Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 32 of 91
Found at i:5527132 original size:32 final size:34
Alignment explanation
Indices: 5527071--5527139 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
5527061 TACATGTTTA
5527071 TTTGCATGATTTGTACATTATATTCAATTGCATG
1 TTTGCATGATTTGTACATTATATTCAATTGCATG
* * *
5527105 TTTGCATGATTTTTA-A-TATATTTAATTGTATG
1 TTTGCATGATTTGTACATTATATTCAATTGCATG
5527137 TTT
1 TTT
5527140 ATTTGTGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 17 0.53
33 1 0.03
34 14 0.44
ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54
Consensus pattern (34 bp):
TTTGCATGATTTGTACATTATATTCAATTGCATG
Found at i:5527220 original size:23 final size:23
Alignment explanation
Indices: 5527194--5527272 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
5527184 ATGTGTGTGA
5527194 TTGCATGTTATTAATATATTTAT
1 TTGCATGTTATTAATATATTTAT
*
5527217 TTGCATGGTTATTAATAT-GTTAT
1 TTGCAT-GTTATTAATATATTTAT
* *
5527240 TTG--TGTGATTTAT-TATTATAT
1 TTGCATGTTATTAATATATT-TAT
*
5527261 TTGCATGGTATT
1 TTGCATGTTATT
5527273 GCATGATTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.02
20 8 0.18
21 7 0.16
23 18 0.40
24 11 0.24
ACGTcount: A:0.25, C:0.04, G:0.15, T:0.56
Consensus pattern (23 bp):
TTGCATGTTATTAATATATTTAT
Found at i:5530082 original size:38 final size:37
Alignment explanation
Indices: 5530036--5530144 Score: 129
Period size: 32 Copynumber: 3.1 Consensus size: 37
5530026 GTTTGCATTA
*
5530036 TAATATATTTAATTACATGTTTATTTGCATGATTTAT
1 TAATATATTTAATTGCATGTTTATTTGCATGATTTAT
* *
5530073 ATATTATATTCAATTGCATG----TTTGCATGATTT-T
1 -TAATATATTTAATTGCATGTTTATTTGCATGATTTAT
**
5530106 TAATATATTTAATTGCATGTTTATTTGTGTGATTTAT
1 TAATATATTTAATTGCATGTTTATTTGCATGATTTAT
5530143 TA
1 TA
5530145 TTACTTGCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
32 17 0.29
33 1 0.02
34 12 0.20
36 10 0.17
37 3 0.05
38 16 0.27
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (37 bp):
TAATATATTTAATTGCATGTTTATTTGCATGATTTAT
Found at i:5530095 original size:66 final size:67
Alignment explanation
Indices: 5530018--5530147 Score: 174
Period size: 70 Copynumber: 1.9 Consensus size: 67
5530008 CTTTTAACTT
*
5530018 AATTGCTTGTTTGC-A-TTATAATATATTTAATTACATGTTTATTTGCATGATTTATATATTATA
1 AATTGCATGTTTGCAATTTATAATATATTTAATTACATGTTTATTTGCATGATTTAT-TATTATA
5530081 TTC
65 TTC
* * **
5530084 AATTGCATGTTTGCATGATTTTTAATATATTTAATTGCATGTTTATTTGTGTGATTTATTATTA
1 AATTGCATGTTTGCA--ATTTATAATATATTTAATTACATGTTTATTTGCATGATTTATTATTA
5530148 CTTGCATGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
66 13 0.24
69 6 0.11
70 36 0.65
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.54
Consensus pattern (67 bp):
AATTGCATGTTTGCAATTTATAATATATTTAATTACATGTTTATTTGCATGATTTATTATTATAT
TC
Found at i:5530189 original size:21 final size:19
Alignment explanation
Indices: 5530139--5530190 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5530129 TTTGTGTGAT
*
5530139 TTATTAT-TACTTGCATGA
1 TTATTATATATTTGCATGA
*
5530157 TTATTTTATATTTGCATGA
1 TTATTATATATTTGCATGA
5530176 TTACTTAATATATTT
1 TTA-TT-ATATATTT
5530191 ATGTGTGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 13 0.46
20 2 0.07
21 7 0.25
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.56
Consensus pattern (19 bp):
TTATTATATATTTGCATGA
Found at i:5530227 original size:23 final size:23
Alignment explanation
Indices: 5530201--5530249 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5530191 ATGTGTGTGA
*
5530201 TTGCACA-TTATTAATATATTTAT
1 TTGCACAGTTATTAATAT-GTTAT
*
5530224 TTGCATAGTTATTAATATGTTAT
1 TTGCACAGTTATTAATATGTTAT
5530247 TTG
1 TTG
5530250 TGTGATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (23 bp):
TTGCACAGTTATTAATATGTTAT
Found at i:5533113 original size:25 final size:25
Alignment explanation
Indices: 5533085--5533140 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
5533075 TCACTATTTT
*
5533085 TTTTTGTTTGTTCTATTTTTTGATA
1 TTTTTGTTTGTTCTAATTTTTGATA
* *
5533110 TTTTTCTTTGTTTTAATTTTTGATA
1 TTTTTGTTTGTTCTAATTTTTGATA
*
5533135 TCTTTG
1 TTTTTG
5533141 ATCTATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.05, G:0.11, T:0.71
Consensus pattern (25 bp):
TTTTTGTTTGTTCTAATTTTTGATA
Found at i:5543294 original size:15 final size:15
Alignment explanation
Indices: 5543271--5543309 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5543261 TGAAAAAAGT
* *
5543271 TATATATATTTTTTA
1 TATAAATATTTTTAA
5543286 TATAAATATTTTTAA
1 TATAAATATTTTTAA
*
5543301 TAAAAATAT
1 TATAAATAT
5543310 GGATAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATAAATATTTTTAA
Found at i:5543462 original size:15 final size:13
Alignment explanation
Indices: 5543426--5543475 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
5543416 GTTTATCGAT
*
5543426 TTAAATTTTTTTA
1 TTAAAATTTTTTA
5543439 TTAAAATTTTTTA
1 TTAAAATTTTTTA
*
5543452 TTAAATTATTTTTTT
1 TTAAA--ATTTTTTA
5543467 TTAAAATTT
1 TTAAAATTT
5543476 CATAAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 21 0.64
15 12 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTAAAATTTTTTA
Found at i:5545344 original size:19 final size:19
Alignment explanation
Indices: 5545322--5545419 Score: 70
Period size: 19 Copynumber: 5.2 Consensus size: 19
5545312 ATGTTTGGGA
*
5545322 TTTGACCTAAGGTTTAGGG
1 TTTGACATAAGGTTTAGGG
** *
5545341 TTTGACATTGGGTTTATGG
1 TTTGACATAAGGTTTAGGG
** *
5545360 TTTGATTTAAAGTTTAGGG
1 TTTGACATAAGGTTTAGGG
* ** *
5545379 TTTGACTTTTGGTTTAGGT
1 TTTGACATAAGGTTTAGGG
* * *
5545398 TTTCACATAGGGTTTAAGG
1 TTTGACATAAGGTTTAGGG
5545417 TTT
1 TTT
5545420 TAGGATTTTT
Statistics
Matches: 58, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
19 58 1.00
ACGTcount: A:0.19, C:0.06, G:0.28, T:0.47
Consensus pattern (19 bp):
TTTGACATAAGGTTTAGGG
Found at i:5545364 original size:38 final size:37
Alignment explanation
Indices: 5545322--5545399 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 37
5545312 ATGTTTGGGA
*
5545322 TTTGACCTAAGGTTTAGGGTTTGACATTGGGTTTATGG
1 TTTGACCTAAAGTTTAGGGTTTGACATTGGGTTTA-GG
** * *
5545360 TTTGATTTAAAGTTTAGGGTTTGACTTTTGGTTTAGG
1 TTTGACCTAAAGTTTAGGGTTTGACATTGGGTTTAGG
5545397 TTT
1 TTT
5545400 TCACATAGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 5 0.14
38 30 0.86
ACGTcount: A:0.18, C:0.05, G:0.28, T:0.49
Consensus pattern (37 bp):
TTTGACCTAAAGTTTAGGGTTTGACATTGGGTTTAGG
Found at i:5550147 original size:15 final size:15
Alignment explanation
Indices: 5550129--5550163 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5550119 TGAAAGTGAA
* *
5550129 AAAGAAAAAGAAATG
1 AAAGAAAAAAAAAAG
5550144 AAAGAAAAAAAAAAG
1 AAAGAAAAAAAAAAG
5550159 AAAGA
1 AAAGA
5550164 TGGAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAGAAAAAAAAAAG
Found at i:5550153 original size:23 final size:23
Alignment explanation
Indices: 5550111--5550163 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5550101 TGAAAAGTAC
** *
5550111 AAAAA-AAATGAAAGTGAAAAAG
1 AAAAAGAAATGAAAGAAAAAAAA
5550133 AAAAAGAAATGAAAGAAAAAAAA
1 AAAAAGAAATGAAAGAAAAAAAA
5550156 AAGAAAGA
1 AA-AAAGA
5550164 TGGAAAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 5 0.19
23 16 0.62
24 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (23 bp):
AAAAAGAAATGAAAGAAAAAAAA
Found at i:5551800 original size:36 final size:36
Alignment explanation
Indices: 5551710--5551839 Score: 138
Period size: 36 Copynumber: 3.6 Consensus size: 36
5551700 TGCAAATCTA
* * *
5551710 TAAGATTTTTTACTATGAATCTTGAATATGAATATC
1 TAAGATTTTTTAATATGAATCTTGAATGTGAATTTC
* *
5551746 T-A-ATTTTTTGAATATGAATCTTGAATGTTAGTTTC
1 TAAGATTTTTT-AATATGAATCTTGAATGTGAATTTC
* * * *
5551781 TAAGATTTTTTAATGTGAATCTTAAAGGTGAACTTC
1 TAAGATTTTTTAATATGAATCTTGAATGTGAATTTC
**
5551817 TAAGATTTTCAAATATGAATCTT
1 TAAGATTTTTTAATATGAATCTT
5551840 TGGATGAGAA
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
34 7 0.09
35 22 0.29
36 41 0.53
37 7 0.09
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (36 bp):
TAAGATTTTTTAATATGAATCTTGAATGTGAATTTC
Found at i:5551957 original size:18 final size:19
Alignment explanation
Indices: 5551904--5551957 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 19
5551894 AATTTTGGGA
*
5551904 ATTT-GTGAATCTTAGGAC
1 ATTTAGTGAATCTTAGAAC
* *
5551922 ATTTA-CGAATCTTGGAAC
1 ATTTAGTGAATCTTAGAAC
5551940 -TTTAGTGAATCTTAGAAC
1 ATTTAGTGAATCTTAGAAC
5551958 CTTTTTAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (19 bp):
ATTTAGTGAATCTTAGAAC
Found at i:5552014 original size:9 final size:9
Alignment explanation
Indices: 5552002--5552047 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
5551992 TCTTTTGCAT
5552002 TGCATTCAC
1 TGCATTCAC
* *
5552011 TGCATCCAT
1 TGCATTCAC
5552020 TGCATTCAC
1 TGCATTCAC
* *
5552029 TGCATCCAT
1 TGCATTCAC
5552038 TGCATTCAC
1 TGCATTCAC
5552047 T
1 T
5552048 ATATGTTATG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.35
Consensus pattern (9 bp):
TGCATTCAC
Found at i:5552022 original size:18 final size:18
Alignment explanation
Indices: 5551999--5552047 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
5551989 GAATCTTTTG
5551999 CATTGCATTCACTGCATC
1 CATTGCATTCACTGCATC
5552017 CATTGCATTCACTGCATC
1 CATTGCATTCACTGCATC
5552035 CATTGCATTCACT
1 CATTGCATTCACT
5552048 ATATGTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.22, C:0.33, G:0.10, T:0.35
Consensus pattern (18 bp):
CATTGCATTCACTGCATC
Found at i:5552372 original size:22 final size:22
Alignment explanation
Indices: 5552331--5552381 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5552321 CATAATCTCC
*
5552331 AAGACCTCTAAACATGATTTAT
1 AAGACCTCTAAACATAATTTAT
* * *
5552353 AAGACCTCTGAATATAATTTGT
1 AAGACCTCTAAACATAATTTAT
*
5552375 AAAACCT
1 AAGACCT
5552382 TCAAGCATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (22 bp):
AAGACCTCTAAACATAATTTAT
Found at i:5553500 original size:20 final size:20
Alignment explanation
Indices: 5553474--5553557 Score: 78
Period size: 20 Copynumber: 4.2 Consensus size: 20
5553464 TTTTCCATGA
*
5553474 ATTTGCATGACTATTAATAT
1 ATTTGCATGATTATTAATAT
* * *
5553494 GTTTGCATAATTATTAATTT
1 ATTTGCATGATTATTAATAT
* *
5553514 ATCTGCATGATTATTAATTT
1 ATTTGCATGATTATTAATAT
* * * *
5553534 ATTTACATAATTATCAATTT
1 ATTTGCATGATTATTAATAT
5553554 ATTT
1 ATTT
5553558 ATTTGTGTGA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.51
Consensus pattern (20 bp):
ATTTGCATGATTATTAATAT
Found at i:5553521 original size:40 final size:40
Alignment explanation
Indices: 5553477--5553555 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
5553467 TCCATGAATT
* * *
5553477 TGCATGACTATTAATATGTTTGCATAATTATTAATTTATC
1 TGCATGACTATTAATATATTTACATAATTATCAATTTATC
* *
5553517 TGCATGATTATTAATTTATTTACATAATTATCAATTTAT
1 TGCATGACTATTAATATATTTACATAATTATCAATTTAT
5553556 TTATTTGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (40 bp):
TGCATGACTATTAATATATTTACATAATTATCAATTTATC
Found at i:5553558 original size:20 final size:20
Alignment explanation
Indices: 5553485--5553558 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
5553475 TTTGCATGAC
* * *
5553485 TATTAATATGTTTGCATAAT
1 TATTAATTTATTTACATAAT
* * *
5553505 TATTAATTTATCTGCATGAT
1 TATTAATTTATTTACATAAT
5553525 TATTAATTTATTTACATAAT
1 TATTAATTTATTTACATAAT
*
5553545 TATCAATTTATTTA
1 TATTAATTTATTTA
5553559 TTTGTGTGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (20 bp):
TATTAATTTATTTACATAAT
Found at i:5554010 original size:18 final size:19
Alignment explanation
Indices: 5553950--5554057 Score: 79
Period size: 18 Copynumber: 5.9 Consensus size: 19
5553940 TGATTTCATG
*
5553950 ATTATATATTTGCATGGT-
1 ATTATATATTTGCATGATA
* * *
5553968 ATTTTATATTAT-TAT-ATG
1 ATTATATATT-TGCATGATA
*
5553986 ATAATATATTTGCATGAT-
1 ATTATATATTTGCATGATA
5554004 ATTATATATTT--AT-ATA
1 ATTATATATTTGCATGATA
5554020 ATTACTAT-TATTGCATGATA
1 ATTA-TATAT-TTGCATGATA
5554040 ATTAATATATTTGCATGA
1 ATT-ATATATTTGCATGA
5554058 CATTCTTGCA
Statistics
Matches: 71, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
15 2 0.03
16 7 0.10
17 7 0.10
18 31 0.44
19 5 0.07
20 17 0.24
21 2 0.03
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTATATATTTGCATGATA
Found at i:5554042 original size:20 final size:20
Alignment explanation
Indices: 5553987--5554057 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
5553977 TATTATATGA
5553987 TAATATATTTGCATGAT-AT
1 TAATATATTTGCATGATAAT
5554006 T-ATATATTT--AT-ATAAT
1 TAATATATTTGCATGATAAT
*
5554022 TACTAT-TATTGCATGATAAT
1 TAATATAT-TTGCATGATAAT
5554042 TAATATATTTGCATGA
1 TAATATATTTGCATGA
5554058 CATTCTTGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
15 2 0.05
16 6 0.14
17 5 0.12
18 8 0.19
19 3 0.07
20 18 0.42
21 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (20 bp):
TAATATATTTGCATGATAAT
Found at i:5556605 original size:20 final size:20
Alignment explanation
Indices: 5556567--5556607 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5556557 TTCATATTTT
*
5556567 AAATAATTATGTTTGAATAA
1 AAATAATTATGTATGAATAA
5556587 AAATAATTATCGTAT-AATAA
1 AAATAATTAT-GTATGAATAA
5556607 A
1 A
5556608 TTATTATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (20 bp):
AAATAATTATGTATGAATAA
Found at i:5561561 original size:14 final size:14
Alignment explanation
Indices: 5561542--5561585 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
5561532 TTTTCTTAAA
5561542 AATTAAATTTCATC
1 AATTAAATTTCATC
*
5561556 AATT-AA-TT-A-A
1 AATTAAATTTCATC
5561566 AATTAAATTTCATC
1 AATTAAATTTCATC
5561580 AATTAA
1 AATTAA
5561586 TTAATGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 4 0.17
11 3 0.12
12 4 0.17
13 3 0.12
14 10 0.42
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTAAATTTCATC
Found at i:5561569 original size:24 final size:24
Alignment explanation
Indices: 5561540--5561589 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
5561530 TTTTTTCTTA
5561540 AAAATTAAATTTCATCAATTAATT
1 AAAATTAAATTTCATCAATTAATT
5561564 AAAATTAAATTTCATCAATTAATT
1 AAAATTAAATTTCATCAATTAATT
5561588 AA
1 AA
5561590 TGAATTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATTAAATTTCATCAATTAATT
Found at i:5563726 original size:13 final size:13
Alignment explanation
Indices: 5563690--5563730 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5563680 TATGAATTTG
5563690 TTTAATTTAA-AT
1 TTTAATTTAATAT
*
5563702 TTT-ATTAAAATAT
1 TTTAATT-TAATAT
5563715 TTTAATTTAATAT
1 TTTAATTTAATAT
5563728 TTT
1 TTT
5563731 TACATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 3 0.12
12 5 0.21
13 13 0.54
14 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAATTTAATAT
Found at i:5564810 original size:2 final size:2
Alignment explanation
Indices: 5564803--5564833 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5564793 TTATCAGGGG
5564803 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5564834 TCTTATTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5564918 original size:81 final size:81
Alignment explanation
Indices: 5564829--5564990 Score: 288
Period size: 81 Copynumber: 2.0 Consensus size: 81
5564819 TATATATATA
* *
5564829 TATATTCTTATTTTTCTTTTGCTTACTGCATCAAATTCATAGCTGTTTGCATTCTGATTTTTTTT
1 TATATTCTTATTTTTCTTCTGCTTACTGCATCAAATTCATAACTGTTTGCATTCTGATTTTTTTT
5564894 TCTATTATCTATGCAT
66 TCTATTATCTATGCAT
*
5564910 TATATTCTTATTTTTCTTCTGCTTACTGCATCAAATTCATAACTGTTTGTATTCTGATTTTTTTT
1 TATATTCTTATTTTTCTTCTGCTTACTGCATCAAATTCATAACTGTTTGCATTCTGATTTTTTTT
*
5564975 TCTATTATTTATGCAT
66 TCTATTATCTATGCAT
5564991 GATGTTCACA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.20, C:0.15, G:0.08, T:0.56
Consensus pattern (81 bp):
TATATTCTTATTTTTCTTCTGCTTACTGCATCAAATTCATAACTGTTTGCATTCTGATTTTTTTT
TCTATTATCTATGCAT
Found at i:5568539 original size:23 final size:23
Alignment explanation
Indices: 5568513--5568556 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
5568503 TTCAAGCGAT
5568513 AAAAGTATGCACTCAAAAGAAGG
1 AAAAGTATGCACTCAAAAGAAGG
5568536 AAAAGTATGCACTCAAAAGAA
1 AAAAGTATGCACTCAAAAGAA
5568557 TCAGCAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.14
Consensus pattern (23 bp):
AAAAGTATGCACTCAAAAGAAGG
Found at i:5569227 original size:19 final size:19
Alignment explanation
Indices: 5569182--5569227 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
5569172 TGGTAATTTT
*
5569182 ATTTTTTAATTTAATTATA
1 ATTTTTTTATTTAATTATA
*
5569201 A-TTATTTATTTATATTA-A
1 ATTTTTTTATTTA-ATTATA
5569219 ATTTTTTTA
1 ATTTTTTTA
5569228 AATAAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTTTATTTAATTATA
Found at i:5569343 original size:91 final size:90
Alignment explanation
Indices: 5569248--5569420 Score: 210
Period size: 91 Copynumber: 1.9 Consensus size: 90
5569238 TTTAAAATAA
* * *
5569248 TTTTTTAATTCTATCAAACTATT-AGATTATTTAAAT-TATGTAATTAAA-TCTTA-TCAAATTA
1 TTTTTTAATCCTATCAAACTATTAAGA--ATTTAAATAT-TGCAATTAAACT-TTACT-AAACTA
*
5569309 TTAAAAAATTTAATCATTTTTTTAAGAAAT
61 TTAAAAAATTTAATAATTTTTTTAAGAAAT
*
5569339 TTTTTTAATCCTATCTAACTATTGAAGAATTTAAATATTGCAATTAAACTTTACTAAACTATTAA
1 TTTTTTAATCCTATCAAACTATT-AAGAATTTAAATATTGCAATTAAACTTTACTAAACTATTAA
*
5569404 AAATTTTAATAATTTTT
65 AAAATTTAATAATTTTT
5569421 GATAAATCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
91 65 0.92
92 3 0.04
93 3 0.04
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.47
Consensus pattern (90 bp):
TTTTTTAATCCTATCAAACTATTAAGAATTTAAATATTGCAATTAAACTTTACTAAACTATTAAA
AAATTTAATAATTTTTTTAAGAAAT
Found at i:5569600 original size:108 final size:109
Alignment explanation
Indices: 5569445--5569689 Score: 277
Period size: 108 Copynumber: 2.3 Consensus size: 109
5569435 ATAAATTTTT
* * * *
5569445 AATCCTATCAAACTAGTAGA-GATTCAAATCTCAAAATTAAATCTTACCAAACAATTGAAAAGCT
1 AATCCTACCAAACTATTAGAGGATTTAAATATCAAAATTAAATCTTACCAAACAATTGAAAAGCT
* *
5569509 TAATTATCTTTTTTTAA-AAAA-TAAAATTA-AAATTTTTTAATT-
66 TAATTATC-TTTTTCAAGAAAATTAAAATTATAAA-TGTTTAATTC
* * * * *
5569551 AATCCTAACCAAATTATTGGAGGATTTAAATATCAAAATTAAA-CTTTACCAAACTATTGGAAGG
1 AATCCT-ACCAAACTATTAGAGGATTTAAATATCAAAATTAAATC-TTACCAAACAATTGAAAAG
* * *
5569615 TTTAATTATCTTTTTCAAGAAAATTAAATTTATAAATGTTTCATTC
64 CTTAATTATCTTTTTCAAGAAAATTAAAATTATAAATGTTTAATTC
*
5569661 AATCCTACCAAACTATTAGATGATTTAAA
1 AATCCTACCAAACTATTAGAGGATTTAAA
5569690 ACCTAAAATA
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
106 6 0.05
107 18 0.16
108 48 0.42
109 34 0.30
110 9 0.08
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (109 bp):
AATCCTACCAAACTATTAGAGGATTTAAATATCAAAATTAAATCTTACCAAACAATTGAAAAGCT
TAATTATCTTTTTCAAGAAAATTAAAATTATAAATGTTTAATTC
Found at i:5569713 original size:109 final size:108
Alignment explanation
Indices: 5569443--5569717 Score: 262
Period size: 109 Copynumber: 2.6 Consensus size: 108
5569433 ACATAAATTT
* * * * *
5569443 TTAATCCT-ATCAAACTAGTAGA-GATTCAAAT-CTCAAAATTAAA-TCTTACCAAACAATTGAA
1 TTAATCCTAACCAAACTATTAGAGGATTTAAATAC-CAAAATTAAACT-TTACCAAACTATTGGA
* * * *
5569504 AAGCTTAATTATCTTTTTTTAAAAAATAAAATTAAAATTTTTTAA
64 AGGTTTAATTATCTTTTTTCAAAAAATAAAATTAAAATTGTTTAA
* * *
5569549 TTAATCCTAACCAAATTATTGGAGGATTTAAATATCAAAATTAAACTTTACCAAACTATTGGAAG
1 TTAATCCTAACCAAACTATTAGAGGATTTAAATACCAAAATTAAACTTTACCAAACTATTGGAAG
* *
5569614 GTTTAATTATC-TTTTTCAAGAAAATTAAATTTATAAA-TGTTTCA
66 GTTTAATTATCTTTTTTCAA-AAAA-TAAAATTA-AAATTGTTTAA
* * *
5569658 TTCAATCCT-ACCAAACTATTAGATGATTTAAA-ACCTAAAA-TAAGATTTTATCAAACTATT
1 TT-AATCCTAACCAAACTATTAGAGGATTTAAATACC-AAAATTAA-ACTTTACCAAACTATT
5569718 AAAAGATTTT
Statistics
Matches: 139, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
106 8 0.06
107 17 0.12
108 52 0.37
109 53 0.38
110 9 0.06
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (108 bp):
TTAATCCTAACCAAACTATTAGAGGATTTAAATACCAAAATTAAACTTTACCAAACTATTGGAAG
GTTTAATTATCTTTTTTCAAAAAATAAAATTAAAATTGTTTAA
Found at i:5572528 original size:40 final size:40
Alignment explanation
Indices: 5572477--5572562 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
5572467 TAAAAACTCA
*
5572477 TTAAATCTTCCAAAACTTTGATAAGATTTAATT-TAGACAT
1 TTAAATATTCCAAAACTTTGATAAGATTTAATTAT-GACAT
* * * * *
5572517 TTAAATATTCCAATAGTTTGGTAATATTTAATTATGAGAT
1 TTAAATATTCCAAAACTTTGATAAGATTTAATTATGACAT
5572557 TTAAAT
1 TTAAAT
5572563 CCTTTAATAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (40 bp):
TTAAATATTCCAAAACTTTGATAAGATTTAATTATGACAT
Found at i:5574325 original size:11 final size:11
Alignment explanation
Indices: 5574311--5574349 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
5574301 AACATACAAG
5574311 AAAAAAAATGA
1 AAAAAAAATGA
5574322 AAAAAAAATGA
1 AAAAAAAATGA
*
5574333 AAAAAAAGTGA
1 AAAAAAAATGA
5574344 AAAAAA
1 AAAAAA
5574350 CATGTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:5576909 original size:18 final size:19
Alignment explanation
Indices: 5576886--5576927 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5576876 ATGCATGATT
*
5576886 GGTTTGTGGGGTAGTTT-A
1 GGTTTGTGAGGTAGTTTAA
*
5576904 GGTTTGTGAGGTGGTTTAA
1 GGTTTGTGAGGTAGTTTAA
5576923 GGTTT
1 GGTTT
5576928 AGGATTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.12, C:0.00, G:0.43, T:0.45
Consensus pattern (19 bp):
GGTTTGTGAGGTAGTTTAA
Found at i:5579876 original size:33 final size:32
Alignment explanation
Indices: 5579834--5580056 Score: 141
Period size: 33 Copynumber: 6.8 Consensus size: 32
5579824 AGTTTAGGTT
5579834 ATTTCATTTTTAAACTTCTATTCAATCCAAGTC
1 ATTTCATTTTTAAACTTC-ATTCAATCCAAGTC
* * *
5579867 ATTTTATTTTTAGACTGTC--TCAGTCCAAGTC
1 ATTTCATTTTTAAACT-TCATTCAATCCAAGTC
* * *
5579898 ATTTCATTTTCATACTTCAATTCAATCCATGTC
1 ATTTCATTTTTAAACTTC-ATTCAATCCAAGTC
* * * * * * *
5579931 ATTTTACTTTTAGATTTCGGTTTAATCTTAAGTC
1 ATTTCATTTTTAAACTTC-ATTCAATC-CAAGTC
* * * *
5579965 ATTTCATTTTTAGATTTCCACT-ATGTCC-AGTC
1 ATTTCATTTTTAAACTT-CATTCA-ATCCAAGTC
* * *
5579997 ATCTCATTTTTAAATTTTAGTTCAATCCAAGTC
1 ATTTCATTTTTAAACTTCA-TTCAATCCAAGTC
5580030 ATTTCATCTTTT-AACTTCAGTTCAATC
1 ATTTCAT-TTTTAAACTTCA-TTCAATC
5580057 TAGATCATTT
Statistics
Matches: 147, Mismatches: 32, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
30 2 0.01
31 25 0.17
32 23 0.16
33 68 0.46
34 28 0.19
35 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (32 bp):
ATTTCATTTTTAAACTTCATTCAATCCAAGTC
Found at i:5580057 original size:99 final size:98
Alignment explanation
Indices: 5579834--5580057 Score: 217
Period size: 99 Copynumber: 2.3 Consensus size: 98
5579824 AGTTTAGGTT
* *
5579834 ATTTCAT-TTTTAAACTTCTA-TTCAATC-CAAGTCATTTTATTTTTAGACTGTCTCAGTCCAAG
1 ATTTCATCTTTT-AACTTC-AGTTCAATCTCAAGTCATTTCATTTTTAGACTGTCACAGTCCAAG
* * *
5579896 TCATTTCATTTTCATACTTCAATTCAATCCATGTC
64 TCATCTCATTTTCAAACTTCAATTCAATCCAAGTC
* * * * * *
5579931 ATTTTA-CTTTTAGATTTCGGTTTAATCTTAAGTCATTTCATTTTTAGA-TTTCCACTATGTCC-
1 ATTTCATCTTTTA-ACTTCAGTTCAATCTCAAGTCATTTCATTTTTAGACTGT-CAC-A-GTCCA
* * * *
5579993 AGTCATCTCATTTTTAAATTTTAGTTCAATCCAAGTC
62 AGTCATCTCATTTTCAAACTTCAATTCAATCCAAGTC
5580030 ATTTCATCTTTTAACTTCAGTTCAATCT
1 ATTTCATCTTTTAACTTCAGTTCAATCT
5580058 AGATCATTTT
Statistics
Matches: 100, Mismatches: 19, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
96 1 0.01
97 21 0.21
98 20 0.20
99 48 0.48
100 10 0.10
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (98 bp):
ATTTCATCTTTTAACTTCAGTTCAATCTCAAGTCATTTCATTTTTAGACTGTCACAGTCCAAGTC
ATCTCATTTTCAAACTTCAATTCAATCCAAGTC
Found at i:5580414 original size:45 final size:46
Alignment explanation
Indices: 5580365--5580546 Score: 137
Period size: 45 Copynumber: 4.0 Consensus size: 46
5580355 AGAATTCTTG
*
5580365 AATTTTTCAAATGAAAATCTTTAAAGTTT-ATATGTGAATTTTTAA
1 AATTTTTCAAATGAAAATCTTTAAATTTTCATATGTGAATTTTTAA
** * * * * * *
5580410 AATTTTTTGAATGTAAATATTTGAATTTTGA-ATGTAAATCTTT-A
1 AATTTTTCAAATGAAAATCTTTAAATTTTCATATGTGAATTTTTAA
* * * *
5580454 AATTTTCTCTAATATG--AATCTTGAGA-TTTCATATATGAATTTTAAA
1 AATTTT-TC-AA-ATGAAAATCTTTAAATTTTCATATGTGAATTTTTAA
* *
5580500 AATTTCTCAAATGAAAAAT-TTTGAATTTT-ATATGTGAATTTTTAA
1 AATTTTTCAAATG-AAAATCTTTAAATTTTCATATGTGAATTTTTAA
5580545 AA
1 AA
5580547 ATTTCATTTG
Statistics
Matches: 102, Mismatches: 25, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
43 3 0.03
44 13 0.13
45 69 0.68
46 14 0.14
47 3 0.03
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (46 bp):
AATTTTTCAAATGAAAATCTTTAAATTTTCATATGTGAATTTTTAA
Found at i:5580440 original size:21 final size:21
Alignment explanation
Indices: 5580414--5580459 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5580404 TTTTAAAATT
*
5580414 TTTTGAATGTAAATATTTGAA
1 TTTTGAATGTAAATATTTAAA
*
5580435 TTTTGAATGTAAATCTTTAAA
1 TTTTGAATGTAAATATTTAAA
5580456 TTTT
1 TTTT
5580460 CTCTAATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (21 bp):
TTTTGAATGTAAATATTTAAA
Found at i:5580570 original size:22 final size:22
Alignment explanation
Indices: 5580518--5580571 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
5580508 AAATGAAAAA
* * *
5580518 TTTTGAATTTTATATGTGAATT
1 TTTTAAATTTCATATGTAAATT
* *
5580540 TTTAAAAATTTCATTTGTAAATT
1 TTT-TAAATTTCATATGTAAATT
5580563 TTTTAAATT
1 TTTTAAATT
5580572 AATCGGAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (22 bp):
TTTTAAATTTCATATGTAAATT
Found at i:5592283 original size:15 final size:16
Alignment explanation
Indices: 5592263--5592296 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5592253 TTTCAAATTG
5592263 TTTTGGGG-TTTGACT
1 TTTTGGGGATTTGACT
5592278 TTTTGGGGATTTTGACT
1 TTTTGGGGA-TTTGACT
5592295 TT
1 TT
5592297 GGGTATTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.09, C:0.06, G:0.29, T:0.56
Consensus pattern (16 bp):
TTTTGGGGATTTGACT
Found at i:5592411 original size:18 final size:18
Alignment explanation
Indices: 5592399--5592601 Score: 101
Period size: 18 Copynumber: 10.9 Consensus size: 18
5592389 AGGTTTATGT
5592399 TTTGACTTTGGTTTAGGG
1 TTTGACTTTGGTTTAGGG
** *
5592417 TTTGACATAGGGTTTAAGG
1 TTTGAC-TTTGGTTTAGGG
*
5592436 TTTGA-TTTGGTTTGGGG
1 TTTGACTTTGGTTTAGGG
* *
5592453 TTTGATTTTGGTTTAAGG
1 TTTGACTTTGGTTTAGGG
* ** *
5592471 TTTAACTTTTCATTTTAAGG
1 TTTGAC-TTT-GGTTTAGGG
* * *
5592491 TTTGGCTTTGCTTTAAGG
1 TTTGACTTTGGTTTAGGG
*
5592509 TTTGA--TCGGTTTTA-GG
1 TTTGACTTTGG-TTTAGGG
* * *
5592525 TTTGACCTTGGTTCTAAGC
1 TTTGACTTTGGTT-TAGGG
*
5592544 TTTGACTTAGGGTTTTAGGG
1 TTTGACTT-TGG-TTTAGGG
*
5592564 TTTGACATTGGGGTTTTA-GG
1 TTTGAC-TT-TGG-TTTAGGG
5592584 TATTGACTTTGGTTTAGG
1 T-TTGACTTTGGTTTAGG
5592602 CTAAGGTTTT
Statistics
Matches: 143, Mismatches: 28, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
16 9 0.06
17 19 0.13
18 40 0.28
19 31 0.22
20 27 0.19
21 17 0.12
ACGTcount: A:0.16, C:0.07, G:0.29, T:0.48
Consensus pattern (18 bp):
TTTGACTTTGGTTTAGGG
Found at i:5592567 original size:20 final size:19
Alignment explanation
Indices: 5592516--5592592 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
5592506 AGGTTTGATC
5592516 GGTTTTAGGTTTGACCTT--
1 GGTTTTAGGTTTGA-CTTAG
* *
5592534 GGTTCTAAGCTTTGACTTAG
1 GGTT-TTAGGTTTGACTTAG
*
5592554 GGTTTTAGGGTTTGACATTGG
1 GGTTTTA-GGTTTGAC-TTAG
5592575 GGTTTTAGGTATTGACTT
1 GGTTTTAGGT-TTGACTT
5592593 TGGTTTAGGC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 7 0.15
19 10 0.21
20 16 0.33
21 15 0.31
ACGTcount: A:0.16, C:0.09, G:0.30, T:0.45
Consensus pattern (19 bp):
GGTTTTAGGTTTGACTTAG
Found at i:5592595 original size:21 final size:20
Alignment explanation
Indices: 5592544--5592592 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
5592534 GGTTCTAAGC
*
5592544 TTTGACTTAGGGTTTTAGGG
1 TTTGACTTGGGGTTTTAGGG
5592564 TTTGACATTGGGGTTTTA-GG
1 TTTGAC-TTGGGGTTTTAGGG
5592584 TATTGACTT
1 T-TTGACTT
5592593 TGGTTTAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.16, C:0.06, G:0.31, T:0.47
Consensus pattern (20 bp):
TTTGACTTGGGGTTTTAGGG
Found at i:5595285 original size:32 final size:32
Alignment explanation
Indices: 5595124--5595333 Score: 129
Period size: 33 Copynumber: 6.5 Consensus size: 32
5595114 TAAAAGTTTA
* * ** *
5595124 AAAATGCAATGACTTGGAATGAAATGAAGTTT
1 AAAATGAAATGACTTGAAATGAACCGAAGTCT
* **
5595156 GAAAATGAAATGACTTGAATTGAATGGAACGTCT
1 -AAAATGAAATGACTTGAAATGAACCGAA-GTCT
* * *
5595190 AAAATGAAATGACCT-AAACTAAACCAAAGTCT
1 AAAATGAAATGACTTGAAA-TGAACCGAAGTCT
** * * * *
5595222 GGGAATGTAATGACCT-AGACTGAACCAAAGTCT
1 -AAAATGAAATGACTTGA-AATGAACCGAAGTCT
**
5595255 AAAATGAAATGACTTGAAATGAATTGAAGTCT
1 AAAATGAAATGACTTGAAATGAACCGAAGTCT
* * * *
5595287 AAAATGAAATTATCTTG-ATTGAACCAAAGTTT
1 AAAATGAAATGA-CTTGAAATGAACCGAAGTCT
*
5595319 AAAATAAAATGACTT
1 AAAATGAAATGACTT
5595334 AGACTAAGCC
Statistics
Matches: 138, Mismatches: 33, Indels: 14
0.75 0.18 0.08
Matches are distributed among these distances:
31 3 0.02
32 59 0.43
33 72 0.52
34 4 0.03
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (32 bp):
AAAATGAAATGACTTGAAATGAACCGAAGTCT
Found at i:5595373 original size:33 final size:32
Alignment explanation
Indices: 5595186--5595387 Score: 156
Period size: 32 Copynumber: 6.2 Consensus size: 32
5595176 TGAATGGAAC
*
5595186 GTCTAAAATGAAATGACCTAAACTAAACCAAA
1 GTCTAAAATGAAATGACCTAAACTGAACCAAA
** * *
5595218 GTCTGGGAATGTAATGACCTAGACTGAACCAAA
1 GTCT-AAAATGAAATGACCTAAACTGAACCAAA
* ***
5595251 GTCTAAAATGAAATGACTTGAAA-TGAATTGAA
1 GTCTAAAATGAAATGACCT-AAACTGAACCAAA
* * ** *
5595283 GTCTAAAATGAAATTATCTTGATTGAACCAAA
1 GTCTAAAATGAAATGACCTAAACTGAACCAAA
* * * *
5595315 GTTTAAAATAAAATGACTTAGACT-AAGCCAAA
1 GTCTAAAATGAAATGACCTAAACTGAA-CCAAA
* * *
5595347 GTCTAGAAATGCAATGACCTAAACTAAACTAAA
1 GTCTA-AAATGAAATGACCTAAACTGAACCAAA
*
5595380 GTATAAAA
1 GTCTAAAA
5595388 ATACAATTAC
Statistics
Matches: 129, Mismatches: 35, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
31 3 0.02
32 72 0.56
33 52 0.40
34 2 0.02
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (32 bp):
GTCTAAAATGAAATGACCTAAACTGAACCAAA
Found at i:5596628 original size:31 final size:32
Alignment explanation
Indices: 5596573--5596687 Score: 101
Period size: 32 Copynumber: 3.6 Consensus size: 32
5596563 TTTTTTTGTG
* *
5596573 AACTCATTCT-TTTTTTCTTCTTTTTTCTTGACA
1 AACTCTTTCTCTTTTTT-TT-TTTTTTCTTGAAA
* *
5596606 AACT-TTTCTCTTTTTTTTTTTTTTACTTCATA
1 AACTCTTTCTCTTTTTTTTTTTTTT-CTTGAAA
* * *
5596638 AACTCTTT-TCCTCTTTTTTTTTTCCTTGAAA
1 AACTCTTTCTCTTTTTTTTTTTTTTCTTGAAA
* *
5596669 AATTCTTTCTCTCTTTTTT
1 AACTCTTTCTCTTTTTTTT
5596688 AAGAACTAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
31 18 0.27
32 35 0.53
33 13 0.20
ACGTcount: A:0.15, C:0.20, G:0.02, T:0.63
Consensus pattern (32 bp):
AACTCTTTCTCTTTTTTTTTTTTTTCTTGAAA
Found at i:5596641 original size:32 final size:34
Alignment explanation
Indices: 5596580--5596660 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
5596570 GTGAACTCAT
* *
5596580 TCTTTTTTTCTTCTTTTTTCTTGACAAA-CTTTT-C
1 TCTTTTTTT-TT-TTTTTACTTCACAAACCTTTTCC
*
5596614 TCTTTTTTTTTTTTTTACTTCATAAACTCTTTTCC
1 TCTTTTTTTTTTTTTTACTTCACAAAC-CTTTTCC
5596649 TCTTTTTTTTTT
1 TCTTTTTTTTTT
5596661 CCTTGAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 12 0.29
33 2 0.05
34 14 0.34
35 13 0.32
ACGTcount: A:0.11, C:0.19, G:0.01, T:0.69
Consensus pattern (34 bp):
TCTTTTTTTTTTTTTTACTTCACAAACCTTTTCC
Found at i:5598697 original size:14 final size:13
Alignment explanation
Indices: 5598644--5598724 Score: 53
Period size: 13 Copynumber: 6.4 Consensus size: 13
5598634 CCATTACTTA
* *
5598644 TTTTTTCTCATAT
1 TTTTTTTTCATCT
* * *
5598657 TGTTTTTCCTTCT
1 TTTTTTTTCATCT
*
5598670 TTTTTTTT--TGT
1 TTTTTTTTCATCT
5598681 TTTTTTCTTCATCT
1 TTTTTT-TTCATCT
5598695 TTTCTTTTTCA-CT
1 TTT-TTTTTCATCT
*
5598708 TTTTCTTTCAT-T
1 TTTTTTTTCATCT
5598720 TTTTT
1 TTTTT
5598725 CACTTTCCTT
Statistics
Matches: 52, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
11 8 0.15
12 13 0.25
13 19 0.37
14 9 0.17
15 3 0.06
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCATCT
Found at i:5598714 original size:19 final size:20
Alignment explanation
Indices: 5598692--5598730 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5598682 TTTTTCTTCA
5598692 TCTTT-TCTTTTTCACTTTT
1 TCTTTATCTTTTTCACTTTT
*
5598711 TCTTTCATTTTTTTCACTTT
1 TCTTT-ATCTTTTTCACTTT
5598731 CCTTTGTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.72
Consensus pattern (20 bp):
TCTTTATCTTTTTCACTTTT
Found at i:5599181 original size:20 final size:21
Alignment explanation
Indices: 5599152--5599190 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5599142 ACTTACTTTC
*
5599152 TTTTACAAAATATTTTTAACT
1 TTTTACAAAAGATTTTTAACT
5599173 TTTTA-AAAAGATTTTTAA
1 TTTTACAAAAGATTTTTAA
5599191 TTCTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (21 bp):
TTTTACAAAAGATTTTTAACT
Found at i:5601377 original size:186 final size:184
Alignment explanation
Indices: 5601061--5601423 Score: 521
Period size: 186 Copynumber: 2.0 Consensus size: 184
5601051 TACTTTTTTC
* * *
5601061 TTTCATTTAGCAATATTTTCTTTTTAGCTTTCATTAAGGCTTTTTTTATACTTTGAAGGGTCAAT
1 TTTCATTTAGCAATAATTTCTTGTTAGCATTCATTAAGGCTTTTTTTATACTTTGAAGGGTCAAT
** **
5601126 CTATTTTATGCCATGTCTATTTTGGCTAAGCAATCAGATGCTTGCTCCATCAAAGTCACCTTGTC
66 CTATTGGATGCCATGTCTATTTTGGCTAAGCAATCAGATGCACGCTCCATCAAAGTCACCTTGTC
5601191 CACACTTCTCTTATCAGGACCAACATTACTATCATCTACAGCATTGTATACTTT
131 CACACTTCTCTTATCAGGACCAACATTACTATCATCTACAGCATTGTATACTTT
* **
5601245 TTTCATTTAGCAATAATTTCTTGTTAGCATTCCTTAAGGCTTTTTTTCCATGTTTTGAAGGGTCA
1 TTTCATTTAGCAATAATTTCTTGTTAGCATTCATTAAGGCTTTTTTT--ATACTTTGAAGGGTCA
* * *
5601310 ATCTATTAGGA-GCCATGTCTATTTTGGCTAAGCAATCAGATGCACGTTCCATTAAAGTCATCTT
64 ATCTATT-GGATGCCATGTCTATTTTGGCTAAGCAATCAGATGCACGCTCCATCAAAGTCACCTT
* * * * * *
5601374 GTCCATATTTCTTTTGTCATGACCAACATTACTATCATCTACAGTATTGT
128 GTCCACACTTCTCTTATCAGGACCAACATTACTATCATCTACAGCATTGT
5601424 TTATTGTCTT
Statistics
Matches: 157, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
184 43 0.27
186 113 0.72
187 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (184 bp):
TTTCATTTAGCAATAATTTCTTGTTAGCATTCATTAAGGCTTTTTTTATACTTTGAAGGGTCAAT
CTATTGGATGCCATGTCTATTTTGGCTAAGCAATCAGATGCACGCTCCATCAAAGTCACCTTGTC
CACACTTCTCTTATCAGGACCAACATTACTATCATCTACAGCATTGTATACTTT
Found at i:5602988 original size:22 final size:23
Alignment explanation
Indices: 5602959--5603011 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
5602949 CTCTTGATTT
* *
5602959 TTTTATTTTTTATTTTTATTTAC
1 TTTTATTTTTTAATTTAATTTAC
5602982 -TTTA-TTTTTAATTTAATTTAC
1 TTTTATTTTTTAATTTAATTTAC
5603003 TTTTATTTT
1 TTTTATTTT
5603012 CAATTTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 15 0.58
22 8 0.31
23 3 0.12
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTTAATTTAATTTAC
Found at i:5603000 original size:21 final size:22
Alignment explanation
Indices: 5602959--5603017 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
5602949 CTCTTGATTT
* *
5602959 TTTTATTTTTTATTTTTATTTAC
1 TTTTA-TTTTTAATTTAATTTAC
5602982 -TTTATTTTTAATTTAATTTAC
1 TTTTATTTTTAATTTAATTTAC
*
5603003 TTTTATTTTCAATTT
1 TTTTATTTTTAATTT
5603018 GTTTTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATTTTTAATTTAATTTAC
Found at i:5603023 original size:22 final size:22
Alignment explanation
Indices: 5602959--5603028 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
5602949 CTCTTGATTT
* *
5602959 TTTTATTTTTTATTTTTATTTAC
1 TTTTATTTTTAATTTAT-TTTAC
*
5602982 -TTTATTTTTAATTTAATTTAC
1 TTTTATTTTTAATTTATTTTAC
* *
5603003 TTTTATTTTCAATTTGTTTTA-
1 TTTTATTTTTAATTTATTTTAC
5603024 TTTTA
1 TTTTA
5603029 CTAATTTCGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 10 0.25
22 30 0.75
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73
Consensus pattern (22 bp):
TTTTATTTTTAATTTATTTTAC
Found at i:5603373 original size:30 final size:30
Alignment explanation
Indices: 5603339--5603402 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
5603329 CTATTAGAGG
5603339 ATTGTTTCTCAAATTAAGTCTTACCAAACT
1 ATTGTTTCTCAAATTAAGTCTTACCAAACT
5603369 ATTGTTTCTCAAATTAAGTCTTACCAAACT
1 ATTGTTTCTCAAATTAAGTCTTACCAAACT
5603399 ATTG
1 ATTG
5603403 GGAGACTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.41
Consensus pattern (30 bp):
ATTGTTTCTCAAATTAAGTCTTACCAAACT
Found at i:5608289 original size:60 final size:60
Alignment explanation
Indices: 5608091--5608301 Score: 210
Period size: 60 Copynumber: 3.5 Consensus size: 60
5608081 GAACTAGGTA
* * * * * *
5608091 TTGGTCATTTTCAAACTCGCGACATCATCTCGATTATTCAT-CTTCGACCTCGACTTAGTT
1 TTGGTCACTTTCAAACTCGCGACATCATCCCGATCATTCATCCAT-GACCTCGACTCAGTC
* * ** *
5608151 TTAGTCACTTTCAGACTCAAGACATCATCTCGATCATTCATCCATGACCTCGACTCAGTC
1 TTGGTCACTTTCAAACTCGCGACATCATCCCGATCATTCATCCATGACCTCGACTCAGTC
* * *** **
5608211 TAGGTCATTTTTTGACTCGCGGTATCATCCCGATCATTCATCCATGACCTCGACTC-GATC
1 TTGGTCACTTTCAAACTCGCGACATCATCCCGATCATTCATCCATGACCTCGACTCAG-TC
* *
5608271 TTGGTCACTTTCAAACTCGTGGCATCATCCC
1 TTGGTCACTTTCAAACTCGCGACATCATCCC
5608302 AGTCATCCGA
Statistics
Matches: 123, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
59 1 0.01
60 120 0.98
61 2 0.02
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.34
Consensus pattern (60 bp):
TTGGTCACTTTCAAACTCGCGACATCATCCCGATCATTCATCCATGACCTCGACTCAGTC
Found at i:5608882 original size:3 final size:3
Alignment explanation
Indices: 5608849--5609026 Score: 71
Period size: 3 Copynumber: 62.0 Consensus size: 3
5608839 GAACCGAGTT
* * *
5608849 TTA TTA TTT TTG TTA -TA TTA -TA TTA -TA TTA TTA -TA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
5608893 -TA TCA -TA TTA TTA TTA TTA CTGTA TTA -TA TGGTA TT- GTA TCA -TA
1 TTA TTA TTA TTA TTA TTA TTA -T-TA TTA TTA T--TA TTA TTA TTA TTA
*
5608937 TTA TTA TTA TTA TTA TTA TTA -TA CTA TGGTA -TA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA TTA TTA TTA TTA TTA
* * * * **
5608980 TAA TTA -TA GTTA TTA CTA TTA TTG TTA -GA TTA TCG TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5609024 TTA
1 TTA
5609027 GCCTTACTGT
Statistics
Matches: 130, Mismatches: 23, Indels: 44
0.66 0.12 0.22
Matches are distributed among these distances:
2 26 0.20
3 93 0.72
4 4 0.03
5 7 0.05
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:5608986 original size:46 final size:48
Alignment explanation
Indices: 5608862--5609002 Score: 128
Period size: 46 Copynumber: 2.9 Consensus size: 48
5608852 TTATTTTTGT
*
5608862 TATATTATATTATATTATTATAGTATTATTA-TATCATATTATTATTATTAC
1 TATAGTATATTATATTA-TATA-TATTATTATTAT--TATTATTATTATTAC
* * ** *
5608913 TGTATTATATGGTATTGTATCATATTATTATTATTATTATTATTA-TAC
1 TATAGTATATTATATTATAT-ATATTATTATTATTATTATTATTATTAC
* *
5608961 TATGGTATATTATATTATATA-ATTA-TAGTTATTACTATTATT
1 TATAGTATATTATATTATATATATTATTA-TTATTATTATTATT
5609003 GTTAGATTAT
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
45 2 0.03
46 17 0.22
47 1 0.01
48 17 0.22
49 11 0.14
50 11 0.14
51 17 0.22
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (48 bp):
TATAGTATATTATATTATATATATTATTATTATTATTATTATTATTAC
Found at i:5609002 original size:26 final size:26
Alignment explanation
Indices: 5608940--5609026 Score: 74
Period size: 26 Copynumber: 3.5 Consensus size: 26
5608930 TATCATATTA
* * * *
5608940 TTATTATTATTATTATTATACTATGG
1 TTATTACTATTATTATTAGATTATAG
5608966 TATATTA-TATTA-TA-TA-ATTATAG
1 T-TATTACTATTATTATTAGATTATAG
* *
5608989 TTATTACTATTATTGTTAGATTATCG
1 TTATTACTATTATTATTAGATTATAG
*
5609015 TTATTATTATTA
1 TTATTACTATTA
5609027 GCCTTACTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
22 5 0.10
23 11 0.22
24 3 0.06
25 4 0.08
26 23 0.45
27 5 0.10
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.56
Consensus pattern (26 bp):
TTATTACTATTATTATTAGATTATAG
Found at i:5609875 original size:5 final size:5
Alignment explanation
Indices: 5609865--5609911 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
5609855 CCCATAATTT
5609865 TTTTA TTTTA -TTTA CTTTATA TTTTTA TTTTA TTTTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA -TTT-TA -TTTTA TTTTA TTTTA -TTTTA TTTT
5609912 CAATTTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
4 4 0.11
5 19 0.51
6 9 0.24
7 5 0.14
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:5609889 original size:16 final size:16
Alignment explanation
Indices: 5609868--5609910 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
5609858 ATAATTTTTT
5609868 TATTTTATTTACTTTA
1 TATTTTATTTACTTTA
*
5609884 TATTTTTATTTTATTTTA
1 TA-TTTTA-TTTACTTTA
5609902 T-TTTTATTT
1 TATTTTATTT
5609911 TCAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 3 0.12
16 7 0.29
17 5 0.21
18 9 0.38
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTTATTTACTTTA
Found at i:5609911 original size:16 final size:17
Alignment explanation
Indices: 5609865--5609911 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
5609855 CCCATAATTT
5609865 TTTTA-TTTTA-TTTAC
1 TTTTATTTTTATTTTAC
5609880 TTTATATTTTTATTTTA-
1 TTT-TATTTTTATTTTAC
5609897 TTTTATTTTTATTTT
1 TTTTATTTTTATTTT
5609912 CAATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.10
16 14 0.48
17 8 0.28
18 4 0.14
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTATTTTAC
Found at i:5609920 original size:15 final size:16
Alignment explanation
Indices: 5609902--5609944 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
5609892 TTTTATTTTA
*
5609902 TTTTTATTTTC-AATT
1 TTTTTATTTACTAATT
5609917 TTTTTACTTTACTAATT
1 TTTTTA-TTTACTAATT
5609934 TTTATTATTTA
1 TTT-TTATTTA
5609945 TTTATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 6 0.25
16 4 0.17
17 11 0.46
18 3 0.12
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATTTACTAATT
Found at i:5609944 original size:17 final size:18
Alignment explanation
Indices: 5609913--5609954 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5609903 TTTTATTTTC
5609913 AATTTTT-TTACTTTACT
1 AATTTTTATTACTTTACT
*
5609930 AATTTTTATTA-TTTATT
1 AATTTTTATTACTTTACT
*
5609947 TATTTTTA
1 AATTTTTA
5609955 CTAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (18 bp):
AATTTTTATTACTTTACT
Found at i:5614603 original size:18 final size:19
Alignment explanation
Indices: 5614576--5614621 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
5614566 CAGATTGAGT
5614576 TTTAAC-TTGTTTTAGGG-
1 TTTAACTTTGTTTTAGGGA
*
5614593 TTTAACTTTGTTTTGGGGA
1 TTTAACTTTGTTTTAGGGA
*
5614612 TTTGACTTTG
1 TTTAACTTTG
5614622 GGTATTTGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.15, C:0.07, G:0.24, T:0.54
Consensus pattern (19 bp):
TTTAACTTTGTTTTAGGGA
Found at i:5614765 original size:18 final size:18
Alignment explanation
Indices: 5614744--5614805 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
5614734 TTTCACCTAG
5614744 GGTTTAAAGTTTGACTTT
1 GGTTTAAAGTTTGACTTT
* * *
5614762 GGTTTAAAATTTAAAGTTT
1 GGTTTAAAGTTT-GACTTT
*
5614781 AGGGTTTAAGGTTTGACTTT
1 --GGTTTAAAGTTTGACTTT
5614801 GGTTT
1 GGTTT
5614806 TGGGTTTGAC
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 16 0.47
19 4 0.12
20 4 0.12
21 10 0.29
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.48
Consensus pattern (18 bp):
GGTTTAAAGTTTGACTTT
Found at i:5614829 original size:18 final size:17
Alignment explanation
Indices: 5614783--5614830 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
5614773 TAAAGTTTAG
*
5614783 GGTTTAAGGTTTGACTTT
1 GGTTT-AGGTTTGACCTT
*
5614801 GGTTTTGGGTTTGACCTT
1 GG-TTTAGGTTTGACCTT
5614819 GTGTTTAGGTTT
1 G-GTTTAGGTTT
5614831 TAACCTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.10, C:0.06, G:0.31, T:0.52
Consensus pattern (17 bp):
GGTTTAGGTTTGACCTT
Found at i:5617046 original size:23 final size:25
Alignment explanation
Indices: 5617007--5617054 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
5616997 TTTTGAAATT
*
5617007 AAAAATTTATAGATTTTTTTAAAAA
1 AAAAATTTATAGATTTTATTAAAAA
5617032 AAAAATTTAT-G-TTTTATTAAAAA
1 AAAAATTTATAGATTTTATTAAAAA
5617055 TAATGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
24 1 0.05
25 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
AAAAATTTATAGATTTTATTAAAAA
Found at i:5618315 original size:25 final size:24
Alignment explanation
Indices: 5618287--5618335 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5618277 ATTTTAATAC
5618287 TTAATTTGCACCTAAATAAATCCTT
1 TTAATTTGCACC-AAATAAATCCTT
* *
5618312 TTAATTTGTATCAAATAAATCCTT
1 TTAATTTGCACCAAATAAATCCTT
5618336 AATATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAATTTGCACCAAATAAATCCTT
Found at i:5618406 original size:30 final size:28
Alignment explanation
Indices: 5618372--5618436 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 28
5618362 ATTTCATTTG
5618372 AAATATAAA-TTTATTTAAATATAAATTAA
1 AAATATAAATTTTATTTAAATAT-AA-TAA
5618401 AAA-ATAAAATTTTATTTAAATATAATAA
1 AAATAT-AAATTTTATTTAAATATAATAA
5618429 AAATATAA
1 AAATATAA
5618437 TGACTTATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
28 10 0.30
29 10 0.30
30 13 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATATAAATTTTATTTAAATATAATAA
Found at i:5618425 original size:18 final size:17
Alignment explanation
Indices: 5618357--5618425 Score: 51
Period size: 18 Copynumber: 4.2 Consensus size: 17
5618347 TGTTCATAAT
5618357 TAAATATTTCATTTGAAATA
1 TAAA-ATTT-ATTT-AAATA
5618377 T-AAATTTATTTAAATA
1 TAAAATTTATTTAAATA
*
5618393 T-AAA-TTA---AAAAA
1 TAAAATTTATTTAAATA
5618405 TAAAATTTTATTTAAATA
1 TAAAA-TTTATTTAAATA
5618423 TAA
1 TAA
5618426 TAAAAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
12 5 0.12
13 3 0.07
15 6 0.15
16 9 0.22
17 4 0.10
18 11 0.27
19 2 0.05
20 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAAATTTATTTAAATA
Found at i:5621234 original size:20 final size:20
Alignment explanation
Indices: 5621209--5621254 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5621199 TATTTTTTTT
5621209 AAAGAGAAAAAAAAAGAGAA
1 AAAGAGAAAAAAAAAGAGAA
* *
5621229 AAAGAGAAAGAGAAAGAGAA
1 AAAGAGAAAAAAAAAGAGAA
*
5621249 AGAGAG
1 AAAGAG
5621255 GAGAGATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (20 bp):
AAAGAGAAAAAAAAAGAGAA
Found at i:5621240 original size:6 final size:6
Alignment explanation
Indices: 5621209--5621253 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
5621199 TATTTTTTTT
* *
5621209 AAAGAG AAAAAA AAAGAG AAAAAGAG AAAGAG AAAGAG AAAGAG A
1 AAAGAG AAAGAG AAAGAG --AAAGAG AAAGAG AAAGAG AAAGAG A
5621254 GGAGAGATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 27 0.82
8 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:5621480 original size:107 final size:106
Alignment explanation
Indices: 5621403--5621612 Score: 339
Period size: 107 Copynumber: 2.0 Consensus size: 106
5621393 GTTTCGTTTG
* * *
5621403 TTTAATAATAAAATGTTCATGTTTAATTTGTATTTGACTCATTTAAATTAAATAAATTCATTTAT
1 TTTAATAATAAAATATTCATGTCTAATTTGTATTTGACTCATTTAAATTAAATAAATTCATTCAT
5621468 GAACATTAAAAAAATATATTCATGAATATATATATATATATA
66 GAACATTAAAAAAATATATT-ATGAATATATATATATATATA
* ** *
5621510 TTTAATAGTATGATATTCATGTCTAATTTGTATTTGACTCATTTAAATTAAATAAATTCGTTCAT
1 TTTAATAATAAAATATTCATGTCTAATTTGTATTTGACTCATTTAAATTAAATAAATTCATTCAT
5621575 GAACATTAAAAAAATATATTCATGAATATATATATATA
66 GAACATTAAAAAAATATATT-ATGAATATATATATATA
5621613 AACAAATATA
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 96 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (106 bp):
TTTAATAATAAAATATTCATGTCTAATTTGTATTTGACTCATTTAAATTAAATAAATTCATTCAT
GAACATTAAAAAAATATATTATGAATATATATATATATATA
Found at i:5621492 original size:23 final size:23
Alignment explanation
Indices: 5621449--5621493 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5621439 ACTCATTTAA
* *
5621449 ATTAAATAAATTCATTTATGAAC
1 ATTAAAAAAATTCATTCATGAAC
5621472 ATTAAAAAAATAT-ATTCATGAA
1 ATTAAAAAAAT-TCATTCATGAA
5621494 TATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (23 bp):
ATTAAAAAAATTCATTCATGAAC
Found at i:5621637 original size:23 final size:23
Alignment explanation
Indices: 5621610--5621665 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
5621600 ATATATATAT
* *
5621610 ATAAACAAATATAGGTGTGAATA
1 ATAAATAAATATAGGTATGAATA
**
5621633 ATAAATAAATATATTTATGAATA
1 ATAAATAAATATAGGTATGAATA
5621656 ATAAATAAAT
1 ATAAATAAAT
5621666 TATAATCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (23 bp):
ATAAATAAATATAGGTATGAATA
Found at i:5621677 original size:19 final size:19
Alignment explanation
Indices: 5621630--5621693 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
5621620 ATAGGTGTGA
*
5621630 ATAATAAATAAATATATTT
1 ATAATAAATAAATATAATT
5621649 ATGAAT-AATAAATA-AATT
1 AT-AATAAATAAATATAATT
* *
5621667 ATAATCAAATAAATTTAAAT
1 ATAAT-AAATAAATATAATT
5621687 A-AATAAA
1 ATAATAAA
5621694 CATACAATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
17 3 0.08
18 8 0.21
19 20 0.53
20 7 0.18
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAATAAATAAATATAATT
Found at i:5622689 original size:22 final size:22
Alignment explanation
Indices: 5622664--5622712 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5622654 AAAGATGTTA
* *
5622664 CAAATATGTAATAATTTGAACT
1 CAAAGATGTAATAATTCGAACT
* *
5622686 CAAAGCTGTAATAATTCGCACT
1 CAAAGATGTAATAATTCGAACT
5622708 CAAAG
1 CAAAG
5622713 TAATTATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (22 bp):
CAAAGATGTAATAATTCGAACT
Found at i:5623362 original size:2 final size:2
Alignment explanation
Indices: 5623355--5623388 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5623345 GTTGATCCTT
5623355 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
5623389 AGACTAAGGA
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):
TA
Found at i:5628473 original size:20 final size:19
Alignment explanation
Indices: 5628450--5628499 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
5628440 TTTTGTTCCT
5628450 TTTTTCTTTCTTTTCCTCTC
1 TTTTTCTTTCTTTT-CTCTC
*
5628470 TTTTACTTT-TTTTCTCTC
1 TTTTTCTTTCTTTTCTCTC
5628488 TGTTTT-TTTCTT
1 T-TTTTCTTTCTT
5628500 GGGGGGTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 9 0.35
19 9 0.35
20 8 0.31
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTCTTTCTTTTCTCTC
Found at i:5631341 original size:19 final size:20
Alignment explanation
Indices: 5631300--5631341 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
5631290 GTGGTTTATC
*
5631300 TTTGTATTGTTGTCTTATGT
1 TTTGTATTGTTGTCTTATAT
5631320 TTTGTATT-TTGT-TTCATAT
1 TTTGTATTGTTGTCTT-ATAT
5631339 TTT
1 TTT
5631342 TTTTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 10 0.50
20 8 0.40
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.69
Consensus pattern (20 bp):
TTTGTATTGTTGTCTTATAT
Found at i:5631775 original size:12 final size:11
Alignment explanation
Indices: 5631756--5631785 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
5631746 AAATTTTTAA
5631756 TTATTTATATT
1 TTATTTATATT
5631767 TTAATTTATATT
1 TT-ATTTATATT
5631779 TTATTTA
1 TTATTTA
5631786 ATTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATTTATATT
Found at i:5635462 original size:145 final size:145
Alignment explanation
Indices: 5635221--5635605 Score: 420
Period size: 145 Copynumber: 2.7 Consensus size: 145
5635211 ATTTTAAAAC
* * * **
5635221 ACCAAAAATCATGAAATATTATGAAACTAAGATATAAAAAGTTTCATGAAATT-TCGAGCTCAAG
1 ACCAAAAATCATAAAATATTATGAAACTAAGATCTAAAAATTTTCACAAAATTCT-GAGCTCAAG
* * *
5635285 AAGATCAAATTATGAAAATACCCTTGTGGGGGTACTTTCATAATTTTACACTTCT-CGGAGTACT
65 AAGACCAAATTATGAAAATACCCTTATAGGGGTACTTTCATAATTTTACACTTCTACGG-GTACT
*
5635349 GCTATGATTTCAAGTGT
129 GCTATGATTTCAAGTAT
* **
5635366 ACCAAAAATCATCAAATATTATGAAACTAAGATCTAAAAATTTTCACAAAATTCTGAGCTCGGGA
1 ACCAAAAATCATAAAATATTATGAAACTAAGATCTAAAAATTTTCACAAAATTCTGAGCTCAAGA
* * ** * * *
5635431 AGGCCAAATTATGAAAATA-CCTTAATAGGGGTATTTTGGTAATTTTATACTTTTATGGGTACTG
66 AGACCAAATTATGAAAATACCCTT-ATAGGGGTACTTTCATAATTTTACACTTCTACGGGTACTG
* *
5635495 CTGTGATTTCAGGTAT
130 CTATGATTTCAAGTAT
* * **
5635511 ACCAAAAATCATAAAATATTATAAAACTAAGATCCGAAAGGTTTT-ACAAAATTCTGAGCTCAA-
1 ACCAAAAATCATAAAATATTATGAAACTAAGAT-CTAAAAATTTTCACAAAATTCTGAGCTCAAG
* ** **
5635574 AAAAGTTAAATTACAAAAATACCCTTATAGGG
65 AAGA-CCAAATTATGAAAATACCCTTATAGGG
5635606 ATATATTGGT
Statistics
Matches: 201, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
144 6 0.03
145 180 0.90
146 15 0.07
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (145 bp):
ACCAAAAATCATAAAATATTATGAAACTAAGATCTAAAAATTTTCACAAAATTCTGAGCTCAAGA
AGACCAAATTATGAAAATACCCTTATAGGGGTACTTTCATAATTTTACACTTCTACGGGTACTGC
TATGATTTCAAGTAT
Found at i:5636275 original size:33 final size:32
Alignment explanation
Indices: 5636237--5636346 Score: 114
Period size: 32 Copynumber: 3.4 Consensus size: 32
5636227 ATTTTCATAC
5636237 CATTTTAAAAAATTAAGTAAAAATATCTATAT
1 CATTTTAAAAAATTAAGTAAAAATATCTATAT
* * * * *
5636269 CGATTTTAAAAAATCAAATTAAAAA-CTCCATCT
1 C-ATTTTAAAAAAT-TAAGTAAAAATATCTATAT
* * * *
5636302 CTTTTTAAAATATTAAGTAAAAATTTCTACAT
1 CATTTTAAAAAATTAAGTAAAAATATCTATAT
5636334 CATTTTAAAAAAT
1 CATTTTAAAAAAT
5636347 AGATATATTA
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
31 8 0.13
32 26 0.43
33 18 0.30
34 8 0.13
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (32 bp):
CATTTTAAAAAATTAAGTAAAAATATCTATAT
Found at i:5636989 original size:21 final size:21
Alignment explanation
Indices: 5636960--5637004 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
5636950 GAATTATTTG
*
5636960 TTTTTAAAATGA-TATGAAAT
1 TTTTTAAAAGGACTATGAAAT
*
5636980 TTTTTAAAAAGGACTTTGAAAT
1 TTTTT-AAAAGGACTATGAAAT
5637002 TTT
1 TTT
5637005 AGCTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 10 0.48
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (21 bp):
TTTTTAAAAGGACTATGAAAT
Found at i:5637662 original size:17 final size:19
Alignment explanation
Indices: 5637642--5637676 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5637632 AGGATGCTAC
5637642 TATTTCA-A-ATTTTTTAA
1 TATTTCATATATTTTTTAA
5637659 TATTTCATATATTTTTTA
1 TATTTCATATATTTTTTA
5637677 TATAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTCATATATTTTTTAA
Found at i:5638202 original size:32 final size:32
Alignment explanation
Indices: 5638157--5638289 Score: 137
Period size: 32 Copynumber: 4.1 Consensus size: 32
5638147 TAAATTTATT
*
5638157 TTTTAAAAATGATATTAAAATTTTTACTTAATA
1 TTTT-AAAATGATATGAAAATTTTTACTTAATA
* *
5638190 TTTGAAAATGATATGAATATTTTT--TTAAT-
1 TTTTAAAATGATATGAAAATTTTTACTTAATA
* * * * *
5638219 TTTTAAAGCTGATATAGAAATTTTTTATTTTATTT
1 TTTTAAA-ATGATAT-GAAAATTTTTA-CTTAATA
5638254 TTTTAAAATGATATGAAAATTTTTACTTAATA
1 TTTTAAAATGATATGAAAATTTTTACTTAATA
5638286 TTTT
1 TTTT
5638290 TGTTTTATTT
Statistics
Matches: 81, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
29 6 0.07
30 11 0.14
31 8 0.10
32 26 0.32
33 13 0.16
34 10 0.12
35 7 0.09
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (32 bp):
TTTTAAAATGATATGAAAATTTTTACTTAATA
Found at i:5638233 original size:62 final size:64
Alignment explanation
Indices: 5638151--5638277 Score: 152
Period size: 64 Copynumber: 2.0 Consensus size: 64
5638141 GATTAATAAA
* *
5638151 TTTATTTTTTAAAAATGATATTA-AAA-TTTTTA-CTTAATATTTGAAAATGATATGAATATTTT
1 TTTAATTTTTAAAAATGATA-TAGAAATTTTTTATCTTAATATTTGAAAATGATATGAAAATTTT
** * * * *
5638213 TTTAATTTTTAAAGCTGATATAGAAATTTTTTATTTTATTTTTTTAAAATGATATGAAAATTTT
1 TTTAATTTTTAAAAATGATATAGAAATTTTTTATCTTAATATTTGAAAATGATATGAAAATTTT
5638277 T
1 T
5638278 ACTTAATATT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
61 2 0.04
62 20 0.37
63 6 0.11
64 26 0.48
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (64 bp):
TTTAATTTTTAAAAATGATATAGAAATTTTTTATCTTAATATTTGAAAATGATATGAAAATTTT
Found at i:5638256 original size:34 final size:33
Alignment explanation
Indices: 5638151--5638290 Score: 121
Period size: 33 Copynumber: 4.3 Consensus size: 33
5638141 GATTAATAAA
* *
5638151 TTTAT-TTTTTAAAAATGATATTAAAATTTTTAC
1 TTTATATTTTT-AAAATGATATGAAAATTTTTAT
* * *
5638184 TTAATA-TTTGAAAATGATATG--AATATTT-T
1 TTTATATTTTTAAAATGATATGAAAATTTTTAT
* *
5638213 TTTA-ATTTTTAAAGCTGATATAGAAATTTTTTAT
1 TTTATATTTTTAAA-ATGATAT-GAAAATTTTTAT
* *
5638247 TTTATTTTTTTAAAATGATATGAAAATTTTTAC
1 TTTATATTTTTAAAATGATATGAAAATTTTTAT
*
5638280 TTAATATTTTT
1 TTTATATTTTT
5638291 GTTTTATTTG
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
28 1 0.01
29 9 0.11
30 12 0.14
31 1 0.01
32 10 0.12
33 31 0.37
34 11 0.13
35 8 0.10
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.54
Consensus pattern (33 bp):
TTTATATTTTTAAAATGATATGAAAATTTTTAT
Found at i:5638544 original size:21 final size:20
Alignment explanation
Indices: 5638502--5638544 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
5638492 ATATTTAATA
**
5638502 TTTTAATAGAAAATAATTTT
1 TTTTAATAGAAAATAACATT
5638522 TTTTAGATAGAAAATAACATT
1 TTTTA-ATAGAAAATAACATT
5638543 TT
1 TT
5638545 CTATTATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTTAATAGAAAATAACATT
Found at i:5644372 original size:21 final size:20
Alignment explanation
Indices: 5644328--5644381 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
5644318 TTGGTTTTTA
5644328 TTTT-TTTATTTTATTTTCT
1 TTTTATTTATTTTATTTTCT
*
5644347 ATTTATTTATTATTATTGTT-T
1 TTTTATTTATT-TTATT-TTCT
5644368 TTTTATTTATTTTA
1 TTTTATTTATTTTA
5644382 CTTATCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.10
20 9 0.30
21 16 0.53
22 2 0.07
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTATTTATTTTATTTTCT
Found at i:5654351 original size:3 final size:3
Alignment explanation
Indices: 5654345--5654395 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
5654335 ACTATTATTG
*
5654345 TAT TAT TAT TACT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5654391 TAT TA
1 TAT TA
5654396 CTAATACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5655428 original size:21 final size:20
Alignment explanation
Indices: 5655356--5655428 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
5655346 GCTTTTCTTT
5655356 TTTATTTTATT-TTCTA-TT-
1 TTTATTTTATTGTT-TATTTA
* *
5655374 TTGATTTTATTATTTATTTA
1 TTTATTTTATTGTTTATTTA
5655394 TTTATTATTATTGTTTATTTA
1 TTTATT-TTATTGTTTATTTA
5655415 TTTATTTTACTTGT
1 TTTATTTTA-TTGT
5655429 CAATTTAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 12 0.26
19 4 0.09
20 8 0.17
21 23 0.49
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.73
Consensus pattern (20 bp):
TTTATTTTATTGTTTATTTA
Found at i:5655434 original size:21 final size:21
Alignment explanation
Indices: 5655389--5655435 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5655379 TTTATTATTT
**
5655389 ATTTATTTATTATTATTGTTT
1 ATTTATTTATTATTATTGTCA
5655410 ATTTATTTATT-TTACTTGTCA
1 ATTTATTTATTATTA-TTGTCA
5655431 ATTTA
1 ATTTA
5655436 AATTGAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (21 bp):
ATTTATTTATTATTATTGTCA
Found at i:5657976 original size:22 final size:22
Alignment explanation
Indices: 5657951--5658053 Score: 72
Period size: 22 Copynumber: 4.8 Consensus size: 22
5657941 TCACAACTGA
*
5657951 AAATTTAAAAATTTGCAATTTG
1 AAATTCAAAAATTTGCAATTTG
* *
5657973 AAATTCAAGAATTCT-CAACTTG
1 AAATTCAAAAATT-TGCAATTTG
* * *
5657995 AAGTTCAAAAAGTCGCAA-TT-
1 AAATTCAAAAATTTGCAATTTG
*
5658015 AAATTCAAAGATTCT-CAATTTG
1 AAATTCAAAAATT-TGCAATTTG
* *
5658037 -AATTTAAAAACTTGCAA
1 AAATTCAAAAATTTGCAA
5658054 AATATTCAAG
Statistics
Matches: 61, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
20 14 0.23
21 16 0.26
22 30 0.49
23 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.33
Consensus pattern (22 bp):
AAATTCAAAAATTTGCAATTTG
Found at i:5658033 original size:20 final size:21
Alignment explanation
Indices: 5657970--5658034 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 21
5657960 AATTTGCAAT
5657970 TTGAAATTC-AAGAATTCTCAA
1 TTGAAATTCAAAG-ATTCTCAA
* * * *
5657991 CTTGAAGTTCAAAAAGTCGCAA
1 -TTGAAATTCAAAGATTCTCAA
5658013 TT-AAATTCAAAGATTCTCAA
1 TTGAAATTCAAAGATTCTCAA
5658033 TT
1 TT
5658035 TGAATTTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 16 0.47
21 2 0.06
22 14 0.41
23 2 0.06
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (21 bp):
TTGAAATTCAAAGATTCTCAA
Found at i:5658176 original size:18 final size:18
Alignment explanation
Indices: 5658113--5658438 Score: 129
Period size: 18 Copynumber: 18.2 Consensus size: 18
5658103 TCAAATGTCA
*
5658113 CAAAAG-TTCAAGGTTCG
1 CAAAAGATTCAAGATTCG
* * **
5658130 CAAAAAATTTAA-ATTTTT
1 CAAAAGATTCAAGA-TTCG
*
5658148 CAAAA-ATTCAAGATTCA
1 CAAAAGATTCAAGATTCG
*
5658165 CAAAAGATTCAAAGATTCAT
1 CAAAAGATTC-AAGATTC-G
*
5658185 AAAAAGATTCAAGATTTC-
1 CAAAAGATTCAAGA-TTCG
*
5658203 TAAAA-ATTCAAGATTCG
1 CAAAAGATTCAAGATTCG
* *
5658220 TAAAAGATTCAAGATTGG
1 CAAAAGATTCAAGATTCG
* * * *
5658238 CAAGAGTTTCAGGATTCA
1 CAAAAGATTCAAGATTCG
*
5658256 C-AAAGATTCAAAGATTTG
1 CAAAAGATTC-AAGATTCG
* *
5658274 C-AAAGAATTTCAAAGTTTCA
1 CAAAAG-A-TTC-AAGATTCG
** * *
5658294 CAATTG--TAAAGATTTG
1 CAAAAGATTCAAGATTCG
* * *
5658310 CAAAAAATTCAA-AGCTCT
1 CAAAAGATTCAAGA-TTCG
*
5658328 CAAAA-ATTCAAGACTCG
1 CAAAAGATTCAAGATTCG
* *
5658345 CAAAAAATTCAAAGATTTG
1 CAAAAGATTC-AAGATTCG
* *
5658364 CAAAA-ATTCAATATTTG
1 CAAAAGATTCAAGATTCG
* *
5658381 TAAAA-ATTCAAGATTCA
1 CAAAAGATTCAAGATTCG
** **
5658398 CAAGTGATTCAAAGATTTA
1 CAAAAGATTC-AAGATTCG
*
5658417 CAAAAGATTCAAGATTTG
1 CAAAAGATTCAAGATTCG
5658435 CAAA
1 CAAA
5658439 GTATTCAAAA
Statistics
Matches: 234, Mismatches: 54, Indels: 41
0.71 0.16 0.12
Matches are distributed among these distances:
16 11 0.05
17 74 0.32
18 87 0.37
19 38 0.16
20 22 0.09
21 2 0.01
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.28
Consensus pattern (18 bp):
CAAAAGATTCAAGATTCG
Found at i:5658181 original size:19 final size:19
Alignment explanation
Indices: 5658148--5658494 Score: 119
Period size: 18 Copynumber: 19.1 Consensus size: 19
5658138 TTAAATTTTT
5658148 CAAAA-ATTC-AAGATTCA
1 CAAAAGATTCAAAGATTCA
5658165 CAAAAGATTCAAAGATTCA
1 CAAAAGATTCAAAGATTCA
*
5658184 TAAAAAGATTC-AAGATTTC-
1 -CAAAAGATTCAAAGA-TTCA
* *
5658203 TAAAA-ATTC-AAGATTCG
1 CAAAAGATTCAAAGATTCA
* **
5658220 TAAAAGATTC-AAGATTGG
1 CAAAAGATTCAAAGATTCA
* * *
5658238 CAAGAGTTTC-AGGATTCA
1 CAAAAGATTCAAAGATTCA
**
5658256 C-AAAGATTCAAAGATTTG
1 CAAAAGATTCAAAGATTCA
*
5658274 C-AAAGAATTTCAAAGTTTCA
1 CAAAAG-A-TTCAAAGATTCA
** **
5658294 CAATTG--T-AAAGATTTG
1 CAAAAGATTCAAAGATTCA
* * *
5658310 CAAAAAATTCAAAG-CTCT
1 CAAAAGATTCAAAGATTCA
* *
5658328 CAAAA-ATTC-AAGACTCG
1 CAAAAGATTCAAAGATTCA
* **
5658345 CAAAAAATTCAAAGATTTG
1 CAAAAGATTCAAAGATTCA
* **
5658364 CAAAA-ATTC-AATATTTG
1 CAAAAGATTCAAAGATTCA
*
5658381 TAAAA-ATTC-AAGATTCA
1 CAAAAGATTCAAAGATTCA
** *
5658398 CAAGTGATTCAAAGATTTA
1 CAAAAGATTCAAAGATTCA
**
5658417 CAAAAGATTC-AAGATTTG
1 CAAAAGATTCAAAGATTCA
**
5658435 C-AAAGTATTCAAA-ATATTT
1 CAAAAG-ATTCAAAGAT-TCA
** * *
5658454 GTAAAGATTAAAAAATTCA
1 CAAAAGATTCAAAGATTCA
5658473 CAAAAGATTTCAAAGATTCA
1 CAAAAGA-TTCAAAGATTCA
5658493 CA
1 CA
5658495 TTTGAAAAAT
Statistics
Matches: 254, Mismatches: 52, Indels: 45
0.72 0.15 0.13
Matches are distributed among these distances:
16 15 0.06
17 63 0.25
18 75 0.30
19 59 0.23
20 40 0.16
21 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (19 bp):
CAAAAGATTCAAAGATTCA
Found at i:5658386 original size:53 final size:53
Alignment explanation
Indices: 5658301--5658438 Score: 145
Period size: 53 Copynumber: 2.6 Consensus size: 53
5658291 TCACAATTGT
** * *
5658301 AAAGATTTGCAAAAAATTCAAAGCTCTCAAAAATTCAAGACTCGCAAAAAATTC
1 AAAGATTTGC-AAAAATTCAAATTTGTCAAAAATTCAAGACTCACAAAAAATTC
* ***
5658355 AAAGATTTGCAAAAATTCAATATTTGT-AAAAATTCAAGATTCACAAGTGATTC
1 AAAGATTTGCAAAAATTCAA-ATTTGTCAAAAATTCAAGACTCACAAAAAATTC
*
5658408 AAAGATTTACAAAAGATTCAAGATTTG-CAAA
1 AAAGATTTGCAAAA-ATTCAA-ATTTGTCAAA
5658439 GTATTCAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
53 44 0.62
54 27 0.38
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (53 bp):
AAAGATTTGCAAAAATTCAAATTTGTCAAAAATTCAAGACTCACAAAAAATTC
Found at i:5658391 original size:35 final size:35
Alignment explanation
Indices: 5658113--5658374 Score: 113
Period size: 35 Copynumber: 7.3 Consensus size: 35
5658103 TCAAATGTCA
* ** * **
5658113 CAAAAGTTCAAGGTTCGCAAAAAATTTAAATTTTT
1 CAAAAATTCAAGACTCGCAAAAAATTCAAAGATTT
* * *
5658148 CAAAAATTCAAGATTCACAAAAGATTCAAAGATTCAT
1 CAAAAATTCAAGACTCGCAAAAAATTCAAAGATT--T
* ** *
5658185 AAAAAGATTCAAGA-TTTCTAAAAATTC-AAGA-TT
1 CAAAA-ATTCAAGACTCGCAAAAAATTCAAAGATTT
* * * ** *
5658218 CGTAAAAGATTCAAGATTGGCAAGAGTTTC-AGGA-TT
1 C--AAAA-ATTCAAGACTCGCAAAAAATTCAAAGATTT
* * *
5658254 CACAAAGATTCAAAGATTTGCAAAGAATTTCAAAG-TTT
1 CA-AAA-ATTC-AAGACTCGCAAA-AAATTCAAAGATTT
* * * * * * *
5658292 CACAATTGTAAAGATTTGCAAAAAATTCAAAGCTCT
1 CAAAAAT-TCAAGACTCGCAAAAAATTCAAAGATTT
5658328 CAAAAATTCAAGACTCGCAAAAAATTCAAAGATTT
1 CAAAAATTCAAGACTCGCAAAAAATTCAAAGATTT
5658363 GCAAAAATTCAA
1 -CAAAAATTCAA
5658375 TATTTGTAAA
Statistics
Matches: 177, Mismatches: 36, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
33 1 0.01
34 1 0.01
35 81 0.46
36 58 0.33
37 22 0.12
38 14 0.08
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (35 bp):
CAAAAATTCAAGACTCGCAAAAAATTCAAAGATTT
Found at i:5658445 original size:37 final size:36
Alignment explanation
Indices: 5658347--5658447 Score: 102
Period size: 37 Copynumber: 2.8 Consensus size: 36
5658337 AAGACTCGCA
* * **
5658347 AAAAATTCAAAGATTTGCAAA-AATTC-AATATTTGT
1 AAAAATTC-AAGATTTGCAAAGTATTCAAAGATTTAC
5658382 AAAAATTCAAGA-TT-CACAAGTGATTCAAAGATTTAC
1 AAAAATTCAAGATTTGCA-AAGT-ATTCAAAGATTTAC
5658418 AAAAGATTCAAGATTTGCAAAGTATTCAAA
1 AAAA-ATTCAAGATTTGCAAAGTATTCAAA
5658448 ATATTTGTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
32 2 0.04
33 4 0.07
34 4 0.07
35 12 0.22
36 10 0.18
37 15 0.27
38 6 0.11
39 2 0.04
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (36 bp):
AAAAATTCAAGATTTGCAAAGTATTCAAAGATTTAC
Found at i:5658460 original size:37 final size:37
Alignment explanation
Indices: 5658351--5658462 Score: 101
Period size: 37 Copynumber: 3.1 Consensus size: 37
5658341 CTCGCAAAAA
* *
5658351 ATTCAAAGATTTGCAAA-AATTC--AATATTTGTAAAA
1 ATTC-AAGATTTGCAAAGTATTCAAAATATTTGTAAAG
***
5658386 ATTCAAGA-TT-CACAAGTGATTCAAAGAT-TTACAAAAG
1 ATTCAAGATTTGCA-AAGT-ATTCAAA-ATATTTGTAAAG
5658423 ATTCAAGATTTGCAAAGTATTCAAAATATTTGTAAAG
1 ATTCAAGATTTGCAAAGTATTCAAAATATTTGTAAAG
5658460 ATT
1 ATT
5658463 AAAAAATTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
32 2 0.03
33 4 0.07
34 4 0.07
35 8 0.13
36 2 0.03
37 30 0.50
38 8 0.13
39 2 0.03
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.33
Consensus pattern (37 bp):
ATTCAAGATTTGCAAAGTATTCAAAATATTTGTAAAG
Found at i:5658603 original size:43 final size:44
Alignment explanation
Indices: 5658479--5658655 Score: 162
Period size: 43 Copynumber: 4.0 Consensus size: 44
5658469 TTCACAAAAG
* * * * *
5658479 ATTTCAAAGATTCACATTTGAAAAATTTTAGAAATTCATA-CCTAAA
1 ATTTCAAAGATTCACAATTG-AAACTCTTAGAGATTCACATCC--AA
* * ** * * * *
5658525 ATTTCGAAGATCCTTATTTGAAAATTTTAGAGATTCACATCTAA
1 ATTTCAAAGATTCACAATTGAAACTCTTAGAGATTCACATCCAA
*
5658569 A-TTCAAAGATTCACAATTGAAACTCTTAGGGATTCACATCCAA
1 ATTTCAAAGATTCACAATTGAAACTCTTAGAGATTCACATCCAA
* *
5658612 ATTTCAAAGATTCACAATTGAAACTCTTAGTGA-TCACATTCAA
1 ATTTCAAAGATTCACAATTGAAACTCTTAGAGATTCACATCCAA
5658655 A
1 A
5658656 ACTTCTAGGT
Statistics
Matches: 111, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
43 44 0.40
44 33 0.30
45 17 0.15
46 17 0.15
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (44 bp):
ATTTCAAAGATTCACAATTGAAACTCTTAGAGATTCACATCCAA
Found at i:5658606 original size:23 final size:23
Alignment explanation
Indices: 5658575--5658649 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 23
5658565 CTAAATTCAA
5658575 AGATTCACAATTGAAACTCTTAG
1 AGATTCACAATTGAAACTCTTAG
* ** *
5658598 GGATTCAC-ATCCAAA-T-TTCAA
1 AGATTCACAATTGAAACTCTT-AG
5658619 AGATTCACAATTGAAACTCTTAG
1 AGATTCACAATTGAAACTCTTAG
*
5658642 TGA-TCACA
1 AGATTCACA
5658650 TTCAAAACTT
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
20 2 0.05
21 9 0.23
22 15 0.38
23 11 0.28
24 2 0.05
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (23 bp):
AGATTCACAATTGAAACTCTTAG
Found at i:5658625 original size:21 final size:21
Alignment explanation
Indices: 5658546--5658627 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
5658536 CCTTATTTGA
* * *
5658546 AAATTTTAGAGATTCACATCT
1 AAATTTCAAAGATTCACATCC
**
5658567 AAA-TTCAAAGATTCACAATTG
1 AAATTTCAAAGATTCAC-ATCC
**
5658588 AAACTCTT-AGGGATTCACATCC
1 AAA-T-TTCAAAGATTCACATCC
5658610 AAATTTCAAAGATTCACA
1 AAATTTCAAAGATTCACA
5658628 ATTGAAACTC
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
20 13 0.28
21 18 0.39
22 5 0.11
23 8 0.17
24 2 0.04
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.30
Consensus pattern (21 bp):
AAATTTCAAAGATTCACATCC
Found at i:5659579 original size:15 final size:15
Alignment explanation
Indices: 5659559--5659612 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
5659549 AACAAATTTC
*
5659559 ATGAATGTAATGTTT
1 ATGAATGCAATGTTT
*
5659574 ATGAATGCAATG--C
1 ATGAATGCAATGTTT
*
5659587 ATGAAAGCAATGTTT
1 ATGAATGCAATGTTT
5659602 ATGAATGCAAT
1 ATGAATGCAAT
5659613 ACATGAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 11 0.34
15 21 0.66
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.33
Consensus pattern (15 bp):
ATGAATGCAATGTTT
Found at i:5659598 original size:28 final size:28
Alignment explanation
Indices: 5659558--5659619 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
5659548 AAACAAATTT
* * *
5659558 CATGAATGTAATGTTTATGAATGCAATG
1 CATGAAAGCAATGTTTATGAATGCAATA
5659586 CATGAAAGCAATGTTTATGAATGCAATA
1 CATGAAAGCAATGTTTATGAATGCAATA
5659614 CATGAA
1 CATGAA
5659620 TATGACTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (28 bp):
CATGAAAGCAATGTTTATGAATGCAATA
Found at i:5666399 original size:2 final size:2
Alignment explanation
Indices: 5666392--5666416 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5666382 ATACAAGTGA
5666392 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 A
5666417 AAATAAGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5667573 original size:64 final size:67
Alignment explanation
Indices: 5667495--5667642 Score: 184
Period size: 68 Copynumber: 2.3 Consensus size: 67
5667485 AAAATAAATT
5667495 TTAGAAAATAATTGAAATATTAAAATTTTC-T-A-TT-TTTTTAAA-ACTAAAATAAATTT-GAA
1 TTAGAAAATAATTGAAATA-TAAAATTTTCTTAACTTATTTTTAAAGA-TAAAATAAATTTAG-A
5667554 AATGG
63 AATGG
* *
5667559 TTAGAAAATAATTGAAATATCAATTTTTCTTTAACTTATTTTTAAAGATAAAATAAATTTAGAAA
1 TTAGAAAATAATTGAAATATAAAATTTTC-TTAACTTATTTTTAAAGATAAAATAAATTTAGAAA
*
5667624 TGT
65 TGG
5667627 TTAGAAAA-AATTGAAA
1 TTAGAAAATAATTGAAA
5667643 GCAAGAGTAT
Statistics
Matches: 74, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
63 8 0.11
64 19 0.26
65 1 0.01
66 1 0.01
67 10 0.14
68 33 0.45
69 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (67 bp):
TTAGAAAATAATTGAAATATAAAATTTTCTTAACTTATTTTTAAAGATAAAATAAATTTAGAAAT
GG
Found at i:5669049 original size:31 final size:31
Alignment explanation
Indices: 5669013--5669075 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
5669003 TGAATACTTA
5669013 ACCTTCAATTTTTTTAAAACTATTAAATATG
1 ACCTTCAATTTTTTTAAAACTATTAAATATG
*
5669044 ACCTTCAATTTTTTTAAAATTATTAAATATG
1 ACCTTCAATTTTTTTAAAACTATTAAATATG
5669075 A
1 A
5669076 TTCACGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (31 bp):
ACCTTCAATTTTTTTAAAACTATTAAATATG
Found at i:5670193 original size:16 final size:16
Alignment explanation
Indices: 5670168--5670198 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5670158 TCCTTCTTTC
*
5670168 CTTTTTTTTTTTTTAT
1 CTTTTATTTTTTTTAT
5670184 CTTTTATTTTTTTTA
1 CTTTTATTTTTTTTA
5670199 AATTTTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (16 bp):
CTTTTATTTTTTTTAT
Found at i:5670227 original size:22 final size:23
Alignment explanation
Indices: 5670199--5670243 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5670189 ATTTTTTTTA
*
5670199 AATTTTTTCA-ATTTTAAAAAAT
1 AATTTTTACATATTTTAAAAAAT
*
5670221 AATTTTTAGATATTTTAAAAAAT
1 AATTTTTACATATTTTAAAAAAT
5670244 TGTTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
AATTTTTACATATTTTAAAAAAT
Found at i:5670255 original size:11 final size:11
Alignment explanation
Indices: 5670239--5670263 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5670229 GATATTTTAA
5670239 AAAATTGTTAT
1 AAAATTGTTAT
5670250 AAAATTGTTAT
1 AAAATTGTTAT
5670261 AAA
1 AAA
5670264 TATTTTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAATTGTTAT
Found at i:5670863 original size:26 final size:27
Alignment explanation
Indices: 5670814--5670872 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
5670804 ATTTTTCTTT
*
5670814 TTTTTTTAATTTATTATTAATTAAATG
1 TTTTTTTAATTTATTATTAATTAAATA
* *
5670841 TTTTTTTATATTT-TTATT-TTTAACTA
1 TTTTTTTA-ATTTATTATTAATTAAATA
5670867 TTTTTT
1 TTTTTT
5670873 ATTAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 11 0.39
27 13 0.46
28 4 0.14
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTTTTAATTTATTATTAATTAAATA
Found at i:5671164 original size:22 final size:22
Alignment explanation
Indices: 5671126--5671168 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5671116 TTTGTTCAGG
*
5671126 TTTCTTTTTCTTTTTCTTTTTT
1 TTTCTTTTTCTTCTTCTTTTTT
5671148 TTTCTTTTT-TATCTTCTTTTT
1 TTTCTTTTTCT-TCTTCTTTTT
5671169 ATTAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTCTTTTTCTTCTTCTTTTTT
Found at i:5676793 original size:34 final size:34
Alignment explanation
Indices: 5676755--5676822 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
5676745 ATATAAAAGA
* *
5676755 AATTTTAAATGCAATTACAACGACTTCAATATCT
1 AATTTTAAATGCAAATACAACGACTCCAATATCT
* *
5676789 AATTTTAAATTCAAATACAATGACTCCAATATCT
1 AATTTTAAATGCAAATACAACGACTCCAATATCT
5676823 GTTGAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (34 bp):
AATTTTAAATGCAAATACAACGACTCCAATATCT
Found at i:5681177 original size:22 final size:21
Alignment explanation
Indices: 5681135--5681183 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
5681125 GTTTTGAAAT
5681135 ATTTTTATAAATACACTAAAA
1 ATTTTTATAAATACACTAAAA
*
5681156 ATTTTTATAAATACATTAAAA
1 ATTTTTATAAATACACTAAAA
*
5681177 AATTTTA
1 ATTTTTA
5681184 GTGTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTTTATAAATACACTAAAA
Done.