Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015161.1 Kokia drynarioides strain JFW-HI SEQ_130205, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 994981
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 641 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:421476 original size:24 final size:24
Alignment explanation
Indices: 421449--421525 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
421439 AGATAGTTTT
421449 TATTATGTAAAGACTAATATCTGG
1 TATTATGTAAAGACTAATATCTGG
* * **
421473 TATTAAGTAAACA-TAGATAGT-TTT
1 TATTATGTAAAGACTA-ATA-TCTGG
421497 TATTATGTAAAGACTAATATCTGG
1 TATTATGTAAAGACTAATATCTGG
421521 TATTA
1 TATTA
421526 ACTAAACATA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
23 3 0.07
24 35 0.85
25 3 0.07
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.40
Consensus pattern (24 bp):
TATTATGTAAAGACTAATATCTGG
Found at i:421510 original size:48 final size:48
Alignment explanation
Indices: 421439--421535 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
421429 GGAAAAGGTA
*
421439 AGATAGTTTTTATTATGTAAAGACTAATATCTGGTATTAAGTAAACAT
1 AGATAGTTTTTATTATGTAAAGACTAATATCTGGTATTAACTAAACAT
421487 AGATAGTTTTTATTATGTAAAGACTAATATCTGGTATTAACTAAACAT
1 AGATAGTTTTTATTATGTAAAGACTAATATCTGGTATTAACTAAACAT
421535 A
1 A
421536 TTGCTCAGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (48 bp):
AGATAGTTTTTATTATGTAAAGACTAATATCTGGTATTAACTAAACAT
Found at i:429199 original size:36 final size:35
Alignment explanation
Indices: 429148--429248 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 35
429138 TGGTAACAGG
*
429148 CATGACCTTCGAGTCAACAGGGAGTAAAATGAGCA
1 CATGACCTTCAAGTCAACAGGGAGTAAAATGAGCA
* *
429183 TCATGACCTTCAAGTCATCAGGGAGAAAAATGAGCA
1 -CATGACCTTCAAGTCAACAGGGAGTAAAATGAGCA
* *
429219 CTATGACCTT-AAGGTCAACAAGGAATAAAA
1 C-ATGACCTTCAA-GTCAACAGGGAGTAAAA
429249 CGAAAAACAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
35 3 0.05
36 53 0.95
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (35 bp):
CATGACCTTCAAGTCAACAGGGAGTAAAATGAGCA
Found at i:429872 original size:21 final size:23
Alignment explanation
Indices: 429818--429873 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
429808 TAATAATTGA
* *
429818 AGTATCGGTAGTTCTGTATACTT
1 AGTATCGGTAGTTCGGGATACTT
*
429841 AAGTATTGGTAGTT-GGGATACTT
1 -AGTATCGGTAGTTCGGGATACTT
429864 -GTATCGGTAG
1 AGTATCGGTAG
429874 AAGTTTCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 9 0.32
23 7 0.25
24 12 0.43
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.39
Consensus pattern (23 bp):
AGTATCGGTAGTTCGGGATACTT
Found at i:432670 original size:18 final size:18
Alignment explanation
Indices: 432647--432681 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
432637 GTTGACCGAC
432647 CTGACTCGTGGACTTTGG
1 CTGACTCGTGGACTTTGG
*
432665 CTGACTCGTTGACTTTG
1 CTGACTCGTGGACTTTG
432682 ATCGATCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.23, G:0.29, T:0.37
Consensus pattern (18 bp):
CTGACTCGTGGACTTTGG
Found at i:433243 original size:2 final size:2
Alignment explanation
Indices: 433236--433276 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
433226 GTACTTTGAG
433236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
433277 CATGAGATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:434429 original size:23 final size:24
Alignment explanation
Indices: 434391--434440 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
434381 AATTTGACTC
*
434391 AAACAACTAAACAGAGTTTAATTG
1 AAACAACTAAACAGAGTTTAACTG
*
434415 AAACAA-TAAATAGAGTTTAACTG
1 AAACAACTAAACAGAGTTTAACTG
434438 AAA
1 AAA
434441 GATTATTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAACTAAACAGAGTTTAACTG
Found at i:436367 original size:24 final size:24
Alignment explanation
Indices: 436340--436390 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
436330 AATTTGACTC
* * *
436340 AAACAACTAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
436364 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
436388 AAA
1 AAA
436391 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:437578 original size:24 final size:24
Alignment explanation
Indices: 437532--437594 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
437522 TAGACTAATA
* * *
437532 AGAATTTAACTCAAATAACTAAAC
1 AGAATTTAACTGAAACAAATAAAC
*
437556 AGAATTTAATTGAAACAAATAAAC
1 AGAATTTAACTGAAACAAATAAAC
*
437580 AGAGTTTAACTGAAA
1 AGAATTTAACTGAAA
437595 GATTATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.54, C:0.11, G:0.10, T:0.25
Consensus pattern (24 bp):
AGAATTTAACTGAAACAAATAAAC
Found at i:438610 original size:22 final size:22
Alignment explanation
Indices: 438583--438634 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
438573 CTCGTACATT
*
438583 ATTAAAACTAATCAAATTGTTG
1 ATTAAAACTAATCAAATTATTG
*
438605 ATTAAAACTAATCCAATTATTG
1 ATTAAAACTAATCAAATTATTG
*
438627 ATAAAAAC
1 ATTAAAAC
438635 ACATTATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.33
Consensus pattern (22 bp):
ATTAAAACTAATCAAATTATTG
Found at i:455960 original size:14 final size:15
Alignment explanation
Indices: 455933--455962 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
455923 ACATGTCTCG
455933 TTTTAATATATTTAT
1 TTTTAATATATTTAT
455948 TTTTAATAT-TTTAT
1 TTTTAATATATTTAT
455962 T
1 T
455963 ATATTCCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAATATATTTAT
Found at i:460198 original size:24 final size:27
Alignment explanation
Indices: 460171--460231 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 27
460161 ACTTTAGACC
460171 TTTTATTTTTTTAATT-TGA-AGTTT-
1 TTTTATTTTTTTAATTATGACAGTTTA
* * *
460195 TTTTACATTTTTTATTTATGACATTTTA
1 TTTTA-TTTTTTTAATTATGACAGTTTA
460223 TTTTATTTT
1 TTTTATTTT
460232 ATAAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
24 5 0.17
25 9 0.31
26 3 0.10
27 7 0.24
28 5 0.17
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.70
Consensus pattern (27 bp):
TTTTATTTTTTTAATTATGACAGTTTA
Found at i:460239 original size:19 final size:19
Alignment explanation
Indices: 460204--460241 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
460194 TTTTTACATT
*
460204 TTTTATTTATGACATTTTA
1 TTTTATTTATGAAATTTTA
460223 TTTTATTTTAT-AAATTTTA
1 TTTTA-TTTATGAAATTTTA
460242 AATTATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTATTTATGAAATTTTA
Found at i:461191 original size:22 final size:20
Alignment explanation
Indices: 461150--461202 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
461140 TTCGAATTCG
*
461150 TTTTAAATTTATCTATATTA
1 TTTTAAATTTATATATATTA
461170 TTTTAAATATATATATATATTA
1 TTTTAAAT-T-TATATATATTA
*
461192 TTTTTAATTTA
1 TTTTAAATTTA
461203 ATTTAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 10 0.34
21 2 0.07
22 17 0.59
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAAATTTATATATATTA
Found at i:465101 original size:43 final size:43
Alignment explanation
Indices: 464945--465238 Score: 305
Period size: 43 Copynumber: 6.9 Consensus size: 43
464935 TCCTTTTTAA
* * * *
464945 ATAATCTTATGCTC-TAC-CGAGTCATAAGTCTTCC-TTTAAAC
1 ATAATCTCATGCTCAT-CTCGAGACATGAGTCTTCCATTTATAC
* * * *
464986 ATAATCTCATGCTCATTTCGAGTCACGAGTCTTCC-TTGA-AC
1 ATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTATAC
* * **
465027 ATAATCTCATGCTCAT-TCTAAGTCACAAGTCTTCCATTTATAC
1 ATAATCTCATGCTCATCTC-GAGACATGAGTCTTCCATTTATAC
* * *
465070 ATAATTTCATGCTCGTCTCGAGACATGAGTCTTACATTTATAC
1 ATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTATAC
* * * *
465113 ATAATCTCATGCTCATCCCGAGACATGAATATTTCATTTATAC
1 ATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTATAC
* * *
465156 ATAATCTCATGCTCATCCCGAAACATGAGTCTTCCATTTGTAC
1 ATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTATAC
*
465199 ATAATCTCATGCTCATC-CTGAGACATGAGTCTTTCATTTA
1 ATAATCTCATGCTCATCTC-GAGACATGAGTCTTCCATTTA
465239 CGCCAAGTGA
Statistics
Matches: 217, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.01
41 45 0.21
42 23 0.11
43 145 0.67
44 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (43 bp):
ATAATCTCATGCTCATCTCGAGACATGAGTCTTCCATTTATAC
Found at i:470000 original size:2 final size:2
Alignment explanation
Indices: 469993--470021 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
469983 TACTAAGTAT
469993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
470022 CTATCTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:470035 original size:5 final size:5
Alignment explanation
Indices: 470025--470051 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
470015 TATATATCTA
470025 TCTTT TCTTT TCTTT TCTTT TCTTT TC
1 TCTTT TCTTT TCTTT TCTTT TCTTT TC
470052 ATAAGGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:471053 original size:15 final size:15
Alignment explanation
Indices: 471014--471056 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
471004 GATAGTGTTC
*
471014 TCAGCATATTCTTTT
1 TCAGCATCTTCTTTT
471029 TCAGCATCTTCTTTCT
1 TCAGCATCTTCTTT-T
*
471045 T-AGCGTCTTCTT
1 TCAGCATCTTCTT
471057 CAAGGACTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 23 0.92
16 2 0.08
ACGTcount: A:0.14, C:0.26, G:0.09, T:0.51
Consensus pattern (15 bp):
TCAGCATCTTCTTTT
Found at i:475976 original size:12 final size:12
Alignment explanation
Indices: 475955--475984 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
475945 AGGCAACTCC
*
475955 CACTTTCTTTGG
1 CACTTCCTTTGG
475967 CACTTCCTTTGG
1 CACTTCCTTTGG
475979 CACTTC
1 CACTTC
475985 ATTGGTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.33, G:0.13, T:0.43
Consensus pattern (12 bp):
CACTTCCTTTGG
Found at i:493643 original size:18 final size:18
Alignment explanation
Indices: 493620--493656 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
493610 CAGTTGTTAG
493620 TGCAGTTAATG-CTATTAT
1 TGCAGTTAA-GACTATTAT
493638 TGCAGTTAAGACTATTAT
1 TGCAGTTAAGACTATTAT
493656 T
1 T
493657 ATGGTTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (18 bp):
TGCAGTTAAGACTATTAT
Found at i:498789 original size:30 final size:30
Alignment explanation
Indices: 498753--498812 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
498743 TGCAAATTAC
498753 CTAAAGTTCCTCAGGTCCCAAGTCAAGGCA
1 CTAAAGTTCCTCAGGTCCCAAGTCAAGGCA
498783 CTAAAGTTCCTCAGGTCCCAAGTCAAGGCA
1 CTAAAGTTCCTCAGGTCCCAAGTCAAGGCA
498813 GTAGAGAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (30 bp):
CTAAAGTTCCTCAGGTCCCAAGTCAAGGCA
Found at i:502488 original size:36 final size:36
Alignment explanation
Indices: 502424--502528 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
502414 TGTAAGTAAT
*
502424 CACATAGGAATACGCTCTAACCAAGACGTATGCAAC
1 CACATAGCAATACGCTCTAACCAAGACGTATGCAAC
* * * * * *
502460 CACTTAGCATTATGCTTTAACCAAGACGTAAGCAAT
1 CACATAGCAATACGCTCTAACCAAGACGTATGCAAC
* *
502496 TACATAGCAATACGCTCTAACCGAGACGTATGC
1 CACATAGCAATACGCTCTAACCAAGACGTATGC
502529 TTTCCATCAA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (36 bp):
CACATAGCAATACGCTCTAACCAAGACGTATGCAAC
Found at i:502491 original size:72 final size:72
Alignment explanation
Indices: 502394--502528 Score: 207
Period size: 72 Copynumber: 1.9 Consensus size: 72
502384 CAATCAAATG
* * * * *
502394 GCATTATGCTTTAATCGAGATGTAAGTAATCACATAGGAATACGCTCTAACCAAGACGTATGCAA
1 GCATTATGCTTTAACCAAGACGTAAGCAATCACATAGCAATACGCTCTAACCAAGACGTATGCAA
502459 CCACTTA
66 CCACTTA
* *
502466 GCATTATGCTTTAACCAAGACGTAAGCAATTACATAGCAATACGCTCTAACCGAGACGTATGC
1 GCATTATGCTTTAACCAAGACGTAAGCAATCACATAGCAATACGCTCTAACCAAGACGTATGC
502529 TTTCCATCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (72 bp):
GCATTATGCTTTAACCAAGACGTAAGCAATCACATAGCAATACGCTCTAACCAAGACGTATGCAA
CCACTTA
Found at i:519633 original size:21 final size:22
Alignment explanation
Indices: 519609--519673 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
519599 GTTCAAGAAA
*
519609 CATTACAGGGGCATCGA-AGTG
1 CATTACAGGGGCATCCATAGTG
*
519630 CATTCATAGGGGCA-CCATAGTG
1 CATT-ACAGGGGCATCCATAGTG
519652 CAATT-CAGGGGCATCACATAGT
1 C-ATTACAGGGGCATC-CATAGT
519674 CTCCATTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 13 0.36
22 14 0.39
23 9 0.25
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.22
Consensus pattern (22 bp):
CATTACAGGGGCATCCATAGTG
Found at i:526856 original size:22 final size:22
Alignment explanation
Indices: 526828--526895 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 22
526818 TTCAAGAAAC
526828 ATTACAGGGGCACCGAAGTGC-
1 ATTACAGGGGCACCGAAGTGCA
*
526849 ATTCACAGAGGCACC-ATAGTGCA
1 ATT-ACAGGGGCACCGA-AGTGCA
* *
526872 ATT-CAGGGGCATCGTAGTGCA
1 ATTACAGGGGCACCGAAGTGCA
526893 ATT
1 ATT
526896 CAAGGGCGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 21 0.54
22 15 0.38
23 3 0.08
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (22 bp):
ATTACAGGGGCACCGAAGTGCA
Found at i:530099 original size:9 final size:9
Alignment explanation
Indices: 530095--530125 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
530085 ATGATGATGG
530095 CGATGAGGA
1 CGATGAGGA
530104 CGATGAGGA
1 CGATGAGGA
*
530113 TGATGAGGA
1 CGATGAGGA
530122 CGAT
1 CGAT
530126 ATTTCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.42, T:0.16
Consensus pattern (9 bp):
CGATGAGGA
Found at i:530296 original size:23 final size:23
Alignment explanation
Indices: 530270--530342 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
530260 TGCAGGTTGG
*
530270 TTTTGGCGCAGCTTTGGTACTAT
1 TTTTGGTGCAGCTTTGGTACTAT
* * *
530293 TTTTGGTGTAGCTTTGGTATTGT
1 TTTTGGTGCAGCTTTGGTACTAT
*
530316 TTTTGGTGCAACTTTGGTACTAT
1 TTTTGGTGCAGCTTTGGTACTAT
530339 TTTT
1 TTTT
530343 TGTGTTATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.12, C:0.11, G:0.25, T:0.52
Consensus pattern (23 bp):
TTTTGGTGCAGCTTTGGTACTAT
Found at i:530360 original size:46 final size:47
Alignment explanation
Indices: 530266--530371 Score: 128
Period size: 46 Copynumber: 2.3 Consensus size: 47
530256 ATTTTGCAGG
* * *
530266 TTGG-TTTTGGCGCAGCTTTGGTACTATTTTTGGTGTAGCTTTGGTA
1 TTGGTTTTTGGTGCAACTTTGGTACTATTTTTGGTGTAGCTTTGATA
* *
530312 TT-GTTTTTGGTGCAACTTTGGTACTATTTTTTGTGTTA-TTTTGATA
1 TTGGTTTTTGGTGCAACTTTGGTACTATTTTTGGTG-TAGCTTTGATA
*
530358 TTGGTTTTTTGTGC
1 TTGGTTTTTGGTGC
530372 TGTTTTGGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
45 1 0.02
46 38 0.75
47 12 0.24
ACGTcount: A:0.11, C:0.08, G:0.25, T:0.55
Consensus pattern (47 bp):
TTGGTTTTTGGTGCAACTTTGGTACTATTTTTGGTGTAGCTTTGATA
Found at i:531056 original size:19 final size:19
Alignment explanation
Indices: 531029--531065 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
531019 ATACTATTTT
*
531029 CAAGGGCATCGAAGTGCAA
1 CAAGAGCATCGAAGTGCAA
531048 CAAGAGCATCGAAGTGCA
1 CAAGAGCATCGAAGTGCA
531066 TATAGGGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.30, T:0.11
Consensus pattern (19 bp):
CAAGAGCATCGAAGTGCAA
Found at i:531092 original size:20 final size:20
Alignment explanation
Indices: 531069--531169 Score: 89
Period size: 20 Copynumber: 5.0 Consensus size: 20
531059 AAGTGCATAT
*
531069 AGGGGTACCGGAGTGCTAAC
1 AGGGGCACCGGAGTGCTAAC
*
531089 AGGGGCACCGAAGTGC-ATAC
1 AGGGGCACCGGAGTGCTA-AC
**
531109 AGGGGCACTAGAGTGCTAAC
1 AGGGGCACCGGAGTGCTAAC
**
531129 AGGGGCACCAAAGTGC-ATAC
1 AGGGGCACCGGAGTGCTA-AC
* **
531149 AAGGGCACTAGAGTGCTAAC
1 AGGGGCACCGGAGTGCTAAC
531169 A
1 A
531170 TTCCATCACT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.03
20 63 0.94
21 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.34, T:0.13
Consensus pattern (20 bp):
AGGGGCACCGGAGTGCTAAC
Found at i:531101 original size:40 final size:40
Alignment explanation
Indices: 531057--531169 Score: 163
Period size: 40 Copynumber: 2.8 Consensus size: 40
531047 ACAAGAGCAT
* * *
531057 CGAAGTGCATATAGGGGTACCGGAGTGCTAACAGGGGCAC
1 CGAAGTGCATACAGGGGCACCAGAGTGCTAACAGGGGCAC
*
531097 CGAAGTGCATACAGGGGCACTAGAGTGCTAACAGGGGCAC
1 CGAAGTGCATACAGGGGCACCAGAGTGCTAACAGGGGCAC
* * *
531137 CAAAGTGCATACAAGGGCACTAGAGTGCTAACA
1 CGAAGTGCATACAGGGGCACCAGAGTGCTAACA
531170 TTCCATCACT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.32, C:0.21, G:0.33, T:0.14
Consensus pattern (40 bp):
CGAAGTGCATACAGGGGCACCAGAGTGCTAACAGGGGCAC
Found at i:533753 original size:17 final size:17
Alignment explanation
Indices: 533731--533769 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
533721 CTCCACCTTG
* *
533731 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
533748 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
533765 ACAAG
1 ACAAG
533770 TTCTCCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:549350 original size:2 final size:2
Alignment explanation
Indices: 549343--549371 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
549333 GTCATAATTA
549343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
549372 ATAATTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:552627 original size:26 final size:27
Alignment explanation
Indices: 552598--552651 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
552588 TTTCTGGTTT
* *
552598 GTAAGAG-TAAAATCTGTTCTGGGCTC
1 GTAAGAGCTAAAATCTATTCTAGGCTC
*
552624 GTAAGAGCTAAACTCTATTCTAGGCTC
1 GTAAGAGCTAAAATCTATTCTAGGCTC
552651 G
1 G
552652 AAGGAGTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (27 bp):
GTAAGAGCTAAAATCTATTCTAGGCTC
Found at i:562324 original size:39 final size:39
Alignment explanation
Indices: 562279--562673 Score: 154
Period size: 39 Copynumber: 10.2 Consensus size: 39
562269 TTCCGATCCT
*
562279 TTACCCCGAGCCTCGAGCAGATCACCATCAGCCAATCTC
1 TTACCCCGAGCCTGGAGCAGATCACCATCAGCCAATCTC
* ** * * ** * *
562318 TTACCCCGAGCCTGGA-CAAATTGCAACCATTCGATCTT
1 TTACCCCGAGCCTGGAGCAGATCACCATCAGCCAATCTC
* * *
562356 TTACCCCGAGCTTGGGGCAGATCACCATCAGCTAATCTC
1 TTACCCCGAGCCTGGAGCAGATCACCATCAGCCAATCTC
* *
562395 TTACCCCGAGCCTGGGGCAGATTGTAGCCATTC-G---ATCTC
1 TTACCCCGAGCCTGGAGCAGA-T-CA-CCA-TCAGCCAATCTC
* * * * *
562434 TTACCCCGAGTCT-AAGGTAAATCACCATCAGCTAATCTC
1 TTACCCCGAGCCTGGA-GCAGATCACCATCAGCCAATCTC
* * * * * ** *
562473 TTACCCCAATCATGGGGTAGAT-TGCAGCAGTCCAATCTC
1 TTACCCCGAGCCTGGAGCAGATCACCATCAG-CCAATCTC
* * * * *
562512 TTACCTCGAGCCCTAG-GCAGATTGCAGCCAT---TCTATCTT
1 TTACCCCGAG-CCTGGAGCAGA-T-CA-CCATCAGCCAATCTC
* * * * * *
562551 TTACCCCGAGCTTGGGGTAGATCACTATTAGCCAATCTT
1 TTACCCCGAGCCTGGAGCAGATCACCATCAGCCAATCTC
* * *
562590 TTACCCCGAGTCTGGGGCAGATTGCAGCCATTC-G---ATCTT
1 TTACCCCGAGCCTGGAGCAGA-T-CA-CCA-TCAGCCAATCTC
* * *
562629 TTACCCTGAGCCTGGGGCAGATCATCATCAGCCAATCTC
1 TTACCCCGAGCCTGGAGCAGATCACCATCAGCCAATCTC
562668 TTACCC
1 TTACCC
562674 GATCATGAGG
Statistics
Matches: 258, Mismatches: 69, Indels: 58
0.67 0.18 0.15
Matches are distributed among these distances:
35 4 0.02
36 10 0.04
37 5 0.02
38 38 0.15
39 180 0.70
40 6 0.02
41 3 0.01
42 7 0.03
43 5 0.02
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (39 bp):
TTACCCCGAGCCTGGAGCAGATCACCATCAGCCAATCTC
Found at i:562365 original size:77 final size:77
Alignment explanation
Indices: 562272--562479 Score: 265
Period size: 78 Copynumber: 2.7 Consensus size: 77
562262 TTGAAGATTC
* *
562272 CGATCCTTTACCCCGAGCCTCGAGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT-GGACA
1 CGATCTTTTACCCCGAGCCT-GAGCAGATCACCATCAGCTAATCTCTTACCCCGAGCCTGGGACA
562336 AATTGCAACCATT
65 AATTGCAACCATT
* * *
562349 CGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCCCGAGCCTGGGGCA
1 CGATCTTTTACCCCGAGCCT-GAGCAGATCACCATCAGCTAATCTCTTACCCCGAGCCTGGGACA
* * *
562414 GATTGTAGCCATT
65 AATTGCAACCATT
* * * * *
562427 CGATCTCTTACCCCGAGTCTAAGGTAAATCACCATCAGCTAATCTCTTACCCC
1 CGATCTTTTACCCCGAGCCTGA-GCAGATCACCATCAGCTAATCTCTTACCCC
562480 AATCATGGGG
Statistics
Matches: 113, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
77 54 0.48
78 59 0.52
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (77 bp):
CGATCTTTTACCCCGAGCCTGAGCAGATCACCATCAGCTAATCTCTTACCCCGAGCCTGGGACAA
ATTGCAACCATT
Found at i:562511 original size:78 final size:78
Alignment explanation
Indices: 562299--562521 Score: 218
Period size: 78 Copynumber: 2.9 Consensus size: 78
562289 CCTCGAGCAG
* * * * * * * * *
562299 ATCACCATCAGCCAATCTCTTACCCCGAGCCT-GGACAAATTGCAACCATTCGATCTTTTACCCC
1 ATCACCATCAGCTAATCTCTTACCCCAAGCATGGGGCAGATTGCAGCCATCCAATCTCTTACCCC
** * *
562363 GAG-CTTGGGGCAG
66 GAGTC-TAAGGTAA
* * * * *
562376 ATCACCATCAGCTAATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATTCGATCTCTTACCCC
1 ATCACCATCAGCTAATCTCTTACCCCAAGCATGGGGCAGATTGCAGCCATCCAATCTCTTACCCC
562441 GAGTCTAAGGTAA
66 GAGTCTAAGGTAA
* * *
562454 ATCACCATCAGCTAATCTCTTACCCCAATCATGGGGTAGATTGCAG-CAGTCCAATCTCTTACCT
1 ATCACCATCAGCTAATCTCTTACCCCAAGCATGGGGCAGATTGCAGCCA-TCCAATCTCTTACCC
562518 CGAG
65 CGAG
562522 CCCTAGGCAG
Statistics
Matches: 125, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
77 33 0.26
78 91 0.73
79 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (78 bp):
ATCACCATCAGCTAATCTCTTACCCCAAGCATGGGGCAGATTGCAGCCATCCAATCTCTTACCCC
GAGTCTAAGGTAA
Found at i:562523 original size:117 final size:116
Alignment explanation
Indices: 562389--562650 Score: 289
Period size: 117 Copynumber: 2.2 Consensus size: 116
562379 ACCATCAGCT
*
562389 AATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATTCGATCTCTTACCCCGAG-TCTAAGGTA
1 AATCTCTTA-CCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCT-TAAGGTA
* *
562453 AATCACCATCAGCTAATCTCTTACCCC-AATCATGGGGTAGATTGCAG-CAGTCC
64 AATCACCATCAGCCAATCTCTTACCCCGAATC-TGGGGCAGATTGCAGCCA-TCC
* * * **
562506 AATCTCTTACCTCGAGCCCT-AGGCAGATTGCAGCCATTCTATCTTTTACCCCGAGCTTGGGGTA
1 AATCTCTTACC-CGAG-CCTGGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCTTAAGGTA
* * * * * *
562570 GATCACTATTAGCCAATCTTTTACCCCGAGTCTGGGGCAGATTGCAGCCATTC
64 AATCACCATCAGCCAATCTCTTACCCCGAATCTGGGGCAGATTGCAGCCATCC
* *
562623 GATCTTTTACCCTGAGCCTGGGGCAGAT
1 AATCTCTTACCC-GAGCCTGGGGCAGAT
562651 CATCATCAGC
Statistics
Matches: 121, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
116 6 0.05
117 106 0.88
118 9 0.07
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (116 bp):
AATCTCTTACCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCTTAAGGTAAA
TCACCATCAGCCAATCTCTTACCCCGAATCTGGGGCAGATTGCAGCCATCC
Found at i:562555 original size:78 final size:78
Alignment explanation
Indices: 562468--562701 Score: 215
Period size: 78 Copynumber: 3.0 Consensus size: 78
562458 CCATCAGCTA
* * ** *
562468 ATCTCTTACCCCAATCATGGGGTAGATTGC-AGCAGTCCAATCTCTTACCTCGAGCCCT-AGGCA
1 ATCTTTTACCCCAAGCATGGGGTAGATCACTAGCAG-CCAATCTCTTACCCCGAG-CCTGAGGCA
*
562531 GATTGCAGCCATTCT
64 GATTGCAGCCATTCG
* * ** * * *
562546 ATCTTTTACCCCGAGCTTGGGGTAGATCACTATTAGCCAATCTTTTACCCCGAGTCTGGGGCAGA
1 ATCTTTTACCCCAAGCATGGGGTAGATCACTAGCAGCCAATCTCTTACCCCGAGCCTGAGGCAGA
562611 TTGCAGCCATTCG
66 TTGCAGCCATTCG
** * * * * * *
562624 ATCTTTTACCCTGAGCCTGGGGCAGATCA-TCATCAGCCAATCTCTTA-CCCGATCATGAGGCAA
1 ATCTTTTACCCCAAGCATGGGGTAGATCACT-AGCAGCCAATCTCTTACCCCGAGCCTGAGGCAG
*
562687 ATTGCAGTCATTCG
65 ATTGCAGCCATTCG
562701 A
1 A
562702 AGCAATATAG
Statistics
Matches: 129, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
77 28 0.22
78 98 0.76
79 3 0.02
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (78 bp):
ATCTTTTACCCCAAGCATGGGGTAGATCACTAGCAGCCAATCTCTTACCCCGAGCCTGAGGCAGA
TTGCAGCCATTCG
Found at i:563144 original size:17 final size:18
Alignment explanation
Indices: 563114--563149 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
563104 AATTGGACCC
*
563114 ATTTTTAATTTTTAATTT
1 ATTTTTAATGTTTAATTT
563132 ATTTTTAA-GTTTAATTT
1 ATTTTTAATGTTTAATTT
563149 A
1 A
563150 GTATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTTTTAATGTTTAATTT
Found at i:563164 original size:17 final size:17
Alignment explanation
Indices: 563135--563217 Score: 73
Period size: 17 Copynumber: 4.9 Consensus size: 17
563125 TTAATTTATT
*
563135 TTTAAGTTT-AATTTAG
1 TTTAAATTTAAATTTAG
* *
563151 TATAAATTTAAATTTAT
1 TTTAAATTTAAATTTAG
* *
563168 TTTGAATTTAAATTCA-
1 TTTAAATTTAAATTTAG
563184 TTCTAAATTTAAATTT-G
1 TT-TAAATTTAAATTTAG
*
563201 TTTTTAATTTAAATTTA
1 -TTTAAATTTAAATTTA
563218 ATTAAAAATT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
16 9 0.17
17 42 0.79
18 2 0.04
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTTAG
Found at i:563165 original size:34 final size:34
Alignment explanation
Indices: 563127--563217 Score: 121
Period size: 34 Copynumber: 2.7 Consensus size: 34
563117 TTTAATTTTT
563127 AATTTATTTTTAAGTTT-AATTTAGTATAAATTTA
1 AATTTATTTTTAA-TTTAAATTTAGTATAAATTTA
* * * *
563161 AATTTATTTTGAATTTAAATTCATTCTAAATTTA
1 AATTTATTTTTAATTTAAATTTAGTATAAATTTA
*
563195 AATTTGTTTTTAATTTAAATTTA
1 AATTTATTTTTAATTTAAATTTA
563218 ATTAAAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
33 3 0.06
34 46 0.94
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.56
Consensus pattern (34 bp):
AATTTATTTTTAATTTAAATTTAGTATAAATTTA
Found at i:563230 original size:34 final size:33
Alignment explanation
Indices: 563127--563230 Score: 111
Period size: 34 Copynumber: 3.1 Consensus size: 33
563117 TTTAATTTTT
*
563127 AATTTATTTTTAAGTTT-AATTTAGTATAAATTTA
1 AATTTATTTTTAA-TTTAAATTTATTA-AAATTTA
* * *
563161 AATTTATTTTGAATTTAAATTCATTCTAAATTTA
1 AATTTATTTTTAATTTAAATTTATT-AAAATTTA
* *
563195 AATTTGTTTTTAATTTAAATTTAATTAAAAATTA
1 AATTTATTTTTAATTTAAATTT-ATTAAAATTTA
563229 AA
1 AA
563231 AGAAAGTCCA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
33 3 0.05
34 52 0.90
35 3 0.05
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (33 bp):
AATTTATTTTTAATTTAAATTTATTAAAATTTA
Found at i:564978 original size:29 final size:28
Alignment explanation
Indices: 564937--565156 Score: 112
Period size: 28 Copynumber: 7.6 Consensus size: 28
564927 CAAACTTTTG
* * *
564937 AAAATCACGTTTTGACCCCCAAAC-TTCAA
1 AAAATTAC-TTTTTACCCCCGAACTTTC-A
* *
564966 AAAATTACTTTTTTA-CCTCGAACTTTCC
1 AAAATTAC-TTTTTACCCCCGAACTTTCA
*
564994 AAAATTACATTTTTA-CCCCTAATCTTTCCA
1 AAAATTAC-TTTTTACCCCCGAA-CTTT-CA
* *
565024 AAAATCATA-TTTTGACCCCCGAACTTTCC
1 AAAAT--TACTTTTTACCCCCGAACTTTCA
* * ** **
565053 AAATTTACATTTTGTCCTTGAACTTTC-
1 AAAATTACTTTTTACCCCCGAACTTTCA
* * *
565080 AAAATCA-TATTTTACCCCTCAAACTTCACA
1 AAAATTACT-TTTTACCCC-CGAACTT-TCA
565110 AAAATTACATTTTTTACCCCCGAAC-TTCA
1 AAAATTAC--TTTTTACCCCCGAACTTTCA
565139 AAAATTACATTTTTACCC
1 AAAATTAC-TTTTTACCC
565157 TGAACATTCC
Statistics
Matches: 144, Mismatches: 33, Indels: 29
0.70 0.16 0.14
Matches are distributed among these distances:
27 13 0.09
28 52 0.36
29 35 0.24
30 22 0.15
31 10 0.07
32 11 0.08
33 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATTACTTTTTACCCCCGAACTTTCA
Found at i:565036 original size:30 final size:29
Alignment explanation
Indices: 564937--565186 Score: 142
Period size: 29 Copynumber: 8.7 Consensus size: 29
564927 CAAACTTTTG
* * * *
564937 AAAATCACGTTTTGACCCCCAAAC-TTCAA
1 AAAATCACATTTTTA-CCCCGAACTTTCCA
* * *
564966 AAAATTACTTTTTTACCTCGAACTTTCC-
1 AAAATCACATTTTTACCCCGAACTTTCCA
* *
564994 AAAATTACATTTTTACCCCTAATCTTTCCA
1 AAAATCACATTTTTACCCCGAA-CTTTCCA
* *
565024 AAAATCATATTTTGACCCCCGAACTTTCC-
1 AAAATCACATTTTTA-CCCCGAACTTTCCA
* * **
565053 AAATTTACATTTTGT-CCTTGAACTTT-C-
1 AAAATCACATTTT-TACCCCGAACTTTCCA
* *
565080 AAAATCATA-TTTTACCCCTCAAAC-TTCACA
1 AAAATCACATTTTTA-CCC-CGAACTTTC-CA
*
565110 AAAATTACATTTTTTACCCCCGAAC-TT-CA
1 AAAATCACA-TTTTTA-CCCCGAACTTTCCA
* * * *
565139 AAAATTACATTTTTACCCTGAACATTCCC
1 AAAATCACATTTTTACCCCGAACTTTCCA
*
565168 AAAATAACATTTTTACCCC
1 AAAATCACATTTTTACCCC
565187 TAAAACTTTT
Statistics
Matches: 174, Mismatches: 32, Indels: 30
0.74 0.14 0.13
Matches are distributed among these distances:
25 1 0.01
26 3 0.02
27 18 0.10
28 45 0.26
29 61 0.35
30 25 0.14
31 12 0.07
32 9 0.05
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATCACATTTTTACCCCGAACTTTCCA
Found at i:565048 original size:59 final size:56
Alignment explanation
Indices: 564976--565189 Score: 183
Period size: 59 Copynumber: 3.7 Consensus size: 56
564966 AAAATTACTT
*
564976 TTTTA-CCTCGAACTTTCCAAAATTACATTTTTACCCCTAATCTTTCCAAAAATCATA
1 TTTTACCCCCGAACTTTCCAAAATTACATTTTTACCCCTAA-CTTT-CAAAAATCATA
* *
565033 TTTTGACCCCCGAACTTTCCAAATTTACATTTTGT--CCTTGAACTTTC-AAAATCATA
1 TTTT-ACCCCCGAACTTTCCAAAATTACATTTT-TACCCCT-AACTTTCAAAAATCATA
* *
565089 TTTTACCCCTCAAAC-TTCACAAAAATTACATTTTTTACCCCCGAAC-TTCAAAAATTACAT-
1 TTTTACCCC-CGAACTTTC-C-AAAATTACA-TTTTTA-CCCCTAACTTTCAAAAA-T-CATA
* * *
565149 TTTTA-CCCTGAACATTCCCAAAATAACATTTTTACCCCTAA
1 TTTTACCCCCGAAC-TTTCCAAAATTACATTTTTACCCCTAA
565190 AACTTTTCAA
Statistics
Matches: 129, Mismatches: 12, Indels: 33
0.74 0.07 0.19
Matches are distributed among these distances:
55 8 0.06
56 24 0.19
57 20 0.16
58 26 0.20
59 37 0.29
60 11 0.09
61 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.36
Consensus pattern (56 bp):
TTTTACCCCCGAACTTTCCAAAATTACATTTTTACCCCTAACTTTCAAAAATCATA
Found at i:565104 original size:28 final size:29
Alignment explanation
Indices: 564981--565216 Score: 111
Period size: 29 Copynumber: 8.1 Consensus size: 29
564971 TACTTTTTTA
564981 CCTCGAACTTTCCAAAATTACAT-TTTTACC
1 CCTCGAACTTTCCAAAA-T-CATATTTTACC
565011 CCT--AATCTTTCCAAAAATCATATTTTGACC
1 CCTCGAA-CTTTCC-AAAATCATATTTT-ACC
* * * **
565041 CC-CGAACTTTCCAAATTTACATTTT-GT
1 CCTCGAACTTTCCAAAATCATATTTTACC
*
565068 CCTTGAACTTT-CAAAATCATATTTTACC
1 CCTCGAACTTTCCAAAATCATATTTTACC
* *
565096 CCTCAAAC-TTCACAAAAATTACATTTTTTACC
1 CCTCGAACTTTC-C-AAAA-T-CATATTTTACC
*
565128 CC-CGAAC-TTCAAAAATTACAT-TTTTA-C
1 CCTCGAACTTTCCAAAA-T-CATATTTTACC
*
565155 CCT-GAACATTCCCAAAATAACAT-TTTTACC
1 CCTCGAAC-TTTCCAAAAT--CATATTTTACC
** * * * *
565185 CCTAAAACTTTTCAAAATTATGTTTTAAC
1 CCTCGAACTTTCCAAAATCATATTTTACC
565214 CCT
1 CCT
565217 AAACTCTCTA
Statistics
Matches: 163, Mismatches: 23, Indels: 41
0.72 0.10 0.18
Matches are distributed among these distances:
27 22 0.13
28 26 0.16
29 56 0.34
30 34 0.21
31 13 0.08
32 12 0.07
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.36
Consensus pattern (29 bp):
CCTCGAACTTTCCAAAATCATATTTTACC
Found at i:565171 original size:29 final size:29
Alignment explanation
Indices: 564966--565187 Score: 158
Period size: 28 Copynumber: 7.7 Consensus size: 29
564956 CAAACTTCAA
* * *
564966 AAAATTACTTTTTTACCTC-GAACTTTCC
1 AAAATTACATTTTTACCCCTGAACTTCCC
*
564994 AAAATTACATTTTTACCCCT-AATCTTTCC
1 AAAATTACATTTTTACCCCTGAA-CTTCCC
* * *
565023 AAAAAT-CATATTTTGACCCCCGAACTTTCC
1 AAAATTACAT-TTTT-ACCCCTGAACTTCCC
* * *
565053 AAATTTACATTTTGT--CCTTGAACTT-TC
1 AAAATTACATTTT-TACCCCTGAACTTCCC
* *
565080 AAAA-T-CATATTTTACCCCTCAAACTTCACA
1 AAAATTACAT-TTTTACCCCT-GAACTTC-CC
* *
565110 AAAATTACATTTTTTACCCCCGAACTT-CA
1 AAAATTACA-TTTTTACCCCTGAACTTCCC
565139 AAAATTACATTTTTA-CCCTGAACATTCCC
1 AAAATTACATTTTTACCCCTGAAC-TTCCC
*
565168 AAAATAACATTTTTACCCCT
1 AAAATTACATTTTTACCCCT
565188 AAAACTTTTC
Statistics
Matches: 156, Mismatches: 19, Indels: 36
0.74 0.09 0.17
Matches are distributed among these distances:
25 4 0.03
26 4 0.03
27 14 0.09
28 43 0.28
29 41 0.26
30 26 0.17
31 12 0.08
32 11 0.07
33 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCTGAACTTCCC
Found at i:572525 original size:21 final size:21
Alignment explanation
Indices: 572501--572543 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
572491 AAACGCATAA
*
572501 AAAAAATA-ACACCCAAACAAC
1 AAAAAATACA-ACCAAAACAAC
*
572522 AAAAACTACAACCAAAACAAC
1 AAAAAATACAACCAAAACAAC
572543 A
1 A
572544 GCAAAACAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.67, C:0.28, G:0.00, T:0.05
Consensus pattern (21 bp):
AAAAAATACAACCAAAACAAC
Found at i:572605 original size:12 final size:11
Alignment explanation
Indices: 572534--572627 Score: 77
Period size: 11 Copynumber: 8.5 Consensus size: 11
572524 AAACTACAAC
*
572534 CAAAACAACAG
1 CAAAAAAACAG
*
572545 CAAAACAACA-
1 CAAAAAAACAG
572555 CAAAAAAAACAG
1 C-AAAAAAACAG
*
572567 CAAAAATAACAA
1 CAAAAA-AACAG
* * *
572579 TAAAACAACAA
1 CAAAAAAACAG
572590 CAAAAAAAGCAG
1 CAAAAAAA-CAG
572602 CAAAAAAA-A-
1 CAAAAAAACAG
572611 CAAAAAAAACAG
1 C-AAAAAAACAG
572623 CAAAA
1 CAAAA
572628 CAGCACCAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
9 1 0.01
10 9 0.13
11 39 0.57
12 20 0.29
ACGTcount: A:0.73, C:0.19, G:0.05, T:0.02
Consensus pattern (11 bp):
CAAAAAAACAG
Found at i:572638 original size:19 final size:18
Alignment explanation
Indices: 572616--572667 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
572606 AAAAACAAAA
**
572616 AAAACAGCAAAACAGCACC
1 AAAACAGCAAAA-AAAACC
*
572635 AAAACAACAAAAAAAACC
1 AAAACAGCAAAAAAAACC
572653 AGAAACAGCAAAAAA
1 A-AAACAGCAAAAAA
572668 TAGTAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.69, C:0.23, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAACAGCAAAAAAAACC
Found at i:572648 original size:32 final size:30
Alignment explanation
Indices: 572560--572667 Score: 80
Period size: 32 Copynumber: 3.5 Consensus size: 30
572550 CAACACAAAA
* *
572560 AAAACAGCA-AAAATAACAATAAAACAACAAC
1 AAAACAGCACAAAA-AACAA-AAAAAAACAGC
* *
572591 AAAAAAAGCAGCAAAAAAAACAAAAAAAACAGC
1 -AAAACAGCA-CAAAAAACA-AAAAAAAACAGC
*
572624 AAAACAGCACCAAAACAACAAAAAAAACCAG-
1 AAAACAGCA-CAAAA-AACAAAAAAAAACAGC
572655 -AAACAGCA-AAAAA
1 AAAACAGCACAAAAA
572668 TAGTAATATA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
27 1 0.02
28 4 0.06
30 8 0.12
32 31 0.48
33 15 0.23
34 5 0.08
ACGTcount: A:0.72, C:0.19, G:0.06, T:0.02
Consensus pattern (30 bp):
AAAACAGCACAAAAAACAAAAAAAAACAGC
Found at i:572649 original size:11 final size:11
Alignment explanation
Indices: 572515--572649 Score: 73
Period size: 11 Copynumber: 12.3 Consensus size: 11
572505 AATAACACCC
572515 AAACAACAAAA
1 AAACAACAAAA
*
572526 ACTACAACCAAAA
1 A-AACAA-CAAAA
* *
572539 CAACAGCAAAA
1 AAACAACAAAA
*
572550 CAAC-ACAAAAA
1 AAACAAC-AAAA
*
572561 AAACAGCAAAA
1 AAACAACAAAA
*
572572 ATAACAATAAAA
1 A-AACAACAAAA
*
572584 CAACAACAAAA
1 AAACAACAAAA
*
572595 AAAGCAGC-AAA
1 AAA-CAACAAAA
572606 AAA-AAC-AAA
1 AAACAACAAAA
**
572615 AAA-AACAGCA
1 AAACAACAAAA
* **
572625 AAACAGCACCA
1 AAACAACAAAA
572636 AAACAACAAAA
1 AAACAACAAAA
572647 AAA
1 AAA
572650 ACCAGAAACA
Statistics
Matches: 95, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
9 11 0.12
10 5 0.05
11 55 0.58
12 19 0.20
13 5 0.05
ACGTcount: A:0.72, C:0.21, G:0.04, T:0.02
Consensus pattern (11 bp):
AAACAACAAAA
Found at i:572649 original size:30 final size:31
Alignment explanation
Indices: 572604--572662 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
572594 AAAAGCAGCA
*
572604 AAAAAAACAAAAAAAACAGCA-AAACAGCACC
1 AAAAAAACAAAAAAAA-ACCAGAAACAGCACC
*
572635 AAAACAAC-AAAAAAAACCAGAAACAGCA
1 AAAAAAACAAAAAAAAACCAGAAACAGCA
572663 AAAAATAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.12
30 15 0.60
31 7 0.28
ACGTcount: A:0.71, C:0.22, G:0.07, T:0.00
Consensus pattern (31 bp):
AAAAAAACAAAAAAAAACCAGAAACAGCACC
Found at i:572666 original size:56 final size:56
Alignment explanation
Indices: 572516--572657 Score: 139
Period size: 56 Copynumber: 2.6 Consensus size: 56
572506 ATAACACCCA
* * * * *
572516 AACAACAAAAACTACAACCAAAACAA-CAGCAAAACAACACAAAAAAAACAGCAAAAAT
1 AACAAC-AAAACAACAA-CAAAAAAACCAG-AAAAAAAAACAAAAAAAACAGCAAAAAC
* * *
572574 AACAATAAAACAACAACAAAAAAAGCAGCAAAAAAAACAAAAAAAACAGC-AAAAC
1 AACAACAAAACAACAACAAAAAAACCAGAAAAAAAAACAAAAAAAACAGCAAAAAC
* *
572629 AGCACCAAAACAAC-A-AAAAAAACCAGAAA
1 AACAACAAAACAACAACAAAAAAACCAGAAA
572658 CAGCAAAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
53 12 0.17
54 1 0.01
55 15 0.21
56 26 0.37
57 12 0.17
58 5 0.07
ACGTcount: A:0.71, C:0.22, G:0.05, T:0.02
Consensus pattern (56 bp):
AACAACAAAACAACAACAAAAAAACCAGAAAAAAAAACAAAAAAAACAGCAAAAAC
Found at i:576158 original size:67 final size:67
Alignment explanation
Indices: 576075--576214 Score: 235
Period size: 67 Copynumber: 2.1 Consensus size: 67
576065 CAAGAGCATA
* *
576075 AAAGAAGTTGTGGGGTAGATTTGTTGATCCCCTCAAGTAAAAATTTTGAATTAGAAGAGAATAGA
1 AAAG-AGTTATGGGGTAGATTTGTTGATCCCCTCAAGTAAAAAATTTGAATTAGAAGAGAATAGA
576140 AGG
65 AGG
* *
576143 AAAGAGTTATGGGGTAGATTTGTTGGTCCCCTCAAGTAAAAAATTTGAATTATAAGAGAATAGAA
1 AAAGAGTTATGGGGTAGATTTGTTGATCCCCTCAAGTAAAAAATTTGAATTAGAAGAGAATAGAA
576208 GG
66 GG
576210 AAAGA
1 AAAGA
576215 TGGCTGTTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
67 64 0.94
68 4 0.06
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.27
Consensus pattern (67 bp):
AAAGAGTTATGGGGTAGATTTGTTGATCCCCTCAAGTAAAAAATTTGAATTAGAAGAGAATAGAA
GG
Found at i:579136 original size:32 final size:33
Alignment explanation
Indices: 579075--579175 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 33
579065 ATTCTAAAAA
* * *
579075 TTCAAACAA-ATATATAATAATACATAAATATT-
1 TTCAAAAAATATATATAAAAATA-AAAAATATTG
579107 TTCAAAAAATATATATAAAAATAAAAAATATTG
1 TTCAAAAAATATATATAAAAATAAAAAATATTG
**
579140 TTGACAAAAAATAATAATTATAAAAATTGAAAATAT
1 TT--CAAAAAAT-AT-A-TATAAAAATAAAAAATAT
579176 ATAAAAATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
32 16 0.28
33 14 0.25
35 8 0.14
36 2 0.04
37 1 0.02
38 16 0.28
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (33 bp):
TTCAAAAAATATATATAAAAATAAAAAATATTG
Found at i:580589 original size:6 final size:6
Alignment explanation
Indices: 580578--580602 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
580568 CTGTCTATCA
580578 CCCTCT CCCTCT CCCTCT CCCTCT C
1 CCCTCT CCCTCT CCCTCT CCCTCT C
580603 TCCCTACCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCTCT
Found at i:582289 original size:9 final size:9
Alignment explanation
Indices: 582275--582335 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 9
582265 GCTAATGATT
582275 TTAAAATTA
1 TTAAAATTA
582284 TTAAAATTA
1 TTAAAATTA
582293 TT----TT-
1 TTAAAATTA
*
582297 TTAAAAATA
1 TTAAAATTA
582306 -TAAAATTA
1 TTAAAATTA
582314 TTAAAATTAA
1 TTAAAATT-A
582324 TTTAAAATTA
1 -TTAAAATTA
582334 TT
1 TT
582336 TTTTAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
8 8 0.19
9 20 0.48
10 2 0.05
11 8 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAAATTA
Found at i:582356 original size:40 final size:40
Alignment explanation
Indices: 582275--582362 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
582265 GCTAATGATT
*
582275 TTAAAATT-ATTAAAATTATTTTTTAAAAATATAAAATTA
1 TTAAAATTAATTAAAATTATTTTTTAAAAATATAAAACTA
*
582314 TTAAAATTAATTTAAAATTATTTTTT-AAAATATATAACTA
1 TTAAAATTAA-TTAAAATTATTTTTTAAAAATATAAAACTA
582354 TTAAAATTA
1 TTAAAATTA
582363 TCATCATCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 8 0.18
40 22 0.49
41 15 0.33
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (40 bp):
TTAAAATTAATTAAAATTATTTTTTAAAAATATAAAACTA
Found at i:582735 original size:24 final size:24
Alignment explanation
Indices: 582708--582768 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
582698 TATTTTTCCA
* *
582708 AGAAACAAACAGAGTATTTTCCTG
1 AGAAACGAACAGAGTATTTTCCTC
* *
582732 AGAAACGAACAAAGTATTTTTCTC
1 AGAAACGAACAGAGTATTTTCCTC
582756 AGAAACGAACAGA
1 AGAAACGAACAGA
582769 AAACTTCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.21
Consensus pattern (24 bp):
AGAAACGAACAGAGTATTTTCCTC
Found at i:592300 original size:21 final size:21
Alignment explanation
Indices: 592245--592302 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
592235 TAGAAGTAAG
* * *
592245 ACTTGTTTCGGTAAAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
592266 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
592287 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
592303 GTCTGAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:599573 original size:21 final size:21
Alignment explanation
Indices: 599549--599606 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
599539 TAGAAGTAAG
599549 ACTTGTTTCAGTAGAAAAGTC
1 ACTTGTTTCAGTAGAAAAGTC
**
599570 ACTTGTATT-AGTAGAACTGTC
1 ACTTGT-TTCAGTAGAAAAGTC
* *
599591 ACTTGTGTCGGTAGAA
1 ACTTGTTTCAGTAGAA
599607 GTTTGCACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.90
22 2 0.06
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (21 bp):
ACTTGTTTCAGTAGAAAAGTC
Found at i:601998 original size:21 final size:21
Alignment explanation
Indices: 601961--602000 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
601951 TAATAAAAAA
*
601961 TTTATAATTTTATAATTTTTT
1 TTTATAATTTTACAATTTTTT
601982 TTTATAAATTTT-CAATTTT
1 TTTAT-AATTTTACAATTTT
602001 AAAAGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATAATTTTACAATTTTTT
Found at i:603253 original size:6 final size:7
Alignment explanation
Indices: 603236--603261 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
603226 CATTATCCTC
603236 AAAAAAG
1 AAAAAAG
603243 AAAAAAG
1 AAAAAAG
603250 AAAAAAG
1 AAAAAAG
603257 AAAAA
1 AAAAA
603262 CCTAATCCAT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:609256 original size:27 final size:27
Alignment explanation
Indices: 609200--609275 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
609190 AGAGCAATAC
* * * **
609200 TCTAATATAGCTCGAGTAAAGCTTTGA
1 TCTATTATAGCTCGGGTAGAGCTTCAA
609227 TCTATTATAGCTCGGGTAGAGCTTCAA
1 TCTATTATAGCTCGGGTAGAGCTTCAA
*
609254 TCTGTTTATAGCTCGGGTAGAG
1 TCT-ATTATAGCTCGGGTAGAG
609276 TTTTGACCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (27 bp):
TCTATTATAGCTCGGGTAGAGCTTCAA
Found at i:609267 original size:28 final size:28
Alignment explanation
Indices: 609205--609308 Score: 129
Period size: 28 Copynumber: 3.8 Consensus size: 28
609195 AATACTCTAA
* * *
609205 TATAGCTCGAGTAAAGCTTTGATCT-AT
1 TATAGCTCGGGTAGAGCTTTGATCTGTT
**
609232 TATAGCTCGGGTAGAGCTTCAATCTGTT
1 TATAGCTCGGGTAGAGCTTTGATCTGTT
* *
609260 TATAGCTCGGGTAGAGTTTTGACCTGTT
1 TATAGCTCGGGTAGAGCTTTGATCTGTT
*
609288 TATAGCTCAGGTAGAGCTTTG
1 TATAGCTCGGGTAGAGCTTTG
609309 GTCTACTTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
27 21 0.32
28 44 0.68
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (28 bp):
TATAGCTCGGGTAGAGCTTTGATCTGTT
Found at i:609318 original size:28 final size:28
Alignment explanation
Indices: 609205--609332 Score: 125
Period size: 28 Copynumber: 4.6 Consensus size: 28
609195 AATACTCTAA
* *
609205 TATAGCTCGAGTAAAGCTTTGATCTA-T
1 TATAGCTCGGGTAGAGCTTTGATCTATT
** *
609232 TATAGCTCGGGTAGAGCTTCAATCTGTT
1 TATAGCTCGGGTAGAGCTTTGATCTATT
* * *
609260 TATAGCTCGGGTAGAGTTTTGACCTGTT
1 TATAGCTCGGGTAGAGCTTTGATCTATT
* * *
609288 TATAGCTCAGGTAGAGCTTTGGTCTACT
1 TATAGCTCGGGTAGAGCTTTGATCTATT
*
609316 TAT-GACTCGGTTAGAGC
1 TATAG-CTCGGGTAGAGC
609333 GTAAATCCAT
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
27 22 0.27
28 60 0.73
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (28 bp):
TATAGCTCGGGTAGAGCTTTGATCTATT
Found at i:610514 original size:28 final size:27
Alignment explanation
Indices: 610445--610763 Score: 147
Period size: 24 Copynumber: 12.3 Consensus size: 27
610435 ATATAAACAC
* *
610445 GCGTTTACACTCGTCAGCTTACAC-A-
1 GCGTTTACGCTCGTCAGCTTATACTAT
*
610470 -CGTTTACGCTTGTCAGCTTATACTTAT
1 GCGTTTACGCTCGTCAGCTTATAC-TAT
* **
610497 GCGTTTACGCTCGCCAGCTTGCAC-A-
1 GCGTTTACGCTCGTCAGCTTATACTAT
*
610522 -CGTTTACGCTCGTCATCTTATACATAT
1 GCGTTTACGCTCGTCAGCTTATAC-TAT
* **
610549 GCGTTTACGCTCGTCAACTTGCAC-A-
1 GCGTTTACGCTCGTCAGCTTATACTAT
* * *
610574 -CATTTACGTTGGTCAGCTTATACATAT
1 GCGTTTACGCTCGTCAGCTTATAC-TAT
** * **
610601 GCGTTTACGCTCACCGGCTTGCAC-A-
1 GCGTTTACGCTCGTCAGCTTATACTAT
*
610626 -CGTTTACGCTTGTCAGCTTATA-TAT
1 GCGTTTACGCTCGTCAGCTTATACTAT
* * **
610651 ACGCGTTTACGATAG-CTAGCTTGCAC-AT
1 --GCGTTTACGCTCGTC-AGCTTATACTAT
* * *
610679 --GTTTACACTCATCAACTTATACATAT
1 GCGTTTACGCTCGTCAGCTTATAC-TAT
* * *
610705 GCGTTTACGCTTGCCAGCTTACAC-A-
1 GCGTTTACGCTCGTCAGCTTATACTAT
*
610730 -CGTTTACGCTCATCAGCTTATACATAT
1 GCGTTTACGCTCGTCAGCTTATAC-TAT
*
610757 GTGTTTA
1 GCGTTTA
610764 GGCTATTTAA
Statistics
Matches: 210, Mismatches: 56, Indels: 53
0.66 0.18 0.17
Matches are distributed among these distances:
24 105 0.50
25 1 0.00
26 10 0.05
27 1 0.00
28 93 0.44
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (27 bp):
GCGTTTACGCTCGTCAGCTTATACTAT
Found at i:610515 original size:52 final size:52
Alignment explanation
Indices: 610445--610763 Score: 395
Period size: 52 Copynumber: 6.1 Consensus size: 52
610435 ATATAAACAC
* * * * *
610445 GCGTTTACACTCGTCAGCTTACACACGTTTACGCTTGTCAGCTTATACTTAT
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATACATAT
*
610497 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCATCTTATACATAT
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATACATAT
* * * * *
610549 GCGTTTACGCTCGTCAACTTGCACACATTTACGTTGGTCAGCTTATACATAT
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATACATAT
* * * * *
610601 GCGTTTACGCTCACCGGCTTGCACACGTTTACGCTTGTCAGCTTATATATAC
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATACATAT
* * * * * * *
610653 GCGTTTACGATAGCTAGCTTGCACATGTTTACACTCATCAACTTATACATAT
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATACATAT
* * *
610705 GCGTTTACGCTTGCCAGCTTACACACGTTTACGCTCATCAGCTTATACATAT
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATACATAT
*
610757 GTGTTTA
1 GCGTTTA
610764 GGCTATTTAA
Statistics
Matches: 226, Mismatches: 41, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 226 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (52 bp):
GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATACATAT
Found at i:611819 original size:3 final size:3
Alignment explanation
Indices: 611811--611859 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
611801 TTTATGACCC
611811 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
611859 T
1 T
611860 TGTAGTTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:612008 original size:28 final size:28
Alignment explanation
Indices: 611966--612066 Score: 125
Period size: 28 Copynumber: 3.6 Consensus size: 28
611956 ATTTCATCTT
*
611966 GGGTAGAGCGA-TATTTTGAATCTTGCTC
1 GGGTAGAGC-ATTATTCTGAATCTTGCTC
* *
611994 GGGTAGAGCATTATTCT-ACTGTTGGCTC
1 GGGTAGAGCATTATTCTGAATCTT-GCTC
* *
612022 GGGTAGAACGTTATTCTGAATCTTGCTC
1 GGGTAGAGCATTATTCTGAATCTTGCTC
612050 GGGTAGAGCATTATTCT
1 GGGTAGAGCATTATTCT
612067 ACTTCTATAT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
27 5 0.08
28 52 0.85
29 4 0.07
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.36
Consensus pattern (28 bp):
GGGTAGAGCATTATTCTGAATCTTGCTC
Found at i:612092 original size:56 final size:56
Alignment explanation
Indices: 611977--612093 Score: 137
Period size: 56 Copynumber: 2.1 Consensus size: 56
611967 GGTAGAGCGA
* * * * ** *
611977 TATTTTGAATCTTGCTCGGGTAGAGCATTATTCTACTGTTGGCTCGGGTAGAACGT
1 TATTCTGAATCTTGCTCGGGTAGAGCATTATTCTACTGTTAGATCAGAAAGAACAT
* *
612033 TATTCTGAATCTTGCTCGGGTAGAGCATTATTCTACT-TCTATATCAGAAAGAGCAT
1 TATTCTGAATCTTGCTCGGGTAGAGCATTATTCTACTGT-TAGATCAGAAAGAACAT
612089 TATTC
1 TATTC
612094 CGTTTGGGCA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 1 0.02
56 50 0.98
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (56 bp):
TATTCTGAATCTTGCTCGGGTAGAGCATTATTCTACTGTTAGATCAGAAAGAACAT
Found at i:612947 original size:20 final size:20
Alignment explanation
Indices: 612922--612960 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
612912 CATGTTTATT
*
612922 TGAAATGATGTAAA-TGAGTA
1 TGAAATAAT-TAAATTGAGTA
612942 TGAAATAATTAAATTGAGT
1 TGAAATAATTAAATTGAGT
612961 TTTAATCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (20 bp):
TGAAATAATTAAATTGAGTA
Found at i:615587 original size:22 final size:22
Alignment explanation
Indices: 615526--615589 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
615516 ATTGACCCAG
* *
615526 ACCCGTTGATCGAACTCAACCC
1 ACCCGTTGATCGAACCCGACCC
** * *
615548 GTCCGTTGAACAAACCCGACCC
1 ACCCGTTGATCGAACCCGACCC
615570 ACCCGTTGATCGAACCCGAC
1 ACCCGTTGATCGAACCCGAC
615590 TTGACTCGTT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.41, G:0.17, T:0.16
Consensus pattern (22 bp):
ACCCGTTGATCGAACCCGACCC
Found at i:615627 original size:25 final size:28
Alignment explanation
Indices: 615575--615630 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 28
615565 GACCCACCCG
*
615575 TTGATCGAACCCGACTTGACTCGTTGACT
1 TTGATCGAACCCGA-TTGACTCATTGACT
615604 TTGATCG-ACCCG-TTGA-TCATTGACT
1 TTGATCGAACCCGATTGACTCATTGACT
615629 TT
1 TT
615631 TTTCGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 10 0.38
26 4 0.15
28 5 0.19
29 7 0.27
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36
Consensus pattern (28 bp):
TTGATCGAACCCGATTGACTCATTGACT
Found at i:621171 original size:21 final size:21
Alignment explanation
Indices: 621147--621203 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
621137 GAAGTAAGAT
*
621147 TTGTTTCGGTAGAAGAGTCAC
1 TTGTATCGGTAGAAGAGTCAC
* **
621168 TTGTATCAGTAGAATTGTCAC
1 TTGTATCGGTAGAAGAGTCAC
621189 TTGTATCGGTAGAAG
1 TTGTATCGGTAGAAG
621204 TTTACATCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (21 bp):
TTGTATCGGTAGAAGAGTCAC
Found at i:626544 original size:19 final size:20
Alignment explanation
Indices: 626502--626546 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
626492 GCATCATCTA
626502 AATTAAGTGTAAAAGGGTTT
1 AATTAAGTGTAAAAGGGTTT
*
626522 AATTAAG-GTTAAGAGGG-TT
1 AATTAAGTG-TAAAAGGGTTT
626541 AATTAA
1 AATTAA
626547 AGCTTAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.33
Consensus pattern (20 bp):
AATTAAGTGTAAAAGGGTTT
Found at i:626553 original size:20 final size:20
Alignment explanation
Indices: 626502--626553 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
626492 GCATCATCTA
*
626502 AATTAAG-TGTAAAAGGGTTT
1 AATTAAGCT-TAAGAGGGTTT
*
626522 AATTAAGGTTAAGAGGG-TT
1 AATTAAGCTTAAGAGGGTTT
626541 AATTAAAGCTTAA
1 AATT-AAGCTTAA
626554 TGATGAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 6 0.21
20 21 0.75
21 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (20 bp):
AATTAAGCTTAAGAGGGTTT
Found at i:641641 original size:17 final size:17
Alignment explanation
Indices: 641616--641709 Score: 81
Period size: 17 Copynumber: 5.8 Consensus size: 17
641606 CCGGGTTCCT
641616 TTTAAATTTATTTTAAC
1 TTTAAATTTATTTTAAC
* *
641633 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAC
* ** *
641650 TTTGAATTTAAATTAAA
1 TTTAAATTTATTTTAAC
641667 TTTAAATTTA----AA-
1 TTTAAATTTATTTTAAC
* *
641679 TGTAAATTTAATTTAAC
1 TTTAAATTTATTTTAAC
641696 TTTAAATTTATTTT
1 TTTAAATTTATTTT
641710 CAAAATTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
12 9 0.15
13 2 0.03
16 2 0.03
17 49 0.79
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAC
Found at i:641657 original size:6 final size:6
Alignment explanation
Indices: 641616--641705 Score: 89
Period size: 6 Copynumber: 15.7 Consensus size: 6
641606 CCGGGTTCCT
* * * * *
641616 TTTAAA TTT-AT TTTAAC TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
641662 -TTAAA TTTAAA TTTAAA TGTAAA TTT-AA TTTAAC TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
641706 TTTTCAAAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
5 17 0.25
6 50 0.75
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:641659 original size:23 final size:23
Alignment explanation
Indices: 641627--641705 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
641617 TTAAATTTAT
* * *
641627 TTTAACTTTAGATTTATTTTAAA
1 TTTAAATTTAAATTTAATTTAAA
* *
641650 TTTGAATTTAAATTAAATTTAAA
1 TTTAAATTTAAATTTAATTTAAA
* *
641673 TTTAAATGTAAATTTAATTTAAC
1 TTTAAATTTAAATTTAATTTAAA
641696 TTTAAATTTA
1 TTTAAATTTA
641706 TTTTCAAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATTTAAA
Found at i:642479 original size:21 final size:20
Alignment explanation
Indices: 642454--642515 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
642444 TAAAATCAGT
*
642454 ATTAATAATAGTCATAATAAC
1 ATTAATAATA-TAATAATAAC
* *
642475 ATTAATAATATTATTATAAC
1 ATTAATAATATAATAATAAC
*
642495 ATTTAACAATAATAATAATAA
1 A-TTAATAAT-ATAATAATAA
642516 TAATAAATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.26
21 17 0.50
22 8 0.24
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (20 bp):
ATTAATAATATAATAATAAC
Found at i:643590 original size:58 final size:58
Alignment explanation
Indices: 643496--643652 Score: 155
Period size: 58 Copynumber: 2.7 Consensus size: 58
643486 TAAACTATCC
*
643496 AAAAATTA-CATTTTTACCCCTCGAACT-TCCAAAAATTCCATATTTTACCCCGA-AACTCT
1 AAAAATTACCA-TATTA-CCCTCGAA-TATCCAAAAATTCCATATTTTACCCCGATAA-TCT
* * * *
643555 CAAAAATTACCAT-TTACACC-CGAATGTCCAAAAATTCCATTTTTTATCCCGATTTATCT
1 -AAAAATTACCATATTAC-CCTCGAATATCCAAAAATTCCATATTTTACCCCGA-TAATCT
*
643614 AAAAATTACCATATTACCCTCGAATAT-CTAAAATTCCAT
1 AAAAATTACCATATTACCCTCGAATATCCAAAAATTCCAT
643653 TTAAAACCCC
Statistics
Matches: 85, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
57 1 0.01
58 54 0.64
59 18 0.21
60 10 0.12
61 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (58 bp):
AAAAATTACCATATTACCCTCGAATATCCAAAAATTCCATATTTTACCCCGATAATCT
Found at i:643605 original size:29 final size:27
Alignment explanation
Indices: 643493--643686 Score: 99
Period size: 30 Copynumber: 6.6 Consensus size: 27
643483 CCCTAAACTA
*
643493 TCCAAAAATTACATTTTTACCCCTCGAACT
1 TCCAAAAATTCCATTTTTA-CCC-CGAA-T
*
643523 TCCAAAAATTCCATATTTTACCCCGAAAC
1 TCCAAAAATTCCAT-TTTTACCCCG-AAT
643552 TCTCAAAAATTACCA--TTTACACCCGAAT
1 TC-CAAAAATT-CCATTTTTAC-CCCGAAT
* *
643580 GTCCAAAAATTCCATTTTTTATCCCGATTT
1 -TCCAAAAATTCCA-TTTTTACCCCGA-AT
* *
643610 ATCTAAAAATTACCA-TATTACCCTCGAAT
1 -TCCAAAAATT-CCATTTTTACCC-CGAAT
* ** *
643639 AT-CTAAAATTCCATTTAAAACCCCAAAATT
1 -TCCAAAAATTCCATTT-TTACCCC-GAA-T
643669 TCCAAAAATTACCATTTT
1 TCCAAAAATT-CCATTTT
643687 GCCCCCGGGT
Statistics
Matches: 128, Mismatches: 18, Indels: 36
0.70 0.10 0.20
Matches are distributed among these distances:
27 6 0.05
28 23 0.18
29 31 0.24
30 51 0.40
31 17 0.13
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (27 bp):
TCCAAAAATTCCATTTTTACCCCGAAT
Found at i:655641 original size:206 final size:206
Alignment explanation
Indices: 655075--655723 Score: 826
Period size: 206 Copynumber: 3.2 Consensus size: 206
655065 GATTATCCAC
* * * *
655075 AAAC-AGCGATGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATTAATGAAACAAGG
1 AAACAAGCGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA-TCA--AAACAAGG
* * *
655139 CTCAAAGCGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGGCGAAGCAA
63 CTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAA
* *
655204 T-AAAGGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTAC
128 TAAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
655268 AGAGAAGCGGATTG
193 AGAGAAGCGGATTG
** * * * * * * * * * *
655282 AAACAAGTAAGGTGGTCATCTTCATAATAAGATACAGAGAAAAATACC-AA-C---TCGAGGCTT
1 AAACAAGCGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAACAAGGCTC
* * * *
655342 AATGCAAGCAAATCTTCGAACCTCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAA
66 AATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAA
* * *
655407 AATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGTTACAGA
131 AAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGA
655472 GAAGCGGATTG
196 GAAGCGGATTG
** * * * * *
655483 AAACAAGCGATACGGTCACCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCATGCTC
1 AAACAAGCGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAACAAGGCTC
*
655548 AATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCAATAA
66 AATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAA
* * * * * *
655613 AAAGGTTAGTTTCCTGATAAGATACTGAGAAGTGGACCAAATTCATCTTCCTAAGGAGATATAGA
131 AAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGA
655678 GAAGCGGATTG
196 GAAGCGGATTG
* *
655689 CAACAAGTGAGGCGGTCATCTTCCTGATGAGATAC
1 AAACAAGCGAGGCGGTCATCTTCCTGATGAGATAC
655724 AATAAGTATA
Statistics
Matches: 373, Mismatches: 62, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
200 62 0.17
201 109 0.29
202 2 0.01
203 1 0.00
206 161 0.43
207 6 0.02
208 32 0.09
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (206 bp):
AAACAAGCGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAACAAGGCTC
AATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAA
AAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGA
GAAGCGGATTG
Found at i:656058 original size:352 final size:350
Alignment explanation
Indices: 655414--656065 Score: 986
Period size: 352 Copynumber: 1.9 Consensus size: 350
655404 TAAAATGGTT
* *
655414 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGTTACAGAGAAGCGG
1 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGACGAGATACAGAGAAGCGG
* * * *
655479 ATTGAAACAAGCGATACGGTCACCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCAT
66 ATTGAAACAAGCAATACGGTCACCATCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
* *
655544 GCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCA
131 GCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGGCGAAACA
* * * * * *
655609 ATAAAAAGGTTAGTTTCCTGATAAGATACTGAGAAGTGGACCAAATTCATCTTCCTAAGGAGATA
196 ATAAAAAGGTTAGTTTCCTGATAAGAAACGGAGAAGTGAACCAAATCCATCTTCCTAAGGAAACA
* *
655674 TAGAGAAGCGGATTGCAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAATAAGTATACCAAC
261 CAGAGAAGCGGA-TCCAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAATAAGTATACCAAC
655739 TCAATGTGAACAAATCTTCGACCCCC
325 TCAATGTGAACAAATCTTCGACCCCC
655765 AGCTTCCTGATGAGATACTGAGAAGT-AGACCAAATTCGTCTTCCTGACGAAGATACAGAGAAGC
1 AGCTTCCTGATGAGATACTGAGAAGTGA-ACCAAATTCGTCTTCCTGACG-AGATACAGAGAAGC
*
655829 GGATTGAAACAAGCAATACGGTCATCATCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCC
64 GGATTGAAACAAGCAATACGGTCACCATCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCC
* * * *
655894 ACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAA
129 ACGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGGCGAAA
* * * *
655959 CAATAAAATGGTTAGCTTT-CTGATGAGAAACGGAGAAGTGAACCAAATCCATCTTCCTGATGAA
194 CAATAAAAAGGTTAG-TTTCCTGATAAGAAACGGAGAAGTGAACCAAATCCATCTTCCTAAGGAA
* *
656023 ACACAGAGAAGTGGA-CCAAAGCAAGTGATGCGGTCATCTTCCT
258 ACACAGAGAAGCGGATCC-AA-CAAGTGAGGCGGTCATCTTCCT
656066 AGTAAGATAC
Statistics
Matches: 269, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
350 2 0.01
351 48 0.18
352 216 0.80
353 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (350 bp):
AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGACGAGATACAGAGAAGCGG
ATTGAAACAAGCAATACGGTCACCATCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
GCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGGCGAAACA
ATAAAAAGGTTAGTTTCCTGATAAGAAACGGAGAAGTGAACCAAATCCATCTTCCTAAGGAAACA
CAGAGAAGCGGATCCAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAATAAGTATACCAACT
CAATGTGAACAAATCTTCGACCCCC
Found at i:657291 original size:3 final size:3
Alignment explanation
Indices: 657201--657275 Score: 71
Period size: 3 Copynumber: 25.0 Consensus size: 3
657191 AAATCAGTGT
* * * * * * *
657201 TAA TAA TAG TCA TAA TAA CAT TAA TAA TAA TAC T-A TAA CATT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
657246 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
657276 ATGGGTTTAA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
2 1 0.02
3 54 0.96
4 1 0.02
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:657538 original size:18 final size:18
Alignment explanation
Indices: 657512--657547 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
657502 TCAAACGTTT
* *
657512 TAAACAAAAAAAGGGAAA
1 TAAAAAAAAAAAGAGAAA
657530 TAAAAAAAAAAAGAGAAA
1 TAAAAAAAAAAAGAGAAA
657548 AGGATGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.06
Consensus pattern (18 bp):
TAAAAAAAAAAAGAGAAA
Found at i:658309 original size:29 final size:28
Alignment explanation
Indices: 658267--658596 Score: 120
Period size: 29 Copynumber: 11.2 Consensus size: 28
658257 TAAACTATCT
*
658267 AAAAATTACATTTTTACCCCT-GAATTACC
1 AAAAATTCCATTTTTA-CCCTAGAATT-CC
* *
658296 AAAAATTCCATTTTTGACCCTAAAATTTCT
1 AAAAATTCCATTTTT-ACCCTAGAA-TTCC
* *
658326 AAAAA-TCATATTTTTACCCTCGAACTTCC
1 AAAAATTC-CATTTTTACCCTAGAA-TTCC
* **
658355 AAAAATTCCATTTTTTA-CCTCGAAACTTTT
1 AAAAATTCCA-TTTTTACCCTAG-AA-TTCC
* * * *
658385 GAAAATTACATTTTCACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCTAGAA-TTCC
* * *
658414 AAAAATTTCATTTTT-CACCTTGAAACTTCT
1 AAAAATTCCATTTTTAC-CCTAG-AA-TTCC
* * * * *
658444 AAAATTTACCA-TTTCACCCTCGGATGTCA
1 AAAAATT-CCATTTTTACCCTAGAAT-TCC
* * *
658473 AAAAAATCCATTTTTAACCCTAAAACTTTC
1 AAAAATTCCATTTTT-ACCCTAGAA-TTCC
*
658503 AAAAATTACC-TTTTTACCCCCA-AATGTCC
1 AAAAATT-CCATTTTTA-CCCTAGAAT-TCC
* * * *
658532 AAAAACTCCATTTTGACCCTAAAACTCTC
1 AAAAATTCCATTTTTACCCTAGAATTC-C
*
658561 AACAATTACCA-TTTTACCCTCA-AATGTCC
1 AAAAATT-CCATTTTTACCCT-AGAAT-TCC
658590 AAAAATT
1 AAAAATT
658597 TTGTTTTTTA
Statistics
Matches: 229, Mismatches: 47, Indels: 50
0.70 0.14 0.15
Matches are distributed among these distances:
28 14 0.06
29 119 0.52
30 88 0.38
31 8 0.03
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAAATTCCATTTTTACCCTAGAATTCC
Found at i:658357 original size:59 final size:58
Alignment explanation
Indices: 658254--658596 Score: 286
Period size: 59 Copynumber: 5.8 Consensus size: 58
658244 CCTAAAAGGT
* *
658254 CCCTAAACTATCTAAAAATTACATTTTTACCC-CTGAATTACCAAAAATTCCATTTTTGA
1 CCCTAAAATTTCTAAAAATTACATTTTTACCCTC-GAATT-CCAAAAATTCCATTTTTGA
* * *
658313 CCCTAAAATTTCTAAAAATCATATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTTA
1 CCCTAAAATTTCTAAAAATTACATTTTTACCCTCGAA-TTCCAAAAATTCCATTTTTGA
* * * * * *
658372 CCTCGAAACTTT-TGAAAATTACATTTTCACCCTCGAACTTCCAAAAATTTCATTTTTCA
1 CC-CTAAAATTTCTAAAAATTACATTTTTACCCTCGAA-TTCCAAAAATTCCATTTTTGA
* * * * * * * * *
658431 CCTTGAAACTTCTAAAATTTACCA-TTTCACCCTCGGATGTCAAAAAAATCCATTTTTAA
1 CCCTAAAATTTCTAAAAATTA-CATTTTTACCCTCGAAT-TCCAAAAATTCCATTTTTGA
* * * *
658490 CCCTAAAACTTTC-AAAAATTACCTTTTTACCCCCAAATGTCCAAAAACTCCA-TTTTGA
1 CCCTAAAA-TTTCTAAAAATTACATTTTTACCCTCGAAT-TCCAAAAATTCCATTTTTGA
* * *
658548 CCCTAAAA-CTCTCAACAATTACCA-TTTTACCCTCAAATGTCCAAAAATT
1 CCCTAAAATTTCT-AAAAATTA-CATTTTTACCCTCGAAT-TCCAAAAATT
658597 TTGTTTTTTA
Statistics
Matches: 231, Mismatches: 42, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
56 2 0.01
58 49 0.21
59 165 0.71
60 15 0.06
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (58 bp):
CCCTAAAATTTCTAAAAATTACATTTTTACCCTCGAATTCCAAAAATTCCATTTTTGA
Found at i:658738 original size:28 final size:28
Alignment explanation
Indices: 658680--658738 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
658670 AAATTTTTCC
*
658680 AAAATTACCATTTTGCCCTCGAGAGTTA
1 AAAATTACCATTTTGCCCTCGAGAGTCA
658708 AAAATTACCATTTTGCCCTCGAGTA-TCA
1 AAAATTACCATTTTGCCCTCGAG-AGTCA
658736 AAA
1 AAA
658739 GTCTCATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.31
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCTCGAGAGTCA
Found at i:664648 original size:20 final size:20
Alignment explanation
Indices: 664625--664666 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
664615 ATCAAAGTTT
664625 AAACAGAGACA-CTGAAGTGC
1 AAACAGAGACATC-GAAGTGC
*
664645 AAACAGAGGCATCGAAGTGC
1 AAACAGAGACATCGAAGTGC
664665 AA
1 AA
664667 TCCCGTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.45, C:0.19, G:0.26, T:0.10
Consensus pattern (20 bp):
AAACAGAGACATCGAAGTGC
Found at i:665169 original size:13 final size:13
Alignment explanation
Indices: 665151--665195 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
665141 GCTCGTATTA
665151 AATTTTTTTATAT
1 AATTTTTTTATAT
665164 AATTTTTTTGA-A-
1 AATTTTTTT-ATAT
*
665176 AATATTTTTATAT
1 AATTTTTTTATAT
665189 AATTTTT
1 AATTTTT
665196 AAATTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.33
13 16 0.59
14 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (13 bp):
AATTTTTTTATAT
Found at i:666924 original size:88 final size:88
Alignment explanation
Indices: 666767--666935 Score: 286
Period size: 88 Copynumber: 1.9 Consensus size: 88
666757 ATGATTAAAA
* *
666767 TGACAAAATTCTTCCAACATAAATAATAATTTTATTTACAAAATTTAAATTACAAAATAGGTGAC
1 TGACAAAATTCTTCCAACATAAATAATAATTTTATTTACAAAATTTAAATTAAAAAATAGGTGAA
666832 ATTAATTATCCAGGCAGGCACTT
66 ATTAATTATCCAGGCAGGCACTT
* *
666855 TGACAAAATTCTTCCAA-ATAAATAATATTTTTATTTACAAATTTTAAATTAAAAAAATAGGTGA
1 TGACAAAATTCTTCCAACATAAATAATAATTTTATTTACAAAATTTAAATT-AAAAAATAGGTGA
666919 AATTAATTATCCAGGCA
65 AATTAATTATCCAGGCA
666936 CTTTATTTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 31 0.41
88 45 0.59
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.34
Consensus pattern (88 bp):
TGACAAAATTCTTCCAACATAAATAATAATTTTATTTACAAAATTTAAATTAAAAAATAGGTGAA
ATTAATTATCCAGGCAGGCACTT
Found at i:670506 original size:48 final size:48
Alignment explanation
Indices: 670452--670549 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
670442 AATCAATAAA
670452 AGTCTAGGAAGTAAATTCACCAACATTGTCAAGACAAATTGTCTTAAT
1 AGTCTAGGAAGTAAATTCACCAACATTGTCAAGACAAATTGTCTTAAT
*
670500 AGTCTAGGAAGTAAATTCACCAACATTGTCAAGACAAATTGTCTTGAT
1 AGTCTAGGAAGTAAATTCACCAACATTGTCAAGACAAATTGTCTTAAT
670548 AG
1 AG
670550 GGAAATCTAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (48 bp):
AGTCTAGGAAGTAAATTCACCAACATTGTCAAGACAAATTGTCTTAAT
Found at i:673162 original size:34 final size:34
Alignment explanation
Indices: 673097--673162 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
673087 ATAATATGAA
* * * **
673097 AAGTTAAAGAAGATGGAAGGTTAGACGTCAAGGG
1 AAGTTAAAGAAGATGAAAAGTTAAAAATCAAGGG
*
673131 AAGTTAAGGAAGATGAAAAGTTAAAAATCAAG
1 AAGTTAAAGAAGATGAAAAGTTAAAAATCAAG
673163 AGAGATGAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.48, C:0.05, G:0.29, T:0.18
Consensus pattern (34 bp):
AAGTTAAAGAAGATGAAAAGTTAAAAATCAAGGG
Found at i:676325 original size:39 final size:43
Alignment explanation
Indices: 676272--676365 Score: 133
Period size: 40 Copynumber: 2.3 Consensus size: 43
676262 ACTTAATTTT
*
676272 AAAATATATTTTAAATTTAA-ATTTTTATTATTT-TTT-TGT-A
1 AAAATA-ATTTTAAATTTAAGATTTTTATTATTTATTTGTATCA
*
676312 AAAATAATTTTAAATTTAAGTTTTTTATTATTTATTTGTATCA
1 AAAATAATTTTAAATTTAAGATTTTTATTATTTATTTGTATCA
676355 AAAATAATTTT
1 AAAATAATTTT
676366 TTTTAATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
39 13 0.27
40 18 0.38
41 3 0.06
42 2 0.04
43 12 0.25
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (43 bp):
AAAATAATTTTAAATTTAAGATTTTTATTATTTATTTGTATCA
Found at i:676379 original size:40 final size:37
Alignment explanation
Indices: 676272--676380 Score: 103
Period size: 40 Copynumber: 2.7 Consensus size: 37
676262 ACTTAATTTT
*
676272 AAAATATATTTTAAATTTAAATTTTTATTATTTTTTTGTA
1 AAAATA-ATTTT-AATTT-AATTTTTATTATTTTTTTATA
676312 AAAATAATTTTAAATTTAAGTTTTTTATTATTTATTTGTATCA
1 AAAATAATTTT-AATTTAA--TTTTTATTATTT-TTT-TAT-A
*
676355 AAAATAATTTT-TTTTAATTATTTATT
1 AAAATAATTTTAATTTAATT-TTTATT
676381 TTGAATTTGT
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
38 2 0.03
39 13 0.21
40 24 0.39
41 8 0.13
42 2 0.03
43 12 0.20
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (37 bp):
AAAATAATTTTAATTTAATTTTTATTATTTTTTTATA
Found at i:678374 original size:13 final size:13
Alignment explanation
Indices: 678356--678380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
678346 AGATATAAGC
678356 TATTTAAATATTT
1 TATTTAAATATTT
678369 TATTTAAATATT
1 TATTTAAATATT
678381 ATCTCAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTAAATATTT
Found at i:679283 original size:41 final size:41
Alignment explanation
Indices: 679194--679285 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 41
679184 TAAAAATTAT
* *
679194 TTATATTAAAAAATACTACCATAAATATAATAAATGTTTCA
1 TTATATTAAAAAATACTACAATAAATATAATAAATATTTCA
* * *
679235 ATGTATTAAAAAA-AC-ACAAATAAATATATATAAATATTTTA
1 TTATATTAAAAAATACTAC-AATAAATATA-ATAAATATTTCA
679276 TTATATTAAA
1 TTATATTAAA
679286 TATAATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
39 2 0.05
40 11 0.26
41 29 0.69
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (41 bp):
TTATATTAAAAAATACTACAATAAATATAATAAATATTTCA
Found at i:679437 original size:30 final size:31
Alignment explanation
Indices: 679372--679439 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
679362 AGTGATTTAA
679372 TATAA-ATATAGAAATATATATAATTATTAT
1 TATAACATATAGAAATATATATAATTATTAT
* *
679402 T-TAACATATATAAATA-ATATAA-TATTTTT
1 TATAACATATAGAAATATATATAATTA-TTAT
679431 TATAACATA
1 TATAACATA
679440 ATTTATTCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 2 0.06
29 13 0.39
30 18 0.55
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (31 bp):
TATAACATATAGAAATATATATAATTATTAT
Found at i:682157 original size:25 final size:26
Alignment explanation
Indices: 682106--682157 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
682096 TTATTATCGA
682106 TATATTATATTACATACAAAAATAAT
1 TATATTATATTACATACAAAAATAAT
*
682132 TATATT-TATCTA-ATATAAAAATAAT
1 TATATTATAT-TACATACAAAAATAAT
682157 T
1 T
682158 TGATACTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
TATATTATATTACATACAAAAATAAT
Found at i:682254 original size:20 final size:22
Alignment explanation
Indices: 682229--682270 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
682219 TTTTAATATT
682229 TATCCTAAACC-T-TTTTAAAA
1 TATCCTAAACCGTATTTTAAAA
682249 TATCCTAAACCGTATTTTAAAA
1 TATCCTAAACCGTATTTTAAAA
682271 AGGACCATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (22 bp):
TATCCTAAACCGTATTTTAAAA
Found at i:691740 original size:45 final size:45
Alignment explanation
Indices: 691691--691804 Score: 210
Period size: 45 Copynumber: 2.5 Consensus size: 45
691681 AGACTTGATG
691691 TATAAATGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATA
1 TATAAATGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATA
*
691736 TATAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATA
1 TATAAATGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATA
*
691781 TATAAATGGAAGACTTATGTCTCG
1 TATAAATGGAAGACTCATGTCTCG
691805 ATAAGAGCAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.30
Consensus pattern (45 bp):
TATAAATGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATA
Found at i:691813 original size:45 final size:45
Alignment explanation
Indices: 691691--691822 Score: 192
Period size: 45 Copynumber: 2.9 Consensus size: 45
691681 AGACTTGATG
* * *
691691 TATAAATGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATA
1 TATAAATGGAAGACTCATGTCTCGAGAAGAGCATGAGATTATATA
* *
691736 TATAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATA
1 TATAAATGGAAGACTCATGTCTCGAGAAGAGCATGAGATTATATA
* * *
691781 TATAAATGGAAGACTTATGTCTCGATAAGAGCATAAGATTAT
1 TATAAATGGAAGACTCATGTCTCGAGAAGAGCATGAGATTAT
691823 TGTAAATGGA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (45 bp):
TATAAATGGAAGACTCATGTCTCGAGAAGAGCATGAGATTATATA
Found at i:698343 original size:4 final size:4
Alignment explanation
Indices: 698336--698360 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
698326 TACATGAATA
698336 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
698361 CAATTAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:698595 original size:15 final size:15
Alignment explanation
Indices: 698588--698681 Score: 67
Period size: 15 Copynumber: 6.5 Consensus size: 15
698578 AATGACATAA
698588 AAATAAATAACAAAT
1 AAATAAATAACAAAT
*
698603 AAATAAATAA-AAACA
1 AAATAAATAACAAA-T
*
698618 AAATAAA-AA-TAAT
1 AAATAAATAACAAAT
698631 AAATAAATAA-AAATT
1 AAATAAATAACAAA-T
*
698646 AAATACTAA-AATAAAT
1 AAATA--AATAACAAAT
*
698662 GAATAAAT-ACAAAT
1 AAATAAATAACAAAT
698676 -AATAAA
1 AAATAAA
698682 ATAAAAGGGA
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
13 13 0.20
14 18 0.27
15 23 0.35
16 7 0.11
17 5 0.08
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.21
Consensus pattern (15 bp):
AAATAAATAACAAAT
Found at i:698597 original size:4 final size:4
Alignment explanation
Indices: 698588--698670 Score: 59
Period size: 4 Copynumber: 21.2 Consensus size: 4
698578 AATGACATAA
* *
698588 AAAT AAAT -AAC AAAT AAAT AAAT AAA- AACA- AAAT AAAA ATAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT
* * *
698635 AAAT AAA- AATT AAAT -ACT AAAAT AAAT GAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A
698671 CAAATAATAA
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
3 9 0.15
4 48 0.77
5 5 0.08
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:698602 original size:11 final size:10
Alignment explanation
Indices: 698570--698686 Score: 73
Period size: 11 Copynumber: 11.3 Consensus size: 10
698560 TAAAAGGTCA
698570 AAATATAAAAT
1 AAATA-AAAAT
*
698581 GACATAAAAAT
1 -AAATAAAAAT
698592 AAATAACAAAT
1 AAATAA-AAAT
698603 AAATAAATAA-
1 AAATAAA-AAT
* *
698613 AAACAAAATAA
1 AAATAAAA-AT
698624 AAATAATAAAT
1 AAATAA-AAAT
698635 AAATAAAAATT
1 AAATAAAAA-T
698646 AAATACTAAAAT
1 AAATA--AAAAT
*
698658 AAAT--GAAT
1 AAATAAAAAT
*
698666 AAATACAAAT
1 AAATAAAAAT
698676 -AAT-AAAAT
1 AAATAAAAAT
698684 AAA
1 AAA
698687 AGGGATTAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 25
0.72 0.07 0.21
Matches are distributed among these distances:
8 11 0.13
9 6 0.07
10 19 0.22
11 35 0.41
12 11 0.13
13 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:698619 original size:18 final size:18
Alignment explanation
Indices: 698588--698687 Score: 73
Period size: 18 Copynumber: 5.4 Consensus size: 18
698578 AATGACATAA
698588 AAATAAATAACAAATAAAT
1 AAATAAA-AACAAATAAAT
698607 AAATAAAAACAAA-ATAA-
1 AAATAAAAACAAATA-AAT
*
698624 AAATAATAAATAAATAAA-
1 AAATAA-AAACAAATAAAT
* *
698642 AATTAAATACTAAAATAAAT
1 AAATAAAAAC--AAATAAAT
* *
698662 GAATAAATACAAAT-AAT
1 AAATAAAAACAAATAAAT
698679 AAAATAAAA
1 -AAATAAAA
698688 GGGATTAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
17 12 0.18
18 31 0.47
19 15 0.23
20 8 0.12
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (18 bp):
AAATAAAAACAAATAAAT
Found at i:698627 original size:54 final size:53
Alignment explanation
Indices: 698569--698687 Score: 129
Period size: 54 Copynumber: 2.2 Consensus size: 53
698559 ATAAAAGGTC
*
698569 AAAATATAAAATGACATAAAAA-TAAATA-ACAAATAAATAAATAAAAACAAAATA
1 AAAATATAAAAT-AAATAAAAATTAAATACA-AAATAAATAAATAAAAAC-AAATA
* *
698623 AAAATA-ATAAATAAATAAAAATTAAATACTAAAATAAATGAATAAATACAAATA
1 AAAATATA-AAATAAATAAAAATTAAATAC-AAAATAAATAAATAAAAACAAATA
698677 ATAAA-ATAAAA
1 A-AAATATAAAA
698688 GGGATTAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
53 9 0.16
54 26 0.46
55 20 0.36
56 1 0.02
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (53 bp):
AAAATATAAAATAAATAAAAATTAAATACAAAATAAATAAATAAAAACAAATA
Found at i:698639 original size:36 final size:36
Alignment explanation
Indices: 698584--698687 Score: 115
Period size: 36 Copynumber: 2.8 Consensus size: 36
698574 ATAAAATGAC
698584 ATAAAAATAAATAACAAATAAATAAATAAAAAC-AAA
1 ATAAAAATAAATAACAAATAAA-AAATAAAAACTAAA
* * *
698620 ATAAAAAT-AATAAATAAATAAAAATTAAATACTAAA
1 ATAAAAATAAAT-AACAAATAAAAAATAAAAACTAAA
698656 ATAAATGAATAAAT-ACAAATAATAAAATAAAA
1 ATAAA--AATAAATAACAAATAA-AAAATAAAA
698688 GGGATTAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
35 11 0.20
36 25 0.45
37 7 0.12
38 10 0.18
39 3 0.05
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (36 bp):
ATAAAAATAAATAACAAATAAAAAATAAAAACTAAA
Found at i:698687 original size:31 final size:29
Alignment explanation
Indices: 698600--698687 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 29
698590 ATAAATAACA
*
698600 AATAAATAAAT-AAAAACAAAATAAAAAT
1 AATAAATAAATAAAAAATAAAATAAAAAT
*
698628 AATAAATAAAT-AAAAATTAAATACTAAAAT
1 AATAAATAAATAAAAAATAAAATA--AAAAT
*
698658 AAATGAATAAATACAAATAATAAAATAAAA
1 -AATAAATAAATA-AAA-AATAAAATAAAA
698688 GGGATTAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
28 21 0.42
30 5 0.10
31 10 0.20
32 3 0.06
33 3 0.06
34 8 0.16
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.22
Consensus pattern (29 bp):
AATAAATAAATAAAAAATAAAATAAAAAT
Found at i:705701 original size:22 final size:22
Alignment explanation
Indices: 705675--705719 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
705665 CTTTTTTGAA
705675 TGGTGATCTCGAAGAAGAAGTC
1 TGGTGATCTCGAAGAAGAAGTC
705697 TGGTGATCTCGAAGAAGAAGTC
1 TGGTGATCTCGAAGAAGAAGTC
705719 T
1 T
705720 ACATGGAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (22 bp):
TGGTGATCTCGAAGAAGAAGTC
Found at i:708619 original size:13 final size:13
Alignment explanation
Indices: 708601--708656 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
708591 TAATTTAAGT
708601 TATTATTAATTAA
1 TATTATTAATTAA
708614 TATTA-TAATATAA
1 TATTATTAAT-TAA
* * *
708627 TAGTATAAATTAT
1 TATTATTAATTAA
708640 TA-T-TTAATTAA
1 TATTATTAATTAA
708651 TATTAT
1 TATTAT
708657 CTTATTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
11 8 0.24
12 6 0.18
13 17 0.50
14 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
TATTATTAATTAA
Found at i:709330 original size:17 final size:18
Alignment explanation
Indices: 709308--709343 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
709298 TAAATGAGTT
709308 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
709325 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
709343 A
1 A
709344 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:709657 original size:18 final size:18
Alignment explanation
Indices: 709634--709670 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
709624 TTTGTGATCA
709634 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
709652 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
709670 A
1 A
709671 TACGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:714682 original size:24 final size:24
Alignment explanation
Indices: 714623--714685 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
714613 AGAAATAATT
*
714623 TTTCAATTAAACTCTGTTTAACTG
1 TTTCAATCAAACTCTGTTTAACTG
* **
714647 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTAACTG
* *
714671 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
714686 TATTAGTGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.48
Consensus pattern (24 bp):
TTTCAATCAAACTCTGTTTAACTG
Found at i:716812 original size:84 final size:84
Alignment explanation
Indices: 716671--716839 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
716661 TTATTTGACC
716671 TAAAAATTTAGCTTATAAATAGGCTCTTTGACACTCATTAGATACACTCATTAAAGTTGAGAACT
1 TAAAAATTTAGCTTATAAATAGGCTCTTTGACACTCATTAGATACACTCATTAAAGTTGAGAACT
716736 CCTAATACTTTTGGAGAAT
66 CCTAATACTTTTGGAGAAT
*
716755 TAAAAATTTAGCTTATAAATAGGCTCTTTGACACTCATTAGATATACTCATTAAAGTTGAGAACT
1 TAAAAATTTAGCTTATAAATAGGCTCTTTGACACTCATTAGATACACTCATTAAAGTTGAGAACT
716820 CCTAATACTTTTGGAGAAT
66 CCTAATACTTTTGGAGAAT
716839 T
1 T
716840 TAGTGTTTAC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (84 bp):
TAAAAATTTAGCTTATAAATAGGCTCTTTGACACTCATTAGATACACTCATTAAAGTTGAGAACT
CCTAATACTTTTGGAGAAT
Done.