Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 25
Found at i:2365107 original size:40 final size:40
Alignment explanation
Indices: 2365048--2365131 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
2365038 AAATGAATGG
2365048 TTTT-TTCTAAACACATGGATCCTATGC-ATATATATAATA
1 TTTTATTCTAAACACATGGATCCTAT-CAATATATATAATA
* * *
2365087 TTTTATTCTAACCCCATGGATTCTATCAATATATATAATA
1 TTTTATTCTAAACACATGGATCCTATCAATATATATAATA
2365127 TTTTA
1 TTTTA
2365132 AAGGTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 5 0.12
40 35 0.88
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (40 bp):
TTTTATTCTAAACACATGGATCCTATCAATATATATAATA
Found at i:2368153 original size:13 final size:12
Alignment explanation
Indices: 2368135--2368175 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
2368125 TCAAATATAG
2368135 ATTTGATTTAGT
1 ATTTGATTTAGT
2368147 AATTTGA-TTA-T
1 -ATTTGATTTAGT
2368158 ATGTTGATTTAGT
1 AT-TTGATTTAGT
2368171 ATTTG
1 ATTTG
2368176 TAAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.08
11 5 0.20
12 9 0.36
13 9 0.36
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (12 bp):
ATTTGATTTAGT
Found at i:2369311 original size:6 final size:6
Alignment explanation
Indices: 2369302--2369338 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
2369292 CATTACCATT
*
2369302 ACCACG ACCATG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
2369339 CGAGACGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.30, C:0.51, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:2369311 original size:12 final size:12
Alignment explanation
Indices: 2369296--2369333 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2369286 TATTACCATT
*
2369296 ACCATTACCACG
1 ACCATGACCACG
2369308 ACCATGACCACG
1 ACCATGACCACG
*
2369320 ACCACGACC-CG
1 ACCATGACCACG
2369331 ACC
1 ACC
2369334 CGACCCGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 5 0.21
12 19 0.79
ACGTcount: A:0.32, C:0.47, G:0.13, T:0.08
Consensus pattern (12 bp):
ACCATGACCACG
Found at i:2369858 original size:6 final size:6
Alignment explanation
Indices: 2369823--2369874 Score: 69
Period size: 5 Copynumber: 9.5 Consensus size: 6
2369813 GTCCGTCTCG
2369823 GGTCG- GGTCG- GGTC-T GGTC-T GGTC-T GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2369866 GGTCGT GGT
1 GGTCGT GGT
2369875 AATACGTGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 23 0.51
6 22 0.49
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2370016 original size:21 final size:23
Alignment explanation
Indices: 2369970--2370024 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
2369960 GATTTTGGAC
*
2369970 TATCGCAA--CGAATTTGGAATA
1 TATCGCAATGCGAACTTGGAATA
2369991 TATCGCAATGCGAACTTGGAA-A
1 TATCGCAATGCGAACTTGGAATA
*
2370013 -ATCGCATTGCGA
1 TATCGCAATGCGA
2370025 TTTAGTTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 19 0.63
22 1 0.03
23 10 0.33
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (23 bp):
TATCGCAATGCGAACTTGGAATA
Found at i:2381093 original size:3 final size:3
Alignment explanation
Indices: 2381085--2381124 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2381075 TCTCGACACT
2381085 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2381125 ATAAGTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2387462 original size:2 final size:2
Alignment explanation
Indices: 2387455--2387493 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2387445 CTCAAGACAA
2387455 AT AT AT AT 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 AT AT AT AT A
2387494 CTACCTGCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2389738 original size:29 final size:29
Alignment explanation
Indices: 2389696--2389755 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
2389686 GTGTTGCCGT
2389696 AGGTCGCCATGGCATCCGGGCGAGCTTGG
1 AGGTCGCCATGGCATCCGGGCGAGCTTGG
2389725 AGGTCGCCATGGCATCCGGGCGAGCTTGG
1 AGGTCGCCATGGCATCCGGGCGAGCTTGG
2389754 AG
1 AG
2389756 TCTCTGTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.15, C:0.27, G:0.42, T:0.17
Consensus pattern (29 bp):
AGGTCGCCATGGCATCCGGGCGAGCTTGG
Found at i:2389807 original size:60 final size:60
Alignment explanation
Indices: 2389742--2389863 Score: 199
Period size: 60 Copynumber: 2.0 Consensus size: 60
2389732 CATGGCATCC
* *
2389742 GGGCGAGCTTGGAGTCTCTGTATGGCTGTGCATGGCGGCATGGCAATGTGGCATGGGTCT
1 GGGCGAGCTTGGAGTCTCTGCATGGCTGTGCATGGCGGCATGGCAACGTGGCATGGGTCT
* **
2389802 GGGCGAGCTTGGAGTCTCTGCATGGTTGTGTGTGGCGGCATGGCAACGTGGCATGGGTCT
1 GGGCGAGCTTGGAGTCTCTGCATGGCTGTGCATGGCGGCATGGCAACGTGGCATGGGTCT
2389862 GG
1 GG
2389864 TGGCAACATG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.12, C:0.18, G:0.43, T:0.26
Consensus pattern (60 bp):
GGGCGAGCTTGGAGTCTCTGCATGGCTGTGCATGGCGGCATGGCAACGTGGCATGGGTCT
Found at i:2389979 original size:29 final size:29
Alignment explanation
Indices: 2389896--2389979 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
2389886 GGCAACGTGG
*
2389896 GTAGGTCGCCAGGGAATCCCAGCAACATT
1 GTAGGTCGCCAGGGAATCCCAGCGACATT
* *
2389925 GTAGGTCACCAGGGCATCCCAGCGACATT
1 GTAGGTCGCCAGGGAATCCCAGCGACATT
*
2389954 GTAGGTCGCCAAGGG-ATCCCAACGAC
1 GTAGGTCGCC-AGGGAATCCCAGCGAC
2389980 CTATGCCTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.26, C:0.30, G:0.29, T:0.15
Consensus pattern (29 bp):
GTAGGTCGCCAGGGAATCCCAGCGACATT
Found at i:2390311 original size:8 final size:9
Alignment explanation
Indices: 2390281--2390318 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2390271 AGGTAAGTTT
2390281 TTTTAATTA
1 TTTTAATTA
2390290 TTTTAATTA
1 TTTTAATTA
*
2390299 GTTT-ATTA
1 TTTTAATTA
2390307 TTTTAAATTA
1 TTTT-AATTA
2390317 TT
1 TT
2390319 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:2390459 original size:27 final size:28
Alignment explanation
Indices: 2390406--2390469 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
2390396 AAAAAATTAA
*
2390406 TTAATTATTGTGTTAGTTAGTCTAATAT
1 TTAATTATTGTGTTAGTTAGTCTAATAG
2390434 TTAATTAGTT-TG-TAGTTAGT-TGAATAG
1 TTAATTA-TTGTGTTAGTTAGTCT-AATAG
2390461 TTAAGTTAT
1 TTAA-TTAT
2390470 ATTTTGGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 1 0.03
27 17 0.53
28 12 0.38
29 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (28 bp):
TTAATTATTGTGTTAGTTAGTCTAATAG
Found at i:2390603 original size:18 final size:18
Alignment explanation
Indices: 2390580--2390634 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
2390570 AATAATTATT
2390580 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
2390598 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
2390610 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
2390627 TAAATTAG
1 TAAATTAG
2390635 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:2390678 original size:21 final size:21
Alignment explanation
Indices: 2390654--2390693 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2390644 AAAAATTAGT
2390654 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
2390675 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
2390694 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:2390940 original size:30 final size:30
Alignment explanation
Indices: 2390872--2390967 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
2390862 ATTAGTTAAT
* *
2390872 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAATTAT-ATTAAAGAA
*
2390903 TTA-TTTATTAGTTTAATTTATATTAAAGAA
1 -TAGTTTATTAGTTTAAATTATATTAAAGAA
*
2390933 TAGTTTATTAG-TTAACGTTATATTAAAGAA
1 TAGTTTATTAGTTTAA-ATTATATTAAAGAA
2390963 TAGTT
1 TAGTT
2390968 AAAGTTATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
29 12 0.21
30 35 0.61
31 8 0.14
32 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAATTATATTAAAGAA
Found at i:2390966 original size:22 final size:22
Alignment explanation
Indices: 2390941--2390986 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2390931 AATAGTTTAT
*
2390941 TAGTTAACGTTATATTAAAGAA
1 TAGTTAAAGTTATATTAAAGAA
2390963 TAGTTAAAGTTATATTAAAGAA
1 TAGTTAAAGTTATATTAAAGAA
2390985 TA
1 TA
2390987 ATTTATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (22 bp):
TAGTTAAAGTTATATTAAAGAA
Found at i:2393383 original size:59 final size:54
Alignment explanation
Indices: 2393320--2393506 Score: 166
Period size: 50 Copynumber: 3.4 Consensus size: 54
2393310 TCGACTATTT
* * * *
2393320 TAAATCATTAGTATCAAATAATTAAGTATTAATAATAAATCATTATTAATAATAATTAG
1 TAAATCATTAGTATCAAATCATTAAATATT--TAA-AAATCATTAAT-A-AATAAGTAG
* *
2393379 TAAATCATTAGTATCAAATCATTAAATATTTAAAAATCATTAATAAATTAGTAT
1 TAAATCATTAGTATCAAATCATTAAATATTTAAAAATCATTAATAAATAAGTAG
* * * * * *
2393433 TAAATCATTAGTATTAAATCATT--AT-TAT-AAAATAATTACTAAATAATTAA
1 TAAATCATTAGTATCAAATCATTAAATATTTAAAAATCATTAATAAATAAGTAG
* * *
2393483 TAAATAATTACTATTAAATCATTA
1 TAAATCATTAGTATCAAATCATTA
2393507 TTATCAGTAT
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
50 38 0.34
51 2 0.02
52 2 0.02
54 28 0.25
55 1 0.01
56 10 0.09
57 3 0.03
59 28 0.25
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (54 bp):
TAAATCATTAGTATCAAATCATTAAATATTTAAAAATCATTAATAAATAAGTAG
Found at i:2393506 original size:14 final size:14
Alignment explanation
Indices: 2393425--2393607 Score: 112
Period size: 14 Copynumber: 14.3 Consensus size: 14
2393415 TCATTAATAA
*
2393425 ATTAGTATTAAATC
1 ATTATTATTAAATC
*
2393439 ATTAGTATTAAATC
1 ATTATTATTAAATC
2393453 ATTATTA-TAAA--
1 ATTATTATTAAATC
* *
2393464 ATAATTACTAAAT-
1 ATTATTATTAAATC
* *
2393477 A--ATTAATAAATA
1 ATTATTATTAAATC
*
2393489 ATTACTATTAAATC
1 ATTATTATTAAATC
2393503 ---ATTATT--ATC
1 ATTATTATTAAATC
*
2393512 AGTATTATTAAATC
1 ATTATTATTAAATC
*
2393526 ATTATTA-T-AATG
1 ATTATTATTAAATC
*
2393538 ATTATTACTAAATC
1 ATTATTATTAAATC
*
2393552 ATTATTA-T-AATG
1 ATTATTATTAAATC
*
2393564 ATTATTATCAAATC
1 ATTATTATTAAATC
* *
2393578 ATTACTA--AAATG
1 ATTATTATTAAATC
*
2393590 ATTATTATCAAATC
1 ATTATTATTAAATC
2393604 ATTA
1 ATTA
2393608 CTAAATCATC
Statistics
Matches: 136, Mismatches: 17, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
9 3 0.02
11 20 0.15
12 41 0.30
13 8 0.06
14 64 0.47
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (14 bp):
ATTATTATTAAATC
Found at i:2393508 original size:11 final size:11
Alignment explanation
Indices: 2393412--2393675 Score: 89
Period size: 11 Copynumber: 21.7 Consensus size: 11
2393402 AAATATTTAA
*
2393412 AAATCATTAAT
1 AAATCATTATT
* *
2393423 AAATTAGTATT
1 AAATCATTATT
2393434 AAATCATTAGTATT
1 AAATCA-T--TATT
2393448 AAATCATTATTAT
1 AAATCATTA-T-T
* *
2393461 AAAATAATTACT
1 -AAATCATTATT
* *
2393473 AAATAATTAAT
1 AAATCATTATT
*
2393484 AAATAATTACTATT
1 AAATCA-T--TATT
2393498 AAATCATTATT
1 AAATCATTATT
*
2393509 ATCAGT-ATTATT
1 A--AATCATTATT
2393521 AAATCATTATT
1 AAATCATTATT
*
2393532 ATAATGATTATTACT
1 A-AATCATTA-T--T
2393547 AAATCATTATT
1 AAATCATTATT
*
2393558 ATAATGATTATTAT
1 A-AATCATTA-T-T
*
2393572 CAAATCATTACTA
1 -AAATCATTA-TT
*
2393585 AAATGATTATTAT
1 AAATCATTA-T-T
*
2393598 CAAATCATTACT
1 -AAATCATTATT
* *
2393610 AAATCATCAAAT
1 AAATCAT-TATT
* * * *
2393622 CATTAAATATT
1 AAATCATTATT
2393633 AAATTCATTATT
1 AAA-TCATTATT
*
2393645 AAATTATTATTT
1 AAATCATTA-TT
*
2393657 AAATTATTATT
1 AAATCATTATT
2393668 AAATCATT
1 AAATCATT
2393676 TTTATTGTTA
Statistics
Matches: 191, Mismatches: 37, Indels: 50
0.69 0.13 0.18
Matches are distributed among these distances:
10 2 0.01
11 69 0.36
12 59 0.31
13 8 0.04
14 50 0.26
15 3 0.02
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (11 bp):
AAATCATTATT
Found at i:2393532 original size:26 final size:26
Alignment explanation
Indices: 2393430--2393607 Score: 179
Period size: 26 Copynumber: 7.1 Consensus size: 26
2393420 AATAAATTAG
* *
2393430 TATTA-AATCATTAGTATTAAATCAT
1 TATTATAATGATTATTATTAAATCAT
* * * *
2393455 TATTATAA-AATAATTACTAAATAAT
1 TATTATAATGATTATTATTAAATCAT
* * *
2393480 TAATA-AATAATTACTATTAAATCAT
1 TATTATAATGATTATTATTAAATCAT
*
2393505 TATTATCA-G--TATTATTAAATCAT
1 TATTATAATGATTATTATTAAATCAT
*
2393528 TATTATAATGATTATTACTAAATCAT
1 TATTATAATGATTATTATTAAATCAT
*
2393554 TATTATAATGATTATTATCAAATCAT
1 TATTATAATGATTATTATTAAATCAT
* * *
2393580 TACTAAAATGATTATTATCAAATCAT
1 TATTATAATGATTATTATTAAATCAT
2393606 TA
1 TA
2393608 CTAAATCATC
Statistics
Matches: 127, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
23 20 0.16
24 3 0.02
25 38 0.30
26 66 0.52
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (26 bp):
TATTATAATGATTATTATTAAATCAT
Found at i:2393541 original size:20 final size:22
Alignment explanation
Indices: 2393495--2393541 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
2393485 AATAATTACT
*
2393495 ATTAAATCATTATTATCAGTATT
1 ATTAAATCATTATTATCAG-ATG
2393518 ATTAAATCATTATTAT-A-ATG
1 ATTAAATCATTATTATCAGATG
2393538 ATTA
1 ATTA
2393542 TTACTAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
22 1 0.04
23 16 0.70
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (22 bp):
ATTAAATCATTATTATCAGATG
Found at i:2393646 original size:12 final size:11
Alignment explanation
Indices: 2393629--2393671 Score: 68
Period size: 12 Copynumber: 3.7 Consensus size: 11
2393619 AATCATTAAA
2393629 TATTAAATTCAT
1 TATTAAATT-AT
2393641 TATTAAATTAT
1 TATTAAATTAT
2393652 TATTTAAATTAT
1 TA-TTAAATTAT
2393664 TATTAAAT
1 TATTAAAT
2393672 CATTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
TATTAAATTAT
Found at i:2394163 original size:21 final size:21
Alignment explanation
Indices: 2394139--2394212 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
2394129 CATTAAAAAT
2394139 TAATGATAATTTCATTATTAC
1 TAATGATAATTTCATTATTAC
* * *
2394160 TAATCATTACTTTCAAATCATTAAC
1 TAATGA-TAATTTC--ATTATT-AC
2394185 AATTAATGATAATTTCATTATTAC
1 ---TAATGATAATTTCATTATTAC
2394209 TAAT
1 TAAT
2394213 CATTACTATC
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 9 0.22
22 6 0.15
24 7 0.17
25 7 0.17
27 6 0.15
28 5 0.12
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.45
Consensus pattern (21 bp):
TAATGATAATTTCATTATTAC
Found at i:2394342 original size:49 final size:49
Alignment explanation
Indices: 2393758--2394338 Score: 1056
Period size: 49 Copynumber: 11.9 Consensus size: 49
2393748 GGTCCCTACA
* * * *
2393758 TTCATTATTACTAAACATTAGTATCAAATCATAAAAAATTAATAATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
* *
2393807 TTAATTATTACTAATCATTA-TATCAAATCATTAAATATTAATGATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
2393855 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
2393904 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
2393953 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
2394002 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
2394051 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
*
2394100 TTCATTATTACTAATCATTAGTATCAAATCATTAAAAATTAATGATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
* *
2394149 TTCATTATTACTAATCATTACTTTCAAATCATTAACAATTAATGATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
2394198 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
*
2394247 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
*
2394296 TTCATTATTACTAATCATTACTATCAAATCATTAAATATTAAT
1 TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAAT
2394339 AATAGATGGG
Statistics
Matches: 516, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
48 44 0.09
49 472 0.91
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (49 bp):
TTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATGATAAT
Found at i:2397549 original size:18 final size:18
Alignment explanation
Indices: 2397490--2397553 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
2397480 ACAATATAAA
* *
2397490 TTAAACAAAATATTTTTT
1 TTAAACACAATAATTTTT
* *
2397508 TTAAAACAACACTAAATATTT
1 TT-AAAC-ACAAT-AATTTTT
2397529 TTAAACACAATAATTTTT
1 TTAAACACAATAATTTTT
2397547 TTAAACA
1 TTAAACA
2397554 GAAATTATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 15 0.41
19 8 0.22
20 7 0.19
21 7 0.19
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAACACAATAATTTTT
Found at i:2397709 original size:22 final size:21
Alignment explanation
Indices: 2397675--2397715 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2397665 CGTATTTATG
2397675 CCTTCTTCCTTTCCTTTCTTTT
1 CCTTCTTCCTTT-CTTTCTTTT
**
2397697 CCTTCTTTGTTTCTTTCTT
1 CCTTCTTCCTTTCTTTCTT
2397716 CGAATCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (21 bp):
CCTTCTTCCTTTCTTTCTTTT
Found at i:2398020 original size:8 final size:8
Alignment explanation
Indices: 2398009--2398033 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2397999 TTTAATAACT
2398009 TAAACTAA
1 TAAACTAA
2398017 TAAACTAA
1 TAAACTAA
2398025 TAAACTAA
1 TAAACTAA
2398033 T
1 T
2398034 TTTTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (8 bp):
TAAACTAA
Found at i:2398086 original size:21 final size:21
Alignment explanation
Indices: 2398053--2398101 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2398043 AATATAATAT
2398053 ATAACTTAAACTAACAAACAA
1 ATAACTTAAACTAACAAACAA
* *
2398074 ATAATTTATACTAACAAACTAA
1 ATAACTTAAACTAACAAAC-AA
*
2398096 TTAACT
1 ATAACT
2398102 ATATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACAA
Found at i:2398868 original size:101 final size:102
Alignment explanation
Indices: 2398748--2398942 Score: 338
Period size: 105 Copynumber: 1.9 Consensus size: 102
2398738 ACCTACACCC
2398748 CATGCACCGATCT-CCCCCCCATGCACACCATACAGCTCCCGCTCCTTGGTCGCCCCGAGTGAAT
1 CATGCACCGATCTCCCCCCCCATGCACACCATACAGCTCCCGCTCCTTGGTCGCCCCGAGTGAAT
*
2398812 GGCGACCTCCTTGGTCGTTGGGCGTGATCTCCATATG
66 GGCAACCTCCTTGGTCGTTGGGCGTGATCTCCATATG
*
2398849 CATGCACCGATCTCCCCCCCCCCCATGCACACCATGCAGCTCCCGCTCCTTGGTCGCCCCGAGTG
1 CATGCACCGATCT---CCCCCCCCATGCACACCATACAGCTCCCGCTCCTTGGTCGCCCCGAGTG
2398914 AATGGCAACCTCCTTGGTCGTTGGGCGTG
63 AATGGCAACCTCCTTGGTCGTTGGGCGTG
2398943 CATGGCGACC
Statistics
Matches: 88, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
101 13 0.15
105 75 0.85
ACGTcount: A:0.15, C:0.41, G:0.23, T:0.22
Consensus pattern (102 bp):
CATGCACCGATCTCCCCCCCCATGCACACCATACAGCTCCCGCTCCTTGGTCGCCCCGAGTGAAT
GGCAACCTCCTTGGTCGTTGGGCGTGATCTCCATATG
Found at i:2399781 original size:75 final size:75
Alignment explanation
Indices: 2399658--2399840 Score: 258
Period size: 75 Copynumber: 2.4 Consensus size: 75
2399648 CTTAATCAGT
* * ** * * *
2399658 TAAAATAAAATAGGTGTTACATATTAAATTAAACTACCTACCGGTTTGTTTGAAGGTTACTAATA
1 TAAAATAAAATAGGTGTTGCCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGATTACTAATA
2399723 ATGTAAACGG
66 ATGTAAACGG
* * *
2399733 TAAAATAAAATAGGTGTTGCCTATTACGTTAAAATATCTGCCGGTTTGTTTAAATATTACTAATA
1 TAAAATAAAATAGGTGTTGCCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGATTACTAATA
2399798 ATGTAAACGG
66 ATGTAAACGG
* *
2399808 TAAAATAAAATATGCGTTGCCTATTACGTTAAA
1 TAAAATAAAATAGGTGTTGCCTATTACGTTAAA
2399841 TAAGCGCTAC
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 96 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAGGTGTTGCCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGATTACTAATA
ATGTAAACGG
Found at i:2399855 original size:23 final size:23
Alignment explanation
Indices: 2399827--2399886 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2399817 ATATGCGTTG
2399827 CCTATTACGTTAAATAAGCGCTA
1 CCTATTACGTTAAATAAGCGCTA
* * * *
2399850 CTTATTACATTAAATAAGTGTTA
1 CCTATTACGTTAAATAAGCGCTA
2399873 CCTATTACGTTAAA
1 CCTATTACGTTAAA
2399887 CTAGCTGCCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (23 bp):
CCTATTACGTTAAATAAGCGCTA
Found at i:2399879 original size:121 final size:121
Alignment explanation
Indices: 2399740--2399984 Score: 373
Period size: 121 Copynumber: 2.0 Consensus size: 121
2399730 CGGTAAAATA
* * * * *
2399740 AAATAGGTGTTGCCTATTACGTTAAAATATCTGCCGGTTTGTTTAAATATTACTAATAATGTAAA
1 AAATAAGTGTTACCTATTACGTTAAAATAGCTGCCGGTTTGTTTAAAGATTAATAATAATGTAAA
* * * * *
2399805 CGGTAAAATAAAATATGCGTTGCCTATTACGTTAAATAAGCGCTACTTATTACATT
66 CAGTAAAATAAAATAGGCGCTACCTATTACGTTAAATAAGCGCTACTTACTACATT
*
2399861 AAATAAGTGTTACCTATTACGTTAAACTAGCTGCCGGTTTGTTTAAAGATTAATAATAATGTAAA
1 AAATAAGTGTTACCTATTACGTTAAAATAGCTGCCGGTTTGTTTAAAGATTAATAATAATGTAAA
* *
2399926 TAGTAAAATAAAATAGGCGCTACCTATTACGTTAAATAAGCGCTACTTACTACGTT
66 CAGTAAAATAAAATAGGCGCTACCTATTACGTTAAATAAGCGCTACTTACTACATT
2399982 AAA
1 AAA
2399985 CTAGATACCG
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 111 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (121 bp):
AAATAAGTGTTACCTATTACGTTAAAATAGCTGCCGGTTTGTTTAAAGATTAATAATAATGTAAA
CAGTAAAATAAAATAGGCGCTACCTATTACGTTAAATAAGCGCTACTTACTACATT
Found at i:2399940 original size:98 final size:98
Alignment explanation
Indices: 2399838--2400033 Score: 284
Period size: 98 Copynumber: 2.0 Consensus size: 98
2399828 CTATTACGTT
* * * * * *
2399838 AAATAAGCGCTACTTATTACATTAAATAAGTGTTACCTATTACGTTAAACTAGCTGCCGGTTTGT
1 AAATAAGCGCTACCTATTACATTAAATAAGCGCTACCTACTACGTTAAACTAGATACCGGTTTGT
*
2399903 TTAAAGATTAATAATAATGTAAATAGTAAAATA
66 TTAAAGATTAATAATAATGTAAACAGTAAAATA
* * *
2399936 AAATAGGCGCTACCTATTACGTTAAATAAGCGCTACTTACTACGTTAAACTAGATACCGGTTTGT
1 AAATAAGCGCTACCTATTACATTAAATAAGCGCTACCTACTACGTTAAACTAGATACCGGTTTGT
* *
2400001 TTAAAGGTTAATAATAATGTAAACGGTAAAATA
66 TTAAAGATTAATAATAATGTAAACAGTAAAATA
2400034 TATACAACTT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 86 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (98 bp):
AAATAAGCGCTACCTATTACATTAAATAAGCGCTACCTACTACGTTAAACTAGATACCGGTTTGT
TTAAAGATTAATAATAATGTAAACAGTAAAATA
Found at i:2399962 original size:23 final size:23
Alignment explanation
Indices: 2399936--2399984 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2399926 TAGTAAAATA
* *
2399936 AAATAGGCGCTACCTATTACGTT
1 AAATAAGCGCTACCTACTACGTT
*
2399959 AAATAAGCGCTACTTACTACGTT
1 AAATAAGCGCTACCTACTACGTT
2399982 AAA
1 AAA
2399985 CTAGATACCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (23 bp):
AAATAAGCGCTACCTACTACGTT
Found at i:2400653 original size:30 final size:30
Alignment explanation
Indices: 2400617--2400687 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
2400607 AGCTTAAACT
2400617 TTGATAATATTTTAGGATCTACCTAATATG
1 TTGATAATATTTTAGGATCTACCTAATATG
2400647 TTGATAATATTTTAGGATCTACCTAATATG
1 TTGATAATATTTTAGGATCTACCTAATATG
2400677 TTGATAATATT
1 TTGATAATATT
2400688 GATAACGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (30 bp):
TTGATAATATTTTAGGATCTACCTAATATG
Found at i:2402782 original size:12 final size:13
Alignment explanation
Indices: 2402765--2402793 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2402755 CTTAATTGCG
2402765 AAAATTAAAA-TT
1 AAAATTAAAATTT
2402777 AAAATTAAAATTT
1 AAAATTAAAATTT
2402790 AAAA
1 AAAA
2402794 ATTTGATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:2404037 original size:20 final size:18
Alignment explanation
Indices: 2404012--2404061 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
2404002 TAAAATAATA
2404012 AATAAATATAATGATACTAT
1 AATAAATATAAT-ATA-TAT
2404032 AATAAATATAATATATAT
1 AATAAATATAATATATAT
*
2404050 ACT-AATATAATA
1 AATAAATATAATA
2404062 AATAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 9 0.31
18 5 0.17
19 3 0.10
20 12 0.41
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (18 bp):
AATAAATATAATATATAT
Found at i:2404038 original size:24 final size:23
Alignment explanation
Indices: 2404006--2404083 Score: 95
Period size: 24 Copynumber: 3.3 Consensus size: 23
2403996 TGGACCTAAA
2404006 ATAATAAATAAATATAATGATACT
1 ATAATAAATAAATATAAT-ATACT
*
2404030 ATAATAAATATAATATATATACTAAT
1 ATAATAAATA-AATATA-ATA-TACT
*
2404056 ATAATAAAT-AATATTATATACT
1 ATAATAAATAAATATAATATACT
2404078 ATAATA
1 ATAATA
2404084 CTATATAACA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
22 9 0.19
23 3 0.06
24 15 0.31
25 7 0.15
26 14 0.29
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (23 bp):
ATAATAAATAAATATAATATACT
Found at i:2404082 original size:27 final size:27
Alignment explanation
Indices: 2404006--2404098 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 27
2403996 TGGACCTAAA
*
2404006 ATAATAAATAAATATAATGATACTATAAT
1 ATAATAAAT-AATATTAT-ATACTATAAT
2404035 A-AAT--ATAATA-TATATAC--TAAT
1 ATAATAAATAATATTATATACTATAAT
2404056 ATAATAAATAATATTATATACTATAAT
1 ATAATAAATAATATTATATACTATAAT
2404083 ACTATATAACATAATA
1 A-TA-ATAA-ATAATA
2404099 ATCTTAGACA
Statistics
Matches: 54, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
21 5 0.09
22 3 0.06
23 4 0.07
24 8 0.15
25 11 0.20
26 2 0.04
27 5 0.09
28 5 0.09
29 5 0.09
30 6 0.11
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (27 bp):
ATAATAAATAATATTATATACTATAAT
Found at i:2404096 original size:15 final size:15
Alignment explanation
Indices: 2404025--2404098 Score: 54
Period size: 15 Copynumber: 5.2 Consensus size: 15
2404015 AAATATAATG
2404025 ATACTATAATAA-AT-
1 ATACTAT-ATAACATA
*
2404039 ATAATATATATAC-TA
1 ATACTATATA-ACATA
2404054 ATA-TA-ATAA-ATA
1 ATACTATATAACATA
*
2404066 ATATTATAT-ACTATA
1 ATACTATATAAC-ATA
2404081 ATACTATATAACATA
1 ATACTATATAACATA
2404096 ATA
1 ATA
2404099 ATCTTAGACA
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
12 6 0.12
13 9 0.18
14 12 0.24
15 20 0.41
16 2 0.04
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
ATACTATATAACATA
Found at i:2405655 original size:21 final size:21
Alignment explanation
Indices: 2405622--2405666 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2405612 AAGTTTTGTA
*
2405622 AAAATTGAAAGTTTAGATACT
1 AAAACTGAAAGTTTAGATACT
* *
2405643 AAAACTGATAGTTTAGGTACT
1 AAAACTGAAAGTTTAGATACT
2405664 AAA
1 AAA
2405667 CACATTAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.31
Consensus pattern (21 bp):
AAAACTGAAAGTTTAGATACT
Found at i:2418010 original size:33 final size:30
Alignment explanation
Indices: 2417967--2418042 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
2417957 TATTAAGGTA
* * *
2417967 TATTTTATTATATTTAGTATTTTTTTAGTAATT
1 TATTTAATTATATTTA--A-TTGTTTAATAATT
*
2418000 TATTTAATTAT-TTTAATTGTTTAATATTT
1 TATTTAATTATATTTAATTGTTTAATAATT
2418029 TATTTAATTA-ATTT
1 TATTTAATTATATTT
2418043 TTTTACAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 23 0.61
30 1 0.03
32 4 0.11
33 10 0.26
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (30 bp):
TATTTAATTATATTTAATTGTTTAATAATT
Found at i:2424085 original size:2 final size:2
Alignment explanation
Indices: 2424078--2424145 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
2424068 ATAAAAGGAG
2424078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2424120 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
2424146 TTGTGAATGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2427047 original size:27 final size:28
Alignment explanation
Indices: 2426997--2427049 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
2426987 TAATAATATT
*
2426997 TTAATTTATTTATTAATTTTTATTAGCA
1 TTAATTTATATATTAATTTTTATTAGCA
2427025 TTAATTT-TATATT-ATTTTATATTAG
1 TTAATTTATATATTAATTTT-TATTAG
2427050 TTGTTATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 11 0.48
28 7 0.30
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (28 bp):
TTAATTTATATATTAATTTTTATTAGCA
Found at i:2428533 original size:16 final size:17
Alignment explanation
Indices: 2428497--2428536 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2428487 ATATGATCAC
*
2428497 AATTAATATCAAATTAA
1 AATTAATATCAAATAAA
*
2428514 AATTAATA-CTAATAAA
1 AATTAATATCAAATAAA
2428530 AATTAAT
1 AATTAAT
2428537 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTAATATCAAATAAA
Found at i:2428711 original size:29 final size:29
Alignment explanation
Indices: 2428655--2428717 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
2428645 TAATATTATT
*
2428655 ATTAATTAAAATTAAAGAATAAATTTAAA
1 ATTAATTAAAAATAAAGAATAAATTTAAA
*
2428684 ATTAATTATCAAAATAAA-AATAAATTAAAA
1 ATTAATTA--AAAATAAAGAATAAATTTAAA
2428714 ATTA
1 ATTA
2428718 TAGAATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 8 0.27
30 15 0.50
31 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
ATTAATTAAAAATAAAGAATAAATTTAAA
Found at i:2428907 original size:123 final size:124
Alignment explanation
Indices: 2428741--2429058 Score: 378
Period size: 123 Copynumber: 2.6 Consensus size: 124
2428731 ACCTAGAAGT
* * *
2428741 CTAAAATCTAAAT-AGGGAAAAGTATAGGGGCTTTTCATGAAATTTAACCATTTAAATTAAAACA
1 CTAAAATCTAAATGAGAG-AAACTATAGGGGTTTTTCATGAAATTTAACCATTTAAATTAAAACA
* * * *
2428805 CAAGTATCGGGTGGGTAGTGTAATTTAG-CTATGCCTATTAATACATA-A-ACATACGTTTGG
65 CAAATATCGGGTGAGTAGTGTAATTTAGAC-ATGCCTACTAA-A-ATAGACACATAAGTTTGG
*
2428865 CTAAAATCT-AATGAGAGAAACTATAGGGGTTTTTCATGAAATTTGACCATTTAAATTAAAACAC
1 CTAAAATCTAAATGAGAGAAACTATAGGGGTTTTTCATGAAATTTAACCATTTAAATTAAAACAC
* * *
2428929 AAATATGGGGTGAGTAGTGTAATTTAGACATGTCTACTAAAATAGACACATAAGTTTGT
66 AAATATCGGGTGAGTAGTGTAATTTAGACATGCCTACTAAAATAGACACATAAGTTTGG
* * * * * * *
2428988 CTAAAATTTAAATGGGAGAAATTATGGGGGATTTTTCATGCAATTTAACCTTTGTAAA-TAACAC
1 CTAAAATCTAAATGAGAGAAACTATAGGGG-TTTTTCATGAAATTTAACCATT-TAAATTAAAAC
2429052 ACAAATA
64 ACAAATA
2429059 AGTAGAGTTG
Statistics
Matches: 168, Mismatches: 19, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
121 3 0.02
122 2 0.01
123 98 0.58
124 30 0.18
125 31 0.18
126 4 0.02
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (124 bp):
CTAAAATCTAAATGAGAGAAACTATAGGGGTTTTTCATGAAATTTAACCATTTAAATTAAAACAC
AAATATCGGGTGAGTAGTGTAATTTAGACATGCCTACTAAAATAGACACATAAGTTTGG
Found at i:2430264 original size:18 final size:18
Alignment explanation
Indices: 2430241--2430276 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2430231 ATTATCGGCT
2430241 TTTCGAGCATCATCACCA
1 TTTCGAGCATCATCACCA
*
2430259 TTTCGAGCATCATTACCA
1 TTTCGAGCATCATCACCA
2430277 ATCAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.31
Consensus pattern (18 bp):
TTTCGAGCATCATCACCA
Found at i:2435945 original size:22 final size:22
Alignment explanation
Indices: 2435919--2435975 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
2435909 CACTCTCTAC
*
2435919 GACGACATCCGTCCCCATCTCT
1 GACGAAATCCGTCCCCATCTCT
*
2435941 GACGAAATCCGTCCCCATCTCC
1 GACGAAATCCGTCCCCATCTCT
* *
2435963 GGCGAAATTCGTC
1 GACGAAATCCGTC
2435976 TATCGCCATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.40, G:0.18, T:0.21
Consensus pattern (22 bp):
GACGAAATCCGTCCCCATCTCT
Found at i:2436383 original size:20 final size:20
Alignment explanation
Indices: 2436360--2436422 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
2436350 TTTGGTGTTA
* *
2436360 CGATTTTCATTTTTGCGTTG
1 CGATTTTCATTTTCGCATTG
*
2436380 CGATTTTCATTTTCACATTG
1 CGATTTTCATTTTCGCATTG
2436400 CGATTTTCATTTTCGCATTG
1 CGATTTTCATTTTCGCATTG
2436420 CGA
1 CGA
2436423 ATTTAAGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (20 bp):
CGATTTTCATTTTCGCATTG
Found at i:2436433 original size:20 final size:20
Alignment explanation
Indices: 2436390--2436434 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2436380 CGATTTTCAT
* * *
2436390 TTTCACATTGCGATTTTCAT
1 TTTCACATTGCGAATTTAAG
*
2436410 TTTCGCATTGCGAATTTAAG
1 TTTCACATTGCGAATTTAAG
2436430 TTTCA
1 TTTCA
2436435 GAAACTACTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (20 bp):
TTTCACATTGCGAATTTAAG
Found at i:2438258 original size:21 final size:21
Alignment explanation
Indices: 2438232--2438280 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2438222 AATGGTGCGC
* *
2438232 TACGTGGTGAGGTATCTA-CTT
1 TACGTGATGAGGTAGC-AGCTT
2438253 TACGTGATGAGGTAGCAGCTT
1 TACGTGATGAGGTAGCAGCTT
2438274 TACGTGA
1 TACGTGA
2438281 GATTGTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (21 bp):
TACGTGATGAGGTAGCAGCTT
Found at i:2438587 original size:21 final size:21
Alignment explanation
Indices: 2438561--2438658 Score: 97
Period size: 21 Copynumber: 4.7 Consensus size: 21
2438551 GATTCACCTG
2438561 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
2438582 TCATCGTTCAAGAAGCCCTTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
2438603 CCACCGTTCAAGAGGCCTCTG
1 TCATCGTTCAAGAGGCCCCTC
* * *
2438624 TCATCATTCAAGTGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
2438645 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
2438659 CCCGATTCAC
Statistics
Matches: 58, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:2438628 original size:42 final size:42
Alignment explanation
Indices: 2438565--2438658 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
2438555 CACCTGTCAT
*
2438565 CGTTCAAGAGGCCCCTCTCATCGTTCAAGAAG-CCCTTCCCAC
1 CGTTCAAGAGGCCCCTCTCATCATTCAAGAAGTCCC-TCCCAC
* * **
2438607 CGTTCAAGAGGCCTCTGTCATCATTCAAGTGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCTCATCATTCAAGAAGTCCCTCCCAC
2438649 CGTTCAAGAG
1 CGTTCAAGAG
2438659 CCCGATTCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 43 0.93
43 3 0.07
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCTCATCATTCAAGAAGTCCCTCCCAC
Found at i:2440300 original size:18 final size:18
Alignment explanation
Indices: 2440277--2440312 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2440267 AAGCCGGTTG
*
2440277 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2440295 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2440313 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2442597 original size:24 final size:24
Alignment explanation
Indices: 2442570--2442623 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2442560 CTGAAACATC
*
2442570 ATCAAAATCCGAGTATTGATCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
2442594 ATCAAAGTTCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2442618 ATCAAA
1 ATCAAA
2442624 TTTTGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2443395 original size:14 final size:15
Alignment explanation
Indices: 2443359--2443396 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2443349 GAAATCATTG
2443359 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
2443374 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
2443389 AAAAATTA
1 AAAAATTA
2443397 GAGATGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:2443656 original size:20 final size:20
Alignment explanation
Indices: 2443552--2443683 Score: 101
Period size: 20 Copynumber: 6.6 Consensus size: 20
2443542 AACTAAAACA
*
2443552 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
* *
2443571 TGTTGAGAATTCGAAAATT-G
1 TGTTGCGAATTTG-AAATTCG
* *
2443591 AGTTACGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTC-G
*
2443612 TGTTGCGAATTTGAAAATCG
1 TGTTGCGAATTTGAAATTCG
* *
2443632 CGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTC-G
*
2443652 TGTTGCG-ATTTACAAATTCG
1 TGTTGCGAATTT-GAAATTCG
* *
2443672 CGTTACGAATTT
1 TGTTGCGAATTT
2443684 AAAAACTGGG
Statistics
Matches: 87, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
19 21 0.24
20 36 0.41
21 30 0.34
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:2443673 original size:40 final size:41
Alignment explanation
Indices: 2443564--2443683 Score: 131
Period size: 40 Copynumber: 3.0 Consensus size: 41
2443554 TTGCGAAATT
* * * *
2443564 AAATTC-GTGTTGAGAATTCGAAAATTGAGTTACGAATTTG
1 AAATTCAGTGTTGCGAATTTGAAAATCGCGTTACGAATTTG
*
2443604 AAATTCAGTGTTGCGAATTTGAAAATCGCGTTGCGAATTTG
1 AAATTCAGTGTTGCGAATTTGAAAATCGCGTTACGAATTTG
* *
2443645 -ACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTACGAATTT
1 AAATTCAGTGTTGCGAATTTGA-AAA-TCGCGTTACGAATTT
2443684 AAAAACTGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
38 1 0.01
39 7 0.10
40 32 0.46
41 29 0.42
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (41 bp):
AAATTCAGTGTTGCGAATTTGAAAATCGCGTTACGAATTTG
Found at i:2444831 original size:15 final size:15
Alignment explanation
Indices: 2444778--2444831 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
2444768 ATTAATTATC
2444778 TATTTGAAATAATAT
1 TATTTGAAATAATAT
*
2444793 TAATTTTAAATTAATTATT
1 T-ATTTGAAA-TAA-TA-T
*
2444812 TATTTGCAATAATAT
1 TATTTGAAATAATAT
2444827 TATTT
1 TATTT
2444832 TTTAAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 7 0.22
16 9 0.28
17 6 0.19
18 8 0.25
19 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (15 bp):
TATTTGAAATAATAT
Found at i:2444847 original size:35 final size:34
Alignment explanation
Indices: 2444767--2444869 Score: 120
Period size: 34 Copynumber: 3.0 Consensus size: 34
2444757 TTTAAAATAT
*
2444767 AATTAATTATCTATTTGAAATAATATTAATTTTA
1 AATTAATTATTTATTTGAAATAATATTAATTTTA
* *
2444801 AATTAATTATTTATTTGCAATAATATTATTTTTTA
1 AATTAATTATTTATTTGAAATAATATTA-ATTTTA
* *
2444836 AATT-ATCTATTTAATTTTAAATAAT-TTAAGTTTA
1 AATTAAT-TATTT-ATTTGAAATAATATTAATTTTA
2444870 GGGTAAATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
34 32 0.54
35 17 0.29
36 10 0.17
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (34 bp):
AATTAATTATTTATTTGAAATAATATTAATTTTA
Found at i:2450643 original size:2 final size:2
Alignment explanation
Indices: 2450638--2450667 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2450628 TTTAAGATGA
2450638 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
2450668 TAAAAGATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2450915 original size:28 final size:26
Alignment explanation
Indices: 2450871--2450924 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
2450861 AAATATCTAA
*
2450871 ATTATTTTATGTATATTTTTAGATATAT
1 ATTATTTTATATATA-TTTTAGA-ATAT
2450899 ATTATTTT-TATATTATTTTAGAATAT
1 ATTATTTTATATA-TATTTTAGAATAT
2450925 TCTTAAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 10 0.42
28 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (26 bp):
ATTATTTTATATATATTTTAGAATAT
Found at i:2452206 original size:2 final size:2
Alignment explanation
Indices: 2452199--2452230 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2452189 CTTCAAATTA
2452199 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
2452231 GTAGAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2461732 original size:13 final size:12
Alignment explanation
Indices: 2461691--2461731 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
2461681 TTAAAATTTA
2461691 CAAATACTAAAT
1 CAAATACTAAAT
2461703 C-AATA-TATAAT
1 CAAATACTA-AAT
2461714 CAAATCACTAAAT
1 CAAAT-ACTAAAT
2461727 CAAAT
1 CAAAT
2461732 CTATATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.08
11 8 0.32
12 4 0.16
13 9 0.36
14 2 0.08
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (12 bp):
CAAATACTAAAT
Found at i:2465063 original size:18 final size:18
Alignment explanation
Indices: 2465025--2465076 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
2465015 GTTTCAGATT
2465025 CAGATTCCAATTCC-T-A
1 CAGATTCCAATTCCTTCA
2465041 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
*
2465059 CAGATTCCAATTTCTTCA
1 CAGATTCCAATTCCTTCA
2465077 TAAACATTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
16 14 0.42
17 1 0.03
18 18 0.55
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.35
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:2465132 original size:18 final size:16
Alignment explanation
Indices: 2465104--2465168 Score: 76
Period size: 18 Copynumber: 3.8 Consensus size: 16
2465094 CAAACACCAC
*
2465104 CTGAGGGAATTGGAAT
1 CTGAAGGAATTGGAAT
2465120 CTGTAAAGGAATTGGAAT
1 CTG--AAGGAATTGGAAT
*
2465138 ATGCGAAGGAATTGGAAT
1 CT--GAAGGAATTGGAAT
2465156 CTGAAGGAATTGG
1 CTGAAGGAATTGG
2465169 TTAGCAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
16 14 0.33
18 27 0.64
20 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.34, T:0.25
Consensus pattern (16 bp):
CTGAAGGAATTGGAAT
Found at i:2465677 original size:37 final size:38
Alignment explanation
Indices: 2465635--2465707 Score: 130
Period size: 37 Copynumber: 1.9 Consensus size: 38
2465625 CCAAACCCCG
*
2465635 ACCCGAATATCACACTTAAAAAACCCGACCC-AACCCA
1 ACCCGAATATCAAACTTAAAAAACCCGACCCGAACCCA
2465672 ACCCGAATATCAAACTTAAAAAACCCGACCCGAACC
1 ACCCGAATATCAAACTTAAAAAACCCGACCCGAACC
2465708 TGATTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 30 0.88
38 4 0.12
ACGTcount: A:0.44, C:0.38, G:0.07, T:0.11
Consensus pattern (38 bp):
ACCCGAATATCAAACTTAAAAAACCCGACCCGAACCCA
Found at i:2467779 original size:21 final size:21
Alignment explanation
Indices: 2467755--2467797 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2467745 TATTTAAATT
*
2467755 AATTAATATATACCAAACATA
1 AATTAATAAATACCAAACATA
* *
2467776 AATTTATAAATATCAAACATA
1 AATTAATAAATACCAAACATA
2467797 A
1 A
2467798 TATCAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTAATAAATACCAAACATA
Found at i:2467812 original size:2 final size:2
Alignment explanation
Indices: 2467805--2467833 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2467795 TAATATCAAA
2467805 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 A
2467834 GTAAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2467879 original size:23 final size:23
Alignment explanation
Indices: 2467852--2467895 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
2467842 AAAAAAATTA
2467852 CAAAT-ACTAAATCAACATATAAT
1 CAAATCACTAAATCAA-ATATAAT
2467875 CAAATCACTAAATCAAATATA
1 CAAATCACTAAATCAAATATA
2467896 TATTTGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (23 bp):
CAAATCACTAAATCAAATATAAT
Found at i:2468733 original size:2 final size:2
Alignment explanation
Indices: 2468726--2468780 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
2468716 TATAAAAATA
2468726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2468766 AG AT AT TT AT A- AT AT
1 AT AT AT AT AT AT AT AT
2468781 TTGATATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2468788 original size:34 final size:36
Alignment explanation
Indices: 2468723--2468792 Score: 92
Period size: 34 Copynumber: 2.0 Consensus size: 36
2468713 TAATATAAAA
*
2468723 ATAATATATATATATATATATATATATATATTATAT
1 ATAATATAGATATATATATATATATATATATTATAT
*
2468759 ATAATATAGATAT-T-TATA-ATATTTGATATTATAT
1 ATAATATAGATATATATATATATATAT-ATATTATAT
2468793 CTAAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.16
34 13 0.42
35 1 0.03
36 12 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (36 bp):
ATAATATAGATATATATATATATATATATATTATAT
Found at i:2469319 original size:17 final size:17
Alignment explanation
Indices: 2469297--2469334 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2469287 CTCCTAAAAG
2469297 TTTTAAGTACTTATATA
1 TTTTAAGTACTTATATA
* *
2469314 TTTTAAGTATTTTTATA
1 TTTTAAGTACTTATATA
2469331 TTTT
1 TTTT
2469335 TATTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTTAAGTACTTATATA
Found at i:2470272 original size:23 final size:24
Alignment explanation
Indices: 2470228--2470274 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
2470218 ATACATTGAC
*
2470228 AAATTATATAAATACAATAACATT
1 AAATTATATAAATACAAAAACATT
2470252 AAATTAT-TAGAA-ACAAAAACATT
1 AAATTATATA-AATACAAAAACATT
2470275 CATTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATTATATAAATACAAAAACATT
Found at i:2473183 original size:8 final size:8
Alignment explanation
Indices: 2473170--2473210 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2473160 CTCATTTTCA
2473170 GAGAATTT
1 GAGAATTT
2473178 GAGAATTT
1 GAGAATTT
*
2473186 -AGAGTTT
1 GAGAATTT
*
2473193 GGGAATTT
1 GAGAATTT
2473201 GAGAATTT
1 GAGAATTT
2473209 GA
1 GA
2473211 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:2473509 original size:126 final size:126
Alignment explanation
Indices: 2473287--2474017 Score: 1102
Period size: 126 Copynumber: 5.9 Consensus size: 126
2473277 GAGTACTATT
* *
2473287 CACATGAAGACGAGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
1 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCA-AGAATATGTTATCATTGC
**
2473352 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATT
65 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC-AGG
2473415 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTC-AGAATATGTTATCATTGCC
1 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAAGAATATGTTATCATTGCC
**
2473479 CTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATT
66 CTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC-AGG
2473541 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
1 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCA-AGAATATGTTATCATTGC
*
2473606 CCTATTATGTCACTCATGT-CCTCGGGGACAC-AGATATATCAGTACCTATTATTTCTCAGGG
65 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACA-GG
* * *
2473667 GACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTCGTCGAGAATATGTTATCATTGCC
1 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAAGAATATGTTATCATTGCC
* *
2473732 CTATTATGTCACTCATGT-CC-CGGGGACACTACATATATCA-TACCTATTATTTCTCAGGG
66 CTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACA-GG
* *
2473791 GACATGAA-G-GCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
1 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCA-AGAATATGTTATCATTGC
*
2473854 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA-CTATTATTCTCA-GGG
65 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATT-TCACAGG
* *
2473915 GACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATG-T-T-ATTGC
1 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCA-AGAATATGTTATCATTGC
2473977 CC---TAT-T-ACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2474018 AATCAGGTAA
Statistics
Matches: 574, Mismatches: 18, Indels: 32
0.92 0.03 0.05
Matches are distributed among these distances:
118 35 0.06
119 1 0.00
120 3 0.01
122 32 0.06
123 45 0.08
124 49 0.09
125 78 0.14
126 239 0.42
127 12 0.02
128 80 0.14
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (126 bp):
CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAAGAATATGTTATCATTGCC
CTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACAGG
Found at i:2473873 original size:248 final size:254
Alignment explanation
Indices: 2473287--2474017 Score: 1149
Period size: 248 Copynumber: 2.9 Consensus size: 254
2473277 GAGTACTATT
* *
2473287 CACATGAAGACGAGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
1 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
* ***
2473352 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA-TTC
66 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-AGGGG
2473416 ACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAATATGTTATCATTGCCCT
130 ACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAATATGTTATCATTGCCCT
* **
2473481 ATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATT
195 ATTATGTCACTCATGTCCCTCGGGGACACTACATATATCAGTACCTATTATTTCACTAGG
2473541 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
1 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
2473606 CCTATTATGTCACTCATGT-CCTCGGGGACAC-AGATATATCAGTACCTATTATTTCTCAGGGGA
66 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGA
*
2473669 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTCGTCGAGAATATGTTATCATTGCCCT
131 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTC-AGAATATGTTATCATTGCCCT
*
2473734 ATTATGTCACTCATGT-CC-CGGGGACACTACATATATCA-TACCTATTATTTCTC-AGGG
195 ATTATGTCACTCATGTCCCTCGGGGACACTACATATATCAGTACCTATTATTTCACTA-GG
* *
2473791 GACATGAA-G-GCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
1 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
2473854 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA-CTATTA-TTCTCAGGGGA
66 CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGA
*
2473917 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATG-T-T-ATTGCCC
131 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTC--AGAATATGTTATCATTGCCC
*
2473979 ---TAT-T-ACTCATGTCCCTCGGGGACACTAGATATATCAGTA
194 TATTATGTCACTCATGTCCCTCGGGGACACTACATATATCAGTA
2474018 AATCAGGTAA
Statistics
Matches: 451, Mismatches: 17, Indels: 28
0.91 0.03 0.06
Matches are distributed among these distances:
241 8 0.02
242 3 0.01
243 22 0.05
244 2 0.00
246 7 0.02
247 1 0.00
248 125 0.28
249 28 0.06
250 34 0.08
251 20 0.04
252 70 0.16
253 49 0.11
254 82 0.18
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (254 bp):
CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGC
CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGA
CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTACATATATCAGTACCTATTATTTCACTAGG
Found at i:2475049 original size:21 final size:20
Alignment explanation
Indices: 2475020--2475110 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 20
2475010 GGTATAAAAC
* *
2475020 CCTGTGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
2475040 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
2475061 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
* *
2475082 CCCTGTGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
2475103 CCCTGCGG
1 -CCTGCGG
2475111 AGATGGCATA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.91
22 3 0.05
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:2475080 original size:42 final size:42
Alignment explanation
Indices: 2475017--2475110 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
2475007 TATGGTATAA
* *
2475017 AACCCTGTGGGCTAGGCATGTAA-CCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACCCT-GCGGGCTAGGAATGT
* * *
2475059 AACCCTGCGGGCTCGGAATGTAACCCTGTGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACCCTGCGGGCTAGGAATGT
2475101 AACCCTGCGG
1 AACCCTGCGG
2475111 AGATGGCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 43 0.93
43 3 0.07
ACGTcount: A:0.20, C:0.26, G:0.34, T:0.20
Consensus pattern (42 bp):
AACCCTGCGGGCTAGGAATGTAACCCTGCGGGCTAGGAATGT
Found at i:2475132 original size:42 final size:42
Alignment explanation
Indices: 2475017--2475134 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
2475007 TATGGTATAA
* * * *
2475017 AACCCTGTGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGATCGGCATGTAACCTGGTGGGCTAGGAATGT
* * *
2475059 AACCCTGCGGGCTCGGAATGTAACCCT-GTGGGCTCGGAATGT
1 AACCCTGCGGGATCGGCATGTAA-CCTGGTGGGCTAGGAATGT
* *
2475101 AACCCTGCGGAGAT-GGCATATAAACTGGTGGGCT
1 AACCCTGCGG-GATCGGCATGTAACCTGGTGGGCT
2475135 TGGCATATGA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.03
42 57 0.89
43 5 0.08
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.21
Consensus pattern (42 bp):
AACCCTGCGGGATCGGCATGTAACCTGGTGGGCTAGGAATGT
Found at i:2475140 original size:21 final size:21
Alignment explanation
Indices: 2475114--2475161 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2475104 CCTGCGGAGA
*
2475114 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
2475135 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
2475156 GGGCAT
1 TGGCAT
2475162 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:2476725 original size:29 final size:32
Alignment explanation
Indices: 2476666--2476743 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 32
2476656 TACATTATAA
* *
2476666 AAAATAAAAATTAATATAAATTCATAATAACTTT
1 AAAATAAAAA-TAATTTAAATTCAT-ATAACATT
2476700 AAAATAAAAATAATTTAAA-T-AT-TAACATT
1 AAAATAAAAATAATTTAAATTCATATAACATT
*
2476729 AATTATAAAAA-AATT
1 AA-AATAAAAATAATT
2476744 ACCATATCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 12 0.30
30 7 0.17
31 2 0.05
32 1 0.03
33 8 0.20
34 10 0.25
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (32 bp):
AAAATAAAAATAATTTAAATTCATATAACATT
Found at i:2485988 original size:38 final size:38
Alignment explanation
Indices: 2485930--2486004 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
2485920 GGAACCAATT
* * *
2485930 TTTAGGTTGCAACCTGATTTTTCATATGAAAACTAGAA
1 TTTAGGTTCCAACCTAATTTTTCATAGGAAAACTAGAA
* *
2485968 TTTAGGTTCCAACTTAATTTTTCATAGGAAAATTAGA
1 TTTAGGTTCCAACCTAATTTTTCATAGGAAAACTAGA
2486005 GTTTTAGTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.39
Consensus pattern (38 bp):
TTTAGGTTCCAACCTAATTTTTCATAGGAAAACTAGAA
Found at i:2486065 original size:19 final size:19
Alignment explanation
Indices: 2486006--2486065 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 19
2485996 AAAATTAGAG
*
2486006 TTTT-AGTTGTATCCTGAT
1 TTTTCAGTTGTAACCTGAT
* * * *
2486024 TTTTCACATAGAAACCAGA-
1 TTTTCA-GTTGTAACCTGAT
2486043 TTTTCAGTTGTAACCTGAT
1 TTTTCAGTTGTAACCTGAT
2486062 TTTT
1 TTTT
2486066 GTATTGGAAT
Statistics
Matches: 30, Mismatches: 9, Indels: 5
0.68 0.20 0.11
Matches are distributed among these distances:
18 12 0.40
19 11 0.37
20 7 0.23
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (19 bp):
TTTTCAGTTGTAACCTGAT
Found at i:2487049 original size:21 final size:21
Alignment explanation
Indices: 2487024--2487098 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 21
2487014 AGTATGTGCA
2487024 GGGGG-AACAGATTCCCCCTTG
1 GGGGGTAAC-GATTCCCCCTTG
*
2487045 GGGGGTATCGATT-CCCC---
1 GGGGGTAACGATTCCCCCTTG
2487062 --GGG-AACAGATTCCCCCTTG
1 GGGGGTAAC-GATTCCCCCTTG
*
2487081 GGGGGTATCGATTCCCCC
1 GGGGGTAACGATTCCCCC
2487099 CTAAATGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
14 2 0.05
15 7 0.17
16 4 0.10
20 4 0.10
21 21 0.50
22 4 0.10
ACGTcount: A:0.16, C:0.31, G:0.32, T:0.21
Consensus pattern (21 bp):
GGGGGTAACGATTCCCCCTTG
Found at i:2487073 original size:36 final size:36
Alignment explanation
Indices: 2487026--2487097 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
2487016 TATGTGCAGG
2487026 GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCCC
2487062 GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCCC
2487098 CCTAAATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCCC
Found at i:2487700 original size:31 final size:31
Alignment explanation
Indices: 2487662--2487833 Score: 308
Period size: 31 Copynumber: 5.5 Consensus size: 31
2487652 AGGGTCGAGG
2487662 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2487693 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2487724 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2487755 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2487786 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2487817 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
2487834 AGAATCTATG
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 138 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2488476 original size:14 final size:14
Alignment explanation
Indices: 2488457--2488489 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2488447 TAACATTTGG
2488457 GTATTGTTCATACA
1 GTATTGTTCATACA
*
2488471 GTATTGTTCATACC
1 GTATTGTTCATACA
2488485 GTATT
1 GTATT
2488490 TTACTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (14 bp):
GTATTGTTCATACA
Found at i:2491057 original size:36 final size:35
Alignment explanation
Indices: 2490992--2491062 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 35
2490982 TATGTGCAGG
2490992 GGGAACAGATTCCCCCCTGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGTATCGATTCCCC
2491027 GGGAACAGATT-CCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCT--GGGGGTATCGATTCCCC
2491063 CCTTAATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 6 0.18
35 11 0.32
36 17 0.50
ACGTcount: A:0.17, C:0.32, G:0.31, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCTGGGGGTATCGATTCCCC
Found at i:2491746 original size:31 final size:31
Alignment explanation
Indices: 2491625--2491735 Score: 195
Period size: 31 Copynumber: 3.6 Consensus size: 31
2491615 AGGGTCGAGG
2491625 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2491656 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2491687 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
2491718 GATTACCTAGGTTTTTCG
1 GTTTACCTATGTTCTTCG
2491736 AAATCTATGG
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2496686 original size:14 final size:14
Alignment explanation
Indices: 2496648--2496687 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2496638 GGGAATTTCA
2496648 TTTTTTTTTTCTGG
1 TTTTTTTTTTCTGG
* **
2496662 TTTCTGGTTTCTGG
1 TTTTTTTTTTCTGG
2496676 TTTTTTTTTTCT
1 TTTTTTTTTTCT
2496688 TTTTCTTTTT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTTCTGG
Found at i:2497628 original size:2 final size:2
Alignment explanation
Indices: 2497621--2497658 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2497611 GATGAGCTTT
2497621 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
2497659 GTTGGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2502923 original size:16 final size:16
Alignment explanation
Indices: 2502899--2502947 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2502889 TATATCTGTA
* *
2502899 AAAAAATTAATTAAAT
1 AAAATATTAAATAAAT
*
2502915 AAAATATTAAAAAAAT
1 AAAATATTAAATAAAT
*
2502931 TAAATACTTAAATAAAT
1 AAAATA-TTAAATAAAT
2502948 TTAAAACAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:2502934 original size:17 final size:19
Alignment explanation
Indices: 2502914--2502953 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
2502904 ATTAATTAAA
2502914 TAAAATA-TTAAA-AAAAT
1 TAAAATACTTAAATAAAAT
*
2502931 T-AAATACTTAAATAAATT
1 TAAAATACTTAAATAAAAT
2502949 TAAAA
1 TAAAA
2502954 CAAAATATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 5 0.26
19 3 0.16
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATACTTAAATAAAAT
Found at i:2503320 original size:2 final size:2
Alignment explanation
Indices: 2503313--2503338 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2503303 TCAAAGGGTA
2503313 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
2503339 GAAAAACGCT
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:2508676 original size:64 final size:64
Alignment explanation
Indices: 2508588--2508749 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 64
2508578 TCCCTTCACG
* * * *
2508588 GGTGCATCGATGCACTACC-CATGCATCGGTGCATAAATC-CTATTCGATG-T-TTGTATTTTAA
1 GGTGCATCGATGCACT-CCTTATGCATCGATGCATAAATCTC-ATTCGATGATCAT-TAATTTAA
2508649 GCA-
63 --AT
* * *
2508652 GGTGCATCGATGCACTCCTTATGCATCGATGTATTAATGTCATTCGATGATCATTAATTTAAAT
1 GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATCTCATTCGATGATCATTAATTTAAAT
2508716 GAGTGCATCGATGCACTCCTTATGCATCGATGCA
1 G-GTGCATCGATGCACTCCTTATGCATCGATGCA
2508750 CCTTCAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
63 3 0.04
64 40 0.48
65 40 0.48
66 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (64 bp):
GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATCTCATTCGATGATCATTAATTTAAAT
Found at i:2514929 original size:22 final size:22
Alignment explanation
Indices: 2514904--2514954 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2514894 TGTTCCAAAG
2514904 GACCACTGGATACATCCCGAAA
1 GACCACTGGATACATCCCGAAA
* *
2514926 GACCACTGGATACGTCCCGAAG
1 GACCACTGGATACATCCCGAAA
2514948 GACCACT
1 GACCACT
2514955 ATGTCCCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.14
Consensus pattern (22 bp):
GACCACTGGATACATCCCGAAA
Found at i:2518812 original size:37 final size:36
Alignment explanation
Indices: 2518770--2518872 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 36
2518760 TAGGTAATCA
*
2518770 GTCCATATGTTCCGAAGAACATATGTAATC-TATAACT
1 GTCCATATGTACCGAAGAACATA-GTAA-CATATAACT
*
2518807 GTCCATATGTACCGAAGAACATAGATAACATGTAACT
1 GTCCATATGTACCGAAGAACATAG-TAACATATAACT
*
2518844 GTCCATATGTCCCGAAGAACATAGGTAAC
1 GTCCATATGTACCGAAGAACATA-GTAAC
2518873 CTTCGACTCT
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
36 2 0.03
37 57 0.95
38 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (36 bp):
GTCCATATGTACCGAAGAACATAGTAACATATAACT
Found at i:2522831 original size:22 final size:22
Alignment explanation
Indices: 2522790--2522831 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2522780 ACATCTAATA
*
2522790 TAACAAAACAATTTAATTCTAT
1 TAACAAAACAATATAATTCTAT
* *
2522812 TAACAAGACAATATACTTCT
1 TAACAAAACAATATAATTCT
2522832 TACACTATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (22 bp):
TAACAAAACAATATAATTCTAT
Found at i:2527830 original size:18 final size:18
Alignment explanation
Indices: 2527788--2527830 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2527778 ACATATAATC
2527788 ATTATCATCCTCATCAGT
1 ATTATCATCCTCATCAGT
** * *
2527806 AACATCATTCTCATCATT
1 ATTATCATCCTCATCAGT
2527824 ATTATCA
1 ATTATCA
2527831 ATATCATTCA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTATCATCCTCATCAGT
Found at i:2528014 original size:23 final size:23
Alignment explanation
Indices: 2527988--2528059 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
2527978 AACCGAAGTG
*
2527988 CCACATAGAAATGTCTCGAATGA
1 CCACATAGAAATGTCTCGAAGGA
* * *
2528011 CCACATAGTATTGTCCCGAAGGA
1 CCACATAGAAATGTCTCGAAGGA
* *
2528034 CCACGTAGAAATGTCTTGAAGGA
1 CCACATAGAAATGTCTCGAAGGA
2528057 CCA
1 CCA
2528060 TGTAGAATTA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (23 bp):
CCACATAGAAATGTCTCGAAGGA
Found at i:2528047 original size:46 final size:46
Alignment explanation
Indices: 2527980--2528086 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 46
2527970 AGAAATTGAA
* * * *
2527980 CCGAAGTG-CCACATAGAAATGTCTCGAATGACCACATAGTATTGTC
1 CCGAAG-GACCACGTAGAAATGTCTCGAAGGACCACATAGAATTATC
* **
2528026 CCGAAGGACCACGTAGAAATGTCTTGAAGGACCATGTAGAATTATC
1 CCGAAGGACCACGTAGAAATGTCTCGAAGGACCACATAGAATTATC
*
2528072 CCGAAGGACCGCGTA
1 CCGAAGGACCACGTA
2528087 CAACCCTCGA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 1 0.02
46 51 0.98
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (46 bp):
CCGAAGGACCACGTAGAAATGTCTCGAAGGACCACATAGAATTATC
Found at i:2528077 original size:23 final size:23
Alignment explanation
Indices: 2527980--2528086 Score: 72
Period size: 23 Copynumber: 4.7 Consensus size: 23
2527970 AGAAATTGAA
* *
2527980 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACGTAGAAATATC
* * * * * *
2528003 TCGAATGACCACATAGTATTGTC
1 CCGAAGGACCACGTAGAAATATC
*
2528026 CCGAAGGACCACGTAGAAATGTC
1 CCGAAGGACCACGTAGAAATATC
** * *
2528049 TTGAAGGACCATGTAGAATTATC
1 CCGAAGGACCACGTAGAAATATC
*
2528072 CCGAAGGACCGCGTA
1 CCGAAGGACCACGTA
2528087 CAACCCTCGA
Statistics
Matches: 65, Mismatches: 18, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
22 1 0.02
23 64 0.98
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATATC
Found at i:2528215 original size:45 final size:45
Alignment explanation
Indices: 2528162--2528261 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
2528152 CATTTATATA
* *
2528162 TTTCACATAACTTGTATCACATAGACATATAATCACATAGATCAC
1 TTTCACATAACTTATATCACATACACATATAATCACATAGATCAC
* * * * * * *
2528207 TTTCACATAGCTTATATCATATTCTCATGTAATCACATATATCAT
1 TTTCACATAACTTATATCACATACACATATAATCACATAGATCAC
2528252 TTATCACATA
1 TT-TCACATA
2528262 GTATGACATA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 38 0.84
46 7 0.16
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (45 bp):
TTTCACATAACTTATATCACATACACATATAATCACATAGATCAC
Found at i:2528724 original size:19 final size:19
Alignment explanation
Indices: 2528696--2528739 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
2528686 TTATGGTATT
*
2528696 GATACTATACTTCAATTTC
1 GATACCATACTTCAATTTC
2528715 GATACCATACTTCAATTTC
1 GATACCATACTTCAATTTC
2528734 GATACC
1 GATACC
2528740 CATTCTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (19 bp):
GATACCATACTTCAATTTC
Found at i:2533193 original size:16 final size:16
Alignment explanation
Indices: 2533165--2533198 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2533155 TGGAAAATTA
2533165 TCCTCCTCATTTTCTT
1 TCCTCCTCATTTTCTT
2533181 TCCT-CTCACTTTTCTT
1 TCCTCCTCA-TTTTCTT
2533197 TC
1 TC
2533199 ATGCCATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (16 bp):
TCCTCCTCATTTTCTT
Found at i:2534075 original size:89 final size:92
Alignment explanation
Indices: 2533899--2534089 Score: 264
Period size: 94 Copynumber: 2.1 Consensus size: 92
2533889 AACCCGAACC
* * * *
2533899 CGACCCGACCCGAATATCACACTTAAAAAACCTGACTCGACCCTACCAAAATAAAGTTTCACCCG
1 CGACCCGACACGAATATCACACTTAAAAAACCTGACCCGACCCGACCAAAATAAAATTTCACCCG
* *
2533964 ACCCGACCCGAATATATGAATTATAAATT
66 A--CGACCCGAATATATGAATTAGAAACT
*
2533993 CGACCCGACACGAATATCACACTTAAAAAAACC-GACCCGATCCGACCAAAATAAAATTTCA-CC
1 CGACCCGACACGAATATCACACTT-AAAAAACCTGACCCGACCCGACCAAAATAAAATTTCACCC
2534056 -A-GACCCGAATATATGAATTAGAAACT
65 GACGACCCGAATATATGAATTAGAAACT
2534082 CGACCCGA
1 CGACCCGA
2534090 AATAATAAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
89 31 0.35
92 1 0.01
93 2 0.02
94 47 0.53
95 8 0.09
ACGTcount: A:0.40, C:0.30, G:0.12, T:0.18
Consensus pattern (92 bp):
CGACCCGACACGAATATCACACTTAAAAAACCTGACCCGACCCGACCAAAATAAAATTTCACCCG
ACGACCCGAATATATGAATTAGAAACT
Found at i:2535617 original size:21 final size:22
Alignment explanation
Indices: 2535569--2535613 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
2535559 ATTTATAAAG
2535569 TTTATTTATCGATTCGTTGATT
1 TTTATTTATCGATTCGTTGATT
* *
2535591 TCTATTTAT-GATT-GTTTATT
1 TTTATTTATCGATTCGTTGATT
2535611 TTT
1 TTT
2535614 TATTAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
20 8 0.40
21 4 0.20
22 8 0.40
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (22 bp):
TTTATTTATCGATTCGTTGATT
Found at i:2537636 original size:33 final size:33
Alignment explanation
Indices: 2537565--2537637 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
2537555 GACTCAACTT
* * *
2537565 CCCTCGAATTCCCTCGCATAGCTCGCTCAGTTG
1 CCCTCGGATGCCCTCGCATAGCTCGCTCAGATG
* *
2537598 CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
1 CCCTCGGATGCCCTCGCATAGCTCGCTCAGATG
*
2537631 GCCTCGG
1 CCCTCGG
2537638 TCGGATGACC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.12, C:0.38, G:0.25, T:0.25
Consensus pattern (33 bp):
CCCTCGGATGCCCTCGCATAGCTCGCTCAGATG
Found at i:2542123 original size:17 final size:17
Alignment explanation
Indices: 2542087--2542140 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 17
2542077 ATATTATGTA
* *
2542087 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAA-TAT
2542105 TTTACTTTATTTAATAT
1 TTTACTTTATTTAATAT
* *
2542122 TTTAC-TAATATAATAT
1 TTTACTTTATTTAATAT
2542138 TTT
1 TTT
2542141 TACAGATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 12 0.38
17 7 0.22
18 13 0.41
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTACTTTATTTAATAT
Found at i:2543824 original size:18 final size:18
Alignment explanation
Indices: 2543801--2543837 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2543791 ACAACCACCA
*
2543801 CAGCCATTTATGATGCCG
1 CAGCCATATATGATGCCG
2543819 CAGCCATATATGATGCCG
1 CAGCCATATATGATGCCG
2543837 C
1 C
2543838 CGCCTTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (18 bp):
CAGCCATATATGATGCCG
Found at i:2544389 original size:26 final size:24
Alignment explanation
Indices: 2544318--2544389 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
2544308 TTATATTTGT
2544318 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
2544343 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
2544365 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
2544390 GTTAGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:2544773 original size:13 final size:13
Alignment explanation
Indices: 2544755--2544783 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2544745 TCTTGTCTAG
2544755 ATCTTTCTCGAAT
1 ATCTTTCTCGAAT
2544768 ATCTTTCTCGAAT
1 ATCTTTCTCGAAT
2544781 ATC
1 ATC
2544784 CATATTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (13 bp):
ATCTTTCTCGAAT
Found at i:2547804 original size:21 final size:21
Alignment explanation
Indices: 2547754--2547804 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2547744 GGGAGAATGG
* **
2547754 TTAAGATTTAGTGTTTAGGGT
1 TTAAGGTTTAGTGCATAGGGT
2547775 TT-AGAGTTTAGTGCATAGGGT
1 TTAAG-GTTTAGTGCATAGGGT
2547796 TTAAGGTTT
1 TTAAGGTTT
2547805 TTAGTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.45
Consensus pattern (21 bp):
TTAAGGTTTAGTGCATAGGGT
Found at i:2549532 original size:37 final size:37
Alignment explanation
Indices: 2549482--2549578 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
2549472 TCCTACTATC
* *
2549482 ATTCAAACTCCTAAAAATAGGATAGAATTTTGCTAGG
1 ATTCAAACTCCTAAAAATAGGATAGAATTCTACTAGG
* **
2549519 ATTCAAACTCCTAAAAATAGGATAGAGTTCTACTATT
1 ATTCAAACTCCTAAAAATAGGATAGAATTCTACTAGG
* *
2549556 ATTTAAACTCCTAAAGATAGGAT
1 ATTCAAACTCCTAAAAATAGGAT
2549579 CCACAAGCAT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
ATTCAAACTCCTAAAAATAGGATAGAATTCTACTAGG
Found at i:2550074 original size:2 final size:2
Alignment explanation
Indices: 2550067--2550095 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2550057 ATTTTTCTAT
2550067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2550096 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2550250 original size:12 final size:12
Alignment explanation
Indices: 2550229--2550259 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2550219 ATTATATGTA
2550229 TATTTA-TTTTT
1 TATTTATTTTTT
2550240 TATTTATTTTTT
1 TATTTATTTTTT
2550252 TATTTATT
1 TATTTATT
2550260 ATTATTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TATTTATTTTTT
Found at i:2550264 original size:29 final size:29
Alignment explanation
Indices: 2550179--2550265 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
2550169 TCTTACTTTA
* * *
2550179 TTTTATTTTATATTTTTA-TGATTACTATT
1 TTTTA-TTTATTTTTTTATTTATTATTATT
* * * * *
2550208 TTTTAGTTAATATTATATGTA-TATTTATT
1 TTTTATTTATTTTTTTATTTATTA-TTATT
2550237 TTTTATTTATTTTTTTATTTATTATTATT
1 TTTTATTTATTTTTTTATTTATTATTATT
2550266 ACTATTTAGT
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
28 9 0.21
29 31 0.74
30 2 0.05
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.70
Consensus pattern (29 bp):
TTTTATTTATTTTTTTATTTATTATTATT
Done.