Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold278
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: 1156311
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 38162 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:677293 original size:21 final size:21
Alignment explanation
Indices: 677267--677320 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
677257 TTCTGCTCTG
*
677267 CTCTGCTTCCCTCACT-GTAGC
1 CTCTGCTTCCCTCACTACT-GC
*
677288 CTCTGCTTCTCTCACTACTGC
1 CTCTGCTTCCCTCACTACTGC
677309 CTCTGCTTCCCT
1 CTCTGCTTCCCT
677321 TGCTGCCGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.07, C:0.44, G:0.11, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCCCTCACTACTGC
Found at i:682924 original size:16 final size:16
Alignment explanation
Indices: 682903--683158 Score: 130
Period size: 16 Copynumber: 15.9 Consensus size: 16
682893 ATAATTAAGC
682903 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
682919 TATGTAAGCTATG---
1 TATGTAAGTTATGTAT
*
682932 --T--AAGTTGTGTAT
1 TATGTAAGTTATGTAT
682944 TATGTAA-TCTATGTAT
1 TATGTAAGT-TATGTAT
682960 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
682976 TATGTATGTTATGTATGT
1 TATGTAAGTTATGTA--T
* *
682994 TATGT-AG-AATGTAAGC
1 TATGTAAGTTATGT-A-T
683010 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* * *
683028 TCTGTATAATGTATCTAAGT
1 TATGTA-AGT-TATGT-A-T
683048 TATGTAAG-T-TGTAAGT
1 TATGTAAGTTATGT-A-T
683064 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
*
683082 TATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
683098 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
* *
683114 AATAT-TAA-ATAAG--T
1 --TATGTAAGTTATGTAT
*
683128 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
*
683144 AATGTAAGTTATGTA
1 TATGTAAGTTATGTA
683159 CGTAATGTAT
Statistics
Matches: 191, Mismatches: 25, Indels: 48
0.72 0.09 0.18
Matches are distributed among these distances:
9 6 0.03
11 1 0.01
12 3 0.02
13 3 0.02
14 4 0.02
15 1 0.01
16 105 0.55
17 11 0.06
18 41 0.21
19 3 0.02
20 13 0.07
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:683014 original size:34 final size:34
Alignment explanation
Indices: 682976--683112 Score: 108
Period size: 34 Copynumber: 4.2 Consensus size: 34
682966 AGTTATGTAT
* *
682976 TATGTATGTTATGTATGTTATGTAGAATGTAAGC
1 TATGTAAGTTATGTAAGTTATGTAGAATGTAAGC
* *
683010 TATGTAAGTTATGTAAGTTCTGTATAA--T--G-
1 TATGTAAGTTATGTAAGTTATGTAGAATGTAAGC
* * *
683039 TATCTAAGTTATGTAAG-T-TGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAGTTATGT-AG-AATGTAAGC
* ** *
683073 TATGTAAGTTATATAAGTTATGTATTATGTAAGT
1 TATGTAAGTTATGTAAGTTATGTAGAATGTAAGC
683107 TATGTA
1 TATGTA
683113 TAATATTAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.04
28 2 0.02
29 17 0.20
30 1 0.01
31 1 0.01
32 1 0.01
33 1 0.01
34 53 0.63
35 2 0.02
36 3 0.04
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.45
Consensus pattern (34 bp):
TATGTAAGTTATGTAAGTTATGTAGAATGTAAGC
Found at i:683047 original size:29 final size:26
Alignment explanation
Indices: 683014--683158 Score: 93
Period size: 25 Copynumber: 5.4 Consensus size: 26
683004 GTAAGCTATG
683014 TAAGTTATGTAAGTTCTGTATAATGTATC
1 TAAGTTATGTAAGTT-TGTA-AAT-TATC
* *
683043 TAAGTTATGTAAG-TTGTAAGTTATG
1 TAAGTTATGTAAGTTTGTAAATTATC
* * *
683068 TAAGTTATGTAAGTTATATAAGTTATG
1 TAAGTTATGTAAGTT-TGTAAATTATC
**
683095 T-A-TTATGTAAGTTATGTATAATATTAAA
1 TAAGTTATGTAAGTT-TG--TAA-ATTATC
* *
683123 TAAGTTATGTAAGTTGTGT--ATAATG
1 TAAGTTATGTAAGTT-TGTAAATTATC
683148 TAAGTTATGTA
1 TAAGTTATGTA
683159 CGTAATGTAT
Statistics
Matches: 98, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
25 43 0.44
26 4 0.04
27 18 0.18
28 6 0.06
29 14 0.14
30 13 0.13
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.45
Consensus pattern (26 bp):
TAAGTTATGTAAGTTTGTAAATTATC
Found at i:683242 original size:16 final size:16
Alignment explanation
Indices: 683223--685030 Score: 98
Period size: 16 Copynumber: 102.1 Consensus size: 16
683213 ATAATGTAAG
*
683223 TTATGTACGTAATGTA
1 TTATGTAAGTAATGTA
*
683239 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683255 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683276 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
683293 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
683310 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683326 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683347 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
683364 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
683381 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683397 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683418 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
683435 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
683452 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683468 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683489 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
683506 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
683523 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683539 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683560 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
683577 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
683594 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683610 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683631 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
683648 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
683665 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683681 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683702 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
683719 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
683736 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683752 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683773 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
683790 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
683807 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683823 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683844 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
683861 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
683878 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683894 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683915 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
683932 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
683949 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
683965 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
683986 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684003 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684020 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684036 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684057 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684074 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684091 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684107 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684128 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684145 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684162 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684178 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684199 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684216 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684233 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684249 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684270 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684287 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684304 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684320 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684341 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684358 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684375 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684391 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684412 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684429 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684446 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684462 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684483 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684500 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684517 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684533 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684554 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684571 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684588 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684604 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684625 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684642 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684659 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684675 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684696 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684713 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684730 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684746 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684767 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684784 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684801 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684817 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684838 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684855 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684872 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684888 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684909 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684926 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
684943 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
* *
684959 TAATATTAAATAAGTTATGTA
1 T--TA-T--GTAAGTAATGTA
*
684980 GGTTGTGT-A-TAATGTAA
1 --TTATGTAAGTAATGT-A
*
684997 GTTATGTACGTAATGTA
1 -TTATGTAAGTAATGTA
*
685014 TTATGTAAGTCATGTA
1 TTATGTAAGTAATGTA
685030 T
1 T
685031 AATATTAAAT
Statistics
Matches: 1315, Mismatches: 227, Indels: 500
0.64 0.11 0.24
Matches are distributed among these distances:
16 665 0.51
17 75 0.06
18 225 0.17
19 25 0.02
20 25 0.02
21 275 0.21
23 25 0.02
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (16 bp):
TTATGTAAGTAATGTA
Found at i:685075 original size:16 final size:17
Alignment explanation
Indices: 685046--685106 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 17
685036 TAAATAAGTT
* *
685046 ATGTAGGTTGTGTA-TA
1 ATGTAAGTTATGTAGTA
685062 ATGTAAGTTATGTACGTA
1 ATGTAAGTTATGTA-GTA
*
685080 ATGT-A-TTATGTAAGTT
1 ATGTAAGTTATGT-AGTA
685096 ATGTAAGTTAT
1 ATGTAAGTTAT
685107 TATGTAAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 24 0.65
17 3 0.08
18 10 0.27
ACGTcount: A:0.31, C:0.02, G:0.23, T:0.44
Consensus pattern (17 bp):
ATGTAAGTTATGTAGTA
Found at i:685107 original size:21 final size:21
Alignment explanation
Indices: 685083--685161 Score: 124
Period size: 21 Copynumber: 3.8 Consensus size: 21
685073 GTACGTAATG
685083 TATTATGTAAGTTATGTAAGT
1 TATTATGTAAGTTATGTAAGT
*
685104 TATTATGTAAGTTATGCAAGT
1 TATTATGTAAGTTATGTAAGT
*
685125 T-TATATATAAGTTATGTAAGT
1 TAT-TATGTAAGTTATGTAAGT
685146 TATTATGTAAGTTATG
1 TATTATGTAAGTTATG
685162 CATTATGTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
20 1 0.02
21 50 0.96
22 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (21 bp):
TATTATGTAAGTTATGTAAGT
Found at i:685119 original size:71 final size:71
Alignment explanation
Indices: 683074--685100 Score: 3957
Period size: 71 Copynumber: 28.5 Consensus size: 71
683064 TATGTAAGTT
* * * * *
683074 ATGTAAGTTATATAAGTTATGTATTATGTAAGTTATGTATAATATTAAATAAGTTATGTAAGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683139 TGTATA
66 TGTATA
* * *
683145 ATGTAAGTTATGTACGTAATGTATTATGTAAGTTC-TATATAATATTAATTAAGTTATGTAAGTT
1 ATGTAAGTTATGTACGTAATGTATTATGTAAG-TCATGTATAATATTAAATAAGTTATGTAGGTT
683209 GTGTATA
65 GTGTATA
683216 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683281 TGTATA
66 TGTATA
683287 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683352 TGTATA
66 TGTATA
683358 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683423 TGTATA
66 TGTATA
683429 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683494 TGTATA
66 TGTATA
683500 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683565 TGTATA
66 TGTATA
683571 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683636 TGTATA
66 TGTATA
683642 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683707 TGTATA
66 TGTATA
683713 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683778 TGTATA
66 TGTATA
683784 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683849 TGTATA
66 TGTATA
683855 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683920 TGTATA
66 TGTATA
683926 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
683991 TGTATA
66 TGTATA
683997 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684062 TGTATA
66 TGTATA
684068 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684133 TGTATA
66 TGTATA
684139 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684204 TGTATA
66 TGTATA
684210 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684275 TGTATA
66 TGTATA
684281 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684346 TGTATA
66 TGTATA
684352 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684417 TGTATA
66 TGTATA
684423 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684488 TGTATA
66 TGTATA
684494 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684559 TGTATA
66 TGTATA
684565 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684630 TGTATA
66 TGTATA
684636 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684701 TGTATA
66 TGTATA
684707 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684772 TGTATA
66 TGTATA
684778 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684843 TGTATA
66 TGTATA
684849 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684914 TGTATA
66 TGTATA
684920 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
684985 TGTATA
66 TGTATA
684991 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
685056 TGTATA
66 TGTATA
*
685062 ATGTAAGTTATGTACGTAATGTATTATGTAAGTTATGTA
1 ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTA
685101 AGTTATTATG
Statistics
Matches: 1944, Mismatches: 10, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
70 2 0.00
71 1941 1.00
72 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (71 bp):
ATGTAAGTTATGTACGTAATGTATTATGTAAGTCATGTATAATATTAAATAAGTTATGTAGGTTG
TGTATA
Found at i:687016 original size:23 final size:22
Alignment explanation
Indices: 686983--687066 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 22
686973 ACCTCAGTTC
*
686983 GAAATTTGGGGAAATGATATCGGG
1 GAAA-TTGGGGAAATGAAATC-GG
**
687007 GAAATTGGGGATTTGAAATCAGG
1 GAAATTGGGGAAATGAAATC-GG
687030 GAAATTGGGAGAATATGAAAT-GG
1 GAAATTGGG-GAA-ATGAAATCGG
*
687053 GAAATTAGGGAAAT
1 GAAATTGGGGAAAT
687067 CAATTTGGGG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.04
22 3 0.06
23 34 0.67
24 6 0.12
25 6 0.12
ACGTcount: A:0.39, C:0.02, G:0.35, T:0.24
Consensus pattern (22 bp):
GAAATTGGGGAAATGAAATCGG
Found at i:687563 original size:22 final size:22
Alignment explanation
Indices: 687507--687565 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
687497 ATAAAATTTA
* *
687507 AACCCTAA-ACCATAAGCCCCT
1 AACCCTAACACCCTAATCCCCT
*
687528 AACCCTTACACCCTAATCCCCT
1 AACCCTAACACCCTAATCCCCT
687550 AACCACTAAC-CCCTAA
1 AACC-CTAACACCCTAA
687566 ATCGTAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 7 0.22
22 21 0.66
23 4 0.12
ACGTcount: A:0.36, C:0.46, G:0.02, T:0.17
Consensus pattern (22 bp):
AACCCTAACACCCTAATCCCCT
Found at i:687588 original size:15 final size:14
Alignment explanation
Indices: 687560--687643 Score: 57
Period size: 13 Copynumber: 6.1 Consensus size: 14
687550 AACCACTAAC
687560 CCCTAAATCGTAAA
1 CCCTAAATCGTAAA
*
687574 CCCTAAACTCTTAAA
1 CCCTAAA-TCGTAAA
* * *
687589 -ACTATATCCTAAA
1 CCCTAAATCGTAAA
* *
687602 -CCTTAATCTTTAAA
1 CCCTAAATC-GTAAA
* *
687616 CCGTAAAT-GTACA
1 CCCTAAATCGTAAA
687629 CCCTAAATCGTAAA
1 CCCTAAATCGTAAA
687643 C
1 C
687644 ACTATATAAG
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
13 21 0.40
14 20 0.38
15 11 0.21
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.27
Consensus pattern (14 bp):
CCCTAAATCGTAAA
Found at i:687754 original size:21 final size:21
Alignment explanation
Indices: 687730--687790 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
687720 TAAACCCTTA
*
687730 AACCCGTAACCTTAAGCC-ACT
1 AACCCCTAACCTTAAGCCTA-T
* *
687751 AACCCCTGACCCTAAGCCTAT
1 AACCCCTAACCTTAAGCCTAT
687772 AACCCCTAAACCTTAAGCC
1 AACCCCT-AACCTTAAGCC
687791 CTCACCCCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.33, C:0.41, G:0.08, T:0.18
Consensus pattern (21 bp):
AACCCCTAACCTTAAGCCTAT
Found at i:687763 original size:43 final size:42
Alignment explanation
Indices: 687716--687799 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
687706 TATACCTTAA
*
687716 ACCCTAAACCCT-TAAACCCGT-AACCTTAAGCCACTAACCCCTG
1 ACCCT-AACCCTAT-AACCCCTAAACCTTAAGCC-CTAACCCCTG
* *
687759 ACCCTAAGCCTATAACCCCTAAACCTTAAGCCCTCACCCCT
1 ACCCTAACCCTATAACCCCTAAACCTTAAGCCCTAACCCCT
687800 AAACACTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 19 0.53
43 17 0.47
ACGTcount: A:0.31, C:0.44, G:0.06, T:0.19
Consensus pattern (42 bp):
ACCCTAACCCTATAACCCCTAAACCTTAAGCCCTAACCCCTG
Found at i:687792 original size:14 final size:14
Alignment explanation
Indices: 687702--687792 Score: 60
Period size: 14 Copynumber: 6.4 Consensus size: 14
687692 AAACTTTTAT
*
687702 ACCCTATACCTTAA
1 ACCCTAAACCTTAA
687716 ACCCTAAACCCTTAA
1 ACCCTAAA-CCTTAA
687731 ACCCGT-AACCTTAA
1 ACCC-TAAACCTTAA
* * * *
687745 GCCACTAACCCCT-G
1 ACC-CTAAACCTTAA
*
687759 ACCCTAAGCCTATAA
1 ACCCTAAACCT-TAA
*
687774 CCCCTAAACCTTAA
1 ACCCTAAACCTTAA
*
687788 GCCCT
1 ACCCT
687793 CACCCCTAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
13 6 0.10
14 26 0.44
15 26 0.44
16 1 0.02
ACGTcount: A:0.33, C:0.41, G:0.05, T:0.21
Consensus pattern (14 bp):
ACCCTAAACCTTAA
Found at i:687797 original size:21 final size:22
Alignment explanation
Indices: 687737--687803 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 22
687727 TTAAACCCGT
687737 AACCTTAAGCCACTAACCCCT-
1 AACCTTAAGCCACTAACCCCTA
* *
687758 GACCCTAAGCCTA-TAACCCCTA
1 AACCTTAAGCC-ACTAACCCCTA
*
687780 AACCTTAAGCC-CTCACCCCTA
1 AACCTTAAGCCACTAACCCCTA
687801 AAC
1 AAC
687804 ACTCAACATG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 28 0.74
22 10 0.26
ACGTcount: A:0.33, C:0.43, G:0.06, T:0.18
Consensus pattern (22 bp):
AACCTTAAGCCACTAACCCCTA
Found at i:687862 original size:13 final size:13
Alignment explanation
Indices: 687822--687866 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
687812 TGTAAATTGA
*
687822 AAACGTACACCAT
1 AAACCTACACCAT
*
687835 AAACACTAAACCAT
1 AAAC-CTACACCAT
687849 AAACCTACACCAT
1 AAACCTACACCAT
687862 AAACC
1 AAACC
687867 GTAAACACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.51, C:0.33, G:0.02, T:0.13
Consensus pattern (13 bp):
AAACCTACACCAT
Found at i:687977 original size:22 final size:24
Alignment explanation
Indices: 687952--687996 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
687942 TATCAATAAC
687952 CCTAACC-CTTAAACCAT-AATAG
1 CCTAACCTCTTAAACCATGAATAG
*
687974 CCTAACCTGTTAAACCATGAATA
1 CCTAACCTCTTAAACCATGAATA
687997 ATAACTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (24 bp):
CCTAACCTCTTAAACCATGAATAG
Found at i:688903 original size:125 final size:124
Alignment explanation
Indices: 688697--689135 Score: 612
Period size: 125 Copynumber: 3.5 Consensus size: 124
688687 TGGCATTTCC
* * * *
688697 AGATAAACACCGCTAGTGCCACTACAGGTCAAAGTTAAACGACAGCGTTCTGCTTAATTATTTGC
1 AGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGGCGTTCTACTTAATTATTTGA
* *
688762 GGAGCATTAGTGGCGTTTTTTGGTATGCGCCGCAAATGCTAGATCATTACTGGCGTTTTT
66 GGAGCATTAGTGGCGTTTTTTGATATGCGCCGCAAATGCTAGATCTTTAC-GGCGTTTTT
* * *
688822 AGATAAACGCTGCTAGTGCCACTACAGGTCAAAGTTAAACGACGGCGTTCTACTTAATTTTTTGT
1 AGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGGCGTTCTACTTAATTATTTGA
* * * * *
688887 TGAGCATTAGTGGCGTTTTTTGATAAT-CGCCACAAATGCTTGATCTTTGGCGGCATTTCTT
66 GGAGCATTAGTGGCGTTTTTTGAT-ATGCGCCGCAAATGCTAGATCTTT-ACGGCGTTT-TT
* *
688948 -GATAAACGCCGCTAGTGTCACTACAGGTCAAAGTTAAACGACGGCGTTCTGCTTAATTATTTGA
1 AGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGGCGTTCTACTTAATTATTTGA
* * **
689012 GGAGCATTAGTGGCGTTTTTTGATAAGTGCCGCAAATGCTAGATCTTTACCGGCGTTTCC
66 GGAGCATTAGTGGCGTTTTTTGATATGCGCCGCAAATGCTAGATCTTTA-CGGCGTTTTT
* * *
689072 AGATAAATGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGAAGGCGTTCTACTTAATTGTTTG
1 AGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGGCGTTCTACTTAATTATTTG
689136 CGGCGCTTTT
Statistics
Matches: 276, Mismatches: 32, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
124 1 0.00
125 270 0.98
126 5 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (124 bp):
AGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGGCGTTCTACTTAATTATTTGA
GGAGCATTAGTGGCGTTTTTTGATATGCGCCGCAAATGCTAGATCTTTACGGCGTTTTT
Found at i:689829 original size:2 final size:2
Alignment explanation
Indices: 689822--689847 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
689812 ATTTAAACTT
689822 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
689848 AATAATTCCA
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:690676 original size:22 final size:22
Alignment explanation
Indices: 690646--690688 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
690636 ACAACAAAAC
*
690646 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
*
690668 AGGCCTTTAGCGGTGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
690689 AGCGCTGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:690838 original size:43 final size:42
Alignment explanation
Indices: 690782--691115 Score: 411
Period size: 43 Copynumber: 7.7 Consensus size: 42
690772 TTCTAGGAAA
*
690782 AAACGCCGCTAAAGGCCAAGACCTTTAGCGGCGCTTCCAACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCC-ACAC
* *
690825 AAACGCCGTTAAAGACCAAGACCTTTAGTGGCGCTTTCCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTCCACAC
690868 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-CCACAC
* *
690911 AAACGCCGCTAAAGACCAAGACTTTTAGCGACGCTTCCCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-CCACAC
* *
690954 AAACGCCGCTAAAGACCAAGACCTTGAGCAGCGCTTCCCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-CCACAC
* *
690997 AAACGTCGCTAAAGA-CAATGACCTTTTTAGCGGCGCTTACACGAC
1 AAACGCCGCTAAAGACCAA-GACC--TTTAGCGGCGCTTCCAC-AC
* * * * *
691042 AAACACCGCTAAAGATCAAGACCTTTAGTGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTCCACAC
*
691085 AAACGCCG-TAAAAGACTAAGACCTTTTAGCG
1 AAACGCCGCT-AAAGACCAAGACC-TTTAGCG
691116 ATGCTTTTTC
Statistics
Matches: 257, Mismatches: 24, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
42 6 0.02
43 201 0.78
44 17 0.07
45 30 0.12
46 3 0.01
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCACAC
Found at i:691297 original size:19 final size:20
Alignment explanation
Indices: 691263--691302 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
691253 CAATTAAACG
* *
691263 AATAATATATAATAAATATC
1 AATAATATAAAATAAAAATC
691283 AATAA-ATAAAATAAAAATC
1 AATAATATAAAATAAAAATC
691302 A
1 A
691303 TATTATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAATATAAAATAAAAATC
Found at i:696912 original size:9 final size:9
Alignment explanation
Indices: 696898--697052 Score: 110
Period size: 9 Copynumber: 17.8 Consensus size: 9
696888 TTTTTATGTA
696898 TTATGTAAG
1 TTATGTAAG
*
696907 TTATGTAAC
1 TTATGTAAG
*
696916 TTACGTAAG
1 TTATGTAAG
** *
696925 TTA-CCAAA
1 TTATGTAAG
*
696933 TTAATGTATG
1 TT-ATGTAAG
696943 TTATGTAAG
1 TTATGTAAG
696952 -T-TGTAAG
1 TTATGTAAG
*
696959 TTAT-TATG
1 TTATGTAAG
696967 TATTATGTAAG
1 --TTATGTAAG
696978 TTATGT-A-
1 TTATGTAAG
*
696985 TTATGTAGG
1 TTATGTAAG
696994 TTATGTAAG
1 TTATGTAAG
*
697003 TTGTGTAAG
1 TTATGTAAG
* *
697012 ATATTTAAG
1 TTATGTAAG
697021 TTATGTAAG
1 TTATGTAAG
* *
697030 TTTTG-CA-
1 TTATGTAAG
697037 TTATGTAAG
1 TTATGTAAG
697046 TTATGTA
1 TTATGTA
697053 TGCTATGTAT
Statistics
Matches: 110, Mismatches: 25, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
7 16 0.15
8 12 0.11
9 72 0.65
10 7 0.06
11 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:696967 original size:19 final size:19
Alignment explanation
Indices: 696943--696981 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
696933 TTAATGTATG
696943 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
696962 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
696981 T
1 T
696982 GTATTATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:697003 original size:25 final size:24
Alignment explanation
Indices: 696963--697068 Score: 88
Period size: 25 Copynumber: 4.2 Consensus size: 24
696953 TGTAAGTTAT
696963 TATGTA-TTATGTAAGTTATGTAT
1 TATGTAGTTATGTAAGTTATGTAT
* *
696986 TATGTAGGTTATGTAAGTTGTGTAAGA
1 TATGTA-GTTATGTAAGTTATGT-A-T
* * *
697013 TATTTAAGTTATGTAAGTTTTGCAT
1 TATGT-AGTTATGTAAGTTATGTAT
* *
697038 TATGTAAGTTATGTATGCTATGTAT
1 TATGT-AGTTATGTAAGTTATGTAT
*
697063 AATGTA
1 TATGTA
697069 AGTTGTTATG
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
23 6 0.09
24 1 0.02
25 38 0.58
26 2 0.03
27 18 0.27
28 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (24 bp):
TATGTAGTTATGTAAGTTATGTAT
Found at i:697042 original size:52 final size:50
Alignment explanation
Indices: 696936--697052 Score: 137
Period size: 52 Copynumber: 2.3 Consensus size: 50
696926 TACCAAATTA
* * * *
696936 ATGTATGTTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTATGTATT
1 ATGTAAGTTATGTAAGTTGTAAGATATTAAG-ATTATGTAAGTTATGCATT
* *
696987 ATGTAGGTTATGTAAGTTGTGTAAGATATTTAAG-TTATGTAAGTTTTGCATT
1 ATGTAAGTTATGTAAG-T-TGTAAGATA-TTAAGATTATGTAAGTTATGCATT
697039 ATGTAAGTTATGTA
1 ATGTAAGTTATGTA
697053 TGCTATGTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 15 0.26
52 30 0.53
53 8 0.14
54 4 0.07
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.48
Consensus pattern (50 bp):
ATGTAAGTTATGTAAGTTGTAAGATATTAAGATTATGTAAGTTATGCATT
Found at i:697097 original size:19 final size:19
Alignment explanation
Indices: 697056--697099 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
697046 TTATGTATGC
**
697056 TATGTATAATGTAAGTTGT
1 TATGTATAATGTAAGTTAA
697075 TATGTATAATGTAAGTTAA
1 TATGTATAATGTAAGTTAA
697094 TATGTA
1 TATGTA
697100 AGTAACGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (19 bp):
TATGTATAATGTAAGTTAA
Found at i:697787 original size:16 final size:16
Alignment explanation
Indices: 697766--697796 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
697756 TATGGAACCA
697766 TATTAAATAATACTAG
1 TATTAAATAATACTAG
697782 TATTAAATAATACTA
1 TATTAAATAATACTA
697797 TTTGAATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
TATTAAATAATACTAG
Found at i:698291 original size:26 final size:26
Alignment explanation
Indices: 698262--698319 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
698252 TTAGATTTAT
*
698262 ATTATTTTATAAGCTATAGAGTAAGA
1 ATTATTTGATAAGCTATAGAGTAAGA
*
698288 ATTATTTGATAAGCTATAGAGTGAGA
1 ATTATTTGATAAGCTATAGAGTAAGA
698314 ATTATT
1 ATTATT
698320 ATGCAACGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (26 bp):
ATTATTTGATAAGCTATAGAGTAAGA
Found at i:699130 original size:26 final size:26
Alignment explanation
Indices: 699101--699158 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
699091 TTAGATTTAT
*
699101 ATTATTTTATAAGCTATAGAGTAAGA
1 ATTATTTGATAAGCTATAGAGTAAGA
*
699127 ATTATTTGATAAGCTATAGAGTGAGA
1 ATTATTTGATAAGCTATAGAGTAAGA
699153 ATTATT
1 ATTATT
699159 ATGCAACGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (26 bp):
ATTATTTGATAAGCTATAGAGTAAGA
Found at i:699407 original size:839 final size:837
Alignment explanation
Indices: 697789--699468 Score: 3191
Period size: 839 Copynumber: 2.0 Consensus size: 837
697779 TAGTATTAAA
697789 TAATACTATTTGAATTGGCTAAAAGAACTATTAGCACATAAACAAAGTCCACTTGCTTAAAACCA
1 TAATACTATTTGAATTGGCTAAAAGAACTATTAGCACATAAACAAAGTCCACTTGCTTAAAACCA
697854 TTTGGGGATTTGCATAATACATGTCAAGACGGTGACTAAATGCAACGGCTATAGCAGTACCTCGA
66 TTTGGGGATTTGCATAATACATGTCAAGACGGTGACTAAATGCAACGGCTATAGCAGTACCTCGA
* *
697919 ACAGCAAGATGATTAACTACCAAACCTTTTGTTTGCAACAGAAAATTTTCCTTCAGAAAATTCTG
131 ACAGCAAGATGATTAACTACCAAACCTTTTGTTTGCAACAGAAAATTTACCTTCAAAAAATTCTG
*
697984 TTCTTTCAATCAAACTAAGGCTGATAGATTAAAACAGAAGAATAAATATTTACCTCCCACGCAAA
196 TTCTTTCAATCAAACTAAGGCTGATACATTAAAACAGAAGAATAAATATTTACCTCCCACGCAAA
698049 AAAGTAGACAAGTTCTGCAGCGAAATACGCAGCAAGCTAGCAGCAAAAAATTGACCTTTCACGCC
261 AAAGTAGACAAGTTCTGCAGCGAAATACGCAGCAAGCTAGCAGCAAAAAATTGACCTTTCACGCC
698114 AAAGAATAGCGTTATCCTTCCAACCCAGCAAGCTAAGCACAACAACGCAAACAACAATTATGAAC
326 AAAGAATAGCGTTATCCTTCCAACCCAGCAAGCTAAGCACAACAACGCAAACAACAATTATGAAC
*
698179 GGTTAGAAACTACTGTAAACTACAAACAGGATATAAACAAATTATGAACAAAAATTTGCAACGAG
391 GGTTACAAACTACTGTAAACTACAAACAGGATATAAACAAATTATGAACAAAAATTTGCAACGAG
698244 AAATGTTATTAGATTTATATTATTTTATAAGCTATAGAGTAAGAATTATTTGATAAGCTATAGAG
456 AAATGTTATTAGATTTATATTATTTTATAAGCTATAGAGTAAGAATTATTTGATAAGCTATAGAG
698309 TGAGAATTATTATGCAACGAGAAATGTTATTAGAAATGCATTACTTGACAGCCTATGGGACCAAA
521 TGAGAATTATTATGCAACGAGAAATGTTATTAGAAATGCATTACTTGACAGCCTATGGGACCAAA
698374 TACAACAATTATTTGATAAGGTATATTCCAACGAAGTGTTCAAGAGAGCACTGCACAAGGTTTTT
586 TACAACAATTATTTGATAAGGTATATTCCAACGAAGTGTTCAAGAGAGCACTGCACAAGGTTTTT
698439 GTCAAGAGTTGGTTCAAATGTGCCAAATTTCTGGCATGGTGAATTTTCCTAACCTTTGTTTTCAC
651 GTCAAGAGTTGGTTCAAATGT--CAAATTTCTGGCATGGTGAATTTTCCTAACCTTTGTTTTCAC
*
698504 TAACCAACTAATTTATCTATATAACAGCTTCCAATGGATGCCGTTTGGTGCCTGAACCTTTGATC
714 TAACCAACTAATTTATCTATATAACAACTTCCAATGGATGCCGTTTGGTGCCTGAACCTTTGATC
698569 AATTTGGTCTTTTAAATGCAGGAATTCGATCGAGACCCCGTAATTCCTATCTATTCAGC
779 AATTTGGTCTTTTAAATGCAGGAATTCGATCGAGACCCCGTAATTCCTATCTATTCAGC
*
698628 TAATACTATTTGCATTGGCTAAAAGAACTATTAGCACATAAACAAAGTCCACTTGCTTAAAACCA
1 TAATACTATTTGAATTGGCTAAAAGAACTATTAGCACATAAACAAAGTCCACTTGCTTAAAACCA
698693 TTTGGGGATTTGCATAATACATGTCAAGACGGTGACTAAATGCAACGGCTATAGCAGTACCTCGA
66 TTTGGGGATTTGCATAATACATGTCAAGACGGTGACTAAATGCAACGGCTATAGCAGTACCTCGA
*
698758 ACAGCAAGATGATTAACTACCAAACCTTTTTTTTGCAACAGAAAATTTACCTTCAAAAAATTCTG
131 ACAGCAAGATGATTAACTACCAAACCTTTTGTTTGCAACAGAAAATTTACCTTCAAAAAATTCTG
* *
698823 TTCTTTCAATCAAACTAAGGCTGATACATTACAACAGAAGAATAAATATTTACCTTCCACGCAAA
196 TTCTTTCAATCAAACTAAGGCTGATACATTAAAACAGAAGAATAAATATTTACCTCCCACGCAAA
*
698888 AAAGTAGACAAGTTCTGCAGCGAAATACGCAGCAAGCTAGCGGCAAAAAATTGACCTTTCACGCC
261 AAAGTAGACAAGTTCTGCAGCGAAATACGCAGCAAGCTAGCAGCAAAAAATTGACCTTTCACGCC
* *
698953 AAAGAATAGTGTTATCCTTCCAACCCAGCAAGCTAAGCACAACAACGCAAACAGCAATTATGAAC
326 AAAGAATAGCGTTATCCTTCCAACCCAGCAAGCTAAGCACAACAACGCAAACAACAATTATGAAC
699018 GGTTACAAACTACTGTAAACTACAAACAGGATATAAACAAATTATGAACAAAAATTTGCAACGAG
391 GGTTACAAACTACTGTAAACTACAAACAGGATATAAACAAATTATGAACAAAAATTTGCAACGAG
699083 AAATGTTATTAGATTTATATTATTTTATAAGCTATAGAGTAAGAATTATTTGATAAGCTATAGAG
456 AAATGTTATTAGATTTATATTATTTTATAAGCTATAGAGTAAGAATTATTTGATAAGCTATAGAG
699148 TGAGAATTATTATGCAACGAGAAATGTTATTAGAAATGCATTACTTGACAGCCTATGGGACCAAA
521 TGAGAATTATTATGCAACGAGAAATGTTATTAGAAATGCATTACTTGACAGCCTATGGGACCAAA
*
699213 TACAGCAATTATTTGATAAGGTATATTCCAACGAAGTGTTCAAGAGAGCACTGCACAAGGTTTTT
586 TACAACAATTATTTGATAAGGTATATTCCAACGAAGTGTTCAAGAGAGCACTGCACAAGGTTTTT
699278 GTCAAGAGTTAGTTGTTCAAATGT-AAATTTCTGGCATGGTGAATTTTCCTAACCTTTGTTTTCA
651 GTCAAGAGTT-G--GTTCAAATGTCAAATTTCTGGCATGGTGAATTTTCCTAACCTTTGTTTTCA
699342 CTAACCAACTAATTTATCTATATAACAACTTCCAATGGATGCCGTTTGGTGCCTGAACCTTTGAT
713 CTAACCAACTAATTTATCTATATAACAACTTCCAATGGATGCCGTTTGGTGCCTGAACCTTTGAT
699407 CAATTTGGTCTTTTAAATGCAGGAATTCGATCGAGACCCCGTAATTCCTATCTATTCAGC
778 CAATTTGGTCTTTTAAATGCAGGAATTCGATCGAGACCCCGTAATTCCTATCTATTCAGC
699467 TA
1 TA
699469 CACCAGATCA
Statistics
Matches: 825, Mismatches: 13, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
839 814 0.99
840 1 0.00
842 10 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (837 bp):
TAATACTATTTGAATTGGCTAAAAGAACTATTAGCACATAAACAAAGTCCACTTGCTTAAAACCA
TTTGGGGATTTGCATAATACATGTCAAGACGGTGACTAAATGCAACGGCTATAGCAGTACCTCGA
ACAGCAAGATGATTAACTACCAAACCTTTTGTTTGCAACAGAAAATTTACCTTCAAAAAATTCTG
TTCTTTCAATCAAACTAAGGCTGATACATTAAAACAGAAGAATAAATATTTACCTCCCACGCAAA
AAAGTAGACAAGTTCTGCAGCGAAATACGCAGCAAGCTAGCAGCAAAAAATTGACCTTTCACGCC
AAAGAATAGCGTTATCCTTCCAACCCAGCAAGCTAAGCACAACAACGCAAACAACAATTATGAAC
GGTTACAAACTACTGTAAACTACAAACAGGATATAAACAAATTATGAACAAAAATTTGCAACGAG
AAATGTTATTAGATTTATATTATTTTATAAGCTATAGAGTAAGAATTATTTGATAAGCTATAGAG
TGAGAATTATTATGCAACGAGAAATGTTATTAGAAATGCATTACTTGACAGCCTATGGGACCAAA
TACAACAATTATTTGATAAGGTATATTCCAACGAAGTGTTCAAGAGAGCACTGCACAAGGTTTTT
GTCAAGAGTTGGTTCAAATGTCAAATTTCTGGCATGGTGAATTTTCCTAACCTTTGTTTTCACTA
ACCAACTAATTTATCTATATAACAACTTCCAATGGATGCCGTTTGGTGCCTGAACCTTTGATCAA
TTTGGTCTTTTAAATGCAGGAATTCGATCGAGACCCCGTAATTCCTATCTATTCAGC
Found at i:700300 original size:24 final size:22
Alignment explanation
Indices: 700264--700307 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
700254 AGGGTTCTAG
700264 ATTTGGGGGATTTTTGGGGAAA
1 ATTTGGGGGATTTTTGGGGAAA
700286 ATTTAGGGGGAATTTTTGGGGA
1 ATTT-GGGGG-ATTTTTGGGGA
700308 GAAAAGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 5 0.25
24 11 0.55
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (22 bp):
ATTTGGGGGATTTTTGGGGAAA
Found at i:700306 original size:12 final size:12
Alignment explanation
Indices: 700265--700306 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
700255 GGGTTCTAGA
700265 TTTGGGGG-ATT
1 TTTGGGGGAATT
* *
700276 TTTGGGGAAAAT
1 TTTGGGGGAATT
*
700288 TTAGGGGGAATT
1 TTTGGGGGAATT
700300 TTTGGGG
1 TTTGGGG
700307 AGAAAAGTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.19, C:0.00, G:0.43, T:0.38
Consensus pattern (12 bp):
TTTGGGGGAATT
Found at i:701090 original size:19 final size:20
Alignment explanation
Indices: 701063--701103 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
701053 AAAATTTTAA
701063 TTAAATAAT-TATTAAAA-TT
1 TTAAATAATAT-TTAAAAGTT
*
701082 TTAAGTAATATTTAAAAGTT
1 TTAAATAATATTTAAAAGTT
701102 TT
1 TT
701104 TGATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAAATAATATTTAAAAGTT
Found at i:701258 original size:2 final size:2
Alignment explanation
Indices: 701201--701248 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
701191 ATTAATTACC
701201 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
701243 TA TA TA
1 TA TA TA
701249 AAAAATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:701867 original size:15 final size:15
Alignment explanation
Indices: 701847--701950 Score: 88
Period size: 15 Copynumber: 6.9 Consensus size: 15
701837 ACCCTTGACA
701847 CCCTAACCCCTAAAT
1 CCCTAACCCCTAAAT
* * *
701862 CTCTAA-CCCTTAAC
1 CCCTAACCCCTAAAT
701876 CCCTAAATCCCCCTAAA-
1 CCCT-AA--CCCCTAAAT
701893 CCCTAACCCCCTAAAT
1 CCCTAA-CCCCTAAAT
* *
701909 CACTAACCCCT-AAC
1 CCCTAACCCCTAAAT
*
701923 CCCTAACCCTTAAAT
1 CCCTAACCCCTAAAT
*
701938 TCCTAACCCCTAA
1 CCCTAACCCCTAA
701951 CCCTTAAACC
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
14 20 0.28
15 34 0.48
16 7 0.10
17 4 0.06
18 6 0.08
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAACCCCTAAAT
Found at i:701876 original size:22 final size:21
Alignment explanation
Indices: 701846--701928 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 21
701836 TACCCTTGAC
*
701846 ACCCTAACCCCTAAATCTCTA
1 ACCCTAACCCCTAAATCACTA
*
701867 ACCCTTAACCCCTAAATCCCCCTAA
1 ACCC-TAACCCCTAAAT--CACT-A
701892 ACCCTAACCCCCTAAATCACTA
1 ACCCTAA-CCCCTAAATCACTA
701914 ACCCCTAACCCCTAA
1 A-CCCTAACCCCTAA
701929 CCCTTAAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.07
22 21 0.39
23 9 0.17
24 6 0.11
25 14 0.26
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.19
Consensus pattern (21 bp):
ACCCTAACCCCTAAATCACTA
Found at i:701879 original size:8 final size:7
Alignment explanation
Indices: 701847--701953 Score: 70
Period size: 7 Copynumber: 14.3 Consensus size: 7
701837 ACCCTTGACA
701847 CCCTAAC
1 CCCTAAC
*
701854 CCCTAAAT
1 CCCT-AAC
*
701862 CTCTAAC
1 CCCTAAC
*
701869 CCTTAAC
1 CCCTAAC
701876 CCCTAAATCC
1 CCCT-AA--C
*
701886 CCCTAAA
1 CCCTAAC
701893 CCCTAACC
1 CCCTAA-C
*
701901 CCCTAAAT
1 CCCT-AAC
*
701909 CACTAAC
1 CCCTAAC
701916 CCCTAAC
1 CCCTAAC
701923 CCCTAAC
1 CCCTAAC
* *
701930 CCTTAAAT
1 CCCT-AAC
*
701938 TCCTAAC
1 CCCTAAC
701945 CCCTAAC
1 CCCTAAC
701952 CC
1 CC
701954 TTAAACCTTA
Statistics
Matches: 75, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
7 48 0.64
8 18 0.24
9 4 0.05
10 5 0.07
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAC
Found at i:701936 original size:29 final size:29
Alignment explanation
Indices: 701885--701964 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
701875 CCCCTAAATC
* *
701885 CCCCTAAACCCTAACCCCCTAAA-TCACTAA
1 CCCCTAACCCCTAA-CCCTTAAATTC-CTAA
701915 CCCCTAACCCCTAACCCTTAAATTCCTAA
1 CCCCTAACCCCTAACCCTTAAATTCCTAA
* *
701944 CCCCTAACCCTTAAACCTTAA
1 CCCCTAACCCCTAACCCTTAA
701965 TCCCAAACCC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 30 0.67
30 15 0.33
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (29 bp):
CCCCTAACCCCTAACCCTTAAATTCCTAA
Found at i:701942 original size:22 final size:22
Alignment explanation
Indices: 701917--701958 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
701907 ATCACTAACC
701917 CCTAACCCCTAACCCTTAAATT
1 CCTAACCCCTAACCCTTAAATT
701939 CCTAACCCCTAACCCTTAAA
1 CCTAACCCCTAACCCTTAAA
701959 CCTTAATCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.43, G:0.00, T:0.24
Consensus pattern (22 bp):
CCTAACCCCTAACCCTTAAATT
Found at i:701975 original size:21 final size:21
Alignment explanation
Indices: 701917--701975 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
701907 ATCACTAACC
*
701917 CCTAACCCCTAACCCTTAAATT
1 CCTAACCCCAAACCCTTAAA-T
*
701939 CCTAACCCCTAACCCTTAAA-
1 CCTAACCCCAAACCCTTAAAT
*
701959 CCTTAATCCCAAACCCT
1 CC-TAACCCCAAACCCT
701976 AATCCATACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 2 0.06
21 12 0.35
22 20 0.59
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (21 bp):
CCTAACCCCAAACCCTTAAAT
Found at i:702569 original size:41 final size:41
Alignment explanation
Indices: 702515--702650 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 41
702505 CTTTACAAAC
* * * **
702515 AAACGCAACTAAAAACCTTAACTTTAGCGGCGCATTA-TTAA
1 AAACGCCACTAAAAACCATAACATTAGCGGCGC-TTAGAAAA
* * * * * *
702556 AAATGCCGCTAAAAGCCCTAAAATTAGTGGCGCTTAGAAAA
1 AAACGCCACTAAAAACCATAACATTAGCGGCGCTTAGAAAA
* **
702597 AAACGCCACTAAAAACCATAACATTAGCGGCG-TTTGTTTAA
1 AAACGCCACTAAAAACCATAACATTAGCGGCGCTTAG-AAAA
702638 AAACGCCACTAAA
1 AAACGCCACTAAA
702651 GCCCTCTAAA
Statistics
Matches: 74, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
40 6 0.08
41 68 0.92
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (41 bp):
AAACGCCACTAAAAACCATAACATTAGCGGCGCTTAGAAAA
Found at i:705265 original size:24 final size:25
Alignment explanation
Indices: 705238--705286 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
705228 ATTATATATT
*
705238 AAATATA-TATTTTTATTTTTAATC
1 AAATATACTATTTTTATTATTAATC
*
705262 AAATATACTTTTTTTTATTATTAAT
1 AAATATAC-TATTTTTATTATTAAT
705287 TTGGCTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
26 14 0.67
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (25 bp):
AAATATACTATTTTTATTATTAATC
Found at i:708369 original size:118 final size:118
Alignment explanation
Indices: 708161--708393 Score: 313
Period size: 118 Copynumber: 2.0 Consensus size: 118
708151 CTGTGCACTG
* * * *
708161 CTAGTTATTCATGGACTAGATAGACTGTAAAAAGAAATTCCAAGGTTCAAATCTAGTCCTGTCTT
1 CTAGTAATTCATGGACTAGATAGACTGTAAAAAGAAATTCCAAGATTCAAATCTAGTCATGACTT
* *
708226 GTGTATGGTATTGAATTTTTATATGCCTCATTATTATCTCCGTGTTCTTTCTA
66 GTGTATGGTATTGAAATTTTATATGCCTCATTATTATCTCCGTATTCTTTCTA
* * * * * *
708279 CTAGTAATTCTTGGGCTAGATAGGCTGTAAAAAGAAATTTCTAGATTTAAATCTAGTCATGACTT
1 CTAGTAATTCATGGACTAGATAGACTGTAAAAAGAAATTCCAAGATTCAAATCTAGTCATGACTT
* * * * *
708344 TTGTTTGGTTTTGAAATTTTATATGCCTTATTATTATCTCTGTATTCTTT
66 GTGTATGGTATTGAAATTTTATATGCCTCATTATTATCTCCGTATTCTTT
708394 TTAGTGGGTG
Statistics
Matches: 98, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
118 98 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (118 bp):
CTAGTAATTCATGGACTAGATAGACTGTAAAAAGAAATTCCAAGATTCAAATCTAGTCATGACTT
GTGTATGGTATTGAAATTTTATATGCCTCATTATTATCTCCGTATTCTTTCTA
Found at i:710923 original size:22 final size:23
Alignment explanation
Indices: 710897--710944 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
710887 AATAACATAG
*
710897 TTTTAATAAATG-CAGAAAAATT
1 TTTTAATAAATGAAAGAAAAATT
*
710919 TTTTAATGAATGAAAAGAAAAATT
1 TTTTAATAAATG-AAAGAAAAATT
710943 TT
1 TT
710945 CAACTGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
24 11 0.50
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (23 bp):
TTTTAATAAATGAAAGAAAAATT
Found at i:713343 original size:23 final size:25
Alignment explanation
Indices: 713309--713371 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
713299 TGGATTTTTT
713309 TTAAA-AA-AATACATT-AT-AAAA
1 TTAAATAATAATACATTGATAAAAA
713330 TTAAATAATAATAC-TTGATAAAAAA
1 TTAAATAATAATACATTGAT-AAAAA
*
713355 CTAGAATAATAATACAT
1 TTA-AATAATAATACAT
713372 AGTAGAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 5 0.15
22 4 0.12
23 7 0.21
25 6 0.18
26 11 0.32
27 1 0.03
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.30
Consensus pattern (25 bp):
TTAAATAATAATACATTGATAAAAA
Found at i:713379 original size:18 final size:18
Alignment explanation
Indices: 713356--713390 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
713346 GATAAAAAAC
713356 TAGAATAATAA-TACATAG
1 TAGAATAA-AATTACATAG
713374 TAGAATAAAATTACATA
1 TAGAATAAAATTACATA
713391 TAAAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.29
Consensus pattern (18 bp):
TAGAATAAAATTACATAG
Found at i:713443 original size:3 final size:3
Alignment explanation
Indices: 713437--713469 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
713427 GTACTTACGC
713437 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
713470 ATTAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:714157 original size:4 final size:4
Alignment explanation
Indices: 714148--714173 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
714138 CCGAGTCAAA
714148 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
714174 TCATCTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:716605 original size:43 final size:43
Alignment explanation
Indices: 716535--716746 Score: 250
Period size: 43 Copynumber: 4.9 Consensus size: 43
716525 CGGCGTTTTT
* *
716535 ATGACCTTTAGCGGCGCTTTGAAAAAAAACGCCGCTAAAGAAC
1 ATGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGAAC
* * *
716578 AGGACCTTTAGCGGCGCTTTCATAAAAAACGCCACTAAAGAAC
1 ATGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGAAC
**
716621 ATGACCTTTAGCGGCGC-TTTACCCAAAAACGCCGCTAAAGAAAC
1 ATGACCTTTAGCGGCGCTTTTA-TAAAAAACGCCGCTAAAG-AAC
* * * *
716665 ATGATCTTTAGCGGCGCTTTTATCACAAACGCAGCTAAA-AAGC
1 ATGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGAA-C
* *
716708 ATGACCTTTAGCGACGCTTTTA-AAGAAAACGCCACTAAA
1 ATGACCTTTAGCGGCGCTTTTATAA-AAAACGCCGCTAAA
716747 AGCATTTTTA
Statistics
Matches: 145, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
42 6 0.04
43 102 0.70
44 33 0.23
45 4 0.03
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (43 bp):
ATGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGAAC
Found at i:716711 original size:87 final size:86
Alignment explanation
Indices: 716535--716746 Score: 268
Period size: 87 Copynumber: 2.5 Consensus size: 86
716525 CGGCGTTTTT
716535 ATGACCTTTAGCGGCGCTTTGAAAAAAAACGCCGCTAAAGAACAGGACCTTTAGCGGCGCTTTCA
1 ATGACCTTTAGCGGCGCTTTGAAAAAAAACGCCGCTAAAGAACAGGACCTTTAGCGGCGCTTTCA
716600 TAAAAAACGCCACTAAAGAAC
66 TAAAAAACGCCACTAAAGAAC
** * *
716621 ATGACCTTTAGCGGCGCTTT-ACCCAAAAACGCCGCTAAAGAAACATGATCTTTAGCGGCGCTTT
1 ATGACCTTTAGCGGCGCTTTGA-AAAAAAACGCCGCTAAAG-AACAGGACCTTTAGCGGCGCTTT
* * *
716685 TATCACAAACG-CAGCTAAA-AAGC
64 CATAAAAAACGCCA-CTAAAGAA-C
* * * *
716708 ATGACCTTTAGCGACGCTTTTAAAGAAAACGCCACTAAA
1 ATGACCTTTAGCGGCGCTTTGAAAAAAAACGCCGCTAAA
716747 AGCATTTTTA
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
85 1 0.01
86 40 0.37
87 67 0.61
88 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (86 bp):
ATGACCTTTAGCGGCGCTTTGAAAAAAAACGCCGCTAAAGAACAGGACCTTTAGCGGCGCTTTCA
TAAAAAACGCCACTAAAGAAC
Found at i:719390 original size:22 final size:22
Alignment explanation
Indices: 719363--719408 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
719353 ATAGTGCCCG
*
719363 GCTCCAGATCCATGAGAATAGC
1 GCTCCAGATCCATGAGAACAGC
719385 GCTCCAGATCCATGAGAACAGC
1 GCTCCAGATCCATGAGAACAGC
719407 GC
1 GC
719409 GTGGGACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.15
Consensus pattern (22 bp):
GCTCCAGATCCATGAGAACAGC
Found at i:720471 original size:15 final size:14
Alignment explanation
Indices: 720453--720485 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
720443 CCCATAATGT
720453 CTAACCCCTAAGCCC
1 CTAACCCCTAA-CCC
720468 CTAACCCCTAACCC
1 CTAACCCCTAACCC
720482 CTAA
1 CTAA
720486 ACCTTAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.30, C:0.52, G:0.03, T:0.15
Consensus pattern (14 bp):
CTAACCCCTAACCC
Found at i:720488 original size:8 final size:7
Alignment explanation
Indices: 720453--720485 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
720443 CCCATAATGT
720453 CTAACCC
1 CTAACCC
720460 CTAAGCCC
1 CTAA-CCC
720468 CTAACCC
1 CTAACCC
720475 CTAACCC
1 CTAACCC
720482 CTAA
1 CTAA
720486 ACCTTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.30, C:0.52, G:0.03, T:0.15
Consensus pattern (7 bp):
CTAACCC
Found at i:720488 original size:15 final size:15
Alignment explanation
Indices: 720453--720509 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
720443 CCCATAATGT
*
720453 CTAACCCCTAAGCCC
1 CTAACCCCTAAACCC
720468 CTAACCCCT-AACCC
1 CTAACCCCTAAACCC
* * *
720482 CTAAACCTTAAATCC
1 CTAACCCCTAAACCC
*
720497 C-AACCCTTAAACC
1 CTAACCCCTAAACC
720510 ATAATCCCTG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
14 21 0.60
15 14 0.40
ACGTcount: A:0.33, C:0.47, G:0.02, T:0.18
Consensus pattern (15 bp):
CTAACCCCTAAACCC
Found at i:720507 original size:21 final size:20
Alignment explanation
Indices: 720477--720517 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
720467 CCTAACCCCT
*
720477 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
720498 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
720518 TGATACATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:723881 original size:40 final size:40
Alignment explanation
Indices: 723826--723907 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
723816 TCACACATGC
*
723826 TCGTTGGTTGTTCATGTATAACTTGTTGCTTCTTGATTGG
1 TCGTTGATTGTTCATGTATAACTTGTTGCTTCTTGATTGG
*
723866 TCGTTGATTGTTCATGTATAACTTGTTGCTTCTTGGTTGG
1 TCGTTGATTGTTCATGTATAACTTGTTGCTTCTTGATTGG
723906 TC
1 TC
723908 AATCTTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.12, C:0.13, G:0.24, T:0.50
Consensus pattern (40 bp):
TCGTTGATTGTTCATGTATAACTTGTTGCTTCTTGATTGG
Found at i:724764 original size:40 final size:40
Alignment explanation
Indices: 724720--724797 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
724710 ACATTTCTTT
*
724720 TATATTTTATAAATCACATATACATATATATATATTATCC
1 TATATTTTACAAATCACATATACATATATATATATTATCC
* *
724760 TATATTTTACAACTTACATATACATATATATATATTAT
1 TATATTTTACAAATCACATATACATATATATATATTAT
724798 ACTTTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (40 bp):
TATATTTTACAAATCACATATACATATATATATATTATCC
Found at i:725758 original size:3 final size:3
Alignment explanation
Indices: 725750--725786 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
725740 CTGCCCGTTT
725750 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
725787 TCGTGAGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:730329 original size:41 final size:41
Alignment explanation
Indices: 730272--730423 Score: 243
Period size: 41 Copynumber: 3.7 Consensus size: 41
730262 CCTTTCGGGG
*
730272 CTTTAGCGACGTTTTTGAAAAAGCGCCGCTGATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTGATGCTCAGAT
*
730313 CTTTAGCGGCGTTTTTGAAAAAGCACCGCTGATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTGATGCTCAGAT
* * *
730354 CTTTAACGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAG-G
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTGATGCTCAGAT
730394 CTTTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 C-TTTAGCGGCGTTTTTGAAAAAGCGCCGC
730424 AAAAATATTT
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 1 0.01
41 102 0.99
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTGATGCTCAGAT
Found at i:730837 original size:7 final size:7
Alignment explanation
Indices: 730825--730850 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
730815 ACAGTAAGGC
730825 GTTAGGG
1 GTTAGGG
730832 GTTAGGG
1 GTTAGGG
730839 GTTAGGG
1 GTTAGGG
730846 GTTAG
1 GTTAG
730851 AGATTAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (7 bp):
GTTAGGG
Found at i:730971 original size:13 final size:13
Alignment explanation
Indices: 730946--730983 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
730936 TATTAAATAA
730946 GGTTTAGGGGTTAG
1 GGTTTA-GGGTTAG
730960 GGATTT-GGGTTAG
1 GG-TTTAGGGTTAG
730973 GGTTTAGGGTT
1 GGTTTAGGGTT
730984 TAGATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 14 0.64
14 2 0.09
15 3 0.14
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.39
Consensus pattern (13 bp):
GGTTTAGGGTTAG
Found at i:730981 original size:74 final size:76
Alignment explanation
Indices: 730894--731037 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 76
730884 TCGGTATCAA
* * *
730894 GTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAA-TT-TATATTAAATAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
730957 TAGGGATTTGG
66 TAGGGATTTGG
* * * **
730968 GTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
731033 TAGGG
66 TAGGG
731038 GTTAGGGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 31 0.52
75 2 0.03
76 27 0.45
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.44
Consensus pattern (76 bp):
GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
TAGGGATTTGG
Found at i:731037 original size:7 final size:7
Alignment explanation
Indices: 731025--731049 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
731015 TAAAGAAGGT
731025 TTAGGGG
1 TTAGGGG
731032 TTAGGGG
1 TTAGGGG
731039 TTAGGGG
1 TTAGGGG
731046 TTAG
1 TTAG
731050 AGATTAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:731166 original size:199 final size:199
Alignment explanation
Indices: 730826--731407 Score: 1164
Period size: 199 Copynumber: 2.9 Consensus size: 199
730816 CAGTAAGGCG
730826 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
1 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
730891 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
66 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
730956 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
131 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
731021 AGGT
196 AGGT
731025 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
1 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
731090 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
66 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
731155 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
131 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
731220 AGGT
196 AGGT
731224 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
1 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
731289 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
66 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
731354 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTA
131 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTA
731408 CGTTAGCGGC
Statistics
Matches: 383, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 383 1.00
ACGTcount: A:0.29, C:0.02, G:0.28, T:0.41
Consensus pattern (199 bp):
TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
AGGT
Found at i:731170 original size:13 final size:13
Alignment explanation
Indices: 731145--731182 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
731135 TATTAAATAA
731145 GGTTTAGGGGTTAG
1 GGTTTA-GGGTTAG
731159 GGATTT-GGGTTAG
1 GG-TTTAGGGTTAG
731172 GGTTTAGGGTT
1 GGTTTAGGGTT
731183 TAGATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 14 0.64
14 2 0.09
15 3 0.14
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.39
Consensus pattern (13 bp):
GGTTTAGGGTTAG
Found at i:731203 original size:74 final size:76
Alignment explanation
Indices: 731093--731236 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 76
731083 TCGGTATCAA
* * *
731093 GTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAA-TT-TATATTAAATAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
731156 TAGGGATTTGG
66 TAGGGATTTGG
* * * **
731167 GTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
731232 TAGGG
66 TAGGG
731237 GTTAGGGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 31 0.52
75 2 0.03
76 27 0.45
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.44
Consensus pattern (76 bp):
GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
TAGGGATTTGG
Found at i:731236 original size:7 final size:7
Alignment explanation
Indices: 731224--731248 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
731214 TAAAGAAGGT
731224 TTAGGGG
1 TTAGGGG
731231 TTAGGGG
1 TTAGGGG
731238 TTAGGGG
1 TTAGGGG
731245 TTAG
1 TTAG
731249 AGATTAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:731369 original size:13 final size:13
Alignment explanation
Indices: 731344--731381 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
731334 TATTAAATAA
731344 GGTTTAGGGGTTAG
1 GGTTTA-GGGTTAG
731358 GGATTT-GGGTTAG
1 GG-TTTAGGGTTAG
731371 GGTTTAGGGTT
1 GGTTTAGGGTT
731382 TAGATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 14 0.64
14 2 0.09
15 3 0.14
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.39
Consensus pattern (13 bp):
GGTTTAGGGTTAG
Found at i:733998 original size:19 final size:19
Alignment explanation
Indices: 733962--733999 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
733952 TTTTTATAAG
*
733962 GGTGTTTTTGTTTTTTGTT
1 GGTGTTTTTGTTTGTTGTT
733981 GGTGTTTTATG-TTGTTGTT
1 GGTGTTTT-TGTTTGTTGTT
734000 TCGATGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.03, C:0.00, G:0.29, T:0.68
Consensus pattern (19 bp):
GGTGTTTTTGTTTGTTGTT
Found at i:735589 original size:43 final size:43
Alignment explanation
Indices: 735522--735752 Score: 268
Period size: 43 Copynumber: 5.4 Consensus size: 43
735512 AGGCTATGTT
* *
735522 TTTAGCGGCGTTT-TTGCGAGAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTTG-GAAAAGCGCCGCTAAAGGTCATGGTC
* *
735565 TTTAGCGGTGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGGC
1 TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
735608 TTTAGTGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
735651 TTTAGCGGCCTTTG-TGATAAAAGCACGGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTTG-GAAAAGCGCCGCTAAAGGTCATGGTC
* * **
735694 TTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCGCGGTC
1 TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTC
*
735737 TTTAGTGGCGTTTGTT
1 TTTAGCGGCGTTTGTT
735753 TCTAAAAATG
Statistics
Matches: 160, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.01
43 155 0.97
44 4 0.03
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:744779 original size:24 final size:24
Alignment explanation
Indices: 744752--744802 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
744742 TTTCTGGGTT
744752 ATTGTTTAA-CTGATTTTAGATGAA
1 ATTGTTTAATC-GATTTTAGATGAA
744776 ATTGTTTAATCGATTTTAGATGAA
1 ATTGTTTAATCGATTTTAGATGAA
744800 ATT
1 ATT
744803 AACCTCCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (24 bp):
ATTGTTTAATCGATTTTAGATGAA
Found at i:755480 original size:5 final size:5
Alignment explanation
Indices: 755472--755510 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
755462 ATATAATATA
755472 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAG
1 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAG
755511 ATAACAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
ATAGT
Found at i:756598 original size:16 final size:18
Alignment explanation
Indices: 756560--756600 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
756550 ACTCTTGTTC
*
756560 GGAACAACCTCTATATTT
1 GGAACAACCTCTACATTT
*
756578 AGAACAA-CTC-ACATTT
1 GGAACAACCTCTACATTT
756594 GGAACAA
1 GGAACAA
756601 GTCAAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 11 0.55
17 3 0.15
18 6 0.30
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (18 bp):
GGAACAACCTCTACATTT
Found at i:757901 original size:15 final size:15
Alignment explanation
Indices: 757881--757910 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
757871 AATTTCATGC
757881 TTCAATCACCATGTT
1 TTCAATCACCATGTT
757896 TTCAATCACCATGTT
1 TTCAATCACCATGTT
757911 ATCACTTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCAATCACCATGTT
Found at i:761307 original size:45 final size:45
Alignment explanation
Indices: 761245--761460 Score: 294
Period size: 45 Copynumber: 4.8 Consensus size: 45
761235 TCTAACATAA
* *
761245 TGCCATTGTGTCATTCAACTATGGTCTTATTCGTTTCTGGTACAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCGTTTCTGGTACAG
* * *
761290 TGCCGTAGTGTCTTTCAACTATGGTCTTATTCATTTTTGGTAGC-G
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCGTTTCTGGTA-CAG
* * * *
761335 TGCCATAGTGTCTTTCAATTATGGTCTTATTCATTT-TCAGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCGTTTCT-GGTACAG
*
761380 TGCCATAGTGTCTTTCAACTATGGTCTTATTCGTTTCTGGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCGTTTCTGGTACAG
761425 TGCCATAGTGTCTTTC-ACTTATGGTCTTATTCGTTT
1 TGCCATAGTGTCTTTCAAC-TATGGTCTTATTCGTTT
761461 TTCAAACCAA
Statistics
Matches: 154, Mismatches: 12, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
44 3 0.02
45 149 0.97
46 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.45
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCGTTTCTGGTACAG
Found at i:763605 original size:13 final size:13
Alignment explanation
Indices: 763587--763625 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
763577 ATACAACAAT
*
763587 AAGAAAAAAATAA
1 AAGAAAAAAAGAA
*
763600 AAGAAAAGAAGAA
1 AAGAAAAAAAGAA
763613 AAGAAAAAAAGAA
1 AAGAAAAAAAGAA
763626 CTAAGAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:768912 original size:21 final size:21
Alignment explanation
Indices: 768883--768922 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
768873 AGAGTATTAT
768883 GGAACAAAAGTATTGCACTAA
1 GGAACAAAAGTATTGCACTAA
*
768904 GGAATAAAAGTATTGCACT
1 GGAACAAAAGTATTGCACT
768923 TGTGAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (21 bp):
GGAACAAAAGTATTGCACTAA
Found at i:770374 original size:50 final size:50
Alignment explanation
Indices: 770315--770446 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 50
770305 TATTGAGGTT
* * *
770315 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATATCTGGGACATGGCATGGGCACCGAG
* *
770365 ATGAGAGGTCTCC-CTTAAGACCATATCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTC-CCACGTAAGACCATATCTGGGACATGGCATGGGCACCGAG
** * *
770415 ATGAGAACTCCCATGTAAGACTATATCTGGGA
1 ATGAGAGGTCCCACGTAAGACCATATCTGGGA
770447 TATGTCATTA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 2 0.03
50 66 0.94
51 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATATCTGGGACATGGCATGGGCACCGAG
Found at i:773559 original size:21 final size:21
Alignment explanation
Indices: 773515--773559 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
773505 AAAAGTTTGG
*
773515 GTTGTATTGGTAGAACCCAGA
1 GTTGTATTGGTAGAACCCACA
*
773536 GTTGTCTTGGTAGAACTCC-CA
1 GTTGTATTGGTAGAAC-CCACA
773557 GTT
1 GTT
773560 ATACCAGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (21 bp):
GTTGTATTGGTAGAACCCACA
Found at i:781177 original size:25 final size:25
Alignment explanation
Indices: 781131--781179 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
781121 CTGTCTTTGA
* *
781131 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATACTGAAACTACTATAGG
781156 TAGTATATACT-AAGACTACTATAG
1 TAGTATATACTGAA-ACTACTATAG
781180 AAAGACTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:786050 original size:18 final size:18
Alignment explanation
Indices: 786008--786050 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
785998 AATAAAAAAC
786008 CGTTTTGTAATTGAATAA
1 CGTTTTGTAATTGAATAA
*
786026 CGATTTGTGAA-TGAATAA
1 CGTTTTGT-AATTGAATAA
*
786044 TGTTTTG
1 CGTTTTG
786051 AAAACGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (18 bp):
CGTTTTGTAATTGAATAA
Found at i:788283 original size:18 final size:18
Alignment explanation
Indices: 788257--788294 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
788247 GCAATAAAAA
*
788257 AACATTTTG-AAATTGAAT
1 AACAATTTGTAAA-TGAAT
788275 AACAATTTGTAAATGAAT
1 AACAATTTGTAAATGAAT
788293 AA
1 AA
788295 TGTTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (18 bp):
AACAATTTGTAAATGAAT
Found at i:789665 original size:5 final size:5
Alignment explanation
Indices: 789657--789696 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
789647 ATATAATATA
789657 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT
1 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT
789697 TAACAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATAGT
Found at i:794212 original size:36 final size:36
Alignment explanation
Indices: 794165--794233 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
794155 GATTATGTAA
794165 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
* *
794201 TCTTAGAGTTCTAATTGTATATAGCTTTTAATT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATT
794234 TTAGCCTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:794214 original size:19 final size:19
Alignment explanation
Indices: 794164--794220 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
794154 TGATTATGTA
794164 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
794183 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
794200 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
794219 AT
1 AT
794221 ATAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:794515 original size:48 final size:48
Alignment explanation
Indices: 794440--794535 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
794430 TGAGGGAATT
* *
794440 CTGTTGAATCCTTTATCTTTGCAAGTTAGGCCGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGAATTAGGCGTTTTTA
* *
794488 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGAATTAGGCGTTTTTA
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGAATTAGGCGTTTTTA
794536 AGTAAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.42
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGAATTAGGCGTTTTTA
Found at i:799228 original size:17 final size:17
Alignment explanation
Indices: 799206--799266 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
799196 AAACTTAGAG
799206 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
799223 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
799242 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
799259 TTTTAATT
1 TTCTAATT
799267 TTAGCTTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 1 0.03
17 18 0.51
18 4 0.11
19 11 0.31
20 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:799548 original size:48 final size:48
Alignment explanation
Indices: 799476--799568 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
799466 GGGAATTCAG
*
799476 TTGAATCCTTTATCTTTGCAAGTTAGGCGGACTTAGGCGTTTTTACTA
1 TTGAATCCTTTATCATTGCAAGTTAGGCGGACTTAGGCGTTTTTACTA
* *
799524 TTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCGTTTTTA
1 TTGAATCCTTTATCATTGCAAGTTAGGCGGACTTAGGCGTTTTTA
799569 AGTAAAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (48 bp):
TTGAATCCTTTATCATTGCAAGTTAGGCGGACTTAGGCGTTTTTACTA
Found at i:804635 original size:10 final size:10
Alignment explanation
Indices: 804605--804675 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
804595 TGAACCACTC
804605 CATTTACTTA
1 CATTTACTTA
*
804615 C-TTTCCATTA
1 CATTTAC-TTA
804625 CATTTACTTA
1 CATTTACTTA
**
804635 C-TTCCCATTA
1 CATTTAC-TTA
804645 CATTTACTTA
1 CATTTACTTA
*
804655 C-TTTCCATTA
1 CATTTAC-TTA
804665 CATTTACTTA
1 CATTTACTTA
804675 C
1 C
804676 TTTCCATTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 11 0.23
10 25 0.53
11 11 0.23
ACGTcount: A:0.25, C:0.27, G:0.00, T:0.48
Consensus pattern (10 bp):
CATTTACTTA
Found at i:804825 original size:25 final size:20
Alignment explanation
Indices: 804605--804834 Score: 327
Period size: 20 Copynumber: 11.5 Consensus size: 20
804595 TGAACCACTC
*
804605 CATTTACTTACTTTCCATTA
1 CATTTACTTACTTTCCATTT
* *
804625 CATTTACTTACTTCCCATTA
1 CATTTACTTACTTTCCATTT
*
804645 CATTTACTTACTTTCCATTA
1 CATTTACTTACTTTCCATTT
804665 CATTTACTTACTTTCCATTT
1 CATTTACTTACTTTCCATTT
* **
804685 CTTTTGTTTACTTTCCATTT
1 CATTTACTTACTTTCCATTT
804705 CATTTACTTACTTTCCATTT
1 CATTTACTTACTTTCCATTT
* *
804725 CTTTTACTTACTTTCTATTT
1 CATTTACTTACTTTCCATTT
*
804745 CATTAACTTACTTT-CAGTTT
1 CATTTACTTACTTTCCA-TTT
* *
804765 CTTTTACTTGCTTTCCATTT
1 CATTTACTTACTTTCCATTT
804785 CATTTACTTACTTTCCATTT
1 CATTTACTTACTTTCCATTT
*
804805 CATTTACTTACTTTCCATTC
1 CATTTACTTACTTTCCATTT
804825 CATTTACTTA
1 CATTTACTTA
804835 GCATAGGCTT
Statistics
Matches: 188, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
19 1 0.01
20 185 0.98
21 2 0.01
ACGTcount: A:0.20, C:0.24, G:0.01, T:0.54
Consensus pattern (20 bp):
CATTTACTTACTTTCCATTT
Found at i:816003 original size:21 final size:19
Alignment explanation
Indices: 815966--816005 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
815956 GCAAGTATGG
*
815966 TTTTTTATTTATTTGAGTT
1 TTTTTTATTTATATGAGTT
815985 TTTTTTATGTTATCATGAGTT
1 TTTTTTAT-TTAT-ATGAGTT
816006 ATGGAATGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.17, C:0.03, G:0.12, T:0.68
Consensus pattern (19 bp):
TTTTTTATTTATATGAGTT
Found at i:819905 original size:50 final size:50
Alignment explanation
Indices: 819848--819974 Score: 141
Period size: 50 Copynumber: 2.5 Consensus size: 50
819838 TATCCCAGAT
* * * *
819848 ATGGTCTTACATGAGA-GTTTTCATATCGGTGCCCATGCCATGTCCCACAC
1 ATGGTCTTACATGAGACCTCTT-ATATCGGTGCCAACGCCATGTCCCACAC
* * *
819898 ATGGTCTTACGA-GGGACCTCTTATGTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTAC-ATGAGACCTCTTATATCGGTGCCAACGCCATGTCCCACAC
* *
819948 ATGGTCTTACATGGGACCTCTCATATC
1 ATGGTCTTACATGAGACCTCTTATATC
819975 CTCAATAGTG
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 1 0.02
50 60 0.92
51 4 0.06
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACATGAGACCTCTTATATCGGTGCCAACGCCATGTCCCACAC
Found at i:824205 original size:18 final size:18
Alignment explanation
Indices: 824182--824219 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
824172 GGACAGCTCA
824182 CACATTTTTGTTCTTATC
1 CACATTTTTGTTCTTATC
824200 CACATTTTTGTTCTTATC
1 CACATTTTTGTTCTTATC
824218 CA
1 CA
824220 GATACGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.05, T:0.53
Consensus pattern (18 bp):
CACATTTTTGTTCTTATC
Found at i:869658 original size:21 final size:22
Alignment explanation
Indices: 869624--869665 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
869614 ATGAACTAAA
*
869624 TTCTTTTTCTCCATCAATTTTC
1 TTCTTGTTCTCCATCAATTTTC
*
869646 TTCTTGTT-TCCATCGATTTT
1 TTCTTGTTCTCCATCAATTTT
869666 AAGACCTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.12, C:0.24, G:0.05, T:0.60
Consensus pattern (22 bp):
TTCTTGTTCTCCATCAATTTTC
Found at i:872484 original size:42 final size:42
Alignment explanation
Indices: 872424--872511 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
872414 ATGCCCGTAT
* * * *
872424 ACGGTTTGCGACAAGGCTGTGTGTATTAAGTTAGTGAGTTAC
1 ACGGTCTGCGACAAGGCTGTGTGTATCAAGTCAGAGAGTTAC
*
872466 ACGGTCTGCGACATGGCTGTGTGTATCAAGTCAGAGAGTTAC
1 ACGGTCTGCGACAAGGCTGTGTGTATCAAGTCAGAGAGTTAC
872508 ACGG
1 ACGG
872512 CCTGACATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (42 bp):
ACGGTCTGCGACAAGGCTGTGTGTATCAAGTCAGAGAGTTAC
Found at i:872519 original size:40 final size:41
Alignment explanation
Indices: 872432--872551 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 41
872422 ATACGGTTTG
* * * *
872432 CGACAAGGCTGTGTGTATTAAGTTAGTGAGTTACACGGTCT
1 CGACATGGCTGTGTGTATCAAGTCAGTGAGTTACACGGCCT
*
872473 GCGACATGGCTGTGTGTATCAAGTCAGAGAGTTACACGGCCT
1 -CGACATGGCTGTGTGTATCAAGTCAGTGAGTTACACGGCCT
* *
872515 -GACAT-ACTGTTGTGTGAACTAAGTCAGTGAGTTACAC
1 CGACATGGCTG-TGTGT-ATC-AAGTCAGTGAGTTACAC
872552 AGTTTAAGAC
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 3 0.04
40 10 0.15
41 2 0.03
42 52 0.78
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (41 bp):
CGACATGGCTGTGTGTATCAAGTCAGTGAGTTACACGGCCT
Found at i:874513 original size:114 final size:114
Alignment explanation
Indices: 874320--874819 Score: 553
Period size: 114 Copynumber: 4.4 Consensus size: 114
874310 AAGCATTCCC
* * * *
874320 TGAGCTTTTGGGGATTTAGCGGCGTTTGTAAGAAATCGCCGCTAATGCTCAGGGCTTTAGCGGCG
1 TGAGCTTTCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCG
* * * * *
874385 TTTTTAAGCAAGCGCCGCAAAAAAACATAATCCCAACGATGCCATTCTC
66 TTTTTGAGAAAGCGCCGCAAAAAAACATAATCCCAACGATGCCGTTTTG
* * * *
874434 TAAGCATTT-GGGGATTTAGCGGCGTTTTTTATAAAGCGCCGCTAATGCTCAGGGCTTTAGCAGT
1 TGAGC-TTTCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGC
*
874498 GTTTTTGAGAAAGCGCCGCAAAAAAACAT-ATGCCCAACGATGTCGTTTTG
65 GTTTTTGAGAAAGCGCCGCAAAAAAACATAAT-CCCAACGATGCCGTTTTG
* * * * *
874548 TGAGCTTTCGGGAATTTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTCAGTGTTTTGGCGGCG
1 TGAGCTTTCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCG
* * * * **
874613 GTTTTGATAAAGCGCCGCAAAAAAACCTAAGT-CCAATGACACCGTTTTG
66 TTTTTGAGAAAGCGCCGCAAAAAAACATAA-TCCCAACGATGCCGTTTTG
* **
874662 TGAGCTTTCGGGGATTTAGCGGCGTTTCTAATAAAGCGCCGCTAATGCTCAGATCTTTTAGCGGC
1 TGAGCTTTCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTCAGGGC-TTTAGCGGC
* * * * * * *
874727 GTTTGCTCA-AAAGCGCCACTAAAAAAAC-TAAACGCAACGACGCCGTTTTC
65 GTTT-TTGAGAAAGCGCCGC-AAAAAAACATAATCCCAACGATGCCGTTTTG
* *
874777 TTAGCTTTCGGGTTATTTAGCGGCG-TTTTAAGTAAAGCGCCGC
1 TGAGCTTTCGGG-GATTTAGCGGCGTTTTTAA-TAAAGCGCCGC
874820 AAAAACCTAA
Statistics
Matches: 327, Mismatches: 48, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
113 5 0.02
114 233 0.71
115 56 0.17
116 33 0.10
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (114 bp):
TGAGCTTTCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCG
TTTTTGAGAAAGCGCCGCAAAAAAACATAATCCCAACGATGCCGTTTTG
Found at i:877129 original size:675 final size:671
Alignment explanation
Indices: 875843--877175 Score: 2396
Period size: 675 Copynumber: 2.0 Consensus size: 671
875833 AATATTAGTT
875843 AAAACACTAAAATTTATAATTTTTACTACTATATATTATAAATATTACTTAACAAAACTATGGAA
1 AAAACACTAAAATTTATAATTTTTACTACTATATATTATAAATATTACTTAACAAAACTATGGAA
* * * * *
875908 TACCTAAACGGCGCCGTTTCAATATAAAATTTGATTTCGTAGTGGCGTTTCCACTAAAAACGCCG
66 TACCAAAACGACACCGTTTCAATAGAAAATTTGATTTCATAGTGGCGTTTCCACTAAAAACGCCG
*
875973 CAATAAACGAGACATTAGCGGCGTTTGGAATAAAAACGCCACAAAAATTCTTAATTTTATAGACA
131 CAATAAACGAGACATTAGCGGCGTTTGGAACAAAAACGCCACAAAAATTCTTAATTTTATAGACA
*
876038 AAACGGCGTAGCTTTCCGCTGCCATTTTAATGGCTTTAGCGGCGCTAGGAGAAAAACGCCACTAA
196 AAACGGCGTAGCTTTCCGCTACCATTTTAATGGCTTTAGCGGCGCTAGGAGAAAAACGCCACTAA
*
876103 AGGTGCGCATTAGGCGCGTTGATAAAAACGCCGCAAGGTTGGGCTGTTGTTTAAACAAAACGACA
261 AGGTGCGCATTAGGCGCGTTGATAAAAACGCCGCAAGGTTGGGCTGTGGTTTAAACAAAACGACA
* *
876168 CCGTTTTGTCTGGGCATTAGTGGTGCTACTGTAAAAACGCCGTAAATTTTCAATCTGTTGTAATT
326 CCGTTTTGTCTGGGCATTAGTGGCGCTACTGTAAAAACGCCGCAAATTTTCAATCTGTTGTAATT
876233 AAGACGCCGTCGTTTTTGTAACCCTCGAAATTATGGACTATTTACCTTAAATACAATTAATAAAT
391 AAGACGCCGTCGTTTTTGTAACCCTCGAAATTATGGACTATTTACCTTAAATACAATTAATAAAT
*
876298 AAGTTAATTTTATTAATTAATAAATAAAATTAAAATAGAAAAATAAAAATGAAATTTAAACACTA
456 AAGTTAATTTTATTAATTAATAAATAAAATTAAAATAGAAAAATAAAAATGAAATTAAAACACTA
876363 AAAATGTTAATTTTATCTAATTTATTATAAATATTACTTAAAGGAAACTAATAAATAAGTTAAAA
521 AAAATGTTAATTTTATCTAATTTATTATAAATATTACTTAAAGGAAACTAATAAATAAGTTAAAA
876428 AAATTAATATATAACATTTGATAATTTAGGAGAGGACCAAATTAACAAATGAAATTAAATTAAAA
586 AAATTAATATATAACATTTGATAATTTAGGAGAGGACCAAATTAACAAATGAAATTAAATTAAAA
876493 TAAAAAAATAAAAAAGAAATA
651 TAAAAAAATAAAAAAGAAATA
876514 AAAACACTAAAATTTATAATTTTTACTACTATATATTATAAATATTACTTAACAAAACTATGGAA
1 AAAACACTAAAATTTATAATTTTTACTACTATATATTATAAATATTACTTAACAAAACTATGGAA
* * * * *
876579 TACCAAAACGACACCGTTTCAATAGAAAATTTGATTTTATAGTGGCGTTTTCATTCAAAATGCCG
66 TACCAAAACGACACCGTTTCAATAGAAAATTTGATTTCATAGTGGCGTTTCCACTAAAAACGCCG
*
876644 CAATAAACGAGACATTAGTGGCGTTTGGAACAAAAACGCCACAAAAAATTCTTAATTTTATAGAC
131 CAATAAACGAGACATTAGCGGCGTTTGGAACAAAAACGCCAC-AAAAATTCTTAATTTTATAGAC
* * * * *
876709 GAAACGGCGTAGCTTTCCGCTACGATTTTTATGGCTTTAGCGGGGCTAGGAGAAAAATGCCACTA
195 AAAACGGCGTAGCTTTCCGCTACCATTTTAATGGCTTTAGCGGCGCTAGGAGAAAAACGCCACTA
* * *
876774 AAGGTGCGCATTAGTGGCGTGTTGATGAAAACGCCGCAAGGTTGGGCTGTGGTTTAAGCAAAACG
260 AAGGTGCGCATTA--GGCGCGTTGATAAAAACGCCGCAAGGTTGGGCTGTGGTTTAAACAAAACG
876839 ACACCGTTTTGTCTGGGGCATTAGTGGCGCTACTGTAAAAACGCCGCAAATTTTCAATCTGTTGT
323 ACACCGTTTTGTCT-GGGCATTAGTGGCGCTACTGTAAAAACGCCGCAAATTTTCAATCTGTTGT
876904 AATTAAGACGCCGTCGTTTTTGTAACCCTCGAAATTATGGACTATTTACCTTAAATACAATTAAT
387 AATTAAGACGCCGTCGTTTTTGTAACCCTCGAAATTATGGACTATTTACCTTAAATACAATTAAT
876969 AAATAAGTTAATTTTATTAATTAATAAATAAAATTAAAATAGAAAAATAAAAATGAAATTAAAAC
452 AAATAAGTTAATTTTATTAATTAATAAATAAAATTAAAATAGAAAAATAAAAATGAAATTAAAAC
877034 ACTAAAAATGTTAATTTTATCTAATTTATTATAAATATTACTTAAAGGAAACTAATAAATAAGTT
517 ACTAAAAATGTTAATTTTATCTAATTTATTATAAATATTACTTAAAGGAAACTAATAAATAAGTT
*
877099 AAAAAAATTAATATATAACATTTGATAATTTAGGAGAGGACCAAATTAACAAATGGAATTAAATT
582 AAAAAAATTAATATATAACATTTGATAATTTAGGAGAGGACCAAATTAACAAATGAAATTAAATT
877164 AAAATAAAAAAA
647 AAAATAAAAAAA
877176 AACACTAAAA
Statistics
Matches: 632, Mismatches: 26, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
671 160 0.25
672 94 0.15
674 60 0.09
675 318 0.50
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (671 bp):
AAAACACTAAAATTTATAATTTTTACTACTATATATTATAAATATTACTTAACAAAACTATGGAA
TACCAAAACGACACCGTTTCAATAGAAAATTTGATTTCATAGTGGCGTTTCCACTAAAAACGCCG
CAATAAACGAGACATTAGCGGCGTTTGGAACAAAAACGCCACAAAAATTCTTAATTTTATAGACA
AAACGGCGTAGCTTTCCGCTACCATTTTAATGGCTTTAGCGGCGCTAGGAGAAAAACGCCACTAA
AGGTGCGCATTAGGCGCGTTGATAAAAACGCCGCAAGGTTGGGCTGTGGTTTAAACAAAACGACA
CCGTTTTGTCTGGGCATTAGTGGCGCTACTGTAAAAACGCCGCAAATTTTCAATCTGTTGTAATT
AAGACGCCGTCGTTTTTGTAACCCTCGAAATTATGGACTATTTACCTTAAATACAATTAATAAAT
AAGTTAATTTTATTAATTAATAAATAAAATTAAAATAGAAAAATAAAAATGAAATTAAAACACTA
AAAATGTTAATTTTATCTAATTTATTATAAATATTACTTAAAGGAAACTAATAAATAAGTTAAAA
AAATTAATATATAACATTTGATAATTTAGGAGAGGACCAAATTAACAAATGAAATTAAATTAAAA
TAAAAAAATAAAAAAGAAATA
Found at i:881345 original size:21 final size:21
Alignment explanation
Indices: 881317--881367 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
881307 GAAAGTATGA
*
881317 AGAA-CAGATGCGGCAGCGAG
1 AGAAGCAGAGGCGGCAGCGAG
*
881337 AGAAGCAGAGGCTGCAGCGAG
1 AGAAGCAGAGGCGGCAGCGAG
*
881358 GGAAGCAGAG
1 AGAAGCAGAG
881368 CAGCGTAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
AGAAGCAGAGGCGGCAGCGAG
Found at i:881787 original size:218 final size:218
Alignment explanation
Indices: 881409--881845 Score: 820
Period size: 218 Copynumber: 2.0 Consensus size: 218
881399 AGCTTCAGAG
881409 TATGATAAAGATGTTTCAGCAATCGCAACAGCCGCCGTCTTAGACTCTCGTGTAAATATACTTCA
1 TATGATAAAGATGTTTCAGCAATCGCAACAGCCGCCGTCTTAGACTCTCGTGTAAATATACTTCA
881474 ATTTTGACTTTTAATTATCATTTTAACTTTTAACATTTTTGTAAGAATAATACAAATTTTATTTT
66 ATTTTGACTTTTAATTATCATTTTAACTTTTAACATTTTTGTAAGAATAATACAAATTTTATTTT
* * *
881539 ATTTACTGATATTTATTATATATTATTCGTTTAATTTTAAATATTATATAGATTTATTGCTTTCG
131 ATTTACTAATATTTATTATATATTATTCGTTTAATCTTAAATATTATATAGATTTATTGCTTTCA
881604 GTTGGTTTAGATTTGGTTTCTTC
196 GTTGGTTTAGATTTGGTTTCTTC
881627 TATGATAAAGATGTTTCAGCAATCGCAACAGCCGCCGTCTTAGACTCTCGTGTAAATATACTTCA
1 TATGATAAAGATGTTTCAGCAATCGCAACAGCCGCCGTCTTAGACTCTCGTGTAAATATACTTCA
*
881692 ATTTTGACTTTTAATTATCATTTTAACTTTTAACATTTTTGTAAGAATAATACGAATTTTATTTT
66 ATTTTGACTTTTAATTATCATTTTAACTTTTAACATTTTTGTAAGAATAATACAAATTTTATTTT
*
881757 ATTTATTAATATTTATTATATATTATTCGTTTAATCTTAAATATTATATAGATTTATTGCTTTCA
131 ATTTACTAATATTTATTATATATTATTCGTTTAATCTTAAATATTATATAGATTTATTGCTTTCA
*
881822 GTTGGTTTAGATTTGGTTTTTTC
196 GTTGGTTTAGATTTGGTTTCTTC
881845 T
1 T
881846 GATTTGTTTT
Statistics
Matches: 213, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
218 213 1.00
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.48
Consensus pattern (218 bp):
TATGATAAAGATGTTTCAGCAATCGCAACAGCCGCCGTCTTAGACTCTCGTGTAAATATACTTCA
ATTTTGACTTTTAATTATCATTTTAACTTTTAACATTTTTGTAAGAATAATACAAATTTTATTTT
ATTTACTAATATTTATTATATATTATTCGTTTAATCTTAAATATTATATAGATTTATTGCTTTCA
GTTGGTTTAGATTTGGTTTCTTC
Found at i:881983 original size:43 final size:44
Alignment explanation
Indices: 881918--882042 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 44
881908 GGCATTTTTA
* * *
881918 AAAAAGCGCCACTAAAGGTCATGATCTTTAGCGGCGTTTGT-GG
1 AAAAAGCGCCGCTAAAGATCATGATCTTTAGCGGCATTTGTAGG
* *
881961 AAAAAGCGCCGCTACAGATCATGTTCTTTAGCGGCATTTGTAGG
1 AAAAAGCGCCGCTAAAGATCATGATCTTTAGCGGCATTTGTAGG
* * * * *
882005 -AAAAGTGCCGCTAAAGACCCTGACCTTTAGCGACATTT
1 AAAAAGCGCCGCTAAAGATCATGATCTTTAGCGGCATTT
882043 TTTTCGTAGC
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
43 67 0.97
44 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.26
Consensus pattern (44 bp):
AAAAAGCGCCGCTAAAGATCATGATCTTTAGCGGCATTTGTAGG
Found at i:891770 original size:34 final size:34
Alignment explanation
Indices: 891727--891796 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
891717 TGTGATTTTT
891727 CAGTACAATAATTTTACTCTTTTACACGCTTCCG
1 CAGTACAATAATTTTACTCTTTTACACGCTTCCG
891761 CAGTACAATAATTTTACTCTTTTACACGCTTCCG
1 CAGTACAATAATTTTACTCTTTTACACGCTTCCG
891795 CA
1 CA
891797 CAACAGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.37
Consensus pattern (34 bp):
CAGTACAATAATTTTACTCTTTTACACGCTTCCG
Found at i:896781 original size:44 final size:44
Alignment explanation
Indices: 896733--896821 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
896723 TTTTTTATTC
*
896733 TGGGTTTTGTTTATA-AGTTTTGAACATTATTCAGTAAAATTTCA
1 TGGGTTTTGTTTATAGA-TTTTGAACATTATTCAGTAAAACTTCA
* * *
896777 TGGGTTTTGTTTATAGATTTTGCATATTTTTCAGTAAAACTTCA
1 TGGGTTTTGTTTATAGATTTTGAACATTATTCAGTAAAACTTCA
896821 T
1 T
896822 AGTTTTCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (44 bp):
TGGGTTTTGTTTATAGATTTTGAACATTATTCAGTAAAACTTCA
Found at i:899304 original size:10 final size:10
Alignment explanation
Indices: 899263--899305 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
899253 AAAAATAGTC
*
899263 AAAATTAATC
1 AAAATTAATT
*
899273 AAAGTTAACTAT
1 AAAATTAA-T-T
899285 AAAATTAATT
1 AAAATTAATT
899295 AAAATTAATT
1 AAAATTAATT
899305 A
1 A
899306 TGTTCTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 19 0.68
11 2 0.07
12 7 0.25
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAATTAATT
Found at i:908124 original size:19 final size:20
Alignment explanation
Indices: 908076--908124 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
908066 ATTCACCATG
908076 TTAA-TATTTTTAACATAAT
1 TTAATTATTTTTAACATAAT
908095 TTAATTA-TTTTATA-AT-AT
1 TTAATTATTTTTA-ACATAAT
908113 TTAATTATTTTT
1 TTAATTATTTTT
908125 CGACAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.33
19 15 0.56
20 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATTATTTTTAACATAAT
Found at i:914907 original size:12 final size:12
Alignment explanation
Indices: 914892--914986 Score: 52
Period size: 12 Copynumber: 8.0 Consensus size: 12
914882 AATTCAAAAA
914892 ATAAAAATATTT
1 ATAAAAATATTT
*
914904 AT-AAAATAATT
1 ATAAAAATATTT
***
914915 ATAAAAATAAAA
1 ATAAAAATATTT
914927 ATAAAAATA-TT
1 ATAAAAATATTT
* * *
914938 CTAATATTATTT
1 ATAAAAATATTT
** *
914950 ATATTAATATTA
1 ATAAAAATATTT
*
914962 ATTAAAAATA-AT
1 A-TAAAAATATTT
914974 ATAAAAAATATTT
1 AT-AAAAATATTT
914987 CCCCACCCCC
Statistics
Matches: 61, Mismatches: 17, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
11 17 0.28
12 37 0.61
13 7 0.11
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAAAAATATTT
Found at i:914909 original size:11 final size:11
Alignment explanation
Indices: 914873--914920 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
914863 CTTATTATAT
914873 TTATAAAATAA
1 TTATAAAATAA
*
914884 TT-CAAAA-AA
1 TTATAAAATAA
*
914893 -TA-AAAATAT
1 TTATAAAATAA
914902 TTATAAAATAA
1 TTATAAAATAA
914913 TTATAAAA
1 TTATAAAA
914921 ATAAAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
8 5 0.17
9 3 0.10
10 6 0.20
11 16 0.53
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
TTATAAAATAA
Found at i:914911 original size:29 final size:29
Alignment explanation
Indices: 914869--914929 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
914859 CCACCTTATT
914869 ATATTTATAAAATAATTCA-AAAAATAAAA
1 ATATTTATAAAATAATT-ATAAAAATAAAA
914898 ATATTTATAAAATAATTATAAAAATAAAA
1 ATATTTATAAAATAATTATAAAAATAAAA
914927 ATA
1 ATA
914930 AAAATATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (29 bp):
ATATTTATAAAATAATTATAAAAATAAAA
Found at i:916306 original size:23 final size:22
Alignment explanation
Indices: 916280--916337 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 22
916270 AGTGCCACAA
* *
916280 CACTTGCATCGTAGTGTCATTTT
1 CACTTGCA-CGTAGTGCCATTAT
916303 CACTTGCAACGTAGTGCCATTAT
1 CACTTGC-ACGTAGTGCCATTAT
916326 CACTTGCACGTA
1 CACTTGCACGTA
916338 TAGAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 5 0.16
23 26 0.81
24 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.34
Consensus pattern (22 bp):
CACTTGCACGTAGTGCCATTAT
Found at i:916533 original size:15 final size:15
Alignment explanation
Indices: 916513--916549 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
916503 AATTTCACTT
916513 GACATTTGTTTTATC
1 GACATTTGTTTTATC
916528 GACATTTGTTTTATC
1 GACATTTGTTTTATC
*
916543 AACATTT
1 GACATTT
916550 AACACTTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (15 bp):
GACATTTGTTTTATC
Found at i:917988 original size:19 final size:19
Alignment explanation
Indices: 917964--918003 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
917954 CCACATGTGA
917964 TGGACCAGATCAATATCTT
1 TGGACCAGATCAATATCTT
917983 TGGACCAGATCAATATCTT
1 TGGACCAGATCAATATCTT
918002 TG
1 TG
918004 TAATAGAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (19 bp):
TGGACCAGATCAATATCTT
Found at i:919648 original size:21 final size:21
Alignment explanation
Indices: 919624--919666 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
919614 GAATCTTAAG
919624 TTAACGAATTTAATGAATAAA
1 TTAACGAATTTAATGAATAAA
*
919645 TTAACGGATTTAATGAATAAA
1 TTAACGAATTTAATGAATAAA
919666 T
1 T
919667 ATACCATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (21 bp):
TTAACGAATTTAATGAATAAA
Found at i:920711 original size:41 final size:41
Alignment explanation
Indices: 920666--920767 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
920656 TTTTCGAATC
920666 CATGAAATGGTTGAAAAGGAAGTTATCCGAAAAGAATAACA
1 CATGAAATGGTTGAAAAGGAAGTTATCCGAAAAGAATAACA
* *
920707 CATGAAAAT-GTTGAAAAGAAAGTTATCCGAAAAGGATAACA
1 CATG-AAATGGTTGAAAAGGAAGTTATCCGAAAAGAATAACA
*
920748 CATGAAAAGGTTGAAAAGGA
1 CATGAAATGGTTGAAAAGGA
920768 TATATTCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
40 3 0.05
41 48 0.87
42 4 0.07
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.19
Consensus pattern (41 bp):
CATGAAATGGTTGAAAAGGAAGTTATCCGAAAAGAATAACA
Found at i:920828 original size:38 final size:40
Alignment explanation
Indices: 920736--920835 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 40
920726 AAGTTATCCG
* *
920736 AAAAGGATAACACATGAAAAGGTTGAAAAGGATATATTCA
1 AAAAGGATAACAAATGAAAAGGTTGAAAAGGATATACTCA
* * *
920776 AAAAGGATATCAAATGAAAAGTTTG-AAAGTGATAT-CT-G
1 AAAAGGATAACAAATGAAAAGGTTGAAAAG-GATATACTCA
*
920814 GAAAGGATAACAAATGAAAAGG
1 AAAAGGATAACAAATGAAAAGG
920836 GATGTGTTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 19 0.37
39 5 0.10
40 27 0.53
ACGTcount: A:0.52, C:0.06, G:0.22, T:0.20
Consensus pattern (40 bp):
AAAAGGATAACAAATGAAAAGGTTGAAAAGGATATACTCA
Found at i:922661 original size:18 final size:19
Alignment explanation
Indices: 922621--922663 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
922611 TTTGGTTTGG
* **
922621 TTTTTTACTTAGTAGTTTT
1 TTTTTAACTTAGTAGTTAC
922640 TTTTTAACTTAGT-GTTAC
1 TTTTTAACTTAGTAGTTAC
922658 TTTTTA
1 TTTTTA
922664 CAGGCTTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.19, C:0.07, G:0.09, T:0.65
Consensus pattern (19 bp):
TTTTTAACTTAGTAGTTAC
Found at i:928941 original size:16 final size:17
Alignment explanation
Indices: 928914--928948 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
928904 ACTCCTCTAA
*
928914 AACCTCTCAAAATCCTT
1 AACCTCTCAAAACCCTT
928931 AACCT-TCAAAACCCTT
1 AACCTCTCAAAACCCTT
928947 AA
1 AA
928949 ATTTTTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (17 bp):
AACCTCTCAAAACCCTT
Found at i:929850 original size:45 final size:44
Alignment explanation
Indices: 929783--929984 Score: 235
Period size: 45 Copynumber: 4.5 Consensus size: 44
929773 GGACGCTGGA
* * * * *
929783 TCTTTCCATTATGGTCCTATTCATTTTCGTCAT-GTTGCCTTAGTG
1 TCTTTCAACTATGGTCTTATTCATTTCCGT-ATAG-TGCCATAGTG
* *
929828 TCTTTCAACTAAGGTCTTATTCATTTCCGTTATAGTGTCATAGTG
1 TCTTTCAACTATGGTCTTATTCATTTCCG-TATAGTGCCATAGTG
* *
929873 TCTTTCAACTATGGTTTTATTCATTTCCGGTATAGTGCCATAATG
1 TCTTTCAACTATGGTCTTATTCATTTCC-GTATAGTGCCATAGTG
* * **
929918 TCTTTCAACTATGGTCTTATTTATTTCCGGTATAGTGTCACGGTG
1 TCTTTCAACTATGGTCTTATTCATTTCC-GTATAGTGCCATAGTG
929963 TCTTTCAACTATGGTCTTATTC
1 TCTTTCAACTATGGTCTTATTC
929985 GTTTTTTCAA
Statistics
Matches: 136, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
45 133 0.98
46 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.46
Consensus pattern (44 bp):
TCTTTCAACTATGGTCTTATTCATTTCCGTATAGTGCCATAGTG
Found at i:943894 original size:18 final size:18
Alignment explanation
Indices: 943859--943900 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
943849 TTTTATCCAT
*
943859 TAAGTTTTTATATTTTAA
1 TAAGTTTTTATATATTAA
943877 TAAGTTTTGTATA-ATTAA
1 TAAGTTTT-TATATATTAA
*
943895 AAAGTT
1 TAAGTT
943901 AGATTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (18 bp):
TAAGTTTTTATATATTAA
Found at i:950174 original size:13 final size:13
Alignment explanation
Indices: 950156--950188 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
950146 CCTTGTGAGA
950156 CACACGACCTGGC
1 CACACGACCTGGC
950169 CACACGACCTGGC
1 CACACGACCTGGC
950182 CACACGA
1 CACACGA
950189 GGATGTGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.27, C:0.45, G:0.21, T:0.06
Consensus pattern (13 bp):
CACACGACCTGGC
Done.