Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 179 of 187
Found at i:54641363 original size:13 final size:13
Alignment explanation
Indices: 54641345--54641369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54641335 AACAAACCCG
54641345 AATATGAATTATT
1 AATATGAATTATT
54641358 AATATGAATTAT
1 AATATGAATTAT
54641370 AAACTCAAAT
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
AATATGAATTATT
Found at i:54641472 original size:151 final size:149
Alignment explanation
Indices: 54641144--54641442 Score: 376
Period size: 151 Copynumber: 2.0 Consensus size: 149
54641134 TTCATTTTTC
*
54641144 AAGAAAATGAAAATAAAAATGATATTTGTTTTTTAAACCAAACAAACCCGAATATGAATTATTAA
1 AAGAAAATGAAAATAAAAATAATATTTGTTTTTTAAACCAAACAAACCCGAATATGAATTATTAA
54641209 TATGAAATATAAACTCAAATTAAAAAAAAAACTTTCAAAATCATTTTATAATTTTTAACCAACTT
66 TATGAAATATAAACTCAAATT-AAAAAAAAAC-TTCAAAATCATTTTATAATTTTTAACCAACTT
** ** * ** * *
54641274 GCTTAGTGTTTTTCATTTTTC
129 AATTAGAATATAACATATTTA
*
54641295 AAGAAAATGAAAATAAAAATGATATTTGTTTTTTAAACCAAACAAACCCGAATATGAATTATTAA
1 AAGAAAATGAAAATAAAAATAATATTTGTTTTTTAAACCAAACAAACCCGAATATGAATTATTAA
* * *
54641360 TATGAATTATAAACTCAAATT-AAAAAAAAC-T-AGAATTA-TTTA-AATTTTTAATTCCATACT
66 TATGAAATATAAACTCAAATTAAAAAAAAACTTCAAAATCATTTTATAATTTTTAA--CCA-ACT
54641420 TAATATA-AATATAACATATTTA
128 TAAT-TAGAATATAACATATTTA
54641442 A
1 A
54641443 TATAATAATG
Statistics
Matches: 132, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
144 9 0.07
145 4 0.03
146 8 0.06
147 15 0.11
148 2 0.02
149 9 0.07
151 85 0.64
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (149 bp):
AAGAAAATGAAAATAAAAATAATATTTGTTTTTTAAACCAAACAAACCCGAATATGAATTATTAA
TATGAAATATAAACTCAAATTAAAAAAAAACTTCAAAATCATTTTATAATTTTTAACCAACTTAA
TTAGAATATAACATATTTA
Found at i:54641515 original size:23 final size:23
Alignment explanation
Indices: 54641489--54641533 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
54641479 ATAATAATTC
* *
54641489 TATTTAAAATTTAATTTTAATCA
1 TATTAAAAATTCAATTTTAATCA
*
54641512 TATTAAAAATTCCATTTTAATC
1 TATTAAAAATTCAATTTTAATC
54641534 TAATCATTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTAAAAATTCAATTTTAATCA
Found at i:54641569 original size:15 final size:16
Alignment explanation
Indices: 54641534--54641570 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
54641524 CATTTTAATC
*
54641534 TAATCATTACATATTA
1 TAATTATTACATATTA
54641550 T-ATTATTA-ATATTA
1 TAATTATTACATATTA
54641564 TAATTAT
1 TAATTAT
54641571 AAAAAACGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 7 0.37
15 11 0.58
16 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTATTACATATTA
Found at i:54643856 original size:35 final size:36
Alignment explanation
Indices: 54643804--54643891 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 36
54643794 TTGGTTGAAT
* * *
54643804 AAATGGTCTATTG-GCTCTACAGAGCAGTATCATGG
1 AAATGATCTACTGAGCTCTACAGAGCAGCATCATGG
** * *
54643839 AAATGATCTACT-AGCTCTATGGATCGGCATCATGG
1 AAATGATCTACTGAGCTCTACAGAGCAGCATCATGG
*
54643874 AAATGATTTACTGAGCTC
1 AAATGATCTACTGAGCTC
54643892 ATTGAAGTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
35 38 0.88
36 5 0.12
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (36 bp):
AAATGATCTACTGAGCTCTACAGAGCAGCATCATGG
Found at i:54644489 original size:28 final size:28
Alignment explanation
Indices: 54644335--54644488 Score: 175
Period size: 28 Copynumber: 5.5 Consensus size: 28
54644325 TTCCAAGGAA
* * *
54644335 TATCTTTTGTGGAAAGTTCGCCAATGAC
1 TATCTTATGTGGAAAGTCCACCAATGAC
* * *
54644363 TATCTTATGTGGAAAGCCCGCCAAAGAC
1 TATCTTATGTGGAAAGTCCACCAATGAC
* * *
54644391 TATCTTATGTGGAAATTCCTCCAAGGAC
1 TATCTTATGTGGAAAGTCCACCAATGAC
* *
54644419 TATCTTATGTGGAAAATCCACCAATGAA
1 TATCTTATGTGGAAAGTCCACCAATGAC
* *
54644447 TATCTGA-GATGGAATGTCCACCAATGAC
1 TATCTTATG-TGGAAAGTCCACCAATGAC
54644475 TATCTTATGTGGAA
1 TATCTTATGTGGAA
54644489 TTTTCACTCA
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
27 1 0.01
28 105 0.98
29 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (28 bp):
TATCTTATGTGGAAAGTCCACCAATGAC
Found at i:54644508 original size:84 final size:84
Alignment explanation
Indices: 54644326--54644488 Score: 211
Period size: 84 Copynumber: 1.9 Consensus size: 84
54644316 AGGGAAGTCT
* * * * * * * *
54644326 TCCAAGGAATATCTTTTGTGGAAAGTTCGCCAATGACTATCTTATGTGGAAAGCCCGCCAAAGAC
1 TCCAAGGACTATCTTATGTGGAAAATCCACCAATGAATATCTGATGTGGAAAGCCCACCAAAGAC
54644391 TATCTTATGTGGAAATTCC
66 TATCTTATGTGGAAATTCC
* * *
54644410 TCCAAGGACTATCTTATGTGGAAAATCCACCAATGAATATCTGA-GATGGAATGTCCACCAATGA
1 TCCAAGGACTATCTTATGTGGAAAATCCACCAATGAATATCTGATG-TGGAAAGCCCACCAAAGA
54644474 CTATCTTATGTGGAA
65 CTATCTTATGTGGAA
54644489 TTTTCACTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
83 1 0.01
84 66 0.99
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (84 bp):
TCCAAGGACTATCTTATGTGGAAAATCCACCAATGAATATCTGATGTGGAAAGCCCACCAAAGAC
TATCTTATGTGGAAATTCC
Found at i:54653426 original size:8 final size:8
Alignment explanation
Indices: 54653413--54653438 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
54653403 TCTGTTTGAA
54653413 AATTTTAC
1 AATTTTAC
54653421 AATTTTAC
1 AATTTTAC
54653429 AATTTTAC
1 AATTTTAC
54653437 AA
1 AA
54653439 ACGAATATAC
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:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (8 bp):
AATTTTAC
Found at i:54656050 original size:24 final size:24
Alignment explanation
Indices: 54655998--54656054 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
54655988 AAGATTCAGT
* * *
54655998 ATTTATGAGTATAATATATTTAGC
1 ATTTATTAGCATAATATATTTAGA
54656022 ATTTATTAGCATAATATATTT-GA
1 ATTTATTAGCATAATATATTTAGA
54656045 ATTTTATTAG
1 A-TTTATTAG
54656055 AATTAGGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.49
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAGA
Found at i:54660432 original size:24 final size:24
Alignment explanation
Indices: 54660399--54660445 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
54660389 TTCTAGAAGA
* *
54660399 TTTAGTATTTATGAGTATAATATG
1 TTTAGCATTTATGAGCATAATATG
*
54660423 TTTAGCATTTATTAGCATAATAT
1 TTTAGCATTTATGAGCATAATAT
54660446 ATTTGACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (24 bp):
TTTAGCATTTATGAGCATAATATG
Found at i:54671266 original size:25 final size:25
Alignment explanation
Indices: 54671230--54671282 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
54671220 AGTGGAGGGC
*
54671230 AAAATAAATTATTACTCCCTATAAA
1 AAAATAAATTATTACTCCCCATAAA
*
54671255 AAAATAAGTTATTACTCCCCATAAA
1 AAAATAAATTATTACTCCCCATAAA
54671280 AAA
1 AAA
54671283 TGATACATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (25 bp):
AAAATAAATTATTACTCCCCATAAA
Found at i:54676031 original size:19 final size:19
Alignment explanation
Indices: 54676009--54676055 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
54675999 AAATTTTCTT
*
54676009 TAAAATTTAAAAAAAATCA
1 TAAAATTTAAAAAAAAGCA
*
54676028 TAAAATTACAAAAAAAAGCA
1 TAAAATT-TAAAAAAAAGCA
*
54676048 AAAAATTT
1 TAAAATTT
54676056 CCCAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAATTTAAAAAAAAGCA
Found at i:54678209 original size:23 final size:23
Alignment explanation
Indices: 54678164--54678209 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54678154 CACACGACCG
* *
54678164 TGTCACACGAACGTTTGCTAGGC
1 TGTCACACGAACGTGTGCCAGGC
**
54678187 TGTCACACGCCCGTGTGCCAGGC
1 TGTCACACGAACGTGTGCCAGGC
54678210 CGTGTAACAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.17, C:0.33, G:0.28, T:0.22
Consensus pattern (23 bp):
TGTCACACGAACGTGTGCCAGGC
Found at i:54678764 original size:22 final size:24
Alignment explanation
Indices: 54678721--54678764 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
54678711 TTATACATAC
*
54678721 TAAATCATCTATTAAAATTTCAAG
1 TAAATCATCTATTAAAAGTTCAAG
*
54678745 TAAA-CATC-ATTATAAGTTCA
1 TAAATCATCTATTAAAAGTTCA
54678765 CATATACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 4 0.22
24 4 0.22
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (24 bp):
TAAATCATCTATTAAAAGTTCAAG
Found at i:54686394 original size:164 final size:164
Alignment explanation
Indices: 54686123--54686451 Score: 622
Period size: 164 Copynumber: 2.0 Consensus size: 164
54686113 CTAGGAGCAA
*
54686123 TAGGTTCATTACCTTTATTGATGTAATCAGGTCCTCTATAGTCTGGTTTAGTTCTCCTTGAAGCC
1 TAGGTTCATTACCTTTATTGATGTAATCAGGTCCTCTATAGTCTGGTTTAGTTCACCTTGAAGCC
54686188 AAAATTACATTAAGCTTCTCACTCTGGCCTCCAAACTTCTTCAAGACAATATTTGCATCATCTAG
66 AAAATTACATTAAGCTTCTCACTCTGGCCTCCAAACTTCTTCAAGACAATATTTGCATCATCTAG
54686253 CTCACTCTTATTTGCTTTCCAAGCACCATCCTTT
131 CTCACTCTTATTTGCTTTCCAAGCACCATCCTTT
* * *
54686287 TAGGTTCCTTACCTTTATTGATGTAATCAGGTCCTCTATTGTCTGGTTTAGTTCACCTTGAAGGC
1 TAGGTTCATTACCTTTATTGATGTAATCAGGTCCTCTATAGTCTGGTTTAGTTCACCTTGAAGCC
54686352 AAAATTACATTAAGCTTCTCACTCTGGCCTCCAAACTTCTTCAAGACAATATTTGCATCATCTAG
66 AAAATTACATTAAGCTTCTCACTCTGGCCTCCAAACTTCTTCAAGACAATATTTGCATCATCTAG
54686417 CTCACTCTTATTTGCTTTCCAAGCACCATCCTTT
131 CTCACTCTTATTTGCTTTCCAAGCACCATCCTTT
54686451 T
1 T
54686452 CTTGGTCCAC
Statistics
Matches: 161, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 161 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (164 bp):
TAGGTTCATTACCTTTATTGATGTAATCAGGTCCTCTATAGTCTGGTTTAGTTCACCTTGAAGCC
AAAATTACATTAAGCTTCTCACTCTGGCCTCCAAACTTCTTCAAGACAATATTTGCATCATCTAG
CTCACTCTTATTTGCTTTCCAAGCACCATCCTTT
Found at i:54688719 original size:22 final size:23
Alignment explanation
Indices: 54688687--54688729 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
54688677 TCTGTCGAAA
54688687 ATTATCAAAATTAATAAAAATAT
1 ATTATCAAAATTAATAAAAATAT
*
54688710 ATTAT-AAAATTAATTAAAAT
1 ATTATCAAAATTAATAAAAAT
54688730 TAAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTATCAAAATTAATAAAAATAT
Found at i:54688784 original size:33 final size:27
Alignment explanation
Indices: 54688719--54688803 Score: 116
Period size: 27 Copynumber: 3.0 Consensus size: 27
54688709 TATTATAAAA
54688719 TTAATTAAAATTAAAATTTTTAATAAT
1 TTAATTAAAATTAAAATTTTTAATAAT
54688746 TTAATTAAAATTAAAATTTTTAATAAT
1 TTAATTAAAATTAAAATTTTTAATAAT
* * *
54688773 TTAAGTATAATTTAATTATTTTATAATAAT
1 TTAATTA-AAATTAA-AATTTT-TAATAAT
54688803 T
1 T
54688804 ATATATTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
27 33 0.63
28 6 0.12
29 5 0.10
30 8 0.15
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TTAATTAAAATTAAAATTTTTAATAAT
Found at i:54690830 original size:27 final size:27
Alignment explanation
Indices: 54690800--54691050 Score: 265
Period size: 27 Copynumber: 9.3 Consensus size: 27
54690790 GGGTATAATA
*
54690800 GTCATTTTACCCTTCGGGAGTATTTCG
1 GTCATTTTACCCTTCGAGAGTATTTCG
* * * *
54690827 GTCATCTTACCTTTCGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGAGTATTTCG
*
54690854 GTCATTTTACCCTTC-AAAGGTATTTCG
1 GTCATTTTACCCTTCGAGA-GTATTTCG
*
54690881 GTCATTTTACCCTTCAAGA-TATTTCG
1 GTCATTTTACCCTTCGAGAGTATTTCG
* * *
54690907 ATCATTTTACCTTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGAGTATTTCG
* * *
54690934 ATCATTTTACCCTTC-AAAGGTATTTCA
1 GTCATTTTACCCTTCGAGA-GTATTTCG
*
54690961 GTCATTTTACCCTTCGAGTGTATTTCG
1 GTCATTTTACCCTTCGAGAGTATTTCG
* * *
54690988 ATTATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGAGTATTTCG
* * * **
54691015 GTCATTTTACCTTTTGAGGGTATTTTT
1 GTCATTTTACCCTTCGAGAGTATTTCG
54691042 GTCATTTTA
1 GTCATTTTA
54691051 GGCCCATTGC
Statistics
Matches: 189, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
26 23 0.12
27 163 0.86
28 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGAGTATTTCG
Found at i:54690928 original size:80 final size:80
Alignment explanation
Indices: 54690799--54691025 Score: 346
Period size: 80 Copynumber: 2.8 Consensus size: 80
54690789 AGGGTATAAT
* * * *
54690799 AGTCATTTTACCCTTCGGGAGTATTTCGGTCATCTTACCTTTCGGGGGTATTTCGGTCATTTTAC
1 AGTCATTTTACCCTTCGAGA-TATTTCGATCATTTTACCTTTCGAGGGTATTTCGGTCATTTTAC
54690864 CCTTCAAAGGTATTTC
65 CCTTCAAAGGTATTTC
* * *
54690880 GGTCATTTTACCCTTCAAGATATTTCGATCATTTTACCTTTCGAGGGTATTTCGATCATTTTACC
1 AGTCATTTTACCCTTCGAGATATTTCGATCATTTTACCTTTCGAGGGTATTTCGGTCATTTTACC
54690945 CTTCAAAGGTATTTC
66 CTTCAAAGGTATTTC
* * *
54690960 AGTCATTTTACCCTTCGAGTGTATTTCGATTATTTTACCCTTCGAGGGTATTTCGGTCATTTTAC
1 AGTCATTTTACCCTTCGAG-ATATTTCGATCATTTTACCTTTCGAGGGTATTTCGGTCATTTTAC
54691025 C
65 C
54691026 TTTTGAGGGT
Statistics
Matches: 132, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
80 73 0.55
81 59 0.45
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (80 bp):
AGTCATTTTACCCTTCGAGATATTTCGATCATTTTACCTTTCGAGGGTATTTCGGTCATTTTACC
CTTCAAAGGTATTTC
Found at i:54695289 original size:39 final size:39
Alignment explanation
Indices: 54695244--54695322 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
54695234 GAAGATAAGT
54695244 AGTTCTTATTGACTCATTATGTTAATGGAAGATCGGAAG
1 AGTTCTTATTGACTCATTATGTTAATGGAAGATCGGAAG
*
54695283 AGTTCTTATTGACTCATTATGTTAATGGAATATCGGAAG
1 AGTTCTTATTGACTCATTATGTTAATGGAAGATCGGAAG
54695322 A
1 A
54695323 TCTTGCTAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (39 bp):
AGTTCTTATTGACTCATTATGTTAATGGAAGATCGGAAG
Found at i:54703706 original size:18 final size:18
Alignment explanation
Indices: 54703683--54703721 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
54703673 ATCTAGATGC
*
54703683 AATTTACCTAAATGTGTG
1 AATTTACCTAAATGTATG
54703701 AATTTACCTAAATGTATG
1 AATTTACCTAAATGTATG
54703719 AAT
1 AAT
54703722 GAATGGCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (18 bp):
AATTTACCTAAATGTATG
Found at i:54710493 original size:24 final size:24
Alignment explanation
Indices: 54710461--54710509 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
54710451 TGACACTTAC
54710461 ATAATTTATACCTGTTCAAGCTCT
1 ATAATTTATACCTGTTCAAGCTCT
54710485 ATAATTTATACCTGTTCAAGCTCT
1 ATAATTTATACCTGTTCAAGCTCT
54710509 A
1 A
54710510 AAATATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (24 bp):
ATAATTTATACCTGTTCAAGCTCT
Found at i:54710939 original size:17 final size:17
Alignment explanation
Indices: 54710917--54710952 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
54710907 TGGACAGTTC
54710917 TACTCATCACTTGGAAA
1 TACTCATCACTTGGAAA
54710934 TACTCATCACTTGGAAA
1 TACTCATCACTTGGAAA
54710951 TA
1 TA
54710953 TTAATATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (17 bp):
TACTCATCACTTGGAAA
Found at i:54717912 original size:3 final size:3
Alignment explanation
Indices: 54717904--54717953 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
54717894 GCAATAAACA
* * *
54717904 ATT ATT ATT ATT ATT AAT ATT ATT ATT ATC ATT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
54717952 AT
1 AT
54717954 CGCGGTGCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:54720655 original size:22 final size:22
Alignment explanation
Indices: 54720630--54720674 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
54720620 CTTATAAGTG
54720630 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
54720652 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
54720674 T
1 T
54720675 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:54724435 original size:22 final size:22
Alignment explanation
Indices: 54724407--54724451 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
54724397 AGGGGGAGTG
54724407 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
54724429 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
54724451 T
1 T
54724452 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:54725814 original size:18 final size:18
Alignment explanation
Indices: 54725791--54725826 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54725781 TTTGCTGCAC
54725791 TAAGAACTTCAAAGGAAG
1 TAAGAACTTCAAAGGAAG
54725809 TAAGAACTTCAAAGGAAG
1 TAAGAACTTCAAAGGAAG
54725827 ATATAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.22, T:0.17
Consensus pattern (18 bp):
TAAGAACTTCAAAGGAAG
Found at i:54729237 original size:39 final size:39
Alignment explanation
Indices: 54729173--54729289 Score: 137
Period size: 39 Copynumber: 3.0 Consensus size: 39
54729163 AGACTAGCTT
* * * *
54729173 TAGATTCTGGCTTAGCATTGATAACCAGTGAAGTAGAAG
1 TAGAGTCTGGATTAGCACTGTTAACCAGTGAAGTAGAAG
*
54729212 TAGAGTCTGGATTAGCAGTGTTAACCAGTGAA-TATGAAG
1 TAGAGTCTGGATTAGCACTGTTAACCAGTGAAGTA-GAAG
* * * *
54729251 TAGAGTCCGGTTTAGCACTGTTAAGCAGTGAAGTTGAAG
1 TAGAGTCTGGATTAGCACTGTTAACCAGTGAAGTAGAAG
54729290 CAGGAGACTC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.03
39 64 0.96
40 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (39 bp):
TAGAGTCTGGATTAGCACTGTTAACCAGTGAAGTAGAAG
Found at i:54737850 original size:4 final size:4
Alignment explanation
Indices: 54737841--54737869 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
54737831 TGAATAAAAT
54737841 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
54737870 CTTTTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:54750996 original size:20 final size:20
Alignment explanation
Indices: 54750968--54751015 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
54750958 ACAATGAATT
*
54750968 GATTCAAATAATAAACAATC
1 GATTTAAATAATAAACAATC
** *
54750988 GATTTAAATAATAATGAATT
1 GATTTAAATAATAAACAATC
54751008 GATTTAAA
1 GATTTAAA
54751016 AGAGCATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (20 bp):
GATTTAAATAATAAACAATC
Found at i:54760780 original size:14 final size:14
Alignment explanation
Indices: 54760763--54760802 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54760753 CGAATGGAAT
*
54760763 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
54760777 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
54760791 GATATGAACAAA
1 GGTAGGAACAAA
54760803 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:54774632 original size:43 final size:43
Alignment explanation
Indices: 54774543--54774751 Score: 226
Period size: 43 Copynumber: 4.9 Consensus size: 43
54774533 GATTCGTACA
* * * * *
54774543 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCAC-GGATCG
1 ATGCCAACATCCCAAACGTGGTCTTACACGAAAACACAAG-TCG
* * *
54774586 ATGCC-GCTATCCCAGACAG-GGTCTTACACGAAAACACAAGTTG
1 ATGCCAAC-ATCCCAAAC-GTGGTCTTACACGAAAACACAAGTCG
*
54774629 ATGCCAACGTCCCAAACGTGGTCTTACACGAAAACACAAGTCG
1 ATGCCAACATCCCAAACGTGGTCTTACACGAAAACACAAGTCG
* ** *
54774672 ATGCCAACGTCCCAAATATGGTCTTACATGAAAACACAAGTCG
1 ATGCCAACATCCCAAACGTGGTCTTACACGAAAACACAAGTCG
* * *
54774715 GTGCCAACATCCCAGACGTGGTCTTACATGAAAACAC
1 ATGCCAACATCCCAAACGTGGTCTTACACGAAAACAC
54774752 TTATCAGAAA
Statistics
Matches: 143, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
42 2 0.01
43 138 0.97
44 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (43 bp):
ATGCCAACATCCCAAACGTGGTCTTACACGAAAACACAAGTCG
Found at i:54776303 original size:112 final size:112
Alignment explanation
Indices: 54776103--54776304 Score: 314
Period size: 112 Copynumber: 1.8 Consensus size: 112
54776093 CAACAGAACA
54776103 TAAATGATGAATTACATTTTGTTCAAGACCGACAACATCGTGTCTTACAAATTGAAAAAGACCAT
1 TAAATGATGAATTACATTTTGTTCAAGACCGACAACATCGTGTCTTACAAATTGAAAAAGACCAT
54776168 GTTTAACGGCAACACGAGCAAGTTTTTAAATACTAATAGAACAAAAT
66 GTTTAACGGCAACACGAGCAAGTTTTTAAATACTAATAGAACAAAAT
** * * * * * *
54776215 TAAATGATGAATTTGATTTTGTTCCAGATCGATACCATTGTGTCTTACAAATTGAAAAGGACCAT
1 TAAATGATGAATTACATTTTGTTCAAGACCGACAACATCGTGTCTTACAAATTGAAAAAGACCAT
* *
54776280 GTTTAATGGCAACACGAGTAAGTTT
66 GTTTAACGGCAACACGAGCAAGTTT
54776305 CTCAGTACTA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
112 80 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (112 bp):
TAAATGATGAATTACATTTTGTTCAAGACCGACAACATCGTGTCTTACAAATTGAAAAAGACCAT
GTTTAACGGCAACACGAGCAAGTTTTTAAATACTAATAGAACAAAAT
Found at i:54782891 original size:28 final size:28
Alignment explanation
Indices: 54782860--54782916 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
54782850 TATGAGTCCT
* * *
54782860 AAGGTTTTAGTCTCTTTTTATGAGCTGA
1 AAGGTTTCAGTCTCCTTTGATGAGCTGA
54782888 AAGGTTTCAGTCTCCTTTGATGAGCTGA
1 AAGGTTTCAGTCTCCTTTGATGAGCTGA
54782916 A
1 A
54782917 CTATCAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (28 bp):
AAGGTTTCAGTCTCCTTTGATGAGCTGA
Found at i:54795178 original size:34 final size:34
Alignment explanation
Indices: 54795129--54795196 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
54795119 ATTCAATTCA
54795129 TTTGTACACACTTAAAAAGGGACCTAGACAACAT
1 TTTGTACACACTTAAAAAGGGACCTAGACAACAT
* *
54795163 TTTGTGCACATTTAAAAAGGGACCTAGACAACAT
1 TTTGTACACACTTAAAAAGGGACCTAGACAACAT
54795197 CCAAATATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (34 bp):
TTTGTACACACTTAAAAAGGGACCTAGACAACAT
Found at i:54796446 original size:22 final size:21
Alignment explanation
Indices: 54796418--54796477 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 21
54796408 GGCAACTTTT
54796418 TTTTTGCGCTTTTTTTTTGCTC
1 TTTTTGCG-TTTTTTTTTGCTC
*
54796440 TTTTTGCTTCTTTTTTTTGCTC
1 TTTTTGCGT-TTTTTTTTGCTC
54796462 TTTTTGCTGTTTTTTT
1 TTTTTGC-GTTTTTTT
54796478 AAAGAATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.12, T:0.73
Consensus pattern (21 bp):
TTTTTGCGTTTTTTTTTGCTC
Found at i:54796456 original size:13 final size:12
Alignment explanation
Indices: 54796415--54796466 Score: 56
Period size: 13 Copynumber: 4.4 Consensus size: 12
54796405 GTAGGCAACT
*
54796415 TTTTTTTTGCGC
1 TTTTTTTTGCTC
54796427 TTTTTTTTTGCTC
1 -TTTTTTTTGCTC
54796440 ---TTTTTGCTTC
1 TTTTTTTTGC-TC
54796450 TTTTTTTTGCTC
1 TTTTTTTTGCTC
54796462 TTTTT
1 TTTTT
54796467 GCTGTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
9 7 0.21
10 2 0.06
12 7 0.21
13 18 0.53
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.75
Consensus pattern (12 bp):
TTTTTTTTGCTC
Found at i:54797063 original size:31 final size:32
Alignment explanation
Indices: 54797004--54797068 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
54796994 GGCAAATTAC
54797004 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
54797036 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
54797067 AA
1 AA
54797069 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:54797771 original size:18 final size:20
Alignment explanation
Indices: 54797748--54797791 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
54797738 ATAAGATACA
*
54797748 TTCCATA-AG-AATTAACCT
1 TTCCATATAGTAATAAACCT
*
54797766 TTCCATATAGTCATAAACCT
1 TTCCATATAGTAATAAACCT
54797786 TTCCAT
1 TTCCAT
54797792 TGAGTCACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 13 0.59
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (20 bp):
TTCCATATAGTAATAAACCT
Found at i:54798880 original size:18 final size:18
Alignment explanation
Indices: 54798857--54798893 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
54798847 AGAAGAAGAA
54798857 AGAAAATTTGATAATATC
1 AGAAAATTTGATAATATC
54798875 AGAAAATTTGATAATATC
1 AGAAAATTTGATAATATC
54798893 A
1 A
54798894 TATTTTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
AGAAAATTTGATAATATC
Found at i:54800541 original size:39 final size:40
Alignment explanation
Indices: 54800496--54800667 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
54800486 GCTCCTCGTT
* * *
54800496 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
54800536 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
54800575 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
54800615 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
54800655 CAAATGCCTTCGG
1 CAAATGCCTTCGG
54800668 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:54800596 original size:40 final size:39
Alignment explanation
Indices: 54800498--54800720 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
54800488 TCCTCGTTCA
* * * *
54800498 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
54800537 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
54800576 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
54800616 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
54800656 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
54800697 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
54800721 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:54800680 original size:80 final size:79
Alignment explanation
Indices: 54800496--54800720 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
54800486 GCTCCTCGTT
* * * * *
54800496 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
54800560 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
54800575 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
54800640 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
54800655 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
54800719 GA
63 GA
54800721 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:54800729 original size:41 final size:41
Alignment explanation
Indices: 54800652--54800729 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
54800642 TTTGTATCTC
* * *
54800652 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
54800693 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
54800730 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:54807187 original size:23 final size:23
Alignment explanation
Indices: 54807158--54807214 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
54807148 AGATGAATCA
54807158 GCCTCCTTGTTACCACCA-TTATCT
1 GCCTCCTTGTTACCACCACTT-T-T
54807182 -CCTCCTTGTTACCACCACTTTT
1 GCCTCCTTGTTACCACCACTTTT
54807204 GCCTCCTTGTT
1 GCCTCCTTGTT
54807215 GAACACTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 1 0.03
23 28 0.90
24 2 0.06
ACGTcount: A:0.12, C:0.39, G:0.09, T:0.40
Consensus pattern (23 bp):
GCCTCCTTGTTACCACCACTTTT
Found at i:54809777 original size:18 final size:19
Alignment explanation
Indices: 54809744--54809782 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
54809734 TAAACGAATT
*
54809744 GAGTTATTCGAGTTAA-TC
1 GAGTTATTCGAATTAACTC
*
54809762 GAGTTATTTGAATTAACTC
1 GAGTTATTCGAATTAACTC
54809781 GA
1 GA
54809783 ATTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (19 bp):
GAGTTATTCGAATTAACTC
Found at i:54810407 original size:17 final size:16
Alignment explanation
Indices: 54810359--54810439 Score: 51
Period size: 17 Copynumber: 4.7 Consensus size: 16
54810349 TTATATCTAC
54810359 TATTTATATTATTAAAT
1 TATTTATATTATT-AAT
*
54810376 TAAATTTCACA-TATTATAT
1 T--ATTT-ATATTATTA-AT
54810395 TATTTATATTATTGAAT
1 TATTTATATTATT-AAT
54810412 TATTTAGTCATT-TTGAA-
1 TATTTA-T-ATTATT-AAT
54810429 TATTTATATTA
1 TATTTATATTA
54810440 AAATTGAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
15 3 0.06
16 3 0.06
17 23 0.43
18 8 0.15
19 14 0.26
20 2 0.04
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (16 bp):
TATTTATATTATTAAT
Found at i:54823088 original size:2 final size:2
Alignment explanation
Indices: 54823081--54823135 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
54823071 TTCTTCTTCT
54823081 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
54823123 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
54823136 GTTTCATGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:54830483 original size:5 final size:5
Alignment explanation
Indices: 54830467--54830580 Score: 156
Period size: 5 Copynumber: 22.8 Consensus size: 5
54830457 TGCAATTTGG
* ** * * * *
54830467 TATGA TACGA TATGA TACAA TATGA TACGG TACGA TACGA TATGA TATGA
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA
*
54830517 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATTA
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA
54830567 TATGA TATGA TATG
1 TATGA TATGA TATG
54830581 GTTAGAATGT
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 97 1.00
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.37
Consensus pattern (5 bp):
TATGA
Found at i:54842180 original size:26 final size:26
Alignment explanation
Indices: 54842128--54842181 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
54842118 TTCTCCTAAA
* *
54842128 TTTCAATTTTATTTAATCATTTAATT
1 TTTCAATTTTATTGAATCATTAAATT
*
54842154 TTTCAA-TTTATTGAATTATTAATATT
1 TTTCAATTTTATTGAATCATTAA-ATT
54842180 TT
1 TT
54842182 ATAATTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTCAATTTTATTGAATCATTAAATT
Found at i:54846805 original size:22 final size:24
Alignment explanation
Indices: 54846754--54846807 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
54846744 GTTTTATGAC
54846754 TAAATTATTGTTATTAAATATGCTT
1 TAAATTATTGTTATT-AATATGCTT
*
54846779 GAAATTATTG-TATT-ATAT-CTTT
1 TAAATTATTGTTATTAATATGC-TT
54846801 TAAATTA
1 TAAATTA
54846808 AATTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 12 0.46
24 4 0.15
25 9 0.35
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (24 bp):
TAAATTATTGTTATTAATATGCTT
Found at i:54848807 original size:27 final size:27
Alignment explanation
Indices: 54848777--54848954 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54848767 ATATTGAGTC
* * * *
54848777 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54848804 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54848831 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54848859 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54848886 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54848913 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54848940 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54848955 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54848916 original size:82 final size:81
Alignment explanation
Indices: 54848798--54848953 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54848788 TGCTATATAA
* *
54848798 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54848863 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54848880 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54848944 CACTTAGTGC
65 CACTTAGTGC
54848954 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54860321 original size:17 final size:15
Alignment explanation
Indices: 54860300--54860336 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
54860290 ATAATTACAT
54860300 AATATATTTGATTAA
1 AATATATTTGATTAA
54860315 AATATATTTGATTAA
1 AATATATTTGATTAA
*
54860330 AACATAT
1 AATATAT
54860337 CTAGCATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (15 bp):
AATATATTTGATTAA
Found at i:54863932 original size:33 final size:32
Alignment explanation
Indices: 54863883--54863944 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
54863873 AATCGAGTTC
54863883 ATAACGATTCATGTTCAAGAAAACTCGAGCCA
1 ATAACGATTCATGTTCAAGAAAACTCGAGCCA
*
54863915 ATAACAGATTCGA-GTTCAAGAAAATTCGAG
1 ATAAC-GATTC-ATGTTCAAGAAAACTCGAG
54863945 TTCGAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 5 0.19
33 21 0.78
34 1 0.04
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (32 bp):
ATAACGATTCATGTTCAAGAAAACTCGAGCCA
Found at i:54863954 original size:16 final size:16
Alignment explanation
Indices: 54863895--54863947 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
54863885 AACGATTCAT
*
54863895 GTTCAAGAAAACTCGA
1 GTTCAAGAAAATTCGA
* *
54863911 G-CCAATAACAGATTCGA
1 GTTCAAGAA-A-ATTCGA
54863928 GTTCAAGAAAATTCGA
1 GTTCAAGAAAATTCGA
54863944 GTTC
1 GTTC
54863948 GAAAAAACCT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 5 0.17
16 12 0.41
17 7 0.24
18 5 0.17
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (16 bp):
GTTCAAGAAAATTCGA
Found at i:54868627 original size:21 final size:21
Alignment explanation
Indices: 54868601--54868647 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
54868591 GGAAGTATCG
54868601 AGACTTCATGAACATG-TCTCA
1 AGACTTCATGAACA-GATCTCA
* *
54868622 AGACTTGATGAATAGATCTCA
1 AGACTTCATGAACAGATCTCA
54868643 AGACT
1 AGACT
54868648 ATGCTCCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (21 bp):
AGACTTCATGAACAGATCTCA
Found at i:54870054 original size:25 final size:26
Alignment explanation
Indices: 54870011--54870063 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
54870001 CCCGCCCATA
*
54870011 TTATTTTTTAAAAATATATTTTATAT
1 TTATTTTTTAAAAATATATTTAATAT
**
54870037 TTATTTTTTAATTA-ATATTTAATAT
1 TTATTTTTTAAAAATATATTTAATAT
54870062 TT
1 TT
54870064 TTATATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATTTTTTAAAAATATATTTAATAT
Found at i:54874767 original size:43 final size:44
Alignment explanation
Indices: 54874708--54874799 Score: 177
Period size: 43 Copynumber: 2.1 Consensus size: 44
54874698 CTTGAGGTTC
54874708 CTGTCTTGATTTCATAGATTAAAGCCGCTTCATGAGCCTTAGGA
1 CTGTCTTGATTTCATAGATTAAAGCCGCTTCATGAGCCTTAGGA
54874752 CTGTC-TGATTTCATAGATTAAAGCCGCTTCATGAGCCTTAGGA
1 CTGTCTTGATTTCATAGATTAAAGCCGCTTCATGAGCCTTAGGA
54874795 CTGTC
1 CTGTC
54874800 ATTGCTTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 43 0.90
44 5 0.10
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (44 bp):
CTGTCTTGATTTCATAGATTAAAGCCGCTTCATGAGCCTTAGGA
Found at i:54887304 original size:9 final size:9
Alignment explanation
Indices: 54887286--54887343 Score: 89
Period size: 9 Copynumber: 6.4 Consensus size: 9
54887276 TTTGGTTAAA
54887286 AATTAACCG
1 AATTAACCG
*
54887295 AATTACCCG
1 AATTAACCG
54887304 AATTAACCG
1 AATTAACCG
54887313 AATTAACCG
1 AATTAACCG
* *
54887322 GATTACCCG
1 AATTAACCG
54887331 AATTAACCG
1 AATTAACCG
54887340 AATT
1 AATT
54887344 GAATCACTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:54887319 original size:27 final size:27
Alignment explanation
Indices: 54887286--54887343 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
54887276 TTTGGTTAAA
54887286 AATTAACCGAATTACCCGAATTAACCG
1 AATTAACCGAATTACCCGAATTAACCG
*
54887313 AATTAACCGGATTACCCGAATTAACCG
1 AATTAACCGAATTACCCGAATTAACCG
54887340 AATT
1 AATT
54887344 GAATCACTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTAACCG
Found at i:54894441 original size:15 final size:17
Alignment explanation
Indices: 54894417--54894459 Score: 72
Period size: 15 Copynumber: 2.6 Consensus size: 17
54894407 GAACAAGGTA
54894417 TAACATTTTACAAGTC-
1 TAACATTTTACAAGTCT
54894433 TAA-ATTTTACAAGTCT
1 TAACATTTTACAAGTCT
54894449 TAACATTTTAC
1 TAACATTTTAC
54894460 TTAAGCCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.48
16 6 0.24
17 7 0.28
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (17 bp):
TAACATTTTACAAGTCT
Found at i:54903703 original size:11 final size:11
Alignment explanation
Indices: 54903658--54903749 Score: 83
Period size: 11 Copynumber: 8.9 Consensus size: 11
54903648 GGCCCATTTT
54903658 TATTTTAAAAA
1 TATTTTAAAAA
54903669 T-TTTT-AAAA
1 TATTTTAAAAA
*
54903678 -ATTTAAAAAA
1 TATTTTAAAAA
54903688 GTATTTTAAAAA
1 -TATTTTAAAAA
54903700 TATTTT--AAA
1 TATTTTAAAAA
54903709 -A--TTAAAAA
1 TATTTTAAAAA
* *
54903717 AATTTAAAAAAA
1 TATTT-TAAAAA
54903729 TATTTTAAAAA
1 TATTTTAAAAA
54903740 TATTTTAAAA
1 TATTTTAAAA
54903750 TTTAAAAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
6 2 0.03
8 4 0.06
9 11 0.17
10 8 0.12
11 23 0.35
12 18 0.27
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:54903723 original size:40 final size:41
Alignment explanation
Indices: 54903658--54903772 Score: 178
Period size: 40 Copynumber: 2.8 Consensus size: 41
54903648 GGCCCATTTT
**
54903658 TATTTTAAAAATTTTTAAAAATTTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTTAAAAAAATTTAAAAAAGTATTTTAAAAA
*
54903700 TATTTTAAAA-TTAAAAAAATTTAAAAAAATATTTTAAAAA
1 TATTTTAAAATTTAAAAAAATTTAAAAAAGTATTTTAAAAA
*
54903740 TATTTTAAAATTTAAAAAAATTAAAAAAAGTAT
1 TATTTTAAAATTTAAAAAAATTTAAAAAAGTAT
54903773 GTCGGGCCAG
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
40 37 0.55
41 24 0.36
42 6 0.09
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (41 bp):
TATTTTAAAATTTAAAAAAATTTAAAAAAGTATTTTAAAAA
Found at i:54903726 original size:17 final size:17
Alignment explanation
Indices: 54903693--54903726 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54903683 AAAAAGTATT
* *
54903693 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAA
54903710 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
54903727 AATATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:54903759 original size:10 final size:10
Alignment explanation
Indices: 54903664--54903768 Score: 60
Period size: 10 Copynumber: 10.5 Consensus size: 10
54903654 TTTTTATTTT
**
54903664 AAAAATTTTT
1 AAAAATTTAA
54903674 AAAAATTTAA
1 AAAAATTTAA
54903684 AAAAGTATTTTAA
1 AAAA--A-TTTAA
*
54903697 AAATATTT--
1 AAAAATTTAA
*
54903705 TAAAA-TTAA
1 AAAAATTTAA
54903714 AAAAATTTAAA
1 AAAAATTT-AA
54903725 AAAATATTTTAA
1 AAAA-A-TTTAA
*
54903737 AAATATTT--
1 AAAAATTTAA
*
54903745 TAAAATTTAA
1 AAAAATTTAA
54903755 AAAAA-TTAA
1 AAAAATTTAA
54903764 AAAAA
1 AAAAA
54903769 GTATGTCGGG
Statistics
Matches: 74, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
7 2 0.03
8 9 0.12
9 13 0.18
10 24 0.32
11 8 0.11
12 7 0.09
13 11 0.15
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:54904798 original size:19 final size:19
Alignment explanation
Indices: 54904776--54904838 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
54904766 ATAAAACCTA
*
54904776 AAAAAAAAGTAAAAAAATT
1 AAAAAATAGTAAAAAAATT
**
54904795 AAAATTTA-TAAAAAAAATT
1 AAAAAATAGT-AAAAAAATT
* *
54904814 AAAAATTAGT-AAAATATT
1 AAAAAATAGTAAAAAAATT
54904832 AAAAAAT
1 AAAAAAT
54904839 TATAAACAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
18 14 0.39
19 21 0.58
20 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAAAATAGTAAAAAAATT
Found at i:54904809 original size:20 final size:20
Alignment explanation
Indices: 54904786--54904827 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
54904776 AAAAAAAAGT
*
54904786 AAAAAAATTAAAATTTA-TA
1 AAAAAAATTAAAAATTAGTA
54904805 AAAAAAATTAAAAATTAGTA
1 AAAAAAATTAAAAATTAGTA
54904825 AAA
1 AAA
54904828 TATTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAAAATTAAAAATTAGTA
Found at i:54904844 original size:28 final size:27
Alignment explanation
Indices: 54904805--54904858 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
54904795 AAAATTTATA
54904805 AAAAAAATTAAA-AATTAGTAAAATATT
1 AAAAAAATTAAACAATT-GTAAAATATT
* *
54904832 AAAAAATTATAAACAATTTTAAAATAT
1 AAAAAAAT-TAAACAATTGTAAAATAT
54904859 GTATTTTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 12 0.52
29 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAAAAATTAAACAATTGTAAAATATT
Found at i:54907974 original size:35 final size:35
Alignment explanation
Indices: 54907935--54908012 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
54907925 GTGTCACCTT
54907935 GAAGGACCTATATATCATTTACACGGTGTCGCCCC
1 GAAGGACCTATATATCATTTACACGGTGTCGCCCC
* **
54907970 GAAGGACCTATATATCATTTACATGGTGTCGCCTT
1 GAAGGACCTATATATCATTTACACGGTGTCGCCCC
54908005 GAAGGACC
1 GAAGGACC
54908013 AGTAGATACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (35 bp):
GAAGGACCTATATATCATTTACACGGTGTCGCCCC
Found at i:54921118 original size:102 final size:103
Alignment explanation
Indices: 54920752--54921109 Score: 549
Period size: 103 Copynumber: 3.5 Consensus size: 103
54920742 ATTGAATATA
*
54920752 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTTCTAAGTGCTGATCCCATCGTATT
1 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCATCGTATT
*
54920817 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCTCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
54920855 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTTCTAAGTGCTGATCCCATCGTATT
1 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCATCGTATT
54920920 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * * * *
54920958 GAGGGGTTGCTAAGTGTTGATTCACCTATTCATTGGTGGTTGCTAAGTGCTGATTCCA-CTGCAT
1 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCATC-GTAT
* *
54921022 CTGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCC
65 TTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* ** * * *
54921060 AAGGGGTTGCTGTGTACTGATTCCCCGATTCATTGGTGGTTGCTAAGTGC
1 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGC
54921110 GGAATCCACC
Statistics
Matches: 238, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
102 72 0.30
103 166 0.70
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.33
Consensus pattern (103 bp):
GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCATCGTATT
TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:54928257 original size:103 final size:103
Alignment explanation
Indices: 54928078--54928279 Score: 386
Period size: 103 Copynumber: 2.0 Consensus size: 103
54928068 ATTGAATATA
*
54928078 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGTTAAGTGCTGATCCCACCGTATT
1 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCACCGTATT
54928143 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCTCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCTCCC
*
54928181 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
1 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCACCGTATT
54928246 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTC
54928280 CACCGCATCT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (103 bp):
GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCACCGTATT
TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCTCCC
Found at i:54928315 original size:42 final size:43
Alignment explanation
Indices: 54928218--54928322 Score: 167
Period size: 43 Copynumber: 2.5 Consensus size: 43
54928208 ATTCATTGGT
* * * *
54928218 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAAGGG
54928261 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTG-AAGGG
1 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAAGGG
54928303 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
54928323 CCCAAGGGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 25 0.43
43 33 0.57
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAAGGG
Found at i:54928385 original size:145 final size:146
Alignment explanation
Indices: 54928115--54928386 Score: 413
Period size: 145 Copynumber: 1.9 Consensus size: 146
54928105 ATTCATCGGT
* * * * *
54928115 GGTTGTTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCTCC
1 GGTTGCTAAGTGCTGATCCCACCGCATCTGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCC
* * * *
54928180 CGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTAT
66 CAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTAGCTAAGTGCGGATCCCACCGTAT
54928245 TTTAAATGTGAAAGGG
131 TTTAAATGTGAAAGGG
*
54928261 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCC
1 GGTTGCTAAGTGCTGATCCCACCGCATCTGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCC
**
54928325 CAAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTAGCTAAGTGCGGAAT-CCACCG
66 CAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTAGCTAAGTGCGG-ATCCCACCG
54928387 ATAACGGTTA
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
145 79 0.70
146 34 0.30
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (146 bp):
GGTTGCTAAGTGCTGATCCCACCGCATCTGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCC
CAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTAGCTAAGTGCGGATCCCACCGTAT
TTTAAATGTGAAAGGG
Found at i:54930577 original size:13 final size:13
Alignment explanation
Indices: 54930559--54930588 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54930549 GAGAATGTAT
*
54930559 AAAACATATCTTG
1 AAAACATAACTTG
54930572 AAAACATAACTTG
1 AAAACATAACTTG
54930585 AAAA
1 AAAA
54930589 TAGAGTTTAT
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:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (13 bp):
AAAACATAACTTG
Found at i:54933870 original size:41 final size:41
Alignment explanation
Indices: 54933813--54933998 Score: 241
Period size: 41 Copynumber: 4.6 Consensus size: 41
54933803 TTTAACATAT
* *
54933813 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* * *
54933854 TCACCGGCACTTAGCCTACAAGGTTTATAACCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
54933895 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* * ** * *
54933936 TCACCAGCACTTAGCCTGCTAGATTTATAGTCTGA--AAAA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
54933975 TTCACCGGCATTTAGCCTGCTAGG
1 -TCACCGGCACTTAGCCTGCTAGG
54933999 CGCTTAGCCT
Statistics
Matches: 127, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
39 2 0.02
40 20 0.16
41 105 0.83
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:54941138 original size:41 final size:41
Alignment explanation
Indices: 54941077--54941185 Score: 139
Period size: 41 Copynumber: 2.6 Consensus size: 41
54941067 CATAATTTAA
*
54941077 CATATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CATA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * * *
54941119 CATATCACCGGCACGTAGCCTGCCAAGTTTATAACCTGATT
1 CATATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
54941160 -TTGATCACCGGCACTTAGCCTGCTAG
1 CAT-ATCACCGGCACTTAGCCTGCTAG
54941186 ATTTATAGTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.02
41 52 0.91
42 4 0.07
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (41 bp):
CATATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:54943743 original size:18 final size:18
Alignment explanation
Indices: 54943722--54943785 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
54943712 AACAGCATGT
*
54943722 GAAAAAGAAAAAGAAAAA
1 GAAAAAGAAAAAGAAAGA
** *
54943740 GAAATTGCAAAAGAAAGA
1 GAAAAAGAAAAAGAAAGA
**
54943758 GAAATAA-AAAAAGTGAGA
1 GAAA-AAGAAAAAGAAAGA
54943776 GAAAAAGAAA
1 GAAAAAGAAA
54943786 TCAAATAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
17 2 0.06
18 33 0.94
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.06
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAAGA
Found at i:54944238 original size:16 final size:15
Alignment explanation
Indices: 54944219--54944248 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54944209 AGTATCAATT
54944219 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
54944235 TTTGATTGGGATGA
1 TTTGATTGGGATGA
54944249 TGGTTTGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:54949448 original size:15 final size:16
Alignment explanation
Indices: 54949422--54949453 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
54949412 ATATTCGCTG
54949422 AAGAACATAAAAATAA
1 AAGAACATAAAAATAA
54949438 AAGAA-ATAAAAATAA
1 AAGAACATAAAAATAA
54949453 A
1 A
54949454 CCTAAAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.12
Consensus pattern (16 bp):
AAGAACATAAAAATAA
Found at i:54952415 original size:12 final size:12
Alignment explanation
Indices: 54952398--54952427 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54952388 CCACACATGT
54952398 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
54952410 CCGTGTGCTAGG
1 CCGTGTGCCAGG
54952422 CCGTGT
1 CCGTGT
54952428 AACTGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:54959784 original size:27 final size:26
Alignment explanation
Indices: 54959723--54959795 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
54959713 TCAAATTTGG
* *
54959723 CTGGCAAACCCCAATTCGCAACTCAA
1 CTGGCGAACCCCAACTCGCAACTCAA
*
54959749 CTGACGAACCCCAACTCGCCAAAC-CAA
1 CTGGCGAACCCCAACTCG-C-AACTCAA
*
54959776 CTGGCGAA-CCCAACTTGCAA
1 CTGGCGAACCCCAACTCGCAA
54959796 TGAATCTGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 2 0.05
25 1 0.03
26 23 0.57
27 11 0.28
28 3 0.08
ACGTcount: A:0.34, C:0.40, G:0.14, T:0.12
Consensus pattern (26 bp):
CTGGCGAACCCCAACTCGCAACTCAA
Found at i:54962613 original size:31 final size:32
Alignment explanation
Indices: 54962575--54962637 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
54962565 TTGTTTCAAA
*
54962575 GGTTTGGAAAGATGAGAAAAACAA-TTTCTCT
1 GGTTTGGAAAGATGAGAAAAAAAATTTTCTCT
54962606 GGTTTGGAAAGATGAGAAAAAAAATTTTCTCT
1 GGTTTGGAAAGATGAGAAAAAAAATTTTCTCT
54962638 TCCCATCCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 23 0.77
32 7 0.23
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (32 bp):
GGTTTGGAAAGATGAGAAAAAAAATTTTCTCT
Found at i:54964800 original size:35 final size:35
Alignment explanation
Indices: 54964721--54964803 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
54964711 AATGGCTATC
* *
54964721 TACTGGCTCTTCAGAGCGACACCGCGTAAACAGTA
1 TACTGGCTCTTCAGAGCGACACCACGAAAACAGTA
** * *
54964756 TACAAGCTCTTCAGAGCGACACCAC-AAAAGATGTT
1 TACTGGCTCTTCAGAGCGACACCACGAAAACA-GTA
54964791 TACTGGCTCTTCA
1 TACTGGCTCTTCA
54964804 AAATCTAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 4 0.10
35 35 0.90
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (35 bp):
TACTGGCTCTTCAGAGCGACACCACGAAAACAGTA
Found at i:54965851 original size:25 final size:26
Alignment explanation
Indices: 54965812--54965870 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
54965802 GACAGTAAAC
*
54965812 GCATGATTCTATATGATGCCTTTGTG
1 GCATGATTCTATATGATGCCTTTGTA
*
54965838 GCATG-TTCTGTATGATGCCTTTGTA
1 GCATGATTCTATATGATGCCTTTGTA
54965863 GCAT-ATTC
1 GCATGATTC
54965871 CATAAGTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (26 bp):
GCATGATTCTATATGATGCCTTTGTA
Found at i:54967814 original size:27 final size:26
Alignment explanation
Indices: 54967714--54967814 Score: 96
Period size: 27 Copynumber: 3.8 Consensus size: 26
54967704 TAATAACGCA
**
54967714 GCAGAGCTGCCAGT-ACAGTATATGTG
1 GCAGAGCCACCAGTAACAGTAT-TGTG
* *
54967740 GCAAAGCCACCAGTAACAATAATTGTG
1 GCAGAGCCACCAGTAACAGT-ATTGTG
* **
54967767 TCAGAGCCACCAGTATTAGTATGTGTG
1 GCAGAGCCACCAGTAACAGTAT-TGTG
*
54967794 GCAGAGCCACCAGAAACAGTA
1 GCAGAGCCACCAGTAACAGTA
54967815 CTTCCTCCAT
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
26 13 0.22
27 44 0.75
28 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.20
Consensus pattern (26 bp):
GCAGAGCCACCAGTAACAGTATTGTG
Found at i:54967975 original size:27 final size:27
Alignment explanation
Indices: 54967930--54968260 Score: 373
Period size: 27 Copynumber: 12.2 Consensus size: 27
54967920 CCTAATAGTC
54967930 ATTTTACCCTATCGAGGGTATTTCGATA
1 ATTTTACCC-ATCGAGGGTATTTCGATA
* *
54967958 ACTTTACCCATCGGGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
54967985 ATTTTACCCATCGAGGGTATTTC-AGTA
1 ATTTTACCCATCGAGGGTATTTCGA-TA
* * *
54968012 ATTTTACCCAT-TAGGGGTATTCCGGTA
1 ATTTTACCCATCGA-GGGTATTTCGATA
* *
54968039 ATTTTACCCATCGAGGGTA-TTCTGGTG
1 ATTTTACCCATCGAGGGTATTTC-GATA
* *
54968066 ATTTTACTCATCGAGGGTATTT-TAGTA
1 ATTTTACCCATCGAGGGTATTTCGA-TA
* * *
54968093 AATTTACCCATTGAGGATATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
*
54968120 ATTTTACCCATCGAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGATA
* *
54968147 ATTTTACCCATCGAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGATA
**
54968174 ATTTTACCCATCGAGGGTATTTTAATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* * *
54968201 ATTTTACCGATCGAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGATA
* ** *
54968228 ATTTTACACATTAAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGATA
54968255 ATTTTA
1 ATTTTA
54968261 AACCCATAAC
Statistics
Matches: 261, Mismatches: 34, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.02
27 245 0.94
28 12 0.05
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCGATA
Found at i:54968080 original size:81 final size:81
Alignment explanation
Indices: 54967930--54968260 Score: 423
Period size: 81 Copynumber: 4.1 Consensus size: 81
54967920 CCTAATAGTC
* * * *
54967930 ATTTTACCCTATCGAGGGTATTTCGATAACTTTACCCATCGGGGGTATTTCGATAATTTTACCCA
1 ATTTTACCC-ATTGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCA
54967995 TCGAGGGTATTTCAGTA
65 TCGAGGGTATTTCAGTA
* * * *
54968012 ATTTTACCCATT-AGGGGTATTCCGGTAATTTTACCCATCGAGGGTA-TTCTGGTGATTTTACTC
1 ATTTTACCCATTGA-GGGTATTTCGATAATTTTACCCATCGAGGGTATTTC-GGTAATTTTACCC
*
54968075 ATCGAGGGTATTTTAGTA
64 ATCGAGGGTATTTCAGTA
* *
54968093 AATTTACCCATTGAGGATATTTCGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCAT
1 ATTTTACCCATTGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCAT
**
54968158 CGAGGGTATTTTGGTA
66 CGAGGGTATTTCAGTA
* ** * * *
54968174 ATTTTACCCATCGAGGGTATTTTAATAATTTTACCGATCGAGGGTATTTTGGTAATTTTACACAT
1 ATTTTACCCATTGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCAT
** *
54968239 TAAGGGTATTTCGGTA
66 CGAGGGTATTTCAGTA
54968255 ATTTTA
1 ATTTTA
54968261 AACCCATAAC
Statistics
Matches: 218, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
80 4 0.02
81 201 0.92
82 13 0.06
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (81 bp):
ATTTTACCCATTGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCAT
CGAGGGTATTTCAGTA
Found at i:54970422 original size:13 final size:13
Alignment explanation
Indices: 54970404--54970445 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
54970394 TGGGTAACAA
*
54970404 AAATTTATATAAT
1 AAATTTATATAAG
54970417 AAATTTATA-AAG
1 AAATTTATATAAG
*
54970429 AAATTGATAT-AG
1 AAATTTATATAAG
54970441 AAATT
1 AAATT
54970446 AATTGTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
AAATTTATATAAG
Found at i:54982253 original size:39 final size:39
Alignment explanation
Indices: 54982089--54982271 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
54982079 TTGAATGCTG
* * * * * * *
54982089 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
54982129 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
54982169 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
54982209 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
54982248 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
54982272 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:54982291 original size:79 final size:80
Alignment explanation
Indices: 54982125--54982306 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
54982115 GCTAAGTGAA
* * * *
54982125 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
54982189 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
54982205 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
54982269 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
54982284 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
54982307 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:54986087 original size:12 final size:13
Alignment explanation
Indices: 54986070--54986098 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
54986060 TTTAGATAAA
54986070 TTAATTCAT-ATT
1 TTAATTCATCATT
54986082 TTAATTCATCATT
1 TTAATTCATCATT
54986095 TTAA
1 TTAA
54986099 ACCTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAATTCATCATT
Found at i:55002087 original size:21 final size:21
Alignment explanation
Indices: 55002029--55002087 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
55002019 TATTTACATA
*
55002029 TACATATATATA-ATAAATCTG
1 TACATATATATATA-AAATATG
55002050 TACATATATATATAAAATAAT-
1 TACATATATATATAAAAT-ATG
55002071 TACATATATATATAAAA
1 TACATATATATATAAAA
55002088 AAATAATGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (21 bp):
TACATATATATATAAAATATG
Found at i:55002466 original size:22 final size:22
Alignment explanation
Indices: 55002441--55002484 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55002431 ATGTGAAAAC
*
55002441 ACCGAGGGGCAATCGGACAAAT
1 ACCGAGGGGCAATCGCACAAAT
55002463 ACCGAGGGGCAATCGCACAAAT
1 ACCGAGGGGCAATCGCACAAAT
55002485 TACCCATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.25, G:0.30, T:0.09
Consensus pattern (22 bp):
ACCGAGGGGCAATCGCACAAAT
Found at i:55003121 original size:21 final size:21
Alignment explanation
Indices: 55003095--55003170 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
55003085 AATCATATCT
55003095 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
* * *
55003116 TCTAAGCTTGCATATCTCATA
1 TCTAAGATTGTATATATCATA
*
55003137 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
55003156 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
55003171 CCTCGAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 17 0.37
21 29 0.63
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:55003130 original size:19 final size:19
Alignment explanation
Indices: 55003108--55003171 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
55003098 AAGATTGTAT
*
55003108 ATATCATATCTAAGCTTGC
1 ATATCATATCTAAGATTGC
55003127 ATATCTCATATCTAAGATTGC
1 ATA--TCATATCTAAGATTGC
*
55003148 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
55003167 ATATC
1 ATATC
55003172 CTCGAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 23 0.56
21 18 0.44
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:55003584 original size:44 final size:44
Alignment explanation
Indices: 55003533--55003704 Score: 168
Period size: 44 Copynumber: 3.9 Consensus size: 44
55003523 CTGCTCTCTG
*
55003533 CAACTTCAGAAAGATAAGATTTGTGGTTTTAATCTGCTCCACTA
1 CAACTTCAGAAAGATAAGATTTGTGGCTTTAATCTGCTCCACTA
** * *
55003577 CAACTTCAGGGAGATAAGATTAT-TGGCTTTAATCTACTCCACTG
1 CAACTTCAGAAAGATAAGATT-TGTGGCTTTAATCTGCTCCACTA
* ** * * *
55003621 CAACTTCCA-AGAGATAAGATTTGTCATCTTCAATCTGCCCCACTT
1 CAACTT-CAGAAAGATAAGATTTGT-GGCTTTAATCTGCTCCACTA
* * *
55003666 CAACTTCAGAAGGATAAGACTTGCTGGCTTAAATCTGCT
1 CAACTTCAGAAAGATAAGATTTG-TGGCTTTAATCTGCT
55003705 TCCCTCTATC
Statistics
Matches: 103, Mismatches: 19, Indels: 11
0.77 0.14 0.08
Matches are distributed among these distances:
43 1 0.01
44 57 0.55
45 44 0.43
46 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (44 bp):
CAACTTCAGAAAGATAAGATTTGTGGCTTTAATCTGCTCCACTA
Found at i:55003851 original size:132 final size:132
Alignment explanation
Indices: 55003685--55004483 Score: 1267
Period size: 132 Copynumber: 6.1 Consensus size: 132
55003675 AAGGATAAGA
* * * *
55003685 CTTGCTGGCTTAAATCTGCTTCCCTCTATCTTGGAAAGATAAGATTTACCGTCCTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* ** * *
55003750 CACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCTACTGCTACTCAGGAAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
55003815 GG
131 GG
* * *
55003817 CTTGGTGGCTTAAATCAGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* * * *
55003882 CACTATTGCTTAGGGAGATAAGATCGACAATCTTTAACCTACTCCGCTGCTGCTTAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
55003947 GG
131 GG
* * * *
55003949 CTTAGTGGCTTAAATCTGCTTCCCACTACCTTGGAAAGATAAGATTT-CCATCTTCGATCTTCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
*
55004013 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTTCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
55004078 GG
131 GG
* *
55004080 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAATGATAAGATTTGCCGTCTTCGATCTTCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* * *
55004145 CACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCTGCTACTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
55004210 GG
131 GG
* * *
55004212 CTTGGTGACTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* *
55004277 CACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACTTACTCCGCTGCTGCTCAGGGAGAACA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAG-ACA
55004342 AGG
130 AGG
55004345 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* * *
55004410 CACTACTACTTAGGAAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
55004475 GG
131 GG
*
55004477 CTCGGTG
1 CTTGGTG
55004484 TTTCACCAGT
Statistics
Matches: 612, Mismatches: 53, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
131 121 0.20
132 367 0.60
133 124 0.20
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
GG
Found at i:55004078 original size:263 final size:264
Alignment explanation
Indices: 55003690--55004478 Score: 1258
Period size: 263 Copynumber: 3.0 Consensus size: 264
55003680 TAAGACTTGC
* *
55003690 TGGCTTAAATCTGCTTCCCTCTATCTTGGAAAGATAAGATTTACCGTCCTCGATCTGCTCCACTA
1 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTCGATCTGCTCCACTA
* * * *
55003755 CTGCTTAGGGAGATAAGATCTATAATCTTCAACCTAC-TCTACTGCTACTCAGGAAGACAAGGCT
66 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTTC-GCTGCTGCTCAGGGAGACAAGGCT
* * *
55003819 TGGTGGCTTAAATCAGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCA
130 TGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCA
* * * *
55003884 CTATTGCTTAGGGAGATAAGATCGACAATCTTTAACCTACTCCGCTGCTGCTTAGGGAGACAAGG
195 CTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGG
55003949 CTTAG
260 CTTAG
* * *
55003954 TGGCTTAAATCTGCTTCCCACTACCTTGGAAAGATAAGATTT-CCATCTTCGATCTTCTCCACTA
1 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTCGATCTGCTCCACTA
55004018 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTTCGCTGCTGCTCAGGGAGACAAGGCTT
66 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTTCGCTGCTGCTCAGGGAGACAAGGCTT
* *
55004083 GGTGGCTTAAATCTGCTTCCCACTATCTTGGAATGATAAGATTTGCCGTCTTCGATCTTCTCCAC
131 GGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCAC
* * *
55004148 TACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCTGCTACTGCTCAGGGAGACAAGGC
196 TACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGC
*
55004213 TTGG
261 TTAG
* * **
55004217 TGACTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTA
1 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTCGATCTGCTCCACTA
* * *
55004282 CTGCTTAGGGAGATAAGATCTACAATTTTCAACTTACTCCGCTGCTGCTCAGGGAGAACAAGGCT
66 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTTCGCTGCTGCTCAGGGAG-ACAAGGCT
55004347 TGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCA
130 TGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCA
* * *
55004412 CTACTACTTAGGAAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGG
195 CTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGG
55004477 CT
260 CT
55004479 CGGTGTTTCA
Statistics
Matches: 483, Mismatches: 39, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
263 237 0.49
264 114 0.24
265 132 0.27
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (264 bp):
TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTCGATCTGCTCCACTA
CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTTCGCTGCTGCTCAGGGAGACAAGGCTT
GGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCAC
TACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGC
TTAG
Found at i:55004166 original size:44 final size:44
Alignment explanation
Indices: 55003853--55004433 Score: 150
Period size: 44 Copynumber: 13.2 Consensus size: 44
55003843 TATCTTGGAA
* ** * *
55003853 AGATAAGATTTGCCATCTTTGATCTGCTCCACTATTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTACTCCACTACTGCTTAGGG
* ** * * * *
55003897 AGATAAGA-TCGACAATCTTTAACCTACTCCGCTGCTGCTTAGGG
1 AGATAAGATTTG-CCGTCTTCAATCTACTCCACTACTGCTTAGGG
* * * * * * * *
55003941 AGACAAGGCTTAG-TGGCTTAAATCTGCTTCCCACTAC--CTT-GGAA
1 AGATAA-GATTTGCCGTCTTCAATCTAC-T-CCACTACTGCTTAGG-G
* * *
55003985 AGATAAGATTT-CCATCTTCGATCTTCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTACTCCACTACTGCTTAGGG
* * ** * * * * *
55004028 AGATAAGATCTACAATCTTCAACCTACTTCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTACTCCACTACTGCTTAGGG
* ** ** * * * *
55004072 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGA
1 AGATAAGATTTGCCGTCTTCAATCTAC-T-CCACTACTGCTTAGGG
* *
55004115 ATGATAAGATTTGCCGTCTTCGATCTTCTCCACTACTGCTTAGGG
1 A-GATAAGATTTGCCGTCTTCAATCTACTCCACTACTGCTTAGGG
* **** * ** *
55004160 AGATAAGATCTATAATCTTCAACCTACTCTGCTACTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTACTCCACTACTGCTTAGGG
* ** ** * * *
55004204 AGACAAGGCTTGGTGACTTAAATCTACTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTCAATCTAC-T-CCACTACTGCTTAGG-G
* * *
55004248 AGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTACTCCACTACTGCTTAGGG
* * ** * * * *
55004292 AGATAAGATCTACAATTTTCAA-CTTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATC-TACTCCACTACTGCTTAGGG
* ** ** * * * *
55004336 AGAACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AG-ATAAGATTTGCCGTCTTCAATCTAC-T-CCACTACTGCTTAGG-G
* * * *
55004381 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTACTTAGGA
1 AGATAAGATTTGCCGTCTTCAATCTACTCCACTACTGCTTAGGG
55004425 AGATAAGAT
1 AGATAAGAT
55004434 CTACAATCTT
Statistics
Matches: 368, Mismatches: 137, Indels: 64
0.65 0.24 0.11
Matches are distributed among these distances:
41 7 0.02
42 19 0.05
43 40 0.11
44 253 0.69
45 28 0.08
46 17 0.05
47 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTGCCGTCTTCAATCTACTCCACTACTGCTTAGGG
Found at i:55007076 original size:6 final size:6
Alignment explanation
Indices: 55007065--55007091 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
55007055 GTTCACCTCA
55007065 TTTTCT TTTTCT TTTTCT TTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTT
55007092 GAGTCTTGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:55010276 original size:23 final size:22
Alignment explanation
Indices: 55010234--55010301 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
55010224 TATTTACATA
*
55010234 TACATATATATATAATAAAT-CT
1 TACATATATATATAA-AAATAAT
55010256 GTACATATATATATATAAAATAAT
1 -TACATATATATATA-AAAATAAT
*
55010280 TACATATATACATAAAAATAAT
1 TACATATATATATAAAAATAAT
55010302 GATTACTCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
22 8 0.20
23 31 0.76
24 2 0.05
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (22 bp):
TACATATATATATAAAAATAAT
Found at i:55011291 original size:21 final size:21
Alignment explanation
Indices: 55011265--55011344 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 21
55011255 AATCATATCT
55011265 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
55011286 TCTAAGATTTCATATATCATATCATA
1 TCTAAGA--T--TGTAT-ATATCATA
*
55011312 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
55011331 TCTAAGATT-TATAT
1 TCTAAGATTGTATAT
55011345 CCTCGAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
19 17 0.35
20 2 0.04
21 7 0.15
22 1 0.02
23 1 0.02
24 1 0.02
25 4 0.08
26 15 0.31
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:55011300 original size:19 final size:19
Alignment explanation
Indices: 55011257--55011345 Score: 58
Period size: 19 Copynumber: 4.4 Consensus size: 19
55011247 GATTACAAAA
55011257 TCATATC-T-TCTAAGATT
1 TCATATCATATCTAAGATT
*
55011274 GTATATATCATATCTAAGATT
1 -T-CATATCATATCTAAGATT
55011295 TCATATATCATATCATATCTAAGATT
1 TC--ATATC--A---TATCTAAGATT
*
55011321 GCATATCATATCTAAGATT
1 TCATATCATATCTAAGATT
55011340 T-ATATC
1 TCATATC
55011346 CTCGAAAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
18 6 0.11
19 16 0.28
20 2 0.04
21 14 0.25
22 1 0.02
23 1 0.02
24 5 0.09
26 12 0.21
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.43
Consensus pattern (19 bp):
TCATATCATATCTAAGATT
Found at i:55011327 original size:45 final size:44
Alignment explanation
Indices: 55011242--55011344 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 44
55011232 AAATTAAATT
* * *
55011242 TCTAAGATTACA-AAATCATATCTTCTAAGATTGTATATATCATA
1 TCTAAGATTTCATATATCATATCTTCTAAGATTG-ACATATCATA
55011286 TCTAAGATTTCATATATCATATCATATCTAAGATTG-CATATCATA
1 TCTAAGATTTCATATATCATATC-T-TCTAAGATTGACATATCATA
55011331 TCTAAGATTT-ATAT
1 TCTAAGATTTCATAT
55011345 CCTCGAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
44 15 0.28
45 27 0.51
46 1 0.02
47 10 0.19
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (44 bp):
TCTAAGATTTCATATATCATATCTTCTAAGATTGACATATCATA
Found at i:55011491 original size:12 final size:13
Alignment explanation
Indices: 55011474--55011502 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55011464 TTTAGATAAA
55011474 TTAATTCAT-ATT
1 TTAATTCATCATT
55011486 TTAATTCATCATT
1 TTAATTCATCATT
55011499 TTAA
1 TTAA
55011503 ACCTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAATTCATCATT
Found at i:55022031 original size:25 final size:25
Alignment explanation
Indices: 55021997--55022049 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
55021987 TTGGTACAAA
55021997 TTTTGAAAAACAGCAATCAATGCAC
1 TTTTGAAAAACAGCAATCAATGCAC
55022022 TTTTGAAAAACAGCAATCAATGCAC
1 TTTTGAAAAACAGCAATCAATGCAC
55022047 TTT
1 TTT
55022050 CTCCCATCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (25 bp):
TTTTGAAAAACAGCAATCAATGCAC
Found at i:55045900 original size:52 final size:52
Alignment explanation
Indices: 55045843--55045946 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
55045833 AAACTTATAA
*
55045843 TCAAAACTTTTCAAATGCAAAACCAATCTACGGATATATATTCTTTTAACTT
1 TCAAAACTTTTCAAATGCAAAACCAATCTACGAATATATATTCTTTTAACTT
55045895 TCAAAACTTTTCAAATGCAAAACCAATCTACGAATATATATTCTTTTAACTT
1 TCAAAACTTTTCAAATGCAAAACCAATCTACGAATATATATTCTTTTAACTT
55045947 CCGTTTATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (52 bp):
TCAAAACTTTTCAAATGCAAAACCAATCTACGAATATATATTCTTTTAACTT
Found at i:55048522 original size:18 final size:17
Alignment explanation
Indices: 55048495--55048529 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55048485 TCTATTTATC
*
55048495 TAATTAAATATTTAATA
1 TAATTAAATATGTAATA
55048512 TAATATAAATATGTAATA
1 TAAT-TAAATATGTAATA
55048530 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TAATTAAATATGTAATA
Found at i:55048711 original size:19 final size:19
Alignment explanation
Indices: 55048658--55048712 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
55048648 TTTAACATAC
55048658 ATAATAATATATATAATAA
1 ATAATAATATATATAATAA
*
55048677 AT-A-AATGT-T-T-AT--
1 ATAATAATATATATAATAA
55048689 ATAATAATATATATAATAA
1 ATAATAATATATATAATAA
55048708 ATAAT
1 ATAAT
55048713 TAATTATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 14
0.63 0.05 0.33
Matches are distributed among these distances:
12 2 0.07
13 1 0.04
14 6 0.22
15 2 0.07
16 2 0.07
17 6 0.22
18 1 0.04
19 7 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAATAATATATATAATAA
Found at i:55048814 original size:7 final size:7
Alignment explanation
Indices: 55048802--55048826 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55048792 TGTACCTTAT
55048802 TATATGA
1 TATATGA
55048809 TATATGA
1 TATATGA
55048816 TATATGA
1 TATATGA
55048823 TATA
1 TATA
55048827 GATTGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
TATATGA
Found at i:55049816 original size:15 final size:15
Alignment explanation
Indices: 55049796--55049827 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55049786 TAATTTATGA
55049796 CATGTACTTCACAGG
1 CATGTACTTCACAGG
55049811 CATGTACTTCACAGG
1 CATGTACTTCACAGG
55049826 CA
1 CA
55049828 CAATTAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (15 bp):
CATGTACTTCACAGG
Found at i:55052248 original size:1 final size:1
Alignment explanation
Indices: 55052242--55052268 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
55052232 TCTTAACTTC
55052242 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
55052269 CAAAAACAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:55056604 original size:14 final size:15
Alignment explanation
Indices: 55056582--55056614 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
55056572 TTTAAATAGA
*
55056582 TTTATTTTTTTTA-T
1 TTTAATTTTTTTACT
55056596 TTTAATTTTTTTACT
1 TTTAATTTTTTTACT
55056611 TTTA
1 TTTA
55056615 TAAATACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTAATTTTTTTACT
Found at i:55058588 original size:19 final size:19
Alignment explanation
Indices: 55058564--55058617 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
55058554 AATCATATCT
55058564 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
55058583 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
55058602 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
55058618 CTTGAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55058613 original size:38 final size:40
Alignment explanation
Indices: 55058541--55058617 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
55058531 AAATTAAATC
55058541 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
55058583 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATC
55058618 CTTGAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:55059288 original size:20 final size:20
Alignment explanation
Indices: 55059263--55059301 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
55059253 ACCCTACTTA
55059263 AAGGTACCAATACCTGACCC
1 AAGGTACCAATACCTGACCC
*
55059283 AAGGTATCAATACCTGACC
1 AAGGTACCAATACCTGACC
55059302 TTTGACATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.31, G:0.15, T:0.18
Consensus pattern (20 bp):
AAGGTACCAATACCTGACCC
Found at i:55060929 original size:21 final size:21
Alignment explanation
Indices: 55060905--55060954 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
55060895 AATAATTCCA
55060905 AAACTTAACCAAAAC-ACACC
1 AAACTTAACCAAAACTACACC
*
55060925 TAAACTT-ACCCAAACTTACACC
1 -AAACTTAACCAAAAC-TACACC
55060947 AAACTTAA
1 AAACTTAA
55060955 AACACATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.28
21 12 0.48
22 6 0.24
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACTTAACCAAAACTACACC
Found at i:55060939 original size:10 final size:11
Alignment explanation
Indices: 55060920--55060953 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
55060910 TAACCAAAAC
55060920 ACACCTAAACTT
1 ACACC-AAACTT
55060932 AC-CCAAACTT
1 ACACCAAACTT
55060942 ACACCAAACTT
1 ACACCAAACTT
55060953 A
1 A
55060954 AAACACATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 11 0.52
12 2 0.10
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (11 bp):
ACACCAAACTT
Found at i:55062640 original size:30 final size:29
Alignment explanation
Indices: 55062604--55062712 Score: 128
Period size: 30 Copynumber: 3.7 Consensus size: 29
55062594 TTTCCGTAAG
55062604 GAAGCCTTTGTGGCGATCTCTGTAAAAAAA
1 GAAGCCTTTGTGGCGATCTCTGT-AAAAAA
** *
55062634 GAAGCCTTTGTGTTGATCTCTGTTAAAAA
1 GAAGCCTTTGTGGCGATCTCTGTAAAAAA
** *
55062663 GAAAGGTTTTGTAGCGATCTCTGTTAAAAAA
1 G-AAGCCTTTGTGGCGATCTCTG-TAAAAAA
*
55062694 GAAGCCTTTGTGGCAATCT
1 GAAGCCTTTGTGGCGATCT
55062713 TTTTCAAAGG
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
29 6 0.09
30 51 0.80
31 7 0.11
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (29 bp):
GAAGCCTTTGTGGCGATCTCTGTAAAAAA
Done.