Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_pilon, 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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 31
Found at i:534360 original size:16 final size:17
Alignment explanation
Indices: 534320--534362 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
534310 AATATATTAA
534320 TATAAAAAAATAATAAC
1 TATAAAAAAATAATAAC
*
534337 TATTTAAAAAAATACTAAC
1 TA--TAAAAAAATAATAAC
534356 -ATAAAAA
1 TATAAAAA
534363 TAAATTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 6 0.26
17 2 0.09
18 1 0.04
19 14 0.61
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (17 bp):
TATAAAAAAATAATAAC
Found at i:534360 original size:35 final size:35
Alignment explanation
Indices: 534290--534362 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
534280 TTATTTTAAT
* * *
534290 AAAAATATAATATTTACATAAATATATTAATATAA
1 AAAAATATAATATTTACATAAAAATACTAACATAA
534325 AAAAATAATAACTATTTA-A-AAAAATACTAACATAA
1 AAAAAT-ATAA-TATTTACATAAAAATACTAACATAA
534360 AAA
1 AAA
534363 TAAATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 22 0.67
36 5 0.15
37 6 0.18
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (35 bp):
AAAAATATAATATTTACATAAAAATACTAACATAA
Found at i:535758 original size:16 final size:16
Alignment explanation
Indices: 535714--535771 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
535704 GTCTCCAACG
*
535714 TTTATGTTCATGTTCA
1 TTTATGTTCGTGTTCA
*
535730 TTTATGTTCGTGTTCT
1 TTTATGTTCGTGTTCA
* *
535746 TTTATGTTTGTGTTCG
1 TTTATGTTCGTGTTCA
*
535762 CTTATGTTCG
1 TTTATGTTCG
535772 ATTATTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.59
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:541727 original size:252 final size:253
Alignment explanation
Indices: 541249--541780 Score: 658
Period size: 252 Copynumber: 2.1 Consensus size: 253
541239 TTTGCAGATT
* *
541249 TTTTCGAGTCAAATTTCAACTTCACGACAAAGGATATTTAGGTTCGAAAGAAAATTCAAAAGAAT
1 TTTTCGAGTCAAATTTTAACTTCACGACAAAGGATATTTAGGTTCGAAAGAAAATTCAAAAGAAC
* * * *
541314 CATCTACAATCTAGCTTAACTCAACAAAGAGTAGTTTTTTTCCAGTCAAGGTTTTTGAAGACCAA
66 CATATACAAACTAGCTTAACTCAACAAAGAGGAGTTATTTTCCAGTCAAGGTTTTTGAAGACCAA
* **
541379 TTTTAACTTCACAACGAAGGATATTGGGTTTGAAAGCAATTTTAAAATCGACTTAACTCGGAATG
131 TTTTAACTTCACAACGAAGGATATTGGGTTAGAAAGCAATTTTAAAATCGACTTAACTCACAATG
* * * *
541444 AAGGAGTCGTTTGCAATCTAGCTTAACTCAACAACGAGGAGATCTTTTCCAGA-C-AAG
196 AAGAAGTCGTCTGCAATCTAGCTTAACTCAACAACAAGGAGATATTTTCCA-ATCAAAG
* * * *
541501 ATTTTCGAGTCAAATTTTAACTTCATGACGAAGGATATTTGGGTTCGAAAGCAAATTCAAAAGAA
1 -TTTTCGAGTCAAATTTTAACTTCACGACAAAGGATATTTAGGTTCGAAAGAAAATTCAAAAGAA
* * *** * * ** * ***
541566 CCATATGCAAACTAGCTTAACTCCACGGCGAGGAGTTATTTTCTATTCAATTTTTTTTAA-ATGG
65 CCATATACAAACTAGCTTAACTCAACAAAGAGGAGTTATTTTCCAGTCAAGGTTTTTGAAGACCA
* * * *
541630 ATTTTAACTTCACAATGAAGGATATTGGGTTCAG-AAGTAATTTTAGAATTGACTTAACTCACAA
130 ATTTTAACTTCACAACGAAGGATATTGGGTT-AGAAAGCAATTTTAAAATCGACTTAACTCACAA
* * *
541694 TGGAGAAGTCGTCTGCAATCTAGCTTAACTCAACTACAAGGAGCTATTTTCCAATCAAAG
194 TGAAGAAGTCGTCTGCAATCTAGCTTAACTCAACAACAAGGAGATATTTTCCAATCAAAG
* *
541754 TTCTCGAGTCAAATTTTAACTTTACGA
1 TTTTCGAGTCAAATTTTAACTTCACGA
541781 TGAATGATAT
Statistics
Matches: 236, Mismatches: 40, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
251 1 0.00
252 127 0.54
253 108 0.46
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (253 bp):
TTTTCGAGTCAAATTTTAACTTCACGACAAAGGATATTTAGGTTCGAAAGAAAATTCAAAAGAAC
CATATACAAACTAGCTTAACTCAACAAAGAGGAGTTATTTTCCAGTCAAGGTTTTTGAAGACCAA
TTTTAACTTCACAACGAAGGATATTGGGTTAGAAAGCAATTTTAAAATCGACTTAACTCACAATG
AAGAAGTCGTCTGCAATCTAGCTTAACTCAACAACAAGGAGATATTTTCCAATCAAAG
Found at i:543490 original size:15 final size:15
Alignment explanation
Indices: 543470--543503 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
543460 CCCTCGTCGA
543470 TTCCGAAGGCATCGC
1 TTCCGAAGGCATCGC
543485 TTCCGAAGGCATCGC
1 TTCCGAAGGCATCGC
543500 TTCC
1 TTCC
543504 TCCGGCGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
TTCCGAAGGCATCGC
Found at i:544501 original size:16 final size:16
Alignment explanation
Indices: 544480--544512 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
544470 TAATAAAAAA
544480 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
544496 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
544512 A
1 A
544513 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:549403 original size:132 final size:132
Alignment explanation
Indices: 549166--549421 Score: 485
Period size: 132 Copynumber: 1.9 Consensus size: 132
549156 CTCTATAATT
* *
549166 TATTGAGTATACATGTAGTCTACTTTTATAGCCTACCATATATAATATATATTTGTTTACCACGT
1 TATTGAGTATACATGTAGTCTACTTTTATAGCCTACCATATATAATACATATTTGTTTACCACAT
*
549231 GATAATCATGATTGAATAAACTAACATGCAGATAAGGTAAAATAAAGATAGTGTTAGCCTGTCCT
66 GATAATCATGATTGAATAAACTAACATGCAGATAAGGTAAAATAAAGATAGAGTTAGCCTGTCCT
549296 TA
131 TA
549298 TATTGAGTATACATGTAGTCTACTTTTATAGCCTACCATATATAATACATATTTGTTTACCACAT
1 TATTGAGTATACATGTAGTCTACTTTTATAGCCTACCATATATAATACATATTTGTTTACCACAT
549363 GATAATCATGATTGAATAAACTAACATGCAGATAAGGTAAAATAAAGATAGAGTTAGCC
66 GATAATCATGATTGAATAAACTAACATGCAGATAAGGTAAAATAAAGATAGAGTTAGCC
549422 ATAGCCTGTC
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 121 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (132 bp):
TATTGAGTATACATGTAGTCTACTTTTATAGCCTACCATATATAATACATATTTGTTTACCACAT
GATAATCATGATTGAATAAACTAACATGCAGATAAGGTAAAATAAAGATAGAGTTAGCCTGTCCT
TA
Found at i:553120 original size:17 final size:17
Alignment explanation
Indices: 553094--553127 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
553084 TAGCATATTT
*
553094 TAAAACAAAACTTAAAA
1 TAAAACAAAAATTAAAA
*
553111 TAAAAGAAAAATTAAAA
1 TAAAACAAAAATTAAAA
553128 CTTGAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAACAAAAATTAAAA
Found at i:555093 original size:19 final size:19
Alignment explanation
Indices: 555066--555105 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
555056 TCATCTTACC
555066 ACTACCCCACCACTAAAAA
1 ACTACCCCACCACTAAAAA
*
555085 ACTATCCCACCACTAAAAA
1 ACTACCCCACCACTAAAAA
555104 AC
1 AC
555106 CAACTTACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.12
Consensus pattern (19 bp):
ACTACCCCACCACTAAAAA
Found at i:555115 original size:19 final size:19
Alignment explanation
Indices: 555071--555109 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
555061 TTACCACTAC
* *
555071 CCCACCACTAAAAAACTAT
1 CCCACCACTAAAAAACCAA
555090 CCCACCACTAAAAAACCAA
1 CCCACCACTAAAAAACCAA
555109 C
1 C
555110 TTACCATCTC
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:0.49, C:0.41, G:0.00, T:0.10
Consensus pattern (19 bp):
CCCACCACTAAAAAACCAA
Found at i:559507 original size:14 final size:16
Alignment explanation
Indices: 559471--559507 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
559461 GAAAAAAGAG
559471 AGAGAAAAGAAGCAAA
1 AGAGAAAAGAAGCAAA
559487 A-AGAAAA-AA-CAAA
1 AGAGAAAAGAAGCAAA
559500 AGAGAAAA
1 AGAGAAAA
559508 TAAACAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.25
14 8 0.40
15 6 0.30
16 1 0.05
ACGTcount: A:0.76, C:0.05, G:0.19, T:0.00
Consensus pattern (16 bp):
AGAGAAAAGAAGCAAA
Found at i:561145 original size:65 final size:63
Alignment explanation
Indices: 561038--561192 Score: 217
Period size: 65 Copynumber: 2.5 Consensus size: 63
561028 CACAATTTAC
**
561038 TCAAGATTGGATTTCAACATTCACAAAAAATGATATCCAACTCAAAACCAATTTGGTGAAACTTA
1 TCAAGATTGGATTTCAAC-TTCACAACGAATGATATCCAACTCAAAACCAATTTGGTGAAAC--A
561103 A
63 A
* *
561104 TCAAGATTGGATTTCAACTTCACGACGAATGATATCTAACTCAAAACCAATTTGGTGAAACAA
1 TCAAGATTGGATTTCAACTTCACAACGAATGATATCCAACTCAAAACCAATTTGGTGAAACAA
*
561167 T--A-TTTGGATTTCAACTTCACAACGAA
1 TCAAGATTGGATTTCAACTTCACAACGAA
561193 GGGTACCAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
60 22 0.27
61 1 0.01
63 3 0.04
65 39 0.47
66 18 0.22
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (63 bp):
TCAAGATTGGATTTCAACTTCACAACGAATGATATCCAACTCAAAACCAATTTGGTGAAACAA
Found at i:561242 original size:125 final size:125
Alignment explanation
Indices: 561113--561388 Score: 283
Period size: 125 Copynumber: 2.2 Consensus size: 125
561103 ATCAAGATTG
**** *
561113 GATTTCAACTTCACGACGAATGATATC-TAACTCAAAACCAATTTGGTGA-AACAATA-TTTGGA
1 GATTTCAACTTCACGACGAATGATATCGTAACT-AAAACC-A-GCAAT-ACAACAATAGATTGGA
* * ** *
561175 TTTCAACTTCACAACGAAGGGTA-CCAATTCGAAGTTCAACTTCACAACGAA-GAAGCCATCCAC
62 TTTCAACTTCACAACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAATG-AGACATCCAC
* * * * * * **
561238 GATTTCAACTTCACTATGAAGGATATCGTACCTAGAAGCAGCAATACAACTCTAGATTGGATTTC
1 GATTTCAACTTCACGACGAATGATATCGTAACTAAAACCAGCAATACAACAATAGATTGGATTTC
* * *
561303 TACTTCACAACGAAGGATATCTAATTCAAAACTCAACTTCACAACGAATGAGATATCCAC
66 AACTTCACAACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAATGAGACATCCAC
561363 GATTTCAACTTCACGACGAATGATAT
1 GATTTCAACTTCACGACGAATGATAT
561389 TGTTCCCACA
Statistics
Matches: 122, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
122 1 0.01
123 6 0.05
124 27 0.22
125 83 0.68
126 5 0.04
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (125 bp):
GATTTCAACTTCACGACGAATGATATCGTAACTAAAACCAGCAATACAACAATAGATTGGATTTC
AACTTCACAACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAATGAGACATCCAC
Found at i:561402 original size:125 final size:123
Alignment explanation
Indices: 561170--561428 Score: 322
Period size: 125 Copynumber: 2.1 Consensus size: 123
561160 GAAACAATAT
* * ** *
561170 TTGGATTTCAACTTCACAACGAAGGGTACCAATTCGAAGTTCAACTTCACAACGAAGAAGCCATC
1 TTGGATTTCAACTTCACAACGAAGGATACCAATTCAAAACTCAACTTCACAACGAAGAAGACATC
* * * *
561235 CACGATTTCAACTTCACTATGAAGGATATCGTACCTAGAAGCAGCAATACAACTCTAGA
66 CACGATTTCAACTTCACGACGAAGGATATCGTACCCACAAGCAGC-ATACAACTCTAGA
* * *
561294 TTGGATTTCTACTTCACAACGAAGGATATCTAATTCAAAACTCAACTTCACAACGAATG-AGATA
1 TTGGATTTCAACTTCACAACGAAGGATA-CCAATTCAAAACTCAACTTCACAACGAA-GAAGACA
* * * * * *
561358 TCCACGATTTCAACTTCACGACGAATGATATTGTTCCCACAAGCATCATCCATCTCTAGA
64 TCCACGATTTCAACTTCACGACGAAGGATATCGTACCCACAAGCAGCATACAACTCTAGA
561418 TTGGATTTCAA
1 TTGGATTTCAA
561429 ACCAATTTGG
Statistics
Matches: 114, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
124 47 0.41
125 66 0.58
126 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (123 bp):
TTGGATTTCAACTTCACAACGAAGGATACCAATTCAAAACTCAACTTCACAACGAAGAAGACATC
CACGATTTCAACTTCACGACGAAGGATATCGTACCCACAAGCAGCATACAACTCTAGA
Found at i:563900 original size:18 final size:18
Alignment explanation
Indices: 563879--563915 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
563869 AACAAGCATG
* *
563879 ACATGCCAAAAACATTCA
1 ACATGACAAAAAAATTCA
563897 ACATGACAAAAAAATTCA
1 ACATGACAAAAAAATTCA
563915 A
1 A
563916 TGGAATTTTC
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:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (18 bp):
ACATGACAAAAAAATTCA
Found at i:571414 original size:18 final size:18
Alignment explanation
Indices: 571391--571464 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
571381 ACCAGTCACA
571391 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
571409 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
571426 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
571440 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
571458 A-CCGACC
1 ACCCGACC
571465 GTTGACCGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
13 12 0.24
17 6 0.12
18 31 0.63
ACGTcount: A:0.18, C:0.50, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:571460 original size:13 final size:13
Alignment explanation
Indices: 571413--571449 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
571403 CCGTTGACCC
571413 GACCCGACCCGTT
1 GACCCGACCCGTT
*
571426 TACCCGACCCGTT
1 GACCCGACCCGTT
571439 GACCCGACCCG
1 GACCCGACCCG
571450 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:571473 original size:7 final size:7
Alignment explanation
Indices: 571461--571494 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
571451 CCCGTTGACC
571461 GACCGTT
1 GACCGTT
571468 GACCGTT
1 GACCGTT
571475 GACCCGTT
1 GA-CCGTT
571483 GACCGTT
1 GACCGTT
571490 GACCG
1 GACCG
571495 GAGTTGACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:571480 original size:31 final size:31
Alignment explanation
Indices: 571395--571471 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
571385 GTCACAACCC
571395 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
571426 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
571457 GA-CCGA-CCGTTGACC
1 GACCCGACCCGTTGACC
571472 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 9 0.20
30 4 0.09
31 31 0.70
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:571483 original size:15 final size:15
Alignment explanation
Indices: 571463--571493 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
571453 CGTTGACCGA
571463 CCGTTGACCGTTGAC
1 CCGTTGACCGTTGAC
571478 CCGTTGACCGTTGAC
1 CCGTTGACCGTTGAC
571493 C
1 C
571494 GGAGTTGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.35, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCGTTGAC
Found at i:572832 original size:18 final size:18
Alignment explanation
Indices: 572806--572841 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
572796 TCGAAAGGAC
*
572806 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
572824 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
572842 CGGATGAAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:574073 original size:24 final size:24
Alignment explanation
Indices: 573969--574075 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
573959 ATATTTTATC
*
573969 TGATTTCTGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
573993 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * * *
574017 TGATTCCTAACCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTT
* *
574041 TGATATCTGATCTGAATTATATTT
1 TGATTTCTGATCTGAATTATGTTT
574065 TGATTTCTGAT
1 TGATTTCTGAT
574076 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:576193 original size:13 final size:13
Alignment explanation
Indices: 576193--576268 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
576183 CCGTTGACCC
576193 GACCCGACCCGTT
1 GACCCGACCCGTT
*
576206 TACCCGACCCGTT
1 GACCCGACCCGTT
576219 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
576237 GACCCGACCCGTT
1 GACCCGACCCGTT
*
576250 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
576265 GACC
1 GACC
576269 GTTGACCGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 29 0.55
15 12 0.23
18 12 0.23
ACGTcount: A:0.16, C:0.45, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:576194 original size:18 final size:18
Alignment explanation
Indices: 576171--576247 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
576161 ACCAGTCACA
576171 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
576189 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
576206 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
576220 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
576238 ACCCGACCCG
1 ACCCGACCCG
576248 TTGACCGTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.17, C:0.51, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:576214 original size:31 final size:31
Alignment explanation
Indices: 576175--576253 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
576165 GTCACAACCC
576175 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
576206 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
576237 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
576254 GTTGACCCGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.16, C:0.48, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:576240 original size:8 final size:8
Alignment explanation
Indices: 576229--576275 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
576219 GACCCGACCC
576229 GACCCGTT
1 GACCCGTT
576237 GACCC---
1 GACCCGTT
576242 GACCCGTT
1 GACCCGTT
576250 GA-CCGTT
1 GACCCGTT
576257 GACCCGTT
1 GACCCGTT
576265 GA-CCGTT
1 GACCCGTT
576272 GACC
1 GACC
576276 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:576257 original size:7 final size:7
Alignment explanation
Indices: 576245--576276 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
576235 TTGACCCGAC
576245 CCGTTGA
1 CCGTTGA
576252 CCGTTGA
1 CCGTTGA
576259 CCCGTTGA
1 -CCGTTGA
576267 CCGTTGA
1 CCGTTGA
576274 CCG
1 CCG
576277 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:576262 original size:15 final size:15
Alignment explanation
Indices: 576229--576275 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
576219 GACCCGACCC
*
576229 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
576242 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
576257 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
576272 GACC
1 GACC
576276 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:577614 original size:18 final size:18
Alignment explanation
Indices: 577588--577623 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
577578 TCGAAAGGAC
*
577588 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
577606 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
577624 CGGATGAAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:578853 original size:24 final size:24
Alignment explanation
Indices: 578749--578855 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
578739 ATATTTTATC
*
578749 TGATTTCTGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
578773 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * * *
578797 TGATTCCTAACCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTT
* *
578821 TGATATCTGATCTGAATTATATTT
1 TGATTTCTGATCTGAATTATGTTT
578845 TGATTTCTGAT
1 TGATTTCTGAT
578856 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:579868 original size:20 final size:22
Alignment explanation
Indices: 579832--579880 Score: 84
Period size: 20 Copynumber: 2.3 Consensus size: 22
579822 ATAAAACTTT
579832 AATTTACTGAGACTAAAATACA
1 AATTTACTGAGACTAAAATACA
579854 AATTTACT-A-ACTAAAATACA
1 AATTTACTGAGACTAAAATACA
579874 AATTTAC
1 AATTTAC
579881 AAAGCTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 18 0.67
21 1 0.04
22 8 0.30
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (22 bp):
AATTTACTGAGACTAAAATACA
Found at i:580340 original size:19 final size:19
Alignment explanation
Indices: 580303--580341 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
580293 TTATTGCGGT
* *
580303 TGTTTGATTGTTGTTTTTG
1 TGTTTGATTGTTCTGTTTG
*
580322 TGTTTGGTTGTTCTGTTTG
1 TGTTTGATTGTTCTGTTTG
580341 T
1 T
580342 TCCAGTTGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.03, G:0.28, T:0.67
Consensus pattern (19 bp):
TGTTTGATTGTTCTGTTTG
Found at i:580393 original size:24 final size:23
Alignment explanation
Indices: 580367--580438 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 23
580357 TTGTTTTTGG
580367 TTTGTTTGTTGTTTGTATCTCC-
1 TTTGTTTGTTGTTTGTATCTCCT
*
580389 --TGTTTGTTGTTCGTATCTCCT
1 TTTGTTTGTTGTTTGTATCTCCT
* *
580410 CTTTGTTGGTTG-TTGTAGCTCCT
1 -TTTGTTTGTTGTTTGTATCTCCT
*
580433 CTTGTT
1 TTTGTT
580439 GATTGTTGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 19 0.46
22 5 0.12
23 9 0.22
24 8 0.20
ACGTcount: A:0.04, C:0.17, G:0.21, T:0.58
Consensus pattern (23 bp):
TTTGTTTGTTGTTTGTATCTCCT
Found at i:580394 original size:20 final size:20
Alignment explanation
Indices: 580369--580422 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
580359 GTTTTTGGTT
580369 TGTTTGTTGTTTGTATCTCC
1 TGTTTGTTGTTTGTATCTCC
*
580389 TGTTTGTTGTTCGTATCTCC
1 TGTTTGTTGTTTGTATCTCC
* *
580409 TCTTTGTTGGTTGT
1 TGTTTGTTGTTTGT
580423 TGTAGCTCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.04, C:0.15, G:0.22, T:0.59
Consensus pattern (20 bp):
TGTTTGTTGTTTGTATCTCC
Found at i:580435 original size:23 final size:22
Alignment explanation
Indices: 580389--580446 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
580379 TTGTATCTCC
* *
580389 TGTTTGTTGTTCGTATCTCCTCTT
1 TGTTGGTTGTT-GTAGCTCCTC-T
580413 TGTTGGTTGTTGTAGCTCCTCT
1 TGTTGGTTGTTGTAGCTCCTCT
*
580435 TGTTGATTGTTG
1 TGTTGGTTGTTG
580447 GTAGGGGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 12 0.39
23 9 0.29
24 10 0.32
ACGTcount: A:0.05, C:0.16, G:0.24, T:0.55
Consensus pattern (22 bp):
TGTTGGTTGTTGTAGCTCCTCT
Found at i:581150 original size:23 final size:23
Alignment explanation
Indices: 581123--581175 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
581113 TCCCAAAAGA
*
581123 CCACATAGGGTTGCACTAAAGTG
1 CCACATAGGGTTGCACCAAAGTG
* *
581146 CCACATAGGTTTGCACCGAAGTG
1 CCACATAGGGTTGCACCAAAGTG
581169 CCACATA
1 CCACATA
581176 TTTTTCCTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
CCACATAGGGTTGCACCAAAGTG
Found at i:581859 original size:54 final size:55
Alignment explanation
Indices: 581793--581912 Score: 152
Period size: 54 Copynumber: 2.2 Consensus size: 55
581783 ACCTATTAAT
581793 GGTAACGATACCAAAATAGCATTCGATGTTTCAAAGGTATCGATACC-TCCTCAA
1 GGTAACGATACCAAAATAGCATTCGATGTTTCAAAGGTATCGATACCATCCTCAA
* ** * * * * *
581847 GGTACCGATACCAATCTGGCATTCGATGTTTTAAGGGTATCGATACCATCTTTAA
1 GGTAACGATACCAAAATAGCATTCGATGTTTCAAAGGTATCGATACCATCCTCAA
*
581902 GGTATCGATAC
1 GGTAACGATAC
581913 TACCTATACG
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
54 41 0.73
55 15 0.27
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (55 bp):
GGTAACGATACCAAAATAGCATTCGATGTTTCAAAGGTATCGATACCATCCTCAA
Found at i:583484 original size:19 final size:20
Alignment explanation
Indices: 583450--583489 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
583440 ATTAAATTAT
583450 ATTATATATGTTTTTT-AAA
1 ATTATATATGTTTTTTCAAA
583469 ATTATATAT-TTATTTTCAAA
1 ATTATATATGTT-TTTTCAAA
583489 A
1 A
583490 ACTATAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 13 0.68
20 4 0.21
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTATATATGTTTTTTCAAA
Found at i:583882 original size:81 final size:81
Alignment explanation
Indices: 583773--584122 Score: 486
Period size: 81 Copynumber: 4.3 Consensus size: 81
583763 AACGATTCTG
* * *
583773 CTCCACTCTTCTTTAGGGGAGATTAGACTTGATATGTTCATCTTTTTCGGGTAGTCATAAT-AAT
1 CTCCACTCTTCTTTAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCA-GATCAAT
* *
583837 TTGGGAACACGGGTCTT
65 TTTGGAAGACGGGTCTT
* * **
583854 CTCCACTCTTCTTTAGGGGAGATCAGACTTTATATGTTCCTTTTTTTCAAGTAGTCAGATCAATT
1 CTCCACTCTTCTTTAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATT
*
583919 TTGGAAGACGGGTTTT
66 TTGGAAGACGGGTCTT
* * * *
583935 CTCTAGTCTTCTTTAGGGGAGATCAGACTTGATATGTTCCTATTTTTTGGGTAGTCAGATCAATT
1 CTCCACTCTTCTTTAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATT
* *
584000 TTGGAAGACGGGTATG
66 TTGGAAGACGGGTCTT
* * *
584016 CTCCACTATTCTTTAGGGGAGATCATACTTGATATGTTCCTCTTTTTCGGGTAGTCGGATCAATT
1 CTCCACTCTTCTTTAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATT
* * *
584081 TTAGAAGATGGGTCTA
66 TTGGAAGACGGGTCTT
584097 CTCCACTCTTCTTTAGGGGAGATCAG
1 CTCCACTCTTCTTTAGGGGAGATCAG
584123 GCTCGAGAAA
Statistics
Matches: 236, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
80 2 0.01
81 234 0.99
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (81 bp):
CTCCACTCTTCTTTAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATT
TTGGAAGACGGGTCTT
Found at i:584308 original size:67 final size:67
Alignment explanation
Indices: 584216--585913 Score: 2085
Period size: 67 Copynumber: 25.5 Consensus size: 67
584206 ATCAAATCAG
* * * * *
584216 AAAGATTGAGTTCACTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTTAGAAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
584281 AC
66 AC
* * ** *
584283 ACAA-ATTTACTTCTCTTCATGAGGAAGTCAAATATTGACTCCTCTTCGCGAGGGAGTAAGGAAT
1 A-AAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAAT
584347 AAC
65 AAC
* * *
584350 AAAGATTGAC--CTCTACATGA-GATAGTCAATGATTGACTCCTCTTCGCGAGGGAGTCAGGAAT
1 AAAGATTGACTTCTCTTCACGAGGA-AGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAAT
584412 AAC
65 AAC
* * * *
584415 AAAGATTGACTTCTTTTCAGGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
584480 AC
66 AC
* * * *
584482 AAAGACTGACTTCTCTTCACGAGGAAGTCAAGGATTTG-CTCCTCTTCGTGAGGGAGCCATGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGA-TTGACTCCTCTTCGCGAGGGAGTCAGGAAT
584546 AAC
65 AAC
* * ** * * *
584549 AAAGATTAACTTCTCTTCAAGACAAATTCAAGGATTGACTCCTCTTTGCGTA-GGATTCAGGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCG-AGGGAGTCAGGAAT
584613 AAC
65 AAC
* * *
584616 AAAGATTTACTTCTCTTCACGAGGAAGTCAATGATTGACTCCTCTTCGTGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
584681 AC
66 AC
* * *
584683 AAAGATTGAGTTCTCTTCACGAGGAAATCAAGGATTGAATCCTCTTCGCGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
584748 AC
66 AC
* * * *
584750 AAAGATTGACTTCTCTTCACAAGGAAATCAAGTATTGACTCCTCTTCGCGAGGAAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
584815 AC
66 AC
* * *
584817 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCTCGAGGTAGTTAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
584882 A-
66 AC
* * * * * *** *
584883 AAAGGATTGATTTTTCTTCAAGAGGAAGTTAGGGATTGACTCCTCTTTATGAGGGAGTCAGAAAT
1 AAA-GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAAT
584948 AAC
65 AAC
* * * ***
584951 AAAGATTGACTTTTCTTCACGAGGAAGTCAGGGATTGACTCATCTTTATGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585016 AC
66 AC
* * ** ***
585018 AAAGATTGACTTATCTTCACGAGGAAGTCAGGGATTGACTAATCTTTATGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585083 AC
66 AC
* * * * *
585085 AAAGATTGACTTCTCTTTATGATGAAGTCAAGGGTTGACTCCTCTTTGCGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585150 AC
66 AC
* * * * * * *
585152 AAAGATTGACTTCTCTTAATGAGAAAGCCAAGGATTGAATCCTCTTCGCAAGGGAGTCATGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585217 AC
66 AC
* * * *
585219 AAAGATTGACTTCTCTTCACAAGGAACTCAAGGATTGACTCTTCTTCGCGAGGGAGTCATGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585284 AC
66 AC
* * * ** * * *
585286 AAAGATTGATTTTTCTTCAAGAGGAAGTCAATTATTGACTCCTCTTTGTGAGTGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
*
585351 AA
66 AC
* * * *
585353 AAAGATTAACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTGTGAGGGACTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
*
585418 AA
66 AC
* * * * * *
585420 AAAGATTGATTTCTCTTAACGAGAAAGTTAAGGAATGACTCCTCTTCGCGAAGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585485 AC
66 AC
* * * * *** *
585487 AAATATTGACTTCTCTTCACAAGGAAGTCAA-G---G-CTCTTTTTTATGAGGGAGTCAGTAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585547 A-
66 AC
* * * * * *
585548 AAAGATTAACTTATCTTCACGAGGAAGTCAATGATTAACTCCACTTCGTGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585613 AC
66 AC
* * * *
585615 AAATATTGACTTCTCTTCATGAGGAAGTCAAAGATTGACTCCTCTTCGCGAGGGAGTCATGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585680 AC
66 AC
* *
585682 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAC-CTCTCTTCGTGAAGGAGTCAGGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTC-CTCTTCGCGAGGGAGTCAGGAAT
585746 AA-
65 AAC
* * * * *
585748 AAAGATTGAATTCTCTTAATGAGGAAGTCAAAGATTGTCTCCTCTTCGCGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585813 AC
66 AC
* **
585815 AAAGATTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTCCTCTTTACGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
585880 AC
66 AC
*
585882 AAAGATTGACTTCTCTTCATGAGGAAGTCAAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG
585914 TTGAAGTTTC
Statistics
Matches: 1412, Mismatches: 198, Indels: 42
0.85 0.12 0.03
Matches are distributed among these distances:
61 27 0.02
62 22 0.02
63 1 0.00
64 2 0.00
65 58 0.04
66 90 0.06
67 1201 0.85
68 11 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (67 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
AC
Found at i:584452 original size:29 final size:29
Alignment explanation
Indices: 584418--584475 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
584408 GAATAACAAA
* * *
584418 GATTGACTTCTTTTCAGGAGGAAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
*
584447 GATTGACTCCTCTTCACGAGGGAGTCAAG
1 GATTGACTCCTCTTCACGAGGAAGTCAAG
584476 AATAACAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (29 bp):
GATTGACTCCTCTTCACGAGGAAGTCAAG
Found at i:584996 original size:29 final size:29
Alignment explanation
Indices: 584954--585078 Score: 88
Period size: 29 Copynumber: 4.0 Consensus size: 29
584944 AAATAACAAA
*
584954 GATTGACTTTTCTTCACGAGGAAGTCAGG
1 GATTGACTTATCTTCACGAGGAAGTCAGG
* * * *
584983 GATTGACTCATCTTTATGAGGGAGTCAGG
1 GATTGACTTATCTTCACGAGGAAGTCAGG
585012 AATAACAAAGATTGACTTATCTTCACGAGGAAGTCAGG
1 ---------GATTGACTTATCTTCACGAGGAAGTCAGG
* * * *
585050 GATTGACTAATCTTTATGAGGGAGTCAGG
1 GATTGACTTATCTTCACGAGGAAGTCAGG
585079 AATAACAAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
29 49 0.66
38 25 0.34
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (29 bp):
GATTGACTTATCTTCACGAGGAAGTCAGG
Found at i:585025 original size:38 final size:38
Alignment explanation
Indices: 584983--585106 Score: 124
Period size: 38 Copynumber: 3.5 Consensus size: 38
584973 GGAAGTCAGG
584983 GATTGACTCATCTTTATGAGGGAGTCAGGAATAACAAA
1 GATTGACTCATCTTTATGAGGGAGTCAGGAATAACAAA
* * * *
585021 GATTGACTTATCTTCACGAGGAAGTCAGG---------
1 GATTGACTCATCTTTATGAGGGAGTCAGGAATAACAAA
*
585050 GATTGACTAATCTTTATGAGGGAGTCAGGAATAACAAA
1 GATTGACTCATCTTTATGAGGGAGTCAGGAATAACAAA
585088 GATTGACTTC-TCTTTATGA
1 GATTGAC-TCATCTTTATGA
585107 TGAAGTCAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
29 25 0.37
38 41 0.61
39 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (38 bp):
GATTGACTCATCTTTATGAGGGAGTCAGGAATAACAAA
Found at i:592294 original size:14 final size:14
Alignment explanation
Indices: 592275--592301 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
592265 AATACATTTT
592275 AAAATAATTTTAAG
1 AAAATAATTTTAAG
592289 AAAATAATTTTAA
1 AAAATAATTTTAA
592302 AAGATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AAAATAATTTTAAG
Found at i:593409 original size:3 final size:3
Alignment explanation
Indices: 593401--593459 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
593391 CGGTTGTTTG
* *
593401 GTT GTT GTT GTT GTT GTA GTT GTT G-T GTT -TG GTT GTT G-T GTTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT G-TT
593444 GTT -TT AGTT GTT GTT G
1 GTT GTT -GTT GTT GTT G
593460 ATGGTTGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
2 7 0.15
3 35 0.76
4 4 0.09
ACGTcount: A:0.03, C:0.00, G:0.34, T:0.63
Consensus pattern (3 bp):
GTT
Found at i:593430 original size:31 final size:31
Alignment explanation
Indices: 593395--593457 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
593385 TTCTTGCGGT
593395 TGTTTGGTTGTTGT-TGTTGTTGTAGTTGTTG
1 TGTTTGGTTGTTGTGT-TTGTTGTAGTTGTTG
*
593426 TGTTTGGTTGTTGTGTTTGTTTTAGTTGTTG
1 TGTTTGGTTGTTGTGTTTGTTGTAGTTGTTG
593457 T
1 T
593458 TGATGGTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.03, C:0.00, G:0.33, T:0.63
Consensus pattern (31 bp):
TGTTTGGTTGTTGTGTTTGTTGTAGTTGTTG
Found at i:593465 original size:31 final size:31
Alignment explanation
Indices: 593399--593468 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
593389 TGCGGTTGTT
*
593399 TGGTTGTTGTTGTTGTTGTAGTTGTTGTGTT
1 TGGTTGTTGTTGTTGTTGTAGTTGTTGTGTA
*
593430 TGGTTGTTG-TGTTTGTTTTAGTTGTTGT-TGA
1 TGGTTGTTGTTG-TTGTTGTAGTTGTTGTGT-A
593461 TGGTTGTT
1 TGGTTGTT
593469 TTTGGTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 3 0.09
31 32 0.91
ACGTcount: A:0.04, C:0.00, G:0.34, T:0.61
Consensus pattern (31 bp):
TGGTTGTTGTTGTTGTTGTAGTTGTTGTGTA
Found at i:593467 original size:22 final size:20
Alignment explanation
Indices: 593393--593470 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 20
593383 TTTTCTTGCG
593393 GTTGTT-TGGTTG--TTGTT
1 GTTGTTGTGGTTGTTTTGTT
* *
593410 GTTGTTGTAGTTGTTGTGTTT
1 GTTGTTGTGGTTGTTTTG-TT
*
593431 GGTTGTTGTGTTTGTTTTAGTT
1 -GTTGTTGTGGTTGTTTT-GTT
593453 GTTGTTGATGGTTGTTTT
1 GTTGTTG-TGGTTGTTTT
593471 TGGTATATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
17 6 0.12
18 5 0.10
20 2 0.04
21 9 0.19
22 25 0.52
23 1 0.02
ACGTcount: A:0.04, C:0.00, G:0.33, T:0.63
Consensus pattern (20 bp):
GTTGTTGTGGTTGTTTTGTT
Found at i:593472 original size:28 final size:29
Alignment explanation
Indices: 593404--593486 Score: 71
Period size: 31 Copynumber: 2.8 Consensus size: 29
593394 TTGTTTGGTT
* * *
593404 GTTGTTGTTGTTGTAGTTGTTG-TGTTTG
1 GTTGTTTTTGTTATAGTTGTTGTTGTATG
*
593432 GTTGTTGTGTTTGTTTTAGTTGTTGTTG-ATG
1 GTTG-T-T-TTTGTTATAGTTGTTGTTGTATG
* *
593463 GTTGTTTTTGGTATATTTGTTGTT
1 GTTGTTTTTGTTATAGTTGTTGTT
593487 TCTATCTCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
28 19 0.42
29 2 0.04
30 2 0.04
31 20 0.44
32 2 0.04
ACGTcount: A:0.06, C:0.00, G:0.31, T:0.63
Consensus pattern (29 bp):
GTTGTTTTTGTTATAGTTGTTGTTGTATG
Found at i:593515 original size:20 final size:20
Alignment explanation
Indices: 593478--593516 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
593468 TTTTGGTATA
*
593478 TTTGTTGTTTCTATCTCCTT
1 TTTGTTGTTTCTAACTCCTT
593498 TTTGTTG-TTCGTAACTCCT
1 TTTGTTGTTTC-TAACTCCT
593517 CCTTGTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.08, C:0.21, G:0.13, T:0.59
Consensus pattern (20 bp):
TTTGTTGTTTCTAACTCCTT
Found at i:594238 original size:3 final size:3
Alignment explanation
Indices: 594230--594263 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
594220 TTGTAATTAA
594230 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
594264 TATATTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:594336 original size:22 final size:20
Alignment explanation
Indices: 594309--594369 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 20
594299 AAATTATATT
594309 AATTATCTATATATATTTTT-
1 AATTAT-TATATATATTTTTA
*
594329 AA-TATTATATTTATTTTTA
1 AATTATTATATATATTTTTA
594348 AATTATATTATATATATGTTTT
1 AA-T-TATTATATATAT-TTTT
594370 TCAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 2 0.06
22 11 0.32
23 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
AATTATTATATATATTTTTA
Found at i:594352 original size:17 final size:18
Alignment explanation
Indices: 594316--594356 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
594306 ATTAATTATC
*
594316 TATATATATTTTTAATAT
1 TATATTTATTTTTAATAT
594334 TATATTTATTTTTAA-AT
1 TATATTTATTTTTAATAT
594351 TATATT
1 TATATT
594357 ATATATATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATTTATTTTTAATAT
Found at i:594369 original size:24 final size:23
Alignment explanation
Indices: 594330--594423 Score: 72
Period size: 23 Copynumber: 4.1 Consensus size: 23
594320 TATATTTTTA
594330 ATATTATATTTATTTTT-AAATT
1 ATATTATATTTATTTTTAAAATT
*
594352 ATATTATATATATGTTTTTCAAAA-T
1 ATATTATAT-T-TATTTTT-AAAATT
* *
594377 -TA-TATATTTATTTTCAAAAAT
1 ATATTATATTTATTTTTAAAATT
*
594398 ATACTAT-TTATATTTTTCAAAATT
1 ATATTATATT-TATTTTT-AAAATT
594422 AT
1 AT
594424 TTTCAAAACT
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
20 4 0.07
21 6 0.10
22 14 0.24
23 15 0.26
24 15 0.26
25 1 0.02
26 3 0.05
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (23 bp):
ATATTATATTTATTTTTAAAATT
Found at i:594380 original size:21 final size:20
Alignment explanation
Indices: 594316--594423 Score: 71
Period size: 21 Copynumber: 5.2 Consensus size: 20
594306 ATTAATTATC
*
594316 TATATATA-TTTTT-AATAT
1 TATATATATTTTTTCAAAAT
* *
594334 TATATTTA-TTTTTAAATTATAT
1 TATATATATTTTTTCAA--A-AT
594356 TATATATATGTTTTTCAAAAT
1 TATATATAT-TTTTTCAAAAT
594377 TATATAT-TTATTTTCAAAAAT
1 TATATATATT-TTTTC-AAAAT
*
594398 ATACTATTTATATTTTTCAAAAT
1 -TA-TATATAT-TTTTTCAAAAT
594421 TAT
1 TAT
594424 TTTCAAAACT
Statistics
Matches: 73, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
18 12 0.16
19 3 0.04
20 6 0.08
21 15 0.21
22 14 0.19
23 9 0.12
24 13 0.18
25 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (20 bp):
TATATATATTTTTTCAAAAT
Found at i:594382 original size:23 final size:21
Alignment explanation
Indices: 594354--594423 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 21
594344 TTTAAATTAT
594354 ATTATATA-TATGTTTTTCAAA
1 ATTATATATTAT-TTTTTCAAA
*
594375 ATTATATATT-TATTTTCAAA
1 ATTATATATTATTTTTTCAAA
*
594395 AATATACTATTTATATTTTTCAAA
1 ATTATA-TA-TTAT-TTTTTCAAA
594419 ATTAT
1 ATTAT
594424 TTTCAAAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 13 0.32
21 11 0.28
22 3 0.08
23 1 0.03
24 12 0.30
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (21 bp):
ATTATATATTATTTTTTCAAA
Found at i:594421 original size:44 final size:45
Alignment explanation
Indices: 594316--594423 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 45
594306 ATTAATTATC
* * *
594316 TATATATATTTTT-AATA-T-TATATTTATTTTTAAATTATATTA
1 TATATATATTTTTCAAAATTATATATTTATTTTCAAATAATATTA
*
594358 TATATATGTTTTTCAAAATTATATATTTATTTTCAAA-AATA-TA
1 TATATATATTTTTCAAAATTATATATTTATTTTCAAATAATATTA
*
594401 CTATTTATATTTTTCAAAATTAT
1 -TATATATATTTTTCAAAATTAT
594424 TTTCAAAACT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
42 12 0.21
43 5 0.09
44 24 0.43
45 15 0.27
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (45 bp):
TATATATATTTTTCAAAATTATATATTTATTTTCAAATAATATTA
Found at i:594449 original size:34 final size:36
Alignment explanation
Indices: 594384--594460 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
594374 AATTATATAT
594384 TTATTTTCAAAAATATACTATTTATATTTTT-CAAAA
1 TTATTTTCAAAAATATACTA-TTATATTTTTCCAAAA
*
594420 TTATTTTCAAAACTATACTA-TATATTTTTCCAAAA
1 TTATTTTCAAAAATATACTATTATATTTTTCCAAAA
*
594455 CTATTT
1 TTATTT
594461 ATTTATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 9 0.24
35 10 0.26
36 19 0.50
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (36 bp):
TTATTTTCAAAAATATACTATTATATTTTTCCAAAA
Found at i:595170 original size:43 final size:43
Alignment explanation
Indices: 595093--595175 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
595083 AGTTGTCTAA
* * * *
595093 TGGTATTATGTCAATGACGTATGTATCTCGACTTGCCATTTTC
1 TGGTATTATGCCAACGACGCATGTATCTCAACTTGCCATTTTC
* *
595136 TGGTATTATGCCGACGACGCATGTGTCTCAACTTGCCATT
1 TGGTATTATGCCAACGACGCATGTATCTCAACTTGCCATT
595176 ATAAATTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (43 bp):
TGGTATTATGCCAACGACGCATGTATCTCAACTTGCCATTTTC
Found at i:599309 original size:7 final size:8
Alignment explanation
Indices: 599284--599312 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
599274 TTAAAAATAA
599284 AAATAATT
1 AAATAATT
599292 AAATAATT
1 AAATAATT
599300 AAAT-ATT
1 AAATAATT
599307 AAATAA
1 AAATAA
599313 AAATAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATAATT
Found at i:599362 original size:4 final size:4
Alignment explanation
Indices: 599345--599452 Score: 69
Period size: 4 Copynumber: 25.8 Consensus size: 4
599335 AAAAGGGTTA
* * *
599345 AAAT AAAT AGAT AAAT AAAT AAAAT CATATT AACAT AAA- GAAT AAATT
1 AAAT AAAT AAAT AAAT AAAT -AAAT -A-AAT AA-AT AAAT AAAT AAA-T
* * *
599393 AAA- AAAT AAAAT AAAA AAAT AAATT AAAAT AAAT AAAT AAAC AAAT AAAA
1 AAAT AAAT -AAAT AAAT AAAT AAA-T -AAAT AAAT AAAT AAAT AAAT AAAT
599443 AAAT -AAT AAA
1 AAAT AAAT AAA
599453 AAGAGTAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
3 8 0.10
4 49 0.60
5 19 0.23
6 5 0.06
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:599409 original size:13 final size:13
Alignment explanation
Indices: 599388--599442 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
599378 CATAAAGAAT
*
599388 AAATTAAAAAATA
1 AAATAAAAAAATA
599401 AAATAAAAAAATA
1 AAATAAAAAAATA
*
599414 AATTAAAATAAAT-
1 AAATAAAA-AAATA
*
599427 AAATAAACAAATA
1 AAATAAAAAAATA
599440 AAA
1 AAA
599443 AAATAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
12 4 0.11
13 28 0.78
14 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:599463 original size:20 final size:20
Alignment explanation
Indices: 599400--599452 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
599390 ATTAAAAAAT
* *
599400 AAAATAAAAAAATAAATTAAA
1 AAAATAAATAAACAAA-TAAA
599421 ATAAATAAATAAACAAATAAA
1 A-AAATAAATAAACAAATAAA
599442 AAAAT-AATAAA
1 AAAATAAATAAA
599453 AAGAGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 6 0.21
20 4 0.14
21 6 0.21
22 13 0.45
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAATAAATAAACAAATAAA
Found at i:600661 original size:21 final size:21
Alignment explanation
Indices: 600635--600697 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
600625 AGAAAAATAA
600635 ATAAATAAATAAATAATAAAT
1 ATAAATAAATAAATAATAAAT
* *
600656 ATAAATAATATTAAT-ATTAAT
1 ATAAATAA-ATAAATAATAAAT
600677 ATAATATATAATAAA-AATAAA
1 ATAA-ATA-AATAAATAATAAA
600698 AATCATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 17 0.50
22 16 0.47
23 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATAAATAAATAATAAAT
Found at i:600738 original size:39 final size:37
Alignment explanation
Indices: 600695--601074 Score: 376
Period size: 39 Copynumber: 10.0 Consensus size: 37
600685 TAATAAAAAT
*
600695 AAAAATCATTTTTAAAACTATATATTATATATGCTTTTA
1 AAAAAT-ATTTTTAAAACTATATATTATATAT-ATTTTA
* *
600734 AAAAAT-TGTTTTCAAAACCATATAATATATATATTTTCA
1 AAAAATAT-TTTT-AAAACTATATATTATATATATTTT-A
** * *
600773 AAAGTTGTTTTTAAAAC--TATA-TA-ATATATTTTC
1 AAAAATATTTTTAAAACTATATATTATATATATTTTA
* *
600806 AAAAATATTTTCAAAACTATATATTATATACATTTTA
1 AAAAATATTTTTAAAACTATATATTATATATATTTTA
* *
600843 AAAAATATTTTTCAAAACTATATATTATATGCATTTTTTC
1 AAAAATATTTTT-AAAACTATATATTATAT--ATATTTTA
*
600883 AAAAATATTTTCCAAAACTATATATTATATATATTTT-
1 AAAAATATTTT-TAAAACTATATATTATATATATTTTA
* *
600920 CAAAATATTTTTAAAAACTATATATTATATATATTTTCT
1 AAAAATATTTTT-AAAACTATATATTATATATATTTT-A
* * *
600959 CAAAATATTTTCAAAAACTATATATTATATATATGTTTT
1 AAAAATATTTT-TAAAACTATATATTATATATAT-TTTA
* *
600998 TAAAATAATTTTAAAACTATATAATATATATATATATATTA
1 AAAAATATTTTTAAAACTATAT-AT-TATATATAT-T-TTA
* *
601039 AAAAATGTTTTTAAAACTATATATTATATATTTTTT
1 AAAAATATTTTTAAAACTATATATTATATATATTTT
601075 TCAAAAATTA
Statistics
Matches: 291, Mismatches: 30, Indels: 42
0.80 0.08 0.12
Matches are distributed among these distances:
33 13 0.04
34 9 0.03
35 6 0.02
36 6 0.02
37 56 0.19
38 47 0.16
39 84 0.29
40 49 0.17
41 21 0.07
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (37 bp):
AAAAATATTTTTAAAACTATATATTATATATATTTTA
Found at i:600795 original size:38 final size:36
Alignment explanation
Indices: 600703--601080 Score: 329
Period size: 38 Copynumber: 10.0 Consensus size: 36
600693 ATAAAAATCA
* *
600703 TTTTT-AAAACTATATATTATATATGCTTTTAAAAAAT
1 TTTTTCAAAACTATATATTATATAT-ATTTT-CAAAAT
* *
600740 TGTTTTCAAAACCATATAATATATATATTTTCAAAAGT
1 T-TTTTCAAAACTATATATTATATATATTTTCAAAA-T
*
600778 TGTTTTTAAAAC--TATA-TA-ATATATTTTCAAAAAT
1 T-TTTTCAAAACTATATATTATATATATTTTC-AAAAT
* * *
600812 ATTTTCAAAACTATATATTATATACATTTTAAAAAAT
1 TTTTTCAAAACTATATATTATATATATTTT-CAAAAT
*
600849 ATTTTTCAAAACTATATATTATATGCATTTTTTCAAAAAT
1 -TTTTTCAAAACTATATATTATAT--ATATTTTC-AAAAT
*
600889 ATTTTCCAAAACTATATATTATATATATTTTCAAAAT
1 -TTTTTCAAAACTATATATTATATATATTTTCAAAAT
*
600926 ATTTTTAAAAACTATATATTATATATATTTTCTCAAAAT
1 -TTTTTCAAAACTATATATTATATATA-TTT-TCAAAAT
* *
600965 ATTTTCAAAAACTATATATTATATATATGTTTTTAAAAT
1 TTTTTC-AAAACTATATATTATATATA--TTTTCAAAAT
* *
601004 AATTTT-AAAACTATATAATATATATATATATATTAAAAAAT
1 -TTTTTCAAAACTATAT-AT-TATATATAT-T-TT-CAAAAT
*
601045 GTTTTT-AAAACTATATATTATATATTTTTTTCAAAA
1 -TTTTTCAAAACTATATATTATATA-TATTTTCAAAA
601081 ATTAATTTCT
Statistics
Matches: 291, Mismatches: 26, Indels: 48
0.80 0.07 0.13
Matches are distributed among these distances:
33 9 0.03
34 11 0.04
35 10 0.03
36 6 0.02
37 52 0.18
38 69 0.24
39 60 0.21
40 55 0.19
41 19 0.07
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (36 bp):
TTTTTCAAAACTATATATTATATATATTTTCAAAAT
Found at i:601081 original size:39 final size:38
Alignment explanation
Indices: 600703--601118 Score: 306
Period size: 39 Copynumber: 10.7 Consensus size: 38
600693 ATAAAAATCA
**
600703 TTTTTAAAACTATATATTATATATGCTTTT-AAAAAAT
1 TTTTTAAAACTATATATTATATATTTTTTTCAAAAAAT
* * * **
600740 TGTTTTCAAAACCATATAATATATA-TATTTTCAAAAGTT
1 T-TTTT-AAAACTATATATTATATATTTTTTTCAAAAAAT
600779 GTTTTTAAAACTATATA--ATATA---TTTTC-AAAAAT
1 -TTTTTAAAACTATATATTATATATTTTTTTCAAAAAAT
* **
600812 ATTTTCAAAACTATATATTATATA-CATTTT-AAAAAAT
1 -TTTTTAAAACTATATATTATATATTTTTTTCAAAAAAT
600849 ATTTTTCAAAACTATATATTATATGCA-TTTTTTCAAAAATAT
1 -TTTTT-AAAACTATATATTATAT--ATTTTTTTCAAAAA-AT
** * *
600891 TTTCCAAAACTATATATTATATA-TATTTTCAAAATAT
1 TTTTTAAAACTATATATTATATATTTTTTTCAAAAAAT
* * *
600928 TTTTAAAAACTATATATTATATATATTTTCTCAAAATAT
1 TTTTTAAAACTATATATTATATAT-TTTTTTCAAAAAAT
**
600967 TTTCAAAAACTATATATTATATATATGTTTTT-AAAATAA-
1 TTTTTAAAACTATATATTATATAT-T-TTTTTCAAAA-AAT
* *
601006 -TTTTAAAACTATATAATATATATATATATATT-AAAAAAT
1 TTTTTAAAACTATAT-AT-TATATAT-TTTTTTCAAAAAAT
601045 GTTTTTAAAACTATATATTATATATTTTTTTCAAAAATTAATT
1 -TTTTTAAAACTATATATTATATATTTTTTTC-AAAA--AA-T
*
601088 TCTTTTAAAAAGTATATTATTATATATTTTT
1 T-TTTT-AAAACTATA-TATTATATATTTTT
601119 CAAACCGTTT
Statistics
Matches: 316, Mismatches: 32, Indels: 54
0.79 0.08 0.13
Matches are distributed among these distances:
33 19 0.06
34 5 0.02
35 5 0.02
36 5 0.02
37 39 0.12
38 64 0.20
39 82 0.26
40 43 0.14
41 22 0.07
42 5 0.02
43 5 0.02
44 8 0.03
45 14 0.04
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.48
Consensus pattern (38 bp):
TTTTTAAAACTATATATTATATATTTTTTTCAAAAAAT
Found at i:601832 original size:85 final size:85
Alignment explanation
Indices: 601716--602125 Score: 608
Period size: 85 Copynumber: 4.8 Consensus size: 85
601706 TGTCATCGAC
* * * * *
601716 CTGAATGTAAT-GAACTCGAAAGTTTTTGTTGACAGCTAGCCCTTCTCGCCTTGAGTTATGTTGT
1 CTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
** *
601780 AAATTTGATATGCTGTTCAG
66 AAATTTGATATGCCCTTGAG
* * *
601800 CTGATTAGAATTGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
1 CTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
*
601865 AATTTTGATATGCCCTTGAG
66 AAATTTGATATGCCCTTGAG
* * *
601885 CTGAATGGAATCGAACTCGAAGG-TTTTATTGACAGATAGCCCTTCTCGCCTTGAGTTATACTGT
1 CTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
*
601949 AAATTTGATATGTCCTTGAG
66 AAATTTGATATGCCCTTGAG
* *
601969 CTGAATGGAATCGAACTTGAAGGTTATTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
1 CTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
602034 AAATTTGATATGCCCTTGAG
66 AAATTTGATATGCCCTTGAG
* * * *
602054 CTGAATGAAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCTCCTTGAGCTATGTTGT
1 CTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
602119 AAATTTG
66 AAATTTG
602126 GTTGGGAGAT
Statistics
Matches: 293, Mismatches: 31, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
84 86 0.29
85 207 0.71
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (85 bp):
CTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
AAATTTGATATGCCCTTGAG
Found at i:602001 original size:169 final size:169
Alignment explanation
Indices: 601716--602125 Score: 617
Period size: 169 Copynumber: 2.4 Consensus size: 169
601706 TGTCATCGAC
* * *
601716 CTGAATGTAAT-GAACTCGAAAGTTTTTGTTGACAGCTAGCCCTTCTCGCCTTGAGTTATGTTGT
1 CTGAATGAAATCGAACTCG-AAGGTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGTTGT
* * * *
601780 AAATTTGATATGCTGTTCAGCTGATTAGAATTGAACTCGAAGGTTTTTGTTGACAGATAGCCCTT
65 AAATTTGATATGCTCTTCAGCTGAATAGAATCGAACTCGAAGGTTATTGTTGACAGATAGCCCTT
*
601845 CTCGCCTTGAGCTATGCTGTAATTTTGATATGCCCTTGAG
130 CTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAG
* * **
601885 CTGAATGGAATCGAACTCGAAGGTTTTATTGACAGATAGCCCTTCTCGCCTTGAGTTATACTGTA
1 CTGAATGAAATCGAACTCGAAGGTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGTTGTA
* * *
601950 AATTTGATATG-TCCTTGAGCTGAATGGAATCGAACTTGAAGGTTATTGTTGACAGATAGCCCTT
66 AATTTGATATGCT-CTTCAGCTGAATAGAATCGAACTCGAAGGTTATTGTTGACAGATAGCCCTT
602014 CTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAG
130 CTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAG
* * *
602054 CTGAATGAAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCTCCTTGAGCTATGTTGT
1 CTGAATGAAATCGAACTCGAAGG-TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGTTGT
602119 AAATTTG
65 AAATTTG
602126 GTTGGGAGAT
Statistics
Matches: 217, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
168 1 0.00
169 166 0.76
170 50 0.23
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (169 bp):
CTGAATGAAATCGAACTCGAAGGTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGTTGTA
AATTTGATATGCTCTTCAGCTGAATAGAATCGAACTCGAAGGTTATTGTTGACAGATAGCCCTTC
TCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAG
Found at i:608955 original size:17 final size:19
Alignment explanation
Indices: 608921--608961 Score: 59
Period size: 17 Copynumber: 2.2 Consensus size: 19
608911 AAAAAAAGAA
608921 AATAAATAAAATAAATAAAT
1 AATAAATAAAAT-AATAAAT
608941 AATAAAT-AAAT-ATAAAT
1 AATAAATAAAATAATAAAT
608958 AATA
1 AATA
608962 TTAATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
19 4 0.19
20 7 0.33
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAAATAAAATAATAAAT
Found at i:608959 original size:4 final size:4
Alignment explanation
Indices: 608920--608952 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
608910 AAAAAAAAGA
608920 AAAT AAAT AAAAT AAAT AAAT -AAT AAAT AAAT A
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT A
608953 TAAATAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.11
4 20 0.74
5 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:608961 original size:20 final size:21
Alignment explanation
Indices: 608921--608959 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
608911 AAAAAAAGAA
608921 AATAAATAAA-ATAAATAAAT
1 AATAAATAAATATAAATAAAT
608941 AATAAATAAATATAAATAA
1 AATAAATAAATATAAATAA
608960 TATTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AATAAATAAATATAAATAAAT
Found at i:608961 original size:24 final size:24
Alignment explanation
Indices: 608920--608987 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
608910 AAAAAAAAGA
608920 AAATAAATA-AAATAAATAAATAAT
1 AAATAAATATAAAT-AATAAATAAT
*
608944 AAATAAATATAAATAAT-ATTAAT
1 AAATAAATATAAATAATAAATAAT
*
608967 ATAATATATGATAAA-AATAAA
1 A-AATAAAT-ATAAATAATAAA
608988 AATCATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.16
24 21 0.57
25 10 0.27
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (24 bp):
AAATAAATATAAATAATAAATAAT
Found at i:608967 original size:9 final size:9
Alignment explanation
Indices: 608922--608974 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 9
608912 AAAAAAGAAA
*
608922 ATAAATAAA
1 ATAAATAAT
608931 ATAAATAAAT
1 ATAAAT-AAT
608941 AATAAATAAAT
1 -ATAAAT-AAT
608952 ATAAATAAT
1 ATAAATAAT
608961 ATTAATATAAT
1 A-TAA-ATAAT
608972 ATA
1 ATA
608975 TGATAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
9 10 0.26
10 13 0.33
11 16 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAAATAAT
Found at i:609079 original size:38 final size:37
Alignment explanation
Indices: 608985--609427 Score: 312
Period size: 39 Copynumber: 11.9 Consensus size: 37
608975 TGATAAAAAT
* * *
608985 AAAAATCATTTTTAAAACTATATATTATATATGCTTTTA
1 AAAAAT-ATTTTTAAAACTATATAATATATAT-ATTTTC
*
609024 AAAAAT-TGTTTTCAAAACCATATAATATATATATTTTC
1 AAAAATAT-TTTT-AAAACTATATAATATATATATTTTC
609062 AAAAATTATTTTTAAAAC--TAT-ATA-ATATATTTTC
1 AAAAA-TATTTTTAAAACTATATAATATATATATTTTC
* * *
609096 AAAAATATTTTCAAAAC-AGTATATTATATACATTTTC
1 AAAAATATTTTTAAAACTA-TATAATATATATATTTTC
* **
609133 AAAAAAATATTTTTCAAAACTATATATTATATGCATTTTC
1 --AAAAATATTTTT-AAAACTATATAATATATATATTTTC
* *
609173 AAAAAGATTTTCCAAAAC----T-ATATAT-TA--TT-
1 AAAAATATTTT-TAAAACTATATAATATATATATTTTC
*
609202 -AAAATATTTTTAAAAACTATATATTATATATATATATTC
1 AAAAATATTTTT-AAAACTATATA--ATATATATATTTTC
*
609241 -AAAATATTTTTAAAAACTATATTATATATATATATATTC
1 AAAAATATTTTT-AAAACTATA-TA-ATATATATATTTTC
* * *
609280 -AAAATATTTTCAAAAACTATATATTATATATATGTTTT
1 AAAAATATTTT-TAAAACTATATAATATATATAT-TTTC
* * * *
609318 TAAAATGTTTTCAAAACTATTTAATATATATATTTTC
1 AAAAATATTTTTAAAACTATATAATATATATATTTTC
* * * *
609355 AAAAATGTTTTCAAAACTATATATTATGTATATTTTC
1 AAAAATATTTTTAAAACTATATAATATATATATTTTC
* *
609392 AAAATTTGATTTTTTTAAA-TATATATATATATATAT
1 AAAA-AT-A-TTTTTAAAACTATATA-ATATATATAT
609428 ATTATATGTT
Statistics
Matches: 337, Mismatches: 34, Indels: 65
0.77 0.08 0.15
Matches are distributed among these distances:
28 14 0.04
30 2 0.01
32 2 0.01
33 16 0.05
34 16 0.05
35 12 0.04
36 7 0.02
37 59 0.18
38 59 0.18
39 109 0.32
40 40 0.12
41 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (37 bp):
AAAAATATTTTTAAAACTATATAATATATATATTTTC
Found at i:609105 original size:12 final size:12
Alignment explanation
Indices: 609054--609111 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
609044 TATAATATAT
609054 ATATTTTCAAAA
1 ATATTTTCAAAA
*
609066 ATTATTTTTAAAA
1 A-TATTTTCAAAA
* * *
609079 CTA-TAT--AAT
1 ATATTTTCAAAA
609088 ATATTTTCAAAA
1 ATATTTTCAAAA
609100 ATATTTTCAAAA
1 ATATTTTCAAAA
609112 CAGTATATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
9 4 0.11
10 2 0.06
11 2 0.06
12 17 0.49
13 10 0.29
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:609210 original size:28 final size:28
Alignment explanation
Indices: 609174--609228 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
609164 TGCATTTTCA
*
609174 AAAAGATTTTCCAAAACTATATATTATT
1 AAAAGATTTTCAAAAACTATATATTATT
* *
609202 AAAATATTTTTAAAAACTATATATTAT
1 AAAAGATTTTCAAAAACTATATATTAT
609229 ATATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (28 bp):
AAAAGATTTTCAAAAACTATATATTATT
Found at i:609247 original size:15 final size:14
Alignment explanation
Indices: 609186--609286 Score: 51
Period size: 15 Copynumber: 7.5 Consensus size: 14
609176 AAGATTTTCC
609186 AAAACTATATATTATT
1 AAAA-TATATA-TATT
609202 AAAATAT-T-T-TT
1 AAAATATATATATT
609213 AAAA-ACTATATATT
1 AAAATA-TATATATT
*
609227 -ATATATATATATT
1 AAAATATATATATT
609240 CAAAATAT-T-T-TT
1 -AAAATATATATATT
*
609252 AAAA-A-CTATATT
1 AAAATATATATATT
*
609264 ATATATATATATATT
1 A-AAATATATATATT
609279 CAAAATAT
1 -AAAATAT
609287 TTTCAAAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 29
0.66 0.05 0.29
Matches are distributed among these distances:
10 3 0.05
11 12 0.18
12 7 0.11
13 14 0.21
14 6 0.09
15 19 0.29
16 5 0.08
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAATATATATATT
Found at i:610941 original size:21 final size:21
Alignment explanation
Indices: 610917--610998 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
610907 GGTTAAGACT
610917 TTTCGATGAAAGGATTTAAAC
1 TTTCGATGAAAGGATTTAAAC
* * * *
610938 TTTCAATGATAGGACTTAACC
1 TTTCGATGAAAGGATTTAAAC
* * * *
610959 TTTTGATTAAAGGGTTTAACAT
1 TTTCGATGAAAGGATTTAA-AC
610981 TTTC-ATGAAAGGATTTAA
1 TTTCGATGAAAGGATTTAA
610999 TCATTTCATG
Statistics
Matches: 45, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
21 42 0.93
22 3 0.07
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (21 bp):
TTTCGATGAAAGGATTTAAAC
Found at i:611005 original size:21 final size:20
Alignment explanation
Indices: 610917--611010 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 20
610907 GGTTAAGACT
610917 TTTCGATGAAAGGATTTAA-A
1 TTTC-ATGAAAGGATTTAACA
* * *
610937 CTTTCAATGATAGGACTTAACCT
1 -TTTC-ATGAAAGGATTTAA-CA
* * *
610960 TTTGATTAAAGGGTTTAACA
1 TTTCATGAAAGGATTTAACA
610980 TTTTCATGAAAGGATTTAATCA
1 -TTTCATGAAAGGATTTAA-CA
611002 TTTCATGAA
1 TTTCATGAA
611011 GAGAATTGTT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.02
21 50 0.89
22 5 0.09
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (20 bp):
TTTCATGAAAGGATTTAACA
Found at i:618664 original size:29 final size:29
Alignment explanation
Indices: 618600--618715 Score: 178
Period size: 29 Copynumber: 3.9 Consensus size: 29
618590 AAATCACATG
* *
618600 TTTAGTACTTAAACTATCAGTTTTATTTCGT
1 TTTAGTACTTAAACTTTCA--CTTATTTCGT
618631 TTTAGTACTTAAACTTTCACTTATTTCGT
1 TTTAGTACTTAAACTTTCACTTATTTCGT
*
618660 TTTAGTACTTAAACTTTCACTTGTTTCGT
1 TTTAGTACTTAAACTTTCACTTATTTCGT
*
618689 TTTAGTACTTAAACTTTCACTTGTTTC
1 TTTAGTACTTAAACTTTCACTTATTTC
618716 AAAATCATAC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
29 64 0.78
31 18 0.22
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (29 bp):
TTTAGTACTTAAACTTTCACTTATTTCGT
Found at i:625866 original size:20 final size:20
Alignment explanation
Indices: 625803--625859 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
625793 GAATGTCCAC
625803 GGGGTACAGATTCCCCCTAG
1 GGGGTACAGATTCCCCCTAG
*
625823 GGGGTACCGATTCCCCCTAG
1 GGGGTACAGATTCCCCCTAG
*
625843 GGGGAACAGATTCCCCC
1 GGGGTACAGATTCCCCC
625860 CCAGGGGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.33, G:0.30, T:0.18
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCTAG
Found at i:627181 original size:19 final size:20
Alignment explanation
Indices: 627157--627204 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
627147 AATGATTTTC
*
627157 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
627176 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
627196 TTTTGAAAA
1 TTTTGAAAA
627205 AAGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:627235 original size:23 final size:24
Alignment explanation
Indices: 627203--627253 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
627193 AAATTTTGAA
* *
627203 AAAAGATTTAGAGCTTTAAAAAAT
1 AAAAGATTTAAAGCTTTAAAAAAG
* *
627227 AAAA-ATTTAAAGTTTTGAAAAAG
1 AAAAGATTTAAAGCTTTAAAAAAG
627250 AAAA
1 AAAA
627254 TTTTGATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.59, C:0.02, G:0.12, T:0.27
Consensus pattern (24 bp):
AAAAGATTTAAAGCTTTAAAAAAG
Found at i:628690 original size:22 final size:21
Alignment explanation
Indices: 628658--628743 Score: 102
Period size: 23 Copynumber: 4.0 Consensus size: 21
628648 AACATAATGT
*
628658 CCAGGGAGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
628679 CCAAGGGGGTACCGATT-CCCC
1 CC-AGGGGGTACAGATTCCCCC
*
628700 CCAGGGGGAACAGATTCCCCCCC
1 CCAGGGGGTACAGATT--CCCCC
*
628723 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
628744 TGTCTAACGA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
20 12 0.22
21 13 0.24
22 12 0.22
23 18 0.33
ACGTcount: A:0.20, C:0.41, G:0.27, T:0.13
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:628717 original size:42 final size:43
Alignment explanation
Indices: 628658--628743 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
628648 AACATAATGT
*
628658 CCAGGGAGTACAGATT-CCCCCCCAAGGGGGTACCGATTCCCC
1 CCAGGGAGAACAGATTCCCCCCCCAAGGGGGTACCGATTCCCC
* *
628700 CCAGGGGGAACAGATTCCCCCCCCCAGGGGGTACCGATTCCCC
1 CCAGGGAGAACAGATTCCCCCCCCAAGGGGGTACCGATTCCCC
628743 C
1 C
628744 TGTCTAACGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 14 0.35
43 26 0.65
ACGTcount: A:0.20, C:0.41, G:0.27, T:0.13
Consensus pattern (43 bp):
CCAGGGAGAACAGATTCCCCCCCCAAGGGGGTACCGATTCCCC
Found at i:631938 original size:21 final size:21
Alignment explanation
Indices: 631913--631992 Score: 124
Period size: 21 Copynumber: 3.8 Consensus size: 21
631903 GAATGTCCAA
631913 GGGGTACAGATTCCCCCCCAG
1 GGGGTACAGATTCCCCCCCAG
*
631934 GGGGTACCGATTCCCCCCCAG
1 GGGGTACAGATTCCCCCCCAG
* *
631955 GGGGAACAAATTCCCCCCCAG
1 GGGGTACAGATTCCCCCCCAG
*
631976 GGGGTACCGATTCCCCC
1 GGGGTACAGATTCCCCC
631993 TGTCTAACGG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.19, C:0.40, G:0.28, T:0.14
Consensus pattern (21 bp):
GGGGTACAGATTCCCCCCCAG
Found at i:631970 original size:42 final size:42
Alignment explanation
Indices: 631913--631992 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
631903 GAATGTCCAA
* *
631913 GGGGTACAGATTCCCCCCCAGGGGGTACCGATTCCCCCCCAG
1 GGGGAACAAATTCCCCCCCAGGGGGTACCGATTCCCCCCCAG
631955 GGGGAACAAATTCCCCCCCAGGGGGTACCGATTCCCCC
1 GGGGAACAAATTCCCCCCCAGGGGGTACCGATTCCCCC
631993 TGTCTAACGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.19, C:0.40, G:0.28, T:0.14
Consensus pattern (42 bp):
GGGGAACAAATTCCCCCCCAGGGGGTACCGATTCCCCCCCAG
Found at i:634225 original size:23 final size:24
Alignment explanation
Indices: 634194--634240 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
634184 AATTAAAATT
*
634194 TTTAAATTTTTTTGAAAG-ATTAG
1 TTTAAATTTTTTTCAAAGAATTAG
*
634217 TTTATATTTTTTTCAAAGAATTAG
1 TTTAAATTTTTTTCAAAGAATTAG
634241 AGTATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (24 bp):
TTTAAATTTTTTTCAAAGAATTAG
Found at i:634246 original size:24 final size:23
Alignment explanation
Indices: 634199--634246 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
634189 AAATTTTTAA
* **
634199 ATTTTTTTGAAAGATTAGTTTAT
1 ATTTTTTTCAAAGATTAGAGTAT
634222 ATTTTTTTCAAAGAATTAGAGTAT
1 ATTTTTTTCAAAG-ATTAGAGTAT
634246 A
1 A
634247 ATTAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (23 bp):
ATTTTTTTCAAAGATTAGAGTAT
Found at i:638946 original size:18 final size:19
Alignment explanation
Indices: 638919--638956 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
638909 GGGTCGACGT
* *
638919 CGGTGCCGGTGAAGG-TGG
1 CGGTGACGGTCAAGGATGG
638937 CGGTGACGGTCAAGGATGG
1 CGGTGACGGTCAAGGATGG
638956 C
1 C
638957 CGGTCAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.16, C:0.18, G:0.50, T:0.16
Consensus pattern (19 bp):
CGGTGACGGTCAAGGATGG
Found at i:639950 original size:27 final size:25
Alignment explanation
Indices: 639913--639996 Score: 109
Period size: 24 Copynumber: 3.4 Consensus size: 25
639903 GAATGACCAG
*
639913 TTTTTTT-ACCGGATTAAAAACCGA
1 TTTTTTTAACCGGATAAAAAACCGA
639937 TTTTTTTCAAACCGGATAAAAAACCGA
1 TTTTTTT--AACCGGATAAAAAACCGA
* *
639964 -TTTTTTATCCGGATAAAAAACCGG
1 TTTTTTTAACCGGATAAAAAACCGA
639988 TTTTTTTAA
1 TTTTTTTAA
639997 AAAACCGGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
24 23 0.44
25 7 0.13
26 6 0.12
27 16 0.31
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (25 bp):
TTTTTTTAACCGGATAAAAAACCGA
Found at i:640009 original size:40 final size:39
Alignment explanation
Indices: 639953--640049 Score: 106
Period size: 41 Copynumber: 2.4 Consensus size: 39
639943 TCAAACCGGA
* *
639953 TAAAAAACCGATTTTTTATCCGGATAAAAAACCGG-TTTTTT
1 TAAAAAACCG-GTTTTTAACC-GA-AAAAAACCGGTTTTTTT
*
639994 TAAAAAACCGGTTTTTTAACCGAAAAAATCCGGTTTTTTT
1 TAAAAAACCGG-TTTTTAACCGAAAAAAACCGGTTTTTTT
**
640034 TTTAAAACCGGTTTTT
1 TAAAAAACCGGTTTTT
640050 TGCAAACCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 14 0.29
40 17 0.35
41 18 0.37
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (39 bp):
TAAAAAACCGGTTTTTAACCGAAAAAAACCGGTTTTTTT
Found at i:640012 original size:16 final size:17
Alignment explanation
Indices: 639977--640010 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
639967 TTTATCCGGA
639977 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
639994 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
640011 AACCGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
TAAAAAACCGGTTTTTT
Found at i:640050 original size:40 final size:41
Alignment explanation
Indices: 639953--640050 Score: 128
Period size: 40 Copynumber: 2.4 Consensus size: 41
639943 TCAAACCGGA
* *
639953 TAAAAAACCGATTTTTTATCCGGATAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTTAACCGGATAAAAAACCGGTTTTTT
*
639994 TAAAAAACCGGTTTTTTAACC-GA-AAAAATCCGGTTTTTTT
1 TAAAAAACCGGTTTTTTAACCGGATAAAAAACCGG-TTTTTT
**
640034 TTTAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
640051 GCAAACCGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
39 9 0.18
40 23 0.45
41 19 0.37
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (41 bp):
TAAAAAACCGGTTTTTTAACCGGATAAAAAACCGGTTTTTT
Found at i:646318 original size:6 final size:6
Alignment explanation
Indices: 646307--646357 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
646297 TTTGATTGTT
* * *
646307 CCTTTC CCTTTC CCTTTC CCTTTC CCTCTC CCTTTC CCTCTC CCTCTC
1 CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC
646355 CCT
1 CCT
646358 CTCCTTCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (6 bp):
CCTTTC
Found at i:646322 original size:12 final size:12
Alignment explanation
Indices: 646311--646361 Score: 84
Period size: 12 Copynumber: 4.2 Consensus size: 12
646301 ATTGTTCCTT
*
646311 TCCCTTTCCCTT
1 TCCCTTTCCCTC
646323 TCCCTTTCCCTC
1 TCCCTTTCCCTC
646335 TCCCTTTCCCTC
1 TCCCTTTCCCTC
*
646347 TCCCTCTCCCTC
1 TCCCTTTCCCTC
646359 TCC
1 TCC
646362 TTCTCTATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (12 bp):
TCCCTTTCCCTC
Found at i:646328 original size:18 final size:18
Alignment explanation
Indices: 646307--646357 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
646297 TTTGATTGTT
*
646307 CCTTTCCCTTTCCCTTTC
1 CCTTTCCCTCTCCCTTTC
646325 CCTTTCCCTCTCCCTTTC
1 CCTTTCCCTCTCCCTTTC
*
646343 CCTCTCCCTCTCCCT
1 CCTTTCCCTCTCCCT
646358 CTCCTTCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (18 bp):
CCTTTCCCTCTCCCTTTC
Found at i:646358 original size:6 final size:6
Alignment explanation
Indices: 646311--646366 Score: 67
Period size: 6 Copynumber: 9.3 Consensus size: 6
646301 ATTGTTCCTT
* * * *
646311 TCCCTT TCCCTT TCCCTT TCCCTC TCCCTT TCCCTC TCCCTC TCCCTC
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC
*
646359 TCCTTC TC
1 TCCCTC TC
646367 TATTCTCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (6 bp):
TCCCTC
Found at i:646366 original size:18 final size:17
Alignment explanation
Indices: 646305--646363 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
646295 TCTTTGATTG
*
646305 TTCCTTTCCCTTTCCCT
1 TTCCTTTCCCTCTCCCT
646322 TTCCCTTTCCCTCTCCCT
1 TT-CCTTTCCCTCTCCCT
*
646340 TTCCCTCTCCCTCTCCCT
1 TT-CCTTTCCCTCTCCCT
*
646358 CTCCTT
1 TTCCTT
646364 CTCTATTCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.14
18 32 0.86
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (17 bp):
TTCCTTTCCCTCTCCCT
Found at i:651831 original size:24 final size:24
Alignment explanation
Indices: 651801--651853 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
651791 AAGTTCGATC
651801 GAAGCCTAAAATTTGAGCTCAATT
1 GAAGCCTAAAATTTGAGCTCAATT
651825 GAAGCCTAAAATTTGAGCTCAATT
1 GAAGCCTAAAATTTGAGCTCAATT
651849 GAAGC
1 GAAGC
651854 AAAAGAATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (24 bp):
GAAGCCTAAAATTTGAGCTCAATT
Found at i:658669 original size:2 final size:2
Alignment explanation
Indices: 658662--658687 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
658652 TATGGAAATG
658662 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
658688 TTAGGTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:662635 original size:17 final size:18
Alignment explanation
Indices: 662613--662646 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
662603 AGGGTTCTAC
662613 GTGGTCCTT-GGGACATA
1 GTGGTCCTTCGGGACATA
662630 GTGGTCCTTCGGGACAT
1 GTGGTCCTTCGGGACAT
662647 TTCATAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:663087 original size:2 final size:2
Alignment explanation
Indices: 663012--663068 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
663002 TATGGAATTG
663012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
663054 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
663069 GGTGTTATGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:663888 original size:23 final size:22
Alignment explanation
Indices: 663844--663888 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
663834 GAGTATATGA
* *
663844 TGGTGTAATAAAGTATAGGAAT
1 TGGTATAATAAAGTATAAGAAT
*
663866 TGGTATAATAGAATTATAAGAAT
1 TGGTATAATA-AAGTATAAGAAT
663889 AAGTGAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (22 bp):
TGGTATAATAAAGTATAAGAAT
Found at i:664072 original size:16 final size:16
Alignment explanation
Indices: 664051--664092 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
664041 CATGTGAAAA
664051 GATATATGTGTTACAT
1 GATATATGTGTTACAT
664067 GATATATGTGTTACAT
1 GATATATGTGTTACAT
664083 GATATATGTG
1 GATATATGTG
664093 ATCTATGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (16 bp):
GATATATGTGTTACAT
Found at i:667285 original size:95 final size:94
Alignment explanation
Indices: 667157--667340 Score: 235
Period size: 95 Copynumber: 1.9 Consensus size: 94
667147 TACCTATGAA
* * ** * *
667157 GTAGTATCGATACCATGGTAAGGGTATCAATACCCGGTAACATCGAA-TATAAAATTTGTATCGA
1 GTAGTATCGATACCATAGTAAGAGTATCAATACCAAGAAACATCGAAGT-TAAAATTGGTATCGA
* *
667221 TACCGTAAGGGGGTATCAGTAGCATAGTAGG
65 TACCGGAA-GGGGTATCAGTACCATAGTAGG
* *
667252 GTAGTATCGATACCATAGTAAGAGTATCGATACCAAGAAACATCGAAGTTAAAATTGGTATTGAT
1 GTAGTATCGATACCATAGTAAGAGTATCAATACCAAGAAACATCGAAGTTAAAATTGGTATCGAT
* *
667317 ACTGGAAGGGGTATCGGTACCATA
66 ACCGGAAGGGGTATCAGTACCATA
667341 TTATAGAAGT
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
94 15 0.20
95 60 0.79
96 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.26
Consensus pattern (94 bp):
GTAGTATCGATACCATAGTAAGAGTATCAATACCAAGAAACATCGAAGTTAAAATTGGTATCGAT
ACCGGAAGGGGTATCAGTACCATAGTAGG
Found at i:667784 original size:59 final size:59
Alignment explanation
Indices: 667709--667915 Score: 256
Period size: 59 Copynumber: 3.5 Consensus size: 59
667699 CTAAGTGTTT
* * *
667709 TAAAATGATAAAAAATTCATACTAAGGGTATGAATTTCAGTATAGGGCACTTCGAGTGC
1 TAAAATGATGAGAAATTCATACTAAGTGTATGAATTTCAGTATAGGGCACTTCGAGTGC
* * * * * *
667768 TAAAATGTTGAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGAACTTGGTGTAC
1 TAAAATGATGAGAAATTCATACTAAGTGTATGAATTTCAGTATAGGGCACTTCGAGTGC
* * *
667827 TGAAATGATGAGAAATTTATACTAACTGTATGAATTTTCA-TATAGGGCACTTC-ATGTGC
1 TAAAATGATGAGAAATTCATACTAAGTGTATGAA-TTTCAGTATAGGGCACTTCGA-GTGC
* *
667886 TAAAATGATAAGAAATTCATATTAAGTGTA
1 TAAAATGATGAGAAATTCATACTAAGTGTA
667916 AGAAATGTTT
Statistics
Matches: 123, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
59 119 0.97
60 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (59 bp):
TAAAATGATGAGAAATTCATACTAAGTGTATGAATTTCAGTATAGGGCACTTCGAGTGC
Found at i:667940 original size:2 final size:2
Alignment explanation
Indices: 667933--667967 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
667923 TTTTATGGGA
667933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
667968 CGAATATAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:668274 original size:68 final size:68
Alignment explanation
Indices: 668165--668559 Score: 603
Period size: 68 Copynumber: 5.8 Consensus size: 68
668155 AGTTAAAAGA
*
668165 TTTGAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
*
668230 GCG
66 GCC
* *
668233 TTTGAGGCCTAACTGTACATATGACAGAAAGGTGTCATTTATGCCAGTTAGATCAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
*
668298 TCC
66 GCC
* *
668301 TTTGAGGCCTAACTGTGCATATGACAGAAAGATGTCATTTATGCTAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
*
668366 TCC
66 GCC
* * * * *
668369 TTTGAGTCCTAAATGTGCATATGACAGAAAGGTTTCATCTATGACAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
668434 GCC
66 GCC
* * *
668437 TTTGAAGCCTAACTGTACATATGATAGAAAGGTGTCATTTATG-CAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
668501 GCC
66 GCC
* * * *
668504 TTTGAGGCCTAACTGTGCATATCACAAAAATGTGTCATTTATGGCAGTTAGATGAA
1 TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
668560 CGATTAAGTA
Statistics
Matches: 296, Mismatches: 30, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
67 61 0.21
68 235 0.79
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
GCC
Found at i:670325 original size:27 final size:29
Alignment explanation
Indices: 670273--670326 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
670263 TTCTATATGC
670273 TTCATTTTTGATACAATATTTATTCATAT
1 TTCATTTTTGATACAATATTTATTCATAT
* *
670302 TTCA-TTTTGAT-CACTATTTGTTCAT
1 TTCATTTTTGATACAATATTTATTCAT
670327 TAATATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 7 0.30
29 4 0.17
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.56
Consensus pattern (29 bp):
TTCATTTTTGATACAATATTTATTCATAT
Found at i:672859 original size:32 final size:32
Alignment explanation
Indices: 672815--672876 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
672805 TCTTACTTGT
*
672815 ACTAACTAATTTCTTTTCTTTTGCTTGTGTAC
1 ACTAACTAATTTCGTTTCTTTTGCTTGTGTAC
* *
672847 ACTAACTTATTTCGTTTCTTTTGTTTGTGT
1 ACTAACTAATTTCGTTTCTTTTGCTTGTGT
672877 CATTTTCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.56
Consensus pattern (32 bp):
ACTAACTAATTTCGTTTCTTTTGCTTGTGTAC
Found at i:688252 original size:16 final size:16
Alignment explanation
Indices: 688231--688264 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
688221 CTCCTCACAT
*
688231 ATCAACATATATATAC
1 ATCAACACATATATAC
688247 ATCAACACATATATAC
1 ATCAACACATATATAC
688263 AT
1 AT
688265 GACACATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (16 bp):
ATCAACACATATATAC
Found at i:688654 original size:36 final size:37
Alignment explanation
Indices: 688606--688686 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 37
688596 AAAAAAGAAC
688606 AAAACAAAGTGTTGTCTCGCTAGAG-TCAGTTTTCT-TA
1 AAAAC-AAGTGTTGTCTCGCTAGAGAT-AGTTTTCTCTA
* * *
688643 AAAACAAGTGTTGTTTCGCTTGAGATAGTTTTCTCTT
1 AAAACAAGTGTTGTCTCGCTAGAGATAGTTTTCTCTA
688680 AAAACAA
1 AAAACAA
688687 ATTTCGTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
36 25 0.64
37 14 0.36
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (37 bp):
AAAACAAGTGTTGTCTCGCTAGAGATAGTTTTCTCTA
Found at i:688684 original size:37 final size:37
Alignment explanation
Indices: 688606--688712 Score: 114
Period size: 37 Copynumber: 2.9 Consensus size: 37
688596 AAAAAAGAAC
* *
688606 AAAACAAAGTGTTGTCTCGCTAGAG-TCAGTTTTCTTA
1 AAAAC-AAGTGTTGTTTCGCTTGAGATCAGTTTTCTTA
*
688643 AAAACAAGTGTTGTTTCGCTTGAGAT-AGTTTTCTCTT
1 AAAACAAGTGTTGTTTCGCTTGAGATCAGTTTTCT-TA
* *
688680 AAAACAAAT-TTCGTTTCGCTTGAGA-CATTTTTC
1 AAAACAAGTGTT-GTTTCGCTTGAGATCAGTTTTC
688713 CTTTGAGATA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
36 27 0.44
37 34 0.56
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (37 bp):
AAAACAAGTGTTGTTTCGCTTGAGATCAGTTTTCTTA
Found at i:688967 original size:29 final size:29
Alignment explanation
Indices: 688914--688969 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
688904 TTTTCTTGAG
688914 AAAACTTTGAGTCTGTTTCACTTGAAAAA
1 AAAACTTTGAGTCTGTTTCACTTGAAAAA
688943 AAAATCTTTGAGTCTGTTTC-CTTGAAA
1 AAAA-CTTTGAGTCTGTTTCACTTGAAA
688970 CAAAGTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (29 bp):
AAAACTTTGAGTCTGTTTCACTTGAAAAA
Found at i:689029 original size:61 final size:62
Alignment explanation
Indices: 688942--689163 Score: 231
Period size: 61 Copynumber: 3.5 Consensus size: 62
688932 CACTTGAAAA
* *
688942 AAAAATCTTTGAGTCTGTTTCCTTGAAACAAAGTTT-TATCTATTGAGATAATTTCTTTT-G
1 AAAAATCTTTGAGTCTGTTTCTTTGAAACAAATTTTGTATCTATTGAGATAATTTCTTTTAG
* *
689002 AAAAATCCTTTGAGT-TGTTTCTATTGAAACAAATTTTGTATCTCA---AGATAGTTTCTTTTAA
1 AAAAAT-CTTTGAGTCTGTTTCT-TTGAAACAAATTTTGTATCT-ATTGAGATAATTTCTTTTAG
* * * *
689063 AAAAATCTTTGAGTCTGTTTCTCTGAAAACAAATTTTTGTCTCTCTTGAGAAAATTTCTTTTGAG
1 AAAAATCTTTGAGTCTGTTTCTTTG-AAACAAA-TTTTGTATCTATTGAGATAATTTCTTTT-AG
*
689128 AAACAAAATCTTTGAGTATGTTTCTTTTGAAACAAA
1 --A-AAAATCTTTGAGTCTGTTTC-TTTGAAACAAA
689164 ACCATATTTG
Statistics
Matches: 134, Mismatches: 12, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
60 35 0.26
61 41 0.31
62 14 0.10
63 1 0.01
64 12 0.09
65 1 0.01
67 1 0.01
68 26 0.19
69 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (62 bp):
AAAAATCTTTGAGTCTGTTTCTTTGAAACAAATTTTGTATCTATTGAGATAATTTCTTTTAG
Found at i:689029 original size:90 final size:91
Alignment explanation
Indices: 688858--689030 Score: 207
Period size: 90 Copynumber: 1.9 Consensus size: 91
688848 GTTTATAATA
* *
688858 TTTGAGTCTGTTTCTCTTGAAACAAATCTTGTCTCCCTTGAGAAAGTTTTCTTGAGAAAACTTTG
1 TTTGAGTCTGTTTCTCTTGAAACAAATCTTGTATCCATTGAGAAAGTTTTCTTGAGAAAACTTTG
688923 AGTCTGTTTCACTTGAAAAAAAAATC
66 AGTCTGTTTCACTTGAAAAAAAAATC
* *
688949 TTTGAGTCTGTTTC-CTTGAAACAAAGT-TT-TATCTATTGAGATAA-TTTCTTTTGA-AAAATC
1 TTTGAGTCTGTTTCTCTTGAAACAAA-TCTTGTATCCATTGAGA-AAGTTT-TCTTGAGAAAA--
689009 CTTTGAGT-TGTTTCTA-TTGAAA
61 CTTTGAGTCTGTTTC-ACTTGAAA
689031 CAAATTTTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
89 16 0.22
90 32 0.44
91 24 0.33
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (91 bp):
TTTGAGTCTGTTTCTCTTGAAACAAATCTTGTATCCATTGAGAAAGTTTTCTTGAGAAAACTTTG
AGTCTGTTTCACTTGAAAAAAAAATC
Found at i:689552 original size:131 final size:129
Alignment explanation
Indices: 689296--689560 Score: 370
Period size: 131 Copynumber: 2.0 Consensus size: 129
689286 TGAAACCATT
* * * *
689296 ATCCCTAAAGATGACATGTCATCCTCATCGCGTAGGAACCGTGTCATCCCCTACCAGACCTCCTT
1 ATCCCTAAAGATGACATGCCATCCTCATCGCATAGGAACCGTGTCATCCCCGACCAGACCTCCTC
* * *
689361 ATCATGTAGAGCTGTGTCACCCCCAGATAACCAACAGTCCTCATCACGTAGGAATCGTGTTATC
66 ATCACGTAGAGCCGTGTCACCCCCAGATAACCAACAGTCATCATCACGTAGGAATCGTGTTATC
* * * * *
689425 ATCCCTAAAGATGGCCTGCCATCCTCATTGCATAGGAACTGTGTCATCCCCCGACTAGACCTCCT
1 ATCCCTAAAGATGACATGCCATCCTCATCGCATAGGAACCGTGTCAT-CCCCGACCAGACCTCCT
* * *
689490 CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCATCATCACGTAGGAATCGTGTTAT
65 CATCACGTA-GAGCCGTGTCACCCCCAGATAACCAACAGTCATCATCACGTAGGAATCGTGTTAT
689555 C
129 C
689556 A-CCCT
1 ATCCCT
689561 TCCTAAAGAT
Statistics
Matches: 119, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
129 41 0.34
130 26 0.22
131 52 0.44
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (129 bp):
ATCCCTAAAGATGACATGCCATCCTCATCGCATAGGAACCGTGTCATCCCCGACCAGACCTCCTC
ATCACGTAGAGCCGTGTCACCCCCAGATAACCAACAGTCATCATCACGTAGGAATCGTGTTATC
Found at i:689767 original size:3 final size:3
Alignment explanation
Indices: 689761--689819 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
689751 CTACAAAAAA
* *
689761 ATT ATT AATT A-T AAT ATT ATT ATAT ATT ATT ATT ATT ATT GTT ATT
1 ATT ATT -ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
* *
689807 GTT ATT AAT ATT A
1 ATT ATT ATT ATT A
689820 CATATTTTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 2 0.04
3 38 0.83
4 6 0.13
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Done.