Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 19 of 24
Found at i:3706333 original size:30 final size:31
Alignment explanation
Indices: 3706293--3706350 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
3706283 GTACTGTGAC
*
3706293 CTTTTCAAAGTCCACGACTCAGTGGCATTTT
1 CTTTTCAAAGTCCACAACTCAGTGGCATTTT
* *
3706324 CTTTT-AAAGTCTACAACTCCGTGGCAT
1 CTTTTCAAAGTCCACAACTCAGTGGCAT
3706351 CCTTTTAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (31 bp):
CTTTTCAAAGTCCACAACTCAGTGGCATTTT
Found at i:3706386 original size:46 final size:46
Alignment explanation
Indices: 3706318--3706406 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
3706308 GACTCAGTGG
* *
3706318 CATTTTCTTTTAAAGTCTACAACTCCGTGGCATCCTTTTAAGTTCA
1 CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTTCA
3706364 CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
3706407 CCCCAACTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (46 bp):
CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTTCA
Found at i:3706413 original size:27 final size:27
Alignment explanation
Indices: 3706370--3707243 Score: 1469
Period size: 27 Copynumber: 32.0 Consensus size: 27
3706360 TTCACATTTT
3706370 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
3706398 CTTTTAAGTCCCCAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
3706425 CTTTCAAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3706452 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706479 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
3706507 TTTTTAAGTCCACAACTCCGTGGCCCC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706534 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706561 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3706588 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706615 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
3706643 CTTTTAAGTCCACAACTCCGTGGCCCC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706670 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706697 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
3706725 CTTTTAAGTCCACAGCTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706752 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
3706780 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706807 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706834 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
3706862 CTTTGAAATTCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
3706890 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706917 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3706944 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
3706972 CTTTTAAGTTCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3706999 CTTTTAGGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3707026 CTTTTAAGTCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3707053 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3707080 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
3707108 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3707135 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3707162 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3707189 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
3707216 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3707243 C
1 C
3707244 ATTCCAAAGC
Statistics
Matches: 797, Mismatches: 42, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
27 589 0.74
28 208 0.26
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:3706538 original size:82 final size:81
Alignment explanation
Indices: 3706370--3707243 Score: 1469
Period size: 82 Copynumber: 10.7 Consensus size: 81
3706360 TTCACATTTT
* * *
3706370 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCCCAACTTCGTGGCACCCTTTCAAGTC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
**
3706435 CACAACTCCGTGGCATT
65 CACAACTCCGTGGCACC
* *
3706452 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
3706517 CACAACTCCGTGGCCCC
65 CACAACTCCGTGGCACC
3706534 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
3706599 ACAACTCCGTGGCATC
66 ACAACTCCGTGGCACC
*
3706615 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCCCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
3706680 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
3706697 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAGCTCCGTGGCATCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
3706762 CACAACTCCGTGGCATCC
65 CACAACTCCGTGGCA-CC
3706780 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
3706845 ACAACTCCGTGGCATCC
66 ACAACTCCGTGGCA-CC
* * *
3706862 CTTTGAAATTCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
3706927 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
3706944 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTTCACAACTCCGTGGCACCCTTTTAGGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
3707009 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
3707026 CTTTTAAGTCCACAACTCCGTGGCACTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
3707091 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
3707108 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
3707173 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
* * *
3707189 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAATCCACAACTCTGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC
3707244 ATTCCAAAGC
Statistics
Matches: 751, Mismatches: 36, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
81 200 0.27
82 470 0.63
83 81 0.11
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.28
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:3706565 original size:109 final size:108
Alignment explanation
Indices: 3706370--3707243 Score: 1469
Period size: 109 Copynumber: 8.0 Consensus size: 108
3706360 TTCACATTTT
* * *
3706370 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCCCAACTTCGTGGCACCCTTTCAAGTC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
** *
3706435 CACAACTCCGTGGCATTCTTTTAAGTCCACAACTCTGTGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
3706479 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCCCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
3706544 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
3706588 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
3706653 CACAACTCCGTGGCCCCCTTTTAAGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
3706697 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAGCTCCGTGGCATCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
3706762 CACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
3706807 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTGAAATT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
3706872 CACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
*
3706917 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
3706982 CACAACTCCGTGGCACCCTTTTAGGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
3707026 CTTTTAAGTCCACAACTCCGTGGCACTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
3707091 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
3707135 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
3707200 ACAACTCCGTGGCATCCTTTTAAATCCACAACTCTGTGGCACC
66 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
3707243 C
1 C
3707244 ATTCCAAAGC
Statistics
Matches: 726, Mismatches: 33, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
108 98 0.13
109 418 0.58
110 210 0.29
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.28
Consensus pattern (108 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:3707284 original size:32 final size:32
Alignment explanation
Indices: 3707226--3708209 Score: 1327
Period size: 32 Copynumber: 31.8 Consensus size: 32
3707216 CTTTTAAATC
* * *
3707226 CACAACTCTGTGGC-ACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707257 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707289 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
3707319 CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3707349 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3707377 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3707405 CACAAGTCGGTGGCAATCTATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
3707435 CACAAGTTAGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707465 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707497 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3707529 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707561 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707593 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3707624 CATAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707656 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707688 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
3707718 CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3707748 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3707776 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3707804 CACAAGTCGGTGGCAATCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
3707834 CACAAGTTAGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707864 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707896 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3707928 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707960 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3707992 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3708023 CATAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3708055 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3708087 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3708119 CACAAGTCGGTGGCGACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3708151 CACAAGTCGGGGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** ** *
3708183 TGCAAGTTAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
3708210 TCACCATTTT
Statistics
Matches: 870, Mismatches: 62, Indels: 41
0.89 0.06 0.04
Matches are distributed among these distances:
28 113 0.13
29 23 0.03
30 136 0.16
31 80 0.09
32 518 0.60
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:3707978 original size:399 final size:399
Alignment explanation
Indices: 3707235--3708157 Score: 1758
Period size: 399 Copynumber: 2.3 Consensus size: 399
3707225 CCACAACTCT
3707235 GTGGC-ACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
3707299 TGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCA
66 TGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCA
*
3707364 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCAATCTATTTC
131 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCAATCCATTTC
3707429 AAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
196 AAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
3707494 CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCC
261 CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCC
3707559 CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCA
326 CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCA
3707624 CATAAGTCG
391 CATAAGTCG
3707633 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
3707698 TGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCA
66 TGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCA
3707763 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCAATCCATTTC
131 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCAATCCATTTC
3707828 AAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
196 AAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
3707893 CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCC
261 CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCC
3707958 CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCA
326 CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCA
3708023 CATAAGTCG
391 CATAAGTCG
*
3708032 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
* * *
3708097 TGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCGACCCTTTTCAAAGCCCACACAAGT
66 TGGCAACCCATTTCAAAG-CC-CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCACACAAGT
3708158 CGGGGGCAAC
Statistics
Matches: 515, Mismatches: 5, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
398 5 0.01
399 474 0.92
400 2 0.00
401 13 0.03
402 1 0.00
403 20 0.04
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (399 bp):
GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
TGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCA
TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCAATCCATTTC
AAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCC
CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCA
CATAAGTCG
Found at i:3708293 original size:45 final size:47
Alignment explanation
Indices: 3708242--3708360 Score: 127
Period size: 49 Copynumber: 2.5 Consensus size: 47
3708232 GTCCGATATT
*
3708242 GCTGGCCTTGAATCAGCATATTGG-CACCTTT-CTAAGCCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCCACCTTTCCTAAGCCCAATGTC
* * * *
3708287 GCTGGCCTTGAGTCAGCACATTGGTCCACTTTTCCCTTAGCCCGATGTC
1 GCTGGCCTTGAATCAGCACATTGG-CCACCTTT-CCTAAGCCCAATGTC
* *
3708336 GCTGACCTTGAAAT-GGCACATTGGC
1 GCTGGCCTTG-AATCAGCACATTGGC
3708361 ATTCCTCTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 22 0.36
47 6 0.10
48 1 0.02
49 30 0.49
50 2 0.03
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (47 bp):
GCTGGCCTTGAATCAGCACATTGGCCACCTTTCCTAAGCCCAATGTC
Found at i:3709080 original size:22 final size:23
Alignment explanation
Indices: 3709046--3709090 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
3709036 GGATCGAAAA
3709046 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
3709068 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
3709091 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:3709483 original size:11 final size:11
Alignment explanation
Indices: 3709445--3709485 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
3709435 AAATTTAGGT
3709445 AAAAAAGAAAG
1 AAAAAAGAAAG
*
3709456 AAAGAAGATGAAG
1 AAAAAAGA--AAG
3709469 AAAAAAGAAAG
1 AAAAAAGAAAG
3709480 AAAAAA
1 AAAAAA
3709486 AATATGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:3715335 original size:9 final size:9
Alignment explanation
Indices: 3715321--3715353 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
3715311 AGAAGGCTCA
3715321 AGCAGAGAC
1 AGCAGAGAC
3715330 AGCAGAGAC
1 AGCAGAGAC
*
3715339 AGCAGAGAT
1 AGCAGAGAC
3715348 AGCAGA
1 AGCAGA
3715354 AAGAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:3716909 original size:2 final size:2
Alignment explanation
Indices: 3716902--3716940 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3716892 TTTTCCGGTG
*
3716902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3716941 GCTCATCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3718696 original size:29 final size:31
Alignment explanation
Indices: 3718652--3718709 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
3718642 ATCAATGATT
*
3718652 GTTTTCAAAAATTAAAAAATTATTTTTAAAA
1 GTTTTCAAAAATTAAAAAATCATTTTTAAAA
*
3718683 GTTTT-AAAAA-TAAAAAATCGTTTTTAA
1 GTTTTCAAAAATTAAAAAATCATTTTTAA
3718710 TAATCATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
30 5 0.20
31 5 0.20
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.41
Consensus pattern (31 bp):
GTTTTCAAAAATTAAAAAATCATTTTTAAAA
Found at i:3720323 original size:2 final size:2
Alignment explanation
Indices: 3720316--3720361 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3720306 ATTCCCATCA
3720316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3720358 AT AT
1 AT AT
3720362 CCCCAATGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3721669 original size:2 final size:2
Alignment explanation
Indices: 3721662--3721692 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3721652 ATGTTTTGAC
3721662 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3721693 AGGAGCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3722653 original size:56 final size:56
Alignment explanation
Indices: 3722571--3722684 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
3722561 CCTAAAAATT
* * *
3722571 GGGTTTATCTTTTCATACTTGGTCATCAACAATATTGAATTAACTTAAAGTAAAAA
1 GGGTTTATCTTTTCATACTTGATCATCAACAATATTGAATCAACTTAAAGAAAAAA
* * * *
3722627 GGGTTTCTCTTTTTATACTTGATCATCAACAATGTTGAATCAGCTTAAAGAAAAAA
1 GGGTTTATCTTTTCATACTTGATCATCAACAATATTGAATCAACTTAAAGAAAAAA
3722683 GG
1 GG
3722685 AAAACAGTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (56 bp):
GGGTTTATCTTTTCATACTTGATCATCAACAATATTGAATCAACTTAAAGAAAAAA
Found at i:3725737 original size:2 final size:2
Alignment explanation
Indices: 3725721--3725754 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3725711 TTTAAATGAG
*
3725721 TA TA T- TA TT TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3725755 TATGGGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:3726190 original size:2 final size:2
Alignment explanation
Indices: 3726183--3726208 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3726173 GAAAGAAGTT
3726183 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3726209 GTGCTAGACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3726650 original size:2 final size:2
Alignment explanation
Indices: 3726600--3726635 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3726590 TTTTATGGGG
*
3726600 AT AT AT AT AT AT TT 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
3726636 TTCTAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3727127 original size:2 final size:2
Alignment explanation
Indices: 3727120--3727172 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
3727110 TTACTATGTG
* *
3727120 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3727162 TA AA TA TA TA T
1 TA TA TA TA TA T
3727173 TCCCTTTAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3729722 original size:13 final size:13
Alignment explanation
Indices: 3729699--3729733 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3729689 ATCTTTTATC
*
3729699 AATTATTTATTTT
1 AATTTTTTATTTT
*
3729712 ATTTTTTTATTTT
1 AATTTTTTATTTT
3729725 AATTTTTTA
1 AATTTTTTA
3729734 AAATATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
AATTTTTTATTTT
Found at i:3735990 original size:20 final size:20
Alignment explanation
Indices: 3735953--3735991 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3735943 TAATTAATAT
* * *
3735953 ATTTTTTTAATATTATAAAA
1 ATTTATTTAAAATAATAAAA
3735973 ATTTATTTAAAATAATAAA
1 ATTTATTTAAAATAATAAA
3735992 TAAAATTTTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTATTTAAAATAATAAAA
Found at i:3737045 original size:2 final size:2
Alignment explanation
Indices: 3737038--3737068 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3737028 AACATATTGC
*
3737038 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3737069 TGATGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3743265 original size:15 final size:15
Alignment explanation
Indices: 3743245--3743278 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3743235 TAAGTTTTTA
**
3743245 TTTTTTAATTTTAAT
1 TTTTTTAATAATAAT
3743260 TTTTTTAATAATAAT
1 TTTTTTAATAATAAT
3743275 TTTT
1 TTTT
3743279 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTAATAATAAT
Found at i:3743875 original size:15 final size:15
Alignment explanation
Indices: 3743838--3743890 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
3743828 ATTATTTTTT
3743838 AATTTAATTTTTATAA
1 AATTTAATTTTTA-AA
*
3743854 AA-ATAATTTTTAAA
1 AATTTAATTTTTAAA
* *
3743868 AATTTAATTTATAAT
1 AATTTAATTTTTAAA
3743883 AATTTAAT
1 AATTTAAT
3743891 AAATTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 4 0.12
15 26 0.81
16 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTAATTTTTAAA
Found at i:3744064 original size:22 final size:22
Alignment explanation
Indices: 3744039--3744088 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3744029 GTTAGAGTTA
3744039 AGATTTAATTTATATT-TTAAAT
1 AGATTTAATTT-TATTATTAAAT
*
3744061 AGATTTAATTTTTTTATTAAAT
1 AGATTTAATTTTATTATTAAAT
*
3744083 ATATTT
1 AGATTT
3744089 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
AGATTTAATTTTATTATTAAAT
Found at i:3744089 original size:33 final size:33
Alignment explanation
Indices: 3744049--3744115 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 33
3744039 AGATTTAATT
*
3744049 TATA-TTTTAAATAGATTTAATTTTTTTA-TTAAA
1 TATATTTTTAAA-A-ATTTAATATTTTTATTTAAA
*
3744082 TATATTTTTTAAAATTTAATATTTTTATTTAAA
1 TATATTTTTAAAAATTTAATATTTTTATTTAAA
3744115 T
1 T
3744116 TCTCTCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 13 0.43
33 11 0.37
34 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATATTTTTAAAAATTTAATATTTTTATTTAAA
Found at i:3745758 original size:2 final size:2
Alignment explanation
Indices: 3745753--3745777 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3745743 ATATATATAT
3745753 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
3745778 AATAAAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3749644 original size:22 final size:21
Alignment explanation
Indices: 3749619--3749660 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3749609 TAATAAAAAA
3749619 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
3749639 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
3749660 A
1 A
3749661 AATCAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:3750118 original size:20 final size:20
Alignment explanation
Indices: 3750080--3750118 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3750070 TTAAAACTTT
* *
3750080 TTAAAAATAATTTTTATTAA
1 TTAAAAATAATTATAATTAA
3750100 TTAAAAATAATTATAATTA
1 TTAAAAATAATTATAATTA
3750119 TTTTTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAAATAATTATAATTAA
Found at i:3751284 original size:18 final size:19
Alignment explanation
Indices: 3751255--3751296 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
3751245 ATATTTGACA
* *
3751255 TAAATATATTTAATTTTTT
1 TAAATATATTTAATATATT
3751274 TAAAT-TATTTAATATATT
1 TAAATATATTTAATATATT
3751292 TAAAT
1 TAAAT
3751297 GATCATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAAATATATTTAATATATT
Found at i:3752741 original size:3 final size:3
Alignment explanation
Indices: 3752733--3752761 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3752723 TGGTCCTAAC
3752733 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
3752762 AGAACAGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:3753148 original size:17 final size:18
Alignment explanation
Indices: 3753126--3753159 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3753116 ATTCGTCAAT
*
3753126 ATATTTTATTTT-TATTG
1 ATATTTAATTTTATATTG
3753143 ATATTTAATTTTATATT
1 ATATTTAATTTTATATT
3753160 TTAAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATATTTAATTTTATATTG
Found at i:3753550 original size:18 final size:16
Alignment explanation
Indices: 3753525--3753568 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
3753515 GTTTTAATTA
3753525 AAAATAAAAGTTAAAT
1 AAAATAAAAGTTAAAT
*
3753541 ATATAATAAAA-TTTAAT
1 A-A-AATAAAAGTTAAAT
3753558 AAAATAAAAGT
1 AAAATAAAAGT
3753569 AGAATAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 7 0.29
16 3 0.12
17 7 0.29
18 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATAAAAGTTAAAT
Found at i:3753770 original size:13 final size:14
Alignment explanation
Indices: 3753742--3753787 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3753732 AGATACGAAT
*
3753742 AATTATATAACATAA
1 AATT-TATAATATAA
3753757 AATTTATAAT-TAA
1 AATTTATAATATAA
3753770 AA--TATAATATAA
1 AATTTATAATATAA
3753782 AATTTA
1 AATTTA
3753788 ACACAATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
11 6 0.22
12 5 0.19
13 5 0.19
14 7 0.26
15 4 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTATAATATAA
Found at i:3753807 original size:29 final size:29
Alignment explanation
Indices: 3753767--3753848 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 29
3753757 AATTTATAAT
*
3753767 TAAAATATAATATAAAATTTAACA-CAATA
1 TAAAA-ATAATATAAAATTTAACATAAATA
*
3753796 TGAAAAATAATAT-AAATTTAATATAAATA
1 T-AAAAATAATATAAAATTTAACATAAATA
*
3753825 TATAAAT-ATATAAAATTTAA-ATAA
1 TAAAAATAATATAAAATTTAACATAA
3753849 CATAATTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 8 0.17
28 22 0.47
29 13 0.28
30 4 0.09
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (29 bp):
TAAAAATAATATAAAATTTAACATAAATA
Found at i:3754248 original size:10 final size:10
Alignment explanation
Indices: 3754233--3754258 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3754223 CATAAATTTT
3754233 AAATTTATAA
1 AAATTTATAA
3754243 AAATTTATAA
1 AAATTTATAA
3754253 AAATTT
1 AAATTT
3754259 CAAATTCATT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAATTTATAA
Found at i:3755068 original size:9 final size:10
Alignment explanation
Indices: 3755050--3755082 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
3755040 ATTTTATATG
3755050 ATTTATATTT
1 ATTTATATTT
3755060 ATTTA-ATTT
1 ATTTATATTT
3755069 ATTTATTATTT
1 ATTTA-TATTT
3755080 ATT
1 ATT
3755083 ATTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 5 0.24
11 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTATATTT
Found at i:3755125 original size:28 final size:28
Alignment explanation
Indices: 3755075--3755158 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
3755065 ATTTATTTAT
* * *
3755075 TATTTATT-ATTTTTATATAAATAATAA
1 TATTTATTAAATTTTAAATTAATAATAA
*
3755102 TATTTATTAAATTTTAAATTAATAAAAA
1 TATTTATTAAATTTTAAATTAATAATAA
*
3755130 TATTTAATTATATATTTAATATTAA-AATA
1 TATTT-ATTAAAT-TTTAA-ATTAATAATA
3755159 TTATAATCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
27 8 0.17
28 20 0.43
29 6 0.13
30 8 0.17
31 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TATTTATTAAATTTTAAATTAATAATAA
Found at i:3755170 original size:17 final size:16
Alignment explanation
Indices: 3755141--3755181 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
3755131 ATTTAATTAT
3755141 ATATT-TAATATTAAA
1 ATATTATAATATTAAA
3755156 ATATTATAATCATTAAA
1 ATATTATAAT-ATTAAA
3755173 ATATGTATA
1 ATAT-TATA
3755182 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.22
16 4 0.17
17 10 0.43
18 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
ATATTATAATATTAAA
Found at i:3755764 original size:18 final size:18
Alignment explanation
Indices: 3755724--3755770 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3755714 ATTCTTTAAG
*
3755724 CTTTTCCTTTTTACTTTTA
1 CTTTTCC-TTTTACCTTTA
3755743 CTTTTCCTTTT-CCTTTA
1 CTTTTCCTTTTACCTTTA
*
3755760 CCTTTACCTTT
1 -CTTTTCCTTT
3755771 ACCCACTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 13 0.52
19 7 0.28
ACGTcount: A:0.09, C:0.28, G:0.00, T:0.64
Consensus pattern (18 bp):
CTTTTCCTTTTACCTTTA
Found at i:3756088 original size:23 final size:23
Alignment explanation
Indices: 3756062--3756106 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3756052 AAATTTTTTT
*
3756062 ATAAAAAAATATATAAATTAAAA
1 ATAAAAAAATACATAAATTAAAA
* *
3756085 ATAAAAAATTACATATATTAAA
1 ATAAAAAAATACATAAATTAAA
3756107 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
ATAAAAAAATACATAAATTAAAA
Found at i:3756771 original size:15 final size:15
Alignment explanation
Indices: 3756743--3756779 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3756733 TTAAATTTTT
3756743 TTATTTT-TTATTTA
1 TTATTTTATTATTTA
3756757 TTATTTTATTATTTA
1 TTATTTTATTATTTA
*
3756772 TTACTTTA
1 TTATTTTA
3756780 AATTCTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTTTATTATTTA
Found at i:3758764 original size:20 final size:20
Alignment explanation
Indices: 3758713--3758855 Score: 80
Period size: 20 Copynumber: 7.2 Consensus size: 20
3758703 TTAATTTAAA
* *
3758713 TTTATAATAAATATATAA-A
1 TTTATAATAAATAAATAATT
* *
3758732 TAT-TAATATATAAATAATT
1 TTTATAATAAATAAATAATT
3758751 TTTATAATAAATAAATAATT
1 TTTATAATAAATAAATAATT
* * ** * *
3758771 AATTATATTTTATACATAATA
1 -TTTATAATAAATAAATAATT
*
3758792 ATTA-AAT-AATAAAT-ATT
1 TTTATAATAAATAAATAATT
* *
3758809 TATTTTAATAATTTATCAATAATT
1 T-TTATAATAA---ATAAATAATT
*
3758833 TTTATAATAAATAATTAATT
1 TTTATAATAAATAAATAATT
3758853 TTT
1 TTT
3758856 TTTTAAATCT
Statistics
Matches: 92, Mismatches: 22, Indels: 19
0.69 0.17 0.14
Matches are distributed among these distances:
17 2 0.02
18 19 0.21
19 9 0.10
20 31 0.34
21 14 0.15
23 13 0.14
24 4 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTATAATAAATAAATAATT
Found at i:3758798 original size:32 final size:33
Alignment explanation
Indices: 3758754--3758815 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
3758744 AATAATTTTT
*
3758754 ATAATAAATAAATAATTAAT-TATATTTTATAC
1 ATAATAAATAAATAATAAATATATATTTTATAC
* *
3758786 ATAATAATTAAATAATAAATATTTATTTTA
1 ATAATAAATAAATAATAAATATATATTTTA
3758816 ATAATTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (33 bp):
ATAATAAATAAATAATAAATATATATTTTATAC
Found at i:3760574 original size:22 final size:21
Alignment explanation
Indices: 3760546--3760600 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3760536 TTTTATTTTT
3760546 TAAATTAAATTAAATAAATAAA
1 TAAATTAAATTAAATAAA-AAA
* *
3760568 TAAATTAATATTTAATTAAAAA
1 TAAATTAA-ATTAAATAAAAAA
*
3760590 TACA-TAAATTA
1 TAAATTAAATTA
3760601 TATGTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.11
21 3 0.11
22 14 0.50
23 8 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATTAAATTAAATAAAAAA
Found at i:3760677 original size:14 final size:15
Alignment explanation
Indices: 3760649--3760677 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3760639 TTAAATTAAA
3760649 TAATTAATTTTAATT
1 TAATTAATTTTAATT
3760664 TAATT-ATTTTAATT
1 TAATTAATTTTAATT
3760678 ACCTATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTAATTTTAATT
Found at i:3764770 original size:2 final size:2
Alignment explanation
Indices: 3764765--3764797 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3764755 ACTAAAAAAT
*
3764765 AC AC AC AC AC AC AC AC GC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3764798 TATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3764802 original size:2 final size:2
Alignment explanation
Indices: 3764797--3764834 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3764787 ACACACACAC
*
3764797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3764835 GAAAAGTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3767252 original size:6 final size:6
Alignment explanation
Indices: 3767243--3767271 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3767233 TTGACTTGGC
3767243 AATGGA AATGGA AATGGA AATGGA AATGG
1 AATGGA AATGGA AATGGA AATGGA AATGG
3767272 CCAACCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (6 bp):
AATGGA
Found at i:3767465 original size:14 final size:13
Alignment explanation
Indices: 3767431--3767488 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 13
3767421 TTATTTTTTA
3767431 ATAAAAATATATT
1 ATAAAAATATATT
** *
3767444 ATTTAAATTTAATT
1 ATAAAAATAT-ATT
3767458 ATAAAAATATA-T
1 ATAAAAATATATT
3767470 -TAAAAATA-A-T
1 ATAAAAATATATT
3767480 ATAAAAATA
1 ATAAAAATA
3767489 AAAATTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.05
11 16 0.43
12 1 0.03
13 8 0.22
14 10 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAAAATATATT
Found at i:3768746 original size:21 final size:21
Alignment explanation
Indices: 3768722--3768787 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
3768712 AGTGCTGCAG
3768722 CTTCGTCTCCGGCTCCTCAGC
1 CTTCGTCTCCGGCTCCTCAGC
* * * *
3768743 CTTCTGCCCCCGCCT-CTCAAC
1 CTTC-GTCTCCGGCTCCTCAGC
* * *
3768764 CTTCTTCTCCAGTTCCTCAGC
1 CTTCGTCTCCGGCTCCTCAGC
3768785 CTT
1 CTT
3768788 TTGCCCCTGC
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
20 4 0.12
21 21 0.66
22 7 0.22
ACGTcount: A:0.08, C:0.48, G:0.12, T:0.32
Consensus pattern (21 bp):
CTTCGTCTCCGGCTCCTCAGC
Found at i:3769379 original size:13 final size:14
Alignment explanation
Indices: 3769361--3769391 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3769351 TCAGCTGCTA
3769361 CACCACCG-TCCTC
1 CACCACCGCTCCTC
3769374 CACCACCGCTCCTC
1 CACCACCGCTCCTC
3769388 CACC
1 CACC
3769392 TCCCACGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.16, C:0.65, G:0.06, T:0.13
Consensus pattern (14 bp):
CACCACCGCTCCTC
Found at i:3770615 original size:2 final size:2
Alignment explanation
Indices: 3770608--3770657 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3770598 AGAATCTACA
3770608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3770650 AT AT AT AT
1 AT AT AT AT
3770658 TGAGCTTAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3773725 original size:20 final size:20
Alignment explanation
Indices: 3773700--3773755 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
3773690 CTGTTTTAAA
3773700 AATATATTAAAAATA-ATTAC
1 AATATA-TAAAAATATATTAC
3773720 AATATATAAAAATATATTA-
1 AATATATAAAAATATATTAC
3773739 ATATAATATAAAAATAT
1 A-AT-ATATAAAAATAT
3773756 GAATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.27
20 12 0.36
21 12 0.36
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATATAAAAATATATTAC
Found at i:3773828 original size:19 final size:18
Alignment explanation
Indices: 3773804--3773888 Score: 54
Period size: 17 Copynumber: 4.8 Consensus size: 18
3773794 GTATGTTTTT
3773804 TTATATTTTTATTTTTATA
1 TTATATTTTTATTTTTA-A
*
3773823 TTATA-TTATA-TTTTAA
1 TTATATTTTTATTTTTAA
* *
3773839 TTATTTTTTTA-TGTTAA
1 TTATATTTTTATTTTTAA
* * *
3773856 TTA-AATATCATATTTTAA
1 TTATATTTTTAT-TTTTAA
3773874 TT-TATTTTATATTTT
1 TTATATTTT-TATTTT
3773889 AGATAGTTTA
Statistics
Matches: 49, Mismatches: 12, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
16 8 0.16
17 17 0.35
18 17 0.35
19 7 0.14
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (18 bp):
TTATATTTTTATTTTTAA
Found at i:3773831 original size:16 final size:15
Alignment explanation
Indices: 3773801--3773848 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
3773791 TTGGTATGTT
3773801 TTTTTATATT-TTTA
1 TTTTTATATTATTTA
3773815 TTTTTATATTATATTA
1 TTTTTATATTAT-TTA
3773831 TATTTTA-ATTATTT-
1 T-TTTTATATTATTTA
3773845 TTTT
1 TTTT
3773849 ATGTTAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.10
14 11 0.35
15 3 0.10
16 9 0.29
17 5 0.16
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTATATTATTTA
Found at i:3773850 original size:35 final size:35
Alignment explanation
Indices: 3773803--3773881 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
3773793 GGTATGTTTT
* * *
3773803 TTTATATTTTTATTTTTATATT-ATATTATATTTTAA
1 TTTATTTTTTTA-TGTTA-ATTAATATCATATTTTAA
3773839 -TTATTTTTTTATGTTAATTAAATATCATATTTTAA
1 TTTATTTTTTTATGTTAATT-AATATCATATTTTAA
3773874 TTTATTTT
1 TTTATTTT
3773882 ATATTTTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 3 0.08
34 4 0.11
35 23 0.62
36 7 0.19
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (35 bp):
TTTATTTTTTTATGTTAATTAATATCATATTTTAA
Found at i:3773978 original size:55 final size:55
Alignment explanation
Indices: 3773865--3773978 Score: 129
Period size: 55 Copynumber: 2.1 Consensus size: 55
3773855 ATTAAATATC
** * * * * * *
3773865 ATATTTTAATTTATTTTATATTTTAGATAGTTTATCATATTTATGTATTTTTATA
1 ATATTTTAATTTAACTTATATATTAGATAATTTATCATATTAATGTAATTTAAAA
* * *
3773920 ATATTTTTATTTAACTTATATATTATATAATTTATCATATTAATTTAATTTAAAA
1 ATATTTTAATTTAACTTATATATTAGATAATTTATCATATTAATGTAATTTAAAA
3773975 ATAT
1 ATAT
3773979 ATATTGATAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (55 bp):
ATATTTTAATTTAACTTATATATTAGATAATTTATCATATTAATGTAATTTAAAA
Found at i:3774036 original size:5 final size:5
Alignment explanation
Indices: 3774026--3774189 Score: 50
Period size: 5 Copynumber: 32.0 Consensus size: 5
3774016 TACGTATTAA
* * * * *
3774026 TATTT TATTT TATTT AAATTT TAATA TATTTAT TAATT TATAT TATTTT
1 TATTT TATTT TATTT -TATTT TATTT TA-TT-T TATTT TATTT TA-TTT
** * * * *
3774075 TATAC TATTT TA-TA TATTA TATAT TATTT TAATTAT T-TTT ATATTA
1 TATTT TATTT TATTT TATTT TATTT TATTT T-ATT-T TATTT -TATTT
* ** * * * *
3774121 TATTT TAATT TATTT TATATT TATAA TA-TT TATTA TA-AT AATTT AATTT
1 TATTT TATTT TATTT TAT-TT TATTT TATTT TATTT TATTT TATTT TATTT
3774170 TAATTT TATTT TA-TT TATTT
1 T-ATTT TATTT TATTT TATTT
3774190 AAAAATTAAC
Statistics
Matches: 113, Mismatches: 32, Indels: 28
0.65 0.18 0.16
Matches are distributed among these distances:
4 11 0.10
5 73 0.65
6 25 0.22
7 4 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.66
Consensus pattern (5 bp):
TATTT
Found at i:3774055 original size:16 final size:17
Alignment explanation
Indices: 3774022--3774112 Score: 53
Period size: 19 Copynumber: 5.1 Consensus size: 17
3774012 TTTTTACGTA
* *
3774022 TTAATATTTTATTTTAT
1 TTAATATTTTAATATAT
3774039 TTAA-ATTTTAATATAT
1 TTAATATTTTAATATAT
* * *
3774055 TTATTAATTTATATTATTT
1 TTAAT-ATTT-TAATATAT
3774074 TTATACTATTTT-ATATAT
1 TTA-A-TATTTTAATATAT
3774092 TATATATTATTTTAAT-TAT
1 T-TA-A-TATTTTAATATAT
3774111 TT
1 TT
3774113 TTATATTATA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
16 13 0.22
17 4 0.07
18 10 0.17
19 24 0.41
20 6 0.10
21 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATATTTTAATATAT
Found at i:3774076 original size:19 final size:19
Alignment explanation
Indices: 3774054--3774156 Score: 70
Period size: 19 Copynumber: 5.3 Consensus size: 19
3774044 TTTTAATATA
*
3774054 TTTATTAATTTATATTATT
1 TTTATTATTTTATATTATT
3774073 TTTATACTATTTTATA-TATT
1 TTTAT--TATTTTATATTATT
*
3774093 ATATATTATTTTA-ATTATT
1 -TTTATTATTTTATATTATT
* *
3774112 TTTA-TATTATATTTTAATT
1 TTTATTATTTTATATT-ATT
*
3774131 TATT-TTATATTTATAATATT
1 T-TTATTAT-TTTATATTATT
3774151 TATTAT
1 T-TTAT
3774157 AATAATTTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
17 6 0.09
18 6 0.09
19 20 0.30
20 16 0.24
21 18 0.27
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATTATTTTATATTATT
Found at i:3774078 original size:11 final size:11
Alignment explanation
Indices: 3774062--3774141 Score: 75
Period size: 10 Copynumber: 7.7 Consensus size: 11
3774052 TATTTATTAA
3774062 TTTATATTATT
1 TTTATATTATT
*
3774073 TTTATACTA-T
1 TTTATATTATT
3774083 TTTATA-TA-T
1 TTTATATTATT
*
3774092 TATATATTA-T
1 TTTATATTATT
3774102 TTTA-ATTATT
1 TTTATATTATT
3774112 TTTATATTATAT
1 TTTATATTAT-T
3774124 TTTA-ATT-TAT
1 TTTATATTAT-T
3774134 TTTATATT
1 TTTATATT
3774142 TATAATATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
9 12 0.20
10 25 0.41
11 19 0.31
12 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATATTATT
Found at i:3774110 original size:39 final size:39
Alignment explanation
Indices: 3774030--3774189 Score: 138
Period size: 39 Copynumber: 4.2 Consensus size: 39
3774020 TATTAATATT
* * *
3774030 TTATTTTATTTAA-ATTTTAATA-TATTTATTAATTTATA
1 TTATTTT-TATAATATTTTAATATTATATATTATTTTATA
*
3774068 TTATTTTTATACTATTTTATATATTATATATTATTTTA-A
1 TTATTTTTATAATATTTTA-ATATTATATATTATTTTATA
3774107 TTATTTTTATATTATATTTTAAT-TTAT-T-TTATATTTATA
1 TTATTTTTATA--ATATTTTAATATTATATATTAT-TTTATA
* * * *
3774146 ATATTTATTATAATAATTTAATTTTA-ATTTTATTTTAT-
1 TTATTT-TTATAATATTTTAATATTATATATTATTTTATA
3774184 TTATTT
1 TTATTT
3774190 AAAAATTAAC
Statistics
Matches: 103, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
37 7 0.07
38 32 0.31
39 34 0.33
40 23 0.22
41 7 0.07
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.66
Consensus pattern (39 bp):
TTATTTTTATAATATTTTAATATTATATATTATTTTATA
Found at i:3774124 original size:22 final size:23
Alignment explanation
Indices: 3774096--3774141 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
3774086 ATATATTATA
3774096 TATTATTTTAA-TTATTTTTATAT
1 TATTATTTTAATTTA-TTTTATAT
3774119 TA-TATTTTAATTTATTTTATAT
1 TATTATTTTAATTTATTTTATAT
3774141 T
1 T
3774142 TATAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTATTTTAATTTATTTTATAT
Found at i:3774138 original size:28 final size:27
Alignment explanation
Indices: 3774029--3774190 Score: 94
Period size: 27 Copynumber: 6.1 Consensus size: 27
3774019 GTATTAATAT
* *
3774029 TTTA-TTTTAT-TTAAATTTTAATATA
1 TTTATTTTTATATTATATTTTAATTTA
3774054 TTTATTAATTTATATTAT-TTTT-A--TA
1 TTTATT--TTTATATTATATTTTAATTTA
* * *
3774079 -CTATTTTATATATTATATATTATTTTA
1 TTTATTTT-TATATTATATTTTAATTTA
*
3774106 ATTATTTTTATATTATATTTTAATTTA
1 TTTATTTTTATATTATATTTTAATTTA
* *
3774133 TTTTATATTTATAATATT-TATTATAA-TAA
1 -TTTAT-TTT-T-ATATTATATTTTAATTTA
* *
3774162 TTTAATTTTA-ATTTTATTTT-ATTTA
1 TTTATTTTTATATTATATTTTAATTTA
3774187 TTTA
1 TTTA
3774191 AAAATTAACA
Statistics
Matches: 108, Mismatches: 13, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
22 2 0.02
23 8 0.07
24 11 0.10
25 18 0.17
26 2 0.02
27 23 0.21
28 23 0.21
29 8 0.07
30 8 0.07
31 5 0.05
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTATTTTTATATTATATTTTAATTTA
Found at i:3774163 original size:55 final size:51
Alignment explanation
Indices: 3774058--3774189 Score: 139
Period size: 51 Copynumber: 2.5 Consensus size: 51
3774048 AATATATTTA
*
3774058 TTAA-TTTATATTAT-TTTTATACTATTTTATATATTATATATTATTTTAA-
1 TTAATTTTATATTATATTTTAT-TTATTTTATATATTATATATTATTTTAAT
*
3774107 TTATTTTTATATTATATTTTAATTTATTTTATAT-TTATAATATTTATTATAATAAT
1 TTAATTTTATATTATATTTT-ATTTATTTTATATATTAT-ATA-TTATT-T--TAAT
*
3774163 TTAATTTTA-ATTTTATTTTATTTATTT
1 TTAATTTTATATTATATTTTATTTATTT
3774190 AAAAATTAAC
Statistics
Matches: 70, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
49 3 0.04
50 14 0.20
51 17 0.24
52 7 0.10
53 1 0.01
54 8 0.11
55 12 0.17
56 8 0.11
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (51 bp):
TTAATTTTATATTATATTTTATTTATTTTATATATTATATATTATTTTAAT
Found at i:3774178 original size:34 final size:32
Alignment explanation
Indices: 3774052--3774196 Score: 91
Period size: 33 Copynumber: 4.4 Consensus size: 32
3774042 AATTTTAATA
* * * *
3774052 TATTTATTAATTTATATTATTTTTATACTATTT
1 TATTTAATAATTTATTTTATATTTATAATA-TT
* * *
3774085 TATATATTATATATTATTTTAATTATTT-TTATATT
1 TATTTAATA-AT-TTATTTT-A-TATTTATAATATT
3774120 ATATTT--TAATTTATTTTATATTTATAATATT
1 -TATTTAATAATTTATTTTATATTTATAATATT
**
3774151 TATTATAATAATTTAATTTTA-ATTTTATTTTATT
1 TATT-TAATAATTT-ATTTTATA-TTTATAATATT
*
3774185 TATTTAAAAATT
1 TATTTAATAATT
3774197 AACATATGAA
Statistics
Matches: 91, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
30 9 0.10
31 8 0.09
32 7 0.08
33 24 0.26
34 23 0.25
35 8 0.09
36 8 0.09
37 4 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (32 bp):
TATTTAATAATTTATTTTATATTTATAATATT
Found at i:3774182 original size:67 final size:66
Alignment explanation
Indices: 3774058--3774187 Score: 158
Period size: 67 Copynumber: 2.0 Consensus size: 66
3774048 AATATATTTA
* * *
3774058 TTAATTTATATTATTTTTATACTATTTTATATATTATATATTATTTTAATTATTTTTATATTATA
1 TTAATTTATATTATATTTATAATATTTTATATAATATATATTATTTTAATTATTTTTAT-TTATA
3774123 TT
65 TT
* *
3774125 TTAATTTATTTTATATTTATAATA-TTTATTATAATA-AT-TTAATTTTAATTTTATTTTATTTA
1 TTAATTTATATTATATTTATAATATTTTA-TATAATATATATT-ATTTTAATTAT-TTTTATTTA
3774187 T
63 T
3774188 TTAAAAATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
65 2 0.04
66 20 0.36
67 33 0.60
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (66 bp):
TTAATTTATATTATATTTATAATATTTTATATAATATATATTATTTTAATTATTTTTATTTATAT
T
Found at i:3774223 original size:20 final size:20
Alignment explanation
Indices: 3774200--3774237 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3774190 AAAAATTAAC
3774200 ATATGAAT-TAAATTATTAGT
1 ATATGAATATAAA-TATTAGT
*
3774220 ATATTAATATAAATATTA
1 ATATGAATATAAATATTA
3774238 TATTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATATGAATATAAATATTAGT
Found at i:3776002 original size:2 final size:2
Alignment explanation
Indices: 3775995--3776023 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3775985 CAACTCTGGG
3775995 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3776024 CCATCTCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3777205 original size:2 final size:2
Alignment explanation
Indices: 3777198--3777223 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3777188 GTTAGCCTTC
3777198 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
3777224 GTTTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3778143 original size:21 final size:21
Alignment explanation
Indices: 3778119--3778161 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3778109 TATTCTAAAG
* *
3778119 AATAGATATATATATATATTT
1 AATAGAAATATAAATATATTT
* *
3778140 AATATAAATATAAATATTTTT
1 AATAGAAATATAAATATATTT
3778161 A
1 A
3778162 TATATTTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AATAGAAATATAAATATATTT
Found at i:3778166 original size:29 final size:29
Alignment explanation
Indices: 3778124--3778216 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
3778114 TAAAGAATAG
*
3778124 ATATATATATATATTTAATATAAATATAA
1 ATATTTATATATATTTAATATAAATATAA
* **
3778153 ATATTTTTATATATTTAA-ATAATTATATTTT
1 ATATTTATATATATTTAATATAA--ATA-TAA
*
3778184 ATATTTATATATAATTTAATATTTAATATAA
1 ATATTTATATAT-ATTTAATA-TAAATATAA
3778215 AT
1 AT
3778217 TTAAAAATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
28 4 0.08
29 16 0.32
30 3 0.06
31 15 0.30
32 9 0.18
33 1 0.02
34 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATATTTATATATATTTAATATAAATATAA
Found at i:3778201 original size:17 final size:16
Alignment explanation
Indices: 3778176--3778219 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
3778166 TTTAAATAAT
*
3778176 TATATTTTATATTTATA
1 TATAATTTATATTTA-A
3778193 TATAATTTAATATTTAA
1 TATAATTT-ATATTTAA
3778210 TATAAATTTA
1 TAT-AATTTA
3778220 AAAATAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATAATTTATATTTAA
Found at i:3778212 original size:25 final size:21
Alignment explanation
Indices: 3778133--3778214 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
3778123 GATATATATA
* *
3778133 TATATTTAATA-TAAATATAAA
1 TATATTTAATATTTAA-ATAAT
*
3778154 TATTTTTATATATTTAAATAAT
1 TATATTTA-ATATTTAAATAAT
* *
3778176 TATATTTTATATTTATAT-A-
1 TATATTTAATATTTAAATAAT
3778195 TA-ATTTAATATTTAATATAA
1 TATATTTAATATTTAA-ATAA
3778215 ATTTAAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
18 11 0.22
19 4 0.08
20 2 0.04
21 16 0.33
22 13 0.27
23 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATATTTAATATTTAAATAAT
Found at i:3778217 original size:18 final size:18
Alignment explanation
Indices: 3778134--3778220 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 18
3778124 ATATATATAT
*
3778134 ATATTTAATATAAATATAA
1 ATATTTAATATAAAT-TTA
* *
3778153 ATATTT-TTATATATTTA
1 ATATTTAATATAAATTTA
* *
3778170 A-A--TAAT-TATATTTT
1 ATATTTAATATAAATTTA
3778184 ATATTT-ATATATAATTTA
1 ATATTTAATATA-AATTTA
3778202 ATATTTAATATAAATTTA
1 ATATTTAATATAAATTTA
3778220 A
1 A
3778221 AAATAAGTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
14 9 0.17
15 2 0.04
16 3 0.06
17 6 0.11
18 23 0.43
19 11 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTAATATAAATTTA
Found at i:3784850 original size:34 final size:34
Alignment explanation
Indices: 3784802--3784867 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
3784792 TTTCCTTAGG
*
3784802 AAGAACTTTTCTGAAATTATTTCTTGGGTCTAGT
1 AAGAACTTTCCTGAAATTATTTCTTGGGTCTAGT
3784836 AAGAACTTTCCTGAAATTATTTCTTGGGTCTA
1 AAGAACTTTCCTGAAATTATTTCTTGGGTCTA
3784868 TAATTAGTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (34 bp):
AAGAACTTTCCTGAAATTATTTCTTGGGTCTAGT
Found at i:3792475 original size:24 final size:24
Alignment explanation
Indices: 3792448--3792495 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3792438 TAGGATACCT
3792448 TCATTTTACGTTGTTCTTATTGCA
1 TCATTTTACGTTGTTCTTATTGCA
3792472 TCATTTTACGTTGTTCTTATTGCA
1 TCATTTTACGTTGTTCTTATTGCA
3792496 GGGTGTTGCA
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:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (24 bp):
TCATTTTACGTTGTTCTTATTGCA
Found at i:3796978 original size:18 final size:18
Alignment explanation
Indices: 3796957--3796992 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3796947 TAATATTATA
3796957 TTATATTATAATTATTTT
1 TTATATTATAATTATTTT
*
3796975 TTATATTATATTTATTTT
1 TTATATTATAATTATTTT
3796993 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATATTATAATTATTTT
Found at i:3797259 original size:2 final size:2
Alignment explanation
Indices: 3797254--3797400 Score: 106
Period size: 2 Copynumber: 79.0 Consensus size: 2
3797244 TGTTATATTT
*
3797254 TA TA TA TA TA TA TA TA TA TA TA T- TA TG T- TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
3797293 T- TA -A TA TA AA TA TA TA TA AA CA -A CTA TA TC TA -A TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA TA
*
3797333 -A TA -A TA TA -A TA TA -A TA TA TA TA TA GTG TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
3797371 TA TA -A TA TA TA CA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3797401 ACATATAATA
Statistics
Matches: 117, Mismatches: 11, Indels: 34
0.72 0.07 0.21
Matches are distributed among these distances:
1 14 0.12
2 99 0.85
3 4 0.03
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3797300 original size:33 final size:35
Alignment explanation
Indices: 3797244--3797309 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3797234 AGTAATTTTT
* *
3797244 TGTTATATTTTATATATATATATATATATATATTA
1 TGTTATATTATATATATATATATAAATATATATTA
3797279 TGTTATATTATATAT-TA-ATATAAATATATAT
1 TGTTATATTATATATATATATATAAATATATAT
3797310 AAACAACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 13 0.45
34 2 0.07
35 14 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (35 bp):
TGTTATATTATATATATATATATAAATATATATTA
Found at i:3797326 original size:29 final size:29
Alignment explanation
Indices: 3797283--3797411 Score: 104
Period size: 29 Copynumber: 4.3 Consensus size: 29
3797273 ATATTATGTT
*
3797283 ATATTATATAT-TAATATAAATATATATA
1 ATATAATATATCTAATATAAATATATATA
*
3797311 A-ACAACTATATCTAATGATATAATA-ATATA
1 ATATAA-TATATCTAAT-ATA-AATATATATA
* **
3797341 ATATAATATATAT-ATAGTGTATATATATA
1 ATATAATATATCTAATA-TAAATATATATA
*
3797370 ATATAATATATACATAATATATATATATATAA
1 ATATAATATAT-C-TAATATAAATATATAT-A
3797402 CATATAATAT
1 -ATATAATAT
3797412 TTTATTTATT
Statistics
Matches: 81, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
27 2 0.02
28 10 0.12
29 23 0.28
30 15 0.19
31 18 0.22
32 4 0.05
33 9 0.11
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (29 bp):
ATATAATATATCTAATATAAATATATATA
Found at i:3797725 original size:29 final size:28
Alignment explanation
Indices: 3797682--3797757 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 28
3797672 TATAATTTAT
** *
3797682 TTAAATAAATT--AAAAAAATTAT-ACG
1 TTAAATAAATTGAAAAAAAAAAATAAAG
*
3797707 TTAAA-AAATTGAAAAAAAATAAATAAAT
1 TTAAATAAATTGAAAAAAAA-AAATAAAG
3797735 TTAAATAAATTGAAAAAAAAAAA
1 TTAAATAAATTGAAAAAAAAAAA
3797758 CAAAAATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 5 0.12
25 5 0.12
26 7 0.17
27 2 0.05
28 9 0.21
29 14 0.33
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (28 bp):
TTAAATAAATTGAAAAAAAAAAATAAAG
Found at i:3798150 original size:17 final size:17
Alignment explanation
Indices: 3798130--3798163 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3798120 AAAAGTAAAG
3798130 TAAAATAAAAAAAATTA
1 TAAAATAAAAAAAATTA
* *
3798147 TAAAATATAATAAATTA
1 TAAAATAAAAAAAATTA
3798164 GTAATTTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATAAAAAAAATTA
Found at i:3798237 original size:7 final size:7
Alignment explanation
Indices: 3798222--3798288 Score: 57
Period size: 7 Copynumber: 9.6 Consensus size: 7
3798212 AATAAATAAA
3798222 ATATTAT
1 ATATTAT
*
3798229 ATGTTAT
1 ATATTAT
3798236 ATATTAT
1 ATATTAT
*
3798243 GTATATATT
1 ATAT-TA-T
3798252 ATATTAT
1 ATATTAT
3798259 ATA-TAT
1 ATATTAT
** *
3798265 GCACTAT
1 ATATTAT
3798272 ATA-TAT
1 ATATTAT
3798278 ATATTAT
1 ATATTAT
3798285 ATAT
1 ATAT
3798289 AGTTGTTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 10 0.21
7 30 0.62
8 4 0.08
9 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (7 bp):
ATATTAT
Found at i:3798249 original size:2 final size:2
Alignment explanation
Indices: 3798233--3798367 Score: 87
Period size: 2 Copynumber: 72.5 Consensus size: 2
3798223 TATTATATGT
* * *
3798233 TA TA TA T- TA TG TA TA TA T- TA TA T- TA TA TA TA TG CA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
3798273 TA TA TA TA T- TA TA TA TA GT- TG TT TA TA TA TA TT TA TA T- TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3798313 -A TA TA TA -A TA TG TA TA TA TA -A CA TA TA -A CA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3798350 TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA T
3798368 GAAAAAAACA
Statistics
Matches: 105, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
1 12 0.11
2 91 0.87
3 2 0.02
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3801518 original size:6 final size:7
Alignment explanation
Indices: 3801496--3801525 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3801486 CCAAAGAAAC
3801496 AAACGAA
1 AAACGAA
3801503 AAACGAA
1 AAACGAA
3801510 AAACGAA
1 AAACGAA
*
3801517 AAATGAA
1 AAACGAA
3801524 AA
1 AA
3801526 TGGGGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.73, C:0.10, G:0.13, T:0.03
Consensus pattern (7 bp):
AAACGAA
Found at i:3801677 original size:2 final size:2
Alignment explanation
Indices: 3801670--3801700 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3801660 TAACAGCGAC
3801670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3801701 CCTTTCCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3803046 original size:7 final size:7
Alignment explanation
Indices: 3803030--3803059 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3803020 ATAAATATCG
3803030 ATAAATA
1 ATAAATA
*
3803037 ATAGATA
1 ATAAATA
3803044 ATAAATA
1 ATAAATA
3803051 ATAAATA
1 ATAAATA
3803058 AT
1 AT
3803060 TAAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (7 bp):
ATAAATA
Found at i:3803198 original size:22 final size:22
Alignment explanation
Indices: 3803127--3803201 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
3803117 TAAAATAAAT
* * *
3803127 TATAAATATTT-TATAATTTTA
1 TATATATATTTATATAAATATA
* *
3803148 TAATATAAATTTATATAAATATC
1 T-ATATATATTTATATAAATATA
* *
3803171 TTTATATATTTATATTAATATA
1 TATATATATTTATATAAATATA
3803193 TATATATAT
1 TATATATAT
3803202 ATATGTATTA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
21 1 0.02
22 33 0.79
23 8 0.19
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (22 bp):
TATATATATTTATATAAATATA
Found at i:3811722 original size:2 final size:2
Alignment explanation
Indices: 3811715--3811748 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3811705 ATGAATATGA
3811715 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
3811749 ATAGAGAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3817057 original size:2 final size:2
Alignment explanation
Indices: 3817050--3817098 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
3817040 TTTTCTTTCG
* *
3817050 TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC GC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3817092 TC TC TC T
1 TC TC TC T
3817099 TCTTCTTGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.04, T:0.47
Consensus pattern (2 bp):
TC
Found at i:3817937 original size:18 final size:19
Alignment explanation
Indices: 3817896--3817937 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3817886 ATCTAATATC
3817896 TATTTACATATTTAATTAT
1 TATTTACATATTTAATTAT
*
3817915 TATTTA-AT-TTTATATTTT
1 TATTTACATATTTA-ATTAT
3817933 TATTT
1 TATTT
3817938 TATAAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 11 0.52
19 6 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTACATATTTAATTAT
Found at i:3817971 original size:17 final size:17
Alignment explanation
Indices: 3817949--3817982 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3817939 ATAAAAAGTA
*
3817949 ATTTAATAAATTCAGAT
1 ATTTAAAAAATTCAGAT
*
3817966 ATTTAAAAAATTTAGAT
1 ATTTAAAAAATTCAGAT
3817983 TTTGACAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (17 bp):
ATTTAAAAAATTCAGAT
Found at i:3818505 original size:16 final size:17
Alignment explanation
Indices: 3818475--3818519 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
3818465 TATTTAATTT
3818475 TTATATTAAAAATATAA
1 TTATATTAAAAATATAA
*
3818492 TTAT-TTAAATATATAAA
1 TTATATTAAAAATAT-AA
3818509 TATATATTAAA
1 T-TATATTAAA
3818520 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.38
17 7 0.29
18 3 0.12
19 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATATTAAAAATATAA
Found at i:3822949 original size:29 final size:28
Alignment explanation
Indices: 3822904--3822982 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
3822894 AAAATATTTT
*
3822904 TATT-TAAATTTAATTTA-AATTTAGATTAA
1 TATTATAAATTTATTTTATAATTTA-A--AA
*
3822933 T-TTATAAATTTATTTTATTATTTAAAA
1 TATTATAAATTTATTTTATAATTTAAAA
3822960 TATTATAAAATTTATTTTATAAT
1 TATTAT-AAATTTATTTTATAAT
3822983 AATATTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
27 3 0.07
28 6 0.14
29 29 0.67
30 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
TATTATAAATTTATTTTATAATTTAAAA
Found at i:3822972 original size:25 final size:26
Alignment explanation
Indices: 3822944--3823019 Score: 63
Period size: 25 Copynumber: 3.0 Consensus size: 26
3822934 TTATAAATTT
3822944 ATTTTATTATT-TAA-AATATTATAAA
1 ATTTTATTATTATAATAATATT-TAAA
* *
3822969 A-TTTATT-TTATAATAATATTTTAT
1 ATTTTATTATTATAATAATATTTAAA
*
3822993 ATTTTATTA-AATAAATAATAATTTAAA
1 ATTTTATTATTAT-AATAAT-ATTTAAA
3823020 TTAAATCGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
23 2 0.05
24 12 0.30
25 15 0.38
26 6 0.15
27 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTTATTATTATAATAATATTTAAA
Found at i:3823456 original size:2 final size:2
Alignment explanation
Indices: 3823412--3823441 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3823402 TCGGTCTAAC
3823412 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
3823442 TGACCTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3823485 original size:2 final size:2
Alignment explanation
Indices: 3823478--3823502 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3823468 TCCAATCATT
3823478 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3823503 ATATATATAT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3823759 original size:14 final size:15
Alignment explanation
Indices: 3823742--3823771 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3823732 CATTTAATAA
3823742 TTTATTTATAT-TAT
1 TTTATTTATATATAT
3823756 TTTATTTATATATAT
1 TTTATTTATATATAT
3823771 T
1 T
3823772 ATCCTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTTATATATAT
Found at i:3824204 original size:23 final size:23
Alignment explanation
Indices: 3824122--3824211 Score: 94
Period size: 23 Copynumber: 3.9 Consensus size: 23
3824112 ACTAATGATA
* **
3824122 ATTTTTTTAATTCCTTAAATATT
1 ATTTTTTAAATTTATTAAATATT
* *
3824145 ATTTTTTAAATTTGTT-AATATA
1 ATTTTTTAAATTTATTAAATATT
3824167 ATTTTTTAAAATTTAATTAAATATT
1 ATTTTTT-AAATTT-ATTAAATATT
*
3824192 ATTTTTT-ATTTTATTAAATA
1 ATTTTTTAAATTTATTAAATA
3824212 ATAATAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
22 20 0.35
23 23 0.40
24 2 0.04
25 12 0.21
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (23 bp):
ATTTTTTAAATTTATTAAATATT
Found at i:3824207 original size:22 final size:23
Alignment explanation
Indices: 3824136--3824211 Score: 84
Period size: 22 Copynumber: 3.3 Consensus size: 23
3824126 TTTTAATTCC
* *
3824136 TTAAATATTATTTTTTAAATTTG
1 TTAAATATTATTTTTTAATTTTA
* *
3824159 TT-AATATAATTTTTTAAAATTTAA
1 TTAAATATTATTTTTT--AATTTTA
3824183 TTAAATATTATTTTTT-ATTTTA
1 TTAAATATTATTTTTTAATTTTA
3824205 TTAAATA
1 TTAAATA
3824212 ATAATAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 24 0.55
23 2 0.05
24 6 0.14
25 12 0.27
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (23 bp):
TTAAATATTATTTTTTAATTTTA
Found at i:3824209 original size:33 final size:33
Alignment explanation
Indices: 3824167--3824318 Score: 87
Period size: 32 Copynumber: 4.4 Consensus size: 33
3824157 TGTTAATATA
3824167 ATTTT-TTAAAATTTAATTAAATATTATTTTTT
1 ATTTTATTAAAATTTAATTAAATATTATTTTTT
* * *
3824199 ATTTTATT-AAA--TAATAATAATAAATACTTTTT
1 ATTTTATTAAAATTTAATTA-AAT-ATTATTTTTT
* * *
3824231 ATTTTTATAAAAACATATAATTAATATTTTAATTTGTTAAT
1 A-TTTTAT-TAAA-ATTTAATTAA-ATATT-ATTT-TT--T
* * *
3824272 ATAATTTTTTAAAATTTACTTAAATATTATTTTTA
1 AT--TTTATTAAAATTTAATTAAATATTATTTTTT
3824307 ATTTTATTAAAA
1 ATTTTATTAAAA
3824319 AATAATAATA
Statistics
Matches: 89, Mismatches: 15, Indels: 31
0.66 0.11 0.23
Matches are distributed among these distances:
30 5 0.06
31 3 0.03
32 17 0.19
33 17 0.19
35 4 0.04
36 1 0.01
37 4 0.04
38 14 0.16
39 6 0.07
40 9 0.10
41 5 0.06
42 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.55
Consensus pattern (33 bp):
ATTTTATTAAAATTTAATTAAATATTATTTTTT
Found at i:3824311 original size:108 final size:111
Alignment explanation
Indices: 3824148--3824439 Score: 379
Period size: 108 Copynumber: 2.6 Consensus size: 111
3824138 AAATATTATT
3824148 TTTTAAATTTGTTAATATAATTTTTTAAAATTTAATTAAATATTATTTTTTATTTTATTAAATAA
1 TTTT-AATTTGTTAATATAATTTTTTAAAATTTAATTAAATATTA-TTTTTATTTTATTAAATAA
*
3824213 TAATAATAA-ATA-C-TTTTT-A-TT-TTTATAAAAACATATAATTAATA
64 TAATAATAATAAACCTTTTTTAATTTATTTATAAAAA-A-ATAATTAATA
* *
3824257 TTTTAATTTGTTAATATAATTTTTTAAAATTTACTTAAATATTATTTTTAATTTTATTAAAAAAT
1 TTTTAATTTGTTAATATAATTTTTTAAAATTTAATTAAATATTATTTTT-ATTTTATTAAATAAT
*
3824322 AATAATAATAAACCTTTTTTAATTTAATTTTTAAAAAAATAATTAATA
65 AATAATAATAAACCTTTTTTAATTT-ATTTATAAAAAAATAATTAATA
* *
3824370 TTTTAATTTATTAATATAAAATTTTTTAAAA-TTAATTAAATATT-TTTTTA--TTATAAAATAA
1 TTTTAATTTGTTAATAT--AATTTTTTAAAATTTAATTAAATATTATTTTTATTTTATTAAATAA
3824431 TAATTAATA
64 TAA-TAATA
3824440 TATTATTATT
Statistics
Matches: 164, Mismatches: 8, Indels: 20
0.85 0.04 0.10
Matches are distributed among these distances:
107 5 0.03
108 61 0.37
109 6 0.04
110 13 0.08
111 10 0.06
112 2 0.01
113 33 0.20
114 13 0.08
115 21 0.13
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (111 bp):
TTTTAATTTGTTAATATAATTTTTTAAAATTTAATTAAATATTATTTTTATTTTATTAAATAATA
ATAATAATAAACCTTTTTTAATTTATTTATAAAAAAATAATTAATA
Found at i:3824457 original size:113 final size:110
Alignment explanation
Indices: 3824148--3824459 Score: 327
Period size: 113 Copynumber: 2.8 Consensus size: 110
3824138 AAATATTATT
* **
3824148 TTTTAAATTTGTTAATATAATTTTTTAAAATTTAATTAAATATTATTTTTTATTTTATTAAATAA
1 TTTT-AATTTGTTAATATAATTTTTTAAAATTTAATTAAATA-T-TTTTTTATTATAAAAAATAA
* *
3824213 TAATAA-TAA-ATACTT--TTTATTTTTATAAAAACATATAATTAATA
63 TAATAATTAATTTACTTAATTTAATTTTATAAAAACATATAATTAATA
*
3824257 TTTTAATTTGTTAATATAATTTTTTAAAATTTACTTAAATATTATTTTTAATTTTATTAAAAAAT
1 TTTTAATTTGTTAATATAATTTTTTAAAATTTAATTAAATATT-TTTTT-A--TTA-TAAAAAAT
* *
3824322 AATAATAATAAACCTTT-TTTAATTTAATTTT-TAAAAA-A-ATAATTAATA
61 AATAATAATTAA--TTTACTTAATTTAATTTTATAAAAACATATAATTAATA
*
3824370 TTTTAATTTATTAATATAAAATTTTTTAAAA-TTAATTAAATATTTTTTTATTATAAAATAATAA
1 TTTTAATTTGTTAATAT--AATTTTTTAAAATTTAATTAAATATTTTTTTATTATAAAA-AATAA
3824434 TTAATATATTATTATTTACTTAATTT
63 -TAATA-ATTA--ATTTACTTAATTT
3824460 TTTAAATTTT
Statistics
Matches: 172, Mismatches: 12, Indels: 34
0.79 0.06 0.16
Matches are distributed among these distances:
106 1 0.01
107 6 0.03
108 37 0.22
109 9 0.05
110 10 0.06
111 19 0.11
112 9 0.05
113 38 0.22
114 16 0.09
115 19 0.11
116 8 0.05
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (110 bp):
TTTTAATTTGTTAATATAATTTTTTAAAATTTAATTAAATATTTTTTTATTATAAAAAATAATAA
TAATTAATTTACTTAATTTAATTTTATAAAAACATATAATTAATA
Found at i:3824627 original size:15 final size:14
Alignment explanation
Indices: 3824583--3824626 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3824573 AACATACTCA
*
3824583 TAAAATAATTTATTT
1 TAAAA-AATTAATTT
3824598 TAAAAAATTAATTT
1 TAAAAAATTAATTT
*
3824612 TATAAAATTAATTT
1 TAAAAAATTAATTT
3824626 T
1 T
3824627 TTTAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 22 0.81
15 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAAAAATTAATTT
Found at i:3825440 original size:14 final size:14
Alignment explanation
Indices: 3825396--3825451 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
3825386 TTTTTTAGTA
3825396 TAAATA-AATATAAT
1 TAAATATAATAT-AT
* *
3825410 TAAAT-TAAAATTTT
1 TAAATATAATA-TAT
3825424 TAAATATAATATAT
1 TAAATATAATATAT
*
3825438 TAAATATATTATAT
1 TAAATATAATATAT
3825452 AATATTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 29 0.85
15 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATATAATATAT
Found at i:3825463 original size:21 final size:21
Alignment explanation
Indices: 3825414--3825480 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
3825404 TATAATTAAA
*
3825414 TTAAAATTTTTAAATATAATAT
1 TTAAAATTATT-AATATAATAT
3825436 ATT-AAATATATT-ATATAATAT
1 -TTAAAAT-TATTAATATAATAT
3825457 TTAAAATTATTGAATATAAT-T
1 TTAAAATTATT-AATATAATAT
3825478 TTA
1 TTA
3825481 TTGATTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
20 6 0.15
21 17 0.44
22 11 0.28
23 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TTAAAATTATTAATATAATAT
Found at i:3826972 original size:9 final size:9
Alignment explanation
Indices: 3826958--3826990 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
3826948 GACGGTGGGG
3826958 AAAAAAGAA
1 AAAAAAGAA
3826967 AAAAAAGAA
1 AAAAAAGAA
*
3826976 AAGAAAGAA
1 AAAAAAGAA
3826985 AAAAAA
1 AAAAAA
3826991 AGGCTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:3826979 original size:14 final size:14
Alignment explanation
Indices: 3826958--3826992 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
3826948 GACGGTGGGG
3826958 AAAAAAGAAA-AAA
1 AAAAAAGAAAGAAA
3826971 AAGAAAAGAAAGAAA
1 AA-AAAAGAAAGAAA
3826986 AAAAAAG
1 AAAAAAG
3826993 GCTAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 13 0.65
15 5 0.25
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAGAAA
Found at i:3827666 original size:2 final size:2
Alignment explanation
Indices: 3827659--3827704 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3827649 TCTCAATTTT
3827659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3827701 TA TA
1 TA TA
3827705 AAAGTTCTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3828045 original size:13 final size:13
Alignment explanation
Indices: 3828029--3828071 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
3828019 AATTAAATTA
3828029 AAAAAATATGTTT
1 AAAAAATATGTTT
* * *
3828042 AAAAAATGTGATG
1 AAAAAATATGTTT
3828055 AAAAAATA-GTTT
1 AAAAAATATGTTT
3828067 AAAAA
1 AAAAA
3828072 CTTTTAGTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (13 bp):
AAAAAATATGTTT
Found at i:3828162 original size:16 final size:18
Alignment explanation
Indices: 3828127--3828163 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3828117 AAATGTTAAA
*
3828127 AAAAATATTTAAAATAAT
1 AAAAATATTAAAAATAAT
3828145 AAAAAT-TTAAAAAT-AT
1 AAAAATATTAAAAATAAT
3828161 AAA
1 AAA
3828164 GATAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 7 0.39
18 6 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATATTAAAAATAAT
Found at i:3831136 original size:1 final size:1
Alignment explanation
Indices: 3831130--3831156 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3831120 TTATATAGCG
3831130 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
3831157 CTACCTCGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3832571 original size:10 final size:11
Alignment explanation
Indices: 3832522--3832642 Score: 63
Period size: 11 Copynumber: 10.8 Consensus size: 11
3832512 ATATTATAAA
*
3832522 TTTATATAAAT
1 TTTATATATAT
*
3832533 TTT-TATA-AG
1 TTTATATATAT
*
3832542 TTTATAATTTAT
1 TTTAT-ATATAT
3832554 TTTATATAT-T
1 TTTATATATAT
*
3832564 TTTTTATATAT
1 TTTATATATAT
*
3832575 TTTAAGTATTATAAA
1 TTT-A-TA-TAT-AT
*
3832590 TTTATATAAAT
1 TTTATATATAT
3832601 TTT-TATATA-
1 TTTATATATAT
* *
3832610 TTAATAATTTAT
1 TTTAT-ATATAT
*
3832622 TTTATTTATAT
1 TTTATATATAT
3832633 TTTGATATAT
1 TTT-ATATAT
3832643 TAATATATTT
Statistics
Matches: 82, Mismatches: 16, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
9 6 0.07
10 20 0.24
11 27 0.33
12 17 0.21
13 4 0.05
14 4 0.05
15 4 0.05
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
TTTATATATAT
Found at i:3832573 original size:14 final size:13
Alignment explanation
Indices: 3832542--3832576 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3832532 TTTTTATAAG
3832542 TTTATA-ATTTAT
1 TTTATATATTTAT
3832554 TTTATATATTT-T
1 TTTATATATTTAT
3832566 TTTATATATTT
1 TTTATATATTT
3832577 TAAGTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATATATTTAT
Found at i:3832596 original size:68 final size:68
Alignment explanation
Indices: 3832513--3832643 Score: 210
Period size: 68 Copynumber: 1.9 Consensus size: 68
3832503 TTTATTAAAA
* * *
3832513 TATTATAAATTTATATAAATTTTTATA-AGTTTATAATTTATTTTATATATTTTTTTATATATTT
1 TATTATAAATTTATATAAATTTTTATATA-TTAATAATTTATTTTATATATATTTTGATATATTT
3832577 TAAG
65 TAAG
*
3832581 TATTATAAATTTATATAAATTTTTATATATTAATAATTTATTTTATTTATATTTTGATATATT
1 TATTATAAATTTATATAAATTTTTATATATTAATAATTTATTTTATATATATTTTGATATATT
3832644 AATATATTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 57 0.98
69 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (68 bp):
TATTATAAATTTATATAAATTTTTATATATTAATAATTTATTTTATATATATTTTGATATATTTT
AAG
Found at i:3833016 original size:18 final size:17
Alignment explanation
Indices: 3832993--3833029 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3832983 TTATTTTATA
*
3832993 TAATTTATCATAATAATT
1 TAATTTATAATAA-AATT
3833011 TAATTTATAATAAAATT
1 TAATTTATAATAAAATT
3833028 TA
1 TA
3833030 TATACTCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTTATAATAAAATT
Found at i:3833162 original size:17 final size:17
Alignment explanation
Indices: 3833133--3833184 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 17
3833123 CAAAGTATTG
3833133 TATATTTATATAATTTT
1 TATATTTATATAATTTT
3833150 TATATATTA-ATAA--TT
1 TATAT-TTATATAATTTT
3833165 TAT-TTTATAT-ATTTT
1 TATATTTATATAATTTT
*
3833180 GATAT
1 TATAT
3833185 GTTTATGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
13 4 0.14
14 3 0.10
15 9 0.31
16 1 0.03
17 9 0.31
18 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TATATTTATATAATTTT
Done.