Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010868.1 Kokia drynarioides strain JFW-HI SEQ_125836, 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: 624094
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:431757 original size:33 final size:33
Alignment explanation
Indices: 431676--431825 Score: 95
Period size: 33 Copynumber: 4.5 Consensus size: 33
431666 TGTATATAGT
* ** * *
431676 CTCACATAATCCTAGGGTTCATAAAATCATATAGG
1 CTCACATAATCCTAGGATTC-GCATA-CATACAGG
*
431711 CTCACATACTCCTAGGATTCGCATACATACAGG
1 CTCACATAATCCTAGGATTCGCATACATACAGG
* * * ** *
431744 CTCGCATAATCCTAGGGTTCGCGTGTATAAACGG
1 CTCACATAATCCTAGGATTCGCATACATACA-GG
* * * * *
431778 TTCACATTATCTTAGGGTTCGCATATATATCA-G
1 CTCACATAATCCTAGGATTCGCATACATA-CAGG
*
431811 TTCACATAATCCTAG
1 CTCACATAATCCTAG
431826 AGTTCACATA
Statistics
Matches: 91, Mismatches: 22, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
33 45 0.49
34 27 0.30
35 19 0.21
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (33 bp):
CTCACATAATCCTAGGATTCGCATACATACAGG
Found at i:431836 original size:33 final size:33
Alignment explanation
Indices: 431777--431840 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
431767 TGTATAAACG
* * * *
431777 GTTCACATTATCTTAGGGTTCGCATATATATCA
1 GTTCACATAATCCTAGAGTTCACATATATATCA
431810 GTTCACATAATCCTAGAGTTCACATATATAT
1 GTTCACATAATCCTAGAGTTCACATATATAT
431841 ATATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (33 bp):
GTTCACATAATCCTAGAGTTCACATATATATCA
Found at i:431840 original size:2 final size:2
Alignment explanation
Indices: 431833--431867 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
431823 TAGAGTTCAC
431833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
431868 GGTTCACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:455508 original size:21 final size:21
Alignment explanation
Indices: 455482--455525 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
455472 GTTGTGAATT
455482 CTGGTTCAACACTTGGCTCAA
1 CTGGTTCAACACTTGGCTCAA
* **
455503 CTGGTTCATCTTTTGGCTCAA
1 CTGGTTCAACACTTGGCTCAA
455524 CT
1 CT
455526 TTTGGTTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (21 bp):
CTGGTTCAACACTTGGCTCAA
Found at i:460781 original size:34 final size:34
Alignment explanation
Indices: 460738--460805 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
460728 AAACTTCACA
460738 TAGTTCGACATTTGTTCTAAAGCCTCCACCAACG
1 TAGTTCGACATTTGTTCTAAAGCCTCCACCAACG
460772 TAGTTCGACATTTGTTCTAAAGCCTCCACCAACG
1 TAGTTCGACATTTGTTCTAAAGCCTCCACCAACG
460806 AAATATTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (34 bp):
TAGTTCGACATTTGTTCTAAAGCCTCCACCAACG
Found at i:461718 original size:23 final size:23
Alignment explanation
Indices: 461692--461744 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
461682 CTGATAACGA
461692 TCCTGAACTCTGGATACACGTCT
1 TCCTGAACTCTGGATACACGTCT
461715 TCCTGAACTCTGGATACACGTCT
1 TCCTGAACTCTGGATACACGTCT
461738 TCCTGAA
1 TCCTGAA
461745 GCTGCTCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (23 bp):
TCCTGAACTCTGGATACACGTCT
Found at i:468673 original size:17 final size:17
Alignment explanation
Indices: 468651--468683 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
468641 TTACTGCACC
468651 TACGACTCCAATTTTTT
1 TACGACTCCAATTTTTT
468668 TACGACTCCAATTTTT
1 TACGACTCCAATTTTT
468684 CAACCACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TACGACTCCAATTTTTT
Found at i:471598 original size:41 final size:41
Alignment explanation
Indices: 471533--471848 Score: 363
Period size: 41 Copynumber: 7.7 Consensus size: 41
471523 ATGCTCTACT
*
471533 GAGTCATAAGTCTTCCTTTAAATATAATCTCATGCTCATCCC
1 GAGTCATGAGTCTTCCTTT-AATATAATCTCATGCTCATCCC
* *
471575 GAGTCACGAGTCTTCCTTTAATATAATCTCATGCTCACCCC
1 GAGTCATGAGTCTTCCTTTAATATAATCTCATGCTCATCCC
* * ***
471616 GAGACATGAGTGC-TCCTTTAACATAATCTCATGCTCATTTTT
1 GAGTCATGAGT-CTTCCTTTAATATAATCTCATGCTCA-TCCC
*
471658 G-GTCATGAGTCTTCCTTTAATATAATCTCATGCTCAGCCC
1 GAGTCATGAGTCTTCCTTTAATATAATCTCATGCTCATCCC
* * **
471698 GAGACATGAGTCTTCCTTTAATATAATCTCATGCTTAAT-TT
1 GAGTCATGAGTCTTCCTTTAATATAATCTCATGC-TCATCCC
* * *
471739 GAGTCAAGAGTCTTCCTTTAATATAATCTTATGCTCACCCC
1 GAGTCATGAGTCTTCCTTTAATATAATCTCATGCTCATCCC
***
471780 GAGAT-ATGAGTC-TCACTTTAATATAATCTCATGCTCATTTT
1 GAG-TCATGAGTCTTC-CTTTAATATAATCTCATGCTCATCCC
*
471821 GAGTCATAAGTCTTCCTTTAATATAATC
1 GAGTCATGAGTCTTCCTTTAATATAATC
471849 AAGGTGATTC
Statistics
Matches: 229, Mismatches: 35, Indels: 21
0.80 0.12 0.07
Matches are distributed among these distances:
40 7 0.03
41 198 0.86
42 24 0.10
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (41 bp):
GAGTCATGAGTCTTCCTTTAATATAATCTCATGCTCATCCC
Found at i:471642 original size:82 final size:81
Alignment explanation
Indices: 471541--471848 Score: 447
Period size: 82 Copynumber: 3.7 Consensus size: 81
471531 CTGAGTCATA
*** *
471541 AGTCTTCCTTTAAATATAATCTCATGCTCATCCCGAGTCACGAGTCTTCCTTTAATATAATCTCA
1 AGTC-TCCTTT-AATATAATCTCATGCTCATTTTGAGTCATGAGTCTTCCTTTAATATAATCTCA
471606 TGCTCACCCCGAGACATG
64 TGCTCACCCCGAGACATG
*
471624 AGTGCTCCTTTAACATAATCTCATGCTCATTTTTG-GTCATGAGTCTTCCTTTAATATAATCTCA
1 AGT-CTCCTTTAATATAATCTCATGCTCA-TTTTGAGTCATGAGTCTTCCTTTAATATAATCTCA
*
471688 TGCTCAGCCCGAGACATG
64 TGCTCACCCCGAGACATG
* * * *
471706 AGTCTTCCTTTAATATAATCTCATGCTTAATTTGAGTCAAGAGTCTTCCTTTAATATAATCTTAT
1 AGTC-TCCTTTAATATAATCTCATGCTCATTTTGAGTCATGAGTCTTCCTTTAATATAATCTCAT
*
471771 GCTCACCCCGAGATATG
65 GCTCACCCCGAGACATG
*
471788 AGTCTCACTTTAATATAATCTCATGCTCATTTTGAGTCATAAGTCTTCCTTTAATATAATC
1 AGTCTC-CTTTAATATAATCTCATGCTCATTTTGAGTCATGAGTCTTCCTTTAATATAATC
471849 AAGGTGATTC
Statistics
Matches: 203, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
81 7 0.03
82 184 0.91
83 11 0.05
84 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (81 bp):
AGTCTCCTTTAATATAATCTCATGCTCATTTTGAGTCATGAGTCTTCCTTTAATATAATCTCATG
CTCACCCCGAGACATG
Found at i:472137 original size:81 final size:81
Alignment explanation
Indices: 472002--472162 Score: 322
Period size: 81 Copynumber: 2.0 Consensus size: 81
471992 AACTGTATAG
472002 CCCCTAATACATATCCTTTGTGTCCCAAATTATTCACGAAGTTCATATGTGTCATATACCATGTC
1 CCCCTAATACATATCCTTTGTGTCCCAAATTATTCACGAAGTTCATATGTGTCATATACCATGTC
472067 CATTCCAATTAACTTC
66 CATTCCAATTAACTTC
472083 CCCCTAATACATATCCTTTGTGTCCCAAATTATTCACGAAGTTCATATGTGTCATATACCATGTC
1 CCCCTAATACATATCCTTTGTGTCCCAAATTATTCACGAAGTTCATATGTGTCATATACCATGTC
472148 CATTCCAATTAACTT
66 CATTCCAATTAACTT
472163 TCATCACAAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.36
Consensus pattern (81 bp):
CCCCTAATACATATCCTTTGTGTCCCAAATTATTCACGAAGTTCATATGTGTCATATACCATGTC
CATTCCAATTAACTTC
Found at i:481192 original size:27 final size:27
Alignment explanation
Indices: 481154--481210 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
481144 ATCAACACAA
481154 AACCGTGAAGTGCATGTGAAGAGGATG
1 AACCGTGAAGTGCATGTGAAGAGGATG
481181 AACCGTGAAGTGCATGTGAAGAGGATG
1 AACCGTGAAGTGCATGTGAAGAGGATG
481208 AAC
1 AAC
481211 ATATTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (27 bp):
AACCGTGAAGTGCATGTGAAGAGGATG
Found at i:482427 original size:3 final size:3
Alignment explanation
Indices: 482405--482504 Score: 94
Period size: 3 Copynumber: 33.7 Consensus size: 3
482395 ATATTTTAGT
* * * *
482405 TTA TTC TTA TT- TTG TTA TTA TTA TTA TTA TTC TTA TTA TTA TTC TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
482452 TTA TTA TTA TTG TTA TTA TTC TTA TTG TTG TTG TTG TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
482500 TTA TT
1 TTA TT
482505 TAATTATAGA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.21, C:0.04, G:0.07, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:484265 original size:32 final size:32
Alignment explanation
Indices: 484231--484800 Score: 840
Period size: 32 Copynumber: 17.8 Consensus size: 32
484221 CAATGATTAT
* *
484231 AGATTGATAGCTCTTACGAGCATATTGATT-AT
1 AGATTGATAGCTCTTACGAGCATACTG-TTCAC
* *
484263 AGATTGACAGCTCTTACGAGCATACTGTTCAT
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
*
484295 AGATTGATAGCTCTTACGAGCATACTGATCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
* * *
484327 ATATTGATAGCTCTTACGAGCATATTTTTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
*
484359 AGATTGATAGCTCTTACGAGCATACTGATCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
* *
484391 AGATTAATAGCTCTTACGAGCATATTGTTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
*
484423 AGATTGATAGCTTTTACGAGCATACTGTTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
* *
484455 AGATTGATAGTTCTTACGAGCATACTATTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
* *
484487 AGATTGATAACTCTTACGAGCATATTGTTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
*
484519 AGATTGATAGCTCTTATGAGCATACTGATT-AC
1 AGATTGATAGCTCTTACGAGCATACTG-TTCAC
*
484551 AGATTGATAGCTCTTACGAGCATATTGTTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
*
484583 AGATTGATAGCTTTTACGAGCATACTGTTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
* *
484615 AGATTGATAGTTCTTACGAGCATACTATTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
* *
484647 AGATTGATAACTCTTACGAGCATATTGTTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
*
484679 AGATTGATAGCTCTTATGAGCATACTGATT-AC
1 AGATTGATAGCTCTTACGAGCATACTG-TTCAC
*
484711 AGATTGATAGCTCTTACGAGCATATTGTTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
* *
484743 AGATTGACAACTCTTACGAGCATACTGTTCAC
1 AGATTGATAGCTCTTACGAGCATACTGTTCAC
*
484775 AGATTGATAGCTCTTACGAGGATACT
1 AGATTGATAGCTCTTACGAGCATACT
484801 TGATACGACT
Statistics
Matches: 482, Mismatches: 51, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
31 6 0.01
32 472 0.98
33 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (32 bp):
AGATTGATAGCTCTTACGAGCATACTGTTCAC
Found at i:486374 original size:32 final size:32
Alignment explanation
Indices: 486329--486527 Score: 235
Period size: 32 Copynumber: 6.2 Consensus size: 32
486319 TTTCGTATCA
486329 ATACTGATT-ACAGATTGATAGCTCTTACGAGC
1 ATACTG-TTCACAGATTGATAGCTCTTACGAGC
*
486361 ATACTGTTCACAGATTGATAGCTCTTACGAGT
1 ATACTGTTCACAGATTGATAGCTCTTACGAGC
* * *
486393 ATATTGATT-ACAGATTGATAGCTATTACGAGT
1 ATACTG-TTCACAGATTGATAGCTCTTACGAGC
*
486425 ATACTATTCACAGATTGATAGCTCTTACGAGC
1 ATACTGTTCACAGATTGATAGCTCTTACGAGC
* *
486457 A-ACTATTCACAGATTGATAGCTCTTATGAGC
1 ATACTGTTCACAGATTGATAGCTCTTACGAGC
* * *
486488 ATACTATTTACTGATTGATTAGCT-TATACGAGC
1 ATACTGTTCACAGATTGA-TAGCTCT-TACGAGC
*
486521 TTACTGT
1 ATACTGT
486528 ATAATGATTG
Statistics
Matches: 148, Mismatches: 13, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
31 34 0.23
32 96 0.65
33 18 0.12
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (32 bp):
ATACTGTTCACAGATTGATAGCTCTTACGAGC
Found at i:486536 original size:33 final size:32
Alignment explanation
Indices: 486479--486592 Score: 95
Period size: 33 Copynumber: 3.5 Consensus size: 32
486469 ATTGATAGCT
* * * *
486479 CTTAT-GAGCATACTATTTACTGATTGATTAG
1 CTTATAGAGCATACTGTATAATGATTGATCAG
* *
486510 CTTATACGAGCTTACTGTATAATGATTGATCAA
1 CTTATA-GAGCATACTGTATAATGATTGATCAG
* * * * *
486543 CTCATAGAGCATACTGGATACTGACTGATGAG
1 CTTATAGAGCATACTGTATAATGATTGATCAG
*
486575 CTTTTATGAGCATACTGT
1 CTTATA-GAGCATACTGT
486593 GAATTTACAT
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
31 5 0.08
32 24 0.38
33 35 0.55
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (32 bp):
CTTATAGAGCATACTGTATAATGATTGATCAG
Found at i:486539 original size:96 final size:96
Alignment explanation
Indices: 486329--486519 Score: 273
Period size: 95 Copynumber: 2.0 Consensus size: 96
486319 TTTCGTATCA
* *
486329 ATACTGATT-ACAGATTGATAGCTCTTACGAGCATACTGTTCACAGATTGATAGCTCTTACGAGT
1 ATACT-ATTCACAGATTGATAGCTCTTACGAGCATACTATTCACAGATTGATAGCTCTTACGAGC
*
486393 ATATTGATTACAGATTGATAGCTATTACGAGT
65 ATACTGATTACAGATTGATAGCTATTACGAGT
*
486425 ATACTATTCACAGATTGATAGCTCTTACGAGCA-ACTATTCACAGATTGATAGCTCTTATGAGCA
1 ATACTATTCACAGATTGATAGCTCTTACGAGCATACTATTCACAGATTGATAGCTCTTACGAGCA
*
486489 TACT-ATTTACTGATTGATTAGCT-TATACGAG
66 TACTGA-TTACAGATTGA-TAGCTAT-TACGAG
486520 CTTACTGTAT
Statistics
Matches: 86, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
94 1 0.01
95 45 0.52
96 40 0.47
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (96 bp):
ATACTATTCACAGATTGATAGCTCTTACGAGCATACTATTCACAGATTGATAGCTCTTACGAGCA
TACTGATTACAGATTGATAGCTATTACGAGT
Found at i:495450 original size:16 final size:16
Alignment explanation
Indices: 495429--495471 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
495419 AATGAGATGA
495429 AAATAATTTTTTAATT
1 AAATAATTTTTTAATT
*
495445 AAATAAATTTAATTAATT
1 AAAT-AATTT-TTTAATT
495463 AAA-AATTTT
1 AAATAATTTT
495472 AAATCCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 9 0.39
17 5 0.22
18 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATAATTTTTTAATT
Found at i:497521 original size:25 final size:25
Alignment explanation
Indices: 497486--497538 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
497476 ACATCAAGAG
* *
497486 AAAAAATAATTTTTCTCT-GTTCTCT
1 AAAAAACAATTTCTCTCTAG-TCTCT
497511 AAAAAACAATTTCTCTCTAGTCTCT
1 AAAAAACAATTTCTCTCTAGTCTCT
497536 AAA
1 AAA
497539 TTCTGATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.40
Consensus pattern (25 bp):
AAAAAACAATTTCTCTCTAGTCTCT
Found at i:498618 original size:15 final size:16
Alignment explanation
Indices: 498598--498638 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
498588 TTTGAAAAGC
498598 ATAAAAAG-AAAAGAA
1 ATAAAAAGTAAAAGAA
498613 AT-AAAAGTAAAAGAA
1 ATAAAAAGTAAAAGAA
498628 AT-AAAAGTAAA
1 ATAAAAAGTAAA
498639 TAATTGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
ATAAAAAGTAAAAGAA
Found at i:499850 original size:9 final size:9
Alignment explanation
Indices: 499836--499865 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
499826 TTAAGTAAAC
499836 AAAACAAGG
1 AAAACAAGG
499845 AAAACAAGG
1 AAAACAAGG
499854 AAAACAA-G
1 AAAACAAGG
499862 AAAA
1 AAAA
499866 TACGAAGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.73, C:0.10, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAACAAGG
Found at i:500316 original size:21 final size:23
Alignment explanation
Indices: 500292--500339 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
500282 TTATGTCTTA
500292 CTCC-ATCTCACC-TCCTTATTT
1 CTCCTATCTCACCATCCTTATTT
* *
500313 CTCCTTCTCTCACCATCCTTTTTT
1 CTCC-TATCTCACCATCCTTATTT
500337 CTC
1 CTC
500340 TTTCTCCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.18
23 7 0.32
24 11 0.50
ACGTcount: A:0.10, C:0.44, G:0.00, T:0.46
Consensus pattern (23 bp):
CTCCTATCTCACCATCCTTATTT
Found at i:500337 original size:24 final size:23
Alignment explanation
Indices: 500297--500345 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
500287 TCTTACTCCA
500297 TCTCACCTCCTTATTTCTCCTTC
1 TCTCACCTCCTTATTTCTCCTTC
* *
500320 TCTCACCATCCTTTTTTCTCTTTC
1 TCTCACC-TCCTTATTTCTCCTTC
500344 TC
1 TC
500346 CATTTTAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.08, C:0.41, G:0.00, T:0.51
Consensus pattern (23 bp):
TCTCACCTCCTTATTTCTCCTTC
Found at i:509602 original size:35 final size:34
Alignment explanation
Indices: 509537--509606 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
509527 TGACAATTGG
* * *
509537 AAATGCAATGACAATGTAATGTAGTGACAATTAA
1 AAATGCAATGACAAGGGAATGTAGTAACAATTAA
* *
509571 AAATGCAATGGCAAAGGGAATGTGGTAACAATTAA
1 AAATGCAATGAC-AAGGGAATGTAGTAACAATTAA
509606 A
1 A
509607 TTACAACTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 11 0.37
35 19 0.63
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (34 bp):
AAATGCAATGACAAGGGAATGTAGTAACAATTAA
Found at i:510022 original size:21 final size:18
Alignment explanation
Indices: 509997--510041 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
509987 TTTAGCTCGA
509997 CTTCTTTTCCTTCCTCTCTTT
1 CTTCTTTT-CTTCCT-TC-TT
*
510018 CTTCTTTTTTTCCTTCTT
1 CTTCTTTTCTTCCTTCTT
510036 CTTCTT
1 CTTCTT
510042 CCACTTCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 5 0.22
21 8 0.35
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
CTTCTTTTCTTCCTTCTT
Found at i:522928 original size:2 final size:2
Alignment explanation
Indices: 522921--522946 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
522911 TTATTTTTAA
522921 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
522947 TGCTATAAAA
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:524617 original size:18 final size:18
Alignment explanation
Indices: 524594--524636 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
524584 TAGCAAGCTG
*
524594 AAGAAGAAGAAGACCCTA
1 AAGAAGAAGAAGACCCAA
*
524612 AAGAAGAAGAAGATCCAA
1 AAGAAGAAGAAGACCCAA
524630 AAGAAGA
1 AAGAAGA
524637 TCCTGAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.60, C:0.12, G:0.23, T:0.05
Consensus pattern (18 bp):
AAGAAGAAGAAGACCCAA
Found at i:529281 original size:7 final size:6
Alignment explanation
Indices: 529263--529301 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
529253 AATGATGCTC
*
529263 AGAAAA ACAAAA ATGAAAA AGAAAA AGAGAAA AGAAAA A
1 AGAAAA AGAAAA A-GAAAA AGAAAA AGA-AAA AGAAAA A
529302 AGAGCATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:529282 original size:13 final size:12
Alignment explanation
Indices: 529263--529301 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
529253 AATGATGCTC
*
529263 AGAAAAACAAAA
1 AGAAAAAGAAAA
529275 ATGAAAAAGAAAA
1 A-GAAAAAGAAAA
529288 AGAGAAAAGAAAA
1 AGA-AAAAGAAAA
529301 A
1 A
529302 AGAGCATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 3 0.12
13 21 0.88
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (12 bp):
AGAAAAAGAAAA
Found at i:529287 original size:19 final size:19
Alignment explanation
Indices: 529263--529301 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
529253 AATGATGCTC
529263 AGAAAAACA-AAAATGAAAA
1 AGAAAAACAGAAAA-GAAAA
*
529282 AGAAAAAGAGAAAAGAAAA
1 AGAAAAACAGAAAAGAAAA
529301 A
1 A
529302 AGAGCATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AGAAAAACAGAAAAGAAAA
Found at i:530701 original size:12 final size:12
Alignment explanation
Indices: 530686--530710 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
530676 TGTTATCATA
530686 ATGAATGCTATT
1 ATGAATGCTATT
530698 ATGAATGCTATT
1 ATGAATGCTATT
530710 A
1 A
530711 ATTCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:531338 original size:31 final size:31
Alignment explanation
Indices: 531303--531364 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
531293 CTTAGTTTAA
531303 CTTAGCTTAATTAGTTTAGAATACTTAGGTT
1 CTTAGCTTAATTAGTTTAGAATACTTAGGTT
531334 CTTAGCTTAATTAGTTTAGAATACTTAGGTT
1 CTTAGCTTAATTAGTTTAGAATACTTAGGTT
531365 AATATCCCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (31 bp):
CTTAGCTTAATTAGTTTAGAATACTTAGGTT
Found at i:538888 original size:15 final size:15
Alignment explanation
Indices: 538870--538900 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
538860 TGTTTTTATT
538870 ATTAACTTAGATTAA
1 ATTAACTTAGATTAA
*
538885 ATTAGCTTAGATTAA
1 ATTAACTTAGATTAA
538900 A
1 A
538901 ACTCTTCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (15 bp):
ATTAACTTAGATTAA
Found at i:548054 original size:26 final size:26
Alignment explanation
Indices: 548022--548075 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
548012 CAACCAGGAA
548022 TGTCGCTACATGAACATGT-ATAGAAT
1 TGTCGCTACATGAACATGTCA-AGAAT
* *
548048 TGTCGCTGCATGAACGTGTCAAGAAT
1 TGTCGCTACATGAACATGTCAAGAAT
548074 TG
1 TG
548076 CACCTAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (26 bp):
TGTCGCTACATGAACATGTCAAGAAT
Found at i:548898 original size:16 final size:16
Alignment explanation
Indices: 548877--548907 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
548867 TTATGGATCC
548877 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
548893 CATTTTATCTTTATT
1 CATTTTACCTTTATT
548908 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:550308 original size:19 final size:19
Alignment explanation
Indices: 550284--550324 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
550274 CAAATGAATG
*
550284 TTACCATAGATAAAAGACA
1 TTACCACAGATAAAAGACA
550303 TTACCACAGATAAAAGACA
1 TTACCACAGATAAAAGACA
550322 TTA
1 TTA
550325 ATGAAACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (19 bp):
TTACCACAGATAAAAGACA
Found at i:553472 original size:18 final size:18
Alignment explanation
Indices: 553446--553485 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
553436 TCTTCTTCAT
553446 TTCTACAGGATCTTCCTC
1 TTCTACAGGATCTTCCTC
* *
553464 TTCTCCAGGATCTTCTTC
1 TTCTACAGGATCTTCCTC
553482 TTCT
1 TTCT
553486 TCTTCAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.33, G:0.10, T:0.45
Consensus pattern (18 bp):
TTCTACAGGATCTTCCTC
Found at i:555034 original size:21 final size:21
Alignment explanation
Indices: 555010--555057 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
555000 AATTTTATAT
*
555010 TAAATATTA-TAAAATTAAAAA
1 TAAATATAATTAAAA-TAAAAA
* *
555031 TAAAAATAATTAACATAAAAA
1 TAAATATAATTAAAATAAAAA
555052 TAAATA
1 TAAATA
555058 ATTAAATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATATAATTAAAATAAAAA
Found at i:556328 original size:23 final size:23
Alignment explanation
Indices: 556302--556348 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
556292 GGAAATGCAC
*
556302 TAAGAAAGTTAATACCTTAAATA
1 TAAGAAAGTTAATACCCTAAATA
556325 TAAGAAAGTTAATACCCTAAATA
1 TAAGAAAGTTAATACCCTAAATA
556348 T
1 T
556349 CAAACAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.30
Consensus pattern (23 bp):
TAAGAAAGTTAATACCCTAAATA
Found at i:561189 original size:13 final size:13
Alignment explanation
Indices: 561171--561195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
561161 TTGTGAAGGA
561171 TATTAATCTAAAT
1 TATTAATCTAAAT
561184 TATTAATCTAAA
1 TATTAATCTAAA
561196 CTAACTTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TATTAATCTAAAT
Found at i:566674 original size:6 final size:7
Alignment explanation
Indices: 566649--566685 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
566639 AAAATCAAGT
*
566649 TAAATAA
1 TAAAAAA
566656 TAAAAAA
1 TAAAAAA
566663 TAAAAAA
1 TAAAAAA
566670 TAAAAAA
1 TAAAAAA
566677 TAAAAAA
1 TAAAAAA
566684 TA
1 TA
566686 TTATATTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAAAAA
Found at i:573248 original size:23 final size:23
Alignment explanation
Indices: 573222--573268 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
573212 TGATTTTAAA
573222 TTTTTTAAAAAAATTAAAATTATT
1 TTTTTTAAAAAAA-TAAAATTATT
* *
573246 TTTTTTGAAATAATAAAATTATT
1 TTTTTTAAAAAAATAAAATTATT
573269 AAATAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTTTTAAAAAAATAAAATTATT
Found at i:574309 original size:22 final size:22
Alignment explanation
Indices: 574266--574309 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
574256 AAAATTATTT
*
574266 AATAATTTTATTATTTCAAAAA
1 AATAATTTTATAATTTCAAAAA
*
574288 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-ATAATTTCAAAA
574310 TCATTTGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTATAATTTCAAAAA
Found at i:577448 original size:16 final size:18
Alignment explanation
Indices: 577429--577464 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
577419 TTTAATAATG
577429 TTAAATTT-AAATT-TTT
1 TTAAATTTGAAATTGTTT
577445 TT-AATTTGAAATTGTTT
1 TTAAATTTGAAATTGTTT
577462 TTA
1 TTA
577465 TTGTGTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
TTAAATTTGAAATTGTTT
Found at i:577450 original size:15 final size:17
Alignment explanation
Indices: 577432--577464 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
577422 AATAATGTTA
577432 AATTT-AAATT-TTTTT
1 AATTTGAAATTGTTTTT
577447 AATTTGAAATTGTTTTT
1 AATTTGAAATTGTTTTT
577464 A
1 A
577465 TTGTGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
AATTTGAAATTGTTTTT
Found at i:581277 original size:24 final size:24
Alignment explanation
Indices: 581197--581528 Score: 179
Period size: 24 Copynumber: 13.4 Consensus size: 24
581187 AAGATAAACA
* *
581197 AGCGTAAATGTGTGCAAGCTGGCG
1 AGCGTAAACGTGTGCAAGCTGACG
* * * *
581221 AGCGTAAACACATAAT-TAAGCTGATG
1 AGCGT-AA-ACGT-GTGCAAGCTGACG
581247 AGCGTAAACGTGTGCAAGCTGACG
1 AGCGTAAACGTGTGCAAGCTGACG
* * *
581271 AGAGTAAATGTGTACAAGCTGACG
1 AGCGTAAACGTGTGCAAGCTGACG
*
581295 AGCGTAAACGTGTGCAAGCTGGCG
1 AGCGTAAACGTGTGCAAGCTGACG
* * *
581319 AGCGTAAACGCATAAT-TAAGTTGACG
1 AGCGTAAACG--T-GTGCAAGCTGACG
* * *
581345 AGCATAAACGTGTGCAAACTGGCG
1 AGCGTAAACGTGTGCAAGCTGACG
* * *
581369 AGCGTTAACGCATAAT-TAAGCTGACG
1 AGCGTAAACG--T-GTGCAAGCTGACG
* **
581395 AGCGTAAACGTGTGCAAACTGGTG
1 AGCGTAAACGTGTGCAAGCTGACG
* * *
581419 AGCGTAAATGCATAAT-TAAGCTGACG
1 AGCGTAAA--CGT-GTGCAAGCTGACG
* * *
581445 AGCGTAAATGTGTGCAAGTTGGCG
1 AGCGTAAACGTGTGCAAGCTGACG
* * * *
581469 AACGTAAATGCATAAT-TAAGCTGACG
1 AGCGTAAA--CGT-GTGCAAGCTGACG
* * *
581495 AGCGTACACATGTGCAAGCTGGCG
1 AGCGTAAACGTGTGCAAGCTGACG
581519 AGCGTAAACG
1 AGCGTAAACG
581529 CATATTAAGC
Statistics
Matches: 223, Mismatches: 65, Indels: 40
0.68 0.20 0.12
Matches are distributed among these distances:
23 5 0.02
24 131 0.59
25 4 0.02
26 78 0.35
27 5 0.02
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.20
Consensus pattern (24 bp):
AGCGTAAACGTGTGCAAGCTGACG
Found at i:581278 original size:50 final size:50
Alignment explanation
Indices: 581197--581553 Score: 477
Period size: 50 Copynumber: 7.2 Consensus size: 50
581187 AAGATAAACA
* * *
581197 AGCGTAAATGTGTGCAAGCTGGCGAGCGTAAACACATAATTAAGCTGATG
1 AGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTAAGCTGACG
* * * ** *
581247 AGCGTAAACGTGTGCAAGCTGACGAGAGTAAATGTGT-A-CAAGCTGACG
1 AGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTAAGCTGACG
*
581295 AGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTAAGTTGACG
1 AGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTAAGCTGACG
* * *
581345 AGCATAAACGTGTGCAAACTGGCGAGCGTTAACGCATAATTAAGCTGACG
1 AGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTAAGCTGACG
* * *
581395 AGCGTAAACGTGTGCAAACTGGTGAGCGTAAATGCATAATTAAGCTGACG
1 AGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTAAGCTGACG
* * * *
581445 AGCGTAAATGTGTGCAAGTTGGCGAACGTAAATGCATAATTAAGCTGACG
1 AGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTAAGCTGACG
* * * *
581495 AGCGTACACATGTGCAAGCTGGCGAGCGTAAACGCAT-ATTAAGCTAATG
1 AGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTAAGCTGACG
581544 AGCGTAAACG
1 AGCGTAAACG
581554 CATAAATATG
Statistics
Matches: 266, Mismatches: 39, Indels: 5
0.86 0.13 0.02
Matches are distributed among these distances:
48 40 0.15
49 20 0.08
50 206 0.77
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (50 bp):
AGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTAAGCTGACG
Found at i:582675 original size:19 final size:19
Alignment explanation
Indices: 582643--582681 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
582633 TTGAGGTATG
*
582643 GATGTTACAAAAAACTCAT
1 GATGTTACAAAAAACCCAT
* *
582662 GATGTTATAGAAAACCCAT
1 GATGTTACAAAAAACCCAT
582681 G
1 G
582682 CCGATGACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (19 bp):
GATGTTACAAAAAACCCAT
Found at i:586138 original size:23 final size:22
Alignment explanation
Indices: 586111--586156 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
586101 ATTTCCGCCG
586111 AAAA-CCTGAAACCTTATACCTTA
1 AAAACCCT-AAACCTTA-ACCTTA
586134 AAAACCCTAAACCTTAACCTTA
1 AAAACCCTAAACCTTAACCTTA
586156 A
1 A
586157 TAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 12 0.55
24 3 0.14
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAACCCTAAACCTTAACCTTA
Found at i:587809 original size:23 final size:23
Alignment explanation
Indices: 587781--587854 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
587771 AATGGTACGA
587781 TCAACAGGTCGGATT-GGGTTCGG
1 TCAACAGGTCGG-TTCGGGTTCGG
*
587804 TTAACAGGTCGGTTCGGGTTCGG
1 TCAACAGGTCGGTTCGGGTTCGG
* * *
587827 TCAACGGGTCAAG-TCGGGTTCGA
1 TCAACAGGTC-GGTTCGGGTTCGG
587850 TCAAC
1 TCAAC
587855 GGGTTACACG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 2 0.05
23 41 0.93
24 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.35, T:0.26
Consensus pattern (23 bp):
TCAACAGGTCGGTTCGGGTTCGG
Found at i:587926 original size:23 final size:23
Alignment explanation
Indices: 587900--587952 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
587890 TGGGTTTGGT
*
587900 TTAATGGTTTGAGTCA-AATGGGC
1 TTAATGGCTTGAGTCATAAT-GGC
* * *
587923 TTAAAGGCTTGGGTCATCATGGC
1 TTAATGGCTTGAGTCATAATGGC
587946 TTAATGG
1 TTAATGG
587953 GTTATGGTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (23 bp):
TTAATGGCTTGAGTCATAATGGC
Found at i:588386 original size:39 final size:39
Alignment explanation
Indices: 588343--588417 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
588333 CAAAGCTTCA
*
588343 TCGAAAAAATCGAAGG-AAAAAGAAGGAGAGAATCTTTTG
1 TCGAAAAAATAGAAGGAAAAAAG-AGGAGAGAATCTTTTG
588382 TCGAAAAAATAGAAGGAAAAAAGAGGAGAGAATCTT
1 TCGAAAAAATAGAAGGAAAAAAGAGGAGAGAATCTT
588418 AGGGATTTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 28 0.82
40 6 0.18
ACGTcount: A:0.52, C:0.07, G:0.25, T:0.16
Consensus pattern (39 bp):
TCGAAAAAATAGAAGGAAAAAAGAGGAGAGAATCTTTTG
Found at i:591803 original size:81 final size:81
Alignment explanation
Indices: 591668--591831 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
591658 AAGATTAGGA
591668 TTGAAAACCCTAAATTTCTCCCTTTTGTGCCATGTGAAGAAGAAAGAAGAAAGAAAATGAAATAG
1 TTGAAAACCCTAAATTTCTCCCTTTTGTGCCATGTGAAGAAGAAAGAAGAAAGAAAATGAAATAG
591733 AAAATCCTAAATTTCT
66 AAAATCCTAAATTTCT
591749 TTGAAAACCCTAAATTTCTCCCTTTTGTGCCATGTGAAGAAGAAAGAAGAAAGAAAATGAAATAG
1 TTGAAAACCCTAAATTTCTCCCTTTTGTGCCATGTGAAGAAGAAAGAAGAAAGAAAATGAAATAG
591814 AAAATCCTAAATTTCT
66 AAAATCCTAAATTTCT
591830 TT
1 TT
591832 CTTTTAGTTC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (81 bp):
TTGAAAACCCTAAATTTCTCCCTTTTGTGCCATGTGAAGAAGAAAGAAGAAAGAAAATGAAATAG
AAAATCCTAAATTTCT
Found at i:595507 original size:15 final size:15
Alignment explanation
Indices: 595462--595508 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
595452 CTCAGTCACT
*
595462 TGAAAAAGAAAAATGA
1 TGAAAAAGAAAAA-AA
*
595478 -GAAAAAGGAAGAAAA
1 TGAAAAA-GAAAAAAA
595493 TGAAAAAGAAAAAAA
1 TGAAAAAGAAAAAAA
595508 T
1 T
595509 TTTAAATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (15 bp):
TGAAAAAGAAAAAAA
Found at i:602732 original size:25 final size:25
Alignment explanation
Indices: 602687--602743 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
602677 TTTGATTCTA
** **
602687 GCTCGTAAGAGCGTATTTCTGTTTG
1 GCTCGTAAGAGCGTAACTCTGACTG
602712 GCTCGTAAGAGCGTAACTCTGACTG
1 GCTCGTAAGAGCGTAACTCTGACTG
602737 GCTCGTA
1 GCTCGTA
602744 TAGGCGATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (25 bp):
GCTCGTAAGAGCGTAACTCTGACTG
Found at i:608683 original size:21 final size:21
Alignment explanation
Indices: 608637--608685 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
608627 CCTATGACAG
* *
608637 TTCTACCGATACAAGTGAGAC
1 TTCTACCAATACAAGTCAGAC
*
608658 ATCTACCAATACAAGTCATG-C
1 TTCTACCAATACAAGTCA-GAC
608679 TTCTACC
1 TTCTACC
608686 GATGCTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (21 bp):
TTCTACCAATACAAGTCAGAC
Found at i:612076 original size:27 final size:27
Alignment explanation
Indices: 612046--612187 Score: 126
Period size: 27 Copynumber: 5.3 Consensus size: 27
612036 AAGATGAAGA
*
612046 AATTTTGATTTTGGCTCTTAAGAGCGT
1 AATTTTGATTCTGGCTCTTAAGAGCGT
* * * * *
612073 AATTCTAATTTTGGCTCGTAAGAGTGT
1 AATTTTGATTCTGGCTCTTAAGAGCGT
* * * *
612100 AATTTTGATTCTGCCTCGTAATAGTGT
1 AATTTTGATTCTGGCTCTTAAGAGCGT
* *
612127 AATTCTAATTCTGGCT-TGTAAGAGCGT
1 AATTTTGATTCTGGCTCT-TAAGAGCGT
*
612154 AATTTTGATTCTGGCT-TGTAAGAGCAT
1 AATTTTGATTCTGGCTCT-TAAGAGCGT
*
612181 ATTTTTG
1 AATTTTG
612188 TTTGGTTCGT
Statistics
Matches: 95, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
27 95 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (27 bp):
AATTTTGATTCTGGCTCTTAAGAGCGT
Found at i:612105 original size:54 final size:54
Alignment explanation
Indices: 612046--612178 Score: 178
Period size: 54 Copynumber: 2.5 Consensus size: 54
612036 AAGATGAAGA
* * *
612046 AATTTTGATTTTGGCTCTTAAGAGCGTAATTCTAATTTTGGCTCGTAAGAGTGT
1 AATTTTGATTCTGGCTCTTAAGAGCGTAATTCTAATTCTGGCTCGTAAGAGCGT
* * * * *
612100 AATTTTGATTCTGCCTCGTAATAGTGTAATTCTAATTCTGGCTTGTAAGAGCGT
1 AATTTTGATTCTGGCTCTTAAGAGCGTAATTCTAATTCTGGCTCGTAAGAGCGT
612154 AATTTTGATTCTGGCT-TGTAAGAGC
1 AATTTTGATTCTGGCTCT-TAAGAGC
612179 ATATTTTTGT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (54 bp):
AATTTTGATTCTGGCTCTTAAGAGCGTAATTCTAATTCTGGCTCGTAAGAGCGT
Found at i:614775 original size:6 final size:6
Alignment explanation
Indices: 614766--614794 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
614756 TCAGTCCTAG
614766 TCTCAA TCTCAA TCTCAA TCTCAA TCTCA
1 TCTCAA TCTCAA TCTCAA TCTCAA TCTCA
614795 TGATATTATA
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:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
TCTCAA
Found at i:616142 original size:7 final size:7
Alignment explanation
Indices: 616127--616160 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
616117 AGTTAGATAC
616127 TTCAAAG
1 TTCAAAG
*
616134 TTTAAAG
1 TTCAAAG
616141 TTCAAAG
1 TTCAAAG
*
616148 TTCAAAC
1 TTCAAAG
616155 TTCAAA
1 TTCAAA
616161 CCCGATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (7 bp):
TTCAAAG
Done.