAAACCAAAC
*
12213977 CCTAGCCCTAAACTCTAAAC
1 CCTAACCCTAAAC-C-AAAC
* * *
12213997 CTTAAACCTAAACCCTAAC
1 CCTAACCCTAAA-CCAAAC
12214016 CCTAACCC-AAACC
1 CCTAACCCTAAACC
12214029 CTAAAAGGTA
Statistics
Matches: 52, Mismatches: 15, Indels: 7
0.70 0.20 0.09
Matches are distributed among these distances:
17 2 0.04
18 26 0.50
19 10 0.19
20 13 0.25
21 1 0.02
ACGTcount: A:0.41, C:0.40, G:0.03, T:0.16
Consensus pattern (18 bp):
CCTAACCCTAAACCAAAC
Found at i:12214009 original size:13 final size:13
Alignment explanation
Indices: 12213932--12214033 Score: 58
Period size: 12 Copynumber: 8.1 Consensus size: 13
12213922 TTAAATCGAG
12213932 ACCCTAAAACCT-A
1 ACCCT-AAACCTAA
12213945 ACCCTAAACC-AA
1 ACCCTAAACCTAA
12213957 ACCCT-AACC-ATA
1 ACCCTAAACCTA-A
**
12213969 AGTC-AAAGCCT-A
1 ACCCTAAA-CCTAA
*
12213981 GCCCTAAACTCTAA
1 ACCCTAAAC-CTAA
*
12213995 ACCTTAAACCTAA
1 ACCCTAAACCTAA
*
12214008 ACCCTAACCCT-A
1 ACCCTAAACCTAA
12214020 ACCC-AAACCCTAA
1 ACCCTAAA-CCTAA
12214033 A
1 A
12214034 AGGTAACCCT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
11 7 0.10
12 27 0.39
13 27 0.39
14 8 0.12
ACGTcount: A:0.43, C:0.38, G:0.03, T:0.16
Consensus pattern (13 bp):
ACCCTAAACCTAA
Found at i:12215397 original size:23 final size:25
Alignment explanation
Indices: 12215344--12215399 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
12215334 GATAAATCAT
* **
12215344 AATAAAAACTATATAAATTATTTTA
1 AATAAAAACTATAGAAATTATAATA
12215369 AATAAAAACT-TAGAAA-TATAATA
1 AATAAAAACTATAGAAATTATAATA
12215392 AATAAAAA
1 AATAAAAA
12215400 TATTCATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 13 0.46
24 5 0.18
25 10 0.36
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (25 bp):
AATAAAAACTATAGAAATTATAATA
Found at i:12216272 original size:30 final size:30
Alignment explanation
Indices: 12216211--12216287 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
12216201 CAAAAAAAGG
*
12216211 TCTTAATTTTAGTATTTTAAAAAATTAATTT
1 TCTTAATTTTAGTATTGTAAAAAA-TAATTT
**
12216242 TCTTAATTTTTTTATTGTAAAAAA-ACATTT
1 TCTTAATTTTAGTATTGTAAAAAATA-ATTT
* **
12216272 TTTTTTTTTTAGTATT
1 TCTTAATTTTAGTATT
12216288 TTTTAATTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 1 0.03
30 15 0.41
31 21 0.57
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (30 bp):
TCTTAATTTTAGTATTGTAAAAAATAATTT
Found at i:12217494 original size:253 final size:253
Alignment explanation
Indices: 12217046--12217556 Score: 1013
Period size: 253 Copynumber: 2.0 Consensus size: 253
12217036 AAATTAAAGA
12217046 AAAAAATGAAAATAAAAATCTTTGTATCGAAAAGAGTTTCTAAATATTTCAATACTTTAATAATT
1 AAAAAATGAAAATAAAAATCTTTGTATCGAAAAGAGTTTCTAAATATTTCAATACTTTAATAATT
12217111 TTTAAAAATCATTTTTCACTCAAAAAATTCTCGAAAATCACTACTTGAACTTCTCAGAATCCCAT
66 TTTAAAAATCATTTTTCACTCAAAAAATTCTCGAAAATCACTACTTGAACTTCTCAGAATCCCAT
12217176 CATTAAAAATATTTTCATTTACTATAAACATTTAATAATAGATATTTTACAAAAATATATATAAT
131 CATTAAAAATATTTTCATTTACTATAAACATTTAATAATAGATATTTTACAAAAATATATATAAT
12217241 TATCGATAATATTTATTTTCATAAACATTATTAATTACTTTAAGCATGCATATTTTAT
196 TATCGATAATATTTATTTTCATAAACATTATTAATTACTTTAAGCATGCATATTTTAT
12217299 AAAAAATGAAAATAAAAATCTTTGTATCGAAAAGAGTTTCTAAATATTTCAATACTTTAATAATT
1 AAAAAATGAAAATAAAAATCTTTGTATCGAAAAGAGTTTCTAAATATTTCAATACTTTAATAATT
*
12217364 TTTAAAAATCATTTTTCACTCAGAAAATTCTCGAAAATCACTACTTGAACTTCTCAGAATCCCAT
66 TTTAAAAATCATTTTTCACTCAAAAAATTCTCGAAAATCACTACTTGAACTTCTCAGAATCCCAT
12217429 CATTAAAAATATTTTCATTTACTATAAACATTTAATAATAGATATTTTACAAAAATATATATAAT
131 CATTAAAAATATTTTCATTTACTATAAACATTTAATAATAGATATTTTACAAAAATATATATAAT
12217494 TATCGATAATATTTATTTTCATAAACATTATTAATTACTTTAAGCATGCATATTTTAT
196 TATCGATAATATTTATTTTCATAAACATTATTAATTACTTTAAGCATGCATATTTTAT
12217552 AAAAA
1 AAAAA
12217557 TATTATTGAC
Statistics
Matches: 257, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 257 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (253 bp):
AAAAAATGAAAATAAAAATCTTTGTATCGAAAAGAGTTTCTAAATATTTCAATACTTTAATAATT
TTTAAAAATCATTTTTCACTCAAAAAATTCTCGAAAATCACTACTTGAACTTCTCAGAATCCCAT
CATTAAAAATATTTTCATTTACTATAAACATTTAATAATAGATATTTTACAAAAATATATATAAT
TATCGATAATATTTATTTTCATAAACATTATTAATTACTTTAAGCATGCATATTTTAT
Found at i:12219164 original size:22 final size:23
Alignment explanation
Indices: 12219137--12219181 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
12219127 GCCAGCCATA
*
12219137 TTTTTCCTTTTTC-TTTTAATTT
1 TTTTTCATTTTTCATTTTAATTT
*
12219159 TTTTTCATTTTTCATTTTTATTT
1 TTTTTCATTTTTCATTTTAATTT
12219182 AATTCAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTCATTTTTCATTTTAATTT
Found at i:12220268 original size:126 final size:125
Alignment explanation
Indices: 12220088--12220413 Score: 352
Period size: 126 Copynumber: 2.6 Consensus size: 125
12220078 TATGCTAAAA
* * *
12220088 GTCTTACAAATCTTAATATCTTTGAATGCTTAAT-ATATCTAAGGCGTTAAAACTTTAAAAATTT
1 GTCTTACAAATCTTGATATCTTTGAATGC-TCATCATATC-AAGGCGTTGAAACTTTAAAAATTT
* * * * * * *****
12220152 AAAATATTTT-GCC-TAGTGATCTTATAGATTATGCCTAAAAGTCTTAGAGATTATGTTTGGAG
64 AAAATATTTTAGCCAAAG-G-TCTTACAAATTATGCCTAAAAGTCTTAAAAATCATGCCCAAAG
* * *
12220214 GTCTTACAAATCTTGATATCTTTGAATGCTCCTCATATCAGAGGCATTGAAACTTTGAAAATTTA
1 GTCTTACAAATCTTGATATCTTTGAATGCTCATCATATCA-AGGCGTTGAAACTTTAAAAATTTA
* * * *
12220279 AAATATTTTATCCAAAGGTCTTACAAATTATGCCTAAAGGTTTTAAAAATCATGCCCAAAT
65 AAATATTTTAGCCAAAGGTCTTACAAATTATGCCTAAAAGTCTTAAAAATCATGCCCAAAG
* * * *
12220340 GTCTTACAAATCTTGACATCTTTAAATGCTCATCGTATCAAAGGCGTTGAAACTTTAAAATTTTA
1 GTCTTACAAATCTTGATATCTTTGAATGCTCATCATATC-AAGGCGTTGAAACTTTAAAAATTTA
12220405 AAATATTTT
65 AAATATTTT
12220414 TCTTGGAGGT
Statistics
Matches: 167, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
125 3 0.02
126 158 0.95
127 4 0.02
128 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (125 bp):
GTCTTACAAATCTTGATATCTTTGAATGCTCATCATATCAAGGCGTTGAAACTTTAAAAATTTAA
AATATTTTAGCCAAAGGTCTTACAAATTATGCCTAAAAGTCTTAAAAATCATGCCCAAAG
Found at i:12220317 original size:22 final size:22
Alignment explanation
Indices: 12220290--12220351 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
12220280 AATATTTTAT
*
12220290 CCAAAGGTCTTACAAATTATGC
1 CCAAAGGTCTTACAAATCATGC
* * *
12220312 CTAAAGGTTTTAAAAATCATGC
1 CCAAAGGTCTTACAAATCATGC
*
12220334 CCAAATGTCTTACAAATC
1 CCAAAGGTCTTACAAATC
12220352 TTGACATCTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (22 bp):
CCAAAGGTCTTACAAATCATGC
Found at i:12220647 original size:23 final size:22
Alignment explanation
Indices: 12220613--12220727 Score: 104
Period size: 22 Copynumber: 5.1 Consensus size: 22
12220603 TATGTTGTAG
*
12220613 CTAATTTGGGCTTAGACTGCCAA
1 CTAATTTAGGCTTAGA-TGCCAA
* *
12220636 TTAATTTAGGCTTAAAGTGCCAA
1 CTAATTTAGGCTTAGA-TGCCAA
* *
12220659 CTAATTTAGGTTTAGGTGCCAA
1 CTAATTTAGGCTTAGATGCCAA
* * * * *
12220681 CTAATATGGGCTTACATGCTAG
1 CTAATTTAGGCTTAGATGCCAA
* *
12220703 TTAATTTAGGCTTGGATGCCAA
1 CTAATTTAGGCTTAGATGCCAA
12220725 CTA
1 CTA
12220728 GATTGGACTT
Statistics
Matches: 69, Mismatches: 23, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
22 38 0.55
23 31 0.45
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (22 bp):
CTAATTTAGGCTTAGATGCCAA
Found at i:12220680 original size:22 final size:23
Alignment explanation
Indices: 12220613--12220694 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
12220603 TATGTTGTAG
* * *
12220613 CTAATTTGGGCTTAGACTGCCAA
1 CTAATTTAGGCTTAAAGTGCCAA
*
12220636 TTAATTTAGGCTTAAAGTGCCAA
1 CTAATTTAGGCTTAAAGTGCCAA
* *
12220659 CTAATTTAGG-TTTAGGTGCCAA
1 CTAATTTAGGCTTAAAGTGCCAA
* *
12220681 CTAATATGGGCTTA
1 CTAATTTAGGCTTA
12220695 CATGCTAGTT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
22 18 0.38
23 30 0.62
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (23 bp):
CTAATTTAGGCTTAAAGTGCCAA
Found at i:12220760 original size:45 final size:44
Alignment explanation
Indices: 12220675--12220760 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 44
12220665 TAGGTTTAGG
* * * *
12220675 TGCCAACTAATATGGGCTTACATGCTAGTTAATTTAGGCTTGGA
1 TGCCAACTAATATGGACTTAAATGCTAGCTAATCTAGGCTTGGA
*
12220719 TGCCAACTAGAT-TGGACTTAAAATGCTAGCTAATCTGGGCTT
1 TGCCAACTA-ATATGGACTT-AAATGCTAGCTAATCTAGGCTT
12220761 TGGTCTAGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 15 0.43
45 20 0.57
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (44 bp):
TGCCAACTAATATGGACTTAAATGCTAGCTAATCTAGGCTTGGA
Found at i:12221401 original size:26 final size:26
Alignment explanation
Indices: 12221340--12221401 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
12221330 CATGTAAGTG
*
12221340 ATGCAAATGCGAATGCCTTTTTCATA
1 ATGCAAATGCGAATGCCTTTGTCATA
* *
12221366 ATGTAAATGCGAATGTCTTTGTCATA
1 ATGCAAATGCGAATGCCTTTGTCATA
*
12221392 ATGCATATGC
1 ATGCAAATGC
12221402 AAGTGATGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (26 bp):
ATGCAAATGCGAATGCCTTTGTCATA
Found at i:12228018 original size:3 final size:3
Alignment explanation
Indices: 12228010--12228035 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12228000 ATGTATTACC
12228010 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12228036 TAAAACGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12228574 original size:31 final size:31
Alignment explanation
Indices: 12228536--12228597 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
12228526 GTAAGGATTT
12228536 GTTCATCTAAAGATTCCTAAATTATTCCTCA
1 GTTCATCTAAAGATTCCTAAATTATTCCTCA
12228567 GTTCATCTAAAGATTCCTAAATTATTCCTCA
1 GTTCATCTAAAGATTCCTAAATTATTCCTCA
12228598 CTAACATCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (31 bp):
GTTCATCTAAAGATTCCTAAATTATTCCTCA
Found at i:12229212 original size:18 final size:21
Alignment explanation
Indices: 12229191--12229229 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12229181 ACTTATATTT
12229191 TTAA-TAAAA-TTT-TTAAAA
1 TTAATTAAAACTTTATTAAAA
12229209 TTAATTAAAACTTTATTAAAA
1 TTAATTAAAACTTTATTAAAA
12229230 AGATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 3 0.17
21 6 0.33
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAATTAAAACTTTATTAAAA
Found at i:12232983 original size:1 final size:1
Alignment explanation
Indices: 12232972--12233015 Score: 79
Period size: 1 Copynumber: 44.0 Consensus size: 1
12232962 TAGTGTAACA
*
12232972 CCCCTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
12233016 AAAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.98, G:0.00, T:0.02
Consensus pattern (1 bp):
C
Found at i:12233821 original size:2 final size:2
Alignment explanation
Indices: 12233810--12233841 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
12233800 TTCTAACTTG
12233810 AT AT AT -T AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12233842 GAATCTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:12235439 original size:17 final size:17
Alignment explanation
Indices: 12235417--12235470 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 17
12235407 TAAGTTCAAG
12235417 TTTAATTTATAATATTA
1 TTTAATTTATAATATTA
12235434 TTTAATTTATAAAATAATTTA
1 TTTAATTTAT--AAT-A-TTA
12235455 TTTAATTT-TAATATTA
1 TTTAATTTATAATATTA
12235471 ATTTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.09
17 11 0.33
18 3 0.09
19 3 0.09
20 2 0.06
21 11 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTTATAATATTA
Done.