Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold33
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: 2032796
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 48244 characters in sequence are not A, C, G, or T
File 3 of 13
Found at i:348025 original size:21 final size:21
Alignment explanation
Indices: 347981--348037 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
347971 GCCAAGGAAA
*
347981 TGTATCGATACAT-TTTTCTG
1 TGTATCGATACATCTATTCTG
*
348001 TGTATCGATACATCTATTCTT
1 TGTATCGATACATCTATTCTG
348022 TGTATCGATACATCTA
1 TGTATCGATACATCTA
348038 GGAAGTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (21 bp):
TGTATCGATACATCTATTCTG
Found at i:348570 original size:10 final size:10
Alignment explanation
Indices: 348544--348572 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
348534 TCCTTTAGCA
348544 AAAAAAAC-C
1 AAAAAAACAC
348553 AAAAAAACAC
1 AAAAAAACAC
348563 AAAAAAACAC
1 AAAAAAACAC
348573 TATTTCCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAC
Found at i:350416 original size:51 final size:51
Alignment explanation
Indices: 350356--350473 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 51
350346 CAGTTCTCCG
350356 TAATCGGGGATA-TCCCAACTCCGATTTCATTT-TCAAAACA-CTAATTTTCTA
1 TAATCGGGGATACT-CCAACTCCGATTTCATTTCT-AAAACATC-AATTTTCTA
*
350407 TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAA-TTT-T-
1 TAATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTA
*
350455 TCATCGGGGATACTCCAAC
1 TAATCGGGGATACTCCAAC
350474 CCCGTTAATC
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
48 18 0.29
49 1 0.02
50 3 0.05
51 37 0.60
52 3 0.05
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (51 bp):
TAATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTA
Found at i:350527 original size:28 final size:27
Alignment explanation
Indices: 350455--350531 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 27
350445 CATCAATTTT
350455 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
350482 TCATCGGGGATACTCCAACCCCGTT-A
1 TCATCGGGGATACTCCAACCCCGTTAA
**
350508 TTTTCGAGGGGATACTCCAACCCC
1 TCATC--GGGGATACTCCAACCCC
350532 CGGCTTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 4 0.09
27 25 0.54
28 17 0.37
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:350660 original size:79 final size:80
Alignment explanation
Indices: 350484--350660 Score: 243
Period size: 80 Copynumber: 2.2 Consensus size: 80
350474 CCCGTTAATC
* *
350484 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
* *
350549 TATTAATTTCTCATA
66 TATGAATTTCTCACA
* * *
350564 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCTAA-CCCCGGTTTTATTTC-CAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
*
350627 TCATCGATTTTC-CACA
66 T-AT-GAATTTCTCACA
350643 ATCGGGGATACTCCAACC
1 ATCGGGGATACTCCAACC
350661 TCGTCTTTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
78 4 0.05
79 37 0.43
80 46 0.53
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
TATGAATTTCTCACA
Found at i:350707 original size:52 final size:51
Alignment explanation
Indices: 350595--350769 Score: 185
Period size: 52 Copynumber: 3.4 Consensus size: 51
350585 TTATCTCCGA
* * * * *
350595 GGGGATACTCTAACCCCGGTTTTATTTCC-AAATCATCGATTTTCCACAATC
1 GGGGATACTCCAACCTC-GTTTTATTTCCAAAAACACCAATTTTCCACAATC
* **
350646 GGGGATACTCCAACCTCGTCTTTATTTTC-AAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCTCGT-TTTATTTCCAAAAACACCAATTTTCC-ACAATC
* *
350698 GGGGATACTCCAA-CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAACCT-CG-TTTTATTTCCAAAAACACCAATTTTCCACAATC
*
350750 GAGGATACTCCAACCTCGTT
1 GGGGATACTCCAACCTCGTT
350770 ATTTCATCGG
Statistics
Matches: 104, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
50 2 0.02
51 40 0.38
52 44 0.42
53 18 0.17
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGTTTTATTTCCAAAAACACCAATTTTCCACAATC
Found at i:350888 original size:290 final size:284
Alignment explanation
Indices: 350384--350946 Score: 815
Period size: 290 Copynumber: 2.0 Consensus size: 284
350374 CTCCGATTTC
* * *
350384 ATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATC
1 ATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCAAAAACACC
* ** *
350449 AATTTTTCATCGGGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCG
66 AATTTTTCATCGAGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACCTCCG
* *
350514 AGGGGATACTCCAACCCCCGGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCA
131 AGGGGATACTCCAACCCCCGGCTTTATTCCCAAAATATTAATTTCTCATAATCGGGGATACTCCA
* * *
350579 ACCCCGTTATCTCCGAGGGGATACTCTAACCCCGGTTTTATTTCCAAATCATCGATTT-TCCACA
196 ACCCCATTATCTCCGAGGGGATACTCCAACCCCGATTTT-TTTCCAAATCATCGATTTCT-CACA
*
350643 ATCGGGGATACTCCAACCTCGTCTTT
259 ACCGGGGATACTCCAACCTCGTCTTT
*
350669 ATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACA
1 ATTTTCAAAACACCAATTTT-CTATAATCGGGGATACTCCAACTCCGATTTTATTT-CAAAAACA
* * *
350734 CCAATTTTTCACAATTGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTA
64 CCAATTTTT--C-ATCGAGGATACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTA
* *
350799 CCTCCGAGGGGATACTCCAA-CCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGAT
125 CCTCCGAGGGGATACTCCAACCCCCGGCTTTATTCCCAAAATATTAATTTCTCATAATCGGGGAT
* * * * * *
350863 ACTCCAACCTCATTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTCTAATCATCGATTTCT
190 ACTCCAACCCCATTATCTCCGAGGGGATACTCCAACCCCGATTTTTTTCCAAATCATCGATTTCT
350928 CACAACCGGGGATACTCCA
255 CACAACCGGGGATACTCCA
350947 GCCCCGTTAT
Statistics
Matches: 246, Mismatches: 25, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
285 19 0.08
286 34 0.14
287 15 0.06
289 35 0.14
290 100 0.41
291 43 0.17
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (284 bp):
ATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCAAAAACACC
AATTTTTCATCGAGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACCTCCG
AGGGGATACTCCAACCCCCGGCTTTATTCCCAAAATATTAATTTCTCATAATCGGGGATACTCCA
ACCCCATTATCTCCGAGGGGATACTCCAACCCCGATTTTTTTCCAAATCATCGATTTCTCACAAC
CGGGGATACTCCAACCTCGTCTTT
Found at i:350957 original size:78 final size:78
Alignment explanation
Indices: 350777--350998 Score: 223
Period size: 78 Copynumber: 2.8 Consensus size: 78
350767 GTTATTTCAT
** * *
350777 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
350842 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * * * * ** *
350856 TGGGGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
350920 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* * * *
350934 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGGACACTCCAACCCCGTTATTA-TCTCCAAAATA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGAT-TTATTC-CCAAAATA
350998 T
64 T
350999 TAAATTTCTC
Statistics
Matches: 112, Mismatches: 27, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
77 3 0.03
78 62 0.55
79 44 0.39
80 3 0.03
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:356078 original size:13 final size:13
Alignment explanation
Indices: 356060--356085 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
356050 TACAAGCCAA
356060 TGTATCGATACAT
1 TGTATCGATACAT
356073 TGTATCGATACAT
1 TGTATCGATACAT
356086 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:356192 original size:20 final size:21
Alignment explanation
Indices: 356145--356197 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
356135 GCCAATCACC
*
356145 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
356166 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
356186 TGTATCGATACA
1 TGTATCGATACA
356198 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:356260 original size:20 final size:20
Alignment explanation
Indices: 356220--356256 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
356210 GTGCATTATG
356220 TATCGATACATTTGAAGGTT
1 TATCGATACATTTGAAGGTT
*
356240 TATCGATATATTT-AAGG
1 TATCGATACATTTGAAGG
356257 GTTTTGACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (20 bp):
TATCGATACATTTGAAGGTT
Found at i:356567 original size:20 final size:20
Alignment explanation
Indices: 356542--356579 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
356532 ACAATAAATA
356542 TATCGATACATTTACTTATG
1 TATCGATACATTTACTTATG
*
356562 TATCGATACATTTCCTTA
1 TATCGATACATTTACTTA
356580 GCAGTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (20 bp):
TATCGATACATTTACTTATG
Found at i:356642 original size:20 final size:20
Alignment explanation
Indices: 356599--356672 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 20
356589 AGGGTGGTTT
***
356599 TGTATTGATACATTTCAAGCA
1 TGTATTGATACA-TTCATTTA
356620 TGTATTGATACATTCATTTA
1 TGTATTGATACATTCATTTA
* * *
356640 TGTATCGATACATTTATTGTT
1 TGTATTGATACATTCATT-TA
*
356661 TATATTGATACA
1 TGTATTGATACA
356673 AATTATAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 21 0.48
21 23 0.52
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (20 bp):
TGTATTGATACATTCATTTA
Found at i:358286 original size:31 final size:32
Alignment explanation
Indices: 358251--358411 Score: 129
Period size: 31 Copynumber: 5.2 Consensus size: 32
358241 AACTCGTTCA
*
358251 GGCTTTGA-TAAGGGTGCTACCAACTTGTGTG
1 GGCTTTGACTAAGGGTGCCACCAACTTGTGTG
* * **
358282 GGCTTTGACTCAA--GTGCCGCCAACTCGTGCA
1 GGCTTTGACT-AAGGGTGCCACCAACTTGTGTG
* *
358313 GGCTTTGACT-AGGTTGCCATCAACTTGTGTG
1 GGCTTTGACTAAGGGTGCCACCAACTTGTGTG
* * * **
358344 GGCTTTGACTTA-GGTGTCGCCAA-TTCGTGCA
1 GGCTTTGACTAAGGGTGCCACCAACTT-GTGTG
* *
358375 GGCTTTGACTAA-GGTGCCACTAACATGTGTG
1 GGCTTTGACTAAGGGTGCCACCAACTTGTGTG
358406 GGCTTT
1 GGCTTT
358412 TAACAAAAAG
Statistics
Matches: 99, Mismatches: 24, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
29 1 0.01
30 2 0.02
31 91 0.92
32 3 0.03
33 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (32 bp):
GGCTTTGACTAAGGGTGCCACCAACTTGTGTG
Found at i:358316 original size:62 final size:63
Alignment explanation
Indices: 358239--358411 Score: 235
Period size: 62 Copynumber: 2.8 Consensus size: 63
358229 AATCATGAAT
* *
358239 CCAACTCGTTCAGGCTTTGA-TAAGGGTGCTACCAACTTGTGTGGGCTTTGACTCAAGTGCCG
1 CCAACTCGTGCAGGCTTTGACTAAGGGTGCCACCAACTTGTGTGGGCTTTGACTCAAGTGCCG
* * * * *
358301 CCAACTCGTGCAGGCTTTGACT-AGGTTGCCATCAACTTGTGTGGGCTTTGACTTAGGTGTCG
1 CCAACTCGTGCAGGCTTTGACTAAGGGTGCCACCAACTTGTGTGGGCTTTGACTCAAGTGCCG
* * *
358363 CCAATTCGTGCAGGCTTTGACTAA-GGTGCCACTAACATGTGTGGGCTTT
1 CCAACTCGTGCAGGCTTTGACTAAGGGTGCCACCAACTTGTGTGGGCTTT
358412 TAACAAAAAG
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
62 95 0.98
63 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (63 bp):
CCAACTCGTGCAGGCTTTGACTAAGGGTGCCACCAACTTGTGTGGGCTTTGACTCAAGTGCCG
Found at i:358504 original size:62 final size:62
Alignment explanation
Indices: 358385--358736 Score: 357
Period size: 62 Copynumber: 5.5 Consensus size: 62
358375 GGCTTTGACT
* * * * * * *
358385 AAGGTGCCACTAACATGTGTGGGCTTTTAACAAAAAGGAAAGGCGTCTTGCTCTTTGAGGACTAA
1 AAGGTGCCACCAACTTGTGTGGGC-TTT-A-AAAAAGAAAAGGCATCCTACTTTTTGAGGACTAA
* * *
358450 AAGGAGCCACCAACTTGTGTGTGCTTTAAAAAAGCAAAGGCATCCTACTTTTTGAGGACTAA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCCTACTTTTTGAGGACTAA
* ** * * *
358512 AAGGT-CCACCAACTTGTGTGGGCTTTAAAAGAGAAAAAAGAAATATGCCCTGCTCTTTGAAGAC
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAA-A-AGAAAAG--GCAT--CCTACTTTTTGAGGAC
358576 TAA
60 TAA
*
358579 AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAAGAAAAAGGCATCCTACTTTTTGAGGACTAT
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAG-AAAAGGCATCCTACTTTTTGAGGACTAA
* * * *
358641 AAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCAAGGCATCTTGCTTTTTGAGGACTA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AAGAA---AAGGCATCCTACTTTTTGAGGACTA
358706 A
62 A
* *
358707 AAAGTGCCACCAACTTGTGTGGGTTTTAAA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAA
358737 GGGATTGTCA
Statistics
Matches: 241, Mismatches: 33, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
61 24 0.10
62 75 0.31
63 11 0.05
64 7 0.03
65 23 0.10
66 56 0.23
67 24 0.10
68 21 0.09
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (62 bp):
AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCCTACTTTTTGAGGACTAA
Found at i:358729 original size:128 final size:127
Alignment explanation
Indices: 358384--358736 Score: 453
Period size: 129 Copynumber: 2.8 Consensus size: 127
358374 AGGCTTTGAC
* * * * *
358384 TAAGGTGCCACTAACATGTGTGGGCTTT-TAACAAAAAGGAAAGGCGTCTTGCTCTTTGAGGACT
1 TAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGG-AAGGCATCTTGCTCTTTGAGGACT
* * *
358448 AAAAGGAGCCACCAACTTGTGTGTGCTTTAAAAAAGCAAAGGCATCCTACTTTTTGAGGACTA
65 AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCCTACTTTTTGAGGACTA
* * ** * *
358511 AAAGGT-CCACCAACTTGTGTGGGCTTTAAAAGAGAAAAAAGAA-ATATGCCCTGCTCTTTGAAG
1 TAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-AGAAAAAGGAAGGCAT--CTTGCTCTTTGAGG
358574 ACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAAGAAAAAGGCATCCTACTTTTTGAGGAC
62 ACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAG-AAAAGGCATCCTACTTTTTGAGGAC
358638 TA
126 TA
* *
358640 TAAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCAAGGCATCTTGCTTTTTGAGGACT
1 TAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGG-AAGGCATCTTGCTCTTTGAGGACT
* *
358705 AAAAAGTGCCACCAACTTGTGTGGGTTTTAAA
65 AAAAGGTGCCACCAACTTGTGTGGGCTTTAAA
358737 GGGATTGTCA
Statistics
Matches: 192, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
126 19 0.10
127 6 0.03
128 58 0.30
129 87 0.45
130 22 0.11
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (127 bp):
TAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGAAGGCATCTTGCTCTTTGAGGACTA
AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCCTACTTTTTGAGGACTA
Found at i:358797 original size:33 final size:31
Alignment explanation
Indices: 358711--358987 Score: 277
Period size: 31 Copynumber: 8.7 Consensus size: 31
358701 GACTAAAAAG
* *
358711 TGCCACCAACTTGTGTGGGTTTTA-AAGGGAT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGG-T
* * *
358742 TGTCATCGACTCGTGTGGGCTTTAGAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAG--AAGGGT
* * *
358775 TGCCACAGACTTGTGTAGGCTTTAGAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* *
358806 TGCCACCGAATTATGTGGGCTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
358837 TGCCACCGACTTATATGGGCTTTAGAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
*
358868 TGCCACCGACTTGTGTGGGCTTTAGAATGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
358899 TGCCACTGACTTATGTGGACTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
* * *
358932 TGCCACCGACTTGTATGGGTTTTAGAAAATGGT
1 TGCCACCGACTTGTGTGGGCTTTAG--AAGGGT
* * *
358965 TGCCACTGACTAGTGTGGACTTT
1 TGCCACCGACTTGTGTGGGCTTT
358988 TAAAAGAGAT
Statistics
Matches: 202, Mismatches: 37, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
31 128 0.63
33 69 0.34
34 5 0.02
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (31 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
Found at i:358823 original size:95 final size:94
Alignment explanation
Indices: 358711--358980 Score: 303
Period size: 95 Copynumber: 2.8 Consensus size: 94
358701 GACTAAAAAG
* * * * *
358711 TGCCACC-AACTTGTGTGGGTTTTA-AAGGGATTGTCATCGACTCGTGTGGGCTTTAGAAAAGGG
1 TGCCACCGAA-TTATGTGGGTTTTAGAAGGG-TTGCCACCGACTTGTATGGGCTTTAGAAAA-GG
*
358774 TTGCCACAGACTTGTGTAGGCTTTAGAGGGGT
63 TTGCCACAGACTTGTGTAGGCTTTAGAAGGGT
* *
358806 TGCCACCGAATTATGTGGGCTTTAGAAGGGTTGCCACCGACTTATATGGGCTTTAG-AAAGGTTG
1 TGCCACCGAATTATGTGGGTTTTAGAAGGGTTGCCACCGACTTGTATGGGCTTTAGAAAAGGTTG
* * *
358870 CCACCGACTTGTGTGGGCTTTAGAATGGT
66 CCACAGACTTGTGTAGGCTTTAGAAGGGT
* * * * *
358899 TGCCACTGACTTATGTGGACTTTAGAGAAGGGTTGCCACCGACTTGTATGGGTTTTAGAAAATGG
1 TGCCACCGAATTATGTGG-GTTT-TAGAAGGGTTGCCACCGACTTGTATGGGCTTTAGAAAA-GG
* *
358964 TTGCCACTGACTAGTGT
63 TTGCCACAGACTTGTGT
358981 GGACTTTTAA
Statistics
Matches: 149, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
93 46 0.31
94 5 0.03
95 71 0.48
96 10 0.07
97 17 0.11
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (94 bp):
TGCCACCGAATTATGTGGGTTTTAGAAGGGTTGCCACCGACTTGTATGGGCTTTAGAAAAGGTTG
CCACAGACTTGTGTAGGCTTTAGAAGGGT
Found at i:359117 original size:63 final size:63
Alignment explanation
Indices: 359042--359419 Score: 252
Period size: 63 Copynumber: 6.0 Consensus size: 63
359032 GATTGTGGAA
* * * *
359042 TTAAGAAGAAAAAAGGTACCATAGAGTTGTGGACTTTAAAAAAGATGCAATGGAGTTGTGAAC
1 TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTTTAAAAAAGATGCCATGGAGTTATGAAC
* * * * * * ** *
359105 TTAAAAAGAAAAAGAGG-GCAATAGAGTTTTGAACTTTAAAAAGGGTGCTACAGAGTTATGGAC
1 TTAAAAAGAAAAA-AGGTGCCATAGAGTTGTGGACTTTAAAAAAGATGCCATGGAGTTATGAAC
* * * ** *
359168 TTAAAAAGATAAAAGATGCCATAGAGTTGTGGACTTAAAAAGAAAAAGGGGGCCATAGAGTTATG
1 TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTT---TA-AAAAA-GATGCCATGGAGTTATG
*
359233 AAT
61 AAC
* * * * * *
359236 TTTAAAAG-----AGGTGCCACAGAGTTATGGACTTAAAATGATAAAGAGTGCCACGGAGTTGTG
1 TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTT-TAA--A-AAAGA-TGCCATGGAGTTATG
359296 AAC
61 AAC
* * * ** *
359299 TTAAAAAG-AAAAAGTGGGCCATGGAGTTGGGGAC-TTAAAAGGGA-GCCATGGAGTTATGGAC
1 TTAAAAAGAAAAAAG-GTGCCATAGAGTTGTGGACTTTAAAAAAGATGCCATGGAGTTATGAAC
* * * * *
359360 TTAAAAAGAAATAGGGTGCCATAGAGTTGTGGACTTTAAAAAGGGTGCCACGGAGTTATG
1 TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTTTAAAAAAGATGCCATGGAGTTATG
359420 GACTATAAGA
Statistics
Matches: 242, Mismatches: 54, Indels: 38
0.72 0.16 0.11
Matches are distributed among these distances:
60 1 0.00
61 41 0.17
62 16 0.07
63 134 0.55
64 4 0.02
66 3 0.01
67 7 0.03
68 36 0.15
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (63 bp):
TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTTTAAAAAAGATGCCATGGAGTTATGAAC
Found at i:359126 original size:34 final size:34
Alignment explanation
Indices: 359080--359402 Score: 173
Period size: 34 Copynumber: 10.0 Consensus size: 34
359070 GTGGACTTTA
* *
359080 AAAAAGA-TGCAATGGAGTTGTGAACTTAAAAAG
1 AAAAAGAGTGCCATAGAGTTGTGAACTTAAAAAG
* * *
359113 AAAAAGAGGGCAATAGAGTTTTGAACTTTAAAAAG
1 AAAAAGAGTGCCATAGAGTTGTGAAC-TTAAAAAG
* * * *
359148 -----G-GTGCTACAGAGTTATGGACTTAAAAAG
1 AAAAAGAGTGCCATAGAGTTGTGAACTTAAAAAG
*
359176 ATAAAAGA-TGCCATAGAGTTGTGGACTTAAAAAG
1 A-AAAAGAGTGCCATAGAGTTGTGAACTTAAAAAG
* * * * *
359210 AAAAAGGGGGCCATAGAGTTATGAATTTTAAAAG
1 AAAAAGAGTGCCATAGAGTTGTGAACTTAAAAAG
* * * *
359244 ----AG-GTGCCACAGAGTTATGGACTTAAAATG
1 AAAAAGAGTGCCATAGAGTTGTGAACTTAAAAAG
* **
359273 ATAAAGAGTGCCACGGAGTTGTGAACTTAAAAAG
1 AAAAAGAGTGCCATAGAGTTGTGAACTTAAAAAG
* * * * *
359307 AAAAAGTGGGCCATGGAGTTGGGGACTT-AAAAG
1 AAAAAGAGTGCCATAGAGTTGTGAACTTAAAAAG
* * * *
359340 -----G-GAGCCATGGAGTTATGGACTTAAAAAG
1 AAAAAGAGTGCCATAGAGTTGTGAACTTAAAAAG
* * *
359368 AAATAGGGTGCCATAGAGTTGTGGACTTTAAAAAG
1 AAAAAGAGTGCCATAGAGTTGTGAAC-TTAAAAAG
359403 GGTGCCACGG
Statistics
Matches: 228, Mismatches: 39, Indels: 44
0.73 0.13 0.14
Matches are distributed among these distances:
27 18 0.08
28 14 0.06
29 35 0.15
30 3 0.01
33 20 0.09
34 122 0.54
35 16 0.07
ACGTcount: A:0.41, C:0.09, G:0.28, T:0.23
Consensus pattern (34 bp):
AAAAAGAGTGCCATAGAGTTGTGAACTTAAAAAG
Found at i:359211 original size:97 final size:96
Alignment explanation
Indices: 359081--359402 Score: 380
Period size: 97 Copynumber: 3.3 Consensus size: 96
359071 TGGACTTTAA
* * * *
359081 AAAAGATGCAATGGAGTTGTGAACTTAAAAAGAAAAAGAGGGCAATAGAGTTTTGAACTTTAAAA
1 AAAAGATGCCATAGAGTTGTGAACTTAAAAAGAAAAAGAGGGCCATAGAGTTATGAACTTT-AAA
*
359146 AGGGTGCTACAGAGTTATGGACTTAAAAAGAT
65 AGGGTGCCACAGAGTTATGGACTTAAAAAGAT
* * *
359178 AAAAGATGCCATAGAGTTGTGGACTTAAAAAGAAAAAGGGGGCCATAGAGTTATGAATTTTAAAA
1 AAAAGATGCCATAGAGTTGTGAACTTAAAAAGAAAAAGAGGGCCATAGAGTTATGAACTTTAAAA
*
359243 GAGGTGCCACAGAGTTATGGACTTAAAATGAT
66 G-GGTGCCACAGAGTTATGGACTTAAAAAGAT
** * * ** *
359275 -AAAGAGTGCCACGGAGTTGTGAACTTAAAAAGAAAAAGTGGGCCATGGAGTTGGGGAC-TTAAA
1 AAAAGA-TGCCATAGAGTTGTGAACTTAAAAAGAAAAAGAGGGCCATAGAGTTATGAACTTTAAA
* **
359338 AGGGAGCCATGGAGTTATGGACTTAAAAAGA-
65 AGGGTGCCACAGAGTTATGGACTTAAAAAGAT
* * *
359369 AATAGGGTGCCATAGAGTTGTGGACTTTAAAAAG
1 AA-AAGATGCCATAGAGTTGTGAAC-TTAAAAAG
359403 GGTGCCACGG
Statistics
Matches: 193, Mismatches: 27, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
95 41 0.21
96 27 0.14
97 125 0.65
ACGTcount: A:0.41, C:0.09, G:0.28, T:0.23
Consensus pattern (96 bp):
AAAAGATGCCATAGAGTTGTGAACTTAAAAAGAAAAAGAGGGCCATAGAGTTATGAACTTTAAAA
GGGTGCCACAGAGTTATGGACTTAAAAAGAT
Found at i:359268 original size:28 final size:28
Alignment explanation
Indices: 359211--359270 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
359201 CTTAAAAAGA
* *
359211 AAAAGGGGGCCATAGAGTTATGAATTTT
1 AAAAGGGGGCCACAGAGTTATGAATCTT
* *
359239 AAAAGAGGTGCCACAGAGTTATGGA-CTT
1 AAAAG-GGGGCCACAGAGTTATGAATCTT
359267 AAAA
1 AAAA
359271 TGATAAAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (28 bp):
AAAAGGGGGCCACAGAGTTATGAATCTT
Found at i:359346 original size:27 final size:27
Alignment explanation
Indices: 359308--359365 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
359298 CTTAAAAAGA
*
359308 AAAAGTGGGCCATGGAGTTGGGGACTT
1 AAAAGTGGGCCATGGAGTTAGGGACTT
*
359335 AAAAG-GGAGCCATGGAGTTATGGACTT
1 AAAAGTGG-GCCATGGAGTTAGGGACTT
359362 AAAA
1 AAAA
359366 AGAAATAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.34, C:0.10, G:0.34, T:0.21
Consensus pattern (27 bp):
AAAAGTGGGCCATGGAGTTAGGGACTT
Found at i:359362 original size:61 final size:63
Alignment explanation
Indices: 358997--359423 Score: 225
Period size: 63 Copynumber: 6.8 Consensus size: 63
358987 TTAAAAGAGA
* * * * * * * *
358997 TGCCATAGAATTGTGGACTTT-GAAA-GGTGCCAC-GAGATTGTGGAATTAAGAAGAAAAAAGG
1 TGCCATAGAGTTGGGGACTTTAAAAAGGGAGCCACGGAG-TTATGGACTTAAAAAGAAAAAGGG
* * * * * * *
359058 TACCATAGAGTTGTGGACTTTAAAAA-AGATGCAATGGAGTTGTGAACTTAAAAAGAAAAAGAGG
1 TGCCATAGAGTTGGGGACTTTAAAAAGGGA-GCCACGGAGTTATGGACTTAAAAAGAAAAAG-GG
* ** * * * * *
359122 -GCAATAGAGTTTTGAACTTTAAAAAGGGTGCTACAGAGTTATGGACTTAAAAAGATAAAA-GA
1 TGCCATAGAGTTGGGGACTTTAAAAAGGGAGCCACGGAGTTATGGACTTAAAAAGA-AAAAGGG
* * * ** * * *
359184 TGCCATAGAGTTGTGGACTTAAAAAGAAAAAGGGGGCCATAGAGTTATGAATTTTAAAAG----A
1 TGCCATAGAGTTGGGGACTT-----TAAAAAGGGAGCCACGGAGTTATGGACTTAAAAAGAAAAA
359245 -GG
61 GGG
* ** * * * * *
359247 TGCCACAGAGTTATGGACTTAAAATGATAAAGAGTGCCACGGAGTTGTGAACTTAAAAAGAAAAA
1 TGCCATAGAGTTGGGGACTT----T-AAAAAGGGAGCCACGGAGTTATGGACTTAAAAAGAAAAA
359312 GTGG
61 G-GG
* * *
359316 -GCCATGGAGTTGGGGAC-TT-AAAAGGGAGCCATGGAGTTATGGACTTAAAAAGAAATAGGG
1 TGCCATAGAGTTGGGGACTTTAAAAAGGGAGCCACGGAGTTATGGACTTAAAAAGAAAAAGGG
* *
359376 TGCCATAGAGTTGTGGACTTTAAAAAGGGTGCCACGGAGTTATGGACT
1 TGCCATAGAGTTGGGGACTTTAAAAAGGGAGCCACGGAGTTATGGACT
359424 ATAAGAAGGT
Statistics
Matches: 284, Mismatches: 60, Indels: 42
0.74 0.16 0.11
Matches are distributed among these distances:
60 2 0.01
61 66 0.23
62 11 0.04
63 150 0.53
64 10 0.04
67 2 0.01
68 41 0.14
69 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.28, T:0.23
Consensus pattern (63 bp):
TGCCATAGAGTTGGGGACTTTAAAAAGGGAGCCACGGAGTTATGGACTTAAAAAGAAAAAGGG
Found at i:359415 original size:29 final size:29
Alignment explanation
Indices: 359307--359474 Score: 119
Period size: 29 Copynumber: 5.7 Consensus size: 29
359297 ACTTAAAAAG
* *
359307 AAAAAGTGG-GCCATGGAGTTGGGGAC-TT
1 AAAAAG-GGTGCCACGGAGTTGTGGACTTT
* * * *
359335 -AAAAGGGAGCCATGGAGTTATGGACTTAAAA
1 AAAAAGGGTGCCACGGAGTTGTGGACTT---T
**
359366 AGAAATAGGGTGCCATAGAGTTGTGGACTTT
1 A-AAA-AGGGTGCCACGGAGTTGTGGACTTT
* *
359397 AAAAAGGGTGCCACGGAGTTATGGACTAT
1 AAAAAGGGTGCCACGGAGTTGTGGACTTT
* **
359426 AAGAA-GGTGCCACGGAGTTGTGCTCTTT
1 AAAAAGGGTGCCACGGAGTTGTGGACTTT
*
359454 AGAAAATGGTGCCACGGAGTT
1 A-AAAAGGGTGCCACGGAGTT
359475 ATAGGCTTTG
Statistics
Matches: 113, Mismatches: 17, Indels: 18
0.76 0.11 0.12
Matches are distributed among these distances:
26 2 0.02
27 20 0.18
28 21 0.19
29 28 0.25
30 17 0.15
31 1 0.01
33 3 0.03
34 21 0.19
ACGTcount: A:0.32, C:0.12, G:0.33, T:0.23
Consensus pattern (29 bp):
AAAAAGGGTGCCACGGAGTTGTGGACTTT
Found at i:359497 original size:30 final size:28
Alignment explanation
Indices: 359383--359513 Score: 86
Period size: 30 Copynumber: 4.5 Consensus size: 28
359373 GGGTGCCATA
* * *
359383 GAGTTGTGGACTTTAAAAAGGGTGCCACG
1 GAGTTATGG-CTTTAAGAAGAGTGCCACG
*
359412 GAGTTATGGACTATAAGAAG-GTGCCACG
1 GAGTTATGG-CTTTAAGAAGAGTGCCACG
* * *
359440 GAGTTGT-GCTCTTTAGAAAATGGTGCCACG
1 GAGTTATGGCT-TTAAGAAGA--GTGCCACG
* *
359470 GAGTTATAGGCTTTGAGAAGAGATGCCACT
1 GAGTTAT-GGCTTTAAGAAGAG-TGCCACG
*
359500 GAGTCATGGACTTT
1 GAGTTATGG-CTTT
359514 TGGAAAAAGA
Statistics
Matches: 82, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
26 2 0.02
27 6 0.07
28 14 0.17
29 20 0.24
30 30 0.37
31 7 0.09
32 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (28 bp):
GAGTTATGGCTTTAAGAAGAGTGCCACG
Found at i:363964 original size:27 final size:26
Alignment explanation
Indices: 363896--363975 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 26
363886 AAATTTTGAA
*
363896 GAAAAGTGA-GGTTGGAGTATGCCCTC
1 GAAAAGCGAGGGTTGGAGTAT-CCCTC
*
363922 GAAAGAGCG-GGATTGGAGTATCCCATC
1 GAAA-AGCGAGGGTTGGAGTATCCC-TC
363949 GGAAAAG-GAGGGTTGGAGTAT-CCTC
1 -GAAAAGCGAGGGTTGGAGTATCCCTC
363974 GA
1 GA
363976 CAATCAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
24 2 0.04
25 2 0.04
26 10 0.22
27 28 0.61
28 4 0.09
ACGTcount: A:0.29, C:0.15, G:0.36, T:0.20
Consensus pattern (26 bp):
GAAAAGCGAGGGTTGGAGTATCCCTC
Found at i:366502 original size:21 final size:20
Alignment explanation
Indices: 366452--366505 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
366442 CATTTGAGAC
* *
366452 ATGTATCGGTACATTCACTT
1 ATGTATCGATACATTCACTA
*
366472 ATGCATCGATACATTCACTA
1 ATGTATCGATACATTCACTA
366492 ATTGTATCGATACA
1 A-TGTATCGATACA
366506 AATTGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:369117 original size:16 final size:16
Alignment explanation
Indices: 369085--369118 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
369075 AAATATTTAT
*
369085 TTATTATTTTATTTTA
1 TTATTATTTTATATTA
*
369101 TTATTATTTTGTATTA
1 TTATTATTTTATATTA
369117 TT
1 TT
369119 GAAAATTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTATTATTTTATATTA
Found at i:370160 original size:22 final size:21
Alignment explanation
Indices: 370135--370179 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
370125 TGCTAACAAA
*
370135 TTTTCTCATTTTTCTTGCTTTT
1 TTTTCTC-TTTCTCTTGCTTTT
*
370157 TTTTCTCTTTCTCTTTCTTTT
1 TTTTCTCTTTCTCTTGCTTTT
370178 TT
1 TT
370180 GCTGAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTCTCTTTCTCTTGCTTTT
Found at i:370673 original size:9 final size:10
Alignment explanation
Indices: 370640--370679 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
370630 ATCTCATTTT
370640 TCACTGTTCA
1 TCACTGTTCA
* *
370650 TAACTATTCA
1 TCACTGTTCA
370660 TCACTGTT-A
1 TCACTGTTCA
370669 TCACTGTTCA
1 TCACTGTTCA
370679 T
1 T
370680 GTATCAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:372821 original size:166 final size:162
Alignment explanation
Indices: 372608--373121 Score: 507
Period size: 166 Copynumber: 3.1 Consensus size: 162
372598 TAAAATGTTC
* * * * *
372608 AAAACTGATTTAATAGGAGTTAAATAATAATATTAGATAAATTTTAAAAATTTTAAATCAAGAAA
1 AAAACTGATTTAATAGGAATCAAATAACAATATTAGATACATTTTAAAAATTTTAAACCAAGAAA
*
372673 AATCCTCCCAAAAATATTTATGGAGTAAAAAACTCGGTTTTTCGAAAAAAAGGGCATTTCAACGA
66 AATCCTCCCAAAAATATTTATGGAGTAGAAAACTCGGTTTTT-GAAAAAAAGGG-ATTTCAA-G-
* *
372738 AAAAAATTCAATACTCATAAAAATGAATTAAATTTTT
127 AAAAAATTCAAAACTCATGAAAATGAA-TAAATTTTT
* * * * *
372775 AAAACTGATTTAAT-GGAATTC-CATGACATTGTTAGATACATTTTAAAAATTTTAGACCAA-AG
1 AAAACTGATTTAATAGGAA-TCAAATAACAATATTAGATACATTTTAAAAATTTTAAACCAAGA-
* * * * *
372837 AAAATCC-CTTCAAAAATATTTATGGAATAGAAAACTCGATTTTTTGAGAAAATAGGGATTTTAA
64 AAAATCCTC-CCAAAAATATTTATGGAGTAGAAAACTCG-GTTTTTGA-AAAAAAGGGA-TTTCA
* * *
372901 AGAAAAACTCCAAAACTCATGAAAATGAGATAAATTTTC
125 AGAAAAAATTCAAAACTCATGAAAATGA-ATAAATTTTT
* * * * **
372940 AAAACTGTTTTAATATGAATCAAATAATAATATTTGAT-CAATTTTAAAAATTAGAAACCAAGAA
1 AAAACTGATTTAATAGGAATCAAATAACAATATTAGATAC-ATTTTAAAAATTTTAAACCAAGAA
* * * * * * *
373004 AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTGGAAACAAGAGAATTTCAAGG
65 AAATCCTCCCAAAAATATTTATGGAGTAGAAAACTCGGT-TTTTGAAAAAAAG-GGATTTCAA-G
*
373069 AAAAAATTCAAAAACTCATGAAGATGAATAAATTTTT
127 AAAAAATTC-AAAACTCATGAAAATGAATAAATTTTT
*
373106 GAAAACTAATTTAATA
1 -AAAACTGATTTAATA
373122 TGAGTTAAAT
Statistics
Matches: 280, Mismatches: 50, Indels: 34
0.77 0.14 0.09
Matches are distributed among these distances:
165 59 0.21
166 157 0.56
167 64 0.23
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (162 bp):
AAAACTGATTTAATAGGAATCAAATAACAATATTAGATACATTTTAAAAATTTTAAACCAAGAAA
AATCCTCCCAAAAATATTTATGGAGTAGAAAACTCGGTTTTTGAAAAAAAGGGATTTCAAGAAAA
AATTCAAAACTCATGAAAATGAATAAATTTTT
Found at i:373140 original size:124 final size:124
Alignment explanation
Indices: 373004--373236 Score: 322
Period size: 124 Copynumber: 1.9 Consensus size: 124
372994 AAACCAAGAA
** * *
373004 AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTGGAAACAAGAGAATTTCAAGG
1 AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTAAAAAAAAGAGAATTTCAAGA
*
373069 AAAAAATTCAAAAACTCATGAAGATGAATAAATTTTTGAAAACTAATTTAATATGAGTT
66 AAAAAATTCAAAAACTCATGAAAATGAATAAATTTTTGAAAACTAATTTAATATGAGTT
* * * * * * *
373128 AAATCCTTCCAAAAACATTTATGGAGTAGAAAATTTCGTATTTTAAAAAAAAGAGAGTTTCAAGA
1 AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTAAAAAAAAGAGAATTTCAAGA
* * * *
373193 AAAAAATTCAAGAATTTATGAAAATGAATGAATTTTTGAAAACT
66 AAAAAATTCAAAAACTCATGAAAATGAATAAATTTTTGAAAACT
373237 GATTAACTGT
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
124 93 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (124 bp):
AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTAAAAAAAAGAGAATTTCAAGA
AAAAAATTCAAAAACTCATGAAAATGAATAAATTTTTGAAAACTAATTTAATATGAGTT
Found at i:374702 original size:85 final size:85
Alignment explanation
Indices: 374500--374809 Score: 232
Period size: 85 Copynumber: 3.6 Consensus size: 85
374490 AGACAGGCTA
* * * * * * * * *
374500 ACAAAGAGATGAAGAAGTCTCTC-AGGCCTAAGCCAACAAGTAGATAAAAGATAAAGAAATCTCT
1 ACAAAAAGATGAAGAAGTCTCACGA-GCCTGAGCCTATAGGCAGACAAAAGATAAAGAAATCTCC
* * * *
374564 CGGGTCAAAGCC-GTAGGGTAG
65 CGGGTCTAACCCAAT-GGGCAG
* * * * * * *
374585 ACAAATAGATAAAGAAGTCTTACGAGCTTGAG-CTGAT-GGACAGACAAAAGATATAGGAGTCTC
1 ACAAAAAGATGAAGAAGTCTCACGAGCCTGAGCCT-ATAGG-CAGACAAAAGATAAAGAAATCTC
* *
374648 CCGGGTCTGACCCGATGGGCAG
64 CCGGGTCTAACCCAATGGGCAG
* * * * **
374670 ACAAAAAGATGAAGAAGTCTCATGGGCCTGAGCCTATAGGTAGACAAAGGATAAAGAAATCTCTT
1 ACAAAAAGATGAAGAAGTCTCACGAGCCTGAGCCTATAGGCAGACAAAAGATAAAGAAATCTCCC
***
374735 GGGTCTAAGTTAATGGGCAG
66 GGGTCTAACCCAATGGGCAG
* * * * *
374755 ACAAAAAGATGAAGAAGTCTCTCGAGCTTGAGCCAATAGGCAAACAAAGGATAAA
1 ACAAAAAGATGAAGAAGTCTCACGAGCCTGAGCCTATAGGCAGACAAAAGATAAA
374810 AATGTCTCTC
Statistics
Matches: 174, Mismatches: 45, Indels: 12
0.75 0.19 0.05
Matches are distributed among these distances:
84 2 0.01
85 166 0.95
86 6 0.03
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18
Consensus pattern (85 bp):
ACAAAAAGATGAAGAAGTCTCACGAGCCTGAGCCTATAGGCAGACAAAAGATAAAGAAATCTCCC
GGGTCTAACCCAATGGGCAG
Found at i:374776 original size:43 final size:43
Alignment explanation
Indices: 374662--374776 Score: 126
Period size: 42 Copynumber: 2.7 Consensus size: 43
374652 GTCTGACCCG
* *
374662 ATGGGCAGACAAAAAGATGAAGAAGTCTCATGGGCCTGAGCCT
1 ATGGGCAGACAAAAAGATGAAGAAGTCTCTTGGGCCTAAGCCT
* * * * * * *
374705 ATAGGTAGAC-AAAGGATAAAGAAATCTCTTGGGTCTAAG-TT
1 ATGGGCAGACAAAAAGATGAAGAAGTCTCTTGGGCCTAAGCCT
374746 AATGGGCAGACAAAAAGATGAAGAAGTCTCT
1 -ATGGGCAGACAAAAAGATGAAGAAGTCTCT
374777 CGAGCTTGAG
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 1 0.02
42 31 0.55
43 24 0.43
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (43 bp):
ATGGGCAGACAAAAAGATGAAGAAGTCTCTTGGGCCTAAGCCT
Found at i:375005 original size:43 final size:42
Alignment explanation
Indices: 374583--375618 Score: 467
Period size: 43 Copynumber: 24.4 Consensus size: 42
374573 GCCGTAGGGT
* *
374583 AGACAAATAGATAAAGAAGTCT-TACGAGCTTGAGCTGATGGAC
1 AGACAAA-AGATAAAGAAGTCTCT-CGAGCTTGAGCCGATGGGC
* * * * *
374626 AGACAAAAGATATAGGAGTCTCCCG-GGTCTGACCCGATGGGC
1 AGACAAAAGATAAAGAAGTCTCTCGAGCT-TGAGCCGATGGGC
* * * * * *
374668 AGACAAAAAGATGAAGAAGTCTCAT-GGGCCTGAGCCTATAGGT
1 AGAC-AAAAGATAAAGAAGTCTC-TCGAGCTTGAGCCGATGGGC
* * * * * ***
374711 AGACAAAGGATAAAGAAATCTCTTG-GGTCTAAGTTAATGGGC
1 AGACAAAAGATAAAGAAGTCTCTCGAGCT-TGAGCCGATGGGC
* * *
374753 AGACAAAAAGATGAAGAAGTCTCTCGAGCTTGAGCCAATAGGC
1 AGAC-AAAAGATAAAGAAGTCTCTCGAGCTTGAGCCGATGGGC
* * * * * * *
374796 AAACAAAGGATAAA-AATGTCTCTCAAG-TCTAAGTCAACGGGC
1 AGACAAAAGATAAAGAA-GTCTCTCGAGCT-TGAGCCGATGGGC
** * * * * * * *
374838 AGACAACGGGTGAAGAAATCTCCCAAGCTTGAGCCGACGAGC
1 AGACAAAAGATAAAGAAGTCTCTCGAGCTTGAGCCGATGGGC
* * * * * * *
374880 AGACAAAGGATATAGGAGTCT-TCTAGGTCTGAGCCGATAGGT
1 AGACAAAAGATAAAGAAGTCTCTCGAGCT-TGAGCCGATGGGC
* * *
374922 AGACAAAATGTTAAAGAAGTCTCTCGTG-TCTGAACCGATGGGC
1 AGACAAAA-GATAAAGAAGTCTCTCGAGCT-TGAGCCGATGGGC
**
374965 AGACAAAAGATAAAAGAAGTCTCTCGAGCTTGAGTTGATGGGC
1 AGACAAAAGAT-AAAGAAGTCTCTCGAGCTTGAGCCGATGGGC
* * * * * *
375008 AGACAAAGGATAAAGAAGTCT-TCAAGGTTTGAGTCAACGGGC
1 AGACAAAAGATAAAGAAGTCTCTCGA-GCTTGAGCCGATGGGC
* * * *
375050 AGACAAACAGATGAAGAAGTCTCTTCGATC-TGAGCCGACGAGC
1 AGACAAA-AGATAAAGAAGTCTC-TCGAGCTTGAGCCGATGGGC
* * * *
375093 AGATAAAAGGATGAAGAAGTCTCTCGAGCTTGAGCTGACGGGC
1 AGACAAAA-GATAAAGAAGTCTCTCGAGCTTGAGCCGATGGGC
* * * * * * * **
375136 AAACAAAGGATATAGGAGTCTC-CTAGGTTTGAGTCGATGAAC
1 AGACAAAAGATAAAGAAGTCTCTCGA-GCTTGAGCCGATGGGC
* * * * * ** *
375178 AGACAATAAAATGAAA-AAGTCTCCCAAGTTTGAGCTGACAGGT
1 AGACAA-AAGAT-AAAGAAGTCTCTCGAGCTTGAGCCGATGGGC
* * * * *
375221 AGACAAAACATAAAGAAAGTCTCCCAAGCTTGATCCGATAGGC
1 AGACAAAAGATAAAG-AAGTCTCTCGAGCTTGAGCCGATGGGC
* * * *** *
375264 AGAAAAAAGATAAAGAAGTCTCTCG-GGTCTGAGTCGACAAGT
1 AGACAAAAGATAAAGAAGTCTCTCGAGCT-TGAGCCGATGGGC
* * * * * *
375306 AGACAAAAAGATGAAGAAGTTTTTTG-GGTCTGAGCCGATGGGT
1 AGAC-AAAAGATAAAGAAGTCTCTCGAGCT-TGAGCCGATGGGC
* *
375349 AGACAAAATATAAAGAAGTCTCTCGAG-TCTGAGCCGACGGGC
1 AGACAAAAGATAAAGAAGTCTCTCGAGCT-TGAGCCGATGGGC
* * **
375391 AAACAAAAAGATGAAA-AAGTCTCTCGAGCTTAAGCTAATGGGC
1 AGAC-AAAAGAT-AAAGAAGTCTCTCGAGCTTGAGCCGATGGGC
* * * * *
375434 AGACAAAGGATATAGGAGTCT-TCTG-GGTCTGAGCCGATTGGC
1 AGACAAAAGATAAAGAAGTCTCTC-GAGCT-TGAGCCGATGGGC
* * *
375476 AGACAAAAGATACAATAAGTCTC-CTAGGCTTGAGCCGATCGGC
1 AGACAAAAGATA-AAGAAGTCTCTCGA-GCTTGAGCCGATGGGC
* * * * *
375519 AAACAAAAGATAAAGAAGTCTCT-TAGGTTTGAGCTGACGGGC
1 AGACAAAAGATAAAGAAGTCTCTCGA-GCTTGAGCCGATGGGC
* * * * * **
375561 AAAGAAAAGATAAAAAAGTCTC-CTAGGTCTGAGCTTATGGGC
1 AGACAAAAGATAAAGAAGTCTCTCGAGCT-TGAGCCGATGGGC
*
375603 AGACAATGAGATAAAG
1 AGACAA-AAGATAAAG
375619 GTTGACCAGA
Statistics
Matches: 751, Mismatches: 195, Indels: 94
0.72 0.19 0.09
Matches are distributed among these distances:
41 29 0.04
42 350 0.47
43 352 0.47
44 17 0.02
45 3 0.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (42 bp):
AGACAAAAGATAAAGAAGTCTCTCGAGCTTGAGCCGATGGGC
Found at i:375022 original size:85 final size:84
Alignment explanation
Indices: 374583--375618 Score: 485
Period size: 85 Copynumber: 12.2 Consensus size: 84
374573 GCCGTAGGGT
* * * * *
374583 AGACAAATAGATAAAGAAGTCT-TACGAG-CTTGAGCTGATGGACAGACAAAAGATATAGGAGTC
1 AGACAAA-AGATAAAGAAGTCTCT-CGAGTC-TGAGCCGACGGGCAGACAAAAGATAAAGAAGTC
* * *
374646 TCCCG-GGTCTGACCCGATGGGC
63 TCTCGAGCT-TGAGCCGATGGGC
* * * * ** * * *
374668 AGACAAAAAGATGAAGAAGTCTCAT-GGGCCTGAGCCTATAGGTAGACAAAGGATAAAGAAATCT
1 AGAC-AAAAGATAAAGAAGTCTC-TCGAGTCTGAGCCGACGGGCAGACAAAAGATAAAGAAGTCT
* * * ***
374732 CTTG-GGTCTAAGTTAATGGGC
64 CTCGAGCT-TGAGCCGATGGGC
* * ** * *
374753 AGACAAAAAGATGAAGAAGTCTCTCGAG-CTTGAGCCAATAGGCAAACAAAGGATAAA-AATGTC
1 AGAC-AAAAGATAAAGAAGTCTCTCGAGTC-TGAGCCGACGGGCAGACAAAAGATAAAGAA-GTC
* * * * *
374816 TCTCAAG-TCTAAGTCAACGGGC
63 TCTCGAGCT-TGAGCCGATGGGC
** * * * * * * * * *
374838 AGACAACGGGTGAAGAAATCTCCCAAG-CTTGAGCCGACGAGCAGACAAAGGATATAGGAGTCT-
1 AGACAAAAGATAAAGAAGTCTCTCGAGTC-TGAGCCGACGGGCAGACAAAAGATAAAGAAGTCTC
* * * *
374901 TCTAGGTCTGAGCCGATAGGT
65 TCGAGCT-TGAGCCGATGGGC
* * * *
374922 AGACAAAATGTTAAAGAAGTCTCTCGTGTCTGAACCGATGGGCAGACAAAAGATAAAAGAAGTCT
1 AGACAAAA-GATAAAGAAGTCTCTCGAGTCTGAGCCGACGGGCAGACAAAAGAT-AAAGAAGTCT
**
374987 CTCGAGCTTGAGTTGATGGGC
64 CTCGAGCTTGAGCCGATGGGC
* * * * * *
375008 AGACAAAGGATAAAGAAGTCT-TCAAGGTTTGAGTCAACGGGCAGACAAACAGATGAAGAAGTCT
1 AGACAAAAGATAAAGAAGTCTCTCGA-GTCTGAGCCGACGGGCAGACAAA-AGATAAAGAAGTCT
* * *
375072 CTTCGATC-TGAGCCGACGAGC
64 C-TCGAGCTTGAGCCGATGGGC
* * * * * * *
375093 AGATAAAAGGATGAAGAAGTCTCTCGAG-CTTGAGCTGACGGGCAAACAAAGGATATAGGAGTCT
1 AGACAAAA-GATAAAGAAGTCTCTCGAGTC-TGAGCCGACGGGCAGACAAAAGATAAAGAAGTCT
* * * **
375157 C-CTAGGTTTGAGTCGATGAAC
64 CTCGA-GCTTGAGCCGATGGGC
* * * * * * * *
375178 AGACAATAAAATGAAA-AAGTCTCCCAAGTTTGAGCTGACAGGTAGACAAAACATAAAGAAAGTC
1 AGACAA-AAGAT-AAAGAAGTCTCTCGAGTCTGAGCCGACGGGCAGACAAAAGATAAAG-AAGTC
* * * *
375242 TCCCAAGCTTGATCCGATAGGC
63 TCTCGAGCTTGAGCCGATGGGC
* * * ** * * * *
375264 AGAAAAAAGATAAAGAAGTCTCTCGGGTCTGAGTCGACAAGTAGACAAAAAGATGAAGAAGTTTT
1 AGACAAAAGATAAAGAAGTCTCTCGAGTCTGAGCCGACGGGCAGAC-AAAAGATAAAGAAGTCTC
* * *
375329 TTG-GGTCTGAGCCGATGGGT
65 TCGAGCT-TGAGCCGATGGGC
* *
375349 AGACAAAATATAAAGAAGTCTCTCGAGTCTGAGCCGACGGGCAAACAAAAAGATGAAA-AAGTCT
1 AGACAAAAGATAAAGAAGTCTCTCGAGTCTGAGCCGACGGGCAGAC-AAAAGAT-AAAGAAGTCT
* **
375413 CTCGAGCTTAAGCTAATGGGC
64 CTCGAGCTTGAGCCGATGGGC
* * * * ** *
375434 AGACAAAGGATATAGGAGTCT-TCTGGGTCTGAGCCGATTGGCAGACAAAAGATACAATAAGTCT
1 AGACAAAAGATAAAGAAGTCTCTC-GAGTCTGAGCCGACGGGCAGACAAAAGATA-AAGAAGTCT
* *
375498 C-CTAGGCTTGAGCCGATCGGC
64 CTCGA-GCTTGAGCCGATGGGC
* * * * * * *
375519 AAACAAAAGATAAAGAAGTCTCT-TAGGTTTGAGCTGACGGGCAAAGAAAAGATAAAAAAGTCTC
1 AGACAAAAGATAAAGAAGTCTCTCGA-GTCTGAGCCGACGGGCAGACAAAAGATAAAGAAGTCTC
* * **
375583 -CTAGGTCTGAGCTTATGGGC
65 TCGAGCT-TGAGCCGATGGGC
*
375603 AGACAATGAGATAAAG
1 AGACAA-AAGATAAAG
375619 GTTGACCAGA
Statistics
Matches: 721, Mismatches: 190, Indels: 80
0.73 0.19 0.08
Matches are distributed among these distances:
83 9 0.01
84 110 0.15
85 484 0.67
86 107 0.15
87 11 0.02
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (84 bp):
AGACAAAAGATAAAGAAGTCTCTCGAGTCTGAGCCGACGGGCAGACAAAAGATAAAGAAGTCTCT
CGAGCTTGAGCCGATGGGC
Found at i:375399 original size:128 final size:128
Alignment explanation
Indices: 374863--375618 Score: 440
Period size: 128 Copynumber: 5.9 Consensus size: 128
374853 AAATCTCCCA
* * * * * * * * * * *
374863 AGCTTGAGCCGACGAGCAGACAAAGGATATAGGAGTCT-TCTAGGTCTGAGCCGATAGGTAGACA
1 AGCTTGAGCCGACGGGCAAACAAAAGATAAAGAAGTCTCTCAAGGTTTGAGTCGACAAGCAGACA
* * * * * *
374927 AAATGTTAAAGAAGTCTC-TCGTGTCTGAACCGATGGGCAGACAAAAGATAAAAGAAGTCTCTCG
66 AAAAGATGAAGAAGTCTCTTAG-GTCTGAGCCGACGGGCAGACAAAAGAT-AAAGAAGTCTCTCG
** * * * * **
374991 AGCTTGAGTTGATGGGCAGACAAAGGATAAAGAAGTCT-TCAAGGTTTGAGTCAACGGGCAGACA
1 AGCTTGAGCCGACGGGCAAACAAAAGATAAAGAAGTCTCTCAAGGTTTGAGTCGACAAGCAGACA
* * * * * *
375055 AACAGATGAAGAAGTCTCTTCGATCTGAGCCGACGAGCAGATAAAAGGATGAAGAAGTCTCTCG
66 AAAAGATGAAGAAGTCTCTTAGGTCTGAGCCGACGGGCAGACAAAA-GATAAAGAAGTCTCTCG
* * * * * *
375119 AGCTTGAGCTGACGGGCAAACAAAGGATATAGGAGTCTC-CTAGGTTTGAGTCGATGAA-CAGAC
1 AGCTTGAGCCGACGGGCAAACAAAAGATAAAGAAGTCTCTCAAGGTTTGAGTCGA-CAAGCAGAC
* ** * * * * * * *
375182 AATAAA-ATGAAAAAGTCTCCCAAGTTTGAGCTGACAGGTAGACAAAACATAAAGAAAGTCTCCC
65 AA-AAAGATGAAGAAGTCTCTTAGGTCTGAGCCGACGGGCAGACAAAAGATAAAG-AAGTCTCTC
*
375246 A
128 G
* ** * * *
375247 AGCTTGATCCGATAGGCAGAA-AAAAGATAAAGAAGTCTCTC-GGGTCTGAGTCGACAAGTAGAC
1 AGCTTGAGCCGACGGGCA-AACAAAAGATAAAGAAGTCTCTCAAGGTTTGAGTCGACAAGCAGAC
* * * * * *
375310 AAAAAGATGAAGAAGTTTTTTGGGTCTGAGCCGATGGGTAGACAAAATATAAAGAAGTCTCTCG
65 AAAAAGATGAAGAAGTCTCTTAGGTCTGAGCCGACGGGCAGACAAAAGATAAAGAAGTCTCTCG
* * * * *
375374 AG-TCTGAGCCGACGGGCAAACAAAAAGATGAAA-AAGTCTCTCGA-GCTTAAG-CTA-ATGGGC
1 AGCT-TGAGCCGACGGGCAAAC-AAAAGAT-AAAGAAGTCTCTCAAGGTTTGAGTCGACA--AGC
* * * ** *
375434 AGAC-AAAGGAT-ATAGGAGTCT-TCTGGGTCTGAGCCGATTGGCAGACAAAAGATACAATAAGT
61 AGACAAAAAGATGA-AGAAGTCTCT-TAGGTCTGAGCCGACGGGCAGACAAAAGATA-AAGAAGT
*
375496 CTC-CT
123 CTCTCG
* **
375501 AGGCTTGAGCCGATC-GGCAAACAAAAGATAAAGAAGTCTCT-TAGGTTTGAG-CTGACGGGCA-
1 A-GCTTGAGCCGA-CGGGCAAACAAAAGATAAAGAAGTCTCTCAAGGTTTGAGTC-GACAAGCAG
* * * ** * *
375562 A-AGAAAAGATAAAAAAGTCTCCTAGGTCTGAGCTTATGGGCAGACAATGAGATAAAG
63 ACA-AAAAGATGAAGAAGTCTCTTAGGTCTGAGCCGACGGGCAGACAA-AAGATAAAG
375619 GTTGACCAGA
Statistics
Matches: 488, Mismatches: 108, Indels: 65
0.74 0.16 0.10
Matches are distributed among these distances:
126 11 0.02
127 135 0.28
128 326 0.67
129 16 0.03
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.20
Consensus pattern (128 bp):
AGCTTGAGCCGACGGGCAAACAAAAGATAAAGAAGTCTCTCAAGGTTTGAGTCGACAAGCAGACA
AAAAGATGAAGAAGTCTCTTAGGTCTGAGCCGACGGGCAGACAAAAGATAAAGAAGTCTCTCG
Found at i:375603 original size:42 final size:42
Alignment explanation
Indices: 375332--375617 Score: 191
Period size: 42 Copynumber: 6.7 Consensus size: 42
375322 AAGTTTTTTG
* * * * * *
375332 GGTCTGAGCCGATGGGTAGACAAAATATAAAGAAGTCT-CTC
1 GGTCTGAGCTGATGGGCAAACAAAAGATAAAAAAGTCTCCTA
* * * *
375373 GAGTCTGAGCCGACGGGCAAACAAAAAGATGAAAAAGTCTCTCGA
1 G-GTCTGAGCTGATGGGCAAAC-AAAAGATAAAAAAGTCTC-CTA
* * * * * * ** * *
375418 GCT-TAAGCTAATGGGCAGACAAAGGATATAGGAGTCTTCTG
1 GGTCTGAGCTGATGGGCAAACAAAAGATAAAAAAGTCTCCTA
* * * *
375459 GGTCTGAGCCGATTGGCAGACAAAAGATACAATAAGTCTCCTA
1 GGTCTGAGCTGATGGGCAAACAAAAGATA-AAAAAGTCTCCTA
* * * *
375502 GG-CTTGAGCCGATCGGCAAACAAAAGATAAAGAAGTCTCTTA
1 GGTC-TGAGCTGATGGGCAAACAAAAGATAAAAAAGTCTCCTA
* * *
375544 GGTTTGAGCTGACGGGCAAAGAAAAGATAAAAAAGTCTCCTA
1 GGTCTGAGCTGATGGGCAAACAAAAGATAAAAAAGTCTCCTA
* * *
375586 GGTCTGAGCTTATGGGCAGACAATGAGATAAA
1 GGTCTGAGCTGATGGGCAAACAA-AAGATAAA
375618 GGTTGACCAG
Statistics
Matches: 186, Mismatches: 50, Indels: 16
0.74 0.20 0.06
Matches are distributed among these distances:
41 4 0.02
42 113 0.61
43 66 0.35
44 1 0.01
45 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (42 bp):
GGTCTGAGCTGATGGGCAAACAAAAGATAAAAAAGTCTCCTA
Found at i:376573 original size:13 final size:13
Alignment explanation
Indices: 376555--376614 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
376545 CCAATGTGGT
376555 AATGTATCGATAC
1 AATGTATCGATAC
376568 AATGTATCGATAC
1 AATGTATCGATAC
*
376581 -AT-T-T-GGT-C
1 AATGTATCGATAC
376589 -ATGTATCGATAC
1 AATGTATCGATAC
376601 AATGTATCGATAC
1 AATGTATCGATAC
376614 A
1 A
376615 TCTTGTATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 2 0.05
11 3 0.08
12 3 0.08
13 26 0.65
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:376594 original size:33 final size:33
Alignment explanation
Indices: 376551--376634 Score: 136
Period size: 33 Copynumber: 2.5 Consensus size: 33
376541 CAAGCCAATG
376551 TGGTAATGTATCGATACAATGTATCGATACAT-T
1 TGGT-ATGTATCGATACAATGTATCGATACATCT
376584 TGGTCATGTATCGATACAATGTATCGATACATCT
1 TGGT-ATGTATCGATACAATGTATCGATACATCT
376618 T-GTATGTATCGATACAA
1 TGGTATGTATCGATACAA
376635 ACAGTTAAGG
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
32 14 0.29
33 33 0.67
34 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (33 bp):
TGGTATGTATCGATACAATGTATCGATACATCT
Found at i:376710 original size:19 final size:20
Alignment explanation
Indices: 376686--376733 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
376676 ATCTTTGCAA
*
376686 GTATCGATACAGTG-GTCAT
1 GTATCGATACAGTGCATCAT
* *
376705 GTATCGATACTGTGCATTAT
1 GTATCGATACAGTGCATCAT
376725 GTATCGATA
1 GTATCGATA
376734 TATCTGAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (20 bp):
GTATCGATACAGTGCATCAT
Found at i:377388 original size:14 final size:14
Alignment explanation
Indices: 377369--377401 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
377359 CCTTAATCAT
377369 AAATTTATTTACAG
1 AAATTTATTTACAG
377383 AAATTTATTTACAG
1 AAATTTATTTACAG
377397 AAATT
1 AAATT
377402 CTCTGATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (14 bp):
AAATTTATTTACAG
Found at i:378203 original size:18 final size:17
Alignment explanation
Indices: 378176--378209 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
378166 TGTGTGGCTT
*
378176 TGTTTTGAGGAACTCGAA
1 TGTTTCGAGGAA-TCGAA
378194 TGTTTCGAGGAATCGA
1 TGTTTCGAGGAATCGA
378210 GCCCTCTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (17 bp):
TGTTTCGAGGAATCGAA
Found at i:385889 original size:35 final size:34
Alignment explanation
Indices: 385833--385898 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
385823 CCTTACAACA
* *
385833 CTATCTTTTCGAAGGCTAAGATAGAACCTCTTCC
1 CTATCTTTTCAAAGGCCAAGATAGAACCTCTTCC
385867 CTATCTTTTGCAAAGGCCAAGATAGAACCTCT
1 CTATCTTTT-CAAAGGCCAAGATAGAACCTCT
385899 CAATCATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (34 bp):
CTATCTTTTCAAAGGCCAAGATAGAACCTCTTCC
Found at i:386409 original size:20 final size:21
Alignment explanation
Indices: 386384--386434 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
386374 CGATACATTA
**
386384 TATCGATACATGACCA-AATG
1 TATCGATACATGAAAAGAATG
*
386404 TATCGATACTTGAAAAGAATG
1 TATCGATACATGAAAAGAATG
386425 TATCGATACA
1 TATCGATACA
386435 GGTCATTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (21 bp):
TATCGATACATGAAAAGAATG
Found at i:386523 original size:33 final size:32
Alignment explanation
Indices: 386467--386534 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
386457 GTAGCCAAAT
*
386467 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
386499 TTGTATTGATACATCACAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
386532 TTG
1 TTG
386535 GCATGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:388358 original size:21 final size:21
Alignment explanation
Indices: 388332--388382 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
388322 CTAATTTGAA
388332 GAAGAAGAATGTGAGCAAACC
1 GAAGAAGAATGTGAGCAAACC
388353 GAAGAAGAATGTGAGCAAACC
1 GAAGAAGAATGTGAGCAAACC
*
388374 AAAGAAGAA
1 GAAGAAGAA
388383 AGCCATGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.53, C:0.12, G:0.27, T:0.08
Consensus pattern (21 bp):
GAAGAAGAATGTGAGCAAACC
Found at i:392346 original size:8 final size:8
Alignment explanation
Indices: 392333--392358 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
392323 ATTTGATTCA
392333 ATTTTGTG
1 ATTTTGTG
392341 ATTTTGTG
1 ATTTTGTG
392349 ATTTTGTG
1 ATTTTGTG
392357 AT
1 AT
392359 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:392578 original size:13 final size:13
Alignment explanation
Indices: 392560--392597 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
392550 CAGCATTCTC
*
392560 TGTATCGATACAT
1 TGTATCGATACAG
392573 TGTATCGATACAG
1 TGTATCGATACAG
392586 TGTATCGATACA
1 TGTATCGATACA
392598 AAGGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:394292 original size:24 final size:22
Alignment explanation
Indices: 394244--394285 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
394234 TGAAAGTGTT
394244 AAATTATTTTACTAAGGGGGAG
1 AAATTATTTTACTAAGGGGGAG
394266 AAATT-TTTTGACTAAGGGGG
1 AAATTATTTT-ACTAAGGGGG
394286 GGAGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (22 bp):
AAATTATTTTACTAAGGGGGAG
Found at i:394976 original size:13 final size:13
Alignment explanation
Indices: 394958--394983 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
394948 ACACACAATA
394958 TGTATCGATACAT
1 TGTATCGATACAT
394971 TGTATCGATACAT
1 TGTATCGATACAT
394984 CACAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:394994 original size:33 final size:32
Alignment explanation
Indices: 394938--395005 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
394928 GTAGCCAAAT
*
394938 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
394970 TTGTATCGATACATCACAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
395003 TTG
1 TTG
395006 GCTTGTAGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:396111 original size:22 final size:23
Alignment explanation
Indices: 396086--396129 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
396076 ACTTTGAATT
396086 ATTT-TTACTTGCAAAAA-ATTTG
1 ATTTATTACTTG-AAAAACATTTG
*
396108 ATTTATTGCTTGAAAAACATTT
1 ATTTATTACTTGAAAAACATTT
396130 AAACTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (23 bp):
ATTTATTACTTGAAAAACATTTG
Found at i:398574 original size:22 final size:20
Alignment explanation
Indices: 398506--398584 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
398496 ACTACTAAGG
*
398506 AAATGTATCAATACATTAAT
1 AAATGTATCGATACATTAAT
398526 AAATGTATCGATACATTAAT
1 AAATGTATCGATACATTAAT
*
398546 AAATGTATATCGATACATTGAT
1 AAATG--TATCGATACATTAAT
***
398568 CCTTGTATCGATACATT
1 AAATGTATCGATACATT
398585 TGGGTATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 36 0.69
22 16 0.31
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (20 bp):
AAATGTATCGATACATTAAT
Found at i:402005 original size:13 final size:13
Alignment explanation
Indices: 401987--402012 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
401977 AATTTTTTTG
401987 TGTATCGATACAT
1 TGTATCGATACAT
402000 TGTATCGATACAT
1 TGTATCGATACAT
402013 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:403215 original size:32 final size:33
Alignment explanation
Indices: 403179--403241 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
403169 TGGTTTTGGA
* *
403179 TTGATGA-TTTGATGAAAAAGAAAGTGTTTTTG
1 TTGATGATTTTGATGAAAAACAAAGAGTTTTTG
403211 TTGATGATTTTGATGAAAAACAAAGAGTTTT
1 TTGATGATTTTGATGAAAAACAAAGAGTTTT
403242 GATGCAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.40
Consensus pattern (33 bp):
TTGATGATTTTGATGAAAAACAAAGAGTTTTTG
Found at i:403397 original size:19 final size:19
Alignment explanation
Indices: 403373--403437 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
403363 CATATAGTTG
403373 AATGTATCGATACAATTTT
1 AATGTATCGATACAATTTT
*
403392 AATGTATTGATAC-A---T
1 AATGTATCGATACAATTTT
403407 --TGTATCGATACAATTTT
1 AATGTATCGATACAATTTT
*
403424 AATGTATTGATACA
1 AATGTATCGATACA
403438 TTGTATCGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 23 0.62
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (19 bp):
AATGTATCGATACAATTTT
Found at i:403411 original size:32 final size:32
Alignment explanation
Indices: 403375--403451 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
403365 TATAGTTGAA
403375 TGTATCGATACAATTTTAATGTATTGATACAT
1 TGTATCGATACAATTTTAATGTATTGATACAT
403407 TGTATCGATACAATTTTAATGTATTGATACAT
1 TGTATCGATACAATTTTAATGTATTGATACAT
403439 TGTATCGATACAA
1 TGTATCGATACAA
403452 AGAACCTGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (32 bp):
TGTATCGATACAATTTTAATGTATTGATACAT
Found at i:403462 original size:32 final size:31
Alignment explanation
Indices: 403375--403471 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 31
403365 TATAGTTGAA
**
403375 TGTATCGATACAATTTTAATGTATTGATACAT
1 TGTATCGATACAA-TAGAATGTATTGATACAT
**
403407 TGTATCGATACAATTTTAATGTATTGATACAT
1 TGTATCGATACAA-TAGAATGTATTGATACAT
*
403439 TGTATCGATACAA-AGAACCTGTATCGATACAT
1 TGTATCGATACAATAGAA--TGTATTGATACAT
403471 T
1 T
403472 TTGGAAAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
30 2 0.03
32 58 0.97
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (31 bp):
TGTATCGATACAATAGAATGTATTGATACAT
Found at i:405245 original size:33 final size:33
Alignment explanation
Indices: 405202--405268 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
405192 TTCAACGATT
405202 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
* *** *
405235 TGTATTGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
405268 T
1 T
405269 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:411364 original size:3 final size:3
Alignment explanation
Indices: 411356--411385 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
411346 GTCAACCTCT
*
411356 TCA TCA TCA TCA TCA TCA TCT TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
411386 CCATTGATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:413139 original size:19 final size:20
Alignment explanation
Indices: 413115--413165 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
413105 CATTTCATGG
413115 TGTATCGATACAAAG-AACA
1 TGTATCGATACAAAGCAACA
* *
413134 TGTATCGATACTAAGCAATA
1 TGTATCGATACAAAGCAACA
413154 TGTATCGATACA
1 TGTATCGATACA
413166 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGCAACA
Found at i:413314 original size:24 final size:23
Alignment explanation
Indices: 413270--413314 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
413260 ATTATTTTTA
* *
413270 CTTGAAAAACATTTGATTTATTG
1 CTTGAAAAACATTTAACTTATTG
413293 CTTGAAAAACATTTAAACTTAT
1 CTTGAAAAACATTT-AACTTAT
413315 CTCTAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (23 bp):
CTTGAAAAACATTTAACTTATTG
Found at i:413630 original size:48 final size:49
Alignment explanation
Indices: 413454--413812 Score: 380
Period size: 48 Copynumber: 7.6 Consensus size: 49
413444 AAATCTTAAC
* * *
413454 ACGAGGGAT-GAAAAGAATTTGACTAGGCCCTAACACCAATACAGTTAA
1 ACGAGGGATAGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAA
* * * * *
413502 AC-AAGGATACAAAA-AGTTTGACCAGACCCTAACACCAATATAATCAA
1 ACGAGGGATAGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAA
* * *
413549 ATGA-GGATA-CAAAGAGTTTGACCAGGCCTTAACACCAATACAGTCAA
1 ACGAGGGATAGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAA
* * *
413596 ACGAGGGA-AGAAAAGAGTTTGACCAAGCCCTAACATCAATAAAGTCAA
1 ACGAGGGATAGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAA
** * * *
413644 ATAAGGGAT-GAAAAGAGTTTGACCAGGCCTTAACACCAATATAGTTAA
1 ACGAGGGATAGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAA
* * * * *
413692 ATGA-AGATA-TAAAGAGTTTGACCAAGCCGTAACACCAATACAGTCAA
1 ACGAGGGATAGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAA
* * *
413739 ACCAGGGA-AGAAAAGAGTTTGACTAGGCCCTAACACCAATAAAGTCAA
1 ACGAGGGATAGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAA
* *
413787 ATGAGAGATA-AAAAGAGTTTGACCAG
1 ACGAGGGATAGAAAAGAGTTTGACCAG
413813 ATACAATCAA
Statistics
Matches: 255, Mismatches: 46, Indels: 20
0.79 0.14 0.06
Matches are distributed among these distances:
46 3 0.01
47 110 0.43
48 141 0.55
49 1 0.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (49 bp):
ACGAGGGATAGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAA
Found at i:413706 original size:95 final size:96
Alignment explanation
Indices: 413457--413811 Score: 420
Period size: 95 Copynumber: 3.7 Consensus size: 96
413447 TCTTAACACG
* * * **
413457 AGGGATGAAAAGAATTTGACTAGGCCCTAACACCAATACAGTTAAACAAG-GATACAAAA-AGTT
1 AGGGATGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAATGAGAGATA-AAAAGAGTT
*
413520 TGACC-AGACCCTAACACCAATATAA-TCAAATG
65 TGACCAAG-CCCTAACACCAATA-AAGTCAAATA
* * *
413552 A-GGAT-ACAAAGAGTTTGACCAGGCCTTAACACCAATACAGTCAAACGAGGGA-AGAAAAGAGT
1 AGGGATGA-AAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAATGAGAGATA-AAAAGAGT
*
413614 TTGACCAAGCCCTAACATCAATAAAGTCAAATA
64 TTGACCAAGCCCTAACACCAATAAAGTCAAATA
* * * *
413647 AGGGATGAAAAGAGTTTGACCAGGCCTTAACACCAATATAGTTAAATGA-AGATATAAAGAGTTT
1 AGGGATGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAATGAGAGATAAAAAGAGTTT
* * **
413711 GACCAAGCCGTAACACCAATACAGTCAAACC
66 GACCAAGCCCTAACACCAATAAAGTCAAATA
* * *
413742 AGGGAAGAAAAGAGTTTGACTAGGCCCTAACACCAATAAAGTCAAATGAGAGATAAAAAGAGTTT
1 AGGGATGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAATGAGAGATAAAAAGAGTTT
413807 GACCA
66 GACCA
413812 GATACAATCA
Statistics
Matches: 227, Mismatches: 24, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
93 1 0.00
94 48 0.21
95 113 0.50
96 64 0.28
97 1 0.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (96 bp):
AGGGATGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAATGAGAGATAAAAAGAGTTT
GACCAAGCCCTAACACCAATAAAGTCAAATA
Found at i:413711 original size:143 final size:142
Alignment explanation
Indices: 413454--413813 Score: 506
Period size: 143 Copynumber: 2.5 Consensus size: 142
413444 AAATCTTAAC
* * * * * *
413454 ACGAGGGATGAAAAGAATTTGACTAGGCCCTAACACCAATACAGTTAAACAA-GGATACAAAAAG
1 ACGAGGGAAGAAAAGAGTTTGACTAGGCCCTAACACCAATAAAGTCAAATAAGGGATA-AAAGAG
* * *
413518 TTTGACCAGACCCTAACACCAATATAATCAAATGAGGATACAAAGAGTTTGACCAGGCCTTAACA
65 TTTGACCAGACCCTAACACCAATATAATCAAATGAAGATACAAAGAGTTTGACCAAGCCGTAACA
413583 CCAATACAGTCAA
130 CCAATACAGTCAA
* * *
413596 ACGAGGGAAGAAAAGAGTTTGACCAAGCCCTAACATCAATAAAGTCAAATAAGGGATGAAAAGAG
1 ACGAGGGAAGAAAAGAGTTTGACTAGGCCCTAACACCAATAAAGTCAAATAAGGGAT-AAAAGAG
* * * * *
413661 TTTGACCAGGCCTTAACACCAATATAGTTAAATGAAGATATAAAGAGTTTGACCAAGCCGTAACA
65 TTTGACCAGACCCTAACACCAATATAATCAAATGAAGATACAAAGAGTTTGACCAAGCCGTAACA
413726 CCAATACAGTCAA
130 CCAATACAGTCAA
* * *
413739 ACCAGGGAAGAAAAGAGTTTGACTAGGCCCTAACACCAATAAAGTCAAATGAGAGATAAAAAGAG
1 ACGAGGGAAGAAAAGAGTTTGACTAGGCCCTAACACCAATAAAGTCAAATAAGGGAT-AAAAGAG
413804 TTTGACCAGA
65 TTTGACCAGA
413814 TACAATCAAA
Statistics
Matches: 191, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
142 44 0.23
143 146 0.76
144 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (142 bp):
ACGAGGGAAGAAAAGAGTTTGACTAGGCCCTAACACCAATAAAGTCAAATAAGGGATAAAAGAGT
TTGACCAGACCCTAACACCAATATAATCAAATGAAGATACAAAGAGTTTGACCAAGCCGTAACAC
CAATACAGTCAA
Found at i:413837 original size:35 final size:35
Alignment explanation
Indices: 413798--413905 Score: 171
Period size: 35 Copynumber: 3.1 Consensus size: 35
413788 TGAGAGATAA
*
413798 AAAGAGTTTGACCAGATACAATCAAACAATGATGG
1 AAAGAGTTTGACCAGATACAGTCAAACAATGATGG
* *
413833 AAAGAGTTTGATCGGATACAGTCAAACAATGATGG
1 AAAGAGTTTGACCAGATACAGTCAAACAATGATGG
* *
413868 AAAGAGTTTGACCAGATACAGTCAAACACTGGTGG
1 AAAGAGTTTGACCAGATACAGTCAAACAATGATGG
413903 AAA
1 AAA
413906 ATTTGATTGA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (35 bp):
AAAGAGTTTGACCAGATACAGTCAAACAATGATGG
Found at i:413981 original size:30 final size:30
Alignment explanation
Indices: 413901--413982 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 30
413891 AAACACTGGT
*
413901 GGAAA-ATTTGATTGAGTACAGTCCAAAGA
1 GGAAAGATTTGATTGAGTATAGTCCAAAGA
* * * * * *
413930 TGAAAGACTCGATCGAATATAGT-CAAGGGA
1 GGAAAGATTTGATTGAGTATAGTCCAA-AGA
413960 GGAAAGATTTGATTGAGTATAGT
1 GGAAAGATTTGATTGAGTATAGT
413983 TGAGTGAGAG
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
29 7 0.18
30 32 0.82
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.26
Consensus pattern (30 bp):
GGAAAGATTTGATTGAGTATAGTCCAAAGA
Found at i:414345 original size:91 final size:91
Alignment explanation
Indices: 414143--414392 Score: 262
Period size: 91 Copynumber: 2.8 Consensus size: 91
414133 AACCTTGGCA
* *
414143 CAAGGAAATCAAACTTTGTGATACATCAATACCATCTAGTAGTTGA-ATGAAGGGGATATGATTG
1 CAAGGAAATCAAGCTTTGTGATACATCAATACCATCTAGTAGTTGAGA--AAGGGAATATGATTG
* * *
414207 GGAATG--TG-T-GGGGTGCA-CCTTTGCCC
64 GGAATGAAGGATCGCGAT--ATCC-TTGCCC
** *
414233 CAAGGAAATCAAGCTTTGTGATATGTTAATACCATCTAGTAGTTGAGAAAGAGG-ATATGATTGG
1 CAAGGAAATCAAGCTTTGTGATACATCAATACCATCTAGTAGTTGAGAAAG-GGAATATGATTGG
414297 GAATGAAGGATCGCGATATCCTTGCCC
65 GAATGAAGGATCGCGATATCCTTGCCC
* * * * * **
414324 TAAGGATATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTGGGTGAGGGAATATGATTGGG
1 CAAGGAAATCAAGCTTTGTGATACATCAATACCATCTAGTAGTTGAGAAAGGGAATATGATTGGG
414389 AATG
66 AATG
414393 TGTGGGCTAT
Statistics
Matches: 135, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
89 18 0.13
90 46 0.34
91 65 0.48
92 3 0.02
93 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (91 bp):
CAAGGAAATCAAGCTTTGTGATACATCAATACCATCTAGTAGTTGAGAAAGGGAATATGATTGGG
AATGAAGGATCGCGATATCCTTGCCC
Found at i:414450 original size:89 final size:90
Alignment explanation
Indices: 414071--414443 Score: 353
Period size: 90 Copynumber: 4.1 Consensus size: 90
414061 TGTAGTCATA
* * * * * * * *
414071 TGATGCATCAGTACTATCTAGTGGTTGAATGAAGGGGATATGATTAGAAATGTGTGCACCACAAC
1 TGATGCATCAATACCATCTAGTAGTTGAATGAAGGGGATATGATTGGGAATGTGTGCGCTACACC
* *
414136 CTTGGCAC-AAGGAAATCAAACTTTG
66 CTT-GCCCTAAGGAAATCAAGCTTTG
* * * *
414161 TGATACATCAATACCATCTAGTAGTTGAATGAAGGGGATATGATTGGGAATGTGTGGGGTGCACC
1 TGATGCATCAATACCATCTAGTAGTTGAATGAAGGGGATATGATTGGGAATGTGTGCGCTACACC
* *
414226 TTTGCCCCAAGGAAATCAAGCTTTG
66 CTTGCCCTAAGGAAATCAAGCTTTG
*** * * * *
414251 TGATATGTTAATACCATCTAGTAGTTG-A-GAAAGAGGATATGATTGGGAATGAAG-GATCGCGA
1 TGATGCATCAATACCATCTAGTAGTTGAATG-AAGGGGATATGATTGGGAATG-TGTG--CGCTA
* * *
414313 TATCCTTGCCCTAAGGATATCAAGCTTTG
62 CACCCTTGCCCTAAGGAAATCAAGCTTTG
* ** * * *
414342 TGATGCATCAATACCATCTAGTGGTTGGGTG-AGGGAATATGATTGGGAATGTGTGGGCTATACC
1 TGATGCATCAATACCATCTAGTAGTTGAATGAAGGGGATATGATTGGGAATGTGTGCGCTACACC
*
414406 CTTGCCCTAAGGAAATC-AGACTTTA
66 CTTGCCCTAAGGAAATCAAG-CTTTG
414431 TGATGCATCAATA
1 TGATGCATCAATA
414444 TTATCTAACG
Statistics
Matches: 231, Mismatches: 43, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
88 3 0.01
89 64 0.28
90 97 0.42
91 66 0.29
93 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (90 bp):
TGATGCATCAATACCATCTAGTAGTTGAATGAAGGGGATATGATTGGGAATGTGTGCGCTACACC
CTTGCCCTAAGGAAATCAAGCTTTG
Found at i:414472 original size:181 final size:181
Alignment explanation
Indices: 414144--414479 Score: 424
Period size: 180 Copynumber: 1.9 Consensus size: 181
414134 ACCTTGGCAC
*
414144 AAGGAAATCAAACTTTGTGATACATCAATACCATCTAGTAGTTGAATGAAGGGGATATGATTGGG
1 AAGGAAATCAAACTTTGTGATACATCAATACCATCTAGTAGTTGAATGAAGGGAATATGATTGGG
* * * * ** * **
414209 AATGTGTGGGGTGCACCTTTGCCCCAAGGAAATCAAGCTTTGTGATATGTTAATACCATCTAGTA
66 AATGTGTGGGCTACACCCTTGCCCCAAGGAAATCAAGCTTTATGATACATCAATACCATCTAACA
*
414274 GTTGAGAAAGAGGATATGATTGGGAATGAAGGATCGCGATATCCTTGCCCT
131 GTTAAGAAAGAGGATATGATTGGGAATGAAGGATCGCGATATCCTTGCCCT
* * * * **
414325 AAGGATATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTGGGTG-AGGGAATATGATTGGG
1 AAGGAAATCAAACTTTGTGATACATCAATACCATCTAGTAGTTGAATGAAGGGAATATGATTGGG
* * * **
414389 AATGTGTGGGCTATACCCTTGCCCTAAGGAAATC-AGACTTTATGATGCATCAATATTATCTAAC
66 AATGTGTGGGCTACACCCTTGCCCCAAGGAAATCAAG-CTTTATGATACATCAATACCATCTAAC
* *
414453 GGTTAAGAAAGCGGGATATGATTGGGA
130 AGTTAAGAAAG-AGGATATGATTGGGA
414480 GTGTATGGAC
Statistics
Matches: 129, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
179 2 0.02
180 71 0.55
181 56 0.43
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (181 bp):
AAGGAAATCAAACTTTGTGATACATCAATACCATCTAGTAGTTGAATGAAGGGAATATGATTGGG
AATGTGTGGGCTACACCCTTGCCCCAAGGAAATCAAGCTTTATGATACATCAATACCATCTAACA
GTTAAGAAAGAGGATATGATTGGGAATGAAGGATCGCGATATCCTTGCCCT
Found at i:471602 original size:50 final size:50
Alignment explanation
Indices: 471547--471672 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 50
471537 AAATTTCTAT
* * * * **
471547 ATTTTTTATCTTGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTG
1 ATTTTTCATCTTGGGGATACTCCAACCCCCGCTTTATTTCCAAAACATCA
** * *
471597 ATTTTTCATCTCAGGGATACTCAAACCCCCGTTTTATTTCCAAAACATCA
1 ATTTTTCATCTTGGGGATACTCCAACCCCCGCTTTATTTCCAAAACATCA
*
471647 ATTTTTCATAATTGGGGATACTCCAA
1 ATTTTTCAT-CTTGGGGATACTCCAA
471673 TCTCGTTATT
Statistics
Matches: 61, Mismatches: 14, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
50 49 0.80
51 12 0.20
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (50 bp):
ATTTTTCATCTTGGGGATACTCCAACCCCCGCTTTATTTCCAAAACATCA
Found at i:471703 original size:79 final size:79
Alignment explanation
Indices: 471610--471862 Score: 265
Period size: 79 Copynumber: 3.2 Consensus size: 79
471600 TTTCATCTCA
* * * * * *
471610 GGGATACTCAAACCCCCGTTTTATTTCCAAAACATCAATTTTTCATAATTGGGGATACTCCAATC
1 GGGATACTCCAACCCCCGCTTTATTTCTAAAACATCGATTTTTCACAATTGGGGATACTCCAACC
*
471675 TCGTTATTTTCGAG
66 CCGTTATTTTCGAG
* * * *
471689 GGGATACTCCAA-CCCCGACTTTATTTCTAAGATATTGATTTCTCACAATTGGGGATACTCCAAC
1 GGGATACTCCAACCCCCG-CTTTATTTCTAAAACATCGATTTTTCACAATTGGGGATACTCCAAC
* *
471753 CCCGTTATTTTGGTG
65 CCCGTTATTTTCGAG
* ** * * * * * *
471768 GGGATATTGTAACCTCGGCCTTATTTCTAAAGCATCGATTTTCCACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCCGCTTTATTTCTAAAACATCGATTTTTCACAATTGGGGATACTCCAACC
*
471833 CCGTTATTTTCAAG
66 CCGTTATTTTCGAG
**
471847 AAGATACTCCAACCCC
1 GGGATACTCCAACCCC
471863 GAAAATACTC
Statistics
Matches: 137, Mismatches: 35, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
78 5 0.04
79 129 0.94
80 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (79 bp):
GGGATACTCCAACCCCCGCTTTATTTCTAAAACATCGATTTTTCACAATTGGGGATACTCCAACC
CCGTTATTTTCGAG
Found at i:471897 original size:44 final size:45
Alignment explanation
Indices: 471822--471908 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 45
471812 ACAATCGGGG
* *
471822 ATACTCCAACCCCGTTATTTTCAAGAAGATACTCCAACCCCGAAA
1 ATACTCCAACCACGATATTTTCAAGAAGATACTCCAACCCCGAAA
*
471867 ATACTCCAACCAC-ATATTTTCGAAG-GGATACTCCAACCCCGA
1 ATACTCCAACCACGATATTTTC-AAGAAGATACTCCAACCCCGA
471909 TTTTATTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 23 0.61
45 15 0.39
ACGTcount: A:0.34, C:0.33, G:0.10, T:0.22
Consensus pattern (45 bp):
ATACTCCAACCACGATATTTTCAAGAAGATACTCCAACCCCGAAA
Found at i:471980 original size:79 final size:79
Alignment explanation
Indices: 471891--472036 Score: 213
Period size: 79 Copynumber: 1.8 Consensus size: 79
471881 TATTTTCGAA
* * * * *
471891 GGGATACTCCAACCCCGATTTTATTTTCA-AAGCATCGATTTTCTATAGTCAGTGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTATTTCCAGAAG-ATAGATTTTCCATAATCAGGGATACTCCAAC
471955 CCCGTTATTTCCAAG
65 CCCGTTATTTCCAAG
* *
471970 GGGATACTCCAACCTCGATTTTATTTCCAGAAGATAGATTTTCCATAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCCAGAAGATAGATTTTCCATAATCAGGGATACTCCAACC
472035 CC
66 CC
472037 ATTGTTATCC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
79 56 0.95
80 3 0.05
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCCGATTTTATTTCCAGAAGATAGATTTTCCATAATCAGGGATACTCCAACC
CCGTTATTTCCAAG
Found at i:475272 original size:28 final size:28
Alignment explanation
Indices: 475232--475303 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
475222 GGAATAAAGC
** *
475232 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
475260 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
475288 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
475304 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:475361 original size:52 final size:50
Alignment explanation
Indices: 475292--475461 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
475282 AAATAACGAG
* * *
475292 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
475344 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
475397 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
475448 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
475462 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:475480 original size:28 final size:28
Alignment explanation
Indices: 475435--475516 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
475425 AGTGTTTTAA
* *
475435 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
475462 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
475489 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
475517 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:477947 original size:13 final size:13
Alignment explanation
Indices: 477929--477954 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
477919 ACAAAGATCC
477929 ATGTATCGATACA
1 ATGTATCGATACA
477942 ATGTATCGATACA
1 ATGTATCGATACA
477955 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:477950 original size:33 final size:33
Alignment explanation
Indices: 477908--477974 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
477898 AAAATTTCCA
***
477908 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
477941 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
477974 A
1 A
477975 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:478018 original size:19 final size:18
Alignment explanation
Indices: 477994--478061 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
477984 CAGTAGCTAA
477994 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
478013 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
478028 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
478045 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
478062 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:478034 original size:13 final size:13
Alignment explanation
Indices: 478016--478040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
478006 ACAATACTTA
478016 TGTATCGATACAT
1 TGTATCGATACAT
478029 TGTATCGATACA
1 TGTATCGATACA
478041 AAACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:478038 original size:32 final size:32
Alignment explanation
Indices: 477997--478059 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
477987 TAGCTAATTA
*
477997 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
478029 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
478060 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:478141 original size:21 final size:21
Alignment explanation
Indices: 478117--478173 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
478107 CATTTGTAGG
478117 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
478138 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
478159 ATGTATCGATACATT
1 ATGTATCGATACATT
478174 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:478184 original size:1 final size:1
Alignment explanation
Indices: 478178--478221 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
478168 TACATTTAAA
***
478178 TTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
478222 CAAACACTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.05, C:0.02, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:478222 original size:19 final size:19
Alignment explanation
Indices: 478187--478224 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
478177 ATTTTTTTTT
478187 TTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTCAA
478206 TTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTCAA
478225 ACACTTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTTTTTTTTCAA
Found at i:486635 original size:79 final size:80
Alignment explanation
Indices: 486511--486852 Score: 399
Period size: 79 Copynumber: 4.3 Consensus size: 80
486501 AGCGCTTTGA
** * * *
486511 AAATAAAATCGGGGTTGGAGTAT-CCTCTCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAA
1 AAATAAAGCCGGGGTTGGAGTATCCCTCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAA
486575 AAATCGATGCTTTAG
66 AAATCGATGCTTTAG
* * * *
486590 AAATAAGGCCGGGGTTGGAGTATCCCTGTC-AAAATAACGGGGTTGGAGTATCCCCGATTATGGA
1 AAATAAAGCCGGGGTTGGAGTATCCCTCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAA
486654 AAATCGATGCTTTAG
66 AAATCGATGCTTTAG
* * * * *
486669 AAATAAGGTCGGGGTTGGAGTAT-CCT-TGCCAAAATAACGGGGTTGAAGTATCCCCAATTGTGA
1 AAATAAAGCCGGGGTTGGAGTATCCCTCT-CGAAAATAACGGGGTTGGAGTATCCCCAATTATGA
* * *
486732 GAAATCAAT-ATCTTAG
65 AAAATCGATGCT-TTAG
* * *
486748 AAATAAAGCTGGGGTTGGAGTATCCC-CTCGGAAATAACGGGATTGGAGTATCCCCAATTATGAA
1 AAATAAAGCCGGGGTTGGAGTATCCCTCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAA
* * *
486812 AAATTGATGTTTTGG
66 AAATCGATGCTTTAG
* *
486827 AAATAAAACCGGGGTTGGAGTTTCCC
1 AAATAAAGCCGGGGTTGGAGTATCCC
486853 CGAGATGAAA
Statistics
Matches: 225, Mismatches: 31, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
77 1 0.00
78 5 0.02
79 210 0.93
80 9 0.04
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (80 bp):
AAATAAAGCCGGGGTTGGAGTATCCCTCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAA
AAATCGATGCTTTAG
Found at i:486794 original size:158 final size:158
Alignment explanation
Indices: 486511--486847 Score: 446
Period size: 158 Copynumber: 2.1 Consensus size: 158
486501 AGCGCTTTGA
* * *
486511 AAATAAAATCGGGGTTGGAGTATCCTCTCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAA
1 AAATAAAATCGGGGTTGGAGTATCCTCTCCAAAATAACAGGGTTGAAGTATCCCCAATTGTGAAA
* * * *
486576 AATCGATGCTTTAGAAATAAGGCCGGGGTTGGAGTATCCCTGTCAAAATAACGGGGTTGGAGTAT
66 AATCAATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCTCTCAAAATAACGGGATTGGAGTAT
* *
486641 CCCCGATTATGGAAAATCGATGCTTTAG
131 CCCCAATTATGAAAAATCGATGCTTTAG
** * *
486669 AAATAAGGTCGGGGTTGGAGTATCCT-TGCCAAAATAACGGGGTTGAAGTATCCCCAATTGTGAG
1 AAATAAAATCGGGGTTGGAGTATCCTCT-CCAAAATAACAGGGTTGAAGTATCCCCAATTGTGAA
* * *
486733 AAATCAAT-ATCTTAGAAATAAAGCTGGGGTTGGAGTATCCC-CTCGGAAATAACGGGATTGGAG
65 AAATCAATGCT-TTAGAAATAAAGCCGGGGTTGGAGTATCCCTCTC-AAAATAACGGGATTGGAG
* * *
486796 TATCCCCAATTATGAAAAATTGATGTTTTGG
128 TATCCCCAATTATGAAAAATCGATGCTTTAG
*
486827 AAATAAAACCGGGGTTGGAGT
1 AAATAAAATCGGGGTTGGAGT
486848 TTCCCCGAGA
Statistics
Matches: 154, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
157 4 0.03
158 150 0.97
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (158 bp):
AAATAAAATCGGGGTTGGAGTATCCTCTCCAAAATAACAGGGTTGAAGTATCCCCAATTGTGAAA
AATCAATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCTCTCAAAATAACGGGATTGGAGTAT
CCCCAATTATGAAAAATCGATGCTTTAG
Found at i:486880 original size:50 final size:50
Alignment explanation
Indices: 486785--486914 Score: 152
Period size: 50 Copynumber: 2.6 Consensus size: 50
486775 TCGGAAATAA
* * * ** * *
486785 CGGGATTGGAGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGA-GATGAAAAATCAATATTTTAGAAATAAAAC
* * *
486836 CGGGGTTGGAGTTTCCCCGAGATGAAAAATCAATATTTTAGAAATAGAGC
1 CGGGGTTGGAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAAC
*
486886 TGGGGTTGGAGTATCCCCGAGATGAAAAA
1 CGGGGTTGGAGTATCCCCGAGATGAAAAA
486915 ACTAAAAATT
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 50 0.75
51 17 0.25
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAAC
Found at i:490809 original size:20 final size:20
Alignment explanation
Indices: 490784--490980 Score: 92
Period size: 20 Copynumber: 9.7 Consensus size: 20
490774 TTTTAATTAG
490784 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
490804 ATGTATCGATACATCTGGAAA
1 ATGTATCGATACAT-TGAAAA
490825 A---A---A-A-A--GATAAA
1 ATGTATCGATACATTGA-AAA
490836 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
* * * * * *
490856 ATATATCCATACAGTCATAC
1 ATGTATCGATACATTGAAAA
490876 ATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACAT-T--G--AAAA
490901 GATAGAATGTATCGATACATT-AAAGA
1 -AT-G----TATCGATACATTGAAA-A
* * *
490927 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
490947 ATGTATTGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
490967 ATGTATCGATACAT
1 ATGTATCGATACAT
490981 CTAGGTACTT
Statistics
Matches: 131, Mismatches: 21, Indels: 50
0.65 0.10 0.25
Matches are distributed among these distances:
10 1 0.01
11 4 0.03
13 1 0.01
14 2 0.02
15 1 0.01
17 1 0.01
18 2 0.02
19 1 0.01
20 83 0.63
21 11 0.08
24 1 0.01
25 7 0.05
26 3 0.02
27 1 0.01
30 1 0.01
31 11 0.08
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:490939 original size:71 final size:72
Alignment explanation
Indices: 490784--490967 Score: 241
Period size: 71 Copynumber: 2.6 Consensus size: 72
490774 TTTTAATTAG
* * *
490784 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGAAAAAAAAGATAAAATGTATCGATACA
1 ATGTATCGATACATTCATACATGTATCGATACATCTGGAAAAAAAAGATAAAATGTATCGATACA
490849 TTGAAAA
66 TTGAAAA
* * * ** *
490856 ATATATCCATACAGTCATACATGTATCGATACATCTGG-GTAAAAAGATAGAATGTATCGATACA
1 ATGTATCGATACATTCATACATGTATCGATACATCTGGAAAAAAAAGATAAAATGTATCGATACA
490920 TT-AAAGA
66 TTGAAA-A
*
490927 ATGTATCGATACATTCATACATGTATTGATACAT-T-GAAAAA
1 ATGTATCGATACATTCATACATGTATCGATACATCTGGAAAAA
490968 TGTATCGATA
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
69 1 0.01
70 6 0.06
71 56 0.59
72 32 0.34
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.29
Consensus pattern (72 bp):
ATGTATCGATACATTCATACATGTATCGATACATCTGGAAAAAAAAGATAAAATGTATCGATACA
TTGAAAA
Found at i:491957 original size:28 final size:28
Alignment explanation
Indices: 491896--492417 Score: 713
Period size: 28 Copynumber: 18.5 Consensus size: 28
491886 TACCAACTCG
* *
491896 TGTGGGCTTTGAAAAGAGGTACCACTGGCT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
491926 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
491954 TGTGGGCTTTAAAAGGGTGACACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
491982 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
492011 TGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
492038 TGTGGGCTTTGAAAGGATGTCACTGACC
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
**
492066 TGTGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
492095 TGCGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
492123 TGCGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
492151 TATGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
492179 TATGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
492207 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
492235 TGTGAGCTTTGAAAAGAGTTACCACTGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * * *
492265 CGTGGGCTTTGAAATGATGCCACTTACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
492293 TGTGGGCTTTGAAAGGATGCCACTGACA
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
492321 TGTGGTCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
492349 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
492377 TGTGGGCTTTAAAAGGGTGTCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
492405 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
492418 GAGATGAACA
Statistics
Matches: 437, Mismatches: 50, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.05
28 329 0.75
29 54 0.12
30 31 0.07
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:493674 original size:9 final size:9
Alignment explanation
Indices: 493651--493701 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
493641 TTTTAGCTAT
493651 TTTTTTCTTG
1 TTTTTT-TTG
*
493661 GTTTTTTTG
1 TTTTTTTTG
493670 TTTTTTTT-
1 TTTTTTTTG
* *
493678 CTTTTTAT-
1 TTTTTTTTG
493686 TTTTTTTTG
1 TTTTTTTTG
493695 TTTTTTT
1 TTTTTTT
493702 AGGTATAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
8 12 0.35
9 17 0.50
10 5 0.15
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:497642 original size:13 final size:13
Alignment explanation
Indices: 497624--497649 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
497614 CAATTTTTTG
497624 TGTATCGATACAT
1 TGTATCGATACAT
497637 TGTATCGATACAT
1 TGTATCGATACAT
497650 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:499913 original size:21 final size:21
Alignment explanation
Indices: 499889--499935 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
499879 TTTGATGCTG
499889 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
499909 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
499930 ATTTTG
1 ATTTTG
499936 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:500074 original size:13 final size:13
Alignment explanation
Indices: 500056--500094 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
500046 ATAATCACCC
*
500056 TGTATCGATACAG
1 TGTATCGATACAA
500069 TGTATCGATACAA
1 TGTATCGATACAA
500082 TGTATCGATACAA
1 TGTATCGATACAA
500095 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:500105 original size:20 final size:20
Alignment explanation
Indices: 500080--500158 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
500070 GTATCGATAC
500080 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
500100 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
500125 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
500145 CATGTATCGATACA
1 AATGTATCGATACA
500159 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:502193 original size:15 final size:15
Alignment explanation
Indices: 502173--502203 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
502163 ATTTCGTTTG
*
502173 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
502188 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
502203 G
1 G
502204 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:504029 original size:21 final size:21
Alignment explanation
Indices: 504000--504044 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
503990 AAGTTTTCAT
*
504000 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
504020 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
504042 TTT
1 TTT
504045 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:509110 original size:19 final size:19
Alignment explanation
Indices: 509088--509135 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
509078 TTTTTTAAAA
*
509088 AATATATAATAAATTTAAT
1 AATATATAATAAAATTAAT
509107 AATATA-AATAAAAATTAAT
1 AATATATAAT-AAAATTAAT
509126 AATAT-TAATA
1 AATATATAATA
509136 TAAAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATATAATAAAATTAAT
Found at i:509137 original size:44 final size:43
Alignment explanation
Indices: 509091--509194 Score: 106
Period size: 41 Copynumber: 2.4 Consensus size: 43
509081 TTTAAAAAAT
* * * *
509091 ATATAATAAATTTAATAATATAAATAAAAATTAATAA-T-ATTA
1 ATATAATAAATTTAATAACAT-AATAAAAAATAAAAATTAATAA
* *
509133 ATATAA-AAATTTATTAACATTATAAAAAATAAAAATTAATAAGA
1 ATATAATAAATTTAATAACATAATAAAAAATAAAAATTAAT-A-A
509177 ATATAATAAATTTAATAA
1 ATATAATAAATTTAATAA
509195 AAAACTTAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
40 12 0.24
41 13 0.26
42 8 0.16
44 7 0.14
45 10 0.20
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (43 bp):
ATATAATAAATTTAATAACATAATAAAAAATAAAAATTAATAA
Found at i:509161 original size:21 final size:21
Alignment explanation
Indices: 509109--509161 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
509099 AATTTAATAA
*
509109 TATAAATAAAAATTAATAATAT
1 TATAAA-AAAAATTAATAACAT
* * *
509131 TAATATAAAAATTTATTAACAT
1 T-ATAAAAAAAATTAATAACAT
509153 TATAAAAAA
1 TATAAAAAA
509162 TAAAAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 7 0.28
22 14 0.56
23 4 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TATAAAAAAAATTAATAACAT
Found at i:509181 original size:25 final size:24
Alignment explanation
Indices: 509112--509187 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 24
509102 TTAATAATAT
*
509112 AAATAAAAATTAAT--AATAT-TA
1 AAATAAAAATTAATAAAATATAAA
* * *
509133 ATATAAAAATTTATTAACATTATAAA
1 AAATAAAAA-TTAATAA-AATATAAA
*
509159 AAATAAAAATTAATAAGAATATAAT
1 AAATAAAAATTAATAA-AATATAAA
509184 AAAT
1 AAAT
509188 TTAATAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
21 8 0.20
22 4 0.10
25 20 0.49
26 9 0.22
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (24 bp):
AAATAAAAATTAATAAAATATAAA
Found at i:510172 original size:14 final size:14
Alignment explanation
Indices: 510127--510172 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
510117 TAATTTATCG
510127 ATATATTTAAA-AT
1 ATATATTTAAATAT
*
510140 ATTATATTT-TATAT
1 A-TATATTTAAATAT
*
510154 TTATATTTAAATAT
1 ATATATTTAAATAT
510168 ATATA
1 ATATA
510173 AAATATGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATATTTAAATAT
Found at i:510770 original size:17 final size:17
Alignment explanation
Indices: 510736--510771 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
510726 AATCACTTTT
* *
510736 TAAATTTAAATTTTTAA
1 TAAATTTAAATATCTAA
510753 TAAATTTAAATATCTAA
1 TAAATTTAAATATCTAA
510770 TA
1 TA
510772 GATAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTTAAATATCTAA
Found at i:510854 original size:48 final size:48
Alignment explanation
Indices: 510752--510865 Score: 115
Period size: 48 Copynumber: 2.4 Consensus size: 48
510742 TAAATTTTTA
** * *
510752 ATAAATTTAA-ATATCTAATAGATAAATTTAAATTCAAATAATATTAT
1 ATAAATTTAATATAGATAATAAATAAAATTAAATTCAAATAATATTAT
* * **
510799 GTGAATTTAATATAGATAATAAATAAAATTAAATTTTAA-AATACTTAT
1 ATAAATTTAATATAGATAATAAATAAAATTAAATTCAAATAATA-TTAT
*
510847 ATAAATTTATATTTAGATA
1 ATAAATTTA-ATATAGATA
510866 TTATAAAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
47 12 0.23
48 33 0.62
49 8 0.15
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (48 bp):
ATAAATTTAATATAGATAATAAATAAAATTAAATTCAAATAATATTAT
Found at i:511189 original size:11 final size:10
Alignment explanation
Indices: 511170--511242 Score: 58
Period size: 11 Copynumber: 6.6 Consensus size: 10
511160 AAAAAATTAA
511170 TTATATTATTT
1 TTAT-TTATTT
511181 TTATGTTATTT
1 TTAT-TTATTT
511192 TATATTTTAATTAT
1 T-TA-TTT-ATT-T
511206 TT-TTTATTT
1 TTATTTATTT
511215 TTATTATATTT
1 TTATT-TATTT
*
511226 TAATTTATTT
1 TTATTTATTT
511236 TATATTT
1 T-TATTT
511243 TATATAATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
9 3 0.06
10 11 0.21
11 27 0.52
12 4 0.08
13 5 0.10
14 2 0.04
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (10 bp):
TTATTTATTT
Found at i:511194 original size:16 final size:15
Alignment explanation
Indices: 511170--511278 Score: 71
Period size: 16 Copynumber: 7.2 Consensus size: 15
511160 AAAAAATTAA
*
511170 TTATATTATTTTTAT
1 TTATTTTATTTTTAT
*
511185 GTTATTTTATATTTTAA
1 -TTATTTTAT-TTTTAT
*
511202 TTATTTT-TTATT-T
1 TTATTTTATTTTTAT
* *
511215 TTATTATATTTTAAT
1 TTATTTTATTTTTAT
511230 TTATTTTATATTTTAT
1 TTATTTTAT-TTTTAT
* * * *
511246 ATAATTTA-TTATAA
1 TTATTTTATTTTTAT
*
511260 TTATTTAATTTTTAAT
1 TTATTTTATTTTT-AT
511276 TTA
1 TTA
511279 AATAAATTTA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
13 6 0.09
14 15 0.22
15 13 0.19
16 30 0.43
17 5 0.07
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (15 bp):
TTATTTTATTTTTAT
Found at i:511207 original size:27 final size:27
Alignment explanation
Indices: 511174--511265 Score: 91
Period size: 27 Copynumber: 3.3 Consensus size: 27
511164 AATTAATTAT
511174 ATTATTTTTATGTTATT-TTATATTTTA
1 ATTATTTTTAT-TTATTATTATATTTTA
511201 ATTATTTTTTATTT-TTATTATATTTTA
1 ATTA-TTTTTATTTATTATTATATTTTA
*
511228 ATTTATTTTATATTTTATATAATT-TATTATA
1 A-TTATTTT-TA-TTTAT-T-ATTATATTTTA
511259 ATTATTT
1 ATTATTT
511266 AATTTTTAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
26 2 0.04
27 21 0.38
28 12 0.21
29 3 0.05
30 7 0.12
31 8 0.14
32 3 0.05
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (27 bp):
ATTATTTTTATTTATTATTATATTTTA
Found at i:511237 original size:10 final size:10
Alignment explanation
Indices: 511208--511270 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
511198 TTAATTATTT
*
511208 TTTATTTTTA
1 TTTATTTTAA
511218 TTATATTTTAA
1 TT-TATTTTAA
511229 TTTATTTTATA
1 TTTATTTTA-A
*
511240 TTT-TATATAA
1 TTTAT-TTTAA
*
511250 TTTATTATAA
1 TTTATTTTAA
511260 -TTA-TTTAA
1 TTTATTTTAA
511268 TTT
1 TTT
511271 TTAATTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 4 0.09
9 5 0.11
10 19 0.42
11 17 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATTTTAA
Found at i:511252 original size:17 final size:17
Alignment explanation
Indices: 511164--511231 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 17
511154 TAGATAAAAA
*
511164 AATTAATTATATTATTTT
1 AATTAATTTTA-TATTTT
* *
511182 TATGTTATTTTATATTTT
1 AAT-TAATTTTATATTTT
*
511200 AATT-ATTTTTTATTTT
1 AATTAATTTTATATTTT
*
511216 TATTATATTTTA-ATTT
1 AATTA-ATTTTATATTT
511232 ATTTTATATT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 14 0.35
17 5 0.12
18 15 0.38
19 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (17 bp):
AATTAATTTTATATTTT
Found at i:516257 original size:59 final size:59
Alignment explanation
Indices: 516161--516420 Score: 371
Period size: 59 Copynumber: 4.4 Consensus size: 59
516151 GTTTGGATAG
* * * *
516161 GGGTCACCTT-GTGGCAATCTTGA-TTTGAGTGATGTGGCGTCACTTATTGTTTGAATTT
1 GGGTCGCCTTGGTGGCGATC-TGAGTTTGAGTGACGTGGCGTCACTTAGTGTTTGAATTT
516219 GGGTCGCCTTGGTGGCGATCTGAGTTTGAGTGACGTGGCGTCACTTAGTGTTTGAATTT
1 GGGTCGCCTTGGTGGCGATCTGAGTTTGAGTGACGTGGCGTCACTTAGTGTTTGAATTT
* * * * *
516278 GGGTTGCCTTGGTGGCAATCTGAGTTTAATTGAAGTGGCGTCACTTAGTGTTTGAATTT
1 GGGTCGCCTTGGTGGCGATCTGAGTTTGAGTGACGTGGCGTCACTTAGTGTTTGAATTT
* * * *
516337 GGGTCGCCTTGGTGGTGATCTGAGTTTGAGTGACTTAGCGTACACTTAGTGTTTAAATTT
1 GGGTCGCCTTGGTGGCGATCTGAGTTTGAGTGACGTGGCGT-CACTTAGTGTTTGAATTT
516397 GGGTCGCCTTGGTGGCGATCTGAG
1 GGGTCGCCTTGGTGGCGATCTGAG
516421 GAGGAGTCTA
Statistics
Matches: 180, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
58 12 0.07
59 128 0.71
60 40 0.22
ACGTcount: A:0.16, C:0.14, G:0.32, T:0.37
Consensus pattern (59 bp):
GGGTCGCCTTGGTGGCGATCTGAGTTTGAGTGACGTGGCGTCACTTAGTGTTTGAATTT
Found at i:533546 original size:78 final size:78
Alignment explanation
Indices: 533428--533666 Score: 232
Period size: 78 Copynumber: 3.1 Consensus size: 78
533418 CAACTAACCT
** * * *
533428 TTACCTAAGTAACTTTAATAGG-CATGTATCAACATGAAAATCCCTAA-ATAACCCTAGAGACTT
1 TTACCTAAGTAACCCTAAT-GGACATGTATCAACATAAAAAT-ACTAACATAACCCTAGAGACTC
* **
533491 GATTTTATTACACCA
64 AATTTTAACACACCA
* *
533506 TTATCTTAA-TAACCCTAATGGACATGTATCAACATAAAAATACTAACATGACCCTAGAGACTCA
1 TTA-CCTAAGTAACCCTAATGGACATGTATCAACATAAAAATACTAACATAACCCTAGAGACTCA
*
533570 ATTTTAACATACCA
65 ATTTTAACACACCA
* * * * * * * * *
533584 TTACCTAAGTAACCCTAATGGATATGTACCGACAAAAAAATTATTAACATAACCTTAAACACTTA
1 TTACCTAAGTAACCCTAATGGACATGTATCAACATAAAAA-TACTAACATAACCCTAGAGACTCA
*
533649 ATTTTAACATACCA
65 ATTTTAACACACCA
533663 TTAC
1 TTAC
533667 TTGTTAGCAT
Statistics
Matches: 134, Mismatches: 22, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
77 10 0.07
78 84 0.63
79 40 0.30
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (78 bp):
TTACCTAAGTAACCCTAATGGACATGTATCAACATAAAAATACTAACATAACCCTAGAGACTCAA
TTTTAACACACCA
Found at i:533665 original size:79 final size:77
Alignment explanation
Indices: 533502--533666 Score: 204
Period size: 79 Copynumber: 2.1 Consensus size: 77
533492 ATTTTATTAC
* * * * * *
533502 ACCATTATCTTAATAACCCTAATGGACATGTATCAACATAAAAATACTAACATGACCCTAGAGAC
1 ACCATTA-CCTAATAACCCTAATGGACATGTACCAACAAAAAAATACTAACATAACCCTAAACAC
533567 TCAATTTTAACAT
65 TCAATTTTAACAT
* * * *
533580 ACCATTACCTAAGTAACCCTAATGGATATGTACCGACAAAAAAATTATTAACATAACCTTAAACA
1 ACCATTACCTAA-TAACCCTAATGGACATGTACCAACAAAAAAA-TACTAACATAACCCTAAACA
*
533645 CTTAATTTTAACAT
64 CTCAATTTTAACAT
533659 ACCATTAC
1 ACCATTAC
533667 TTGTTAGCAT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
77 4 0.05
78 34 0.46
79 36 0.49
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (77 bp):
ACCATTACCTAATAACCCTAATGGACATGTACCAACAAAAAAATACTAACATAACCCTAAACACT
CAATTTTAACAT
Found at i:538309 original size:2 final size:2
Alignment explanation
Indices: 538304--538343 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
538294 TATATATATA
538304 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
538344 AAGTGGGAGG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:539955 original size:2 final size:2
Alignment explanation
Indices: 539948--539978 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
539938 AAACCTTATC
539948 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
539979 GACAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:540417 original size:13 final size:13
Alignment explanation
Indices: 540401--540430 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
540391 TATTAAAGAT
*
540401 TAAATTTAAAAAA
1 TAAATTAAAAAAA
540414 TAAATTAAAAAAA
1 TAAATTAAAAAAA
540427 TAAA
1 TAAA
540431 ATATGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
TAAATTAAAAAAA
Found at i:543079 original size:29 final size:31
Alignment explanation
Indices: 543026--543090 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
543016 TTAAAAAAAT
*
543026 AAAATTTATAAATATTATAAATATAA-ATAA
1 AAAATTTATAAATATAATAAATATAATATAA
* * *
543056 AAAATTT-TAAATATAATTATTATAATATTA
1 AAAATTTATAAATATAATAAATATAATATAA
543086 AAAAT
1 AAAAT
543091 AATTAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAATTTATAAATATAATAAATATAATATAA
Done.