Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 3 of 135
Found at i:683966 original size:11 final size:11
Alignment explanation
Indices: 683931--683972 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
683921 ATCAAAAATT
683931 TATTTT-AAAA
1 TATTTTAAAAA
683941 -ATTTTAAAAA
1 TATTTTAAAAA
683951 GTATTTTAAAAA
1 -TATTTTAAAAA
683963 TATTTTAAAA
1 TATTTTAAAA
683973 TTAAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.17
10 4 0.14
11 10 0.34
12 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:692999 original size:28 final size:28
Alignment explanation
Indices: 692917--693011 Score: 75
Period size: 31 Copynumber: 3.2 Consensus size: 28
692907 CTTTTTTATT
*
692917 AAATTATAAAATAGTGATTCAATTATTAA
1 AAATTATAAAATA-TCATTCAATTATTAA
**** * *
692946 TAAATTTATCTTTTCATTATTTAATTATTAA
1 -AAA-TTATAAAAT-ATCATTCAATTATTAA
692977 AAATTATAAAATATCATTCAATTAATT-A
1 AAATTATAAAATATCATTCAATT-ATTAA
693005 AAATTAT
1 AAATTAT
693012 TTTTTACCAC
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
28 17 0.34
29 8 0.16
30 6 0.12
31 18 0.36
32 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (28 bp):
AAATTATAAAATATCATTCAATTATTAA
Found at i:693398 original size:219 final size:220
Alignment explanation
Indices: 693008--693446 Score: 871
Period size: 219 Copynumber: 2.0 Consensus size: 220
692998 TTAATTAAAA
693008 TTATTTTTTACCACTAATAAACTAATGTAAAAATAAAGACATTAAAAATTCAAAATAATAATAGA
1 TTATTTTTTACCACTAATAAACTAATGTAAAAATAAAGACATTAAAAATTCAAAATAATAATAGA
693073 TTTTTAAAAAAAATAGAACTGTATTTTGTTTTAATGTAATATAAAAGCAAAAAAGTTTTCTTAAA
66 TTTTTAAAAAAAATAGAACTGTATTTTGTTTTAATGTAATATAAAAGCAAAAAAGTTTTCTTAAA
693138 AGAAAAGTCTCCTTGTCTAATAAGTCAACTATTGAAAGATATAAATGAACAAACTGACTTTATCT
131 AGAAAAGTCTCCTTGTCTAATAAGTCAACTATTGAAAGATATAAATGAACAAACTGACTTTATCT
693203 GACATGTGAGCCATCGGATTGATCT
196 GACATGTGAGCCATCGGATTGATCT
693228 TTATTTTTTA-CACTAATAAACTAATGTAAAAATAAAGACATTAAAAATTCAAAATAATAATAGA
1 TTATTTTTTACCACTAATAAACTAATGTAAAAATAAAGACATTAAAAATTCAAAATAATAATAGA
693292 TTTTTAAAAAAAATAGAACTGTATTTTGTTTTAATGTAATATAAAAGCAAAAAAGTTTTCTTAAA
66 TTTTTAAAAAAAATAGAACTGTATTTTGTTTTAATGTAATATAAAAGCAAAAAAGTTTTCTTAAA
693357 AGAAAAGTCTCCTTGTCTAATAAGTCAACTATTGAAAGATATAAATGAACAAACTGACTTTATCT
131 AGAAAAGTCTCCTTGTCTAATAAGTCAACTATTGAAAGATATAAATGAACAAACTGACTTTATCT
693422 GACATGTGAGCCATCGGATTGATCT
196 GACATGTGAGCCATCGGATTGATCT
693447 GTATCTTCCT
Statistics
Matches: 219, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
219 209 0.95
220 10 0.05
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (220 bp):
TTATTTTTTACCACTAATAAACTAATGTAAAAATAAAGACATTAAAAATTCAAAATAATAATAGA
TTTTTAAAAAAAATAGAACTGTATTTTGTTTTAATGTAATATAAAAGCAAAAAAGTTTTCTTAAA
AGAAAAGTCTCCTTGTCTAATAAGTCAACTATTGAAAGATATAAATGAACAAACTGACTTTATCT
GACATGTGAGCCATCGGATTGATCT
Found at i:694534 original size:85 final size:87
Alignment explanation
Indices: 694425--694593 Score: 234
Period size: 85 Copynumber: 2.0 Consensus size: 87
694415 GTTTCAATCT
* * *
694425 TACTACACTCCTCCTATTAGAATATGATTTTACAAGCCTATAAATAGACATACTCTACTCCTCTT
1 TACTACACTCCT-CTATTAAAATATGATTTTACAAGCCTATAAATAGACATAATCTACTCCGCTT
* *
694490 GTAATCATTCGAATTCGACTTAG
65 ATAATCATTCAAATTCGACTTAG
* * *
694513 TACTACACT-CT-TATTAAAATATGGTTTTACAAGCCTATGAATAGACCTAATCTACTCCGCTTA
1 TACTACACTCCTCTATTAAAATATGATTTTACAAGCCTATAAATAGACATAATCTACTCCGCTTA
*
694576 TAATTATTCAAATTCGAC
66 TAATCATTCAAATTCGAC
694594 ATAATGAATT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
85 61 0.85
87 2 0.03
88 9 0.12
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (87 bp):
TACTACACTCCTCTATTAAAATATGATTTTACAAGCCTATAAATAGACATAATCTACTCCGCTTA
TAATCATTCAAATTCGACTTAG
Found at i:699186 original size:2 final size:2
Alignment explanation
Indices: 699179--699203 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
699169 CCTTTTCGAT
699179 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
699204 ACCCAGGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:703022 original size:6 final size:6
Alignment explanation
Indices: 703011--703041 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
703001 AATGAAGGAG
703011 CCATAC CCATAC CCATAC CCATAC CCATAC C
1 CCATAC CCATAC CCATAC CCATAC CCATAC C
703042 AGATCCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CCATAC
Found at i:713433 original size:154 final size:154
Alignment explanation
Indices: 713228--713513 Score: 511
Period size: 154 Copynumber: 1.9 Consensus size: 154
713218 TTACTTTCAA
*
713228 TAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
1 TAAAAAACACAATAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
* *
713293 TATAAAATAATATATTTTTTAAAAGTAACAAAATCTGGGGAAAA-AATACGAACAAAGGGCCGAA
66 TATAAAATAATATATTTTTTAAAAGTAACAAAATC-CGAGAAAAGAATACGAACAAAGGGCCGAA
713357 ATAAAGGTTTTTTACTAAATTTATT
130 ATAAAGGTTTTTTACTAAATTTATT
*
713382 TAAAAAACACAATTAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
1 TAAAAAACACAATAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
*
713447 TATAAAATAATATATTTTTTAAAAGTAATAAAATCCGAGAAAAGAATACGAACAAAGGGCCGAAA
66 TATAAAATAATATATTTTTTAAAAGTAACAAAATCCGAGAAAAGAATACGAACAAAGGGCCGAAA
713512 TA
131 TA
713514 TGAACAATTG
Statistics
Matches: 126, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
153 6 0.05
154 120 0.95
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (154 bp):
TAAAAAACACAATAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
TATAAAATAATATATTTTTTAAAAGTAACAAAATCCGAGAAAAGAATACGAACAAAGGGCCGAAA
TAAAGGTTTTTTACTAAATTTATT
Found at i:714699 original size:3 final size:3
Alignment explanation
Indices: 714691--714726 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
714681 NNNNNNNNAT
714691 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
714727 GTCCATTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:732713 original size:3 final size:3
Alignment explanation
Indices: 732705--732743 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
732695 ATTTTGAATA
732705 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAGG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG
732744 TTGAAACTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:732905 original size:16 final size:17
Alignment explanation
Indices: 732875--732908 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
732865 GGAAGTTGGA
732875 GGAGAGGGGAAGGGATG
1 GGAGAGGGGAAGGGATG
*
732892 GGAG-GGGGAGGGGATG
1 GGAGAGGGGAAGGGATG
732908 G
1 G
732909 CTTTTGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.71, T:0.06
Consensus pattern (17 bp):
GGAGAGGGGAAGGGATG
Found at i:734709 original size:78 final size:79
Alignment explanation
Indices: 734613--734770 Score: 309
Period size: 78 Copynumber: 2.0 Consensus size: 79
734603 GGTTGCGGCT
734613 TACTTCGTAAATAATTTATATTAAATATTTAAAAGTATTTAAATTTAACACATTATAATATTTAT
1 TACTTCGTAAATAATTTATATTAAATATTTAAAAGTATTTAAATTTAACACATTATAATATTTAT
734678 AAATTTGAATAGCA
66 AAATTTGAATAGCA
734692 TACTTCGT-AATAATTTATATTAAATATTTAAAAGTATTTAAATTTAACACATTATAATATTTAT
1 TACTTCGTAAATAATTTATATTAAATATTTAAAAGTATTTAAATTTAACACATTATAATATTTAT
734756 AAATTTGAATAGCA
66 AAATTTGAATAGCA
734770 T
1 T
734771 TTAAGTTAAT
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 71 0.90
79 8 0.10
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (79 bp):
TACTTCGTAAATAATTTATATTAAATATTTAAAAGTATTTAAATTTAACACATTATAATATTTAT
AAATTTGAATAGCA
Found at i:756193 original size:19 final size:19
Alignment explanation
Indices: 756150--756193 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
756140 ATTATTTTCG
756150 ATATAAGTATATATATAAA
1 ATATAAGTATATATATAAA
* * * *
756169 AAATAATTATATTTATCAA
1 ATATAAGTATATATATAAA
756188 ATATAA
1 ATATAA
756194 AATAAATTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
ATATAAGTATATATATAAA
Found at i:762511 original size:4 final size:4
Alignment explanation
Indices: 762502--762556 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
762492 AATGAGAAGG
762502 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
762550 CATA CAT
1 CATA CAT
762557 GTGGTGTTCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:775199 original size:29 final size:30
Alignment explanation
Indices: 775129--775200 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
775119 AATAAGGCTT
* *
775129 ATAGGTCGGTTTTAAAATTTATTTAGGCAT
1 ATAGGTCGATTTTAAAATTTATTTAGGCAA
* * *
775159 TTAGG-CTAATTTTAAAA-TTATTTAGGGAA
1 ATAGGTC-GATTTTAAAATTTATTTAGGCAA
775188 ATAGGTCGATTTT
1 ATAGGTCGATTTT
775201 GAGGAAAAGC
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (30 bp):
ATAGGTCGATTTTAAAATTTATTTAGGCAA
Found at i:798004 original size:4 final size:4
Alignment explanation
Indices: 797995--798020 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
797985 TGAAAGGAGG
797995 GAAT GAAT GAAT GAAT GAAT GAAT GA
1 GAAT GAAT GAAT GAAT GAAT GAAT GA
798021 GGAACAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:803493 original size:42 final size:42
Alignment explanation
Indices: 803446--803544 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
803436 TATACGAACA
* * *
803446 GCACTAAGTGCGCGAAACTAAAATGACAATGTTGAATAACGG
1 GCACTAAGTGTGCGAAACAAAAATGACAATGTCGAATAACGG
*
803488 GCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACGG
1 GCACTAAGTGTGCGAAACAAAAATGACAATGTCGAATAACGG
803530 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
803545 TATCAATATC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.18
Consensus pattern (42 bp):
GCACTAAGTGTGCGAAACAAAAATGACAATGTCGAATAACGG
Found at i:808273 original size:16 final size:16
Alignment explanation
Indices: 808252--808287 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
808242 ATATCGACTC
808252 AAAAAAGAA-AAAAGA
1 AAAAAAGAAGAAAAGA
808267 GAAAAAAGAAGAAAAGA
1 -AAAAAAGAAGAAAAGA
808284 AAAA
1 AAAA
808288 CCCTTTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAGAAAAGA
Found at i:818849 original size:40 final size:37
Alignment explanation
Indices: 818805--818912 Score: 119
Period size: 40 Copynumber: 2.8 Consensus size: 37
818795 TGTTTGATTA
*
818805 AAAATATATATATTTAATATATAATTCGAATTAAAAGTCT
1 AAAATATATATATTTAATATATAATTCG-ATTAAAA--AT
* *
818845 AAAATATATATATTTAATAAAAAGTATATTTGATTAAAAAT
1 AAAATATATATATTTAAT--ATA-TA-ATTCGATTAAAAAT
818886 -AAATATATATATTTAATATATAATTCG
1 AAAATATATATATTTAATATATAATTCG
818913 GGCCGAGCCC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
36 4 0.07
37 2 0.03
38 2 0.03
40 35 0.59
41 1 0.02
42 2 0.03
43 9 0.15
44 4 0.07
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (37 bp):
AAAATATATATATTTAATATATAATTCGATTAAAAAT
Found at i:818901 original size:20 final size:20
Alignment explanation
Indices: 818845--818903 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
818835 TTAAAAGTCT
818845 AAAATATATATATTTAATAA
1 AAAATATATATATTTAATAA
* *
818865 AAAGTATATTTGA-TTAA-AA
1 AAAATATATAT-ATTTAATAA
818884 ATAAATATATATATTTAATA
1 A-AAATATATATATTTAATA
818904 TATAATTCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 4 0.13
20 25 0.81
21 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAATATATATATTTAATAA
Found at i:820157 original size:3 final size:3
Alignment explanation
Indices: 820149--820182 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
820139 TTAAGGGTTC
820149 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
820183 TGCATTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:830753 original size:20 final size:20
Alignment explanation
Indices: 830728--830765 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
830718 ATTTAACCAA
830728 AAAATT-AAGTATGAAAAAAC
1 AAAATTCAAG-ATGAAAAAAC
830748 AAAATTCAAGATGAAAAA
1 AAAATTCAAGATGAAAAA
830766 TATAAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAATTCAAGATGAAAAAAC
Found at i:851295 original size:72 final size:72
Alignment explanation
Indices: 851191--851338 Score: 233
Period size: 72 Copynumber: 2.1 Consensus size: 72
851181 CAATTTCTTC
* * * *
851191 CAAATTTGACATACTCCCCATCCACCTTGGTATGTCCCCAGAAAGCTCGTTATTGCTTAAATCCA
1 CAAACTTGACATACTCCCCATCCACATTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
851256 ATGTTGA
66 ATGTTGA
* * *
851263 CAAACTTGACATATTCTCCATCGACATTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
1 CAAACTTGACATACTCCCCATCCACATTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
851328 ATGTTGA
66 ATGTTGA
851335 CAAA
1 CAAA
851339 AAGGAGCAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (72 bp):
CAAACTTGACATACTCCCCATCCACATTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
ATGTTGA
Found at i:851375 original size:72 final size:72
Alignment explanation
Indices: 851225--851376 Score: 173
Period size: 72 Copynumber: 2.1 Consensus size: 72
851215 CCTTGGTATG
* *** *** *
851225 TCCCCAGAAAGCTCGTTATTGCTTAAATCCAATGTTGACAAACTTGACATATTCTCCATCGACAT
1 TCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTGACAAAAAGGACATATTAGACAACGACAT
*
851290 TGGTATC
66 TGGGATC
*
851297 TCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTGACAAAAAGGAGCA-ATTAGACAAGGA-A
1 TCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTGACAAAAAGGA-CATATTAGACAACGACA
851360 TCTGGGATC
65 T-TGGGATC
*
851369 TTCCCAGA
1 TCCCCAGA
851377 GAAATGATTC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
71 2 0.03
72 63 0.94
73 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (72 bp):
TCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTGACAAAAAGGACATATTAGACAACGACAT
TGGGATC
Found at i:858281 original size:15 final size:16
Alignment explanation
Indices: 858261--858290 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
858251 GTACTACAAG
858261 ATTATTTT-TTTAAAA
1 ATTATTTTATTTAAAA
858276 ATTATTTTATTTAAA
1 ATTATTTTATTTAAA
858291 TGCCTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATTTTATTTAAAA
Found at i:858716 original size:25 final size:25
Alignment explanation
Indices: 858634--858703 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
858624 GAATTTTAGC
858634 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
*
858659 GCTCTCTGATTATTAGCACATTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
858684 GCTCTCTGA-TATTTAGCACG
1 GCTCTCTGATTA-TTAGCACG
858704 CCAGTGCTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 2 0.05
25 40 0.95
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:858723 original size:22 final size:22
Alignment explanation
Indices: 858657--858762 Score: 77
Period size: 22 Copynumber: 4.5 Consensus size: 22
858647 TAGCACGTTG
**
858657 GTGCTCTCTGATTATTAGCACATTG
1 GTGCTCTCTG--T-TTAGCACATCA
**
858682 GTGCTCTCTGATATTTAGCACGCCA
1 GTGCTCTCTG---TTTAGCACATCA
*
858707 GTGCTCTCTGTTTAGCACATCT
1 GTGCTCTCTGTTTAGCACATCA
* * * *
858729 GTGCTTTCTGTATAGCACTTTA
1 GTGCTCTCTGTTTAGCACATCA
858751 GTGCTCTCTGTT
1 GTGCTCTCTGTT
858763 CATTGGTGCA
Statistics
Matches: 64, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
22 36 0.56
25 27 0.42
26 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.41
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACATCA
Found at i:865032 original size:13 final size:13
Alignment explanation
Indices: 865014--865038 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
865004 GTTTTATTTT
865014 TTATTTAAAATTG
1 TTATTTAAAATTG
865027 TTATTTAAAATT
1 TTATTTAAAATT
865039 ATGTTACATA
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTATTTAAAATTG
Found at i:873250 original size:15 final size:15
Alignment explanation
Indices: 873232--873263 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
873222 AGATGACTAT
873232 ATAAAAAATGAATAA
1 ATAAAAAATGAATAA
*
873247 ATAAAAAATGTATAA
1 ATAAAAAATGAATAA
873262 AT
1 AT
873264 TATTAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (15 bp):
ATAAAAAATGAATAA
Found at i:877590 original size:13 final size:13
Alignment explanation
Indices: 877572--877601 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
877562 TCACTCTATC
877572 ATATAAGTAAAGA
1 ATATAAGTAAAGA
877585 ATATAAGTAAAGA
1 ATATAAGTAAAGA
877598 ATAT
1 ATAT
877602 TTGTTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (13 bp):
ATATAAGTAAAGA
Found at i:883003 original size:2 final size:2
Alignment explanation
Indices: 882996--883020 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
882986 CCAAAAATGA
882996 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
883021 CTTTGGGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:887045 original size:21 final size:21
Alignment explanation
Indices: 887008--887080 Score: 94
Period size: 21 Copynumber: 3.4 Consensus size: 21
886998 TGATCAGTAT
*
887008 ACGACACAT-AAGTGCCTGAA
1 ACGACACATGAGGTGCCTGAA
*
887028 ACGACACATGAGGTGCCTGAT
1 ACGACACATGAGGTGCCTGAA
*
887049 ACGACACACGAGGTGCCTGAGA
1 ACGACACATGAGGTGCCTGA-A
887071 TACGACACAT
1 -ACGACACAT
887081 AAAGTGCTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 9 0.20
21 28 0.62
23 8 0.18
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (21 bp):
ACGACACATGAGGTGCCTGAA
Found at i:887087 original size:23 final size:23
Alignment explanation
Indices: 887006--887114 Score: 104
Period size: 23 Copynumber: 5.0 Consensus size: 23
886996 CCTGATCAGT
887006 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
* *
887027 A-ACGACACATGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
** *
887047 ATACGACACACGAGGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
*
887070 ATACGACACATAAAGTGCTTGATG
1 ATACGACACATAAAGTGCCTGA-G
*
887094 -TACAACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
887115 TCGGCAAAGC
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
20 10 0.14
21 25 0.34
23 38 0.51
24 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:888197 original size:15 final size:16
Alignment explanation
Indices: 888165--888197 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
888155 GTTTTCCCTT
*
888165 TTATTTTTCTTTCTCC
1 TTATTTTTCTTTCCCC
888181 TTATTTTTC-TTCCCC
1 TTATTTTTCTTTCCCC
888196 TT
1 TT
888198 TCCTTCCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTTTCTTTCCCC
Found at i:888264 original size:18 final size:18
Alignment explanation
Indices: 888241--888292 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
888231 TTTTAAGCTA
888241 TTTTGTTTCTATTTCTTC
1 TTTTGTTTCTATTTCTTC
*
888259 TTTTGTTTCT-TTTATTC
1 TTTTGTTTCTATTTCTTC
*
888276 TTTTATTT-TATTCTCTT
1 TTTTGTTTCTATT-TCTT
888293 TTATGCATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 1 0.03
17 15 0.52
18 13 0.45
ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTTGTTTCTATTTCTTC
Found at i:888460 original size:7 final size:7
Alignment explanation
Indices: 888448--888497 Score: 82
Period size: 7 Copynumber: 7.0 Consensus size: 7
888438 CTTTATCTTT
888448 ACCCTAA
1 ACCCTAA
888455 ACCCTAAA
1 ACCCT-AA
888463 ACCCTAA
1 ACCCTAA
*
888470 ATCCTAA
1 ACCCTAA
888477 ACCCTAA
1 ACCCTAA
888484 ACCCTAA
1 ACCCTAA
888491 ACCCTAA
1 ACCCTAA
888498 TATAATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
7 33 0.82
8 7 0.17
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (7 bp):
ACCCTAA
Found at i:888505 original size:5 final size:5
Alignment explanation
Indices: 888495--888534 Score: 62
Period size: 5 Copynumber: 7.6 Consensus size: 5
888485 CCCTAAACCC
888495 TAATA TAATA TAATA TAATA TAATA TAATAA TATATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAAT-A TA-ATA TAA
888535 AACATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 25 0.76
6 6 0.18
7 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:890658 original size:24 final size:24
Alignment explanation
Indices: 890631--890677 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
890621 AGCCTATAAT
890631 GGGTAGCTCCAAAAAGCAATTAAC
1 GGGTAGCTCCAAAAAGCAATTAAC
* * *
890655 GGGTAGCTTCGAAGAGCAATTAA
1 GGGTAGCTCCAAAAAGCAATTAA
890678 TGGGAAGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (24 bp):
GGGTAGCTCCAAAAAGCAATTAAC
Found at i:890787 original size:26 final size:25
Alignment explanation
Indices: 890723--890788 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
890713 ATACGAGCAC
* * *
890723 TAACGGGAAGCTTACAAAGAGCTTT
1 TAACGGGAAGCTCACAAAGAGCATA
*
890748 TAATCGGAAAGCTCACAAAGAGCCATA
1 TAA-CGGGAAGCTCACAAAGAG-CATA
*
890775 TAACGGGACGCTCA
1 TAACGGGAAGCTCA
890789 TAAGAGCTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 3 0.09
26 25 0.76
27 5 0.15
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (25 bp):
TAACGGGAAGCTCACAAAGAGCATA
Found at i:900455 original size:17 final size:18
Alignment explanation
Indices: 900419--900469 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
900409 TAGGGGTGTG
*
900419 CAAAATTCGGGTAAAACCGA
1 CAAAATTC-GGT-TAACCGA
900439 -AAAATTCGGTTAACCGA
1 CAAAATTCGGTTAACCGA
**
900456 CCGAATTCGGTTAA
1 CAAAATTCGGTTAA
900470 TCGGTCGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.22
18 14 0.52
19 7 0.26
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (18 bp):
CAAAATTCGGTTAACCGA
Found at i:900749 original size:9 final size:9
Alignment explanation
Indices: 900735--900811 Score: 75
Period size: 9 Copynumber: 8.6 Consensus size: 9
900725 GTAGTGATTC
900735 AATTTGGTT
1 AATTTGGTT
900744 AATTTGGTT
1 AATTTGGTT
* *
900753 AATTCGGGT
1 AATTTGGTT
900762 AATTTCGGTT
1 AATTT-GGTT
*
900772 AA-TTGGGT
1 AATTTGGTT
* *
900780 AATTCGGAT
1 AATTTGGTT
*
900789 AATTCGGTT
1 AATTTGGTT
*
900798 AATTCGGTT
1 AATTTGGTT
900807 AATTT
1 AATTT
900812 TTAACCAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
8 5 0.09
9 47 0.82
10 5 0.09
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.45
Consensus pattern (9 bp):
AATTTGGTT
Found at i:900764 original size:18 final size:18
Alignment explanation
Indices: 900743--900810 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
900733 TCAATTTGGT
*
900743 TAATTTGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
900761 TAATTTCGGTTAATT-GGG
1 TAA-TTCGGTTAATTCGGG
* *
900779 TAATTCGGATAATTCGGT
1 TAATTCGGTTAATTCGGG
900797 TAATTCGGTTAATT
1 TAATTCGGTTAATT
900811 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.23
18 24 0.55
19 10 0.23
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGG
Found at i:901635 original size:12 final size:12
Alignment explanation
Indices: 901618--901643 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
901608 GATAAGTATT
901618 ATATTTATTTAA
1 ATATTTATTTAA
901630 ATATTTATTTAA
1 ATATTTATTTAA
901642 AT
1 AT
901644 TTTTTGTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATTTATTTAA
Found at i:910288 original size:8 final size:8
Alignment explanation
Indices: 910275--910315 Score: 73
Period size: 8 Copynumber: 5.0 Consensus size: 8
910265 TCTTTTATAT
910275 ATATAATA
1 ATATAATA
910283 ATATAATA
1 ATATAATA
910291 ATATAATA
1 ATATAATA
910299 ATATAATTA
1 ATATAA-TA
910308 ATATAATA
1 ATATAATA
910316 CTTATTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 24 0.75
9 8 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:919855 original size:28 final size:29
Alignment explanation
Indices: 919801--919855 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
919791 TTTCTATGTG
* * **
919801 TTTATAATGTTATTAATTAGTTTAATATT
1 TTTATAATGTAATTAATTAATCAAATATT
919830 TTTATAAT-TAATTAATTAATCAAATA
1 TTTATAATGTAATTAATTAATCAAATA
919856 GTTAATATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 14 0.64
29 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (29 bp):
TTTATAATGTAATTAATTAATCAAATATT
Found at i:926092 original size:7 final size:7
Alignment explanation
Indices: 926080--926107 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
926070 TTAGGATGAG
926080 TTTTAAA
1 TTTTAAA
926087 TTTTAAA
1 TTTTAAA
926094 TTTTAAA
1 TTTTAAA
926101 TTTTAAA
1 TTTTAAA
926108 ATAAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTTAAA
Found at i:927858 original size:44 final size:44
Alignment explanation
Indices: 927810--927899 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
927800 TAAATTTTAA
* *
927810 GATTCAAAAATTAAATCATTTAAATCTTACTTTTTAAGAATATG
1 GATTCAAAAATTAAATCACTTAAATCTTACTTTTTAAAAATATG
*
927854 GATTCAAAAATTAAATTACTTAAATCTTACTTTTTAAAAATATG
1 GATTCAAAAATTAAATCACTTAAATCTTACTTTTTAAAAATATG
927898 GA
1 GA
927900 GTTAAATACA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (44 bp):
GATTCAAAAATTAAATCACTTAAATCTTACTTTTTAAAAATATG
Found at i:930248 original size:23 final size:22
Alignment explanation
Indices: 930215--930257 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
930205 TTCTTTTGTT
*
930215 TTATATATATAATAATATAATA
1 TTATATATATAATAAAATAATA
930237 TTATATTATATAATAAAATAA
1 TTATA-TATATAATAAAATAA
930258 CATACTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATATATATAATAAAATAATA
Found at i:947118 original size:123 final size:123
Alignment explanation
Indices: 946890--947419 Score: 657
Period size: 123 Copynumber: 4.3 Consensus size: 123
946880 TTTCAAATCA
* * * *
946890 TGAACATGAACTATAAAATACACAT----AA-AAAAAAATTGAATGAGCTAATTGTATTAATCTG
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAG
* *
946950 ATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTAAAAAAAATTGAATTGAAACCT
66 ATCCGATATATAATTACTT-AAAAAGAAAATGCCTTTTAAAAAAATTGAATTGAAACCT
** *
947009 TGAATATGAACTATAAAATAGAC-TGAAGAATGTAAAAATTGAATGAGTTAATTGTATTAATCAT
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAG
*
947073 ATCCGATATATAATTACTTAAAAAAGAAGATGCCTTTTAAAAAAATTGAATTGAAACCT
66 ATCCGATATATAATTACTT-AAAAAGAAAATGCCTTTTAAAAAAATTGAATTGAAACCT
*
947132 TGAATATGAACTAGAACTATAAAATAGACATGAATAATAAAAAAATTGAATGAGTTAATTGTATT
1 TG-A-AT--A-T-GAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATT
* * **
947197 AATCGGATCCGATATGA-AATTACTTAAAAAGAAAATGCCTTTT--AAAAGTTGGCTTGAAACCT
60 AATCAGATCCGATAT-ATAATTACTTAAAAAGAAAATGCCTTTTAAAAAAATTGAATTGAAACCT
* * *
947259 TGAACATAAACTATAAAACAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAG
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAG
* * * *
947324 ATCCGATATGTAATTACTTAAAAAGAAAATGTCTTTTAAAAAAATTGACTTGAAAACTT
66 ATCCGATATATAATTACTTAAAAAGAAAATGCCTTTTAAAAAAATTGAATTG-AAACCT
* * * * *
947383 TAAAAAT-AACTTTAAAATAAATATGAAGAATAAAAAA
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAA
947420 TTAGTTATTG
Statistics
Matches: 359, Mismatches: 35, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
118 1 0.00
119 21 0.06
121 88 0.25
122 3 0.01
123 124 0.35
124 11 0.03
125 3 0.01
126 1 0.00
127 19 0.05
128 1 0.00
129 33 0.09
130 53 0.15
131 1 0.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (123 bp):
TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAG
ATCCGATATATAATTACTTAAAAAGAAAATGCCTTTTAAAAAAATTGAATTGAAACCT
Found at i:947292 original size:121 final size:122
Alignment explanation
Indices: 946917--947481 Score: 620
Period size: 123 Copynumber: 4.6 Consensus size: 122
946907 ATACACATAA
* * *
946917 AAAAAAATTGAATGAGCTAATTGTATTAATCTGATCCGATATGTAATTACTTAAAAAAGAAAATG
1 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGAAATTACTTAAAAAAGAAAATG
* * *
946982 CCTTTAAAAAAAATTGAATTGAAACCTTGAATATGAACTATAAAATAGAC-TGAAGAAT
66 CCTTT--TAAAAATTGAATTGAAACCTTGAAAATAAACTATAAAATAGACATGAAGAAT
** * *
947040 GTAAAAATTGAATGAGTTAATTGTATTAATCATATCCGATAT-ATAATTACTTAAAAAAGAAGAT
1 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGA-AATTACTTAAAAAAGAAAAT
*
947104 GCCTTTTAAAAAAATTGAATTGAAACCTTGAATATGAACTAGAACTATAAAATAGACATGAATAA
65 GCCTTTT--AAAAATTGAATTGAAACCTTG-A-A--AA-TA-AACTATAAAATAGACATGAAGAA
947169 T
122 T
*
947170 AAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCGATATGAAATTACTT-AAAAAGAAAATG
1 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGAAATTACTTAAAAAAGAAAATG
* ** * *
947234 CCTTTTAAAAGTTGGCTTGAAACCTTGAACATAAACTATAAAACAGACATGAAGAAT
66 CCTTTTAAAAATTGAATTGAAACCTTGAAAATAAACTATAAAATAGACATGAAGAAT
*
947291 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGTAATTACTT-AAAAAGAAAATG
1 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGAAATTACTTAAAAAAGAAAATG
* * * * * * *
947355 TCTTTTAAAAAAATTGACTTGAAAACTTTAAAA-ATAACTTTAAAATAAATATGAAGAAT
66 CCTTTT--AAAAATTGAATTGAAACCTTGAAAATA-AACTATAAAATAGACATGAAGAAT
* * * *
947414 -AAAAAA-T---T-AGTT-ATTGTATTAATTAGATCCAATATGAAAATTTC-TATAAAA-AAAAT
1 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATG-AAATTACTTAAAAAAGAAAAT
947470 G-CTTTTAGAAAA
65 GCCTTTTA-AAAA
947482 AATTACTGTA
Statistics
Matches: 386, Mismatches: 39, Indels: 43
0.82 0.08 0.09
Matches are distributed among these distances:
113 1 0.00
114 4 0.01
115 5 0.01
116 29 0.08
117 13 0.03
118 1 0.00
121 90 0.23
122 9 0.02
123 124 0.32
124 1 0.00
125 2 0.01
126 1 0.00
127 19 0.05
128 1 0.00
129 32 0.08
130 53 0.14
131 1 0.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (122 bp):
AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGAAATTACTTAAAAAAGAAAATG
CCTTTTAAAAATTGAATTGAAACCTTGAAAATAAACTATAAAATAGACATGAAGAAT
Found at i:963013 original size:6 final size:6
Alignment explanation
Indices: 963002--963028 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
962992 AACAGTTATA
963002 CCAGCT CCAGCT CCAGCT CCAGCT CCA
1 CCAGCT CCAGCT CCAGCT CCAGCT CCA
963029 TGTTTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.15, T:0.15
Consensus pattern (6 bp):
CCAGCT
Found at i:963922 original size:75 final size:75
Alignment explanation
Indices: 963837--964066 Score: 451
Period size: 75 Copynumber: 3.1 Consensus size: 75
963827 GGCTTTAAAT
963837 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATTAGTTTTTTGA
1 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATTAGTTTTTTGA
963902 TAAATAAAGA
66 TAAATAAAGA
963912 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATTAGTTTTTTGA
1 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATTAGTTTTTTGA
963977 TAAATAAAGA
66 TAAATAAAGA
*
963987 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATCAGTTTTTTGA
1 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATTAGTTTTTTGA
964052 TAAATAAAGA
66 TAAATAAAGA
964062 TTTTA
1 TTTTA
964067 AATTATAAAA
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 154 1.00
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (75 bp):
TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATTAGTTTTTTGA
TAAATAAAGA
Found at i:966068 original size:51 final size:51
Alignment explanation
Indices: 965989--966243 Score: 361
Period size: 51 Copynumber: 5.0 Consensus size: 51
965979 GATGCCGAAC
* *
965989 CAGCAAGGTGGAAACATCGAAT-CTCAAACATACACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATAC-CAAACATATACTCAGCTACCACAACAG
* ** *
966040 CAGCAAGGTGGTAACATCAAATACCAAACATATACTCAACTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
* * *
966091 CAGCAAGGTGGAAACGTTGAATACCAAACATATACTCAGCTGCCACAACAA
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
* * *
966142 CAGCAAGGTGGAAACATTGAATCCCAAACTTATACTCAGCTACAACAACAG
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
*
966193 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCCT-CCACAACAG
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAG-CTACCACAACAG
966244 TACTTAATGG
Statistics
Matches: 183, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
51 180 0.98
52 3 0.02
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.16
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
Found at i:968159 original size:51 final size:51
Alignment explanation
Indices: 968083--968185 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
968073 CCTTGGAACT
968083 TTTTACTGATTATAATTTGTTATTGATCCCTTTTGCCTATATCTGTTTGTG
1 TTTTACTGATTATAATTTGTTATTGATCCCTTTTGCCTATATCTGTTTGTG
968134 TTTTACTGATTATAATTTGTTATTGATCCCTTTTGCCTATATCTGTTTGTG
1 TTTTACTGATTATAATTTGTTATTGATCCCTTTTGCCTATATCTGTTTGTG
968185 T
1 T
968186 ATGTCCTTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (51 bp):
TTTTACTGATTATAATTTGTTATTGATCCCTTTTGCCTATATCTGTTTGTG
Found at i:968174 original size:27 final size:27
Alignment explanation
Indices: 968093--968174 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 27
968083 TTTTACTGAT
968093 TATAATTTGTTATTGATCCCTTTTGCC
1 TATAATTTGTTATTGATCCCTTTTGCC
* **
968120 TAT-ATCTGTT-TGTG-T---TTTACTGAT
1 TATAATTTGTTAT-TGATCCCTTT--TGCC
968144 TATAATTTGTTATTGATCCCTTTTGCC
1 TATAATTTGTTATTGATCCCTTTTGCC
968171 TATA
1 TATA
968175 TCTGTTTGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
22 3 0.08
24 5 0.12
25 10 0.25
26 10 0.25
27 9 0.22
29 3 0.08
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.54
Consensus pattern (27 bp):
TATAATTTGTTATTGATCCCTTTTGCC
Found at i:971730 original size:3 final size:3
Alignment explanation
Indices: 971722--971762 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
971712 CGGTCTCAAC
971722 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
971763 CAATTAGTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:974877 original size:3 final size:3
Alignment explanation
Indices: 974869--974906 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
974859 CAATGGGAGA
974869 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
974907 ATCGAAGAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:980177 original size:34 final size:35
Alignment explanation
Indices: 980123--980196 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 35
980113 TCCTTACACC
980123 TCTTTTGTTCTCCTTTCAACTTCAAAGGTAGGCAA
1 TCTTTTGTTCTCCTTTCAACTTCAAAGGTAGGCAA
980158 TCTTTTGTTC-CCTTTCAACTTCAAAGGTAGGCAA
1 TCTTTTGTTCTCCTTTCAACTTCAAAGGTAGGCAA
980192 -CTTTT
1 TCTTTT
980197 ACCCATACAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 5 0.13
34 24 0.62
35 10 0.26
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (35 bp):
TCTTTTGTTCTCCTTTCAACTTCAAAGGTAGGCAA
Found at i:993193 original size:20 final size:21
Alignment explanation
Indices: 993161--993199 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
993151 ACTAAAGATA
993161 TTTAAAAATTTTAC-TATTAT
1 TTTAAAAATTTTACATATTAT
993181 TTTAATAAA-TTTACATATT
1 TTTAA-AAATTTTACATATT
993200 TAAATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAAAATTTTACATATTAT
Found at i:994669 original size:33 final size:33
Alignment explanation
Indices: 994631--994732 Score: 145
Period size: 33 Copynumber: 3.2 Consensus size: 33
994621 AGATTAATTT
* * *
994631 ATATTTGATGTATCATTATATTAAATTATTTAA
1 ATATTTCATATATCATTCTATTAAATTATTTAA
994664 ATATTTCATATATCATTCTATTAAATTATTTAA
1 ATATTTCATATATCATTCTATTAAATTATTTAA
* *
994697 ATA--TCATTTACCATTCTATTAAATTATTTAA
1 ATATTTCATATATCATTCTATTAAATTATTTAA
994728 ATATT
1 ATATT
994733 ATATAACTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
31 29 0.47
33 33 0.53
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (33 bp):
ATATTTCATATATCATTCTATTAAATTATTTAA
Found at i:994715 original size:31 final size:31
Alignment explanation
Indices: 994644--994737 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 31
994634 TTTGATGTAT
* *
994644 CATTATATTAAATTATTTAAATATTTCATATAT
1 CATTCTATTAAATTATTTAAATA--TCATATAC
*
994677 CATTCTATTAAATTATTTAAATATCATTTAC
1 CATTCTATTAAATTATTTAAATATCATATAC
*
994708 CATTCTATTAAATTATTTAAATATTATATA
1 CATTCTATTAAATTATTTAAATATCATATA
994738 ACTTAACTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 34 0.61
33 22 0.39
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (31 bp):
CATTCTATTAAATTATTTAAATATCATATAC
Found at i:1000675 original size:24 final size:25
Alignment explanation
Indices: 1000647--1000705 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
1000637 ATTGGCTTGT
* *
1000647 ATGAGCTTCCCGTTA-ATGGCTCTC
1 ATGAGCTTCCCATTACATGGCTCAC
*
1000671 CTGAGCTTCCCATTACATGGCTCAC
1 ATGAGCTTCCCATTACATGGCTCAC
1000696 ATGAGCTTCC
1 ATGAGCTTCC
1000706 TCTTATGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCATTACATGGCTCAC
Found at i:1003044 original size:18 final size:18
Alignment explanation
Indices: 1003021--1003058 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1003011 TTTTGCTAAC
1003021 ACATAACCCAACTATTAT
1 ACATAACCCAACTATTAT
1003039 ACATAACCCAACTATTAT
1 ACATAACCCAACTATTAT
1003057 AC
1 AC
1003059 TTTTATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (18 bp):
ACATAACCCAACTATTAT
Found at i:1008662 original size:19 final size:18
Alignment explanation
Indices: 1008609--1008662 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
1008599 ACGAAACAGA
*
1008609 GAAGGAAAGAAGGAAAGG
1 GAAGGAAAGAAGAAAAGG
* * *
1008627 AAAGAAAAAGAAAAAAAGG
1 GAAG-GAAAGAAGAAAAGG
1008646 GAAGGAAAGGAAGAAAA
1 GAAGGAAA-GAAGAAAA
1008663 TTTGGGATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
GAAGGAAAGAAGAAAAGG
Found at i:1009456 original size:15 final size:14
Alignment explanation
Indices: 1009420--1009460 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
1009410 ATATTGAATT
1009420 AAATGAATTAAA-A
1 AAATGAATTAAATA
*
1009433 ATATGAATTAAATA
1 AAATGAATTAAATA
1009447 AAAGTGAATTAAAT
1 AAA-TGAATTAAAT
1009461 TATGATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.46
14 3 0.12
15 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (14 bp):
AAATGAATTAAATA
Found at i:1019143 original size:26 final size:26
Alignment explanation
Indices: 1019085--1019137 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1019075 TGATTCCTTG
*
1019085 TGGAACTCTAAGGGAATTGCCTACCT
1 TGGAACTCTAAGGGAATTGCCCACCT
* *
1019111 TGGAACTCTAAGGGAGTTGCCCCCCT
1 TGGAACTCTAAGGGAATTGCCCACCT
1019137 T
1 T
1019138 TTAACTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (26 bp):
TGGAACTCTAAGGGAATTGCCCACCT
Found at i:1027868 original size:34 final size:34
Alignment explanation
Indices: 1027825--1027892 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1027815 TAAGCAATAC
1027825 ATAACCTTCCATTTTTGTAAACTTACCCTTCAAG
1 ATAACCTTCCATTTTTGTAAACTTACCCTTCAAG
1027859 ATAACCTTCCATTTTTGTAAACTTACCCTTCAAG
1 ATAACCTTCCATTTTTGTAAACTTACCCTTCAAG
1027893 CAACCATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (34 bp):
ATAACCTTCCATTTTTGTAAACTTACCCTTCAAG
Found at i:1032472 original size:72 final size:73
Alignment explanation
Indices: 1032323--1032523 Score: 260
Period size: 72 Copynumber: 2.7 Consensus size: 73
1032313 CAATATTATT
* * *
1032323 AACTACTCTAACATTACTAAATATATTTCACTTAAATTGCAATTTAAATTTATACAATTTTGTTC
1 AACTACTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATACAATTTTGTTC
**
1032388 ATCCATGG
66 ATCCATAA
* * * *
1032396 AACTACTCTGACATTATTAAATATATTTTATTTAAA-TACAATTCAAATTTATACAATTTTGTTG
1 AACTACTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATACAATTTTGTTC
1032460 ATCCATAA
66 ATCCATAA
* * **
1032468 AACTATTGTTTGACATTACTAAATGCATTTCATTTAAATTGCAATTCAAATTTATA
1 AACTA--CTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATA
1032524 AGAAATTTAA
Statistics
Matches: 109, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
72 36 0.33
73 32 0.29
74 25 0.23
75 16 0.15
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.42
Consensus pattern (73 bp):
AACTACTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATACAATTTTGTTC
ATCCATAA
Found at i:1033021 original size:2 final size:2
Alignment explanation
Indices: 1033009--1033037 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1032999 GTTGATTAAA
1033009 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1033038 GTAAATGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1045293 original size:2 final size:2
Alignment explanation
Indices: 1045286--1045312 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1045276 ATTCAAGGGT
1045286 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1045313 TTATGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1045935 original size:19 final size:19
Alignment explanation
Indices: 1045911--1045953 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1045901 TGATACATAA
*
1045911 TTTATA-TTAAAATCTCAAT
1 TTTATAGTT-AAATCACAAT
1045930 TTTATAGTTAAATCACAAT
1 TTTATAGTTAAATCACAAT
1045949 TTTAT
1 TTTAT
1045954 TTACTAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (19 bp):
TTTATAGTTAAATCACAAT
Found at i:1048393 original size:30 final size:32
Alignment explanation
Indices: 1048345--1048407 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
1048335 TAATAAAGTT
*
1048345 AAAATTATACTTTGATTTTTTAAAAATAATAA
1 AAAATTATACTTTAATTTTTTAAAAATAATAA
*
1048377 AAAATTA-A-TTTAATTTTTTAAAAATTATAA
1 AAAATTATACTTTAATTTTTTAAAAATAATAA
1048407 A
1 A
1048408 GATAAGGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 21 0.72
31 1 0.03
32 7 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
AAAATTATACTTTAATTTTTTAAAAATAATAA
Found at i:1049148 original size:24 final size:25
Alignment explanation
Indices: 1049098--1049151 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
1049088 ATTATATACA
* *
1049098 AATAAATTTAACAAAAATAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
*
1049123 AATAAATTCAAC-ACAAGAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
1049147 AATAA
1 AATAA
1049152 CCCATCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.67, C:0.15, G:0.02, T:0.17
Consensus pattern (25 bp):
AATAAATTCAACAAAAAGAAAACAC
Found at i:1052048 original size:3 final size:3
Alignment explanation
Indices: 1052040--1052066 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1052030 TATATTGATG
1052040 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1052067 GTTATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1053945 original size:14 final size:14
Alignment explanation
Indices: 1053928--1053968 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1053918 ATTCATTCTT
1053928 TTTTATTTTTAAAA
1 TTTTATTTTTAAAA
*
1053942 TTTTAATTTTAAAA
1 TTTTATTTTTAAAA
1053956 -TTTATTTATTAAA
1 TTTTATTT-TTAAA
1053969 TTTATTGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTATTTTTAAAA
Found at i:1054655 original size:16 final size:16
Alignment explanation
Indices: 1054634--1054670 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1054624 TGGAAAGATG
1054634 GAAAACT-GAAGGAGTA
1 GAAAACTAGAAGGA-TA
1054650 GAAAACTAGAAGGATA
1 GAAAACTAGAAGGATA
1054666 GAAAA
1 GAAAA
1054671 TATAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.57, C:0.05, G:0.27, T:0.11
Consensus pattern (16 bp):
GAAAACTAGAAGGATA
Found at i:1058546 original size:3 final size:3
Alignment explanation
Indices: 1058538--1058565 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1058528 TTATATTGAT
1058538 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1058566 GTTATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:1069828 original size:75 final size:75
Alignment explanation
Indices: 1069705--1069847 Score: 216
Period size: 75 Copynumber: 1.9 Consensus size: 75
1069695 CAGGCTATGC
* * *
1069705 TCCTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAGGACCTGGTCATCCTCCAAGTCCACCAC
1 TCCTCCTCCAAGGCCAAGTCCTCAAGAGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACCAC
1069770 ATGCCGGGCA
66 ATGCCGGGCA
* * *
1069780 TCCTCCTCCAAGGCCAAGT-CTCTATGAGCCACCACCAAGACCAGGTCATCCTCCAGGTCCACTA
1 TCCTCCTCCAAGGCCAAGTCCTC-AAGAGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACCA
1069844 CATG
65 CATG
1069848 AGCATCCTCC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 3 0.05
75 58 0.95
ACGTcount: A:0.24, C:0.42, G:0.17, T:0.17
Consensus pattern (75 bp):
TCCTCCTCCAAGGCCAAGTCCTCAAGAGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACCAC
ATGCCGGGCA
Found at i:1069884 original size:27 final size:24
Alignment explanation
Indices: 1069826--1069871 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1069816 AAGACCAGGT
* *
1069826 CATCCTCCAGGTCCACTACATGAG
1 CATCCTCCAAGTCCACCACATGAG
1069850 CATCCTCCAAGTCCACCACATG
1 CATCCTCCAAGTCCACCACATG
1069872 TTGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (24 bp):
CATCCTCCAAGTCCACCACATGAG
Found at i:1069911 original size:99 final size:99
Alignment explanation
Indices: 1069751--1069933 Score: 251
Period size: 99 Copynumber: 1.8 Consensus size: 99
1069741 AGGACCTGGT
* * *
1069751 CATCCTCCAAGTCCACCACATGCCGGGCATCCTCCTCCAAGGCCAAGTCTCTATGAGCCACCACC
1 CATCCTCCAAGTCCACCACATGCCGAGCATCCTCCTCCAAGGCCAAGTCCCCATGAGCCACCACC
1069816 AAGACCAGGTCATCCTCCAGGTCCACTACATGAG
66 AAGACCAGGTCATCCTCCAGGTCCACTACATGAG
** * * **
1069850 CATCCTCCAAGTCCACCACATGTTGAGCATCCTCCTCCAAGG-CTAGATCCCCATGCGCCACCGT
1 CATCCTCCAAGTCCACCACATGCCGAGCATCCTCCTCCAAGGCCAAG-TCCCCATGAGCCACCAC
* *
1069914 TAGGACCAGGTCATCCTCCA
65 CAAGACCAGGTCATCCTCCA
1069934 AGCCCACCAC
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
98 3 0.04
99 69 0.96
ACGTcount: A:0.24, C:0.40, G:0.17, T:0.19
Consensus pattern (99 bp):
CATCCTCCAAGTCCACCACATGCCGAGCATCCTCCTCCAAGGCCAAGTCCCCATGAGCCACCACC
AAGACCAGGTCATCCTCCAGGTCCACTACATGAG
Found at i:1070128 original size:90 final size:90
Alignment explanation
Indices: 1069917--1070151 Score: 226
Period size: 90 Copynumber: 2.6 Consensus size: 90
1069907 CCACCGTTAG
* * *
1069917 GACCAGGTCATCCTCCAAGCCCACCACATAATGATCA-TCTTCATCCAGACCATGCTCCCCCTCC
1 GACCAGGTCATCCTCCAAG-TCACCACATAATGAGCATTC-TCATCCAGGCCATGCT--CCCTCC
* * **
1069981 AGGGCCAGGTCCCCATGTGCCACCACCAA
62 AGGACCAAGTCCCCATACGCCACCACCAA
* * * * **
1070010 GACCTGGACATCCTCCAGGTGCATCACATGCTGAGCATTCTCATCCAGGCCATGCT-CCTCCAGG
1 GACCAGGTCATCCTCCAAGT-CACCACATAATGAGCATTCTCATCCAGGCCATGCTCCCTCCAGG
1070074 ACCAAGTCCCCATACGCCACCACC-A
65 ACCAAGTCCCCATACGCCACCACCAA
* * *
1070099 GAACCAGGTCATCTTCCAAGTCAACCACATATTG-GTCATCCTCATCCAGGCCA
1 G-ACCAGGTCATCCTCCAAGTC-ACCACATAATGAG-CATTCTCATCCAGGCCA
1070152 GATCCCCATG
Statistics
Matches: 116, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
89 4 0.03
90 67 0.58
93 43 0.37
94 2 0.02
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (90 bp):
GACCAGGTCATCCTCCAAGTCACCACATAATGAGCATTCTCATCCAGGCCATGCTCCCTCCAGGA
CCAAGTCCCCATACGCCACCACCAA
Found at i:1071664 original size:26 final size:27
Alignment explanation
Indices: 1071635--1071688 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1071625 CATAGTTTAG
1071635 TGTCTGCC-GTTTTTGGCACGTTTCTT
1 TGTCTGCCAGTTTTTGGCACGTTTCTT
*
1071661 TGTCTGCCATTTTTTGGCACGTTTCTT
1 TGTCTGCCAGTTTTTGGCACGTTTCTT
1071688 T
1 T
1071689 ATTGTTCTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.06, C:0.22, G:0.20, T:0.52
Consensus pattern (27 bp):
TGTCTGCCAGTTTTTGGCACGTTTCTT
Found at i:1088193 original size:82 final size:82
Alignment explanation
Indices: 1088056--1088217 Score: 279
Period size: 82 Copynumber: 2.0 Consensus size: 82
1088046 GAAGACTCAT
* *
1088056 AATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGATGTCTCTATTCCATCGCTTAGGAT
1 AATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTATCTATTCCATCGCTTAGGAT
*
1088121 TCTGCAAAATTAAATGC
66 TCTGCAAAATCAAATGC
* *
1088138 AATTTGATAATCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTATCTATTCCATCGTTTAGGAT
1 AATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTATCTATTCCATCGCTTAGGAT
1088203 TCTGCAAAATCAAAT
66 TCTGCAAAATCAAAT
1088218 CAGACACAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (82 bp):
AATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTATCTATTCCATCGCTTAGGAT
TCTGCAAAATCAAATGC
Found at i:1089372 original size:27 final size:27
Alignment explanation
Indices: 1089340--1089393 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1089330 TAAACTGAGC
1089340 CGTAAATATTTTTATAAATATTTACGG
1 CGTAAATATTTTTATAAATATTTACGG
1089367 CGTAAATATTTTTATAAATATTTACGG
1 CGTAAATATTTTTATAAATATTTACGG
1089394 AGTGTCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (27 bp):
CGTAAATATTTTTATAAATATTTACGG
Found at i:1089566 original size:17 final size:17
Alignment explanation
Indices: 1089544--1089604 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
1089534 TAAAGAATGA
1089544 CCTAAATAGCAATTATG
1 CCTAAATAGCAATTATG
** * *
1089561 CCTAAATAAAAAGATAAGG
1 CCTAAAT-AGCA-ATTATG
1089580 CCTAAATAGCAATTATG
1 CCTAAATAGCAATTATG
1089597 CCTAAATA
1 CCTAAATA
1089605 AAAAGATGAG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
17 19 0.56
18 4 0.12
19 11 0.32
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (17 bp):
CCTAAATAGCAATTATG
Found at i:1089587 original size:36 final size:36
Alignment explanation
Indices: 1089544--1089616 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1089534 TAAAGAATGA
1089544 CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
1 CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
*
1089580 CCTAAATAGCAATTATGCCTAAATAAAAAGATGAGG
1 CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
1089616 C
1 C
1089617 AACATAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (36 bp):
CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
Found at i:1094478 original size:23 final size:23
Alignment explanation
Indices: 1094428--1094471 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1094418 AATAGTTCAG
*
1094428 AAGAAAAAGCGCGTCAAAAGACA
1 AAGAAAAAACGCGTCAAAAGACA
*
1094451 AAGAAAAAACGTGTCAAAAGA
1 AAGAAAAAACGCGTCAAAAGA
1094472 TAGAGAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.14, G:0.20, T:0.07
Consensus pattern (23 bp):
AAGAAAAAACGCGTCAAAAGACA
Found at i:1099827 original size:81 final size:80
Alignment explanation
Indices: 1099651--1099828 Score: 191
Period size: 81 Copynumber: 2.2 Consensus size: 80
1099641 AGAAAACTAC
* *
1099651 TAGGAAAAGCCTAAAGGCTAAGCTAGGAAGATGCCTGACAATGATATAGTAAATTGGCAGATAGT
1 TAGG-AAAGACTAAAGGCTAAGCTACGAAGATGCCTGACAATGATATAGTAAATTGGCAGATAGT
* *
1099716 AATAAGGGTTGAGATT
65 AATAAGGATCGAGATT
* * * * *
1099732 TAGGAAAAGCCTAAATGCTAAGCTACGAAGATGCCTGACAATGATTTTATTTCAAATT-TCTA-A
1 TAGG-AAAGACTAAAGGCTAAGCTACGAAGATGCCTGACAATGA-TATA-GT-AAATTGGC-AGA
*
1099795 TAGTAATAAGGATCGAGTTT
61 TAGTAATAAGGATCGAGATT
1099815 TAGG-AAGACTAAAG
1 TAGGAAAGACTAAAG
1099829 CAAAGCGTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
81 50 0.60
82 3 0.04
83 24 0.29
84 6 0.07
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.26
Consensus pattern (80 bp):
TAGGAAAGACTAAAGGCTAAGCTACGAAGATGCCTGACAATGATATAGTAAATTGGCAGATAGTA
ATAAGGATCGAGATT
Found at i:1101633 original size:42 final size:42
Alignment explanation
Indices: 1101580--1101703 Score: 124
Period size: 42 Copynumber: 3.0 Consensus size: 42
1101570 AGGCTGCACA
* * * * *
1101580 GAAGCACATAAGTGCTAAACAGAAACCCGTAAGAGTTGAGC-
1 GAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAACT
* *
1101621 GAAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAACT
1 G-AAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAACT
* * * * *
1101664 GAAGCTCAAAAGAGCTAAACGGAAACTCATTAGGGTTAAA
1 GAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAA
1101704 TAGAAACTCA
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 67 0.97
43 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAACT
Found at i:1101692 original size:21 final size:21
Alignment explanation
Indices: 1101577--1101715 Score: 82
Period size: 21 Copynumber: 6.6 Consensus size: 21
1101567 CGAAGGCTGC
* * *
1101577 ACAGAAGCACATAAGTGCTAA
1 ACAGAAACTCATAAGAGCTAA
* * * *
1101598 ACAGAAACCCGTAAGAGTTGA
1 ACAGAAACTCATAAGAGCTAA
* *
1101619 GC-GAAAGCTCATAAGAGCTGA
1 ACAGAAA-CTCATAAGAGCTAA
* * *
1101640 ACAGAAACCCATAAGGGTTAA
1 ACAGAAACTCATAAGAGCTAA
* * *
1101661 ACTGAAGCTCAAAAGAGCTAA
1 ACAGAAACTCATAAGAGCTAA
* * * *
1101682 ACGGAAACTCATTAGGGTTAA
1 ACAGAAACTCATAAGAGCTAA
*
1101703 ATAGAAACTCATA
1 ACAGAAACTCATA
1101716 TAAGTTAACA
Statistics
Matches: 86, Mismatches: 30, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
20 4 0.05
21 78 0.91
22 4 0.05
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.17
Consensus pattern (21 bp):
ACAGAAACTCATAAGAGCTAA
Found at i:1106759 original size:21 final size:21
Alignment explanation
Indices: 1106665--1106775 Score: 64
Period size: 21 Copynumber: 5.3 Consensus size: 21
1106655 AACTCATATA
* *
1106665 AGTTTTCGTTCAACCCTAATG
1 AGTTTCCGTTCAACCCTTATG
* * * *
1106686 GGTTTCCATT-AAGCTCTTTTG
1 AGTTTCCGTTCAA-CCCTTATG
* * * *
1106707 AGCTTCTGTTTAACCCTTTTG
1 AGTTTCCGTTCAACCCTTATG
* * *
1106728 AGATTT-TGTTCAGCTCTTATG
1 AG-TTTCCGTTCAACCCTTATG
1106749 AGTTTCCGTTCAACCCTTATG
1 AGTTTCCGTTCAACCCTTATG
*
1106770 GGTTTC
1 AGTTTC
1106776 TGTTTAGCAT
Statistics
Matches: 66, Mismatches: 20, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
20 5 0.08
21 57 0.86
22 4 0.06
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (21 bp):
AGTTTCCGTTCAACCCTTATG
Found at i:1106790 original size:42 final size:42
Alignment explanation
Indices: 1106647--1106779 Score: 117
Period size: 42 Copynumber: 3.2 Consensus size: 42
1106637 TCTCTCGAGC
* * * *
1106647 TTCTGTTTAA-CTCATATAAGTTTTCGTTCAACCCTAATGGGT
1 TTCTG-TTAAGCTCTTATGAGTTTCCGTTCAACCCTTATGGGT
** * * * * * *
1106689 TTCCATTAAGCTCTTTTGAGCTTCTGTTTAACCCTTTTGAGAT
1 TTCTGTTAAGCTCTTATGAGTTTCCGTTCAACCCTTATG-GGT
*
1106732 TT-TGTTCAGCTCTTATGAGTTTCCGTTCAACCCTTATGGGT
1 TTCTGTTAAGCTCTTATGAGTTTCCGTTCAACCCTTATGGGT
1106773 TTCTGTT
1 TTCTGTT
1106780 TAGCATTTAT
Statistics
Matches: 67, Mismatches: 21, Indels: 6
0.71 0.22 0.06
Matches are distributed among these distances:
41 8 0.12
42 55 0.82
43 4 0.06
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.46
Consensus pattern (42 bp):
TTCTGTTAAGCTCTTATGAGTTTCCGTTCAACCCTTATGGGT
Found at i:1107824 original size:20 final size:20
Alignment explanation
Indices: 1107795--1107842 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1107785 CTGCATCTAA
*
1107795 GAAAAATTTTGAACTTTTGG
1 GAAAAATTTTGAAATTTTGG
*
1107815 GAAAATTTTTGAAATTTTGG
1 GAAAAATTTTGAAATTTTGG
1107835 GAAAAATT
1 GAAAAATT
1107843 CTCTAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (20 bp):
GAAAAATTTTGAAATTTTGG
Found at i:1109133 original size:27 final size:28
Alignment explanation
Indices: 1109082--1109157 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
1109072 TGACTATTTT
**
1109082 TTAAAAGATTAAT-A-ATTAATTTAAAC-
1 TTAAAA-ATTAATAATATTAAAATAAACA
1109108 TTAAAAATTAATAATATTAAAATAAACA
1 TTAAAAATTAATAATATTAAAATAAACA
**
1109136 AAAAAAATT-ATAAATATTAAAA
1 TTAAAAATTAAT-AATATTAAAA
1109158 ACTAAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
25 6 0.14
26 7 0.17
27 12 0.29
28 17 0.40
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (28 bp):
TTAAAAATTAATAATATTAAAATAAACA
Found at i:1115804 original size:5 final size:5
Alignment explanation
Indices: 1115794--1115819 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1115784 TGAGCATTCG
1115794 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
1115820 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:1116579 original size:9 final size:9
Alignment explanation
Indices: 1116565--1116601 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1116555 TATAGTTTGA
1116565 TATTCGAAT
1 TATTCGAAT
1116574 TATTCGAAT
1 TATTCGAAT
*
1116583 TATTCGAGT
1 TATTCGAAT
1116592 TATTCGAAT
1 TATTCGAAT
1116601 T
1 T
1116602 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1121567 original size:18 final size:18
Alignment explanation
Indices: 1121544--1121579 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1121534 AGATTTATAT
1121544 TTTTTATTCCACAAGCAA
1 TTTTTATTCCACAAGCAA
1121562 TTTTTATTCCACAAGCAA
1 TTTTTATTCCACAAGCAA
1121580 CTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (18 bp):
TTTTTATTCCACAAGCAA
Found at i:1121584 original size:17 final size:18
Alignment explanation
Indices: 1121546--1121584 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1121536 ATTTATATTT
*
1121546 TTTATTCCACAAGCAATT
1 TTTATTCCACAAGCAATC
1121564 TTTATTCCACAAGCAA-C
1 TTTATTCCACAAGCAATC
1121581 TTTA
1 TTTA
1121585 AAAAATTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.38
Consensus pattern (18 bp):
TTTATTCCACAAGCAATC
Found at i:1124118 original size:33 final size:32
Alignment explanation
Indices: 1124057--1124125 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 32
1124047 TTTTAAAATG
*
1124057 AAAATTTTTTATTTAAGGCTTTATAATTT-AT
1 AAAATTTTTTATTTAAGGCTTTAAAATTTAAT
*
1124088 AAAATTATTTTAATTTAA-TCTATTAAAATTTAAT
1 AAAATT-TTTT-ATTTAAGGCT-TTAAAATTTAAT
1124122 AAAA
1 AAAA
1124126 ATATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 6 0.19
32 6 0.19
33 14 0.44
34 6 0.19
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
AAAATTTTTTATTTAAGGCTTTAAAATTTAAT
Found at i:1132131 original size:19 final size:18
Alignment explanation
Indices: 1132109--1132172 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
1132099 TTGTAAAATT
*
1132109 TTATAAAGTCATAAGAAAA
1 TTATAAAAT-ATAAGAAAA
1132128 TTATAAAAATATAAGAAAA
1 TTAT-AAAATATAAGAAAA
*
1132147 TT-TAAAATTCTAA-AAAA
1 TTATAAAA-TATAAGAAAA
1132164 TATATAAAA
1 T-TATAAAA
1132173 ATTATTGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 9 0.23
18 6 0.15
19 20 0.51
20 4 0.10
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
TTATAAAATATAAGAAAA
Found at i:1132160 original size:26 final size:27
Alignment explanation
Indices: 1132124--1132175 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1132114 AAGTCATAAG
1132124 AAAATTAT-AAAAATATA-AGAAAATTT
1 AAAATTATAAAAAATATATA-AAAATTT
*
1132150 AAAATTCTAAAAAATATATAAAAATT
1 AAAATTATAAAAAATATATAAAAATT
1132176 ATTGTATCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 15 0.65
28 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAATTATAAAAAATATATAAAAATTT
Found at i:1132172 original size:10 final size:9
Alignment explanation
Indices: 1132084--1132177 Score: 52
Period size: 10 Copynumber: 10.1 Consensus size: 9
1132074 AAGGCTCTTT
1132084 TAAAAATTA
1 TAAAAATTA
*
1132093 TAAAAATTG
1 TAAAAATTA
*
1132102 T-AAAATTT
1 TAAAAATTA
* *
1132110 TATAAAGTCA
1 TA-AAAATTA
1132120 TAAGAAAATTA
1 T-A-AAAATTA
1132131 TAAAAA-TA
1 TAAAAATTA
1132139 TAAGAAAATT-
1 T-A-AAAATTA
*
1132149 T-AAAATTC
1 TAAAAATTA
1132157 TAAAAAATATA
1 T-AAAAAT-TA
1132168 TAAAAATTA
1 TAAAAATTA
1132177 T
1 T
1132178 TGTATCCCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 20
0.69 0.09 0.21
Matches are distributed among these distances:
7 6 0.09
8 11 0.17
9 17 0.26
10 22 0.33
11 10 0.15
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:1132828 original size:19 final size:19
Alignment explanation
Indices: 1132804--1132860 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1132794 ATTTTTGATG
* *
1132804 TATTTTTATAGATTTTTAC
1 TATTTTTATAAAATTTTAC
1132823 TATTTTTATAAAATTTTAC
1 TATTTTTATAAAATTTTAC
*
1132842 AATTTTTTATAAATATTTT
1 TA-TTTTTATAAA-ATTTT
1132861 TATAATTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
20 10 0.30
21 5 0.15
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTTTTATAAAATTTTAC
Found at i:1141266 original size:21 final size:21
Alignment explanation
Indices: 1141240--1141282 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1141230 ATTTTAAAAG
1141240 TAAAAAATATATTGCATTGAA
1 TAAAAAATATATTGCATTGAA
*
1141261 TAAAAATTATATTGCATTGAA
1 TAAAAAATATATTGCATTGAA
1141282 T
1 T
1141283 CTTCAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (21 bp):
TAAAAAATATATTGCATTGAA
Found at i:1148110 original size:15 final size:14
Alignment explanation
Indices: 1148092--1148145 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1148082 TTATATTTAC
1148092 ACAAATATATATATT
1 ACAAATATATATA-T
*
1148107 ACAAATATATCTAT
1 ACAAATATATATAT
* *
1148121 ATAAATATATTTAT
1 ACAAATATATATAT
1148135 ATCTAAATATA
1 A-C-AAATATA
1148146 AGTTTCAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 14 0.42
15 12 0.36
16 7 0.21
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ACAAATATATATAT
Found at i:1148224 original size:98 final size:99
Alignment explanation
Indices: 1148094--1148290 Score: 387
Period size: 98 Copynumber: 2.0 Consensus size: 99
1148084 ATATTTACAC
1148094 AAATATATATATTACAAATATATCTATATAAATATATTTATATCTAAATATAAGTTTCAAATTAA
1 AAATATATATATTACAAATATATCTATATAAATATATTTATATCTAAATATAAGTTTCAAATTAA
1148159 TAACTTTTAATTTTAAATGTAATTATGGAAATTT
66 TAACTTTTAATTTTAAATGTAATTATGGAAATTT
1148193 AAATATATAT-TTACAAATATATCTATATAAATATATTTATATCTAAATATAAGTTTCAAATTAA
1 AAATATATATATTACAAATATATCTATATAAATATATTTATATCTAAATATAAGTTTCAAATTAA
1148257 TAACTTTTAATTTTAAATGTAATTATGGAAATTT
66 TAACTTTTAATTTTAAATGTAATTATGGAAATTT
1148291 TAAAATGGTT
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 88 0.90
99 10 0.10
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (99 bp):
AAATATATATATTACAAATATATCTATATAAATATATTTATATCTAAATATAAGTTTCAAATTAA
TAACTTTTAATTTTAAATGTAATTATGGAAATTT
Found at i:1150305 original size:17 final size:17
Alignment explanation
Indices: 1150275--1150320 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1150265 CAACATTTTT
1150275 AAAAGTATTT-TAAATTC
1 AAAA-TATTTATAAATTC
1150292 AAAATATTTATAAAATTC
1 AAAATATTTAT-AAATTC
*
1150310 TAAAT-TTTATA
1 AAAATATTTATA
1150321 TTTTTTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.23
17 10 0.38
18 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AAAATATTTATAAATTC
Found at i:1150309 original size:18 final size:17
Alignment explanation
Indices: 1150286--1150320 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1150276 AAAGTATTTT
1150286 AAATTCAAAATATTTATA
1 AAATTCAAAAT-TTTATA
*
1150304 AAATTCTAAATTTTATA
1 AAATTCAAAATTTTATA
1150321 TTTTTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTCAAAATTTTATA
Found at i:1151179 original size:18 final size:18
Alignment explanation
Indices: 1151144--1151181 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1151134 CGGTAAAGTA
*
1151144 TAAAAAACGAAATCTTAT
1 TAAAAAACGAAATATTAT
1151162 TAAAAAAC-AATATATTAT
1 TAAAAAACGAA-ATATTAT
1151180 TA
1 TA
1151182 TTATTGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAAAAACGAAATATTAT
Found at i:1156946 original size:69 final size:69
Alignment explanation
Indices: 1156835--1157115 Score: 553
Period size: 69 Copynumber: 4.1 Consensus size: 69
1156825 TGAAAAATTA
1156835 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
1 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
1156900 GTTG
66 GTTG
1156904 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
1 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
1156969 GTTG
66 GTTG
1156973 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
1 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
1157038 GTTG
66 GTTG
*
1157042 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAATG
1 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
1157107 GTTG
66 GTTG
1157111 GACCT
1 GACCT
1157116 TTCATACAAT
Statistics
Matches: 211, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 211 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (69 bp):
GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
GTTG
Found at i:1170085 original size:91 final size:91
Alignment explanation
Indices: 1169951--1170135 Score: 370
Period size: 91 Copynumber: 2.0 Consensus size: 91
1169941 TAGATGACCT
1169951 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
1 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
1170016 ATCTGGAAAGTCTCTACTTATCTTTG
66 ATCTGGAAAGTCTCTACTTATCTTTG
1170042 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
1 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
1170107 ATCTGGAAAGTCTCTACTTATCTTTG
66 ATCTGGAAAGTCTCTACTTATCTTTG
1170133 TTT
1 TTT
1170136 GATGAAGATG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (91 bp):
TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
ATCTGGAAAGTCTCTACTTATCTTTG
Found at i:1170805 original size:3 final size:3
Alignment explanation
Indices: 1170797--1170861 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
1170787 TGACGAAGAG
* * ** * *
1170797 GAT GAT GAT GAC GAC GAT GAT GAT GGG GAT GAA GAT GAT GAT GAT GAC
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
1170845 GAT GAT GGT GAG GAT GA
1 GAT GAT GAT GAT GAT GA
1170862 AGAAGAGGAG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.05, G:0.40, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:1170817 original size:15 final size:15
Alignment explanation
Indices: 1170797--1170851 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
1170787 TGACGAAGAG
*
1170797 GATGATGATGACGAC
1 GATGATGATGATGAC
*
1170812 GATGATGATGGGGATGAA
1 GATGATGAT---GATGAC
1170830 GATGATGATGATGAC
1 GATGATGATGATGAC
1170845 GATGATG
1 GATGATG
1170852 GTGAGGATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 21 0.62
18 13 0.38
ACGTcount: A:0.33, C:0.05, G:0.38, T:0.24
Consensus pattern (15 bp):
GATGATGATGATGAC
Found at i:1170878 original size:15 final size:15
Alignment explanation
Indices: 1170854--1170888 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1170844 CGATGATGGT
*
1170854 GAGGATGAAGAAGAG
1 GAGGACGAAGAAGAG
*
1170869 GAGGACGAAGAAGAT
1 GAGGACGAAGAAGAG
1170884 GAGGA
1 GAGGA
1170889 TGATGAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.46, T:0.06
Consensus pattern (15 bp):
GAGGACGAAGAAGAG
Found at i:1180256 original size:18 final size:18
Alignment explanation
Indices: 1180233--1180272 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1180223 TGCTAAAAAG
*
1180233 AAAAATT-CATAATTGATT
1 AAAAATTCCA-AAATGATT
1180251 AAAAATTCCAAAATGATT
1 AAAAATTCCAAAATGATT
1180269 AAAA
1 AAAA
1180273 TTAGCCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAAATTCCAAAATGATT
Found at i:1193765 original size:15 final size:16
Alignment explanation
Indices: 1193738--1193767 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1193728 TACAAATATA
1193738 TAATAATTTAAAATAC
1 TAATAATTTAAAATAC
1193754 TAATAA-TTAAAATA
1 TAATAATTTAAAATA
1193768 TTCAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAATTTAAAATAC
Found at i:1198572 original size:27 final size:27
Alignment explanation
Indices: 1198539--1198597 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1198529 TTTTGGTTAA
*
1198539 AAATTAACCGAATTACCGAAATTAACC
1 AAATTAACCGAATTACCCAAATTAACC
*
1198566 AAATTAATCGAATTACCCAAATTAACC
1 AAATTAACCGAATTACCCAAATTAACC
*
1198593 GAATT
1 AAATT
1198598 GAATCACTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (27 bp):
AAATTAACCGAATTACCCAAATTAACC
Found at i:1198579 original size:18 final size:18
Alignment explanation
Indices: 1198540--1198597 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
1198530 TTTGGTTAAA
*
1198540 AATTAACCGAATT-ACCG
1 AATTAACCAAATTAACCG
*
1198557 AAATTAACCAAATTAATCG
1 -AATTAACCAAATTAACCG
*
1198576 AATTACCCAAATTAACCG
1 AATTAACCAAATTAACCG
1198594 AATT
1 AATT
1198598 GAATCACTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 32 0.91
19 3 0.09
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (18 bp):
AATTAACCAAATTAACCG
Found at i:1198597 original size:9 final size:9
Alignment explanation
Indices: 1198540--1198597 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
1198530 TTTGGTTAAA
1198540 AATTAACCG
1 AATTAACCG
1198549 AATT-ACCG
1 AATTAACCG
*
1198557 AAATTAACCA
1 -AATTAACCG
*
1198567 AATTAATCG
1 AATTAACCG
* *
1198576 AATTACCCA
1 AATTAACCG
1198585 AATTAACCG
1 AATTAACCG
1198594 AATT
1 AATT
1198598 GAATCACTCC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
8 4 0.10
9 32 0.82
10 3 0.08
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:1198782 original size:18 final size:18
Alignment explanation
Indices: 1198743--1198785 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1198733 TATAATTGGG
*
1198743 TTGGGTTGGGTTGGGTAA
1 TTGGGTTGGGTTGGATAA
*
1198761 TTGGGTT-GGTGTGGATAC
1 TTGGGTTGGGT-TGGATAA
1198779 TTGGGTT
1 TTGGGTT
1198786 TGGATTGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.09, C:0.02, G:0.47, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTTGGATAA
Found at i:1199124 original size:14 final size:14
Alignment explanation
Indices: 1199101--1199148 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
1199091 GTTACTGAAC
1199101 TATTTAAATTTTTT
1 TATTTAAATTTTTT
*
1199115 TATTTTAATTATTAATT
1 TATTTAAATT-TT--TT
*
1199132 TATTTAAATGTTTT
1 TATTTAAATTTTTT
1199146 TAT
1 TAT
1199149 GTAAGTCCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 14 0.50
15 2 0.07
16 2 0.07
17 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TATTTAAATTTTTT
Done.