Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 17 of 125
Found at i:2926377 original size:23 final size:22
Alignment explanation
Indices: 2926329--2926378 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
2926319 ATAGTTATTA
2926329 TTTTTCTTCTTTCTTTTTTTGGT
1 TTTTTCTTCTTTCTTTTTTT-GT
* *
2926352 TTTTTTTTCCTTTCTTTTTCT-T
1 TTTTTCTT-CTTTCTTTTTTTGT
2926374 TTTTT
1 TTTTT
2926379 AGAGATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.25
23 7 0.29
24 11 0.46
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (22 bp):
TTTTTCTTCTTTCTTTTTTTGT
Found at i:2927408 original size:3 final size:3
Alignment explanation
Indices: 2927402--2927453 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
2927392 AAAAAAAGTA
*
2927402 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2927450 AAT A
1 AAT A
2927454 CCATCAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2928322 original size:22 final size:22
Alignment explanation
Indices: 2928281--2928322 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2928271 AAAAAAAAAA
*
2928281 AAAAAACCACCACAAGCCTACC
1 AAAAAACCACCACAAACCTACC
2928303 AAAAAACCACC-CAAAACCTA
1 AAAAAACCACCAC-AAACCTA
2928323 TCATAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.55, C:0.38, G:0.02, T:0.05
Consensus pattern (22 bp):
AAAAAACCACCACAAACCTACC
Found at i:2929880 original size:23 final size:21
Alignment explanation
Indices: 2929831--2929904 Score: 60
Period size: 23 Copynumber: 3.4 Consensus size: 21
2929821 CCTTGAAACC
2929831 CTTAAACCAAAACTTTAAAAT
1 CTTAAACCAAAACTTTAAAAT
*
2929852 CATAAACCCTAAAACTTTAAAA-
1 CTTAAA-CC-AAAACTTTAAAAT
* **
2929874 CTTTAAAGTCAAAACCCTAAAAT
1 C-TTAAA-CCAAAACTTTAAAAT
*
2929897 CCTAAACC
1 CTTAAACC
2929905 TTGAAACCTC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
21 6 0.15
22 17 0.41
23 18 0.44
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.24
Consensus pattern (21 bp):
CTTAAACCAAAACTTTAAAAT
Found at i:2929927 original size:16 final size:16
Alignment explanation
Indices: 2929908--2929941 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2929898 CTAAACCTTG
*
2929908 AAACCTCGAAACCCCA
1 AAACCTCAAAACCCCA
*
2929924 AAACCTCAAAACCTCA
1 AAACCTCAAAACCCCA
2929940 AA
1 AA
2929942 CCAAAATCCT
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:0.50, C:0.38, G:0.03, T:0.09
Consensus pattern (16 bp):
AAACCTCAAAACCCCA
Found at i:2929947 original size:21 final size:20
Alignment explanation
Indices: 2929921--2929961 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2929911 CCTCGAAACC
2929921 CCAAAA-CCTCAAAACCTCAAA
1 CCAAAATCCT-AAAACC-CAAA
2929942 CCAAAATCCTAAAACCCAAA
1 CCAAAATCCTAAAACCCAAA
2929962 GCCTTAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 12 0.63
22 3 0.16
ACGTcount: A:0.54, C:0.37, G:0.00, T:0.10
Consensus pattern (20 bp):
CCAAAATCCTAAAACCCAAA
Found at i:2931500 original size:17 final size:18
Alignment explanation
Indices: 2931466--2931501 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2931456 TTCAAAAATT
*
2931466 ATAAAAATCTTTTTTTTC
1 ATAAAAATCATTTTTTTC
2931484 ATAAAAAT-ATTTTTTTC
1 ATAAAAATCATTTTTTTC
2931501 A
1 A
2931502 ATTCATTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAAAAATCATTTTTTTC
Found at i:2931642 original size:2 final size:2
Alignment explanation
Indices: 2931637--2931661 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2931627 TATATATATA
2931637 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2931662 ATATCATTTG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2948935 original size:23 final size:24
Alignment explanation
Indices: 2948890--2948967 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 24
2948880 TTAATGTTAG
* *
2948890 ATAATATTAATA-TTAATTAAATA
1 ATAATATTAATACTTAGTTTAATA
2948913 ATAATATTAA-ACTTAGTTTAATA
1 ATAATATTAATACTTAGTTTAATA
* *
2948936 TTAA-ATTAATTACATAGTATTAA-A
1 ATAATATTAA-TACTTAGT-TTAATA
2948960 ATAATATT
1 ATAATATT
2948968 CAAAATAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
22 6 0.13
23 22 0.49
24 10 0.22
25 7 0.16
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (24 bp):
ATAATATTAATACTTAGTTTAATA
Found at i:2948988 original size:31 final size:30
Alignment explanation
Indices: 2948931--2948995 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
2948921 AAACTTAGTT
* *
2948931 TAATATTAAATTAATTACATAGTATTAAAA
1 TAATATTAAAATAATTACATAATATTAAAA
*
2948961 TAATATTCAAAATAATTA-ATTAATATTAAAT
1 TAATATT-AAAATAATTACA-TAATATTAAAA
2948992 TAAT
1 TAAT
2948996 TAAATCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (30 bp):
TAATATTAAAATAATTACATAATATTAAAA
Found at i:2949025 original size:18 final size:20
Alignment explanation
Indices: 2949002--2949045 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
2948992 TAATTAAATC
2949002 ATATTA-AATTTT-TATTTA
1 ATATTATAATTTTATATTTA
2949020 ATATTATAATTTTAATATTTA
1 ATATTATAATTTT-ATATTTA
2949041 ATATT
1 ATATT
2949046 CTGAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
21 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTATAATTTTATATTTA
Found at i:2949055 original size:21 final size:20
Alignment explanation
Indices: 2949014--2949617 Score: 192
Period size: 21 Copynumber: 28.2 Consensus size: 20
2949004 ATTAAATTTT
*
2949014 TATTTAATATTATAATTTTAA
1 TATTTAATATTATAA-ATTAA
*
2949035 TATTTAATATTCTGAAATTAA
1 TATTTAATATTAT-AAATTAA
* *
2949056 CATTCAATATTATTAAATTAA
1 TATTTAATATTA-TAAATTAA
** *
2949077 TATCCAATATTACTAAATTAT
1 TATTTAATATTA-TAAATTAA
2949098 TATTTCAA-ATTATTAAATTAAA
1 TATTT-AATATTA-TAAATT-AA
2949120 TAATATTAA-ATTAATAAGAAATTAA
1 T-AT-TTAATATT-AT---AAATTAA
**
2949145 TATTTGTTATTAAATTAATACTTAA
1 TATTTAATATT--A-TAA-A-TTAA
* * *
2949170 TTATACTAAAAATATTAAATTAA
1 -TAT-TTAATATTA-TAAATTAA
*
2949193 TATTTAATA--ATAAATCAA
1 TATTTAATATTATAAATTAA
*
2949211 TATTTAATATTTTTAAAATT-A
1 TATTTAATA-TTAT-AAATTAA
*
2949232 TATGTAATCATATTTATTAAATTAA
1 TAT-T--TAATA-TTA-TAAATTAA
* *
2949257 TTATTTAATAATATTAAATAAA
1 -TATTTAATATTA-TAAATTAA
* *
2949279 TATTTTTTAAAATT-CAAA-TAA
1 TA---TTTAATATTATAAATTAA
* * *
2949300 TATTGAATAGTATTAAAGTAA
1 TATTTAATATTA-TAAATTAA
*
2949321 T-TTTAATAATATTCAAA-TAA
1 TATTTAATATTA-T-AAATTAA
* *
2949341 TATTGAATAATATCAAAATTGAA
1 TATTTAATATTAT--AAATT-AA
* * *
2949364 -AATCAATA-T-TAAAGTAA
1 TATTTAATATTATAAATTAA
*
2949381 TATTTAATATTATTCAATTAA
1 TATTTAATATTA-TAAATTAA
* *
2949402 TATTTAAGATTATTAAATGAA
1 TATTTAATATTA-TAAATTAA
*
2949423 TATTTTATATTATTAAATTAA
1 TATTTAATATTA-TAAATTAA
*
2949444 TATTTAATCCTATTTATTAAATTATT
1 TATTTAA---TA-TTA-TAAATTA-A
*
2949470 TATTTAATATTAGTCAATTAA
1 TATTTAATATTA-TAAATTAA
**
2949491 TATGAAATATTATTAAATTAA
1 TATTTAATATTA-TAAATTAA
* *
2949512 TATTTAATATAATTAAACTAA
1 TATTTAATATTA-TAAATTAA
* * **
2949533 TATTTAAGATAAT-TCTTAA
1 TATTTAATATTATAAATTAA
**
2949552 TATTTAATATTATTAAA-CCA
1 TATTTAATATTA-TAAATTAA
* *
2949572 TAGTTAATATTGCTAAATTAA
1 TATTTAATATT-ATAAATTAA
* *
2949593 TATTTACTAATATTAAATTAA
1 TATTTAATATTA-TAAATTAA
2949614 TATT
1 TATT
2949618 AGTATTTAAT
Statistics
Matches: 445, Mismatches: 86, Indels: 104
0.70 0.14 0.16
Matches are distributed among these distances:
17 2 0.00
18 32 0.07
19 15 0.03
20 36 0.08
21 211 0.47
22 44 0.10
23 24 0.05
24 31 0.07
25 28 0.06
26 19 0.04
27 3 0.01
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (20 bp):
TATTTAATATTATAAATTAA
Found at i:2949418 original size:42 final size:42
Alignment explanation
Indices: 2949370--2949617 Score: 223
Period size: 42 Copynumber: 5.9 Consensus size: 42
2949360 TGAAAATCAA
* *
2949370 TATTAAAGTAATATTTAATATTATTCAATTAATATTTAAGAT
1 TATTAAATTAATATTTAATATTATTAAATTAATATTTAAGAT
* * *
2949412 TATTAAATGAATATTTTATATTATTAAATTAATATTTAATCCTATT
1 TATTAAATTAATATTTAATATTATTAAATTAATATTTAA---GA-T
* * * ** *
2949458 TATTAAATTATTTATTTAATATTAGTCAATTAATATGAAATAT
1 TATTAAATTA-ATATTTAATATTATTAAATTAATATTTAAGAT
* *
2949501 TATTAAATTAATATTTAATATAATTAAACTAATATTTAAGAT
1 TATTAAATTAATATTTAATATTATTAAATTAATATTTAAGAT
* * ** * *
2949543 AATT--CTTAATATTTAATATTATTAAA-CCATAGTTAATAT
1 TATTAAATTAATATTTAATATTATTAAATTAATATTTAAGAT
** * *
2949582 TGCTAAATTAATATTTACTAATATTAAATTAATATT
1 TATTAAATTAATATTTAATATTATTAAATTAATATT
2949618 AGTATTTAAT
Statistics
Matches: 162, Mismatches: 36, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
39 10 0.06
40 20 0.12
41 19 0.12
42 66 0.41
43 11 0.07
44 2 0.01
45 1 0.01
46 10 0.06
47 23 0.14
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (42 bp):
TATTAAATTAATATTTAATATTATTAAATTAATATTTAAGAT
Found at i:2949623 original size:27 final size:27
Alignment explanation
Indices: 2949588--2949658 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
2949578 ATATTGCTAA
*
2949588 ATTAATATTTACTAATATTAAATTAAT
1 ATTAATATTTAATAATATTAAATTAAT
* *
2949615 ATTAGTATTTAATATTATTAAATTAAT
1 ATTAATATTTAATAATATTAAATTAAT
* *
2949642 TTTAATTAATTAATAAT
1 ATTAA-TATTTAATAAT
2949659 TAATTATTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 27 0.75
28 9 0.25
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
ATTAATATTTAATAATATTAAATTAAT
Found at i:2949653 original size:19 final size:19
Alignment explanation
Indices: 2949608--2949673 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 19
2949598 ACTAATATTA
*
2949608 AATTAATATTAGTATTTAATAT
1 AATTAA-ATTAAT-TTTAAT-T
*
2949630 TATTAAATTAATTTTAATT
1 AATTAAATTAATTTTAATT
2949649 AATTAATAATTAATTATTATATT
1 AATT-A-AATTAATT-TTA-ATT
2949672 AA
1 AA
2949674 CTTATTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.11
20 7 0.19
21 13 0.35
22 8 0.22
23 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
AATTAAATTAATTTTAATT
Found at i:2949665 original size:33 final size:33
Alignment explanation
Indices: 2949628--2949690 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
2949618 AGTATTTAAT
2949628 ATTATTAAATTAA-TT-TTAATTAATTAATAATTA
1 ATTATTAAATTAACTTATT-ATTAA-TAATAATTA
*
2949661 ATTATTATATTAACTTATTATTAATAATAA
1 ATTATTAAATTAACTTATTATTAATAATAA
2949691 AATTTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 18 0.67
34 7 0.26
35 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (33 bp):
ATTATTAAATTAACTTATTATTAATAATAATTA
Found at i:2949685 original size:27 final size:27
Alignment explanation
Indices: 2949603--2949684 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
2949593 TATTTACTAA
2949603 TATTAAATTAA-TATTAGTATTTAA-TAT
1 TATTAAATTAATTATTA-TA-TTAATTAT
2949630 TATTAAATTAATT-TTA-ATTAATTA-
1 TATTAAATTAATTATTATATTAATTAT
2949654 -A-T-AATTAATTATTATATTAACTTAT
1 TATTAAATTAATTATTATATTAA-TTAT
2949679 TATTAA
1 TATTAA
2949685 TAATAAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
21 8 0.17
22 4 0.09
23 6 0.13
24 7 0.15
25 3 0.07
26 1 0.02
27 15 0.33
28 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (27 bp):
TATTAAATTAATTATTATATTAATTAT
Found at i:2950584 original size:2 final size:2
Alignment explanation
Indices: 2950579--2950614 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2950569 TCATTGGATC
2950579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2950615 GAAATGGCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2955981 original size:11 final size:12
Alignment explanation
Indices: 2955958--2955988 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2955948 TTTTTTTAAT
2955958 AATTT-AATAAA
1 AATTTCAATAAA
2955969 AATTTCAATAAA
1 AATTTCAATAAA
2955981 AATTTCAA
1 AATTTCAA
2955989 ATCATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
AATTTCAATAAA
Found at i:2963583 original size:42 final size:42
Alignment explanation
Indices: 2963521--2963644 Score: 153
Period size: 42 Copynumber: 3.0 Consensus size: 42
2963511 CATGATCGTC
* *
2963521 AAGGAGC-ATTTACTTGTCAAAAGTTGTGGTGCCTTTATTTA
1 AAGGAGCAATTTACTTTTCAAAAGTTATGGTGCCTTTATTTA
* * * *
2963562 AATGAGCAATTTACTTTTCAAAAGTTACGGTGCCTTTGTTTG
1 AAGGAGCAATTTACTTTTCAAAAGTTATGGTGCCTTTATTTA
* * *
2963604 GAGGAGCAATTTAC-TTTCAAAAGTTATAGTGCCTCTATTTA
1 AAGGAGCAATTTACTTTTCAAAAGTTATGGTGCCTTTATTTA
2963645 GAGAAGTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
41 28 0.41
42 41 0.59
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (42 bp):
AAGGAGCAATTTACTTTTCAAAAGTTATGGTGCCTTTATTTA
Found at i:2963721 original size:41 final size:41
Alignment explanation
Indices: 2963656--2963945 Score: 321
Period size: 41 Copynumber: 7.0 Consensus size: 41
2963646 AGAAGTTTTG
* * ** * **
2963656 TTTATTTTTTAAAGTCATCAAGCCTCTAATTAGAGGAGCTT
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
*
2963697 TTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
* *
2963738 TTTATTTTTCTAAAAGTCGTTGAGACTCTGATTAGAGGAACCA
1 TTTATTTTTC--AAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
* * *
2963781 TTTATTTTTTAAAGTCGTTGAGCCTCAGATTAAAGGAGCCA
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
* * *
2963822 TTTATTTTTTCAAAGTCGTTAAACCTCT-ATTTAAAGGAGCCA
1 TTTA-TTTTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCCA
* *
2963864 TTTATTTTTTCAAAAGTCGTTAAGCCTCTGATTAGAGGAACCA
1 TTTA-TTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
* * * *
2963907 TTTATTTTTTAAAGTCATTGAACCTCTGTTTAGAGGAGC
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC
2963946 TTTGATCAAA
Statistics
Matches: 214, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
41 99 0.46
42 47 0.22
43 67 0.31
44 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (41 bp):
TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
Found at i:2963723 original size:84 final size:84
Alignment explanation
Indices: 2963656--2963924 Score: 232
Period size: 84 Copynumber: 3.2 Consensus size: 84
2963646 AGAAGTTTTG
* * **
2963656 TTTATTTTT-T-AAAGTCATCAAGCCTCTAATTAGAGGAGCTTTTTATTTTTCAAAGTCGTTGAG
1 TTTATTTTTCTAAAAGTCATCAAGACTCTAATTAGAGGAACCATTTATTTTTCAAAGTCGTTGAG
* *
2963719 CCTCTGTTTAGAGGAGCCA
66 CCTCTATTTAGAGAAGCCA
* ** * *
2963738 TTTATTTTTCTAAAAGTCGTTGAGACTCTGATTAGAGGAACCATTTATTTTTTAAAGTCGTTGAG
1 TTTATTTTTCTAAAAGTCATCAAGACTCTAATTAGAGGAACCATTTATTTTTCAAAGTCGTTGAG
* * *
2963803 CCTC-AGATTAAAGGAGCCA
66 CCTCTA-TTTAGAGAAGCCA
* * * * * *
2963822 TTTATTTTT-TCAAAGTCGTTAA-ACCTCTATTTAAAGGAGCCATTTATTTTTTCAAAAGTCGTT
1 TTTATTTTTCTAAAAGTCATCAAGA-CTCTAATTAGAGGAACCATTTA-TTTTTC-AAAGTCGTT
*
2963885 AAGCCTCTGA-TTAGAGGAA-CCA
63 GAGCCTCT-ATTTAGA-GAAGCCA
2963907 TTTATTTTT-T-AAAGTCAT
1 TTTATTTTTCTAAAAGTCAT
2963925 TGAACCTCTG
Statistics
Matches: 155, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
82 10 0.06
83 30 0.19
84 80 0.52
85 32 0.21
86 2 0.01
87 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (84 bp):
TTTATTTTTCTAAAAGTCATCAAGACTCTAATTAGAGGAACCATTTATTTTTCAAAGTCGTTGAG
CCTCTATTTAGAGAAGCCA
Found at i:2963944 original size:126 final size:125
Alignment explanation
Indices: 2963656--2963945 Score: 404
Period size: 126 Copynumber: 2.3 Consensus size: 125
2963646 AGAAGTTTTG
* * ** * *
2963656 TTTATTTTTTAAAGTCA-TCAAGCCTCTAATTAGAGGAGCTTTTTATTTTTCAAAGTCGTTGAGC
1 TTTATTTTTTAAAGTCATTGAA-CCTCTGATTAGAGGAGCCATTTATTTTTCAAAGTCGTTAAAC
* * *
2963720 CTCTGTTTAGAGGAGCCATTTATTTTTCTAAAAGTCGTTGAGACTCTGATTAGAGGAACCA
65 CTCTATTTAAAGGAGCCATTTATTTTTCTAAAAGTCGTTAAGACTCTGATTAGAGGAACCA
* * * *
2963781 TTTATTTTTTAAAGTCGTTGAGCCTCAGATTAAAGGAGCCATTTATTTTTTCAAAGTCGTTAAAC
1 TTTATTTTTTAAAGTCATTGAACCTCTGATTAGAGGAGCCATTTA-TTTTTCAAAGTCGTTAAAC
*
2963846 CTCTATTTAAAGGAGCCATTTATTTTT-TCAAAAGTCGTTAAGCCTCTGATTAGAGGAACCA
65 CTCTATTTAAAGGAGCCATTTATTTTTCT-AAAAGTCGTTAAGACTCTGATTAGAGGAACCA
*
2963907 TTTATTTTTTAAAGTCATTGAACCTCTGTTTAGAGGAGC
1 TTTATTTTTTAAAGTCATTGAACCTCTGATTAGAGGAGC
2963946 TTTGATCAAA
Statistics
Matches: 143, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
125 35 0.24
126 108 0.76
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (125 bp):
TTTATTTTTTAAAGTCATTGAACCTCTGATTAGAGGAGCCATTTATTTTTCAAAGTCGTTAAACC
TCTATTTAAAGGAGCCATTTATTTTTCTAAAAGTCGTTAAGACTCTGATTAGAGGAACCA
Found at i:2964170 original size:6 final size:6
Alignment explanation
Indices: 2964144--2964198 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
2964134 AAATGGCCCA
* * *
2964144 TTTTAT TTTTAG TTTTAT TATTT-T TATTAT TTATTAT TTATAT TTTT-T
1 TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT TT-TTAT TTTTAT TTTTAT
2964192 TTTTAT T
1 TTTTAT T
2964199 AGTTATCCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
5 7 0.18
6 23 0.59
7 9 0.23
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:2964187 original size:13 final size:13
Alignment explanation
Indices: 2964145--2964286 Score: 54
Period size: 14 Copynumber: 10.4 Consensus size: 13
2964135 AATGGCCCAT
*
2964145 TTTATTTTTAGTTT
1 TTTATTTTTA-TTA
2964159 TATTATTTTTATTA
1 T-TTATTTTTATTA
2964173 TTTATTATTTA-TA
1 TTTATT-TTTATTA
*
2964186 TTTTTTTTTTATTA
1 -TTTATTTTTATTA
* ** *
2964200 GTTATCCATTAATA
1 TTTAT-TTTTATTA
*
2964214 TTATTTTTTTATTA
1 TT-TATTTTTATTA
* * *
2964228 TTTATCTATTAATG
1 TTTAT-TTTTATTA
* *
2964242 TATATTTTTAATA
1 TTTATTTTTATTA
* *
2964255 CTTATCTATTATTA
1 TTTAT-TTTTATTA
*
2964269 -TTATTATTTTTTA
1 TTTATT-TTTATTA
2964282 TTTAT
1 TTTAT
2964287 CTAGTAATTT
Statistics
Matches: 93, Mismatches: 25, Indels: 20
0.67 0.18 0.14
Matches are distributed among these distances:
12 1 0.01
13 34 0.37
14 47 0.51
15 11 0.12
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (13 bp):
TTTATTTTTATTA
Found at i:2964191 original size:24 final size:24
Alignment explanation
Indices: 2964146--2964198 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2964136 ATGGCCCATT
2964146 TTATTTTTAGTTTTATTATTTTTA
1 TTATTTTTAGTTTTATTATTTTTA
*
2964170 TTATTTATTA-TTTATATT-TTTTTT
1 TTATTT-TTAGTTT-TATTATTTTTA
2964194 TTATT
1 TTATT
2964199 AGTTATCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (24 bp):
TTATTTTTAGTTTTATTATTTTTA
Found at i:2964195 original size:28 final size:28
Alignment explanation
Indices: 2964158--2964287 Score: 104
Period size: 27 Copynumber: 4.7 Consensus size: 28
2964148 ATTTTTAGTT
* * *
2964158 TTATTATTTTTATTATTTAT-TATTTATA
1 TTATT-TTTTTATTAGTTATCCATTAATA
*
2964186 TTTTTTTTTTATTAGTTATCCATTAATA
1 TTATTTTTTTATTAGTTATCCATTAATA
* *
2964214 TTATTTTTTTATTATTTATCTATTAAT-
1 TTATTTTTTTATTAGTTATCCATTAATA
* * * * * *
2964241 GTATATTTTTAATACTTATCTATTATTA
1 TTATTTTTTTATTAGTTATCCATTAATA
* *
2964269 TTATTATTTT-TTATTTATC
1 TTATTTTTTTATTAGTTATC
2964288 TAGTAATTTT
Statistics
Matches: 83, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
27 42 0.51
28 41 0.49
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TTATTTTTTTATTAGTTATCCATTAATA
Found at i:2964306 original size:58 final size:55
Alignment explanation
Indices: 2964191--2964294 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 55
2964181 TTATATTTTT
* * * *
2964191 TTTTTATTAGTTATCCATTAATATTATTTTTTTATTATTTATCTATTAATGTATA
1 TTTTTAATACTTATCCATTAATATTATTATTTTATTATTTATCTAGTAATGTATA
* *
2964246 TTTTTAATACTTATCTATTATTATTATTATTTT-TTATTTATCTAGTAAT
1 TTTTTAATACTTATCCATTAATATTATTATTTTATTATTTATCTAGTAAT
2964295 TTTCTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 15 0.35
55 28 0.65
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (55 bp):
TTTTTAATACTTATCCATTAATATTATTATTTTATTATTTATCTAGTAATGTATA
Found at i:2965187 original size:3 final size:3
Alignment explanation
Indices: 2965181--2965251 Score: 65
Period size: 3 Copynumber: 23.0 Consensus size: 3
2965171 TTTTCCTTAT
* *
2965181 TTA TTA TTA TTA TT- TCTT TTA TTA TTA TTA TTTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
2965227 TTA TT- TCA TTA TTA TGTA TTGA TTA
1 TTA TTA TTA TTA TTA T-TA TT-A TTA
2965252 GATTAAAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
2 2 0.04
3 45 0.79
4 10 0.18
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2965202 original size:22 final size:22
Alignment explanation
Indices: 2965182--2965231 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
2965172 TTTCCTTATT
2965182 TATTATTA-TTATT-TCTTTTAT
1 TATTATTATTTATTAT-TTTTAT
2965203 TATTATTATTTATTATTTTTAT
1 TATTATTATTTATTATTTTTAT
2965225 TATTATT
1 TATTATT
2965232 TCATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.30
22 18 0.67
23 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTATTATTTATTATTTTTAT
Found at i:2965203 original size:18 final size:18
Alignment explanation
Indices: 2965180--2965246 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
2965170 TTTTTCCTTA
2965180 TTTATTATTATTATTTCT
1 TTTATTATTATTATTTCT
*
2965198 TTTATTATTATTATTTAT
1 TTTATTATTATTATTTCT
*
2965216 TATTTTTATTATTATTTC-
1 T-TTATTATTATTATTTCT
*
2965234 ATTATTATGTATT
1 TTTATTAT-TATT
2965247 GATTAGATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 6 0.14
18 22 0.52
19 14 0.33
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (18 bp):
TTTATTATTATTATTTCT
Found at i:2965225 original size:34 final size:34
Alignment explanation
Indices: 2965181--2965251 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
2965171 TTTTCCTTAT
* * *
2965181 TTATTATTATTATTTCTTTTATTATTAT-TATTTA
1 TTATTATTATTA-TTATTTCATTATTATGTATTGA
*
2965215 TTATTTTTATTATTATTTCATTATTATGTATTGA
1 TTATTATTATTATTATTTCATTATTATGTATTGA
2965249 TTA
1 TTA
2965252 GATTAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 13 0.41
34 19 0.59
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (34 bp):
TTATTATTATTATTATTTCATTATTATGTATTGA
Found at i:2965251 original size:14 final size:14
Alignment explanation
Indices: 2965177--2965246 Score: 73
Period size: 13 Copynumber: 5.4 Consensus size: 14
2965167 TTTTTTTTCC
2965177 TTATTT-ATTATTA
1 TTATTTCATTATTA
2965190 TTATTTC-TT-TTA
1 TTATTTCATTATTA
2965202 TTA-TT-ATTATTTA
1 TTATTTCATTA-TTA
2965215 TTATTT--TTATTA
1 TTATTTCATTATTA
2965227 TTATTTCATTATTA
1 TTATTTCATTATTA
2965241 TGTATT
1 T-TATT
2965247 GATTAGATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
11 4 0.08
12 15 0.31
13 17 0.35
14 9 0.18
15 4 0.08
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (14 bp):
TTATTTCATTATTA
Found at i:2965284 original size:5 final size:5
Alignment explanation
Indices: 2965274--2965312 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
2965264 TTAGTAATCC
2965274 TTATT TTATT TTATTT TTATT TTATT TTATT TTACTT TT
1 TTATT TTATT TTA-TT TTATT TTATT TTATT TTA-TT TT
2965313 TGATTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 23 0.72
6 9 0.28
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:2965293 original size:11 final size:11
Alignment explanation
Indices: 2965277--2965319 Score: 61
Period size: 10 Copynumber: 3.8 Consensus size: 11
2965267 GTAATCCTTA
2965277 TTTTATTTTAT
1 TTTTATTTTAT
2965288 TTTTATTTTA-
1 TTTTATTTTAT
2965298 TTTTATTTTACT
1 TTTTATTTTA-T
2965310 TTTTGATTTT
1 TTTT-ATTTT
2965320 CTTTAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.34
11 10 0.34
12 4 0.14
13 5 0.17
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:2965312 original size:16 final size:16
Alignment explanation
Indices: 2965274--2965306 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2965264 TTAGTAATCC
2965274 TTATTTTATTTTATTT
1 TTATTTTATTTTATTT
2965290 TTATTTTATTTTATTT
1 TTATTTTATTTTATTT
2965306 T
1 T
2965307 ACTTTTTGAT
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:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTATTTTATTTTATTT
Found at i:2965407 original size:59 final size:58
Alignment explanation
Indices: 2965332--2965495 Score: 231
Period size: 59 Copynumber: 2.8 Consensus size: 58
2965322 TTAAATAAAA
* *
2965332 TTCTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTT
1 TTCT-AAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTGAAAATAAG-TT
* * * *
2965392 TTCTAAAAAATATTTTTGAGAAAAATTTGAAAGCATTAATTTTCCTTGAAAATAAGTT
1 TTCTAAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTGAAAATAAGTT
* *
2965450 TTCTGAAAAATA-TTTTGAGAAAAAATTAAAAGTATCAATTTTTCTT
1 TTCTAAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTT
2965496 ATACAAAAGC
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
57 29 0.31
58 13 0.14
59 47 0.51
60 4 0.04
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (58 bp):
TTCTAAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTGAAAATAAGTT
Found at i:2968125 original size:21 final size:21
Alignment explanation
Indices: 2968101--2968141 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2968091 TTTTTATATT
*
2968101 TTTTATTGTTATTTTTTATCC
1 TTTTATTGTTATTATTTATCC
*
2968122 TTTTATTTTTATTATTTATC
1 TTTTATTGTTATTATTTATC
2968142 TATATTATTA
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:0.17, C:0.07, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTATTGTTATTATTTATCC
Found at i:2969114 original size:34 final size:34
Alignment explanation
Indices: 2969076--2969193 Score: 91
Period size: 34 Copynumber: 3.3 Consensus size: 34
2969066 TTTATCAATG
2969076 TAATTTTAATTGGTAAATTTTTGTTTATTTAATT
1 TAATTTTAATTGGTAAATTTTTGTTTATTTAATT
* * *
2969110 TAATTTTCATT--T-TATTTGTGTGAATTTATTTATTT
1 TAATTTTAATTGGTAAATTT-T-TG--TTTATTTAATT
*
2969145 TAACTTATTTTAATTGGTAAATTTTTGTTTACTTAATTT
1 T-A---ATTTTAATTGGTAAATTTTTGTTTATTTAA-TT
2969184 TAA-TTTAATT
1 TAATTTTAATT
2969194 TTATTTGTGT
Statistics
Matches: 65, Mismatches: 7, Indels: 24
0.68 0.07 0.25
Matches are distributed among these distances:
31 4 0.06
32 2 0.03
33 2 0.03
34 17 0.26
35 12 0.18
36 1 0.02
38 8 0.12
39 11 0.17
40 2 0.03
41 2 0.03
42 4 0.06
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (34 bp):
TAATTTTAATTGGTAAATTTTTGTTTATTTAATT
Found at i:2969158 original size:73 final size:74
Alignment explanation
Indices: 2969078--2969221 Score: 238
Period size: 73 Copynumber: 2.0 Consensus size: 74
2969068 TATCAATGTA
* * *
2969078 ATTTTAATTGGTAAATTTTTGTTTATTTAA-TTTAATTTTCATTTTATTTGTGTGAA-TTTATTT
1 ATTTTAATTGGTAAATTTTTGTTTACTTAATTTTAA-TTTAATTTTATTTGTGTAAATTTTATTT
2969141 ATTTTAACTT
65 ATTTTAACTT
2969151 ATTTTAATTGGTAAATTTTTGTTTACTTAATTTTAATTTAATTTTATTTGTGTAAATTTTATTTA
1 ATTTTAATTGGTAAATTTTTGTTTACTTAATTTTAATTTAATTTTATTTGTGTAAATTTTATTTA
2969216 TTTTAA
66 TTTTAA
2969222 TTGATATTTA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
73 47 0.71
74 19 0.29
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (74 bp):
ATTTTAATTGGTAAATTTTTGTTTACTTAATTTTAATTTAATTTTATTTGTGTAAATTTTATTTA
TTTTAACTT
Found at i:2969223 original size:15 final size:15
Alignment explanation
Indices: 2969182--2969233 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
2969172 TTTACTTAAT
*
2969182 TTTAATTTAATTTTA
1 TTTATTTTAATTTTA
* * *
2969197 TTTGTGTAAATTTTA
1 TTTATTTTAATTTTA
*
2969212 TTTATTTTAATTGATA
1 TTTATTTTAATT-TTA
2969228 TTTATT
1 TTTATT
2969234 AAATGACAAG
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
15 20 0.71
16 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:2970721 original size:12 final size:12
Alignment explanation
Indices: 2970704--2970730 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2970694 GAGAATATAC
2970704 ATACATACATAT
1 ATACATACATAT
2970716 ATACATACATAT
1 ATACATACATAT
2970728 ATA
1 ATA
2970731 ATATAGTTAT
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:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
ATACATACATAT
Found at i:2974188 original size:26 final size:26
Alignment explanation
Indices: 2974159--2974212 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2974149 AATATAATGA
*
2974159 TATTAATATTTATATAAA-TATTTTAT
1 TATT-ATATTTATATAAATTATATTAT
* *
2974185 TATTTTATTTTTATAAATTATATTAT
1 TATTATATTTATATAAATTATATTAT
2974211 TA
1 TA
2974213 AAAGGTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTATATTTATATAAATTATATTAT
Found at i:2974878 original size:20 final size:19
Alignment explanation
Indices: 2974855--2974902 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2974845 ATTTGATGAA
2974855 ATAAAAAATAAT-TGTAAAAG
1 ATAAAAAATAATAT-T-AAAG
*
2974875 ATAAATAATAATATTAAAG
1 ATAAAAAATAATATTAAAG
2974894 ATAAAAAAT
1 ATAAAAAAT
2974903 GTAAAATGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.48
20 12 0.48
21 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (19 bp):
ATAAAAAATAATATTAAAG
Found at i:2980048 original size:17 final size:17
Alignment explanation
Indices: 2980020--2980052 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2980010 TTGAAAAAAA
2980020 AAAATCTCAAAAGTTTTG
1 AAAATCTCAAAA-TTTTG
2980038 AAAAT-TCAAAATTTT
1 AAAATCTCAAAATTTT
2980053 ACCCGTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (17 bp):
AAAATCTCAAAATTTTG
Found at i:2981102 original size:19 final size:19
Alignment explanation
Indices: 2981064--2981102 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2981054 ATAGCCTTGA
*
2981064 TTTTTCATTTATTCTTTTT
1 TTTTTCATTTATTCTATTT
*
2981083 TTTTTCATTT-TTCTAATT
1 TTTTTCATTTATTCTATTT
2981101 TT
1 TT
2981103 GAGGTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTCATTTATTCTATTT
Found at i:2981375 original size:19 final size:18
Alignment explanation
Indices: 2981337--2981375 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2981327 ATAAAATAAT
* *
2981337 TTTATTAATTTTCAATTA
1 TTTATTAATTTACAAATA
2981355 TTTATTAATTTCACAAATA
1 TTTATTAATTT-ACAAATA
2981374 TT
1 TT
2981376 AATATATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATTAATTTACAAATA
Found at i:2982381 original size:20 final size:20
Alignment explanation
Indices: 2982340--2982383 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2982330 GTCATCTACC
**
2982340 AATATTATTAATTAAGTGTT
1 AATATTATTAATTAAGCCTT
2982360 AATATT-TTAATTAAGCCCTT
1 AATATTATTAATTAAG-CCTT
2982380 AATA
1 AATA
2982384 AATTACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (20 bp):
AATATTATTAATTAAGCCTT
Found at i:2983496 original size:17 final size:19
Alignment explanation
Indices: 2983474--2983508 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2983464 TGAAAAATCA
2983474 AATTTATT-AA-TAAAATT
1 AATTTATTCAATTAAAATT
2983491 AATTTATTCAATTAAAAT
1 AATTTATTCAATTAAAAT
2983509 ATTTAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTTATTCAATTAAAATT
Found at i:2993296 original size:13 final size:13
Alignment explanation
Indices: 2993278--2993303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2993268 GTTTCTAGTC
2993278 GAGCTTTTTTCAG
1 GAGCTTTTTTCAG
2993291 GAGCTTTTTTCAG
1 GAGCTTTTTTCAG
2993304 CCGTCGAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
GAGCTTTTTTCAG
Found at i:2993437 original size:32 final size:32
Alignment explanation
Indices: 2993401--2993508 Score: 101
Period size: 32 Copynumber: 3.2 Consensus size: 32
2993391 AATGTTTCTC
2993401 TAAAAAATAAATTTATGAATTTTATCAAACTA
1 TAAAAAATAAATTTATGAATTTTATCAAACTA
** * * * *
2993433 TAAAAAA-ATCTTTTAATGGATTTAAATTTATAATCTC
1 TAAAAAATA-AATTT-ATGAATTT-TA-TCA-AA-CTA
2993470 TAAAAAATAAATTTATGAATTTTATCAAACTA
1 TAAAAAATAAATTTATGAATTTTATCAAACTA
2993502 TAAAAAA
1 TAAAAAA
2993509 ATCTTTTAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
31 1 0.02
32 19 0.33
33 9 0.16
34 3 0.05
35 3 0.05
36 9 0.16
37 12 0.21
38 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (32 bp):
TAAAAAATAAATTTATGAATTTTATCAAACTA
Found at i:2993481 original size:69 final size:69
Alignment explanation
Indices: 2993397--2993535 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
2993387 AAAAAATGTT
2993397 TCTCTAAAAAATAAATTTATGAATTTTATCAAACTATAAAAAAATCTTTTAATGGATTTAAATTT
1 TCTCTAAAAAATAAATTTATGAATTTTATCAAACTATAAAAAAATCTTTTAATGGATTTAAATTT
2993462 ATAA
66 ATAA
2993466 TCTCTAAAAAATAAATTTATGAATTTTATCAAACTATAAAAAAATCTTTTAATGGATTTAAATTT
1 TCTCTAAAAAATAAATTTATGAATTTTATCAAACTATAAAAAAATCTTTTAATGGATTTAAATTT
2993531 ATAA
66 ATAA
2993535 T
1 T
2993536 ATATATATAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.41
Consensus pattern (69 bp):
TCTCTAAAAAATAAATTTATGAATTTTATCAAACTATAAAAAAATCTTTTAATGGATTTAAATTT
ATAA
Found at i:2997254 original size:15 final size:15
Alignment explanation
Indices: 2997234--2997262 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2997224 TTAATTTCTT
2997234 TAAATTAAAAGTGTA
1 TAAATTAAAAGTGTA
2997249 TAAATTAAAAGTGT
1 TAAATTAAAAGTGT
2997263 TTGATTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (15 bp):
TAAATTAAAAGTGTA
Found at i:2998038 original size:15 final size:15
Alignment explanation
Indices: 2998020--2998062 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2998010 AAAAATGATG
*
2998020 AAAAATAAAAAAATA
1 AAAAATAAAAAAAGA
*
2998035 AAAAATAAAAAAAGG
1 AAAAATAAAAAAAGA
*
2998050 AAAAAGAAAAAAA
1 AAAAATAAAAAAA
2998063 ATTGATAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAATAAAAAAAGA
Found at i:2998360 original size:14 final size:13
Alignment explanation
Indices: 2998327--2998379 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
2998317 AAGATGTGCC
*
2998327 AAAAAAATGAAAA
1 AAAAAAAAGAAAA
*
2998340 ATGAAAAAGAGCAAAA
1 A--AAAAAAAG-AAAA
2998356 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
2998369 AAAAAAAAGAA
1 AAAAAAAAGAA
2998380 GACTTAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 16 0.47
14 7 0.21
15 6 0.18
16 5 0.15
ACGTcount: A:0.83, C:0.02, G:0.11, T:0.04
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:2998362 original size:16 final size:14
Alignment explanation
Indices: 2998327--2998376 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
2998317 AAGATGTGCC
*
2998327 AAAAAAATGAAAAA
1 AAAAAAAAGAAAAA
* * *
2998341 TGAAAAAGAGCAAAA
1 -AAAAAAAAGAAAAA
2998356 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
2998370 AAAAAAA
1 AAAAAAA
2998377 GAAGACTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.84, C:0.02, G:0.10, T:0.04
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:2998381 original size:16 final size:15
Alignment explanation
Indices: 2998352--2998381 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
2998342 GAAAAAGAGC
2998352 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
2998367 AAAAAAAAAAGAAGA
1 AAAAAAAAAA-AAGA
2998382 CTTAAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:2999541 original size:46 final size:46
Alignment explanation
Indices: 2999491--2999708 Score: 166
Period size: 45 Copynumber: 4.9 Consensus size: 46
2999481 GGATGAGAAC
*
2999491 TTTGAAACTTTGGATGTGAATCTTTAAAATTTTTCAAATGTGAATA
1 TTTGAAATTTTGGATGTGAATCTTTAAAATTTTTCAAATGTGAATA
* * ** *
2999537 TTTGAAATTTTGG--GTGAAATC-CTGAAATTTTATCAAATGAAAATT
1 TTTGAAATTTTGGATGTG-AATCTTTAAAATTTT-TCAAATGTGAATA
* * * ** *
2999582 TTTGAAATTTTGAATGTAAAAT-TCTAAAATTTTTTTAATGTGAATC
1 TTTGAAATTTTGGATGT-GAATCTTTAAAATTTTTCAAATGTGAATA
* * ** *
2999628 TTTGAAATTTTGGTTATGAATCTTT-AAATTTTTTGAA--TGAAAA
1 TTTGAAATTTTGGATGTGAATCTTTAAAATTTTTCAAATGTGAATA
* * *
2999671 TTT-TAACTTTGAATGTGAATCTTTAAAATTTTT-AAATG
1 TTTGAAATTTTGGATGTGAATCTTTAAAATTTTTCAAATG
2999709 AAAAATGTGA
Statistics
Matches: 134, Mismatches: 28, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
42 18 0.13
43 15 0.11
44 11 0.08
45 40 0.30
46 36 0.27
47 14 0.10
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (46 bp):
TTTGAAATTTTGGATGTGAATCTTTAAAATTTTTCAAATGTGAATA
Found at i:2999667 original size:21 final size:21
Alignment explanation
Indices: 2999612--2999668 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 21
2999602 ATTCTAAAAT
2999612 TTTTTTAATGTGAATCTTTGAAA
1 TTTTTTAA--TGAATCTTTGAAA
2999635 TTTTGGTT-ATGAATCTTT-AAA
1 TTTT--TTAATGAATCTTTGAAA
2999656 TTTTTTGAATGAA
1 TTTTTT-AATGAA
2999669 AATTTTAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
19 2 0.07
21 12 0.40
22 9 0.30
23 4 0.13
24 1 0.03
25 2 0.07
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.53
Consensus pattern (21 bp):
TTTTTTAATGAATCTTTGAAA
Found at i:2999718 original size:30 final size:30
Alignment explanation
Indices: 2999682--2999742 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2999672 TTTAACTTTG
2999682 AATGTGAATCTTTAAAATTTTTAAATGAAA
1 AATGTGAATCTTTAAAATTTTTAAATGAAA
2999712 AATGTGAATCTTTAAAATTTTTAAATGAAA
1 AATGTGAATCTTTAAAATTTTTAAATGAAA
2999742 A
1 A
2999743 TCTTTGAATT
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:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (30 bp):
AATGTGAATCTTTAAAATTTTTAAATGAAA
Found at i:2999922 original size:19 final size:19
Alignment explanation
Indices: 2999898--2999977 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
2999888 TTCTTGTGAA
* *
2999898 TTTGAATCTTTTGTGAATC
1 TTTGAATCTCTTGCGAATC
* *
2999917 TTTGAAACTCTTGCAAATC
1 TTTGAATCTCTTGCGAATC
*
2999936 TTTGAAAT-TCTTGTGAATC
1 TTTG-AATCTCTTGCGAATC
*
2999955 --TAAATCTCTTGCGAATC
1 TTTGAATCTCTTGCGAATC
2999972 TTTGAA
1 TTTGAA
2999978 AATTTTGTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
16 3 0.06
17 11 0.23
19 31 0.66
20 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (19 bp):
TTTGAATCTCTTGCGAATC
Found at i:2999964 original size:36 final size:36
Alignment explanation
Indices: 2999921--3000010 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
2999911 TGAATCTTTG
* *
2999921 AAACTCTTGCAAATCTTTG-AAATTCTTGTGAATCTA
1 AAACTCTTGCAAATCTTTGAAAATT-TTGTAAAACTA
* *
2999957 AATCTCTTGCGAATCTTTGAAAATTTTGTAAAACTA
1 AAACTCTTGCAAATCTTTGAAAATTTTGTAAAACTA
*
2999993 AAACTCTTGTAAATCTTT
1 AAACTCTTGCAAATCTTT
3000011 AACCTTGGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
36 41 0.89
37 5 0.11
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (36 bp):
AAACTCTTGCAAATCTTTGAAAATTTTGTAAAACTA
Found at i:3000073 original size:17 final size:17
Alignment explanation
Indices: 3000053--3000090 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3000043 AAAATCCTTG
* *
3000053 TGAATCTAGAACTTTTA
1 TGAATCTAAAACTTCTA
3000070 TGAATCTAAAACTTCTA
1 TGAATCTAAAACTTCTA
3000087 TGAA
1 TGAA
3000091 ACTTGAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (17 bp):
TGAATCTAAAACTTCTA
Found at i:3000441 original size:44 final size:44
Alignment explanation
Indices: 3000393--3000552 Score: 157
Period size: 44 Copynumber: 3.6 Consensus size: 44
3000383 TTGACATTTT
3000393 TTATTTCCTATTTTTAAAGTTGTTTA-CTCTCTATACAGAGGAGC
1 TTATTTCCTATTTTTAAAGTTGTTTAGCTCTCTATA-AGAGGAGC
* *
3000437 TTATTTCTTATTTTTAAAATTGTTTAGC-CTCTATATAGAGGAG-
1 TTATTTCCTATTTTTAAAGTTGTTTAGCTCTCTATA-AGAGGAGC
* * * * * * *
3000480 TCGATTTCTTAGTTTTAAAGTTGCTTAGCATTTGTATAA-AGAAGC
1 T-TATTTCCTATTTTTAAAGTTGTTTAGC-TCTCTATAAGAGGAGC
**
3000525 CCATTTCCTATTTTTAAAGTTGTTTAGC
1 TTATTTCCTATTTTTAAAGTTGTTTAGC
3000553 CTTTGTTTAG
Statistics
Matches: 96, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
43 1 0.01
44 88 0.92
45 2 0.02
46 5 0.05
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.46
Consensus pattern (44 bp):
TTATTTCCTATTTTTAAAGTTGTTTAGCTCTCTATAAGAGGAGC
Found at i:3003429 original size:30 final size:30
Alignment explanation
Indices: 3003353--3003455 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 30
3003343 TATTTTTAAG
* * *
3003353 AATTTAATTTTTATTGA-ATTA-TTTAAAGA
1 AATTTAATCTTTA-TAATATTATTTTAAAAA
*
3003382 AATTTTATCTTTATAATATTATTTTAAAAA
1 AATTTAATCTTTATAATATTATTTTAAAAA
* * *
3003412 AATTTAAT-TTATGTAATATTAGTTTTTTAAAG
1 AATTTAATCTT-TATAATATTA--TTTTAAAAA
3003444 AATTTAATCTTT
1 AATTTAATCTTT
3003456 GTGTATTATT
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.03
29 17 0.28
30 23 0.38
32 16 0.27
33 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (30 bp):
AATTTAATCTTTATAATATTATTTTAAAAA
Found at i:3008672 original size:2 final size:2
Alignment explanation
Indices: 3008659--3008688 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3008649 AAGCGTTGTA
*
3008659 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3008689 TTCAAATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3011476 original size:19 final size:19
Alignment explanation
Indices: 3011454--3011491 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3011444 GTCCTAACAA
3011454 CCAAACCAAACCCTAGCTC
1 CCAAACCAAACCCTAGCTC
*
3011473 CCAAGCCAAACCCTAGCTC
1 CCAAACCAAACCCTAGCTC
3011492 GACCCCAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.47, G:0.08, T:0.11
Consensus pattern (19 bp):
CCAAACCAAACCCTAGCTC
Found at i:3012205 original size:17 final size:17
Alignment explanation
Indices: 3012181--3012227 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
3012171 CCGGTTTAGG
3012181 TATTTTTATTTTTTTTA
1 TATTTTTATTTTTTTTA
* **
3012198 TTTTTTTAAATTTTTTA
1 TATTTTTATTTTTTTTA
*
3012215 TATTATTATTTTT
1 TATTTTTATTTTT
3012228 AGTTTTATTT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TATTTTTATTTTTTTTA
Found at i:3012301 original size:3 final size:3
Alignment explanation
Indices: 3012295--3012359 Score: 64
Period size: 3 Copynumber: 22.7 Consensus size: 3
3012285 TTAATTTTTT
* * * *
3012295 TAA TAA TAA TAA AAA TAA AAA CAA TAA -AA TAA TAA TAA -AA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3012341 TAA TAA GAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
3012360 TTTTTTTATT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
2 6 0.12
3 44 0.88
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.25
Consensus pattern (3 bp):
TAA
Found at i:3012345 original size:20 final size:19
Alignment explanation
Indices: 3012295--3012360 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
3012285 TTAATTTTTT
3012295 TAATAATAATAAAAATAAAAA
1 TAAT-ATAATAAAAAT-AAAA
* * *
3012316 CAATAAAATAATAATAAAA
1 TAATATAATAAAAATAAAA
*
3012335 TAATGATAATAAGAATAAAA
1 TAAT-ATAATAAAAATAAAA
3012355 TAATAT
1 TAATAT
3012361 TTTTTTATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 9 0.24
20 26 0.68
21 3 0.08
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.26
Consensus pattern (19 bp):
TAATATAATAAAAATAAAA
Found at i:3012478 original size:3 final size:3
Alignment explanation
Indices: 3012470--3012509 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3012460 TTAAAAAAGG
3012470 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3012510 ATTTTTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3012692 original size:30 final size:31
Alignment explanation
Indices: 3012641--3012708 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
3012631 AAAATTGTTA
*
3012641 AAAAATCTAAATCCTAAAACCTTTCAAACCC
1 AAAAATCTAAAACCTAAAACCTTTCAAACCC
* *
3012672 AAAAAT-TAAAACCTTAAACCTTTTAAA-CC
1 AAAAATCTAAAACCTAAAACCTTTCAAACCC
3012701 ATAAAATC
1 A-AAAATC
3012709 AAGGCCTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 3 0.09
30 23 0.72
31 6 0.19
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (31 bp):
AAAAATCTAAAACCTAAAACCTTTCAAACCC
Found at i:3012869 original size:68 final size:66
Alignment explanation
Indices: 3012797--3012923 Score: 157
Period size: 68 Copynumber: 1.9 Consensus size: 66
3012787 AAAATTGTAA
* * *
3012797 CCTTAAACCCTCTAAACTCTAAAACCAAAACCCTAAA-CCTCAAACTTTCCAAACCCTAAAAACT
1 CCTTAAAACCTCTAAACCCTAAAACCAAAACCATAAACCCT-AAAC-TT-CAAACCCTAAAAACT
3012861 CAAG
63 CAAG
* ** *
3012865 CCTTAAAACCTTTAAACCCTAAAACTGAAACCATAGACCCTAAACTTCAAACCCTAAAA
1 CCTTAAAACCTCTAAACCCTAAAACCAAAACCATAAACCCTAAACTTCAAACCCTAAAA
3012924 TCCAAAATCC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
66 12 0.24
67 2 0.04
68 34 0.67
69 3 0.06
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (66 bp):
CCTTAAAACCTCTAAACCCTAAAACCAAAACCATAAACCCTAAACTTCAAACCCTAAAAACTCAA
G
Found at i:3015321 original size:16 final size:17
Alignment explanation
Indices: 3015300--3015342 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3015290 ATAAAAAATA
*
3015300 TTTTAAATTATTTG-TT
1 TTTTAAATAATTTGTTT
3015316 TTTTAAA-AATTTGTTT
1 TTTTAAATAATTTGTTT
3015332 TTTTAAATAAT
1 TTTTAAATAAT
3015343 ATTAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 16 0.67
17 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTTAAATAATTTGTTT
Found at i:3015384 original size:25 final size:24
Alignment explanation
Indices: 3015354--3015474 Score: 79
Period size: 24 Copynumber: 4.9 Consensus size: 24
3015344 TTAATATAAC
*
3015354 TATTAAAATATTAAAAATTAATTAT
1 TATTAAAATATTAAAAATT-ATTAA
3015379 TATTAAAGTATATT-AAAATTATTAA
1 TATTAAA--ATATTAAAAATTATTAA
*
3015404 TATTCAAAA-ATTAAAATATTGTTAA
1 TATT-AAAATATTAAAA-ATTATTAA
* ** *
3015429 AATT-ATTTATTAATATATTATTAA
1 TATTAAAATATTAA-AAATTATTAA
* *
3015453 TA-TAATATATTATAATATTATT
1 TATTAAAATATTA-AAAATTATT
3015475 TATTAATTAA
Statistics
Matches: 78, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
23 5 0.06
24 32 0.41
25 27 0.35
26 9 0.12
27 5 0.06
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTAAAATATTAAAAATTATTAA
Found at i:3015450 original size:15 final size:15
Alignment explanation
Indices: 3015430--3015599 Score: 100
Period size: 15 Copynumber: 11.1 Consensus size: 15
3015420 TATTGTTAAA
3015430 ATTATTTATTAATAT
1 ATTATTTATTAATAT
*
3015445 ATTATTAATATAATAT
1 ATTATTTAT-TAATAT
* *
3015461 ATTA--TAATATTAT
1 ATTATTTATTAATAT
*
3015474 -TTATTAATTAATAT
1 ATTATTTATTAATAT
**
3015488 AACA-TTATTTAATAT
1 ATTATTTA-TTAATAT
* **
3015503 AATAAATA-TAATAAT
1 ATTATTTATTAAT-AT
* *
3015518 ATTTACTAATATAATAT
1 A-TTATTTAT-TAATAT
3015535 -TTATTTATTAATAT
1 ATTATTTATTAATAT
*
3015549 ATTAGTTATTAATAT
1 ATTATTTATTAATAT
3015564 ATTATTTATTAAATAAAAAT
1 ATTATTTATT-AAT----AT
3015584 ATTATTTATTAATAT
1 ATTATTTATTAATAT
3015599 A
1 A
3015600 ATAATATTTT
Statistics
Matches: 119, Mismatches: 20, Indels: 32
0.70 0.12 0.19
Matches are distributed among these distances:
12 3 0.03
13 5 0.04
14 19 0.16
15 53 0.45
16 18 0.15
17 2 0.02
18 4 0.03
19 3 0.03
20 12 0.10
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (15 bp):
ATTATTTATTAATAT
Found at i:3015546 original size:46 final size:46
Alignment explanation
Indices: 3015446--3015604 Score: 153
Period size: 46 Copynumber: 3.3 Consensus size: 46
3015436 TATTAATATA
* * *
3015446 TTATTAATATAATATATTATAATATTATTTATTAAT-TAATA-TAACA
1 TTATTAATATAATA-ATTATAATAATATTTATTAATATAATATTTA-T
* *
3015492 TTATTTAATATAATAAATATAATAATATTTACTAATATAATATTTAT
1 TTA-TTAATATAATAATTATAATAATATTTATTAATATAATATTTAT
* * *
3015539 TTATTAATATATTAGTTATTAATATATTATTTATTAA-ATAAAAATATTAT
1 TTATTAATATAATAATTA-TAATA-A-TATTTATTAATAT-AATAT-TTAT
3015589 TTATTAATATAATAAT
1 TTATTAATATAATAAT
3015605 ATTTTGAGTC
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
46 33 0.35
47 24 0.26
48 5 0.05
49 13 0.14
50 18 0.19
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (46 bp):
TTATTAATATAATAATTATAATAATATTTATTAATATAATATTTAT
Found at i:3015587 original size:20 final size:21
Alignment explanation
Indices: 3015562--3015607 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
3015552 AGTTATTAAT
3015562 ATATTATTTATTAA-ATAAAA
1 ATATTATTTATTAATATAAAA
*
3015582 ATATTATTTATTAATATAATA
1 ATATTATTTATTAATATAAAA
3015603 ATATT
1 ATATT
3015608 TTGAGTCGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTATTTATTAATATAAAA
Found at i:3030640 original size:28 final size:29
Alignment explanation
Indices: 3030598--3030654 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3030588 TGTTTTTTTT
* *
3030598 TTAATGTATTCTA-TTTTTTTAGTATAAA
1 TTAATATATTATATTTTTTTTAGTATAAA
*
3030626 TTAATATATTATATTTTTTTTCGTATAAA
1 TTAATATATTATATTTTTTTTAGTATAAA
3030655 AGATTTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (29 bp):
TTAATATATTATATTTTTTTTAGTATAAA
Found at i:3030919 original size:14 final size:13
Alignment explanation
Indices: 3030901--3030939 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
3030891 AATCATTAAA
3030901 TAAAAATTAAAAT
1 TAAAAATTAAAAT
3030914 TAAAAATTAAAAT
1 TAAAAATTAAAAT
*
3030927 TGATAAATTAAAA
1 T-AAAAATTAAAA
3030940 GGTCTTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
TAAAAATTAAAAT
Found at i:3031078 original size:18 final size:18
Alignment explanation
Indices: 3031044--3031078 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3031034 ATCATTAAAT
*
3031044 AATTATTAGTTAAATTTA
1 AATTATTAATTAAATTTA
*
3031062 AATTATTAATTATATTT
1 AATTATTAATTAAATTT
3031079 TTAATATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AATTATTAATTAAATTTA
Found at i:3032393 original size:72 final size:72
Alignment explanation
Indices: 3032307--3032440 Score: 171
Period size: 72 Copynumber: 1.9 Consensus size: 72
3032297 AACAAAACTT
3032307 TTTATATTAAAAATAT-TATATTTATTAAATTATAAAAAATAATTTTTCATATTTTTAACAAATA
1 TTTATATTAAAAATATCTAT-TTTATTAAATTATAAAAAATAATTTTTCATATTTTTAACAAATA
3032371 TCAAGTTG
65 TCAAGTTG
* * * * * * * * *
3032379 TTTATTTTAGAAATATCTCTTTTGTTGAATTATAGAAAATATTTTTTTATCTTTTTAACAAA
1 TTTATATTAAAAATATCTATTTTATTAAATTATAAAAAATAATTTTTCATATTTTTAACAAA
3032441 AATTATATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 50 0.96
73 2 0.04
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.50
Consensus pattern (72 bp):
TTTATATTAAAAATATCTATTTTATTAAATTATAAAAAATAATTTTTCATATTTTTAACAAATAT
CAAGTTG
Found at i:3035600 original size:24 final size:25
Alignment explanation
Indices: 3035573--3035625 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
3035563 AAATAAAAAA
*
3035573 TTTTATTAATATATTAAAT-TT-AATT
1 TTTTATT-ATATA-AAAATGTTAAATT
3035598 TTTTATTATATAAAAATGTTAAATT
1 TTTTATTATATAAAAATGTTAAATT
3035623 TTT
1 TTT
3035626 AAATTTTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 4 0.16
24 7 0.28
25 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTATTATATAAAAATGTTAAATT
Found at i:3035626 original size:24 final size:25
Alignment explanation
Indices: 3035555--3035626 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 25
3035545 AAAGTAAGAA
** *
3035555 TAATA-ATAAAATAAAAAATTTTAT
1 TAATATATAAAATTTAAATTTTTAT
* *
3035579 TAATATATTAAATTTAATTTTTTAT
1 TAATATATAAAATTTAAATTTTTAT
3035604 T-ATATA-AAAATGTTAAATTTTTA
1 TAATATATAAAAT-TTAAATTTTTA
3035627 AATTTTAAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 4 0.10
24 20 0.51
25 15 0.38
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (25 bp):
TAATATATAAAATTTAAATTTTTAT
Found at i:3039930 original size:31 final size:31
Alignment explanation
Indices: 3039889--3039948 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3039879 AAATTTACAC
* * *
3039889 ATTAAAAAAATGATATCATTTGATTTATTTT
1 ATTAAAAAAATAATATCATCTAATTTATTTT
*
3039920 ATTAATAAAATAATATCATCTAATTTATT
1 ATTAAAAAAATAATATCATCTAATTTATT
3039949 AATAATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTAAAAAAATAATATCATCTAATTTATTTT
Found at i:3043242 original size:12 final size:12
Alignment explanation
Indices: 3043201--3043245 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
3043191 ATCTCTACTC
3043201 ATATATAAATGTAA
1 ATATATAAA--TAA
*
3043215 ATAAATAAATAA
1 ATATATAAATAA
*
3043227 ATATATAAATAT
1 ATATATAAATAA
3043239 ATATATA
1 ATATATA
3043246 TTTATATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 20 0.71
14 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (12 bp):
ATATATAAATAA
Found at i:3050892 original size:33 final size:31
Alignment explanation
Indices: 3050848--3050969 Score: 104
Period size: 33 Copynumber: 3.7 Consensus size: 31
3050838 CAAGACGATG
*
3050848 AGTATGGATGATGCTCCTTTAAGCAGGACAAAT
1 AGTAGGGATGATGCTCCTTTAAGCAGG-C-AAT
* *
3050881 AGTAGGAATGATGCTGCTCATTTAAGCAGG-AGT
1 AGTAGGGATGATGCT-C-C-TTTAAGCAGGCAAT
* * *
3050914 AGTAGGGATGATGCACCTATAAACAGGCCAAT
1 AGTAGGGATGATGCTCCTTTAAGCAGG-CAAT
3050946 CAGTAGGGATGATGC-CCTTGTAAG
1 -AGTAGGGATGATGCTCCTT-TAAG
3050970 TGGGCCAACT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
30 8 0.11
31 1 0.01
32 6 0.08
33 45 0.62
34 1 0.01
35 1 0.01
36 10 0.14
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (31 bp):
AGTAGGGATGATGCTCCTTTAAGCAGGCAAT
Found at i:3057028 original size:28 final size:28
Alignment explanation
Indices: 3056988--3057045 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
3056978 GCAAAGCAAA
3056988 AACAGACTTATGATTTTCCCAATAAACT
1 AACAGACTTATGATTTTCCCAATAAACT
*
3057016 AACAGATTTATGATTTTCCCAATAAACT
1 AACAGACTTATGATTTTCCCAATAAACT
3057044 AA
1 AA
3057046 GGCTCCGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (28 bp):
AACAGACTTATGATTTTCCCAATAAACT
Found at i:3057808 original size:42 final size:42
Alignment explanation
Indices: 3057750--3057833 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
3057740 ATTTACAGTA
3057750 AAAAAAAAAATACAAATAAAAATTTGACGTTTAGAAGAGATT
1 AAAAAAAAAATACAAATAAAAATTTGACGTTTAGAAGAGATT
3057792 AAAAAAAAAATACAAATAAAAATTTGACGTTTAGAAGAGATT
1 AAAAAAAAAATACAAATAAAAATTTGACGTTTAGAAGAGATT
3057834 CAGAGGGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.24
Consensus pattern (42 bp):
AAAAAAAAAATACAAATAAAAATTTGACGTTTAGAAGAGATT
Found at i:3064173 original size:17 final size:19
Alignment explanation
Indices: 3064143--3064189 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
3064133 TATTAAATAT
3064143 TTTAATATAAAATATTA-A
1 TTTAATATAAAATATTATA
3064161 TTTAATA-AAAATATTATA
1 TTTAATATAAAATATTATA
3064179 TTTATATATAA
1 TTTA-ATATAA
3064190 TTAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
19 3 0.12
20 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAATATAAAATATTATA
Found at i:3064206 original size:12 final size:12
Alignment explanation
Indices: 3064159--3064218 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
3064149 ATAAAATATT
*
3064159 AATTTA-ATAAA
1 AATTTATATTAA
*
3064170 AATATTATATTTA
1 AAT-TTATATTAA
* *
3064183 TATATA-ATTAA
1 AATTTATATTAA
3064194 AATTTATATTAA
1 AATTTATATTAA
*
3064206 AAATTATATTAA
1 AATTTATATTAA
3064218 A
1 A
3064219 TTAATTTTGA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
11 11 0.29
12 22 0.58
13 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AATTTATATTAA
Found at i:3075229 original size:187 final size:187
Alignment explanation
Indices: 3074908--3075880 Score: 1014
Period size: 187 Copynumber: 5.2 Consensus size: 187
3074898 TTGAAGGAAT
* * * * * * * * *
3074908 TTATTGAAGGCGTCTTCTAGTGTAAAATGCCTTCAATATTTCATTATTCAAATTTTAAGATAGTT
1 TTATTAAAGGCGTCTTTTAGTGAAAAACGACTTCAATATATCAGTACTCAAATTTTAAGATGGTT
* * * *
3074973 AGTGAAGACGTTTATTCTAGAAAAACACCTTCACTAATTTTTTTT-AATTTATTTACATAATTAT
66 AGTGAAGGCGTTTATTCTAGAAAAATACCTTCAATAATTTTTTTTAAATTT-TGTACATAATTAT
* * *
3075037 TGAAGGTATTTTTTGAGAATAAACACCTTAAATAATTTTATTTTAAAAATTTTTGGGA
130 TGAAGGTATTTTTTGAGAACAAACGCCTTCAATAATTTTATTTTAAAAATTTTTGGGA
*
3075095 TTATTAAAGGCGTCTTTTAGTGAAAAACGACTTCAATATATCAGTACTCAAATTTTAAGACGGTT
1 TTATTAAAGGCGTCTTTTAGTGAAAAACGACTTCAATATATCAGTACTCAAATTTTAAGATGGTT
* *
3075160 AGTAAAGGCGTTTATTTTTA-AAAAATACCTTCAATAATTTTTTTTAAATTTTGTACATAATTAT
66 AGTGAAGGCGTTTA-TTCTAGAAAAATACCTTCAATAATTTTTTTTAAATTTTGTACATAATTAT
* * * * *
3075224 TGAAGGCT-TCTTTTAAGAACAAACGCCTTCAATAATTTTCTTTTAAAATTTTTTGAGA
130 TGAAGG-TATTTTTTGAGAACAAACGCCTTCAATAATTTTATTTTAAAAATTTTTGGGA
* ** * * *
3075282 TTATTAAAGGTGTCTTTCGGTGAAAAA-TACCTTCAATAT-TCCACTACTCAAATTTTAAGATAG
1 TTATTAAAGGCGTCTTTTAGTGAAAAACGA-CTTCAATATAT-CAGTACTCAAATTTTAAGATGG
* ** * * * * * *
3075345 TTAATGAATACGTTTATTCTAAAAAAATTCCTTCATTGATTCTATTT-AATTTATGTACATAATT
64 TTAGTGAAGGCGTTTATTCTAGAAAAATACCTTCAATAATTTTTTTTAAATTT-TGTACATAATT
* *
3075409 ATTGAAGGTATTTTTTGAGAACAAATGCCTTCAATAATTTTATTTTAAAAAATTTTGGGA
128 ATTGAAGGTATTTTTTGAGAACAAACGCCTTCAATAATTTTATTTTAAAAATTTTTGGGA
* * * * * *
3075469 TTATTAAAGGCATATTCTATTGAACAATAC--CTTCAATATACCAGTACTCAAATTTTAAGACGG
1 TTATTAAAGGCGTCTTTTAGTGAA-AA-ACGACTTCAATATATCAGTACTCAAATTTTAAGATGG
* * * * *
3075532 TTAGTTAAAGCATTTATTCTAGAAAAATACTTTCAATAA-TTTTTTTAAATTTTATACATAATTA
64 TTAGTGAAGGCGTTTATTCTAGAAAAATACCTTCAATAATTTTTTTTAAATTTTGTACATAATTA
* * ** * *
3075596 TTGAAGGCATTTTTTGAGAACAAACGCCTTCAATAATTTTTTTTTAAAAATAGTCGAGA
129 TTGAAGGTATTTTTTGAGAACAAACGCCTTCAATAATTTTATTTTAAAAATTTTTGGGA
* * * * * * * *
3075655 TTATTAAATGTGTTTTTTAGTAAAAAAAACGTCTTCAATATTTAATTACTCAAATTTTAAGATGG
1 TTATTAAAGGCGTCTTTTAGT--GAAAAACGACTTCAATATATCAGTACTCAAATTTTAAGATGG
* * * * * ** * * *
3075720 TTAGTGAATGCGTTTATTATAGAAAAACACCTTTACTAATTCGTTTTAATTTTTTTACATAGTTA
64 TTAGTGAAGGCGTTTATTCTAGAAAAATACCTTCAATAATTTTTTTTAAATTTTGTACATAATTA
* * * *
3075785 TTGAAGGTATTTTTT-AGAACAAACACTTTCAATAATTTTCTTTTAAAAATTTTTAGGA
129 TTGAAGGTATTTTTTGAGAACAAACGCCTTCAATAATTTTATTTTAAAAATTTTTGGGA
* * * *
3075843 TTATTAAAGGCATTTTTTAGT-ATAAAACGCCTTTAATA
1 TTATTAAAGGCGTCTTTTAGTGA-AAAACGACTTCAATA
3075881 ATGTTAAAAG
Statistics
Matches: 648, Mismatches: 119, Indels: 39
0.80 0.15 0.05
Matches are distributed among these distances:
185 1 0.00
186 109 0.17
187 377 0.58
188 126 0.19
189 35 0.05
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (187 bp):
TTATTAAAGGCGTCTTTTAGTGAAAAACGACTTCAATATATCAGTACTCAAATTTTAAGATGGTT
AGTGAAGGCGTTTATTCTAGAAAAATACCTTCAATAATTTTTTTTAAATTTTGTACATAATTATT
GAAGGTATTTTTTGAGAACAAACGCCTTCAATAATTTTATTTTAAAAATTTTTGGGA
Found at i:3075806 original size:374 final size:372
Alignment explanation
Indices: 3074937--3075855 Score: 1258
Period size: 374 Copynumber: 2.5 Consensus size: 372
3074927 GTGTAAAATG
*
3074937 CCTTCAATATTTCATTATTCAAATTTTAAGATAGTTAGTGAA-GACGTTTATTCTAGAAAAACAC
1 CCTTCAATATTTCATTACTCAAATTTTAAGATAGTTAGTGAATG-CGTTTATTCTAGAAAAACAC
* *
3075001 CTTCACTAATTTTTTTTAATTTATTTACATAATTATTGAAGGTATTTTTTGAGAATAAACACCTT
65 CTTCACTAA-TTCTTTTAATTTATTTACATAATTATTGAAGGTATTTTTTGAGAACAAACACCTT
* * * *
3075066 AAATAATTTTATTTTAAAAATTTTTGGGATTATTAAAGGCGTCTTTTAGTGAAAAACGACTTCAA
129 CAATAATTTTATTTTAAAAATTTTTGGGATTATTAAAGGCATATTCTAGTGAAAAAC-ACTTCAA
* * *
3075131 TATATCAGTACTCAAATTTTAAGACGGTTAGTAAAGGCGTTTATTTTTAAAAAATACCTTCAATA
193 TATACCAGTACTCAAATTTTAAGACGGTTAGTAAAGGCATTTATTTCTAAAAAATACCTTCAATA
*
3075196 ATTTTTTTTAAATTTTGTACATAATTATTGAAGGCTTCTTTTAAGAACAAACGCCTTCAATAATT
258 ATTTTTTTTAAATTTTATACATAATTATTGAAGGCTTCTTTTAAGAACAAACGCCTTCAATAATT
* ** * * * *
3075261 TTCTTTTAAAATTTTTTGAGATTATTAAAGGTGTCTTTCGGTGAAAAATA
323 TTCTTTTAAAAATAGTCGAGATTATTAAAGGTGTCTTTCAGTAAAAAAAA
* * * * * **
3075311 CCTTCAATATTCCACTACTCAAATTTTAAGATAGTTAATGAATACGTTTATTCTAAAAAAATTCC
1 CCTTCAATATTTCATTACTCAAATTTTAAGATAGTTAGTGAATGCGTTTATTCTAGAAAAACACC
* * * **
3075376 TTCATTGATTCTATTTAATTTATGTACATAATTATTGAAGGTATTTTTTGAGAACAAATGCCTTC
66 TTCACTAATTCT-TTTAATTTATTTACATAATTATTGAAGGTATTTTTTGAGAACAAACACCTTC
* *
3075441 AATAATTTTATTTTAAAAAATTTTGGGATTATTAAAGGCATATTCTATTGAACAATAC-CTTCAA
130 AATAATTTTATTTTAAAAATTTTTGGGATTATTAAAGGCATATTCTAGTGAA-AA-ACACTTCAA
*
3075505 TATACCAGTACTCAAATTTTAAGACGGTTAGTTAAA-GCATTTA-TTCTAGAAAAATACTTTCAA
193 TATACCAGTACTCAAATTTTAAGACGGTTAG-TAAAGGCATTTATTTCTA-AAAAATACCTTCAA
*
3075568 TAA-TTTTTTTAAATTTTATACATAATTATTGAAGGCATT-TTTTGAGAACAAACGCCTTCAATA
256 TAATTTTTTTTAAATTTTATACATAATTATTGAAGGC-TTCTTTTAAGAACAAACGCCTTCAATA
* * * *
3075631 ATTTTTTTTTAAAAATAGTCGAGATTATTAAATGTGTTTTTTAGTAAAAAAAA
320 ATTTTCTTTTAAAAATAGTCGAGATTATTAAAGGTGTCTTTCAGTAAAAAAAA
* * *
3075684 CGTCTTCAATATTTAATTACTCAAATTTTAAGATGGTTAGTGAATGCGTTTATTATAGAAAAACA
1 C--CTTCAATATTTCATTACTCAAATTTTAAGATAGTTAGTGAATGCGTTTATTCTAGAAAAACA
* * * *
3075749 CCTTTACTAATTCGTTTTAATTTTTTTACATAGTTATTGAAGGTATTTTTT-AGAACAAACACTT
64 CCTTCACTAATTC-TTTTAATTTATTTACATAATTATTGAAGGTATTTTTTGAGAACAAACACCT
* *
3075813 TCAATAATTTTCTTTTAAAAATTTTTAGGATTATTAAAGGCAT
128 TCAATAATTTTATTTTAAAAATTTTTGGGATTATTAAAGGCAT
3075856 TTTTTAGTAT
Statistics
Matches: 475, Mismatches: 60, Indels: 20
0.86 0.11 0.04
Matches are distributed among these distances:
373 105 0.22
374 266 0.56
375 101 0.21
376 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (372 bp):
CCTTCAATATTTCATTACTCAAATTTTAAGATAGTTAGTGAATGCGTTTATTCTAGAAAAACACC
TTCACTAATTCTTTTAATTTATTTACATAATTATTGAAGGTATTTTTTGAGAACAAACACCTTCA
ATAATTTTATTTTAAAAATTTTTGGGATTATTAAAGGCATATTCTAGTGAAAAACACTTCAATAT
ACCAGTACTCAAATTTTAAGACGGTTAGTAAAGGCATTTATTTCTAAAAAATACCTTCAATAATT
TTTTTTAAATTTTATACATAATTATTGAAGGCTTCTTTTAAGAACAAACGCCTTCAATAATTTTC
TTTTAAAAATAGTCGAGATTATTAAAGGTGTCTTTCAGTAAAAAAAA
Found at i:3076734 original size:25 final size:25
Alignment explanation
Indices: 3076677--3076735 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
3076667 ATGCTAAATC
* *
3076677 GTATG-CTGAATGATTTGTTGAATG
1 GTATGTCTGAATGATTTGTTAAAGG
* * *
3076701 GTGTTTCTGAATGGTTTGTTAAAGG
1 GTATGTCTGAATGATTTGTTAAAGG
3076726 GTATGTCTGA
1 GTATGTCTGA
3076736 GTACATTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
24 3 0.11
25 24 0.89
ACGTcount: A:0.22, C:0.05, G:0.31, T:0.42
Consensus pattern (25 bp):
GTATGTCTGAATGATTTGTTAAAGG
Found at i:3079978 original size:36 final size:35
Alignment explanation
Indices: 3079915--3079985 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
3079905 ATATATAAAC
*
3079915 CAAATATTTTTTGGGCATAAATATACAATTGACTT
1 CAAATATTTTTTGGGCATAAATATACAACTGACTT
*
3079950 CAAATGTTTTTTGGGCATAAACCT-TACAACTGACTT
1 CAAATATTTTTTGGGCATAAA--TATACAACTGACTT
3079986 GACATATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 20 0.62
36 11 0.34
37 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (35 bp):
CAAATATTTTTTGGGCATAAATATACAACTGACTT
Found at i:3081878 original size:9 final size:9
Alignment explanation
Indices: 3081864--3081889 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3081854 CTCTGCGCCC
3081864 CAACAGCCT
1 CAACAGCCT
3081873 CAACAGCCT
1 CAACAGCCT
3081882 CAACAGCC
1 CAACAGCC
3081890 CCACTCCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.46, G:0.12, T:0.08
Consensus pattern (9 bp):
CAACAGCCT
Found at i:3087729 original size:3 final size:3
Alignment explanation
Indices: 3087721--3087752 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3087711 TAAAAGATAA
3087721 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
3087753 TAATAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3089086 original size:31 final size:31
Alignment explanation
Indices: 3089039--3089099 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3089029 CAACCATGAC
*
3089039 CATTTAATCTGAAATAAACCATATAAAAAAA
1 CATTGAATCTGAAATAAACCATATAAAAAAA
* *
3089070 CATTGAATTTGAAATAAATCATATAAAAAA
1 CATTGAATCTGAAATAAACCATATAAAAAA
3089100 GAAATTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (31 bp):
CATTGAATCTGAAATAAACCATATAAAAAAA
Found at i:3100187 original size:30 final size:30
Alignment explanation
Indices: 3100153--3100210 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3100143 CGCTAACGTA
3100153 TAGAAATTATAATTATTCTTAATTGTTAGT
1 TAGAAATTATAATTATTCTTAATTGTTAGT
* *
3100183 TAGAAATTATAATTATTTTTTATTGTTA
1 TAGAAATTATAATTATTCTTAATTGTTA
3100211 AATTGTAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (30 bp):
TAGAAATTATAATTATTCTTAATTGTTAGT
Found at i:3100953 original size:20 final size:19
Alignment explanation
Indices: 3100884--3100953 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 19
3100874 TTTAAAATTC
*
3100884 AATAAAGATAATATTTTAA
1 AATAAAAATAATATTTTAA
* *
3100903 AGATAAAAATACAATTTTTGTTA
1 A-ATAAAAAT--AATATTT-TAA
*
3100926 AA-AAAAATAATGTTTCTAA
1 AATAAAAATAATATTT-TAA
3100945 AATAAAAAT
1 AATAAAAAT
3100954 GTAGTTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
19 11 0.28
20 13 0.32
21 6 0.15
22 7 0.17
23 3 0.08
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (19 bp):
AATAAAAATAATATTTTAA
Found at i:3101107 original size:113 final size:113
Alignment explanation
Indices: 3100813--3101097 Score: 320
Period size: 113 Copynumber: 2.5 Consensus size: 113
3100803 AGAATTCAAC
* *
3100813 AAAAACAATTTTTTTAAGATAAAAAATATAATCTTTATTAAAAACATGAAAAAATATAGTATTTA
1 AAAAATAATTTTTTTAAGATAAAAAATATAATCTTTATTAAAAACAT-AAAAAAT-TAATATTTA
* *
3100878 AAATTCAATAAAGATAATATTTTAAAGATAAAAATACAATTTTTGTTAAA
64 AAATTCAATAAAGATAACATTTTAAAGATAAAAACACAATTTTTGTTAAA
* * * * * * * * ** *
3100928 AAAAATAATGTTTCTAAAAT-AAAAATGTAGTTTTTATTGAAAACGTAAAAAATTTTTTTTTTAA
1 AAAAATAATTTTTTTAAGATAAAAAATATAATCTTTATTAAAAACATAAAAAA-TTAATATTTAA
* ** ** *
3100992 AATTCAATAAAGATAACGTTTTTGAGATAAAAACATGATTTTTGTTGAA
65 AATTCAATAAAGATAACATTTTAAAGATAAAAACACAATTTTTGTTAAA
* * *
3101041 AAAAATAATTTTTTTAGGATAAAAAATACAATCTTTATTAAAAATATAAAAAATTAA
1 AAAAATAATTTTTTTAAGATAAAAAATATAATCTTTATTAAAAACATAAAAAATTAA
3101098 AACGTAAAAT
Statistics
Matches: 135, Mismatches: 33, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
113 72 0.53
114 47 0.35
115 16 0.12
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (113 bp):
AAAAATAATTTTTTTAAGATAAAAAATATAATCTTTATTAAAAACATAAAAAATTAATATTTAAA
ATTCAATAAAGATAACATTTTAAAGATAAAAACACAATTTTTGTTAAA
Found at i:3101707 original size:13 final size:13
Alignment explanation
Indices: 3101689--3101715 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3101679 TTATAAAACT
3101689 ATATATATTTTTA
1 ATATATATTTTTA
3101702 ATATATATTTTTA
1 ATATATATTTTTA
3101715 A
1 A
3101716 GAATATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATATATTTTTA
Found at i:3108622 original size:22 final size:22
Alignment explanation
Indices: 3108597--3108683 Score: 72
Period size: 22 Copynumber: 4.0 Consensus size: 22
3108587 ATTAAAATAT
3108597 ATTTTATATTATATTTTATTAA
1 ATTTTATATTATATTTTATTAA
* *
3108619 A-TTTATATATAAATTTTGTTAAA
1 ATTTTATAT-TATATTTTATT-AA
* *
3108642 ATTTTAAATTATATTATT-TTTA
1 ATTTTATATTATATT-TTATTAA
* *
3108664 TTTTTATATCAT-TTTTATTA
1 ATTTTATATTATATTTTATTA
3108684 GTATTATCAT
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
20 2 0.04
21 11 0.22
22 20 0.39
23 10 0.20
24 8 0.16
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (22 bp):
ATTTTATATTATATTTTATTAA
Found at i:3108672 original size:17 final size:17
Alignment explanation
Indices: 3108650--3108682 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3108640 AAATTTTAAA
*
3108650 TTATATTATTTTTATTT
1 TTATATCATTTTTATTT
3108667 TTATATCATTTTTATT
1 TTATATCATTTTTATT
3108683 AGTATTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATATCATTTTTATTT
Found at i:3108691 original size:18 final size:17
Alignment explanation
Indices: 3108651--3108693 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3108641 AATTTTAAAT
* **
3108651 TATATTATTTTTATTTT
1 TATATCATTTTTATTAG
3108668 TATATCATTTTTATTAG
1 TATATCATTTTTATTAG
3108685 TATTATCAT
1 TA-TATCAT
3108694 ATTAGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (17 bp):
TATATCATTTTTATTAG
Found at i:3111848 original size:16 final size:16
Alignment explanation
Indices: 3111814--3111847 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3111804 ATATTTACTT
3111814 AAATATTTTTATTTTA
1 AAATATTTTTATTTTA
3111830 AAATA-TTTTATTTTA
1 AAATATTTTTATTTTA
3111845 AAA
1 AAA
3111848 ACTTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATATTTTTATTTTA
Found at i:3112155 original size:27 final size:25
Alignment explanation
Indices: 3112088--3112176 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 25
3112078 TTAGGGTTTA
*
3112088 GATTTAGAGTTTAAAATTTAAGATTTTT
1 GATTTA-AGTTT-GAATTTAAGA-TTTT
*
3112116 TATTTGAAGTTTGAGATTTAAGATTTT
1 GATTT-AAGTTTGA-ATTTAAGATTTT
*
3112143 GATTTATGATTTGAAGTTTAAG-TTTT
1 GATTTAAG-TTTGAA-TTTAAGATTTT
3112169 GGATTTAA
1 -GATTTAA
3112177 AGTTCAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
26 7 0.14
27 26 0.51
28 17 0.33
29 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (25 bp):
GATTTAAGTTTGAATTTAAGATTTT
Found at i:3113570 original size:23 final size:22
Alignment explanation
Indices: 3113527--3113610 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 22
3113517 ATCAAACATA
3113527 AAATATAT-ATTTTTAT-TTTT
1 AAATATATCATTTTTATATTTT
3113547 AAATAATATCATTTTTATATTTT
1 AAAT-ATATCATTTTTATATTTT
** * *
3113570 ATTTTATATCAATTTTATATTAT
1 A-AATATATCATTTTTATATTTT
*
3113593 ACAATCATATCATATTTA
1 A-AAT-ATATCATTTTTA
3113611 AAATTATCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.08
21 4 0.08
22 8 0.16
23 23 0.46
24 11 0.22
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATATATCATTTTTATATTTT
Found at i:3113822 original size:20 final size:20
Alignment explanation
Indices: 3113784--3113828 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3113774 ATTATTTATA
* * *
3113784 TATATTTATATAATTATATT
1 TATATTTAAAAAATAATATT
3113804 TATATTTAAAAAATAATATT
1 TATATTTAAAAAATAATATT
3113824 T-TATT
1 TATATT
3113829 AATTTCGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATTTAAAAAATAATATT
Found at i:3114557 original size:52 final size:52
Alignment explanation
Indices: 3114500--3114602 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
3114490 TTGCCATTAC
3114500 TTATTCAACCAAATTTAAGGTTTAAACTTTATTTAAATGAATGATGAAAAAT
1 TTATTCAACCAAATTTAAGGTTTAAACTTTATTTAAATGAATGATGAAAAAT
*
3114552 TTATTCAACCAAATTTAAGGTTTAAATTTTATTTAAATGAATGATGAAAAA
1 TTATTCAACCAAATTTAAGGTTTAAACTTTATTTAAATGAATGATGAAAAA
3114603 AATTTTCCAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.39
Consensus pattern (52 bp):
TTATTCAACCAAATTTAAGGTTTAAACTTTATTTAAATGAATGATGAAAAAT
Found at i:3117755 original size:1 final size:1
Alignment explanation
Indices: 3117751--3117781 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
3117741 TACTCTTCAT
3117751 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3117782 CTTACTTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3118787 original size:17 final size:18
Alignment explanation
Indices: 3118765--3118804 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3118755 TTTTTTATTT
* *
3118765 TATAAAATTAA-AAAATA
1 TATAAAACTAATAAAAAA
3118782 TATAAAACTAATAAAAAA
1 TATAAAACTAATAAAAAA
3118800 TATAA
1 TATAA
3118805 TTTATTCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
TATAAAACTAATAAAAAA
Found at i:3125114 original size:3 final size:3
Alignment explanation
Indices: 3125106--3125131 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3125096 CAAATGATGT
3125106 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3125132 TCTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3137407 original size:61 final size:61
Alignment explanation
Indices: 3137302--3137438 Score: 159
Period size: 61 Copynumber: 2.3 Consensus size: 61
3137292 TCATTATATT
* * * * * *
3137302 ATCACTTG-TTTTTATCTCAACTCAGTCCAAATCAACTTTTTGACTCGTGGTTTGATCCCA
1 ATCACTTGCTTTTGATCCCAACTCAATCCAAATCAACTGTCTGACTCGTAGTTTGATCCCA
* * * * *
3137362 ATCACTTGCTTTTGATCCCAACTCAATCTAAGTCATCTGTCTGACTCGTAGTTTGATCTCG
1 ATCACTTGCTTTTGATCCCAACTCAATCCAAATCAACTGTCTGACTCGTAGTTTGATCCCA
*
3137423 ATCACTTACTTTTGAT
1 ATCACTTGCTTTTGAT
3137439 ATTGACTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 8 0.12
61 56 0.88
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (61 bp):
ATCACTTGCTTTTGATCCCAACTCAATCCAAATCAACTGTCTGACTCGTAGTTTGATCCCA
Found at i:3138360 original size:22 final size:21
Alignment explanation
Indices: 3138335--3138375 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3138325 GAAGTTTGGG
*
3138335 AGTTTGAAGTTTTTGGGTTTTA
1 AGTTTGAA-TTTTTAGGTTTTA
3138357 AGTTTGAATTTTTAGGTTT
1 AGTTTGAATTTTTAGGTTT
3138376 GGGTTGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (21 bp):
AGTTTGAATTTTTAGGTTTTA
Found at i:3138766 original size:19 final size:19
Alignment explanation
Indices: 3138731--3138774 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
3138721 AAATCGCAGG
*
3138731 TTTTTTTTTCTTTATTTTA
1 TTTTTTTTTCTTGATTTTA
3138750 TTTTTATTTT-TTGATTTTA
1 TTTTT-TTTTCTTGATTTTA
3138769 TTTTTT
1 TTTTTT
3138775 ACCATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 18 0.78
20 4 0.17
ACGTcount: A:0.11, C:0.02, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTCTTGATTTTA
Found at i:3138798 original size:16 final size:16
Alignment explanation
Indices: 3138764--3138804 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
3138754 TATTTTTTGA
*
3138764 TTTTATTTTTTACCAT
1 TTTTATTTTTTAACAT
**
3138780 TTTTATTTTTTAAGTT
1 TTTTATTTTTTAACAT
3138796 TTTTATTTT
1 TTTTATTTT
3138805 ATCTTCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTATTTTTTAACAT
Found at i:3142022 original size:21 final size:21
Alignment explanation
Indices: 3141978--3142130 Score: 114
Period size: 21 Copynumber: 7.2 Consensus size: 21
3141968 CATAATTTTG
* *
3141978 ATTTCGATAACTTTTAAT-TAA
1 ATTTTGATAACTTTTGATAT-A
* *
3141999 ATTTTGGTACCTTTTGATATA
1 ATTTTGATAACTTTTGATATA
* *
3142020 ATTTTAATAACTTTTGATATT
1 ATTTTGATAACTTTTGATATA
* *
3142041 AGTTTGATAACTTATGATATA
1 ATTTTGATAACTTTTGATATA
* *
3142062 ATTTTAATAATCATTT-ATATA
1 ATTTTGATAA-CTTTTGATATA
* * *
3142083 ATTTTGATAATTTTTTTATAAA
1 ATTTTGATAA-CTTTTGATATA
* *
3142105 ATTTAG-TAACCTTTTGATGTA
1 ATTTTGATAA-CTTTTGATATA
3142126 ATTTT
1 ATTTT
3142131 AATTACCTTT
Statistics
Matches: 102, Mismatches: 27, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
21 89 0.87
22 13 0.13
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (21 bp):
ATTTTGATAACTTTTGATATA
Found at i:3143041 original size:33 final size:30
Alignment explanation
Indices: 3143004--3143118 Score: 86
Period size: 33 Copynumber: 3.6 Consensus size: 30
3142994 GTTAAAATTA
**
3143004 TATATCATTTTTAAAAATTAAGTAAAATTTTTT
1 TATATCA-TTTTAAAAATTAAGTAAAA--ACTT
* * *
3143037 TATATCGATATAAAAAATTAAATAAAAACTT
1 TATATC-ATTTTAAAAATTAAGTAAAAACTT
* *
3143068 TATATCATTTTAAAATATTATGTAAAAAATT
1 TATATCATTTTAAAA-ATTAAGTAAAAACTT
*
3143099 TCAAAATCATTTTCAAAAAT
1 T--ATATCATTTT-AAAAAT
3143119 AGATTTATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
30 7 0.11
31 21 0.32
33 33 0.50
34 5 0.08
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (30 bp):
TATATCATTTTAAAAATTAAGTAAAAACTT
Found at i:3143223 original size:14 final size:14
Alignment explanation
Indices: 3143206--3143236 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3143196 TGTTTTCTTT
*
3143206 TTTTATAAAATGTA
1 TTTTATAAAATATA
3143220 TTTTATAAAATATA
1 TTTTATAAAATATA
3143234 TTT
1 TTT
3143237 AAAAAGGAAA
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TTTTATAAAATATA
Done.