Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold84
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: 4163231
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 246351 characters in sequence are not A, C, G, or T
File 2 of 11
Found at i:466932 original size:22 final size:22
Alignment explanation
Indices: 466902--466949 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
466892 CTACAATCAC
466902 TTCTAAAGGAAGTGAAGGAATA
1 TTCTAAAGGAAGTGAAGGAATA
*
466924 TTCTGAAGGAAGTGAAGGAATA
1 TTCTAAAGGAAGTGAAGGAATA
466946 TTCT
1 TTCT
466950 TAAGCCTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.06, G:0.27, T:0.27
Consensus pattern (22 bp):
TTCTAAAGGAAGTGAAGGAATA
Found at i:486629 original size:17 final size:16
Alignment explanation
Indices: 486603--486638 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
486593 TGAGAGCTAA
*
486603 GAGAGTTGAGAGAGGAT
1 GAGAGATGAGA-AGGAT
486620 GAGAGATGAGAAGGAT
1 GAGAGATGAGAAGGAT
486636 GAG
1 GAG
486639 GGATAAGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.47, T:0.14
Consensus pattern (16 bp):
GAGAGATGAGAAGGAT
Found at i:494463 original size:56 final size:52
Alignment explanation
Indices: 494397--494538 Score: 153
Period size: 50 Copynumber: 2.7 Consensus size: 52
494387 GGAATGAGAC
* * *
494397 CCCATGTAAGACTATGTCTAGGACATGGCATTGGCATTATTGAGGTTATGAGAGGT
1 CCCACGTAAGACCATGTCTAGGACATGGCATTGGCA-TATCGA-G--ATGAGAGGT
* * **
494453 CTCACGTAAGACCATGTCTGGGACATGGTGTTGG--TATCGAGATGAGAGGT
1 CCCACGTAAGACCATGTCTAGGACATGGCATTGGCATATCGAGATGAGAGGT
* *
494503 CCCCCGTAAGACCATGTCTAAGACATGGCATTGGCA
1 CCCACGTAAGACCATGTCTAGGACATGGCATTGGCA
494539 CTGATATGAG
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
50 37 0.52
52 1 0.01
53 5 0.07
56 28 0.39
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (52 bp):
CCCACGTAAGACCATGTCTAGGACATGGCATTGGCATATCGAGATGAGAGGT
Found at i:494502 original size:50 final size:50
Alignment explanation
Indices: 494402--494637 Score: 152
Period size: 50 Copynumber: 4.6 Consensus size: 50
494392 GAGACCCCAT
* * *
494402 GTAAGACTATGTCTAGGACATGGCATTGGCATTATTGAGGTTATGAGAGGTCTCAC
1 GTAAGACCATGTCTGGGACATGGCATTGGC---ACTGA-G--ATGAGAGGTCTCAC
** * * *
494458 GTAAGACCATGTCTGGGACATGGTGTTGGTA-TCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACT-GAGATGAGAGGTCTCAC
** * ** *
494508 GTAAGACCATGTCTAAGACATGGCATTGGCACTGATATGAGAACTCTCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCTCAC
* ** * * * * * ** * *
494558 GTAAGACCATATCTGGGTTATGGCATTTGCAGT-ATAGGAAACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCTCAC
*
494607 GTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
494638 TGTTATTATC
Statistics
Matches: 143, Mismatches: 35, Indels: 11
0.76 0.19 0.06
Matches are distributed among these distances:
49 37 0.26
50 75 0.52
51 1 0.01
52 2 0.01
53 3 0.02
56 25 0.17
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCTCAC
Found at i:494630 original size:49 final size:50
Alignment explanation
Indices: 494508--494634 Score: 143
Period size: 49 Copynumber: 2.6 Consensus size: 50
494498 GAGGTCCCCC
** * * *
494508 GTAAGACCATGTCTAAGACATGGCATTGGCACTGATATGAGAACTCTCAT
1 GTAAGACCATGTCTGGGACATGGCATTTGCACTGATAGGAGAACTCCCAT
* ** *
494558 GTAAGACCATATCTGGGTTATGGCATTTGCAGT-ATAGGA-AACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTTGCACTGATAGGAGAAC-TCCCAT
494607 GTAAGACCATGTCTGGGACATGGC-TTTG
1 GTAAGACCATGTCTGGGACATGGCATTTG
494635 GCATGTTATT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 7 0.11
49 31 0.48
50 26 0.41
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTTGCACTGATAGGAGAACTCCCAT
Found at i:495882 original size:42 final size:41
Alignment explanation
Indices: 495734--495887 Score: 161
Period size: 42 Copynumber: 3.7 Consensus size: 41
495724 AGCTCGTACA
* * *
495734 ATGCCAACGTCTCGGACGTGGTCTTACATGTAATCACATATCT
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAA-CACA-ATCT
* *
495777 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAACA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAACACAAT-CT
* * *
495818 ATTCCAATGTCCCAGACATGGTCTTACACGTAACACAAGTCT
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAACACAA-TCT
495860 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
495888 AGATAACATA
Statistics
Matches: 91, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
40 2 0.02
41 30 0.33
42 33 0.36
43 25 0.27
44 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAACACAATCT
Found at i:505221 original size:27 final size:27
Alignment explanation
Indices: 505191--505381 Score: 150
Period size: 27 Copynumber: 7.1 Consensus size: 27
505181 CCCAATATTT
* * * *
505191 GTAAAATGACCATAATGCCCCTATAAG
1 GTAAAATGATCGTAATACCCCTATAGG
* *
505218 GTAAAATGATCGTAATACCCTTGTAGG
1 GTAAAATGATCGTAATACCCCTATAGG
** * * *
505245 GTAAAATGATCAAAAAATCCTTATAGG
1 GTAAAATGATCGTAATACCCCTATAGG
* * * * *
505272 GTCAAATGACCGTAATGCCCTTGTAGG
1 GTAAAATGATCGTAATACCCCTATAGG
505299 GTAAAATGATCGTAATA-CCCTCATAGG
1 GTAAAATGATCGTAATACCCCT-ATAGG
* ** * * *
505326 GTTAAATGATCAAAATACTCCTGTAAG
1 GTAAAATGATCGTAATACCCCTATAGG
* *
505353 GTAAAATGATCGTAATGCCCCTAGAGG
1 GTAAAATGATCGTAATACCCCTATAGG
505380 GT
1 GT
505382 CAATGACTAT
Statistics
Matches: 124, Mismatches: 38, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
26 3 0.02
27 118 0.95
28 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (27 bp):
GTAAAATGATCGTAATACCCCTATAGG
Found at i:505279 original size:54 final size:54
Alignment explanation
Indices: 505212--505363 Score: 171
Period size: 54 Copynumber: 2.8 Consensus size: 54
505202 ATAATGCCCC
* *
505212 TATAAGGTAAAATGATCGTAATACCCTTGTAGGGTAAAATGATCAAAAAATCCT
1 TATAGGGTAAAATGATCGTAATACCCTTGTAGGGTAAAATGATCAAAAAACCCT
* * * ** *
505266 TATAGGGTCAAATGACCGTAATGCCCTTGTAGGGTAAAATGATCGTAATACCCT
1 TATAGGGTAAAATGATCGTAATACCCTTGTAGGGTAAAATGATCAAAAAACCCT
* * ** *
505320 CATAGGGTTAAATGATCAAAATACTCC-TGTAAGGTAAAATGATC
1 TATAGGGTAAAATGATCGTAATAC-CCTTGTAGGGTAAAATGATC
505364 GTAATGCCCC
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
54 80 0.98
55 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (54 bp):
TATAGGGTAAAATGATCGTAATACCCTTGTAGGGTAAAATGATCAAAAAACCCT
Found at i:505333 original size:81 final size:81
Alignment explanation
Indices: 505191--505375 Score: 248
Period size: 81 Copynumber: 2.3 Consensus size: 81
505181 CCCAATATTT
* **
505191 GTAAAATGACCATAATGCCCCTATAAGGTAAAATGATCGTAATACCCTTGTAGGGTAAAATGATC
1 GTAAAATGACCGTAATGCCCCTATAAGGTAAAATGATCGTAATACCCTCATAGGGTAAAATGATC
505256 AAAA-AATCCT-TATAGG
66 AAAATAATCCTGTA-A-G
* * * * *
505272 GTCAAATGACCGTAATGCCCTTGTAGGGTAAAATGATCGTAATACCCTCATAGGGTTAAATGATC
1 GTAAAATGACCGTAATGCCCCTATAAGGTAAAATGATCGTAATACCCTCATAGGGTAAAATGATC
*
505337 AAAATACTCCTGTAAG
66 AAAATAATCCTGTAAG
*
505353 GTAAAATGATCGTAATGCCCCTA
1 GTAAAATGACCGTAATGCCCCTA
505376 GAGGGTCAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 81 0.91
82 6 0.07
83 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (81 bp):
GTAAAATGACCGTAATGCCCCTATAAGGTAAAATGATCGTAATACCCTCATAGGGTAAAATGATC
AAAATAATCCTGTAAG
Found at i:505463 original size:24 final size:24
Alignment explanation
Indices: 505436--505492 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
505426 TGATGTAAAC
* *
505436 GACTCATTTGTCTGTGATTGGTAT
1 GACTGATTTGTCTGTGATTGGCAT
* * *
505460 GACTGATCTGTTTGTGATTTGCAT
1 GACTGATTTGTCTGTGATTGGCAT
505484 GACTGATTT
1 GACTGATTT
505493 TGAGTATGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.46
Consensus pattern (24 bp):
GACTGATTTGTCTGTGATTGGCAT
Found at i:505731 original size:32 final size:31
Alignment explanation
Indices: 505662--505738 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 31
505652 TGCTGCGATG
505662 CTACTGATGGCTTTGTGTCGATCATACTACCA
1 CTACTGATGGC-TTGTGTCGATCATACTACCA
* *
505694 TTACTGATGG-TTGTGTACCGATCATA-TCACTA
1 CTACTGATGGCTTGTGT--CGATCATACT-ACCA
505726 CTACTGATGGCTT
1 CTACTGATGGCTT
505739 TGTGCCAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 6 0.16
31 1 0.03
32 29 0.76
33 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (31 bp):
CTACTGATGGCTTGTGTCGATCATACTACCA
Found at i:511652 original size:16 final size:17
Alignment explanation
Indices: 511625--511660 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
511615 AAAGAGTTGA
511625 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
511642 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
511658 GAG
1 GAG
511661 GGATAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.53, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:520066 original size:10 final size:10
Alignment explanation
Indices: 520048--520086 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
520038 TTTCATGTGG
*
520048 TTCAGCTCAC
1 TTCAGCTCAA
*
520058 TTGAGCTCAA
1 TTCAGCTCAA
*
520068 GTCAGCTCAA
1 TTCAGCTCAA
520078 TTCAGCTCA
1 TTCAGCTCA
520087 TTGAGCTCGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (10 bp):
TTCAGCTCAA
Found at i:520074 original size:20 final size:20
Alignment explanation
Indices: 520049--520086 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
520039 TTCATGTGGT
* *
520049 TCAGCTCACTTGAGCTCAAG
1 TCAGCTCAATTCAGCTCAAG
520069 TCAGCTCAATTCAGCTCA
1 TCAGCTCAATTCAGCTCA
520087 TTGAGCTCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (20 bp):
TCAGCTCAATTCAGCTCAAG
Found at i:527519 original size:50 final size:50
Alignment explanation
Indices: 527439--527605 Score: 158
Period size: 50 Copynumber: 3.2 Consensus size: 50
527429 AGATACTATA
* * ** * *
527439 TCCCAGATATGGTCTTACATGA-GAGTTCTCATATCAATTCCCACGCCATG
1 TCCCAGACATGGTCTTAC-GGAGGACCTCTCATATCAATACCAACGCCATG
* **
527489 TCCCAGACATGGTCTTACGGAGGACCTCTCATCTCGGTACCAACGCCATG
1 TCCCAGACATGGTCTTACGGAGGACCTCTCATATCAATACCAACGCCATG
*
527539 TCCCAGACATGGTCTTACGTG-GGACCTCTCATAGCCTCAATAATGCCAATGCCATG
1 TCCCAGACATGGTCTTACG-GAGGACCTCTCATA---TCAAT-A--CCAACGCCATG
527595 TCCCAGACATG
1 TCCCAGACATG
527606 ACCTTACATG
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
49 2 0.02
50 68 0.71
51 1 0.01
53 3 0.03
54 1 0.01
56 21 0.22
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACGGAGGACCTCTCATATCAATACCAACGCCATG
Found at i:527876 original size:30 final size:29
Alignment explanation
Indices: 527828--527885 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
527818 TCTTTGACTC
527828 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTT-CCCCT
* * * *
527858 AAACTTTTGCATATTTACACTTTTCCCC
1 AAACTTTGGCAAAATTACAATTTTCCCC
527886 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.38
Consensus pattern (29 bp):
AAACTTTGGCAAAATTACAATTTTCCCCT
Found at i:534404 original size:24 final size:24
Alignment explanation
Indices: 534374--534419 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
534364 TATCATGACC
*
534374 TTTACTT-TTTTCTGTACTTACTCT
1 TTTACTTGTTTACT-TACTTACTCT
534398 TTTACTTGTTTACTTACTTACT
1 TTTACTTGTTTACTTACTTACT
534420 TACTGATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.15, C:0.20, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTACTTGTTTACTTACTTACTCT
Found at i:537561 original size:51 final size:54
Alignment explanation
Indices: 537449--537569 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 54
537439 AAACCAGGTC
* * * *
537449 AGTGAGTTAAACGGGCTAGTCAAACGAATGTGTAGTTGGCCGTATGACCCAGGTA
1 AGTGAGTTACACGGGCTAGTCAAACG-AGGCGTAGTTGGCCGTATGACCCAAGTA
* * *
537504 AGTGAGTTACACGGGCTAGTCACACG-GGCGT-G-TGGCCGTGTGACCCAAGTG
1 AGTGAGTTACACGGGCTAGTCAAACGAGGCGTAGTTGGCCGTATGACCCAAGTA
537555 AGTGAGTTACACGGG
1 AGTGAGTTACACGGG
537570 GTTGGACATG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 31 0.53
52 1 0.02
53 3 0.05
55 24 0.41
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (54 bp):
AGTGAGTTACACGGGCTAGTCAAACGAGGCGTAGTTGGCCGTATGACCCAAGTA
Found at i:546890 original size:22 final size:23
Alignment explanation
Indices: 546843--546890 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
546833 AACCCTATTT
*
546843 TCTAACTGAAAACCATACTTACC
1 TCTAACTGAAAACCATACTTAAC
*
546866 TCTAA-TGAAAACACCTA-TTAAC
1 TCTAACTGAAAAC-CATACTTAAC
546888 TCT
1 TCT
546891 TAATTCCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.40, C:0.27, G:0.04, T:0.29
Consensus pattern (23 bp):
TCTAACTGAAAACCATACTTAAC
Found at i:551094 original size:23 final size:23
Alignment explanation
Indices: 551067--551110 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
551057 TTCATGAAAA
*
551067 CATAAATGCT-TATATGTTATGTT
1 CATAAAAGCTATA-ATGTTATGTT
551090 CATAAAAGCTATAATGTTATG
1 CATAAAAGCTATAATGTTATG
551111 CAATGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (23 bp):
CATAAAAGCTATAATGTTATGTT
Found at i:558163 original size:11 final size:12
Alignment explanation
Indices: 558134--558168 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
558124 TGTCAAACAC
558134 AAATATCACAGA
1 AAATATCACAGA
*
558146 TAATATCACA-A
1 AAATATCACAGA
558157 AAATATCACAGA
1 AAATATCACAGA
558169 GAAGTTCCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.20
Consensus pattern (12 bp):
AAATATCACAGA
Found at i:565419 original size:23 final size:23
Alignment explanation
Indices: 565392--565437 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
565382 CAAAATTAAT
565392 ATTAA-CTAAATACAAATGAATGA
1 ATTAATCTAAATAC-AATGAATGA
*
565415 ATTAATCTAAATGCAATGAATGA
1 ATTAATCTAAATACAATGAATGA
565438 GATGAGATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (23 bp):
ATTAATCTAAATACAATGAATGA
Found at i:576964 original size:21 final size:21
Alignment explanation
Indices: 576914--576968 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
576904 GTTCTCCTAA
576914 GACAAATTAAACATACATTAG
1 GACAAATTAAACATACATTAG
* ** *
576935 AACTTATTAAACATGCATTAG
1 GACAAATTAAACATACATTAG
*
576956 GACACATTAAACA
1 GACAAATTAAACA
576969 CGCCTAGAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.25
Consensus pattern (21 bp):
GACAAATTAAACATACATTAG
Found at i:579558 original size:10 final size:10
Alignment explanation
Indices: 579540--579587 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
579530 CAAATCTGTC
579540 AAAAA-TAAT
1 AAAAATTAAT
579549 AAAAATTAAT
1 AAAAATTAAT
*
579559 AAAAATTTGAT
1 AAAAA-TTAAT
579570 ATAAAATTAAT
1 A-AAAATTAAT
*
579581 TAAAATT
1 AAAAATT
579588 CAAAATCTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
9 5 0.15
10 15 0.45
11 9 0.27
12 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAAATTAAT
Found at i:587256 original size:18 final size:19
Alignment explanation
Indices: 587230--587266 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
587220 AATTTTGGAA
587230 TGGAAAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
*
587248 TGGAGAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
587267 ATGTGAGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Found at i:587853 original size:22 final size:21
Alignment explanation
Indices: 587811--587859 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
587801 TGCAAATCTG
587811 TCAAAA-ATAATAAAAAATAA
1 TCAAAATATAATAAAAAATAA
* *
587831 TCAAAATATGATATAAAATTAA
1 TCAAAATATAATA-AAAAATAA
*
587853 TTAAAAT
1 TCAAAAT
587860 TCAACATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.25
21 5 0.21
22 13 0.54
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
TCAAAATATAATAAAAAATAA
Found at i:591051 original size:22 final size:22
Alignment explanation
Indices: 591023--591067 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
591013 ATTATGATGA
591023 TTGATATG-ATGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
591045 TTGATATGTATGTGATTATATT
1 TTGATATGTATGAGATTATATT
591067 T
1 T
591068 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:610928 original size:19 final size:18
Alignment explanation
Indices: 610884--610930 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
610874 AATAGTTTCG
*
610884 AAAGGAAGA-AAAAATAA
1 AAAGGAAAATAAAAATAA
* *
610901 AGAGAAAAATAAAAATAAA
1 AAAGGAAAATAAAAAT-AA
610920 AAAGGAAAATA
1 AAAGGAAAATA
610931 TATCTTATAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 11 0.48
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (18 bp):
AAAGGAAAATAAAAATAA
Found at i:616020 original size:25 final size:25
Alignment explanation
Indices: 615992--616080 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 25
615982 TTACCAACAC
615992 TCAGCTCGTATGAGCTTACTGTTAT
1 TCAGCTCGTATGAGCTTACTGTTAT
* * *
616017 TCAGCTCGGAGGAGCTTA-TCATTAT
1 TCAGCTCGTATGAGCTTACT-GTTAT
* * *
616042 TCAGCTCGAAAGAGCTTACCGTT-T
1 TCAGCTCGTATGAGCTTACTGTTAT
*
616066 ACAGCTCGTATGAGC
1 TCAGCTCGTATGAGC
616081 ATACATGTAC
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
24 14 0.27
25 38 0.73
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (25 bp):
TCAGCTCGTATGAGCTTACTGTTAT
Found at i:624713 original size:19 final size:19
Alignment explanation
Indices: 624689--624727 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
624679 GGATGAAACC
*
624689 ATGAGGGTATGCATTTATT
1 ATGAGGGTATGCATTGATT
*
624708 ATGAGGTTATGCATTGATT
1 ATGAGGGTATGCATTGATT
624727 A
1 A
624728 CCGACAGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41
Consensus pattern (19 bp):
ATGAGGGTATGCATTGATT
Found at i:641111 original size:36 final size:36
Alignment explanation
Indices: 641064--641135 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
641054 GCATCACTAA
641064 ACTGATACTTGTCGCTATGTTGCAACAGCGGATGAT
1 ACTGATACTTGTCGCTATGTTGCAACAGCGGATGAT
641100 ACTGATACTTGTCGCTATGTTGCAACAGCGGATGAT
1 ACTGATACTTGTCGCTATGTTGCAACAGCGGATGAT
641136 CGATGTCGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (36 bp):
ACTGATACTTGTCGCTATGTTGCAACAGCGGATGAT
Found at i:648822 original size:12 final size:12
Alignment explanation
Indices: 648807--648848 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
648797 AAAATAAAAT
648807 AAAAATTTGAAAA
1 AAAAATTTG-AAA
648820 AAAAATTTGAAA
1 AAAAATTTGAAA
* *
648832 AAAAAATTCAAA
1 AAAAATTTGAAA
648844 AAAAA
1 AAAAA
648849 GAGTTTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (12 bp):
AAAAATTTGAAA
Found at i:648823 original size:13 final size:13
Alignment explanation
Indices: 648802--648848 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
648792 TAAAAAAAAT
648802 AAAATAAAAATTTG
1 AAAA-AAAAATTTG
648816 AAAAAAAAATTTG
1 AAAAAAAAATTTG
*
648829 AAAAAAAAA-TTC
1 AAAAAAAAATTTG
648841 AAAAAAAA
1 AAAAAAAA
648849 GAGTTTGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 10 0.31
13 18 0.56
14 4 0.12
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (13 bp):
AAAAAAAAATTTG
Found at i:648935 original size:26 final size:26
Alignment explanation
Indices: 648896--648955 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
648886 GTATTGAAGA
*
648896 AAAAAAAAGAAAAAAAATTCGGAATT-
1 AAAAAAAAGAAAAAAAA-TCGAAATTG
*
648922 AAAAAAAAGGAAAAAAATCGAAATTG
1 AAAAAAAAGAAAAAAAATCGAAATTG
648948 AAAAAAAA
1 AAAAAAAA
648956 AAGAGTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 7 0.23
26 24 0.77
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (26 bp):
AAAAAAAAGAAAAAAAATCGAAATTG
Found at i:656772 original size:19 final size:19
Alignment explanation
Indices: 656748--656787 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
656738 ATCCATGTGG
656748 TTTGATCCTCGATTTGGCT
1 TTTGATCCTCGATTTGGCT
656767 TTTGATCCTCGATTTGGCT
1 TTTGATCCTCGATTTGGCT
656786 TT
1 TT
656788 CTTACAAGTG
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:0.10, C:0.20, G:0.20, T:0.50
Consensus pattern (19 bp):
TTTGATCCTCGATTTGGCT
Found at i:661981 original size:11 final size:11
Alignment explanation
Indices: 661965--661990 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
661955 AGCTAAAGAA
661965 AACTAGAATTG
1 AACTAGAATTG
661976 AACTAGAATTG
1 AACTAGAATTG
661987 AACT
1 AACT
661991 TTGAGTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (11 bp):
AACTAGAATTG
Found at i:672232 original size:13 final size:12
Alignment explanation
Indices: 672216--672249 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
672206 AAAAAAAATC
672216 AAAAAAATTCGAA
1 AAAAAAATTC-AA
*
672229 AAAAATATTCAA
1 AAAAAAATTCAA
672241 AAAAAAATT
1 AAAAAAATT
672250 TGTATTCGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:681348 original size:12 final size:12
Alignment explanation
Indices: 681333--681362 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
681323 TCAAGTTGTT
681333 ACACGGCCTAGC
1 ACACGGCCTAGC
681345 ACACGGCCTAGC
1 ACACGGCCTAGC
681357 ACACGG
1 ACACGG
681363 GCGTTTCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.40, G:0.27, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:688690 original size:322 final size:322
Alignment explanation
Indices: 687719--688688 Score: 1823
Period size: 322 Copynumber: 3.0 Consensus size: 322
687709 CAATCTTTTG
687719 TTTTAAAAATTAATGAGTTTTTCACTTGTTACAGATGATAAATAATCTATTTAGAAATCAAATAA
1 TTTTAAAAATTAATGAGTTTTTCACTTGTTACAGATGATAAATAATCTATTTAGAAATCAAATAA
687784 TACATAATGAAGAGTTATAATTTAATCCTACTTAGTAGAGGGTTAAAAAGTTATAAACCTAATAG
66 TACATAATGAAGAGTTATAATTTAATCCTACTTAGTAGAGGGTTAAAAAGTTATAAACCTAATAG
* *
687849 AACTAAACTAAACAAACGCCAATGGGTAGTTTAAATTCGAATAACAAAGTTATAAACCTAATAAA
131 AACTAAACTAAACAAACGCCAGTGGTTAGTTTAAATTCGAATAACAAAGTTATAAACCTAATAAA
*
687914 ACTAACCTAATAGAAATTATATTTAATATTTCTACATTCAACGAGATTACTATGACCAAATGATT
196 ACTAACCTAATAGAAATTATATTTAATATTTCTACATTCAACGAGTTTACTATGACCAAATGATT
*
687979 TATTTCCATTCTCAAACTTCATTTATTTTGAAAACCATAAATTCATTTCCAGGTCATTTTCA
261 TATTTCCATTCTCAAACTTCATTTATTTTGAAAACCATAAATTCATTTCCAGGCCATTTTCA
*
688041 TTTTAAAAATTTATGAGTTTTTCACTTGTTACAGATGATAAATAATCTATTTAGAAATCAAATAA
1 TTTTAAAAATTAATGAGTTTTTCACTTGTTACAGATGATAAATAATCTATTTAGAAATCAAATAA
688106 TACATAATGAAGAGTTATAATTTAATCCTACTTAGTAGAGGGTTAAAAAGTTATAAACCTAATAG
66 TACATAATGAAGAGTTATAATTTAATCCTACTTAGTAGAGGGTTAAAAAGTTATAAACCTAATAG
* *
688171 AACTAAACGAAACAAACGCCAGTGGTTAGTTTAAATTCGAATAAAAAAGTTATAAACCTAATAAA
131 AACTAAACTAAACAAACGCCAGTGGTTAGTTTAAATTCGAATAACAAAGTTATAAACCTAATAAA
*
688236 ACTAACCTAATAGAAATTATATTTAATATTTCTACATTCAACGAGTTTAATATGACCAAATGATT
196 ACTAACCTAATAGAAATTATATTTAATATTTCTACATTCAACGAGTTTACTATGACCAAATGATT
688301 TATTTCCATTCTCAAACTTCATTTATTTTGAAAACCATAAATTCATTTCCAGGCCATTTTCA
261 TATTTCCATTCTCAAACTTCATTTATTTTGAAAACCATAAATTCATTTCCAGGCCATTTTCA
*
688363 TTTTTAAAATTAATGAGTTTTTCACTTGTTACAGATGATAAATAATCTATTTAGAAATCAAATAA
1 TTTTAAAAATTAATGAGTTTTTCACTTGTTACAGATGATAAATAATCTATTTAGAAATCAAATAA
688428 TACATAATGAAGAGTTATAATTTAATCCTACTTAGTAGAGGGTTAAAAAGTTATAAACCTAATAG
66 TACATAATGAAGAGTTATAATTTAATCCTACTTAGTAGAGGGTTAAAAAGTTATAAACCTAATAG
*
688493 AACTAAACTAAACAAACGCCAGTGGTTAGTTTAAATTCGAATAACAAAGTTATAAACCTAATAGA
131 AACTAAACTAAACAAACGCCAGTGGTTAGTTTAAATTCGAATAACAAAGTTATAAACCTAATAAA
* *
688558 ACTAACCTAATAGAAATTATATTTCATATTTCTACACTCAACGAGTTTACTATGACCAAATGATT
196 ACTAACCTAATAGAAATTATATTTAATATTTCTACATTCAACGAGTTTACTATGACCAAATGATT
*
688623 TATTTCCATCCTCAAACTTCATTTATTTTGAAAACCATAAATTCATTTCCAGGCCATTTTCA
261 TATTTCCATTCTCAAACTTCATTTATTTTGAAAACCATAAATTCATTTCCAGGCCATTTTCA
688685 TTTT
1 TTTT
688689 TATTTTTGAG
Statistics
Matches: 631, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
322 631 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (322 bp):
TTTTAAAAATTAATGAGTTTTTCACTTGTTACAGATGATAAATAATCTATTTAGAAATCAAATAA
TACATAATGAAGAGTTATAATTTAATCCTACTTAGTAGAGGGTTAAAAAGTTATAAACCTAATAG
AACTAAACTAAACAAACGCCAGTGGTTAGTTTAAATTCGAATAACAAAGTTATAAACCTAATAAA
ACTAACCTAATAGAAATTATATTTAATATTTCTACATTCAACGAGTTTACTATGACCAAATGATT
TATTTCCATTCTCAAACTTCATTTATTTTGAAAACCATAAATTCATTTCCAGGCCATTTTCA
Found at i:697489 original size:8 final size:8
Alignment explanation
Indices: 697468--697527 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 8
697458 TAAATTTTAA
*
697468 TTTAATTA
1 TTTAATTT
*
697476 TCTAATTT
1 TTTAATTT
697484 TTTAATTT
1 TTTAATTT
697492 TTTAATTT
1 TTTAATTT
* *
697500 ATTAATAT
1 TTTAATTT
*
697508 TTTATATTA
1 TTTA-ATTT
*
697517 ATTAATTT
1 TTTAATTT
697525 TTT
1 TTT
697528 CAGAAAATAA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
8 35 0.88
9 5 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAATTT
Found at i:697527 original size:17 final size:16
Alignment explanation
Indices: 697485--697527 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
697475 ATCTAATTTT
*
697485 TTAATTTTTTAATTTA
1 TTAATTTTTTAATTAA
*
697501 TTAATATTTTATATTAA
1 TTAATTTTTTA-ATTAA
697518 TTAATTTTTT
1 TTAATTTTTT
697528 CAGAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATTTTTTAATTAA
Found at i:705698 original size:21 final size:20
Alignment explanation
Indices: 705665--705713 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
705655 CATGTATGAT
*
705665 TAAATTA-AATAATAAAATA
1 TAAATTATATTAATAAAATA
*
705684 TAAAGTTATATTAATGAAATA
1 TAAA-TTATATTAATAAAATA
*
705705 TTAATTATA
1 TAAATTATA
705714 CAATGTCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 13 0.52
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
TAAATTATATTAATAAAATA
Found at i:705984 original size:19 final size:19
Alignment explanation
Indices: 705962--705999 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
705952 TCAATCATCC
705962 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
705981 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
706000 AATCTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:710839 original size:34 final size:34
Alignment explanation
Indices: 710795--710862 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
710785 AATTTCTAAG
* *
710795 CCGCTGTGTTTGTTGTTAGAGAAAGATACAGTGT
1 CCGCTATGTTTATTGTTAGAGAAAGATACAGTGT
710829 CCGCTATGTTTATTGTTAGAGAAAGATACAGTGT
1 CCGCTATGTTTATTGTTAGAGAAAGATACAGTGT
710863 TCGATTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (34 bp):
CCGCTATGTTTATTGTTAGAGAAAGATACAGTGT
Found at i:716794 original size:19 final size:19
Alignment explanation
Indices: 716772--716809 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
716762 TCAATCATCC
716772 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
716791 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
716810 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:741643 original size:67 final size:68
Alignment explanation
Indices: 741518--741645 Score: 215
Period size: 68 Copynumber: 1.9 Consensus size: 68
741508 TTTAACAAAA
*
741518 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTATTTTTCTTCAAAACACATGGTTGCTGC
1 TTTTTTCTCTCATTCTCTCTCTTGCCAAACACCACTTATTTTTCTTCAAAACACATGGTTGCTGC
741583 CAT
66 CAT
*
741586 TTTTTTCTCTCATTCTCTCTCTTGCCAAACACCA-TT-TTTCTTCTTCAAAACATATGGTTG
1 TTTTTTCTCTCATTCTCTCTCTTGCCAAACACCACTTATTT-TTCTTCAAAACACATGGTTG
741646 GCTCATTTCA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
66 3 0.05
67 21 0.37
68 33 0.58
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.45
Consensus pattern (68 bp):
TTTTTTCTCTCATTCTCTCTCTTGCCAAACACCACTTATTTTTCTTCAAAACACATGGTTGCTGC
CAT
Found at i:742682 original size:17 final size:16
Alignment explanation
Indices: 742650--742688 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
742640 ACATAATTAT
*
742650 TAGTAAAAGGTTAATA
1 TAGTAAAAGGTAAATA
742666 TAGTAATAAGGTAAATA
1 TAGTAA-AAGGTAAATA
742683 TAGTAA
1 TAGTAA
742689 CTTTATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (16 bp):
TAGTAAAAGGTAAATA
Found at i:743616 original size:42 final size:42
Alignment explanation
Indices: 743557--743653 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
743547 TATGAATGGA
* *
743557 ACTAAGTGTGCGGAATTAAAATAATGATGTTGGATAATGGGC
1 ACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACGGGC
* * *
743599 ACTAAGTGTGTGAAATTAAAATGATGATGTTGTATAACGGGC
1 ACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACGGGC
743641 ACTAAGTGTGCGA
1 ACTAAGTGTGCGA
743654 TACCGAGAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.35, C:0.08, G:0.28, T:0.29
Consensus pattern (42 bp):
ACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACGGGC
Found at i:769403 original size:12 final size:12
Alignment explanation
Indices: 769386--769410 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
769376 TTAAATGAAT
769386 TAAAAAGCCAAA
1 TAAAAAGCCAAA
769398 TAAAAAGCCAAA
1 TAAAAAGCCAAA
769410 T
1 T
769411 TTTGCTCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.16, G:0.08, T:0.12
Consensus pattern (12 bp):
TAAAAAGCCAAA
Found at i:801025 original size:24 final size:24
Alignment explanation
Indices: 800998--801044 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
800988 ATTTATTTTC
800998 TTTTTTGTTT-CTCTATTTGTTTGA
1 TTTTTT-TTTACTCTATTTGTTTGA
*
801022 TTTTTTTTTACTCTTTTTGTTTG
1 TTTTTTTTTACTCTATTTGTTTG
801045 GAGTATATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.06, C:0.09, G:0.11, T:0.74
Consensus pattern (24 bp):
TTTTTTTTTACTCTATTTGTTTGA
Found at i:803263 original size:34 final size:35
Alignment explanation
Indices: 803205--803271 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
803195 CAAACATTAG
803205 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
803240 AAAATATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
803272 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:803377 original size:2 final size:2
Alignment explanation
Indices: 803370--803395 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
803360 ATGGATACAT
803370 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
803396 CAAAAAAAGC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:806066 original size:28 final size:28
Alignment explanation
Indices: 806026--806081 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
806016 AAAATCATCA
806026 TTTAAGTGGGTGGATTTACCCTTGTTGG
1 TTTAAGTGGGTGGATTTACCCTTGTTGG
806054 TTTAAGTGGGTGGATTTACCCTTGTTGG
1 TTTAAGTGGGTGGATTTACCCTTGTTGG
806082 CATTATGTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.11, G:0.32, T:0.43
Consensus pattern (28 bp):
TTTAAGTGGGTGGATTTACCCTTGTTGG
Found at i:817320 original size:57 final size:57
Alignment explanation
Indices: 817203--817321 Score: 148
Period size: 57 Copynumber: 2.1 Consensus size: 57
817193 GTTAGGTCAA
* * * * * *
817203 ATCTTGTCTTTTTAATCCCTTGATACTTGTTTCCAGTTATGCCCTTAATTTTTGCAG
1 ATCTTGCCTTCTTAATCCCTTGATACTTGCTGCCAGTTATGCCCTTAATCTTGGCAG
* * * *
817260 ATCTTGCCTTCTTAATTCCTTGATCCTTGCTGCCAGTTATGCCCTTGATCTTGGCTG
1 ATCTTGCCTTCTTAATCCCTTGATACTTGCTGCCAGTTATGCCCTTAATCTTGGCAG
817317 ATCTT
1 ATCTT
817322 TTGTTGTTTG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.15, C:0.24, G:0.14, T:0.46
Consensus pattern (57 bp):
ATCTTGCCTTCTTAATCCCTTGATACTTGCTGCCAGTTATGCCCTTAATCTTGGCAG
Found at i:818979 original size:18 final size:19
Alignment explanation
Indices: 818946--818981 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
818936 AAGATTTATA
*
818946 TATTAAGAACCGAATAAAC
1 TATTAAGAACCAAATAAAC
818965 TATTAA-AACCAAATAAA
1 TATTAAGAACCAAATAAA
818982 TCAAATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (19 bp):
TATTAAGAACCAAATAAAC
Found at i:825021 original size:27 final size:27
Alignment explanation
Indices: 824991--825076 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 27
824981 GACTACCGCA
* *
824991 TGTTTATTGTCCCGACGGGCTATCCCG
1 TGTTTACTGTCCCGACGGACTATCCCG
**
825018 TGTTTACTGTTTCGACGGACTATCCCG
1 TGTTTACTGTCCCGACGGACTATCCCG
* * * *
825045 TGATCACTGTCCTGACGGACTATCCTG
1 TGTTTACTGTCCCGACGGACTATCCCG
825072 TGTTT
1 TGTTT
825077 GCTATTCTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.14, C:0.27, G:0.23, T:0.36
Consensus pattern (27 bp):
TGTTTACTGTCCCGACGGACTATCCCG
Found at i:828161 original size:14 final size:15
Alignment explanation
Indices: 828144--828172 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
828134 TTTTTTTCTA
828144 TAGATTT-TTCCTTG
1 TAGATTTCTTCCTTG
828158 TAGATTTCTTCCTTG
1 TAGATTTCTTCCTTG
828173 GTAAAGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (15 bp):
TAGATTTCTTCCTTG
Found at i:833647 original size:20 final size:20
Alignment explanation
Indices: 833622--833663 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
833612 AGATTCAATC
833622 AACATCATTGAGGGTGGATT
1 AACATCATTGAGGGTGGATT
833642 AACATCATTGAGGGTGGATT
1 AACATCATTGAGGGTGGATT
833662 AA
1 AA
833664 AACATGACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (20 bp):
AACATCATTGAGGGTGGATT
Found at i:842424 original size:45 final size:45
Alignment explanation
Indices: 842338--842426 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
842328 TGTGAACCAA
* ** * *
842338 ACATCATAGATTAGTAAGGTGGTTTCTATATGTTGATTCCACCGG
1 ACATCATAGATTAATAAGGTGGTCGCTATATGCTGAATCCACCGG
* *
842383 ACATCATTGATTAATAAGGTGGTCGCTATGTGCTGAATCCACCG
1 ACATCATAGATTAATAAGGTGGTCGCTATATGCTGAATCCACCG
842427 AGTATCTGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (45 bp):
ACATCATAGATTAATAAGGTGGTCGCTATATGCTGAATCCACCGG
Found at i:847158 original size:13 final size:13
Alignment explanation
Indices: 847140--847172 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
847130 GGGACACACA
847140 GCCGTGTCGCCTG
1 GCCGTGTCGCCTG
847153 GCCGTGTCGCCTG
1 GCCGTGTCGCCTG
847166 GCCGTGT
1 GCCGTGT
847173 GTCACACACG
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:0.00, C:0.36, G:0.39, T:0.24
Consensus pattern (13 bp):
GCCGTGTCGCCTG
Found at i:865080 original size:13 final size:14
Alignment explanation
Indices: 865051--865080 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
865041 AAAATTGCTT
865051 AAAAATCAAGCCAA
1 AAAAATCAAGCCAA
*
865065 AAAAATCAAGTCAA
1 AAAAATCAAGCCAA
865079 AA
1 AA
865081 GCCACGAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGCCAA
Found at i:865229 original size:11 final size:11
Alignment explanation
Indices: 865215--865246 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
865205 CTCACGCATC
865215 CCTCAATCATT
1 CCTCAATCATT
865226 CCTCAATCATT
1 CCTCAATCATT
865237 -CTC-ATCATT
1 CCTCAATCATT
865246 C
1 C
865247 ATCATTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.30
10 3 0.15
11 11 0.55
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (11 bp):
CCTCAATCATT
Found at i:873160 original size:24 final size:24
Alignment explanation
Indices: 873128--873176 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
873118 TGAGAATGCC
873128 AAAATGTGTAAAGAAAGATCAAAG
1 AAAATGTGTAAAGAAAGATCAAAG
873152 AAAATGTGTAAAGAAAGATCAAAG
1 AAAATGTGTAAAGAAAGATCAAAG
873176 A
1 A
873177 GATGGTACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.04, G:0.20, T:0.16
Consensus pattern (24 bp):
AAAATGTGTAAAGAAAGATCAAAG
Found at i:874001 original size:156 final size:156
Alignment explanation
Indices: 873712--874018 Score: 596
Period size: 156 Copynumber: 2.0 Consensus size: 156
873702 AATCAGTTTT
*
873712 TTTAGTAAGATATAGTCTGAGTTTGAGGCCCAAGACAGCAAAAAGGAGGGAAAAATTCATGCCTT
1 TTTAGTAAGATATAGTATGAGTTTGAGGCCCAAGACAGCAAAAAGGAGGGAAAAATTCATGCCTT
*
873777 GCCGTCACACCCATTGCTTGCCGCCCAAATAACCCTAATGTAGCTAATTTTTTGCTACATGTTGC
66 GCCGTCACACCCATTGCTTGCCGCCCAAATAACCCTAATGTAGCTAATTTTTTGCTACATGTTCC
873842 CCTAATTTTTCCTATATAAACCTCTG
131 CCTAATTTTTCCTATATAAACCTCTG
873868 TTTAGTAAGATATAGTATGAGTTTGAGGCCCAAGACAGCAAAAAGGAGGGAAAAATTCATGCCTT
1 TTTAGTAAGATATAGTATGAGTTTGAGGCCCAAGACAGCAAAAAGGAGGGAAAAATTCATGCCTT
873933 GCCGTCACACCCATTGCTTGCCGCCCAAATAACCCTAATGTAGCTAATTTTTTGCTACATGTTCC
66 GCCGTCACACCCATTGCTTGCCGCCCAAATAACCCTAATGTAGCTAATTTTTTGCTACATGTTCC
873998 CCTAATTTTTCCTATATAAAC
131 CCTAATTTTTCCTATATAAAC
874019 TTCTTTTCAT
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 149 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (156 bp):
TTTAGTAAGATATAGTATGAGTTTGAGGCCCAAGACAGCAAAAAGGAGGGAAAAATTCATGCCTT
GCCGTCACACCCATTGCTTGCCGCCCAAATAACCCTAATGTAGCTAATTTTTTGCTACATGTTCC
CCTAATTTTTCCTATATAAACCTCTG
Found at i:877696 original size:27 final size:27
Alignment explanation
Indices: 877665--877871 Score: 245
Period size: 27 Copynumber: 7.7 Consensus size: 27
877655 AGCTGAAAAG
* * **
877665 CCCCCAGAGGGTAAATTGATTGAAATA
1 CCCCCATAGGGTAAAATGACCGAAATA
*
877692 CCCCCATAGGGTAAATTGACCGAAATA
1 CCCCCATAGGGTAAAATGACCGAAATA
*
877719 CCCCCATAGGGTAAAATGACCAAAATA
1 CCCCCATAGGGTAAAATGACCGAAATA
* *
877746 CCTCCATAGGGTAAAATGATCGAAATA
1 CCCCCATAGGGTAAAATGACCGAAATA
* * *
877773 CCCGC-TAGGGTACAATGACCAAAATA
1 CCCCCATAGGGTAAAATGACCGAAATA
**
877799 CCCTAATAGGGTAAAATGACCGAAATA
1 CCCCCATAGGGTAAAATGACCGAAATA
* * *
877826 CCCCTATAAGATAAAATGACCGAAATA
1 CCCCCATAGGGTAAAATGACCGAAATA
* *
877853 CCTCCATTGGGTAAAATGA
1 CCCCCATAGGGTAAAATGA
877872 GTGTTATACC
Statistics
Matches: 153, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
26 21 0.14
27 132 0.86
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (27 bp):
CCCCCATAGGGTAAAATGACCGAAATA
Found at i:877808 original size:80 final size:81
Alignment explanation
Indices: 877672--877867 Score: 245
Period size: 80 Copynumber: 2.4 Consensus size: 81
877662 AAGCCCCCAG
* * * *
877672 AGGGTAAATTGATTGAAATACCCCCATAGGGTAAATTGACCGAAATACCCCCATAGGGTAAAATG
1 AGGGTAAAATGATCGAAATACCCCCATAGGGTAAATTGACCAAAATACCCCAATAGGGTAAAATG
877737 ACCAAAATACCTCC-AT
66 ACCAAAATACC-CCTAT
* *
877753 AGGGTAAAATGATCGAAATACCCGC-TAGGGTACAA-TGACCAAAATACCCTAATAGGGTAAAAT
1 AGGGTAAAATGATCGAAATACCCCCATAGGGTA-AATTGACCAAAATACCCCAATAGGGTAAAAT
*
877816 GACCGAAATACCCCTAT
65 GACCAAAATACCCCTAT
* * * * *
877833 AAGATAAAATGACCGAAATACCTCCATTGGGTAAA
1 AGGGTAAAATGATCGAAATACCCCCATAGGGTAAA
877868 ATGAGTGTTA
Statistics
Matches: 99, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
79 2 0.02
80 67 0.68
81 30 0.30
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (81 bp):
AGGGTAAAATGATCGAAATACCCCCATAGGGTAAATTGACCAAAATACCCCAATAGGGTAAAATG
ACCAAAATACCCCTAT
Found at i:877881 original size:54 final size:53
Alignment explanation
Indices: 877687--877899 Score: 189
Period size: 54 Copynumber: 4.0 Consensus size: 53
877677 AAATTGATTG
* * * * * *
877687 AAATACCCCCATAGGGTAAATTGACCGAAATACCCCCATAGGGTAAAATGACCA
1 AAATACCTCCATAGGGTAAAATGA-TGAAATACCCCTATAAGATAAAATGACCA
* * *
877741 AAATACCTCCATAGGGTAAAATGATCGAAATACCCGC--TAGGGTACAATGACCA
1 AAATACCTCCATAGGGTAAAATGAT-GAAATACCC-CTATAAGATAAAATGACCA
* * *
877794 AAATACC-CTAATAGGGTAAAATGACCGAAATACCCCTATAAGATAAAATGACCG
1 AAATACCTC-CATAGGGTAAAATGA-TGAAATACCCCTATAAGATAAAATGACCA
* ** ** *
877848 AAATACCTCCATTGGGTAAAATGAGTGTTATACCCCTAGGAGATGAAATGAC
1 AAATACCTCCATAGGGTAAAATGA-TGAAATACCCCTATAAGATAAAATGAC
877900 TGTTATGGCC
Statistics
Matches: 133, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
52 2 0.02
53 45 0.34
54 84 0.63
55 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (53 bp):
AAATACCTCCATAGGGTAAAATGATGAAATACCCCTATAAGATAAAATGACCA
Found at i:878158 original size:25 final size:26
Alignment explanation
Indices: 878106--878185 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
878096 TTTGCCACAT
* *
878106 ATACTTTTACTGGCATCTTTGCTACG
1 ATACTATTACTGGCATCTTTGCTGCG
* *
878132 ATACTATTACT-GCAGCTTTGTTGCG
1 ATACTATTACTGGCATCTTTGCTGCG
878157 ATACTATTACTGGCATCTTTGCTGCG
1 ATACTATTACTGGCATCTTTGCTGCG
878183 ATA
1 ATA
878186 TTGGTGTGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 22 0.47
26 25 0.53
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (26 bp):
ATACTATTACTGGCATCTTTGCTGCG
Found at i:878514 original size:28 final size:28
Alignment explanation
Indices: 878287--878508 Score: 257
Period size: 28 Copynumber: 7.9 Consensus size: 28
878277 TATTGCACTG
* *
878287 CATTGTTACTTTATTGGGCTAAGACCCA
1 CATTGTTACTGTATTGGGCTAAGGCCCA
* *
878315 CACTGATT-TTGTATTGGGCTAAGGCCCA
1 CATTG-TTACTGTATTGGGCTAAGGCCCA
* * *
878343 TATTGTTACTATTTTGGGCTAAGGCCCA
1 CATTGTTACTGTATTGGGCTAAGGCCCA
* *
878371 TATTGTTACTATATTGGGCTAAGGCCCA
1 CATTGTTACTGTATTGGGCTAAGGCCCA
* *
878399 CATTGTTATTGTATCGGGCTAAGGCCCA
1 CATTGTTACTGTATTGGGCTAAGGCCCA
* ** *
878427 CATTGTTATTGTATCAGGCTAAGACCCA
1 CATTGTTACTGTATTGGGCTAAGGCCCA
* *
878455 CATTATTACTGTATTGGGCTAAGGTCCA
1 CATTGTTACTGTATTGGGCTAAGGCCCA
* *
878483 CACTGTTACTGTAATGGGCTAAGGCC
1 CATTGTTACTGTATTGGGCTAAGGCC
878509 TACACTATAC
Statistics
Matches: 166, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
27 2 0.01
28 162 0.98
29 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (28 bp):
CATTGTTACTGTATTGGGCTAAGGCCCA
Found at i:879828 original size:53 final size:53
Alignment explanation
Indices: 879748--879890 Score: 216
Period size: 53 Copynumber: 2.7 Consensus size: 53
879738 CAAAGTAGGG
879748 TAAAATGATCGAAATAGCCCCATAGGGTAAAATGACCAAAATACCCC-AGAGGA
1 TAAAATGATCGAAATA-CCCCATAGGGTAAAATGACCAAAATACCCCTAGAGGA
* * *
879801 TAAAATGATCGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCTATAGGG
1 TAAAATGATCGAAATACCCC-ATAGGGTAAAATGACCAAAATACCCCTAGAGGA
*
879855 TAAAATGACCGAAATACCCCCATAGGGTAAAATGAC
1 TAAAATGATCGAAATA-CCCCATAGGGTAAAATGAC
879891 TGTTATACCC
Statistics
Matches: 83, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
52 4 0.05
53 41 0.49
54 34 0.41
55 4 0.05
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.17
Consensus pattern (53 bp):
TAAAATGATCGAAATACCCCATAGGGTAAAATGACCAAAATACCCCTAGAGGA
Found at i:879900 original size:27 final size:27
Alignment explanation
Indices: 879743--879890 Score: 217
Period size: 27 Copynumber: 5.5 Consensus size: 27
879733 GACCTCAAAG
* *
879743 TAGGGTAAAATGATCGAAATAGCCCCA
1 TAGGGTAAAATGACCGAAATACCCCCA
*
879770 TAGGGTAAAATGACCAAAATA-CCCCA
1 TAGGGTAAAATGACCGAAATACCCCCA
* * * *
879796 GAGGATAAAATGATCGAAATACCCCTA
1 TAGGGTAAAATGACCGAAATACCCCCA
*
879823 TAGGGTAAAATGACCGAAATACCCCTA
1 TAGGGTAAAATGACCGAAATACCCCCA
879850 TAGGGTAAAATGACCGAAATACCCCCA
1 TAGGGTAAAATGACCGAAATACCCCCA
879877 TAGGGTAAAATGAC
1 TAGGGTAAAATGAC
879891 TGTTATACCC
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
26 22 0.20
27 87 0.80
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (27 bp):
TAGGGTAAAATGACCGAAATACCCCCA
Found at i:880304 original size:28 final size:28
Alignment explanation
Indices: 880260--880432 Score: 143
Period size: 28 Copynumber: 6.2 Consensus size: 28
880250 ACTACACTGT
* * *
880260 TACTGTATTGGGCTAAGGCCCACAGTAA
1 TACTGTATTGGGTTAAGGCCCAAACTAA
* *
880288 -ATCTGTATTAGGTTAAGGCCCAAACTAT
1 TA-CTGTATTGGGTTAAGGCCCAAACTAA
* * **
880316 TACTGTATTGGGTTAAGGCCTAAATTGT
1 TACTGTATTGGGTTAAGGCCCAAACTAA
* * **
880344 TACTATATTGGGTTAAGGCCCACACTGT
1 TACTGTATTGGGTTAAGGCCCAAACTAA
* * * **
880372 TACTGTATTGGGCTAAGGCCTACACTGT
1 TACTGTATTGGGTTAAGGCCCAAACTAA
* *
880400 TACTGTATTGGGCTAAGGCCCACACT-A
1 TACTGTATTGGGTTAAGGCCCAAACTAA
880427 TACTGT
1 TACTGT
880433 CACTGAATAG
Statistics
Matches: 125, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
27 7 0.06
28 117 0.94
29 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (28 bp):
TACTGTATTGGGTTAAGGCCCAAACTAA
Found at i:880358 original size:56 final size:56
Alignment explanation
Indices: 880253--880432 Score: 204
Period size: 56 Copynumber: 3.2 Consensus size: 56
880243 TTATTGCACT
* * * * * *
880253 ACACTGTTACTGTATTGGGCTAAGGCC--CACAGTAAATCTGTATTAGGTTAAGGCCC
1 ACACTATTACTGTATTGGGCTAAGGCCTAAACTGT-TA-CTATATTGGGTTAAGGCCC
* * *
880309 AAACTATTACTGTATTGGGTTAAGGCCTAAATTGTTACTATATTGGGTTAAGGCCC
1 ACACTATTACTGTATTGGGCTAAGGCCTAAACTGTTACTATATTGGGTTAAGGCCC
* * * *
880365 ACACTGTTACTGTATTGGGCTAAGGCCTACACTGTTACTGTATTGGGCTAAGGCCC
1 ACACTATTACTGTATTGGGCTAAGGCCTAAACTGTTACTATATTGGGTTAAGGCCC
880421 ACACTA-TACTGT
1 ACACTATTACTGT
880433 CACTGAATAG
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
55 6 0.06
56 95 0.90
57 1 0.01
58 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (56 bp):
ACACTATTACTGTATTGGGCTAAGGCCTAAACTGTTACTATATTGGGTTAAGGCCC
Found at i:880403 original size:84 final size:84
Alignment explanation
Indices: 880257--880419 Score: 213
Period size: 84 Copynumber: 1.9 Consensus size: 84
880247 TGCACTACAC
* *
880257 TGTTACTGTATTGGGCTAAGGCCCACAGTAAATCTGTATTAGGTTAAGGCCCAAACTATTACTGT
1 TGTTACTATATTGGGCTAAGGCCCACAGTAAATCTGTATTAGGCTAAGGCCCAAACTATTACTGT
*
880322 ATTGGGTTAAGGCCTAAAT
66 ATTGGGCTAAGGCCTAAAT
* * * * * *
880341 TGTTACTATATTGGGTTAAGGCCCACACTGT-TA-CTGTATTGGGCTAAGGCCTACACTGTTACT
1 TGTTACTATATTGGGCTAAGGCCCACA--GTAAATCTGTATTAGGCTAAGGCCCAAACTATTACT
880404 GTATTGGGCTAAGGCC
64 GTATTGGGCTAAGGCC
880420 CACACTATAC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 65 0.96
85 1 0.01
86 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
TGTTACTATATTGGGCTAAGGCCCACAGTAAATCTGTATTAGGCTAAGGCCCAAACTATTACTGT
ATTGGGCTAAGGCCTAAAT
Found at i:881333 original size:23 final size:24
Alignment explanation
Indices: 881292--881338 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
881282 CAATAAAATA
881292 TAAAATTATATTTAATAATTCATTT
1 TAAAATTATATTTAATAATT-ATTT
*
881317 TAAAA-TAT-TTTATTAATTATTT
1 TAAAATTATATTTAATAATTATTT
881339 GGGTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 9 0.43
24 3 0.14
25 5 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TAAAATTATATTTAATAATTATTT
Found at i:896143 original size:44 final size:44
Alignment explanation
Indices: 896080--896167 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
896070 TTAAAATTTA
896080 CATAGAATTTTTGTGAATTGTGAATAATTATGAAT-TGTACTAGT
1 CATAGAATTTTTGTGAATTGTGAATAATTATG-ATCTGTACTAGT
896124 CATAGAATTTTTGTGAATTGTGAATAATTATGATCTGTACTAGT
1 CATAGAATTTTTGTGAATTGTGAATAATTATGATCTGTACTAGT
896168 ATATGAAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 2 0.05
44 41 0.95
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (44 bp):
CATAGAATTTTTGTGAATTGTGAATAATTATGATCTGTACTAGT
Found at i:905620 original size:43 final size:44
Alignment explanation
Indices: 905568--905654 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 44
905558 TTCTCTGTTC
905568 AGTTTCAGATCTGATCGTTTAGAGTTTTCTTAGAA-TTTTCCTG
1 AGTTTCAGATCTGATCGTTTAGAGTTTTCTTAGAAGTTTTCCTG
905611 AGTTTCAGATCTGATCGTTTAGAGTTTTCTTAGAAGTTTTCCTG
1 AGTTTCAGATCTGATCGTTTAGAGTTTTCTTAGAAGTTTTCCTG
905655 TGACTTGACA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 35 0.81
44 8 0.19
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.46
Consensus pattern (44 bp):
AGTTTCAGATCTGATCGTTTAGAGTTTTCTTAGAAGTTTTCCTG
Found at i:906576 original size:13 final size:13
Alignment explanation
Indices: 906543--906580 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
906533 TTTCATGTCC
*
906543 ACACAGCC-TGAG
1 ACACAGCCGTGTG
*
906555 ACACGGCCGTGTG
1 ACACAGCCGTGTG
906568 ACACAGCCGTGTG
1 ACACAGCCGTGTG
906581 TGACACACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.13
Consensus pattern (13 bp):
ACACAGCCGTGTG
Found at i:912600 original size:22 final size:22
Alignment explanation
Indices: 912575--912619 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
912565 ATTATGATGA
912575 TTGATATGT-TGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
912597 TTGATATGTATGTGATTATATT
1 TTGATATGTATGAGATTATATT
912619 T
1 T
912620 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:926024 original size:11 final size:11
Alignment explanation
Indices: 926008--926036 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
925998 GTTGATAAAG
926008 TGTAATTATAT
1 TGTAATTATAT
926019 TGTAATTATAT
1 TGTAATTATAT
926030 TGTAATT
1 TGTAATT
926037 CCTTATGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (11 bp):
TGTAATTATAT
Found at i:933218 original size:31 final size:32
Alignment explanation
Indices: 933165--933231 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 32
933155 ACTATCATAA
** * *
933165 TATATGAATATGTGTGTGTTGT-GATATTTGTC
1 TATATGAATATGTGACTATTGTGGA-AATTGTC
933197 TATATG-ATATGTGACTATTGTGGAAATTGTC
1 TATATGAATATGTGACTATTGTGGAAATTGTC
933228 TATA
1 TATA
933232 ACTATGTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
31 22 0.73
32 8 0.27
ACGTcount: A:0.27, C:0.04, G:0.22, T:0.46
Consensus pattern (32 bp):
TATATGAATATGTGACTATTGTGGAAATTGTC
Found at i:941139 original size:34 final size:34
Alignment explanation
Indices: 941096--941182 Score: 138
Period size: 34 Copynumber: 2.6 Consensus size: 34
941086 CTATAGTGCC
941096 TTGGTGTGGTGTAGTTATCACTCTATCGAGCCAT
1 TTGGTGTGGTGTAGTTATCACTCTATCGAGCCAT
* * *
941130 TTGGTGTGGTGTAGTTATCACTTTATTGAGCTAT
1 TTGGTGTGGTGTAGTTATCACTCTATCGAGCCAT
*
941164 TTAGTGTGGTGTAGTTATC
1 TTGGTGTGGTGTAGTTATC
941183 CACGTATCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.44
Consensus pattern (34 bp):
TTGGTGTGGTGTAGTTATCACTCTATCGAGCCAT
Found at i:947856 original size:34 final size:34
Alignment explanation
Indices: 947786--947870 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
947776 CTACGATGCC
*
947786 TTGGTGTGGTGTAGTTATCGCTCTATCGAACAAT
1 TTGGTGTGGTGTAGTTATCACTCTATCGAACAAT
* * * *
947820 TTGGTGTGTTGTAGTTATCACTCTATTGAGCTAT
1 TTGGTGTGGTGTAGTTATCACTCTATCGAACAAT
* *
947854 TTGGTATAGTGTAGTTA
1 TTGGTGTGGTGTAGTTA
947871 CCTACGTATC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.44
Consensus pattern (34 bp):
TTGGTGTGGTGTAGTTATCACTCTATCGAACAAT
Found at i:951449 original size:15 final size:14
Alignment explanation
Indices: 951418--951452 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
951408 ATTTTGTATG
*
951418 AAAATTTTAATTTT
1 AAAATTTTAAATTT
951432 AAAATTTTAAAATTT
1 AAAATTTT-AAATTT
951447 AAAATT
1 AAAATT
951453 GAAATGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAAATTTTAAATTT
Found at i:952571 original size:61 final size:61
Alignment explanation
Indices: 952461--952603 Score: 169
Period size: 61 Copynumber: 2.3 Consensus size: 61
952451 ATTAAGAAAC
* * *
952461 CATCATTGTCGAGCAATCCAGGGTGGTAAGCAATTGCTACCGGGGAACCTGAGATGGCAAT
1 CATCGTTGTCGAGCAATCCAGGGTGGTAAGCAATTGCTACCAGGCAACCTGAGATGGCAAT
* * * * ** * *
952522 CATCGTTGTCAAGCAATCCAGTGTGGTAAGCCATTGTTTTCAGGCAACCTGGGATGGCAGT
1 CATCGTTGTCGAGCAATCCAGGGTGGTAAGCAATTGCTACCAGGCAACCTGAGATGGCAAT
* *
952583 CATTGTTGTCGGGCAATCCAG
1 CATCGTTGTCGAGCAATCCAG
952604 AATGACATTA
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (61 bp):
CATCGTTGTCGAGCAATCCAGGGTGGTAAGCAATTGCTACCAGGCAACCTGAGATGGCAAT
Found at i:964584 original size:20 final size:20
Alignment explanation
Indices: 964538--964576 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
964528 TACAAATGAC
964538 ATTTGAATTTGATTATTTGAT
1 ATTT-AATTTGATTATTTGAT
964559 ATTTAATTTGA-TATTTGA
1 ATTTAATTTGATTATTTGA
964577 ATGGTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (20 bp):
ATTTAATTTGATTATTTGAT
Found at i:965599 original size:18 final size:19
Alignment explanation
Indices: 965573--965614 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
965563 TTTTAACTTC
965573 TTTTAAT-AATAACAAT-TA
1 TTTTAATAAATAA-AATATA
*
965591 TTTTTATAAATAAAATATA
1 TTTTAATAAATAAAATATA
965610 TTTTA
1 TTTTA
965615 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTAATAAATAAAATATA
Found at i:975112 original size:32 final size:33
Alignment explanation
Indices: 975060--975138 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
975050 TCTTTTTCAA
* * *
975060 TATCAGTAACAGTTTGGGCCTTAGCCCATC-TCAG
1 TATCAGTAGCAG-TAGGGCCTTAGCACATCAT-AG
*
975094 TA-CAGTATCAGTAGGGCCTTAGCACATCATAG
1 TATCAGTAGCAGTAGGGCCTTAGCACATCATAG
975126 TATCAGTAGCAGT
1 TATCAGTAGCAGT
975139 CATGCAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 19 0.49
33 18 0.46
34 2 0.05
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (33 bp):
TATCAGTAGCAGTAGGGCCTTAGCACATCATAG
Found at i:979144 original size:27 final size:26
Alignment explanation
Indices: 979105--979218 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 26
979095 AGAGGTCAAT
**
979105 AAATGACCGAAATACCCTCATAGGGTA
1 AAATGACTAAAATACCC-CATAGGGTA
* *
979132 AAATAACTAAAATACCCCTATTGGGTA
1 AAATGACTAAAATACCCC-ATAGGGTA
* *
979159 AAATGACTGAAATACCCCCAAAGGGTA
1 AAATGACTAAAATA-CCCCATAGGGTA
979186 AAATGA-TCAAAATACCCACATAGGGTA
1 AAATGACT-AAAATACCC-CATAGGGTA
979213 AAATGA
1 AAATGA
979219 GTGTTATACC
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
26 5 0.07
27 64 0.88
28 4 0.05
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (26 bp):
AAATGACTAAAATACCCCATAGGGTA
Found at i:979229 original size:54 final size:54
Alignment explanation
Indices: 979105--979218 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
979095 AGAGGTCAAT
* * * *
979105 AAATGACCGAAATACCCTCATAGGGTAAAATAACTAAAATACCCCTATTGGGTA
1 AAATGACTGAAATACCCCCAAAGGGTAAAATAACTAAAATACCCCTATAGGGTA
*
979159 AAATGACTGAAATACCCCCAAAGGGTAAAATGA-TCAAAATACCCAC-ATAGGGTA
1 AAATGACTGAAATACCCCCAAAGGGTAAAATAACT-AAAATACCC-CTATAGGGTA
979213 AAATGA
1 AAATGA
979219 GTGTTATACC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
53 1 0.02
54 51 0.96
55 1 0.02
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (54 bp):
AAATGACTGAAATACCCCCAAAGGGTAAAATAACTAAAATACCCCTATAGGGTA
Found at i:979428 original size:26 final size:26
Alignment explanation
Indices: 979383--979445 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
979373 TGGAGCTAGT
* * *
979383 ATACTATTATTGGTAGCTTTGCTGCA
1 ATACTATTACTGGCAACTTTGCTGCA
* *
979409 ATACTATTACTGGCAACTTTGTTGCG
1 ATACTATTACTGGCAACTTTGCTGCA
*
979435 ATACGATTACT
1 ATACTATTACT
979446 CGTTGGTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (26 bp):
ATACTATTACTGGCAACTTTGCTGCA
Found at i:979617 original size:33 final size:33
Alignment explanation
Indices: 979560--979631 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
979550 TGCATTATTG
* * * *
979560 CACTGTACTGATACTGTATTGGGCTAAGGCCCA
1 CACTGTACTGATACGGAATAGGGCTAAGACCCA
* *
979593 CACTGTACTGTTACGGAATAGGGCTTAGACCCA
1 CACTGTACTGATACGGAATAGGGCTAAGACCCA
*
979626 GACTGT
1 CACTGT
979632 CATTGCTTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (33 bp):
CACTGTACTGATACGGAATAGGGCTAAGACCCA
Found at i:981099 original size:13 final size:13
Alignment explanation
Indices: 981081--981106 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
981071 AATGTGGACG
981081 CCTAAAGAAAGGA
1 CCTAAAGAAAGGA
981094 CCTAAAGAAAGGA
1 CCTAAAGAAAGGA
981107 ATTTTTGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (13 bp):
CCTAAAGAAAGGA
Found at i:992746 original size:41 final size:42
Alignment explanation
Indices: 992641--992752 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 42
992631 TTCTGATATA
* * *
992641 TGTTATCGTGTAAGACCACGTCTGGGGCATTGGCATCGACTTG
1 TGTTA-CGTGTAAGACCATGTCTGGGACATTAGCATCGACTTG
*
992684 TGTTACGTTTAAGACCATGTCTGGGACATTAGCATCGTA-TT-
1 TGTTACGTGTAAGACCATGTCTGGGACATTAGCATCG-ACTTG
992725 TGTTACGTGTAAGAACC-TGTCTGGGACA
1 TGTTACGTGTAAG-ACCATGTCTGGGACA
992753 GTGGCGTAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
41 23 0.37
42 33 0.53
43 6 0.10
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (42 bp):
TGTTACGTGTAAGACCATGTCTGGGACATTAGCATCGACTTG
Found at i:997402 original size:27 final size:27
Alignment explanation
Indices: 997364--997478 Score: 230
Period size: 27 Copynumber: 4.3 Consensus size: 27
997354 CTAGGCTGAA
997364 TGGGCCGCACAAACATGTGGGCCCACT
1 TGGGCCGCACAAACATGTGGGCCCACT
997391 TGGGCCGCACAAACATGTGGGCCCACT
1 TGGGCCGCACAAACATGTGGGCCCACT
997418 TGGGCCGCACAAACATGTGGGCCCACT
1 TGGGCCGCACAAACATGTGGGCCCACT
997445 TGGGCCGCACAAACATGTGGGCCCACT
1 TGGGCCGCACAAACATGTGGGCCCACT
997472 TGGGCCG
1 TGGGCCG
997479 AGTAATGGGC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (27 bp):
TGGGCCGCACAAACATGTGGGCCCACT
Found at i:997626 original size:27 final size:27
Alignment explanation
Indices: 997570--997629 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
997560 GAGGTCAATG
*
997570 AATGACCAAAATACCCCTATAGGGTAA
1 AATGACCAAAATACCCCTATAGGATAA
* *
997597 AATGACCGAAATACCCCTA-AGAGATGA
1 AATGACCAAAATACCCCTATAG-GATAA
997624 AATGAC
1 AATGAC
997630 TGATATGGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.17
Consensus pattern (27 bp):
AATGACCAAAATACCCCTATAGGATAA
Found at i:1018067 original size:37 final size:37
Alignment explanation
Indices: 1018011--1018105 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
1018001 CTTAGTGCCA
* *
1018011 TGGCATGTTATCAGG-TGGATTAGGTCTTACGAGCATT
1 TGGCATGTTTTC-GGTTGGATTAGATCTTACGAGCATT
* * * *
1018048 TGGCGTGTTTTTGGTTGGATTAGATCTTATGAGTATT
1 TGGCATGTTTTCGGTTGGATTAGATCTTACGAGCATT
1018085 TGGCATGTTTTCGGTTGGATT
1 TGGCATGTTTTCGGTTGGATT
1018106 GCTTGTGTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 2 0.04
37 47 0.96
ACGTcount: A:0.17, C:0.09, G:0.31, T:0.43
Consensus pattern (37 bp):
TGGCATGTTTTCGGTTGGATTAGATCTTACGAGCATT
Found at i:1026262 original size:9 final size:9
Alignment explanation
Indices: 1026248--1026274 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1026238 ATAATTACAT
1026248 TTAGTCACA
1 TTAGTCACA
1026257 TTAGTCACA
1 TTAGTCACA
1026266 TTAGTCACA
1 TTAGTCACA
1026275 GTCTATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (9 bp):
TTAGTCACA
Found at i:1036415 original size:115 final size:116
Alignment explanation
Indices: 1036238--1036484 Score: 347
Period size: 115 Copynumber: 2.1 Consensus size: 116
1036228 GGTTGAAACC
* * *
1036238 ATCCCTTTTAATTAATCGATGGTTGTCACCAACCCTTTTCATAGTTGATGGTCGCCACCATCCCT
1 ATCCCTTTTCA-TATTCGATGGTCGTCACCAACCCTTTTCATAGTTGATGGTCGCCACCATCCCT
** *
1036303 TTTTGTAATCGATAG-CTGAAGCTATCCATTTTCATAATCGACAACCGAAGCT
65 TTTCATAATCGATAGTC-GAAGCTATCCATATTCATAATCGACAACCGAAGCT
* *
1036355 ATCCCTTTTCATATTCGATGGTCGTCACCATCCC-TTTCATAGTTGATGGTCGTCACCATCCCTT
1 ATCCCTTTTCATATTCGATGGTCGTCACCAACCCTTTTCATAGTTGATGGTCGCCACCATCCCTT
* * * *
1036419 TTCATAATCGATAGTCGAAGCTATCCCTATTCATATTCGATAGCCGAAGCT
66 TTCATAATCGATAGTCGAAGCTATCCATATTCATAATCGACAACCGAAGCT
1036470 ATCCC-TTTCATATTC
1 ATCCCTTTTCATATTC
1036485 AATGACCAAA
Statistics
Matches: 117, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
114 10 0.09
115 76 0.65
116 21 0.18
117 10 0.09
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (116 bp):
ATCCCTTTTCATATTCGATGGTCGTCACCAACCCTTTTCATAGTTGATGGTCGCCACCATCCCTT
TTCATAATCGATAGTCGAAGCTATCCATATTCATAATCGACAACCGAAGCT
Found at i:1036435 original size:29 final size:29
Alignment explanation
Indices: 1036235--1036461 Score: 131
Period size: 29 Copynumber: 7.8 Consensus size: 29
1036225 GATGGTTGAA
* * *
1036235 ACCATCCCTTTTAATTAATCGATGGTTGTC
1 ACCATCCCTTTTCA-TAATCGATAGTCGTC
* * * * *
1036265 ACCAACCCTTTTCATAGTTGATGGTCGCC
1 ACCATCCCTTTTCATAATCGATAGTCGTC
** *
1036294 ACCATCCCTTTTTGTAATCGATAG-C-TGA
1 ACCATCCCTTTTCATAATCGATAGTCGT-C
* * * ** *
1036322 AGCTATCCATTTTCATAATCGACAACCG-A
1 A-CCATCCCTTTTCATAATCGATAGTCGTC
* * *
1036351 AGCTATCCCTTTTCATATTCGATGGTCGTC
1 A-CCATCCCTTTTCATAATCGATAGTCGTC
* * *
1036381 ACCATCCC-TTTCATAGTTGATGGTCGTC
1 ACCATCCCTTTTCATAATCGATAGTCGTC
*
1036409 ACCATCCCTTTTCATAATCGATAGTCG-A
1 ACCATCCCTTTTCATAATCGATAGTCGTC
* * *
1036437 AGCTATCCCTATTCATATTCGATAG
1 A-CCATCCCTTTTCATAATCGATAG
1036462 CCGAAGCTAT
Statistics
Matches: 153, Mismatches: 37, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
28 29 0.19
29 110 0.72
30 14 0.09
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (29 bp):
ACCATCCCTTTTCATAATCGATAGTCGTC
Found at i:1036452 original size:86 final size:86
Alignment explanation
Indices: 1036326--1036538 Score: 250
Period size: 86 Copynumber: 2.5 Consensus size: 86
1036316 AGCTGAAGCT
* * ** * * *
1036326 ATCCATTTTCATAATCGACAACCGAAGCTATCCCTTTTCATATTCGATGGTCGTCA-CCATCCCT
1 ATCCCTTTTCATAATCGATAGTCGAAGCTATCCCTTTTCATATTCGATAGCCG-AAGCCATCCCT
* ** ***
1036390 TTCATAGTT-GATGGTCGTCACC
65 TTCATA-TTCAATGACCAAAACC
* *
1036412 ATCCCTTTTCATAATCGATAGTCGAAGCTATCCCTATTCATATTCGATAGCCGAAGCTATCCCTT
1 ATCCCTTTTCATAATCGATAGTCGAAGCTATCCCTTTTCATATTCGATAGCCGAAGCCATCCCTT
*
1036477 TCATATTCAATGACCAAAACT
66 TCATATTCAATGACCAAAACC
1036498 ATCCCTTTTCATAATCGATAGTCGAAGCTATCCCTTTTCAT
1 ATCCCTTTTCATAATCGATAGTCGAAGCTATCCCTTTTCAT
1036539 TGGTCGATGA
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
85 3 0.03
86 105 0.97
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (86 bp):
ATCCCTTTTCATAATCGATAGTCGAAGCTATCCCTTTTCATATTCGATAGCCGAAGCCATCCCTT
TCATATTCAATGACCAAAACC
Found at i:1036466 original size:29 final size:29
Alignment explanation
Indices: 1036297--1036538 Score: 190
Period size: 29 Copynumber: 8.4 Consensus size: 29
1036287 GGTCGCCACC
** * *
1036297 ATCCCTTTTTGTAATCGATAGCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
* * * *
1036326 ATCCATTTTCATAATCGACAACCGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
* * * *
1036355 ATCCCTTTTCATATTCGATGGTCGTCA-CC
1 ATCCCTTTTCATATTCGATAGCCG-AAGCT
* * * *
1036384 ATCCC-TTTCATAGTT-GATGGTCGTCA-CC
1 ATCCCTTTTCATA-TTCGATAGCCG-AAGCT
* *
1036412 ATCCCTTTTCATAATCGATAGTCGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
*
1036441 ATCCCTATTCATATTCGATAGCCGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
* * *
1036470 ATCCC-TTTCATATTCAAT-GACCAAAACT
1 ATCCCTTTTCATATTCGATAG-CCGAAGCT
* *
1036498 ATCCCTTTTCATAATCGATAGTCGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
1036527 ATCCCTTTTCAT
1 ATCCCTTTTCAT
1036539 TGGTCGATGA
Statistics
Matches: 175, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
27 1 0.01
28 49 0.28
29 123 0.70
30 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (29 bp):
ATCCCTTTTCATATTCGATAGCCGAAGCT
Found at i:1036479 original size:57 final size:58
Alignment explanation
Indices: 1036297--1036538 Score: 199
Period size: 57 Copynumber: 4.2 Consensus size: 58
1036287 GGTCGCCACC
** * * *
1036297 ATCCCTTTTTGTAATCGATAG-CTGAAGCTATCCATTTTCATAATCGACAACCGAAGCT
1 ATCCCTTTTCATAATCGATAGTC-GAAGCTATCCCTTTTCATAATCGATAGCCGAAGCT
* * * * * * * * * *
1036355 ATCCCTTTTCATATTCGATGGTCGTCA-CCATCCC-TTTCATAGTTGATGGTCGTCA-CC
1 ATCCCTTTTCATAATCGATAGTCG-AAGCTATCCCTTTTCATAATCGATAGCCG-AAGCT
* *
1036412 ATCCCTTTTCATAATCGATAGTCGAAGCTATCCCTATTCATATTCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGTCGAAGCTATCCCTTTTCATAATCGATAGCCGAAGCT
* * * * * *
1036470 ATCCC-TTTCATATTCAAT-GACCAAAACTATCCCTTTTCATAATCGATAGTCGAAGCT
1 ATCCCTTTTCATAATCGATAG-TCGAAGCTATCCCTTTTCATAATCGATAGCCGAAGCT
1036527 ATCCCTTTTCAT
1 ATCCCTTTTCAT
1036539 TGGTCGATGA
Statistics
Matches: 142, Mismatches: 34, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
56 2 0.01
57 89 0.63
58 49 0.35
59 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (58 bp):
ATCCCTTTTCATAATCGATAGTCGAAGCTATCCCTTTTCATAATCGATAGCCGAAGCT
Found at i:1036508 original size:115 final size:116
Alignment explanation
Indices: 1036265--1036510 Score: 318
Period size: 115 Copynumber: 2.1 Consensus size: 116
1036255 GATGGTTGTC
* **
1036265 ACCAACCCTTTTCATAGTTGATGGTCGCCACCATCCCTTTTTGTAATCGATAGCTGAAGCTATCC
1 ACCATCCCTTTTCATAGTTGATGGTCGCCACCATCCCTTTTCATAATCGATAGCTGAAGCTATCC
* * ** ***
1036330 ATTTTCATAATCGACAACCGAAGCTATCCCTTTTCATATTCGATGGTCGTC
66 ATATTCATAATCGACAACCGAAGCTATCCCTTTTCATATTCAATGACCAAA
*
1036381 ACCATCCC-TTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCGATAG-TCGAAGCTATC
1 ACCATCCCTTTTCATAGTTGATGGTCGCCACCATCCCTTTTCATAATCGATAGCT-GAAGCTATC
* * * *
1036444 CCTATTCATATTCGATAGCCGAAGCTATCCC-TTTCATATTCAATGACCAAA
65 CATATTCATAATCGACAACCGAAGCTATCCCTTTTCATATTCAATGACCAAA
*
1036495 ACTATCCCTTTTCATA
1 ACCATCCCTTTTCATA
1036511 ATCGATAGTC
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
114 22 0.20
115 83 0.74
116 7 0.06
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.34
Consensus pattern (116 bp):
ACCATCCCTTTTCATAGTTGATGGTCGCCACCATCCCTTTTCATAATCGATAGCTGAAGCTATCC
ATATTCATAATCGACAACCGAAGCTATCCCTTTTCATATTCAATGACCAAA
Found at i:1036805 original size:14 final size:14
Alignment explanation
Indices: 1036782--1036833 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
1036772 AAATAACAAC
1036782 TAAT-ATTTAAAAT
1 TAATCATTTAAAAT
* *
1036795 TTATCATTTAACAAA
1 TAATCATTTAA-AAT
*
1036810 TAAT-ATTTCAAAT
1 TAATCATTTAAAAT
1036823 TAATCATTTAA
1 TAATCATTTAA
1036834 CATCAAAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 9 0.30
14 16 0.53
15 5 0.17
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATCATTTAAAAT
Found at i:1036807 original size:28 final size:28
Alignment explanation
Indices: 1036775--1036835 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
1036765 TACTTTTAAA
* *
1036775 TAACAACTAATATTTAAAATTTATCATT
1 TAACAAATAATATTTAAAATTAATCATT
*
1036803 TAACAAATAATATTTCAAATTAATCATT
1 TAACAAATAATATTTAAAATTAATCATT
1036831 TAACA
1 TAACA
1036836 TCAAAAACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.39
Consensus pattern (28 bp):
TAACAAATAATATTTAAAATTAATCATT
Found at i:1037843 original size:21 final size:21
Alignment explanation
Indices: 1037817--1037858 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1037807 ATTATTTTGT
1037817 TTCTCTT-TCCTTTTTACTCTC
1 TTCTCTTAT-CTTTTTACTCTC
*
1037838 TTCTCTTATCTTTTTTCTCTC
1 TTCTCTTATCTTTTTACTCTC
1037859 CTTTTTCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64
Consensus pattern (21 bp):
TTCTCTTATCTTTTTACTCTC
Found at i:1048717 original size:18 final size:18
Alignment explanation
Indices: 1048694--1048730 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1048684 ATCCCAATGA
1048694 ATGATAAGAAAGTATGGG
1 ATGATAAGAAAGTATGGG
1048712 ATGATAAGAAAGTATGGG
1 ATGATAAGAAAGTATGGG
1048730 A
1 A
1048731 GCCATTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (18 bp):
ATGATAAGAAAGTATGGG
Found at i:1053101 original size:11 final size:11
Alignment explanation
Indices: 1053087--1053123 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1053077 CTTCATTCAT
*
1053087 CATCCCTCAAT
1 CATCCCTCAAG
1053098 CATCCCTCAAG
1 CATCCCTCAAG
*
1053109 CATCCATCAAG
1 CATCCCTCAAG
1053120 CATC
1 CATC
1053124 ATTCTCTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.30, C:0.43, G:0.05, T:0.22
Consensus pattern (11 bp):
CATCCCTCAAG
Found at i:1055452 original size:29 final size:29
Alignment explanation
Indices: 1055410--1055469 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
1055400 CATATTCTAG
*
1055410 TGTCAGAATGGGCCTGCTAGTTTGGTGGT
1 TGTCAGAATGGGCCTGCTAGTCTGGTGGT
* * *
1055439 TGTCCGAATGGGCCTGTTGGTCTGGTGGT
1 TGTCAGAATGGGCCTGCTAGTCTGGTGGT
1055468 TG
1 TG
1055470 GTTGTGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.10, C:0.15, G:0.40, T:0.35
Consensus pattern (29 bp):
TGTCAGAATGGGCCTGCTAGTCTGGTGGT
Found at i:1058014 original size:27 final size:26
Alignment explanation
Indices: 1057984--1058303 Score: 352
Period size: 27 Copynumber: 11.8 Consensus size: 26
1057974 CCTCAAAATA
* *
1057984 GGTAATATGATCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCC-CATAG
*
1058011 GGTAAAATGACCAAAATACCCCGATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
* *
1058038 GGTAAAATGATCGAAATACCCCCATAA
1 GGTAAAATGACCGAAATA-CCCCATAG
*
1058065 GGTAAAATGACCGAAATACCCCTATAT
1 GGTAAAATGACCGAAATACCCC-ATAG
**
1058092 AATAAAATGACCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCC-CATAG
*
1058119 GGTAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
** * *
1058146 GGTAAAAATGATAGAAATACCCCCGTAA
1 GGT-AAAATGACCGAAATA-CCCCATAG
1058174 GGTAATAATGACCGAAATACTCCCATAG
1 GGTAA-AATGACCGAAATAC-CCCATAG
*
1058202 GGTAAAATGACTGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
* * *
1058229 GGTAAAATAACCGAAATACCCTATAC
1 GGTAAAATGACCGAAATACCCCATAG
*
1058255 GGTAAAATGACCGAAATATCCCCATAT
1 GGTAAAATGACCGAAATA-CCCCATAG
* *
1058282 GGTAAAATGACTGATATACCCC
1 GGTAAAATGACCGAAATACCCC
1058304 TAGTAGATGA
Statistics
Matches: 251, Mismatches: 32, Indels: 21
0.83 0.11 0.07
Matches are distributed among these distances:
26 32 0.13
27 167 0.67
28 52 0.21
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.20
Consensus pattern (26 bp):
GGTAAAATGACCGAAATACCCCATAG
Found at i:1058220 original size:137 final size:135
Alignment explanation
Indices: 1057984--1058292 Score: 401
Period size: 137 Copynumber: 2.3 Consensus size: 135
1057974 CCTCAAAATA
* * * *
1057984 GGTAATATGATCGAAATACCCTCATAGGGT-AAAATGACCAAAATACCCCGATAGGGTAAAATGA
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAAATGACCAAAATACCCCGATAAGGTAAAATGA
* * *
1058048 TCGAAATACCCCCATAAGGTAAAATGACCGAAATACCCCTATATAATAAAATGACCGAAATACCC
66 CCGAAATACCCCCATAAGGTAAAATGACCGAAATACCCCTATAGAATAAAATAACCGAAATACCC
*
1058113 TCATAG
131 T-ATAC
* *
1058119 GGTAAAATGACTGAAATACCCCCATAGGGTAAAAATGA-TAGAAATACCCCCG-TAAGGTAATAA
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAAATGACCA-AAATA-CCCCGATAAGGTAA-AA
* * * **
1058182 TGACCGAAATACTCCCATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATAACCGAAATA
63 TGACCGAAATACCCCCATAAGGTAAAATGACCGAAATACCCCTATAGAATAAAATAACCGAAATA
1058247 CCCTATAC
128 CCCTATAC
* *
1058255 GGTAAAATGACCGAAATATCCCCATATGGT-AAAATGAC
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAAAATGAC
1058293 TGATATACCC
Statistics
Matches: 151, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
135 34 0.23
136 49 0.32
137 68 0.45
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.20
Consensus pattern (135 bp):
GGTAAAATGACCGAAATACCCCCATAGGGTAAAAATGACCAAAATACCCCGATAAGGTAAAATGA
CCGAAATACCCCCATAAGGTAAAATGACCGAAATACCCCTATAGAATAAAATAACCGAAATACCC
TATAC
Found at i:1060503 original size:25 final size:25
Alignment explanation
Indices: 1060487--1060551 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
1060477 CTGTAGATCG
*
1060487 GTATGATCTCATGAGCTATAAATCA
1 GTATGATCTCACGAGCTATAAATCA
*
1060512 GTATGCTCTCACGAGCTATAAATCA
1 GTATGATCTCACGAGCTATAAATCA
* *
1060537 GTATGCTCACACGAG
1 GTATGATCTCACGAG
1060552 TTGTAGGTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (25 bp):
GTATGATCTCACGAGCTATAAATCA
Found at i:1060562 original size:25 final size:25
Alignment explanation
Indices: 1060499--1060551 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1060489 ATGATCTCAT
*
1060499 GAGCTATAAATCAGTATGCTCTCAC
1 GAGCTATAAATCAGTATGCTCACAC
1060524 GAGCTATAAATCAGTATGCTCACAC
1 GAGCTATAAATCAGTATGCTCACAC
1060549 GAG
1 GAG
1060552 TTGTAGGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (25 bp):
GAGCTATAAATCAGTATGCTCACAC
Found at i:1062534 original size:40 final size:40
Alignment explanation
Indices: 1062485--1062625 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
1062475 TTTGCAATTT
1062485 TGGTGGCTTGTCCACAATATTGGCAATTTATCTGCATTAC
1 TGGTGGCTTGTCCACAATATTGGCAATTTATCTGCATTAC
* * * ** ** *
1062525 TGGTAGCTTGTCCACATTACTGGCAGCTCGTCTGCAATAC
1 TGGTGGCTTGTCCACAATATTGGCAATTTATCTGCATTAC
* * * * **
1062565 TAGTGGCTTGTCCAC-ATTTCTGGCATTTTATCTGTATTGT
1 TGGTGGCTTGTCCACAATAT-TGGCAATTTATCTGCATTAC
*
1062605 TGGTGGCTTATCCACAA-ATTG
1 TGGTGGCTTGTCCACAATATTG
1062626 ATGTGTTATT
Statistics
Matches: 75, Mismatches: 24, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
39 3 0.04
40 71 0.95
41 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (40 bp):
TGGTGGCTTGTCCACAATATTGGCAATTTATCTGCATTAC
Found at i:1062544 original size:20 final size:20
Alignment explanation
Indices: 1062519--1062587 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
1062509 AATTTATCTG
1062519 CATTACTGGTAGCTTGTCCA
1 CATTACTGGTAGCTTGTCCA
* * **
1062539 CATTACTGGCAGCTCGTCTG
1 CATTACTGGTAGCTTGTCCA
* * *
1062559 CAATACTAGTGGCTTGTCCA
1 CATTACTGGTAGCTTGTCCA
*
1062579 CATTTCTGG
1 CATTACTGG
1062588 CATTTTATCT
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (20 bp):
CATTACTGGTAGCTTGTCCA
Found at i:1062619 original size:80 final size:80
Alignment explanation
Indices: 1062462--1062620 Score: 194
Period size: 80 Copynumber: 2.0 Consensus size: 80
1062452 AAGGAAGAAG
* * ** *
1062462 TACTGGCAGCTTGTTTGCAATTTTGGTGGCTTGTCCACAATATTGGCAATTTATCTGCATTACTG
1 TACTGGCAGCTCGTCTGCAATACTAGTGGCTTGTCCACAATATTGGCAATTTATCTGCATTACTG
*
1062527 GTAGCTTGTCCACAT
66 GTAGCTTATCCACAT
* * * **
1062542 TACTGGCAGCTCGTCTGCAATACTAGTGGCTTGTCCAC-ATTTCTGGCATTTTATCTGTATTGTT
1 TACTGGCAGCTCGTCTGCAATACTAGTGGCTTGTCCACAATAT-TGGCAATTTATCTGCATTACT
*
1062606 GGTGGCTTATCCACA
65 GGTAGCTTATCCACA
1062621 AATTGATGTG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
79 3 0.05
80 63 0.95
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (80 bp):
TACTGGCAGCTCGTCTGCAATACTAGTGGCTTGTCCACAATATTGGCAATTTATCTGCATTACTG
GTAGCTTATCCACAT
Found at i:1064270 original size:16 final size:16
Alignment explanation
Indices: 1064249--1064280 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1064239 TCAAATCTAT
*
1064249 TTGAAGTGATTTAAAA
1 TTGAAGTGATGTAAAA
1064265 TTGAAGTGATGTAAAA
1 TTGAAGTGATGTAAAA
1064281 GGCATGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (16 bp):
TTGAAGTGATGTAAAA
Found at i:1077205 original size:20 final size:20
Alignment explanation
Indices: 1077161--1077236 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
1077151 AGCTAATAAC
*
1077161 GAGCTC-AATGAGCTGAATT
1 GAGCTCAAATGAGCTGACTT
1077180 CG-GCTCAAATGAGCTGACTT
1 -GAGCTCAAATGAGCTGACTT
* * *
1077200 GAGCTCGAATGATCTAACTT
1 GAGCTCAAATGAGCTGACTT
* *
1077220 GAGGTCAAGTGAGCTGA
1 GAGCTCAAATGAGCTGA
1077237 ACCACAGGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 5 0.11
20 40 0.89
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (20 bp):
GAGCTCAAATGAGCTGACTT
Found at i:1081623 original size:10 final size:10
Alignment explanation
Indices: 1081608--1081663 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
1081598 ACGAGCTCAA
1081608 TGAGCTGAAT
1 TGAGCTGAAT
1081618 TGAGCTCGAA-
1 TGAGCT-GAAT
*
1081628 TGAGCTGACT
1 TGAGCTGAAT
1081638 TGAGCTCGAA-
1 TGAGCT-GAAT
*
1081648 TGAGCTGACT
1 TGAGCTGAAT
1081658 TGAGCT
1 TGAGCT
1081664 CAAGTGAGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 4 0.10
10 30 0.77
11 5 0.13
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (10 bp):
TGAGCTGAAT
Done.