Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 51 of 427
Found at i:12279923 original size:59 final size:59
Alignment explanation
Indices: 12279835--12280446 Score: 829
Period size: 59 Copynumber: 10.2 Consensus size: 59
12279825 AATATATATG
* * *
12279835 TAATTGATTTTCAATTAATTAAATAAATAATCATATTTCATAATAATTCTATGAATAAT
1 TAATTAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAAT
* *
12279894 TAATAAATTTTCGATTAATTAAATAAATAATCATATTTTATAATAATTTTATGAATAAT
1 TAATTAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAAT
* * * *
12279953 TAATAAAATTTT-GATTAATTAAATAAATAATCATATTCCATAATAAATTTACGAATAAT
1 TAAT-TAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAAT
* *
12280012 TAATTAATTTCCGATTAATAAAATAAATAATCATATTTCATAATAATTTTATGAATAAT
1 TAATTAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAAT
* *
12280071 TAATAAAATTTT-GATTAATTAAATAAATAATCATATTTCATAATAATTTTACGAATAAT
1 TAAT-TAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAAT
*
12280130 TAATTAATTTTAGATTAATTAATTAAATAAATAATCATATTTCATAATAATTTTA-GAAATAAT
1 TAATTAATTTTCG----ATTAATTAAATAAATAATCATATTTCATAATAATTTTATG-AATAAT
* * *
12280193 TAATTAATTTCCGATTAAATAAATAAATAATCATATTTCATAATAATTTTAAGAATAAT
1 TAATTAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAAT
* * * *
12280252 TAATTAA-CTTCTGATTAATTAAATAAATAATCATATCTTGATAATAATTTTAGGAACAAT
1 TAATTAATTTTC-GATTAATTAAATAAATAATCATAT-TTCATAATAATTTTATGAATAAT
* *
12280312 TAATTAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAGTTTTAGGAATAATTAAT
1 TAATTAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAATTTTATG---AA-TAAT
*
12280375 TAATTTTTAATTTTTGATTAATTAAATAAATAATCATATTTCATAATAATTTTA-GAATAAT
1 TAA---TTAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAAT
12280436 TAATTAATTTT
1 TAATTAATTTT
12280447 TAATTTTTTT
Statistics
Matches: 498, Mismatches: 35, Indels: 41
0.87 0.06 0.07
Matches are distributed among these distances:
58 21 0.04
59 290 0.58
60 64 0.13
61 10 0.02
62 5 0.01
63 61 0.12
65 1 0.00
66 46 0.09
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (59 bp):
TAATTAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAAT
Found at i:12281388 original size:27 final size:29
Alignment explanation
Indices: 12281330--12281392 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 29
12281320 TTTTATATAT
* *
12281330 TATATATACATTCTTTATATATCATATTA
1 TATATATACATTCTTTATATACCATATCA
*
12281359 TATATATACATT-TTTA-ATACCGTATCA
1 TATATATACATTCTTTATATACCATATCA
12281386 TATATAT
1 TATATAT
12281393 TATTATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 15 0.48
28 4 0.13
29 12 0.39
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (29 bp):
TATATATACATTCTTTATATACCATATCA
Found at i:12281485 original size:22 final size:20
Alignment explanation
Indices: 12281435--12281485 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
12281425 TTATTATTAA
*
12281435 TATTAGTACATATATTTTAT
1 TATTAGTATATATATTTTAT
*
12281455 TA-TACGTATATATACTTTTTTT
1 TATTA-GTATATATA--TTTTAT
12281477 TATTAGTAT
1 TATTAGTAT
12281486 TTTTCTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.08
20 10 0.40
22 11 0.44
23 2 0.08
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (20 bp):
TATTAGTATATATATTTTAT
Found at i:12281524 original size:21 final size:21
Alignment explanation
Indices: 12281500--12281550 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
12281490 CTCATATATC
12281500 ATTATATTTTTTATTAT-ACCT
1 ATTAT-TTTTTTATTATCACCT
* *
12281521 ATTATTTTCATTATTATCACTT
1 ATTATTTT-TTTATTATCACCT
12281543 ATTATTTT
1 ATTATTTT
12281551 ATTTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 12 0.46
22 11 0.42
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTATTTTTTTATTATCACCT
Found at i:12281643 original size:2 final size:2
Alignment explanation
Indices: 12281622--12281671 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
12281612 ATATTTATTT
* * *
12281622 TA TA TA TG TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
12281663 TG TA TA TA T
1 TA TA TA TA T
12281672 TTTAACATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12285499 original size:21 final size:21
Alignment explanation
Indices: 12285465--12285522 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
12285455 CTCATATATC
*
12285465 ATTATATTATTTATTAT-ACCT
1 ATTATTTTA-TTATTATCACCT
*
12285486 ATTATTTTCATTATTATCACTT
1 ATTATTTT-ATTATTATCACCT
12285508 ATTATTTTATT-TTAT
1 ATTATTTTATTATTAT
12285523 TTTAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 4 0.12
21 17 0.52
22 12 0.36
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTATTTTATTATTATCACCT
Found at i:12285624 original size:38 final size:37
Alignment explanation
Indices: 12285527--12285626 Score: 96
Period size: 38 Copynumber: 2.6 Consensus size: 37
12285517 TTTTATTTTA
12285527 ATAT-TATTATGTATATATTTTTCATATATGTTATGTAC
1 ATATATATTATGTATATA-TTTT-ATATATGTTATGTAC
* * * * *
12285565 ATACAT-TTTTCAATATTTATTTTATATATGTATATGTAT
1 ATATATATTAT--GTATATATTTTATATATGT-TATGTAC
12285604 ATATATATTATGTATATATTTTA
1 ATATATATTATGTATATATTTTA
12285627 ACATTACAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
38 24 0.50
39 16 0.33
40 8 0.17
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (37 bp):
ATATATATTATGTATATATTTTATATATGTTATGTAC
Found at i:12288108 original size:6 final size:7
Alignment explanation
Indices: 12288088--12288112 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12288078 TAATGTACAT
12288088 AATAAAA
1 AATAAAA
12288095 AATAAAA
1 AATAAAA
12288102 AATAAAA
1 AATAAAA
12288109 AATA
1 AATA
12288113 TATATTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AATAAAA
Found at i:12288464 original size:39 final size:37
Alignment explanation
Indices: 12288421--12288537 Score: 114
Period size: 39 Copynumber: 3.1 Consensus size: 37
12288411 ATATTAAGGG
* *
12288421 ATAATTAATACTAATACTAATAATAGTAAAATACTAATA
1 ATAATTAATA-TAATAATAATAGTAGTAAAATA-TAATA
*
12288460 ATAA-TAATGATAATAATAATAGTAG-AAAATAAAATA
1 ATAATTAAT-ATAATAATAATAGTAGTAAAATATAATA
* *
12288496 ATAATAATAATAGTAATATTAATAGTGGT-AAATATAATA
1 ATAAT--TAATA-TAATAATAATAGTAGTAAAATATAATA
12288535 ATA
1 ATA
12288538 GAATACGAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
36 8 0.12
37 6 0.09
38 18 0.27
39 34 0.52
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (37 bp):
ATAATTAATATAATAATAATAGTAGTAAAATATAATA
Found at i:12288537 original size:3 final size:3
Alignment explanation
Indices: 12288421--12288519 Score: 85
Period size: 3 Copynumber: 33.0 Consensus size: 3
12288411 ATATTAAGGG
* * * *
12288421 ATA ATTA ATA CTA ATA CTA ATA ATA GTA A-A ATA CTA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
12288466 ATG ATA ATA ATA ATA GTA GAAA ATA A-A ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
12288511 ATA TTA ATA
1 ATA ATA ATA
12288520 GTGGTAAATA
Statistics
Matches: 74, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
2 4 0.05
3 66 0.89
4 4 0.05
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12289260 original size:71 final size:72
Alignment explanation
Indices: 12289144--12289287 Score: 281
Period size: 71 Copynumber: 2.0 Consensus size: 72
12289134 GATCCTAGTC
12289144 CCAATGGGTCGGGTAATCGGGCTACCCCAAAACGATGTCGTTTTGGGCGCGTTT-GGGGTCTTTC
1 CCAATGGGTCGGGTAATCGGGCTACCCCAAAACGATGTCGTTTTGGGCGCGTTTGGGGGTCTTTC
12289208 AAAACGG
66 AAAACGG
12289215 CCAATGGGTCGGGTAATCGGGCTACCCCAAAACGATGTCGTTTTGGGCGCGTTTGGGGGTCTTTC
1 CCAATGGGTCGGGTAATCGGGCTACCCCAAAACGATGTCGTTTTGGGCGCGTTTGGGGGTCTTTC
12289280 AAAACGG
66 AAAACGG
12289287 C
1 C
12289288 GCCGTTTTCT
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 54 0.75
72 18 0.25
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.25
Consensus pattern (72 bp):
CCAATGGGTCGGGTAATCGGGCTACCCCAAAACGATGTCGTTTTGGGCGCGTTTGGGGGTCTTTC
AAAACGG
Found at i:12291993 original size:43 final size:43
Alignment explanation
Indices: 12291932--12292099 Score: 201
Period size: 43 Copynumber: 3.9 Consensus size: 43
12291922 TGGCATTTTT
* * *
12291932 TCCTACAAACGCCACTATAGAACGTGATCTTTAGCGGCGCTTT
1 TCCTACAAACGCCACTATAGAACATGATCTTTAGCGACGCTTC
** * *
12291975 TCCTACAAACGCTGCTATAGAACATGATCTTTAGCAATGCTTC
1 TCCTACAAACGCCACTATAGAACATGATCTTTAGCGACGCTTC
* * * *
12292018 TCCAACAAACGCCGCTATAGAACATGGTATTTAGCGACGCTTC
1 TCCTACAAACGCCACTATAGAACATGATCTTTAGCGACGCTTC
* * * *
12292061 GCCTACAAACACTACTAAAGAACATGATCTTTAGCGACG
1 TCCTACAAACGCCACTATAGAACATGATCTTTAGCGACG
12292100 TTTTGTTCTT
Statistics
Matches: 104, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 104 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (43 bp):
TCCTACAAACGCCACTATAGAACATGATCTTTAGCGACGCTTC
Found at i:12292083 original size:86 final size:86
Alignment explanation
Indices: 12291936--12292095 Score: 230
Period size: 86 Copynumber: 1.9 Consensus size: 86
12291926 ATTTTTTCCT
* * * ** * * *
12291936 ACAAACGCCACTATAGAACGTGATCTTTAGCGGCGCTTTTCCTACAAACGCTGCTATAGAACATG
1 ACAAACGCCACTATAGAACATGATATTTAGCGACGCTTCGCCTACAAACACTACTAAAGAACATG
12292001 ATCTTTAGCAATGCTTCTCCA
66 ATCTTTAGCAATGCTTCTCCA
* *
12292022 ACAAACGCCGCTATAGAACATGGTATTTAGCGACGCTTCGCCTACAAACACTACTAAAGAACATG
1 ACAAACGCCACTATAGAACATGATATTTAGCGACGCTTCGCCTACAAACACTACTAAAGAACATG
12292087 ATCTTTAGC
66 ATCTTTAGC
12292096 GACGTTTTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 64 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (86 bp):
ACAAACGCCACTATAGAACATGATATTTAGCGACGCTTCGCCTACAAACACTACTAAAGAACATG
ATCTTTAGCAATGCTTCTCCA
Found at i:12293077 original size:22 final size:22
Alignment explanation
Indices: 12293043--12293094 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
12293033 AAAAGCAATG
12293043 CAAATAAAATCC-AACA-AAAC
1 CAAATAAAATCCAAACATAAAC
*
12293063 CAAATATATAATCCAAACATAAAT
1 CAAATA-A-AATCCAAACATAAAC
12293087 CAAATAAA
1 CAAATAAA
12293095 TAGTAATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 6 0.22
21 1 0.04
22 6 0.22
23 5 0.19
24 9 0.33
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.17
Consensus pattern (22 bp):
CAAATAAAATCCAAACATAAAC
Found at i:12296463 original size:227 final size:227
Alignment explanation
Indices: 12296067--12296753 Score: 1178
Period size: 227 Copynumber: 3.0 Consensus size: 227
12296057 AATTTAAGAA
* * * * *
12296067 CTCTTAAACCTTTAGACCCACCTATGCTCCTTGGGAGGCTCACAAGGTTACTGCAATCTTTCAGA
1 CTCTTAAACCTTTACACCCACCTTTGCTGCTTGCGAGGCTCACAAGGTT-TTGCAATCTTTCAGA
* *
12296132 TTTAATATTTCAAGAGATTCCCATTCAATTTTGGTTGGAAGACTCCTAAGATTTTAGCAGCCTCC
65 TTTAATGTTTCAAGAGATTCCCATTCAATTTTGGTTGGAAGACTCCTAAGATTTTTGCAGCCTCC
12296197 TAAGTTCAAAAGTTTAAGCCTCGTAAGAACTCCTATGGATGGATGAACATCTATTAATCTGGTAC
130 TAAGTTCAAAAGTTTAAGCCTCGTAAGAACTCCTATGGATGGATGAACATCTATTAATCTGGTAC
12296262 ATCCTTCCAAAATCAAAACTTCAAGATTTGGAG
195 ATCCTTCCAAAATCAAAACTTCAAGATTTGGAG
*
12296295 CTCTTAAACCTTTACACCCACCTTTGCTGCTTGCGAGACTCACAAGGTTTTGCAATCTTTCAGAT
1 CTCTTAAACCTTTACACCCACCTTTGCTGCTTGCGAGGCTCACAAGGTTTTGCAATCTTTCAGAT
12296360 TTAATGTTTCAAGAGATTCCCATTCAATTTTGGTTGGAAGACTCCTAAGATTTTTGCAGCCTCCT
66 TTAATGTTTCAAGAGATTCCCATTCAATTTTGGTTGGAAGACTCCTAAGATTTTTGCAGCCTCCT
* * *
12296425 AAGTTCAAAAGTTTGAGTCTCGTAAGAACTCCTATGGATGGATGAACATCTATTAATTTGGTACA
131 AAGTTCAAAAGTTTAAGCCTCGTAAGAACTCCTATGGATGGATGAACATCTATTAATCTGGTACA
12296490 TCCTTCCAAAATCAAAACTTCAAGATTTGGAG
196 TCCTTCCAAAATCAAAACTTCAAGATTTGGAG
* *
12296522 CCCTTAAACCTTTACACCCACCTTTGCTGCTTGTGAGGCTCACAAGGTTTTTGCAATCTTTCAGA
1 CTCTTAAACCTTTACACCCACCTTTGCTGCTTGCGAGGCTCACAAGG-TTTTGCAATCTTTCAGA
*
12296587 TTTAATGTTTCAAGAGATTCCCATTCAATTTTGGTTGGAAGACTCCTAAGATTTTTGCAGCCTCT
65 TTTAATGTTTCAAGAGATTCCCATTCAATTTTGGTTGGAAGACTCCTAAGATTTTTGCAGCCTCC
*
12296652 TAAGTTCAAAAGTTTAAGCCTCGTAAGAACTCCTATGGATGGATGAACATCTTTTAATCTGGTAC
130 TAAGTTCAAAAGTTTAAGCCTCGTAAGAACTCCTATGGATGGATGAACATCTATTAATCTGGTAC
** *
12296717 -TCCCTTTTAAAATCAAAACTTCAAGATTTGGAC
195 AT-CCTTCCAAAATCAAAACTTCAAGATTTGGAG
12296750 CTCT
1 CTCT
12296754 AGTAAAGTCT
Statistics
Matches: 434, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
227 217 0.50
228 217 0.50
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (227 bp):
CTCTTAAACCTTTACACCCACCTTTGCTGCTTGCGAGGCTCACAAGGTTTTGCAATCTTTCAGAT
TTAATGTTTCAAGAGATTCCCATTCAATTTTGGTTGGAAGACTCCTAAGATTTTTGCAGCCTCCT
AAGTTCAAAAGTTTAAGCCTCGTAAGAACTCCTATGGATGGATGAACATCTATTAATCTGGTACA
TCCTTCCAAAATCAAAACTTCAAGATTTGGAG
Found at i:12297623 original size:43 final size:43
Alignment explanation
Indices: 12297243--12297646 Score: 349
Period size: 43 Copynumber: 9.4 Consensus size: 43
12297233 TATTTGAAAA
* * ** * *
12297243 AAACGCCGCTATAGAACATGACTTTTAGCGGCATTTTTTCTAC
1 AAACGCCGCTATAGAACGTGACCTTTAGCGGCGCTTTTCCAAC
* * * ** * *
12297286 AAACGCCACTATAGAATGTGACATTTAGCCACACTTTTACAAC
1 AAACGCCGCTATAGAACGTGACCTTTAGCGGCGCTTTTCCAAC
* * * * * **
12297329 AAAAGCCGCTAGAGAACGTGACCTTTAACGGTGTTTTTCCTTC
1 AAACGCCGCTATAGAACGTGACCTTTAGCGGCGCTTTTCCAAC
* * * * *
12297372 AAACGCCGCTACAGAACATTACCTTTAGTGGCACTTTTCCAAC
1 AAACGCCGCTATAGAACGTGACCTTTAGCGGCGCTTTTCCAAC
* * * * ** * *
12297415 AAACGACGCTGTAAAACGTGACATTTAGCGATGCTTTGCCTAC
1 AAACGCCGCTATAGAACGTGACCTTTAGCGGCGCTTTTCCAAC
* * * * *
12297458 AAACGACGCTGTAGAACGTGGCCTGTAGCGGCGCTTTTACAAC
1 AAACGCCGCTATAGAACGTGACCTTTAGCGGCGCTTTTCCAAC
* * *
12297501 AAATGCCGCTATAGAACGTGGCCTTTAGCGGCGTTTTTCCAAC
1 AAACGCCGCTATAGAACGTGACCTTTAGCGGCGCTTTTCCAAC
* * *
12297544 AAACGCCGCTATAGAACGTGGCCTTTAGCTGCGCTTTTCCTAC
1 AAACGCCGCTATAGAACGTGACCTTTAGCGGCGCTTTTCCAAC
* * * ***
12297587 AAACGCCGCTATAGAACGTGGCCTTTAGCAGTGCTTTTCCCGT
1 AAACGCCGCTATAGAACGTGACCTTTAGCGGCGCTTTTCCAAC
*
12297630 AAACGCCACTATAGAAC
1 AAACGCCGCTATAGAAC
12297647 TTGGTTTTTA
Statistics
Matches: 289, Mismatches: 72, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 289 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGAACGTGACCTTTAGCGGCGCTTTTCCAAC
Found at i:12297642 original size:129 final size:128
Alignment explanation
Indices: 12297243--12297646 Score: 405
Period size: 129 Copynumber: 3.1 Consensus size: 128
12297233 TATTTGAAAA
* * * * *
12297243 AAACGCCGCTATAGAACATGACTTTTAGCGGCATTTTTTCTACAAACGCCACTATAGAATGTGAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCATTTTTCCAACAAACGCCGCTATAGAACGTGAC
* * * * * * * * * *
12297308 ATTTAGCCACACTTTTACAACAAAAGCCGCTAGAGAACGTGACCTTTAACGGTG-TTTTTCCTT
66 ATTTAG-CGCGCTTTTCCTACAAACGCCGCTATAGAACGTGGCCTTTAGCGGTGCTTTTACCAT
* * * * * * *
12297371 CAAACGCCGCTACAGAACATTACCTTTAGTGGCACTTTTCCAACAAACGACGCTGTAAAACGTGA
1 -AAACGCCGCTATAGAACATGACCTTTAGCGGCATTTTTCCAACAAACGCCGCTATAGAACGTGA
* * * * * * * *
12297436 CATTTAGCGATGCTTTGCCTACAAACGACGCTGTAGAACGTGGCCTGTAGCGGCGCTTTTACAAC
65 CATTTAGCG-CGCTTTTCCTACAAACGCCGCTATAGAACGTGGCCTTTAGCGGTGCTTTTACCAT
* * * * *
12297501 AAATGCCGCTATAGAACGTGGCCTTTAGCGGCGTTTTTCCAACAAACGCCGCTATAGAACGTGGC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCATTTTTCCAACAAACGCCGCTATAGAACGTGAC
* * * *
12297566 CTTTAGCTGCGCTTTTCCTACAAACGCCGCTATAGAACGTGGCCTTTAGCAGTGCTTTTCCCGT
66 ATTTAGC-GCGCTTTTCCTACAAACGCCGCTATAGAACGTGGCCTTTAGCGGTGCTTTTACCAT
*
12297630 AAACGCCACTATAGAAC
1 AAACGCCGCTATAGAAC
12297647 TTGGTTTTTA
Statistics
Matches: 216, Mismatches: 56, Indels: 6
0.78 0.20 0.02
Matches are distributed among these distances:
128 1 0.00
129 209 0.97
130 6 0.03
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (128 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCATTTTTCCAACAAACGCCGCTATAGAACGTGAC
ATTTAGCGCGCTTTTCCTACAAACGCCGCTATAGAACGTGGCCTTTAGCGGTGCTTTTACCAT
Found at i:12297667 original size:43 final size:43
Alignment explanation
Indices: 12297509--12297668 Score: 131
Period size: 43 Copynumber: 3.7 Consensus size: 43
12297499 ACAAATGCCG
* * ** *** *
12297509 CTATAGAACGTGGCCTTTAGCGGCGTTTTTCCAACAAACGCCG
1 CTATAGAACGTGGCCTTTAACAGCACTTTTCCCGTAAACGCCA
* * * *** *
12297552 CTATAGAACGTGGCCTTTAGCTGCGCTTTTCCTACAAACGCCG
1 CTATAGAACGTGGCCTTTAACAGCACTTTTCCCGTAAACGCCA
* **
12297595 CTATAGAACGTGGCCTTTAGCAGTGCTTTTCCCGTAAACGCCA
1 CTATAGAACGTGGCCTTTAACAGCACTTTTCCCGTAAACGCCA
* **
12297638 CTATAGAACTTGGTTTTTAACAGCACTTTTC
1 CTATAGAACGTGGCCTTTAACAGCACTTTTC
12297669 GCAAAAATGC
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 102 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (43 bp):
CTATAGAACGTGGCCTTTAACAGCACTTTTCCCGTAAACGCCA
Found at i:12308594 original size:19 final size:19
Alignment explanation
Indices: 12308558--12308594 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12308548 GAAGTATCAA
*
12308558 TTGGATTTGCTGTTTTTGG
1 TTGGATTTGCTGTATTTGG
*
12308577 TTGGATTTGTTGTATTTG
1 TTGGATTTGCTGTATTTG
12308595 TTGTTTTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.03, G:0.30, T:0.59
Consensus pattern (19 bp):
TTGGATTTGCTGTATTTGG
Found at i:12308822 original size:86 final size:86
Alignment explanation
Indices: 12308677--12309111 Score: 385
Period size: 86 Copynumber: 5.1 Consensus size: 86
12308667 GCTTTTTTGC
** * * * * *
12308677 GAAAAGCGCCGCTAAAAATCAA-GCTCTATAACAGCGTTTGCGGGAAAAGCGTCGCTAAAGGCCA
1 GAAAAGCGCCGCT-AAAGGCAACGTTCTATAGCAGCGTTTGAGGGAAAAGCGCCGCTAAAGGTCA
* *
12308741 CTTTCTATAGCGGCATTTGTGG
65 CATTCTATAGCGGCATTTGTTG
* * * *
12308763 GAAAAGCACCGCTAAAGGCAACGTTCTATAGCAGCGTTTGTGGGAAAAGCGCTGCTAAAGGACAC
1 GAAAAGCGCCGCTAAAGGCAACGTTCTATAGCAGCGTTTGAGGGAAAAGCGCCGCTAAAGGTCAC
*
12308828 ATTCTATAGCGGCGTTTGTTG
66 ATTCTATAGCGGCATTTGTTG
* * * *
12308849 TAAAAGCGCCG-TAACAGGTC-ACGTTCTATAGCTGCGTTTGTA-GGTAAAGCGCCGCTAAATGT
1 GAAAAGCGCCGCTAA-AGG-CAACGTTCTATAGCAGCGTTTG-AGGGAAAAGCGCCGCTAAAGGT
* * * *
12308911 CACGTTCTATAGCGTCGTTTTTTG
63 CACATTCTATAGCGGCATTTGTTG
** * * * * ** *
12308935 GAAAAGCGCTACTAAAGGTAATGTTCTATAGCGGCGTTTGAAGGAAAAATGCCGCTGAAGGTCA-
1 GAAAAGCGCCGCTAAAGGCAACGTTCTATAGCAGCGTTTGAGGGAAAAGCGCCGCTAAAGGTCAC
*
12308999 AGTTCTATAGCGGCATTAGTTG
66 A-TTCTATAGCGGCATTTGTTG
* * * * * * * * * *
12309021 TAAAAGCGCTGCTAAAGGTAACATTCTATAGCGGTGTTCGAGGGAAAAGCACCACTAAAAGTCAC
1 GAAAAGCGCCGCTAAAGGCAACGTTCTATAGCAGCGTTTGAGGGAAAAGCGCCGCTAAAGGTCAC
* * *
12309086 ATTCTATAGTGGTATTTGTAG
66 ATTCTATAGCGGCATTTGTTG
12309107 GAAAA
1 GAAAA
12309112 ATGTCACTAA
Statistics
Matches: 283, Mismatches: 57, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
85 10 0.04
86 268 0.95
87 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (86 bp):
GAAAAGCGCCGCTAAAGGCAACGTTCTATAGCAGCGTTTGAGGGAAAAGCGCCGCTAAAGGTCAC
ATTCTATAGCGGCATTTGTTG
Found at i:12309039 original size:43 final size:43
Alignment explanation
Indices: 12308677--12309094 Score: 335
Period size: 43 Copynumber: 9.7 Consensus size: 43
12308667 GCTTTTTTGC
** * * * *
12308677 GAAAAGCGCCGCTAAAAATCAAGCTCTATAACAGCGTTTGCGG
1 GAAAAGCGCCGCTAAAGGTCAAGTTCTATAGCGGCGTTTGTGG
* * ** *
12308720 GAAAAGCGTCGCTAAAGGCCACTTTCTATAGCGGCATTTGTGG
1 GAAAAGCGCCGCTAAAGGTCAAGTTCTATAGCGGCGTTTGTGG
* *
12308763 GAAAAGCACCGCTAAAGG-CAACGTTCTATAGCAGCGTTTGTGG
1 GAAAAGCGCCGCTAAAGGTCAA-GTTCTATAGCGGCGTTTGTGG
* * *
12308806 GAAAAGCGCTGCTAAAGGACACA-TTCTATAGCGGCGTTTGTTG
1 GAAAAGCGCCGCTAAAGGTCA-AGTTCTATAGCGGCGTTTGTGG
* * * *
12308849 TAAAAGCGCCG-TAACAGGTCACGTTCTATAGCTGCGTTTGTAG
1 GAAAAGCGCCGCTAA-AGGTCAAGTTCTATAGCGGCGTTTGTGG
* * * * * *
12308892 GTAAAGCGCCGCTAAATGTCACGTTCTATAGCGTCGTTTTTTG
1 GAAAAGCGCCGCTAAAGGTCAAGTTCTATAGCGGCGTTTGTGG
** **
12308935 GAAAAGCGCTACTAAAGGT-AATGTTCTATAGCGGCGTTTGAAG
1 GAAAAGCGCCGCTAAAGGTCAA-GTTCTATAGCGGCGTTTGTGG
** * * * *
12308978 GAAAAATGCCGCTGAAGGTCAAGTTCTATAGCGGCATTAGTTG
1 GAAAAGCGCCGCTAAAGGTCAAGTTCTATAGCGGCGTTTGTGG
* * * * * *
12309021 TAAAAGCGCTGCTAAAGGT-AACATTCTATAGCGGTGTTCGAGG
1 GAAAAGCGCCGCTAAAGGTCAA-GTTCTATAGCGGCGTTTGTGG
* * *
12309064 GAAAAGCACCACTAAAAGTCACA-TTCTATAG
1 GAAAAGCGCCGCTAAAGGTCA-AGTTCTATAG
12309095 TGGTATTTGT
Statistics
Matches: 296, Mismatches: 68, Indels: 22
0.77 0.18 0.06
Matches are distributed among these distances:
42 8 0.03
43 278 0.94
44 8 0.03
45 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (43 bp):
GAAAAGCGCCGCTAAAGGTCAAGTTCTATAGCGGCGTTTGTGG
Found at i:12311913 original size:137 final size:137
Alignment explanation
Indices: 12311655--12311938 Score: 453
Period size: 137 Copynumber: 2.1 Consensus size: 137
12311645 TAGAGAATAT
* * *
12311655 AAATAAAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATTTTTTATCGAATTTA
1 AAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTA
* ** *
12311720 TTAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGCAAATTAATATTCT
66 TTAATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTCT
*
12311785 TTTGGAAA
131 TTT-AAAA
*
12311793 GAATATAATTAATATATGAATTTGATTCATACAAAATATTAATT-TATATATTTTACCGAATTTA
1 AAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTA
* *
12311857 TTAATATAAATAATTATATTAATTAATTTCAATCAAAATATAAAAGATATGAAAATTAATATTCT
66 TTAATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTCT
12311922 TTTAAAA
131 TTTAAAA
12311929 AAATATAATT
1 AAATATAATT
12311939 TCTTTTTTAA
Statistics
Matches: 134, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
136 12 0.09
137 80 0.60
138 42 0.31
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (137 bp):
AAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTA
TTAATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTCT
TTTAAAA
Found at i:12317527 original size:17 final size:17
Alignment explanation
Indices: 12317505--12317539 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12317495 TCGAAGTAAG
12317505 GTTCATGTTTGAAATTT
1 GTTCATGTTTGAAATTT
12317522 GTTCATGTTTGAAATTT
1 GTTCATGTTTGAAATTT
12317539 G
1 G
12317540 ACCCATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51
Consensus pattern (17 bp):
GTTCATGTTTGAAATTT
Found at i:12317881 original size:36 final size:35
Alignment explanation
Indices: 12317841--12317909 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
12317831 AGCCCCCAGA
*
12317841 AAAAACCTAACCCAAAAA-AAAAAAGAAGAAAAAATG
1 AAAAACCTAA-CAAAAAATAAAAAAGAA-AAAAAATG
*
12317877 AAAAACCTAACAAAAAATAAAAAATAAAAAAAA
1 AAAAACCTAACAAAAAATAAAAAAGAAAAAAAA
12317910 CCTAGCCACC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 12 0.40
36 18 0.60
ACGTcount: A:0.77, C:0.12, G:0.04, T:0.07
Consensus pattern (35 bp):
AAAAACCTAACAAAAAATAAAAAAGAAAAAAAATG
Found at i:12317900 original size:19 final size:19
Alignment explanation
Indices: 12317840--12317900 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
12317830 AAGCCCCCAG
*
12317840 AAAAAACCTAACCCAAAAA-
1 AAAAAACCTAA-CAAAAAAT
* *
12317859 AAAAAA--GAAGAAAAAAT
1 AAAAAACCTAACAAAAAAT
*
12317876 GAAAAACCTAACAAAAAAT
1 AAAAAACCTAACAAAAAAT
12317895 AAAAAA
1 AAAAAA
12317901 TAAAAAAAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
16 5 0.16
17 7 0.22
19 20 0.62
ACGTcount: A:0.75, C:0.13, G:0.05, T:0.07
Consensus pattern (19 bp):
AAAAAACCTAACAAAAAAT
Found at i:12317900 original size:28 final size:29
Alignment explanation
Indices: 12317859--12317913 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
12317849 AACCCAAAAA
*
12317859 AAAAAAGAAGAAAA-AATGAAAAACCTAAC
1 AAAAAAGAAGAAAATAA-AAAAAACCTAAC
*
12317888 AAAAAATAA-AAAATAAAAAAAACCTA
1 AAAAAAGAAGAAAATAAAAAAAACCTA
12317914 GCCACCTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.76, C:0.09, G:0.05, T:0.09
Consensus pattern (29 bp):
AAAAAAGAAGAAAATAAAAAAAACCTAAC
Found at i:12318142 original size:18 final size:17
Alignment explanation
Indices: 12318103--12318141 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12318093 CCTAAAGGTG
*
12318103 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
12318120 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
12318137 ATTTT
1 ATTTT
12318142 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:12318401 original size:29 final size:29
Alignment explanation
Indices: 12318345--12318401 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
12318335 TCTCTTCTTT
* *
12318345 TTTCATTTATTTTTCGTATTTACCTTAGA
1 TTTCATTTATTTTGCGTATTTAACTTAGA
*
12318374 TTTCATATTATTTTGC-TATTTAATTTAG
1 TTTCAT-TTATTTTGCGTATTTAACTTAG
12318402 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTCATTTATTTTGCGTATTTAACTTAGA
Found at i:12318662 original size:11 final size:11
Alignment explanation
Indices: 12318644--12318673 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12318634 GTGTATATTG
12318644 TATATATTATA
1 TATATATTATA
*
12318655 TTTATATTATA
1 TATATATTATA
12318666 TATATATT
1 TATATATT
12318674 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:12318923 original size:12 final size:12
Alignment explanation
Indices: 12318906--12318931 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12318896 TCATATATCG
12318906 TTATATTTATTA
1 TTATATTTATTA
12318918 TTATATTTATTA
1 TTATATTTATTA
12318930 TT
1 TT
12318932 TTTCTCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTTATTA
Found at i:12322916 original size:12 final size:12
Alignment explanation
Indices: 12322899--12322934 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
12322889 AACATTTTGA
12322899 CATTCATGCATT
1 CATTCATGCATT
12322911 CATTCATGCATT
1 CATTCATGCATT
*
12322923 CATTCATACATT
1 CATTCATGCATT
12322935 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:12329500 original size:46 final size:44
Alignment explanation
Indices: 12329441--12329555 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
12329431 ACAGGACAGA
* *
12329441 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
12329487 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
12329531 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
12329556 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:12329536 original size:44 final size:45
Alignment explanation
Indices: 12329441--12329574 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
12329431 ACAGGACAGA
* *
12329441 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
12329487 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
12329531 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
12329575 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:12336392 original size:46 final size:44
Alignment explanation
Indices: 12336333--12336447 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
12336323 ACAGGACAGA
* *
12336333 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
12336379 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
12336423 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
12336448 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:12336428 original size:44 final size:45
Alignment explanation
Indices: 12336333--12336466 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
12336323 ACAGGACAGA
* *
12336333 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
12336379 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
12336423 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
12336467 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:12343289 original size:46 final size:44
Alignment explanation
Indices: 12343230--12343344 Score: 140
Period size: 44 Copynumber: 2.6 Consensus size: 44
12343220 ACAGGACAGA
* *
12343230 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* * *
12343276 ATAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
12343320 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
12343345 GTCAAAGACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 34 0.58
46 25 0.42
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:12343336 original size:44 final size:45
Alignment explanation
Indices: 12343230--12343363 Score: 135
Period size: 46 Copynumber: 3.0 Consensus size: 45
12343220 ACAGGACAGA
* * *
12343230 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * * *
12343276 ATAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * * *
12343320 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
12343364 CAGGATATTG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
44 35 0.49
45 1 0.01
46 36 0.50
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:12347408 original size:72 final size:72
Alignment explanation
Indices: 12347286--12347661 Score: 388
Period size: 72 Copynumber: 5.2 Consensus size: 72
12347276 AAGCCTTTTT
* * * * * *
12347286 ATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTCGAACCTCAGGTCACGCTGAGGT
1 ATTTTTGTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
12347351 ATTTTCA
66 ATTTTCA
* ** *
12347358 ATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGACGT
1 ATTTTTGTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
*
12347423 AATTTCA
66 ATTTTCA
* ** * * * * * *
12347430 ATTTCTGTTGTCAAAAAAATCAACTCGTATTGCAAGCGGCGAGTTAAGCCTCAGGTCACACGCCG
1 ATTTTTG-TGT-TTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTG
12347495 AGGTATTTTCA
62 AGGTATTTTCA
*
12347506 A-TTTT-TG---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT
1 ATTTTTGTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
*
12347566 AATTTCA
66 ATTTTCA
* * ** * *
12347573 ATTTCTGT-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTTTGTGTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
12347637 TATTTTCA
65 TATTTTCA
*
12347645 ATTTCTGT-TTTCAAAAA
1 ATTTTTGTGTTT-AAAAA
12347662 AAAAAAAAAT
Statistics
Matches: 252, Mismatches: 42, Indels: 20
0.80 0.13 0.06
Matches are distributed among these distances:
67 18 0.07
68 3 0.01
69 36 0.14
72 137 0.54
73 5 0.02
74 33 0.13
75 3 0.01
76 17 0.07
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (72 bp):
ATTTTTGTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
ATTTTCA
Found at i:12348509 original size:36 final size:37
Alignment explanation
Indices: 12348469--12348539 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
12348459 GCCCCCCAAA
** *
12348469 AAAAACCTAACCCAAAAA-AAAAAAGAAGAAAAAATG
1 AAAAACCTAACAAAAAAATAAAAAAGAAAAAAAAATG
*
12348505 AAAAACCTAACAAAAAAATAAAAAATAAAAAAAAA
1 AAAAACCTAACAAAAAAATAAAAAAGAAAAAAAAA
12348540 CCTAGCCACC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 16 0.53
37 14 0.47
ACGTcount: A:0.77, C:0.11, G:0.04, T:0.07
Consensus pattern (37 bp):
AAAAACCTAACAAAAAAATAAAAAAGAAAAAAAAATG
Found at i:12348535 original size:34 final size:35
Alignment explanation
Indices: 12348469--12348536 Score: 95
Period size: 34 Copynumber: 1.9 Consensus size: 35
12348459 GCCCCCCAAA
12348469 AAAAACCTAACCCAAAAAAAAAAAGAAGAAAAAATG
1 AAAAACCTAA-CCAAAAAAAAAAAGAAGAAAAAATG
*
12348505 AAAAACCTAA-CAAAAAAATAAAA-AATAAAAAA
1 AAAAACCTAACCAAAAAAA-AAAAGAAGAAAAAA
12348537 AAACCTAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 16 0.53
35 4 0.13
36 10 0.33
ACGTcount: A:0.76, C:0.12, G:0.04, T:0.07
Consensus pattern (35 bp):
AAAAACCTAACCAAAAAAAAAAAGAAGAAAAAATG
Found at i:12348539 original size:30 final size:33
Alignment explanation
Indices: 12348466--12348543 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
12348456 TAAGCCCCCC
12348466 AAAAAAAACCTAACCCAAAAAAAAAAAGAAGAAA
1 AAAAAAAACCTAA-CCAAAAAAAAAAAGAAGAAA
* *
12348500 AAATGAAAAACCTAA-CAAAAAAATAAA-AA-ATA
1 AAA--AAAAACCTAACCAAAAAAAAAAAGAAGAAA
12348532 AAAAAAAACCTA
1 AAAAAAAACCTA
12348544 GCCACCTAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 9 0.22
32 5 0.12
33 2 0.05
34 14 0.35
36 10 0.25
ACGTcount: A:0.76, C:0.13, G:0.04, T:0.08
Consensus pattern (33 bp):
AAAAAAAACCTAACCAAAAAAAAAAAGAAGAAA
Found at i:12348771 original size:18 final size:17
Alignment explanation
Indices: 12348732--12348770 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12348722 CCTAAAGGTG
*
12348732 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
12348749 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
12348766 ATTTT
1 ATTTT
12348771 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:12349049 original size:29 final size:29
Alignment explanation
Indices: 12348993--12349049 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
12348983 TCTCTTCTTT
* *
12348993 TTTCATTTATTTTTCGTATTTACCTTAGA
1 TTTCATTTATTTTGCGTATTTAACTTAGA
*
12349022 TTTCATATTATTTTGC-TATTTAATTTAG
1 TTTCAT-TTATTTTGCGTATTTAACTTAG
12349050 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTCATTTATTTTGCGTATTTAACTTAGA
Found at i:12349309 original size:11 final size:11
Alignment explanation
Indices: 12349291--12349320 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12349281 GTGTATATTG
12349291 TATATATTATA
1 TATATATTATA
*
12349302 TTTATATTATA
1 TATATATTATA
12349313 TATATATT
1 TATATATT
12349321 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:12355310 original size:34 final size:32
Alignment explanation
Indices: 12355250--12355356 Score: 93
Period size: 34 Copynumber: 3.4 Consensus size: 32
12355240 AATTTTTATA
* *
12355250 ATTATTTTAAAATAATTTGTTAGTAATTTAGG
1 ATTATATTAAAATTATTTGTTAGTAATTTAGG
*
12355282 ATTATATTATAAATTATTATGTTTGTAA-TT---
1 ATTATATTA-AAATTATT-TGTTAGTAATTTAGG
*
12355312 A-T-T-TTAAAATTAATTTATTAGTAATTTAGG
1 ATTATATTAAAATT-ATTTGTTAGTAATTTAGG
12355342 ATTATATTATAAATT
1 ATTATATTA-AAATT
12355357 GTTGTGTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
26 12 0.20
27 8 0.14
28 1 0.02
29 1 0.02
30 2 0.03
31 1 0.02
32 9 0.15
33 12 0.20
34 13 0.22
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.52
Consensus pattern (32 bp):
ATTATATTAAAATTATTTGTTAGTAATTTAGG
Found at i:12355337 original size:60 final size:59
Alignment explanation
Indices: 12355248--12355365 Score: 200
Period size: 60 Copynumber: 2.0 Consensus size: 59
12355238 GTAATTTTTA
*
12355248 TAATTATTTTAAAATAATTTGTTAGTAATTTAGGATTATATTATAAATTATTATGTTTG
1 TAATTATTTTAAAATAATTTATTAGTAATTTAGGATTATATTATAAATTATTATGTTTG
* *
12355307 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATATTATAAATTGTTGTGTTT
1 TAATTATTTTAAAA-TAATTTATTAGTAATTTAGGATTATATTATAAATTATTATGTTT
12355366 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
59 14 0.25
60 41 0.75
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.53
Consensus pattern (59 bp):
TAATTATTTTAAAATAATTTATTAGTAATTTAGGATTATATTATAAATTATTATGTTTG
Found at i:12355460 original size:72 final size:72
Alignment explanation
Indices: 12355372--12355543 Score: 274
Period size: 72 Copynumber: 2.4 Consensus size: 72
12355362 GTTTAGTTTA
* * *
12355372 GTATTTTGTGAGTTTTTAATAATGTAAAATTATTTCGTTAAAAAATTTGTTAGTAATTTATTATA
1 GTATTTTGTGAGTTTTTAGTAATGTAAAATTATTTCGTTAAAAAATTTATTAGTAATTCATTATA
12355437 AATTGTT
66 AATTGTT
* * *
12355444 G-AGTTTTGTGAGTTTTTAGTAATGTAAAATTATTTTGTTAAATATTTTATTAGTAATTCATTAT
1 GTA-TTTTGTGAGTTTTTAGTAATGTAAAATTATTTCGTTAAAAAATTTATTAGTAATTCATTAT
12355508 AAATTGTT
65 AAATTGTT
12355516 GTATTTTGTGAGTTTTTAGTAATGTAAA
1 GTATTTTGTGAGTTTTTAGTAATGTAAA
12355544 TGTTTTAAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
71 1 0.01
72 90 0.98
73 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.52
Consensus pattern (72 bp):
GTATTTTGTGAGTTTTTAGTAATGTAAAATTATTTCGTTAAAAAATTTATTAGTAATTCATTATA
AATTGTT
Found at i:12355463 original size:38 final size:38
Alignment explanation
Indices: 12355421--12355538 Score: 95
Period size: 38 Copynumber: 3.2 Consensus size: 38
12355411 AAAAAATTTG
12355421 TTAGTAATTTATTATAAATTGTTGAGTTTTGTGAGTTT
1 TTAGTAATTTATTATAAATTGTTGAGTTTTGTGAGTTT
* * ** *** *
12355459 TTAGTAA--T-GTA-AAATTATTTTGTTAAAT-ATTTT
1 TTAGTAATTTATTATAAATTGTTGAGTTTTGTGAGTTT
*
12355492 ATTAGTAATTCATTATAAATTGTTGTA-TTTTGTGAGTTT
1 -TTAGTAATTTATTATAAATTGTTG-AGTTTTGTGAGTTT
12355531 TTAGTAAT
1 TTAGTAAT
12355539 GTAAATGTTT
Statistics
Matches: 56, Mismatches: 17, Indels: 14
0.64 0.20 0.16
Matches are distributed among these distances:
33 4 0.07
34 18 0.32
35 2 0.04
36 1 0.02
37 2 0.04
38 25 0.45
39 4 0.07
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (38 bp):
TTAGTAATTTATTATAAATTGTTGAGTTTTGTGAGTTT
Found at i:12355563 original size:72 final size:73
Alignment explanation
Indices: 12355372--12355565 Score: 238
Period size: 72 Copynumber: 2.7 Consensus size: 73
12355362 GTTTAGTTTA
* ** * *
12355372 GTATTTTGTGAGTTTTTAATAATGTAAAATTATTTCGTTAAAA-AA-TTTGTTAGTAATTTATTA
1 GTATTTTGTGAGTTTTTAGTAATGTAAAATTATTT-AATAAAATAATTTTATTAGTAATTCATTA
12355435 TAAATTGTT
65 TAAATTGTT
** *
12355444 G-AGTTTTGTGAGTTTTTAGTAATGTAAAATTATTTTGTTAAAT-ATTTTATTAGTAATTCATTA
1 GTA-TTTTGTGAGTTTTTAGTAATGTAAAATTATTTAATAAAATAATTTTATTAGTAATTCATTA
12355507 TAAATTGTT
65 TAAATTGTT
*
12355516 GTATTTTGTGAGTTTTTAGTAATGT-AAATGT-TTTAAAAAAATAATTTTAT
1 GTATTTTGTGAGTTTTTAGTAATGTAAAAT-TATTTAATAAAATAATTTTAT
12355566 AGTTATTTTG
Statistics
Matches: 106, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
71 17 0.16
72 88 0.83
73 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (73 bp):
GTATTTTGTGAGTTTTTAGTAATGTAAAATTATTTAATAAAATAATTTTATTAGTAATTCATTAT
AAATTGTT
Found at i:12355723 original size:12 final size:12
Alignment explanation
Indices: 12355706--12355731 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12355696 GCCACCAATA
12355706 AAAAAATATTTT
1 AAAAAATATTTT
12355718 AAAAAATATTTT
1 AAAAAATATTTT
12355730 AA
1 AA
12355732 TATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAAAATATTTT
Found at i:12356298 original size:30 final size:30
Alignment explanation
Indices: 12356176--12356291 Score: 178
Period size: 30 Copynumber: 3.9 Consensus size: 30
12356166 AAAACCCTAG
12356176 CCACCTTGCCTCCCACTTGCACCTACTCCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
* * *
12356206 CCACCTTGCCTCCCACTTGCATCTATTTCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
*
12356236 CCACCTTGCCTCCTACTTGCACCTACTCCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
* *
12356266 TCACCTTGTCTCCCACTTGCACCTAC
1 CCACCTTGCCTCCCACTTGCACCTAC
12356292 ACCATCAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.16, C:0.48, G:0.07, T:0.28
Consensus pattern (30 bp):
CCACCTTGCCTCCCACTTGCACCTACTCCA
Found at i:12356833 original size:3 final size:3
Alignment explanation
Indices: 12356817--12356891 Score: 50
Period size: 3 Copynumber: 24.3 Consensus size: 3
12356807 TTTTATTTTT
* *
12356817 TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA TT- TCTCA TGTA TATA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-T-A T-TA T-TA
12356865 TTA TTA TT- TATA TTA TTA TTA -TA TTA T
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA T
12356892 ATATACCCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
2 5 0.09
3 44 0.76
4 7 0.12
5 2 0.03
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:12356884 original size:18 final size:18
Alignment explanation
Indices: 12356809--12356895 Score: 88
Period size: 18 Copynumber: 4.7 Consensus size: 18
12356799 TTTATTTTTT
* *
12356809 TTATT-TTTTTATTTTTA
1 TTATTATTTATATTATTA
*
12356826 CTATTATTTATATTATTA
1 TTATTATTTATATTATTA
*
12356844 TTATTATTTCTCATGTATATA
1 TTATTATTTAT-AT-TAT-TA
12356865 TTATTATTTATATTATTA
1 TTATTATTTATATTATTA
12356883 TTA-TATTATATAT
1 TTATTATT-TATAT
12356896 ACCCACTCCA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
17 8 0.14
18 29 0.49
19 5 0.08
20 5 0.08
21 12 0.20
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TTATTATTTATATTATTA
Found at i:12357220 original size:3 final size:3
Alignment explanation
Indices: 12357212--12357336 Score: 53
Period size: 3 Copynumber: 40.3 Consensus size: 3
12357202 ATTTCTATAT
* * *
12357212 TTA TTA TTA TTA TTA TTA TTA TATA GTA GTG TGTA TT- TCTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA T-TA TTA T-TA
* * * *
12357260 CATA TATA TATA TT- TTA -TA TATA GTA TTA TTA TTTA CT- TTA CT-
1 -TTA T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA TTA
* *
12357303 TTA ATA TTA TTA TTA TTA TTA TTA GTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12357337 ATCCAACCCA
Statistics
Matches: 93, Mismatches: 16, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
2 7 0.08
3 65 0.70
4 21 0.23
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:12357280 original size:13 final size:15
Alignment explanation
Indices: 12357262--12357338 Score: 51
Period size: 13 Copynumber: 5.3 Consensus size: 15
12357252 ATTATATACA
12357262 TATATATA-TATT-T
1 TATATATAGTATTAT
12357275 TATATATAGTATTAT
1 TATATATAGTATTAT
*
12357290 TAT-T-TACT-TTACT
1 TATATATAGTATTA-T
*
12357303 T-TA-ATATTATTAT
1 TATATATAGTATTAT
12357316 TATTATTATTAGTATTAT
1 TA-TA-TA-TAGTATTAT
12357334 TATAT
1 TATAT
12357339 CCAACCCAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 19
0.69 0.04 0.26
Matches are distributed among these distances:
12 4 0.08
13 18 0.36
14 8 0.16
15 6 0.12
16 1 0.02
17 3 0.06
18 10 0.20
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (15 bp):
TATATATAGTATTAT
Found at i:12359622 original size:7 final size:7
Alignment explanation
Indices: 12359610--12359670 Score: 77
Period size: 7 Copynumber: 8.6 Consensus size: 7
12359600 TATAAACATG
12359610 GGGTTTA
1 GGGTTTA
12359617 GGGTTTA
1 GGGTTTA
*
12359624 AGGTTTA
1 GGGTTTA
12359631 GGGTTTA
1 GGGTTTA
*
12359638 AGGTTTA
1 GGGTTTA
**
12359645 AAGTTTA
1 GGGTTTA
12359652 GGGTTTA
1 GGGTTTA
12359659 GGGTTTAA
1 GGGTTT-A
12359667 GGGT
1 GGGT
12359671 CATCAATTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
7 42 0.89
8 5 0.11
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (7 bp):
GGGTTTA
Found at i:12359630 original size:14 final size:14
Alignment explanation
Indices: 12359611--12359668 Score: 89
Period size: 14 Copynumber: 4.1 Consensus size: 14
12359601 ATAAACATGG
12359611 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
12359625 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
** *
12359639 GGTTTAAAGTTTAG
1 GGTTTAGGGTTTAA
12359653 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
12359667 GG
1 GG
12359669 GTCATCAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.41
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:12359636 original size:21 final size:21
Alignment explanation
Indices: 12359610--12359668 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
12359600 TATAAACATG
12359610 GGGTTTAGGGTTTAAGGTTTA
1 GGGTTTAGGGTTTAAGGTTTA
* *
12359631 GGGTTTAAGGTTTAAAGTTTA
1 GGGTTTAGGGTTTAAGGTTTA
12359652 GGGTTTAGGGTTTAAGG
1 GGGTTTAGGGTTTAAGG
12359669 GTCATCAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (21 bp):
GGGTTTAGGGTTTAAGGTTTA
Found at i:12365013 original size:23 final size:22
Alignment explanation
Indices: 12364983--12365041 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
12364973 TGGGCAGTAG
12364983 AAGAAGAAGAGAAAAAAAAATAA
1 AAGAAGAAGAGAAAAAAAAA-AA
* *
12365006 AAGAAGAAACAGAAAAGAAAAAA
1 AAGAAG-AAGAGAAAAAAAAAAA
* *
12365029 AAGAGGAGGAGAA
1 AAGAAGAAGAGAA
12365042 GAAGAACTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 5 0.17
23 13 0.43
24 12 0.40
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (22 bp):
AAGAAGAAGAGAAAAAAAAAAA
Found at i:12365956 original size:14 final size:15
Alignment explanation
Indices: 12365930--12365958 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12365920 GCTTCATCTT
12365930 CTTCTTCTTCCTCTG
1 CTTCTTCTTCCTCTG
12365945 CTTCTT-TTCCTCTG
1 CTTCTTCTTCCTCTG
12365959 GTTTTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.38, G:0.07, T:0.55
Consensus pattern (15 bp):
CTTCTTCTTCCTCTG
Found at i:12366243 original size:21 final size:21
Alignment explanation
Indices: 12366219--12366259 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
12366209 CTACGTGGCA
12366219 AGTTAACTGGCCACGTCAGCT
1 AGTTAACTGGCCACGTCAGCT
*
12366240 AGTTAACTTGCCACGTCAGC
1 AGTTAACTGGCCACGTCAGC
12366260 ACTCCCGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (21 bp):
AGTTAACTGGCCACGTCAGCT
Found at i:12380575 original size:48 final size:48
Alignment explanation
Indices: 12380519--12380610 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
12380509 TCTAGTAAGA
* *
12380519 TGGCACGCGAACAATAATGAAGAGAAAAGTGGTCCTTCGTTACGAAGC
1 TGGCACGCGAACAATAACGAAGAAAAAAGTGGTCCTTCGTTACGAAGC
12380567 TGGCACGCGAACAATAACGAAGAAAAAAGTGGTCCTTCGTTACG
1 TGGCACGCGAACAATAACGAAGAAAAAAGTGGTCCTTCGTTACG
12380611 GGTTGGTTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (48 bp):
TGGCACGCGAACAATAACGAAGAAAAAAGTGGTCCTTCGTTACGAAGC
Found at i:12388680 original size:28 final size:28
Alignment explanation
Indices: 12388649--12388702 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
12388639 GAAGCTCATC
*
12388649 AGGACTATCTTT-TATGTGGAAGTCCGCT
1 AGGACTAT-TTTCAATGTGGAAGTCCGCT
12388677 AGGACTATTTTCAATGTGGAAGTCCG
1 AGGACTATTTTCAATGTGGAAGTCCG
12388703 TCAAGATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (28 bp):
AGGACTATTTTCAATGTGGAAGTCCGCT
Found at i:12394488 original size:21 final size:22
Alignment explanation
Indices: 12394444--12394492 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
12394434 TTGTTTCTTT
*
12394444 TATTTTAAAAAATAACGTGTAATA
1 TATTTTAAAAAAT-A-GAGTAATA
12394468 TATTTTAAAAAAT-GAGTAATA
1 TATTTTAAAAAATAGAGTAATA
12394489 TATT
1 TATT
12394493 AATAAAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
24 13 0.54
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (22 bp):
TATTTTAAAAAATAGAGTAATA
Found at i:12394563 original size:13 final size:13
Alignment explanation
Indices: 12394547--12394571 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12394537 TTTTAAAATA
12394547 TAAAAATAACGTG
1 TAAAAATAACGTG
12394560 TAAAAATAACGT
1 TAAAAATAACGT
12394572 CTATAGATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
TAAAAATAACGTG
Found at i:12403195 original size:19 final size:19
Alignment explanation
Indices: 12403171--12403216 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
12403161 TGATTTATTC
12403171 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
*
12403190 TAAGATTTATCTATCTAAA
1 TAAGATTTATCTACCTAAA
12403209 TAA-ATTTA
1 TAAGATTTA
12403217 AAATATATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:12412749 original size:25 final size:25
Alignment explanation
Indices: 12412721--12412769 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
12412711 TTTTGCAAAT
12412721 TAATTTTTAAAATAAATTTAAAAAC
1 TAATTTTTAAAATAAATTTAAAAAC
* *
12412746 TAATTTTTTAAATAAGTTTAAAAA
1 TAATTTTTAAAATAAATTTAAAAA
12412770 ATAAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATTTTTAAAATAAATTTAAAAAC
Found at i:12415365 original size:42 final size:44
Alignment explanation
Indices: 12415292--12415383 Score: 145
Period size: 42 Copynumber: 2.2 Consensus size: 44
12415282 TCCTAATTGG
12415292 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
12415335 GAAAATAGTTCCCTT-TTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
12415378 -AAAATA
1 GAAAATA
12415384 TTTCTAGAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 30 0.65
43 16 0.35
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:12415427 original size:19 final size:18
Alignment explanation
Indices: 12415405--12415444 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
12415395 TGAATAAAAC
12415405 TTATCTATCC-AAATAAGAT
1 TTATCTA-CCTAAATAA-AT
12415424 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
12415442 TTA
1 TTA
12415445 AAATATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:12419930 original size:43 final size:44
Alignment explanation
Indices: 12419869--12419961 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 44
12419859 TCGTAATTGG
* *
12419869 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCACTTATTCTAATAAACTACCAAAACATAAAATA
* *
12419912 GAAAATAGTTCACTTATTCTAGTAAACTACCAAAAGATAAAATA
1 GAAAATAGTTCACTTATTCTAATAAACTACCAAAACATAAAATA
12419956 -AAAATA
1 GAAAATA
12419962 TTTCTAGAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 44 0.98
44 1 0.02
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (44 bp):
GAAAATAGTTCACTTATTCTAATAAACTACCAAAACATAAAATA
Found at i:12419999 original size:19 final size:19
Alignment explanation
Indices: 12419975--12420017 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12419965 CTAGAATATG
12419975 AATAAGACTTATCTATCC-A
1 AATAAGACTTATCTA-CCTA
*
12419994 AATAAGATTTATCTACCTA
1 AATAAGACTTATCTACCTA
12420013 AATAA
1 AATAA
12420018 ATTTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (19 bp):
AATAAGACTTATCTACCTA
Found at i:12421612 original size:19 final size:21
Alignment explanation
Indices: 12421580--12421618 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
12421570 GGATTGCACG
12421580 ATACTCATCCGTGTC-AATCT
1 ATACTCATCCGTGTCGAATCT
*
12421600 ATAC-CATCGGTGTCGAATC
1 ATACTCATCCGTGTCGAATC
12421619 AGAAGGCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (21 bp):
ATACTCATCCGTGTCGAATCT
Found at i:12422634 original size:31 final size:32
Alignment explanation
Indices: 12422599--12422670 Score: 114
Period size: 31 Copynumber: 2.3 Consensus size: 32
12422589 TAAAATTCCA
12422599 AAATTCAAAAAATA-AAAATATTAAAATTAA-C
1 AAATTCAAAAAATATAAAA-ATTAAAATTAACC
12422630 AAATTCAAAAAATATAAAAATTAAAATTAACC
1 AAATTCAAAAAATATAAAAATTAAAATTAACC
12422662 AAATT-AAAA
1 AAATTCAAAA
12422671 TACATGAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
31 29 0.74
32 10 0.26
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (32 bp):
AAATTCAAAAAATATAAAAATTAAAATTAACC
Found at i:12422665 original size:15 final size:14
Alignment explanation
Indices: 12422618--12422671 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
12422608 AAATAAAAAT
12422618 ATTAAAATTAACAA
1 ATTAAAATTAACAA
12422632 ATTCAAAAAATATAA-AA
1 ATT---AAAAT-TAACAA
12422649 ATTAAAATTAACCAA
1 ATTAAAATTAA-CAA
12422664 ATTAAAAT
1 ATTAAAAT
12422672 ACATGAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.09
14 8 0.24
15 10 0.29
17 10 0.29
18 3 0.09
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
ATTAAAATTAACAA
Found at i:12424096 original size:15 final size:15
Alignment explanation
Indices: 12424078--12424110 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12424068 AATTAATTTA
12424078 TTTTTAAAAAATTAT
1 TTTTTAAAAAATTAT
*
12424093 TTTTTAGAAAATTAT
1 TTTTTAAAAAATTAT
12424108 TTT
1 TTT
12424111 AAGTAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTTAAAAAATTAT
Found at i:12428355 original size:2 final size:2
Alignment explanation
Indices: 12428348--12428377 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12428338 CTATAAAAGG
12428348 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
12428378 CCTGAACTAT
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):
AT
Found at i:12430521 original size:16 final size:16
Alignment explanation
Indices: 12430492--12430540 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
12430482 ACTTTTAATA
*
12430492 TACT-GGCACTAAGCC
1 TACTAGGCACAAAGCC
*
12430507 TGCTAGGCACAAAGCC
1 TACTAGGCACAAAGCC
*
12430523 TACTAGGTACAAAGCC
1 TACTAGGCACAAAGCC
12430539 TA
1 TA
12430541 AATAACTCCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 3 0.10
16 26 0.90
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (16 bp):
TACTAGGCACAAAGCC
Found at i:12430594 original size:22 final size:22
Alignment explanation
Indices: 12430566--12430607 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12430556 AAGCCTGCTA
12430566 GGCACAAAGCCTGAATAACATT
1 GGCACAAAGCCTGAATAACATT
*
12430588 GGCACAAGGCCTGAATAACA
1 GGCACAAAGCCTGAATAACA
12430608 ATATTATTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.14
Consensus pattern (22 bp):
GGCACAAAGCCTGAATAACATT
Found at i:12430600 original size:38 final size:38
Alignment explanation
Indices: 12430512--12430584 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
12430502 AAGCCTGCTA
* *
12430512 GGCACAAAGCCTACTAGGTACAAAGCCTAAATAACTCC
1 GGCACAAAGCCTGCTAGGCACAAAGCCTAAATAACTCC
* *
12430550 GACACAAAGCCTGCTAGGCACAAAGCCTGAATAAC
1 GGCACAAAGCCTGCTAGGCACAAAGCCTAAATAAC
12430585 ATTGGCACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.40, C:0.29, G:0.18, T:0.14
Consensus pattern (38 bp):
GGCACAAAGCCTGCTAGGCACAAAGCCTAAATAACTCC
Found at i:12441613 original size:38 final size:38
Alignment explanation
Indices: 12441571--12441647 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
12441561 CCTCATTGTC
12441571 ATTTTGTAAACAAAGAGTAATCATACTTACTTTGCTGA
1 ATTTTGTAAACAAAGAGTAATCATACTTACTTTGCTGA
12441609 ATTTTGTAAACAAAGAGTAATCATACTTACTTTGCTGA
1 ATTTTGTAAACAAAGAGTAATCATACTTACTTTGCTGA
12441647 A
1 A
12441648 ATCTAGCAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (38 bp):
ATTTTGTAAACAAAGAGTAATCATACTTACTTTGCTGA
Found at i:12446980 original size:11 final size:11
Alignment explanation
Indices: 12446964--12447006 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
12446954 ATAAAAATAT
12446964 TTTAATTTAAA
1 TTTAATTTAAA
12446975 TTTAATTTAAAA
1 TTTAATTT-AAA
*
12446987 TATATATTTAATA
1 TTTA-ATTTAA-A
12447000 TTTAATT
1 TTTAATT
12447007 AATATATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 8 0.30
12 11 0.41
13 8 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:12447743 original size:23 final size:24
Alignment explanation
Indices: 12447712--12447760 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
12447702 ATTTCAAACC
*
12447712 AAACTTTTC-AAAGCACTTTCCAA
1 AAACATTTCAAAAGCACTTTCCAA
* *
12447735 AAACATTTCAAAATCACTTTCGAA
1 AAACATTTCAAAAGCACTTTCCAA
12447759 AA
1 AA
12447761 TCAGCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.45, C:0.22, G:0.04, T:0.29
Consensus pattern (24 bp):
AAACATTTCAAAAGCACTTTCCAA
Found at i:12453075 original size:20 final size:20
Alignment explanation
Indices: 12453050--12453093 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12453040 AATAATTTTT
* *
12453050 AAATTTTAAAATATT-TATAA
1 AAATTTCAAAAAATTCTA-AA
12453070 AAATTTCAAAAAATTCTAAA
1 AAATTTCAAAAAATTCTAAA
12453090 AAAT
1 AAAT
12453094 ATATAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTCAAAAAATTCTAAA
Found at i:12453093 original size:10 final size:9
Alignment explanation
Indices: 12453021--12453093 Score: 65
Period size: 9 Copynumber: 7.8 Consensus size: 9
12453011 TTTACAAAAA
12453021 AAAAAATTT
1 AAAAAATTT
*
12453030 AAAATATTT
1 AAAAAATTT
*
12453039 AAATAATTT
1 AAAAAATTT
** *
12453048 TTAAATTTT
1 AAAAAATTT
*
12453057 AAAATATTT
1 AAAAAATTT
12453066 ATAAAAATTT
1 A-AAAAATTT
12453076 CAAAAAATTCT
1 -AAAAAATT-T
12453087 AAAAAAT
1 AAAAAAT
12453094 ATATAAAGTT
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
9 26 0.53
10 21 0.43
11 2 0.04
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAAAATTT
Found at i:12472535 original size:14 final size:14
Alignment explanation
Indices: 12472511--12472546 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12472501 ATATTTTTTT
12472511 AAAAATT-ATATAA
1 AAAAATTAATATAA
12472524 AAAAATTAATATAA
1 AAAAATTAATATAA
12472538 AAGAAATTA
1 AA-AAATTA
12472547 CTACGGGCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.33
14 8 0.38
15 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AAAAATTAATATAA
Found at i:12477809 original size:53 final size:52
Alignment explanation
Indices: 12477708--12477844 Score: 136
Period size: 53 Copynumber: 2.6 Consensus size: 52
12477698 TGGAGGTTTG
* **
12477708 GGGAAGTAAAAGTTTTGGGGAAAACG-AAAGGAAAAAAAGTTTTTAGGGTCT-A
1 GGGAAGTAAAAGTTTTGGGGAAAA-GTAAAGG-GAAAAAGTTTCGAGGGTCTGA
* *
12477760 GGAGAAGTAAAAGTTTT-GGGAGAAAGTAATAGGGAAAATGTTTCGAGGGTTTGA
1 GG-GAAGTAAAAGTTTTGGGGA-AAAGTAA-AGGGAAAAAGTTTCGAGGGTCTGA
*
12477814 GGGAAAGTAAAATTTTTGGGGGAAAAGTAAA
1 GGG-AAGTAAAAGTTTT-GGGGAAAAGTAAA
12477845 AGGGCTTGGA
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
52 7 0.10
53 34 0.48
54 19 0.27
55 7 0.10
56 4 0.06
ACGTcount: A:0.41, C:0.02, G:0.33, T:0.24
Consensus pattern (52 bp):
GGGAAGTAAAAGTTTTGGGGAAAAGTAAAGGGAAAAAGTTTCGAGGGTCTGA
Found at i:12481926 original size:31 final size:31
Alignment explanation
Indices: 12481891--12481967 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
12481881 CCAACCTAAC
12481891 TAAGATAAACACCAATTGTTAAGGATACATA
1 TAAGATAAACACCAATTGTTAAGGATACATA
*
12481922 TAAGATAAACACCAATTGTTAAGGATACCTA
1 TAAGATAAACACCAATTGTTAAGGATACATA
12481953 TAAGATAAACACCAA
1 TAAGATAAACACCAA
12481968 CTTAAGTAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (31 bp):
TAAGATAAACACCAATTGTTAAGGATACATA
Found at i:12497789 original size:11 final size:11
Alignment explanation
Indices: 12497773--12497799 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12497763 GCTATATGAG
12497773 CCCATTTTTTC
1 CCCATTTTTTC
12497784 CCCATTTTTTC
1 CCCATTTTTTC
12497795 CCCAT
1 CCCAT
12497800 CTTAGCAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.11, C:0.41, G:0.00, T:0.48
Consensus pattern (11 bp):
CCCATTTTTTC
Found at i:12507912 original size:6 final size:6
Alignment explanation
Indices: 12507901--12507926 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12507891 TGACGCTGGC
12507901 GGTGCT GGTGCT GGTGCT GGTGCT GG
1 GGTGCT GGTGCT GGTGCT GGTGCT GG
12507927 GAATAGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.54, T:0.31
Consensus pattern (6 bp):
GGTGCT
Found at i:12508429 original size:46 final size:47
Alignment explanation
Indices: 12508379--12508474 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 47
12508369 TAGCAGCATG
*
12508379 ACTTTCTTTTTAAAGGGTTAGGTAAGTCCCTCACCC-TTTAAGTCAA
1 ACTTTCTTTTTAAAGGGTTAGGTAAGGCCCTCACCCTTTTAAGTCAA
12508425 ACTTTCTTTTTAAAGGGTTAGGTAAGGCCCTCACCCTTTTAAGTCAA
1 ACTTTCTTTTTAAAGGGTTAGGTAAGGCCCTCACCCTTTTAAGTCAA
12508472 ACT
1 ACT
12508475 ATCATAAAGC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 35 0.73
47 13 0.27
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (47 bp):
ACTTTCTTTTTAAAGGGTTAGGTAAGGCCCTCACCCTTTTAAGTCAA
Found at i:12512743 original size:40 final size:40
Alignment explanation
Indices: 12512679--12512816 Score: 134
Period size: 40 Copynumber: 3.5 Consensus size: 40
12512669 CTTTTCAGGT
* * * *
12512679 CAAATCCTATCCGCCTTAAGTTACCTTAGTGAATCA-GCAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCACG-AA
* * *
12512719 TAAATCCTATTCACTTTAAATTACCATGGTGAATCACGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCACGAA
* ** ** *
12512759 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCACGAA
*
12512799 CGAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
12512817 TATTCTCGAG
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 78 0.99
41 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.30
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAATTACCATAGTGAATCACGAA
Found at i:12515049 original size:27 final size:25
Alignment explanation
Indices: 12515014--12515080 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
12515004 TATGGTGTTC
*
12515014 AAAAT-ATGTACATAATGTGAAGTTAA
1 AAAATAATGTACATAAAGT--AGTTAA
* *
12515040 AAAATAATGTGCGTAAAGTAGTTAA
1 AAAATAATGTACATAAAGTAGTTAA
12515065 AAAATATATGTACATA
1 AAAATA-ATGTACATA
12515081 TTTATATGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 12 0.35
26 12 0.35
27 10 0.29
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (25 bp):
AAAATAATGTACATAAAGTAGTTAA
Found at i:12515359 original size:25 final size:25
Alignment explanation
Indices: 12515331--12515383 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
12515321 ATATTATGTG
*
12515331 AAATAATGTATAGAATACA-ATATTA
1 AAAT-ATGTACAGAATACACATATTA
* *
12515356 AAATATTTACATAATACACATATTA
1 AAATATGTACAGAATACACATATTA
12515381 AAA
1 AAA
12515384 ATAACTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.32
Consensus pattern (25 bp):
AAATATGTACAGAATACACATATTA
Found at i:12515394 original size:25 final size:24
Alignment explanation
Indices: 12515344--12515396 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
12515334 TAATGTATAG
**
12515344 AATACAATATTAAAATATTTACAT
1 AATACAATATTAAAATAACTACAT
12515368 AATACACATATTAAAAATAACTA-AT
1 AATACA-ATATT-AAAATAACTACAT
12515393 AATA
1 AATA
12515397 ATATTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 11 0.44
26 8 0.32
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.32
Consensus pattern (24 bp):
AATACAATATTAAAATAACTACAT
Found at i:12516678 original size:16 final size:16
Alignment explanation
Indices: 12516659--12516696 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
12516649 TTTCTGTGTT
12516659 TTTGGGTTTGTAAGGG
1 TTTGGGTTTGTAAGGG
12516675 TTTGGGTTTGTAAGGG
1 TTTGGGTTTGTAAGGG
12516691 TTTGGG
1 TTTGGG
12516697 GTTATTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.11, C:0.00, G:0.45, T:0.45
Consensus pattern (16 bp):
TTTGGGTTTGTAAGGG
Found at i:12518817 original size:92 final size:93
Alignment explanation
Indices: 12518680--12518867 Score: 297
Period size: 92 Copynumber: 2.0 Consensus size: 93
12518670 ACTTCTTCTT
* *
12518680 TTTTTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATACATCAAAAAAGCGCTCAAAATTTT
1 TTTTTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATACATCAAAAAAACCCTCAAAATTTT
*
12518745 TCAAAAAAAAAGA-AATTAAGCCCCTAC
66 TCAAAAAAAAAAACAATTAAGCCCCTAC
* * * * *
12518772 TTTTTTTTTGCACTTAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAAACCCTCAAACTTTT
1 TTTTTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATACATCAAAAAAACCCTCAAAATTTT
12518837 TCAAAAAAAAAAACAATTAAGCCCCTAC
66 TCAAAAAAAAAAACAATTAAGCCCCTAC
12518865 TTT
1 TTT
12518868 ATTAAAAAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 70 0.80
93 17 0.20
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (93 bp):
TTTTTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATACATCAAAAAAACCCTCAAAATTTT
TCAAAAAAAAAAACAATTAAGCCCCTAC
Found at i:12518905 original size:16 final size:16
Alignment explanation
Indices: 12518873--12518940 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
12518863 ACTTTATTAA
12518873 AAAATTATAAAAAATT
1 AAAATTATAAAAAATT
*
12518889 AAAATCTATAAATATTATT
1 AAAAT-TATAAA-A-AATT
* *
12518908 AAATTTATTAAAAATT
1 AAAATTATAAAAAATT
*
12518924 CAAA-TATTAAAAAATT
1 AAAATTA-TAAAAAATT
12518940 A
1 A
12518941 TTAAAAAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
15 2 0.05
16 18 0.45
17 7 0.17
18 6 0.15
19 7 0.17
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATTATAAAAAATT
Found at i:12518941 original size:35 final size:35
Alignment explanation
Indices: 12518877--12518945 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
12518867 TATTAAAAAA
*
12518877 TTATAAAAAATTAAAATCTATAAATATTATTAAAT
1 TTATAAAAAATTAAAATCTATAAAAATTATTAAAT
*
12518912 TTATTAAAAATTCAAATAT-TA-AAAAATTATTAAA
1 TTATAAAAAATT-AAA-ATCTATAAAAATTATTAAA
12518946 AAATAGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 23 0.77
36 5 0.17
37 2 0.07
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (35 bp):
TTATAAAAAATTAAAATCTATAAAAATTATTAAAT
Found at i:12518955 original size:27 final size:27
Alignment explanation
Indices: 12518876--12518964 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
12518866 TTATTAAAAA
* *
12518876 ATTATAAAAA--ATTAAAATCTATAAAT
1 ATTATAAAAATTATTAAAA-ATACAAAT
* * *
12518902 ATTATTAAATTTATTAAAAATTCAAAT
1 ATTATAAAAATTATTAAAAATACAAAT
*
12518929 ATTA-AAAAATTATTAAAAAATAGAAAT
1 ATTATAAAAATTATT-AAAAATACAAAT
12518956 ATATATAAA
1 AT-TATAAA
12518965 TTGTAAAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
26 16 0.33
27 21 0.43
28 9 0.18
29 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (27 bp):
ATTATAAAAATTATTAAAAATACAAAT
Found at i:12519023 original size:29 final size:28
Alignment explanation
Indices: 12518972--12519059 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 28
12518962 AAATTGTAAA
*
12518972 AAAATATAAA-AAATTTGTTAAAATTTTAT
1 AAAATATAAACAAA-TT-ATAAAATTTTAT
** *
12519001 AAAA-ATCGTACAAATTTATAAAA-TATAT
1 AAAATAT-AAACAAA-TTATAAAATTTTAT
12519029 AGAAATATAAACAAATTATAAAATTTTAT
1 A-AAATATAAACAAATTATAAAATTTTAT
12519058 AA
1 AA
12519060 CTTCGTAAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
28 16 0.34
29 23 0.49
30 8 0.17
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATATAAACAAATTATAAAATTTTAT
Found at i:12519158 original size:11 final size:11
Alignment explanation
Indices: 12519142--12519175 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12519132 AAAAGAAGCA
12519142 TTTTATAATTT
1 TTTTATAATTT
12519153 TTTTATAATTT
1 TTTTATAATTT
*
12519164 TTAT-TAATTT
1 TTTTATAATTT
12519174 TT
1 TT
12519176 ATTCTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:12519402 original size:36 final size:35
Alignment explanation
Indices: 12519318--12519396 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 35
12519308 TAAAAAATTC
*
12519318 TAATTTTTAATAAATTTTATATTTTATTAAAATTTAA
1 TAATTTTT-CTAAATTTTATATTTTATT-AAATTTAA
* * *
12519355 TAATTTTTCTAAATTTTATTTTTTATT-ATTTTTA
1 TAATTTTTCTAAATTTTATATTTTATTAAATTTAA
12519389 TAATTTTT
1 TAATTTTT
12519397 TTCTAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 13 0.34
36 17 0.45
37 8 0.21
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (35 bp):
TAATTTTTCTAAATTTTATATTTTATTAAATTTAA
Found at i:12519407 original size:9 final size:9
Alignment explanation
Indices: 12519318--12519396 Score: 56
Period size: 9 Copynumber: 8.9 Consensus size: 9
12519308 TAAAAAATTC
12519318 TAATTTTTAA
1 TAATTTTT-A
*
12519328 TAAATTTTA
1 TAATTTTTA
*
12519337 TATTTTATTA
1 TAATTT-TTA
* *
12519347 -AAATTTAA
1 TAATTTTTA
*
12519355 TAATTTTTC
1 TAATTTTTA
*
12519364 TAAATTTTA
1 TAATTTTTA
12519373 T--TTTTTA
1 TAATTTTTA
*
12519380 TTATTTTTA
1 TAATTTTTA
12519389 TAATTTTT
1 TAATTTTT
12519397 TTCTAATTTT
Statistics
Matches: 52, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
7 6 0.12
8 2 0.04
9 34 0.65
10 10 0.19
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (9 bp):
TAATTTTTA
Found at i:12519773 original size:33 final size:32
Alignment explanation
Indices: 12519729--12519795 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
12519719 AAAACTTCAG
* *
12519729 TTGACCGTTTCTTGATTTATGCTCCAATTCTTT
1 TTGACCATTTCTTGATTTATACTCCAATT-TTT
*
12519762 TTGACCATTTCTTTATTTATACTCCAATTTTT
1 TTGACCATTTCTTGATTTATACTCCAATTTTT
12519794 TT
1 TT
12519796 ATACTTTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 5 0.16
33 26 0.84
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.55
Consensus pattern (32 bp):
TTGACCATTTCTTGATTTATACTCCAATTTTT
Found at i:12524508 original size:10 final size:10
Alignment explanation
Indices: 12524495--12524522 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
12524485 ATACAATTCA
12524495 ATATTAACAC
1 ATATTAACAC
12524505 ATATTAACAC
1 ATATTAACAC
12524515 ATATTAAC
1 ATATTAAC
12524523 TACAATTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (10 bp):
ATATTAACAC
Found at i:12524918 original size:22 final size:22
Alignment explanation
Indices: 12524884--12524936 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
12524874 CAATTTAATC
12524884 CTAAC-TAAGTTTACTTACTTTT
1 CTAACTTAAGTTTACTT-CTTTT
*
12524906 CTAACTTAATTTATACTTCTTTT
1 CTAACTTAAGTT-TACTTCTTTT
12524929 CT-ACTTAA
1 CTAACTTAA
12524937 TTTTTGCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 11 0.39
23 12 0.43
24 5 0.18
ACGTcount: A:0.28, C:0.19, G:0.02, T:0.51
Consensus pattern (22 bp):
CTAACTTAAGTTTACTTCTTTT
Found at i:12524937 original size:22 final size:24
Alignment explanation
Indices: 12524895--12524939 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
12524885 TAACTAAGTT
12524895 TACTTACTTTTCTAACTTAATTTA
1 TACTTACTTTTCTAACTTAATTTA
12524919 TACTT-CTTTTCT-ACTTAATTT
1 TACTTACTTTTCTAACTTAATTT
12524940 TTGCCATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.43
23 7 0.33
24 5 0.24
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTTA
Found at i:12525340 original size:9 final size:9
Alignment explanation
Indices: 12525316--12525350 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
12525306 GTCTCTGTTC
*
12525316 TTTCTTTCC
1 TTTCTTTCT
12525325 TTT-TTTCT
1 TTTCTTTCT
12525333 TTTCTTTCT
1 TTTCTTTCT
12525342 TTTCTTTCT
1 TTTCTTTCT
12525351 ATCTTTTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:12525349 original size:13 final size:13
Alignment explanation
Indices: 12525316--12525357 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
12525306 GTCTCTGTTC
*
12525316 TTTCTTTCCTT-T
1 TTTCTTTCTTTCT
12525328 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
*
12525342 TTTCTTTCTATCT
1 TTTCTTTCTTTCT
12525355 TTT
1 TTT
12525358 AGATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 17 0.65
14 5 0.19
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTCTTTCT
Found at i:12525395 original size:3 final size:3
Alignment explanation
Indices: 12525387--12525441 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
12525377 TATTAGTTAT
* *
12525387 TAA TAA TAA TAA TAA TAA TAA TCA TAA TAA TACA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
*
12525433 TTA TAA TAA
1 TAA TAA TAA
12525442 ATATCTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 43 0.96
4 2 0.04
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12526806 original size:11 final size:11
Alignment explanation
Indices: 12526790--12526820 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12526780 TATATATATT
12526790 TAAAAATTATA
1 TAAAAATTATA
*
12526801 TAAAAATAATA
1 TAAAAATTATA
12526812 TAAAAATTA
1 TAAAAATTA
12526821 ATACTGGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:12527241 original size:17 final size:20
Alignment explanation
Indices: 12527204--12527247 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
12527194 ACATAATACG
12527204 AATAT-AAAATAAGATAAAT
1 AATATAAAAATAAGATAAAT
12527223 AAT-TAAAAATAA-A-AAAT
1 AATATAAAAATAAGATAAAT
12527240 AATATAAA
1 AATATAAA
12527248 TACACAAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 6 0.26
19 10 0.43
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AATATAAAAATAAGATAAAT
Found at i:12529469 original size:30 final size:31
Alignment explanation
Indices: 12529404--12529471 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
12529394 ACTGTTAATC
* * *
12529404 AGTGACTATTTTGTCACTTTTTTATAACGTT
1 AGTGACTATTTTATAACTTTTTGATAACGTT
12529435 AGTGACTATTTTATAACTTTTTGA-AA-GTT
1 AGTGACTATTTTATAACTTTTTGATAACGTT
12529464 GAGTGACT
1 -AGTGACT
12529472 GAAATGAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 9 0.27
31 21 0.64
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.47
Consensus pattern (31 bp):
AGTGACTATTTTATAACTTTTTGATAACGTT
Found at i:12530617 original size:46 final size:45
Alignment explanation
Indices: 12530567--12530666 Score: 107
Period size: 46 Copynumber: 2.2 Consensus size: 45
12530557 TTACAAATTG
* *
12530567 AAGTTGC-CAATACGGTGTAGTTAAACCACTCAAACGGTGCAAATAA
1 AAGTTGCTCAA-ACGGTGTAGATAAACCACTC-AACGGTGAAAATAA
* * * *
12530613 AAGTTTCTTAAACGGTGTGGATAAACCACTCAATGGTGAAAAT-A
1 AAGTTGCTCAAACGGTGTAGATAAACCACTCAACGGTGAAAATAA
12530657 AA-TTGCTCAA
1 AAGTTGCTCAA
12530667 CTTCGGAACT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
43 6 0.13
44 3 0.07
45 10 0.22
46 24 0.53
47 2 0.04
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (45 bp):
AAGTTGCTCAAACGGTGTAGATAAACCACTCAACGGTGAAAATAA
Found at i:12535319 original size:31 final size:29
Alignment explanation
Indices: 12535279--12535336 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
12535269 TTAATATCAA
*
12535279 GTGGTAAATTTTAATTAAATAATCAAAGTCG
1 GTGGAAAATTTTAA-TAAA-AATCAAAGTCG
*
12535310 GTGGAAAATTTTAATAAAATTCAAAGT
1 GTGGAAAATTTTAATAAAAATCAAAGT
12535337 TTAGTAGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 4 0.16
31 13 0.52
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (29 bp):
GTGGAAAATTTTAATAAAAATCAAAGTCG
Found at i:12540283 original size:47 final size:47
Alignment explanation
Indices: 12540214--12540339 Score: 155
Period size: 47 Copynumber: 2.7 Consensus size: 47
12540204 CTTTACATAA
* * * *
12540214 TGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCTCAC
1 TGATGCCATATCCCAGATATGGTCTTACACAGT-AGCACATATCACAC
* * *
12540261 TGATGTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
* *
12540308 CGATGCCATATCCCAGATATGGTCTTATACAG
1 TGATGCCATATCCCAGATATGGTCTTACACAG
12540340 AAATCACTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 67 0.97
48 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (47 bp):
TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
Found at i:12540355 original size:7 final size:7
Alignment explanation
Indices: 12540343--12540371 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
12540333 TATACAGAAA
12540343 TCACTTG
1 TCACTTG
12540350 TCACTTG
1 TCACTTG
12540357 TCACTTG
1 TCACTTG
12540364 TCACTTG
1 TCACTTG
12540371 T
1 T
12540372 AGCCAAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:12540405 original size:31 final size:31
Alignment explanation
Indices: 12540370--12540547 Score: 257
Period size: 31 Copynumber: 5.7 Consensus size: 31
12540360 CTTGTCACTT
* *
12540370 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
12540401 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
12540432 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
12540463 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
12540494 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
12540525 GTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
12540548 GTTGTCATTT
Statistics
Matches: 136, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 136 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:12540631 original size:50 final size:50
Alignment explanation
Indices: 12540525--12540701 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
12540515 CACTGATCAG
* * * * *
12540525 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGGTAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT
* *
12540576 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
12540626 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
12540676 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
12540702 GTTTCCATGG
Statistics
Matches: 112, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
50 88 0.79
51 24 0.21
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:12556935 original size:29 final size:29
Alignment explanation
Indices: 12556902--12556968 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
12556892 AAAACAAATC
*
12556902 ATTTTAATAAATAAATATCAATTA-ATATT
1 ATTTTAATAAA-AAATATCAAATATATATT
* *
12556931 ATTTTGAT-AAAAATATTAAATATATATT
1 ATTTTAATAAAAAATATCAAATATATATT
12556959 ATTTTAATAA
1 ATTTTAATAA
12556969 TTTTCCTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 10 0.31
28 14 0.44
29 8 0.25
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
ATTTTAATAAAAAATATCAAATATATATT
Done.