Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 32 of 33
Found at i:5925492 original size:21 final size:20
Alignment explanation
Indices: 5925452--5925499 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
5925442 AAATAAAGGG
*
5925452 AAAA-AAAGATAAATAAATA
1 AAAATAAAGATAAAGAAATA
5925471 AAAATAAAGATAAAGGAAATA
1 AAAATAAAGATAAA-GAAATA
*
5925492 ACAATAAA
1 AAAATAAA
5925500 ATGAATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.16
20 9 0.36
21 12 0.48
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAATAAAGATAAAGAAATA
Found at i:5925571 original size:2 final size:2
Alignment explanation
Indices: 5925564--5925594 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5925554 ACATGTACGC
5925564 AT AT 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 AT AT A
5925595 AAGAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5925769 original size:15 final size:16
Alignment explanation
Indices: 5925759--5925789 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5925749 TAAAATTCAA
5925759 AAAAAATAAATTAAAT
1 AAAAAATAAATTAAAT
5925775 AAAAAATAAA-TAAAT
1 AAAAAATAAATTAAAT
5925790 GAATTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAATAAATTAAAT
Found at i:5925797 original size:20 final size:19
Alignment explanation
Indices: 5925752--5925797 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
5925742 TATAATATAA
* *
5925752 AATTCAAAAAAAATAAATT
1 AATTAAAAAAAAATAAATG
*
5925771 AAATAAAAAATAAATAAATG
1 AATTAAAAAA-AAATAAATG
5925791 AATTAAA
1 AATTAAA
5925798 CTGCTCAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AATTAAAAAAAAATAAATG
Found at i:5929651 original size:2 final size:2
Alignment explanation
Indices: 5929646--5929702 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
5929636 CTATATAGTT
5929646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5929687 TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA T
5929703 GGTTTAGGGT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5929674 original size:33 final size:33
Alignment explanation
Indices: 5929565--5929753 Score: 132
Period size: 33 Copynumber: 5.8 Consensus size: 33
5929555 TTTATACAAG
*
5929565 ATATATATAGTTTATACATAGTAGTATATA-AGTAT
1 ATATATATAGTTTATATATA-TA-TATATATA-TAT
* * *
5929600 AAACTATATGGTTTATATATAGTTTATAT-TA-AT
1 ATA-TATATAGTTTATATATA-TATATATATATAT
*
5929633 AAACTATATAGTTTATATATATATATATATATAT
1 ATA-TATATAGTTTATATATATATATATATATAT
5929667 ATATATATA---TATATATATA-ATATATATAT
1 ATATATATAGTTTATATATATATATATATATAT
* ** *
5929696 ATA-ATATGGTTTAGGGT-TA-ATTTATATA-AT
1 ATATATATAGTTTA-TATATATATATATATATAT
*
5929726 -TATATATAGTTTATATATAAACTATATA
1 ATATATATAGTTTATATATATA-TATATA
5929754 GTTTATACAT
Statistics
Matches: 126, Mismatches: 15, Indels: 29
0.74 0.09 0.17
Matches are distributed among these distances:
28 4 0.03
29 16 0.13
30 24 0.19
31 11 0.09
32 12 0.10
33 30 0.24
34 4 0.03
35 8 0.06
36 17 0.13
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (33 bp):
ATATATATAGTTTATATATATATATATATATAT
Found at i:5929871 original size:9 final size:9
Alignment explanation
Indices: 5929842--5929884 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
5929832 ATGGGCAATA
5929842 TATATAAAC
1 TATATAAAC
5929851 TA-ATAAAC
1 TATATAAAC
*
5929859 TATATAAATTA
1 TATATAAA--C
5929870 TATATAAAC
1 TATATAAAC
5929879 TATATA
1 TATATA
5929885 TAAACTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 8 0.28
9 13 0.45
11 8 0.28
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (9 bp):
TATATAAAC
Found at i:5929875 original size:11 final size:11
Alignment explanation
Indices: 5929840--5930024 Score: 62
Period size: 11 Copynumber: 18.1 Consensus size: 11
5929830 ATATGGGCAA
5929840 TATATATAAAC
1 TATATATAAAC
5929851 --TA-ATAAAC
1 TATATATAAAC
*
5929859 --TATATAAAT
1 TATATATAAAC
5929868 TATATATAAAC
1 TATATATAAAC
5929879 TATATATAAAC
1 TATATATAAAC
* **
5929890 TGTATATTTTA-
1 TATATA-TAAAC
* *
5929901 TATTTATATAC
1 TATATATAAAC
5929912 TATATAT--A-
1 TATATATAAAC
5929920 -AT-TATAAA-
1 TATATATAAAC
**
5929928 T-TATATAGGC
1 TATATATAAAC
* *
5929938 TATGTATAAAT
1 TATATATAAAC
** *
5929949 TATATAGTTTAT
1 TATATA-TAAAC
5929961 TA-ATATAAAC
1 TATATATAAAC
5929971 TATATATAAAC
1 TATATATAAAC
* *
5929982 CATACAT--AC
1 TATATATAAAC
* *
5929991 AATATGTAAAC
1 TATATATAAAC
5930002 TATATATAAA-
1 TATATATAAAC
*
5930012 AACTATATAAAC
1 TA-TATATAAAC
5930024 T
1 T
5930025 TTACTTTATA
Statistics
Matches: 127, Mismatches: 30, Indels: 33
0.67 0.16 0.17
Matches are distributed among these distances:
6 3 0.02
7 2 0.02
8 10 0.08
9 18 0.14
10 9 0.07
11 78 0.61
12 7 0.06
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (11 bp):
TATATATAAAC
Found at i:5930075 original size:2 final size:2
Alignment explanation
Indices: 5930056--5930177 Score: 82
Period size: 2 Copynumber: 63.0 Consensus size: 2
5930046 TACTATAGTT
* * *
5930056 TA TA TT TA TA TT TA TA TA TA GA TA TA TA TA TCA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * *
5930098 TA T- TT TA TA TT TA TA TA -A GTA TA CA T- TA TA CT- TA TA -A GTA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA
5930138 TA TA -A TA TA -A GTA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5930178 AGTATACATT
Statistics
Matches: 95, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
1 9 0.09
2 80 0.84
3 6 0.06
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5930135 original size:19 final size:20
Alignment explanation
Indices: 5930109--5930216 Score: 71
Period size: 19 Copynumber: 5.3 Consensus size: 20
5930099 ATTTTATATT
5930109 TATATAAGTATACATTATAC
1 TATATAAGTATACATTATAC
* * *
5930129 T-TATAAGTATATAATATAAG
1 TATATAAGTATACATTAT-AC
* *
5930149 TATATATA-TATATATATATATA
1 TATATA-AGTATACAT-TATA-C
5930171 TAATATAAGTATACATTATAC
1 T-ATATAAGTATACATTATAC
* * *
5930192 T-TACAAGTATATAATATA-
1 TATATAAGTATACATTATAC
5930210 TATATAA
1 TATATAA
5930217 AGTGTAAAGT
Statistics
Matches: 69, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
18 1 0.01
19 32 0.46
20 3 0.04
21 12 0.17
22 10 0.14
23 11 0.16
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
TATATAAGTATACATTATAC
Found at i:5930182 original size:63 final size:62
Alignment explanation
Indices: 5930088--5930209 Score: 192
Period size: 63 Copynumber: 2.0 Consensus size: 62
5930078 TATATATATC
* * *
5930088 ATATATAATATATTTTATATTTATATAAGTATACATTATACTTATAAGTATATAATATAAGT
1 ATATATAATATATTATATATTAATATAAGTATACATTATACTTACAAGTATATAATATAAGT
5930150 ATATAT-ATATATATATATATATAATATAAGTATACATTATACTTACAAGTATATAATATA
1 ATATATAATATAT-TATATAT-TAATATAAGTATACATTATACTTACAAGTATATAATATA
5930210 TATATAAAGT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
61 6 0.11
62 12 0.22
63 37 0.67
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (62 bp):
ATATATAATATATTATATATTAATATAAGTATACATTATACTTACAAGTATATAATATAAGT
Found at i:5931369 original size:13 final size:13
Alignment explanation
Indices: 5931351--5931375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5931341 TTATTTACTT
5931351 TTTGTTTTTTATA
1 TTTGTTTTTTATA
5931364 TTTGTTTTTTAT
1 TTTGTTTTTTAT
5931376 TTCTTTTCAT
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:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTGTTTTTTATA
Found at i:5931495 original size:3 final size:3
Alignment explanation
Indices: 5931487--5931518 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5931477 ATTATATTTA
5931487 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5931519 ATTAGTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5932987 original size:14 final size:14
Alignment explanation
Indices: 5932970--5933016 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
5932960 TTTTAGACCC
5932970 TTAATTTTCTATTT
1 TTAATTTTCTATTT
5932984 TTAATATTT-TAGTTT
1 TTAAT-TTTCTA-TTT
*
5932999 TTAAATTATCTATTT
1 TT-AATTTTCTATTT
5933014 TTA
1 TTA
5933017 TTATTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 8 0.29
15 15 0.54
16 5 0.18
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (14 bp):
TTAATTTTCTATTT
Found at i:5933022 original size:60 final size:60
Alignment explanation
Indices: 5932968--5933084 Score: 157
Period size: 60 Copynumber: 1.9 Consensus size: 60
5932958 TATTTTAGAC
*
5932968 CCTTAA-TTTTCTATTTTTAATATTTTAGT-TTTTAAATTATCTATTTTTATTATTTTAATA
1 CCTTAAGTTTT-TATTTGTAATATTTTAGTATTTTAAATT-TCTATTTTTATTATTTTAATA
* * * *
5933028 CCTTAAGTTTTTGTTTGTGATATTTTGGTATTTTAAATTTCTATTTTTGTTATTTTA
1 CCTTAAGTTTTTATTTGTAATATTTTAGTATTTTAAATTTCTATTTTTATTATTTTA
5933085 TCACTAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 37 0.74
61 13 0.26
ACGTcount: A:0.24, C:0.06, G:0.07, T:0.63
Consensus pattern (60 bp):
CCTTAAGTTTTTATTTGTAATATTTTAGTATTTTAAATTTCTATTTTTATTATTTTAATA
Found at i:5933082 original size:30 final size:30
Alignment explanation
Indices: 5932970--5933084 Score: 97
Period size: 30 Copynumber: 3.8 Consensus size: 30
5932960 TTTTAGACCC
*
5932970 TTAATTTTCTATTTTTAATATTTTAGT-TT
1 TTAAATTTCTATTTTTAATATTTTAGTATT
* * **
5932999 TTAAATTATCTATTTTTATTATTTTAATACC
1 TTAAATT-TCTATTTTTAATATTTTAGTATT
* * * * * *
5933030 TTAAGTTTTTGTTTGTGATATTTTGGTATT
1 TTAAATTTCTATTTTTAATATTTTAGTATT
**
5933060 TTAAATTTCTATTTTTGTTATTTTA
1 TTAAATTTCTATTTTTAATATTTTA
5933085 TCACTAATTT
Statistics
Matches: 63, Mismatches: 21, Indels: 3
0.72 0.24 0.03
Matches are distributed among these distances:
29 6 0.10
30 51 0.81
31 6 0.10
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.64
Consensus pattern (30 bp):
TTAAATTTCTATTTTTAATATTTTAGTATT
Found at i:5934349 original size:17 final size:17
Alignment explanation
Indices: 5934329--5934379 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
5934319 TTGCTAATTG
*
5934329 TTTTCTATTTTTATATT
1 TTTTCTAATTTTATATT
*
5934346 TTTTTTAATTTTATA-T
1 TTTTCTAATTTTATATT
*
5934362 TTTT-TAATTTTATGTT
1 TTTTCTAATTTTATATT
5934378 TT
1 TT
5934380 ATTTGTGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.30
16 8 0.27
17 13 0.43
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTCTAATTTTATATT
Found at i:5934364 original size:15 final size:15
Alignment explanation
Indices: 5934346--5934379 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5934336 TTTTTATATT
5934346 TTTTTTAATTTTATA
1 TTTTTTAATTTTATA
*
5934361 TTTTTTAATTTTATG
1 TTTTTTAATTTTATA
5934376 TTTT
1 TTTT
5934380 ATTTGTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTTAATTTTATA
Found at i:5934454 original size:11 final size:11
Alignment explanation
Indices: 5934438--5934465 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5934428 TTATTTTCTA
5934438 TTTTCTATTTG
1 TTTTCTATTTG
5934449 TTTTCTATTTG
1 TTTTCTATTTG
5934460 TTTTCT
1 TTTTCT
5934466 GTTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.11, G:0.07, T:0.75
Consensus pattern (11 bp):
TTTTCTATTTG
Found at i:5934583 original size:4 final size:4
Alignment explanation
Indices: 5934574--5934687 Score: 52
Period size: 4 Copynumber: 27.2 Consensus size: 4
5934564 GTTTTATGTT
* * * *
5934574 TTTA TTTA TTTTA TGTTT TTTA TTTGT TTTA TTTGT TTTA TTTGT TTTA
1 TTTA TTTA -TTTA T-TTA TTTA TTT-A TTTA TTT-A TTTA TTT-A TTTA
* * * * * *
5934623 TTTG TTTT TTTA TTTA TTT- TATTA TTTA GTT- TCTG TTTA TTTA CTTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
*
5934670 TTTT TGTTA TTTA TTTA T
1 TTTA T-TTA TTTA TTTA T
5934688 ATTTTGTTTT
Statistics
Matches: 81, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
3 2 0.02
4 59 0.73
5 20 0.25
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:5934587 original size:9 final size:9
Alignment explanation
Indices: 5934573--5934687 Score: 82
Period size: 9 Copynumber: 13.1 Consensus size: 9
5934563 TGTTTTATGT
5934573 TTTTATTTA
1 TTTTATTTA
5934582 TTTTATGTT-
1 TTTTAT-TTA
*
5934591 TTTTATTTG
1 TTTTATTTA
*
5934600 TTTTATTTG
1 TTTTATTTA
*
5934609 TTTTATTTG
1 TTTTATTTA
*
5934618 TTTTATTTG
1 TTTTATTTA
5934627 TTTT-TTTA
1 TTTTATTTA
5934635 -TTTATTT-
1 TTTTATTTA
*
5934642 TATTATTTA
1 TTTTATTTA
*
5934651 GTTTCTGTTTA
1 -TTT-TATTTA
*
5934662 -TTTACTTA
1 TTTTATTTA
5934670 TTTT-TGTTA
1 TTTTAT-TTA
5934679 -TTTATTTA
1 TTTTATTTA
5934687 T
1 T
5934688 ATTTTGTTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
7 3 0.03
8 24 0.27
9 52 0.59
10 4 0.05
11 5 0.06
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.76
Consensus pattern (9 bp):
TTTTATTTA
Found at i:5934593 original size:18 final size:18
Alignment explanation
Indices: 5934565--5934697 Score: 111
Period size: 18 Copynumber: 7.6 Consensus size: 18
5934555 TCTTATATTG
5934565 TTTTATG-TTTTTATTTA
1 TTTTATGTTTTTTATTTA
*
5934582 TTTTATGTTTTTTATTTG
1 TTTTATGTTTTTTATTTA
*
5934600 TTTTAT-TTGTTTTATTTG
1 TTTTATGTT-TTTTATTTA
5934618 TTTTAT-TTGTTTT-TTTA
1 TTTTATGTT-TTTTATTTA
*
5934635 -TTTAT-TTTATTATTTA
1 TTTTATGTTTTTTATTTA
* * *
5934651 GTTTCTGTTTATTTACTTA
1 TTTTATGTTT-TTTATTTA
*
5934670 TTTT-TGTTATTTATTTA
1 TTTTATGTTTTTTATTTA
5934687 TATTT-TGTTTT
1 T-TTTATGTTTT
5934698 CTGTTTATAT
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
15 3 0.03
16 11 0.11
17 24 0.24
18 52 0.53
19 9 0.09
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.76
Consensus pattern (18 bp):
TTTTATGTTTTTTATTTA
Found at i:5936186 original size:2 final size:2
Alignment explanation
Indices: 5936179--5936204 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5936169 GGTAAATGTC
5936179 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
5936205 TTTCTAGTTC
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:5937233 original size:22 final size:22
Alignment explanation
Indices: 5937208--5937267 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
5937198 TTGGACTTGA
* * *
5937208 TCTGAATGTTGATTTGAATTTG
1 TCTGAATGTTGATTAGAAATCG
**
5937230 TCTGAATACTGATTAGAAATCG
1 TCTGAATGTTGATTAGAAATCG
*
5937252 TTTGAATGTTGATTAG
1 TCTGAATGTTGATTAG
5937268 TTTTGGTCTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (22 bp):
TCTGAATGTTGATTAGAAATCG
Found at i:5937326 original size:18 final size:18
Alignment explanation
Indices: 5937286--5937327 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5937276 TAAATGATGA
* *
5937286 ATTGTTGCTTGTTAGTTG
1 ATTGTTGCTTGTAAATTG
5937304 ATTGTTGCCTTGTAAATTG
1 ATTGTTG-CTTGTAAATTG
5937323 -TTGTT
1 ATTGTT
5937328 ATTGGTCTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.14, C:0.07, G:0.24, T:0.55
Consensus pattern (18 bp):
ATTGTTGCTTGTAAATTG
Found at i:5943091 original size:20 final size:20
Alignment explanation
Indices: 5943066--5943105 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5943056 CAGAACTAAA
*
5943066 TTACTTGTTCCGTCGAACTC
1 TTACTTGCTCCGTCGAACTC
*
5943086 TTACTTGCTCCGTCGGACTC
1 TTACTTGCTCCGTCGAACTC
5943106 AAAAAGTAAT
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:0.12, C:0.33, G:0.17, T:0.38
Consensus pattern (20 bp):
TTACTTGCTCCGTCGAACTC
Found at i:5949210 original size:14 final size:15
Alignment explanation
Indices: 5949187--5949216 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5949177 ATAACGTCCA
5949187 CGACATCCGCAACCG
1 CGACATCCGCAACCG
5949202 CGACA-CCGCAACCG
1 CGACATCCGCAACCG
5949216 C
1 C
5949217 ATTCGCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.27, C:0.50, G:0.20, T:0.03
Consensus pattern (15 bp):
CGACATCCGCAACCG
Found at i:5955128 original size:26 final size:26
Alignment explanation
Indices: 5955098--5955149 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5955088 TAACACTAAC
5955098 ATTTCCAATCCGTCTAAGCTGATTAG
1 ATTTCCAATCCGTCTAAGCTGATTAG
5955124 ATTTCCAATCCGTCTAAGCTGATTAG
1 ATTTCCAATCCGTCTAAGCTGATTAG
5955150 TTGTACCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (26 bp):
ATTTCCAATCCGTCTAAGCTGATTAG
Found at i:5959198 original size:30 final size:30
Alignment explanation
Indices: 5959150--5959210 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
5959140 AAAATTATAT
5959150 TCTTTTTGTATTGAA-TTTTATTCACTTTTAA
1 TCTTTTTGTATTGAATTTTTA-T-ACTTTTAA
*
5959181 TCTTTTT-TATTGTATTTTTATACTTTTAA
1 TCTTTTTGTATTGAATTTTTATACTTTTAA
5959210 T
1 T
5959211 TACAATTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 9 0.32
30 7 0.25
31 12 0.43
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (30 bp):
TCTTTTTGTATTGAATTTTTATACTTTTAA
Found at i:5961750 original size:19 final size:19
Alignment explanation
Indices: 5961718--5961769 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
5961708 ATCAGTATCC
*
5961718 CTTA-GTATCGATACCTCT
1 CTTAGGTATCAATACCTCT
5961736 CTTAGGTATCAATACCTCT
1 CTTAGGTATCAATACCTCT
5961755 CTTAGGTATCAATAC
1 CTTAGGTATCAATAC
5961770 TCTACTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 4 0.12
19 28 0.88
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (19 bp):
CTTAGGTATCAATACCTCT
Found at i:5962840 original size:18 final size:18
Alignment explanation
Indices: 5962817--5962869 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
5962807 CATAGAAATT
*
5962817 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
5962835 TGTCCCGAAGGACCACTC
1 TGTCCCGAAGGACCACTA
5962853 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
5962870 GAATCTCGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5965505 original size:17 final size:17
Alignment explanation
Indices: 5965483--5965519 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
5965473 CCATTACAAG
5965483 GAATCTAAACGTGCTTT
1 GAATCTAAACGTGCTTT
5965500 GAATCTAAACGTGCTTT
1 GAATCTAAACGTGCTTT
5965517 GAA
1 GAA
5965520 GAGATGGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (17 bp):
GAATCTAAACGTGCTTT
Found at i:5973072 original size:18 final size:18
Alignment explanation
Indices: 5973031--5973074 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5973021 AAAAAAAATT
*
5973031 GATGAGAGAAAGAGAGTC
1 GATGAGAGAAAGAGAGCC
* * *
5973049 GGTGAGGGACAGAGAGCC
1 GATGAGAGAAAGAGAGCC
5973067 GATGAGAG
1 GATGAGAG
5973075 GTGGAGGTTG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.45, T:0.09
Consensus pattern (18 bp):
GATGAGAGAAAGAGAGCC
Found at i:5973126 original size:10 final size:10
Alignment explanation
Indices: 5973111--5973142 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5973101 GGTGGAGAGC
5973111 AGTGAATATT
1 AGTGAATATT
5973121 AGTGAATA--
1 AGTGAATATT
5973129 AGTGAATATT
1 AGTGAATATT
5973139 AGTG
1 AGTG
5973143 TGGGCTCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (10 bp):
AGTGAATATT
Found at i:5973799 original size:3 final size:3
Alignment explanation
Indices: 5973791--5973828 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5973781 CAAATACATA
5973791 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5973829 AGTATGAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5973864 original size:21 final size:21
Alignment explanation
Indices: 5973838--5973880 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5973828 AAGTATGAAT
5973838 AAAAATTAGAAATAAAATTTC
1 AAAAATTAGAAATAAAATTTC
5973859 AAAAATTAGAAATAAAATTTC
1 AAAAATTAGAAATAAAATTTC
5973880 A
1 A
5973881 CACTCAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAAATTAGAAATAAAATTTC
Found at i:5976189 original size:31 final size:30
Alignment explanation
Indices: 5976113--5976190 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 30
5976103 ACTTTTAAAA
* * *
5976113 TTTACAATACAGTCCCCTAACATTAATCCG
1 TTTACAATATAGTCCCCCAACATTAATACG
** * * *
5976143 TTTGTAATATGGTCCCCCAACATTTAGTATG
1 TTTACAATATAGTCCCCCAACA-TTAATACG
5976174 TTTACAATATAGTCCCC
1 TTTACAATATAGTCCCC
5976191 GACCGTTGAC
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
30 17 0.47
31 19 0.53
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (30 bp):
TTTACAATATAGTCCCCCAACATTAATACG
Found at i:5978169 original size:31 final size:30
Alignment explanation
Indices: 5978126--5978234 Score: 146
Period size: 31 Copynumber: 3.5 Consensus size: 30
5978116 TTAAACGGCT
* *
5978126 GGGGACCATATTGCAAACAGACTAAATGTTA
1 GGGGACCGTATTGCAAAC-GACTAAATGTTG
*
5978157 GGGGACCGTATTGTAAACGAACTAAATGTTG
1 GGGGACCGTATTGCAAACG-ACTAAATGTTG
*
5978188 GGGGACCGTATTGCAAACGGACTAAATATTG
1 GGGGACCGTATTGCAAAC-GACTAAATGTTG
*
5978219 GGGGACTGTATTGCAA
1 GGGGACCGTATTGCAA
5978235 GTTTTAAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
30 1 0.01
31 68 0.97
32 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (30 bp):
GGGGACCGTATTGCAAACGACTAAATGTTG
Found at i:5978598 original size:23 final size:23
Alignment explanation
Indices: 5978537--5978603 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 23
5978527 TCTTCAAGCC
* *
5978537 AAATATAAAGACTCCAAGAATGAT
1 AAATAAAAAGACTCTAA-AATGAT
5978561 AAATGAAAAAGACTCTAAAATGAT
1 AAAT-AAAAAGACTCTAAAATGAT
*
5978585 AAATAAAAAAACTCTAAAA
1 AAATAAAAAGACTCTAAAA
5978604 ATACAATGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
23 14 0.36
24 14 0.36
25 11 0.28
ACGTcount: A:0.61, C:0.10, G:0.09, T:0.19
Consensus pattern (23 bp):
AAATAAAAAGACTCTAAAATGAT
Found at i:5978604 original size:24 final size:24
Alignment explanation
Indices: 5978537--5978605 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
5978527 TCTTCAAGCC
* * *
5978537 AAATATAAAGACTCCAAGAATGAT
1 AAATAAAAAGACTCTAAAAATGAT
5978561 AAATGAAAAAGACTCT-AAAATGAT
1 AAAT-AAAAAGACTCTAAAAATGAT
*
5978585 AAATAAAAAAACTCTAAAAAT
1 AAATAAAAAGACTCTAAAAAT
5978606 ACAATGCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.26
24 20 0.51
25 9 0.23
ACGTcount: A:0.61, C:0.10, G:0.09, T:0.20
Consensus pattern (24 bp):
AAATAAAAAGACTCTAAAAATGAT
Found at i:5981929 original size:27 final size:28
Alignment explanation
Indices: 5981873--5981935 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
5981863 AGCTTACCAT
* *
5981873 TAAACTTGTATTATAATTAATTTTATTTA
1 TAAATTTGTATTATAATT-ATTTTAATTA
5981902 TAACATTTGT-TTATAATT-TTTTAATTA
1 TAA-ATTTGTATTATAATTATTTTAATTA
5981929 TAAATTT
1 TAAATTT
5981936 ATAACGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.13
27 11 0.35
29 11 0.35
30 5 0.16
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (28 bp):
TAAATTTGTATTATAATTATTTTAATTA
Found at i:5984595 original size:13 final size:15
Alignment explanation
Indices: 5984565--5984596 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
5984555 AGTGAGAAAA
5984565 AGAAAAACATACGAG
1 AGAAAAACATACGAG
5984580 AGAAAAA-ATA-GAG
1 AGAAAAACATACGAG
5984593 AGAA
1 AGAA
5984597 TTGAGAGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.66, C:0.06, G:0.22, T:0.06
Consensus pattern (15 bp):
AGAAAAACATACGAG
Found at i:5990137 original size:17 final size:16
Alignment explanation
Indices: 5990096--5990138 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
5990086 TAACGACACA
5990096 TTAATATTTAATTATTT
1 TTAA-ATTTAATTATTT
*
5990113 TATTAATTTAATTATGTT
1 T-TAAATTTAATTAT-TT
5990131 TTAAATTT
1 TTAAATTT
5990139 TTGAATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTAAATTTAATTATTT
Found at i:5991710 original size:10 final size:10
Alignment explanation
Indices: 5991677--5991709 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5991667 GTCTGTTTGG
5991677 TTTTAATTTA
1 TTTTAATTTA
*
5991687 ATTTAATTTA
1 TTTTAATTTA
5991697 TTTT-ATTTA
1 TTTTAATTTA
5991706 TTTT
1 TTTT
5991710 TTAGAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:5992559 original size:30 final size:30
Alignment explanation
Indices: 5992508--5992586 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
5992498 TAGATGAACT
** *
5992508 TAATTAATTTTTTGGCT-AAGTTCGAGGGCC
1 TAATTAATTTTTT-TATAAAGTTCGAGGACC
* *
5992538 TAATTAATTTTTTTATAAAGTTTGAGGACT
1 TAATTAATTTTTTTATAAAGTTCGAGGACC
*
5992568 TATTTAATTTTTTTATAAA
1 TAATTAATTTTTTTATAAA
5992587 AAATAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 1 0.02
30 41 0.98
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.49
Consensus pattern (30 bp):
TAATTAATTTTTTTATAAAGTTCGAGGACC
Found at i:5992853 original size:22 final size:20
Alignment explanation
Indices: 5992810--5992859 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
5992800 GACCAACAAA
5992810 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* *
5992830 TTTGCAACGCGAATTTCCCAAT
1 TTCGCAACGCGAA-CT-CCAAT
5992852 TTCGCAAC
1 TTCGCAAC
5992860 TCAGTCTCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.48
21 1 0.04
22 12 0.48
ACGTcount: A:0.28, C:0.32, G:0.14, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:5995116 original size:42 final size:42
Alignment explanation
Indices: 5995057--5995155 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
5995047 CCCCCCACTT
* * * *
5995057 CGAGAGCCATCACCTGATCGAGTCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
5995099 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
5995141 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
5995156 ATTTCATCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.27, C:0.36, G:0.19, T:0.17
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
Found at i:5995319 original size:21 final size:21
Alignment explanation
Indices: 5995270--5995319 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
5995260 GTTAGGGAAG
*
5995270 TTACATGATGAGGTCAGTACT
1 TTACGTGATGAGGTCAGTACT
** *
5995291 TTGTGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
5995312 TTACGTGA
1 TTACGTGA
5995320 CGACAACTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:5995379 original size:21 final size:21
Alignment explanation
Indices: 5995355--5995454 Score: 76
Period size: 21 Copynumber: 4.8 Consensus size: 21
5995345 GTACGGTCTA
*
5995355 TACGTGGTGAGGTAGCTATTT
1 TACGTGGTGAGGTAGCTACTT
* ** * *
5995376 TACGTGATGA-CAATGGTGCTT
1 TACGTGGTGAGGTA-GCTACTT
* *
5995397 TATGTGGTGAGGTATCTACTT
1 TACGTGGTGAGGTAGCTACTT
* *
5995418 TACGTGGAGAGGTATCTACTT
1 TACGTGGTGAGGTAGCTACTT
**
5995439 TACGTTATGAGGTAGC
1 TACGTGGTGAGGTAGC
5995455 CGCTCTACGT
Statistics
Matches: 58, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (21 bp):
TACGTGGTGAGGTAGCTACTT
Found at i:5995773 original size:21 final size:21
Alignment explanation
Indices: 5995747--5995822 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
5995737 ATTCACCTGT
*
5995747 CATCGTTCAAGAGGCCCCTTC
1 CATCGTTCAAGAGGCCCCTCC
**
5995768 CATCGTTCAAGAGGCATCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
5995789 CATCGTTCAATAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
5995810 CACCATTCAAGAG
1 CATCGTTCAAGAG
5995823 CCCGATTCAC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:5998176 original size:20 final size:20
Alignment explanation
Indices: 5998151--5998338 Score: 67
Period size: 20 Copynumber: 9.3 Consensus size: 20
5998141 TAAAATCCGT
5998151 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTCGAAAATCGA
**
5998171 GTTGCGAAAAC-AAAATTC-A
1 GTTGCGAATTCGAAAA-TCGA
* * **
5998190 TGTTGCGATTTAGAAAATCTT
1 -GTTGCGAATTCGAAAATCGA
*** * * *
5998211 GTTGCGAAAAGGAAACTTGT
1 GTTGCGAATTCGAAAATCGA
*** * *
5998231 GTTGCGAAAAAGAAATTCGC
1 GTTGCGAATTCGAAAATCGA
* *
5998251 TTTGCGAATTC-AGAAATTGA
1 GTTGCGAATTCGA-AAATCGA
* * *
5998271 GTTGCGAATTTGAAATTCCA
1 GTTGCGAATTCGAAAATCGA
* * * *
5998291 TGTTGCGAATTTGGAAATAGC
1 -GTTGCGAATTCGAAAATCGA
* *
5998312 GTTGCGAATTTGAAAATCGC
1 GTTGCGAATTCGAAAATCGA
5998332 GTTGCGA
1 GTTGCGA
5998339 GAAAGAAATT
Statistics
Matches: 124, Mismatches: 37, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
19 6 0.05
20 98 0.79
21 20 0.16
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTCGAAAATCGA
Found at i:5998234 original size:40 final size:40
Alignment explanation
Indices: 5998142--5998238 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 40
5998132 TTGTGAAATT
* *
5998142 AAAATCCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAAC
1 AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAC
* * ** *
5998182 AAAATTCATGTTGCGATTTAGAAAATCTTGTTGCGAAAAGG
1 AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAA-C
*
5998223 AAACTT-GTGTTGCGAA
1 AAAATTCGTGTTGCGAA
5998239 AAAGAAATTC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
40 41 0.89
41 5 0.11
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (40 bp):
AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAC
Found at i:6001275 original size:7 final size:7
Alignment explanation
Indices: 6001263--6001287 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6001253 ATTTTTTAAA
6001263 AAAATTT
1 AAAATTT
6001270 AAAATTT
1 AAAATTT
6001277 AAAATTT
1 AAAATTT
6001284 AAAA
1 AAAA
6001288 CTCTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:6003359 original size:2 final size:2
Alignment explanation
Indices: 6003352--6003418 Score: 113
Period size: 2 Copynumber: 35.0 Consensus size: 2
6003342 ATGGCCCGTA
6003352 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6003392 AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6003419 TAAATATTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 3 0.05
2 59 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6003376 original size:19 final size:19
Alignment explanation
Indices: 6003352--6003418 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
6003342 ATGGCCCGTA
6003352 ATATATATATATATATAAT
1 ATATATATATATATATAAT
6003371 ATATATATATATATAT-AT
1 ATATATATATATATATAAT
6003389 -TATATATATATATATAAT
1 ATATATATATATATATAAT
6003407 ATATATATATAT
1 ATATATATATAT
6003419 TAAATATTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
17 15 0.33
18 4 0.09
19 27 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATATATATATATAAT
Found at i:6003425 original size:15 final size:14
Alignment explanation
Indices: 6003352--6003418 Score: 113
Period size: 13 Copynumber: 5.0 Consensus size: 14
6003342 ATGGCCCGTA
6003352 ATATATATATATAT
1 ATATATATATATAT
6003366 ATA-ATATATATAT
1 ATATATATATATAT
6003379 ATATATATAT-TAT
1 ATATATATATATAT
6003392 ATATATATATATA-
1 ATATATATATATAT
6003405 ATATATATATATAT
1 ATATATATATATAT
6003419 TAAATATTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
13 39 0.78
14 11 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:6003425 original size:17 final size:17
Alignment explanation
Indices: 6003350--6003418 Score: 120
Period size: 17 Copynumber: 3.9 Consensus size: 17
6003340 CTATGGCCCG
6003350 TAATATATATATATATA
1 TAATATATATATATATA
6003367 TAATATATATATATATA
1 TAATATATATATATATA
6003384 TATATTATATATATATATA
1 TA-A-TATATATATATATA
6003403 TAATATATATATATAT
1 TAATATATATATATAT
6003419 TAAATATTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
17 32 0.64
18 2 0.04
19 16 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATATATATATATA
Found at i:6003921 original size:14 final size:14
Alignment explanation
Indices: 6003902--6003935 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6003892 TAGACACAGT
6003902 TATATATAATTATA
1 TATATATAATTATA
*
6003916 TATATATGATTATA
1 TATATATAATTATA
*
6003930 AATATA
1 TATATA
6003936 AATATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TATATATAATTATA
Found at i:6004822 original size:29 final size:28
Alignment explanation
Indices: 6004781--6004837 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
6004771 AAAACCTAAT
* * *
6004781 ATTTTTATAAATAATATTTGAGACTCAA
1 ATTTTTATAAATAAAATTTAAAACTCAA
*
6004809 ATTTTTAATTAATAAAATTTAAAACTCAA
1 ATTTTT-ATAAATAAAATTTAAAACTCAA
6004838 TATTCGAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (28 bp):
ATTTTTATAAATAAAATTTAAAACTCAA
Found at i:6010155 original size:23 final size:24
Alignment explanation
Indices: 6010129--6010194 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 24
6010119 ATATAATATT
*
6010129 ATATTATGTATTAATGGAGAAG-A
1 ATATTATGTATTAATGGAAAAGTA
* *
6010152 ATATTATGCATTAATGAAAAAGTATA
1 ATATTATGTATTAATGGAAAAG--TA
*
6010178 ATATTATATATTAATGG
1 ATATTATGTATTAATGG
6010195 TGGATATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.56
26 15 0.44
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (24 bp):
ATATTATGTATTAATGGAAAAGTA
Found at i:6010857 original size:2 final size:2
Alignment explanation
Indices: 6010850--6010880 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6010840 AGCAATATTA
6010850 AT AT 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 AT AT A
6010881 CACTCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6011577 original size:31 final size:29
Alignment explanation
Indices: 6011539--6011597 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
6011529 CAGAAAACTA
6011539 AATAAAAATATATATATAATTGATACAAGTT
1 AATAAAAA-A-ATATATAATTGATACAAGTT
*
6011570 AATAAAAAAGTATATAATTGATACAAGT
1 AATAAAAAAATATATAATTGATACAAGT
6011598 ATCAATAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 18 0.67
30 1 0.04
31 8 0.30
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.32
Consensus pattern (29 bp):
AATAAAAAAATATATAATTGATACAAGTT
Found at i:6021107 original size:16 final size:16
Alignment explanation
Indices: 6021086--6021117 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6021076 CTGTCTTATA
6021086 AAATACCTCCTTGGGC
1 AAATACCTCCTTGGGC
6021102 AAATACCTCCTTGGGC
1 AAATACCTCCTTGGGC
6021118 TATAACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (16 bp):
AAATACCTCCTTGGGC
Found at i:6023682 original size:31 final size:31
Alignment explanation
Indices: 6023647--6023742 Score: 153
Period size: 30 Copynumber: 3.2 Consensus size: 31
6023637 GAATACAAAG
*
6023647 ATTAAATTGATATTTTATATAAATTTTAAAA
1 ATTAAATTAATATTTTATATAAATTTTAAAA
6023678 ATTAAATTAATATTTTATATAAATTTT-AAA
1 ATTAAATTAATATTTTATATAAATTTTAAAA
6023708 ATTAAATTAATATTTTATATGAAA--TTAAAA
1 ATTAAATTAATATTTTATAT-AAATTTTAAAA
6023738 ATTAA
1 ATTAA
6023743 TTATTTTTAC
Statistics
Matches: 62, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
29 2 0.03
30 31 0.50
31 29 0.47
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
ATTAAATTAATATTTTATATAAATTTTAAAA
Found at i:6031419 original size:24 final size:25
Alignment explanation
Indices: 6031366--6031422 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 25
6031356 AAACTTTAAT
*
6031366 TTAAAAATATTAAATATTGAATTTCA
1 TTAAAAA-ATTAAATATTGAATTACA
6031392 -TAAAAAA-TAAATATCTG-ATTACA
1 TTAAAAAATTAAATAT-TGAATTACA
6031415 TTAAAAAA
1 TTAAAAAA
6031423 ATCAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 12 0.43
24 10 0.36
25 6 0.21
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (25 bp):
TTAAAAAATTAAATATTGAATTACA
Found at i:6031444 original size:12 final size:12
Alignment explanation
Indices: 6031421--6031453 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6031411 TACATTAAAA
6031421 AAATCAAAATCAC
1 AAATC-AAATCAC
6031434 AAATCAAATCAC
1 AAATCAAATCAC
6031446 AAAT-AAAT
1 AAATCAAAT
6031454 ATTAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 11 0.55
13 5 0.25
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (12 bp):
AAATCAAATCAC
Found at i:6040265 original size:31 final size:31
Alignment explanation
Indices: 6040229--6040309 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 31
6040219 TCCGAACCCG
6040229 ACCTGAACCCGAATTGAACCGA-AAATATGA
1 ACCTGAACCCGAATTGAACCGACAAATATGA
* * * *
6040259 TACCTGAACCCGAACTGCATCTGACTAATATGA
1 -ACCTGAACCCGAATTG-AACCGACAAATATGA
6040292 ACCTGAACCCGAGATTGA
1 ACCTGAACCCGA-ATTGA
6040310 CCTGGTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
31 15 0.36
32 17 0.40
33 10 0.24
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (31 bp):
ACCTGAACCCGAATTGAACCGACAAATATGA
Found at i:6040354 original size:15 final size:16
Alignment explanation
Indices: 6040334--6040367 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6040324 GGTATTACCC
6040334 GACCTG-TTTCAACCT
1 GACCTGTTTTCAACCT
*
6040349 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
6040365 GAC
1 GAC
6040368 ATGTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:6040468 original size:19 final size:19
Alignment explanation
Indices: 6040432--6040467 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6040422 ATTACCATAG
6040432 ATAAAATTATAAGATTTTA
1 ATAAAATTATAAGATTTTA
6040451 ATAAAATTATAAG-TTTT
1 ATAAAATTATAAGATTTT
6040468 TTAACTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (19 bp):
ATAAAATTATAAGATTTTA
Found at i:6041978 original size:101 final size:101
Alignment explanation
Indices: 6041861--6042062 Score: 325
Period size: 101 Copynumber: 2.0 Consensus size: 101
6041851 TGGAGCGATG
* * *
6041861 GGTTGTTTGGAGAGAGGGAAACAATTAATAGCAGAAGAAAAAGAAAAATAGGAGGGAAATGATAA
1 GGTTGTTTGGAGAGAGGGAAACAATTAAGAGCAAAAGAAAAAGAAAAATAGGAGGGAAATGACAA
6041926 TTCTGGTTTGGTTATCTGGCG-TCACCGCCTTATATA
66 TTCTGGTTTGGTTATCTGGCGCT-ACCGCCTTATATA
* *
6041962 GGTTGTTTGGAGAGAGGGAAACAATTAAGATCAAAAGAAAAATAAAAATAGGAGGGAAATGACAA
1 GGTTGTTTGGAGAGAGGGAAACAATTAAGAGCAAAAGAAAAAGAAAAATAGGAGGGAAATGACAA
* *
6042027 TTCTGGTTTGGTTATTTGGCGCTACCGTCTTATATA
66 TTCTGGTTTGGTTATCTGGCGCTACCGCCTTATATA
6042063 ATTTATATTA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 92 0.99
102 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.27
Consensus pattern (101 bp):
GGTTGTTTGGAGAGAGGGAAACAATTAAGAGCAAAAGAAAAAGAAAAATAGGAGGGAAATGACAA
TTCTGGTTTGGTTATCTGGCGCTACCGCCTTATATA
Found at i:6042178 original size:25 final size:28
Alignment explanation
Indices: 6042059--6042262 Score: 154
Period size: 28 Copynumber: 7.2 Consensus size: 28
6042049 TACCGTCTTA
* *
6042059 TATAATTTATATTAATA-AA--GTAT-T
1 TATAATTAATATTAATATAATTATATAT
*
6042083 TATAATTAATATTAAAATAATTATATAT
1 TATAATTAATATTAATATAATTATATAT
* *
6042111 TATAATTAATATAAAAATAATTATATAT
1 TATAATTAATATTAATATAATTATATAT
*
6042139 TATAATTAATATTAATTTAATTA-ATAT
1 TATAATTAATATTAATATAATTATATAT
*
6042166 TA-ACTT-ATATTAATATAATATAGTTTATAATT
1 TATAATTAATATTAATATAAT-TA---TAT-A-T
* *
6042198 TGTAATTAATATTAATATAA-AATATAGT
1 TATAATTAATATTAATATAATTATATA-T
* *
6042226 CTATAAAATTAATATTAATATAAACTATATGT
1 -TAT--AATTAATATTAATAT-AATTATATAT
6042258 TATAA
1 TATAA
6042263 ATTATATAGT
Statistics
Matches: 146, Mismatches: 16, Indels: 31
0.76 0.08 0.16
Matches are distributed among these distances:
24 15 0.10
25 14 0.10
26 5 0.03
27 9 0.06
28 50 0.34
29 7 0.05
30 2 0.01
31 19 0.13
32 6 0.04
33 7 0.05
34 12 0.08
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (28 bp):
TATAATTAATATTAATATAATTATATAT
Found at i:6042239 original size:31 final size:30
Alignment explanation
Indices: 6042201--6042385 Score: 126
Period size: 31 Copynumber: 5.8 Consensus size: 30
6042191 TATAATTTGT
*
6042201 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAACTATAGT-TATAA
6042232 AATTAATATTAATATAAACTATATGTTAT-A
1 AATTAATATTAATATAAACTATA-GTTATAA
* * *
6042262 AATTATATAGTATAGTTTATAAACTATAATTCATAT
1 AATTA-ATA-T-TA--ATATAAACTATAGTT-ATAA
*
6042298 AATTAATATTAATAT--AGTATAGTTTATAA
1 AATTAATATTAATATAAACTATAG-TTATAA
*
6042327 ACTATATACTATATTAATATAAATTATAGTTA-AGA
1 A--AT-TA--ATATTAATATAAACTATAGTTATA-A
* *
6042362 TAATTAACATTAATATAAATTATA
1 -AATTAATATTAATATAAACTATA
6042386 TAGTACATTA
Statistics
Matches: 126, Mismatches: 10, Indels: 36
0.73 0.06 0.21
Matches are distributed among these distances:
29 9 0.07
30 8 0.06
31 50 0.40
32 5 0.04
33 6 0.05
34 16 0.13
35 20 0.16
36 12 0.10
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAACTATAGTTATAA
Found at i:6042253 original size:24 final size:25
Alignment explanation
Indices: 6042208--6042254 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
6042198 TGTAATTAAT
**
6042208 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
6042233 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
6042255 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:6042313 original size:131 final size:132
Alignment explanation
Indices: 6042172--6042421 Score: 312
Period size: 131 Copynumber: 1.9 Consensus size: 132
6042162 ATATTAACTT
** * *
6042172 ATATTAATATAATATAGTTTATAATTTGTA-ATTAATATTAATATAAAATATAGTCTATA-A-AA
1 ATATTAATATAATATAGTTTATAAACTATATACT-ATATTAATATAAAATATAGT-TA-AGATAA
* * * *
6042234 TTAATATTAATATAAACTATAT-GT-TATAAATTATATAGTATAGTTTATAAACTATAATTCATA
63 TTAACATTAATATAAACTATATAGTACATAAA-TATAAACTATAGTTTATAAACTATAATTCATA
6042297 TAATTA
127 TAATTA
* *
6042303 ATATTAATATAGTATAGTTTATAAACTATATACTATATTAATATAAATTATAGTTAAGATAATTA
1 ATATTAATATAATATAGTTTATAAACTATATACTATATTAATATAAAATATAGTTAAGATAATTA
* * *
6042368 ACATTAATATAAATTATATAGTACATTAATATAAACTATAGTTTATAAATTATA
66 ACATTAATATAAACTATATAGTACATAAATATAAACTATAGTTTATAAACTATA
6042422 TACTATAGGT
Statistics
Matches: 101, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
129 1 0.01
130 3 0.03
131 67 0.66
132 26 0.26
133 4 0.04
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (132 bp):
ATATTAATATAATATAGTTTATAAACTATATACTATATTAATATAAAATATAGTTAAGATAATTA
ACATTAATATAAACTATATAGTACATAAATATAAACTATAGTTTATAAACTATAATTCATATAAT
TA
Found at i:6042315 original size:43 final size:40
Alignment explanation
Indices: 6042266--6042356 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 40
6042256 GTTATAAATT
* *
6042266 ATATAGTATAGTTTATAAACTATAATTCATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTAT-ATAC-TAT-ATTAATATAA
6042309 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
6042349 ATTATAGT
1 A-TATAGT
6042357 TAAGATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 10 0.22
41 9 0.20
42 3 0.07
43 23 0.51
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
Found at i:6042354 original size:15 final size:15
Alignment explanation
Indices: 6042336--6042386 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
6042326 AACTATATAC
6042336 TATATTAATATAAAT
1 TATATTAATATAAAT
*
6042351 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
*
6042366 TAACATTAATATAAAT
1 T-ATATTAATATAAAT
6042382 TATAT
1 TATAT
6042387 AGTACATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:6042355 original size:36 final size:34
Alignment explanation
Indices: 6042171--6042357 Score: 114
Period size: 31 Copynumber: 5.6 Consensus size: 34
6042161 AATATTAACT
* *
6042171 TATATTAATAT-AA-TATAGTTTAT-AATTTGTAA
1 TATATTAATATAAACTATAGTTTATAAATATAT-A
* *
6042203 TTAATATTAATATAAAATATAGTCTATAAA-AT-TA
1 -T-ATATTAATATAAACTATAGTTTATAAATATATA
6042237 -ATATTAATATAAACTATA-TGTTATAAATTATATA
1 TATATTAATATAAACTATAGT-TTATAAA-TATATA
* * *
6042271 GTATAGTT--TATAAACTATAATTCATATA-AT-TA
1 -TATA-TTAATATAAACTATAGTTTATAAATATATA
*
6042303 -ATATTAATAT--AGTATAGTTTATAAACTATATA
1 TATATTAATATAAACTATAGTTTATAAA-TATATA
*
6042335 CTATATTAATATAAATTATAGTT
1 -TATATTAATATAAACTATAGTT
6042358 AAGATAATTA
Statistics
Matches: 122, Mismatches: 11, Indels: 39
0.71 0.06 0.23
Matches are distributed among these distances:
29 13 0.11
30 4 0.03
31 28 0.23
32 4 0.03
33 5 0.04
34 23 0.19
35 19 0.16
36 22 0.18
37 4 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (34 bp):
TATATTAATATAAACTATAGTTTATAAATATATA
Found at i:6042426 original size:21 final size:21
Alignment explanation
Indices: 6042397--6042449 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
6042387 AGTACATTAA
* *
6042397 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
6042418 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
6042439 TATAAACTATA
1 TATAAACTATA
6042450 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:6042553 original size:57 final size:55
Alignment explanation
Indices: 6042480--6042617 Score: 168
Period size: 59 Copynumber: 2.4 Consensus size: 55
6042470 TTGTTTATAA
**
6042480 ACTATAAGTTACATATATAGTTTATATAAAATATAAATAGATTGTATGTATACATAT
1 ACTATAAGTTACATATATAGTTTATATAAAATATAAATAG-TT-TATACATACATAT
* * * * * *
6042537 ACTATAGGTTATATATATATAGTTTATATATAGTATACATAGTTTATACATACATGT
1 ACTATAAG-T-TACATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
6042594 ACTATAAGTTACATATATAGTTTA
1 ACTATAAGTTACATATATAGTTTA
6042618 CATGTATACA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
55 14 0.20
56 1 0.01
57 24 0.35
58 3 0.04
59 27 0.39
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (55 bp):
ACTATAAGTTACATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
Found at i:6042563 original size:15 final size:16
Alignment explanation
Indices: 6042533--6042573 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
6042523 GTATGTATAC
6042533 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
*
6042549 ATATA-TATAGTTTAT
1 ATATACTATAGGTTAT
*
6042564 ATATAGTATA
1 ATATACTATA
6042574 CATAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:6042563 original size:59 final size:57
Alignment explanation
Indices: 6042480--6042612 Score: 162
Period size: 57 Copynumber: 2.3 Consensus size: 57
6042470 TTGTTTATAA
**
6042480 ACTATAAGTTAC--ATATATAGTTTATATAAAATATAAATAGATTGTATGTATACATAT
1 ACTATAAGTTACATATATATAGTTTATATAAAATATAAATAG-TT-TATACATACATAT
* * * * * *
6042537 ACTATAGGTTATATATATATAGTTTATATATAGTATACATAGTTTATACATACATGT
1 ACTATAAGTTACATATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
6042594 ACTATAAGTTACATATATA
1 ACTATAAGTTACATATATA
6042613 GTTTACATGT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 37 0.58
58 2 0.03
59 25 0.39
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (57 bp):
ACTATAAGTTACATATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
Found at i:6042573 original size:20 final size:19
Alignment explanation
Indices: 6042546--6042584 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
6042536 TACTATAGGT
*
6042546 TATATATATATAGTTTATA
1 TATATATACATAGTTTATA
6042565 TATAGTATACATAGTTTATA
1 TATA-TATACATAGTTTATA
6042585 CATACATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (19 bp):
TATATATACATAGTTTATA
Found at i:6042614 original size:35 final size:36
Alignment explanation
Indices: 6042575--6042648 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
6042565 TATAGTATAC
*
6042575 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
6042610 ATAGTTTACATGTATACATATACTATATGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
6042647 AT
1 AT
6042649 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:6042682 original size:7 final size:7
Alignment explanation
Indices: 6042670--6042709 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
6042660 TATGCATAAT
6042670 GTTTAGG
1 GTTTAGG
*
6042677 GTTTAGA
1 GTTTAGG
6042684 GTTTATGG
1 GTTTA-GG
6042692 G-TTAGG
1 GTTTAGG
6042698 GTTTAGG
1 GTTTAGG
6042705 GTTTA
1 GTTTA
6042710 TATTTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 3 0.10
7 24 0.83
8 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:6042732 original size:35 final size:34
Alignment explanation
Indices: 6042693--6042772 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 34
6042683 AGTTTATGGG
*
6042693 TTAGGGTTTAGGGTTTATATTTTAATATTTAGGAT
1 TTAGGGTTTAGGGTTTATA-TATAATATTTAGGAT
* * *
6042728 TTAGGATTTAGGGTTTATATATACTATTTAGGGT
1 TTAGGGTTTAGGGTTTATATATAATATTTAGGAT
6042762 TTAGGGATTTA
1 TTAGGG-TTTA
6042773 AGATTTCTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 17 0.44
35 22 0.56
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (34 bp):
TTAGGGTTTAGGGTTTATATATAATATTTAGGAT
Found at i:6042789 original size:35 final size:34
Alignment explanation
Indices: 6042718--6042789 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 34
6042708 TATATTTTAA
* * *
6042718 TATTTAGGATTTAGGATTTAGGGTTTATATATAC
1 TATTTAGGATTTAGGATTTAAGATTTATATAAAC
* *
6042752 TATTTAGGGTTTAGGGATTTAAGATTTCTATAAAC
1 TATTTAGGATTTA-GGATTTAAGATTTATATAAAC
6042787 TAT
1 TAT
6042790 ATATTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 12 0.38
35 20 0.62
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (34 bp):
TATTTAGGATTTAGGATTTAAGATTTATATAAAC
Found at i:6043155 original size:2 final size:2
Alignment explanation
Indices: 6043148--6043291 Score: 194
Period size: 2 Copynumber: 75.0 Consensus size: 2
6043138 GCATAGTGTT
6043148 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
6043190 TA TA TA TA TA TA TA TA -A CA TA TA TGA TA TA TA T- TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
* * *
6043229 TT TA TA T- TA TA TT TA TA -A TA TA AA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6043268 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
6043292 ATTAAAAGTA
Statistics
Matches: 127, Mismatches: 7, Indels: 16
0.85 0.05 0.11
Matches are distributed among these distances:
1 7 0.06
2 118 0.93
3 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6043659 original size:2 final size:2
Alignment explanation
Indices: 6043652--6043678 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6043642 ACTTTGAATA
6043652 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
6043679 AATTAATATA
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:6043810 original size:17 final size:17
Alignment explanation
Indices: 6043753--6043826 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 17
6043743 TAAACATAAT
* *
6043753 TATATATATAGCTTATA
1 TATAAATATAGTTTATA
6043770 -ATAATTATATAGTTTATAA
1 TATAA--ATATAGTTTAT-A
6043789 TATAAATATAGTTTATA
1 TATAAATATAGTTTATA
*
6043806 TATAAATTTA-TATTATA
1 TATAAATATAGT-TTATA
6043823 TATA
1 TATA
6043827 TATTATTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
16 4 0.08
17 19 0.39
18 21 0.43
19 1 0.02
20 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (17 bp):
TATAAATATAGTTTATA
Found at i:6049856 original size:13 final size:13
Alignment explanation
Indices: 6049837--6049925 Score: 88
Period size: 13 Copynumber: 6.3 Consensus size: 13
6049827 GTCACAACCC
6049837 GACCCGACCCGTT
1 GACCCGACCCGTT
*
6049850 TACCCGACCCGTT
1 GACCCGACCCGTT
*
6049863 GACCTGACCCGTT
1 GACCCGACCCGTT
6049876 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
6049894 GACCCGACCCGTT
1 GACCCGACCCGTT
*
6049907 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
6049922 GACC
1 GACC
6049926 GTTGACCGGA
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
13 40 0.62
15 12 0.19
18 12 0.19
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:6049866 original size:8 final size:8
Alignment explanation
Indices: 6049855--6049932 Score: 64
Period size: 8 Copynumber: 10.5 Consensus size: 8
6049845 CCGTTTACCC
6049855 GACCCGTT
1 GACCCGTT
6049863 GA-CC--T
1 GACCCGTT
6049868 GACCCGTT
1 GACCCGTT
**
6049876 GACCCGACCC
1 GACCCG--TT
6049886 GACCCGTT
1 GACCCGTT
6049894 GACCC---
1 GACCCGTT
6049899 GACCCGTT
1 GACCCGTT
6049907 GA-CCGTT
1 GACCCGTT
6049914 GACCCGTT
1 GACCCGTT
6049922 GA-CCGTT
1 GACCCGTT
6049929 GACC
1 GACC
6049933 GGAATTGACC
Statistics
Matches: 56, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
5 8 0.14
6 2 0.04
7 16 0.29
8 24 0.43
10 6 0.11
ACGTcount: A:0.15, C:0.41, G:0.24, T:0.19
Consensus pattern (8 bp):
GACCCGTT
Found at i:6049871 original size:26 final size:26
Alignment explanation
Indices: 6049837--6049925 Score: 88
Period size: 31 Copynumber: 3.2 Consensus size: 26
6049827 GTCACAACCC
*
6049837 GACCCGACCCGTTTACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGTT
*
6049863 GACCTGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTT-----GACCCGACCCGTT
*
6049894 GACCCGACCCGTTGACCGTTGACCCGTT
1 GACCCGACCCGTTGACC--CGACCCGTT
6049922 GACC
1 GACC
6049926 GTTGACCGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
26 16 0.31
28 12 0.23
31 24 0.46
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (26 bp):
GACCCGACCCGTTGACCCGACCCGTT
Found at i:6049872 original size:18 final size:18
Alignment explanation
Indices: 6049863--6049904 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
6049853 CCGACCCGTT
*
6049863 GACCTGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
6049881 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
6049899 GACCCG
1 GACCCG
6049905 TTGACCGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.24, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:6049882 original size:44 final size:45
Alignment explanation
Indices: 6049833--6049925 Score: 161
Period size: 44 Copynumber: 2.1 Consensus size: 45
6049823 ACCGGTCACA
*
6049833 ACCCGACCCGACCCGTTTACCCGACCCGTTGACC-TGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTGACCGTGACCCGTTG
6049877 ACCCGACCCGACCCGTTGACCCGACCCGTTGACCGTTGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTGACCG-TGACCCGTTG
6049923 ACC
1 ACC
6049926 GTTGACCGGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 33 0.72
46 13 0.28
ACGTcount: A:0.16, C:0.45, G:0.22, T:0.17
Consensus pattern (45 bp):
ACCCGACCCGACCCGTTGACCCGACCCGTTGACCGTGACCCGTTG
Found at i:6049886 original size:31 final size:31
Alignment explanation
Indices: 6049851--6049910 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
6049841 CGACCCGTTT
*
6049851 ACCCGACCCGTTGACCTGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCGACCCGTTGACCCG
6049882 ACCCGACCCGTTGACCCGACCCGTTGACC
1 ACCCGACCCGTTGACCCGACCCGTTGACC
6049911 GTTGACCCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGTTGACCCG
Found at i:6049914 original size:7 final size:7
Alignment explanation
Indices: 6049902--6049933 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
6049892 TTGACCCGAC
6049902 CCGTTGA
1 CCGTTGA
6049909 CCGTTGA
1 CCGTTGA
6049916 CCCGTTGA
1 -CCGTTGA
6049924 CCGTTGA
1 CCGTTGA
6049931 CCG
1 CCG
6049934 GAATTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:6055604 original size:36 final size:36
Alignment explanation
Indices: 6055562--6055676 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
6055552 ATTAAAAGAT
** *
6055562 ATTAAAAGGATATCAATATCTTTTCGAATATTTTAA
1 ATTAAAAGGATATCAATATCTTTTTAAATATTTAAA
* * *
6055598 ATTAAAA-GATATTTATTAT-TTTTTTAA-ATTTAAA
1 ATTAAAAGGATA-TCAATATCTTTTTAAATATTTAAA
* * * *
6055632 TATTAAAACGATAACAATATCTTTTTAAATAATTCAA
1 -ATTAAAAGGATATCAATATCTTTTTAAATATTTAAA
6055669 ATTAAAAG
1 ATTAAAAG
6055677 ATAATTAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
34 6 0.10
35 21 0.34
36 30 0.48
37 5 0.08
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (36 bp):
ATTAAAAGGATATCAATATCTTTTTAAATATTTAAA
Found at i:6055657 original size:35 final size:34
Alignment explanation
Indices: 6055560--6055679 Score: 100
Period size: 35 Copynumber: 3.4 Consensus size: 34
6055550 ATATTAAAAG
* *
6055560 ATATTAAAAGGATATCAATATCTTTTCGAATATTTTA
1 ATATTAAAA-GATATCAATATCTTTT-TAA-ATTTAA
* * *
6055597 A-ATTAAAAGATATTTATTATTTTTTTAAATTTAA
1 ATATTAAAAGATA-TCAATATCTTTTTAAATTTAA
* *
6055631 ATATTAAAACGATAACAATATCTTTTTAAATAATTCA
1 ATATTAAAA-GATATCAATATCTTTTTAAAT--TTAA
6055668 A-ATTAAAAGATA
1 ATATTAAAAGATA
6055680 ATTAAAATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
34 6 0.09
35 30 0.44
36 27 0.40
37 5 0.07
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (34 bp):
ATATTAAAAGATATCAATATCTTTTTAAATTTAA
Found at i:6055690 original size:71 final size:71
Alignment explanation
Indices: 6055560--6055692 Score: 185
Period size: 71 Copynumber: 1.9 Consensus size: 71
6055550 ATATTAAAAG
* * * * * * **
6055560 ATATTAAAAGGATATCAATATCTTTTCGAATATTTTAAATTAAAAGATATTTATTATTTTTTTAA
1 ATATTAAAACGATAACAATATCTTTTCAAATAATTCAAATTAAAAGATAATTAAAATTTTTTTAA
6055625 ATTTAA
66 ATTTAA
*
6055631 ATATTAAAACGATAACAATATCTTTTTAAATAATTCAAATTAAAAGATAATTAAAATTTTTT
1 ATATTAAAACGATAACAATATCTTTTCAAATAATTCAAATTAAAAGATAATTAAAATTTTTT
6055693 CTTTTAGAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 53 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (71 bp):
ATATTAAAACGATAACAATATCTTTTCAAATAATTCAAATTAAAAGATAATTAAAATTTTTTTAA
ATTTAA
Found at i:6055692 original size:35 final size:33
Alignment explanation
Indices: 6055591--6055692 Score: 80
Period size: 35 Copynumber: 2.9 Consensus size: 33
6055581 CTTTTCGAAT
* * * *
6055591 ATTTTAAATTAAAAGATATTTATTATTTTTTTAA
1 ATTTAAAATTAAAAGATAATTA-AAATTTTTTAA
* *
6055625 ATTTAAATATTAAAACGATAA-CAATATCTTTTTAA
1 ATTTAAA-ATTAAAA-GATAATTAAAAT-TTTTTAA
*
6055660 ATAATTCAAATTAAAAGATAATTAAAATTTTTT
1 AT--TTAAAATTAAAAGATAATTAAAATTTTTT
6055693 CTTTTAGAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
34 7 0.13
35 27 0.51
36 15 0.28
37 4 0.08
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (33 bp):
ATTTAAAATTAAAAGATAATTAAAATTTTTTAA
Found at i:6063173 original size:201 final size:201
Alignment explanation
Indices: 6062909--6063948 Score: 1204
Period size: 201 Copynumber: 5.2 Consensus size: 201
6062899 AGGGTAATTT
* * * * *
6062909 TAAAAAGTGTCGACACGAATTTAA-AAAGTGTCGATACGTTATGTT-GA-CTGGTTTTCTCATAA
1 TAAAAAGTATCGACAC-AAATAAATAAAGTGTCGATACATTAT-TTAGACCT-ATTTTCTCATAA
* * *
6062971 AATCGGTAAATTTAAATCGGTTACATTGTAAAGTGATCTATTACATTATAATTTTCGGTCTCGAT
63 AACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGAT
* * *
6063036 GTATTTGGGGTCGACACTTTTTATAAATGTGTCGACATTTTATGCGTGCACATAGTATGGGAATT
128 GTATTTGGGGTCGACACTTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGAATT
6063101 CATTATGGA
193 CATTATGGA
6063110 TAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAAC
1 TAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAAC
* *
6063175 CGGTAAATTTAAACCAGTTATATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTA
66 CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTA
*
6063240 TTTGGGGTCGACACTTTTTATAAATGTATTGACACTTTATGCGTGCACATAGTTTGGGAATTCAT
131 TTTGGGGTCGACACTTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGAATTCAT
6063305 TATGGA
196 TATGGA
*
6063311 TAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACTTATTTTCTCATAAAAC
1 TAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAAC
* * *
6063376 CGGTAAATTTAAA-CGATTACATTGTAAAGTGACCTATTATATTATAATTTTCGG--TCAATGTA
66 CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTA
*
6063438 -TTGGGGTCGACAC-TTTTATAAATGTATCGACACTTTATGTGTGCACATAGTTTGGGAATTCAT
131 TTTGGGGTCGACACTTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGAATTCAT
6063501 TATGGA
196 TATGGA
6063507 TAAAAAGTATCGACACAAAT-AATAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAAC
1 TAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAAC
* *
6063571 CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACA-TATTATATCTAT-GTGTTTCGA
66 CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTA-TA-AT-TTTCG-GTCTCGA
* * ** * * * * *
6063634 TGTTTTTAGTATCGACACTTGTTATAAATGTATCGACACTTTGT-CGTGCACTTGGTTTGGAAAA
127 TGTATTTGGGGTCGACACTTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGG-GAA
* *
6063698 TACATTCTGGA
191 TTCATTATGGA
*** ** ** * * * *
6063709 -AAATAAGTATCGACACTTGT-TGTAGTTGTGTCGATACTTTATGTATACCTGTTTTCTCAT-AA
1 TAAA-AAGTATCGACACAAATAAATA-AAGTGTCGATACATTATTTAGACCTATTTTCTCATAAA
** ** * ** * *
6063771 ACCGGTGTATTTAGGCCGGTTACATTGTTATTTTACCTATTACA-TAT-ATCTAT-GTGT-TCGA
64 ACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAAT-TTTCG-GTCTCGA
* * ** * * * **
6063832 TGTTTTTAGTATCGACACTTGTTATAAATGTATCGACACTTTATGCGTGC-CTGTCGTTTGGCCA
127 TGTATTTGGGGTCGACACTTTTTATAAATGTATCGACACTTTATGCGTGCAC-ATAGTTTGGGAA
* *
6063896 TTCATTCTAGA
191 TTCATTATGGA
* * **
6063907 CAATAAGTATCGACACAAAT-TCTAATAGTGTCGATACATTAT
1 TAAAAAGTATCGACACAAATAAATAA-AGTGTCGATACATTAT
6063949 GTTGACCAGT
Statistics
Matches: 747, Mismatches: 73, Indels: 41
0.87 0.08 0.05
Matches are distributed among these distances:
195 58 0.08
196 102 0.14
197 16 0.02
198 98 0.13
199 24 0.03
200 50 0.07
201 279 0.37
202 91 0.12
203 29 0.04
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (201 bp):
TAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAAC
CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTA
TTTGGGGTCGACACTTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGAATTCAT
TATGGA
Found at i:6063766 original size:398 final size:396
Alignment explanation
Indices: 6062772--6063948 Score: 1216
Period size: 398 Copynumber: 2.9 Consensus size: 396
6062762 TTTCTACCGT
* * *
6062772 TTACATTGTAAA-TATACCTATTACATTATAATTATCGGTATCGATGT-TTTAGTATCGACACTT
1 TTACATTGTAAAGT-GACCTATTACATTATAATTATCGGTCTCGATGTATTTAGGATCGACACTT
* *
6062835 GTTATAAATGTATCGACACTTTGT-CGTGCACTTAGTTTGGAAAATACATTCTGGAAAATAATGA
65 GTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGG-AAATACA---T------T-AT--
* * * *
6062899 AGGGTAATTTTAAAAAGTGTCGACACGAATTTAA-AAAGTGTCGATACGTTATGT-TGA-CTGGT
117 --GG--A---TAAAAAGTATCGACAC-AAATAAATAAAGTGTCGATACATTATGTAT-ACCT-GT
* *
6062961 TTTCTCATAAAATCGGTAAATTTAAATCGGTTACATTGTAAAGTGATCTATTACATTATAATTTT
172 TTTCTCATAAAACCGGTAAATTTAAA-CGGTTACATTGTAAAGTGACCTATTACATTATAATTTT
* *
6063026 CGGTCTCGATGTATTTGGGGTCGACACTTTTTATAAATGTGTCGACATTTTATGCGTGCACATAG
236 CGG--TCGATGTA-TTGGGGTCGACAC-TTTTATAAATGTATCGACACTTTATGCGTGCACATAG
*
6063091 TATGGGAATTCATTATGGATAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAG
297 TTTGGGAATTCATTATGGATAAAAAGTATCGACACAAAT-AATAAAGTGTCGATACATTATTTAG
6063156 ACCTATTTTCTCATAAAACCGGTAAATTTAAACCAG
361 ACCTATTTTCTCATAAAACCGGTAAATTTAAACCAG
* * * * *
6063192 TTATATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTATTTGGGGTCGACACTTT
1 TTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGTATTTAGGATCGACACTTG
* * *
6063257 TTATAAATGTATTGACACTTTATGCGTGCACATAGTTTGGGAATTCATTATGGATAAAAAGTATC
66 TTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGAAATACATTATGGATAAAAAGTATC
* * * *
6063322 GACACAAATAAATAAAGTGTCGATACATTATTTAGACTTATTTTCTCATAAAACCGGTAAATTTA
131 GACACAAATAAATAAAGTGTCGATACATTATGTATACCTGTTTTCTCATAAAACCGGTAAATTTA
* * *
6063387 AACGATTACATTGTAAAGTGACCTATTATATTATAATTTTCGGTCAATGTATTGGGGTCGACACT
196 AACGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCGATGTATTGGGGTCGACACT
*
6063452 TTTATAAATGTATCGACACTTTATGTGTGCACATAGTTTGGGAATTCATTATGGATAAAAAGTAT
261 TTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGAATTCATTATGGATAAAAAGTAT
6063517 CGACACAAATAATAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTA
326 CGACACAAATAATAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTA
*
6063582 AACCGG
391 AACCAG
* * *
6063588 TTACATTGTAAAGTGACCTATTACA-TATTATATCTAT-GTGTTTCGATGTTTTTAGTATCGACA
1 TTACATTGTAAAGTGACCTATTACATTA-TA-AT-TATCG-GTCTCGATGTATTTAGGATCGACA
* * * *
6063651 CTTGTTATAAATGTATCGACACTTTGT-CGTGCACTTGGTTTGGAAAATACATTCTGGA-AAATA
62 CTTGTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGG-AAATACATTATGGATAAA-A
*** ** ** *
6063714 AGTATCGACACTTGT-TGTAGTTGTGTCGATACTTTATGTATACCTGTTTTCTCAT-AAACCGGT
125 AGTATCGACACAAATAAATA-AAGTGTCGATACATTATGTATACCTGTTTTCTCATAAAACCGGT
** ** * ** * * *
6063777 GTATTTAGGCCGGTTACATTGTTATTTTACCTATTACA-TAT-ATCTATGT-GTTCGATGTTTTT
189 AAATTTA-AACGGTTACATTGTAAAGTGACCTATTACATTATAAT-T-T-TCGGTCGATG-TATT
* ** * * ** *
6063839 AGTATCGACACTTGTTATAAATGTATCGACACTTTATGCGTGC-CTGTCGTTTGGCCATTCATTC
249 GGGGTCGACACTT-TTATAAATGTATCGACACTTTATGCGTGCAC-ATAGTTTGGGAATTCATTA
* * * **
6063903 TAGACAATAAGTATCGACACAAATTCTAATAGTGTCGATACATTAT
312 TGGATAAAAAGTATCGACACAAATAATAA-AGTGTCGATACATTAT
6063949 GTTGACCAGT
Statistics
Matches: 651, Mismatches: 85, Indels: 61
0.82 0.11 0.08
Matches are distributed among these distances:
395 2 0.00
396 88 0.14
397 111 0.17
398 139 0.21
399 22 0.03
400 66 0.10
401 59 0.09
402 60 0.09
403 1 0.00
405 1 0.00
407 2 0.00
411 2 0.00
412 1 0.00
418 1 0.00
420 41 0.06
421 40 0.06
422 15 0.02
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (396 bp):
TTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGTATTTAGGATCGACACTTG
TTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGAAATACATTATGGATAAAAAGTATC
GACACAAATAAATAAAGTGTCGATACATTATGTATACCTGTTTTCTCATAAAACCGGTAAATTTA
AACGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCGATGTATTGGGGTCGACACT
TTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGAATTCATTATGGATAAAAAGTAT
CGACACAAATAATAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTA
AACCAG
Found at i:6063994 original size:596 final size:598
Alignment explanation
Indices: 6062909--6064020 Score: 1274
Period size: 596 Copynumber: 1.9 Consensus size: 598
6062899 AGGGTAATTT
* * * * *
6062909 TAAAAAGTGTCGACACGAATTTAAAAAGTGTCGATACGTTATGTTGACTGGTTTTCTCATAAAAT
1 TAAAAAGTATCGACACGAATATAAAAAGTGTCGATACATTATGTTGACTGATTTTCTCATAAAAC
* * *
6062974 CGGTAAATTTAAATCGGTTACATTGTAAAGTGATCTATTACATTATAATTTTCGGTCTCGATGTA
66 CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGTA
* * * * * * *
6063039 TTTGGGGTCGACACTTTTTATAAATGTGTCGACATTTTATGCGTGCACATAGTATGGGAATTCAT
131 TTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATGCGTGCACATAGTATGGAAATACAT
*
6063104 TATGGATAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACCTATTTTCTCA
196 TATGGATAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATGTAGACCTATTTTCTCA
* *
6063169 TAAAACCGGTAAATTTAAACCAGTTATATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTC
261 TAAAACCGGTAAATTTAAACCAGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTC
* * * * *
6063234 GATGTATTTGGGGTCGACACTTTTTATAAATGTATTGACACTTTATGCGTGCACATAGTTTGGGA
326 GATGTATTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGCA
* * * *
6063299 ATTCATTATGGATAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACTTATT
391 ATTCATTATAGACAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACTCAGT
* *
6063364 TTCTCATAAAACCGGTAAATTTAAACGATTACATTGTAAAGTGACCTATTATATTATAATTTTCG
456 TTCTCATAAAACCGATAAATGTAAACGATTACATTGTAAAGTGACCTATTATATTATAATTTTCG
6063429 GTCAATGTATTGGGGTCGACACTTTTATAAATGTATCGACACTTTATGTGTGCACATAGTTTGGG
521 GTCAATGTATTGGGGTCGACACTTTTATAAATGTATCGACACTTTATGTGTGCACATAGTTTGGG
6063494 AATTCATTATGGA
586 AATTCATTATGGA
6063507 TAAAAAGTATCGACAC-AA-ATAATAAAGTGTCGATACATTAT-TTAGACCT-ATTTTCTCATAA
1 TAAAAAGTATCGACACGAATATAA-AAAGTGTCGATACATTATGTT-GA-CTGATTTTCTCATAA
*
6063568 AACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACA-TATTATATCTAT-GTGTTT
63 AACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTA-TA-AT-TATCG-GTCT
* * * * * *
6063631 CGATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACACTTTGT-CGTGCACTTGGTTTGGA
124 CGATGTATTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATGCGTGCACATAGTATGG-
* *** ** ** * *
6063695 AAATACATTCTGGA-AAATAAGTATCGACACTTGT-TGTAGTTGTGTCGATACTTTATGTATACC
188 AAATACATTATGGATAAA-AAGTATCGACACAAATAAATA-AAGTGTCGATACATTATGTAGACC
* ** ** * * ** *
6063758 TGTTTTCTCAT-AAACCGGTGTATTTAGGCCGGTTACATTGTTATTTTACCTATTACA-TAT-AT
251 TATTTTCTCATAAAACCGGTAAATTTAAACCAGTTACATTGTAAAGTGACCTATTACATTATAAT
* *
6063820 CTAT-GTGT-TCGATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACACTTTATGCGTGC-
316 -TATCG-GTCTCGATGTATTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATGCGTGCA
* * * * * **
6063882 CTGTCGTTTGGCCATTCATTCTAGACAATAAGTATCGACACAAAT-TCTAATAGTGTCGATACAT
379 C-ATAGTTTGGCAATTCATTATAGACAAAAAGTATCGACACAAATAAATAA-AGTGTCGATACAT
* ** * * * *
6063946 TATGTT-GAC-CAGTTT-T-ATAATTAACCGATATATGTATATTGGTTACATTGTTAATTTACCT
442 TAT-TTAGACTCAGTTTCTCATAA--AACCGATAAATGTA-AACGATTACATTGTAAAGTGACCT
6064007 ATTATATTATAATT
503 ATTATATTATAATT
6064021 ATTTGTTTCG
Statistics
Matches: 424, Mismatches: 72, Indels: 38
0.79 0.13 0.07
Matches are distributed among these distances:
593 4 0.01
594 1 0.00
595 19 0.04
596 144 0.34
597 85 0.20
598 74 0.17
599 97 0.23
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (598 bp):
TAAAAAGTATCGACACGAATATAAAAAGTGTCGATACATTATGTTGACTGATTTTCTCATAAAAC
CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTCGATGTA
TTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATGCGTGCACATAGTATGGAAATACAT
TATGGATAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATGTAGACCTATTTTCTCA
TAAAACCGGTAAATTTAAACCAGTTACATTGTAAAGTGACCTATTACATTATAATTATCGGTCTC
GATGTATTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGCA
ATTCATTATAGACAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACTCAGT
TTCTCATAAAACCGATAAATGTAAACGATTACATTGTAAAGTGACCTATTATATTATAATTTTCG
GTCAATGTATTGGGGTCGACACTTTTATAAATGTATCGACACTTTATGTGTGCACATAGTTTGGG
AATTCATTATGGA
Found at i:6068068 original size:203 final size:201
Alignment explanation
Indices: 6067430--6068186 Score: 814
Period size: 201 Copynumber: 3.8 Consensus size: 201
6067420 ATGAATTTAA
* * * *
6067430 AAAGTTTCGATACATTATGTTGACCGATTTTCTCATAAAATCGATAAATTTAAACCGGTTACATT
1 AAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACATT
* * * * *
6067495 GTAAAGTGACCTATTACATTATAATTTTTGGTCTCGATGTATTTGGGGTTGA-AGCTTTTTATAA
66 GTAAAGTGACCTATTACATTATAATTTATGGTCTCGATGTATTTAGGATCGACA-CTTGTTATAA
* * *
6067559 TTATATCGACACTTTATGCGTGCACATAGTTT-GAGAATTCATTATGGATAAAAAGTATCGACAC
130 ATGTATCGACACTTTGT-CGTGCACATAGTTTGGAGAATTCATTATGGATAAAAAGTATCGACAC
6067623 AAATAAAT
194 AAATAAAT
* * * *
6067631 AAAGTGTCAATACATTATTTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCAGTAACATT
1 AAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACATT
* * *
6067696 GTAAAGTGACCTATTACATTATAATTT-TCGGTCTCGATGTATTTGGGGTCGACACTTTTTATAA
66 GTAAAGTGACCTATTACATTATAATTTAT-GGTCTCGATGTATTTAGGATCGACACTTGTTATAA
*
6067760 ATGTATCGACACTTTATGT-GTGCACATAGTTTGG-GAATTCATTAGGGATAAAAAGTATCGACA
130 ATGTATCGACAC-TT-TGTCGTGCACATAGTTTGGAGAATTCATTATGGATAAAAAGTATCGACA
6067823 CAAATAAAT
193 CAAATAAAT
* * * *
6067832 AAAGTGTCGATACATTATTTAGACCCATTTTCTCATAAAACCGGTAAGTTTAAACCGGTTACATT
1 AAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACATT
* * * * * *
6067897 GTAAAGTGGCCTATTACA-TATTATATCTATGTGTTTCGATGTTTTTAGTATCGACGCTTGTTAT
66 GTAAAGTGACCTATTACATTA-TA-ATTTATG-GTCTCGATGTATTTAGGATCGACACTTGTTAT
* * * * * *
6067961 AAATGTATCGACACTTTGTCGTGCACTTGGTTTGGAAAATACATTCTGGA-AAATAAGTATCGAT
128 AAATGTATCGACACTTTGTCGTGCACATAGTTTGGAGAATTCATTATGGATAAA-AAGTATCGAC
*** **
6068025 ACTTGT-TGT
192 ACAAATAAAT
** * * * ** **
6068034 AGTTGTGTCGATACTTTATGTATACCTGTTTTCTCAT-AAACCGATGTATTTAGGCCGGTTACAT
1 A-AAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACAT
* ** * * * * * *
6068098 TGTTATTTTACCTATTACATTAT-ATTTATGTGTTTCAATGTTTTTAGTATCGACACTAGTTATA
65 TGTAAAGTGACCTATTACATTATAATTTATG-GTCTCGATGTATTTAGGATCGACACTTGTTATA
6068162 AATGTATCGACACTTTGTCGTGCAC
129 AATGTATCGACACTTTGTCGTGCAC
6068187 TTGTTATAAA
Statistics
Matches: 480, Mismatches: 62, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
200 65 0.14
201 257 0.54
202 64 0.13
203 94 0.20
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (201 bp):
AAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATAAATTTAAACCGGTTACATT
GTAAAGTGACCTATTACATTATAATTTATGGTCTCGATGTATTTAGGATCGACACTTGTTATAAA
TGTATCGACACTTTGTCGTGCACATAGTTTGGAGAATTCATTATGGATAAAAAGTATCGACACAA
ATAAAT
Found at i:6069656 original size:3 final size:3
Alignment explanation
Indices: 6069648--6069697 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
6069638 ACTTGTTTGG
* * * * *
6069648 ATC ATC ATC ATC ATC ATT ATC ATC ATC TTC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
6069696 AT
1 AT
6069698 TGACCGCTTG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.42
Consensus pattern (3 bp):
ATC
Found at i:6070508 original size:2 final size:2
Alignment explanation
Indices: 6070501--6070534 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6070491 GTTTCCTGAG
6070501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6070535 TCCCCATGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6071931 original size:23 final size:22
Alignment explanation
Indices: 6071905--6071968 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
6071895 CAGCTCATAT
6071905 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
*
6071928 AATTGCA-CTGGAGTGCCGCGTAG
1 AATTGCACCT--AGTGCCACGTAG
6071951 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
6071969 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 2 0.06
23 31 0.89
24 1 0.03
25 1 0.03
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:6072109 original size:103 final size:103
Alignment explanation
Indices: 6071984--6072201 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
6071974 TAATGTCCAT
*
6071984 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCA
*
6072049 TACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
6072087 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCA
6072152 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
6072190 AAGGACCACATA
1 AAGGACCACATA
6072202 GACCCTCTAC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:6072757 original size:64 final size:67
Alignment explanation
Indices: 6072647--6072774 Score: 210
Period size: 64 Copynumber: 2.0 Consensus size: 67
6072637 ATTTTTATCT
6072647 TTTAATGGTGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
1 TTTAATGGTGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
6072712 TA
66 TA
*
6072714 TTTAATGG-GG-ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGGTGGTATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTT
6072775 TCTTTTTAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
63 1 0.02
64 33 0.56
65 15 0.25
66 2 0.03
67 8 0.14
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (67 bp):
TTTAATGGTGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
TA
Found at i:6072792 original size:64 final size:62
Alignment explanation
Indices: 6072659--6072819 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 62
6072649 TAATGGTGGT
* * *
6072659 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* *
6072724 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
6072788 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
6072820 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:6074009 original size:199 final size:199
Alignment explanation
Indices: 6073612--6074634 Score: 1642
Period size: 199 Copynumber: 5.2 Consensus size: 199
6073602 AATGTTCTTA
* * *
6073612 GGATCTATACTTGTTATAAATGTATTGACACTTTTTCGTGCACTTGGTTTAGAAATTCATTCTGG
1 GGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATTCATTATGG
*
6073677 ACCAAAAGTATCGACACTTG-TTTATTTGTGTCGATACTTTTTGTACACTTGTTTTCTCAAAAAC
66 ACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAAC
*** * * * * * *
6073741 CGGTATATTTAGACTAATTACATTGTTAATTAACATATTACATTCTAATTAAGGGTTTTGATATT
131 CGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTAGATTATAATTATGGGTTTCGATATT
6073806 TTTG
196 TTTG
* * *
6073810 GGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGTTTTAGAAATTCATTATGG
1 GGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATTCATTATGG
*
6073875 ACCAAAAGTATCGACACTTATTTTATTTGTGTCTG-TACTTTTTGTACACCTGTTTTCTCAAAAA
66 ACCAAAAGTATCGACACTTGTTTTATTTGTGTC-GATACTTTTTGTACACCTGTTTTCTCAAAAA
* * * *
6073939 CTGGTATATTTAGACCGGTTACATTTTTAATTTACCTATTAGATTATAATTATGAGTTTCGATGT
130 CCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTAGATTATAATTATGGGTTTCGATAT
6074004 TTTTG
195 TTTTG
* *
6074009 GGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATTCATTCTAG
1 GGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATTCATTATGG
* * * * * *
6074074 ACCAACATTATCGACACTTGTTTTATTTGTGTCGATACTTTTTTTACACTTGTTTTCTAAAAAAA
66 ACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAAC
* *
6074139 CGGTATATTTAGACCGGTTACATTGTTAATTTACCAATTACATTATAATTATGGGTTTCGATATT
131 CGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTAGATTATAATTATGGGTTTCGATATT
6074204 TTTG
196 TTTG
* * *
6074208 GGATCGATACTTGTTATAAATGTATCGATACTTTTTCCTGCACTTGGTTCAGAAATTCATTATGG
1 GGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATTCATTATGG
*
6074273 ACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAAC
66 ACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAAC
6074338 CGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTAGATTATAATTATGGGTTTCGATATT
131 CGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTAGATTATAATTATGGGTTTCGATATT
6074403 TTTG
196 TTTG
* * *
6074407 GGATCGATACTTGATATAAATGTATCGACACTTTTTCGTACACTTGGTTTAGAAATTCATTTTGG
1 GGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATTCATTATGG
*
6074472 ACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATA-TTTTTGTACACCCT-TCTTCTC-AAAA
66 ACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACA-CCTGTTTTCTCAAAAA
6074534 CCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTAGATTATAATTATGGGTTTCGATAT
130 CCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTAGATTATAATTATGGGTTTCGATAT
6074599 TTTTG
195 TTTTG
6074604 GGATCGATACTTGTTATAAATGTATCGACAC
1 GGATCGATACTTGTTATAAATGTATCGACAC
6074635 ATAAGTTTAC
Statistics
Matches: 760, Mismatches: 61, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
197 104 0.14
198 95 0.12
199 560 0.74
200 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (199 bp):
GGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATTCATTATGG
ACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAAC
CGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTAGATTATAATTATGGGTTTCGATATT
TTTG
Found at i:6074982 original size:19 final size:19
Alignment explanation
Indices: 6074958--6075007 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
6074948 TTACATTTAC
*
6074958 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
**
6074977 ATACAAAATTAAAAATTTT
1 ATACAAAATTAAAAATCGT
6074996 ATACAAAATTAA
1 ATACAAAATTAA
6075008 CCCTACATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:6078487 original size:19 final size:19
Alignment explanation
Indices: 6078458--6078524 Score: 118
Period size: 19 Copynumber: 3.6 Consensus size: 19
6078448 CATTTATACA
*
6078458 ACCTA-AATATCATTTTCT
1 ACCTATAATATCATTTTTT
6078476 ACCTATAATATCATTTTTT
1 ACCTATAATATCATTTTTT
6078495 ACCTATAATATCATTTTTT
1 ACCTATAATATCATTTTTT
6078514 ACCTATAATAT
1 ACCTATAATAT
6078525 TAAATAAAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.11
19 42 0.89
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (19 bp):
ACCTATAATATCATTTTTT
Found at i:6079209 original size:161 final size:162
Alignment explanation
Indices: 6079015--6079347 Score: 553
Period size: 162 Copynumber: 2.1 Consensus size: 162
6079005 TTTGAGACCA
*
6079015 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA-TTTTTTAAAGTATCGACACT
1 GTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
* *
6079079 TTATAAGCGCTATAACTTGTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCG
66 TTATAAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
*
6079144 ACACTTTCAACATATCCGATATCTTTTTACCG
131 ACACTTTCAAAATATCCGATATCTTTTTACCG
*
6079176 GTTTTTTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
1 GTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
*
6079241 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
66 TTATAAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
* * * *
6079306 ACACTTTCAAAATATTCGGTAGT-TATTTACCT
131 ACACTTTCAAAATATCCGATA-TCTTTTTACCG
6079338 GTTTTGTCAT
1 GTTTTGTCAT
6079348 TTTGAGACCA
Statistics
Matches: 159, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
161 42 0.26
162 116 0.73
163 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (162 bp):
GTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
TTATAAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
ACACTTTCAAAATATCCGATATCTTTTTACCG
Found at i:6079600 original size:182 final size:182
Alignment explanation
Indices: 6079172--6079603 Score: 595
Period size: 182 Copynumber: 2.4 Consensus size: 182
6079162 ATATCTTTTT
* *
6079172 ACCGGTTTTTTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTT--TTAAAGTATC
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTCATT--AGTATC
6079235 GACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAA
64 GACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAA
* * * *
6079300 GTATCGACACTTTCAAAATATTCGGTAGTTATTTACCTGTTTTGTCATTTTGAG
129 GTATCGACACTTTCAAAATATCCGGTAGGTATTTACCGGTTTTGTCATTTCGAG
* * * *
6079354 ACCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGAATCGATACA-TTTTCATAAAGTATCG
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTCAT-TAGTATCG
* * *
6079418 ATACTTTTTAGGCGCTATAACTTCTTCTGTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAA
65 ACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTATATTAAA
* * *
6079482 TTATCGACACTTTCAACATATCCGGTAGCGT-TTTACCGGTTTTTTCATTTCGAG
129 GTATCGACACTTTCAAAATATCCGGTAG-GTATTTACCGGTTTTGTCATTTCGAG
* * * * *
6079536 ACCGGTTTTGTCATATTTTTACCTGTAATATTGCTATGGAGCGATATATTTTTCATTTGTATCGA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTCATTAGTATCGA
6079601 CAC
66 CAC
6079604 AAACCGACAA
Statistics
Matches: 218, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
181 6 0.03
182 203 0.93
183 9 0.04
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (182 bp):
ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTCATTAGTATCGA
CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGT
ATCGACACTTTCAAAATATCCGGTAGGTATTTACCGGTTTTGTCATTTCGAG
Found at i:6081511 original size:2 final size:2
Alignment explanation
Indices: 6081506--6081563 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
6081496 TTTTCCAATT
6081506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6081548 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
6081564 CTTTTTAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6084399 original size:41 final size:41
Alignment explanation
Indices: 6084307--6084431 Score: 234
Period size: 40 Copynumber: 3.0 Consensus size: 41
6084297 GCTCTATCGG
6084307 TTATATTTTTTTTATGAATATTTTGTGTTGTATTCATAAGTT
1 TTATA-TTTTTTTATGAATATTTTGTGTTGTATTCATAAGTT
6084349 TTATA-TTTTTTATGAATATTTTGTGTTGTATTCATAAGTT
1 TTATATTTTTTTATGAATATTTTGTGTTGTATTCATAAGTT
6084389 TTATATTTTTTTATGAATATTTTGTGTTGTATTCATAAGTT
1 TTATATTTTTTTATGAATATTTTGTGTTGTATTCATAAGTT
6084430 TT
1 TT
6084432 CTTTTCAACA
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
40 40 0.49
41 37 0.45
42 5 0.06
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.62
Consensus pattern (41 bp):
TTATATTTTTTTATGAATATTTTGTGTTGTATTCATAAGTT
Found at i:6085137 original size:31 final size:31
Alignment explanation
Indices: 6085102--6085163 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
6085092 TAGACTATCA
6085102 ATAACTAGCATAGTTACTAGCAGAGTACTAT
1 ATAACTAGCATAGTTACTAGCAGAGTACTAT
* *
6085133 ATAACTAGTATAGTTACTCGCAGAGTACTAT
1 ATAACTAGCATAGTTACTAGCAGAGTACTAT
6085164 CAAGTAGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (31 bp):
ATAACTAGCATAGTTACTAGCAGAGTACTAT
Found at i:6085335 original size:68 final size:69
Alignment explanation
Indices: 6085226--6085360 Score: 218
Period size: 68 Copynumber: 2.0 Consensus size: 69
6085216 CTTTAAATCC
* *
6085226 CACCTTTTGATTTTGTGACAATTGAAACAACACATTGTATGAACATTATTATCCAG-CATTTAAT
1 CACCTTTTGATTTTGTGACAATTGAAACAACACATGGTATGAACATCATTATCCAGTCATTTAAT
6085290 CACA
66 CACA
* * *
6085294 CACCTTTTGATTTTGTGCCAATTGAAACAGCTCATGGTATGAACATCATTATCCAGTCATTTAAT
1 CACCTTTTGATTTTGTGACAATTGAAACAACACATGGTATGAACATCATTATCCAGTCATTTAAT
6085359 CA
66 CA
6085361 ACAGAAAGAC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
68 51 0.84
69 10 0.16
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (69 bp):
CACCTTTTGATTTTGTGACAATTGAAACAACACATGGTATGAACATCATTATCCAGTCATTTAAT
CACA
Found at i:6085595 original size:18 final size:17
Alignment explanation
Indices: 6085562--6085618 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
6085552 TATTTGCTCA
*
6085562 ATATAT-AAAAATTTAT
1 ATATATGAAATATTTAT
* *
6085578 TTATTTGAAGATATTTAT
1 ATATATGAA-ATATTTAT
6085596 ATATATGAAATA-TTAGT
1 ATATATGAAATATTTA-T
6085613 ATATAT
1 ATATAT
6085619 TATATATACA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 7 0.21
17 12 0.36
18 14 0.42
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
ATATATGAAATATTTAT
Done.