Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 79 of 318
Found at i:27036778 original size:16 final size:17
Alignment explanation
Indices: 27036759--27036799 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
27036749 TTGAAGATGC
27036759 AAATTAAATT-TTA-TA
1 AAATTAAATTATTAGTA
*
27036774 AAAAT-AATTATTAGTA
1 AAATTAAATTATTAGTA
27036790 AAATTAAATT
1 AAATTAAATT
27036800 CAAGATGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 4 0.19
15 7 0.33
16 6 0.29
17 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AAATTAAATTATTAGTA
Found at i:27038661 original size:21 final size:21
Alignment explanation
Indices: 27038618--27038673 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
27038608 AAGCAGATGG
*
27038618 AGCCACTGCAAATAAATTATAT
1 AGCCACTGCAAA-CAATTATAT
*
27038640 AGCCACTGCAAACAATTGTAT
1 AGCCACTGCAAACAATTATAT
*
27038661 AACCACTGCAAAC
1 AGCCACTGCAAAC
27038674 GGGGGAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.21
Consensus pattern (21 bp):
AGCCACTGCAAACAATTATAT
Found at i:27039782 original size:33 final size:33
Alignment explanation
Indices: 27039740--27039875 Score: 149
Period size: 33 Copynumber: 4.3 Consensus size: 33
27039730 AAAAATGGCA
*
27039740 AGAGGAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
** *
27039773 AGAGAAACAAAA-A----ACCA-CTATAGAAAAT
1 AGAGAAACAAAACATGGTA-CAGAAACAGAAAAT
* *
27039801 AGAGGAACAAAATATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
* *
27039834 AAAGAAACAAAACACGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
27039867 AGAGAAACA
1 AGAGAAACA
27039876 TAAAGCAGAC
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
28 20 0.24
29 3 0.04
32 3 0.04
33 57 0.69
ACGTcount: A:0.61, C:0.12, G:0.18, T:0.09
Consensus pattern (33 bp):
AGAGAAACAAAACATGGTACAGAAACAGAAAAT
Found at i:27041477 original size:27 final size:30
Alignment explanation
Indices: 27041447--27041501 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
27041437 TAGCCTAATA
27041447 TGCAATTTTA-T-A-AAAATTTTAATTTTG
1 TGCAATTTTATTCATAAAATTTTAATTTTG
27041474 TGCAATTTTATTCATAAAATTTTAATTT
1 TGCAATTTTATTCATAAAATTTTAATTT
27041502 GATACAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 10 0.40
28 1 0.04
29 1 0.04
30 13 0.52
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (30 bp):
TGCAATTTTATTCATAAAATTTTAATTTTG
Found at i:27045375 original size:47 final size:48
Alignment explanation
Indices: 27045318--27045532 Score: 189
Period size: 47 Copynumber: 4.6 Consensus size: 48
27045308 AGAGCCAATA
* *
27045318 TAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA-GGGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGC-TCGAGACGATGAGCTAGTG
* *
27045366 TAAGA-CATGTCTGGGACAT-GTATCGGCCTCGAGAC-ATAAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGG-CTCGAGACGATGAGCTAGTG
* * *
27045412 TAAGA-CATGT-TGGGACAT-GTATTGGCTACGAGATGAT-AG-TCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCT-CGAGACGATGAGCT-AGTG
* * * * *
27045457 TAAGACCATGTCTGGGACATGGAATCGACTTGAGA-TATGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCTCGAGACGATGAGCTAGTG
* * *
27045504 TAAAACCATGTCTAGGACATGACATCGGC
1 TAAGACCATGTCTGGGACATGGCATCGGC
27045533 ACCTTACCCA
Statistics
Matches: 140, Mismatches: 17, Indels: 21
0.79 0.10 0.12
Matches are distributed among these distances:
44 3 0.02
45 31 0.22
46 38 0.27
47 57 0.41
48 11 0.08
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATCGGCTCGAGACGATGAGCTAGTG
Found at i:27045444 original size:45 final size:46
Alignment explanation
Indices: 27045318--27045477 Score: 159
Period size: 46 Copynumber: 3.4 Consensus size: 46
27045308 AGAGCCAATA
* * * **
27045318 TAAGACCATGTCTGGGACATGGCATCGGCATTGAGA-CGAGGGCTAGTG
1 TAAGA-CATGTCTGGGACAT-GTATCGGCCTCGAGATC-ATAGCTAGTG
27045366 TAAGACATGTCTGGGACATGTATCGGCCTCGAGA-CATAAGCTAGTG
1 TAAGACATGTCTGGGACATGTATCGGCCTCGAGATCAT-AGCTAGTG
* *
27045412 TAAGACATGT-TGGGACATGTATTGG-CTACGAGATGATAG-TCAGTG
1 TAAGACATGTCTGGGACATGTATCGGCCT-CGAGATCATAGCT-AGTG
27045457 TAAGACCATGTCTGGGACATG
1 TAAGA-CATGTCTGGGACATG
27045478 GAATCGACTT
Statistics
Matches: 99, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
44 3 0.03
45 31 0.31
46 37 0.37
47 23 0.23
48 5 0.05
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (46 bp):
TAAGACATGTCTGGGACATGTATCGGCCTCGAGATCATAGCTAGTG
Found at i:27053678 original size:30 final size:30
Alignment explanation
Indices: 27053642--27053703 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
27053632 AAAAAAATTA
27053642 ATGTGGATGTCACGTTAGCAAAGTTAACAT
1 ATGTGGATGTCACGTTAGCAAAGTTAACAT
*
27053672 ATGTGGATGTTACGTTAGCAAAGTTAACAT
1 ATGTGGATGTCACGTTAGCAAAGTTAACAT
27053702 AT
1 AT
27053704 ATTAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (30 bp):
ATGTGGATGTCACGTTAGCAAAGTTAACAT
Found at i:27067289 original size:21 final size:20
Alignment explanation
Indices: 27067247--27067291 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
27067237 GTCTTAACAG
*
27067247 AACTGCTGATGTGGCAAGTT
1 AACTGCTGATGTGCCAAGTT
27067267 AACTGGCTGATGTGACCAA-TT
1 AACT-GCTGATGTG-CCAAGTT
27067288 AACT
1 AACT
27067292 TGCCACGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (20 bp):
AACTGCTGATGTGCCAAGTT
Found at i:27068353 original size:5 final size:5
Alignment explanation
Indices: 27068343--27068439 Score: 194
Period size: 5 Copynumber: 19.4 Consensus size: 5
27068333 TTGTTTAATA
27068343 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
27068393 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
27068440 ATAAAAGAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 92 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:27073009 original size:44 final size:44
Alignment explanation
Indices: 27072954--27073497 Score: 269
Period size: 44 Copynumber: 11.9 Consensus size: 44
27072944 ATATGCTCCA
* *
27072954 CTTCAGTCTGCTTCACTGCAACTTCAGGGAGATAAGACTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAG
* * * * *
27072998 CTTCAACCTGCTCCACTGAAACTTCAGAGAGATAAGGTCTGTAATTTCTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-----G--ACTTGTAG
* * * *
27073049 GTTCAATCTACTCCACTGTAACTTCAGGGAGATAAGA-TTCGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-G-TAG
* *
27073094 CTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT-AG
* **
27073139 -TTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGATTTTCAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-GACT-TG----T-AG
* * * *
27073189 CTTCAATTTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAG
* * * * * * **
27073233 CTTCAACCTACCCCACTACAAATTCAGGGGGATAAGGTTTGT-G
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAG
* * * * * *
27073276 ACTTCAATCTGCACTACTGCGACTACAAGGAGATAAGA-TTCGCTAT
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-G-TAG
* *
27073322 CTTCAGTCTGCTCCACTGCAACTTTAGGG-GCATAAGAC-T-TA-
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAG-ATAAGACTTGTAG
* ** * * * * * * * *
27073363 TTTTGATTTGCTCTATTGGAACTTCAGAGAGATCAGATCTGTAATTTATAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGAT-A-A---G--ACTTGTAG
* * *
27073414 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGACTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAG
* ** *
27073459 CTTTAGCCTGCTCTACTGCAACTTC-GGGAAGATAAGACT
1 CTTCAATCTGCTCCACTGCAACTTCAGGG-AGATAAGACT
27073498 GTGAATTTAC
Statistics
Matches: 374, Mismatches: 89, Indels: 73
0.70 0.17 0.14
Matches are distributed among these distances:
41 21 0.06
42 4 0.01
43 6 0.02
44 131 0.35
45 101 0.27
46 7 0.02
48 1 0.00
49 4 0.01
50 8 0.02
51 91 0.24
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAG
Found at i:27073206 original size:140 final size:140
Alignment explanation
Indices: 27072954--27073224 Score: 420
Period size: 140 Copynumber: 1.9 Consensus size: 140
27072944 ATATGCTCCA
*
27072954 CTTCAGTCTGCTTCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCTGCTCCACTGAAA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCTGCTCCACTGAAA
* *
27073019 CTTCAGAGAGATAAGGTCTGTAATTTCTAGGTTCAATCTACTCCACTGTAACTTCAGGGAGATAA
66 CTTCAGAGAGATAAGGTCTGTAATTTCTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAA
27073084 GATTCGCTAT
131 GATTCGCTAT
* *
27073094 CTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAAG-TTCAACCTGCTCCACTGCA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT-AGCTTCAACCTGCTCCACTGAA
* * * * *
27073158 ACTTCAGGGAGATAAGGTTTGTGATTT-TCAGCTTCAATTTGCTCCACTGCAACTTCAGGGAGAT
65 ACTTCAGAGAGATAAGGTCTGTAATTTCT-AGCTTCAATCTACTCCACTGCAACTTCAGGGAGAT
27073222 AAG
129 AAG
27073225 GCTGGTGGCT
Statistics
Matches: 119, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
139 1 0.01
140 116 0.97
141 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (140 bp):
CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCTGCTCCACTGAAA
CTTCAGAGAGATAAGGTCTGTAATTTCTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAA
GATTCGCTAT
Found at i:27073238 original size:95 final size:95
Alignment explanation
Indices: 27073102--27073276 Score: 253
Period size: 95 Copynumber: 1.8 Consensus size: 95
27073092 ATCTTCAGTC
* * * * * *
27073102 TGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAAGTTCAACCTGCTCCACTGCAACTTCAGGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGTAAGTTCAACCTACCCCACTACAAATTCAGGG
27073167 AGATAAGGTTTGTGATTTTCAGCTTCAATT
66 AGATAAGGTTTGTGATTTTCAGCTTCAATT
* *
27073197 TGCTCCACTGCAACTTCAGGGAGATAAGGCTGGT-GGCTTCAACCTACCCCACTACAAATTCAGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGTAAG-TTCAACCTACCCCACTACAAATTCAGG
*
27073261 GGGATAAGGTTTGTGA
65 GAGATAAGGTTTGTGA
27073277 CTTCAATCTG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
94 1 0.01
95 69 0.99
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (95 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTGGTAAGTTCAACCTACCCCACTACAAATTCAGGG
AGATAAGGTTTGTGATTTTCAGCTTCAATT
Found at i:27081493 original size:19 final size:19
Alignment explanation
Indices: 27081471--27081508 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
27081461 GGCCTTTTCG
* *
27081471 TGAAATTTAGTGCATATGA
1 TGAAATGTAGTGCAAATGA
27081490 TGAAATGTAGTGCAAATGA
1 TGAAATGTAGTGCAAATGA
27081509 ATGAGTGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (19 bp):
TGAAATGTAGTGCAAATGA
Found at i:27084396 original size:26 final size:27
Alignment explanation
Indices: 27084345--27084396 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
27084335 GAAACCATTT
**
27084345 TTTTGAAAAACGGGGATCGATTTTATA
1 TTTTGAAAAACGGGGATCGAGGTTATA
27084372 TTTTGAAAAACGGGGATCG-GGTTAT
1 TTTTGAAAAACGGGGATCGAGGTTAT
27084397 CTCATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.35
Consensus pattern (27 bp):
TTTTGAAAAACGGGGATCGAGGTTATA
Found at i:27085178 original size:45 final size:45
Alignment explanation
Indices: 27085083--27085178 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
27085073 GATTTTCTCG
* *** *
27085083 ATACTGTTACCGTTACTGTTATTTATTCGACACTTTGTTTGTCGA
1 ATACTGTTACCGTTAATGTTACAAATTCGACACTTTGTGTGTCGA
*
27085128 ATACTGTTACCGTTAATGTTACAAATTC-AGCACTTTGTGTGTTGA
1 ATACTGTTACCGTTAATGTTACAAATTCGA-CACTTTGTGTGTCGA
*
27085173 TTACTG
1 ATACTG
27085179 CTACTGTTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 42 0.98
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (45 bp):
ATACTGTTACCGTTAATGTTACAAATTCGACACTTTGTGTGTCGA
Found at i:27088321 original size:19 final size:20
Alignment explanation
Indices: 27088297--27088336 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27088287 TTGCTACTGT
27088297 TTTGC-TTCGTTTCTGCTTC
1 TTTGCTTTCGTTTCTGCTTC
* *
27088316 TTTGCTTTCTTTTCTGTTTC
1 TTTGCTTTCGTTTCTGCTTC
27088336 T
1 T
27088337 GTTTTGTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.00, C:0.23, G:0.12, T:0.65
Consensus pattern (20 bp):
TTTGCTTTCGTTTCTGCTTC
Found at i:27093585 original size:25 final size:23
Alignment explanation
Indices: 27093552--27093614 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
27093542 AAATGTCCAA
*
27093552 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAGTATAATCAT
27093575 CCAAAACACACCAGTATAATCAT
1 CCAAAACACACCAGTATAATCAT
27093598 CCAAAACACACCAGTAT
1 CCAAAACACACCAGTAT
27093615 CATATAATCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.46, C:0.33, G:0.05, T:0.16
Consensus pattern (23 bp):
CCAAAACACACCAGTATAATCAT
Found at i:27093620 original size:28 final size:26
Alignment explanation
Indices: 27093552--27093669 Score: 113
Period size: 23 Copynumber: 4.6 Consensus size: 26
27093542 AAATGTCCAA
*
27093552 CCAAAACACACCAG---TATAATCCT
1 CCAAAACACACCAGATATATAATCAT
27093575 CCAAAACACACCAG---TATAATCAT
1 CCAAAACACACCAGATATATAATCAT
*
27093598 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG-AT-ATATAATCAT
*
27093626 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG-AT-ATATAAT-CAT
*
27093655 CCAAAACGCACCAGA
1 CCAAAACACACCAGA
27093670 ATAGCACAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
23 36 0.44
28 31 0.38
29 14 0.17
ACGTcount: A:0.46, C:0.33, G:0.05, T:0.16
Consensus pattern (26 bp):
CCAAAACACACCAGATATATAATCAT
Found at i:27093671 original size:29 final size:29
Alignment explanation
Indices: 27093566--27093672 Score: 122
Period size: 28 Copynumber: 4.0 Consensus size: 29
27093556 AACACACCAG
27093566 TATAATCC-TCCAAAACACACCAG-----
1 TATAATCCATCCAAAACACACCAGAATAA
* *
27093589 TATAAT-CATCCAAAACACACCAGTATCA
1 TATAATCCATCCAAAACACACCAGAATAA
*
27093617 TATAATCC-TCCCAAACACACCAGAATAA
1 TATAATCCATCCAAAACACACCAGAATAA
*
27093645 TATAATCCATCCAAAACGCACCAGAATA
1 TATAATCCATCCAAAACACACCAGAATA
27093673 GCACAAAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
22 1 0.01
23 21 0.30
28 31 0.44
29 18 0.25
ACGTcount: A:0.46, C:0.31, G:0.05, T:0.19
Consensus pattern (29 bp):
TATAATCCATCCAAAACACACCAGAATAA
Found at i:27096926 original size:21 final size:21
Alignment explanation
Indices: 27096887--27096927 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27096877 CAATGTGGCA
*
27096887 AGTTAACTGGCCACTTCAGCT
1 AGTTAACTGGCCACATCAGCT
* *
27096908 AGTTAACTTGTCACATCAGC
1 AGTTAACTGGCCACATCAGC
27096928 GGTTATGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:27097024 original size:30 final size:31
Alignment explanation
Indices: 27096958--27097026 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
27096948 ACTGTTAGTC
* *
27096958 AGTGACTGTTTTGTCACTTTTTTATAACGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
*
27096989 AGTGACTGTTTTGTTA-TTTTTCA-AAAGTTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAG-TT
*
27097019 GGTGACTG
1 AGTGACTG
27097027 CAATGAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 15 0.45
31 15 0.45
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.49
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTCATAAAGTT
Found at i:27097232 original size:41 final size:41
Alignment explanation
Indices: 27097175--27097256 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
27097165 AAAATACAGC
27097175 TGACTAGGTGATGTGGCAGCCTATGTTGGACAATATTTTTT
1 TGACTAGGTGATGTGGCAGCCTATGTTGGACAATATTTTTT
27097216 TGACTAGGTGATGTGGCAGCCTATGTTGGACAATATTTTTT
1 TGACTAGGTGATGTGGCAGCCTATGTTGGACAATATTTTTT
27097257 AGACAAACGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (41 bp):
TGACTAGGTGATGTGGCAGCCTATGTTGGACAATATTTTTT
Found at i:27101044 original size:8 final size:8
Alignment explanation
Indices: 27101033--27101101 Score: 50
Period size: 8 Copynumber: 7.9 Consensus size: 8
27101023 ATAAAAACTC
27101033 TATAAAAT
1 TATAAAAT
27101041 TATAAAAGT
1 TATAAAA-T
27101050 TATTAGAAAT
1 TA-TA-AAAT
*
27101060 TGTAAAA-
1 TATAAAAT
27101067 TATTAAAAT
1 TA-TAAAAT
27101076 TATAAAAAT
1 TAT-AAAAT
27101085 TATTAGAAAT
1 TA-TA-AAAT
*
27101095 TGTAAAA
1 TATAAAA
27101102 AATTTTAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
7 1 0.02
8 19 0.38
9 17 0.34
10 10 0.20
11 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (8 bp):
TATAAAAT
Found at i:27101074 original size:35 final size:35
Alignment explanation
Indices: 27101035--27101101 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
27101025 AAAAACTCTA
*
27101035 TAAAATTATAAAAGTTATTAGAAATTGTAAAATAT
1 TAAAATTATAAAAATTATTAGAAATTGTAAAATAT
27101070 TAAAATTATAAAAATTATTAGAAATTGTAAAA
1 TAAAATTATAAAAATTATTAGAAATTGTAAAA
27101102 AATTTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (35 bp):
TAAAATTATAAAAATTATTAGAAATTGTAAAATAT
Found at i:27101085 original size:9 final size:9
Alignment explanation
Indices: 27101016--27101102 Score: 54
Period size: 9 Copynumber: 9.6 Consensus size: 9
27101006 TAAAATTGTA
*
27101016 AAAAAATAT
1 AAAAATTAT
27101025 AAAAACTCTAT
1 AAAAA-T-TAT
27101036 -AAAATTAT
1 AAAAATTAT
*
27101044 AAAAGTTATT
1 AAAAATTA-T
* *
27101054 AGAAATTGT
1 AAAAATTAT
27101063 -AAAA-TAT
1 AAAAATTAT
*
27101070 TAAAATTAT
1 AAAAATTAT
27101079 AAAAATTATT
1 AAAAATTA-T
* *
27101089 AGAAATTGT
1 AAAAATTAT
27101098 AAAAA
1 AAAAA
27101103 ATTTTAAAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
7 2 0.03
8 10 0.17
9 28 0.47
10 17 0.28
11 3 0.05
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:27101102 original size:19 final size:19
Alignment explanation
Indices: 27101037--27101102 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
27101027 AAACTCTATA
*
27101037 AAATTATAAAAGTTATTAG
1 AAATTATAAAAATTATTAG
*
27101056 AAATTGT-AAAA-TATTA-
1 AAATTATAAAAATTATTAG
27101072 AAATTATAAAAATTATTAG
1 AAATTATAAAAATTATTAG
*
27101091 AAATTGTAAAAA
1 AAATTATAAAAA
27101103 ATTTTAAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.15
17 9 0.22
18 8 0.20
19 17 0.43
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (19 bp):
AAATTATAAAAATTATTAG
Found at i:27103776 original size:23 final size:23
Alignment explanation
Indices: 27103750--27103799 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
27103740 TAACTAAAAT
27103750 ATTAGTAATTTCTAATAGTTCAC
1 ATTAGTAATTTCTAATAGTTCAC
27103773 ATTAGTAATTTCTAATAGTTCAC
1 ATTAGTAATTTCTAATAGTTCAC
27103796 ATTA
1 ATTA
27103800 AATGCATTAG
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:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (23 bp):
ATTAGTAATTTCTAATAGTTCAC
Found at i:27109976 original size:11 final size:12
Alignment explanation
Indices: 27109953--27109985 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
27109943 GATGTATCTA
27109953 TTAATTCAATTT
1 TTAATTCAATTT
27109965 TTAATT-AATTT
1 TTAATTCAATTT
*
27109976 TTAGTTCAAT
1 TTAATTCAAT
27109986 ACTGACTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (12 bp):
TTAATTCAATTT
Found at i:27118802 original size:57 final size:58
Alignment explanation
Indices: 27118726--27118843 Score: 159
Period size: 57 Copynumber: 2.1 Consensus size: 58
27118716 CATTTTTAGG
** * *
27118726 TCATTTTCATTTTGGAGAAAACCA-CATTCATTTCCAAATGATTC-CATTTTTCCATTT
1 TCATTTTCATTTTACAGAAAACCATAATT-ATTTCCAAATGATTCTCATTTCTCCATTT
* *
27118783 TCATTTTTATTTTACAGAAAACCATAATTATTTCCAAATGTTTCTCATTTCTCCATTT
1 TCATTTTCATTTTACAGAAAACCATAATTATTTCCAAATGATTCTCATTTCTCCATTT
27118841 TCA
1 TCA
27118844 CAATTTCTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
57 35 0.66
58 18 0.34
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (58 bp):
TCATTTTCATTTTACAGAAAACCATAATTATTTCCAAATGATTCTCATTTCTCCATTT
Found at i:27119633 original size:5 final size:5
Alignment explanation
Indices: 27119623--27119664 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
27119613 GTAACACTTA
27119623 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
27119665 TATAATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:27119765 original size:20 final size:21
Alignment explanation
Indices: 27119742--27119785 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
27119732 AAGTAAAACG
*
27119742 AAAGAAAAAGAAATAGG-GAA
1 AAAGAAAAAGAAAAAGGAGAA
*
27119762 AAAGAGAAAGAAAAAGGAGAA
1 AAAGAAAAAGAAAAAGGAGAA
27119783 AAA
1 AAA
27119786 AGCTAGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAGAAAAAGGAGAA
Found at i:27122818 original size:18 final size:18
Alignment explanation
Indices: 27122797--27122831 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27122787 AAAAAGCTGA
27122797 CTGAAACGAAAAAAAAAC
1 CTGAAACGAAAAAAAAAC
*
27122815 CTGAAATGAAAAAAAAA
1 CTGAAACGAAAAAAAAA
27122832 AGGCTGCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.11, G:0.11, T:0.09
Consensus pattern (18 bp):
CTGAAACGAAAAAAAAAC
Found at i:27123047 original size:18 final size:17
Alignment explanation
Indices: 27123007--27123048 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
27122997 CTCATTTAGG
27123007 GAAGAAATGAGAGAAAA
1 GAAGAAATGAGAGAAAA
27123024 GAAAGAAA-GAAGAGAAGAA
1 G-AAGAAATG-AGAGAA-AA
27123043 GAAGAA
1 GAAGAA
27123049 GGAGCAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 17 0.77
19 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (17 bp):
GAAGAAATGAGAGAAAA
Found at i:27123222 original size:11 final size:11
Alignment explanation
Indices: 27123190--27123222 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
27123180 TATTATTGTT
27123190 GATTTGAATTT-
1 GATTT-AATTTA
27123201 GATTTAATTTA
1 GATTTAATTTA
27123212 GATTTAATTTA
1 GATTTAATTTA
27123223 TAAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (11 bp):
GATTTAATTTA
Found at i:27124381 original size:27 final size:26
Alignment explanation
Indices: 27124351--27124422 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
27124341 TATAAAAAAG
*
27124351 AAAATATGAAAAAAATATATTAATGAA
1 AAAATATGAAAAAAATATAAT-ATGAA
* *
27124378 AAAATACGAAAAGAAATAGAATATGAA
1 AAAATATGAAAA-AAATATAATATGAA
*
27124405 AAAA-ATAGAATAAAATAT
1 AAAATAT-GAAAAAAATAT
27124423 GAAAAATAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
26 6 0.16
27 24 0.65
28 7 0.19
ACGTcount: A:0.68, C:0.01, G:0.10, T:0.21
Consensus pattern (26 bp):
AAAATATGAAAAAAATATAATATGAA
Found at i:27124412 original size:16 final size:17
Alignment explanation
Indices: 27124380--27124416 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
27124370 TTAATGAAAA
27124380 AATACGAAAAGAAATAG
1 AATACGAAAAGAAATAG
*
27124397 AATATGAAAA-AAATAG
1 AATACGAAAAGAAATAG
27124413 AATA
1 AATA
27124417 AAATATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.68, C:0.03, G:0.14, T:0.16
Consensus pattern (17 bp):
AATACGAAAAGAAATAG
Found at i:27124427 original size:19 final size:19
Alignment explanation
Indices: 27124405--27124463 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
27124395 AGAATATGAA
27124405 AAAAATAGAATAAAATATG
1 AAAAATAGAATAAAATATG
*
27124424 AAAAATAGTATAAAA-AT-
1 AAAAATAGAATAAAATATG
27124441 AATATAA-A-AATAAAATATG
1 AA-A-AATAGAATAAAATATG
27124460 AAAA
1 AAAA
27124464 TAGTATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
17 9 0.26
18 7 0.21
19 18 0.53
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (19 bp):
AAAAATAGAATAAAATATG
Found at i:27124463 original size:14 final size:11
Alignment explanation
Indices: 27124397--27124453 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
27124387 AAAGAAATAG
27124397 AATATGAAAAA-
1 AATAT-AAAAAT
* *
27124408 AATAGAATAA-
1 AATATAAAAAT
27124418 AATATGAAAAAT
1 AATAT-AAAAAT
*
27124430 AGTATAAAAAT
1 AATATAAAAAT
27124441 AATATAAAAAT
1 AATATAAAAAT
27124452 AA
1 AA
27124454 AATATGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
10 8 0.21
11 26 0.68
12 4 0.11
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:27124485 original size:36 final size:34
Alignment explanation
Indices: 27124403--27124470 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
27124393 ATAGAATATG
*
27124403 AAAAAAAT-AGAATAAAATATGAAAAATAGTATA
1 AAAAAAATAAAAATAAAATATGAAAAATAGTATA
27124436 AAAATAATATAAAAATAAAATATG-AAAATAGTATA
1 AAAA-AA-ATAAAAATAAAATATGAAAAATAGTATA
27124471 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 4 0.13
34 2 0.06
35 13 0.42
36 12 0.39
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (34 bp):
AAAAAAATAAAAATAAAATATGAAAAATAGTATA
Found at i:27124744 original size:140 final size:138
Alignment explanation
Indices: 27124446--27124782 Score: 446
Period size: 140 Copynumber: 2.4 Consensus size: 138
27124436 AAAATAATAT
* *
27124446 AAAAATAAAATATGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATATAAACA
1 AAAAATAAAATAAGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAACA
* **
27124511 AATGGACAAAATTAGGATTATTTAAAAACACTAAAATAATACATTTGAAACATTATGTACGGGAA
66 AATGGACAAAATAAGGATTATTTAAAAACACTAAAATAATACATTTGAAACATTATGTACGAAAA
27124576 TAAGATAA
131 TAAGATAA
* * ** *
27124584 ATAAAATAAAATACGAAAATAGTATATTTTAAAAATTAAAATTTGAATATTTTAGAAAAT-CAAA
1 A-AAAATAAAATAAGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTA-AAAATACAAA
** * *
27124648 CAAA-GAGACAAAATCAAGG-TTATTTTAAAAACTTTAGAATAATATATTTGAAACATTATGTAC
64 CAAATG-GACAAAAT-AAGGATTA-TTTAAAAACACTAAAATAATACATTTGAAACATTATGTAC
*
27124711 TAAAATAAGATAA
126 GAAAATAAGATAA
* *
27124724 AAAAATAAAAATAAGAAAATAATATATTTTAAAAAATAGAATCCGAAAATTTTAAAAAT
1 AAAAAT-AAAATAAGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAAT
27124783 TTTAGAAATA
Statistics
Matches: 172, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
138 2 0.01
139 75 0.44
140 95 0.55
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (138 bp):
AAAAATAAAATAAGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAACA
AATGGACAAAATAAGGATTATTTAAAAACACTAAAATAATACATTTGAAACATTATGTACGAAAA
TAAGATAA
Found at i:27126774 original size:12 final size:12
Alignment explanation
Indices: 27126741--27126774 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27126731 GCTAATATAG
*
27126741 AGCCAGATCAAC
1 AGCCAGATCCAC
*
27126753 AGCCTGATCCAC
1 AGCCAGATCCAC
27126765 AGCCAGATCC
1 AGCCAGATCC
27126775 CGAGCTTGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.38, G:0.18, T:0.12
Consensus pattern (12 bp):
AGCCAGATCCAC
Found at i:27130618 original size:16 final size:16
Alignment explanation
Indices: 27130599--27130631 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27130589 TTTTACTGAA
27130599 TTTTTTTCCTTCT-TTC
1 TTTTTTT-CTTCTCTTC
27130615 TTTTTTTCTTCTCTTC
1 TTTTTTTCTTCTCTTC
27130631 T
1 T
27130632 CCCTCCCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTTCTTCTCTTC
Found at i:27130776 original size:27 final size:27
Alignment explanation
Indices: 27130746--27130802 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
27130736 GTCATCAACT
* *
27130746 AGTGCCGTCTCTGGCAGAGGCAAGACC
1 AGTGCCGCCTCTGACAGAGGCAAGACC
27130773 AGTGCCGCCTCTGACAGAGGCAAGACC
1 AGTGCCGCCTCTGACAGAGGCAAGACC
27130800 AGT
1 AGT
27130803 ATTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.30, G:0.32, T:0.14
Consensus pattern (27 bp):
AGTGCCGCCTCTGACAGAGGCAAGACC
Found at i:27132017 original size:18 final size:18
Alignment explanation
Indices: 27131976--27132023 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
27131966 TTGATATTGA
* *
27131976 TTATTACAAAATATTATC
1 TTATTATAAAATATAATC
27131994 TTATTATAAAATATAAT-
1 TTATTATAAAATATAATC
27132011 TTAATTATCAAAA
1 TT-ATTAT-AAAA
27132024 GGAATTGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 2 0.08
18 20 0.77
19 4 0.15
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATTATAAAATATAATC
Found at i:27138782 original size:17 final size:17
Alignment explanation
Indices: 27138727--27138783 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
27138717 TAGAAATAAA
*
27138727 TTAAAAACCATAAAACT
1 TTAAAAACCATAAAAAT
* **
27138744 TTCAAAACC-T-AATTT
1 TTAAAAACCATAAAAAT
27138759 ATTAAAAACCATAAAAAT
1 -TTAAAAACCATAAAAAT
27138777 TTAAAAA
1 TTAAAAA
27138784 AATTAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 3 0.10
16 9 0.29
17 16 0.52
18 3 0.10
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (17 bp):
TTAAAAACCATAAAAAT
Found at i:27138915 original size:15 final size:16
Alignment explanation
Indices: 27138886--27138915 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27138876 CTCATTTTAT
27138886 TAAAATTTATAATATA
1 TAAAATTTATAATATA
27138902 TAAAATTT-TAATAT
1 TAAAATTTATAATAT
27138916 TGGCTTTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAATTTATAATATA
Found at i:27139168 original size:10 final size:10
Alignment explanation
Indices: 27139155--27139218 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
27139145 AGTAAAATAA
27139155 TTTTATAAAT
1 TTTTATAAAT
*
27139165 TTTTAT-GAT
1 TTTTATAAAT
* *
27139174 TTTCATTAAT
1 TTTTATAAAT
*
27139184 TTCTAATAAA-
1 TT-TTATAAAT
27139194 TTTTATAAAT
1 TTTTATAAAT
27139204 TATTT-TAAAT
1 T-TTTATAAAT
27139214 TTTTA
1 TTTTA
27139219 GGGTTTTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 16 0.37
10 19 0.44
11 8 0.19
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:27145015 original size:32 final size:30
Alignment explanation
Indices: 27144974--27145035 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 30
27144964 TCATATTTAG
**
27144974 ATTATTAAAATGTTCATATTTATATTACATTT
1 ATTATTAAAACATTCATATTTA-ATTA-ATTT
27145006 ATTATTAAAACATTCATATTTAATTAATTT
1 ATTATTAAAACATTCATATTTAATTAATTT
27145036 CTAACAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.14
31 4 0.14
32 20 0.71
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTATTAAAACATTCATATTTAATTAATTT
Found at i:27145162 original size:9 final size:9
Alignment explanation
Indices: 27145125--27145181 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
27145115 ATTTCTAATA
27145125 TTATAATTT
1 TTATAATTT
27145134 TTAATCAATTT
1 TT-AT-AATTT
* *
27145145 TAATGATTT
1 TTATAATTT
27145154 TTATAATTT
1 TTATAATTT
*
27145163 TT-TATGTTT
1 TTATA-ATTT
27145172 TTATAATTT
1 TTATAATTT
27145181 T
1 T
27145182 AAAATGAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
8 2 0.05
9 24 0.63
10 6 0.16
11 6 0.16
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (9 bp):
TTATAATTT
Found at i:27145163 original size:18 final size:18
Alignment explanation
Indices: 27145130--27145183 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
27145120 TAATATTATA
27145130 ATTTTTAATCAATTTTAATG
1 ATTTTT-AT-AATTTTAATG
*
27145150 ATTTTTATAATTTTTTATG
1 ATTTTTATAA-TTTTAATG
27145169 -TTTTTATAATTTTAA
1 ATTTTTATAATTTTAA
27145184 AATGAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 5 0.16
18 11 0.35
19 9 0.29
20 6 0.19
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (18 bp):
ATTTTTATAATTTTAATG
Found at i:27150020 original size:23 final size:22
Alignment explanation
Indices: 27149985--27150028 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
27149975 GAATAATTTT
* *
27149985 AAAATATATAATATGTATATGTA
1 AAAATATAAAATAAGTA-ATGTA
*
27150008 AAAATGTAAAATAAGTAATGT
1 AAAATATAAAATAAGTAATGT
27150029 GTAAATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (22 bp):
AAAATATAAAATAAGTAATGTA
Found at i:27152075 original size:47 final size:47
Alignment explanation
Indices: 27151960--27152166 Score: 209
Period size: 47 Copynumber: 4.2 Consensus size: 47
27151950 TGCACATAGT
* ** * * *
27151960 CACATATTACACACCGAAGCCATAGCCCAGCCATGGTCTTACAC-GGAT
1 CACATA-T-CACACCGATGCCATAGCCCAGATATGGTCTTATACAGAAG
* * *
27152008 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGAAG
* *
27152055 CACATATCACACCGATGCCATATCCCAGATATGGTCTTATACGGAAG
1 CACATATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGAAG
* *
27152102 CACATAATCACATATCTCCGATGCCATAGCCCAGCTATGGTCTTATACAGAAAT
1 CACAT-ATCAC--A---CCGATGCCATAGCCCAGATATGGTCTTATACAG-AAG
27152156 CACATATCACA
1 CACATATCACA
27152167 TGTTGCCATG
Statistics
Matches: 136, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
46 29 0.21
47 52 0.38
48 11 0.08
50 1 0.01
51 1 0.01
53 35 0.26
54 7 0.05
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (47 bp):
CACATATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGAAG
Found at i:27152082 original size:93 final size:98
Alignment explanation
Indices: 27151942--27152166 Score: 246
Period size: 93 Copynumber: 2.3 Consensus size: 98
27151932 ATAGTAAAAC
** *
27151942 TATGGTCTTGCACA-TAGTCACATATTACACACCGAAGCCATAGCCCAGCCATGGTCTTACACGG
1 TATGGTCTTATACAGTAG-CACATA-T-CACACCGAAGCCATAGCCCAGACATGGTCTTACACGG
* *
27152006 -ATCACAT-ATCAC-A-CT-GATGCCATATCCCAGA
63 AAGCACATAATCACAATCTCGATGCCATAGCCCAGA
* * * *
27152037 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCAGATATGGTCTTATACGGAAG
1 TATGGTCTTATACAGTAGCACATATCACACCGAAGCCATAGCCCAGACATGGTCTTACACGGAAG
*
27152102 CACATAATCACATATCTCCGATGCCATAGCCCAGC
66 CACATAATCACA-ATCT-CGATGCCATAGCCCAGA
* *
27152137 TATGGTCTTATACAGAAATCACATATCACA
1 TATGGTCTTATACAG-TAGCACATATCACA
27152167 TGTTGCCATG
Statistics
Matches: 109, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
93 32 0.29
94 7 0.06
95 23 0.21
96 3 0.03
97 1 0.01
98 2 0.02
100 29 0.27
101 12 0.11
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (98 bp):
TATGGTCTTATACAGTAGCACATATCACACCGAAGCCATAGCCCAGACATGGTCTTACACGGAAG
CACATAATCACAATCTCGATGCCATAGCCCAGA
Found at i:27152135 original size:53 final size:53
Alignment explanation
Indices: 27152066--27152167 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
27152056 ACATATCACA
* *
27152066 CCGATGCCATATCCCAGATATGGTCTTATAC-GGAAGCACATAATCACATATCT
1 CCGATGCCATAGCCCAGATATGGTCTTATACAGAAAGCACAT-ATCACATATCT
* *
27152119 CCGATGCCATAGCCCAGCTATGGTCTTATACAGAAATCACATATCACAT
1 CCGATGCCATAGCCCAGATATGGTCTTATACAGAAAGCACATATCACAT
27152168 GTTGCCATGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 36 0.82
54 8 0.18
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.25
Consensus pattern (53 bp):
CCGATGCCATAGCCCAGATATGGTCTTATACAGAAAGCACATATCACATATCT
Found at i:27154237 original size:11 final size:10
Alignment explanation
Indices: 27154190--27154239 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
27154180 ATAAATAAGT
27154190 AAAGAAACA-
1 AAAGAAACAG
27154199 AAAGAAACAG
1 AAAGAAACAG
**
27154209 AAAGAAATTG
1 AAAGAAACAG
27154219 AAACGAAACAG
1 AAA-GAAACAG
27154230 AGAAGAAACA
1 A-AAGAAACA
27154240 TGGGAGAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 9 0.26
10 11 0.32
11 12 0.35
12 2 0.06
ACGTcount: A:0.68, C:0.10, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAACAG
Found at i:27154265 original size:6 final size:6
Alignment explanation
Indices: 27154254--27154280 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27154244 AGAAAGAAAG
27154254 AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA
27154281 TTTGGGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:27155062 original size:30 final size:30
Alignment explanation
Indices: 27155026--27155086 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
27155016 TTATGTGTCG
27155026 AATACTGTTACTGTTACTGTTATCGATTCA
1 AATACTGTTACTGTTACTGTTATCGATTCA
27155056 AATACTGTTACTGTTACTGTTATCGATTCA
1 AATACTGTTACTGTTACTGTTATCGATTCA
27155086 A
1 A
27155087 CACTTTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (30 bp):
AATACTGTTACTGTTACTGTTATCGATTCA
Found at i:27155106 original size:75 final size:75
Alignment explanation
Indices: 27154983--27155122 Score: 217
Period size: 75 Copynumber: 1.9 Consensus size: 75
27154973 CGACTACTGT
* *
27154983 TACTGTTACCGTTACTGTTACCTATTCGACACTTTATGTGTCGAATACTGTTACTGTTACTGTTA
1 TACTGTTACCGTTACTGTTACCGATTCAACACTTTATGTGTCGAATACTGTTACTGTTACTGTTA
27155048 TCGATTCAAA
66 TCGATTCAAA
* * * * *
27155058 TACTGTTACTGTTACTGTTATCGATTCAACACTTTGTGTGTTGAATACTGTTACTGTTATTGTTA
1 TACTGTTACCGTTACTGTTACCGATTCAACACTTTATGTGTCGAATACTGTTACTGTTACTGTTA
27155123 CTGTTCTGGA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (75 bp):
TACTGTTACCGTTACTGTTACCGATTCAACACTTTATGTGTCGAATACTGTTACTGTTACTGTTA
TCGATTCAAA
Found at i:27155317 original size:18 final size:18
Alignment explanation
Indices: 27155296--27155478 Score: 174
Period size: 18 Copynumber: 10.2 Consensus size: 18
27155286 TAACTGATTA
27155296 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
27155314 TTACCGAATAATTGACTG
1 TTACTGAATAATTGACTG
* *
27155332 TTACTGGATAATAGACTG
1 TTACTGAATAATTGACTG
* * *
27155350 TTACTGAATAACTGAATA
1 TTACTGAATAATTGACTG
*
27155368 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* *
27155386 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
* *
27155404 TCACTGAATAAGTGACTG
1 TTACTGAATAATTGACTG
* *
27155422 TTACTGAATAACTTAATTG
1 TTACTGAATAA-TTGACTG
* *
27155441 CTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
*
27155458 TTACTAAATAATTGACTG
1 TTACTGAATAATTGACTG
27155476 TTA
1 TTA
27155479 TTGGATAACC
Statistics
Matches: 134, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
17 13 0.10
18 108 0.81
19 13 0.10
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:27155573 original size:18 final size:18
Alignment explanation
Indices: 27155284--27155579 Score: 139
Period size: 18 Copynumber: 16.1 Consensus size: 18
27155274 AAAGGTATAA
* *
27155284 AATAACTGATTATTACTG
1 AATAAATGATTGTTACTG
* * *
27155302 AATAATTGACTGTTACCG
1 AATAAATGATTGTTACTG
* *
27155320 AATAATTGACTGTTACTG
1 AATAAATGATTGTTACTG
* *
27155338 GAT-AATAGACTGTTACTG
1 AATAAAT-GATTGTTACTG
* * *
27155356 AATAACTGAATATTACTG
1 AATAAATGATTGTTACTG
* **
27155374 AATAATTGATCATTACTG
1 AATAAATGATTGTTACTG
* *
27155392 AATAACTGATTGTCACTG
1 AATAAATGATTGTTACTG
* *
27155410 AATAAGTGACTGTTACTG
1 AATAAATGATTGTTACTG
* * *
27155428 AATAACTTAATTGCTACTG
1 AATAA-ATGATTGTTACTG
** *
27155447 AATATCTGATT-TTACTA
1 AATAAATGATTGTTACTG
* * *
27155464 AATAATTGACTGTTATTG
1 AATAAATGATTGTTACTG
* *
27155482 GATAACCGATCAATTGATCGATACTG
1 AATAA---AT-GATTG-T---TACTG
* * * *
27155508 AATAACTGGTTATTATTG
1 AATAAATGATTGTTACTG
* *
27155526 AATAATTGATTGTTACCG
1 AATAAATGATTGTTACTG
*
27155544 AATAAGTGATTGTTACTG
1 AATAAATGATTGTTACTG
*
27155562 AATAAATAATTGTT-CTG
1 AATAAATGATTGTTACTG
27155579 A
1 A
27155580 TTGTTAATGA
Statistics
Matches: 211, Mismatches: 55, Indels: 25
0.73 0.19 0.09
Matches are distributed among these distances:
17 18 0.09
18 161 0.76
19 15 0.07
21 2 0.01
22 5 0.02
23 2 0.01
26 8 0.04
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (18 bp):
AATAAATGATTGTTACTG
Found at i:27167453 original size:21 final size:21
Alignment explanation
Indices: 27167412--27167456 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
27167402 GAAAATCTAA
* *
27167412 GTTTTATAAGGAATTAATTGG
1 GTTTTACAAGGAATAAATTGG
27167433 GTTTTACAAGGAA-AAACTTGG
1 GTTTTACAAGGAATAAA-TTGG
27167454 GTT
1 GTT
27167457 ATTTTATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.38
Consensus pattern (21 bp):
GTTTTACAAGGAATAAATTGG
Found at i:27170058 original size:68 final size:67
Alignment explanation
Indices: 27169921--27170071 Score: 205
Period size: 68 Copynumber: 2.2 Consensus size: 67
27169911 TAGCCTAGCC
* * * * *
27169921 ATGGTCTTACACATTTTACACCATATTTAATGTCATGGTAGACCCTCTATGTTGTCATAGTCGAG
1 ATGGTCTTACACATTTTACACCAAATTTAATGTCATGGTAGACCCTCTATATTGCCATAATCGAA
27169986 CT
66 CT
* * *
27169988 ATGGTCTCACACATTTTAC-CCAAATGCTTAATGTCCTGGTGGACCCTCTATATTGCCATAATCG
1 ATGGTCTTACACATTTTACACCAAAT--TTAATGTCATGGTAGACCCTCTATATTGCCATAATCG
27170052 AACT
64 AACT
27170056 ATGGTCTTACACATTT
1 ATGGTCTTACACATTT
27170072 AAATCTCCTT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
66 5 0.07
67 18 0.25
68 50 0.68
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (67 bp):
ATGGTCTTACACATTTTACACCAAATTTAATGTCATGGTAGACCCTCTATATTGCCATAATCGAA
CT
Found at i:27180738 original size:19 final size:20
Alignment explanation
Indices: 27180716--27180754 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
27180706 TGAATCGGTC
27180716 TTTTTCT-TTTTTC-TTTTT
1 TTTTTCTATTTTTCATTTTT
27180734 TTTTTCTATTTTTCTATTTTT
1 TTTTTCTATTTTTC-ATTTTT
27180755 CTTCTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
21 5 0.28
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCTATTTTTCATTTTT
Found at i:27180759 original size:19 final size:18
Alignment explanation
Indices: 27180719--27180762 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
27180709 ATCGGTCTTT
* *
27180719 TTCTTTTTTCTTTTTTTT
1 TTCTTTTTTCTATTTTTC
27180737 TTCTATTTTTCTATTTTTC
1 TTCT-TTTTTCTATTTTTC
27180756 TTCTTTT
1 TTCTTTT
27180763 CTACTTATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (18 bp):
TTCTTTTTTCTATTTTTC
Found at i:27181464 original size:22 final size:22
Alignment explanation
Indices: 27181426--27181482 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
27181416 ATATTTTTGC
* * *
27181426 TATTATCTATTATTATCATATT
1 TATTATATATTTTTATCATATA
*
27181448 TATTAT-TATTTTCTATCCTATA
1 TATTATATATTTT-TATCATATA
27181470 TATTTATATATTT
1 TA-TTATATATTT
27181483 CTTTTTAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.17
22 15 0.52
23 4 0.14
24 5 0.17
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATATATTTTTATCATATA
Found at i:27181696 original size:3 final size:3
Alignment explanation
Indices: 27181686--27181728 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
27181676 TATTTTTTTG
* * *
27181686 TAT T-T TAT TAT TAT TAG TAT TAT TAT TAT TAT TGT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
27181729 ATGTATATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:27181887 original size:23 final size:23
Alignment explanation
Indices: 27181844--27181887 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
27181834 ACATTTTTTA
* *
27181844 AATACTATATTATATATATATAT
1 AATACCATATTATATACATATAT
*
27181867 AATACCATATTATGTACATAT
1 AATACCATATTATATACATAT
27181888 TATTATTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (23 bp):
AATACCATATTATATACATATAT
Found at i:27182063 original size:26 final size:27
Alignment explanation
Indices: 27182019--27182071 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
27182009 ATTATACTTA
* * *
27182019 TTATTTTCACTATTGTTACTTATTATT
1 TTATTTTCAATATTATTACGTATTATT
27182046 TTATTTT-AATATTATTACGTATTATT
1 TTATTTTCAATATTATTACGTATTATT
27182072 CGGTATACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (27 bp):
TTATTTTCAATATTATTACGTATTATT
Found at i:27183015 original size:15 final size:16
Alignment explanation
Indices: 27182997--27183034 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
27182987 TTTAGCTCTA
27182997 AGTTTTTATGGT-TTT
1 AGTTTTTATGGTGTTT
*
27183012 AGTTTTT-TGTTGTTT
1 AGTTTTTATGGTGTTT
27183027 AGTTTTTA
1 AGTTTTTA
27183035 AATAAAACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.13, C:0.00, G:0.18, T:0.68
Consensus pattern (16 bp):
AGTTTTTATGGTGTTT
Found at i:27191045 original size:50 final size:50
Alignment explanation
Indices: 27190991--27191100 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
27190981 CATGTAAACA
* * *
27190991 GGAAGCTCTTCCAAGCTATATAACGGGAAGCTCATGTGAGCTAAATAACG
1 GGAAGCTCATCCAAGCTAAATAACGGGAAGCTCATGCGAGCTAAATAACG
*** * ** *
27191041 GGAAGCTCATGGGAGCTAAATAAGGGGAAGCTCATGCGAGCTGTATATCG
1 GGAAGCTCATCCAAGCTAAATAACGGGAAGCTCATGCGAGCTAAATAACG
27191091 GGAAGCTCAT
1 GGAAGCTCAT
27191101 GAGAGCTGTG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (50 bp):
GGAAGCTCATCCAAGCTAAATAACGGGAAGCTCATGCGAGCTAAATAACG
Found at i:27191109 original size:25 final size:25
Alignment explanation
Indices: 27191004--27191107 Score: 136
Period size: 25 Copynumber: 4.2 Consensus size: 25
27190994 AGCTCTTCCA
*
27191004 AGCTATATAACGGGAAGCTCATGTG
1 AGCTATATAACGGGAAGCTCATGAG
* *
27191029 AGCTAAATAACGGGAAGCTCATGGG
1 AGCTATATAACGGGAAGCTCATGAG
* * *
27191054 AGCTAAATAAGGGGAAGCTCATGCG
1 AGCTATATAACGGGAAGCTCATGAG
* *
27191079 AGCTGTATATCGGGAAGCTCATGAG
1 AGCTATATAACGGGAAGCTCATGAG
27191104 AGCT
1 AGCT
27191108 GTGGTGTGTC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 70 1.00
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (25 bp):
AGCTATATAACGGGAAGCTCATGAG
Found at i:27193541 original size:13 final size:13
Alignment explanation
Indices: 27193525--27193557 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
27193515 TTGCCCACGA
27193525 TTTCAACCCACAG
1 TTTCAACCCACAG
*
27193538 TTTCAACCCACGG
1 TTTCAACCCACAG
27193551 TTTCAAC
1 TTTCAAC
27193558 AAGTAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.36, G:0.09, T:0.27
Consensus pattern (13 bp):
TTTCAACCCACAG
Found at i:27209615 original size:41 final size:41
Alignment explanation
Indices: 27209570--27209656 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
27209560 AATTAGTAGG
27209570 AAAGTAATTT-TAATGTTTAATATATTAAATTTTATACTTAA
1 AAAGT-ATTTCTAATGTTTAATATATTAAATTTTATACTTAA
* * * * *
27209611 AAAGTATTTCTAATGTTTGATATGTTAAGTTTTATAGTTAG
1 AAAGTATTTCTAATGTTTAATATATTAAATTTTATACTTAA
27209652 AAAGT
1 AAAGT
27209657 GTTTTTGACA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 4 0.10
41 36 0.90
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.47
Consensus pattern (41 bp):
AAAGTATTTCTAATGTTTAATATATTAAATTTTATACTTAA
Found at i:27211490 original size:21 final size:23
Alignment explanation
Indices: 27211443--27211496 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
27211433 CATTCAAGAT
**
27211443 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
27211466 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
27211487 AAAAT-ATATA
1 AAAATAATATA
27211497 ATGTGTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:27211550 original size:52 final size:49
Alignment explanation
Indices: 27211434--27211567 Score: 114
Period size: 52 Copynumber: 2.7 Consensus size: 49
27211424 ATTAGTACCC
* * * *
27211434 ATTCAAGATAAAATAATATATAAAACTCTTTAAA-A-ATAATATATAAACA
1 ATTCAAAAT-AAATAATGTATAAAAAT-TTGAAATACATAATATATAAACA
* *
27211483 ATTCAAAATATATAATGTGTGAAAAAAGTTTGAAATACATAATATATGAAA-A
1 ATTCAAAATAAATAATGTAT--AAAAA-TTTGAAATACATAATATAT-AAACA
*
27211535 TATT-AAAGTAAATAATGTATAAAAATTTGAAAT
1 -ATTCAAAATAAATAATGTATAAAAATTTGAAAT
27211568 GAGCATTCTA
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
48 8 0.12
49 16 0.23
50 14 0.20
51 2 0.03
52 23 0.33
53 6 0.09
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.32
Consensus pattern (49 bp):
ATTCAAAATAAATAATGTATAAAAATTTGAAATACATAATATATAAACA
Found at i:27212247 original size:25 final size:25
Alignment explanation
Indices: 27212162--27212257 Score: 67
Period size: 25 Copynumber: 3.8 Consensus size: 25
27212152 GAATGTAATA
*
27212162 ATTATATTGATGATAT-TTTA-AATT
1 ATTATATT-ATGATATATTTATTATT
*
27212186 AATTA-ATTA-GATAAATATTATT-TT
1 -ATTATATTATGATATAT-TTATTATT
27212210 ATTAATATTTTATGATATATTTATTATT
1 ATT-ATA--TTATGATATATTTATTATT
* *
27212238 ATTATATTATTATTTATTTA
1 ATTATATTATGATATATTTA
27212258 GTATAAAAGG
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
22 4 0.07
23 5 0.09
24 9 0.16
25 17 0.30
27 11 0.19
28 11 0.19
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
ATTATATTATGATATATTTATTATT
Found at i:27212492 original size:20 final size:20
Alignment explanation
Indices: 27212455--27212492 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27212445 TGATGGGGAG
*
27212455 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
27212475 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
27212493 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:27214509 original size:51 final size:46
Alignment explanation
Indices: 27214383--27214557 Score: 278
Period size: 46 Copynumber: 3.7 Consensus size: 46
27214373 AGTGTGCTCT
* *
27214383 CTGATATGAAATGTGTAAGACCATGGTTGAAATATACCACGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
27214429 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
*
27214475 TTGATATGAAATGAAATGGGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATG---T--GTAAGACCATGGTTGAAAGATACCATGGCAGC
27214526 CTGATATGAAATGTGTAAGACCATGGTTGAAA
1 CTGATATGAAATGTGTAAGACCATGGTTGAAA
27214558 CCTGATATAA
Statistics
Matches: 120, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
46 74 0.62
48 1 0.01
49 1 0.01
51 44 0.37
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.25
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
Found at i:27214564 original size:33 final size:33
Alignment explanation
Indices: 27214525--27214590 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
27214515 ACCATGGCAG
*
27214525 CCTGATATGAAATGTGTAAGACCATGGTTGAAA
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAA
27214558 CCTGATATAAAATGTGTAAGACCATGGTTGAAA
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAA
27214591 GATACCATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (33 bp):
CCTGATATAAAATGTGTAAGACCATGGTTGAAA
Found at i:27214584 original size:79 final size:79
Alignment explanation
Indices: 27214488--27214636 Score: 244
Period size: 79 Copynumber: 1.9 Consensus size: 79
27214478 ATATGAAATG
* ***
27214488 AAATGGGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATGTGTAAGACCATGGT
1 AAATGGGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAACAAGACCATGGT
27214553 TGAAACCTGATATA
66 TGAAACCTGATATA
* *
27214567 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAGACCATGGT
1 AAATGGGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAACAAGACCATGGT
27214632 TGAAA
66 TGAAA
27214637 GATACCATGG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (79 bp):
AAATGGGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAACAAGACCATGGT
TGAAACCTGATATA
Found at i:27214617 original size:46 final size:46
Alignment explanation
Indices: 27214560--27214684 Score: 162
Period size: 46 Copynumber: 2.7 Consensus size: 46
27214550 GGTTGAAACC
* * *
27214560 TGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
** *
27214606 TGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGTAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
**
27214652 TGATA-GAAAATGAGTAAGACCACAGTTGAAAGA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGA
27214685 CACTATAGCA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 1 0.01
46 67 0.99
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:27214680 original size:125 final size:127
Alignment explanation
Indices: 27214428--27214682 Score: 363
Period size: 130 Copynumber: 2.0 Consensus size: 127
27214418 ACCACGGCAG
* * *
27214428 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCTTGATATGAAATGAAATG
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAAA--
* * * * **
27214493 GGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATGTGTAAGACCATGGTTGAAA
64 -GCAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGAGTAAGACCACAGTTGAAA
27214558 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATG-AA-C
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAAAGC
*
27214621 AAGACCATGGTTGAAAGATACCATGGTAACATGATA-GAAAATGAGTAAGACCACAGTTGAAA
66 AAGACCATGGTTGAAAGATACCATGGCAACATGATATG-AAATGAGTAAGACCACAGTTGAAA
27214683 GACACTATAG
Statistics
Matches: 114, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
124 1 0.01
125 54 0.47
129 2 0.02
130 57 0.50
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.23
Consensus pattern (127 bp):
CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAAAGC
AAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGAGTAAGACCACAGTTGAAA
Found at i:27215346 original size:15 final size:15
Alignment explanation
Indices: 27215328--27215358 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27215318 GAAAAATAAA
27215328 TAGATAAATAAAAAT
1 TAGATAAATAAAAAT
*
27215343 TAGATAAATAATAAT
1 TAGATAAATAAAAAT
27215358 T
1 T
27215359 GTATTAGAAT
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:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
TAGATAAATAAAAAT
Found at i:27216399 original size:9 final size:9
Alignment explanation
Indices: 27216385--27216449 Score: 60
Period size: 9 Copynumber: 7.0 Consensus size: 9
27216375 CAATAATATC
27216385 TTATAATTT
1 TTATAATTT
27216394 TTATAATTT
1 TTATAATTT
27216403 TTATAATATT
1 TTATAAT-TT
* *
27216413 CTATTATTT
1 TTATAATTT
*
27216422 TCA-AATTT
1 TTATAATTT
27216430 TTATATGATTT
1 TTATA--ATTT
*
27216441 TAATAATTT
1 TTATAATTT
27216450 ATAGACTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
8 6 0.13
9 24 0.53
10 7 0.16
11 8 0.18
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (9 bp):
TTATAATTT
Found at i:27216408 original size:18 final size:18
Alignment explanation
Indices: 27216385--27216449 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
27216375 CAATAATATC
27216385 TTATAATTTTTATAATTT
1 TTATAATTTTTATAATTT
* *
27216403 TTATAATATTCTATTATTT
1 TTATAAT-TTTTATAATTT
*
27216422 TCA-AATTTTTATATGATTT
1 TTATAATTTTTATA--ATTT
*
27216441 TAATAATTT
1 TTATAATTT
27216450 ATAGACTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.14
18 10 0.27
19 17 0.46
20 5 0.14
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATAATTTTTATAATTT
Found at i:27216409 original size:28 final size:27
Alignment explanation
Indices: 27216377--27216434 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
27216367 TATTTTCACA
*
27216377 ATAATA-TCTTATAATTTTTATAATTTTT
1 ATAATATTC-TATAATTTTCA-AATTTTT
*
27216405 ATAATATTCTATTATTTTCAAATTTTT
1 ATAATATTCTATAATTTTCAAATTTTT
27216432 ATA
1 ATA
27216435 TGATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 10 0.37
28 15 0.56
29 2 0.07
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (27 bp):
ATAATATTCTATAATTTTCAAATTTTT
Found at i:27219961 original size:27 final size:27
Alignment explanation
Indices: 27219922--27219973 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
27219912 TTTAGGTTAG
* *
27219922 AAAATGAAAAAAAAGTAAGGAAAAAAT
1 AAAAAGAAAAAAAAGTAAAGAAAAAAT
* *
27219949 AAAAAGAACAAAAATTAAAGAAAAA
1 AAAAAGAAAAAAAAGTAAAGAAAAA
27219974 GAAATTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.10
Consensus pattern (27 bp):
AAAAAGAAAAAAAAGTAAAGAAAAAAT
Found at i:27219978 original size:15 final size:14
Alignment explanation
Indices: 27219927--27219982 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
27219917 GTTAGAAAAT
* *
27219927 GAAAAAAAAGTAAG
1 GAAAAAAAATTAAA
27219941 GAAAAAATAA--AAA
1 GAAAAAA-AATTAAA
*
27219954 GAACAAAAATTAAA
1 GAAAAAAAATTAAA
27219968 GAAAAAGAAATTAAA
1 GAAAAA-AAATTAAA
27219983 AAAGAAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
12 2 0.06
13 8 0.23
14 15 0.43
15 10 0.29
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.11
Consensus pattern (14 bp):
GAAAAAAAATTAAA
Found at i:27220627 original size:53 final size:53
Alignment explanation
Indices: 27220542--27220650 Score: 173
Period size: 53 Copynumber: 2.1 Consensus size: 53
27220532 GTAAAATTGG
*
27220542 TCTGTTTATTGGTTAGTGAACAATAGAACCCGGCAAACCTTTTCATTTTCCTA
1 TCTGTTTATTCGTTAGTGAACAATAGAACCCGGCAAACCTTTTCATTTTCCTA
* * * *
27220595 TCTGTTTGTTCGTTAGTGAACAATAGAGCCCGGCATACCTTTTGATTTTCCTA
1 TCTGTTTATTCGTTAGTGAACAATAGAACCCGGCAAACCTTTTCATTTTCCTA
27220648 TCT
1 TCT
27220651 TCTCAGATCC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (53 bp):
TCTGTTTATTCGTTAGTGAACAATAGAACCCGGCAAACCTTTTCATTTTCCTA
Found at i:27229338 original size:19 final size:18
Alignment explanation
Indices: 27229316--27229355 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
27229306 TGAATAAAAC
27229316 TTATCTATCC-AAATAAGAT
1 TTATCTA-CCTAAATAA-AT
27229335 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
27229353 TTA
1 TTA
27229356 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:27233992 original size:43 final size:44
Alignment explanation
Indices: 27233931--27234023 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
27233921 TCCTAATTGG
27233931 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
27233974 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
27234018 -AAAATA
1 GAAAATA
27234024 TTTCTAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:27234067 original size:19 final size:18
Alignment explanation
Indices: 27234045--27234084 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
27234035 TGAATAAAAC
27234045 TTATCTATCC-AAATAAGAT
1 TTATCTA-CCTAAATAA-AT
27234064 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
27234082 TTA
1 TTA
27234085 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:27237102 original size:39 final size:39
Alignment explanation
Indices: 27237055--27237129 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
27237045 CTAGCTTCGA
* * *
27237055 TTTTGTTTTCAAGGATTCTAGTTTTGATTTGATAGCTTT
1 TTTTGTTTTCAAAGATTCGAGTTTTGATTCGATAGCTTT
*
27237094 TTTTGTTTTCAAAGTTTCGAGTTTTGATTCGATAGC
1 TTTTGTTTTCAAAGATTCGAGTTTTGATTCGATAGC
27237130 ATTTGAGTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.19, C:0.09, G:0.19, T:0.53
Consensus pattern (39 bp):
TTTTGTTTTCAAAGATTCGAGTTTTGATTCGATAGCTTT
Found at i:27238775 original size:30 final size:30
Alignment explanation
Indices: 27238720--27238777 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
27238710 AATTCAGCTG
*
27238720 AAAATTAAAAATTTAGTTGCTCTATTTTTT
1 AAAATTAAAAATTTAGGTGCTCTATTTTTT
*
27238750 AAAATTTAAAATTTAGGT-CTACTATTTT
1 AAAATTAAAAATTTAGGTGCT-CTATTTT
27238778 AACATTGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (30 bp):
AAAATTAAAAATTTAGGTGCTCTATTTTTT
Found at i:27242236 original size:29 final size:29
Alignment explanation
Indices: 27242203--27242282 Score: 124
Period size: 29 Copynumber: 2.8 Consensus size: 29
27242193 TTCAAATCTG
* *
27242203 AAAAGTAGAAGGATTAAATTCTTGAAAAT
1 AAAAGTACAAGGACTAAATTCTTGAAAAT
*
27242232 AAAAGTACAAGAACTAAATTCTTGAAAAT
1 AAAAGTACAAGGACTAAATTCTTGAAAAT
*
27242261 AAAAATACAAGGACTAAATTCT
1 AAAAGTACAAGGACTAAATTCT
27242283 AAATTTGTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (29 bp):
AAAAGTACAAGGACTAAATTCTTGAAAAT
Found at i:27245165 original size:14 final size:14
Alignment explanation
Indices: 27245136--27245173 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
27245126 GAGTTCTGAA
*
27245136 TTTAGAATTT-GAG
1 TTTAAAATTTAGAG
*
27245149 TTTAAATTTTAGAG
1 TTTAAAATTTAGAG
27245163 TTTAAAATTTA
1 TTTAAAATTTA
27245174 TAATTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TTTAAAATTTAGAG
Found at i:27250443 original size:15 final size:15
Alignment explanation
Indices: 27250420--27250455 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27250410 GTTCCAAATG
*
27250420 TTGCAACAAGTTCTA
1 TTGCTACAAGTTCTA
*
27250435 TTGCTACAAGTTCTG
1 TTGCTACAAGTTCTA
27250450 TTGCTA
1 TTGCTA
27250456 AATTGTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (15 bp):
TTGCTACAAGTTCTA
Found at i:27252966 original size:36 final size:36
Alignment explanation
Indices: 27252919--27252990 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
27252909 GAGTGAGACA
27252919 TTGAATGTGATGGAAAAGGTGTAGTGGAGGTAGGTG
1 TTGAATGTGATGGAAAAGGTGTAGTGGAGGTAGGTG
* *
27252955 TTGAATGTGATGGGATAGGTGTAGTGGAGGTAGGTG
1 TTGAATGTGATGGAAAAGGTGTAGTGGAGGTAGGTG
27252991 GCGTATTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.00, G:0.46, T:0.29
Consensus pattern (36 bp):
TTGAATGTGATGGAAAAGGTGTAGTGGAGGTAGGTG
Found at i:27256253 original size:48 final size:48
Alignment explanation
Indices: 27256199--27256296 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
27256189 AGGGATCGAG
27256199 ACACAATACAATATGAAGACACAAAATTTATTTATATGATAAATATGA
1 ACACAATACAATATGAAGACACAAAATTTATTTATATGATAAATATGA
27256247 ACACAATACAATATGAAGACACAAAATTTATTTATATGATAAATATGA
1 ACACAATACAATATGAAGACACAAAATTTATTTATATGATAAATATGA
27256295 AC
1 AC
27256297 TAATCCAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.29
Consensus pattern (48 bp):
ACACAATACAATATGAAGACACAAAATTTATTTATATGATAAATATGA
Found at i:27279549 original size:32 final size:32
Alignment explanation
Indices: 27279513--27279578 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
27279503 GTTAAACAAT
27279513 TTAGTTTCAAATTGTTCATATGAATTCTTAAC
1 TTAGTTTCAAATTGTTCATATGAATTCTTAAC
27279545 TTAGTTTCAAATTGTTCATATGAATTCTTAAC
1 TTAGTTTCAAATTGTTCATATGAATTCTTAAC
27279577 TT
1 TT
27279579 TGACATAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (32 bp):
TTAGTTTCAAATTGTTCATATGAATTCTTAAC
Found at i:27279727 original size:86 final size:86
Alignment explanation
Indices: 27279616--27279790 Score: 296
Period size: 86 Copynumber: 2.0 Consensus size: 86
27279606 TTAGTGAACA
* ** *
27279616 AATTTACAGCGTTTCTTGCCTTGCTTCTCCTCATGTAGTTCTTACTTCCCTGATTTTGTTTTGAC
1 AATTTACAGCGCTTCTCCCCCTGCTTCTCCTCATGTAGTTCTTACTTCCCTGATTTTGTTTTGAC
27279681 TTAGAAATGATTACAAGACCT
66 TTAGAAATGATTACAAGACCT
27279702 AATTTACAGCGCTTCTCCCCCTGCTTCTCCTCATGTAGTTCTTACTTCCCTGATTTTGTTTTGAC
1 AATTTACAGCGCTTCTCCCCCTGCTTCTCCTCATGTAGTTCTTACTTCCCTGATTTTGTTTTGAC
* *
27279767 TTAGTAATGATTACATGACCT
66 TTAGAAATGATTACAAGACCT
27279788 AAT
1 AAT
27279791 GTTTGGTTGC
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (86 bp):
AATTTACAGCGCTTCTCCCCCTGCTTCTCCTCATGTAGTTCTTACTTCCCTGATTTTGTTTTGAC
TTAGAAATGATTACAAGACCT
Found at i:27286926 original size:27 final size:27
Alignment explanation
Indices: 27286891--27286942 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
27286881 TTATTTTTGA
* *
27286891 ACTATCCTAATATATACAATGATTTAG
1 ACTAGCCTAATATATACAATAATTTAG
* *
27286918 ACTAGCCTATTATATATAATAATTT
1 ACTAGCCTAATATATACAATAATTT
27286943 GCTTTTAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (27 bp):
ACTAGCCTAATATATACAATAATTTAG
Found at i:27297642 original size:14 final size:14
Alignment explanation
Indices: 27297623--27297653 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27297613 TGCTACTATT
27297623 TTACTATTATGTTG
1 TTACTATTATGTTG
*
27297637 TTACTATTTTGTTG
1 TTACTATTATGTTG
27297651 TTA
1 TTA
27297654 TTGTTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:27297697 original size:17 final size:17
Alignment explanation
Indices: 27297675--27297707 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27297665 TTATATAAAA
27297675 TTTATT-TTATTGTTAAT
1 TTTATTATTATT-TTAAT
27297692 TTTATTATTATTTTAA
1 TTTATTATTATTTTAA
27297708 AGACATTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTATTATTATTTTAAT
Found at i:27297724 original size:30 final size:30
Alignment explanation
Indices: 27297688--27297748 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
27297678 ATTTTATTGT
27297688 TAATTTTATTATTATTTTAAAGACATTTGC
1 TAATTTTATTATTATTTTAAAGACATTTGC
* * *
27297718 TAATTTTGTTATTATTTTAGAGGCATTTGC
1 TAATTTTATTATTATTTTAAAGACATTTGC
27297748 T
1 T
27297749 TGTTAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (30 bp):
TAATTTTATTATTATTTTAAAGACATTTGC
Found at i:27299451 original size:11 final size:11
Alignment explanation
Indices: 27299437--27299475 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
27299427 TTTTTGTCAC
*
27299437 TATTTTGCTAT
1 TATTTTGTTAT
*
27299448 TATTTTATTAT
1 TATTTTGTTAT
*
27299459 TATGTTGTTAT
1 TATTTTGTTAT
27299470 TATTTT
1 TATTTT
27299476 ATTGTTAATG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.69
Consensus pattern (11 bp):
TATTTTGTTAT
Found at i:27303030 original size:18 final size:18
Alignment explanation
Indices: 27302996--27303030 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27302986 TTGTTAATTT
* *
27302996 GATAAAAGTTTTGTATTA
1 GATAAAAGTTATATATTA
27303014 GATAAAAGTTATATATT
1 GATAAAAGTTATATATT
27303031 TTGATACTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (18 bp):
GATAAAAGTTATATATTA
Found at i:27308368 original size:22 final size:22
Alignment explanation
Indices: 27308343--27308394 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
27308333 TCAAACTCAA
*
27308343 GACTTGAATTACTT-ATTCGATT
1 GACTTGAATGACTTGA-TCGATT
**
27308365 GACTCAAATGACTTGATCGATT
1 GACTTGAATGACTTGATCGATT
*
27308387 AACTTGAA
1 GACTTGAA
27308395 ATTCAAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (22 bp):
GACTTGAATGACTTGATCGATT
Found at i:27311192 original size:20 final size:20
Alignment explanation
Indices: 27311154--27311192 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
27311144 TTAAAATTAA
*
27311154 AATTAAAGAAGATATAATTT
1 AATTAAAGAAAATATAATTT
27311174 AATTAAATGAAAATA-AATT
1 AATTAAA-GAAAATATAATT
27311193 ACTTATTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
AATTAAAGAAAATATAATTT
Found at i:27313066 original size:18 final size:18
Alignment explanation
Indices: 27313043--27313082 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
27313033 CGAATAATAT
27313043 AATAAACATATTTA-AAAA
1 AATAAA-ATATTTATAAAA
27313061 AAT-AAATATTTATAAAA
1 AATAAAATATTTATAAAA
27313078 AATAA
1 AATAA
27313083 TTTAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAAATATTTATAAAA
Found at i:27313071 original size:16 final size:17
Alignment explanation
Indices: 27313050--27313082 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27313040 TATAATAAAC
27313050 ATATTTA-AAAAAATAA
1 ATATTTATAAAAAATAA
27313066 ATATTTATAAAAAATAA
1 ATATTTATAAAAAATAA
27313083 TTTAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATTTATAAAAAATAA
Found at i:27314568 original size:20 final size:20
Alignment explanation
Indices: 27314500--27314569 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
27314490 AAATTGAGCT
*
27314500 TTCTTAAATAAATTGTTAAAAA
1 TTCTAAAAT-AATT-TTAAAAA
** * *
27314522 AACTAAAATAATTTTTAAAT
1 TTCTAAAATAATTTTAAAAA
27314542 TTC-AAAAT-ATTTATAAAAA
1 TTCTAAAATAATTT-TAAAAA
27314561 TTCTAAAAT
1 TTCTAAAAT
27314570 TTATATTTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 4 0.11
19 12 0.32
20 11 0.30
21 4 0.11
22 6 0.16
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (20 bp):
TTCTAAAATAATTTTAAAAA
Found at i:27322156 original size:20 final size:20
Alignment explanation
Indices: 27322131--27322171 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
27322121 CTTAAGGCAC
*
27322131 TAGACTCAACATGTTTCTTT
1 TAGACTCAACATGTTTATTT
27322151 TAGACTCAACATGTTTATTT
1 TAGACTCAACATGTTTATTT
27322171 T
1 T
27322172 CTCTCTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (20 bp):
TAGACTCAACATGTTTATTT
Found at i:27322543 original size:17 final size:17
Alignment explanation
Indices: 27322523--27322557 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
27322513 GAATTATTTG
27322523 TTAAAAATTA-ATAATAT
1 TTAAAAA-TACATAATAT
27322540 TTAAAAATACATAATAT
1 TTAAAAATACATAATAT
27322557 T
1 T
27322558 ACTTAGATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATACATAATAT
Found at i:27323594 original size:3 final size:3
Alignment explanation
Indices: 27323588--27323619 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
27323578 AAACTTTAGT
27323588 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
27323620 GCAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27335162 original size:33 final size:33
Alignment explanation
Indices: 27335120--27335185 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
27335110 AAATTGAGAC
* *
27335120 AAGATGAGAGAGAAAGTCAACCTTGGAAGCTAT
1 AAGATGAGAGAGAAAATCAACCATGGAAGCTAT
27335153 AAGATGAGAGAGAAAATCAACCATGGAAGCTAT
1 AAGATGAGAGAGAAAATCAACCATGGAAGCTAT
27335186 CTTTCAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.26, T:0.17
Consensus pattern (33 bp):
AAGATGAGAGAGAAAATCAACCATGGAAGCTAT
Found at i:27338005 original size:14 final size:14
Alignment explanation
Indices: 27337986--27338015 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27337976 CTTCACTTTA
*
27337986 TATTCATCTCTCAT
1 TATTCATCACTCAT
27338000 TATTCATCACTCAT
1 TATTCATCACTCAT
27338014 TA
1 TA
27338016 CTATAACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTCATCACTCAT
Found at i:27338960 original size:6 final size:6
Alignment explanation
Indices: 27338951--27338979 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
27338941 GGAACAGGGT
27338951 CAGAGA CAGAGA CAGAGA CAGAGA CAGAG
1 CAGAGA CAGAGA CAGAGA CAGAGA CAGAG
27338980 TGATTGACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.34, T:0.00
Consensus pattern (6 bp):
CAGAGA
Found at i:27339380 original size:43 final size:43
Alignment explanation
Indices: 27339332--27339418 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
27339322 TAATAAATGG
27339332 TATTAATTTTTTAATGTAGTTTAGTGATGACATGCAACGTTGA
1 TATTAATTTTTTAATGTAGTTTAGTGATGACATGCAACGTTGA
* *
27339375 TATTAATTTTTTAATGTGGTTTAGTGATGACATGCGACGTTGA
1 TATTAATTTTTTAATGTAGTTTAGTGATGACATGCAACGTTGA
27339418 T
1 T
27339419 GACATCAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (43 bp):
TATTAATTTTTTAATGTAGTTTAGTGATGACATGCAACGTTGA
Found at i:27343139 original size:30 final size:32
Alignment explanation
Indices: 27343103--27343171 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
27343093 TACTTTCAGT
* *
27343103 TCAGTCACTCAACTTTCTT-AAAA-TAACAAA
1 TCAGTCACTCAACGTTATTGAAAATTAACAAA
* *
27343133 TCAGTCA-TTAACGTTATTGAAAATTGACAAA
1 TCAGTCACTCAACGTTATTGAAAATTAACAAA
27343164 TCAGTCAC
1 TCAGTCAC
27343172 CCATAAACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 8 0.25
30 11 0.34
31 13 0.41
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (32 bp):
TCAGTCACTCAACGTTATTGAAAATTAACAAA
Done.