Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 127 of 205
Found at i:38332759 original size:33 final size:33
Alignment explanation
Indices: 38332701--38332764 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
38332691 TTGCATTATT
* * *
38332701 ACACTGTACTATTATTGTATTGGGCTAAGGCTC
1 ACACTGTACTATTACTGAATAGGGCTAAGGCTC
* *
38332734 ACACTGTACTGTTACTGAATAGGGCTCAGGC
1 ACACTGTACTATTACTGAATAGGGCTAAGGC
38332765 CTAGACTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (33 bp):
ACACTGTACTATTACTGAATAGGGCTAAGGCTC
Found at i:38343695 original size:28 final size:28
Alignment explanation
Indices: 38343662--38343735 Score: 148
Period size: 28 Copynumber: 2.6 Consensus size: 28
38343652 GCCATGTATG
38343662 ACACACGGCCAAGCGACATGGCCGTGTC
1 ACACACGGCCAAGCGACATGGCCGTGTC
38343690 ACACACGGCCAAGCGACATGGCCGTGTC
1 ACACACGGCCAAGCGACATGGCCGTGTC
38343718 ACACACGGCCAAGCGACA
1 ACACACGGCCAAGCGACA
38343736 CAGTCGTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.28, C:0.36, G:0.27, T:0.08
Consensus pattern (28 bp):
ACACACGGCCAAGCGACATGGCCGTGTC
Found at i:38346707 original size:27 final size:26
Alignment explanation
Indices: 38346677--38346745 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 26
38346667 CCTATGAAGG
38346677 TATTTCAGTCATTTTAC-CTTTTAGGGA
1 TATTTC-GTCATTTTACACTTTT-GGGA
38346704 TA-TTCGATCATTTTACACTTTTGGGA
1 TATTTCG-TCATTTTACACTTTTGGGA
38346730 TATTTCGGTCATTTTA
1 TATTTC-GTCATTTTA
38346746 GTGAACCCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
25 1 0.03
26 18 0.47
27 18 0.47
28 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (26 bp):
TATTTCGTCATTTTACACTTTTGGGA
Found at i:38346719 original size:26 final size:27
Alignment explanation
Indices: 38346677--38346745 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
38346667 CCTATGAAGG
38346677 TATTTC-AGTCATTTTAC-CTTTTAGGGA
1 TATTTCGA-TCATTTTACACTTTT-GGGA
38346704 TA-TTCGATCATTTTACACTTTTGGGA
1 TATTTCGATCATTTTACACTTTTGGGA
*
38346730 TATTTCGGTCATTTTA
1 TATTTCGATCATTTTA
38346746 GTGAACCCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 18 0.47
27 20 0.53
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (27 bp):
TATTTCGATCATTTTACACTTTTGGGA
Found at i:38354831 original size:14 final size:14
Alignment explanation
Indices: 38354808--38354849 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
38354798 ACAGAAAAGT
*
38354808 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
38354822 AAATCATTTTACGG
1 AAAACATTTTACAG
38354836 AAAACATTTTACAG
1 AAAACATTTTACAG
38354850 CCAATCAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:38354833 original size:34 final size:35
Alignment explanation
Indices: 38354773--38354839 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
38354763 CAAACACCAG
* *
38354773 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
38354808 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
38354840 CATTTTACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:38356706 original size:50 final size:50
Alignment explanation
Indices: 38356630--38356733 Score: 154
Period size: 50 Copynumber: 2.1 Consensus size: 50
38356620 TATTGAGGTT
* * *
38356630 ATGAAAGGTCCCATGTAAGACAATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAAAGGTCCCACGTAAGACAATGTCTGGGACATGGCATGGGCACCGAG
* * *
38356680 ATGAAAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAAAGGTCCCACGTAAGACAATGTCTGGGACATGGCATGGGCACCGAG
38356730 ATGA
1 ATGA
38356734 GAACTCCTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (50 bp):
ATGAAAGGTCCCACGTAAGACAATGTCTGGGACATGGCATGGGCACCGAG
Found at i:38356748 original size:50 final size:50
Alignment explanation
Indices: 38356630--38356761 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 50
38356620 TATTGAGGTT
* * * * *
38356630 ATGAAAGGTCCCATGTAAGACAATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAAAGCTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* * *
38356680 ATGAAAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAAAGCTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
** *
38356730 ATGAGAA-CTCCTGTGTAAGACCATATCTGGGA
1 ATGA-AAGCTCCCCTGTAAGACCATGTCTGGGA
38356762 TATGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
50 68 0.97
51 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (50 bp):
ATGAAAGCTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
Found at i:38357045 original size:12 final size:12
Alignment explanation
Indices: 38357028--38357082 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
38357018 ATGAGTTATT
38357028 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
38357040 TAAGTAAACAAG
1 TAAGTAAGCAAG
*
38357052 TAAG-AGAGTAAG
1 TAAGTA-AGCAAG
*
38357064 TAAAG-AAGAAAG
1 T-AAGTAAGCAAG
38357076 TAAGTAA
1 TAAGTAA
38357083 AGAAGAAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 4 0.11
12 28 0.78
13 4 0.11
ACGTcount: A:0.56, C:0.04, G:0.24, T:0.16
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:38357054 original size:20 final size:19
Alignment explanation
Indices: 38357029--38357082 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
38357019 TGAGTTATTT
38357029 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAG-AAGTAAGTAAAC
*
38357049 AAGTAAGAGAGTAAGTAAAG
1 AAGTAAGA-AGTAAGTAAAC
*
38357069 AAGAAAGTAAGTAA
1 AAGTAAG-AAGTAA
38357083 AGAAGAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.57, C:0.04, G:0.24, T:0.15
Consensus pattern (19 bp):
AAGTAAGAAGTAAGTAAAC
Found at i:38357072 original size:16 final size:16
Alignment explanation
Indices: 38357053--38357094 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
38357043 GTAAACAAGT
*
38357053 AAGAGAGTAAGTAAAG
1 AAGAAAGTAAGTAAAG
38357069 AAGAAAGTAAGTAAAG
1 AAGAAAGTAAGTAAAG
38357085 AAGAAAGTAA
1 AAGAAAGTAA
38357095 AAATCATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (16 bp):
AAGAAAGTAAGTAAAG
Found at i:38363412 original size:15 final size:15
Alignment explanation
Indices: 38363392--38363425 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38363382 TCTAGTTTTG
38363392 ATGTATCTGATAGTC
1 ATGTATCTGATAGTC
* *
38363407 ATGTATCTGTTAGTG
1 ATGTATCTGATAGTC
38363422 ATGT
1 ATGT
38363426 GTCCAATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44
Consensus pattern (15 bp):
ATGTATCTGATAGTC
Found at i:38367738 original size:18 final size:18
Alignment explanation
Indices: 38367715--38367755 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
38367705 ATATTTATGC
38367715 CTTTATTCTGCCTTAGTT
1 CTTTATTCTGCCTTAGTT
* **
38367733 CTTTATTTTGTTTTAGTT
1 CTTTATTCTGCCTTAGTT
38367751 CTTTA
1 CTTTA
38367756 AGAAAAAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.10, T:0.63
Consensus pattern (18 bp):
CTTTATTCTGCCTTAGTT
Found at i:38368812 original size:171 final size:171
Alignment explanation
Indices: 38368527--38368867 Score: 628
Period size: 171 Copynumber: 2.0 Consensus size: 171
38368517 GCAACTCAGT
* * * *
38368527 AGGAAGCTGCCTCAACTCACCAACATGATGATGCCTCGAGAGAAAAGTTCCCATTCAAGAGGAAA
1 AGGAAGCTGCCCCAACTCACCAACAAGATAATGCCTCAAGAGAAAAGTTCCCATTCAAGAGGAAA
* *
38368592 CCAACCACTGTTAGATGGATGCTTTCTACTCAAGAGTCATTTGTGATAGACCTATTGATGACATT
66 CCAACCACTGTTAGATGGATGCCTTCTACTCAAGAGTCATCTGTGATAGACCTATTGATGACATT
38368657 GTGAACTAGATGTTTATTTTGTTGACCTTTTGATCTTGTGC
131 GTGAACTAGATGTTTATTTTGTTGACCTTTTGATCTTGTGC
38368698 AGGAAGCTGCCCCAACTCACCAACAAGATAATGCCTCAAGAGAAAAGTTCCCATTCAAGAGGAAA
1 AGGAAGCTGCCCCAACTCACCAACAAGATAATGCCTCAAGAGAAAAGTTCCCATTCAAGAGGAAA
38368763 CCAACCACTGTTAGATGGATGCCTTCTACTCAAGAGTCATCTGTGATAGACCTATTGATGACATT
66 CCAACCACTGTTAGATGGATGCCTTCTACTCAAGAGTCATCTGTGATAGACCTATTGATGACATT
38368828 GTGAACTAGATGTTTATTTTGTTGACCTTTTGATCTTGTG
131 GTGAACTAGATGTTTATTTTGTTGACCTTTTGATCTTGTG
38368868 TAAATTTGCC
Statistics
Matches: 164, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
171 164 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (171 bp):
AGGAAGCTGCCCCAACTCACCAACAAGATAATGCCTCAAGAGAAAAGTTCCCATTCAAGAGGAAA
CCAACCACTGTTAGATGGATGCCTTCTACTCAAGAGTCATCTGTGATAGACCTATTGATGACATT
GTGAACTAGATGTTTATTTTGTTGACCTTTTGATCTTGTGC
Found at i:38374189 original size:61 final size:58
Alignment explanation
Indices: 38374114--38374225 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
38374104 ATTATCTTAG
*
38374114 TATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTCTATTAATTTAATAGATTAAA
1 TATTAAATTAAATTTAATATTTATC-T-T-GATAAGTATTATATTAATTTAATAGATTAAA
* *
38374175 TATTTAATTTAATTTAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 TATTAAATTAAATTTAATATTTATCTTGATAAGTATTATATTAATTTAATA
38374226 TTAAAGTGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
58 23 0.48
59 1 0.02
60 1 0.02
61 23 0.48
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (58 bp):
TATTAAATTAAATTTAATATTTATCTTGATAAGTATTATATTAATTTAATAGATTAAA
Found at i:38374244 original size:58 final size:59
Alignment explanation
Indices: 38374114--38374246 Score: 166
Period size: 58 Copynumber: 2.2 Consensus size: 59
38374104 ATTATCTTAG
* *
38374114 TATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTCTATTAATTTAATAGATTAAA
1 TATT-AATTTAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATA-ATTAAA
38374175 TATTTAATTTAATTTAATATTTATC-T-T-GATAAGTATTATATTAATTTAAT-ATTAAA
1 TA-TTAATTTAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATAATTAAA
38374231 GTGATTAAGTTTAATT
1 -T-ATTAA-TTTAATT
38374247 ATAGTTGAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
56 6 0.09
57 5 0.08
58 30 0.45
59 1 0.02
60 1 0.02
61 21 0.32
62 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (59 bp):
TATTAATTTAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATAATTAAA
Found at i:38381486 original size:15 final size:15
Alignment explanation
Indices: 38381448--38381487 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
38381438 CATTGATCTA
38381448 TGAAATA-ATTAAAT
1 TGAAATATATTAAAT
*
38381462 T-AAATTTATTAAAT
1 TGAAATATATTAAAT
38381476 TGAAATATATTA
1 TGAAATATATTA
38381488 TAATATTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 4 0.18
14 9 0.41
15 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (15 bp):
TGAAATATATTAAAT
Found at i:38384386 original size:22 final size:21
Alignment explanation
Indices: 38384343--38384393 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
38384333 CATCTCCTTA
* *
38384343 TATATATGTTTTATAATTATT
1 TATATATGTTATATAATAATT
*
38384364 TATATCATGTTATATTATAATT
1 TATAT-ATGTTATATAATAATT
38384386 TGATATAT
1 T-ATATAT
38384394 ATTTATGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 16 0.64
23 4 0.16
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (21 bp):
TATATATGTTATATAATAATT
Found at i:38392313 original size:45 final size:45
Alignment explanation
Indices: 38392258--38392344 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
38392248 AAATAGGGTA
* *
38392258 ACTCAAAGGAGGAGGGGAGCGAGCTAGGTCCTCGTGCTCATCTTG
1 ACTCAAAGGAGGAGGGGAGCGAGCTAGGTCCTCATACTCATCTTG
*
38392303 ACTCGAAGGAGGAGGGGAGCGAGCTAGGTCCTCATACTCATC
1 ACTCAAAGGAGGAGGGGAGCGAGCTAGGTCCTCATACTCATC
38392345 CTGAGGATCC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.24, C:0.23, G:0.34, T:0.18
Consensus pattern (45 bp):
ACTCAAAGGAGGAGGGGAGCGAGCTAGGTCCTCATACTCATCTTG
Found at i:38393526 original size:3 final size:3
Alignment explanation
Indices: 38393518--38393652 Score: 58
Period size: 3 Copynumber: 44.3 Consensus size: 3
38393508 AGCTGTACAC
* * * * *
38393518 TAA TAA TAA -CA TAA TAA GAA T-A TAA GAA AAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
38393564 CAG TAGT TCAA CTAA TAA TAC TAA TAC TAA TAC TAA TAC TAA TAA TAA
1 TAA TA-A T-AA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
38393612 TAG TAA CAG TAA TAA AAA TAG TAC TAA TAA TAAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA T
38393653 GAACCAAAAA
Statistics
Matches: 93, Mismatches: 33, Indels: 12
0.67 0.24 0.09
Matches are distributed among these distances:
2 3 0.03
3 82 0.88
4 6 0.06
5 2 0.02
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:38393600 original size:18 final size:18
Alignment explanation
Indices: 38393579--38393644 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
38393569 GTTCAACTAA
*
38393579 TAATACTAATACTAATAC
1 TAATACTAATAATAATAC
*
38393597 TAATACTAATAATAATAG
1 TAATACTAATAATAATAC
* *
38393615 TAACAGTAATAA-AA-A-
1 TAATACTAATAATAATAC
*
38393630 TAGTACTAATAATAA
1 TAATACTAATAATAA
38393645 ATAATAATGA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 9 0.22
16 3 0.08
17 2 0.05
18 26 0.65
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (18 bp):
TAATACTAATAATAATAC
Found at i:38395959 original size:20 final size:20
Alignment explanation
Indices: 38395934--38395986 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
38395924 GGCAAAGACG
38395934 GCCTAGGGTGATATCACATA
1 GCCTAGGGTGATATCACATA
* *
38395954 GCCTAGGGTGACATCACATG
1 GCCTAGGGTGATATCACATA
*
38395974 GCCTAGAGTGATA
1 GCCTAGGGTGATA
38395987 GGGTGATATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (20 bp):
GCCTAGGGTGATATCACATA
Found at i:38398218 original size:32 final size:32
Alignment explanation
Indices: 38398177--38398240 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
38398167 GCTTTTTGTA
38398177 GTCAATACAAACTCTACATCCTGTAAGTGTTC
1 GTCAATACAAACTCTACATCCTGTAAGTGTTC
38398209 GTCAATACAAACTCTACATCCTGTAAGTGTTC
1 GTCAATACAAACTCTACATCCTGTAAGTGTTC
38398241 TTTTTGGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (32 bp):
GTCAATACAAACTCTACATCCTGTAAGTGTTC
Found at i:38402349 original size:131 final size:131
Alignment explanation
Indices: 38402104--38402365 Score: 445
Period size: 131 Copynumber: 2.0 Consensus size: 131
38402094 TTTTCTTGAC
* *
38402104 TATCCTATGATGGCTCACTCCTATCTTCATTTTTGACATATATATGTCTTAGAATGTCTGAAAAA
1 TATCCTATGATGGCTCACTCCTATCTTCATTTTTGACATATATATGTCTTAGAATATCCGAAAAA
38402169 CCTAAAAATCACGTCTTTCCACTGTTTGGGGTCCAAATTTGTGAAATTGACACAGCCTGCCACAT
66 CCTAAAAATCACGTCTTTCCACTGTTTGGGGTCCAAATTTGTGAAATTGACACAGCCTGCCACAT
38402234 G
131 G
* *
38402235 TATCCTATGATGGCTCACTCTTATCTTCTTTTTTTGACATATATATGTCTTAGAATATCCGAAAA
1 TATCCTATGATGGCTCACTCCTATCTTC-ATTTTTGACATATATATGTCTTAGAATATCCGAAAA
** *
38402300 ACCTAAAAATCATTTCTTTCCACTGTTT-GGGTCCAAATTTGTGAAATTGACACGGCCTGCCACA
65 ACCTAAAAATCACGTCTTTCCACTGTTTGGGGTCCAAATTTGTGAAATTGACACAGCCTGCCACA
38402364 TG
130 TG
38402366 GTCATATGGC
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
131 64 0.52
132 59 0.48
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (131 bp):
TATCCTATGATGGCTCACTCCTATCTTCATTTTTGACATATATATGTCTTAGAATATCCGAAAAA
CCTAAAAATCACGTCTTTCCACTGTTTGGGGTCCAAATTTGTGAAATTGACACAGCCTGCCACAT
G
Found at i:38403843 original size:12 final size:12
Alignment explanation
Indices: 38403826--38403850 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38403816 TGGGGGATAT
38403826 GATGGAAGAAGA
1 GATGGAAGAAGA
38403838 GATGGAAGAAGA
1 GATGGAAGAAGA
38403850 G
1 G
38403851 GCAATAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GATGGAAGAAGA
Found at i:38408566 original size:11 final size:11
Alignment explanation
Indices: 38408547--38408585 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
38408537 AAGAGAGAAT
*
38408547 GATGCTTGAGG
1 GATGATTGAGG
*
38408558 GATGATTGAGA
1 GATGATTGAGG
*
38408569 GATGCTTGAGG
1 GATGATTGAGG
38408580 GATGAT
1 GATGAT
38408586 GAATGAAGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.41, T:0.28
Consensus pattern (11 bp):
GATGATTGAGG
Found at i:38417272 original size:29 final size:29
Alignment explanation
Indices: 38417230--38417289 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
38417220 TGGAATTAAC
38417230 TTGTTACACTCAGTTTCAACACTCGTGAT
1 TTGTTACACTCAGTTTCAACACTCGTGAT
*
38417259 TTGTTACGCTCAGTTTCAACACTCGTGAT
1 TTGTTACACTCAGTTTCAACACTCGTGAT
38417288 TT
1 TT
38417290 CACCTTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (29 bp):
TTGTTACACTCAGTTTCAACACTCGTGAT
Found at i:38435558 original size:39 final size:41
Alignment explanation
Indices: 38435463--38435606 Score: 160
Period size: 39 Copynumber: 3.6 Consensus size: 41
38435453 TTGAATGATG
*
38435463 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
38435502 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
38435542 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
38435581 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
38435607 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 6, Indels: 15
0.81 0.05 0.13
Matches are distributed among these distances:
38 2 0.02
39 50 0.55
40 27 0.30
41 11 0.12
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:38435620 original size:40 final size:39
Alignment explanation
Indices: 38435543--38435625 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 39
38435533 GATACTAATT
** *
38435543 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTATAA
* *
38435582 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATAT
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTATAA
38435622 CCGG
1 CCGG
38435626 TTAAATTCCG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 10 0.27
40 27 0.73
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.22
Consensus pattern (39 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTATAA
Found at i:38444887 original size:12 final size:12
Alignment explanation
Indices: 38444870--38444897 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38444860 AGGTTTCCAA
38444870 AAATGAAAATGG
1 AAATGAAAATGG
38444882 AAATGAAAATGG
1 AAATGAAAATGG
38444894 AAAT
1 AAAT
38444898 AATCCATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (12 bp):
AAATGAAAATGG
Found at i:38449740 original size:14 final size:15
Alignment explanation
Indices: 38449711--38449743 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
38449701 AAGTGAGTAA
38449711 AAAAGAAAGAAAAAG
1 AAAAGAAAGAAAAAG
*
38449726 AAAAGAACG-AAAAG
1 AAAAGAAAGAAAAAG
38449740 AAAA
1 AAAA
38449744 ATACTCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAAG
Found at i:38456788 original size:21 final size:21
Alignment explanation
Indices: 38456762--38456824 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38456752 TTGGTATTTG
38456762 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
38456783 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
38456804 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
38456825 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:38461555 original size:31 final size:31
Alignment explanation
Indices: 38461519--38461589 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
38461509 AAGAAAAGAT
*
38461519 AATAGTTCAGCGACTTAAATAAAAACTTTTA
1 AATAGTTCAGCGACTTAAATAAAAACTTTCA
*
38461550 AATAGTTCAGTGACTTAAATAAAAACTTTCA
1 AATAGTTCAGCGACTTAAATAAAAACTTTCA
38461581 AATAGTTCA
1 AATAGTTCA
38461590 ATAACTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (31 bp):
AATAGTTCAGCGACTTAAATAAAAACTTTCA
Found at i:38461607 original size:30 final size:31
Alignment explanation
Indices: 38461531--38461608 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
38461521 TAGTTCAGCG
* * *
38461531 ACTTAAATAAAAACTTTTAAATAGTTCAGTG
1 ACTTAAATAAAAACTTTCAAATAGTTCAATA
38461562 ACTTAAATAAAAACTTTCAAATAGTTCAATA
1 ACTTAAATAAAAACTTTCAAATAGTTCAATA
* *
38461593 AC-TAAATTATAACTTT
1 ACTTAAATAAAAACTTT
38461609 TTTTAGTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 12 0.29
31 30 0.71
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAGTTCAATA
Found at i:38463061 original size:175 final size:175
Alignment explanation
Indices: 38462769--38463086 Score: 591
Period size: 175 Copynumber: 1.8 Consensus size: 175
38462759 ATGCCCTAAC
38462769 AACAAACATGGATCTCTTTGATCTTTTCTAGATATTTACTTTAGCAGACTTGAGGCTTATTGCAT
1 AACAAACATGGATCTCTTTGATCTTTTCTAGATATTTACTTTAGCAGACTTGAGGCTTATTGCAT
* *
38462834 GTTAAAGTCCCCACACCTTTGCTAGCATGGTTGTTATTTGAAGTGATTTGAATAATTAACGGGAA
66 GCTAAAGTCCCCACACCTTTGCTAGCACGGTTGTTATTTGAAGTGATTTGAATAATTAACGGGAA
38462899 TCTGTGGTGATTAAAGGTACTCATGCTCGGGTCAGGCTAGGTTTA
131 TCTGTGGTGATTAAAGGTACTCATGCTCGGGTCAGGCTAGGTTTA
*
38462944 AACAAACATGGATCTCTTTGATCTTTTTTAGATATTTACTTTAGCAGACTTGAGGCTTATTGCAT
1 AACAAACATGGATCTCTTTGATCTTTTCTAGATATTTACTTTAGCAGACTTGAGGCTTATTGCAT
*
38463009 GCTAAAGTCCCCACACCTTTGCTAGCACGGTTGTTATTTGAAGTGCTTTGAATAATTAACGGGAA
66 GCTAAAGTCCCCACACCTTTGCTAGCACGGTTGTTATTTGAAGTGATTTGAATAATTAACGGGAA
*
38463074 TCTGTGGTTATTA
131 TCTGTGGTGATTA
38463087 GATGTGCTCA
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 138 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (175 bp):
AACAAACATGGATCTCTTTGATCTTTTCTAGATATTTACTTTAGCAGACTTGAGGCTTATTGCAT
GCTAAAGTCCCCACACCTTTGCTAGCACGGTTGTTATTTGAAGTGATTTGAATAATTAACGGGAA
TCTGTGGTGATTAAAGGTACTCATGCTCGGGTCAGGCTAGGTTTA
Found at i:38468073 original size:21 final size:21
Alignment explanation
Indices: 38468043--38468087 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
38468033 TACACCAAAA
* *
38468043 TAGGCTTTTAGCGGCATTTTT
1 TAGGCCTTTAGCGGCACTTTT
38468064 TAGGCCTTTAGCGGCACTTTT
1 TAGGCCTTTAGCGGCACTTTT
38468085 TAG
1 TAG
38468088 CGCTGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (21 bp):
TAGGCCTTTAGCGGCACTTTT
Found at i:38468231 original size:43 final size:43
Alignment explanation
Indices: 38468166--38468380 Score: 171
Period size: 43 Copynumber: 5.2 Consensus size: 43
38468156 TTATAGAAAT
* * *
38468166 AAACGCCGCTAAAGAAT-GTGTTCTTTAGTGGCGCTTTTCTCAC
1 AAACGCCGCTAAAG-GTCATGTTCTTTAGCGGCGCTTTTCTCAC
* *
38468209 AAACGCCGCTAATGGTCATGTTC-TT-------CATTTCTCAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCTCAC
* *
38468244 AAACGCCGCTAAAGGTCATGTTCTTTAACGACGCTTTTCTCAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCTCAC
** ** *
38468287 AAACGCCGCTAAAATTCATGTTCTTTAGCGGCGCTTCCCTCAT
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCTCAC
** ** * *
38468330 AAACGCCGCT-ATTGTCTGATGACCTTTAGCGGCGCTTTTCTTAA
1 AAACGCCGCTAAAGGTC--ATGTTCTTTAGCGGCGCTTTTCTCAC
38468374 AAACGCC
1 AAACGCC
38468381 ACAAATTTTG
Statistics
Matches: 139, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
35 31 0.22
36 2 0.01
42 6 0.04
43 73 0.53
44 27 0.19
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCTCAC
Found at i:38468247 original size:35 final size:35
Alignment explanation
Indices: 38468201--38468268 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
38468191 TAGTGGCGCT
*
38468201 TTTCTCACAAACGCCGCTAATGGTCATGTTCTTCA
1 TTTCTCACAAACGCCGCTAAAGGTCATGTTCTTCA
38468236 TTTCTCACAAACGCCGCTAAAGGTCATGTTCTT
1 TTTCTCACAAACGCCGCTAAAGGTCATGTTCTT
38468269 TAACGACGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.34
Consensus pattern (35 bp):
TTTCTCACAAACGCCGCTAAAGGTCATGTTCTTCA
Found at i:38468306 original size:78 final size:78
Alignment explanation
Indices: 38468166--38468311 Score: 204
Period size: 78 Copynumber: 1.9 Consensus size: 78
38468156 TTATAGAAAT
* ** * **
38468166 AAACGCCGCTAAAGAATGTGTTCTTTAGTGGCGCTTTTCTCACAAACGCCGCTAATGGTCATGTT
1 AAACGCCGCTAAAGAATATGTTCTTTAACGACGCTTTTCTCACAAACGCCGCTAAAAGTCATGTT
38468231 CTTCATTTCTCAC
66 CTTCATTTCTCAC
* *
38468244 AAACGCCGCTAAAG-GTCATGTTCTTTAACGACGCTTTTCTCACAAACGCCGCTAAAATTCATGT
1 AAACGCCGCTAAAGAAT-ATGTTCTTTAACGACGCTTTTCTCACAAACGCCGCTAAAAGTCATGT
38468308 TCTT
65 TCTT
38468312 TAGCGGCGCT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
77 1 0.02
78 58 0.98
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (78 bp):
AAACGCCGCTAAAGAATATGTTCTTTAACGACGCTTTTCTCACAAACGCCGCTAAAAGTCATGTT
CTTCATTTCTCAC
Found at i:38470758 original size:37 final size:37
Alignment explanation
Indices: 38470717--38470804 Score: 158
Period size: 37 Copynumber: 2.4 Consensus size: 37
38470707 TATGTATGTC
*
38470717 ATGTATGTCATGTATAATATTAATTAAGTTGTGTATT
1 ATGTATGTTATGTATAATATTAATTAAGTTGTGTATT
38470754 ATGTATGTTATGTATAATATTAATTAAGTTGTGTATT
1 ATGTATGTTATGTATAATATTAATTAAGTTGTGTATT
*
38470791 ATGTAAGTTATGTA
1 ATGTATGTTATGTA
38470805 AGAAATGTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.49
Consensus pattern (37 bp):
ATGTATGTTATGTATAATATTAATTAAGTTGTGTATT
Found at i:38470758 original size:46 final size:43
Alignment explanation
Indices: 38470702--38470804 Score: 119
Period size: 37 Copynumber: 2.4 Consensus size: 43
38470692 GTAAGTTATA
38470702 TGTATTATGTATGTCATGTATGTCATGTATAATATTAATTAAGTTG
1 TGTATTATGTATGT-ATGTAT-T-ATGTATAATATTAATTAAGTTG
38470748 TG---TAT-TATGTATG--TTATGTATAATATTAATTAAGTTG
1 TGTATTATGTATGTATGTATTATGTATAATATTAATTAAGTTG
*
38470785 TGTATTATGTAAGTTATGTA
1 TGTATTATGTATG-TATGTA
38470805 AGAAATGTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
37 24 0.49
38 1 0.02
39 1 0.02
40 3 0.06
41 6 0.12
42 9 0.18
43 3 0.06
46 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (43 bp):
TGTATTATGTATGTATGTATTATGTATAATATTAATTAAGTTG
Found at i:38470767 original size:16 final size:16
Alignment explanation
Indices: 38470669--38470768 Score: 57
Period size: 16 Copynumber: 6.2 Consensus size: 16
38470659 AAGTTATGTA
38470669 GTATTATGT-TAGTTAT
1 GTATTATGTAT-GTTAT
* *
38470685 GTACTATGTAAGTTATAT
1 GTATTATGTATG-T-TAT
*
38470703 GTATTATGTATGTCAT
1 GTATTATGTATGTTAT
**
38470719 GTATGTCATGTATAATAT
1 GTAT-T-ATGTATGTTAT
* *
38470737 -TA--AT-TAAGTTGT
1 GTATTATGTATGTTAT
38470749 GTATTATGTATGTTAT
1 GTATTATGTATGTTAT
38470765 GTAT
1 GTAT
38470769 AATATTAATT
Statistics
Matches: 61, Mismatches: 14, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
12 4 0.07
13 4 0.07
15 2 0.03
16 25 0.41
17 5 0.08
18 21 0.34
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (16 bp):
GTATTATGTATGTTAT
Found at i:38470788 original size:21 final size:21
Alignment explanation
Indices: 38470727--38470789 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
38470717 ATGTATGTCA
38470727 TGTATAATATTAATTAAGTTG
1 TGTATAATATTAATTAAGTTG
*
38470748 TGTAT--TATGT-A-T--GTTA
1 TGTATAATAT-TAATTAAGTTG
38470764 TGTATAATATTAATTAAGTTG
1 TGTATAATATTAATTAAGTTG
38470785 TGTAT
1 TGTAT
38470790 TATGTAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
16 8 0.24
17 1 0.03
18 5 0.15
19 5 0.15
20 1 0.03
21 13 0.39
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
TGTATAATATTAATTAAGTTG
Found at i:38470803 original size:9 final size:9
Alignment explanation
Indices: 38470789--38470928 Score: 82
Period size: 9 Copynumber: 16.2 Consensus size: 9
38470779 AAGTTGTGTA
38470789 TTATGTAAG
1 TTATGTAAG
38470798 TTATGTAAG
1 TTATGTAAG
**
38470807 AAATGT-A-
1 TTATGTAAG
38470814 TTATGTAAG
1 TTATGTAAG
*
38470823 TTGTGT-A-
1 TTATGTAAG
* *
38470830 TAATGTTAG
1 TTATGTAAG
**
38470839 TTATCAAAG
1 TTATGTAAG
38470848 TTATGT-A-
1 TTATGTAAG
*
38470855 CTATGTAAG
1 TTATGTAAG
*
38470864 TTATTTAAG
1 TTATGTAAG
38470873 TTATGTAAG
1 TTATGTAAG
*
38470882 TTGTGT-A-
1 TTATGTAAG
38470889 TTATGTAAG
1 TTATGTAAG
*
38470898 TTAT-TATG
1 TTATGTAAG
38470906 TTATTATGTAAG
1 ---TTATGTAAG
*
38470918 TTATGCAAG
1 TTATGTAAG
38470927 TT
1 TT
38470929 TATATATAAG
Statistics
Matches: 97, Mismatches: 22, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
7 18 0.19
8 11 0.11
9 61 0.63
11 4 0.04
12 3 0.03
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:38470854 original size:41 final size:41
Alignment explanation
Indices: 38470778--38470865 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
38470768 TAATATTAAT
* ** *
38470778 TAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATG
1 TAAGTTGTGTATAATGTAAGTTATCAAAGAAATGTACTATG
* **
38470819 TAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTACTATG
1 TAAGTTGTGTATAATGTAAGTTATCAAAGAAATGTACTATG
38470860 TAAGTT
1 TAAGTT
38470866 ATTTAAGTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.44
Consensus pattern (41 bp):
TAAGTTGTGTATAATGTAAGTTATCAAAGAAATGTACTATG
Found at i:38470875 original size:34 final size:34
Alignment explanation
Indices: 38470837--38470902 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
38470827 GTATAATGTT
38470837 AGTTATCAAAGTTATGTACTATGTAAGTTATTTA
1 AGTTATCAAAGTTATGTACTATGTAAGTTATTTA
** * *
38470871 AGTTATGTAAGTTGTGTATTATGTAAGTTATT
1 AGTTATCAAAGTTATGTACTATGTAAGTTATT
38470903 ATGTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (34 bp):
AGTTATCAAAGTTATGTACTATGTAAGTTATTTA
Found at i:38470892 original size:25 final size:24
Alignment explanation
Indices: 38470778--38470928 Score: 100
Period size: 25 Copynumber: 6.2 Consensus size: 24
38470768 TAATATTAAT
38470778 TAAGTTGTGTATTATGTAAGTTATG
1 TAAGTTGT-TATTATGTAAGTTATG
* *
38470803 TAAGAAATG-TATTATGTAAGTTGTG
1 TAAG--TTGTTATTATGTAAGTTATG
* **
38470828 TATA-ATGTTAGTTATCAAAGTTATG
1 TA-AGTTGTTA-TTATGTAAGTTATG
* * *
38470853 T-ACTATGTAAGTTATTTAAGTTATG
1 TAAGT-TGTTA-TTATGTAAGTTATG
38470878 TAAGTTGTGTATTATGTAAGTTAT-
1 TAAGTTGT-TATTATGTAAGTTATG
38470902 T-A--TGTTATTATGTAAGTTATG
1 TAAGTTGTTATTATGTAAGTTATG
*
38470923 CAAGTT
1 TAAGTT
38470929 TATATATAAG
Statistics
Matches: 100, Mismatches: 13, Indels: 27
0.71 0.09 0.19
Matches are distributed among these distances:
20 15 0.15
21 3 0.03
22 1 0.01
23 5 0.05
24 4 0.04
25 66 0.66
26 4 0.04
27 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (24 bp):
TAAGTTGTTATTATGTAAGTTATG
Found at i:38470939 original size:12 final size:12
Alignment explanation
Indices: 38470924--38470952 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
38470914 TAAGTTATGC
38470924 AAGTTTATATAT
1 AAGTTTATATAT
38470936 AAGTTTATATAT
1 AAGTTTATATAT
38470948 AAGTT
1 AAGTT
38470953 ATGTAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
AAGTTTATATAT
Found at i:38471366 original size:14 final size:15
Alignment explanation
Indices: 38471347--38471377 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38471337 ACAGAAACAG
38471347 AAATAGA-AAACAAA
1 AAATAGAGAAACAAA
38471361 AAATAGAGAAACAAA
1 AAATAGAGAAACAAA
38471376 AA
1 AA
38471378 CTGCTACAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.77, C:0.06, G:0.10, T:0.06
Consensus pattern (15 bp):
AAATAGAGAAACAAA
Found at i:38472460 original size:83 final size:83
Alignment explanation
Indices: 38472373--38472592 Score: 261
Period size: 84 Copynumber: 2.6 Consensus size: 83
38472363 TGCATATTTC
* * *
38472373 CGGCGTTT-CTAGCAAAAACGCCAGTATAA-ATTCAT-TTC-ATGAAGCGAAACGGTGCCGCATT
1 CGGCGTTTCCTA--AAAAACGCCACTATAAGATT-ATATTCTA-GAAGAGAAACGGTGCCACATT
38472434 -GACAAACATTAATTCACTCTTG
62 AG-CAAACATTAATTCACTCTTG
* * * *
38472456 CGGCGTTTGCTTAAAAAACGCCACTATAAGATTTTATTCTAGTAGAGAAACGGTGCCATATTAGC
1 CGGCGTTT-CCTAAAAAACGCCACTATAAGATTATATTCTAGAAGAGAAACGGTGCCACATTAGC
38472521 AAACATTAATTCACTCTTG
65 AAACATTAATTCACTCTTG
* *
38472540 CGGCGTTTTCCTAAAAAACGCCACTATAAGATTTTATTCTAGTAGAGAAACGG
1 CGGCG-TTTCCTAAAAAACGCCACTATAAGATTATATTCTAGAAGAGAAACGG
38472593 CTCCGCTTTG
Statistics
Matches: 122, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
83 24 0.20
84 91 0.75
85 7 0.06
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (83 bp):
CGGCGTTTCCTAAAAAACGCCACTATAAGATTATATTCTAGAAGAGAAACGGTGCCACATTAGCA
AACATTAATTCACTCTTG
Found at i:38472614 original size:84 final size:84
Alignment explanation
Indices: 38472418--38472592 Score: 298
Period size: 84 Copynumber: 2.1 Consensus size: 84
38472408 TTCATGAAGC
** *
38472418 GAAACGGTGCCGCATT-GACAAACATTAATTCACTCTTGCGGCGTTTGCTTAAAAAACGCCACTA
1 GAAACGGTGCCATATTAG-CAAACATTAATTCACTCTTGCGGCGTTTGCCTAAAAAACGCCACTA
38472482 TAAGATTTTATTCTAGTAGA
65 TAAGATTTTATTCTAGTAGA
*
38472502 GAAACGGTGCCATATTAGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTAT
1 GAAACGGTGCCATATTAGCAAACATTAATTCACTCTTGCGGCGTTTGCCTAAAAAACGCCACTAT
38472567 AAGATTTTATTCTAGTAGA
66 AAGATTTTATTCTAGTAGA
38472586 GAAACGG
1 GAAACGG
38472593 CTCCGCTTTG
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
84 85 0.99
85 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (84 bp):
GAAACGGTGCCATATTAGCAAACATTAATTCACTCTTGCGGCGTTTGCCTAAAAAACGCCACTAT
AAGATTTTATTCTAGTAGA
Found at i:38473150 original size:82 final size:81
Alignment explanation
Indices: 38473056--38473302 Score: 314
Period size: 90 Copynumber: 2.9 Consensus size: 81
38473046 TATAAAGAAC
* * *
38473056 TTATTTAATATATAAATTAAAAAGTACTAATTAATCTAAATCTTAAACCCTAACCTGACCCCAAA
1 TTATTTAATATATAAATTAAAAA-CACTAATTAATCTAAATCCTAAACCCTAACCCGACCCCAAA
38473121 TCTCTAACCCCTAAACT
65 TCTCTAACCCCTAAACT
* *
38473138 TTATTTAATATATAAATTAACAAACACTAATTAATCTAAATCCTAAACCCTGAACCCGACCTCGA
1 TTATTTAATATATAAATTAA-AAACACTAATTAATCTAAATCCTAAACCCT-AACCCGACCCCAA
38473203 ATCCCTAACCCCTAACCCCTAAACT
64 AT--CT-----CTAACCCCTAAACT
* * * *
38473228 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGATCCTAAA
1 TTATTTAATATATAAATT-AAAAACACTAATTAATCTAAATCCTAAACCCTAACCCGACCCCAAA
38473293 TCTCTAACCC
65 TCTCTAACCC
38473303 TTAACCCCTA
Statistics
Matches: 144, Mismatches: 11, Indels: 20
0.82 0.06 0.11
Matches are distributed among these distances:
82 52 0.36
83 15 0.10
85 2 0.01
87 2 0.01
89 11 0.08
90 60 0.42
91 2 0.01
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (81 bp):
TTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTAACCCGACCCCAAAT
CTCTAACCCCTAAACT
Found at i:38473415 original size:103 final size:103
Alignment explanation
Indices: 38473202--38473417 Score: 285
Period size: 102 Copynumber: 2.1 Consensus size: 103
38473192 CCCGACCTCG
*
38473202 AATCCCTAACCCCTAACCCCTAAACTTTATTTAATATATAAATTAAAAAACACTAATTAATCTAA
1 AATCCCTAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAA
* * * *
38473267 ACCCTAAACCATAACCCGATCCTAAATCTCTAACCCTT
66 ACCCTAAACCATAACCCGAACATAAATCCCTAAACCTT
* * * *
38473305 AACCCCTAACCCCTAACCCTTAAACCTTATTTAATATAT-AATTAAAACATACTAATTAATCTAA
1 AATCCCTAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAA
* *
38473369 ACCCTAAACTC-TAA-CCTAACATCGAATCCCTAAACCTT
66 ACCCTAAAC-CATAACCCGAACAT-AAATCCCTAAACCTT
38473407 AAATCCCTAAC
1 -AATCCCTAAC
38473418 TCTTAACATC
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
101 5 0.05
102 47 0.48
103 46 0.47
ACGTcount: A:0.42, C:0.30, G:0.01, T:0.28
Consensus pattern (103 bp):
AATCCCTAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAA
ACCCTAAACCATAACCCGAACATAAATCCCTAAACCTT
Found at i:38473425 original size:36 final size:33
Alignment explanation
Indices: 38473365--38473451 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
38473355 ACTAATTAAT
* *
38473365 CTAAACCCTAAACTCTAACCTAACATCGAATCC
1 CTAAACCCTAAACCCTAACCTAACATCGAACCC
* *
38473398 CTAAACCTTAAATCCCTAACTCTTAACATCTAACCC
1 CTAAACCCTAAA-CCCTAAC-C-TAACATCGAACCC
*
38473434 CT-AA-CCTAACCCCTAACC
1 CTAAACCCTAAACCCTAACC
38473452 CCTAACCCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
32 1 0.02
33 18 0.40
34 10 0.22
35 3 0.07
36 13 0.29
ACGTcount: A:0.37, C:0.39, G:0.01, T:0.23
Consensus pattern (33 bp):
CTAAACCCTAAACCCTAACCTAACATCGAACCC
Found at i:38473437 original size:7 final size:7
Alignment explanation
Indices: 38473427--38473463 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
38473417 CTCTTAACAT
38473427 CTAACCC
1 CTAACCC
38473434 CTAA--C
1 CTAACCC
38473439 CTAACCC
1 CTAACCC
38473446 CTAACCC
1 CTAACCC
38473453 CTAACCC
1 CTAACCC
38473460 CTAA
1 CTAA
38473464 ACCTTAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.18
7 23 0.82
ACGTcount: A:0.32, C:0.51, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAACCC
Found at i:38473450 original size:26 final size:26
Alignment explanation
Indices: 38473412--38473463 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
38473402 ACCTTAAATC
* * *
38473412 CCTAACTCTTAACATCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
*
38473438 CCTAACCCCTAACCCCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
38473464 ACCTTAAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (26 bp):
CCTAACCCCTAACACCTAACCCCTAA
Found at i:38473616 original size:21 final size:22
Alignment explanation
Indices: 38473574--38473619 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
38473564 ATCCTAAATT
*
38473574 AACCATATATATATACACCCTA
1 AACCATATATATATAAACCCTA
*
38473596 AACCATATTTAT-TAAACCCTA
1 AACCATATATATATAAACCCTA
38473617 AAC
1 AAC
38473620 TATAATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (22 bp):
AACCATATATATATAAACCCTA
Found at i:38474336 original size:114 final size:113
Alignment explanation
Indices: 38474080--38474755 Score: 840
Period size: 114 Copynumber: 6.0 Consensus size: 113
38474070 TAGATTATTT
* * * * * *
38474080 TAAATCCCTCAGCATTAGCGGCGCATCCTTAAAAACGCCACTAAATCCCCGAAAGCTAAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * * * * *
38474145 GGCATCGTCGGGCTTAGGTTTTTTGCGGCACTTT-TCCAAAAATGTCGC
66 GGCGTCGTTGGGCTTAGTTTTTTTGTGGCGCTTTAT-CAAAAACGTCGC
* * * *
38474193 TAAAGCCCTGAGCATTAGCGGCGCGTACTTAAAAAAGCTGCTAAATCCTCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * *
38474258 GGCGTCATTGGGCTTATGTTTTTTTGTGGCCCTTTATCAAAAACGCCGC
66 GGCGTCGTTGGGCTTA-GTTTTTTTGTGGCGCTTTATCAAAAACGTCGC
* *
38474307 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTAAGAAAAT
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * *
38474372 GACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATAAAAAACATCGC
66 GGCGTCGTTGGGCTTA-GTTTTTTTGTGGCGCTTTATCAAAAACGTCGC
* *
38474421 TAAAGCCCTGAGCATTAGCAGCGCTTTA-TTAAAAACGCCCCTAAATCCCCGAAAGCTCAGAAAA
1 TAAAGCCCTGAGCATTAGCGGCGC-TTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
38474485 CGGCGTCGTTGGGCTTAGATTTTTTTGT-G-GC---ATCAAAAACGTCGC
65 CGGCGTCGTTGGGCTTAG-TTTTTTTGTGGCGCTTTATCAAAAACGTCGC
*
38474530 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAATGCCGCTAAATCCCCGAAAGCTCAG---A-
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* *
38474591 GGCGTCATTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCGC
66 GGCGTCGTTGGGCTTA-GTTTTTTTGTGGCGCTTTATCAAAAACGTCGC
* * *
38474640 TAAAGCCTTGAGCATTAGTGGCACTTTA-TTAAAAACGCCGCTAAATCCCCGAAAGCTC-GAAAA
1 TAAAGCCCTGAGCATTAGCGGCGC-TTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAG-AAA
* * * * *
38474703 ACGACGTCGTTGGGCTTAGGTATTTTGCGGCGCGTTT-TCGAAAACGTCGC
64 ACGGCGTCGTTGGGCTTAGTTTTTTTGTGGCGC-TTTATCAAAAACGTCGC
38474753 TAA
1 TAA
38474756 TGCTTATTTT
Statistics
Matches: 492, Mismatches: 53, Indels: 36
0.85 0.09 0.06
Matches are distributed among these distances:
105 24 0.05
106 3 0.01
107 2 0.00
108 3 0.01
109 66 0.13
110 63 0.13
111 3 0.01
112 2 0.00
113 98 0.20
114 224 0.46
115 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (113 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
GGCGTCGTTGGGCTTAGTTTTTTTGTGGCGCTTTATCAAAAACGTCGC
Found at i:38474686 original size:219 final size:222
Alignment explanation
Indices: 38474080--38474721 Score: 850
Period size: 219 Copynumber: 2.9 Consensus size: 222
38474070 TAGATTATTT
* * * * *
38474080 TAAATCCCTCAGCATTAGCGGCGCATCCTTAAAAACGCCACTAAATCCCCGAAAGCTAAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTAAG--AAC
* * * * *
38474145 GGCATCGTCGGGCTTAGG-TTTTTTGCGGCACTTT-TCCAAAAATGTCGCTAAAGCCCTGAGCAT
64 GGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTAT-CAAAAACGTCGCTAAAGCCCTGAGCAT
* * * * *
38474208 TAGCGGCGC-GTACTTAAAAAAGCTGCTAAATCCTCGAAAGCTCAGAAAACGGCGTCATTGGGCT
128 TAGCGGCGCTTTA-TTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCT
38474272 TATGTTTTTTTGTGGCCCTTTATCAAAAACGCCGC
192 TA-GTTTTTTTGTGG-CC--TATCAAAAACGCCGC
*
38474307 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTAAGAAAAT
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTAAG--AAC
* * *
38474372 GACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATAAAAAACATCGCTAAAGCCCTGAGCATT
64 GGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGTCGCTAAAGCCCTGAGCATT
* *
38474437 AGCAGCGCTTTATTAAAAACGCCCCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
129 AGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
*
38474502 GATTTTTTTGTGG-C-ATCAAAAACGTCGC
194 G-TTTTTTTGTGGCCTATCAAAAACGCCGC
* *
38474530 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAATGCCGCTAAATCCCCGAAAGCTCAG-A-GG
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTAAGAACGG
* * *
38474593 CGTCATTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCGCTAAAGCCTTGAGCATTAG
66 CGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGTCGCTAAAGCCCTGAGCATTAG
* * *
38474658 TGGCACTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTC-GAAAAACGACGTCGTTGGGCTTAG
131 CGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCAG-AAAACGGCGTCGTTGGGCTTAG
38474722 GTATTTTGCG
Statistics
Matches: 375, Mismatches: 35, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
218 1 0.00
219 118 0.31
220 1 0.00
223 71 0.19
226 1 0.00
227 75 0.20
228 105 0.28
229 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (222 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTAAGAACGG
CGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGTCGCTAAAGCCCTGAGCATTAG
CGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGT
TTTTTTGTGGCCTATCAAAAACGCCGC
Found at i:38474711 original size:333 final size:336
Alignment explanation
Indices: 38474080--38474728 Score: 959
Period size: 333 Copynumber: 1.9 Consensus size: 336
38474070 TAGATTATTT
* * *
38474080 TAAATCCCTCAGCATTAGCGGCGCATCCTTAAAAACGCCACTAAATCCCCGAAAGCTAAGAAAAC
1 TAAAGCCCTCAGCATTAGCAGCGCATCATTAAAAACGCCACTAAATCCCCGAAAGCTAAGAAAAC
*
38474145 GGCATCGTCGGGCTTAGGTTTTTTGCGGCACTTTTCCAAAAATGTCGCTAAAGCCCTGAGCATTA
66 GGCATCGTCGGGCTTAGGTTTTTTGCGGCA---TTCCAAAAACGTCGCTAAAGCCCTGAGCATTA
* * *
38474210 GCGGCGCGTACTTAAAAAAGCTGCTAAATCCTCGAAAGCTCAGAAAACGGCGTCATTGGGCTTAT
128 GCGGCGCGTACTTAAAAAAGCCGCTAAATCCCCGAAAGCTCAG--AACGGCGTCATTGGGCTTAG
*
38474275 GTTTTTTTGTGGCCCTTTATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAA
191 GTTTTTTTGTGGCCCTTTATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTACTTAAA
* *
38474340 AACGCCGCTAAATCCCCGAAAGCTAAGAAAATGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCT
256 AACGCCGCTAAATCCCCGAAAGCTAAGAAAACGACGTCGTTGGGCTTAGGTATTTTTGTGGCGCT
38474405 TTATAAAAAACATCGC
321 TTATAAAAAACATCGC
* * * * *
38474421 TAAAGCCCTGAGCATTAGCAGCGCTTTATTAAAAACGCCCCTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTCAGCATTAGCAGCGCATCATTAAAAACGCCACTAAATCCCCGAAAGCTAAGAAAAC
* * * *
38474486 GGCGTCGTTGGGCTTAGATTTTTTTGTGGCA-T-CAAAAACGTCGCTAAAGCCCTGAGCATTAGC
66 GGCATCGTCGGGCTTAG-GTTTTTTGCGGCATTCCAAAAACGTCGCTAAAGCCCTGAGCATTAGC
* *
38474549 GGCGCTTACTTAAAAATGCCGCTAAATCCCCGAAAGCTCAG-A-GGCGTCATTGGGCTTAGGTTT
130 GGCGCGTACTTAAAAAAGCCGCTAAATCCCCGAAAGCTCAGAACGGCGTCATTGGGCTTAGGTTT
* * *
38474612 TTTTGTGGCGCTTTATCAAAAACGCCGCTAAAGCCTTGAGCATTAGTGGCACTTTA-TTAAAAAC
195 TTTTGTGGCCCTTTATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCAC-TTACTTAAAAAC
*
38474676 GCCGCTAAATCCCCGAAAGCT-CGAAAAACGACGTCGTTGGGCTTAGGTATTTT
259 GCCGCTAAATCCCCGAAAGCTAAG-AAAACGACGTCGTTGGGCTTAGGTATTTT
38474729 GCGGCGCGTT
Statistics
Matches: 280, Mismatches: 25, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
332 1 0.00
333 124 0.44
334 4 0.01
337 67 0.24
338 1 0.00
341 72 0.26
342 11 0.04
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (336 bp):
TAAAGCCCTCAGCATTAGCAGCGCATCATTAAAAACGCCACTAAATCCCCGAAAGCTAAGAAAAC
GGCATCGTCGGGCTTAGGTTTTTTGCGGCATTCCAAAAACGTCGCTAAAGCCCTGAGCATTAGCG
GCGCGTACTTAAAAAAGCCGCTAAATCCCCGAAAGCTCAGAACGGCGTCATTGGGCTTAGGTTTT
TTTGTGGCCCTTTATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTACTTAAAAACGC
CGCTAAATCCCCGAAAGCTAAGAAAACGACGTCGTTGGGCTTAGGTATTTTTGTGGCGCTTTATA
AAAAACATCGC
Found at i:38474844 original size:12 final size:12
Alignment explanation
Indices: 38474827--38474851 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38474817 TTTATCCAAC
38474827 CGCCGCTAAAAG
1 CGCCGCTAAAAG
38474839 CGCCGCTAAAAG
1 CGCCGCTAAAAG
38474851 C
1 C
38474852 CTGTTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.24, T:0.08
Consensus pattern (12 bp):
CGCCGCTAAAAG
Found at i:38479431 original size:40 final size:40
Alignment explanation
Indices: 38479367--38479498 Score: 196
Period size: 40 Copynumber: 3.3 Consensus size: 40
38479357 TCTTCGGAAT
* *
38479367 TTAG-CCGGATATAACAACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATCAACTAGCACAAATGCCTTCGGGTC
*
38479406 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATCAACTAGCACAAATGCCTTCGGGTC
* *
38479446 TTAGCCCGGATAAAATC-ACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCAACTAGCACAAATGCCTTCGGGTC
38479486 TTAGCCCGGATAT
1 TTAGCCCGGATAT
38479499 CATTCAAATG
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
39 5 0.06
40 75 0.89
41 4 0.05
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATATCAACTAGCACAAATGCCTTCGGGTC
Found at i:38483927 original size:24 final size:24
Alignment explanation
Indices: 38483899--38483946 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
38483889 ATGATTGTTT
*
38483899 GCGAATTATTTTGAGTCATTATTG
1 GCGAATTATTTTGAGACATTATTG
38483923 GCGAATTATTTTGAGACATTATTG
1 GCGAATTATTTTGAGACATTATTG
38483947 ATGAAAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (24 bp):
GCGAATTATTTTGAGACATTATTG
Found at i:38489045 original size:24 final size:25
Alignment explanation
Indices: 38489013--38489059 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
38489003 TTATTGAGTG
*
38489013 AAAAATTCTCT-TTGAGTTTTCTCC
1 AAAAATTCTCTCTTGAATTTTCTCC
38489037 AAAAATTCTCTCTTGAATTTTCT
1 AAAAATTCTCTCTTGAATTTTCT
38489060 TTAGAAGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (25 bp):
AAAAATTCTCTCTTGAATTTTCTCC
Found at i:38490787 original size:24 final size:25
Alignment explanation
Indices: 38490755--38490801 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
38490745 TTATTGAGTG
*
38490755 AAAAATTCTCT-TTGAGTTTTCTCC
1 AAAAATTCTCTCTTGAATTTTCTCC
38490779 AAAAATTCTCTCTTGAATTTTCT
1 AAAAATTCTCTCTTGAATTTTCT
38490802 TTAGAAGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (25 bp):
AAAAATTCTCTCTTGAATTTTCTCC
Found at i:38493560 original size:156 final size:156
Alignment explanation
Indices: 38493276--38493583 Score: 508
Period size: 156 Copynumber: 2.0 Consensus size: 156
38493266 CAACCGAGTC
* * *
38493276 TCGTGCAGATTTGAAAATTATTGATAAAACTTTTGGTGACTTAGTTCTTAAAAGATCCCCTCAGT
1 TCGTGCAGATTTGAAAATTATTAATAAAACTTTTAGTGACTTAGTTCTTAAAAAATCCCCTCAGT
* * *
38493341 TTGATCCGATTAATTGTTACTCTTCGATTGTGGTTGATAAAGTCATTGCAAAAGGAACCGTGAGT
66 TTGATCCAATTAAGTGTTACTCTTCGATTGTGGTTGATAAAGTCATTACAAAAGGAACCGTGAGT
*
38493406 TGTTATTTTCTTGATTTGCCTTGTGT
131 TGTTATTCTCTTGATTTGCCTTGTGT
*
38493432 TCGTGCAGATTTGAAAATTATTAATAAAACTTTTAGTGACTTAGTTCTTAAAAAATCCCCTCATT
1 TCGTGCAGATTTGAAAATTATTAATAAAACTTTTAGTGACTTAGTTCTTAAAAAATCCCCTCAGT
* ** *
38493497 TTGATCCAATTAAGTGTTATTCTTCGATTGTGGTTGATAAAGTCATTATGAAAGGAAGCGTGAGT
66 TTGATCCAATTAAGTGTTACTCTTCGATTGTGGTTGATAAAGTCATTACAAAAGGAACCGTGAGT
38493562 TGTTATTCTCTTGATTTGCCTT
131 TGTTATTCTCTTGATTTGCCTT
38493584 TTGTAAAATC
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
156 140 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (156 bp):
TCGTGCAGATTTGAAAATTATTAATAAAACTTTTAGTGACTTAGTTCTTAAAAAATCCCCTCAGT
TTGATCCAATTAAGTGTTACTCTTCGATTGTGGTTGATAAAGTCATTACAAAAGGAACCGTGAGT
TGTTATTCTCTTGATTTGCCTTGTGT
Found at i:38495112 original size:12 final size:12
Alignment explanation
Indices: 38495095--38495119 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38495085 CCTTATACAC
38495095 ATTACACATTGA
1 ATTACACATTGA
38495107 ATTACACATTGA
1 ATTACACATTGA
38495119 A
1 A
38495120 ATCAGATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:38500189 original size:50 final size:51
Alignment explanation
Indices: 38500126--38500258 Score: 151
Period size: 50 Copynumber: 2.6 Consensus size: 51
38500116 TATCATTCGA
* * ** *
38500126 TACACGTAATAGCCTTCACATAGTACTACACACGTGGTCAAA-CTTTCCGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAAGCCTTCCGG
* * *
38500176 TTCACGTAGTAGCCTACACATAGTACTACACACTTGACCAAAGCCTTCTGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAAGCCTTCCGG
* * * *
38500227 TAAACATAGTAGCCTGCACATAGTACAACACA
1 TACACGTAGTAGCCTACACATAGTACTACACA
38500259 TGTGTTTATA
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 36 0.52
51 33 0.48
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (51 bp):
TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAAGCCTTCCGG
Found at i:38500250 original size:51 final size:50
Alignment explanation
Indices: 38500135--38500258 Score: 140
Period size: 51 Copynumber: 2.5 Consensus size: 50
38500125 ATACACGTAA
* ** * ** *
38500135 TAGCCTTCACATAGTACTACACACGTGGTCAAACTTTCCGGTTCACGTAG
1 TAGCCTACACATAGTACTACACACGTGACCAAACCTTCCGGTAAACATAG
* *
38500185 TAGCCTACACATAGTACTACACACTTGACCAAAGCCTTCTGGTAAACATAG
1 TAGCCTACACATAGTACTACACACGTGACCAAA-CCTTCCGGTAAACATAG
* *
38500236 TAGCCTGCACATAGTACAACACA
1 TAGCCTACACATAGTACTACACA
38500259 TGTGTTTATA
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 29 0.47
51 33 0.53
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.24
Consensus pattern (50 bp):
TAGCCTACACATAGTACTACACACGTGACCAAACCTTCCGGTAAACATAG
Found at i:38502267 original size:39 final size:39
Alignment explanation
Indices: 38502213--38502294 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
38502203 ACTCAGTCCA
38502213 ATACAAAGGGGTTCTACACTTACGTCCATATAATGCTTC
1 ATACAAAGGGGTTCTACACTTACGTCCATATAATGCTTC
38502252 ATACAAAGGGGTTCTACACTTACGTCCATATAATGCTTC
1 ATACAAAGGGGTTCTACACTTACGTCCATATAATGCTTC
38502291 ATAC
1 ATAC
38502295 GGTGTCATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (39 bp):
ATACAAAGGGGTTCTACACTTACGTCCATATAATGCTTC
Found at i:38507843 original size:50 final size:51
Alignment explanation
Indices: 38507783--38507919 Score: 204
Period size: 50 Copynumber: 2.7 Consensus size: 51
38507773 TATCATTCGA
* * *
38507783 TACACGTAGTAGCCTTCACATAGTATTACACACGTGATCAAA-CTTTCCGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAAGCCTTCCGG
* *
38507833 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAGCCTTCCGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAAGCCTTCCGG
* *
38507884 TACACATAGTAGCCTACACATAGTACAACACACGTG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTG
38507920 TTTATAGGCG
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 39 0.50
51 39 0.50
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
TACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAAGCCTTCCGG
Found at i:38514582 original size:26 final size:26
Alignment explanation
Indices: 38514529--38514586 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
38514519 TTTTATTGGA
*
38514529 GGTAAAATTGTTAAAATTTTAACGAG
1 GGTAAAATTGTTAAAACTTTAACGAG
*
38514555 GGTAAAATTGTTAAAAACTTT-ACTAG
1 GGTAAAATTGTT-AAAACTTTAACGAG
38514581 GGTAAA
1 GGTAAA
38514587 TTTGGGATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (26 bp):
GGTAAAATTGTTAAAACTTTAACGAG
Found at i:38522375 original size:6 final size:6
Alignment explanation
Indices: 38522364--38522390 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38522354 AAGTGACTTT
38522364 TTATAA TTATAA TTATAA TTATAA TTA
1 TTATAA TTATAA TTATAA TTATAA TTA
38522391 CTATGTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:38533725 original size:24 final size:24
Alignment explanation
Indices: 38533698--38533744 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
38533688 AAAGTCAAAT
* *
38533698 ATATTATGCTAATAAATGCTAAAA
1 ATATTATACTAATAAATACTAAAA
*
38533722 ATATTATACTCATAAATACTAAA
1 ATATTATACTAATAAATACTAAA
38533745 TCTTCTAGAA
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:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (24 bp):
ATATTATACTAATAAATACTAAAA
Found at i:38536742 original size:43 final size:42
Alignment explanation
Indices: 38536593--38536742 Score: 137
Period size: 43 Copynumber: 3.5 Consensus size: 42
38536583 TATGATTTTG
*
38536593 TGTAAGACCACGTCTGGGAC-GTTGGCATCG-ATTTGAGATTTACG
1 TGTAAGACCACGTCTGGGACAG-TGGCATCGTATTT--GA-TTACA
* * * * * *
38536637 TGTAAGACCATGTTTGGGACA-TCAGCATTGTATATGATTTCA
1 TGTAAGACCACGTCTGGGACAGT-GGCATCGTATTTGATTACA
*
38536679 TGTAAGACC-CTGTCTAGGACAGTGGCATCGCTATTTGATTACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATCG-TATTTGATTACA
38536722 TGTAAGACCACGTCTGGGACA
1 TGTAAGACCACGTCTGGGACA
38536743 TTGGTATTGT
Statistics
Matches: 84, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
42 25 0.30
43 32 0.38
44 24 0.29
45 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCGTATTTGATTACA
Found at i:38537023 original size:10 final size:11
Alignment explanation
Indices: 38537006--38537057 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
38536996 GACCCATTTT
38537006 TATTTTAAAAA
1 TATTTTAAAAA
38537017 T-TTTT-AAAA
1 TATTTTAAAAA
**
38537026 -ATTAAAAAAA
1 TATTTTAAAAA
38537036 GTATTTTAAAAA
1 -TATTTTAAAAA
38537048 TATTTTAAAA
1 TATTTTAAAA
38537058 TTAAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 6 0.18
10 8 0.24
11 11 0.33
12 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:38537072 original size:8 final size:9
Alignment explanation
Indices: 38537054--38537103 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
38537044 AAAATATTTT
38537054 AAAATTAAA
1 AAAATTAAA
38537063 AAAATTAAA
1 AAAATTAAA
***
38537072 AAAAGTATTTT
1 AAAA-T-TAAA
38537083 AAAATTAAA
1 AAAATTAAA
38537092 AAAATTAAA
1 AAAATTAAA
38537101 AAA
1 AAA
38537104 GTATTTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 26 0.79
10 2 0.06
11 5 0.15
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (9 bp):
AAAATTAAA
Found at i:38537115 original size:40 final size:40
Alignment explanation
Indices: 38537026--38537147 Score: 142
Period size: 40 Copynumber: 3.0 Consensus size: 40
38537016 ATTTTTAAAA
***
38537026 ATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA--
1 ATTAAAAAAAGTATTTT-AAAAT-TAAAAAAATTAAAAAAGT
38537066 ATTAAAAAAAGTATTTTAAAATTAAAAAAATTAAAAAAGT
1 ATTAAAAAAAGTATTTTAAAATTAAAAAAATTAAAAAAGT
** *
38537106 ATTTTAAAAA-TATTTTAAAATTAAAAAAAATTTAAAAAGT
1 ATTAAAAAAAGTATTTTAAAATT-AAAAAAATTAAAAAAGT
38537146 AT
1 AT
38537148 CTGCCCGGCC
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
38 13 0.18
39 17 0.23
40 43 0.59
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (40 bp):
ATTAAAAAAAGTATTTTAAAATTAAAAAAATTAAAAAAGT
Found at i:38537116 original size:29 final size:29
Alignment explanation
Indices: 38537043--38537114 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 29
38537033 AAAGTATTTT
38537043 AAAAA-TATTTTAAAATTAAAAAAATTAA
1 AAAAAGTATTTTAAAATTAAAAAAATTAA
38537071 AAAAAGTATTTTAAAATTAAAAAAATT-A
1 AAAAAGTATTTTAAAATTAAAAAAATTAA
38537099 AAAAAGTATTTTAAAA
1 AAAAAGTATTTTAAAA
38537115 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 22 0.51
29 21 0.49
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAAAGTATTTTAAAATTAAAAAAATTAA
Found at i:38539996 original size:24 final size:24
Alignment explanation
Indices: 38539969--38540025 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
38539959 AACCCTAATT
38539969 CTAATCAAA-GTAAAATATATTATG
1 CTAAT-AAATGTAAAATATATTATG
* *
38539993 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTAAAATATATTATG
*
38540017 CTCATAAAT
1 CTAATAAAT
38540026 ACTAAATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (24 bp):
CTAATAAATGTAAAATATATTATG
Found at i:38540031 original size:24 final size:24
Alignment explanation
Indices: 38539981--38540032 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
38539971 AATCAAAGTA
* **
38539981 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
38540005 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
38540029 AAAT
1 AAAT
38540033 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:38543870 original size:104 final size:103
Alignment explanation
Indices: 38543690--38543956 Score: 390
Period size: 104 Copynumber: 2.6 Consensus size: 103
38543680 TAACCGTTAT
* * * **
38543690 CGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCATCACTTAGCAACCCCTCGTTGG
1 CGGTGGAT-ACGCACTTAGCACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGG
**
38543755 AATCAGCACATAGCAACCCCCTTTTTCATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
38543794 CGGTGGATATCGCACTTAGCATCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGG
1 CGGTGGATA-CGCACTTAGCACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGG
38543859 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* * * **
38543898 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 CGGTGGAT-ACGCACTTAGCACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCT
38543957 TTATATACAA
Statistics
Matches: 147, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
104 146 0.99
105 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (103 bp):
CGGTGGATACGCACTTAGCACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:38544317 original size:29 final size:29
Alignment explanation
Indices: 38544284--38544347 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
38544274 TAATCCACCA
38544284 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
38544313 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
38544343 CCCAA
1 CCCAA
38544348 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:38544321 original size:30 final size:30
Alignment explanation
Indices: 38544291--38544347 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38544281 CCACCCAACT
38544291 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
38544320 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
38544348 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:38545304 original size:8 final size:8
Alignment explanation
Indices: 38545293--38545326 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
38545283 TAGTTAATTT
38545293 TTTAAAAA
1 TTTAAAAA
38545301 TTTAAAAA
1 TTTAAAAA
38545309 TATTAAAAAA
1 T-TT-AAAAA
38545319 TTTAAAAA
1 TTTAAAAA
38545327 CATTAGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 14 0.58
9 4 0.17
10 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TTTAAAAA
Found at i:38545319 original size:18 final size:18
Alignment explanation
Indices: 38545296--38545331 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38545286 TTAATTTTTT
*
38545296 AAAAATTTAAAAATATTA
1 AAAAATTTAAAAACATTA
38545314 AAAAATTTAAAAACATTA
1 AAAAATTTAAAAACATTA
38545332 GATTGACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATTTAAAAACATTA
Found at i:38545829 original size:14 final size:14
Alignment explanation
Indices: 38545796--38545839 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
38545786 ATTTATTAGG
38545796 TTAAATTTAAA--T
1 TTAAATTTAAATTT
38545808 TTAAATTTAAATTT
1 TTAAATTTAAATTT
* *
38545822 TTACATTTTAATTT
1 TTAAATTTAAATTT
38545836 TTAA
1 TTAA
38545840 CATATTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 11 0.41
14 16 0.59
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATTTAAATTT
Found at i:38545836 original size:6 final size:6
Alignment explanation
Indices: 38545796--38545821 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
38545786 ATTTATTAGG
38545796 TTAAAT TTAAAT TTAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TTAAAT TT
38545822 TTACATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:38558583 original size:13 final size:13
Alignment explanation
Indices: 38558551--38558588 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
38558541 TCTCCAATTC
38558551 TTCT-TCTTCTTT
1 TTCTCTCTTCTTT
38558563 TTCGTCTCTTCTTT
1 TTC-TCTCTTCTTT
38558577 TTCTCTCTTCTT
1 TTCTCTCTTCTT
38558589 CTTTTATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.12
13 10 0.42
14 11 0.46
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (13 bp):
TTCTCTCTTCTTT
Found at i:38559512 original size:5 final size:5
Alignment explanation
Indices: 38559498--38559535 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
38559488 ACAACTAAAG
* *
38559498 CTTTA CTTTA ATTTA CTTTA CTTTA CTTTA ATTTA CTT
1 CTTTA CTTTA CTTTA CTTTA CTTTA CTTTA CTTTA CTT
38559536 ATGCATTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.61
Consensus pattern (5 bp):
CTTTA
Found at i:38559514 original size:10 final size:10
Alignment explanation
Indices: 38559499--38559535 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
38559489 CAACTAAAGC
38559499 TTTACTTTAA
1 TTTACTTTAA
*
38559509 TTTACTTTAC
1 TTTACTTTAA
38559519 TTTACTTTAA
1 TTTACTTTAA
38559529 TTTACTT
1 TTTACTT
38559536 ATGCATTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTACTTTAA
Found at i:38561312 original size:39 final size:37
Alignment explanation
Indices: 38561269--38561355 Score: 104
Period size: 37 Copynumber: 2.3 Consensus size: 37
38561259 TTAACTTTTT
*
38561269 ATCATATATAACATGATATTTAACATTTTATGCGTTTAA
1 ATCATATATAACATGATATTTAA-A-CTTATGCGTTTAA
* *
38561308 ATCATGT-TATATATGATATTTAAACTTATGCGTTTAA
1 ATCATATATA-ACATGATATTTAAACTTATGCGTTTAA
*
38561345 ATCATACATAA
1 ATCATATATAA
38561356 GCTTAATATC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
37 18 0.44
38 5 0.12
39 18 0.44
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (37 bp):
ATCATATATAACATGATATTTAAACTTATGCGTTTAA
Found at i:38564368 original size:8 final size:9
Alignment explanation
Indices: 38564332--38564366 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
38564322 ATTATTTTAG
38564332 AAAATTTTT
1 AAAATTTTT
38564341 AAAATTTTT
1 AAAATTTTT
38564350 AAAATTTTT
1 AAAATTTTT
38564359 AAAATTTT
1 AAAATTTT
38564367 AACTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AAAATTTTT
Found at i:38564440 original size:20 final size:20
Alignment explanation
Indices: 38564417--38564459 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
38564407 TTTATAAATA
*
38564417 TTTTGAATTTTAAAAATTAT
1 TTTTCAATTTTAAAAATTAT
* * *
38564437 TTTTCATTTTTGAAAATTGT
1 TTTTCAATTTTAAAAATTAT
38564457 TTT
1 TTT
38564460 AAATTTTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTCAATTTTAAAAATTAT
Found at i:38564867 original size:19 final size:19
Alignment explanation
Indices: 38564814--38564897 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
38564804 ATACACCTCA
*
38564814 TGTGCCAGGATGCACTTCG
1 TGTGCTAGGATGCACTTCG
* ** *
38564833 TGCG-TCAATATACACTTCG
1 TGTGCT-AGGATGCACTTCG
38564852 TGTGCTAGGATGCACTTCG
1 TGTGCTAGGATGCACTTCG
* * **
38564871 TGTGCCAGTATGCACTTTA
1 TGTGCTAGGATGCACTTCG
38564890 TGTGCTAG
1 TGTGCTAG
38564898 TTTACAATCT
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 48 0.98
20 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (19 bp):
TGTGCTAGGATGCACTTCG
Found at i:38564887 original size:38 final size:38
Alignment explanation
Indices: 38564804--38564897 Score: 116
Period size: 38 Copynumber: 2.5 Consensus size: 38
38564794 ATGCGCTCGG
* * *
38564804 ATACACCTCATGTGCCAGGATGCACTTCGTGCGTCAAT
1 ATACACTTCATGTGCTAGGATGCACTTCGTGCGCCAAT
* * *
38564842 ATACACTTCGTGTGCTAGGATGCACTTCGTGTGCCAGT
1 ATACACTTCATGTGCTAGGATGCACTTCGTGCGCCAAT
* *
38564880 ATGCACTTTATGTGCTAG
1 ATACACTTCATGTGCTAG
38564898 TTTACAATCT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (38 bp):
ATACACTTCATGTGCTAGGATGCACTTCGTGCGCCAAT
Found at i:38569980 original size:33 final size:33
Alignment explanation
Indices: 38569938--38570139 Score: 170
Period size: 33 Copynumber: 5.6 Consensus size: 33
38569928 TCCCCCAAGG
38569938 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
38569971 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-AA--T-CAT-TG---GT
*
38570013 GGTTGCTAAGTGCTGATTTCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
38570046 GGCTGCTAAGTGCTGATTCCACCGTATCTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
* *
38570088 GGTTGCTAAGTGCTGATTCGCCAAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
38570121 GGTTGCTAAGTGCTGATTC
1 GGTTGCTAAGTGCTGATTC
38570140 TACTGTATCT
Statistics
Matches: 137, Mismatches: 14, Indels: 36
0.73 0.07 0.19
Matches are distributed among these distances:
33 59 0.43
34 9 0.07
35 2 0.01
36 4 0.03
37 5 0.04
38 5 0.04
39 4 0.03
40 2 0.01
41 8 0.06
42 39 0.28
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:38570030 original size:42 final size:41
Alignment explanation
Indices: 38569971--38570183 Score: 161
Period size: 33 Copynumber: 5.5 Consensus size: 41
38569961 AATCATTGGT
38569971 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTAACTT-AATGTGAAAGG
* * *
38570013 GGTTGCTAAGTGCTGATTTC-CCG-AA--TCAT-TG---GT
1 GGTTGCTAAGTGCTGATTCCACCGTAACTTAATGTGAAAGG
* *
38570046 GGCTGCTAAGTGCTGATTCCACCGTATCTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTAACTT-AATGTGAAAGG
* * * *
38570088 GGTTGCTAAGTGCTGATT-CGCC--AA-ATCAT-TG---GT
1 GGTTGCTAAGTGCTGATTCCACCGTAACTTAATGTGAAAGG
* * *
38570121 GGTTGCTAAGTGCTGATTCTACTGTATCTTTTAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTAAC--TTAATGTGAAAGG
*
38570164 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
38570184 CCGAATCACT
Statistics
Matches: 129, Mismatches: 23, Indels: 37
0.68 0.12 0.20
Matches are distributed among these distances:
33 38 0.29
34 4 0.03
35 1 0.01
36 5 0.04
37 5 0.04
38 4 0.03
39 6 0.05
40 4 0.03
41 6 0.05
42 37 0.29
43 19 0.15
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTAACTTAATGTGAAAGG
Found at i:38570057 original size:75 final size:75
Alignment explanation
Indices: 38569934--38570217 Score: 451
Period size: 75 Copynumber: 3.8 Consensus size: 75
38569924 TGATTCCCCC
*
38569934 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
38569999 TTGAATGTGA
66 TTGAATGTGA
* *
38570009 AAGGGGTTGCTAAGTGCTGATTTCCCGAATCATTGGTGGCTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
38570074 TTGAATGTGA
66 TTGAATGTGA
* * * *
38570084 AAGGGGTTGCTAAGTGCTGATTCGCCAAATCATTGGTGGTTGCTAAGTGCTGATTCTACTGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
38570149 TTTTAATGTGA
66 -TTGAATGTGA
* * * *
38570160 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGAATCCA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCA
38570218 TCGAGTAACG
Statistics
Matches: 191, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
75 131 0.69
76 60 0.31
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTGAATGTGA
Found at i:38570131 original size:150 final size:151
Alignment explanation
Indices: 38569934--38570217 Score: 453
Period size: 151 Copynumber: 1.9 Consensus size: 151
38569924 TGATTCCCCC
*
38569934 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
* * * *
38569999 -TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTTCCCGAATCATTGGTGGCTGCTAAGTGCTGAT
66 TTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGGCTGCTAAGTGCTGAA
38570063 TCCACCGTATCTTGAATGTGA
131 TCCACCGTATCTTGAATGTGA
* * * *
38570084 AAGGGGTTGCTAAGTGCTGATTCGCCAAATCATTGGTGGTTGCTAAGTGCTGATTCTACTGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
* * *
38570149 TTTTAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGAA
66 TTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGGCTGCTAAGTGCTGAA
38570214 TCCA
131 TCCA
38570218 TCGAGTAACG
Statistics
Matches: 121, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
150 60 0.50
151 61 0.50
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (151 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
TTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGGCTGCTAAGTGCTGAA
TCCACCGTATCTTGAATGTGA
Found at i:38577387 original size:27 final size:27
Alignment explanation
Indices: 38577357--38577409 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
38577347 TTGAATATAA
* *
38577357 AAGGGGTTGCTAAGTGTTGATTCCCCC
1 AAGGGGTTGCGAAGTGCTGATTCCCCC
38577384 AAGGGGTTGCGAAGTGCTGATTCCCC
1 AAGGGGTTGCGAAGTGCTGATTCCCC
38577410 GAATCATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (27 bp):
AAGGGGTTGCGAAGTGCTGATTCCCCC
Found at i:38577432 original size:33 final size:33
Alignment explanation
Indices: 38577388--38577628 Score: 178
Period size: 33 Copynumber: 6.7 Consensus size: 33
38577378 TCCCCCAAGG
*
38577388 GGTTGCGAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
38577421 GGTTGCTAAGTGTTGATTCCACCGTAACTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-AA--T-CAT-TG---GT
*
38577463 GGTTGCTAAGTGCTGATTTCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
38577496 GGTTGCTAAGTGCTGATTCCACC-ATATCTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGA-ATC----AT-TG---GT
* *
38577538 GGTTGGTAAGTGCTGATTCCCCAAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
38577571 GGTTGCTAAGTGTTGATTCCTCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
38577604 GGTTGCCAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
38577629 GTAACAGATA
Statistics
Matches: 166, Mismatches: 21, Indels: 41
0.73 0.09 0.18
Matches are distributed among these distances:
33 85 0.51
34 11 0.07
35 2 0.01
36 4 0.02
37 5 0.03
38 5 0.03
39 4 0.02
40 2 0.01
41 8 0.05
42 40 0.24
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:38577480 original size:42 final size:42
Alignment explanation
Indices: 38577421--38577557 Score: 148
Period size: 42 Copynumber: 3.5 Consensus size: 42
38577411 AATCATTGGT
*
38577421 GGTTGCTAAGTGTTGATTCCACCGTAACTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAAAGG
* * *
38577463 GGTTGCTAAGTGCTGATTTC-CCG-AA--T-CAT-TG---GT
1 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAAAGG
* *
38577496 GGTTGCTAAGTGCTGATTCCACCATATCTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAAAGG
*
38577538 GGTTGGTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
38577558 CCAAATCATT
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
33 20 0.26
34 2 0.03
35 1 0.01
36 2 0.03
37 3 0.04
38 3 0.04
39 2 0.03
40 2 0.03
41 3 0.04
42 38 0.50
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAAAGG
Found at i:38577507 original size:75 final size:75
Alignment explanation
Indices: 38577384--38577590 Score: 351
Period size: 75 Copynumber: 2.8 Consensus size: 75
38577374 TGATTCCCCC
* *
38577384 AAGGGGTTGCGAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCATAAC
38577449 TTGAATGTGA
66 TTGAATGTGA
* * *
38577459 AAGGGGTTGCTAAGTGCTGATTTCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCATAAC
38577524 TTGAATGTGA
66 TTGAATGTGA
* *
38577534 AAGGGGTTGGTAAGTGCTGATTCCCCAAATCATTGGTGGTTGCTAAGTGTTGATTCC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCC
38577591 TCGAATCACT
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 123 1.00
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCATAAC
TTGAATGTGA
Found at i:38578992 original size:35 final size:35
Alignment explanation
Indices: 38578935--38579051 Score: 126
Period size: 35 Copynumber: 3.3 Consensus size: 35
38578925 ACTCGATATT
** *
38578935 TTGGTGTGTTTCGGTTGTATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* * *
38578970 TTGGTGTTTTTTGGAGGGATTAGCTCTTATGAGCG
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* * * *
38579005 TTGGTGTGTTTCGGATGGACTGGCTCTTATGAGAA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
*
38579040 TCTAGTGTGTTT
1 T-TGGTGTGTTT
38579052 GGGTAGTTTG
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 58 0.87
36 9 0.13
ACGTcount: A:0.15, C:0.10, G:0.32, T:0.44
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
Found at i:38585852 original size:3 final size:3
Alignment explanation
Indices: 38585846--38585926 Score: 67
Period size: 3 Copynumber: 26.3 Consensus size: 3
38585836 ACTTTTTTTA
* * *
38585846 TAT TAT T-T TAT TAT TAT CAT TAT TAT TAT ATAG TAT TAT TAAT TGAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT T-AT T-AT
* *
38585893 TAT T-T TAT TAT TTT TAT TAT TATT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
38585927 GTATTCATTA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
2 4 0.06
3 49 0.79
4 9 0.15
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:38585924 original size:10 final size:10
Alignment explanation
Indices: 38585842--38585937 Score: 70
Period size: 10 Copynumber: 9.1 Consensus size: 10
38585832 TCATACTTTT
38585842 TTTA-TATTA
1 TTTATTATTA
38585851 TTTTATTATTA
1 -TTTATTATTA
38585862 TCATTATTATTA
1 T--TTATTATTA
* *
38585874 TATAGTATTA
1 TTTATTATTA
* *
38585884 TTAATTGAATA
1 TTTATT-ATTA
38585895 TTTTATTATT-
1 -TTTATTATTA
38585905 TTTATTATTA
1 TTTATTATTA
*
38585915 TTTCTTATTA
1 TTTATTATTA
38585925 TTGTATTCATTA
1 TT-TATT-ATTA
38585937 T
1 T
38585938 AATATTGTCA
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
9 9 0.13
10 26 0.38
11 13 0.19
12 20 0.29
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (10 bp):
TTTATTATTA
Found at i:38589184 original size:43 final size:43
Alignment explanation
Indices: 38589119--38589216 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
38589109 TGCAGGGGTC
* * *
38589119 ACACGCCTGTGTGGTTAGACCGTGTGGTTCACATGGCCAAGGG
1 ACACGCCCGTGTGGTCAAACCGTGTGGTTCACATGGCCAAGGG
38589162 ACACGCCCGTGTGGTCAAACCGTGTGGTTCACATGGCCAAGGG
1 ACACGCCCGTGTGGTCAAACCGTGTGGTTCACATGGCCAAGGG
*
38589205 ACACACCCGTGT
1 ACACGCCCGTGT
38589217 CTTAGGCCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.20, C:0.28, G:0.32, T:0.20
Consensus pattern (43 bp):
ACACGCCCGTGTGGTCAAACCGTGTGGTTCACATGGCCAAGGG
Found at i:38590650 original size:24 final size:26
Alignment explanation
Indices: 38590614--38590677 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 26
38590604 ATCAGGGCCA
38590614 TATAA-CAAGAAGCTCAT-AAGAG-C
1 TATAATCAAGAAGCTCATGAAGAGCC
* *
38590637 TATAATCAGGAAGCTCGTGAAGAGCC
1 TATAATCAAGAAGCTCATGAAGAGCC
*
38590663 TTTAATCAAG-AGCTC
1 TATAATCAAGAAGCTC
38590678 CAGATAGCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 5 0.15
24 10 0.29
25 10 0.29
26 9 0.26
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (26 bp):
TATAATCAAGAAGCTCATGAAGAGCC
Found at i:38594611 original size:2 final size:2
Alignment explanation
Indices: 38594604--38594628 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38594594 ACTTCAGAGT
38594604 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 T
38594629 TTTAAAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38597449 original size:9 final size:9
Alignment explanation
Indices: 38597435--38597474 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
38597425 GGAAAGGGAG
*
38597435 GGTGGTAGT
1 GGTGGTAGA
*
38597444 GGTGGTGGA
1 GGTGGTAGA
38597453 GGTGGTAGA
1 GGTGGTAGA
*
38597462 GGTGGCAGA
1 GGTGGTAGA
38597471 GGTG
1 GGTG
38597475 TTCGTATTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.15, C:0.03, G:0.60, T:0.23
Consensus pattern (9 bp):
GGTGGTAGA
Found at i:38603213 original size:52 final size:52
Alignment explanation
Indices: 38603145--38603249 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
38603135 ATAATTGAAC
38603145 TCATATTAGTTCTAAGAAGTAAAAGTATGATTGAGAGAGTGTTAAATTGTAT
1 TCATATTAGTTCTAAGAAGTAAAAGTATGATTGAGAGAGTGTTAAATTGTAT
38603197 TCATATTAGTTCTAAGAAGTAAAAGTATGATTGAGAGAGTGTTAAATTGTAT
1 TCATATTAGTTCTAAGAAGTAAAAGTATGATTGAGAGAGTGTTAAATTGTAT
38603249 T
1 T
38603250 TTATTTATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (52 bp):
TCATATTAGTTCTAAGAAGTAAAAGTATGATTGAGAGAGTGTTAAATTGTAT
Found at i:38603297 original size:30 final size:28
Alignment explanation
Indices: 38603261--38603329 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 28
38603251 TATTTATTTA
*
38603261 TATTAAAAAATAAGTAAATTAGTTTT-TG
1 TATTAAAAAA-AAGTAAATTAATTTTGTG
38603289 TAAGTTAAATCAAAAAGTAAATTAATTTTGTG
1 T-A-TTAAA--AAAAAGTAAATTAATTTTGTG
38603321 TATTAAAAA
1 TATTAAAAA
38603330 TTTCATACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
28 3 0.09
29 1 0.03
30 10 0.29
31 15 0.43
32 6 0.17
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (28 bp):
TATTAAAAAAAAGTAAATTAATTTTGTG
Found at i:38605271 original size:6 final size:6
Alignment explanation
Indices: 38605255--38605287 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
38605245 AAATCAAGTA
38605255 ATTTT- ATTTTG ATTTTG ATTTTG ATTTTG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
38605288 GAGTTAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (6 bp):
ATTTTG
Found at i:38605523 original size:25 final size:25
Alignment explanation
Indices: 38605481--38605532 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
38605471 ATTTGTATAA
*
38605481 ACTAAATTGATTAATTGAACTAAAT
1 ACTAAATTAATTAATTGAACTAAAT
**
38605506 ACTAAATTAATTGGTTGAACTAAAT
1 ACTAAATTAATTAATTGAACTAAAT
38605531 AC
1 AC
38605533 ATTCAGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (25 bp):
ACTAAATTAATTAATTGAACTAAAT
Found at i:38607267 original size:10 final size:10
Alignment explanation
Indices: 38607244--38607277 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
38607234 TTAATGCATT
38607244 TTCAAAAGAAA
1 TTCAAAA-AAA
38607255 TTCAAAAAAA
1 TTCAAAAAAA
*
38607265 TTCCAAAAAA
1 TTCAAAAAAA
38607275 TTC
1 TTC
38607278 CATTTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (10 bp):
TTCAAAAAAA
Found at i:38608501 original size:30 final size:30
Alignment explanation
Indices: 38608465--38608533 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
38608455 ACTGTAGGGG
38608465 TCACACGGCCATGTGGCCAGGCCGTGTGAC
1 TCACACGGCCATGTGGCCAGGCCGTGTGAC
38608495 TCACACGGCCATGTGGCCAGGCCGTGTGAC
1 TCACACGGCCATGTGGCCAGGCCGTGTGAC
38608525 TCACACGGC
1 TCACACGGC
38608534 TGAGACACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.17, C:0.35, G:0.32, T:0.16
Consensus pattern (30 bp):
TCACACGGCCATGTGGCCAGGCCGTGTGAC
Found at i:38608714 original size:12 final size:12
Alignment explanation
Indices: 38608697--38608726 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
38608687 CCTCACACGC
38608697 CCGTGTGCTAGG
1 CCGTGTGCTAGG
38608709 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
38608721 TCGTGT
1 CCGTGT
38608727 AACAGCCTGA
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:0.23, G:0.40, T:0.30
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:38612466 original size:22 final size:22
Alignment explanation
Indices: 38612420--38612478 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
38612410 TTGACTTGGG
*
38612420 TATCGCAATACCTAAACAAGGA
1 TATCGCAATACCTAAACAAGAA
**
38612442 TATCGCAATACCTAAACTCGAA
1 TATCGCAATACCTAAACAAGAA
* *
38612464 TATTGCAATAGCTAA
1 TATCGCAATACCTAA
38612479 GACTGACGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (22 bp):
TATCGCAATACCTAAACAAGAA
Found at i:38612727 original size:25 final size:25
Alignment explanation
Indices: 38612671--38612727 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
38612661 TTTAGGTTAG
*
38612671 GGTTAGGGTTTTTTTTTTCATTTGTA
1 GGTTA-GGTTTTTCTTTTCATTTGTA
* *
38612697 GTTTAGGTTTTATCTTTTCCTTT-TA
1 GGTTAGGTTTT-TCTTTTCATTTGTA
38612722 GGTTAG
1 GGTTAG
38612728 ACTTTAATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.12, C:0.07, G:0.21, T:0.60
Consensus pattern (25 bp):
GGTTAGGTTTTTCTTTTCATTTGTA
Done.