Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 63 of 109
Found at i:12651788 original size:27 final size:26
Alignment explanation
Indices: 12651750--12651807 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
12651740 GTATGATGAC
*
12651750 ATTATTTAATTTAATTTTATTCATAAT
1 ATTATTTAATTTAATCTTATT-ATAAT
* *
12651777 ATTATTTTATTTTATCTTATTATAAT
1 ATTATTTAATTTAATCTTATTATAAT
*
12651803 TTTAT
1 ATTAT
12651808 GTACCAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (26 bp):
ATTATTTAATTTAATCTTATTATAAT
Found at i:12651806 original size:21 final size:22
Alignment explanation
Indices: 12651751--12651807 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
12651741 TATGATGACA
*
12651751 TTATT-TAATTTAATTTTATTC
1 TTATTATAATTTTATTTTATTC
* * *
12651772 ATAATATTATTTTATTTTA-TC
1 TTATTATAATTTTATTTTATTC
12651793 TTATTATAATTTTAT
1 TTATTATAATTTTAT
12651808 GTACCAAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTATAATTTTATTTTATTC
Found at i:12652811 original size:30 final size:30
Alignment explanation
Indices: 12652775--12652831 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
12652765 CTTGCCGTGG
12652775 CTTGATCCCTTAAAGTTTCTTTTTCTCTTC
1 CTTGATCCCTTAAAGTTTCTTTTTCTCTTC
12652805 CTTGATCCCTTAAAGTTTCTTTTTCTC
1 CTTGATCCCTTAAAGTTTCTTTTTCTC
12652832 CTCGGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.14, C:0.26, G:0.07, T:0.53
Consensus pattern (30 bp):
CTTGATCCCTTAAAGTTTCTTTTTCTCTTC
Found at i:12653178 original size:2 final size:2
Alignment explanation
Indices: 12653171--12653200 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12653161 AAGGCATGCA
12653171 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
12653201 TTTGTAGCGT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12653846 original size:19 final size:18
Alignment explanation
Indices: 12653802--12653836 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12653792 ATATTATAAA
*
12653802 TATAGTAAGAAAAAATAT
1 TATAGTAAGAAAAAAAAT
12653820 TATAGTAAGAAAAAAAA
1 TATAGTAAGAAAAAAAA
12653837 GTTCATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (18 bp):
TATAGTAAGAAAAAAAAT
Found at i:12654232 original size:15 final size:16
Alignment explanation
Indices: 12654212--12654241 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12654202 GTTTAGTAAC
12654212 ATTTTT-AATAATTTG
1 ATTTTTAAATAATTTG
12654227 ATTTTTAAATAATTT
1 ATTTTTAAATAATTT
12654242 TTGTTTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
ATTTTTAAATAATTTG
Found at i:12654983 original size:3 final size:3
Alignment explanation
Indices: 12654975--12655017 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
12654965 AAATACAATG
12654975 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12655018 ATAATTGACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12655457 original size:11 final size:11
Alignment explanation
Indices: 12655422--12655525 Score: 71
Period size: 11 Copynumber: 9.7 Consensus size: 11
12655412 ATGGGTAAGC
12655422 TTATTT-TATT
1 TTATTTATATT
12655432 TT-TTTAT-TT
1 TTATTTATATT
12655441 TGTATTTATATT
1 T-TATTTATATT
12655453 TTATTTATATT
1 TTATTTATATT
*
12655464 ATTA-TTATTTT
1 -TTATTTATATT
12655475 TTATTTTATATAT
1 TTA-TTTATAT-T
* *
12655488 ATATTTAT-GT
1 TTATTTATATT
12655498 TTATTT-TA-T
1 TTATTTATATT
*
12655507 GTATTTAT-TAT
1 TTATTTATAT-T
12655518 TTATTTAT
1 TTATTTAT
12655526 TAATATATAT
Statistics
Matches: 75, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
9 13 0.17
10 14 0.19
11 29 0.39
12 16 0.21
13 3 0.04
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (11 bp):
TTATTTATATT
Found at i:12655493 original size:46 final size:45
Alignment explanation
Indices: 12655443--12655549 Score: 123
Period size: 46 Copynumber: 2.3 Consensus size: 45
12655433 TTTTATTTTG
12655443 TATTTATATTTTATTTATAT-TA-TTATTATTT-TTTATTTTATATATA
1 TATTTATATTTTATTT-TATGTATTTATTATTTATTTA--TTA-ATATA
*
12655489 TATTTAT-GTTTATTTTATGTATTTATTATTTATTTATTAATATA
1 TATTTATATTTTATTTTATGTATTTATTATTTATTTATTAATATA
12655533 TATTTATTATTATTATT
1 TATTTA-TATT-TTATT
12655550 ACTATTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
44 14 0.26
45 13 0.25
46 17 0.32
47 9 0.17
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (45 bp):
TATTTATATTTTATTTTATGTATTTATTATTTATTTATTAATATA
Found at i:12655521 original size:4 final size:4
Alignment explanation
Indices: 12655426--12655540 Score: 62
Period size: 4 Copynumber: 28.5 Consensus size: 4
12655416 GTAAGCTTAT
* * *
12655426 TTTA TTTT TTTA TTT- TGTA TTTA TAT- TTTA TTTA TATTA -TTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA
* * *
12655471 TTT- TTTA TTTTA TATA TATA TTTA TGTTTA TTTTA TGTA TTTA -TTA
1 TTTA TTTA -TTTA TTTA TTTA TTTA --TTTA -TTTA TTTA TTTA TTTA
*
12655517 TTTA TTTA TTAATA TATA TTTA TT
1 TTTA TTTA TT--TA TTTA TTTA TT
12655541 ATTATTATTA
Statistics
Matches: 87, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
3 16 0.18
4 53 0.61
5 11 0.13
6 7 0.08
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:12655526 original size:11 final size:11
Alignment explanation
Indices: 12655434--12655543 Score: 65
Period size: 11 Copynumber: 10.2 Consensus size: 11
12655424 ATTTTATTTT
12655434 TTTATTT-TGTA
1 TTTATTTAT-TA
12655445 TTTATATT-TTA
1 TTTAT-TTATTA
12655456 TTTATATTATTA
1 TTTAT-TTATTA
*
12655468 -TTATTTTTTA
1 TTTATTTATTA
*
12655478 TTT-TATA-TA
1 TTTATTTATTA
* *
12655487 TATATTTA-TG
1 TTTATTTATTA
12655497 TTTA-TT-TTA
1 TTTATTTATTA
*
12655506 TGTATTTATTA
1 TTTATTTATTA
12655517 TTTATTTATTAA
1 TTTATTTATT-A
12655529 TATATATTTATTA
1 T-T-TATTTATTA
12655542 TT
1 TT
12655544 ATTATTACTA
Statistics
Matches: 79, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
9 10 0.13
10 16 0.20
11 33 0.42
12 9 0.11
13 3 0.04
14 8 0.10
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:12655693 original size:39 final size:41
Alignment explanation
Indices: 12655627--12655703 Score: 106
Period size: 39 Copynumber: 1.9 Consensus size: 41
12655617 ATATAGTATA
*
12655627 ATTTATCTATTATTTATTTTTAGTTATCCGTTAACATTATT
1 ATTTATCTATTATTTATTTTTAGTTATCCATTAACATTATT
*
12655668 ATTTATCTGATTA-TT-TTTTTA-TTATCTATTAACATT
1 ATTTATCT-ATTATTTATTTTTAGTTATCCATTAACATT
12655704 TTTTTTGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 13 0.39
40 6 0.18
41 10 0.30
42 4 0.12
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (41 bp):
ATTTATCTATTATTTATTTTTAGTTATCCATTAACATTATT
Found at i:12656607 original size:6 final size:6
Alignment explanation
Indices: 12656556--12656631 Score: 70
Period size: 6 Copynumber: 12.8 Consensus size: 6
12656546 GATTTGTTTA
* *
12656556 ATTTTT -TTTCT ATTTTT ATTTATT -TTCCTTT A-TTTT ATTTTC ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTT-TT ATT--TTT ATTTTT ATTTTT ATTTTT
*
12656604 ATTTTT ATTTTT -TTTAT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
12656632 CTTTAAATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
5 12 0.21
6 39 0.68
7 5 0.09
8 1 0.02
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:12656614 original size:23 final size:23
Alignment explanation
Indices: 12656584--12656631 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
12656574 TTTATTTTCC
12656584 TTTATTTTATTTT-CATTTTTATT
1 TTTATTTT-TTTTACATTTTTATT
*
12656607 TTTATTTTTTTTATATTTTTATT
1 TTTATTTTTTTTACATTTTTATT
12656630 TT
1 TT
12656632 CTTTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTATTTTTTTTACATTTTTATT
Found at i:12656631 original size:17 final size:17
Alignment explanation
Indices: 12656556--12656636 Score: 76
Period size: 17 Copynumber: 4.6 Consensus size: 17
12656546 GATTTGTTTA
*
12656556 ATTTTTTTTCTATTTTT
1 ATTTTTTTTATATTTTT
*
12656573 ATTTATTTTCCTTTA-TTTT
1 ATTT-TTTT--TATATTTTT
12656592 ATTTTCATTTT-TATTTTT
1 ATTTT--TTTTATATTTTT
12656610 ATTTTTTTTATATTTTT
1 ATTTTTTTTATATTTTT
*
12656627 ATTTTCTTTA
1 ATTTTTTTTA
12656637 AATAAAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
16 4 0.07
17 22 0.40
18 15 0.27
19 8 0.15
20 6 0.11
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (17 bp):
ATTTTTTTTATATTTTT
Found at i:12656741 original size:60 final size:59
Alignment explanation
Indices: 12656628--12656866 Score: 253
Period size: 60 Copynumber: 4.1 Consensus size: 59
12656618 TATATTTTTA
* * * *
12656628 TTTTCTTTAAATAAAATTT-AAAAAAA--TATTTTTGGGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAATAAATTTTCAAAAAAAGTTTTTTTTTGGAAAAAGTTGAAAGTATCAAT
*
12656684 TTTTCTTAAAGATAAATTTTCAAAAAAAGTTTTTTTTTTGG-AAAAGTTGAAAATATCAAT
1 TTTTCTTAAA-ATAAATTTTCAAAAAAAG-TTTTTTTTTGGAAAAAGTTGAAAGTATCAAT
* * * * *
12656744 TTTTCTCGAAATTAAAGTTTCAAAAAAA---TATTTCTGGAAAAAAGTTGAAAGTATCAA-
1 TTTTCT-TAAAATAAATTTTCAAAAAAAGTTTTTTTTTGG-AAAAAGTTGAAAGTATCAAT
*
12656801 TTTTCTTTAAAAATAAATTTTCAAAAAAAAG-TTTTTTTTAGAAAAAGTTGAAAGTATCAAT
1 TTTTC-TT-AAAATAAATTTTC-AAAAAAAGTTTTTTTTTGGAAAAAGTTGAAAGTATCAAT
12656862 TTTTC
1 TTTTC
12656867 CTTGTATAAA
Statistics
Matches: 152, Mismatches: 17, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
56 16 0.11
57 13 0.09
58 36 0.24
59 7 0.05
60 58 0.38
61 22 0.14
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (59 bp):
TTTTCTTAAAATAAATTTTCAAAAAAAGTTTTTTTTTGGAAAAAGTTGAAAGTATCAAT
Found at i:12656775 original size:118 final size:117
Alignment explanation
Indices: 12656639--12656866 Score: 352
Period size: 118 Copynumber: 1.9 Consensus size: 117
12656629 TTTCTTTAAA
* * *
12656639 TAAAATTTAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTT-TCTTAAAGATAAATTT
1 TAAAATTTAAAAAAATATTTCTGGAAAAAAGTTGAAAGTATCAATTTTCT-TTAAAAATAAATTT
* *
12656703 TC-AAAAAAAGTTTTTTTTTTGGAAAAGTTGAAAATATCAATTTTTCTCGAAAT
65 TCAAAAAAAAG-TTTTTTTTAGAAAAAGTTGAAAATATCAATTTTTCTCGAAAT
*
12656756 TAAAGTTTCAAAAAAATATTTCTGGAAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTT
1 TAAAATTT-AAAAAAATATTTCTGGAAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTT
*
12656821 TCAAAAAAAAGTTTTTTTTAGAAAAAGTTGAAAGTATCAATTTTTC
65 TCAAAAAAAAGTTTTTTTTAGAAAAAGTTGAAAATATCAATTTTTC
12656867 CTTGTATAAA
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
117 7 0.07
118 85 0.84
119 9 0.09
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.39
Consensus pattern (117 bp):
TAAAATTTAAAAAAATATTTCTGGAAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTTT
CAAAAAAAAGTTTTTTTTAGAAAAAGTTGAAAATATCAATTTTTCTCGAAAT
Found at i:12656901 original size:11 final size:10
Alignment explanation
Indices: 12656885--12656921 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
12656875 AAAGCAATCA
*
12656885 TTTTTTTTCT
1 TTTTTTTTAT
12656895 TTTTTTTTAT
1 TTTTTTTTAT
*
12656905 TTTTTTTTAA
1 TTTTTTTTAT
12656915 TTTTTTT
1 TTTTTTT
12656922 AATGTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.08, C:0.03, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:12659882 original size:13 final size:13
Alignment explanation
Indices: 12659864--12659888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12659854 GATGTTGATG
12659864 TTGTTTTGATGAC
1 TTGTTTTGATGAC
12659877 TTGTTTTGATGA
1 TTGTTTTGATGA
12659889 GTCTCAAACT
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:0.16, C:0.04, G:0.24, T:0.56
Consensus pattern (13 bp):
TTGTTTTGATGAC
Found at i:12659885 original size:24 final size:23
Alignment explanation
Indices: 12659835--12659887 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 23
12659825 AAAATGATAC
*
12659835 TTTTGTTGTTGTGTTTGATGATG
1 TTTTGATGTTGTGTTTGATGATG
12659858 --TTGATGTTGT-TTTGATGACTTG
1 TTTTGATGTTGTGTTTGATGA--TG
12659880 TTTTGATG
1 TTTTGATG
12659888 AGTCTCAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 8 0.32
21 9 0.36
22 2 0.08
24 6 0.24
ACGTcount: A:0.11, C:0.02, G:0.28, T:0.58
Consensus pattern (23 bp):
TTTTGATGTTGTGTTTGATGATG
Found at i:12664619 original size:4 final size:4
Alignment explanation
Indices: 12664610--12664658 Score: 50
Period size: 4 Copynumber: 13.0 Consensus size: 4
12664600 TAGGGCCAAA
* * *
12664610 TATT TATT TATT TATC T-TT TATA TA-T TATT T-GT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
12664655 TATT
1 TATT
12664659 CTTCTTTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
3 6 0.17
4 30 0.83
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:12672223 original size:9 final size:9
Alignment explanation
Indices: 12672204--12672298 Score: 57
Period size: 9 Copynumber: 10.1 Consensus size: 9
12672194 TGGGTGAAAG
*
12672204 AATGAAGAA
1 AATGAAAAA
12672213 AATGAAAAA
1 AATGAAAAA
* * *
12672222 AAAGAATAC
1 AATGAAAAA
*
12672231 AATTAAAAA
1 AATGAAAAA
* *
12672240 GAAAGGAAAA
1 -AATGAAAAA
12672250 AA-GAAAACA
1 AATGAAAA-A
12672259 AATGAAAAA
1 AATGAAAAA
*
12672268 AAAGAAAGAAA
1 AATG-AA-AAA
*
12672279 AAAGAGAAAA
1 AATGA-AAAA
12672289 AATGAAAAA
1 AATGAAAAA
12672298 A
1 A
12672299 GAATACTCAA
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
8 4 0.06
9 33 0.50
10 21 0.32
11 8 0.12
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (9 bp):
AATGAAAAA
Found at i:12672256 original size:17 final size:17
Alignment explanation
Indices: 12672236--12672301 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
12672226 AATACAATTA
*
12672236 AAAAGAAAGGAAAAAAG
1 AAAAGAAATGAAAAAAG
*
12672253 AAAACAAATG--AAAA-
1 AAAAGAAATGAAAAAAG
12672267 AAAAGAAA-GAAAAAAG
1 AAAAGAAATGAAAAAAG
12672283 AGAAA-AAATGAAAAAAG
1 A-AAAGAAATGAAAAAAG
12672300 AA
1 AA
12672302 TACTCAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
13 1 0.02
14 7 0.17
15 8 0.20
16 5 0.12
17 20 0.49
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAAGAAATGAAAAAAG
Found at i:12672266 original size:27 final size:28
Alignment explanation
Indices: 12672204--12672298 Score: 86
Period size: 27 Copynumber: 3.4 Consensus size: 28
12672194 TGGGTGAAAG
* * * *
12672204 AATGAAGAAAATGAAAAAAAAGAATACA
1 AATGAAAAAAAAGAGAAAAAAGAAAACA
* * *
12672232 ATTAAAAAGAAAG-GAAAAAAGAAAACA
1 AATGAAAAAAAAGAGAAAAAAGAAAACA
12672259 AATGAAAAAAAAGAAAGAAAAAAGAGAAA-A
1 AATGAAAAAAAAG--AGAAAAAAGA-AAACA
12672289 AATGAAAAAA
1 AATGAAAAAA
12672299 GAATACTCAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 22 0.42
28 8 0.15
30 20 0.38
31 3 0.06
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (28 bp):
AATGAAAAAAAAGAGAAAAAAGAAAACA
Found at i:12672292 original size:30 final size:31
Alignment explanation
Indices: 12672235--12672298 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
12672225 GAATACAATT
12672235 AAAAAGAAAGGAAAAAAGAAAACAAATGAAA
1 AAAAAGAAAGGAAAAAAGAAAACAAATGAAA
12672266 AAAAAGAAA-GAAAAAAGAGAAA-AAATGAAA
1 AAAAAGAAAGGAAAAAAGA-AAACAAATGAAA
12672296 AAA
1 AAA
12672299 GAATACTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.03
Consensus pattern (31 bp):
AAAAAGAAAGGAAAAAAGAAAACAAATGAAA
Found at i:12673771 original size:45 final size:44
Alignment explanation
Indices: 12673701--12673935 Score: 296
Period size: 45 Copynumber: 5.2 Consensus size: 44
12673691 GCCAAAAAGT
* * * *
12673701 AATTTATTTATTTT-AAAGTCCTGGTTGCCTCTGTTTAGAAAAGT
1 AATTTATTT-TTTTCAAAGTCGTGGTTGCCTCTATTTAGAAGAGC
* *
12673745 AATTTATTTTATTTCAAAGTCGTGGTTGCCTCTGTTTAGAGGAGC
1 AATTTATTTT-TTTCAAAGTCGTGGTTGCCTCTATTTAGAAGAGC
*
12673790 AATTTATTTTTTTCAAAGTCAGTGGTTGCCTCTATTTAGAGGAGC
1 AATTTATTTTTTTCAAAGTC-GTGGTTGCCTCTATTTAGAAGAGC
* *
12673835 AATTTATTTTTTTTTCAAAAGTTGTGGTTGCTTCTATTTAGAAGAGC
1 AATTTA--TTTTTTTC-AAAGTCGTGGTTGCCTCTATTTAGAAGAGC
*
12673882 AATTTA-TTTTTTCAAAAGTTGTGG-TGCCTCTATTTAGAAGAGC
1 AATTTATTTTTTTC-AAAGTCGTGGTTGCCTCTATTTAGAAGAGC
12673925 AATTTATTTTT
1 AATTTATTTTT
12673936 GAAATTGTGG
Statistics
Matches: 175, Mismatches: 9, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
43 25 0.14
44 44 0.25
45 65 0.37
47 36 0.21
48 5 0.03
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.46
Consensus pattern (44 bp):
AATTTATTTTTTTCAAAGTCGTGGTTGCCTCTATTTAGAAGAGC
Found at i:12673959 original size:40 final size:43
Alignment explanation
Indices: 12673726--12673964 Score: 191
Period size: 45 Copynumber: 5.4 Consensus size: 43
12673716 AAGTCCTGGT
** * * *
12673726 TGCCTCTGTTTAGAAAAGTAATTTATTTTATTTC-AAAGTCGTGG
1 TGCCTCTACTTAGAAGAGCAATTTA-TTT-TTTCAAAAGTTGTGG
** * *
12673770 TTGCCTCTGTTTAGAGGAGCAATTTATTTTTTTC-AAAGTCAGTGG
1 -TGCCTCTACTTAGAAGAGCAATTTA-TTTTTTCAAAAGT-TGTGG
* *
12673815 TTGCCTCTATTTAGAGGAGCAATTTATTTTTTTTTCAAAAGTTGTGG
1 -TGCCTCTACTTAGAAGAGCAATTTA---TTTTTTCAAAAGTTGTGG
* *
12673862 TTGCTTCTATTTAGAAGAGCAATTTATTTTTTCAAAAGTTGTGG
1 -TGCCTCTACTTAGAAGAGCAATTTATTTTTTCAAAAGTTGTGG
* *
12673906 TGCCTCTATTTAGAAGAGCAATTTA-TTTTT-GAAA-TTGTGG
1 TGCCTCTACTTAGAAGAGCAATTTATTTTTTCAAAAGTTGTGG
* * *
12673946 TGCCTTTGCTTAGAGGAGC
1 TGCCTCTACTTAGAAGAGC
12673965 TTTGTTTATT
Statistics
Matches: 176, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
40 21 0.12
41 3 0.02
42 5 0.03
43 24 0.14
44 27 0.15
45 55 0.31
47 36 0.20
48 5 0.03
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.43
Consensus pattern (43 bp):
TGCCTCTACTTAGAAGAGCAATTTATTTTTTCAAAAGTTGTGG
Found at i:12674079 original size:43 final size:43
Alignment explanation
Indices: 12673756--12674118 Score: 254
Period size: 44 Copynumber: 8.3 Consensus size: 43
12673746 ATTTATTTTA
* * * *
12673756 TTTCAAAGTCGTGGTTGCCTCTGTTTAGAGGAGCAATTTATT-TT
1 TTTCAAAGTTGTGG-TGCCTCTATTTAGAGGAGC-TTTTTTTATT
*
12673800 TTTCAAAGTCAGTGGTTGCCTCTATTTAGAGGAGCAATTTATTTT-TT
1 TTTCAAAGT-TGTGG-TGCCTCTATTTAGAGGAGC--TTT-TTTTATT
* * ** *
12673847 TTTCAAAAGTTGTGGTTGCTTCTATTTAGAAGAGCAATTTAT-TT
1 TTTC-AAAGTTGTGG-TGCCTCTATTTAGAGGAGCTTTTTTTATT
* **
12673891 TTTCAAAAGTTGTGGTGCCTCTATTTAGAAGAGC--AATTTATT
1 TTTC-AAAGTTGTGGTGCCTCTATTTAGAGGAGCTTTTTTTATT
* * ** *
12673933 TTTGAAA-TTGTGGTGCCTTTGCTTAGAGGAGCTTTGTTTATT
1 TTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCTTTTTTTATT
** * * * *
12673975 TTTCTAAAGTCATTGAGCCTCTGTTTAGAGGAGAC-TTGTTTACTT
1 TTTC-AAAGTTGTGGTGCCTCTATTTAGAGGAG-CTTTTTTTA-TT
* * *
12674020 TTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTTTTTATT
1 TTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCTTTTTTTATT
* * * * *
12674063 TTTCAAAGTCGTTGAGCCTCTATTTAGATGAGCTTTGTTTATTT
1 TTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCTTTTTTTA-TT
*
12674107 TTTAAAAGTTGT
1 TTTCAAAGTTGT
12674119 TGAGTCTTTA
Statistics
Matches: 269, Mismatches: 37, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
40 21 0.08
41 5 0.02
42 14 0.05
43 61 0.23
44 98 0.36
45 31 0.12
46 3 0.01
47 31 0.12
48 5 0.02
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (43 bp):
TTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCTTTTTTTATT
Found at i:12674089 original size:87 final size:86
Alignment explanation
Indices: 12673747--12674118 Score: 281
Period size: 87 Copynumber: 4.2 Consensus size: 86
12673737 AGAAAAGTAA
* * *
12673747 TTTATTTTATTTCAAAGTCGTGGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTTTC-AAAGTCA
1 TTTA-TTT-TTTCAAAGTTGTGG-AGCCTCTGTTTAGAGGAGC-ATTTTTTTTTTTCAAAAGTC-
*
12673811 GTGGTTGCCTCTATTTAGAGGAGCAATT-
61 GTGG-AGCCTCTATTTAGAGGAGC--TTG
* * * * * * * *
12673839 TATTTTTTTTTCAAAAGTTGTGGTTGCTTCTATTTAGAAGAGCAATTTATTTTTTCAAAAGTTGT
1 T-TTATTTTTTC-AAAGTTGTGG-AGCCTCTGTTTAGAGGAGCATTTTTTTTTTTCAAAAGTCGT
* * **
12673904 GGTGCCTCTATTTAGAAGAGC-AA
63 GGAGCCTCTATTTAGAGGAGCTTG
* * * * * * *
12673927 TTTA-TTTTTGAAA-TTGTGGTGCCTTTGCTTAGAGGAGC-TTTGTTTATTTTTCTAAAGTCATT
1 TTTATTTTTTCAAAGTTGTGGAGCCTCTGTTTAGAGGAGCATTT-TTT-TTTTTCAAAAGTCGTG
*
12673989 GAGCCTCTGTTTAGAGGAGACTTG
64 GAGCCTCTATTTAGAGGAG-CTTG
* * * *
12674013 TTTACTTTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTTTTTATTTTTC-AAAGTCGTTG
1 TTTATTTTTTCAAAGTTGTGGAGCCTCTGTTTAGAGGAGCATTTTTT-TTTTTCAAAAGTCGTGG
*
12674077 AGCCTCTATTTAGATGAGCTTTG
65 AGCCTCTATTTAGAGGAGC-TTG
*
12674100 TTTATTTTTTAAAAGTTGT
1 TTTATTTTTTCAAAGTTGT
12674119 TGAGTCTTTA
Statistics
Matches: 229, Mismatches: 39, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
82 2 0.01
83 16 0.07
84 34 0.15
85 4 0.02
86 10 0.04
87 55 0.24
88 32 0.14
89 3 0.01
90 18 0.08
91 18 0.08
92 35 0.15
93 2 0.01
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.46
Consensus pattern (86 bp):
TTTATTTTTTCAAAGTTGTGGAGCCTCTGTTTAGAGGAGCATTTTTTTTTTTCAAAAGTCGTGGA
GCCTCTATTTAGAGGAGCTTG
Found at i:12674138 original size:87 final size:88
Alignment explanation
Indices: 12673947--12674143 Score: 272
Period size: 87 Copynumber: 2.2 Consensus size: 88
12673937 AAATTGTGGT
*
12673947 GCCTTTGCTTAGAGGAGCTTTGTTTATTTTTCTAAAGTCATTGAGCCTCTGTTTAGAGGAGACTT
1 GCCTTTGCTTAGAGGAGCTTTGTTTATTTTTCTAAAGTCATTGAGCCTCTATTTAGAGGAGACTT
*
12674012 GTTTACTTTTTCAAAGTTGTTGA
66 GTTTACTTTTTAAAAGTTGTTGA
* * * * *
12674035 GCCTCTGTTTAGAGGAGCTTTTTTTATTTTTC-AAAGTCGTTGAGCCTCTATTTAGATGAG-CTT
1 GCCTTTGCTTAGAGGAGCTTTGTTTATTTTTCTAAAGTCATTGAGCCTCTATTTAGAGGAGAC-T
*
12674098 TGTTTATTTTTTAAAAGTTGTTGA
65 TGTTTACTTTTTAAAAGTTGTTGA
* * *
12674122 GTCTTTACTTAAAGGAGCTTTG
1 GCCTTTGCTTAGAGGAGCTTTG
12674144 ATAAAAAAAA
Statistics
Matches: 94, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
86 1 0.01
87 64 0.68
88 29 0.31
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.46
Consensus pattern (88 bp):
GCCTTTGCTTAGAGGAGCTTTGTTTATTTTTCTAAAGTCATTGAGCCTCTATTTAGAGGAGACTT
GTTTACTTTTTAAAAGTTGTTGA
Found at i:12674325 original size:4 final size:4
Alignment explanation
Indices: 12674316--12674368 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
12674306 AGGCCCAAAG
* * *
12674316 ATTT ATTT ATTT ATTT ATTT ATCT -TTT ATAT A-TT ATTT -GTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
12674361 ATTT ATTT
1 ATTT ATTT
12674369 TTTCTTCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
3 6 0.15
4 34 0.85
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:12675230 original size:23 final size:23
Alignment explanation
Indices: 12675204--12675248 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12675194 CGTTTCCATT
* *
12675204 ATTTTTGTATTTGTTTTTTTTAA
1 ATTTTTGTATTTATTTATTTTAA
*
12675227 ATTTTTGTGTTTATTTATTTTA
1 ATTTTTGTATTTATTTATTTTA
12675249 GGAGTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (23 bp):
ATTTTTGTATTTATTTATTTTAA
Found at i:12678613 original size:14 final size:14
Alignment explanation
Indices: 12678570--12678613 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
12678560 TCAAATATTT
* *
12678570 TTTATATTTTTAAT
1 TTTATTTTTTTAAA
12678584 TTTATATTTATTTAAA
1 TTTAT-TTT-TTTAAA
12678600 TTTATTTTTTTAAA
1 TTTATTTTTTTAAA
12678614 AAAATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 11 0.42
15 5 0.19
16 10 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATTTTTTTAAA
Found at i:12689338 original size:2 final size:2
Alignment explanation
Indices: 12689331--12689360 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12689321 CATTATACCA
12689331 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12689361 ATACTGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12689353 original size:17 final size:17
Alignment explanation
Indices: 12689331--12689363 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12689321 CATTATACCA
12689331 ATATATATATATAATAT
1 ATATATATATATAATAT
12689348 ATATATATATATAATA
1 ATATATATATATAATA
12689364 CTGATATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATATATATAATAT
Found at i:12694932 original size:4 final size:4
Alignment explanation
Indices: 12694925--12694951 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12694915 TGATTTATTT
12694925 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
12694952 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:12696278 original size:3 final size:3
Alignment explanation
Indices: 12696270--12696296 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12696260 CCAAAATACA
12696270 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
12696297 TGATAAATGG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12709819 original size:34 final size:32
Alignment explanation
Indices: 12709754--12709819 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 32
12709744 AAAAAAAATC
* * **
12709754 ATATATTAATTATTTGAGTAAAATGTTTGGAT
1 ATATATTAATCATTTGAGCAAAACATTTGGAT
12709786 ATATATTCAATCATTTGAGCCAAAACATTTGGAT
1 ATATATT-AATCATTTGAG-CAAAACATTTGGAT
12709820 TAAATCTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 7 0.25
33 10 0.36
34 11 0.39
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (32 bp):
ATATATTAATCATTTGAGCAAAACATTTGGAT
Found at i:12711241 original size:12 final size:12
Alignment explanation
Indices: 12711224--12711249 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12711214 ATGATGAGTA
12711224 TAAACCCACTTT
1 TAAACCCACTTT
12711236 TAAACCCACTTT
1 TAAACCCACTTT
12711248 TA
1 TA
12711250 CCTTAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAACCCACTTT
Found at i:12711591 original size:22 final size:22
Alignment explanation
Indices: 12711543--12711613 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
12711533 TTATAGTTAC
*
12711543 TAATTTAATTT-ATT-ATAAAT
1 TAATATAATTTAATTAATAAAT
*
12711563 T-TTATATATTATAATTAATAAAT
1 TAATATA-ATT-TAATTAATAAAT
*
12711586 TAATATAATTTTATTAATAAAT
1 TAATATAATTTAATTAATAAAT
*
12711608 AAATAT
1 TAATAT
12711614 CAACCATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.07
20 4 0.10
21 1 0.02
22 19 0.46
23 10 0.24
24 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATATAATTTAATTAATAAAT
Found at i:12712683 original size:28 final size:28
Alignment explanation
Indices: 12712651--12712717 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
12712641 AAGAAAAAAG
12712651 AAAACTTGCAATATTACAGTACATAAAT
1 AAAACTTGCAATATTACAGTACATAAAT
*
12712679 AAAACTTGCAATATTACAGTACGTAAAT
1 AAAACTTGCAATATTACAGTACATAAAT
12712707 AAAACTTGCAA
1 AAAACTTGCAA
12712718 AAGCATTAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (28 bp):
AAAACTTGCAATATTACAGTACATAAAT
Found at i:12715790 original size:13 final size:13
Alignment explanation
Indices: 12715765--12715802 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
12715755 ATTTTGTTTC
12715765 AAGAAAAAA--AA
1 AAGAAAAAATCAA
12715776 AAGAAAAAATCAA
1 AAGAAAAAATCAA
*
12715789 AAGTAAAAATCAA
1 AAGAAAAAATCAA
12715802 A
1 A
12715803 GTTAGATCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 9 0.38
13 15 0.62
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (13 bp):
AAGAAAAAATCAA
Found at i:12716132 original size:17 final size:15
Alignment explanation
Indices: 12716112--12716158 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
12716102 TTTTAGCATA
12716112 TTGTTAGTTATTATATT
1 TTGTT-GTTA-TATATT
12716129 TTGTTGTTATATATT
1 TTGTTGTTATATATT
*
12716144 AT-TTGTTA-ATATT
1 TTGTTGTTATATATT
12716157 TT
1 TT
12716159 ATTATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 7 0.25
16 4 0.14
17 5 0.18
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (15 bp):
TTGTTGTTATATATT
Found at i:12716301 original size:14 final size:15
Alignment explanation
Indices: 12716284--12716316 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12716274 GTTAATTCAT
*
12716284 TTTTTATAT-TATTA
1 TTTTTAAATATATTA
12716298 TTTTTAAATATATTA
1 TTTTTAAATATATTA
12716313 TTTT
1 TTTT
12716317 ATGAGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAAATATATTA
Found at i:12716678 original size:61 final size:61
Alignment explanation
Indices: 12716570--12716685 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
12716560 TAAATTTTAG
* *
12716570 TTTACTAAGTTTTATATATTTCATAATTCCATCATCTATGGTAAGAATTTGTGAGTTTAAA
1 TTTACTAAGTTTTATATATTTCATAATTCCATCATCTATGATAAGAATTTATGAGTTTAAA
* * * * * *
12716631 TTTACTATA-TTTTATGTATTTTATAATTCTATTATTTATGATGAGAATTTATGAG
1 TTTACTA-AGTTTTATATATTTCATAATTCCATCATCTATGATAAGAATTTATGAG
12716686 ATTTTTACTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
61 45 0.98
62 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (61 bp):
TTTACTAAGTTTTATATATTTCATAATTCCATCATCTATGATAAGAATTTATGAGTTTAAA
Found at i:12717239 original size:13 final size:13
Alignment explanation
Indices: 12717221--12717246 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12717211 AAAAGGTTGT
12717221 GGAGCCGCAATTG
1 GGAGCCGCAATTG
12717234 GGAGCCGCAATTG
1 GGAGCCGCAATTG
12717247 ACGAGGCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.15
Consensus pattern (13 bp):
GGAGCCGCAATTG
Found at i:12728286 original size:14 final size:14
Alignment explanation
Indices: 12728267--12728296 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12728257 AGCAATAAGA
12728267 TTTCCTAATCTTTC
1 TTTCCTAATCTTTC
*
12728281 TTTCCTAATGTTTC
1 TTTCCTAATCTTTC
12728295 TT
1 TT
12728297 AGGGTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.60
Consensus pattern (14 bp):
TTTCCTAATCTTTC
Found at i:12731949 original size:22 final size:21
Alignment explanation
Indices: 12731924--12731981 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 21
12731914 CACCACTTTA
12731924 TTGTTTTTTTTTTTCTTTTATT
1 TTGTTTTTTTTTTTCTTTT-TT
*
12731946 TTGTTTTGGTTTTTCTCTTTTTT
1 TTGTTTT--TTTTTTTCTTTTTT
*
12731969 TT-TTTCTTTTTTT
1 TTGTTTTTTTTTTT
12731982 GCAAGTTAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 6 0.19
22 10 0.32
23 4 0.13
24 11 0.35
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.84
Consensus pattern (21 bp):
TTGTTTTTTTTTTTCTTTTTT
Found at i:12736266 original size:10 final size:8
Alignment explanation
Indices: 12736239--12736273 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
12736229 TATTTTTTAA
12736239 ATATAAAT
1 ATATAAAT
12736247 ATATAAAT
1 ATATAAAT
12736255 ATATAATTAT
1 ATATAA--AT
12736265 ATATAAAT
1 ATATAAAT
12736273 A
1 A
12736274 AAAAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:12736280 original size:18 final size:18
Alignment explanation
Indices: 12736245--12736296 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
12736235 TTAAATATAA
* *
12736245 ATATATAAATATATAATT
1 ATATATAAATAAAAAATT
12736263 ATATATAAATAAAAAATT
1 ATATATAAATAAAAAATT
* *
12736281 TTA-AAAAATAAAAAAT
1 ATATATAAATAAAAAAT
12736297 AATTTTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATATATAAATAAAAAATT
Found at i:12739384 original size:2 final size:2
Alignment explanation
Indices: 12739377--12739402 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12739367 GATTCATCAG
12739377 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
12739403 GTCTGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12739977 original size:16 final size:16
Alignment explanation
Indices: 12739956--12739989 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
12739946 AGCATGCTTG
12739956 TTGGCATAATTGCAGA
1 TTGGCATAATTGCAGA
12739972 TTGGCATAATTGCAGA
1 TTGGCATAATTGCAGA
12739988 TT
1 TT
12739990 CTTTATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (16 bp):
TTGGCATAATTGCAGA
Found at i:12741873 original size:2 final size:2
Alignment explanation
Indices: 12741862--12741892 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12741852 AACATGCACT
12741862 TA TA -A 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
12741893 ATTTCTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12745069 original size:19 final size:20
Alignment explanation
Indices: 12745033--12745070 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12745023 TTAACACGAT
12745033 AATCTTTAAAATAAAATAAC
1 AATCTTTAAAATAAAATAAC
*
12745053 AATCTTTATAA-AAAATAA
1 AATCTTTAAAATAAAATAA
12745071 TTGTTAGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
AATCTTTAAAATAAAATAAC
Found at i:12745814 original size:29 final size:28
Alignment explanation
Indices: 12745781--12745869 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
12745771 GAAGTTTTGG
12745781 TTTTAGGGTTTAGAGTATTTAGGATTTAA
1 TTTTAGGGTTTAGAG-ATTTAGGATTTAA
* * * *
12745810 TTTTAGGGTTTGGAGGTTTGGGGTTTAA
1 TTTTAGGGTTTAGAGATTTAGGATTTAA
* *
12745838 TTATAGGGTTT-GAAGGTTT-GAGATTTAA
1 TTTTAGGGTTTAG-AGATTTAG-GATTTAA
12745866 TTTT
1 TTTT
12745870 TATGGTTTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.04
28 35 0.69
29 14 0.27
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.48
Consensus pattern (28 bp):
TTTTAGGGTTTAGAGATTTAGGATTTAA
Found at i:12745885 original size:29 final size:28
Alignment explanation
Indices: 12745803--12745885 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 28
12745793 GAGTATTTAG
* *
12745803 GATTTAATTTTAGGGTTTGGAGGTTTGG
1 GATTTAATTTTAGGGTTTGAAGGTTTGA
* *
12745831 GGTTTAATTATAGGGTTTGAAGGTTTGA
1 GATTTAATTTTAGGGTTTGAAGGTTTGA
*
12745859 GATTTAATTTTTATGGTTTGAAGGTTT
1 GATTTAA-TTTTAGGGTTTGAAGGTTT
12745886 TAAGGTTTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 30 0.64
29 17 0.36
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (28 bp):
GATTTAATTTTAGGGTTTGAAGGTTTGA
Found at i:12746317 original size:17 final size:18
Alignment explanation
Indices: 12746274--12746320 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
12746264 ATCATGCATA
*
12746274 AATATATAAAAAA-ACTC
1 AATATATAAAAAATAATC
*
12746291 AAAATA-AAAAAATAAT-
1 AATATATAAAAAATAATC
12746307 AATATATAAAAAAT
1 AATATATAAAAAAT
12746321 TAGAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (18 bp):
AATATATAAAAAATAATC
Found at i:12746328 original size:33 final size:34
Alignment explanation
Indices: 12746274--12746337 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
12746264 ATCATGCATA
12746274 AATATATAAAAAAACTCAAAA-TAAAAAAATAAT
1 AATATATAAAAAAACTCAAAATTAAAAAAATAAT
* *
12746307 AATATAT-AAAAAATTAGAAAATTAAAAAAAT
1 AATATATAAAAAAACT-CAAAATTAAAAAAAT
12746338 TTTTTTTACC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 7 0.26
33 11 0.41
34 9 0.33
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (34 bp):
AATATATAAAAAAACTCAAAATTAAAAAAATAAT
Found at i:12747104 original size:11 final size:11
Alignment explanation
Indices: 12747088--12747134 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
12747078 ATTAGGTGGA
12747088 GTAGGGTGGCT
1 GTAGGGTGGCT
12747099 GTAGGGATGGC-
1 GTAGGG-TGGCT
*
12747110 -TAGGGTAGGTT
1 GTAGGGT-GGCT
12747121 GTAGGGTGGCT
1 GTAGGGTGGCT
12747132 GTA
1 GTA
12747135 AGGTAAGAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
9 1 0.03
10 7 0.23
11 12 0.40
12 10 0.33
ACGTcount: A:0.15, C:0.06, G:0.51, T:0.28
Consensus pattern (11 bp):
GTAGGGTGGCT
Found at i:12747113 original size:21 final size:21
Alignment explanation
Indices: 12747089--12747131 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12747079 TTAGGTGGAG
12747089 TAGGGT-GGCTGTAGGGATGGC
1 TAGGGTAGGCTGTAGGG-TGGC
*
12747110 TAGGGTAGGTTGTAGGGTGGC
1 TAGGGTAGGCTGTAGGGTGGC
12747131 T
1 T
12747132 GTAAGGTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.14, C:0.07, G:0.51, T:0.28
Consensus pattern (21 bp):
TAGGGTAGGCTGTAGGGTGGC
Found at i:12747292 original size:16 final size:17
Alignment explanation
Indices: 12747256--12747301 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
12747246 TTTAGTTTTA
* *
12747256 ATTAAACAATATTATTT
1 ATTAAAAAAAATTATTT
12747273 ATTAAAAAAAATTA-TT
1 ATTAAAAAAAATTATTT
*
12747289 ATTAACAAAAATT
1 ATTAAAAAAAATT
12747302 GAAATTAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTAAAAAAAATTATTT
Found at i:12749338 original size:37 final size:37
Alignment explanation
Indices: 12749297--12749370 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
12749287 AAGAACCTAT
*
12749297 TCGAATATGAGTGGTAATGTTCTACAGTGATTGAGAA
1 TCGAATATAAGTGGTAATGTTCTACAGTGATTGAGAA
*
12749334 TCGAATATAAGTGGTAATGTTCTGCAGTGATTGAGAA
1 TCGAATATAAGTGGTAATGTTCTACAGTGATTGAGAA
12749371 ATGCTAGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.32
Consensus pattern (37 bp):
TCGAATATAAGTGGTAATGTTCTACAGTGATTGAGAA
Found at i:12757264 original size:19 final size:20
Alignment explanation
Indices: 12757240--12757279 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
12757230 TGATAGTGAA
12757240 AATTTGTGAGAG-TTTCAGT
1 AATTTGTGAGAGTTTTCAGT
12757259 AATTTGTGAGAGTTTTCAGT
1 AATTTGTGAGAGTTTTCAGT
12757279 A
1 A
12757280 TCTGAGACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.42
Consensus pattern (20 bp):
AATTTGTGAGAGTTTTCAGT
Found at i:12767743 original size:98 final size:98
Alignment explanation
Indices: 12767620--12767807 Score: 281
Period size: 98 Copynumber: 1.9 Consensus size: 98
12767610 AAATCTTATT
*
12767620 GAATCCTAGATTATTTGAGATTTGAAGACTGAAAAA-TGTTCTATAAAATCG-CGCTAAAACACT
1 GAATCCTAGATTATTTGAGATTTGAA-AATGAAAAAGTGTTCTATAAAAT-GACGCTAAAACACT
* *
12767683 ACCAAAAATAGAGGGGGAAGCCTAGAGGTTATATG
64 ACCAAAAACAAAGGGGGAAGCCTAGAGGTTATATG
* * * *
12767718 GAATCCTAGATTATTTGAGATTTGAAAATTAAAAAGTTTTCTATAAAATGACGCTAGAACACTGC
1 GAATCCTAGATTATTTGAGATTTGAAAATGAAAAAGTGTTCTATAAAATGACGCTAAAACACTAC
12767783 CAAAAACAAAGGGGGAAGCCTAGAG
66 CAAAAACAAAGGGGGAAGCCTAGAG
12767808 ATTCTACCAA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
97 8 0.10
98 73 0.90
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (98 bp):
GAATCCTAGATTATTTGAGATTTGAAAATGAAAAAGTGTTCTATAAAATGACGCTAAAACACTAC
CAAAAACAAAGGGGGAAGCCTAGAGGTTATATG
Found at i:12768497 original size:12 final size:11
Alignment explanation
Indices: 12768471--12768562 Score: 57
Period size: 12 Copynumber: 8.1 Consensus size: 11
12768461 TTGATTTTGA
12768471 TTTTAT-TTA-
1 TTTTATGTTAT
12768480 TTTTATGTTGAT
1 TTTTATGTT-AT
12768492 TTTTATGTTAT
1 TTTTATGTTAT
*
12768503 TTATTTTGTTTATT
1 TT-TTATG-TTA-T
*
12768517 TTTTATGATAT
1 TTTTATGTTAT
*
12768528 TATTGT-TATTAT
1 T-TT-TATGTTAT
*
12768540 TATTACTGTTA-
1 TTTTA-TGTTAT
12768551 TTTTATGTTAT
1 TTTTATGTTAT
12768562 T
1 T
12768563 ACTAGTAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
9 6 0.09
10 8 0.12
11 13 0.20
12 26 0.41
13 8 0.12
14 3 0.05
ACGTcount: A:0.21, C:0.01, G:0.09, T:0.70
Consensus pattern (11 bp):
TTTTATGTTAT
Found at i:12768528 original size:25 final size:26
Alignment explanation
Indices: 12768474--12768536 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
12768464 ATTTTGATTT
*
12768474 TATTTATTTTATGTTGATTTTTATGT
1 TATTTATTTTATGTTGATTTTTATGA
*
12768500 TATTTA-TTT-TGTTTATTTTTTATGA
1 TATTTATTTTATGTTGA-TTTTTATGA
12768525 TA-TTATTGTTAT
1 TATTTATT-TTAT
12768537 TATTATTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
24 8 0.26
25 14 0.45
26 8 0.26
27 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.70
Consensus pattern (26 bp):
TATTTATTTTATGTTGATTTTTATGA
Found at i:12768783 original size:16 final size:17
Alignment explanation
Indices: 12768764--12768802 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
12768754 TTTTCCTAAA
*
12768764 AAATAAAATTAAA-AAT
1 AAATAAAATAAAATAAT
12768780 AAATAAAATAAAATAAT
1 AAATAAAATAAAATAAT
12768797 -AATAAA
1 AAATAAA
12768803 TTGTTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAATAAAATAAT
Found at i:12768802 original size:20 final size:21
Alignment explanation
Indices: 12768763--12768803 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
12768753 TTTTTCCTAA
12768763 AAAATAAAATTAAAAATAAAT
1 AAAATAAAATTAAAAATAAAT
*
12768784 AAAATAAAA-TAATAATAAAT
1 AAAATAAAATTAAAAATAAAT
12768804 TGTTTAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATAAAATTAAAAATAAAT
Found at i:12769152 original size:19 final size:19
Alignment explanation
Indices: 12769127--12769170 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12769117 ATAAAAAAGG
*
12769127 AAATAACAATAAACAATAA
1 AAATAACAAAAAACAATAA
* *
12769146 CAATAACAAAAAATAATAA
1 AAATAACAAAAAACAATAA
12769165 AAATAA
1 AAATAA
12769171 TCACAATAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (19 bp):
AAATAACAAAAAACAATAA
Found at i:12771697 original size:39 final size:39
Alignment explanation
Indices: 12771637--12771722 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
12771627 CAATAACAGG
* *
12771637 ATTAAAGTAATTCATTCTGATGACTCATAGTTTTTGAGA
1 ATTAGAGTAATTCATTCTGATGACTCATAGTTTTCGAGA
* *
12771676 ATTAGAGTAATTCATTTTGATGACTCATGGTTTTCGAGA
1 ATTAGAGTAATTCATTCTGATGACTCATAGTTTTCGAGA
12771715 ATTAGAGT
1 ATTAGAGT
12771723 TCTCTTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (39 bp):
ATTAGAGTAATTCATTCTGATGACTCATAGTTTTCGAGA
Found at i:12784992 original size:25 final size:26
Alignment explanation
Indices: 12784964--12785021 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
12784954 AATCATTATA
12784964 TTTTTA-TTGTATT-AAAATAAGATTT
1 TTTTTATTTGTATTCAAAA-AAGATTT
*
12784989 TTTTTATTTGTATTCAAAAAAGTTTT
1 TTTTTATTTGTATTCAAAAAAGATTT
12785015 TATTTTA
1 T-TTTTA
12785022 ATTAAAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 6 0.21
26 14 0.48
27 9 0.31
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (26 bp):
TTTTTATTTGTATTCAAAAAAGATTT
Found at i:12784993 original size:26 final size:25
Alignment explanation
Indices: 12784964--12785015 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
12784954 AATCATTATA
12784964 TTTTTA-TTGTATT-AAAATAAGATTT
1 TTTTTATTTGTATTCAAAA-AAG-TTT
12784989 TTTTTATTTGTATTCAAAAAAGTTT
1 TTTTTATTTGTATTCAAAAAAGTTT
12785014 TT
1 TT
12785016 ATTTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 11 0.44
26 10 0.40
27 4 0.16
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (25 bp):
TTTTTATTTGTATTCAAAAAAGTTT
Found at i:12785028 original size:21 final size:21
Alignment explanation
Indices: 12784989--12785033 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
12784979 AATAAGATTT
12784989 TTTTTATTTGTATTCAAAAAAG
1 TTTTTATTTGTATTC-AAAAAG
12785011 TTTTTATTT-TAATT-AAAAAG
1 TTTTTATTTGT-ATTCAAAAAG
12785031 TTT
1 TTT
12785034 ATTTATGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.41
21 1 0.05
22 12 0.55
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTTATTTGTATTCAAAAAG
Found at i:12785080 original size:30 final size:31
Alignment explanation
Indices: 12785042--12785127 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 31
12785032 TTATTTATGC
12785042 TAAG-AATTTATTTAAGTACAAATTAAAAAT
1 TAAGAAATTTATTTAAGTACAAATTAAAAAT
* *
12785072 TAA-AAATTTTTTTGAA-TACAAATTAAAATT
1 TAAGAAATTTATTT-AAGTACAAATTAAAAAT
** *
12785102 TAAGTGA-TTATTTAAGTGCAAATTAA
1 TAAGAAATTTATTTAAGTACAAATTAA
12785128 GTGTTAAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
29 2 0.04
30 41 0.89
31 3 0.07
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (31 bp):
TAAGAAATTTATTTAAGTACAAATTAAAAAT
Found at i:12789425 original size:19 final size:17
Alignment explanation
Indices: 12789374--12789416 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
12789364 ATATTTTTTT
12789374 AATTTTGATTTTTTTGGG
1 AATTTTGA-TTTTTTGGG
* *
12789392 ATTTTCTTATTTTTTGGG
1 AATTT-TGATTTTTTGGG
12789410 AATTTTG
1 AATTTTG
12789417 GATTATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
17 1 0.05
18 17 0.85
19 2 0.10
ACGTcount: A:0.16, C:0.02, G:0.19, T:0.63
Consensus pattern (17 bp):
AATTTTGATTTTTTGGG
Found at i:12789724 original size:24 final size:24
Alignment explanation
Indices: 12789678--12789737 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
12789668 CTTGAGTTTC
12789678 GGATATCACCACCAAAGGAAACTT
1 GGATATCACCACCAAAGGAAACTT
** *
12789702 GGATATCGTCACCAAAAGG-AACTA
1 GGATATCACCACC-AAAGGAAACTT
*
12789726 AGATATCACCAC
1 GGATATCACCAC
12789738 TAAGAAAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.17
Consensus pattern (24 bp):
GGATATCACCACCAAAGGAAACTT
Found at i:12790260 original size:52 final size:54
Alignment explanation
Indices: 12790203--12790307 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 54
12790193 GCTAATGATG
* *
12790203 CAAAAGCAAAGTC-AAAGATGCAAATGCTTAAAATCTT-TTTTCTTAAATTTTC
1 CAAAAGCAAAGTCAAAAGATACAAACGCTTAAAATCTTCTTTTCTTAAATTTTC
* * *
12790255 CAAAAGCCAAGTCAAAATATACAAACGTTTAAAATCTTCTTTTCTTAAATTTT
1 CAAAAGCAAAGTCAAAAGATACAAACGCTTAAAATCTTCTTTTCTTAAATTTT
12790308 TCAAGAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 12 0.26
53 20 0.43
54 14 0.30
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (54 bp):
CAAAAGCAAAGTCAAAAGATACAAACGCTTAAAATCTTCTTTTCTTAAATTTTC
Found at i:12794293 original size:31 final size:32
Alignment explanation
Indices: 12794258--12794319 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
12794248 ATGGTCCATA
*
12794258 TACTCCAACGAAATTTAAAATTTAGT-TCTTG
1 TACTCCAACGAAACTTAAAATTTAGTCTCTTG
** *
12794289 TACTCGTACGAAACTTGAAATTTAGTCTCTT
1 TACTCCAACGAAACTTAAAATTTAGTCTCTT
12794320 TAATATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (32 bp):
TACTCCAACGAAACTTAAAATTTAGTCTCTTG
Found at i:12796573 original size:13 final size:13
Alignment explanation
Indices: 12796552--12796600 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
12796542 GTAAAAAGGG
12796552 AAGAA-ATAAAGA
1 AAGAAGATAAAGA
12796564 AAGAAGATAAAAGA
1 AAGAAGAT-AAAGA
*
12796578 AACATAGA-AAAGA
1 AAGA-AGATAAAGA
12796591 AA-AAGATAAA
1 AAGAAGATAAA
12796601 AACAATAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
11 3 0.09
12 9 0.28
13 9 0.28
14 8 0.25
15 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.08
Consensus pattern (13 bp):
AAGAAGATAAAGA
Found at i:12796601 original size:13 final size:13
Alignment explanation
Indices: 12796559--12796601 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
12796549 GGGAAGAAAT
12796559 AAAGAAAGAAGATA
1 AAAGAAA-AAGATA
* * *
12796573 AAAGAAACATAGA
1 AAAGAAAAAGATA
12796586 AAAGAAAAAGATA
1 AAAGAAAAAGATA
12796599 AAA
1 AAA
12796602 ACAATAATAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.07
Consensus pattern (13 bp):
AAAGAAAAAGATA
Found at i:12796612 original size:3 final size:3
Alignment explanation
Indices: 12796604--12796660 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
12796594 AGATAAAAAC
12796604 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12796652 AAT AAT AAT
1 AAT AAT AAT
12796661 TTAAAATGAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12797776 original size:44 final size:45
Alignment explanation
Indices: 12797721--12797812 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 45
12797711 GGAGTTTTAA
* *
12797721 TGAAATTTAAAC-TTAAATACTCAGATTTCACCACTGAGTGAATT
1 TGAAAATTAAACTTTAAATACTCAGATATCACCACTGAGTGAATT
* **
12797765 TGAAAATTAAACTTTGAATACTCAGATATCGTCACTGAGTGAATT
1 TGAAAATTAAACTTTAAATACTCAGATATCACCACTGAGTGAATT
12797810 TGA
1 TGA
12797813 TTAAAACTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 11 0.26
45 31 0.74
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (45 bp):
TGAAAATTAAACTTTAAATACTCAGATATCACCACTGAGTGAATT
Found at i:12798115 original size:162 final size:156
Alignment explanation
Indices: 12797715--12798164 Score: 481
Period size: 162 Copynumber: 2.8 Consensus size: 156
12797705 TTAAAGGGAG
* * * * *
12797715 TTTTAATGAAATTTAAACTTAAATACTC-AGATTTCACCACTGAGTGAATTTGAAAATTAAACTT
1 TTTTAATAAAATTTAGACTTGAATA-TCGAGATATCACCACTGAGTGAATTTGAAAATTGAACTT
** * *
12797779 TGAATACTCAGATATCGTCACTGAGTGAATTTGATTAAAACTCGAATATCACCACTAAGAGAATT
65 TGAATACT-AGATATCACCACTGAGTGAATTTGATTAAAACTCAAATATCACCACCAAGAGAATT
* * * * * * *
12797844 TTAATTTTAGATTTCACCATTGAGAACA
129 TTAATCTCAGATATCAACATTAAAAAAA
** * *
12797872 TTTTAATAAAATTTAGACTTGAATATTTAGATATCACCACTGAGTTAATTTGAAAATTGAATTTT
1 TTTTAATAAAATTTAGACTTGAATATCGAGATATCACCACTGAGTGAATTTGAAAATTGAACTTT
*
12797937 GAATACCTAGATATCACCACTGAGTGAATTTGATTAAAACTCAAATATCATCACCAAGAGAATTT
66 GAATA-CTAGATATCACCACTGAGTGAATTTGATTAAAACTCAAATATCACCACCAAGAGAATTT
*
12798002 TAATGAAAGCTCGGATATCAACATTAAAAAAA
130 TAAT-----CTCAGATATCAACATTAAAAAAA
* ** *
12798034 TTTTAATAAAATTTAGACTTGAATACTCGA-ATATTATGACTGAGTGAATTTGAAAATTGAACTC
1 TTTTAATAAAATTTAGACTTGAATA-TCGAGATATCACCACTGAGTGAATTTGAAAATTGAACTT
* ** ** * * * *
12798098 TAAATACTAGAATATCACCACCAAGTGAATTTGATTAAAGTTTAGATATCACCATCGAGAGAATT
65 TGAATACTAG-ATATCACCACTGAGTGAATTTGATTAAAACTCAAATATCACCACCAAGAGAATT
12798163 TT
129 TT
12798165 CATAAAAGTT
Statistics
Matches: 245, Mismatches: 39, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
156 1 0.00
157 116 0.47
158 2 0.01
161 4 0.02
162 120 0.49
163 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (156 bp):
TTTTAATAAAATTTAGACTTGAATATCGAGATATCACCACTGAGTGAATTTGAAAATTGAACTTT
GAATACTAGATATCACCACTGAGTGAATTTGATTAAAACTCAAATATCACCACCAAGAGAATTTT
AATCTCAGATATCAACATTAAAAAAA
Found at i:12798199 original size:162 final size:162
Alignment explanation
Indices: 12797715--12798248 Score: 419
Period size: 162 Copynumber: 3.3 Consensus size: 162
12797705 TTAAAGGGAG
* * * * * *
12797715 TTTTAATGAAATTTAAACTTAAATACTC-AGATTTCACCACTGAGTGAATTTGAAAATTAAACTT
1 TTTTAATAAAATTTAGACTTGAATA-TCGAGATATCACCACTGAGTGAATTTGAAAATTGAACTC
* ** ** * *
12797779 TGAATA-CTCAGATATCGTCACTGAGTGAATTTGATTAAAACTCGAATATCACCACTAAGAGAAT
65 TAAATACCT-AGATATCACCACCAAGTGAATTTGATTAAAACTCAAATATCACCACCAAGAGAAT
* * * * * **
12797843 TTTAAT-----TTTAGATTTCACCA-TTGAGAACA
129 TTTAATAAAAGCTCAAATATCAACAGTAAAGAA-A
** * * *
12797872 TTTTAATAAAATTTAGACTTGAATATTTAGATATCACCACTGAGTTAATTTGAAAATTGAATTTT
1 TTTTAATAAAATTTAGACTTGAATATCGAGATATCACCACTGAGTGAATTTGAAAATTGAACTCT
* ** *
12797937 GAATACCTAGATATCACCACTGAGTGAATTTGATTAAAACTCAAATATCATCACCAAGAGAATTT
66 AAATACCTAGATATCACCACCAAGTGAATTTGATTAAAACTCAAATATCACCACCAAGAGAATTT
* ** * *
12798002 TAATGAAAGCTCGGATATCAACATTAAAAAAA
131 TAATAAAAGCTCAAATATCAACAGTAAAGAAA
* **
12798034 TTTTAATAAAATTTAGACTTGAATACTCGA-ATATTATGACTGAGTGAATTTGAAAATTGAACTC
1 TTTTAATAAAATTTAGACTTGAATA-TCGAGATATCACCACTGAGTGAATTTGAAAATTGAACTC
** * * * *
12798098 TAAATA-CTAGAATATCACCACCAAGTGAATTTGATTAAAGTTTAGATATCACCATCGAGAGAAT
65 TAAATACCTAG-ATATCACCACCAAGTGAATTTGATTAAAACTCAAATATCACCACCAAGAGAAT
* * * * *
12798162 TTTCATAAAAGTTTAAATTTTGCTAC-GT-AAGAAA
129 TTTAATAAAAGCTCAAA-TAT-CAACAGTAAAGAAA
* * * * **
12798196 TTTTAATAAAATATAGCCTTGACTATTTG-GATATCACCACCAAGTGAATTTGA
1 TTTTAATAAAATTTAGACTTGAATA-TCGAGATATCACCACTGAGTGAATTTGA
12798249 TTAAAACTTG
Statistics
Matches: 305, Mismatches: 59, Indels: 21
0.79 0.15 0.05
Matches are distributed among these distances:
156 1 0.00
157 116 0.38
158 2 0.01
161 4 0.01
162 170 0.56
163 9 0.03
164 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (162 bp):
TTTTAATAAAATTTAGACTTGAATATCGAGATATCACCACTGAGTGAATTTGAAAATTGAACTCT
AAATACCTAGATATCACCACCAAGTGAATTTGATTAAAACTCAAATATCACCACCAAGAGAATTT
TAATAAAAGCTCAAATATCAACAGTAAAGAAA
Found at i:12798297 original size:117 final size:117
Alignment explanation
Indices: 12798100--12798365 Score: 306
Period size: 117 Copynumber: 2.3 Consensus size: 117
12798090 TTGAACTCTA
**
12798100 AATAC-TAGAATATCACCACCAAGTGAATTTGATTAAAGTTTAGATATCACCATCGAGAGAATTT
1 AATACTTA-AATATCACCACCAAGTGAATTTGATTAAAACTTAGATATCACCATCGAGAGAATTT
* * * *
12798164 TCATAAAAGTTTAAATTTTG-CTACGT-AAGAAATTTTAATAAAATATAGCCTTG
65 TAATAAAAGCTCAAATTTTGTC-A-GTGAAGAAATTTTAATAAAATATAGACTTG
* * ** * *
12798217 ACTATTTGGATATCACCACCAAGTGAATTTGATTAAAACTT-GCATATTACCATTGAGAGAATTT
1 AATACTTAAATATCACCACCAAGTGAATTTGATTAAAACTTAG-ATATCACCATCGAGAGAATTT
* * * *
12798281 TAATGAAAGCTCAAATTTTGTCATTGAAGAAATTTTAATAAAATTTAGACTTT
65 TAATAAAAGCTCAAATTTTGTCAGTGAAGAAATTTTAATAAAATATAGACTTG
* *
12798334 AATACTTAAATATTACCACCGAGTGAATTTGA
1 AATACTTAAATATCACCACCAAGTGAATTTGA
12798366 AAATTGAACT
Statistics
Matches: 123, Mismatches: 22, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
116 2 0.02
117 119 0.97
118 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (117 bp):
AATACTTAAATATCACCACCAAGTGAATTTGATTAAAACTTAGATATCACCATCGAGAGAATTTT
AATAAAAGCTCAAATTTTGTCAGTGAAGAAATTTTAATAAAATATAGACTTG
Found at i:12804865 original size:40 final size:40
Alignment explanation
Indices: 12804821--12804901 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
12804811 ATATTATTTT
*
12804821 TATTATATAT-AATTA-ATTAAT-AATATCATGTTATTAATAA
1 TATTAT-TATCAATTATATTAATCAAT-T-ATATTATTAATAA
*
12804861 TATTATTATCATTTATATTAATCAATTATATTATTAATAA
1 TATTATTATCAATTATATTAATCAATTATATTATTAATAA
12804901 T
1 T
12804902 TAAATTAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
39 3 0.08
40 23 0.64
41 7 0.19
42 3 0.08
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (40 bp):
TATTATTATCAATTATATTAATCAATTATATTATTAATAA
Found at i:12804908 original size:15 final size:16
Alignment explanation
Indices: 12804876--12804908 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12804866 TTATCATTTA
*
12804876 TATTAATCAATTATAT
1 TATTAATCAATTAAAT
12804892 TATTAAT-AATTAAAT
1 TATTAATCAATTAAAT
12804907 TA
1 TA
12804909 AGATATCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTAATCAATTAAAT
Found at i:12805727 original size:31 final size:31
Alignment explanation
Indices: 12805691--12805784 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
12805681 TATTAAAGAC
* *
12805691 TAAATTTTAAATTTCGTGTTAATATAAGGAT
1 TAAATTTCAAATTTCGTGTAAATATAAGGAT
* * * * *
12805722 TAAATTTCAAATTACGTGCAAGTAAAAGAAT
1 TAAATTTCAAATTTCGTGTAAATATAAGGAT
* * *
12805753 TAAATTTCAACTTTCGTATAAATATAGGGAT
1 TAAATTTCAAATTTCGTGTAAATATAAGGAT
12805784 T
1 T
12805785 TTTTTACATA
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.38
Consensus pattern (31 bp):
TAAATTTCAAATTTCGTGTAAATATAAGGAT
Found at i:12806546 original size:13 final size:13
Alignment explanation
Indices: 12806528--12806553 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12806518 ATTGGTGAAA
12806528 ACTTTATTGCAAT
1 ACTTTATTGCAAT
12806541 ACTTTATTGCAAT
1 ACTTTATTGCAAT
12806554 TAAGATGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
ACTTTATTGCAAT
Found at i:12809890 original size:11 final size:13
Alignment explanation
Indices: 12809871--12809902 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
12809861 ATATTAACAG
12809871 ATATTATAT-TTT
1 ATATTATATATTT
12809883 AT-TTATATATTT
1 ATATTATATATTT
12809895 ATATTATA
1 ATATTATA
12809903 AACACTTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 7 0.39
13 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTATATATTT
Found at i:12810936 original size:20 final size:20
Alignment explanation
Indices: 12810899--12810936 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12810889 ATCTTTTATA
*
12810899 TAATACTTGAATTTTAAAAT
1 TAATACTTGAATTATAAAAT
12810919 TAATACTT-AACTTATAAA
1 TAATACTTGAA-TTATAAA
12810937 TTTATTAGTT
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:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (20 bp):
TAATACTTGAATTATAAAAT
Found at i:12811088 original size:30 final size:28
Alignment explanation
Indices: 12811002--12811105 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 28
12810992 ACAACATATG
* *
12811002 AATATTAATTAATAAA--TTTACAATTTA
1 AATATTATTTAA-AAATTTTTAAAATTTA
*
12811029 AATATAATATTAAAAATTTTTAAAATTTA
1 AATATTAT-TTAAAAATTTTTAAAATTTA
* *
12811058 AATATTATTTAAATATTTTATTATAATTTA
1 AATATTATTTAAA-AATTT-TTAAAATTTA
* *
12811088 AAAATTATTCATAAAATT
1 AATATTATTTA-AAAATT
12811106 AACCTATTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
27 9 0.15
28 9 0.15
29 21 0.34
30 21 0.34
31 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
AATATTATTTAAAAATTTTTAAAATTTA
Found at i:12814198 original size:12 final size:10
Alignment explanation
Indices: 12814167--12814202 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
12814157 TTTTATATGT
12814167 AAATCTATTA
1 AAATCTATTA
12814177 AAATCTATTA
1 AAATCTATTA
12814187 GAAATCCTATTA
1 -AAAT-CTATTA
12814199 AAAT
1 AAAT
12814203 ATACAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
11 8 0.33
12 6 0.25
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (10 bp):
AAATCTATTA
Found at i:12819475 original size:3 final size:3
Alignment explanation
Indices: 12819458--12819575 Score: 74
Period size: 3 Copynumber: 41.3 Consensus size: 3
12819448 AACAAAAATA
*
12819458 AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT -AT AAT -AT GAT -AT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
12819500 AAT AAT AGT AGT AAT -GT AAT ACACT AAT -AT AAT -AT ACT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT AAT AAT
* *
12819544 AAT AAT -AC AAT AGT AAT AAT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12819576 TGATACAATA
Statistics
Matches: 91, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
2 16 0.18
3 68 0.75
4 5 0.05
5 2 0.02
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12819493 original size:8 final size:8
Alignment explanation
Indices: 12819471--12819576 Score: 70
Period size: 8 Copynumber: 12.2 Consensus size: 8
12819461 AAAATAAATA
12819471 ATAATAAT
1 ATAATAAT
12819479 AATAATAAT
1 -ATAATAAT
12819488 ATAATATGAT
1 ATAATA--AT
12819498 ATAATAAT
1 ATAATAAT
*
12819506 AGTAGTAAT
1 A-TAATAAT
*
12819515 GTAATACACT
1 ATAATA-A-T
12819525 A-ATATAAT
1 ATA-ATAAT
* *
12819533 ATACTAAAA
1 ATAAT-AAT
12819542 ATAATAAT
1 ATAATAAT
* *
12819550 ACAATAGT
1 ATAATAAT
12819558 AATAATAAT
1 -ATAATAAT
12819567 ATAATAAT
1 ATAATAAT
12819575 AT
1 AT
12819577 GATACAATAT
Statistics
Matches: 76, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
8 34 0.45
9 30 0.39
10 12 0.16
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.34
Consensus pattern (8 bp):
ATAATAAT
Found at i:12819494 original size:5 final size:5
Alignment explanation
Indices: 12819454--12819595 Score: 58
Period size: 5 Copynumber: 26.8 Consensus size: 5
12819444 GAAAAACAAA
* *
12819454 AATA- AATAA AATA- AATAAT AATAAT AATAAT AATAT AATAT GATAT
1 AATAT AATAT AATAT AAT-AT AAT-AT AAT-AT AATAT AATAT AATAT
* * * * *
12819500 AATAAT AGTAGT AATGT AATACACT AATAT AATAT ACTAAA AATAAT AATAC
1 AAT-AT AATA-T AATAT AAT--A-T AATAT AATAT AAT-AT AAT-AT AATAT
* * *
12819552 AATAGT AATAAT AATAT -A-AT AATAT GATAC AATAT CATAT AATA
1 AATA-T AAT-AT AATAT AATAT AATAT AATAT AATAT AATAT AATA
12819596 AAGTATGATA
Statistics
Matches: 107, Mismatches: 18, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
3 2 0.02
4 9 0.08
5 53 0.50
6 38 0.36
7 1 0.01
8 4 0.04
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (5 bp):
AATAT
Found at i:12819504 original size:30 final size:29
Alignment explanation
Indices: 12819468--12819596 Score: 102
Period size: 30 Copynumber: 4.2 Consensus size: 29
12819458 AATAAAATAA
*
12819468 ATAATAATAATAATAATAATATAATATGAT
1 ATAATAATAATAATAATAATACAATA-GAT
* * *
12819498 ATAATAATAGTAGTAATGTAATACACTA-AT
1 ATAATAATAATAATAA--TAATACAATAGAT
*
12819528 ATAATATACTAAAAATAATAATACAATAG-T
1 ATAATA-A-TAATAATAATAATACAATAGAT
*
12819558 AATAATAAT-ATAATAATATGATACAATATCAT
1 -ATAATAATAATAATAATA--ATACAATA-GAT
12819590 ATAATAA
1 ATAATAA
12819597 AGTATGATAA
Statistics
Matches: 79, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
28 8 0.10
29 1 0.01
30 41 0.52
31 14 0.18
32 15 0.19
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (29 bp):
ATAATAATAATAATAATAATACAATAGAT
Found at i:12820444 original size:66 final size:66
Alignment explanation
Indices: 12820310--12820433 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 66
12820300 TGACTAGGAC
* *
12820310 AAATTATGAGTCCAAAAAATAAAGCAACCAAGACTGAGTCGATGTCAAAGATAAATGACCGGAAT
1 AAATCATGAGTCCAAAAAATAAAGCAACCAAGACCGAGTCGATGTCAAAGATAAATGACCGGAAT
12820375 G
66 G
* * * * *
12820376 AAATCATGAGTCTAAAAGATAATGCGACCAAGACCGAGTCGA-GATCATAGATAAATGA
1 AAATCATGAGTCCAAAAAATAAAGCAACCAAGACCGAGTCGATG-TCAAAGATAAATGA
12820434 TTGGGATGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 1 0.02
66 49 0.98
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (66 bp):
AAATCATGAGTCCAAAAAATAAAGCAACCAAGACCGAGTCGATGTCAAAGATAAATGACCGGAAT
G
Found at i:12820453 original size:66 final size:66
Alignment explanation
Indices: 12820317--12820461 Score: 150
Period size: 66 Copynumber: 2.2 Consensus size: 66
12820307 GACAAATTAT
* *
12820317 GAGTCCAAAAAATAAAGCAACCAAGACTGAGTCGATGTCAAAGATAAATGACCGGAATGAAATCA
1 GAGTCCAAAAAATAAAGCAACCAAGACCGAGTCGATGTCAAAGATAAATGACCGGAATGAAACCA
*
12820382 T
66 C
* * * * * ** *
12820383 GAGTCTAAAAGATAATGCGACCAAGACCGAGTCGA-GATCATAGATAAATGATTGGGATGAAACC
1 GAGTCCAAAAAATAAAGCAACCAAGACCGAGTCGATG-TCAAAGATAAATGACCGGAATGAAACC
*
12820447 GC
65 AC
12820449 GAGT-CAAGAAAAT
1 GAGTCCAA-AAAAT
12820462 GATCTGGATT
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
65 3 0.05
66 60 0.95
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (66 bp):
GAGTCCAAAAAATAAAGCAACCAAGACCGAGTCGATGTCAAAGATAAATGACCGGAATGAAACCA
C
Found at i:12820594 original size:121 final size:121
Alignment explanation
Indices: 12820386--12820607 Score: 284
Period size: 121 Copynumber: 1.8 Consensus size: 121
12820376 AAATCATGAG
* * * * * *
12820386 TCTAAAAGATAATGCGACCAAGACCGAGTCGAGATCATAGATAAATGATTGGGATGAAACCGCGA
1 TCTAAAAGATAAAGCGACCAAGACCGAGTCAAGATCAAAGATAAATAACTGGGATGAAACCGCAA
* ** *
12820451 GTCAAGAAAATGATCTGGATTGAGCCGAGATCGAATAATCAAGACAAAATCGCAAA
66 GTCAAGAAAATAATCTAAATTGAACCGAGATCGAATAATCAAGACAAAATCGCAAA
* * * *
12820507 TCTAAAAGATAAAGCGATCAAGACCGAGTTAAGATCAAAGATGAATAACCT-GGATGAAATCGCA
1 TCTAAAAGATAAAGCGACCAAGACCGAGTCAAGATCAAAGATAAATAA-CTGGGATGAAACCGCA
* *
12820571 AGTTACGAAAATAATCTAAATTGAACCGAGATCGAAT
65 AGTCAAGAAAATAATCTAAATTGAACCGAGATCGAAT
12820608 GAGTGATAAG
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
121 83 0.99
122 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (121 bp):
TCTAAAAGATAAAGCGACCAAGACCGAGTCAAGATCAAAGATAAATAACTGGGATGAAACCGCAA
GTCAAGAAAATAATCTAAATTGAACCGAGATCGAATAATCAAGACAAAATCGCAAA
Found at i:12820889 original size:37 final size:37
Alignment explanation
Indices: 12820813--12820890 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 37
12820803 ATAATAATAG
*
12820813 TTTATTTTAAATAATGCATCAATTTAACTTCAATATT
1 TTTATTTTAAATAATGCATCAATTTAACATCAATATT
* *
12820850 TTTATTTTAAAAATAATGCATCATTTTAA-AT-AATCTT
1 TTTATTTT--AAATAATGCATCAATTTAACATCAATATT
12820887 TTTA
1 TTTA
12820891 GAACTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 17 0.47
38 1 0.03
39 18 0.50
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (37 bp):
TTTATTTTAAATAATGCATCAATTTAACATCAATATT
Found at i:12821145 original size:2 final size:2
Alignment explanation
Indices: 12821138--12821164 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12821128 ATAGTGTTTA
12821138 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
12821165 GAAAGGGGAC
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:12822196 original size:3 final size:3
Alignment explanation
Indices: 12822188--12822231 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
12822178 TTTTGTTCCT
12822188 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12822232 TCATTTTCGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12834320 original size:10 final size:10
Alignment explanation
Indices: 12834307--12834351 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
12834297 TTTTAAAAAA
12834307 CTTTCATTTC
1 CTTTCATTTC
12834317 CTTTCATTTC
1 CTTTCATTTC
*
12834327 ATTTCATTTC
1 CTTTCATTTC
* * *
12834337 ATTTCCTTTT
1 CTTTCATTTC
12834347 CTTTC
1 CTTTC
12834352 CTCTAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (10 bp):
CTTTCATTTC
Found at i:12834326 original size:15 final size:15
Alignment explanation
Indices: 12834308--12834351 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
12834298 TTTAAAAAAC
12834308 TTTCATTTCCTTTCA
1 TTTCATTTCCTTTCA
*
12834323 TTTCATTTCATTTCA
1 TTTCATTTCCTTTCA
* *
12834338 TTTCCTTTTCTTTC
1 TTTCATTTCCTTTC
12834352 CTCTAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.11, C:0.25, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTCATTTCCTTTCA
Found at i:12834350 original size:5 final size:5
Alignment explanation
Indices: 12834308--12834341 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
12834298 TTTAAAAAAC
*
12834308 TTTCA TTTCC TTTCA TTTCA TTTCA TTTCA TTTC
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTC
12834342 CTTTTCTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTCA
Found at i:12838644 original size:29 final size:30
Alignment explanation
Indices: 12838591--12838659 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
12838581 AAGATTAAAT
* *
12838591 TTTATTATTTTATTTAAATAAATTTT-TATA
1 TTTATAATTTTATGTAAATAAATTTTATA-A
12838621 TTT-TAATTTGTATGTAAAT-AATTTTATAA
1 TTTATAATTT-TATGTAAATAAATTTTATAA
12838650 TTTATAATTT
1 TTTATAATTT
12838660 ATAATTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (30 bp):
TTTATAATTTTATGTAAATAAATTTTATAA
Found at i:12838655 original size:7 final size:7
Alignment explanation
Indices: 12838638--12838669 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
12838628 TTGTATGTAA
12838638 ATAATTTT
1 ATAA-TTT
12838646 ATAATTT
1 ATAATTT
12838653 ATAATTT
1 ATAATTT
12838660 ATAATTT
1 ATAATTT
12838667 ATA
1 ATA
12838670 TTCAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATAATTT
Found at i:12838719 original size:18 final size:19
Alignment explanation
Indices: 12838698--12838733 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12838688 GTAAATCAGT
12838698 ATTTTAT-TAAAAATAAAA
1 ATTTTATGTAAAAATAAAA
*
12838716 ATTTTATGTAAATATAAA
1 ATTTTATGTAAAAATAAA
12838734 TAAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTTTATGTAAAAATAAAA
Found at i:12838738 original size:29 final size:28
Alignment explanation
Indices: 12838705--12838793 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
12838695 AGTATTTTAT
*
12838705 TAAAAATAAAAATTTTATGTAAATATAAA
1 TAAAAATAAAAA-TTTATTTAAATATAAA
** *
12838734 TAAAAAATAATGATTTATTTAAGTAT-AA
1 T-AAAAATAAAAATTTATTTAAATATAAA
12838762 TAAAAATATAAAAATTTATTTAAATA-AAA
1 T-AAAA-ATAAAAATTTATTTAAATATAAA
12838791 TAA
1 TAA
12838794 TAAAATTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
28 10 0.20
29 31 0.62
30 9 0.18
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
TAAAAATAAAAATTTATTTAAATATAAA
Found at i:12839894 original size:17 final size:17
Alignment explanation
Indices: 12839872--12839906 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12839862 TAAAAAATTA
12839872 TTTAGA-TTTGAATTTTT
1 TTTAGATTTTG-ATTTTT
12839889 TTTAGATTTTGATTTTT
1 TTTAGATTTTGATTTTT
12839906 T
1 T
12839907 AATACAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (17 bp):
TTTAGATTTTGATTTTT
Found at i:12840231 original size:14 final size:15
Alignment explanation
Indices: 12840212--12840241 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12840202 TAGATCCAGG
12840212 TTTTTAGG-TTTTTT
1 TTTTTAGGATTTTTT
12840226 TTTTTAGGATTTTTT
1 TTTTTAGGATTTTTT
12840241 T
1 T
12840242 ATGAAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (15 bp):
TTTTTAGGATTTTTT
Found at i:12842387 original size:19 final size:19
Alignment explanation
Indices: 12842360--12842413 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 19
12842350 GGGTTAAGTG
12842360 TTGGTTTTAGGGTTTGGGGT
1 TTGG-TTTAGGGTTTGGGGT
*
12842380 TTGGTTTAGGATTTGGGGT
1 TTGGTTTAGGGTTTGGGGT
12842399 TTAGGTTTAGGGTTT
1 TT-GGTTTAGGGTTT
12842414 AGTTTTAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (19 bp):
TTGGTTTAGGGTTTGGGGT
Found at i:12842414 original size:7 final size:7
Alignment explanation
Indices: 12842365--12842705 Score: 136
Period size: 7 Copynumber: 51.4 Consensus size: 7
12842355 AAGTGTTGGT
12842365 TTTAGGG
1 TTTAGGG
*
12842372 TTTGGGG
1 TTTAGGG
12842379 TTT--GG
1 TTTAGGG
*
12842384 TTTAGGA
1 TTTAGGG
*
12842391 TTTGGGG
1 TTTAGGG
12842398 TTTA-GG
1 TTTAGGG
12842404 TTTAGGG
1 TTTAGGG
*
12842411 TTTA-GT
1 TTTAGGG
*
12842417 TTTAAGG
1 TTTAGGG
*
12842424 TTTAAGG
1 TTTAGGG
12842431 TTTA-GG
1 TTTAGGG
*
12842437 TTTAGGA
1 TTTAGGG
12842444 TTT-GGG
1 TTTAGGG
12842450 ATTTA-GG
1 -TTTAGGG
*
12842457 TTTAAGG
1 TTTAGGG
***
12842464 TTTAAAA
1 TTTAGGG
*
12842471 TTTA-GT
1 TTTAGGG
12842477 TTTAGGG
1 TTTAGGG
12842484 TTTAGGG
1 TTTAGGG
*
12842491 TTTATGG
1 TTTAGGG
*
12842498 TTTA-TG
1 TTTAGGG
* *
12842504 ATTA-GA
1 TTTAGGG
*
12842510 ATTAGGG
1 TTTAGGG
* *
12842517 TTTTGAG
1 TTTAGGG
12842524 TTTA-GG
1 TTTAGGG
12842530 TTTAGGG
1 TTTAGGG
* *
12842537 ATTAAGG
1 TTTAGGG
*
12842544 TCTT-GAG
1 T-TTAGGG
*
12842551 TTTA-AG
1 TTTAGGG
12842557 TTTA-GG
1 TTTAGGG
* *
12842563 TTTTGTGA
1 TTTAG-GG
12842571 TTT-GGAG
1 TTTAGG-G
12842578 TTTA-GG
1 TTTAGGG
*
12842584 TTTAAGGC
1 TTT-AGGG
12842592 TTTA-GG
1 TTTAGGG
*
12842598 TTT-TGG
1 TTTAGGG
12842604 TTTAGGG
1 TTTAGGG
12842611 TTTAGGG
1 TTTAGGG
12842618 TTTA--G
1 TTTAGGG
*
12842623 TTTA-TG
1 TTTAGGG
12842629 -TTAGGG
1 TTTAGGG
12842635 TTTAGGG
1 TTTAGGG
* *
12842642 TTCAAGG
1 TTTAGGG
*
12842649 TTTA-GA
1 TTTAGGG
*
12842655 TTTAAGG
1 TTTAGGG
* *
12842662 TTCAAGG
1 TTTAGGG
12842669 TTTAGGG
1 TTTAGGG
*
12842676 TTTA-TG
1 TTTAGGG
*
12842682 TTTAAGG
1 TTTAGGG
*
12842689 TTTAGGA
1 TTTAGGG
12842696 TTTAGGG
1 TTTAGGG
12842703 TTT
1 TTT
12842706 TGCATGGTGG
Statistics
Matches: 257, Mismatches: 51, Indels: 52
0.71 0.14 0.14
Matches are distributed among these distances:
5 13 0.05
6 78 0.30
7 156 0.61
8 10 0.04
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:12842414 original size:27 final size:26
Alignment explanation
Indices: 12842382--12842705 Score: 127
Period size: 27 Copynumber: 12.2 Consensus size: 26
12842372 TTTGGGGTTT
12842382 GGTTTAGGATTTGGGGTTTAGGTTTAG
1 GGTTTAGGATTT-GGGTTTAGGTTTAG
* *
12842409 GGTTTA-GTTTTAAGGTTTAAGGTTTA-
1 GGTTTAGGATTT-GGGTTT-AGGTTTAG
*
12842435 GGTTTAGGATTTGGGATTTAGGTTTAA
1 GGTTTAGGATTTGGG-TTTAGGTTTAG
** * *
12842462 GGTTTAAAATTTAGTTTTAGGGTTTAG
1 GGTTTAGGATTTGGGTTTA-GGTTTAG
* *
12842489 GGTTT---A--T-GGTTTATGATTA-
1 GGTTTAGGATTTGGGTTTAGGTTTAG
** * *
12842508 GAATTAGGGTTTTGAGTTTAGGTTTAG
1 GGTTTA-GGATTTGGGTTTAGGTTTAG
* * *
12842535 GGATTAAGG-TCTTGAGTTTAAGTTTA-
1 GG-TTTAGGAT-TTGGGTTTAGGTTTAG
*
12842561 GGTTTTGTGATTTGGAGTTTAGGTTTAAG
1 GGTTTAG-GATTTGG-GTTTAGGTTT-AG
* *
12842590 GCTTTAGG-TTTTGGTTTAGGGTTTAG
1 GGTTTAGGATTTGGGTTTA-GGTTTAG
* * *
12842616 GGTTTAGTTTATGTTAGGGTTTAGGGTTCAA
1 GGTTTAG--GAT-TT-GGGTTTA-GGTTTAG
* *
12842647 GGTTTA-GATTTAAGGTTCAAGGTTTAG
1 GGTTTAGGATTT-GGGTT-TAGGTTTAG
* *
12842674 GGTTTATG-TTTAAGGTTTAGGATTTAG
1 GGTTTAGGATTT-GGGTTTAGG-TTTAG
12842701 GGTTT
1 GGTTT
12842706 TGCATGGTGG
Statistics
Matches: 227, Mismatches: 41, Indels: 58
0.70 0.13 0.18
Matches are distributed among these distances:
19 3 0.01
20 4 0.02
21 5 0.02
22 1 0.00
24 1 0.00
25 4 0.02
26 60 0.26
27 115 0.51
28 8 0.04
29 6 0.03
30 2 0.01
31 18 0.08
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (26 bp):
GGTTTAGGATTTGGGTTTAGGTTTAG
Found at i:12842424 original size:20 final size:20
Alignment explanation
Indices: 12842365--12842701 Score: 173
Period size: 20 Copynumber: 16.6 Consensus size: 20
12842355 AAGTGTTGGT
*
12842365 TTTAGGGTTTGGGGTTT--GG
1 TTTAGGGTTT-AGGTTTAAGG
* *
12842384 TTTAGGATTTGGGGTTT-AGG
1 TTTAGGGTTT-AGGTTTAAGG
*
12842404 TTTAGGGTTTAGTTTTAAGG
1 TTTAGGGTTTAGGTTTAAGG
*
12842424 TTTAAGGTTTAGGTTT-AGG
1 TTTAGGGTTTAGGTTTAAGG
12842443 ATTT-GGGATTTAGGTTTAAGG
1 -TTTAGGG-TTTAGGTTTAAGG
*** * *
12842464 TTTAAAATTTAGTTTTAGGG
1 TTTAGGGTTTAGGTTTAAGG
*
12842484 TTTAGGGTTTATGGTTTATGATTAGA
1 TTTAGGGTTTA-GG-TT-T-A--AGG
* *
12842510 ATTAGGGTTTTGAGTTT-AGG
1 TTTAGGGTTTAG-GTTTAAGG
* *
12842530 TTTAGGGATTAAGGTCTTGA-G
1 TTTAGGG-TTTAGGT-TTAAGG
* *
12842551 TTTA-AGTTTAGGTTT-TGTG
1 TTTAGGGTTTAGGTTTAAG-G
12842570 ATTT-GGAGTTTAGGTTTAAGG
1 -TTTAGG-GTTTAGGTTTAAGG
* *
12842591 CTTTA-GGTTTTGGTTTAGGG
1 -TTTAGGGTTTAGGTTTAAGG
*
12842611 TTTAGGGTTTA-GTTT-ATG
1 TTTAGGGTTTAGGTTTAAGG
*
12842629 -TTAGGGTTTAGGGTTCAAGG
1 TTTAGGGTTTA-GGTTTAAGG
* *
12842649 TTTA-GATTTAAGGTTCAAGG
1 TTTAGGGTTT-AGGTTTAAGG
*
12842669 TTTAGGGTTTATGTTTAAGG
1 TTTAGGGTTTAGGTTTAAGG
*
12842689 TTTAGGATTTAGG
1 TTTAGGGTTTAGG
12842702 GTTTTGCATG
Statistics
Matches: 245, Mismatches: 43, Indels: 59
0.71 0.12 0.17
Matches are distributed among these distances:
17 10 0.04
18 3 0.01
19 43 0.18
20 131 0.53
21 37 0.15
22 4 0.02
23 1 0.00
24 2 0.01
25 3 0.01
26 11 0.04
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (20 bp):
TTTAGGGTTTAGGTTTAAGG
Found at i:12842486 original size:53 final size:53
Alignment explanation
Indices: 12842365--12842494 Score: 156
Period size: 53 Copynumber: 2.5 Consensus size: 53
12842355 AAGTGTTGGT
* * * * **
12842365 TTTAGGGTTTGGGGTTT-GGTTTAGGATTTGGGGTTTAGGTTTAGGGTTTAGT
1 TTTAAGGTTTAGGGTTTAGGTTTAGGATTTGGGATTTAGGTTTAAGGTTTAAA
*
12842417 TTTAAGGTTTAAGGTTTAGGTTTAGGATTTGGGATTTAGGTTTAAGGTTTAAAA
1 TTTAAGGTTTAGGGTTTAGGTTTAGGATTTGGGATTTAGGTTTAAGGTTT-AAA
*
12842471 TTT-AGTTTTAGGGTTTAGGGTTTA
1 TTTAAGGTTTAGGGTTTA-GGTTTA
12842495 TGGTTTATGA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
52 14 0.21
53 42 0.64
54 10 0.15
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (53 bp):
TTTAAGGTTTAGGGTTTAGGTTTAGGATTTGGGATTTAGGTTTAAGGTTTAAA
Found at i:12843687 original size:20 final size:22
Alignment explanation
Indices: 12843662--12843705 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
12843652 AAATCAAAGC
*
12843662 AAAATG-ATATGAAAA-GTATG
1 AAAATGAATATAAAAATGTATG
12843682 AAAATGAATATAAAAATGTATG
1 AAAATGAATATAAAAATGTATG
12843704 AA
1 AA
12843706 GAATATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 8 0.38
22 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (22 bp):
AAAATGAATATAAAAATGTATG
Found at i:12844379 original size:145 final size:143
Alignment explanation
Indices: 12844087--12844411 Score: 336
Period size: 146 Copynumber: 2.2 Consensus size: 143
12844077 TTCTTTTTAT
* * * * *
12844087 GATTTCAATGCACCAAAAATCATAAAATAA-T-ATAAAAATATGATATAAAAATTTTTACGAAAA
1 GATTTTAATGCA-CAAAAATAATAAAATAATTAAAAAAAACATGATATAAAAATTTTCACGAAAA
* * * * * **
12844150 ATCGACCTCGAAAAGGTCAAATTACGAAAATACCTTTAAAGGGTATTTTAGTAATTTCATTCCTT
65 ATCAACCTCGAAAAGATCAAATTACAAAAATACCTCTAAAGAGTATTTTAGTAATTTCACACCTT
*
12844215 TCAAGGTATGATCAA
130 TC-AGATATGATCAA
** *
12844230 GATTTTTAATGCATCAAAAATAATAAAATAATTAAAAAAAACATGATATGAAGCA-TTTCATGAA
1 GA-TTTTAATGCA-CAAAAATAATAAAATAATTAAAAAAAACATGATAT-AAAAATTTTCACGAA
* * * *
12844294 AAATCAATCTCGAGAAGATCAAATTATAAAAATATCTCTAAA-AGTATTTTAGTAATTTCACACC
63 AAATCAACCTCGAAAAGATCAAATTACAAAAATACCTCTAAAGAGTATTTTAGTAATTTCACACC
12844358 TTTC-GATATGCGATCAA
128 TTTCAGATAT--GATCAA
* *
12844375 GATTTTAATGCACTAAAAATTATTAAATAATATAAAA
1 GATTTTAATGCAC-AAAAATAATAAAATAAT-TAAAA
12844412 TTATGATTTA
Statistics
Matches: 151, Mismatches: 23, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
143 7 0.05
144 50 0.33
145 37 0.25
146 54 0.36
147 3 0.02
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (143 bp):
GATTTTAATGCACAAAAATAATAAAATAATTAAAAAAAACATGATATAAAAATTTTCACGAAAAA
TCAACCTCGAAAAGATCAAATTACAAAAATACCTCTAAAGAGTATTTTAGTAATTTCACACCTTT
CAGATATGATCAA
Found at i:12845201 original size:65 final size:65
Alignment explanation
Indices: 12845066--12845199 Score: 157
Period size: 64 Copynumber: 2.1 Consensus size: 65
12845056 ATTAAGTAGA
* ** * **
12845066 TTTTTATTTAAGAAAAATTTGATAATTTCAACTTTTCTTTAAAAATCTTTTTTTTTATTATTATT
1 TTTTTATTTAAGAAAAATTTGATAATTTCAACTTTTCTTTAAAAATCTTTTTGTGAAATACAATT
* *
12845131 TTTTTATTTAAG-AAAATTTGATACTTTCAACTTTT-TTTTAAAA-CGTTTCTTGTGAAATACAA
1 TTTTTATTTAAGAAAAATTTGATAATTTCAACTTTTCTTTAAAAATC-TTT-TTGTGAAATACAA
12845193 TT
64 TT
12845195 TTTTT
1 TTTTT
12845200 TAAAACAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 10 0.17
64 36 0.61
65 12 0.20
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.56
Consensus pattern (65 bp):
TTTTTATTTAAGAAAAATTTGATAATTTCAACTTTTCTTTAAAAATCTTTTTGTGAAATACAATT
Done.