Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1836
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1164857
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 152653 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:726761 original size:19 final size:20
Alignment explanation
Indices: 726734--726791 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
726724 CACAGGTAAC
726734 TCACTACACAGCAGGTAAGA
1 TCACTACACAGCAGGTAAGA
* * * *
726754 TTAC-ACAC-TCGGGTAA-C
1 TCACTACACAGCAGGTAAGA
726771 TCACTACACAGCAGGTAAGA
1 TCACTACACAGCAGGTAAGA
726791 T
1 T
726792 ACGCAGGTAA
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
17 3 0.11
18 10 0.37
19 10 0.37
20 4 0.15
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
TCACTACACAGCAGGTAAGA
Found at i:729262 original size:19 final size:19
Alignment explanation
Indices: 729238--729335 Score: 178
Period size: 19 Copynumber: 5.2 Consensus size: 19
729228 AGTTTTAGTT
*
729238 ATTGTCAGTGGTTGTATAC
1 ATTGTCAGTGATTGTATAC
729257 ATTGTCAGTGATTGTATAC
1 ATTGTCAGTGATTGTATAC
729276 ATTGTCAGTGATTGTATAC
1 ATTGTCAGTGATTGTATAC
729295 ATTGTCAGTGATTGTATAC
1 ATTGTCAGTGATTGTATAC
*
729314 ATTGTCAGTGGTTGTATAC
1 ATTGTCAGTGATTGTATAC
729333 ATT
1 ATT
729336 TGGCTGTTGG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 77 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.43
Consensus pattern (19 bp):
ATTGTCAGTGATTGTATAC
Found at i:729993 original size:40 final size:40
Alignment explanation
Indices: 729919--730086 Score: 124
Period size: 40 Copynumber: 4.0 Consensus size: 40
729909 AATAGATGTA
* * *
729919 TATGTACAACACTTACTGTACAATAAAGTAACATCAGATG
1 TATGTACTACACTAACTGTACAATAAAGTTACATCAGATG
*
729959 TATGTACTACACTAACTGTACAATAGA-TCTACATCCATTGTTCATG
1 TATGTACTACACTAACTGTACAATAAAGT-TACAT-CA--G---ATG
* * * *
730005 TGTCTACTACACTAACTGTACAATAAAGTTACATTAGGTG
1 TATGTACTACACTAACTGTACAATAAAGTTACATCAGATG
* * * * * *
730045 TGTGT-CATGCACTAACTTTACAATAGATTTACATGAGATG
1 TATGTAC-TACACTAACTGTACAATAAAGTTACATCAGATG
730085 TA
1 TA
730087 CATGTATGTA
Statistics
Matches: 102, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
39 2 0.02
40 62 0.61
41 2 0.02
43 2 0.02
45 1 0.01
46 32 0.31
47 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.33
Consensus pattern (40 bp):
TATGTACTACACTAACTGTACAATAAAGTTACATCAGATG
Found at i:730099 original size:86 final size:86
Alignment explanation
Indices: 729919--730099 Score: 204
Period size: 86 Copynumber: 2.1 Consensus size: 86
729909 AATAGATGTA
* *
729919 TATGTACAACACTTACTGTACAATAAAGTAACATCAGATGTATGTACTACACTAACTGTACAATA
1 TATGTACTACACTAACTGTACAATAAAGTAACATCAGATGTATGTACTACACTAACTGTACAATA
* *
729984 GATCTACATCCATTGTTCATG
66 GATCTACATCCAATGTACATG
* * * * * * * *
730005 TGTCTACTACACTAACTGTACAATAAAGTTACATTAGGTGTGTGT-CATGCACTAACTTTACAAT
1 TATGTACTACACTAACTGTACAATAAAGTAACATCAGATGTATGTAC-TACACTAACTGTACAAT
* *
730069 AGATTTACAT-GAGATGTACATG
65 AGATCTACATCCA-ATGTACATG
730091 TATGTACTA
1 TATGTACTA
730100 TATCACCTAT
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
85 2 0.03
86 75 0.97
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (86 bp):
TATGTACTACACTAACTGTACAATAAAGTAACATCAGATGTATGTACTACACTAACTGTACAATA
GATCTACATCCAATGTACATG
Found at i:730402 original size:6 final size:6
Alignment explanation
Indices: 730391--730420 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
730381 GTGTGTTGTC
*
730391 TGTCGT TGTCGT TGTCGT CGTCGT TGTCGT
1 TGTCGT TGTCGT TGTCGT TGTCGT TGTCGT
730421 CGTTAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.20, G:0.33, T:0.47
Consensus pattern (6 bp):
TGTCGT
Found at i:730408 original size:12 final size:12
Alignment explanation
Indices: 730391--730423 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
730381 GTGTGTTGTC
*
730391 TGTCGTTGTCGT
1 TGTCGTCGTCGT
730403 TGTCGTCGTCGT
1 TGTCGTCGTCGT
730415 TGTCGTCGT
1 TGTCGTCGT
730424 TAACTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.33, T:0.45
Consensus pattern (12 bp):
TGTCGTCGTCGT
Found at i:731201 original size:333 final size:332
Alignment explanation
Indices: 730593--731436 Score: 1237
Period size: 333 Copynumber: 2.5 Consensus size: 332
730583 GTTATTTTTC
* * * ** * ***
730593 AAAAATCTTCTTCTCAAAAACTGTTTGGCCTGAAAAGCTAAAACTT-GTGTGGAGGCATCCTCAG
1 AAAAATCTTCTCCTCAAAAACTATTAGGCCACAAAAGCTCAAA-TTAAAATGGA-GCATCCTCAG
* * *
730657 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGAGGGGCCACAAGAAGGGG
64 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGG
* * * *
730722 ATTAAGTTTTACATAGGAATATATAGAGAAAATCTTAAAAAATCTTCTTCTCAAAAACTATTGGG
129 ATGAATTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTCCTCAAAAACTATTGGG
* *
730787 CCACAAAAGCTCAAATTAATATGGAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCA
194 CCACAAAAGCTCAAATTAAAATGGAAGCATCCACAGGTAGTGTAGATTCAAGTTTGTTCAAATCA
* * *
730852 TGATCCCTTGGGGTAGGGGGGGGCCACAATTGGGGGATCAATTTTT-ACATAGGAATATATAGAG
259 TGATCCCTCGGGGTAGGGGGGGGCCACAATAGGGGGATCAATTTTTAAAATAGGAATATATAGAG
730916 AAAATCTTT
324 AAAATCTTT
* *
730925 AAAAATCTTCTCCTCAAAAACTATTGGGCCACAAAAGCTCAAATTAAAATTGGAGCATCCACAGG
1 AAAAATCTTCTCCTCAAAAACTATTAGGCCACAAAAGCTCAAATTAAAA-TGGAGCATCCTCAGG
* *
730990 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGAGGGTAGGGTGGGGCCACAATAGGGGGA
65 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGA
*
731055 TGAATTTTTAAAATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTCCTCAAAAACTATTGGG
130 TGAATTTTT-ACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTCCTCAAAAACTATTGGG
731120 CCACAAAAGCTCAAATTAAAATTGG-AGCATCCACAGGTAGTGTAGATTCAAGTTTGTTCAAATC
194 CCACAAAAGCTCAAATTAAAA-TGGAAGCATCCACAGGTAGTGTAGATTCAAGTTTGTTCAAATC
* * *
731184 ATGGTCCC-CGAGGGTAGGGTGGGGCCACAATAGGGGGATGAATTTTTAAAATAGGAATATATAG
258 ATGATCCCTCG-GGGTAGGGGGGGGCCACAATAGGGGGATCAATTTTTAAAATAGGAATATATAG
731248 AGAAAATCTTT
322 AGAAAATCTTT
* ** * **
731259 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTTAAATTTGAATGGAAGCATCCTCAGG
1 AAAAATCTTCTCCTCAAAAACTATTAGGCCACAAAAGCTCAAATTAAAATGG-AGCATCCTCAGG
* * * *
731324 TAGTGTAGATTCAATTTTTTTTCAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATTGGGGG
65 TAGTGTAGATTCAA-GTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGG
731389 ATGAATTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCT
129 ATGAATTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCT
731437 TNNNNNNNNN
Statistics
Matches: 461, Mismatches: 43, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
331 2 0.00
332 115 0.25
333 157 0.34
334 133 0.29
335 54 0.12
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (332 bp):
AAAAATCTTCTCCTCAAAAACTATTAGGCCACAAAAGCTCAAATTAAAATGGAGCATCCTCAGGT
AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGAT
GAATTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTCCTCAAAAACTATTGGGCC
ACAAAAGCTCAAATTAAAATGGAAGCATCCACAGGTAGTGTAGATTCAAGTTTGTTCAAATCATG
ATCCCTCGGGGTAGGGGGGGGCCACAATAGGGGGATCAATTTTTAAAATAGGAATATATAGAGAA
AATCTTT
Found at i:731437 original size:167 final size:166
Alignment explanation
Indices: 730593--731437 Score: 1237
Period size: 167 Copynumber: 5.1 Consensus size: 166
730583 GTTATTTTTC
* * ** * * *** *
730593 AAAAATCTTCTTCTCAAAAACTGTTTGGCCTGAAAAGCTAAAACTTGTGTGGAGGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTGGGCCACAAAAGCTCAAATTTAAATGGAAGCATCCTCAGG
* * *
730658 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGAGGGGCCACAAGAAGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGA
* * *
730723 TTAAGTTTTACATAGGAATATATAGAGAAAATCTTA
131 TGAATTTTTACATAGGAATATATAGAGAAAATCTTT
730759 AAAAATCTTCTTCTCAAAAACTATTGGGCCACAAAAGCTCAAA-TTAATATGGAAGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTGGGCCACAAAAGCTCAAATTTAA-ATGGAAGCATCCTCAG
* * * *
730823 GTAGTGTAGATTCAAGTTTGTTCAAATCATGATCCCTTGGGGTAGGGGGGGGCCACAATTGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGG
*
730888 ATCAATTTTTACATAGGAATATATAGAGAAAATCTTT
130 ATGAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * *
730925 AAAAATCTTCTCCTCAAAAACTATTGGGCCACAAAAGCTCAAATTAAAATTGG-AGCATCCACAG
1 AAAAATCTTCTTCTCAAAAACTATTGGGCCACAAAAGCTCAAATTTAAA-TGGAAGCATCCTCAG
* *
730989 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGAGGGTAGGGTGGGGCCACAATAGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGG
*
731054 ATGAATTTTTAAAATAGGAATATATAGAGAAAATCTTT
130 ATGAATTTTT-ACATAGGAATATATAGAGAAAATCTTT
* * *
731092 AAAAATCTTCTCCTCAAAAACTATTGGGCCACAAAAGCTCAAATTAAAATTGG-AGCATCCACAG
1 AAAAATCTTCTTCTCAAAAACTATTGGGCCACAAAAGCTCAAATTTAAA-TGGAAGCATCCTCAG
* *
731156 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGAGGGTAGGGTGGGGCCACAATAGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGG
*
731221 ATGAATTTTTAAAATAGGAATATATAGAGAAAATCTTT
130 ATGAATTTTT-ACATAGGAATATATAGAGAAAATCTTT
* ** * *
731259 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTTAAATTTGAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTGGGCCACAAAAGCTCAAATTTAAATGGAAGCATCCTCAGG
* * * *
731324 TAGTGTAGATTCAATTTTTTTTCAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATTGGGGG
66 TAGTGTAGATTCAA-GTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGG
731389 ATGAATTTTTACATAGGAATATATAGAGAAAATCTTT
130 ATGAATTTTTACATAGGAATATATAGAGAAAATCTTT
731426 AAAAATCTTCTT
1 AAAAATCTTCTT
731438 NNNNNNNNNN
Statistics
Matches: 629, Mismatches: 44, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
165 2 0.00
166 269 0.43
167 304 0.48
168 54 0.09
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAAAAACTATTGGGCCACAAAAGCTCAAATTTAAATGGAAGCATCCTCAGG
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGA
TGAATTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:735048 original size:2 final size:2
Alignment explanation
Indices: 735041--735080 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
735031 GACAATTCAC
735041 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
735081 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:743734 original size:13 final size:13
Alignment explanation
Indices: 743710--743743 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
743700 CTTATTTTGA
743710 AAAATTTA-AATC
1 AAAATTTACAATC
743722 AAAATTTACAATC
1 AAAATTTACAATC
743735 AAAATTTAC
1 AAAATTTAC
743744 TTATTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTTACAATC
Found at i:748568 original size:46 final size:46
Alignment explanation
Indices: 748501--748612 Score: 224
Period size: 46 Copynumber: 2.4 Consensus size: 46
748491 NNNNNNNNNN
748501 CTAACGTGCGGGACCAGCACAGTTTGTCCGATATCACATACTCCCA
1 CTAACGTGCGGGACCAGCACAGTTTGTCCGATATCACATACTCCCA
748547 CTAACGTGCGGGACCAGCACAGTTTGTCCGATATCACATACTCCCA
1 CTAACGTGCGGGACCAGCACAGTTTGTCCGATATCACATACTCCCA
748593 CTAACGTGCGGGACCAGCAC
1 CTAACGTGCGGGACCAGCAC
748613 GGAAAGCTCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.20
Consensus pattern (46 bp):
CTAACGTGCGGGACCAGCACAGTTTGTCCGATATCACATACTCCCA
Found at i:749400 original size:24 final size:23
Alignment explanation
Indices: 749372--749418 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
749362 TCTCATAGCG
*
749372 GCTGGTACATTTTAAATCTAAAA
1 GCTGGCACATTTTAAATCTAAAA
749395 NGCTGGCACATTTTAAATCTAAAA
1 -GCTGGCACATTTTAAATCTAAAA
749419 CCTGTTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.32
Consensus pattern (23 bp):
GCTGGCACATTTTAAATCTAAAA
Found at i:753347 original size:23 final size:23
Alignment explanation
Indices: 751975--753340 Score: 2228
Period size: 23 Copynumber: 58.1 Consensus size: 23
751965 ATTAACATTA
* *
751975 TTCATGTAATGTTCTAGCAGTAC
1 TTCATGTAATGTTCTAACAATAC
*
751998 TTTATGTAATGTTCTAACAATACTTC
1 TTCATGTAATGTTCTAACAATA---C
752024 ATGTACATGTAATGTTCTAACAATAC
1 -T-T-CATGTAATGTTCTAACAATAC
*
752050 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752073 TTCATGTACATGTAATGTGCTAACAATAC
1 TTCATGTA-ATG---T-T-CTAACAATAC
752102 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752125 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752148 TTCATGTAATGTTCTAACAATACTTC
1 TTCATGTAATGTTCTAACAATA---C
752174 ATGTACATGTAATGTTCTAACAATAC
1 -T-T-CATGTAATGTTCTAACAATAC
752200 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752223 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752246 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752269 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752292 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752315 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752338 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752361 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752384 TTCATGTAATGTTCTAACAATACTTC
1 TTCATGTAATGTTCTAACAATA---C
752410 ATGTACATGTAATGTTCTAACAATAC
1 -T-T-CATGTAATGTTCTAACAATAC
752436 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752459 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752482 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752505 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752528 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752551 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752574 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752597 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752620 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752643 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752666 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752689 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752712 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752735 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752758 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752781 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752804 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752827 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752850 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752873 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752896 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752919 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752942 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
752965 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
752988 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
753011 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
753034 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
753057 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
753080 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
753103 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
753126 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
753149 TTCATGTACTGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
753172 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
753195 TTCGTGTAATGTTCTAACAATATTTC
1 TTCATGTAATGTTCTAACAATA---C
753221 ATGTACATGTAATGTTCTAACAATAC
1 -T-T-CATGTAATGTTCTAACAATAC
753247 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
753270 TTCATGTAATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
753293 TTCATGTTATGTTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
*
753316 TTCATGTAATATTCTAACAATAC
1 TTCATGTAATGTTCTAACAATAC
753339 TT
1 TT
753341 TGTGTAACTT
Statistics
Matches: 1264, Mismatches: 49, Indels: 60
0.92 0.04 0.04
Matches are distributed among these distances:
23 1135 0.90
24 7 0.01
25 5 0.00
26 8 0.01
27 5 0.00
28 8 0.01
29 96 0.08
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (23 bp):
TTCATGTAATGTTCTAACAATAC
Found at i:769763 original size:29 final size:29
Alignment explanation
Indices: 769713--770478 Score: 1102
Period size: 29 Copynumber: 26.4 Consensus size: 29
769703 TGGTATATTC
** *
769713 ACACTAGCCAGTGGAGGTACTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
* * *
769742 ACACTAGTCAGTAAATGAACTTGATACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
*
769771 ACATTAGCCAGTAAAGGAACTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
*
769800 ACACTAGCCAGTAAAGGAACTTGAAACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
769829 ACACTAGCCAGTAAAGGAACTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
*
769858 ACACTAGCCAGTAAAGGAACTTGAAACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
*
769887 ACACTAGTCAGTAGAA-GAACTTGACACTT
1 ACACTAGCCAGTA-AAGGAACTTGACACTT
*
769916 ACACTAGTCAGTAGAA-GAACTTGACACTT
1 ACACTAGCCAGTA-AAGGAACTTGACACTT
*
769945 ACACTAGTCAGTAGAA-GAACTTGACACTT
1 ACACTAGCCAGTA-AAGGAACTTGACACTT
*
769974 ACACTAGTCAGTAGAA-GAACTTGACACTT
1 ACACTAGCCAGTA-AAGGAACTTGACACTT
* *
770003 ACACTAGTCAGTAGAA-GACCTTGACACTT
1 ACACTAGCCAGTA-AAGGAACTTGACACTT
* * *
770032 ACACTAGTCTGTAGAA-GAAGTTGACACTT
1 ACACTAGCCAGTA-AAGGAACTTGACACTT
* * *
770061 ACACTAGTCAGTAGAA-GATCTTGTCACTT
1 ACACTAGCCAGTA-AAGGAACTTGACACTT
*
770090 ACACTAGCCAGTAAAGGAACCTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
* *
770119 ACACTAGCTAGAAAAGGAACTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
770148 ACACTAGCCAGTAAAGGAACTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
*
770177 ACACTAGCCAGTAAATGAACTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
770206 ACACTAGCCAGTAGAA-GAACTTGACACTT
1 ACACTAGCCAGTA-AAGGAACTTGACACTT
*
770235 ACACTAGCCAGTAAAGGAACTTTACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
*
770264 ACACTAGTCAGTAGAA-GAACTTGACACTT
1 ACACTAGCCAGTA-AAGGAACTTGACACTT
*
770293 ACACTAGCCAGTTAAGGAACTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
*
770322 ACACTAGTCAGTAGAA-GAACTTGACACTT
1 ACACTAGCCAGTA-AAGGAACTTGACACTT
*
770351 ACACTAGCCAGTAAAGGAATTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
770380 ACACTAGCCAGTAAAGGAACTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
770409 ACACTAGCCAGTAAAGGAACTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
770438 ACACTAGCCAGTAAAGGAACTTGACACTT
1 ACACTAGCCAGTAAAGGAACTTGACACTT
770467 ACACTAGCCAGT
1 ACACTAGCCAGT
770479 GGAGGTACTC
Statistics
Matches: 685, Mismatches: 44, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
28 8 0.01
29 669 0.98
30 8 0.01
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (29 bp):
ACACTAGCCAGTAAAGGAACTTGACACTT
Found at i:781313 original size:26 final size:26
Alignment explanation
Indices: 781277--781330 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
781267 ATAACACAAG
*
781277 AAAAATAACCCTGTATACAGTATTTC
1 AAAAATAACCCTGTATAAAGTATTTC
*
781303 AAAAATAACCCTGTGTAAAGTATTTC
1 AAAAATAACCCTGTATAAAGTATTTC
781329 AA
1 AA
781331 TTCATCCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (26 bp):
AAAAATAACCCTGTATAAAGTATTTC
Found at i:781553 original size:14 final size:14
Alignment explanation
Indices: 781534--781565 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
781524 ATGGCAACAT
781534 GAGAGAGAGAGAAA
1 GAGAGAGAGAGAAA
781548 GAGAGAGAGAGAAA
1 GAGAGAGAGAGAAA
781562 GAGA
1 GAGA
781566 CAATTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (14 bp):
GAGAGAGAGAGAAA
Found at i:787769 original size:32 final size:32
Alignment explanation
Indices: 787728--787795 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
787718 CTGCTTATAA
787728 TTGCCAGTTCACAAACCAGCTAAATAAATGAT
1 TTGCCAGTTCACAAACCAGCTAAATAAATGAT
787760 TTGCCAGTTCACAAACCAGCTAAATAAATGAT
1 TTGCCAGTTCACAAACCAGCTAAATAAATGAT
787792 TTGC
1 TTGC
787796 AATCTCTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.26
Consensus pattern (32 bp):
TTGCCAGTTCACAAACCAGCTAAATAAATGAT
Found at i:787994 original size:43 final size:43
Alignment explanation
Indices: 787933--788106 Score: 348
Period size: 43 Copynumber: 4.0 Consensus size: 43
787923 AATTAAAGTA
787933 TACACAATAGATAACTATGGACTGACTCACATGATGGAGTGTC
1 TACACAATAGATAACTATGGACTGACTCACATGATGGAGTGTC
787976 TACACAATAGATAACTATGGACTGACTCACATGATGGAGTGTC
1 TACACAATAGATAACTATGGACTGACTCACATGATGGAGTGTC
788019 TACACAATAGATAACTATGGACTGACTCACATGATGGAGTGTC
1 TACACAATAGATAACTATGGACTGACTCACATGATGGAGTGTC
788062 TACACAATAGATAACTATGGACTGACTCACATGATGGAGTGTC
1 TACACAATAGATAACTATGGACTGACTCACATGATGGAGTGTC
788105 TA
1 TA
788107 AGTTATTTTT
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 131 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (43 bp):
TACACAATAGATAACTATGGACTGACTCACATGATGGAGTGTC
Found at i:788505 original size:14 final size:14
Alignment explanation
Indices: 788486--788526 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
788476 GAGCAAATTT
788486 AGCTATCTATACAA
1 AGCTATCTATACAA
788500 AGCTATCTATACAA
1 AGCTATCTATACAA
788514 AGCTATCTATACA
1 AGCTATCTATACA
788527 GTACTAAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (14 bp):
AGCTATCTATACAA
Found at i:788614 original size:12 final size:12
Alignment explanation
Indices: 788597--788623 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
788587 ATTTTGAACA
788597 TACATGTATATG
1 TACATGTATATG
788609 TACATGTATATG
1 TACATGTATATG
788621 TAC
1 TAC
788624 TATTTAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (12 bp):
TACATGTATATG
Found at i:790752 original size:2 final size:2
Alignment explanation
Indices: 790745--790789 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
790735 AAAACAGAAG
*
790745 GA GA GA GA GT GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
790787 GA G
1 GA G
790790 TTAGATGAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.51, T:0.02
Consensus pattern (2 bp):
GA
Found at i:793381 original size:1 final size:1
Alignment explanation
Indices: 793338--793363 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
793328 GCAAATTGAA
793338 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
793364 ANNNNNNNNG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:796288 original size:2 final size:2
Alignment explanation
Indices: 796281--796324 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
796271 TTATTAGCAT
796281 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
796323 GA
1 GA
796325 TTTTCATTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:798398 original size:25 final size:25
Alignment explanation
Indices: 798369--799625 Score: 1478
Period size: 25 Copynumber: 50.4 Consensus size: 25
798359 TTTTAGATCT
*
798369 ATTGGGATGTATTCACGTACAGATG
1 ATTGGGATGTATTCACGTACTGATG
*
798394 ATTGGGATGTATTCAGGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* * *
798419 ATTGGGATGTATTTACGTACTAAAG
1 ATTGGGATGTATTCACGTACTGATG
*
798444 ATTGGGATGTATTCAGGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* * *
798469 ATTGAGATGTATCCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
798494 ATTGGGATGTATTCATGTACTGATA
1 ATTGGGATGTATTCACGTACTGATG
* * *
798519 ATTGGGATATATTCATGGACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* * *
798544 ATTGAGATGAATTCACGTACTAATG
1 ATTGGGATGTATTCACGTACTGATG
*
798569 ATTGGGATGTATTAACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
798594 ATTGGGATGTATTCATGTATTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
798619 ATTGGGATGTATTTACGTACTGATA
1 ATTGGGATGTATTCACGTACTGATG
*
798644 ATTGGGATGTA-TCAACGTACTGGTG
1 ATTGGGATGTATTC-ACGTACTGATG
* *
798669 ATTGGGATCTATTCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
798694 ATTGGGAAGTATTCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
798719 ATTGGAATGTAATCACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* * *
798744 ATTAAGG-CGTATTCACGTAGTGATG
1 ATT-GGGATGTATTCACGTACTGATG
* * * *
798769 ATTGGGATATTTTCATGTACCGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
798794 ATTGGGATGTATTCACATCCTGATG
1 ATTGGGATGTATTCACGTACTGATG
* * *
798819 ATTGGAATGTATCCAGGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
*
798844 ATTGGGATGTATTCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
798869 ATTGGGCTGTAATCACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
** * *
798894 ATTGAAATGTTTTCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* * * * *
798919 ATTGAGATGTGTACATGCACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* * *
798944 ATTTGGATGTATTCATGCACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
798969 ATTGAGATGTATTCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
798994 ATTGGGATGTATTCACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
799019 ATTGGGATTTATTTACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
799044 ATTGGAATGTATTCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
*
799069 ATTTGGATGTATTCACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
799094 ATTGGGATATATTCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
** *
799119 ATTGGTTTGTATTCACGTACTAATG
1 ATTGGGATGTATTCACGTACTGATG
* *
799144 ATTGAGATGTATTGACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
799169 ATTGGGATGTATCCAGGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
799194 ATTGGGATGT-TTCACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* * *
799218 ATTGAGATGTTTTCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* * *
799243 ATTGAGATGTGTTCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
*
799268 ATTGGGATGTATTCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
799293 ACTGGGATGTATTTACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
*
799318 ATTGGGATGTATTCACGTACTGGTG
1 ATTGGGATGTATTCACGTACTGATG
* * * *
799343 ATTGGAATATATCCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
799368 ATTGGGATGTGTTCAAGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
799393 ATTGGGATGTATTCACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
** *
799418 ATTGAAATGTATTCACGTACTAATG
1 ATTGGGATGTATTCACGTACTGATG
* * *
799443 ATTGAGATGTATTAACGTACTGGTG
1 ATTGGGATGTATTCACGTACTGATG
* * * *
799468 ATTGGAATATATCCATGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
* *
799493 ATTGGGATGTGTTCAAGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
*
799518 ATTGAGATGTATTCACGTACTGATG
1 ATTGGGATGTATTCACGTACTGATG
** *
799543 ATTGGGATGTA-TCATATACTGACG
1 ATTGGGATGTATTCACGTACTGATG
* *
799567 ATTGGGATGTATTCATGTACTGATA
1 ATTGGGATGTATTCACGTACTGATG
* * * *
799592 ATTGAGATGTATCCATGTTCTGATG
1 ATTGGGATGTATTCACGTACTGATG
799617 ATTGGGATG
1 ATTGGGATG
799626 CATCTGTTTA
Statistics
Matches: 1045, Mismatches: 181, Indels: 12
0.84 0.15 0.01
Matches are distributed among these distances:
24 45 0.04
25 997 0.95
26 3 0.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.37
Consensus pattern (25 bp):
ATTGGGATGTATTCACGTACTGATG
Found at i:799719 original size:30 final size:30
Alignment explanation
Indices: 799666--799723 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
799656 ATGAACTGAA
*
799666 TGATGATTGGGATGTATAAGCGAAATGCAC
1 TGATGAATGGGATGTATAAGCGAAATGCAC
* * *
799696 TGATGAATGGGGTGTTTAGGCGAAATGC
1 TGATGAATGGGATGTATAAGCGAAATGC
799724 CATTTTAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.28
Consensus pattern (30 bp):
TGATGAATGGGATGTATAAGCGAAATGCAC
Found at i:805196 original size:35 final size:34
Alignment explanation
Indices: 805149--805272 Score: 104
Period size: 35 Copynumber: 3.6 Consensus size: 34
805139 TATAGCAAAA
* * *
805149 GAGTAGTAAGTATTTGTAACTCATCTCAGGAGATG
1 GAGTAGTGAGTATTTGTAACT-ATATCAGGACATG
* * * * * * *
805184 AAGTAGTGAGTATCTGCAATTTATTTAAGGACAGG
1 GAGTAGTGAGTATTTGTAA-CTATATCAGGACATG
* *
805219 GAGTAGTCAGTATTCGTAAACTATATCAGGACATG
1 GAGTAGTGAGTATTTGT-AACTATATCAGGACATG
*
805254 GAGTAGTGATTATTTGTAA
1 GAGTAGTGAGTATTTGTAA
805273 TTAATGTAAG
Statistics
Matches: 66, Mismatches: 21, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
34 2 0.03
35 61 0.92
36 3 0.05
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (34 bp):
GAGTAGTGAGTATTTGTAACTATATCAGGACATG
Found at i:805262 original size:70 final size:70
Alignment explanation
Indices: 805149--805290 Score: 178
Period size: 70 Copynumber: 2.0 Consensus size: 70
805139 TATAGCAAAA
* * * * *
805149 GAGTAGTAAGTATTTGTAACTCATCTCAGGAGATGAAGTAGTGAGTATCTGCAATTTATTTAAGG
1 GAGTAGTAAGTATTCGTAACTCATATCAGGACATGAAGTAGTGAGTATCTGCAATTAATGTAAGG
805214 ACAGG
66 ACAGG
* * * * *
805219 GAGTAGTCAGTATTCGTAAACT-ATATCAGGACATGGAGTAGTGATTATTTGTAATTAATGTAAG
1 GAGTAGTAAGTATTCGT-AACTCATATCAGGACATGAAGTAGTGAGTATCTGCAATTAATGTAAG
805283 GACAGG
65 GACAGG
805289 GA
1 GA
805291 AAAATTCGAG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
70 57 0.93
71 4 0.07
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (70 bp):
GAGTAGTAAGTATTCGTAACTCATATCAGGACATGAAGTAGTGAGTATCTGCAATTAATGTAAGG
ACAGG
Found at i:809572 original size:2 final size:2
Alignment explanation
Indices: 809565--809592 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
809555 NNNNNNNNNN
809565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
809593 CACACATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:812814 original size:4 final size:4
Alignment explanation
Indices: 812805--812867 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
812795 ATCTTTTCGA
812805 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
812853 CTAT CTAT CTAT CTA
1 CTAT CTAT CTAT CTA
812868 ATCGATACTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.49
Consensus pattern (4 bp):
CTAT
Found at i:816712 original size:11 final size:11
Alignment explanation
Indices: 816696--816725 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
816686 AATAACATAT
816696 ATTTTAGTAGA
1 ATTTTAGTAGA
*
816707 ATTTTAGTAGT
1 ATTTTAGTAGA
816718 ATTTTAGT
1 ATTTTAGT
816726 CTATCAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (11 bp):
ATTTTAGTAGA
Found at i:823803 original size:101 final size:102
Alignment explanation
Indices: 823671--823884 Score: 403
Period size: 101 Copynumber: 2.1 Consensus size: 102
823661 AATCTTGCTG
823671 ATGGATGGGTCGTATAGCCATTGTTTTTCATAGACTAAGGATCTATATGAACGTGTTGCTATACG
1 ATGGATGGGTCG-ATAGCCATTGTTTTTCATAGACTAAGGATCTATATGAACGTGTTGCTATACG
823736 TAGTTACACACATTTACTTATATTGATAAGTCATACCT
65 TAGTTACACACATTTACTTATATTGATAAGTCATACCT
823774 ATGGATGGGTCG-TAGCCATTGTTTTTCATAGACTAAGGATCTATATGAACGTGTTGCTATACGT
1 ATGGATGGGTCGATAGCCATTGTTTTTCATAGACTAAGGATCTATATGAACGTGTTGCTATACGT
823838 AGTTACACACATTTACTTATATTGATAAGTCATACCT
66 AGTTACACACATTTACTTATATTGATAAGTCATACCT
*
823875 ATGGAAGGGT
1 ATGGATGGGT
823885 TGTTACACAC
Statistics
Matches: 110, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
101 98 0.89
103 12 0.11
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (102 bp):
ATGGATGGGTCGATAGCCATTGTTTTTCATAGACTAAGGATCTATATGAACGTGTTGCTATACGT
AGTTACACACATTTACTTATATTGATAAGTCATACCT
Found at i:823908 original size:47 final size:47
Alignment explanation
Indices: 823839--823934 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
823829 GCTATACGTA
823839 GTTACACACATTTACTTATATTGATAAGTCATACCTATGGAAGGGTT
1 GTTACACACATTTACTTATATTGATAAGTCATACCTATGGAAGGGTT
823886 GTTACACACATTTACTTATATTGATAAGTCATACCTATGGAAGGGTT
1 GTTACACACATTTACTTATATTGATAAGTCATACCTATGGAAGGGTT
823933 GT
1 GT
823935 AGCCATTGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (47 bp):
GTTACACACATTTACTTATATTGATAAGTCATACCTATGGAAGGGTT
Found at i:825187 original size:2 final size:2
Alignment explanation
Indices: 825180--825220 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
825170 AGTGATTACA
* * *
825180 AC AC AC AC AC AC AC AC AT GC AC AC GC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
825221 TTCTGATTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.46, G:0.05, T:0.02
Consensus pattern (2 bp):
AC
Found at i:837942 original size:8 final size:8
Alignment explanation
Indices: 837921--837994 Score: 123
Period size: 8 Copynumber: 9.4 Consensus size: 8
837911 GATCACATTT
837921 TGTCCGTC
1 TGTCCGTC
837929 -GTCCGTC
1 TGTCCGTC
837936 TGTCCGTC
1 TGTCCGTC
837944 TGTCCGTC
1 TGTCCGTC
*
837952 CGTCCGTC
1 TGTCCGTC
837960 TGTCCGTC
1 TGTCCGTC
837968 TGTCCGTC
1 TGTCCGTC
837976 TGTCCGTC
1 TGTCCGTC
*
837984 TGCCCGTC
1 TGTCCGTC
837992 TGT
1 TGT
837995 AAACTTTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
7 7 0.11
8 54 0.89
ACGTcount: A:0.00, C:0.39, G:0.26, T:0.35
Consensus pattern (8 bp):
TGTCCGTC
Found at i:837952 original size:4 final size:4
Alignment explanation
Indices: 837922--837983 Score: 72
Period size: 4 Copynumber: 15.8 Consensus size: 4
837912 ATCACATTTT
* * * *
837922 GTCC GT-C GTCC GTCT GTCC GTCT GTCC GTCC GTCC GTCT GTCC GTCT
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
*
837969 GTCC GTCT GTCC GTC
1 GTCC GTCC GTCC GTC
837984 TGCCCGTCTG
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
3 3 0.06
4 44 0.94
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (4 bp):
GTCC
Found at i:839884 original size:166 final size:165
Alignment explanation
Indices: 839501--840423 Score: 1178
Period size: 166 Copynumber: 5.6 Consensus size: 165
839491 AACTACTCCT
* * * * *
839501 GGGGGTAGGGTGGGGCCACAA-TGGAGGGTCGAAGTTTAACATATGAATATAAAAAGTAATTCTT
1 GGGGGTAGGGTGGGGCCACAATTGG-GGATCGAAGTTTAACATAGGAATATATACAGTAAATCTT
* * * * *
839565 TAAAAATCTTCTTCTCAG-AATTAATCGGCCAGGAAAGCTGACACTTGTGTGGATGCATCCTTAG
65 TAAAAATCTTCTTCTCAGAAACTAATC-ACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* *
839629 GTAGTGAAGATTCAAATTTGTGAAAATCATGACCCCC
129 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC
* * * *
839666 GAGGGTAGGGTGGGGCCACAATAGGGGATCGACGTTTTACATAGGAATATATACAGTAAATCTTT
1 GGGGGTAGGGTGGGGCCACAATTGGGGATCGAAGTTTAACATAGGAATATATACAGTAAATCTTT
* * *
839731 AAAAATCTTCTTCTCAGAAACTAATCACCAGGAAAGCTGACACTTGTGTGTATGCATCCTCAGGT
66 AAAAATCTTCTTCTCAGAAACTAATCACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT
* *
839796 AGTGTAAATTTTAAAGTTGTGAAAATCATGACCCCC
131 AGTGTAGA-TTCAAAGTTGTGAAAATCATGACCCCC
*
839832 GGGGGTAGGGCGGGGCCACAATTGGGGATCGAAGTTTAACATAGGAATATATACAGTAAATCTTT
1 GGGGGTAGGGTGGGGCCACAATTGGGGATCGAAGTTTAACATAGGAATATATACAGTAAATCTTT
* *
839897 AAAAATCTTCTTCTCAGAAACTAATTCGCC-GGCAAAGCTGGAACTTGTGTGGAAGCATCCTCAG
66 AAAAATCTTCTTCTCAGAAACTAA-TCACCAGG-AAAGCTGAAACTTGTGTGGAAGCATCCTCAG
*
839961 GTAGTGTAGATTCAAA-TATGTGAAAATCATGACCCCT
129 GTAGTGTAGATTCAAAGT-TGTGAAAATCATGACCCCC
* * * *
839998 GGGGGTAGGTTGGGGCCACAATGGGGGATCGAAGTTTAACATATGATTATATACAGTAAATCTTT
1 GGGGGTAGGGTGGGGCCACAATTGGGGATCGAAGTTTAACATAGGAATATATACAGTAAATCTTT
* * *
840063 AAAAATCTTCTTCTCAGAAACTAATTAGCCAGGAAAGCTAAAACTTGTGTGGAAGCATACTCAGG
66 AAAAATCTTCTTCTCAGAAACTAATCA-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* *
840128 TAGTGTAGATTCAAATTTGTGAAAATCATGACCCCT
130 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC
* * * * * * * * * * *
840164 GGGGGTAGGTTTGGGCCACAA-TGGGAGGTTGATGTTTTACATAGGAATAAACAGAGTTATTCTT
1 GGGGGTAGGGTGGGGCCACAATTGGG-GATCGAAGTTTAACATAGGAATATATACAGTAAATCTT
*
840228 TAAAAATCTTCTTCTCAGAAACTAATCACCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGG
65 TAAAAATCTTCTTCTCAGAAACTAATCACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
** *
840293 TAGTGTAGATTCAAAGTTGTGAAAAAAATGATCCCC
130 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC
* ** * * * * **
840329 AGGGGTAGGGTGGGATCACAATGGGGGGGTCAAAGTTTAACAAAGGAATATATAGGGTAAATCTT
1 GGGGGTAGGGTGGGGCCACAAT-TGGGGATCGAAGTTTAACATAGGAATATATACAGTAAATCTT
840394 TAAAAA---TCTTCTCAGAAACTAATCAGCCAG
65 TAAAAATCTTCTTCTCAGAAACTAATCA-CCAG
840424 ATGATTCTTT
Statistics
Matches: 667, Mismatches: 78, Indels: 27
0.86 0.10 0.03
Matches are distributed among these distances:
163 19 0.03
164 4 0.01
165 198 0.30
166 400 0.60
167 46 0.07
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (165 bp):
GGGGGTAGGGTGGGGCCACAATTGGGGATCGAAGTTTAACATAGGAATATATACAGTAAATCTTT
AAAAATCTTCTTCTCAGAAACTAATCACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT
AGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC
Found at i:841156 original size:1 final size:1
Alignment explanation
Indices: 841145--841181 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
841135 GGTCGGTGGT
*
841145 GGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
841182 CATAAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.03, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:846982 original size:32 final size:32
Alignment explanation
Indices: 846946--847023 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
846936 CATAGTGGGT
*
846946 CAATGCCTGTATTGTTTTACACCATTGTCGGC
1 CAATGCCTGCATTGTTTTACACCATTGTCGGC
**
846978 CAATGCCTGCATTGTTTTACTTCATTGTCGGC
1 CAATGCCTGCATTGTTTTACACCATTGTCGGC
*
847010 CAATGCATGCATTG
1 CAATGCCTGCATTG
847024 GAAGACTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (32 bp):
CAATGCCTGCATTGTTTTACACCATTGTCGGC
Found at i:849318 original size:2 final size:2
Alignment explanation
Indices: 849311--849349 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
849301 NNNNNNNNNN
849311 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
849350 GGGTAGGGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:851314 original size:27 final size:28
Alignment explanation
Indices: 851276--851331 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
851266 ATTTTTAAAT
*
851276 CGGATAAAAAC-GAAGTTTAAC-AAAAAA
1 CGGATAAAAACGGAAATTT-ACGAAAAAA
851303 CGGATAAAAACGGAAATTTACGAAAAAA
1 CGGATAAAAACGGAAATTTACGAAAAAA
851331 C
1 C
851332 TCTAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.14
Consensus pattern (28 bp):
CGGATAAAAACGGAAATTTACGAAAAAA
Found at i:856052 original size:20 final size:20
Alignment explanation
Indices: 856023--856062 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
856013 TTTCAGATGC
* *
856023 TGGAGGAGGTTAAGGTTTTT
1 TGGAGCAGGTTAAAGTTTTT
856043 TGGAGCAGGTTAAAGTTTTT
1 TGGAGCAGGTTAAAGTTTTT
856063 GTTGCAGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.03, G:0.35, T:0.40
Consensus pattern (20 bp):
TGGAGCAGGTTAAAGTTTTT
Found at i:856323 original size:179 final size:179
Alignment explanation
Indices: 856013--856575 Score: 741
Period size: 175 Copynumber: 3.2 Consensus size: 179
856003 GGGTTCTAAA
* * *
856013 TTTCAGATGCTGGAGGAGGTTAAGGTTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTT
1 TTTCAGATGCTGGAGGAGGTTAAGG-TTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTC
** * ** *
856078 TGATAGCA--ATATCTAAG-TA-ACTGCTGGTCCTAACTTCAACAAACTTGCATGGATGGTG-TG
65 TGAT-G-ATTATATCTTGGTTATAATATTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCT-
* **
856138 TCTTATGATACTGATGCACCAGACA-GCTTGAATGCTGAATTTGAGCTGTAGG
127 TCTTATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCCATAGG
*
856190 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
1 TTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
*
856255 GATGATTATATCTTGGTTACTAATATTGGTCTTAACTTCACCAAACTTGCATGGATGGTGCTTCT
66 GATGATTATATCTTGGTTA-TAATATTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCTTCT
* * *
856320 TATGATACTGATGCTCCAGAGAGGCTTGAATGATGAATCTGAGCCATAGG
130 TATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCCATAGG
* * * *
856370 TTTCAGATGCTGGAGGAGGTAAAGCTTTTTAGAACTGGTAAAAG--TTTGTTGCAGGTGCCCTCT
1 TTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * *
856433 GATGATTATATCTTGGTTATCA-CTT-GTCCTAACTTCACCAAACTTGCATGGATGGTGCATCTT
66 GATGATTATATCTTGGTTATAATATTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCTTCTT
* *
856496 ATGATACTGATGCAACTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
131 ATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCCATAGG
* * **
856545 TTTCGGATGCTTGATAAGGTTAAGGTTTTTA
1 TTTCAGATGCTGGAGGAGGTTAAGGTTTTTA
856576 TAACAGGTCT
Statistics
Matches: 342, Mismatches: 37, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
174 1 0.00
175 106 0.31
176 49 0.14
177 28 0.08
178 38 0.11
179 57 0.17
180 63 0.18
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (179 bp):
TTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
GATGATTATATCTTGGTTATAATATTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCTTCTT
ATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCCATAGG
Found at i:857086 original size:20 final size:20
Alignment explanation
Indices: 857039--857087 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
857029 ACATGATTCC
* *
857039 TATGATAAAGTATTGTATAA
1 TATGATACACTATTGTATAA
* *
857059 CATGATACACTATTGTTTAA
1 TATGATACACTATTGTATAA
857079 TATGATACA
1 TATGATACA
857088 ATATGATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (20 bp):
TATGATACACTATTGTATAA
Found at i:857307 original size:20 final size:18
Alignment explanation
Indices: 857278--857331 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
857268 TGATATTGCA
857278 ATATATAATATTGTATCTT
1 ATATA-AATATTGTATCTT
*
857297 ATGATACAATATTGTATATT
1 AT-ATA-AATATTGTATCTT
857317 ATATAAA-ATTGTATC
1 ATATAAATATTGTATC
857332 AAACAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 7 0.23
18 2 0.06
19 5 0.16
20 17 0.55
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (18 bp):
ATATAAATATTGTATCTT
Found at i:858845 original size:15 final size:15
Alignment explanation
Indices: 858827--859006 Score: 60
Period size: 15 Copynumber: 11.2 Consensus size: 15
858817 ATCACATGCA
858827 ATTGTATTATATGAT
1 ATTGTATTATATGAT
*
858842 ATTGTTATATTATATAAT
1 ATTG---TATTATATGAT
* * *
858860 ATAGTATCATATGGT
1 ATTGTATTATATGAT
*
858875 ATTGT-TTAATATAAT
1 ATTGTATT-ATATGAT
* *
858890 ATTGGT-TTTTATCAT
1 ATT-GTATTATATGAT
* *
858905 ATATGATTTTATCCCATGAA
1 AT-TG-TATTAT---ATGAT
858925 ATTGTATTATATGAT
1 ATTGTATTATATGAT
**
858940 ATTGTAAAATAT-ATT
1 ATTGTATTATATGA-T
* *
858955 TTTGTATTATGTGAT
1 ATTGTATTATATGAT
*
858970 ACAATATGTATAATATGAT
1 ---AT-TGTATTATATGAT
* *
858989 ATTATATTATATAAT
1 ATTGTATTATATGAT
859004 ATT
1 ATT
859007 TTACTTTATC
Statistics
Matches: 120, Mismatches: 28, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
14 2 0.02
15 69 0.57
16 9 0.08
17 3 0.03
18 19 0.16
19 13 0.11
20 5 0.04
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.50
Consensus pattern (15 bp):
ATTGTATTATATGAT
Found at i:858878 original size:33 final size:30
Alignment explanation
Indices: 858830--858891 Score: 79
Period size: 33 Copynumber: 2.0 Consensus size: 30
858820 ACATGCAATT
*
858830 GTATTATATGATATTGTTATATTATATAATATA
1 GTATCATATGATATTGTT-TA--ATATAATATA
*
858863 GTATCATATGGTATTGTTTAATATAATAT
1 GTATCATATGATATTGTTTAATATAATAT
858892 TGGTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
32 2 0.07
33 16 0.59
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (30 bp):
GTATCATATGATATTGTTTAATATAATATA
Found at i:860286 original size:20 final size:20
Alignment explanation
Indices: 860263--860333 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
860253 CTTATGTTAC
* *
860263 AATATTATAATGTATTATGT
1 AATATTATATTGTATTATAT
* * *
860283 AATATGATATTGTGTCATAT
1 AATATTATATTGTATTATAT
*
860303 AATAATATATTGTATTATAT
1 AATATTATATTGTATTATAT
* *
860323 ATTAATATATT
1 AATATTATATT
860334 ATGATATTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.49
Consensus pattern (20 bp):
AATATTATATTGTATTATAT
Found at i:860663 original size:16 final size:16
Alignment explanation
Indices: 860642--860676 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
860632 TTAAGGTGGT
860642 CTCATACAA-GTGATGC
1 CTCATA-AAGGTGATGC
860658 CTCATAAAGGTGATGC
1 CTCATAAAGGTGATGC
860674 CTC
1 CTC
860677 GTCTCGGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (16 bp):
CTCATAAAGGTGATGC
Found at i:870435 original size:16 final size:16
Alignment explanation
Indices: 870414--870460 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
870404 CAAATTATGT
870414 TGTGTATTTGATGCAA
1 TGTGTATTTGATGCAA
870430 TGTGTATTTGATGCAA
1 TGTGTATTTGATGCAA
870446 TGTGTATTTGATGCA
1 TGTGTATTTGATGCA
870461 TACCCTGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (16 bp):
TGTGTATTTGATGCAA
Found at i:871953 original size:21 final size:21
Alignment explanation
Indices: 871927--871999 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
871917 GGTGAGTGAC
* *
871927 CATCACTAATTAAATTGATTA
1 CATCACTGATTACATTGATTA
*
871948 CATCACTGATTACATTGAATA
1 CATCACTGATTACATTGATTA
*
871969 CATAACTGATTACATTGATTA
1 CATCACTGATTACATTGATTA
*
871990 CATAACTGAT
1 CATCACTGAT
872000 ATCATGGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (21 bp):
CATCACTGATTACATTGATTA
Found at i:871959 original size:12 final size:11
Alignment explanation
Indices: 871942--871999 Score: 52
Period size: 12 Copynumber: 5.4 Consensus size: 11
871932 CTAATTAAAT
871942 TGATTACATCAC
1 TGATTACAT-AC
871954 TGATTACAT--
1 TGATTACATAC
*
871963 TGAATACATAAC
1 TGATTACAT-AC
871975 TGATTACAT--
1 TGATTACATAC
871984 TGATTACATAAC
1 TGATTACAT-AC
871996 TGAT
1 TGAT
872000 ATCATGGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
9 17 0.45
12 21 0.55
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (11 bp):
TGATTACATAC
Found at i:872010 original size:21 final size:21
Alignment explanation
Indices: 871935--871999 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
871925 ACCATCACTA
* *
871935 ATTAAATTGATTACATCACTG
1 ATTACATTGATTACATAACTG
*
871956 ATTACATTGAATACATAACTG
1 ATTACATTGATTACATAACTG
871977 ATTACATTGATTACATAACTG
1 ATTACATTGATTACATAACTG
871998 AT
1 AT
872000 ATCATGGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (21 bp):
ATTACATTGATTACATAACTG
Found at i:875347 original size:154 final size:152
Alignment explanation
Indices: 875059--875365 Score: 343
Period size: 154 Copynumber: 2.0 Consensus size: 152
875049 AAATTTGTTC
* * *
875059 AAATCATGATCCCTAGGGGTAGGGTGGGGCCACAAAGTGGGGCAAATGTTTACATAGGATTATAT
1 AAATCATGATCCCCAGGGGTAGGGTGGGGCCACAAAGTAGGGCAAATGTTTACATAGGAATATAT
* * * * * *
875124 AGAGAAAAATTTTAAACCATCTTTTTCTCCAAAACTGATAATCCAGAAAAACTGTAACTTTTTTG
66 AGAGAAAAATTTTAAACAATCTTCTTCTCCAAAACTGATAATCCAGAAAAACTGAAACTTATGTA
875189 GAAGCATCCTCAAAGTAGGGTAG
131 GAAGCATCCTC-AAGTAGGGTAG
* * * * * * *
875212 AAATCATGATCCCCAGGGGTAGGGTGGGGTCACAACTGTAGGTCAAATTTTTCCCTATGAATATA
1 AAATCATGATCCCCAGGGGTAGGGTGGGGCCACAA-AGTAGGGCAAATGTTTACATAGGAATATA
* ** *
875277 TTA-AGAAAAATCTTTAAA-AATCTTCTTCT-CAGAAAGTG-TTTTACCAGAAAAGCTGAAACTT
65 -TAGAGAAAAAT-TTTAAACAATCTTCTTCTCCA-AAACTGATAAT-CCAGAAAAACTGAAACTT
*
875338 ATGTAGAAGCATCCTCAGGTAGGGTAG
126 ATGTAGAAGCATCCTCAAGTAGGGTAG
875365 A
1 A
875366 TTCAAGTTTG
Statistics
Matches: 128, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
153 48 0.38
154 72 0.56
155 8 0.06
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (152 bp):
AAATCATGATCCCCAGGGGTAGGGTGGGGCCACAAAGTAGGGCAAATGTTTACATAGGAATATAT
AGAGAAAAATTTTAAACAATCTTCTTCTCCAAAACTGATAATCCAGAAAAACTGAAACTTATGTA
GAAGCATCCTCAAGTAGGGTAG
Found at i:877584 original size:178 final size:180
Alignment explanation
Indices: 877123--877666 Score: 943
Period size: 180 Copynumber: 3.0 Consensus size: 180
877113 GGCTGCCAAA
877123 AGGGTACCCTTATTGTACAGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTTATTGTACAGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
* *
877188 GATCAATTGTACTTATATTAGAGGTGT-CTATATTGCTAGGATTTTGATTTCTGATAATTTATGA
66 GATCAATTGTACATATATCAGAGGTGTGC-ATATTGCTAGGATTTTGATTTCTGATAATTTATGA
* *
877252 AAAAAATACCAGCTTTTGAACTTGGTCATTTTTTGGCAAAATATTGCATAA
130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
877303 AGGGTACCCTTATTGTACAGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTTATTGTACAGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
*
877368 GATCAATTGAACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA
877433 AAAAATACCAGCTTTTGAACTTAGTCA-TTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
* * * *
877482 AGGGTACCCTCATTGTACGGATAACT-CTCCTACAGTTCTCAAGATAGGAAGTTATTCTTTTGCA
1 AGGGTACCCTTATTGTACAGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
* * *
877546 GATCAATTGTTCATATATCAGAGGTGTGCATTTTGCTAGGATTTTGATTTCTGATAATTAATG-A
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA
877610 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
877660 AGGGTAC
1 AGGGTAC
877667 TCCATTTCAC
Statistics
Matches: 349, Mismatches: 13, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
177 28 0.08
178 124 0.36
179 45 0.13
180 151 0.43
181 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (180 bp):
AGGGTACCCTTATTGTACAGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA
AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:882759 original size:21 final size:22
Alignment explanation
Indices: 882733--882817 Score: 140
Period size: 21 Copynumber: 4.0 Consensus size: 22
882723 TGCGTCTTTT
*
882733 TACCCCAGTGA-ACCCCAATGA
1 TACCCCAATGATACCCCAATGA
882754 TACCCCAATGA-ACCCCAATGA
1 TACCCCAATGATACCCCAATGA
882775 TACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA
882797 -ACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA
882818 ACTTTGAAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
21 52 0.84
22 10 0.16
ACGTcount: A:0.36, C:0.38, G:0.11, T:0.15
Consensus pattern (22 bp):
TACCCCAATGATACCCCAATGA
Found at i:882760 original size:11 final size:11
Alignment explanation
Indices: 882733--882817 Score: 140
Period size: 11 Copynumber: 8.0 Consensus size: 11
882723 TGCGTCTTTT
*
882733 TACCCCAGTGA
1 TACCCCAATGA
882744 -ACCCCAATGA
1 TACCCCAATGA
882754 TACCCCAATGA
1 TACCCCAATGA
882765 -ACCCCAATGA
1 TACCCCAATGA
882775 TACCCCAATGA
1 TACCCCAATGA
882786 TACCCCAATGA
1 TACCCCAATGA
882797 -ACCCCAATGA
1 TACCCCAATGA
882807 TACCCCAATGA
1 TACCCCAATGA
882818 ACTTTGAAAT
Statistics
Matches: 70, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
10 29 0.41
11 41 0.59
ACGTcount: A:0.36, C:0.38, G:0.11, T:0.15
Consensus pattern (11 bp):
TACCCCAATGA
Found at i:882781 original size:32 final size:32
Alignment explanation
Indices: 882733--882819 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
882723 TGCGTCTTTT
*
882733 TACCCCAGTGA-ACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA-ACCCCAATGA
882765 -ACCCCAATGATACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA-ACCCCAATGA
882797 -ACCCCAATGATACCCCAATGAAC
1 TACCCCAATGATACCCCAATGAAC
882820 TTTGAAATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 11 0.21
32 42 0.79
ACGTcount: A:0.37, C:0.38, G:0.10, T:0.15
Consensus pattern (32 bp):
TACCCCAATGATACCCCAATGAACCCCAATGA
Found at i:883821 original size:7 final size:7
Alignment explanation
Indices: 883809--883875 Score: 62
Period size: 7 Copynumber: 9.6 Consensus size: 7
883799 GAGAAGGATC
883809 ATTCGAG
1 ATTCGAG
883816 ATTCGAG
1 ATTCGAG
* *
883823 ATTCAAA
1 ATTCGAG
* *
883830 ATACAAG
1 ATTCGAG
*
883837 ATTCGAA
1 ATTCGAG
*
883844 ATACGAG
1 ATTCGAG
*
883851 ATTCAAG
1 ATTCGAG
*
883858 ATTCGAA
1 ATTCGAG
883865 ATTCGAG
1 ATTCGAG
883872 ATTC
1 ATTC
883876 AATATCTAAA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:883857 original size:21 final size:21
Alignment explanation
Indices: 883833--883877 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
883823 ATTCAAAATA
883833 CAAGATTCGAAATACGAGATT
1 CAAGATTCGAAATACGAGATT
*
883854 CAAGATTCGAAATTCGAGATT
1 CAAGATTCGAAATACGAGATT
883875 CAA
1 CAA
883878 TATCTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (21 bp):
CAAGATTCGAAATACGAGATT
Found at i:885190 original size:50 final size:50
Alignment explanation
Indices: 885115--885248 Score: 180
Period size: 50 Copynumber: 2.7 Consensus size: 50
885105 ATGTACCATC
**** *
885115 TTAACGCACTTTGAAAAAAAATTTCAAAGTGGGTTAACTTGGTCCAAAAT
1 TTAACGCACTTTGAAAATTTTTTTCAAAGTGCGTTAACTTGGTCCAAAAT
* *
885165 TTAACGCACTTTGAAAATTTTTTTCAAAGTGCGTTGATTTGGTCCAAAAT
1 TTAACGCACTTTGAAAATTTTTTTCAAAGTGCGTTAACTTGGTCCAAAAT
*
885215 TTGACGCACTTTG-AAATATTTTTTCAAAGTGCGT
1 TTAACGCACTTTGAAAAT-TTTTTTCAAAGTGCGT
885249 AATTTTTTCA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
49 4 0.05
50 71 0.95
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (50 bp):
TTAACGCACTTTGAAAATTTTTTTCAAAGTGCGTTAACTTGGTCCAAAAT
Found at i:885255 original size:18 final size:18
Alignment explanation
Indices: 885232--885266 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
885222 ACTTTGAAAT
885232 ATTTTTTCAAAGTGCGTA
1 ATTTTTTCAAAGTGCGTA
885250 ATTTTTTCAAAGTGCGT
1 ATTTTTTCAAAGTGCGT
885267 TGCCACAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (18 bp):
ATTTTTTCAAAGTGCGTA
Found at i:885857 original size:7 final size:7
Alignment explanation
Indices: 885842--885908 Score: 62
Period size: 7 Copynumber: 9.6 Consensus size: 7
885832 TTTAGATATT
885842 GAATCTC
1 GAATCTC
*
885849 GAATTTC
1 GAATCTC
*
885856 GAATCTT
1 GAATCTC
885863 GAATCTC
1 GAATCTC
* * *
885870 GTATATT
1 GAATCTC
885877 GAATCTC
1 GAATCTC
* * *
885884 GTATTTT
1 GAATCTC
885891 GAATCTC
1 GAATCTC
885898 GAATCTC
1 GAATCTC
885905 GAAT
1 GAAT
885909 GATCCTTCTC
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (7 bp):
GAATCTC
Found at i:885883 original size:35 final size:35
Alignment explanation
Indices: 885837--885905 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
885827 GTTAATTTAG
*
885837 ATATTGAATCTCGAATTTCGAATCTTGAATCTCGT
1 ATATTGAATCTCGAATTTCGAATCTCGAATCTCGT
* *
885872 ATATTGAATCTCGTATTTTGAATCTCGAATCTCG
1 ATATTGAATCTCGAATTTCGAATCTCGAATCTCG
885906 AATGATCCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (35 bp):
ATATTGAATCTCGAATTTCGAATCTCGAATCTCGT
Found at i:885908 original size:14 final size:14
Alignment explanation
Indices: 885842--885908 Score: 71
Period size: 14 Copynumber: 4.8 Consensus size: 14
885832 TTTAGATATT
* *
885842 GAATCTCGAATTTC
1 GAATCTTGAATCTC
885856 GAATCTTGAATCTC
1 GAATCTTGAATCTC
* *
885870 GTATATTGAATCTC
1 GAATCTTGAATCTC
* *
885884 GTATTTTGAATCTC
1 GAATCTTGAATCTC
*
885898 GAATCTCGAAT
1 GAATCTTGAAT
885909 GATCCTTCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 45 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (14 bp):
GAATCTTGAATCTC
Found at i:887138 original size:21 final size:21
Alignment explanation
Indices: 887112--887426 Score: 240
Period size: 21 Copynumber: 15.2 Consensus size: 21
887102 TCTCTATGCT
*
887112 ATTATTAATTTGTTAAAACAA
1 ATTATTAATTTGTTATAACAA
887133 ATTATTAATTTGTTATAACAA
1 ATTATTAATTTGTTATAACAA
** *
887154 ATTGA-TAACAT-CTATAACAA
1 ATT-ATTAATTTGTTATAACAA
*
887174 ATTATTAATCTT-TTATAACAG
1 ATTATTAAT-TTGTTATAACAA
* * * *
887195 ACTAGTAATATGTTATAACAT
1 ATTATTAATTTGTTATAACAA
*
887216 ATTAGTAA-TTG-T-TAACAA
1 ATTATTAATTTGTTATAACAA
* * *
887234 ATTAATAATCTGTTATTACAA
1 ATTATTAATTTGTTATAACAA
* *
887255 ATTACTT-ATCTGTTATTACAA
1 ATTA-TTAATTTGTTATAACAA
*
887276 ATTACTT-ATCTGTTATAACAA
1 ATTA-TTAATTTGTTATAACAA
887297 ATTGA-TAATTTGTTATAACAA
1 ATT-ATTAATTTGTTATAACAA
* *
887318 ATTGA-TAAATTGTTATAACAG
1 ATT-ATTAATTTGTTATAACAA
*
887339 ATTGA-TAATTTGTTACAACAA
1 ATT-ATTAATTTGTTATAACAA
* *
887360 ATTACTAATCTGTTATAACAA
1 ATTATTAATTTGTTATAACAA
* * * *
887381 AGTAATAATCTGTTATATCAA
1 ATTATTAATTTGTTATAACAA
*
887402 ATTACTT-ATTTGTTTTAACAA
1 ATTA-TTAATTTGTTATAACAA
887423 ATTA
1 ATTA
887427 AGAAAAAATA
Statistics
Matches: 246, Mismatches: 36, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
18 12 0.05
19 4 0.02
20 20 0.08
21 206 0.84
22 4 0.02
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (21 bp):
ATTATTAATTTGTTATAACAA
Found at i:905729 original size:13 final size:12
Alignment explanation
Indices: 905711--905745 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
905701 CAACTAAACC
905711 CTGGGTTTACTTT
1 CTGGGTTTAC-TT
905724 CTGGGTTTAC-T
1 CTGGGTTTACTT
905735 CTGGGTTTACT
1 CTGGGTTTACT
905746 AGAGTGGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.49
Consensus pattern (12 bp):
CTGGGTTTACTT
Found at i:905775 original size:11 final size:11
Alignment explanation
Indices: 905761--905794 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
905751 GGACCCAAAT
905761 TAAACCCAGAG
1 TAAACCCAGAG
905772 TAAACCCCA-AG
1 TAAA-CCCAGAG
905783 TAAACCCAGAG
1 TAAACCCAGAG
905794 T
1 T
905795 GGACACAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 4 0.19
11 13 0.62
12 4 0.19
ACGTcount: A:0.44, C:0.29, G:0.15, T:0.12
Consensus pattern (11 bp):
TAAACCCAGAG
Found at i:905778 original size:22 final size:22
Alignment explanation
Indices: 905753--905794 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
905743 ACTAGAGTGG
*
905753 ACCCAAATTAAACCCAGAGTAA
1 ACCCAAAGTAAACCCAGAGTAA
*
905775 ACCCCAAGTAAACCCAGAGT
1 ACCCAAAGTAAACCCAGAGT
905795 GGACACAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.31, G:0.12, T:0.12
Consensus pattern (22 bp):
ACCCAAAGTAAACCCAGAGTAA
Found at i:905983 original size:22 final size:22
Alignment explanation
Indices: 905958--906015 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
905948 AAGCAATTCT
* *
905958 CGAGTAAATCGAAAGTAAACCC
1 CGAGTAAACCCAAAGTAAACCC
905980 CGAGTAAACCCAAAGTAAACCC
1 CGAGTAAACCCAAAGTAAACCC
**
906002 CGAGTGGACCCAAA
1 CGAGTAAACCCAAA
906016 TTTTCAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.10
Consensus pattern (22 bp):
CGAGTAAACCCAAAGTAAACCC
Found at i:905985 original size:11 final size:11
Alignment explanation
Indices: 905971--906006 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
905961 GTAAATCGAA
905971 AGTAAACCCCG
1 AGTAAACCCCG
**
905982 AGTAAACCCAA
1 AGTAAACCCCG
905993 AGTAAACCCCG
1 AGTAAACCCCG
906004 AGT
1 AGT
906007 GGACCCAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.42, C:0.31, G:0.17, T:0.11
Consensus pattern (11 bp):
AGTAAACCCCG
Found at i:910531 original size:2 final size:2
Alignment explanation
Indices: 910524--910594 Score: 106
Period size: 2 Copynumber: 35.0 Consensus size: 2
910514 AAAAGTTTTG
* *
910524 GA GA GA GA GA GA GA GCC TA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA G-A GA GA GA GA GA GA GA GA GA GA GA GA GA
*
910567 GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
910595 AGTAGTAGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.49, C:0.03, G:0.46, T:0.01
Consensus pattern (2 bp):
GA
Found at i:918202 original size:16 final size:13
Alignment explanation
Indices: 918169--918193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
918159 CAGGGATGGG
918169 GTAATGGTAATTT
1 GTAATGGTAATTT
918182 GTAATGGTAATT
1 GTAATGGTAATT
918194 GAGTGTAATT
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:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (13 bp):
GTAATGGTAATTT
Found at i:919351 original size:37 final size:33
Alignment explanation
Indices: 919270--919341 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 33
919260 TAAATTTTGA
919270 TGAAAATGTAATTTGTAATTTAATTAATTACATC
1 TGAAAATGTAA-TTGTAATTTAATTAATTACATC
* *
919304 TGTAAA-GTAATTGTAATTTAATTAATTACATT
1 TGAAAATGTAATTGTAATTTAATTAATTACATC
919336 TGAAAA
1 TGAAAA
919342 CTCTTGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 26 0.74
33 4 0.11
34 5 0.14
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (33 bp):
TGAAAATGTAATTGTAATTTAATTAATTACATC
Found at i:923669 original size:17 final size:18
Alignment explanation
Indices: 923638--923680 Score: 79
Period size: 17 Copynumber: 2.4 Consensus size: 18
923628 TTTGTCCTAC
923638 ATCCTACACCCTATGTTG
1 ATCCTACACCCTATGTTG
923656 ATCCTACA-CCTATGTTG
1 ATCCTACACCCTATGTTG
923673 ATCCTACA
1 ATCCTACA
923681 TTAGAGTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.26, C:0.33, G:0.09, T:0.33
Consensus pattern (18 bp):
ATCCTACACCCTATGTTG
Found at i:933712 original size:2 final size:2
Alignment explanation
Indices: 933705--933730 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
933695 TCAAAACTTC
933705 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
933731 GAGTGGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:937405 original size:2 final size:2
Alignment explanation
Indices: 937398--937427 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
937388 ATAGATGCAA
937398 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
937428 AAAATGTTGC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:940253 original size:2 final size:2
Alignment explanation
Indices: 940246--940376 Score: 137
Period size: 2 Copynumber: 67.5 Consensus size: 2
940236 AATAAATAAA
* *
940246 CT CT CT CT CT CT TT TT CT CAT -T CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT CT CT CT
* * * * * *
940288 CT CT TT CT TT CC CT CT -T CT -T CT TT CT CT TT C- CT TT C- CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
940326 NT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
940368 CT CT CT CT C
1 CT CT CT CT C
940377 AACGTTTATC
Statistics
Matches: 107, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
1 5 0.05
2 101 0.94
3 1 0.01
ACGTcount: A:0.01, C:0.44, G:0.00, T:0.54
Consensus pattern (2 bp):
CT
Found at i:940626 original size:151 final size:151
Alignment explanation
Indices: 940389--940666 Score: 511
Period size: 151 Copynumber: 1.8 Consensus size: 151
940379 CGTTTATCTC
* *
940389 TTTATCTCTTTATTTTATCAAACAAAATATTTTCAGTCATTAATTTAGTACAAATTATTAATTTA
1 TTTATCTCTTTATTTTATCAAACAAAATATTTTCAGTCATTAATTAAGTACAAATTATAAATTTA
940454 AAGCTTTAATGTAAGTCAAAATGATGTCCATATTTTGAAAAGAACTAAACTCTCTCTCTCTCATT
66 AAGCTTTAATGTAAGTCAAAATGATGTCCATATTTTGAAAAGAACTAAACTCTCTCTCTCTCATT
940519 CTCTCTCTCGCTCTCTCAACG
131 CTCTCTCTCGCTCTCTCAACG
*
940540 TTTATCTCTTTATTTTATCAAACAAAATATTTTCAGTCATTAATTAAGTACAAATTATAAATTTC
1 TTTATCTCTTTATTTTATCAAACAAAATATTTTCAGTCATTAATTAAGTACAAATTATAAATTTA
**
940605 AAGCTTTAATGTAAGTCAAAATGATGTCCATATTTTGAAAATTACTAAACTCTCTCTCTCTC
66 AAGCTTTAATGTAAGTCAAAATGATGTCCATATTTTGAAAAGAACTAAACTCTCTCTCTCTC
940667 TCAACGTTTA
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
151 122 1.00
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (151 bp):
TTTATCTCTTTATTTTATCAAACAAAATATTTTCAGTCATTAATTAAGTACAAATTATAAATTTA
AAGCTTTAATGTAAGTCAAAATGATGTCCATATTTTGAAAAGAACTAAACTCTCTCTCTCTCATT
CTCTCTCTCGCTCTCTCAACG
Found at i:943085 original size:4 final size:4
Alignment explanation
Indices: 943076--943198 Score: 183
Period size: 4 Copynumber: 30.8 Consensus size: 4
943066 CTGATAAATT
* * * * * * *
943076 GATA GATA GATA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
943124 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
943172 GATA GATA GATA GATA GATA GATA GAT
1 GATA GATA GATA GATA GATA GATA GAT
943199 GAATAATAGC
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 117 1.00
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (4 bp):
GATA
Found at i:943665 original size:2 final size:2
Alignment explanation
Indices: 943658--943711 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
943648 AGACTGAAAA
943658 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
943700 TC TC TC TC TC TC
1 TC TC TC TC TC TC
943712 CCATGCCAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:944905 original size:14 final size:14
Alignment explanation
Indices: 944882--944911 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
944872 TTTGGCCTTT
*
944882 ATCTTTAAACAGTC
1 ATCTTGAAACAGTC
944896 ATCTTGAAACAGTC
1 ATCTTGAAACAGTC
944910 AT
1 AT
944912 AGAAAAACCC
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:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (14 bp):
ATCTTGAAACAGTC
Found at i:947630 original size:56 final size:56
Alignment explanation
Indices: 947558--947674 Score: 198
Period size: 56 Copynumber: 2.1 Consensus size: 56
947548 ATTTATAGCC
* * *
947558 CATTTCACAGAAAATATTGCATTGTTATTTTACTTTGCACTTATTTAAAATATGTG
1 CATTTCACAGAAAATATTGCATTGTAATTTTACTTTGCACTTATCTAAAATATGTA
*
947614 CATTTCACAGAAAATATTGCATTGTAATTTTACTTTGCACTTATCTAAAATGTGTA
1 CATTTCACAGAAAATATTGCATTGTAATTTTACTTTGCACTTATCTAAAATATGTA
947670 CATTT
1 CATTT
947675 GCATAATGAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (56 bp):
CATTTCACAGAAAATATTGCATTGTAATTTTACTTTGCACTTATCTAAAATATGTA
Found at i:959473 original size:1 final size:1
Alignment explanation
Indices: 959469--959511 Score: 68
Period size: 1 Copynumber: 43.0 Consensus size: 1
959459 CCCCCCCCCC
* *
959469 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
959512 CAAAGAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:959520 original size:9 final size:9
Alignment explanation
Indices: 959468--959524 Score: 73
Period size: 9 Copynumber: 6.4 Consensus size: 9
959458 CCCCCCCCCC
959468 CAAAAAAAA
1 CAAAAAAAA
959477 -AAAAAAAA
1 CAAAAAAAA
959485 -AAAAAAAA
1 CAAAAAAAA
*
959493 AAAAAAAAA
1 CAAAAAAAA
959502 CAACAAAAAA
1 CAA-AAAAAA
*
959512 CAAAGAAAA
1 CAAAAAAAA
959521 CAAA
1 CAAA
959525 CAAATGGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
8 16 0.36
9 19 0.43
10 9 0.20
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:959525 original size:23 final size:23
Alignment explanation
Indices: 959470--959527 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
959460 CCCCCCCCCA
959470 AAAAAAAAAAAAA-AA-AAAAAA
1 AAAAAAAAAAAAACAACAAAAAA
959491 AAAAA--AAAAAACAACAAAAAA
1 AAAAAAAAAAAAACAACAAAAAA
* * *
959512 CAAAGAAAACAAACAA
1 AAAAAAAAAAAAACAA
959528 ATGGCATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.20
20 2 0.07
21 14 0.47
23 8 0.27
ACGTcount: A:0.90, C:0.09, G:0.02, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAAACAACAAAAAA
Found at i:963138 original size:2 final size:2
Alignment explanation
Indices: 963131--963171 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
963121 ATGTTATAAC
*
963131 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AT AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
963172 TAATATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.02
Consensus pattern (2 bp):
AG
Found at i:963514 original size:10 final size:10
Alignment explanation
Indices: 963499--963523 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
963489 TGTCAAACTA
963499 TACTTCTATT
1 TACTTCTATT
963509 TACTTCTATT
1 TACTTCTATT
963519 TACTT
1 TACTT
963524 GAAACGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (10 bp):
TACTTCTATT
Found at i:964167 original size:2 final size:2
Alignment explanation
Indices: 964160--964185 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
964150 AAATGTGTAA
964160 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
964186 GCTATTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:994741 original size:13 final size:13
Alignment explanation
Indices: 994723--994753 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
994713 CATTAGAAAT
994723 ATAAATAATAAAA
1 ATAAATAATAAAA
*
994736 ATAAATAATAATA
1 ATAAATAATAAAA
994749 ATAAA
1 ATAAA
994754 ATTTTGAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAATAATAAAA
Found at i:1008505 original size:1 final size:1
Alignment explanation
Indices: 1008499--1008527 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1008489 NNNNNNNNNN
1008499 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1008528 CAGACAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1014811 original size:4 final size:4
Alignment explanation
Indices: 1014802--1014840 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
1014792 AAAAAGACAC
1014802 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1014841 CAAGCACAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:1015363 original size:2 final size:2
Alignment explanation
Indices: 1015358--1015404 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1015348 ATTCTCACAC
1015358 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
1015400 GG AG A
1 AG AG A
1015405 CACTGGATGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1015751 original size:131 final size:131
Alignment explanation
Indices: 1015528--1015857 Score: 529
Period size: 131 Copynumber: 2.5 Consensus size: 131
1015518 TCAGCAAGTA
* *
1015528 TCCGTTAGGTTTCAGTCA-GCAGAAACTTT-AGTCTAAGATTCCTGATGGTTTCCGCAATGCGGA
1 TCCGCTAGGTTTCAGT-ATGCTGAAACTTTAAGT-TAAGATTCCTGATGGTTTCCGCAATGCGGA
* * *
1015591 AACTAAATTTGAATCGTGTGAATAGTTGTGTAAATCATTATGGAAATATCAATTAGTTTCAGAAC
64 AACTAAATTTGAATCATGTGAAAAGTTGTGTAAATCATTATGGAAATATCAATCAGTTTCAGAAC
1015656 ATT
129 ATT
1015659 TCCGCTAGGTTTCAGTATGCTGAAACTTTAAGTTAAGATTCCTGATGGTTTCCGCAATGCGGAAA
1 TCCGCTAGGTTTCAGTATGCTGAAACTTTAAGTTAAGATTCCTGATGGTTTCCGCAATGCGGAAA
*
1015724 CTAAATTTGAATCATGTGAAAAGTTGTGTAAATTATTATGGAAATATCAATCAGTTTCAGAACAT
66 CTAAATTTGAATCATGTGAAAAGTTGTGTAAATCATTATGGAAATATCAATCAGTTTCAGAACAT
1015789 T
131 T
** * * *
1015790 TCCGCTAGGTTTCAGTATGCTGAAACTTTAAGTTAAGATTCCAAATGGTTTACGCATTGCTGAAA
1 TCCGCTAGGTTTCAGTATGCTGAAACTTTAAGTTAAGATTCCTGATGGTTTCCGCAATGCGGAAA
1015855 CTA
66 CTA
1015858 TTACTAAAAT
Statistics
Matches: 186, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
130 1 0.01
131 182 0.98
132 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (131 bp):
TCCGCTAGGTTTCAGTATGCTGAAACTTTAAGTTAAGATTCCTGATGGTTTCCGCAATGCGGAAA
CTAAATTTGAATCATGTGAAAAGTTGTGTAAATCATTATGGAAATATCAATCAGTTTCAGAACAT
T
Found at i:1017558 original size:23 final size:23
Alignment explanation
Indices: 1017530--1017577 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1017520 AAACTTGTTT
1017530 AATTTCATTAGACATTTGTAAAC
1 AATTTCATTAGACATTTGTAAAC
1017553 AATTTCATTAGACATTTGTAAAC
1 AATTTCATTAGACATTTGTAAAC
1017576 AA
1 AA
1017578 ATGGTCGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (23 bp):
AATTTCATTAGACATTTGTAAAC
Found at i:1021050 original size:17 final size:17
Alignment explanation
Indices: 1021028--1021061 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1021018 GTTTCCCGAA
1021028 AGTGACGGAGTTAGGGT
1 AGTGACGGAGTTAGGGT
1021045 AGTGACGGAGTTAGGGT
1 AGTGACGGAGTTAGGGT
1021062 GCTATGCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.47, T:0.24
Consensus pattern (17 bp):
AGTGACGGAGTTAGGGT
Found at i:1023829 original size:88 final size:88
Alignment explanation
Indices: 1023718--1023928 Score: 359
Period size: 88 Copynumber: 2.4 Consensus size: 88
1023708 AAAATATAAA
* * * * **
1023718 AAGTTTCAGTAAGTTTCAGTTGCGGAAACCCTTTGTAAATAATATGTTTCCCAATTGTATATGGA
1 AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
*
1023783 GGTTGAAACTATGCAGAAACTTC
66 GATTGAAACTATGCAGAAACTTC
1023806 AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
1 AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
1023871 GATTGAAACTATGCAGAAACTTC
66 GATTGAAACTATGCAGAAACTTC
1023894 AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTG
1 AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTG
1023929 GATTCATGGA
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 116 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (88 bp):
AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
GATTGAAACTATGCAGAAACTTC
Found at i:1050852 original size:2 final size:2
Alignment explanation
Indices: 1050845--1050886 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1050835 AATTGCATTT
*
1050845 GA GA GA GA GA GA GA GA GA GA GA TA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1050887 TTTTTAAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
GA
Found at i:1051717 original size:9 final size:9
Alignment explanation
Indices: 1051703--1051732 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
1051693 CAGAATGATA
1051703 AGTCAGAAT
1 AGTCAGAAT
1051712 AGTCAGAAT
1 AGTCAGAAT
1051721 AGTCAGAAT
1 AGTCAGAAT
1051730 AGT
1 AGT
1051733 GGCAAGTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.23
Consensus pattern (9 bp):
AGTCAGAAT
Found at i:1054258 original size:2 final size:2
Alignment explanation
Indices: 1054251--1054308 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1054241 GAGCATTTCA
1054251 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1054293 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
1054309 ATATTTGGGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1062700 original size:38 final size:38
Alignment explanation
Indices: 1062658--1062733 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
1062648 GATTTATAAA
* *
1062658 ATTCCTCTTTATAATCAGATCAATTGATTGAATTTGAT
1 ATTCCTCTTTACAATCAGATCAACTGATTGAATTTGAT
*
1062696 ATTCCTCTTTACAATCAGATCAGCTGATTGAATTTGAT
1 ATTCCTCTTTACAATCAGATCAACTGATTGAATTTGAT
1062734 TCTCAATTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (38 bp):
ATTCCTCTTTACAATCAGATCAACTGATTGAATTTGAT
Found at i:1068210 original size:16 final size:16
Alignment explanation
Indices: 1068184--1068225 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1068174 AAGTTTACTC
1068184 ATTTGTAGGGGT-TCATA
1 ATTT-TAGGGGTAT-ATA
*
1068201 ATTTTAGGGGTATGTA
1 ATTTTAGGGGTATATA
1068217 ATTTTAGGG
1 ATTTTAGGG
1068226 TTATTTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.24, C:0.02, G:0.31, T:0.43
Consensus pattern (16 bp):
ATTTTAGGGGTATATA
Found at i:1076002 original size:348 final size:347
Alignment explanation
Indices: 1075364--1076061 Score: 1369
Period size: 348 Copynumber: 2.0 Consensus size: 347
1075354 GAAGGCTAAT
1075364 TCAAAATTGAAAATATGGCATTATATTTACATTTTCTAGTGACCTTTTCTGTAATAAATGTAACA
1 TCAAAATTGAAAATATGGCATTATATTTACATTTTCTAGTGACCTTTTCTGTAATAAATGTAACA
*
1075429 CTAAACGTAATTCCCTAAATTAAATGACGCAAATGACGTACCGCTGGGGTGCAAGTGGGGTTTGC
66 CTAAACGTAATTCACTAAATTAAATGACGCAAATGACGTACCGCTGGGGTGCAAGTGGGGTTTGC
1075494 ATCATTATACGAAATGTAATAACACAAAGATGTCACTAATTTAATATTCATTCCTACAATTACTG
131 ATCATTATACGAAATGTAATAACACAAAGATGTCACTAATTTAATATTCATTCCTACAATTACTG
1075559 AAAATTATTTAACTATACGGAATAAGAAATCTTTCCTTGATCATTATGAGGTAATCAATACGGTC
196 AAAATTATTTAACTATACGGAATAAGAAATCTTTCCTTGATCATTATGAGGTAATCAATACGGTC
1075624 AGGTTTGATCAAATTTATCATGAAGCCGTTAGCGCTTTATTGGATCTGACCACACCCCGACTATA
261 AGGTTTGATCAAATTTATCATGAAGCCGTTAGCGCTTTATTGGATCTGACCACACCCCGACTATA
1075689 GTGATCACCTCACAGTCAAAAC
326 GTGATCACCTCACAGTCAAAAC
1075711 TNCAAAATTGAAAATATGGCATTATATTTACATTTTCTAGTGACCTTTTCTGTAATAAATGTAAC
1 T-CAAAATTGAAAATATGGCATTATATTTACATTTTCTAGTGACCTTTTCTGTAATAAATGTAAC
1075776 ACTAAACGTAATTCACTAAATTAAATGACGCAAATGACGTACCGCTGGGGTGCAAGTGGGGTTTG
65 ACTAAACGTAATTCACTAAATTAAATGACGCAAATGACGTACCGCTGGGGTGCAAGTGGGGTTTG
*
1075841 CATCATTATACGAAATGTAATAACACAAAGATGTCACTAATTTAATATTCATTCCTATAATTACT
130 CATCATTATACGAAATGTAATAACACAAAGATGTCACTAATTTAATATTCATTCCTACAATTACT
1075906 GAAAATTATTTAACTATACGGAATAAGAAATCTTTCCTTGATCATTATGAGGTAATCAATACGGT
195 GAAAATTATTTAACTATACGGAATAAGAAATCTTTCCTTGATCATTATGAGGTAATCAATACGGT
1075971 CAGGTTTGATCAAATTTATCATGAAGCCGTTAGCGCTTTATTGGATCTGACCACACCCCGACTAT
260 CAGGTTTGATCAAATTTATCATGAAGCCGTTAGCGCTTTATTGGATCTGACCACACCCCGACTAT
1076036 AGTGATCACCTCACAGTCAAAAC
325 AGTGATCACCTCACAGTCAAAAC
1076059 TCA
1 TCA
1076062 GATTGATTTC
Statistics
Matches: 348, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
347 3 0.01
348 345 0.99
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (347 bp):
TCAAAATTGAAAATATGGCATTATATTTACATTTTCTAGTGACCTTTTCTGTAATAAATGTAACA
CTAAACGTAATTCACTAAATTAAATGACGCAAATGACGTACCGCTGGGGTGCAAGTGGGGTTTGC
ATCATTATACGAAATGTAATAACACAAAGATGTCACTAATTTAATATTCATTCCTACAATTACTG
AAAATTATTTAACTATACGGAATAAGAAATCTTTCCTTGATCATTATGAGGTAATCAATACGGTC
AGGTTTGATCAAATTTATCATGAAGCCGTTAGCGCTTTATTGGATCTGACCACACCCCGACTATA
GTGATCACCTCACAGTCAAAAC
Found at i:1076781 original size:2 final size:2
Alignment explanation
Indices: 1076774--1076818 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1076764 CTCTTTTATC
1076774 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1076816 AG A
1 AG A
1076819 CCTTGTTCCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1080642 original size:50 final size:50
Alignment explanation
Indices: 1080567--1080700 Score: 187
Period size: 50 Copynumber: 2.7 Consensus size: 50
1080557 ATGTACCATC
* *** *
1080567 TTAACGCACTTTGAAAAAAAATTTCAAAGTGGGTTAACTTGGTCCAAAAT
1 TTAACGCACTTTGAAATATTTTTTCAAAGTGCGTTAACTTGGTCCAAAAT
* * *
1080617 TTAACGCACTTTGAAATTTTTTTTCAAAGTGCGTTGATTTGGTCCAAAAT
1 TTAACGCACTTTGAAATATTTTTTCAAAGTGCGTTAACTTGGTCCAAAAT
*
1080667 TTGACGCACTTTGAAATATTTTTTCAAAGTGCGT
1 TTAACGCACTTTGAAATATTTTTTCAAAGTGCGT
1080701 AATTTTTTCA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 74 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (50 bp):
TTAACGCACTTTGAAATATTTTTTCAAAGTGCGTTAACTTGGTCCAAAAT
Found at i:1080707 original size:18 final size:18
Alignment explanation
Indices: 1080684--1080718 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1080674 ACTTTGAAAT
1080684 ATTTTTTCAAAGTGCGTA
1 ATTTTTTCAAAGTGCGTA
1080702 ATTTTTTCAAAGTGCGT
1 ATTTTTTCAAAGTGCGT
1080719 TGCCACAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (18 bp):
ATTTTTTCAAAGTGCGTA
Found at i:1081405 original size:2 final size:2
Alignment explanation
Indices: 1081398--1081523 Score: 206
Period size: 2 Copynumber: 65.0 Consensus size: 2
1081388 AAGATAAAGG
1081398 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
1081439 CT CT CT CT C- CT -T CT CT CT CT CG CT CG CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1081479 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1081520 CT CT
1 CT CT
1081524 GATAGATGTC
Statistics
Matches: 116, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
1 4 0.03
2 112 0.97
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1083571 original size:23 final size:24
Alignment explanation
Indices: 1083533--1083580 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1083523 TACACTATGC
* *
1083533 ATTAGTTTGCTAATAATGTATGGG
1 ATTAGTTTACTAATAATGCATGGG
1083557 ATTAGTTTACT-ATAATGCATGGG
1 ATTAGTTTACTAATAATGCATGGG
1083580 A
1 A
1083581 AATGTGACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (24 bp):
ATTAGTTTACTAATAATGCATGGG
Found at i:1090797 original size:2 final size:2
Alignment explanation
Indices: 1090790--1090832 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1090780 GTAGAAGGTA
1090790 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1090832 A
1 A
1090833 TTAAAAGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1092770 original size:2 final size:2
Alignment explanation
Indices: 1092763--1092804 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1092753 AGTAGATGAT
1092763 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1092805 AACATACAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1098435 original size:2 final size:2
Alignment explanation
Indices: 1098428--1098457 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1098418 ACGAATTTTC
1098428 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1098458 GTGTTATTAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1098524 original size:8 final size:8
Alignment explanation
Indices: 1098511--1098562 Score: 68
Period size: 8 Copynumber: 6.5 Consensus size: 8
1098501 TTTCCTCTGC
*
1098511 GTCCGTCA
1 GTCCGTCT
1098519 GTCCGTCT
1 GTCCGTCT
*
1098527 GTCTGTCT
1 GTCCGTCT
1098535 GTCCGTCT
1 GTCCGTCT
**
1098543 GTCTTTCT
1 GTCCGTCT
1098551 GTCCGTCT
1 GTCCGTCT
1098559 GTCC
1 GTCC
1098563 CACTTCAGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.02, C:0.35, G:0.23, T:0.40
Consensus pattern (8 bp):
GTCCGTCT
Found at i:1098530 original size:4 final size:4
Alignment explanation
Indices: 1098523--1098561 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1098513 CCGTCAGTCC
* * *
1098523 GTCT GTCT GTCT GTCC GTCT GTCT TTCT GTCC GTCT GTC
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTC
1098562 CCACTTCAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.23, T:0.46
Consensus pattern (4 bp):
GTCT
Found at i:1098540 original size:16 final size:16
Alignment explanation
Indices: 1098519--1098561 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1098509 GCGTCCGTCA
1098519 GTCCGTCTGTCTGTCT
1 GTCCGTCTGTCTGTCT
*
1098535 GTCCGTCTGTCTTTCT
1 GTCCGTCTGTCTGTCT
1098551 GTCCGTCTGTC
1 GTCCGTCTGTC
1098562 CCACTTCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.00, C:0.33, G:0.23, T:0.44
Consensus pattern (16 bp):
GTCCGTCTGTCTGTCT
Found at i:1100063 original size:4 final size:4
Alignment explanation
Indices: 1100048--1100085 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1100038 ATCACCCGTT
* *
1100048 GTCC GT-C GTCC GTCC GTCC GTCC GTCT GTCT GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
1100086 AGTCTGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.42, G:0.26, T:0.32
Consensus pattern (4 bp):
GTCC
Found at i:1100811 original size:166 final size:166
Alignment explanation
Indices: 1100259--1101273 Score: 1212
Period size: 166 Copynumber: 6.1 Consensus size: 166
1100249 GGTGCATGTC
* * * *
1100259 TTTAAAAATCTTCTTCTAAAGACCCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGTAT
1 TTTAAAAATCTTCATATCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGTAT
*
1100324 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGAACCAAAACTGGGGCCCCAGGCGGG
66 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
*
1100389 GTTCAAAGTTTAACATTGAAATACATTA-GAAAAATG
131 GTTCAAAGTTTAACATAGAAATACA-TAGGAAAAATG
* * *
1100425 TTTAAAAGTCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGTAT
1 TTTAAAAATCTTCATATCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGTAT
* * * * *
1100490 ATATAGTGAAGATTCTAATTTGT-AAACTTGTGACCCCCGGACCGAAACTGGGGCCCAAGGCGGG
66 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
* * *
1100554 GTTCAAAATTTAACATGGAAATACGTAGGAAAAATG
131 GTTCAAAGTTTAACATAGAAATACATAGGAAAAATG
* * * *
1100590 TTTAAAAATCATCTTCTCAAGACCCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGTAT
1 TTTAAAAATCTTCATATCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGTAT
* * * * * **
1100655 ATATAGTGAAGATTCTAAATTATATAAATCCTGACTCCCGGACTAAAACTAAGGCCCCAGGCGGG
66 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
* * *
1100720 GTTTAAAGTTTAACATAGAAATCCATAGGATAAATG
131 GTTCAAAGTTTAACATAGAAATACATAGGAAAAATG
* * * * * * *
1100756 TTTAAAAATCATCATATCACGAACCACTGCACCAGAAAAGCCAATATTCACACAAAAGTTTTTAT
1 TTTAAAAATCTTCATATCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGTAT
* * **
1100821 ATATAGTAAAAATTCTAAATTGTAAAAATTATGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
66 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
* * *
1100886 GTTCAAAGTTTAACAT-GAAAATCCATAGGATAAAGG
131 GTTCAAAGTTTAACATAG-AAATACATAGGAAAAATG
* * *
1100922 TTTAAAAAT-TTCCT-TCTTAAAAACCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGA
1 TTTAAAAATCTTCATATC--AAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGT
* *
1100985 ATATATAGTGAAGATTTTAAATTGTAAAAATCGTGACCCCCGGACCAAGACTGGGGCCCCAGGCG
64 ATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCG
* * * ** *
1101050 GTCCGG-GCTACAACTTAAACATAGAAATATGTAGGAAAATTG
129 G---GGTTC-A-AAGTTTAACATAGAAATACATAGGAAAAATG
* * * * *
1101092 TTTAAAAATCTTCATATCAAGAACCACTGAACCAAAAATTCCAATATTTATACAAAAGCTTGTAT
1 TTTAAAAATCTTCATATCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGTAT
* * * * * * *
1101157 GTATAGTGAAGATTCTAAATTTTTAAAATTGTGA-CCCCGGGCAAAAACTGGGCCCCCAGGCGGG
66 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
*
1101221 GTTCAAAG-TTAACAT----AT--ATAAGAAAAATG
131 GTTCAAAGTTTAACATAGAAATACATAGGAAAAATG
* *
1101250 TTTAAAAATCTTCTTCTCAAGAAC
1 TTTAAAAATCTTCATATCAAGAAC
1101274 TACAATGCAA
Statistics
Matches: 731, Mismatches: 104, Indels: 36
0.84 0.12 0.04
Matches are distributed among these distances:
158 31 0.04
160 2 0.00
164 10 0.01
165 155 0.21
166 397 0.54
167 1 0.00
168 1 0.00
169 28 0.04
170 99 0.14
171 5 0.01
172 2 0.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (166 bp):
TTTAAAAATCTTCATATCAAGAACCACTGCACCAGAAATGCCAACATTTACACAAAAGCTTGTAT
ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
GTTCAAAGTTTAACATAGAAATACATAGGAAAAATG
Found at i:1114319 original size:26 final size:27
Alignment explanation
Indices: 1114283--1114380 Score: 110
Period size: 26 Copynumber: 3.7 Consensus size: 27
1114273 CAAGAAAATC
*
1114283 CCCA-TCAACAAAATCAGGTAAAGATT
1 CCCATTCAACAAAATCAGGTAAAGAAT
* * *
1114309 CCCATT-GACAAAATCAGATAAGGAAT
1 CCCATTCAACAAAATCAGGTAAAGAAT
*
1114335 CCCATTCAACAAAATCAGGTAATGGAAT
1 CCCATTCAACAAAATCAGGTAA-AGAAT
* *
1114363 TCCAATCAACAAAATCAG
1 CCCATTCAACAAAATCAG
1114381 ATAAGGAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 26 0.43
27 14 0.23
28 21 0.34
ACGTcount: A:0.46, C:0.22, G:0.12, T:0.19
Consensus pattern (27 bp):
CCCATTCAACAAAATCAGGTAAAGAAT
Found at i:1114388 original size:55 final size:52
Alignment explanation
Indices: 1114283--1114388 Score: 149
Period size: 55 Copynumber: 2.0 Consensus size: 52
1114273 CAAGAAAATC
* **
1114283 CCCATCAACAAAATCAGGTAAAGATTCCCATTGACAAAATCAGATAAGGAAT
1 CCCATCAACAAAATCAGGTAAAGATTCCAATCAACAAAATCAGATAAGGAAT
*
1114335 CCCATTCAACAAAATCAGGTAATGGAATTCCAATCAACAAAATCAGATAAGGAA
1 CCCA-TCAACAAAATCAGGTAA-AG-ATTCCAATCAACAAAATCAGATAAGGAA
1114389 ATTTCTATAC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
52 4 0.09
53 17 0.36
54 1 0.02
55 25 0.53
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (52 bp):
CCCATCAACAAAATCAGGTAAAGATTCCAATCAACAAAATCAGATAAGGAAT
Found at i:1114391 original size:28 final size:27
Alignment explanation
Indices: 1114286--1114388 Score: 118
Period size: 28 Copynumber: 3.8 Consensus size: 27
1114276 GAAAATCCCC
* * *
1114286 ATCAACAAAATCAGGTAAAG-ATTCCC
1 ATCAACAAAATCAGATAAGGAATTCCA
** *
1114312 ATTGACAAAATCAGATAAGGAATCCCA
1 ATCAACAAAATCAGATAAGGAATTCCA
* *
1114339 TTCAACAAAATCAGGTAATGGAATTCCA
1 ATCAACAAAATCAGATAA-GGAATTCCA
1114367 ATCAACAAAATCAGATAAGGAA
1 ATCAACAAAATCAGATAAGGAA
1114389 ATTTCTATAC
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
26 16 0.26
27 22 0.35
28 24 0.39
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (27 bp):
ATCAACAAAATCAGATAAGGAATTCCA
Found at i:1115886 original size:16 final size:16
Alignment explanation
Indices: 1115861--1115891 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1115851 GAATTTCTTA
*
1115861 TACGGTTATAACGAAT
1 TACGGATATAACGAAT
1115877 TACGGATATAACGAA
1 TACGGATATAACGAA
1115892 GTAATTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (16 bp):
TACGGATATAACGAAT
Found at i:1117627 original size:15 final size:15
Alignment explanation
Indices: 1117603--1117632 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1117593 CAGTAGTGAA
1117603 GAAGAAGAGGAGGAG
1 GAAGAAGAGGAGGAG
*
1117618 GAAGATGAGGAGGAG
1 GAAGAAGAGGAGGAG
1117633 AACAGTAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.53, T:0.03
Consensus pattern (15 bp):
GAAGAAGAGGAGGAG
Done.