Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008817.1 Hibiscus syriacus cultivar Beakdansim tig00111983_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: 1047399
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 1 of 4
Found at i:2439 original size:2 final size:2
Alignment explanation
Indices: 2432--2456 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2422 AGCATCAAAT
2432 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2457 TAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7860 original size:15 final size:15
Alignment explanation
Indices: 7840--7871 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
7830 ACATACTATA
7840 AAACTAGTCAAAAGC
1 AAACTAGTCAAAAGC
7855 AAACTAGTCAAAAGC
1 AAACTAGTCAAAAGC
7870 AA
1 AA
7872 CAGCTATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.12
Consensus pattern (15 bp):
AAACTAGTCAAAAGC
Found at i:10268 original size:14 final size:14
Alignment explanation
Indices: 10249--10276 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10239 AAGGTGTTAC
10249 TTTGGATTGCATTA
1 TTTGGATTGCATTA
10263 TTTGGATTGCATTA
1 TTTGGATTGCATTA
10277 GCAGTTGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
TTTGGATTGCATTA
Found at i:22526 original size:33 final size:32
Alignment explanation
Indices: 22484--22550 Score: 71
Period size: 32 Copynumber: 2.0 Consensus size: 32
22474 ATATATTTAA
*
22484 AAATCAATAAAAATACAATAAATAAAGAATTAA
1 AAATCAAT-AAAATACAATAAAAAAAGAATTAA
* * **
22517 AAGTGAATAAAATTTAATAAAAAAAGAATGTAA
1 AAATCAATAAAATACAATAAAAAAAGAAT-TAA
22550 A
1 A
22551 GCTAAAGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.22
Consensus pattern (32 bp):
AAATCAATAAAATACAATAAAAAAAGAATTAA
Found at i:37489 original size:22 final size:22
Alignment explanation
Indices: 37461--37509 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
37451 GCTTTATGAT
37461 CTTTTGCAGAGAGGAGACATTC
1 CTTTTGCAGAGAGGAGACATTC
37483 CTTTTGCAGAGAGGAGACATTC
1 CTTTTGCAGAGAGGAGACATTC
37505 CTTTT
1 CTTTT
37510 AGTTGTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (22 bp):
CTTTTGCAGAGAGGAGACATTC
Found at i:56780 original size:16 final size:17
Alignment explanation
Indices: 56753--56784 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
56743 ATAAAAAGGT
56753 TAAATAATTTCTAATTC
1 TAAATAATTTCTAATTC
56770 TAAAT-ATTTCTAATT
1 TAAATAATTTCTAATT
56785 GTTTTTAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATAATTTCTAATTC
Found at i:57504 original size:2 final size:2
Alignment explanation
Indices: 57497--57532 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
57487 ATCGTTTTTC
57497 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
57533 TCAAAAGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65018 original size:32 final size:32
Alignment explanation
Indices: 64982--65120 Score: 233
Period size: 32 Copynumber: 4.3 Consensus size: 32
64972 TGAATTTAAG
*
64982 ACAATTAGTGCAGTGTCTTAACAGATTAGGTA
1 ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
65014 ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
1 ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
65046 ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
1 ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
** * *
65078 ACAATTAGTGCAGTGTCTTGGTAGATTGGGCA
1 ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
65110 ACAATTAGTGC
1 ACAATTAGTGC
65121 CCTTTCGCTA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 102 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (32 bp):
ACAATTAGTGCAGTGTCTTGACAGATTAGGTA
Found at i:68137 original size:21 final size:21
Alignment explanation
Indices: 68112--68151 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
68102 TATTAATCGA
68112 TTATT-ATATAATAAATTAAAC
1 TTATTAATAT-ATAAATTAAAC
*
68133 TTATTAATATTTAAATTAA
1 TTATTAATATATAAATTAA
68152 TTTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATTAATATATAAATTAAAC
Found at i:68256 original size:23 final size:21
Alignment explanation
Indices: 68215--68256 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
68205 AATGATTATA
*
68215 ATTAAAATTTATAATATAAGG
1 ATTAAAATTTATAAAATAAGG
68236 ATTAAAATTATTATAAAATAA
1 ATTAAAA-T-TTATAAAATAA
68257 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTAAAATTTATAAAATAAGG
Found at i:90275 original size:21 final size:21
Alignment explanation
Indices: 90245--90461 Score: 130
Period size: 21 Copynumber: 10.4 Consensus size: 21
90235 GATTTACATA
* *
90245 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCGAAG
*
90266 TTCGTGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
*
90287 TTCGCGTTGCGA-A-TCTGGAAA
1 TTCGCGTTGCGATAGTC--GAAG
* **
90308 CT-GATTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* *
90328 TTCGCGTTGCGATTTATTAC-AAA
1 TTCGCGTTGCGA--TAGT-CGAAG
*
90351 TT--TGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* * * *
90370 TTTGCGTTGCGATTTATTCTAAA
1 TTCGCGTTGCGA--TAGTCGAAG
90393 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* * *
90412 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCGAAG
90435 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
90454 TTCGCGTT
1 TTCGCGTT
90462 TCTATTTATT
Statistics
Matches: 147, Mismatches: 30, Indels: 38
0.68 0.14 0.18
Matches are distributed among these distances:
18 1 0.01
19 25 0.17
20 12 0.08
21 83 0.56
22 2 0.01
23 23 0.16
24 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:90297 original size:42 final size:41
Alignment explanation
Indices: 90245--90491 Score: 268
Period size: 42 Copynumber: 5.9 Consensus size: 41
90235 GATTTACATA
* * *
90245 TTCGCATTGCGA-TAGTCCAAGTTCGTGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAATTC--GTTGCGATAGTCGAAG
** *
90287 TTCGCGTTGCGA--ATCTGGAAACT-GATTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTAT-TCCAAATTCG--TTGCGATAGTCGAAG
* *
90328 TTCGCGTTGCGATTTATTACAAATTTGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTCGAAG
* *
90370 TTTGCGTTGCGATTTATTCTAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTCGAAG
90412 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTCGAAG
* * *
90454 TTCGCGTTTCTATTTATTCCAAGTTCGTTGCGATAGTC
1 TTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTC
90492 CAAAATCTCA
Statistics
Matches: 180, Mismatches: 18, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
39 1 0.01
41 28 0.16
42 143 0.79
43 5 0.03
44 3 0.02
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATTATTCCAAATTCGTTGCGATAGTCGAAG
Found at i:90424 original size:84 final size:84
Alignment explanation
Indices: 90271--90491 Score: 297
Period size: 84 Copynumber: 2.6 Consensus size: 84
90261 CCAAGTTCGT
** *
90271 GTTGCGATAGTCGAAGTTCGCGTTGCGA---ATCTGGAAACT-GATTTGCGATAGTCGAAGTTCG
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT-TCCAAATTCG--TTGCGATAGTCGAAGTTCG
*
90332 CGTTGCGATTTATTACAAATTT
63 CGTTGCGATTTATTACAAATTC
* *
90354 GTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCTAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
*
90419 TGCGATTTATTCCAAATTC
66 TGCGATTTATTACAAATTC
* * *
90438 GTTGCGATAGTCGAAGTTCGCGTTTCTATTTATTCCAAGTTCGTTGCGATAGTC
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
90492 CAAAATCTCA
Statistics
Matches: 123, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
83 27 0.22
84 88 0.72
85 5 0.04
86 3 0.02
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.37
Consensus pattern (84 bp):
GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
TGCGATTTATTACAAATTC
Found at i:90594 original size:6 final size:6
Alignment explanation
Indices: 90583--90650 Score: 118
Period size: 6 Copynumber: 11.3 Consensus size: 6
90573 AAACACGTAT
*
90583 GACCAC GACCAC GACCAC GACAAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
*
90631 GACCAC GACCAC AACCAC GA
1 GACCAC GACCAC GACCAC GA
90651 GACGAGACGG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.37, C:0.47, G:0.16, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:91434 original size:21 final size:21
Alignment explanation
Indices: 91406--91619 Score: 121
Period size: 21 Copynumber: 10.3 Consensus size: 21
91396 ATTTTGGACT
91406 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * * *
91427 ATAGCAACGCGAGCTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
91448 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
91469 ATCGCAACACGAACTTCGACT--
1 ATCGC-A-ACGAACTTGGAATAA
91490 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
91511 ATCGCAACGCGAACTT-CAACT--
1 ATCGCAA--CGAACTTGGAA-TAA
* *
91532 ATCGCAACGAACTAGGACT--
1 ATCGCAACGAACTTGGAATAA
* *
91551 ATAGCAACGCGAATTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
*
91574 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
91595 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAACTTGGAATAA
91614 ATCGCA
1 ATCGCA
91620 TTGCGATAGT
Statistics
Matches: 150, Mismatches: 25, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
19 47 0.31
20 2 0.01
21 52 0.35
22 3 0.02
23 46 0.31
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:91461 original size:42 final size:42
Alignment explanation
Indices: 91402--91563 Score: 247
Period size: 42 Copynumber: 3.9 Consensus size: 42
91392 TGCGATTTTG
*
91402 GACTATCGCAACGAACTTGGAATAAATAGCAACGCGAGCTTC
1 GACTATCGCAACGAACTTGGAATAAATAGCAACGCGAACTTC
* *
91444 GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATAGCAACGCGAACTTC
*
91486 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATAGCAACGCGAACTTC
* * *
91528 AACTATCGCAACGAACTAGGACT--ATAGCAACGCGAA
1 GACTATCGCAACGAACTTGGAATAAATAGCAACGCGAA
91564 TTTGGAATAA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
40 12 0.11
42 100 0.89
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATAGCAACGCGAACTTC
Found at i:91515 original size:63 final size:62
Alignment explanation
Indices: 91448--91605 Score: 173
Period size: 63 Copynumber: 2.5 Consensus size: 62
91438 AGCTTCGACT
* *
91448 ATCGCAA-CGAACTTGGAA-TAAATCGCAACACGAACTTCGACTATCGCAA-CGAACTTGGAATA
1 ATCGCAACCGAACTTGGAACT--ATCGC-A-ACGAACTACGACTATAGCAACCGAACTTGGAATA
91510 A
62 A
* * *
91511 ATCGCAACGCGAACTT-CAACTATCGCAACGAACTAGGACTATAGCAACGCGAATTTGGAATAA
1 ATCGCAAC-CGAACTTGGAACTATCGCAACGAACTACGACTATAGCAAC-CGAACTTGGAATAA
91574 ATCGCAACGCGAACTTGG-ACTATCGCAACGAA
1 ATCGCAAC-CGAACTTGGAACTATCGCAACGAA
91606 TTTGGAAAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
61 17 0.20
62 1 0.01
63 55 0.66
64 2 0.02
65 8 0.10
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (62 bp):
ATCGCAACCGAACTTGGAACTATCGCAACGAACTACGACTATAGCAACCGAACTTGGAATAA
Found at i:91578 original size:42 final size:39
Alignment explanation
Indices: 91532--91619 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 39
91522 AACTTCAACT
91532 ATCGCAA-CGAACTAGGACTATAGCAACGCGAATTTGGAATAA
1 ATCGCAACCGAACTAGGACTATAGCAA--CGAATTTGG-A-AA
* *
91574 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAAC-CGAACTAGGACTATAGCAACGAATTTGGAAA
91614 ATCGCA
1 ATCGCA
91620 TTGCGATAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
40 8 0.19
41 1 0.02
42 16 0.38
44 17 0.40
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (39 bp):
ATCGCAACCGAACTAGGACTATAGCAACGAATTTGGAAA
Found at i:91578 original size:84 final size:83
Alignment explanation
Indices: 91405--91592 Score: 234
Period size: 84 Copynumber: 2.2 Consensus size: 83
91395 GATTTTGGAC
* * *
91405 TATCGCAACGAACTTGGAATAAATAGCAACGCGAGCTTCGACTATCGCAACGAACTTGGAATAAA
1 TATCGCAACGAACTTGGAATAAATAGCAACGCGAACTTCAACTATCGCAACGAACTAGGAAT-AA
* *
91470 TCGCAACACGAACTTCGAC
65 TAGCAACACGAACTTCGAA
* *
91489 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCAACTATCGCAACGAACTAGGACT-AT
1 TATCGCAACGAACTTGGAATAAATAGCAACGCGAACTTCAACTATCGCAACGAACTAGGAATAAT
* * *
91553 AGCAACGCGAATTTGGAA
66 AGCAACACGAACTTCGAA
91571 TAAATCGCAACGCGAACTTGGA
1 T--ATCGCAA--CGAACTTGGA
91593 CTATCGCAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
82 16 0.18
84 64 0.71
86 10 0.11
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (83 bp):
TATCGCAACGAACTTGGAATAAATAGCAACGCGAACTTCAACTATCGCAACGAACTAGGAATAAT
AGCAACACGAACTTCGAA
Found at i:91617 original size:19 final size:20
Alignment explanation
Indices: 91554--91619 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 20
91544 TAGGACTATA
91554 GCAACGCGAATTTGGAATAAATC
1 GCAAC-CGAATTTGG-A-AAATC
* **
91577 GCAACGCGAACTTGGACTATC
1 GCAAC-CGAATTTGGAAAATC
91598 GCAA-CGAATTTGGAAAATC
1 GCAACCGAATTTGGAAAATC
91617 GCA
1 GCA
91620 TTGCGATAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 15 0.41
21 7 0.19
22 1 0.03
23 14 0.38
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (20 bp):
GCAACCGAATTTGGAAAATC
Found at i:96461 original size:21 final size:21
Alignment explanation
Indices: 96436--96502 Score: 134
Period size: 21 Copynumber: 3.2 Consensus size: 21
96426 GTATATGATT
96436 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
96457 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
96478 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
96499 CTTA
1 CTTA
96503 TGGACATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.34
Consensus pattern (21 bp):
CTTAAGGAATGATATGTGGTC
Found at i:96537 original size:21 final size:22
Alignment explanation
Indices: 96511--96561 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
96501 TATGGACATT
*
96511 ATTATATG-GCACTACGGTGAA
1 ATTATACGTGCACTACGGTGAA
* *
96532 ATTATACGTGCACTTCGGTGCA
1 ATTATACGTGCACTACGGTGAA
*
96554 ATGATACG
1 ATTATACG
96562 AGCTGTGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (22 bp):
ATTATACGTGCACTACGGTGAA
Found at i:101918 original size:21 final size:21
Alignment explanation
Indices: 101893--101938 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
101883 GTATATGATT
101893 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
101914 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
101935 CTTA
1 CTTA
101939 TGGACATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.35
Consensus pattern (21 bp):
CTTAAGGAATGATATGTGGTC
Found at i:101997 original size:22 final size:22
Alignment explanation
Indices: 101955--101997 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
101945 TTATTATATG
**
101955 GCACTACGGTGCAATTCTACGT
1 GCACTACGGTGCAATGATACGT
*
101977 GCACTTCGGTGCAATGATACG
1 GCACTACGGTGCAATGATACG
101998 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GCACTACGGTGCAATGATACGT
Found at i:106957 original size:43 final size:42
Alignment explanation
Indices: 106904--107254 Score: 416
Period size: 43 Copynumber: 8.2 Consensus size: 42
106894 TGAGAACCAA
*
106904 AAACGCCGCAATAGGTTAAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAATAGG-TCAGATCTATAGCGGCGTTTTTGGAAC
*
106947 AAACGCCGCAATAGGTCAAGATCTATAGTGGCG-TTTTGGAAC
1 AAACGCCGCAATAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * * *
106989 AAACGCCGCAAAAGGTTGATATCTATAGCGACGTTTTTGGAAC
1 AAACGCCGCAATAGG-TCAGATCTATAGCGGCGTTTTTGGAAC
* * *
107032 AAACGGCGCAATAGGTCAGATATATAGCAGCGTTTCTTGGAAC
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTT-TTGGAAC
* * *
107075 AAACGCTGTAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * * * * *
107117 AAACACCGCAAAAGGGTGATATCTATAGAGGCATTTTTGGAAC
1 AAACGCCGCAATA-GGTCAGATCTATAGCGGCGTTTTTGGAAC
107160 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTTGGAAC
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCG-TTTTTGGAAC
* * * * * *
107203 AAACACTGTAAAAGATCAGATATATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
107246 AAACGCCGC
1 AAACGCCGC
107255 TAATTTCTTT
Statistics
Matches: 259, Mismatches: 42, Indels: 14
0.82 0.13 0.04
Matches are distributed among these distances:
42 91 0.35
43 168 0.65
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (42 bp):
AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:107047 original size:85 final size:84
Alignment explanation
Indices: 106904--107254 Score: 416
Period size: 85 Copynumber: 4.1 Consensus size: 84
106894 TGAGAACCAA
* * *
106904 AAACGCCGCAATAGGTTAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCAAGAT
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-AGAT
* *
106969 CTATAGTGGCG-TTTTGGAAC
64 ATATAGCGGCGTTTTTGGAAC
* * * * *
106989 AAACGCCGCAAAAGGTTGATATCTATAGCGACGTTTTTGGAACAAACGGCGCAATAGGTCAGATA
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATA
*
107054 TATAGCAGCGTTTCTTGGAAC
65 TATAGCGGCGTTT-TTGGAAC
* * * * * *
107075 AAACGCTGTAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGGTGATATC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA-GGTCAGATA
* *
107140 TATAGAGGCATTTTTGGAAC
65 TATAGCGGCGTTTTTGGAAC
* * * * *
107160 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTTGGAACAAACACTGTAAAAGATCAGATA
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAACAAACGCCGCAAAAGGTCAGATA
107225 TATAGCGGCGTTTTTGGATAC
65 TATAGCGGCGTTTTTGGA-AC
107246 AAACGCCGC
1 AAACGCCGC
107255 TAATTTCTTT
Statistics
Matches: 228, Mismatches: 33, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
84 12 0.05
85 148 0.65
86 68 0.30
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (84 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATAT
ATAGCGGCGTTTTTGGAAC
Found at i:107092 original size:128 final size:127
Alignment explanation
Indices: 106904--107254 Score: 506
Period size: 128 Copynumber: 2.7 Consensus size: 127
106894 TGAGAACCAA
* * * *
106904 AAACGCCGCAATAGGTTAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCAAGAT
1 AAACGCCGCAATAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAACGCTGTAAAAGGTC-AGAT
* * * *
106969 CTATAGTGGCG-TTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGACGTTTTTGGAAC
64 CTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGGTGATATCTATAGAGACATTTTTGGAAC
* * *
107032 AAACGGCGCAATAGGTCAGATATATAGCAGCGTTTCTTGGAACAAACGCTGTAAAAGGTCAGATC
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTT-TTGGAACAAACGCTGTAAAAGGTCAGATC
* *
107097 TATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGGTGATATCTATAGAGGCATTTTTGGAAC
65 TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGGTGATATCTATAGAGACATTTTTGGAAC
* * *
107160 AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTTGGAACAAACACTGTAAAAGATCAGATA
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCG-TTTTTGGAACAAACGCTGTAAAAGGTCAGATC
107225 TATAGCGGCGTTTTTGGATACAAACGCCGC
65 TATAGCGGCGTTTTTGGA-ACAAACGCCGC
107255 TAATTTCTTT
Statistics
Matches: 199, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
127 31 0.16
128 155 0.78
129 13 0.07
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (127 bp):
AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCTGTAAAAGGTCAGATCT
ATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGGTGATATCTATAGAGACATTTTTGGAAC
Found at i:111314 original size:41 final size:41
Alignment explanation
Indices: 111253--111488 Score: 255
Period size: 41 Copynumber: 5.7 Consensus size: 41
111243 TTGTAAACTT
111253 GCGGCGTTTGT-TAAACAAACGCCACTAAAACATGAGTCTATA
1 GCGGCGTTTGTAT-AA-AAACGCCACTAAAACATGAGTCTATA
*
111295 GCGGCGTTTGTATAAAAACGCCACTAAAGTACA--AGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAA--ACATGAGTCTATA
* ***
111336 GTGGCGTTTGTATAAAAAC-CCACTAAGGTATGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAACATGAGTCTATA
* * * *
111376 GCGGCGTTTGTAAACACAAACGCCACTAAATCACGATTCTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAACATGAGTCTATA
** *
111419 GCGGCGTTTGTATAAAAACGCCACTAAATGTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAA-ACATGAGTCTATA
* *
111461 GCGGCGTTTTTATGAAAACGCCACTAAA
1 GCGGCGTTTGTATAAAAACGCCACTAAA
111489 GTACAGTCTT
Statistics
Matches: 164, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
40 26 0.16
41 52 0.32
42 52 0.32
43 33 0.20
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAACATGAGTCTATA
Found at i:111428 original size:83 final size:82
Alignment explanation
Indices: 111253--111610 Score: 321
Period size: 83 Copynumber: 4.3 Consensus size: 82
111243 TTGTAAACTT
** *
111253 GCGGCGTTTGT-TAAACAAACGCCACTAAAACATGAGTCTATAGCGGCGTTTGTATAAAAACGCC
1 GCGGCGTTTGTAT-AA-AAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTAAAAAAACGCC
*
111317 ACTAAAGTACAAGTCTTTA
64 ACTAAAGTACAAGTCTATA
* *
111336 GTGGCGTTTGTATAAAAAC-CCACTAAGGTATGAGTCTATAGCGGCGTTTGTAAACACAAACGCC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTAAA-A-AAACGCC
* *
111400 ACTAAA-TCACGATTCTATA
64 ACTAAAGT-ACAAGTCTATA
* * **
111419 GCGGCGTTTGTATAAAAACGCCACTAAATGTATGAGTCTTTAGCGGCGTTTTTATGAAAACGCCA
1 GCGGCGTTTGTATAAAAACGCCACTAAA-GTATGAGTCTATAGCGGCGTTTGTAAAAAAACGCCA
*
111484 CTAAAGTAC-AGTCTTTA
65 CTAAAGTACAAGTCTATA
* * * * * * * * * * * * *
111501 ACAGCGTTTTTACAGAAACGCCACTAAAGTA-CAGTCTTTAACAGCGTTTTTATAGAAACGCCGC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTAAAAAAACGCCAC
*** *
111565 TAAAGTACGCTTCTTTA
66 TAAAGTACAAGTCTATA
* * *
111582 GCGACGTTTGTTCTAAAAACGCCGCTAAA
1 GCGGCGTTTG-TATAAAAACGCCACTAAA
111611 AATGCTGCTA
Statistics
Matches: 229, Mismatches: 37, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
80 35 0.15
81 46 0.20
82 49 0.21
83 66 0.29
84 10 0.04
85 23 0.10
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (82 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTAAAAAAACGCCAC
TAAAGTACAAGTCTATA
Found at i:111508 original size:40 final size:40
Alignment explanation
Indices: 111253--111610 Score: 310
Period size: 40 Copynumber: 8.7 Consensus size: 40
111243 TTGTAAACTT
** * *
111253 GCGGCGTTTGTTA-AACAAACGCCACTAAAACATGAGTCTATA
1 GCGGCGTTT-TTATAA-AAACGCCACTAAAGTA-CAGTCTTTA
*
111295 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTTTA
1 GCGGCGTTTTTATAAAAACGCCACTAAAGTAC-AGTCTTTA
* * * * *
111336 GTGGCGTTTGTATAAAAAC-CCACTAAGGTATGAGTCTATA
1 GCGGCGTTTTTATAAAAACGCCACTAAAGTA-CAGTCTTTA
* * * *
111376 GCGGCGTTTGTAAACACAAACGCCACTAAA-TCACGATTCTATA
1 GCGGCGTTTTTATA-A-AAACGCCACTAAAGT-AC-AGTCTTTA
* *
111419 GCGGCGTTTGTATAAAAACGCCACTAAATGTATGAGTCTTTA
1 GCGGCGTTTTTATAAAAACGCCACTAAA-GTA-CAGTCTTTA
*
111461 GCGGCGTTTTTATGAAAACGCCACTAAAGTACAGTCTTTA
1 GCGGCGTTTTTATAAAAACGCCACTAAAGTACAGTCTTTA
* * * *
111501 ACAGCGTTTTTACAGAAACGCCACTAAAGTACAGTCTTTA
1 GCGGCGTTTTTATAAAAACGCCACTAAAGTACAGTCTTTA
* * * *
111541 ACAGCGTTTTTATAGAAACGCCGCTAAAGTAC-GCTTCTTTA
1 GCGGCGTTTTTATAAAAACGCCACTAAAGTACAG--TCTTTA
* * *
111582 GCGACGTTTGTTCTAAAAACGCCGCTAAA
1 GCGGCGTTT-TTATAAAAACGCCACTAAA
111611 AATGCTGCTA
Statistics
Matches: 269, Mismatches: 33, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.00
40 102 0.38
41 70 0.26
42 67 0.25
43 29 0.11
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (40 bp):
GCGGCGTTTTTATAAAAACGCCACTAAAGTACAGTCTTTA
Found at i:115551 original size:258 final size:259
Alignment explanation
Indices: 115087--115608 Score: 989
Period size: 259 Copynumber: 2.0 Consensus size: 259
115077 ATAGCTGGTG
115087 GCTTAGAGCAGGCAGCGGCGCCCGAGGGAGGTGCCCATATTTTTCCAAAAGGTTTCGTTTTTCAG
1 GCTTAGAGCAGGCAGCGGCGCCCGAGGGAGGTGCCCATATTTTTCCAAAAGGTTTCGTTTTTCAG
115152 CTACCTGGTCCTGGTTCATGTGTGTATAATAGCTAGGGTTTACTTTAGTTCTTTTCTCCTATAGG
66 CTACCTGGTCCTGGTTCATGTGTGTATAATAGCTAGGGTTTACTTTAGTTCTTTTCTCCTATAGG
115217 CTGGAGCATATGACAGTGTTGCAATTATCATCAAAATGGGATTCCGCTACTTAATAGAGACAGCT
131 CTGGAGCATATGACAGTGTTGCAATTATCATCAAAATGGGATTCCGCTACTTAATAGAGACAGCT
115282 TAATAAAACCCTAG-TTTTAATGGACTAAACATGATCATGTTATTTTCA-AATTAACAAGAGAA
196 TAATAAAACCCTAGTTTTTAATGGACTAAACATGATCATGTTATTTTCATAATTAACAAGAGAA
115344 GCTTAGAGCAGGCAGCGGCGCCCGAGGGAGGTGCCCATA-TTTTCCAAAAGGTTTCGTTTTTCAG
1 GCTTAGAGCAGGCAGCGGCGCCCGAGGGAGGTGCCCATATTTTTCCAAAAGGTTTCGTTTTTCAG
115408 CTACCTGGTCCTGGTTCATGTGTGTGTATAATAGCTAGGGTTTACTTTAGTTCTTTTCTCCTATA
66 CTACCTGGTCCTGGTTCA--TGTGTGTATAATAGCTAGGGTTTACTTTAGTTCTTTTCTCCTATA
115473 GGCTGGAGCATATGACAGTTGTTGCAATTATCATCAAAATGGGATTCCGCTACTTAATAGAGACA
129 GGCTGGAGCATATGACAG-TGTTGCAATTATCATCAAAATGGGATTCCGCTACTTAATAGAGACA
115538 GCTTAAT-AAACCCTAGTTTTTAATGGACTAAACATGATCATGTTATTTTCATAATTAACAAGAG
193 GCTTAATAAAACCCTAGTTTTTAATGGACTAAACATGATCATGTTATTTTCATAATTAACAAGAG
115602 AA
258 AA
115604 GCTTA
1 GCTTA
115609 AGAAAAGGGA
Statistics
Matches: 260, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
256 43 0.17
257 39 0.15
258 72 0.28
259 87 0.33
260 19 0.07
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (259 bp):
GCTTAGAGCAGGCAGCGGCGCCCGAGGGAGGTGCCCATATTTTTCCAAAAGGTTTCGTTTTTCAG
CTACCTGGTCCTGGTTCATGTGTGTATAATAGCTAGGGTTTACTTTAGTTCTTTTCTCCTATAGG
CTGGAGCATATGACAGTGTTGCAATTATCATCAAAATGGGATTCCGCTACTTAATAGAGACAGCT
TAATAAAACCCTAGTTTTTAATGGACTAAACATGATCATGTTATTTTCATAATTAACAAGAGAA
Found at i:117079 original size:26 final size:26
Alignment explanation
Indices: 117050--117122 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
117040 TGCAAAACGA
*
117050 AAATATAATTAAACTTTCATAGTAAC
1 AAATATAATAAAACTTTCATAGTAAC
*
117076 AAATCA-AGTAAAACTTTCATAGTAAC
1 AAAT-ATAATAAAACTTTCATAGTAAC
117102 -AATATCAAGTAAAACTTTCAT
1 AAATAT-AA-TAAAACTTTCAT
117123 CAATGAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 1 0.03
25 3 0.08
26 23 0.57
27 13 0.32
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (26 bp):
AAATATAATAAAACTTTCATAGTAAC
Found at i:117116 original size:27 final size:26
Alignment explanation
Indices: 117060--117122 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
117050 AAATATAATT
117060 AAACTTTCATAGTAACAAATCAAGTA
1 AAACTTTCATAGTAACAAATCAAGTA
117086 AAACTTTCATAGTAACAATATCAAGTA
1 AAACTTTCATAGTAACAA-ATCAAGTA
117113 AAACTTTCAT
1 AAACTTTCAT
117123 CAATGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 18 0.50
27 18 0.50
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (26 bp):
AAACTTTCATAGTAACAAATCAAGTA
Found at i:117142 original size:28 final size:27
Alignment explanation
Indices: 117060--117143 Score: 91
Period size: 26 Copynumber: 3.1 Consensus size: 27
117050 AAATATAATT
* *
117060 AAACTTTCATAGTAACAA-ATCAAGTA
1 AAACTTTCATAATAACAATATCAACTA
* *
117086 AAACTTTCATAGTAACAATATCAAGTA
1 AAACTTTCATAATAACAATATCAACTA
*
117113 AAACTTTCATCAATGAA-AATATTAACTA
1 AAACTTTCAT-AAT-AACAATATCAACTA
117141 AAA
1 AAA
117144 TTTAATAGCT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 18 0.35
27 18 0.35
28 14 0.27
29 2 0.04
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (27 bp):
AAACTTTCATAATAACAATATCAACTA
Found at i:117703 original size:17 final size:15
Alignment explanation
Indices: 117681--117718 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 15
117671 AGGTTAAAGA
117681 GGAGCCTGGAGCTGGCT
1 GGAGCCTGGAGC-GG-T
117698 GGAGCCTGGAGCGGT
1 GGAGCCTGGAGCGGT
117713 GGAGCC
1 GGAGCC
117719 AACTGCCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.33
16 2 0.10
17 12 0.57
ACGTcount: A:0.13, C:0.24, G:0.50, T:0.13
Consensus pattern (15 bp):
GGAGCCTGGAGCGGT
Found at i:117868 original size:24 final size:23
Alignment explanation
Indices: 117840--117888 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
117830 TTGTTTACTT
* *
117840 TAATTTAATATATAATATTATTAA
1 TAATTAAATATATAATAATA-TAA
117864 TAATTAAATATATAATAATATAA
1 TAATTAAATATATAATAATATAA
117887 TA
1 TA
117889 TTATTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATTAAATATATAATAATATAA
Found at i:118751 original size:14 final size:14
Alignment explanation
Indices: 118732--118759 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
118722 AAGTGAAAGA
118732 ATAGTTATATAATT
1 ATAGTTATATAATT
118746 ATAGTTATATAATT
1 ATAGTTATATAATT
118760 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:123322 original size:2 final size:2
Alignment explanation
Indices: 123304--123342 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
123294 CCTGTCTGTT
* *
123304 TA TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
123343 CCTTTGCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:124937 original size:2 final size:2
Alignment explanation
Indices: 124930--124955 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
124920 ACTAAAAATA
124930 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
124956 GATGTTTTTA
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:128674 original size:42 final size:42
Alignment explanation
Indices: 128628--128710 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
128618 GTCGCCTCAC
*
128628 TCATTCAAGGATTATTCTTTCTGTTCTTCAATTAATAAGTGG
1 TCATTCAAGGATTATTCTTTCTGTTCTTCAATTAAAAAGTGG
* *
128670 TCATTCATGGATTATTCTTTTTGTTCTTCAATTAAAAAGTG
1 TCATTCAAGGATTATTCTTTCTGTTCTTCAATTAAAAAGTG
128711 ACGAAATTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (42 bp):
TCATTCAAGGATTATTCTTTCTGTTCTTCAATTAAAAAGTGG
Found at i:130907 original size:32 final size:33
Alignment explanation
Indices: 130807--130909 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
130797 ACAAAGTTTA
* *
130807 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
**
130839 TAATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
130872 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
130904 CGATAA
1 CGATAA
130910 TTGAAACAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.22
33 50 0.78
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:130928 original size:21 final size:21
Alignment explanation
Indices: 130904--130945 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
130894 ACTTCAAGTT
130904 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
130925 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
130946 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:146238 original size:37 final size:37
Alignment explanation
Indices: 146165--146239 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
146155 ATTGGAAAAT
* *
146165 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
146202 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
146239 A
1 A
146240 AGGTTTTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:148550 original size:33 final size:33
Alignment explanation
Indices: 148508--148572 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
148498 ACTTACAGTA
148508 CCTAGCCAGCATGCTCTTTTAACATAAAATGTT
1 CCTAGCCAGCATGCTCTTTTAACATAAAATGTT
*
148541 CCTAGCCAGCATGCTCTTTTAACATGAAATGT
1 CCTAGCCAGCATGCTCTTTTAACATAAAATGT
148573 ATCAAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (33 bp):
CCTAGCCAGCATGCTCTTTTAACATAAAATGTT
Found at i:153820 original size:43 final size:42
Alignment explanation
Indices: 153767--154022 Score: 305
Period size: 43 Copynumber: 6.0 Consensus size: 42
153757 TTGGTAACAA
* *** * **
153767 AAAAATGCCGCAATAGGTAACGATATATAGCGGCGTTTGTTGG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TTCC
153810 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCC
153852 AACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCC
1 AA-AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT-CC
* * *
153896 ACAAATGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT-CC
* * * * *
153939 ACAAACGCCGCAATAAGTGTTGAGATTTAGTGGCGTTTTTCT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCC
* * * *
153981 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGTGTTTTTCC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCC
154023 CACAAACACC
Statistics
Matches: 192, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
42 42 0.22
43 147 0.77
44 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCC
Found at i:153884 original size:86 final size:85
Alignment explanation
Indices: 153773--154084 Score: 347
Period size: 86 Copynumber: 3.6 Consensus size: 85
153763 ACAAAAAAAT
*** * *
153773 GCCGCAATAGGTAACGATATATAGCGGCGTTTGTTGGAAAAACGCCGCAATAGGTGTTGATATTT
1 GCCGCAATAGGTGTTGATATATAGCGGCGTTT-TTCGAAAAACGCCGCAATAGGTGTTGAGATTT
*
153838 AGCGGCGTTTTTCCAACAAAC
65 AGCGGCGTTTTTCCCACAAAC
* * * *
153859 GCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCCACAAATGCCGCAATAGGTGTTGAGATTT
1 GCCGCAATAGGTGTTGATATATAGCGGCGTTTTT-CGAAAAACGCCGCAATAGGTGTTGAGATTT
153924 AGCGGCGTTTTTCCCACAAAC
65 AGCGGCGTTTTTCCCACAAAC
* * * * * * *
153945 GCCGCAATAAGTGTTGAGATTTAGTGGCGTTTTTCTACAAACGCCGCAATAGGTCTTGAGATTTA
1 GCCGCAATAGGTGTTGATATATAGCGGCGTTTTTCGAAAAACGCCGCAATAGGTGTTGAGATTTA
*
154010 GCGGTGTTTTTCCCACAAAC
66 GCGGCGTTTTTCCCACAAAC
* * * * * * * *
154030 ACCGTAAAAGAT-CTGGTATATAGCGGCGTTTTTTAGAACAAACGCCGCAAAAGGT
1 GCCGCAATAGGTGTTGATATATAGCGGCG-TTTTTCGAA-AAACGCCGCAATAGGT
154085 CATATCTATA
Statistics
Matches: 192, Mismatches: 31, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
84 11 0.06
85 62 0.32
86 119 0.62
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (85 bp):
GCCGCAATAGGTGTTGATATATAGCGGCGTTTTTCGAAAAACGCCGCAATAGGTGTTGAGATTTA
GCGGCGTTTTTCCCACAAAC
Found at i:153912 original size:129 final size:128
Alignment explanation
Indices: 153769--154028 Score: 360
Period size: 129 Copynumber: 2.0 Consensus size: 128
153759 GGTAACAAAA
* ** *
153769 AAATGCCGCAATAGGTAACGATATATAGCGGCGTTTGTT-GGAAAAACGCCGCAATAGGTGTTGA
1 AAATGCCGCAATAGGTAACGAGATATAGCGGCGTTT-TTCCCAAAAACGCCGCAATAAGTGTTGA
* * *
153833 TATTTAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCCAC
65 GATTTAGCGGCGTTTTT-CAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCAC
*** * *
153898 AAATGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAAGTGTTGAG
1 AAATGCCGCAATAGGTAACGAGATATAGCGGCGTTTTTCCCAAAAACGCCGCAATAAGTGTTGAG
* * *
153963 ATTTAGTGGCGTTTTTCTACAAACGCCGCAATAGGTCTTGAGATTTAGCGGTGTTTTTCCCAC
66 ATTTAGCGGCGTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCAC
154026 AAA
1 AAA
154029 CACCGTAAAA
Statistics
Matches: 115, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
128 48 0.42
129 67 0.58
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (128 bp):
AAATGCCGCAATAGGTAACGAGATATAGCGGCGTTTTTCCCAAAAACGCCGCAATAAGTGTTGAG
ATTTAGCGGCGTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCAC
Found at i:154004 original size:42 final size:43
Alignment explanation
Indices: 153812--154029 Score: 348
Period size: 43 Copynumber: 5.1 Consensus size: 43
153802 TTTGTTGGAA
* *
153812 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
153855 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
153898 AAATGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* * *
153941 AAACGCCGCAATAAGTGTTGAGATTTAGTGGCGTTTTT-CTAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* *
153983 AAACGCCGCAATAGGTCTTGAGATTTAGCGGTGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
154026 AAAC
1 AAAC
154030 ACCGTAAAAG
Statistics
Matches: 162, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
42 37 0.23
43 125 0.77
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
Found at i:154063 original size:128 final size:130
Alignment explanation
Indices: 153790--154079 Score: 365
Period size: 128 Copynumber: 2.3 Consensus size: 130
153780 TAGGTAACGA
* * *
153790 TATATAGCGGCGTTTGTTGGAA-AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAA
1 TATATAGCGGCGTTT-TTTGAACAAACGCCGCAATAAGTGTTGAGATTTAGCGGCGTTTTTCCAA
* * ** * * *
153854 CAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCCACAAATGCCGCAATAGGTGTTGA
65 CAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATGCTGA
153919 G
130 G
* *** * *
153920 -ATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAAGTGTTGAGATTTAGTGGCGTTTTT-CTAC
1 TATATAGCGGCGTTTTTTGAACAAACGCCGCAATAAGTGTTGAGATTTAGCGGCGTTTTTCCAAC
* *
153983 AAACGCCGCAATAGGTCTTGAGATTTAGCGGTGTTTTTCCCACAAACACCGTAAAAGAT-CTG-G
66 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATGCTGAG
154046 TATATAGCGGCGTTTTTTAGAACAAACGCCGCAA
1 TATATAGCGGCGTTTTTT-GAACAAACGCCGCAA
154080 AAGGTCATAT
Statistics
Matches: 136, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
126 1 0.01
127 17 0.12
128 70 0.51
129 48 0.35
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (130 bp):
TATATAGCGGCGTTTTTTGAACAAACGCCGCAATAAGTGTTGAGATTTAGCGGCGTTTTTCCAAC
AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATGCTGAG
Found at i:154258 original size:21 final size:21
Alignment explanation
Indices: 154232--154290 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
154222 ATTTTCCAAT
*
154232 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
154253 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
154274 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
154291 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:157282 original size:41 final size:40
Alignment explanation
Indices: 157149--157552 Score: 156
Period size: 41 Copynumber: 9.8 Consensus size: 40
157139 AATATACCAA
* * *
157149 ACTA-TTGCGGCGTTTGTAAAAAAATGCCTCT-ACAGTACT
1 ACTATTTGCGGCGTTTGT-AAAAAACGCCGCTAAAAGTACT
* * * *
157188 ACTATGTTGCGGCGTTTGTTAAAAAAAACGTCACTG-TAGATGAAAT
1 ACTAT-TTGCGGCGTTTG-T--AAAAAACG-C-C-GCTAAAAGTACT
157234 -CTA-TTGCGGCGTTTGTAAAAAACGCCGCTAAAAGTACT
1 ACTATTTGCGGCGTTTGTAAAAAACGCCGCTAAAAGTACT
* * * * *
157272 ACTATTTTGCGGCGTTTGTTGAAAAACGCCACTATAGATTA-A
1 ACTA-TTTGCGGCGTTTG-TAAAAAACGCCGCTA-AAAGTACT
*
157314 ACCTA-TTACGGCGTTTGTAAAAAACGCCGCT-AAAGTACT
1 A-CTATTTGCGGCGTTTGTAAAAAACGCCGCTAAAAGTACT
* ** ** * * * * *
157353 ACTCTATAACAACGTTTGTTAAGAAACGCCACTATGGATGAAC-
1 ACTAT-TTGCGGCGTTTG-TAAAAAACGCCGCTA--AAAGTACT
157396 -CTA-TTGTC-GCGTTTGTATAAAAACGCCGCT-AAAGTACT
1 ACTATTTG-CGGCGTTTGTA-AAAAACGCCGCTAAAAGTACT
* * * * *
157434 ACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAAC-
1 ACTAT-TTGCGGCGTTTG-T-AAAAAACGCCGCTA-A-AAGTACT
* * * * *
157478 CCTA-TTGCGGCATTTTTATACAAACGCCGCT-AAAGTATT
1 ACTATTTGCGGCGTTTGTA-AAAAACGCCGCTAAAAGTACT
157517 ACTATATTGCGGCGTTTTGTATAAAAACGCCGCTAA
1 ACTAT-TTGCGGCG-TTTGTA-AAAAACGCCGCTAA
157553 CGTTACCATT
Statistics
Matches: 266, Mismatches: 59, Indels: 76
0.66 0.15 0.19
Matches are distributed among these distances:
37 5 0.02
38 16 0.06
39 17 0.06
40 48 0.18
41 75 0.28
42 56 0.21
43 29 0.11
44 8 0.03
45 9 0.03
46 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (40 bp):
ACTATTTGCGGCGTTTGTAAAAAACGCCGCTAAAAGTACT
Found at i:157386 original size:81 final size:82
Alignment explanation
Indices: 157107--157547 Score: 446
Period size: 83 Copynumber: 5.3 Consensus size: 82
157097 GAAGCAGAAA
* * * **
157107 ATGTTGCGGCGTTT-TTAAAGCCAAACGCCACGAATATACCAAA-CTATTGCGGCGTTTGTAAAA
1 ATGTTGCGGCGTTTGTTAAA--AAAACGCCAC-TATAGATGAAACCTATTGCGGCGTTTGT-AAA
* * *
157170 AAATGCCTCTACAGTACTACT
62 AAACGCCGCTAAAGTACTACT
* * *
157191 ATGTTGCGGCGTTTGTTAAAAAAAACGTCACTGTAGATGAAATCTATTGCGGCGTTTGTAAAAAA
1 ATGTTGCGGCGTTTGTT-AAAAAAACGCCACTATAGATGAAACCTATTGCGGCGTTTGTAAAAAA
157256 CGCCGCTAAAAGTACTACT
65 CGCCGCT-AAAGTACTACT
* * * *
157275 ATTTTGCGGCGTTTGTT-GAAAAACGCCACTATAGATTAAACCTATTACGGCGTTTGTAAAAAAC
1 ATGTTGCGGCGTTTGTTAAAAAAACGCCACTATAGATGAAACCTATTGCGGCGTTTGTAAAAAAC
157339 GCCGCTAAAGTACTACT
66 GCCGCTAAAGTACTACT
* * ** ** * *
157356 CTATAACAACGTTTGTT-AAGAAACGCCACTATGGATG-AACCTATTGTC-GCGTTTGTATAAAA
1 ATGTTGCGGCGTTTGTTAAAAAAACGCCACTATAGATGAAACCTATTG-CGGCGTTTGTA-AAAA
157418 ACGCCGCTAAAGTACTACT
64 ACGCCGCTAAAGTACTACT
* * * * * * *
157437 CTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGCGGCATTTTTATACAAA
1 ATGTTGCGGCGTTTGTTAAAAAAACGCCACTATAGATGAAACCTATTGCGGCGTTTGTA-AAAAA
*
157502 CGCCGCTAAAGTATTACT
65 CGCCGCTAAAGTACTACT
* *
157520 ATATTGCGGCGTTT-TGTATAAAAACGCC
1 ATGTTGCGGCGTTTGT-TAAAAAAACGCC
157548 GCTAACGTTA
Statistics
Matches: 301, Mismatches: 46, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
80 17 0.06
81 74 0.25
82 66 0.22
83 75 0.25
84 64 0.21
85 2 0.01
86 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (82 bp):
ATGTTGCGGCGTTTGTTAAAAAAACGCCACTATAGATGAAACCTATTGCGGCGTTTGTAAAAAAC
GCCGCTAAAGTACTACT
Found at i:158251 original size:26 final size:27
Alignment explanation
Indices: 158218--158269 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
158208 TTTTTACCTA
*
158218 TTAAAATTTTATAA-ATTATCTTCTAC
1 TTAAAATTATATAAGATTATCTTCTAC
158244 TTAAAATTATATAAGATTATCTTCTA
1 TTAAAATTATATAAGATTATCTTCTA
158270 GGAACAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAAAATTATATAAGATTATCTTCTAC
Found at i:160484 original size:60 final size:59
Alignment explanation
Indices: 160395--160509 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 59
160385 AAAAGACGAG
**
160395 TTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACGTCCTATAGTCGAAAGATTA
1 TTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACACCCTATAGTC-AAAGATTA
*
160455 TTTTGTAACTTTTAATAGTCAGGAG-ACTCAACAAAGCAGCACCCTATAGTCAAAG
1 TTTTGTAACTTTTAATAGT-AGGAGAACTCAACAAAGCAACACCCTATAGTCAAAG
160510 GACCATTTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
59 4 0.08
60 42 0.82
61 5 0.10
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (59 bp):
TTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACACCCTATAGTCAAAGATTA
Found at i:160526 original size:60 final size:60
Alignment explanation
Indices: 160386--160526 Score: 171
Period size: 60 Copynumber: 2.3 Consensus size: 60
160376 TTTTACGGAA
* **
160386 AAAGACGAGTTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACGTCCTATAGTCG
1 AAAGACCA-TTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACACCCTATAGTCG
** *
160447 AAAGATTATTTTGTAACTTTTAATAGTCAGGAG-ACTCAACAAAGCAGCACCCTATAGTC-
1 AAAGACCATTTTGTAACTTTTAATAGT-AGGAGAACTCAACAAAGCAACACCCTATAGTCG
160506 AAAGGACCATTTGTGT-ACTTT
1 AAA-GACCATTT-TGTAACTTT
160527 ACCCCAAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
59 3 0.04
60 53 0.76
61 14 0.20
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (60 bp):
AAAGACCATTTTGTAACTTTTAATAGTAGGAGAACTCAACAAAGCAACACCCTATAGTCG
Found at i:165422 original size:3 final size:3
Alignment explanation
Indices: 165409--165441 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
165399 ATATATATAT
165409 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
165442 TTTATCGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:171000 original size:41 final size:41
Alignment explanation
Indices: 170942--171019 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
170932 TTGACGTTAC
*
170942 AATTCGATCGATGATAATATCAAGTTTGATAAAATTTCAAT
1 AATTCGATCGATAATAATATCAAGTTTGATAAAATTTCAAT
*
170983 AATTCGACTC-ATAATAATATCGAGTTTGATAAAATTT
1 AATTCGA-TCGATAATAATATCAAGTTTGATAAAATTT
171020 TGATAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (41 bp):
AATTCGATCGATAATAATATCAAGTTTGATAAAATTTCAAT
Found at i:177705 original size:21 final size:22
Alignment explanation
Indices: 177679--177719 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
177669 ATTCATACCT
177679 TATAAA-ACATAATTAAATCGA
1 TATAAAGACATAATTAAATCGA
* *
177700 TATAAAGATATATTTAAATC
1 TATAAAGACATAATTAAATC
177720 TACATACGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (22 bp):
TATAAAGACATAATTAAATCGA
Found at i:178405 original size:2 final size:2
Alignment explanation
Indices: 178400--178429 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
178390 CGTGTGTGTG
178400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
178430 GTTACTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:180615 original size:27 final size:27
Alignment explanation
Indices: 180583--180637 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
180573 ACAAAAAGAA
*
180583 GAAATATAATTACATGACAATAGTTTT
1 GAAATATAATTACATGACAATAGATTT
180610 GAAATATAATTACATGACAATAGATTT
1 GAAATATAATTACATGACAATAGATTT
180637 G
1 G
180638 TCCCTGACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (27 bp):
GAAATATAATTACATGACAATAGATTT
Found at i:185084 original size:17 final size:17
Alignment explanation
Indices: 185062--185094 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
185052 AATTTTTGAA
185062 GAAATATAT-TAAAATTT
1 GAAATA-ATGTAAAATTT
185079 GAAATAATGTAAAATT
1 GAAATAATGTAAAATT
185095 ATAAAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (17 bp):
GAAATAATGTAAAATTT
Found at i:192284 original size:18 final size:17
Alignment explanation
Indices: 192261--192299 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
192251 AAAGGCGATG
192261 GCGGCATCATATATGACT
1 GCGGCATCATATATGA-T
192279 GCGGCATCATATATGAT
1 GCGGCATCATATATGAT
192296 GCGG
1 GCGG
192300 TGGCTGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (17 bp):
GCGGCATCATATATGAT
Found at i:193961 original size:110 final size:111
Alignment explanation
Indices: 193767--193979 Score: 365
Period size: 110 Copynumber: 1.9 Consensus size: 111
193757 ATTACAAAAA
* * * *
193767 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
193832 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
193878 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
193942 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
193980 AAAAATATAT
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 63 0.66
111 33 0.34
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:198495 original size:14 final size:15
Alignment explanation
Indices: 198467--198496 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
198457 TATTTTATTC
198467 ATAATATTTAATTTT
1 ATAATATTTAATTTT
198482 ATAATA-TTAATTTT
1 ATAATATTTAATTTT
198496 A
1 A
198497 CAAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAATATTTAATTTT
Found at i:206141 original size:15 final size:15
Alignment explanation
Indices: 206118--206148 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
206108 TCTTTTTTAG
206118 TAATGAAAAATGTAC
1 TAATGAAAAATGTAC
*
206133 TAATTAAAAATGTAC
1 TAATGAAAAATGTAC
206148 T
1 T
206149 CCTCTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (15 bp):
TAATGAAAAATGTAC
Found at i:219539 original size:29 final size:29
Alignment explanation
Indices: 219506--219591 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
219496 GCCCCAACAC
* *
219506 ATAGGTCGTCATGTC-CTCCGGGCGACTTT
1 ATAGGTCGACATG-CACTCCGGGCGACCTT
219535 ATAGGTCGACATGCACTCCGGGCGACCTT
1 ATAGGTCGACATGCACTCCGGGCGACCTT
*
219564 ATAGGTCGCCATGCACTCCGGGCGACCT
1 ATAGGTCGACATGCACTCCGGGCGACCT
219592 ACCTTTGCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
28 1 0.02
29 52 0.98
ACGTcount: A:0.17, C:0.31, G:0.28, T:0.23
Consensus pattern (29 bp):
ATAGGTCGACATGCACTCCGGGCGACCTT
Found at i:219683 original size:34 final size:33
Alignment explanation
Indices: 219612--219721 Score: 157
Period size: 33 Copynumber: 3.3 Consensus size: 33
219602 GCTCGCTCGG
*
219612 TCGGATGCCCTCGCATAACTCGCTCGGCTGCCC
1 TCGGATGCCCTCGCATAGCTCGCTCGGCTGCCC
*
219645 TCGGATTCCCTCGCATAGCTCGCTCGGCTTGCCC
1 TCGGATGCCCTCGCATAGCTCGCTCGGC-TGCCC
* * * *
219679 TCGGATGCTCTCGCATAGCTCGATCGGATGGCC
1 TCGGATGCCCTCGCATAGCTCGCTCGGCTGCCC
219712 TCGGATGCCC
1 TCGGATGCCC
219722 AGCGTGTTGG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 39 0.57
34 29 0.43
ACGTcount: A:0.12, C:0.38, G:0.26, T:0.24
Consensus pattern (33 bp):
TCGGATGCCCTCGCATAGCTCGCTCGGCTGCCC
Found at i:225451 original size:60 final size:60
Alignment explanation
Indices: 225385--225506 Score: 149
Period size: 60 Copynumber: 2.0 Consensus size: 60
225375 CATCATATTT
* * * * *
225385 CCTAAACTAT-AACCCTCATTTTAAATTGGTCCTTCAAA-TTTTGAACATTTCAATTTCATC
1 CCTAAACTATGAA-CATCATTTTAAATTAGTCCCT-AAACTTTTGAACATTCCAAATTCATC
*
225445 CCTAAACTATGAACATCCTTTTAAATTAGTCCCTAAACTTTTTGAACATTCCAAATTCATC
1 CCTAAACTATGAACATCATTTTAAATTAGTCCCTAAAC-TTTTGAACATTCCAAATTCATC
225506 C
1 C
225507 AAATATGCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
59 3 0.06
60 27 0.51
61 23 0.43
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (60 bp):
CCTAAACTATGAACATCATTTTAAATTAGTCCCTAAACTTTTGAACATTCCAAATTCATC
Found at i:225710 original size:60 final size:59
Alignment explanation
Indices: 225613--225749 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 59
225603 ATTAGTATAT
* * *
225613 ATGT-ATAGTTTAGGATGCAATTGGAATTTTCAAAAAGTTTG-GGAGCCAATTTAAAATG
1 ATGTCATAGTTTAGGATGAAATTGAAATGTTCAAAAAGTTTGAGGA-CCAATTTAAAATG
* * *
225671 AATGTCATAGTTTGGGAATGAAATTGAAATGTTC-AAAAGTTTGAGGACTAATTTAGAATG
1 -ATGTCATAGTTTAGG-ATGAAATTGAAATGTTCAAAAAGTTTGAGGACCAATTTAAAATG
225731 ATAGTCATAGTTTATGGAT
1 AT-GTCATAGTTTA-GGAT
225750 AAAACGTGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
59 6 0.09
60 41 0.62
61 19 0.29
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (59 bp):
ATGTCATAGTTTAGGATGAAATTGAAATGTTCAAAAAGTTTGAGGACCAATTTAAAATG
Found at i:226077 original size:21 final size:21
Alignment explanation
Indices: 226048--226100 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
226038 ATTCTGACTA
226048 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
226069 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
226090 TCGCAATGCGA
1 TCGCATTGCGA
226101 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:226333 original size:22 final size:22
Alignment explanation
Indices: 226308--226382 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
226298 CACTCTCTAA
* *
226308 GACGACATCTGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
226330 GACGAAATCAGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
* *
226352 GACGATATCAGTCTCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
226374 G-CGAAATCA
1 GACGAAATCA
226383 TTCACGCTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 7 0.15
22 41 0.85
ACGTcount: A:0.25, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GACGAAATCAGTCCCCATCTCC
Found at i:226781 original size:20 final size:20
Alignment explanation
Indices: 226708--226798 Score: 103
Period size: 20 Copynumber: 4.6 Consensus size: 20
226698 GCGATTCTGT
226708 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
226727 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
226747 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
226767 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
226787 TGTTGCGATTTT
1 CGTTGCGATTTT
226799 AAGTTTCAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
19 12 0.19
20 51 0.81
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:226805 original size:20 final size:20
Alignment explanation
Indices: 226762--226805 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
226752 CGATAGTCAT
* *
226762 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
226782 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
226802 TTTC
1 TTTC
226806 AGAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:228783 original size:20 final size:20
Alignment explanation
Indices: 228758--228804 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
228748 CAACAACAAA
228758 ATCGCAATGCGAAA-ATGACT
1 ATCGCAATGC-AAATATGACT
*
228778 ATCGCAATGCAAATTTGACT
1 ATCGCAATGCAAATATGACT
228798 ATCGCAA
1 ATCGCAA
228805 CGAGAGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCAAATATGACT
Found at i:228876 original size:20 final size:20
Alignment explanation
Indices: 228849--228917 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
228839 GCGATTCTCT
**
228849 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
228869 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
228889 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
228909 CGTTGCGAT
1 CGTTGCGAT
228918 TTTAAGTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:228927 original size:20 final size:20
Alignment explanation
Indices: 228849--228927 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
228839 GCGATTCTCT
*
228849 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* * *
228869 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
228889 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
228909 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
228928 AGATTCTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:229494 original size:21 final size:21
Alignment explanation
Indices: 229403--229507 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
229393 GACTCACCTG
*
229403 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
229425 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
229445 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
229466 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
229487 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
229508 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:229500 original size:42 final size:42
Alignment explanation
Indices: 229400--229510 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
229390 CCCGACTCAC
* * * *
229400 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
229442 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
229484 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
229511 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:231167 original size:33 final size:34
Alignment explanation
Indices: 231105--231180 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
231095 ACTAAATTCG
231105 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
*
231139 CGTTGCGATTTTCA-TTTCGCATTTCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
231172 CGTTGCGAT
1 CGTTGCGAT
231181 AGTTATTTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 27 0.66
34 14 0.34
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:231189 original size:33 final size:33
Alignment explanation
Indices: 231105--231200 Score: 122
Period size: 33 Copynumber: 2.8 Consensus size: 33
231095 ACTAAATTCG
*
231105 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATGTTCA-TTTCGCATTGCGATTCTCT
* *
231139 CGTTGCGATTTTCATTTCGCATTTCGATTCTCT
1 CGTTGCGATGTTCATTTCGCATTGCGATTCTCT
*
231172 CGTTGCGATAGTT-ATTTCCGCGTTGCGAT
1 CGTTGCGAT-GTTCATTT-CGCATTGCGAT
231201 AGTCAATTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
CGTTGCGATGTTCATTTCGCATTGCGATTCTCT
Found at i:231197 original size:20 final size:20
Alignment explanation
Indices: 231172--231260 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
231162 TCGATTCTCT
*
231172 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
231192 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
231212 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
231232 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
231252 CGTTGCGAT
1 CGTTGCGAT
231261 TTCCGCGTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:231227 original size:40 final size:40
Alignment explanation
Indices: 231172--231260 Score: 153
Period size: 40 Copynumber: 2.2 Consensus size: 40
231162 TCGATTCTCT
231172 CGTTGCGATAGTTATTTCCGCGTTGCGATAGTCA-ATTCCG
1 CGTTGCGATAGTTATTTCCGCGTTGCGATAGTCATATT-CG
*
231212 CGTTGCGATAGTTATTTCCGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTTATTTCCGCGTTGCGATAGTCATATTCG
231252 CGTTGCGAT
1 CGTTGCGAT
231261 TTCCGCGTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 44 0.94
41 3 0.06
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTTATTTCCGCGTTGCGATAGTCATATTCG
Found at i:233719 original size:24 final size:24
Alignment explanation
Indices: 233685--233738 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
233675 CTGAAAAATC
233685 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
233709 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
233733 ATCAAA
1 ATCAAA
233739 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:234605 original size:20 final size:20
Alignment explanation
Indices: 234580--234629 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
234570 AAATTCAGTA
*
234580 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAAAATCTCG
*
234600 TTGCGATAGTCAAAATCTTG
1 TTGCGATAGTCAAAATCTCG
234620 TTGCGATAGT
1 TTGCGATAGT
234630 TTGCGATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAAAATCTCG
Found at i:234653 original size:30 final size:30
Alignment explanation
Indices: 234600--234656 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
234590 CAGAATCTCG
**
234600 TTGCGATAGTCAAAATCTTGTTGCGATAGT
1 TTGCGATAGTCAAAATCGCGTTGCGATAGT
* *
234630 TTGCGATAGTCAGATTCGCGTTGCGAT
1 TTGCGATAGTCAAAATCGCGTTGCGAT
234657 TTACATATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (30 bp):
TTGCGATAGTCAAAATCGCGTTGCGATAGT
Found at i:234666 original size:20 final size:20
Alignment explanation
Indices: 234643--234735 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
234633 CGATAGTCAG
* *
234643 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
234663 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
234683 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
234703 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
234723 ATTCGCATTGCGA
1 ATTCGCATTGCGA
234736 ATTAGGAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:239034 original size:22 final size:21
Alignment explanation
Indices: 238980--239041 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
238970 TATGAGAGAT
*
238980 GGAGATAGG-CGGATTTCGCC
1 GGAGATGGGACGGATTTCGCC
*
239000 GGAGATGGGACGGATTTCGTC
1 GGAGATGGGACGGATTTCGCC
*
239021 GGAGATGGGGACGGATGTCGC
1 GGAGAT-GGGACGGATTTCGC
239042 TGTAGAGAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.22
21 16 0.44
22 12 0.33
ACGTcount: A:0.19, C:0.16, G:0.45, T:0.19
Consensus pattern (21 bp):
GGAGATGGGACGGATTTCGCC
Found at i:239246 original size:20 final size:20
Alignment explanation
Indices: 239196--239467 Score: 195
Period size: 20 Copynumber: 13.6 Consensus size: 20
239186 TAAACAAGCT
* * *
239196 TTGCGAATTTAACTTCCGCT
1 TTGCGAATTTGACTTTCGCG
239216 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
** *
239236 TTGCGAATTTGAAATTCAACG
1 TTGCGAATTTGACTTTC-GCG
*
239257 TTGCGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GCG
*
239277 TTGCG-ATTT-ACAAATTCGCG
1 TTGCGAATTTGAC--TTTCGCG
*
239297 TTGCG-ATTT-ACATATTCGCA
1 TTGCGAATTTGAC-T-TTCGCG
* *
239317 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGCG
*
239337 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGCG
* *
239357 TTACGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGCG
*
239377 TTGCGAATTTGACTTAT-GTG
1 TTGCGAATTTGACTT-TCGCG
*
239397 TTGCGAATTTGACTTAT-GTG
1 TTGCGAATTTGACTT-TCGCG
* **
239417 TTGCG-ATTTATAAATTCGCG
1 TTGCGAATTT-GACTTTCGCG
*
239437 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC--TTTCGCG
239457 TTGCGAATTTG
1 TTGCGAATTTG
239468 GAAACTGTGT
Statistics
Matches: 210, Mismatches: 28, Indels: 26
0.80 0.11 0.10
Matches are distributed among these distances:
18 3 0.01
19 10 0.05
20 168 0.80
21 27 0.13
22 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:239410 original size:60 final size:61
Alignment explanation
Indices: 239216--239442 Score: 240
Period size: 60 Copynumber: 3.8 Consensus size: 61
239206 AACTTCCGCT
* * * *
239216 TTGCGAATTTGACTTTCGCGTTGCGAATTTGA-AATTCAACGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTATTC-GCGTTGCGAATTTGACTTATGTG
* * *
239277 TTGCG-ATTT-ACAAATTCGCGTTGCG-ATTT-ACATATTCGCATTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGAC-TATTCGCGTTGCGAATTTGACTTATGTG
*
239337 TTGCGAATTTGACTATCGCGTTACGAATTTGACTA-TCGCGTTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTATGTG
*
239397 TTGCGAATTTGACTTAT-GTGTTGCG-ATTT-A-TAAATTCGCGTTGCGA
1 TTGCGAATTTGAC-TATCGCGTTGCGAATTTGACT--ATTCGCGTTGCGA
239443 TTTACAGATT
Statistics
Matches: 142, Mismatches: 12, Indels: 25
0.79 0.07 0.14
Matches are distributed among these distances:
57 1 0.01
58 1 0.01
59 8 0.06
60 95 0.67
61 33 0.23
62 4 0.03
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (61 bp):
TTGCGAATTTGACTATCGCGTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTTATGTG
Found at i:241945 original size:106 final size:104
Alignment explanation
Indices: 241761--242064 Score: 352
Period size: 106 Copynumber: 2.9 Consensus size: 104
241751 TTATAAACGG
* * * *
241761 TAAAATAGTAAATTACTTATTTT-TTATT-ATATTATCAACATATT---TAGCACCTAATATATT
1 TAAAATAGTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGGTAACGCCTAA-ATGTT
* * ** *
241821 ATGAGAGTTTAAGCTGATGGGCCTTAAATATTTGACGATAA
65 ATCAAAGTTTAAGCTGATGGGCCTTAAA-ATCCGACAATAA
*
241862 -AAAATATGTTAATTACTTATTTTGTTATTAATATTATCAACGTATTAGGTAACGCCTAGAATGT
1 TAAAATA-GTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGGTAACGCCTA-AATGT
*
241926 TATCAAAGTTTAAGTTGATGGGCCCTT-AAATCCGACAATAA
64 TATCAAAGTTTAAGCTGATGGG-CCTTAAAATCCGACAATAA
* *
241967 TAAAATAGATTAATTATTTATTTTGTTATTAATATTATCAACATATTAGGTACCGCCTAAAATGT
1 TAAAATAG-TTAATTACTTATTTTGTTATTAATATTATCAACATATTAGGTAACGCCT-AAATGT
* *
242032 TAACAAAGTTTAAGCTGATGAGCCTTATAAATC
64 TATCAAAGTTTAAGCTGATGGGCCTTA-AAATC
242065 TCATGATAAC
Statistics
Matches: 173, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
100 6 0.03
101 15 0.09
102 5 0.03
103 15 0.09
105 14 0.08
106 107 0.62
107 11 0.06
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (104 bp):
TAAAATAGTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGGTAACGCCTAAATGTTA
TCAAAGTTTAAGCTGATGGGCCTTAAAATCCGACAATAA
Found at i:243935 original size:15 final size:15
Alignment explanation
Indices: 243915--243969 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
243905 AACCGGGTAT
243915 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
*
243930 CGGGTACCCGCA-AATC
1 CGGGTACCCG-ATTA-C
*
243946 CGGATACCCGATTAC
1 CGGGTACCCGATTAC
243961 CGGGTACCC
1 CGGGTACCC
243970 ATAACATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 21 0.64
16 12 0.36
ACGTcount: A:0.22, C:0.36, G:0.25, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:244209 original size:65 final size:65
Alignment explanation
Indices: 244133--244254 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 65
244123 GCACGATTAG
*
244133 TGTTACCTTGGTATAAATAT-GAGCGGTGTCTAGGTGGGTCAGCTGAACCAAATAGCCTCAGATA
1 TGTTACCTTGGTATAAATATGGA-CGGTGTCTAGGTAGGTCAGCTGAACCAAATAGCCTCAGATA
244197 A
65 A
* * * * *
244198 TGTTATCTTGGTGTAGATATGGACGGTGTTTAGGTAGGTCAGTTGAACCAAATAGCC
1 TGTTACCTTGGTATAAATATGGACGGTGTCTAGGTAGGTCAGCTGAACCAAATAGCC
244255 ACAAATGACG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
65 48 0.96
66 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (65 bp):
TGTTACCTTGGTATAAATATGGACGGTGTCTAGGTAGGTCAGCTGAACCAAATAGCCTCAGATAA
Found at i:244655 original size:12 final size:11
Alignment explanation
Indices: 244634--244664 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
244624 ATTTTTAATT
244634 TTTAATTATTA
1 TTTAATTATTA
244645 TTTATATTATTA
1 TTTA-ATTATTA
244657 TTTAATTA
1 TTTAATTA
244665 ATTTTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:252899 original size:26 final size:24
Alignment explanation
Indices: 252870--252930 Score: 95
Period size: 26 Copynumber: 2.5 Consensus size: 24
252860 TTTTTCGGAT
*
252870 AAAAAACCGGTTTTTTATCCGGTTGA
1 AAAAAACCGGTTTTTAATCCGG-T-A
252896 AAAAAACCGGTTTTTAATCCGGTA
1 AAAAAACCGGTTTTTAATCCGGTA
252920 AAAAAACCGGT
1 AAAAAACCGGT
252931 CGTTCAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 12 0.35
25 1 0.03
26 21 0.62
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (24 bp):
AAAAAACCGGTTTTTAATCCGGTA
Found at i:255485 original size:204 final size:204
Alignment explanation
Indices: 255135--255544 Score: 721
Period size: 204 Copynumber: 2.0 Consensus size: 204
255125 TCAGAAGGTG
*
255135 TTGAATGTCCTTCAGCTCCCCAAACGCCATTGCTAAAACTAGAAACTGTTGAGGATGATGGGGGT
1 TTGAATGTCCTTCAGCTCCCCAAACGCCATTGCTAAAACTAGAAACTGTTGAGGATGATGGGGAT
* * * *
255200 GGAAATTCAGGACCCCGTGCATACCTATTACTAAAAGTATCATGCTGACTTGATTGGCCACTGTG
66 GGAAATTCAGGACCCCGCGCATACCTATTACTAAAAGCATCATGCCGACTTGATTGACCACTGTG
255265 GAACATATGGCTTCTTTGTGGTGCATTTATGCCAGTTTGATTAGGCAATGACTCAAAAGAGCTTG
131 GAACATATGGCTTCTTTGTGGTGCATTTATGCCAGTTTGATTAGGCAATGACTCAAAAGAGCTTG
255330 TGTTAAACT
196 TGTTAAACT
255339 TTGAATGTCCTTCAGCTCCCCAAACGCCATTGCTAAAACTAGAAACTGTTGAGGATGATGGGGAT
1 TTGAATGTCCTTCAGCTCCCCAAACGCCATTGCTAAAACTAGAAACTGTTGAGGATGATGGGGAT
* *
255404 GGAAATTCAGGACCCCGCGGATACCTATTACTAAAAGCATCATGCCGACTTGCTTGACCACTGTG
66 GGAAATTCAGGACCCCGCGCATACCTATTACTAAAAGCATCATGCCGACTTGATTGACCACTGTG
* * *
255469 GAACATCTGGCTTCTTTGTGGTGCATTTATGCCAGTTTGATTAGGCAATGACTCAATAGAGCTTT
131 GAACATATGGCTTCTTTGTGGTGCATTTATGCCAGTTTGATTAGGCAATGACTCAAAAGAGCTTG
*
255534 TTTTAAACT
196 TGTTAAACT
255543 TT
1 TT
255545 TCTCCAATTG
Statistics
Matches: 195, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
204 195 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (204 bp):
TTGAATGTCCTTCAGCTCCCCAAACGCCATTGCTAAAACTAGAAACTGTTGAGGATGATGGGGAT
GGAAATTCAGGACCCCGCGCATACCTATTACTAAAAGCATCATGCCGACTTGATTGACCACTGTG
GAACATATGGCTTCTTTGTGGTGCATTTATGCCAGTTTGATTAGGCAATGACTCAAAAGAGCTTG
TGTTAAACT
Found at i:256171 original size:27 final size:27
Alignment explanation
Indices: 256141--256201 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
256131 TATACTGAAC
256141 CATTTCAGGAATTGGATCATACGACGA
1 CATTTCAGGAATTGGATCATACGACGA
* * *
256168 CATTTCAGGAATTGTATTATAGGACGA
1 CATTTCAGGAATTGGATCATACGACGA
256195 CATTTCA
1 CATTTCA
256202 AAGTTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (27 bp):
CATTTCAGGAATTGGATCATACGACGA
Found at i:256486 original size:17 final size:18
Alignment explanation
Indices: 256455--256488 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
256445 GCCCAAAACA
256455 TATCAACTAGAATCTTTT
1 TATCAACTAGAATCTTTT
*
256473 TATC-ACTAGCATCTTT
1 TATCAACTAGAATCTTT
256489 CACACCTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (18 bp):
TATCAACTAGAATCTTTT
Found at i:262440 original size:23 final size:23
Alignment explanation
Indices: 262414--262463 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
262404 TTCATAAAAT
262414 ATTGTGTCATATGTGAATTATCA
1 ATTGTGTCATATGTGAATTATCA
262437 ATTGTGTCATATGTGAATTATCA
1 ATTGTGTCATATGTGAATTATCA
262460 ATTG
1 ATTG
262464 GTTTATTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (23 bp):
ATTGTGTCATATGTGAATTATCA
Found at i:263437 original size:28 final size:28
Alignment explanation
Indices: 263397--263455 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
263387 TACATACCTC
263397 ATATTAATTGCCAATACCATGTGATGGG
1 ATATTAATTGCCAATACCATGTGATGGG
263425 ATATTAATTGCCAATACCATGTGATGGG
1 ATATTAATTGCCAATACCATGTGATGGG
263453 ATA
1 ATA
263456 GCCACCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (28 bp):
ATATTAATTGCCAATACCATGTGATGGG
Found at i:264213 original size:23 final size:25
Alignment explanation
Indices: 264178--264233 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
264168 TCCAATCTTC
*
264178 ATTATCTAT-ATTCCTTTACA-AAAT
1 ATTAT-TATAATTCCTTTAAATAAAT
*
264202 ATT-TTATAATTCTTTTAAATAAAT
1 ATTATTATAATTCCTTTAAATAAAT
264226 ATTATTAT
1 ATTATTAT
264234 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.11
23 10 0.37
24 10 0.37
25 4 0.15
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTATTATAATTCCTTTAAATAAAT
Found at i:280133 original size:34 final size:35
Alignment explanation
Indices: 280090--280191 Score: 170
Period size: 34 Copynumber: 2.9 Consensus size: 35
280080 TTTCGTCCTA
280090 TTAGGATTCAAACTCCTAAAAATAGGATAGAA-TT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
280124 TTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
280159 TGCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 T--TAGGATTCAAACTCCTAAAAATAGGATAGA
280192 GTTATACTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
34 31 0.49
35 3 0.05
37 29 0.46
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (35 bp):
TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:280656 original size:62 final size:60
Alignment explanation
Indices: 280590--280704 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 60
280580 GGATATTTTA
* * *
280590 TTCATTTATTTTATTATTCATGTTATTA-TATTATATGTATATATATATATATATAAATTATT
1 TTCATTTATTTT-TTACT-ATATT-TTACTATTATATATATATATATATATATATAAATTATT
280652 TTCATTTATTTTTTACTATATTTTACTATTATATATATATATATATATATATA
1 TTCATTTATTTTTTACTATATTTTACTATTATATATATATATATATATATATA
280705 TTTCTTTAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 3 0.06
60 30 0.61
61 4 0.08
62 12 0.24
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (60 bp):
TTCATTTATTTTTTACTATATTTTACTATTATATATATATATATATATATATAAATTATT
Found at i:280688 original size:2 final size:2
Alignment explanation
Indices: 280681--280705 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
280671 ATTTTACTAT
280681 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
280706 TTCTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:284884 original size:19 final size:21
Alignment explanation
Indices: 284862--284908 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
284852 AACAAAAAGG
284862 GCAAAAA-GAAAAAA-AAGAA
1 GCAAAAAGGAAAAAACAAGAA
284881 GCAAAAAAGGAAAAAACAAGAA
1 GC-AAAAAGGAAAAAACAAGAA
284903 -CAAAAA
1 GCAAAAA
284909 AAGAAAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 2 0.08
20 10 0.40
21 8 0.32
22 5 0.20
ACGTcount: A:0.77, C:0.09, G:0.15, T:0.00
Consensus pattern (21 bp):
GCAAAAAGGAAAAAACAAGAA
Found at i:284901 original size:22 final size:20
Alignment explanation
Indices: 284864--284931 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
284854 CAAAAAGGGC
284864 AAAAAGAAAAAA-AAGAAGCA
1 AAAAAGAAAAAACAAGAA-CA
284884 AAAAAGGAAAAAACAAGAACAA
1 AAAAA-GAAAAAACAAGAAC-A
* * *
284906 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
284926 AAAAAG
1 AAAAAG
284932 GGAACAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.29
21 19 0.45
22 11 0.26
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:284912 original size:11 final size:11
Alignment explanation
Indices: 284871--284913 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
284861 GGCAAAAAGA
284871 AAAAAAAGAAGC
1 AAAAAAAGAA-C
*
284883 AAAAAAGGAA-
1 AAAAAAAGAAC
*
284893 AAAACAAGAAC
1 AAAAAAAGAAC
284904 AAAAAAAGAA
1 AAAAAAAGAA
284914 AGAACAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.31
11 9 0.35
12 9 0.35
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAC
Found at i:286447 original size:36 final size:36
Alignment explanation
Indices: 286407--286528 Score: 106
Period size: 36 Copynumber: 3.4 Consensus size: 36
286397 ACTCATGATT
* * *
286407 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
* * * * *
286443 GTTT-TCACTAGAA-GAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAGATTTGTCTCCCTTGAGACA
* *
286478 GTTTCCCTTGAAACAA-ATTTTGTCTCCCTTGAGACA
1 GTTTCTCTTAAAACAAGA-TTTGTCTCCCTTGAGACA
*
286514 GTTTCTCTTGAAACA
1 GTTTCTCTTAAAACA
286529 TAAACATTGA
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
35 27 0.40
36 41 0.60
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
Found at i:286690 original size:101 final size:101
Alignment explanation
Indices: 286585--286768 Score: 282
Period size: 101 Copynumber: 1.8 Consensus size: 101
286575 ATAGTTTCCC
*
286585 TTGAAACAAAATTTTGTCTCTC-TTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCTTGAG
1 TTGAAAC-AAATTTCGTCTC-CATTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAG
286648 ACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTCT
64 ACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTCT
** * *
286686 TTGAAACAAATTTCGTCTCCATTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTCGTCTCCATTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGAC
*
286751 AGTTTCTCTTGAAACAAA
66 AGTTTCCCTTGAAACAAA
286769 TTTCGTCTAT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
99 1 0.01
100 26 0.35
101 48 0.64
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (101 bp):
TTGAAACAAATTTCGTCTCCATTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGAC
AGTTTCCCTTGAAACAAAATATTTGAATATGTTTCT
Found at i:286712 original size:137 final size:137
Alignment explanation
Indices: 286459--286867 Score: 536
Period size: 137 Copynumber: 3.0 Consensus size: 137
286449 ACTAGAAGAG
* *
286459 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * * *
286524 AAACATAAACA-TTGAAAACATTTCCCTTGAAATAAATTTCGTCT-CTCTGAGATAGTTTCCCTT
66 AAACA-AAATATTTGAATATATTTCCCTTGAAACAAATTTCGTCTCCT-TGAGACAGTTTCTCTT
286587 GAAACAAAA
129 GAAACAAAA
*
286596 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
286661 AAACAAAATATTTGAATATGTTT-CTTTGAAACAAATTTCGTCTCCATTGAGACAGTTTCTTTTG
66 AAACAAAATATTTGAATATATTTCCCTTGAAACAAATTTCGTCTCC-TTGAGACAGTTTCTCTTG
* * *
286725 GAACTAAG
130 AAACAAAA
* * * *
286733 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAATTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * * *
286798 AAACAAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTG
66 AAACAAAATATTTGAATATATTTCCCTTGAAACAAATTTCGTCT-CCTTGAGACAGTTTCTCTTG
286863 AAACA
130 AAACA
286868 CAAAATCTTC
Statistics
Matches: 236, Mismatches: 31, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
136 22 0.09
137 176 0.75
138 36 0.15
139 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (137 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
AAACAAAATATTTGAATATATTTCCCTTGAAACAAATTTCGTCTCCTTGAGACAGTTTCTCTTGA
AACAAAA
Found at i:286798 original size:36 final size:35
Alignment explanation
Indices: 286463--286804 Score: 223
Period size: 36 Copynumber: 9.9 Consensus size: 35
286453 GAAGAGTTTT
* *
286463 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCT-TCTTGAGACAGTTTCTCTTGAAACAAATTTC
*
286499 GTCTCCCTTGAGACAGTTTCTCTTGAAACATAA----
1 GTCT-TCTTGAGACAGTTTCTCTTGAAACA-AATTTC
* * * * *
286532 -AC--ATTGAAAACA-TTTCCCTTGAAATAAATTTC
1 GTCTTCTTG-AGACAGTTTCTCTTGAAACAAATTTC
* * *
286564 GTC-TCTCTGAGATAGTTTCCCTTGAAACAAAATTTT
1 GTCTTCT-TGAGACAGTTTCTCTTGAAAC-AAATTTC
* * *
286600 GTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTT
1 GTCT-TCTTGAGACAGTTTCTCTTGAAACAAATTTC
*
286636 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA----
1 GTCT-TCTTGAGACAGTTTCTCTTGAAACAAATTTC
* * *
286668 AT-AT-TTGA-ATATGTTTCT-TTGAAACAAATTTC
1 GTCTTCTTGAGACA-GTTTCTCTTGAAACAAATTTC
* * * * *
286700 GTCTCCATTGAGACAGTTTCTTTTGGAACTAAGTTTT
1 GTCTTC-TTGAGACAGTTTCTCTTGAAAC-AAATTTC
286737 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTC
1 GTCT-TCTTGAGACAGTTTCTCTTGAAACAAATTTC
* *
286773 GTCTATCTTGAGACAATTTCCCTTGAAACAAA
1 GTCT-TCTTGAGACAGTTTCTCTTGAAACAAA
286805 ATCTTTGAAT
Statistics
Matches: 246, Mismatches: 35, Indels: 50
0.74 0.11 0.15
Matches are distributed among these distances:
28 14 0.06
29 24 0.10
30 5 0.02
32 3 0.01
33 1 0.00
34 4 0.02
35 24 0.10
36 117 0.48
37 50 0.20
38 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (35 bp):
GTCTTCTTGAGACAGTTTCTCTTGAAACAAATTTC
Found at i:286866 original size:65 final size:65
Alignment explanation
Indices: 286762--286936 Score: 224
Period size: 65 Copynumber: 2.6 Consensus size: 65
286752 GTTTCTCTTG
* ** * **
286762 AAACAAATTTCGTCTATCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
*
286827 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
286892 TA
64 TA
* ** *
286894 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAA
286937 CAGATATCTT
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
65 32 0.33
66 6 0.06
67 31 0.32
68 27 0.28
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:287757 original size:105 final size:105
Alignment explanation
Indices: 287539--288304 Score: 1069
Period size: 105 Copynumber: 7.3 Consensus size: 105
287529 GCCATCTGCG
* * * * * *
287539 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
287604 TGGA-CGACTGGTTATCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* *
287648 ATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
287713 ACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
287753 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
287818 ACCGCTGCTTGTCAACAACAACTTCTTAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
287858 ATTTCAACTTCACAACAAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
287923 ACTGCTACTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
287963 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
288028 ACCGCTGCTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
288068 ATTTCAAATTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
288133 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
288168 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
288233 A-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * *
288274 ATTTCAACTTCACGACGGAGGATATTAGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
288305 TGGAACAATG
Statistics
Matches: 598, Mismatches: 51, Indels: 19
0.90 0.08 0.03
Matches are distributed among these distances:
99 2 0.00
100 78 0.13
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 402 0.67
106 77 0.13
107 5 0.01
109 21 0.04
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:288882 original size:34 final size:34
Alignment explanation
Indices: 288839--288939 Score: 175
Period size: 34 Copynumber: 2.9 Consensus size: 34
288829 TTTCGTCCTA
288839 TTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATT
*
288873 TTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATT
288907 TGCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 T--TAGGATTCAAACTCCTAAAAATAGGATAGA
288940 GTTATACTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 34 0.54
36 29 0.46
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (34 bp):
TTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:289366 original size:18 final size:17
Alignment explanation
Indices: 289327--289369 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
289317 ATTATATGGA
289327 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
289343 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
289361 TATTATTAT
1 TATTATTAT
289370 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:289380 original size:2 final size:2
Alignment explanation
Indices: 289367--289460 Score: 70
Period size: 2 Copynumber: 47.5 Consensus size: 2
289357 TTATTATTAT
* *
289367 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
289407 TT TCA TT TA T- TT TT TA CTA TA T- TT TA CTA TA TA TA TA TA TA
1 TA T-A TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
289448 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
289461 TTCTTTAATA
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
1 4 0.05
2 67 0.88
3 5 0.07
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (2 bp):
TA
Found at i:289879 original size:2 final size:2
Alignment explanation
Indices: 289872--289923 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
289862 TAATACTTTG
289872 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
*
289914 AT AT TT AT AT
1 AT AT AT AT AT
289924 TTTTCCTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:291049 original size:2 final size:2
Alignment explanation
Indices: 291042--291075 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
291032 AACTTAATTT
291042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
291076 ATTGGATATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:308373 original size:90 final size:90
Alignment explanation
Indices: 308212--308406 Score: 264
Period size: 90 Copynumber: 2.2 Consensus size: 90
308202 ATATTCGTCG
* *
308212 GCACATGGTTGCTTGAGGATTTCTTGTACCATTGTGCAGCAGAAACTGGAGGAAAATCAGAAGAG
1 GCACCTGGTTGCTTGAGGATTGCTTGTACCATTGTGCAGCAGAAACTGGAGGAAAATCAGAAGAG
* * * *
308277 AGTGGTTCAGGGTATCCAGTCATTA
66 AATGGTTCAGAGTATCCACTCATCA
* * * * * *
308302 GCACCTGGTTGCTTGAGGATTGCTTGTGCCTTTGTGTAGCCGAAACTGGAGGAAAATCATAAGCG
1 GCACCTGGTTGCTTGAGGATTGCTTGTACCATTGTGCAGCAGAAACTGGAGGAAAATCAGAAGAG
* *
308367 AATGGTTCTGAGTATCCACTCGTCA
66 AATGGTTCAGAGTATCCACTCATCA
308392 GCACCTGGTTGCTTG
1 GCACCTGGTTGCTTG
308407 TGCCTTTGTG
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (90 bp):
GCACCTGGTTGCTTGAGGATTGCTTGTACCATTGTGCAGCAGAAACTGGAGGAAAATCAGAAGAG
AATGGTTCAGAGTATCCACTCATCA
Found at i:309307 original size:17 final size:17
Alignment explanation
Indices: 309270--309306 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
309260 TAATATTTTT
309270 AATTTTTTAAAATATCAA
1 AATTTTTTAAAATAT-AA
309288 AATTTTTTAAATATATAA
1 AATTTTTTAAA-ATATAA
309306 A
1 A
309307 TGTGTTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTTTTAAAATATAA
Found at i:311271 original size:234 final size:234
Alignment explanation
Indices: 310862--311334 Score: 937
Period size: 234 Copynumber: 2.0 Consensus size: 234
310852 ATGACGAAAC
310862 AGTTGTGCACCATAGGATATACAATTGATGGTAGGCTATTAGAGTTGGTGGGAGATAGTGTCTGC
1 AGTTGTGCACCATAGGATATACAATTGATGGTAGGCTATTAGAGTTGGTGGGAGATAGTGTCTGC
310927 TATCCTCCCGATTTCCTAAAGCTTATGGTTCCTTCTATCTTCTAAACAAGATATTTGTTTAAATC
66 TATCCTCCCGATTTCCTAAAGCTTATGGTTCCTTCTATCTTCTAAACAAGATATTTGTTTAAATC
310992 ATTATAGAGTTGGATGAATTTAGTTTGGTGCCTCGTATGGCCTTATTGTTTTAAGTCCTTTACAT
131 ATTATAGAGTTGGATGAATTTAGTTTGGTGCCTCGTATGGCCTTATTGTTTTAAGTCCTTTACAT
311057 ACATGCTAAAGACGGTAGCCAGTGATGTTTGTAGAATGA
196 ACATGCTAAAGACGGTAGCCAGTGATGTTTGTAGAATGA
311096 AGTTGTGCACCATAGGATATACAATTGATGGTAGGCTATTAGAGTTGGTGGGAGATAGTGTCTGC
1 AGTTGTGCACCATAGGATATACAATTGATGGTAGGCTATTAGAGTTGGTGGGAGATAGTGTCTGC
311161 TATCCTCCCGATTTCCTAAAGCTTATGGTTCCTTCTATCTTCTAAACAAGATATTTGTTTAAATC
66 TATCCTCCCGATTTCCTAAAGCTTATGGTTCCTTCTATCTTCTAAACAAGATATTTGTTTAAATC
311226 ATTATAGAGTTGGATGAATTTAGTTTGGTGCCTCGTATGGCCTTATTGTTTTAAGTCCTTTACAT
131 ATTATAGAGTTGGATGAATTTAGTTTGGTGCCTCGTATGGCCTTATTGTTTTAAGTCCTTTACAT
*
311291 ACATGCTAAAGACTGTAGCCAGTGATGTTTGTAGAATGA
196 ACATGCTAAAGACGGTAGCCAGTGATGTTTGTAGAATGA
311330 AGTTG
1 AGTTG
311335 ACTGTTTATG
Statistics
Matches: 238, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
234 238 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (234 bp):
AGTTGTGCACCATAGGATATACAATTGATGGTAGGCTATTAGAGTTGGTGGGAGATAGTGTCTGC
TATCCTCCCGATTTCCTAAAGCTTATGGTTCCTTCTATCTTCTAAACAAGATATTTGTTTAAATC
ATTATAGAGTTGGATGAATTTAGTTTGGTGCCTCGTATGGCCTTATTGTTTTAAGTCCTTTACAT
ACATGCTAAAGACGGTAGCCAGTGATGTTTGTAGAATGA
Done.