Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 14 of 325
Found at i:5355454 original size:18 final size:15
Alignment explanation
Indices: 5355438--5355469 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5355428 TATTCTGTTC
5355438 TTTCTTATTATTTTG
1 TTTCTTATTATTTTG
5355453 TTTCTTATTA-TTTG
1 TTTCTTATTATTTTG
5355467 TTT
1 TTT
5355470 TATTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (15 bp):
TTTCTTATTATTTTG
Found at i:5355650 original size:14 final size:15
Alignment explanation
Indices: 5355623--5355668 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
5355613 ACTCTATTTA
5355623 ATTAATATAAAATAAT
1 ATTAATAT-AAATAAT
5355639 ATTAATAT-AATAAT
1 ATTAATATAAATAAT
*
5355653 ATTTACT-TAAATAAT
1 A-TTAATATAAATAAT
5355668 A
1 A
5355669 AGTAAACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 8 0.30
15 11 0.41
16 8 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAATATAAATAAT
Found at i:5374006 original size:23 final size:24
Alignment explanation
Indices: 5373970--5374017 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
5373960 AAACATATAT
5373970 TTTTATACATTAAAAATTATTTAAA
1 TTTTATACATTAAAAATT-TTTAAA
*
5373995 TTTTAT-CA-TAAATATTTTTAAA
1 TTTTATACATTAAAAATTTTTAAA
5374017 T
1 T
5374018 GATTATCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 7 0.32
24 2 0.09
25 6 0.27
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTATACATTAAAAATTTTTAAA
Found at i:5374023 original size:23 final size:23
Alignment explanation
Indices: 5373980--5374024 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5373970 TTTTATACAT
*
5373980 TAAAAATTATTTAAATTTTATCA
1 TAAAAATTATTTAAATATTATCA
*
5374003 TAAATATT-TTTAAATGATTATC
1 TAAAAATTATTTAAAT-ATTATC
5374025 CTTCAAAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAATTATTTAAATATTATCA
Found at i:5375181 original size:12 final size:14
Alignment explanation
Indices: 5375145--5375175 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5375135 CCTACACTCT
*
5375145 TATAGATTTAAAAA
1 TATATATTTAAAAA
5375159 TATATATTTAAAAA
1 TATATATTTAAAAA
5375173 TAT
1 TAT
5375176 TTTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TATATATTTAAAAA
Found at i:5378702 original size:10 final size:8
Alignment explanation
Indices: 5378675--5378702 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5378665 TTCTCAACTC
5378675 ATATCCAT
1 ATATCCAT
5378683 ATATCCAT
1 ATATCCAT
5378691 ATATCCAT
1 ATATCCAT
5378699 ATAT
1 ATAT
5378703 TAAATCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATCCAT
Found at i:5379955 original size:30 final size:30
Alignment explanation
Indices: 5379921--5379977 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
5379911 TATAAAATTT
*
5379921 ATTTTATTATTAATTTAAAGGTATTTGTTA
1 ATTTTATTATTAATTTAAAGGCATTTGTTA
* * *
5379951 ATTTTGTTATTATTTTAGAGGCATTTG
1 ATTTTATTATTAATTTAAAGGCATTTG
5379978 CTTATTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (30 bp):
ATTTTATTATTAATTTAAAGGCATTTGTTA
Found at i:5382060 original size:28 final size:28
Alignment explanation
Indices: 5382028--5382090 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
5382018 TCCCATATTA
5382028 ATGGGGTATACGAAAAGTTTCATAACTT
1 ATGGGGTATACGAAAAGTTTCATAACTT
* * *
5382056 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATACGAAAAGTTTCATAACTT
5382084 ATGGGGT
1 ATGGGGT
5382091 TGATAATGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (28 bp):
ATGGGGTATACGAAAAGTTTCATAACTT
Found at i:5384973 original size:23 final size:23
Alignment explanation
Indices: 5384943--5385027 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 23
5384933 GCTTTACTGA
5384943 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
5384966 TCAGGCACCTCT-TGTGTCGTA--
1 TCAGGCA-CTTTATGTGTCGTATT
* **
5384987 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACTTTATGTGTCGTATT
5385009 T-AGGCACTTTATGTGTCGT
1 TCAGGCACTTTATGTGTCGT
5385028 CTACTGATCA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 30 0.59
22 1 0.02
23 16 0.31
24 3 0.06
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:5393986 original size:12 final size:12
Alignment explanation
Indices: 5393969--5393993 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5393959 TAGAACCAAC
5393969 AGTTCATTATCT
1 AGTTCATTATCT
5393981 AGTTCATTATCT
1 AGTTCATTATCT
5393993 A
1 A
5393994 ATGGATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (12 bp):
AGTTCATTATCT
Found at i:5394111 original size:33 final size:33
Alignment explanation
Indices: 5394072--5394137 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
5394062 GGAAGACTAT
5394072 TGGATCAAATGGCAAAGACATTGTTGAGAAAAA
1 TGGATCAAATGGCAAAGACATTGTTGAGAAAAA
*
5394105 TGGATCAAATGGCAAAGACATTTTTGAGAAAAA
1 TGGATCAAATGGCAAAGACATTGTTGAGAAAAA
5394138 AGATGGCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (33 bp):
TGGATCAAATGGCAAAGACATTGTTGAGAAAAA
Found at i:5394215 original size:12 final size:12
Alignment explanation
Indices: 5394198--5394222 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5394188 AAGATATATG
5394198 GTCATGAAATAA
1 GTCATGAAATAA
5394210 GTCATGAAATAA
1 GTCATGAAATAA
5394222 G
1 G
5394223 AATTAAGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (12 bp):
GTCATGAAATAA
Found at i:5395348 original size:16 final size:16
Alignment explanation
Indices: 5395327--5395359 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5395317 CAAGGGGCCA
5395327 ACATTATTAGTTTAGT
1 ACATTATTAGTTTAGT
5395343 ACATTATTAGTTTAGT
1 ACATTATTAGTTTAGT
5395359 A
1 A
5395360 GTGGCAGTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (16 bp):
ACATTATTAGTTTAGT
Found at i:5412362 original size:21 final size:22
Alignment explanation
Indices: 5412324--5412364 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5412314 AAACATAAGC
*
5412324 AAATTTTCAAAAATAGTTTATA
1 AAATTTTCAAAAAAAGTTTATA
5412346 AAATTTT-AAAAAAAGTTTA
1 AAATTTTCAAAAAAAGTTTA
5412365 ATATTAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATTTTCAAAAAAAGTTTATA
Found at i:5412516 original size:15 final size:16
Alignment explanation
Indices: 5412498--5412530 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5412488 ATTTTTGTAT
*
5412498 TATTTT-AATATTAAA
1 TATTTTAAAGATTAAA
5412513 TATTTTAAAGATTAAA
1 TATTTTAAAGATTAAA
5412529 TA
1 TA
5412531 AATTCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TATTTTAAAGATTAAA
Found at i:5420535 original size:29 final size:29
Alignment explanation
Indices: 5420493--5420548 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5420483 GTGAAAGCAT
*
5420493 ATATCTGACATTAGAATATAAATCCATCC
1 ATATCTGACATTAGAATATAAAACCATCC
* * *
5420522 ATATCTTACGTTAGCATATAAAACCAT
1 ATATCTGACATTAGAATATAAAACCAT
5420549 TAATATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (29 bp):
ATATCTGACATTAGAATATAAAACCATCC
Found at i:5455969 original size:46 final size:46
Alignment explanation
Indices: 5455902--5456247 Score: 444
Period size: 46 Copynumber: 7.5 Consensus size: 46
5455892 GGGTATTACA
*
5455902 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATTATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
* * *
5455948 AAATGTGTAAGACCATGGTTGAAAAATACCATGGCAACAGGATATA
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
*
5455994 AAATGTGTAAGACCATGGTTGAAAGATACCATTGCAACATGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
* *
5456040 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATA
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
**
5456086 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-CGG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
* ** * * * *
5456131 GAATGAATAAGACCATCGTTGAAAGATACCATGGCAATATAACATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
**** * * *
5456177 AAATAAACAAGACAATGGTTGAAAGATACCATGGCAACCTGACA-G
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
* *
5456222 AAAATGAGTAAGACCATAGTTGAAAG
1 -AAATGTGTAAGACCATGGTTGAAAG
5456248 GCACTATGGC
Statistics
Matches: 262, Mismatches: 36, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
45 37 0.14
46 225 0.86
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (46 bp):
AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
Found at i:5456258 original size:137 final size:138
Alignment explanation
Indices: 5455910--5456247 Score: 428
Period size: 137 Copynumber: 2.5 Consensus size: 138
5455900 CAAAATGTGT
* *
5455910 AAGACCATGGTTGAAAGATACCATGGCAACATTATATG-AAATGTGTAAGACCATGGTTGAAAAA
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATA-GAAAATGTGTAAGACCATGGTTGAAAGA
* * ** * * * *
5455974 TACCATGGCAACAGGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATTGCAACATGATAT
65 TACCATGGCAACATGATAGAAAATGAATAAGACCATCGTTGAAAGATACCATGGCAACATAACAT
****
5456039 GAAATGTGT
130 GAAATAAAC
* *
5456048 AAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGTGTAAGACCATGGTTGAAAGAT
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGTGTAAGACCATGGTTGAAAGAT
* ** *
5456113 ACCATGGCAACATGA-CGGGAATGAATAAGACCATCGTTGAAAGATACCATGGCAATATAACATG
66 ACCATGGCAACATGATAGAAAATGAATAAGACCATCGTTGAAAGATACCATGGCAACATAACATG
5456177 AAATAAAC
131 AAATAAAC
* * * * *
5456185 AAGACAATGGTTGAAAGATACCATGGCAACCTGACAGAAAATGAGTAAGACCATAGTTGAAAG
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGTGTAAGACCATGGTTGAAAG
5456248 GCACTATGGC
Statistics
Matches: 172, Mismatches: 27, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
137 98 0.57
138 74 0.43
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.21
Consensus pattern (138 bp):
AAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGTGTAAGACCATGGTTGAAAGAT
ACCATGGCAACATGATAGAAAATGAATAAGACCATCGTTGAAAGATACCATGGCAACATAACATG
AAATAAAC
Found at i:5456274 original size:91 final size:90
Alignment explanation
Indices: 5456002--5456258 Score: 239
Period size: 91 Copynumber: 2.8 Consensus size: 90
5455992 TAAAATGTGT
* * * ** *
5456002 AAGACCATGGTTGAAAGATACCATTGCAACATGA-TATGAAATGTGTAAGACCATGGTTGAAAGA
1 AAGACAATGGTTGAAAGATACCATGGCAACATGACGA--AAATGAATAAGACCATAGTTGAAAGA
* * * * ****
5456066 TACCATGGCAACAGGATATA-AAATGTGT
64 CACCATGGCAATA-TA-ACAGAAATAAAC
* ** * *
5456094 AAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAATGAATAAGACCATCGTTGAAAGATA
1 AAGACAATGGTTGAAAGATACCATGGCAACATGACGAAAATGAATAAGACCATAGTTGAAAGACA
5456159 CCATGGCAATATAACATGAAATAAAC
66 CCATGGCAATATAACA-GAAATAAAC
* * *
5456185 AAGACAATGGTTGAAAGATACCATGGCAACCTGACAGAAAATGAGTAAGACCATAGTTGAAAGGC
1 AAGACAATGGTTGAAAGATACCATGGCAACATGAC-GAAAATGAATAAGACCATAGTTGAAAGAC
*
5456250 ACTATGGCA
65 ACCATGGCA
5456259 TCATGTCAAA
Statistics
Matches: 138, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
89 2 0.01
90 1 0.01
91 71 0.51
92 64 0.46
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (90 bp):
AAGACAATGGTTGAAAGATACCATGGCAACATGACGAAAATGAATAAGACCATAGTTGAAAGACA
CCATGGCAATATAACAGAAATAAAC
Found at i:5456565 original size:16 final size:17
Alignment explanation
Indices: 5456544--5456576 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5456534 ATGATGGAGC
5456544 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
5456560 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
5456577 TATTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:5456630 original size:24 final size:24
Alignment explanation
Indices: 5456603--5456650 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5456593 GTAAGAGAAT
5456603 GATATGTTTCATGACATGTACATA
1 GATATGTTTCATGACATGTACATA
5456627 GATATGTTTCATGACATGTACATA
1 GATATGTTTCATGACATGTACATA
5456651 TATGATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (24 bp):
GATATGTTTCATGACATGTACATA
Found at i:5457627 original size:16 final size:16
Alignment explanation
Indices: 5457606--5457636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5457596 GATATTTTAA
5457606 TATATTATATTAATAT
1 TATATTATATTAATAT
*
5457622 TATATTATGTTAATA
1 TATATTATATTAATA
5457637 AAATAATAAA
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:5457751 original size:17 final size:16
Alignment explanation
Indices: 5457724--5457757 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5457714 GGAGAAAAAG
*
5457724 AGAAAAAAAAAGGGAA
1 AGAAAAAAAAAGAGAA
5457740 AGAAAAATAAAAGAGAA
1 AGAAAAA-AAAAGAGAA
5457757 A
1 A
5457758 ACTAAAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AGAAAAAAAAAGAGAA
Found at i:5463357 original size:33 final size:37
Alignment explanation
Indices: 5463277--5463357 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 37
5463267 ACTAATTACA
5463277 AATATTTAATTGTTATATTTAAATATTTAAAATATATT
1 AATATTT-ATTGTTATATTTAAATATTTAAAATATATT
* *
5463315 -TTATATATTG-TA-A-TTAAAT-TTTATAAATA-ATT
1 AATATTTATTGTTATATTTAAATATTTA-AAATATATT
5463347 AATATTTATTG
1 AATATTTATTG
5463358 CTTGAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
32 7 0.19
33 19 0.51
34 1 0.03
35 2 0.05
36 4 0.11
37 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (37 bp):
AATATTTATTGTTATATTTAAATATTTAAAATATATT
Found at i:5464508 original size:8 final size:8
Alignment explanation
Indices: 5464495--5464527 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
5464485 CAAAACTTTC
5464495 AAATACAT
1 AAATACAT
5464503 AAATACAT
1 AAATACAT
5464511 AAATACAT
1 AAATACAT
5464519 AAA-ACAT
1 AAATACAT
5464526 AA
1 AA
5464528 TATCATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (8 bp):
AAATACAT
Found at i:5464705 original size:20 final size:20
Alignment explanation
Indices: 5464668--5464706 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5464658 CTTCTTCTTT
* * *
5464668 TTTTTGTTTTTTTGTTTTTG
1 TTTTTGTCTTTGTCTTTTTG
5464688 TTTTTGTCTTTGTCTTTTT
1 TTTTTGTCTTTGTCTTTTT
5464707 CCTTTCCTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.05, G:0.13, T:0.82
Consensus pattern (20 bp):
TTTTTGTCTTTGTCTTTTTG
Found at i:5464752 original size:14 final size:16
Alignment explanation
Indices: 5464712--5464752 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
5464702 TTTTTCCTTT
5464712 CCTTTATATTTTTCTC
1 CCTTTATATTTTTCTC
*
5464728 CCTTTCT-TTTTT-TC
1 CCTTTATATTTTTCTC
5464742 CCTTT-TATTTT
1 CCTTTATATTTT
5464753 GCCGCCCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.04
14 11 0.48
15 5 0.22
16 6 0.26
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.68
Consensus pattern (16 bp):
CCTTTATATTTTTCTC
Found at i:5466538 original size:21 final size:21
Alignment explanation
Indices: 5466506--5466554 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5466496 TCGTTGACAC
*
5466506 CCTTTTTACTTT-TTTTTTTGT
1 CCTTTTTACTTTCATTTTTT-T
5466527 CCTTCTTT-CTTTCATTTTTTT
1 CCTT-TTTACTTTCATTTTTTT
5466548 CCTTTTT
1 CCTTTTT
5466555 TTTAAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 9 0.36
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (21 bp):
CCTTTTTACTTTCATTTTTTT
Found at i:5466640 original size:23 final size:20
Alignment explanation
Indices: 5466609--5466664 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
5466599 AAAAAAATTG
*
5466609 AAATGTATATTTGAAATGTTTT
1 AAATATATATTTGAAA--TTTT
*
5466631 ATAATATATATTTTTAAATTTT
1 A-AATATATA-TTTGAAATTTT
5466653 AAATATATATTT
1 AAATATATATTT
5466665 TTTAAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 3 0.10
21 8 0.27
22 6 0.20
23 7 0.23
24 6 0.20
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
AAATATATATTTGAAATTTT
Found at i:5466657 original size:21 final size:23
Alignment explanation
Indices: 5466627--5466672 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
5466617 ATTTGAAATG
5466627 TTTTATAATATATA-TTTTTAAA
1 TTTTATAATATATATTTTTTAAA
5466649 TTTTA-AATATATATTTTTTAAA
1 TTTTATAATATATATTTTTTAAA
5466671 TT
1 TT
5466673 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTATAATATATATTTTTTAAA
Found at i:5466677 original size:12 final size:12
Alignment explanation
Indices: 5466660--5466705 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
5466650 TTTAAATATA
5466660 TATTTTTTAAAT
1 TATTTTTTAAAT
5466672 TATTTTTTAAA-
1 TATTTTTTAAAT
*
5466683 -A-TTTTAAATAT
1 TATTTTTTAA-AT
5466694 TATTTTTTAAAT
1 TATTTTTTAAAT
5466706 ATTAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
12 14 0.50
13 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTTTTAAAT
Found at i:5466686 original size:22 final size:22
Alignment explanation
Indices: 5466670--5466720 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
5466660 TATTTTTTAA
5466670 ATTATTTTTTAAAATTTTAAAT
1 ATTATTTTTTAAAATTTTAAAT
*
5466692 ATTATTTTTT-AAATATTAAAT
1 ATTATTTTTTAAAATTTTAAAT
5466713 A-TATTTTT
1 ATTATTTTT
5466721 AATAATATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 7 0.25
21 11 0.39
22 10 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTATTTTTTAAAATTTTAAAT
Found at i:5466688 original size:35 final size:35
Alignment explanation
Indices: 5466627--5466707 Score: 121
Period size: 34 Copynumber: 2.3 Consensus size: 35
5466617 ATTTGAAATG
5466627 TTTTATAATATATATTTTTAAATTTTAAATATATATT
1 TTTTA-AATATATATTTTTAAATTTTAAATAT-TATT
5466664 TTTTAAAT-TAT-TTTTTAAAATTTTAAATATTATT
1 TTTTAAATATATATTTTT-AAATTTTAAATATTATT
5466698 TTTTAAATAT
1 TTTTAAATAT
5466708 TAAATATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
34 17 0.40
35 17 0.40
36 3 0.07
37 5 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (35 bp):
TTTTAAATATATATTTTTAAATTTTAAATATTATT
Found at i:5466689 original size:20 final size:19
Alignment explanation
Indices: 5466627--5466720 Score: 70
Period size: 22 Copynumber: 4.8 Consensus size: 19
5466617 ATTTGAAATG
5466627 TTTTATAATATATATTTTTAAA
1 TTTTA-AAT-TAT-TTTTTAAA
* *
5466649 TTTTAAA-TATATATT---
1 TTTTAAATTATTTTTTAAA
5466664 TTTTAAATTATTTTTTAAAA
1 TTTTAAATTATTTTTT-AAA
5466684 TTTTAAATATTATTTTTTAAA
1 TTTT-AA-ATTATTTTTTAAA
*
5466705 TATTAAATATATTTTT
1 TTTTAAAT-TATTTTT
5466721 AATAATATAG
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
15 7 0.12
16 6 0.10
18 3 0.05
19 5 0.08
20 13 0.22
21 10 0.17
22 15 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAAATTATTTTTTAAA
Found at i:5466699 original size:21 final size:21
Alignment explanation
Indices: 5466670--5466728 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
5466660 TATTTTTTAA
*
5466670 ATTATTTTTTAAAATTTTAAAT
1 ATTA-TTTTTAAAATATTAAAT
*
5466692 ATTATTTTTTAAATATTAAAT
1 ATTATTTTTAAAATATTAAAT
5466713 A-TATTTTTAATAATAT
1 ATTATTTTTAA-AATAT
5466729 AGAACATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.24
21 21 0.64
22 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATTTTTAAAATATTAAAT
Found at i:5466703 original size:14 final size:14
Alignment explanation
Indices: 5466649--5466709 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
5466639 TATTTTTAAA
5466649 TTTTAAATATATATT
1 TTTTAAATAT-TATT
5466664 TTTT-AA-ATTATT
1 TTTTAAATATTATT
5466676 TTTT-AA-A--A--
1 TTTTAAATATTATT
5466684 TTTTAAATATTATT
1 TTTTAAATATTATT
5466698 TTTTAAATATTA
1 TTTTAAATATTA
5466710 AATATATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
12 12 0.30
13 2 0.05
14 14 0.35
15 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAAATATTATT
Found at i:5466721 original size:33 final size:35
Alignment explanation
Indices: 5466646--5466722 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 35
5466636 ATATATTTTT
***
5466646 AAATTTTAAATATATATTTTTTAAATTATTTTTTA
1 AAATTTTAAATATATATTTTTTAAATTATTAAATA
5466681 AAATTTTAAATAT-TATTTTTTAAA-TATTAAATA
1 AAATTTTAAATATATATTTTTTAAATTATTAAATA
* *
5466714 TATTTTTAA
1 AAATTTTAA
5466723 TAATATAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 13 0.35
34 11 0.30
35 13 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (35 bp):
AAATTTTAAATATATATTTTTTAAATTATTAAATA
Found at i:5466898 original size:15 final size:13
Alignment explanation
Indices: 5466857--5466904 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
5466847 AATAAGGATA
*
5466857 AAAAAGTAAAAAAC
1 AAAAAG-AAAAAAG
5466871 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
5466884 AAAGAAGGAAAAAAG
1 AAA-AA-GAAAAAAG
*
5466899 TAAAAG
1 AAAAAG
5466905 GGTGCTAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 10 0.33
14 10 0.33
15 10 0.33
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:5466905 original size:14 final size:14
Alignment explanation
Indices: 5466857--5466905 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
5466847 AATAAGGATA
* *
5466857 AAAAAGTAAAAAAC
1 AAAAAGGAAAAAAG
5466871 AAAAA-GAAAAAAG
1 AAAAAGGAAAAAAG
5466884 AAAGAAGGAAAAAAG
1 AAA-AAGGAAAAAAG
*
5466899 TAAAAGG
1 AAAAAGG
5466906 GTGCTAGCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 9 0.30
14 11 0.37
15 10 0.33
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAAAGGAAAAAAG
Found at i:5467255 original size:289 final size:289
Alignment explanation
Indices: 5466933--5467804 Score: 1744
Period size: 289 Copynumber: 3.0 Consensus size: 289
5466923 GGCGTCAAAT
5466933 AAAATGCCTCTACCAGAAAATGAATTTTTTTTAAAGTTCCCTATATTTTTAGAAATTACAGTATT
1 AAAATGCCTCTACCAGAAAATGAATTTTTTTTAAAGTTCCCTATATTTTTAGAAATTACAGTATT
5466998 TCTCTGACATTTATACAAGTAACACCATTCTACTTAACTCTACCAAAAAATTGATTTTTTTTCCT
66 TCTCTGACATTTATACAAGTAACACCATTCTACTTAACTCTACCAAAAAATTGATTTTTTTTCCT
5467063 TATTGCTTATGTGGTATGTTGGTAGAGCTAAATTCTTAAGCTCCACCAACTTTTAATATAGATTT
131 TATTGCTTATGTGGTATGTTGGTAGAGCTAAATTCTTAAGCTCCACCAACTTTTAATATAGATTT
5467128 TAGGTTATTTTTATGTTTAATTAAAAAAAGATAATTAGTTAAATTTTTCGAGTTATTTTTATAAA
196 TAGGTTATTTTTATGTTTAATTAAAAAAAGATAATTAGTTAAATTTTTCGAGTTATTTTTATAAA
5467193 AAAACCGAAATACTCCGCGGGTTGTTGAG
261 AAAACCGAAATACTCCGCGGGTTGTTGAG
5467222 AAAATGCCTCTACCAGAAAATGAATTTTTTTTAAAGTTCCCTATATTTTTAGAAATTACAGTATT
1 AAAATGCCTCTACCAGAAAATGAATTTTTTTTAAAGTTCCCTATATTTTTAGAAATTACAGTATT
5467287 TCTCTGACATTTATACAAGTAACACCATTCTACTTAACTCTACCAAAAAATTGATTTTTTTTCCT
66 TCTCTGACATTTATACAAGTAACACCATTCTACTTAACTCTACCAAAAAATTGATTTTTTTTCCT
5467352 TATTGCTTATGTGGTATGTTGGTAGAGCTAAATTCTTAAGCTCCACCAACTTTTAATATAGATTT
131 TATTGCTTATGTGGTATGTTGGTAGAGCTAAATTCTTAAGCTCCACCAACTTTTAATATAGATTT
5467417 TAGGTTATTTTTATGTTTAATTAAAAAAAGATAATTAGTTAAATTTTTCGAGTTATTTTTATAAA
196 TAGGTTATTTTTATGTTTAATTAAAAAAAGATAATTAGTTAAATTTTTCGAGTTATTTTTATAAA
5467482 AAAACCGAAATACTCCGCGGGTTGTTGAG
261 AAAACCGAAATACTCCGCGGGTTGTTGAG
5467511 AAAATGCCTCTACCAGAAAATGAATTTTTTTTAAAGTTCCCTATATTTTTAGAAATTACAGTATT
1 AAAATGCCTCTACCAGAAAATGAATTTTTTTTAAAGTTCCCTATATTTTTAGAAATTACAGTATT
5467576 TCTCTGACATTTATACAAGTAACACCATTCTACTTAACTCTACCAAAAAATTGATTTTTTTTCCT
66 TCTCTGACATTTATACAAGTAACACCATTCTACTTAACTCTACCAAAAAATTGATTTTTTTTCCT
5467641 TATTGCTTATGTGGTATGTTGGTAGAGCTAAATTCTTAAGCTCCACCAACTTTTAATATAGATTT
131 TATTGCTTATGTGGTATGTTGGTAGAGCTAAATTCTTAAGCTCCACCAACTTTTAATATAGATTT
5467706 TAGGTTATTTTTATGTTTAATTAAAAAAAGATAATTAGTTAAATTTTTCGAGTTATTTTTATAAA
196 TAGGTTATTTTTATGTTTAATTAAAAAAAGATAATTAGTTAAATTTTTCGAGTTATTTTTATAAA
5467771 AAAACCGAAATACTCCGCGGGTTGTTGAG
261 AAAACCGAAATACTCCGCGGGTTGTTGAG
5467800 AAAAT
1 AAAAT
5467805 CTCTGTCGAG
Statistics
Matches: 583, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
289 583 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (289 bp):
AAAATGCCTCTACCAGAAAATGAATTTTTTTTAAAGTTCCCTATATTTTTAGAAATTACAGTATT
TCTCTGACATTTATACAAGTAACACCATTCTACTTAACTCTACCAAAAAATTGATTTTTTTTCCT
TATTGCTTATGTGGTATGTTGGTAGAGCTAAATTCTTAAGCTCCACCAACTTTTAATATAGATTT
TAGGTTATTTTTATGTTTAATTAAAAAAAGATAATTAGTTAAATTTTTCGAGTTATTTTTATAAA
AAAACCGAAATACTCCGCGGGTTGTTGAG
Found at i:5483519 original size:27 final size:27
Alignment explanation
Indices: 5483445--5483520 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 27
5483435 AAAGGTATAG
*
5483445 ATATTTAATTAAGAAAAAAAAATCTCAA
1 ATATTTAATTAA-ATAAAAAAATCTCAA
*
5483473 ATA-CTAATTAAATATTAAAAAA-CTCAA
1 ATATTTAATTAAATA--AAAAAATCTCAA
5483500 ATATTTAATTACAATAAAAAA
1 ATATTTAATTA-AATAAAAAA
5483521 TTAATATCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
26 2 0.05
27 20 0.49
28 15 0.37
29 4 0.10
ACGTcount: A:0.61, C:0.08, G:0.01, T:0.30
Consensus pattern (27 bp):
ATATTTAATTAAATAAAAAAATCTCAA
Found at i:5483548 original size:23 final size:24
Alignment explanation
Indices: 5483489--5483553 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
5483479 ATTAAATATT
* **
5483489 AAAAAACTCAAATATTTAATTACA
1 AAAAAACTCTAATATCAAATTACA
*
5483513 ATAAAAAAT-TAATATCAAATTA-A
1 A-AAAAACTCTAATATCAAATTACA
5483536 AAAAAACTCTAATATCAA
1 AAAAAACTCTAATATCAA
5483554 TTTCAATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 6 0.18
23 11 0.32
24 11 0.32
25 6 0.18
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAAAACTCTAATATCAAATTACA
Found at i:5491611 original size:21 final size:21
Alignment explanation
Indices: 5491586--5491654 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
5491576 TATAATGATT
5491586 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
5491607 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
5491627 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
5491647 ATTATTAT
1 ATTATTAT
5491655 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:5491667 original size:15 final size:14
Alignment explanation
Indices: 5491641--5491671 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
5491631 TATGGTTTTA
5491641 TATTAGATTATTAT
1 TATTAGATTATTAT
5491655 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
5491670 TA
1 TA
5491672 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:5491992 original size:14 final size:15
Alignment explanation
Indices: 5491973--5492001 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5491963 ATAAAGCATA
5491973 AAAAGAAACA-AAAC
1 AAAAGAAACAGAAAC
5491987 AAAAGAAACAGAAAC
1 AAAAGAAACAGAAAC
5492002 GAAGCAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.76, C:0.14, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAGAAACAGAAAC
Found at i:5515388 original size:32 final size:32
Alignment explanation
Indices: 5515350--5515414 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
5515340 AAATCTTTTG
5515350 TATTTAGGATAAGTATCCTCATTTCAAACATT
1 TATTTAGGATAAGTATCCTCATTTCAAACATT
*
5515382 TATTTAGGATAAGTATCCTTATTTCAAACATT
1 TATTTAGGATAAGTATCCTCATTTCAAACATT
5515414 T
1 T
5515415 GTAAGTTTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (32 bp):
TATTTAGGATAAGTATCCTCATTTCAAACATT
Found at i:5526572 original size:23 final size:24
Alignment explanation
Indices: 5526512--5526572 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
5526502 ATATATAAAC
5526512 ATTTATTTTA-ATATTTTTAACAT
1 ATTTATTTTATATATTTTTAACAT
* *
5526535 ATTTAATTTATTATATTTTTTA-A-
1 ATTTATTTTA-TATATTTTTAACAT
5526558 ATTTATTTTTATATA
1 ATTTA-TTTTATATA
5526573 ATAGACTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 18 0.56
24 5 0.16
25 9 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
ATTTATTTTATATATTTTTAACAT
Found at i:5531365 original size:15 final size:15
Alignment explanation
Indices: 5531345--5531374 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5531335 GTTGTTGTTG
5531345 TTTTTTTT-TTTTTC
1 TTTTTTTTCTTTTTC
5531359 TTTTTTTTCTTTTTC
1 TTTTTTTTCTTTTTC
5531374 T
1 T
5531375 GATTTGAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:5543917 original size:21 final size:21
Alignment explanation
Indices: 5543891--5543931 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5543881 ATCTGCTCAA
* *
5543891 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5543912 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5543932 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5557503 original size:17 final size:16
Alignment explanation
Indices: 5557487--5557538 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5557477 CATTTTATAT
5557487 TATATAAAATTAAATA
1 TATATAAAATTAAATA
*
5557503 TATATAACA-T-AATA
1 TATATAAAATTAAATA
*
5557517 CTATATAGAAATTAAAAA
1 -TATATA-AAATTAAATA
5557535 TATA
1 TATA
5557539 GTTTTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 4 0.14
15 7 0.24
16 10 0.34
17 5 0.17
18 3 0.10
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
TATATAAAATTAAATA
Found at i:5558755 original size:21 final size:21
Alignment explanation
Indices: 5558729--5558781 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5558719 CGCTGTTTCT
*
5558729 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
5558750 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
5558771 AATCTCACCGC
1 AATCTCACCGC
5558782 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:5561433 original size:8 final size:8
Alignment explanation
Indices: 5561420--5561448 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
5561410 ACCAAATTGA
5561420 AAAAAAAG
1 AAAAAAAG
5561428 AAAAAAAG
1 AAAAAAAG
5561436 AAAAAAAG
1 AAAAAAAG
5561444 AAAAA
1 AAAAA
5561449 GGAAAGCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5577684 original size:17 final size:18
Alignment explanation
Indices: 5577662--5577695 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5577652 TAAAATAAAT
*
5577662 TCTTCTGTATC-CATTTA
1 TCTTCTCTATCTCATTTA
5577679 TCTTCTCTATCTCATTT
1 TCTTCTCTATCTCATTT
5577696 TAAGTTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.26, G:0.03, T:0.56
Consensus pattern (18 bp):
TCTTCTCTATCTCATTTA
Found at i:5594897 original size:41 final size:41
Alignment explanation
Indices: 5594852--5594930 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
5594842 TTGTTGAGTC
5594852 AACTTGTCCAATGATTTTGTTTGAACTGATACCCTAGATAG
1 AACTTGTCCAATGATTTTGTTTGAACTGATACCCTAGATAG
*
5594893 AACTTGTCCAATGATTTTGTTTGAACTGGTACCCTAGA
1 AACTTGTCCAATGATTTTGTTTGAACTGATACCCTAGA
5594931 CAAAACTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (41 bp):
AACTTGTCCAATGATTTTGTTTGAACTGATACCCTAGATAG
Found at i:5596289 original size:15 final size:15
Alignment explanation
Indices: 5596271--5596309 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
5596261 AGAATTAAAT
5596271 AAAATGATTATTATA
1 AAAATGATTATTATA
* *
5596286 AAAATGAATATTCTA
1 AAAATGATTATTATA
5596301 AAAAT-ATTA
1 AAAATGATTA
5596310 GTTTTGAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (15 bp):
AAAATGATTATTATA
Found at i:5604933 original size:6 final size:6
Alignment explanation
Indices: 5604924--5604953 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5604914 TGCTTGGGTT
5604924 TGGCTG TGGCTG TGGCTG TGGCTG TGGCTG
1 TGGCTG TGGCTG TGGCTG TGGCTG TGGCTG
5604954 CCTTCCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
TGGCTG
Found at i:5605266 original size:25 final size:25
Alignment explanation
Indices: 5605217--5605267 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5605207 ATACTTTTAC
* *
5605217 AAATATTAAATTATTTTTCTTTTCA
1 AAATATTAAATTATTTTTATGTTCA
5605242 AAATAATTAAA-TATTTTTATGTTCA
1 AAAT-ATTAAATTATTTTTATGTTCA
5605267 A
1 A
5605268 TTAAAAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (25 bp):
AAATATTAAATTATTTTTATGTTCA
Found at i:5616483 original size:15 final size:16
Alignment explanation
Indices: 5616447--5616483 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5616437 GATTTGAAAC
5616447 TAATA-TATTAATTTT
1 TAATATTATTAATTTT
5616462 TAA-ATTATTAA-TTT
1 TAATATTATTAATTTT
5616476 TAATATTA
1 TAATATTA
5616484 CAATTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATATTATTAATTTT
Found at i:5617047 original size:15 final size:15
Alignment explanation
Indices: 5617024--5617065 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
5617014 ACATTAATTC
5617024 AAATAAAAAAATTTA
1 AAATAAAAAAATTTA
* * *
5617039 AAAT-TAAAATTTTT
1 AAATAAAAAAATTTA
5617053 AAATAAAAAAATT
1 AAATAAAAAAATT
5617066 AATTATTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATAAAAAAATTTA
Found at i:5617943 original size:13 final size:14
Alignment explanation
Indices: 5617927--5617956 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5617917 ATTAAGAGTG
5617927 AAATTT-AATTAAA
1 AAATTTAAATTAAA
5617940 AAATTTAAATTAAA
1 AAATTTAAATTAAA
5617954 AAA
1 AAA
5617957 AATGTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTTAAATTAAA
Found at i:5619952 original size:33 final size:31
Alignment explanation
Indices: 5619905--5619969 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 31
5619895 TTTTCAATTT
5619905 TTAAATAAAAAAATAATATATTTTAGTACAC
1 TTAAATAAAAAAATAATATATTTTAGTACAC
5619936 TTAAATTATAAAAAATAATATATTTTAGTACAC
1 TTAAA-TA-AAAAAATAATATATTTTAGTACAC
5619969 T
1 T
5619970 AACAACAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 5 0.16
32 2 0.06
33 25 0.78
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.38
Consensus pattern (31 bp):
TTAAATAAAAAAATAATATATTTTAGTACAC
Found at i:5625084 original size:16 final size:15
Alignment explanation
Indices: 5625063--5625093 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5625053 AGCGTTGACA
5625063 AGGAAACAGAGAAATT
1 AGGAAACAG-GAAATT
5625079 AGGAAACAGGAAATT
1 AGGAAACAGGAAATT
5625094 CCGAGATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.06, G:0.26, T:0.13
Consensus pattern (15 bp):
AGGAAACAGGAAATT
Found at i:5629237 original size:411 final size:411
Alignment explanation
Indices: 5628470--5629299 Score: 1419
Period size: 411 Copynumber: 2.0 Consensus size: 411
5628460 TGACTCTAAT
**
5628470 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTTGCCAAAAAGTTATGATGATTAGAAG
1 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCACCAAAAAGTTATGATGATTAGAAG
* * *
5628535 TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGTGTAACTGATTGAAGGTCTGCCTCA
66 TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACCGATTGAAGATCTGCCTCA
* *
5628600 AGATCAGCTACTCTCTTTTCTAACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAAG
131 AGATCAGCTACTCTCTTTTCTAACCCCTCCAAATCAGCAGCTACTGACCCATAATAATTTTCAAG
*
5628665 ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAATCGCCCTCCCTAACC
196 ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCTAACC
*
5628730 ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGT
261 ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGC
*
5628795 TCCTCCCATTTTTGCACCAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAGTTCATTTCGTTC
326 TCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAGTTCATTTCGTTC
* *
5628860 TACCAAACTATAAATCTTGCC
391 TACCAAACTATAAAACTTACC
* *
5628881 CTGAAGGTTTTCATTCTCAACTTCAAATTGAGCTGCCTTCACC-GAAAGATTATGATGATTAGAA
1 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCACCAAAAAG-TTATGATGATTAGAA
5628945 GTCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACCGATTGAAGATCTGCCTC
65 GTCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACCGATTGAAGATCTGCCTC
* * *
5629010 AAGATCAGCTACTCTCTTTTCTGACCCCTCCAACTCAGCAGCTACTGACCTATAATAATTTTCAA
130 AAGATCAGCTACTCTCTTTTCTAACCCCTCCAAATCAGCAGCTACTGACCCATAATAATTTTCAA
*
5629075 GATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTTCCTAAC
195 GATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCTAAC
* *
5629140 CATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAGGGCATGTTGATTCCATCCAAAAG
260 CATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAG
* * *
5629205 CTCCTCCCATTTTTGCAACAAGTGGTTCCTTTCCATTAAGGATTGTTCCAGCATTTCATTTCGTT
325 CTCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAGTTCATTTCGTT
* *
5629270 CTGCCAACCTATAAAACTTACC
390 CTACCAAACTATAAAACTTACC
5629292 CTGAAGGT
1 CTGAAGGT
5629300 CCTCATATTT
Statistics
Matches: 393, Mismatches: 25, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
410 4 0.01
411 389 0.99
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (411 bp):
CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCACCAAAAAGTTATGATGATTAGAAG
TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACCGATTGAAGATCTGCCTCA
AGATCAGCTACTCTCTTTTCTAACCCCTCCAAATCAGCAGCTACTGACCCATAATAATTTTCAAG
ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCTAACC
ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGC
TCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAGTTCATTTCGTTC
TACCAAACTATAAAACTTACC
Found at i:5642032 original size:21 final size:21
Alignment explanation
Indices: 5642008--5642060 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5641998 CATTGTTTTT
*
5642008 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
5642029 AATCTCACTGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
5642050 AATCTCACCGC
1 AATCTCACCGC
5642061 CACCGCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:5642229 original size:15 final size:15
Alignment explanation
Indices: 5642209--5642239 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5642199 GTCATGTAAG
5642209 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
5642224 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
5642239 T
1 T
5642240 ATATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:5642429 original size:17 final size:17
Alignment explanation
Indices: 5642396--5642434 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
5642386 TAAGCTTTTG
5642396 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
5642413 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
5642430 ATTTT
1 ATTTT
5642435 CTACAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:5644202 original size:17 final size:17
Alignment explanation
Indices: 5644185--5644252 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 17
5644175 CTTCACATCT
*
5644185 TTTTGTTTTC-TTTTTC
1 TTTTGTTTTCATATTTC
*
5644201 TTTTATTTTCATATTTC
1 TTTTGTTTTCATATTTC
5644218 TTTTG-TTT--T-TTTC
1 TTTTGTTTTCATATTTC
*
5644231 TTTTATTTTCATATTTCC
1 TTTTGTTTTCATATTT-C
5644249 TTTT
1 TTTT
5644253 TTTATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 8 0.19
14 4 0.10
16 13 0.31
17 12 0.29
18 5 0.12
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTGTTTTCATATTTC
Found at i:5644231 original size:30 final size:30
Alignment explanation
Indices: 5644190--5644268 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
5644180 CATCTTTTTG
*
5644190 TTTTCTTTTTCTTTTATTTTCATATTT-CT
1 TTTTTTTTTTCTTTTATTTTCATATTTCCT
5644219 TTTGTTTTTTTCTTTTATTTTCATATTTCCT
1 TTT-TTTTTTTCTTTTATTTTCATATTTCCT
*
5644250 TTTTTTATTT-TTTTATTTT
1 TTTTTTTTTTCTTTTATTTT
5644269 GTTCCTTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 12 0.26
30 29 0.63
31 5 0.11
ACGTcount: A:0.10, C:0.10, G:0.01, T:0.78
Consensus pattern (30 bp):
TTTTTTTTTTCTTTTATTTTCATATTTCCT
Found at i:5644251 original size:18 final size:17
Alignment explanation
Indices: 5644197--5644252 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
5644187 TTGTTTTCTT
5644197 TTTCTTTTATTTTCATA
1 TTTCTTTTATTTTCATA
*
5644214 TTTCTTTT-GTTT--T-
1 TTTCTTTTATTTTCATA
5644227 TTTCTTTTATTTTCATA
1 TTTCTTTTATTTTCATA
5644244 TTTCCTTTT
1 TTT-CTTTT
5644253 TTTATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 8 0.25
14 4 0.12
16 4 0.12
17 11 0.34
18 5 0.16
ACGTcount: A:0.11, C:0.12, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTCTTTTATTTTCATA
Found at i:5644268 original size:13 final size:14
Alignment explanation
Indices: 5644197--5644268 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 14
5644187 TTGTTTTCTT
5644197 TTTCTTTTATTTTCATA
1 TTTCTTTTA-TTT--TA
*
5644214 TTTCTTTTGTTTT-
1 TTTCTTTTATTTTA
5644227 TTTCTTTTATTTTCATA
1 TTTCTTTTA-TTT--TA
*
5644244 TTTCCTTT-TTTTA
1 TTTCTTTTATTTTA
5644257 TTT-TTTTATTTT
1 TTTCTTTTATTTT
5644269 GTTCCTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
12 3 0.07
13 17 0.37
14 4 0.09
15 3 0.07
16 4 0.09
17 15 0.33
ACGTcount: A:0.11, C:0.10, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTCTTTTATTTTA
Found at i:5644307 original size:10 final size:9
Alignment explanation
Indices: 5644289--5644351 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
5644279 AAATTTTGTC
*
5644289 TTTTTCTTT
1 TTTTTATTT
*
5644298 TTTTTACTT
1 TTTTTATTT
*
5644307 TTTTGATTT
1 TTTTTATTT
*
5644316 TTTTT-CTT
1 TTTTTATTT
*
5644324 ATTTTATTT
1 TTTTTATTT
5644333 TGTTTTATTT
1 T-TTTTATTT
5644343 TTTATTATT
1 TTT-TTATT
5644352 AACTTTAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
8 6 0.14
9 22 0.52
10 14 0.33
ACGTcount: A:0.11, C:0.05, G:0.03, T:0.81
Consensus pattern (9 bp):
TTTTTATTT
Found at i:5644309 original size:17 final size:17
Alignment explanation
Indices: 5644289--5644348 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
5644279 AAATTTTGTC
*
5644289 TTTTTCTTTTTTTTACT
1 TTTTTATTTTTTTTACT
5644306 TTTTTGATTTTTTTT-CT
1 TTTTT-ATTTTTTTTACT
5644323 TATTTTATTTTGTTTTA-T
1 T-TTTTATTTT-TTTTACT
5644341 TTTTTATT
1 TTTTTATT
5644349 ATTAACTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 20 0.53
18 18 0.47
ACGTcount: A:0.10, C:0.05, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTTTTTACT
Found at i:5644328 original size:27 final size:27
Alignment explanation
Indices: 5644289--5644345 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
5644279 AAATTTTGTC
*
5644289 TTTTTCTTTTTTTTACTTT-TTTGATTT
1 TTTTTC-TTATTTTACTTTGTTTGATTT
* *
5644316 TTTTTCTTATTTTATTTTGTTTTATTT
1 TTTTTCTTATTTTACTTTGTTTGATTT
5644343 TTT
1 TTT
5644346 ATTATTAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.09, C:0.05, G:0.04, T:0.82
Consensus pattern (27 bp):
TTTTTCTTATTTTACTTTGTTTGATTT
Found at i:5644530 original size:14 final size:14
Alignment explanation
Indices: 5644513--5644539 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5644503 TTTTTTAAAA
5644513 TTTTAAATATTAAT
1 TTTTAAATATTAAT
5644527 TTTTAAATATTAA
1 TTTTAAATATTAA
5644540 CCATATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAATATTAAT
Found at i:5644539 original size:37 final size:35
Alignment explanation
Indices: 5644397--5644539 Score: 110
Period size: 37 Copynumber: 4.0 Consensus size: 35
5644387 TTTATAATAC
* * *
5644397 TTTTTTAAAATTTTAATTATCATTTTTAAAAAT-A
1 TTTTTTAAAATTTTAAATATAATTTTTAAAATTAA
* * * * *
5644431 TTTTTT-TAACTTTAGATATATATTTGTGAAATTAA
1 TTTTTTAAAATTTTAAATATA-ATTTTTAAAATTAA
* * * * *
5644466 ATTTTTATATATTTTAAAAATGTATTTTTCAAATTAA
1 TTTTTTA-AAATTTTAAATAT-AATTTTTAAAATTAA
5644503 TTTTTTAAAATTTTAAATATTAATTTTTAAATATTAA
1 TTTTTTAAAATTTTAAATA-TAATTTTTAAA-ATTAA
5644540 CCATATTTTT
Statistics
Matches: 80, Mismatches: 22, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
33 9 0.11
34 15 0.19
35 6 0.08
36 18 0.22
37 32 0.40
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (35 bp):
TTTTTTAAAATTTTAAATATAATTTTTAAAATTAA
Found at i:5644546 original size:23 final size:23
Alignment explanation
Indices: 5644498--5644539 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
5644488 TATTTTTCAA
*
5644498 ATTAATTTTTTAAAATTTTAAAT
1 ATTAATTTTTTAAAATATTAAAT
5644521 ATTAA-TTTTT-AAATATTAA
1 ATTAATTTTTTAAAATATTAA
5644540 CCATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 5 0.28
23 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTAATTTTTTAAAATATTAAAT
Found at i:5644616 original size:22 final size:22
Alignment explanation
Indices: 5644591--5644634 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5644581 TTGTAAATAC
5644591 AATTTCTTTAA-TTTCTTTTTAA
1 AATTT-TTTAACTTTCTTTTTAA
*
5644613 AATTTTTTAACTTTTTTTTTAA
1 AATTTTTTAACTTTCTTTTTAA
5644635 TTTTTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (22 bp):
AATTTTTTAACTTTCTTTTTAA
Found at i:5644755 original size:17 final size:17
Alignment explanation
Indices: 5644735--5644782 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
5644725 TTTTTTACTT
5644735 TTTTATTAAATTTTGTC
1 TTTTATTAAATTTTGTC
* *
5644752 TTTTACTTAATTTTTTTC
1 TTTTA-TTAAATTTTGTC
*
5644770 TTTT-TTAAGTTTT
1 TTTTATTAAATTTT
5644783 ATATTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 8 0.30
17 5 0.19
18 14 0.52
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTATTAAATTTTGTC
Found at i:5644956 original size:34 final size:33
Alignment explanation
Indices: 5644868--5644957 Score: 78
Period size: 33 Copynumber: 2.7 Consensus size: 33
5644858 ATTTTTACAA
* *
5644868 TTTTTTA-AAATTTTAATTATTATTTTTAAAATT
1 TTTTTTATAAATTTTAAATA-TATTTGTAAAATT
* * *
5644901 ATTTTT-T-AACTTTAGAGATATATTTGTGAAATT
1 TTTTTTATAAATTTTA-A-ATATATTTGTAAAATT
5644934 GTTTTTTATAAATTTTAAATATAT
1 -TTTTTTATAAATTTTAAATATAT
5644958 ATTTTCAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
32 6 0.14
33 17 0.39
34 13 0.30
35 2 0.05
36 6 0.14
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.58
Consensus pattern (33 bp):
TTTTTTATAAATTTTAAATATATTTGTAAAATT
Found at i:5645193 original size:7 final size:7
Alignment explanation
Indices: 5645165--5645226 Score: 58
Period size: 7 Copynumber: 9.1 Consensus size: 7
5645155 TGATTATTAA
5645165 TAAAT-T
1 TAAATAT
5645171 TAAATAT
1 TAAATAT
5645178 T-AATA-
1 TAAATAT
5645183 TAAATAT
1 TAAATAT
*
5645190 TAAAAAAT
1 T-AAATAT
5645198 TAAATAT
1 TAAATAT
** *
5645205 TATTTTT
1 TAAATAT
5645212 TAAATAT
1 TAAATAT
5645219 TAAATAT
1 TAAATAT
5645226 T
1 T
5645227 TTTTTCTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
5 1 0.02
6 13 0.30
7 24 0.55
8 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATAT
Found at i:5645220 original size:21 final size:21
Alignment explanation
Indices: 5645169--5645231 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
5645159 TATTAATAAA
* * *
5645169 TTTAAATATT-AATATAAATA
1 TTTAAATATTAAATATTATTT
* *
5645189 TTAAAAAATTAAATATTATTT
1 TTTAAATATTAAATATTATTT
5645210 TTTAAATATTAAATATT-TTT
1 TTTAAATATTAAATATTATTT
5645230 TT
1 TT
5645232 CTTTTTTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAAATATTAAATATTATTT
Found at i:5645416 original size:27 final size:28
Alignment explanation
Indices: 5645368--5645425 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
5645358 TTAAATACAA
*
5645368 TTTTTAAATACATTTAAAAAATCATAAT
1 TTTTTAAATACATATAAAAAATCATAAT
* *
5645396 TTTTTTAATA-ATATAAGAAATCATAAT
1 TTTTTAAATACATATAAAAAATCATAAT
5645423 TTT
1 TTT
5645426 ATTTTGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (28 bp):
TTTTTAAATACATATAAAAAATCATAAT
Found at i:5645502 original size:24 final size:21
Alignment explanation
Indices: 5645475--5645525 Score: 50
Period size: 21 Copynumber: 2.3 Consensus size: 21
5645465 GTAATGTATA
5645475 TTTAAAATGTTTTATAATA-TACTT
1 TTTAAAA--TTTTA-AATATTA-TT
*
5645499 TTTACAATTTTAAATATTATT
1 TTTAAAATTTTAAATATTATT
5645520 TTTAAA
1 TTTAAA
5645526 TTCTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 11 0.46
22 7 0.29
24 6 0.25
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAAAATTTTAAATATTATT
Found at i:5645527 original size:20 final size:22
Alignment explanation
Indices: 5645484--5645527 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
5645474 ATTTAAAATG
5645484 TTTTATAATATACTTTTTACAA
1 TTTTATAATATACTTTTTACAA
5645506 TTTTA-AATATTA-TTTTTA-AA
1 TTTTATAATA-TACTTTTTACAA
5645526 TT
1 TT
5645528 CTTTTTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 10 0.48
22 7 0.33
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTATAATATACTTTTTACAA
Found at i:5647565 original size:9 final size:9
Alignment explanation
Indices: 5647494--5647565 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
5647484 TTTTAAAGTT
5647494 AATAATAAAA
1 AATAA-AAAA
5647504 AATAAAACAA
1 AATAAAA-AA
*
5647514 AATAAACAA
1 AATAAAAAA
* *
5647523 AAT-GAAAT
1 AATAAAAAA
*
5647531 AAGAAAAAA
1 AATAAAAAA
*
5647540 AATCAAAAA
1 AATAAAAAA
*
5647549 AGTAAAAAAA
1 AAT-AAAAAA
5647559 AATAAAA
1 AATAAAA
5647566 GGACAATTTA
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
8 4 0.09
9 23 0.49
10 20 0.43
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.12
Consensus pattern (9 bp):
AATAAAAAA
Found at i:5651295 original size:9 final size:9
Alignment explanation
Indices: 5651274--5651307 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
5651264 GATGTGATAA
*
5651274 AAAAAATTT
1 AAAAATTTT
5651283 -AAAATTTT
1 AAAAATTTT
5651291 AAAAATTTT
1 AAAAATTTT
5651300 AAAAATTT
1 AAAAATTT
5651308 AATTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAAATTTT
Found at i:5651300 original size:17 final size:17
Alignment explanation
Indices: 5651274--5651309 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5651264 GATGTGATAA
*
5651274 AAAAAATTTAAAATTTT
1 AAAAAATTTAAAAATTT
*
5651291 AAAAATTTTAAAAATTT
1 AAAAAATTTAAAAATTT
5651308 AA
1 AA
5651310 TTTTTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAAATTTAAAAATTT
Found at i:5651303 original size:25 final size:26
Alignment explanation
Indices: 5651275--5651339 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
5651265 ATGTGATAAA
5651275 AAAAATTTAAAATTTTAAAAAT-TTT
1 AAAAATTTAAAATTTTAAAAATATTT
** *
5651300 AAAAATTTAATTTTTTAAATATATTT
1 AAAAATTTAAAATTTTAAAAATATTT
*
5651326 AATAATTTATAAAT
1 AAAAATTTA-AAAT
5651340 AAATGATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 19 0.59
26 11 0.34
27 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAAATTTAAAATTTTAAAAATATTT
Found at i:5654577 original size:3 final size:3
Alignment explanation
Indices: 5654569--5654621 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
5654559 GAAGAAACCC
* * * * **
5654569 CAT CAT CAT CAT CAT CAT CAT CAT CGT CTT CCT CTT CAT TTT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
5654617 CAT CA
1 CAT CA
5654622 AATGACAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.25, C:0.34, G:0.02, T:0.40
Consensus pattern (3 bp):
CAT
Found at i:5656009 original size:26 final size:26
Alignment explanation
Indices: 5655980--5656087 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
5655970 TGGTACAAAT
5655980 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5656006 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5656032 TTATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5656058 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5656084 TGAT
1 TGAT
5656088 GGGCAGTTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5667868 original size:15 final size:14
Alignment explanation
Indices: 5667844--5667888 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
5667834 AAGTATAAAA
*
5667844 TATTTATTAATTTT
1 TATTTTTTAATTTT
*
5667858 GTATTTTTTAAATTT
1 -TATTTTTTAATTTT
5667873 TATTTTTGTAATTTT
1 TATTTTT-TAATTTT
5667888 T
1 T
5667889 TTGAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:5667890 original size:24 final size:22
Alignment explanation
Indices: 5667848--5667899 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
5667838 ATAAAATATT
*
5667848 TATTAATTTTGTATTTTTTAAA
1 TATTATTTTTGTATTTTTTAAA
* *
5667870 TTTTATTTTTGTAATTTTTTTGAA
1 TATTATTTTTGT-A-TTTTTTAAA
5667894 TATTAT
1 TATTAT
5667900 ACAATATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 10 0.42
23 1 0.04
24 13 0.54
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (22 bp):
TATTATTTTTGTATTTTTTAAA
Found at i:5684521 original size:12 final size:12
Alignment explanation
Indices: 5684506--5684665 Score: 76
Period size: 12 Copynumber: 13.3 Consensus size: 12
5684496 CCGCCTTTTG
*
5684506 CTTTGCCTCTGC
1 CTTTGTCTCTGC
* *
5684518 CTTTGGCTCTGT
1 CTTTGTCTCTGC
*
5684530 CTTTTTCTCTGC
1 CTTTGTCTCTGC
* *
5684542 CTCTGTCTCTGT
1 CTTTGTCTCTGC
5684554 CTTT-TGCTCTGC
1 CTTTGT-CTCTGC
* *
5684566 CTCTGTATCTGTC
1 CTTTGTCTCTG-C
* *
5684579 TTTTGT-TCTAC
1 CTTTGTCTCTGC
* *
5684590 CTCTGTCTCTGT
1 CTTTGTCTCTGC
*
5684602 CTTT-TGCTGTGC
1 CTTTGT-CTCTGC
**
5684614 CTCCGTCTCTGC
1 CTTTGTCTCTGC
*
5684626 CTTT-TGGTCTGC
1 CTTTGT-CTCTGC
* *
5684638 CTCTGGCTCTGC
1 CTTTGTCTCTGC
* *
5684650 CTCTATCTCTGC
1 CTTTGTCTCTGC
5684662 CTTT
1 CTTT
5684666 TGCTCTTTCT
Statistics
Matches: 106, Mismatches: 34, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
11 8 0.08
12 91 0.86
13 7 0.07
ACGTcount: A:0.02, C:0.33, G:0.17, T:0.48
Consensus pattern (12 bp):
CTTTGTCTCTGC
Found at i:5684651 original size:24 final size:24
Alignment explanation
Indices: 5684507--5684648 Score: 176
Period size: 24 Copynumber: 5.9 Consensus size: 24
5684497 CGCCTTTTGC
* *
5684507 TTTGCCTCTGCCTTTGGCTCTGTCT
1 TTTG-CTCTGCCTCTGTCTCTGTCT
*
5684532 TTTTCTCTGCCTCTGTCTCTGTCT
1 TTTGCTCTGCCTCTGTCTCTGTCT
*
5684556 TTTGCTCTGCCTCTGTATCTGTCT
1 TTTGCTCTGCCTCTGTCTCTGTCT
* *
5684580 TTTGTTCTACCTCTGTCTCTGTCT
1 TTTGCTCTGCCTCTGTCTCTGTCT
* * *
5684604 TTTGCTGTGCCTCCGTCTCTGCCT
1 TTTGCTCTGCCTCTGTCTCTGTCT
* *
5684628 TTTGGTCTGCCTCTGGCTCTG
1 TTTGCTCTGCCTCTGTCTCTG
5684649 CCTCTATCTC
Statistics
Matches: 100, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
24 97 0.97
25 3 0.03
ACGTcount: A:0.01, C:0.32, G:0.18, T:0.49
Consensus pattern (24 bp):
TTTGCTCTGCCTCTGTCTCTGTCT
Found at i:5685064 original size:18 final size:18
Alignment explanation
Indices: 5685043--5685079 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5685033 ACGGACTCTG
5685043 AGGCTCGGGCTCAGTCTC
1 AGGCTCGGGCTCAGTCTC
* *
5685061 AGGCTCTGTCTCAGTCTC
1 AGGCTCGGGCTCAGTCTC
5685079 A
1 A
5685080 TTATGTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (18 bp):
AGGCTCGGGCTCAGTCTC
Found at i:5688925 original size:27 final size:27
Alignment explanation
Indices: 5688871--5688921 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5688861 TGGGCCCCAC
* *
5688871 CACAACCATTTGCGCCTCTGAGGTAGG
1 CACAACCATTTGCGCCTCAGAGGAAGG
*
5688898 CACAATCATTTGCGCCTCAG-GGAA
1 CACAACCATTTGCGCCTCAGAGGAA
5688922 AGGCTCGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 3 0.14
27 18 0.86
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (27 bp):
CACAACCATTTGCGCCTCAGAGGAAGG
Found at i:5692450 original size:42 final size:42
Alignment explanation
Indices: 5692403--5692485 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
5692393 TCTACAGGGA
5692403 GAGGCATATTGAAATATTAGTAGTCTATTTGTAGTATCATTG
1 GAGGCATATTGAAATATTAGTAGTCTATTTGTAGTATCATTG
* *
5692445 GAGGCATATTGAAATCTTAGTAGTCTGTTTGTAGTATCATT
1 GAGGCATATTGAAATATTAGTAGTCTATTTGTAGTATCATT
5692486 AGATTATTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (42 bp):
GAGGCATATTGAAATATTAGTAGTCTATTTGTAGTATCATTG
Found at i:5693407 original size:82 final size:82
Alignment explanation
Indices: 5693268--5693431 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
5693258 CTGGTGCCCT
*
5693268 ATTTGCAAAGCATCAGCAGAACCCACCCAGTCTTGTTCGCCTACTTCATATTTGAGTTGAATTTG
1 ATTTGCAAAGCATCAGCAGAACCCACCCAGTCTTGTTCGCCTACTTCATATTCGAGTTGAATTTG
5693333 ACAAAAAGGAAGCAAGA
66 ACAAAAAGGAAGCAAGA
5693350 ATTTGCAAAGCATCAGCAGAACCCACCCAGTCTTGTTCGCCTACTTCATATTCGAGTTGAATTTG
1 ATTTGCAAAGCATCAGCAGAACCCACCCAGTCTTGTTCGCCTACTTCATATTCGAGTTGAATTTG
5693415 ACAAAAAGGAAGCAAGA
66 ACAAAAAGGAAGCAAGA
5693432 GACCGAGTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (82 bp):
ATTTGCAAAGCATCAGCAGAACCCACCCAGTCTTGTTCGCCTACTTCATATTCGAGTTGAATTTG
ACAAAAAGGAAGCAAGA
Found at i:5703563 original size:12 final size:12
Alignment explanation
Indices: 5703546--5703572 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5703536 TGGAATTGCA
5703546 AAAAAAAAAAAG
1 AAAAAAAAAAAG
5703558 AAAAAAAAAAAG
1 AAAAAAAAAAAG
5703570 AAA
1 AAA
5703573 GAAGAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:5703566 original size:16 final size:16
Alignment explanation
Indices: 5703545--5703575 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5703535 TTGGAATTGC
5703545 AAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAGAAA
*
5703561 AAAAAAAAGAAAGAA
1 AAAAAAAAAAAAGAA
5703576 GAAGAAGCAA
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:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAA
Found at i:5709292 original size:5 final size:5
Alignment explanation
Indices: 5709282--5709306 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5709272 GTAGAAGTAG
5709282 AGTGA AGTGA AGTGA AGTGA AGTGA
1 AGTGA AGTGA AGTGA AGTGA AGTGA
5709307 TGGGTATCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (5 bp):
AGTGA
Found at i:5709341 original size:29 final size:29
Alignment explanation
Indices: 5709299--5709357 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5709289 TGAAGTGAAG
5709299 TGAAGTGATGGGTATCCGTGGAACGGAAT
1 TGAAGTGATGGGTATCCGTGGAACGGAAT
5709328 TGAAGTGATGGGTATCCGTGGAACGGAAT
1 TGAAGTGATGGGTATCCGTGGAACGGAAT
5709357 T
1 T
5709358 AAATAGGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.37, T:0.25
Consensus pattern (29 bp):
TGAAGTGATGGGTATCCGTGGAACGGAAT
Found at i:5709657 original size:19 final size:17
Alignment explanation
Indices: 5709620--5709653 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
5709610 CATGTGTCTC
5709620 TTTTTTTAAAATATTTA
1 TTTTTTTAAAATATTTA
5709637 TTTTTTTATAAATATTT
1 TTTTTTTA-AAATATTT
5709654 TATTACACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTTAAAATATTTA
Found at i:5709807 original size:27 final size:27
Alignment explanation
Indices: 5709759--5709810 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5709749 AATATAAATG
**
5709759 TTATATGTATTAAACATGTTTTATTTA
1 TTATATGTATTAAACACATTTTATTTA
* *
5709786 TTATATTTATTAAATACATTTTATT
1 TTATATGTATTAAACACATTTTATT
5709811 CAAATAAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (27 bp):
TTATATGTATTAAACACATTTTATTTA
Found at i:5723311 original size:6 final size:6
Alignment explanation
Indices: 5723300--5723325 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5723290 AAATTGTATA
5723300 TTTGTT TTTGTT TTTGTT TTTGTT TT
1 TTTGTT TTTGTT TTTGTT TTTGTT TT
5723326 GACTGAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:5729300 original size:12 final size:12
Alignment explanation
Indices: 5729283--5729318 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5729273 ATAGTCGTAG
5729283 TCATCATAATCA
1 TCATCATAATCA
*
5729295 TCATCATAACCA
1 TCATCATAATCA
*
5729307 TCATCACAATCA
1 TCATCATAATCA
5729319 ATTCCATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.28
Consensus pattern (12 bp):
TCATCATAATCA
Found at i:5731633 original size:16 final size:16
Alignment explanation
Indices: 5731612--5731643 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5731602 TCAAGCCATG
*
5731612 CAAATATATTGTCAGA
1 CAAATATATTGACAGA
5731628 CAAATATATTGACAGA
1 CAAATATATTGACAGA
5731644 TTTTGCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (16 bp):
CAAATATATTGACAGA
Found at i:5736233 original size:64 final size:64
Alignment explanation
Indices: 5736161--5736284 Score: 203
Period size: 64 Copynumber: 1.9 Consensus size: 64
5736151 TATCTGTTTC
* ** *
5736161 GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTTGGGATGAGTGGAGCTATGTTGCTCCTGG
1 GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGTTGCTCCTGG
*
5736225 GAATGATGAAAAGGTTTAAATGTTTCAATATTGTTGGGGATGAGAAGAACTATGTTGCTC
1 GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGTTGCTC
5736285 TGACTCTTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (64 bp):
GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGTTGCTCCTGG
Found at i:5738376 original size:25 final size:24
Alignment explanation
Indices: 5738348--5738395 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
5738338 CAAAAAAAAA
* *
5738348 TTGTCTAAGTCACTTCGTTTTTTTT
1 TTGTCCAACTCACTTC-TTTTTTTT
*
5738373 TTGTCCAACTTACTTCTTTTTTT
1 TTGTCCAACTCACTTCTTTTTTT
5738396 CTTTTTGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.12, C:0.19, G:0.08, T:0.60
Consensus pattern (24 bp):
TTGTCCAACTCACTTCTTTTTTTT
Found at i:5742709 original size:30 final size:30
Alignment explanation
Indices: 5742673--5742733 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
5742663 TAGGTTGTCA
5742673 ACAGTAAAAACTAGGTGATGTACAACTTTG
1 ACAGTAAAAACTAGGTGATGTACAACTTTG
5742703 ACAGTAAAAACTAGGTGATGTACAACTTTG
1 ACAGTAAAAACTAGGTGATGTACAACTTTG
5742733 A
1 A
5742734 GAAACTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (30 bp):
ACAGTAAAAACTAGGTGATGTACAACTTTG
Found at i:5744297 original size:18 final size:19
Alignment explanation
Indices: 5744274--5744318 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5744264 AATGCCTGGA
*
5744274 TTTTCTTTTCTTTTCT-CT
1 TTTTCTTTCCTTTTCTACT
*
5744292 TTTTCTATCCTTTTCTACT
1 TTTTCTTTCCTTTTCTACT
5744311 TTCTTCTT
1 TT-TTCTT
5744319 CTGTTTGGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 14 0.64
19 4 0.18
20 4 0.18
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCTTTCCTTTTCTACT
Found at i:5745120 original size:10 final size:10
Alignment explanation
Indices: 5745105--5745130 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5745095 AATATACAAA
5745105 ATATATACAT
1 ATATATACAT
5745115 ATATATACAT
1 ATATATACAT
5745125 ATATAT
1 ATATAT
5745131 TTTGCGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATACAT
Found at i:5752525 original size:17 final size:17
Alignment explanation
Indices: 5752503--5752536 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5752493 ATTGAAATGC
5752503 CCTTTTGCTCAAGTTTG
1 CCTTTTGCTCAAGTTTG
5752520 CCTTTTGCTCAAGTTTG
1 CCTTTTGCTCAAGTTTG
5752537 ACTTCGCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (17 bp):
CCTTTTGCTCAAGTTTG
Found at i:5776582 original size:35 final size:35
Alignment explanation
Indices: 5776543--5776614 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
5776533 ATATTTTATC
5776543 TCACTATTACCATTACATTTAAAT-TCAAATACATA
1 TCACTATTACCATTACATTTAAATCT-AAATACATA
*
5776578 TCACTATTATCATTACATTTAAATCTAAATACATA
1 TCACTATTACCATTACATTTAAATCTAAATACATA
5776613 TC
1 TC
5776615 TCACTGTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (35 bp):
TCACTATTACCATTACATTTAAATCTAAATACATA
Found at i:5778154 original size:25 final size:26
Alignment explanation
Indices: 5778087--5778154 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 26
5778077 ATTTTTCTCG
5778087 AAAAATTATAAGT-AAAATCATAATCAA
1 AAAAATTATAA-TCAAAAT-ATAATCAA
* * *
5778114 AATAATTACAACCAAAAT-TAAT-ATA
1 AAAAATTATAATCAAAATATAATCA-A
5778139 AAAAATTATAATCAAA
1 AAAAATTATAATCAAA
5778155 TTGATAATTG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
24 1 0.03
25 18 0.55
27 14 0.42
ACGTcount: A:0.63, C:0.09, G:0.01, T:0.26
Consensus pattern (26 bp):
AAAAATTATAATCAAAATATAATCAA
Found at i:5780002 original size:16 final size:16
Alignment explanation
Indices: 5779978--5780011 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5779968 TATAAAATTT
*
5779978 TATTGTTTTCATTTTA
1 TATTATTTTCATTTTA
*
5779994 TATTATTTTTATTTTA
1 TATTATTTTCATTTTA
5780010 TA
1 TA
5780012 GTGACTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (16 bp):
TATTATTTTCATTTTA
Found at i:5780647 original size:18 final size:19
Alignment explanation
Indices: 5780611--5780647 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5780601 ATTTATTAAA
5780611 GAATATTTTATATAATTGAC
1 GAATATTTTATAT-ATTGAC
5780631 GAATATTTTATAT-TTGA
1 GAATATTTTATATATTGA
5780648 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49
Consensus pattern (19 bp):
GAATATTTTATATATTGAC
Found at i:5783743 original size:16 final size:15
Alignment explanation
Indices: 5783718--5783765 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
5783708 CTATTTTAAG
5783718 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
5783733 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
5783750 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
5783765 T
1 T
5783766 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:5789816 original size:38 final size:39
Alignment explanation
Indices: 5789732--5789866 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
5789722 ACCAATATGG
*
5789732 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
5789771 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
5789809 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
5789850 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5789867 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:5791456 original size:5 final size:5
Alignment explanation
Indices: 5791438--5791473 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
5791428 TTTCTTTTAT
5791438 ATATA ATAATA ATATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA
5791474 CTTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Done.