Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 102 of 221
Found at i:31413989 original size:44 final size:44
Alignment explanation
Indices: 31413882--31414268 Score: 342
Period size: 44 Copynumber: 8.7 Consensus size: 44
31413872 GGCTTCTTTG
* * * *
31413882 ATCTGCTTCGCTGTCAGTACAGGAAGGTAAGATCCGCTATCTTCA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAG-GCTGGTATCTTCA
* * * *
31413927 GTATGCTTCGCTGTCAGTACAAGAAGGCAAGGCTGGTGTCTTCA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGGTATCTTCA
* * * * * *
31413971 ATCTACTTCACTATCAGTACAGGAAGGCAAGATCTGCTATCTTTA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAG-GCTGGTATCTTCA
* * * *
31414016 GTCTGCTCCGTTGTCAGTACAGGAAGGCAAGGCTGGTATCTTCG
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGGTATCTTCA
* * ** * *
31414060 ATCTGTTTCGCTGTTAGTACAGGAAGGCAAGATTTGCTATATTCA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAG-GCTGGTATCTTCA
* * * * * * * *
31414105 GTCTGCTCCACTGTTAGTACAGAAAAGCAAGGCTGGTGTCTTCG
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGGTATCTTCA
* * * **
31414149 ATCTGCTTCGCTATTAGTACAGGAAGGCAAGATCTACTATCTTCA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAG-GCTGGTATCTTCA
* * * * * **
31414194 GTCTGCTCCGCTGTCAGTATAAGAAGGCAAGGCTGGTGTCTTTG
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGGTATCTTCA
31414238 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAG
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAG
31414269 ATCCGCTATC
Statistics
Matches: 262, Mismatches: 77, Indels: 7
0.76 0.22 0.02
Matches are distributed among these distances:
44 135 0.52
45 127 0.48
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (44 bp):
ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGGTATCTTCA
Found at i:31414046 original size:89 final size:89
Alignment explanation
Indices: 31413876--31414282 Score: 555
Period size: 89 Copynumber: 4.6 Consensus size: 89
31413866 AGGATTGGCT
* * * * * *
31413876 TCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGTAAGATCCGCTATCTTCAGTATGCTTCGCTGT
1 TCTTCGATCTGCTTCGCTATCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGT
31413941 CAGTACAAGAAGGCAAGGCTGGTG
66 CAGTACAAGAAGGCAAGGCTGGTG
* * * * *
31413965 TCTTCAATCTACTTCACTATCAGTACAGGAAGGCAAGATCTGCTATCTTTAGTCTGCTCCGTTGT
1 TCTTCGATCTGCTTCGCTATCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGT
* *
31414030 CAGTACAGGAAGGCAAGGCTGGTA
66 CAGTACAAGAAGGCAAGGCTGGTG
* * * * * *
31414054 TCTTCGATCTGTTTCGCTGTTAGTACAGGAAGGCAAGATTTGCTATATTCAGTCTGCTCCACTGT
1 TCTTCGATCTGCTTCGCTATCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGT
* *
31414119 TAGTAC-AGAAAAGCAAGGCTGGTG
66 CAGTACAAG-AAGGCAAGGCTGGTG
* *
31414143 TCTTCGATCTGCTTCGCTATTAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCCGCTGT
1 TCTTCGATCTGCTTCGCTATCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGT
*
31414208 CAGTATAAGAAGGCAAGGCTGGTG
66 CAGTACAAGAAGGCAAGGCTGGTG
* * *
31414232 TCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCCGCTATCTTCA
1 TCTTCGATCTGCTTCGCTATCAGTACAGGAAGGCAAGATCTGCTATCTTCA
31414283 TTGATATTTT
Statistics
Matches: 274, Mismatches: 42, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
88 1 0.00
89 271 0.99
90 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (89 bp):
TCTTCGATCTGCTTCGCTATCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGT
CAGTACAAGAAGGCAAGGCTGGTG
Found at i:31414588 original size:24 final size:24
Alignment explanation
Indices: 31414561--31414612 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
31414551 GCCCATACTG
31414561 TAATCTTCAAAGTTCAATCCACTA
1 TAATCTTCAAAGTTCAATCCACTA
* *
31414585 TAATCTTCAAGGTTCAATCCACTG
1 TAATCTTCAAAGTTCAATCCACTA
31414609 TAAT
1 TAAT
31414613 TTTGGGACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (24 bp):
TAATCTTCAAAGTTCAATCCACTA
Found at i:31415519 original size:19 final size:19
Alignment explanation
Indices: 31415493--31415545 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
31415483 TTGGCCTCTC
31415493 CTTTTTCTTTTTTCGTTCTT
1 CTTTTTCTTTTTT-GTTCTT
*
31415513 C-TTTTCTTTTCTTTTTCTT
1 CTTTTTCTTTT-TTGTTCTT
31415532 CTTGTTTCTTTTTT
1 CTT-TTTCTTTTTT
31415546 TTCAAGTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 15 0.52
20 6 0.21
21 8 0.28
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (19 bp):
CTTTTTCTTTTTTGTTCTT
Found at i:31422478 original size:9 final size:9
Alignment explanation
Indices: 31422469--31422572 Score: 154
Period size: 9 Copynumber: 11.6 Consensus size: 9
31422459 TCAATTAGGT
*
31422469 TAATTCGGT
1 TAATTCGGG
31422478 TAATTCGGG
1 TAATTCGGG
31422487 TAATTCGGG
1 TAATTCGGG
*
31422496 TAATTCGGT
1 TAATTCGGG
31422505 TAATTCGGG
1 TAATTCGGG
**
31422514 TAATTTAGG
1 TAATTCGGG
31422523 TAATTCGGG
1 TAATTCGGG
31422532 TAATTCGGG
1 TAATTCGGG
31422541 TAATTCGGG
1 TAATTCGGG
*
31422550 TAATTCGGT
1 TAATTCGGG
*
31422559 TAATTCGGT
1 TAATTCGGG
31422568 TAATT
1 TAATT
31422573 TTTAACCAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 87 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (9 bp):
TAATTCGGG
Found at i:31422499 original size:27 final size:27
Alignment explanation
Indices: 31422469--31422572 Score: 172
Period size: 27 Copynumber: 3.9 Consensus size: 27
31422459 TCAATTAGGT
31422469 TAATTCGGTTAATTCGGGTAATTCGGG
1 TAATTCGGTTAATTCGGGTAATTCGGG
**
31422496 TAATTCGGTTAATTCGGGTAATTTAGG
1 TAATTCGGTTAATTCGGGTAATTCGGG
*
31422523 TAATTCGGGTAATTCGGGTAATTCGGG
1 TAATTCGGTTAATTCGGGTAATTCGGG
*
31422550 TAATTCGGTTAATTCGGTTAATT
1 TAATTCGGTTAATTCGGGTAATT
31422573 TTTAACCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (27 bp):
TAATTCGGTTAATTCGGGTAATTCGGG
Found at i:31429056 original size:45 final size:45
Alignment explanation
Indices: 31428978--31429072 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
31428968 TACTATGTGA
* *
31428978 ACCGAACATTATTAATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGCTGATTCC
* * * *
31429023 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCT
1 ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGCTGATTCC
31429068 ACCGA
1 ACCGA
31429073 GTATCTGTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (45 bp):
ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGCTGATTCC
Found at i:31437087 original size:89 final size:87
Alignment explanation
Indices: 31436968--31437143 Score: 246
Period size: 89 Copynumber: 2.0 Consensus size: 87
31436958 ATTAAGTCTC
* *
31436968 TTTTTTCCACTCAATTGAGCACTTGGACTTTCAAAATGTATCAAAAAGACCTTCAAACTTCTTTA
1 TTTTTTCCACTCAATTGAGCACTTGAACTTTCAAAATGTATCAAAAAGACCCTC-AA-TTCTTTA
31437033 AAAAAAAGCAATTAATCCC-CTGCT
64 AAAAAAAGCAATTAA-CCCTCTGCT
* * * * **
31437057 TTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATGTATCAAAAAGACCCTCAATTTTTTTCA
1 TTTTTTCCACTCAATTGAGCACTTGAACTTTCAAAATGTATCAAAAAGACCCTCAATTCTTTAAA
31437122 AAAAAGCAATTAACCCTCTGCT
66 AAAAAGCAATTAACCCTCTGCT
31437144 CTTATTAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
86 3 0.04
87 24 0.31
88 2 0.03
89 49 0.63
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (87 bp):
TTTTTTCCACTCAATTGAGCACTTGAACTTTCAAAATGTATCAAAAAGACCCTCAATTCTTTAAA
AAAAAGCAATTAACCCTCTGCT
Found at i:31437533 original size:56 final size:57
Alignment explanation
Indices: 31437473--31437593 Score: 156
Period size: 56 Copynumber: 2.1 Consensus size: 57
31437463 ATTTACGAAA
*
31437473 TTTATATTTCTTTACATTTTGT-ATTTCTTATGACTTTATAAAAAATTTT-AATTTTT
1 TTTATATTTCTATACATTTTGTAATTTCTTATGACTTT-TAAAAAATTTTAAATTTTT
* * * *
31437529 TTTATATTTCTATATATTTTGTAATTTTTTATGGCTTTTATAAAATTTTACAATTTTT
1 TTTATATTTCTATACATTTTGTAATTTCTTATGACTTTTAAAAAATTTTA-AATTTTT
*
31437587 TATATAT
1 TTTATAT
31437594 ATTTTACTAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
56 30 0.54
57 13 0.23
58 13 0.23
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (57 bp):
TTTATATTTCTATACATTTTGTAATTTCTTATGACTTTTAAAAAATTTTAAATTTTT
Found at i:31437816 original size:89 final size:92
Alignment explanation
Indices: 31437715--31437945 Score: 244
Period size: 89 Copynumber: 2.5 Consensus size: 92
31437705 ATTTTTAATA
*
31437715 AAAGC-AGTGGCTTAATTACTTTTTTTGAAAATATTTGAGGGTCTTTTTGATGCATTTTGAAAGT
1 AAAGCAAG-GGCTTAATTACTTTTTTTGAAAAAATTTGAGGGTCTTTTTGATGCATTTTGAAAGT
* * * *
31437779 TTAAGTACTCAATTGAGTGCAGAAAAAAG
65 TCAAGTACCCAAATGAGTCCA-AAAAAAG
* * * * * * *
31437808 -TA-C-A-GGCTTAATTGC-TTTTTT-AAAAAGGTTTAAGGTTTTTTTTTTATGCATTTTGAAAG
1 AAAGCAAGGGCTTAATTACTTTTTTTGAAAAA-ATTTGAGG-GTCTTTTTGATGCATTTTGAAAG
31437867 TTCAAGTACCCAAATGAGTCCAAAAAAAG
64 TTCAAGTACCCAAATGAGTCCAAAAAAAG
31437896 AAAAAGCAAGGGCTTAATTACTTTTTTTGAAAAAATTTGAGGG-CTTTTTG
1 --AAAGCAAGGGCTTAATTACTTTTTTTGAAAAAATTTGAGGGTCTTTTTG
31437946 CACCCTGAAG
Statistics
Matches: 109, Mismatches: 19, Indels: 20
0.74 0.13 0.14
Matches are distributed among these distances:
87 4 0.04
88 19 0.17
89 48 0.44
91 3 0.03
92 2 0.02
93 6 0.06
94 10 0.09
95 12 0.11
96 5 0.05
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.38
Consensus pattern (92 bp):
AAAGCAAGGGCTTAATTACTTTTTTTGAAAAAATTTGAGGGTCTTTTTGATGCATTTTGAAAGTT
CAAGTACCCAAATGAGTCCAAAAAAAG
Found at i:31438935 original size:19 final size:20
Alignment explanation
Indices: 31438911--31438955 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
31438901 AATAACCCAG
*
31438911 AAAATATTAATT-TTTTTAA
1 AAAATATCAATTATTTTTAA
*
31438930 AAAATATCAATTAATTTTTTA
1 AAAATATCAATT-ATTTTTAA
31438951 AAAAT
1 AAAAT
31438956 TATTTTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
21 11 0.50
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATATCAATTATTTTTAA
Found at i:31448659 original size:68 final size:68
Alignment explanation
Indices: 31448571--31449142 Score: 649
Period size: 68 Copynumber: 8.4 Consensus size: 68
31448561 GAGGTTTAAG
* * * **
31448571 GTGTAAGACCATAACTCGGCTATGGAAACATGTGGAGTCTACTAGGACATTAAACATTAGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
31448636 ATT
66 ATT
*
31448639 GTGTAAGACCATAGCCCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
31448704 ATT
66 ATT
** ** * ** * *
31448707 GTGTAAGACCATAGCTCAACTATGGCAACACATGGATTCCGCTAGGACATTAAACATTGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
31448772 ATT
66 ATT
* *
31448775 CTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
31448840 ATT
66 ATT
* ** * * ** * *
31448843 GTGTAAGATCATAGCTCGAATATGGCAACATGTAGAGCCCGCTAGGACATTAAACATGGGTTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
*
31448908 ACT
66 ATT
* * * * * *
31448911 GTGTAAGATCATAGCTTGGCTATGGAAATATGTGGAGTGTGCCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
*
31448976 AAT
66 ATT
* ** * ** *
31448979 GTGTAAGATCATAGCTCGATTACGAAAACATGTGGAGTCCACCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
31449044 ATT
66 ATT
* ** *** * * * *
31449047 GTGTAAGACCGTAATTTAACTATGGCAACATGTAGAGTCTGCCAAGACATTAAACATGGGGCTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
*
31449112 AAT
66 ATT
* * *
31449115 GTGTAAAACCATAGCTCGACTGTGGCAA
1 GTGTAAGACCATAGCTCGGCTATGGCAA
31449143 AGTATGGAGC
Statistics
Matches: 420, Mismatches: 84, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 420 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (68 bp):
GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
ATT
Found at i:31448815 original size:136 final size:136
Alignment explanation
Indices: 31448571--31449142 Score: 714
Period size: 136 Copynumber: 4.2 Consensus size: 136
31448561 GAGGTTTAAG
* * * * *
31448571 GTGTAAGACCATAACTCGGCTATGGAAACATGTGGAGTCTACTAGGACATTAAACATTAGGTTAC
1 GTGTAAGACCATAGCTCGACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
* *
31448636 ATTGTGTAAGACCATAGCCCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGT
66 ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
*
31448701 TACATT
131 TACAAT
* ** * *
31448707 GTGTAAGACCATAGCTCAACTATGGCAACACATGGATTCCGCTAGGACATTAAACATTGGGTTAC
1 GTGTAAGACCATAGCTCGACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
*
31448772 ATTCTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
66 ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
*
31448837 TACATT
131 TACAAT
* * * * *
31448843 GTGTAAGATCATAGCTCGAATATGGCAACATGTAGAGCCCGCTAGGACATTAAACA-TGGGTTTA
1 GTGTAAGACCATAGCTCGACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGG-TTA
* * * * * * * *
31448907 CACTGTGTAAGATCATAGCTTGGCTATGGAAATATGTGGAGTGTGCCAGGACATTAAACATGGGG
65 CATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGG
31448972 TTACAAT
130 TTACAAT
* * * ** * *
31448979 GTGTAAGATCATAGCTCGATTACGAAAACATGTGGAGTCCACCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
* ** *** * * *
31449044 ATTGTGTAAGACCGTAATTTAACTATGGCAACATGTAGAGTCTGCCAAGACATTAAACATGGGGC
66 ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
31449109 TACAAT
131 TACAAT
* *
31449115 GTGTAAAACCATAGCTCGACTGTGGCAA
1 GTGTAAGACCATAGCTCGACTATGGCAA
31449143 AGTATGGAGC
Statistics
Matches: 374, Mismatches: 60, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
135 4 0.01
136 367 0.98
137 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (136 bp):
GTGTAAGACCATAGCTCGACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
TACAAT
Found at i:31451506 original size:40 final size:40
Alignment explanation
Indices: 31451462--31451649 Score: 313
Period size: 40 Copynumber: 4.7 Consensus size: 40
31451452 GCAAACACAT
* * *
31451462 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
31451502 TTGCCTTCGGGTCTTAACCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
31451542 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
31451582 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
31451622 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
31451650 TCCAGTGCTC
Statistics
Matches: 142, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:31460700 original size:21 final size:19
Alignment explanation
Indices: 31460674--31460722 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
31460664 TGTAGAAGAC
31460674 TAATGATTCCCTTCAGTGGTA
1 TAATGATTCCCTT-AG-GGTA
*
31460695 TAATGATATTCCCTTTGGGTA
1 TAATG--ATTCCCTTAGGGTA
31460716 TAATGAT
1 TAATGAT
31460723 ATCCACGCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
21 14 0.56
22 1 0.04
23 8 0.32
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (19 bp):
TAATGATTCCCTTAGGGTA
Found at i:31460708 original size:23 final size:21
Alignment explanation
Indices: 31460679--31460724 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
31460669 AAGACTAATG
31460679 ATTCCCTTCAGTGGTATAATGAT
1 ATTCCCTT-AG-GGTATAATGAT
*
31460702 ATTCCCTTTGGGTATAATGAT
1 ATTCCCTTAGGGTATAATGAT
31460723 AT
1 AT
31460725 CCACGCCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 1 0.05
23 8 0.36
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (21 bp):
ATTCCCTTAGGGTATAATGAT
Found at i:31462580 original size:6 final size:6
Alignment explanation
Indices: 31462561--31462599 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
31462551 GAAATCCATG
* *
31462561 TTCATT TATCATT TTCATT TCCATT TTCATT TCCATT TT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TT
31462600 TAGAAAACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (6 bp):
TTCATT
Found at i:31462587 original size:12 final size:12
Alignment explanation
Indices: 31462555--31462599 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
31462545 TTTTTAGAAA
*
31462555 TCCATGTTCATT
1 TCCATTTTCATT
*
31462567 TATCATTTTCATT
1 T-CCATTTTCATT
31462580 TCCATTTTCATT
1 TCCATTTTCATT
31462592 TCCATTTT
1 TCCATTTT
31462600 TAGAAAACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.58
Consensus pattern (12 bp):
TCCATTTTCATT
Found at i:31462647 original size:15 final size:15
Alignment explanation
Indices: 31462627--31462656 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31462617 TTCCAAATGA
31462627 TTTCATTTTCTCCAT
1 TTTCATTTTCTCCAT
*
31462642 TTTCATTTTGTCCAT
1 TTTCATTTTCTCCAT
31462657 GCAATTCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTCATTTTCTCCAT
Found at i:31464115 original size:239 final size:239
Alignment explanation
Indices: 31463690--31464151 Score: 701
Period size: 239 Copynumber: 1.9 Consensus size: 239
31463680 GATATGAGCT
*
31463690 TGTGTCTATTCCATGTTGTATGAACCCGTAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
1 TGTGTCTATTCCATGTTGTATGAACCCATAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
* *
31463755 TGTATGTATTTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
66 TGCATATATTTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
* * * *
31463820 ATAGAAATAAATACAATATATTGCGTGAAATGCTTTTATGTATATGATGAGGAGAAAGGAGGAAT
131 ATAGAAATAAATACAATAAATTGAGTGAAATGCTTGTATGAATATGATGAGGAGAAAGGAGGAAT
*
31463885 ATACTTTGATGGGGTAGTTAAAGATAGGAACACTTTGATGAGTC
196 ATACTTTGATGGGGCAGTTAAAGATAGGAACACTTTGATGAGTC
* * * **
31463929 TGTGTCTATTTCGTGTTGTATGAACCCATAGTTGTGTATGAACCTGGTGACTGGGTATGCTTGCA
1 TGTGTCTATTCCATGTTGTATGAACCCATAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
* * * *
31463994 TGCATATATGTT-GGATGTTTATTTAGTTATAATTTGAAGTGTTAATGGGTGGTGTATTGTATGC
66 TGCATATAT-TTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGC
* * * *
31464058 TATAGAAATAAATACAATAAATTGATTGAAATGCTTGTATGAATATGATGCGGAGAAATGAGGGA
130 TATAGAAATAAATACAATAAATTGAGTGAAATGCTTGTATGAATATGATGAGGAGAAAGGAGGAA
* *
31464123 TATACTTTGATGGGGCGGTTGAAGATAGG
195 TATACTTTGATGGGGCAGTTAAAGATAGG
31464152 TGAAAGCTCG
Statistics
Matches: 199, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
239 197 0.99
240 2 0.01
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.36
Consensus pattern (239 bp):
TGTGTCTATTCCATGTTGTATGAACCCATAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
TGCATATATTTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
ATAGAAATAAATACAATAAATTGAGTGAAATGCTTGTATGAATATGATGAGGAGAAAGGAGGAAT
ATACTTTGATGGGGCAGTTAAAGATAGGAACACTTTGATGAGTC
Found at i:31466767 original size:21 final size:20
Alignment explanation
Indices: 31466722--31466767 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
31466712 TTGTTGGAAT
31466722 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
31466741 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
31466762 GGTTGA
1 GGTTGA
31466768 TTGCATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:31470724 original size:53 final size:55
Alignment explanation
Indices: 31470601--31470730 Score: 149
Period size: 53 Copynumber: 2.4 Consensus size: 55
31470591 ATTCAAAAAG
* * *
31470601 AAAATCAAAAATCAAAATAAAATGATAGAAAAAAGAAGAAGAAAAAAGAAAAATCA
1 AAAATC-AAGATCAAAATAAAATGAGAGAAAAAAGAAGAAGAAAAAAGAAAAAACA
* * * *
31470657 AAAATCAAGGTCAAAATGAAAATGAGAG-AAAAAG-A-AAGAAGAATGAAAAAAGA
1 AAAATCAAGATCAAAAT-AAAATGAGAGAAAAAAGAAGAAGAAAAAAGAAAAAACA
*
31470710 AAAATCTAGATCAAAATAAAA
1 AAAATCAAGATCAAAATAAAA
31470731 AATGACAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
52 4 0.06
53 29 0.45
54 1 0.02
55 15 0.23
56 15 0.23
ACGTcount: A:0.69, C:0.05, G:0.14, T:0.12
Consensus pattern (55 bp):
AAAATCAAGATCAAAATAAAATGAGAGAAAAAAGAAGAAGAAAAAAGAAAAAACA
Found at i:31471633 original size:14 final size:14
Alignment explanation
Indices: 31471613--31471655 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
31471603 AAAAAAAGGG
*
31471613 ATGAAAAATG-ACA
1 ATGAAAAATGAAAA
31471626 ATGAAAAATGAAAA
1 ATGAAAAATGAAAA
*
31471640 ATGAAAAGT-AAAA
1 ATGAAAAATGAAAA
31471653 ATG
1 ATG
31471656 GAGAGGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.65, C:0.02, G:0.16, T:0.16
Consensus pattern (14 bp):
ATGAAAAATGAAAA
Found at i:31471639 original size:6 final size:7
Alignment explanation
Indices: 31471613--31471655 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
31471603 AAAAAAAGGG
31471613 ATGAAAA
1 ATGAAAA
*
31471620 ATG-ACA
1 ATGAAAA
31471626 ATGAAAA
1 ATGAAAA
31471633 ATGAAAA
1 ATGAAAA
31471640 ATGAAAA
1 ATGAAAA
*
31471647 GT-AAAA
1 ATGAAAA
31471653 ATG
1 ATG
31471656 GAGAGGCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 10 0.33
7 20 0.67
ACGTcount: A:0.65, C:0.02, G:0.16, T:0.16
Consensus pattern (7 bp):
ATGAAAA
Found at i:31471652 original size:20 final size:20
Alignment explanation
Indices: 31471613--31471655 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
31471603 AAAAAAAGGG
*
31471613 ATGAAAAATGACAATGAAAA
1 ATGAAAAATGAAAATGAAAA
31471633 ATGAAAAATGAAAA-GTAAAA
1 ATGAAAAATGAAAATG-AAAA
31471653 ATG
1 ATG
31471656 GAGAGGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.65, C:0.02, G:0.16, T:0.16
Consensus pattern (20 bp):
ATGAAAAATGAAAATGAAAA
Found at i:31473052 original size:87 final size:87
Alignment explanation
Indices: 31472870--31473454 Score: 888
Period size: 87 Copynumber: 6.7 Consensus size: 87
31472860 CAGATCAGTG
* * *
31472870 AAGATAGCAGATCTTGCCTTCTTGCATTGACAGCGAAGTAGATCG-AAA-AAAGCCTTACCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
31472933 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
*
31472955 AAGATAGCAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
31473020 TCGGTTGCAATGGAGCTAGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
*
31473042 AAGATGGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
31473107 TCGGTTGCAGTAGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* * * * *
31473129 AAGATGGCAGATATTGTCTTCTTGCATTGACAACGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
31473194 TCAGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
*
31473216 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
31473281 TCGGTTGTAGTGGAGCTGGTCA
66 TCGGTTGCAGTGGAGCTGGTTA
* * * *
31473303 AAGATGGCAGATCTTGCCTTCCTACATTGATAGCGAAGCAGATCGAAAACAAAACCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
31473368 TCGGTTGCAGTAGAGCAGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* * * *
31473390 AAGATAGCAGATCTTGCCTTCCAGCACTGACAGCGAAGCAAATCGAAGATAC-CAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTC
31473454 C
64 C
31473455 CAAGTAGTGC
Statistics
Matches: 453, Mismatches: 43, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
85 42 0.09
86 3 0.01
87 394 0.87
88 12 0.03
89 2 0.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
TCGGTTGCAGTGGAGCTGGTTA
Found at i:31473651 original size:100 final size:99
Alignment explanation
Indices: 31473473--31473852 Score: 487
Period size: 100 Copynumber: 3.8 Consensus size: 99
31473463 GCAATAGAAT
* * * * *
31473473 AGATTAAAGCCACGA-CGGCGTATCTTGCTTCCCCAACATTGCAGTTAAGAAGACTAAAGCCACA
1 AGATTAAAGCCA-AATCGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCACA
* * *
31473537 GCGGCGAGTGTTACTTCCCTGGCGATGCAGTGGAAC
65 TC-GCGAATCTTACTTCCCTGGCGATGCAGTGGAAC
* *
31473573 AGATTAAAGCCATATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCACAT
1 AGATTAAAGCCAAATCGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCACAT
31473638 CGTCGAATCTTACTTCCCTGGCGATGCAGTGGAAC
66 CG-CGAATCTTACTTCCCTGGCGATGCAGTGGAAC
* * *
31473673 AGATTAAAACCACAA-CGGCGAATCTCGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
1 AGATTAAAGCCA-AATCGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCAC-
* * *
31473737 ATAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAC
64 ATCGCGAATCTTACTTCCCTGGCGATGCAGTGGAAC
* * *
31473773 AGATTAAAGCCACAAT-GGCAAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTGAAGCTACA
1 AGATTAAAGCCA-AATCGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCAC-
* *
31473837 ATGGCAAATCTTACTT
64 ATCGCGAATCTTACTT
31473853 TCCAAAAGTT
Statistics
Matches: 252, Mismatches: 23, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
99 2 0.01
100 246 0.98
101 4 0.02
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (99 bp):
AGATTAAAGCCAAATCGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCACAT
CGCGAATCTTACTTCCCTGGCGATGCAGTGGAAC
Found at i:31473838 original size:50 final size:50
Alignment explanation
Indices: 31473473--31473848 Score: 310
Period size: 50 Copynumber: 7.5 Consensus size: 50
31473463 GCAATAGAAT
* * * * *
31473473 AGATTAAAGCCACGACGGCGTATCTTGCTTCCCCAACATTGCAGTTAAGA
1 AGATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* ** * * * * * ** *
31473523 AGACTAAAGCCACAGCGGCGAGTGTTACTTCCCTGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAATGGCGAATCTTGCTTCCCCGAC-ATTGCAGTTAAAA
* *
31473573 AGATTAAAGCCA-TATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAAT-GGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * ** *
31473623 AGATTAAAGCCAC-ATCGTCGAATCTTACTTCCCTGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAAT-GGCGAATCTTGCTTCCCCGAC-ATTGCAGTTAAAA
* * *
31473673 AGATTAAAACCACAACGGCGAATCTCGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * ** ** *
31473723 AGATTAAAGCTACAATAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
*
31473773 AGATTAAAGCCACAATGGCAAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * *
31473823 AGATTGAAGCTACAATGGCAAATCTT
1 AGATTAAAGCCACAATGGCGAATCTT
31473849 ACTTTCCAAA
Statistics
Matches: 248, Mismatches: 71, Indels: 14
0.74 0.21 0.04
Matches are distributed among these distances:
49 2 0.01
50 243 0.98
51 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:31474238 original size:15 final size:15
Alignment explanation
Indices: 31474214--31474273 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
31474204 ATTACATTAG
31474214 CCCAACTAGCCTAAA
1 CCCAACTAGCCTAAA
* *
31474229 CCCAATTAGCCTAAG
1 CCCAACTAGCCTAAA
* *
31474244 CCCAA-TACCCT-AG
1 CCCAACTAGCCTAAA
31474257 CCCAACTAGCCTAAA
1 CCCAACTAGCCTAAA
31474272 CC
1 CC
31474274 AGAAATTAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 7 0.18
14 10 0.26
15 21 0.55
ACGTcount: A:0.35, C:0.42, G:0.08, T:0.15
Consensus pattern (15 bp):
CCCAACTAGCCTAAA
Found at i:31475410 original size:20 final size:20
Alignment explanation
Indices: 31475387--31475435 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
31475377 TTGTTTAAGT
* *
31475387 TTAATATATTTTTAATTTTA
1 TTAATATATTTTCAATATTA
31475407 TTAATACTA-TTTCAATATTA
1 TTAATA-TATTTTCAATATTA
31475427 -TAATATATT
1 TTAATATATT
31475436 ATTATTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 15 0.60
21 2 0.08
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATATATTTTCAATATTA
Found at i:31483605 original size:22 final size:23
Alignment explanation
Indices: 31483559--31483608 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
31483549 TGTTTGTTTG
*
31483559 ATAAAGAAATATTACTATTTTTT
1 ATAAAGAAATATTACTAGTTTTT
* *
31483582 ATAAAGTAGTATTACT-GTTTTT
1 ATAAAGAAATATTACTAGTTTTT
31483604 ATAAA
1 ATAAA
31483609 ATATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (23 bp):
ATAAAGAAATATTACTAGTTTTT
Found at i:31485370 original size:17 final size:18
Alignment explanation
Indices: 31485348--31485387 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
31485338 TCCATTAAAA
31485348 TATTATTTT-TTAAATTT
1 TATTATTTTATTAAATTT
* *
31485365 TATTATTTTATTTATTTT
1 TATTATTTTATTAAATTT
31485383 TATTA
1 TATTA
31485388 AAATATTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTATTTTATTAAATTT
Found at i:31485479 original size:22 final size:22
Alignment explanation
Indices: 31485454--31485496 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31485444 AACATTTTAA
*
31485454 ATATTACATGTACCTTTTATTG
1 ATATTACATGTACATTTTATTG
31485476 ATATTACATGTACATTTTATT
1 ATATTACATGTACATTTTATT
31485497 AATAGACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (22 bp):
ATATTACATGTACATTTTATTG
Found at i:31486344 original size:19 final size:17
Alignment explanation
Indices: 31486309--31486350 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
31486299 GGTTTTTCAC
31486309 AAAA-ATATATATATTA
1 AAAATATATATATATTA
31486325 AAAATATATATTATATTTA
1 AAAATATATA-TATA-TTA
31486344 AAAATAT
1 AAAATAT
31486351 TTATCTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.17
17 5 0.22
18 4 0.17
19 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATATATATATATTA
Found at i:31486638 original size:16 final size:16
Alignment explanation
Indices: 31486608--31486658 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
31486598 GGTTCATTGG
31486608 AATGGAATA-AGGTTGT
1 AATGGAATAGA-GTTGT
*
31486624 AATTGAATAGAGTTGT
1 AATGGAATAGAGTTGT
*
31486640 AATGGAATAGAGCTGT
1 AATGGAATAGAGTTGT
31486656 AAT
1 AAT
31486659 CAGTAATTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 30 0.97
17 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.31
Consensus pattern (16 bp):
AATGGAATAGAGTTGT
Found at i:31486848 original size:20 final size:21
Alignment explanation
Indices: 31486823--31486870 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
31486813 GTTATTAAAT
* *
31486823 TTTAATATAATTAAAT-ATAA
1 TTTAATAAAAATAAATAATAA
31486843 TTTAATAAAAATAAATAAATAA
1 TTTAATAAAAATAAAT-AATAA
31486865 TTTAAT
1 TTTAAT
31486871 CATATTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.58
22 10 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAATAAAAATAAATAATAA
Found at i:31486943 original size:24 final size:24
Alignment explanation
Indices: 31486888--31486946 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
31486878 TAGTATACTT
*
31486888 ATTACTAA-ATATAAGTTAATAAA
1 ATTAATAATATATAAGTTAATAAA
* * *
31486911 AATAATAATATATAATTTAATAAC
1 ATTAATAATATATAAGTTAATAAA
*
31486935 ATTATTAATATA
1 ATTAATAATATA
31486947 ATTATTTGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (24 bp):
ATTAATAATATATAAGTTAATAAA
Found at i:31491525 original size:30 final size:30
Alignment explanation
Indices: 31491489--31491549 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
31491479 ATTTTTGAAT
31491489 TCCTTGAACTTTTCAAGGGACTCAGACTTA
1 TCCTTGAACTTTTCAAGGGACTCAGACTTA
*
31491519 TCCTTGAACTTTTCAAGGGACTTAGACTTA
1 TCCTTGAACTTTTCAAGGGACTCAGACTTA
31491549 T
1 T
31491550 GGCGTATGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (30 bp):
TCCTTGAACTTTTCAAGGGACTCAGACTTA
Found at i:31493831 original size:12 final size:13
Alignment explanation
Indices: 31493814--31493842 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
31493804 CTCATACATG
31493814 AATAAATAAA-GC
1 AATAAATAAATGC
31493826 AATAAATAAATGC
1 AATAAATAAATGC
31493839 AATA
1 AATA
31493843 GTTATAGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:31500959 original size:19 final size:19
Alignment explanation
Indices: 31500912--31500963 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
31500902 GATTATGTAA
31500912 TCTTAGAGTTCTAA--GTG
1 TCTTAGAGTTCTAATTGTG
* *
31500929 T-ATACAGCTTCTAATTGTG
1 TCTTAGAG-TTCTAATTGTG
31500948 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
31500964 ATATACAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
19 12 0.44
20 4 0.15
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.44
Consensus pattern (19 bp):
TCTTAGAGTTCTAATTGTG
Found at i:31506003 original size:19 final size:19
Alignment explanation
Indices: 31505953--31506009 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
31505943 TGATTATGTA
31505953 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
31505972 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
31505989 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
31506008 AT
1 AT
31506010 ACAACTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:31507843 original size:19 final size:18
Alignment explanation
Indices: 31507819--31507881 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 18
31507809 CCCTAGTTCC
31507819 TTTTCTTTTCGTTATTCTT
1 TTTTCTTTTC-TTATTCTT
31507838 TTTTC-TTTCTT-TTCTT
1 TTTTCTTTTCTTATTCTT
* *
31507854 TTTTGTTTTCATACTTCTT
1 TTTTCTTTTCTTA-TTCTT
*
31507873 TTTCCTTTT
1 TTTTCTTTT
31507882 TTCTTTTATC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
16 9 0.24
17 7 0.19
18 4 0.11
19 17 0.46
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTCTTTTCTTATTCTT
Found at i:31507863 original size:35 final size:33
Alignment explanation
Indices: 31507819--31507888 Score: 79
Period size: 35 Copynumber: 2.1 Consensus size: 33
31507809 CCCTAGTTCC
* *
31507819 TTTTCTTTTCGTTA-TTCTTTTTTCTTTCTTTTCTT
1 TTTTCTTTTC-ATACTTC-TTTTTCCTT-TTTTCTT
*
31507854 TTTTGTTTTCATACTTCTTTTTCCTTTTTTCTT
1 TTTTCTTTTCATACTTCTTTTTCCTTTTTTCTT
31507887 TT
1 TT
31507889 ATCAATCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
33 9 0.29
34 10 0.32
35 12 0.39
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (33 bp):
TTTTCTTTTCATACTTCTTTTTCCTTTTTTCTT
Found at i:31509900 original size:9 final size:9
Alignment explanation
Indices: 31509864--31509968 Score: 67
Period size: 9 Copynumber: 11.6 Consensus size: 9
31509854 AATATGTGGC
31509864 AAAAATTAT
1 AAAAATTAT
*
31509873 AAAAA--AG
1 AAAAATTAT
*
31509880 AAAAATAAAT
1 AAAAAT-TAT
31509890 AAAAATTAT
1 AAAAATTAT
31509899 AAAAATTATT
1 AAAAATTA-T
**
31509909 AAATTTTAAT
1 AAAAATT-AT
31509919 AAAAA-TAT
1 AAAAATTAT
31509927 AAAAA-TATT
1 AAAAATTA-T
31509936 AAAAATTATAT
1 AAAAA-T-TAT
**
31509947 AAAAATCGT
1 AAAAATTAT
31509956 AAAAA-TAT
1 AAAAATTAT
31509964 AAAAA
1 AAAAA
31509969 AATATAAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
7 6 0.08
8 15 0.20
9 28 0.37
10 18 0.24
11 7 0.09
12 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:31509932 original size:20 final size:20
Alignment explanation
Indices: 31509880--31509982 Score: 69
Period size: 20 Copynumber: 5.4 Consensus size: 20
31509870 TATAAAAAAG
31509880 AAAAATAA-ATAAAAAT-TAT
1 AAAAATAATATAAAAATAT-T
* *
31509899 AAAAAT--TAT-TAAATTTT
1 AAAAATAATATAAAAATATT
31509916 AATAAA-AATATAAAAATATT
1 AA-AAATAATATAAAAATATT
* **
31509936 AAAAATTATATAAAAATCGT
1 AAAAATAATATAAAAATATT
*
31509956 AAAAAT-ATAAAAAAATA-T
1 AAAAATAATATAAAAATATT
31509974 AAAATATAA
1 AAAA-ATAA
31509983 AATTGTAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
17 7 0.10
18 11 0.16
19 23 0.34
20 26 0.39
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (20 bp):
AAAAATAATATAAAAATATT
Found at i:31509958 original size:29 final size:27
Alignment explanation
Indices: 31509864--31509984 Score: 99
Period size: 28 Copynumber: 4.4 Consensus size: 27
31509854 AATATGTGGC
* *
31509864 AAAAATTATAAAAA-A-GAAAAATAAAT
1 AAAAA-TATAAAAATATTAAAAATATAT
* *
31509890 AAAAATTATAAAAATTATT-AAATTTTAAT
1 AAAAA-TATAAAAA-TATTAAAAATAT-AT
31509919 AAAAATATAAAAATATTAAAAATTATAT
1 AAAAATATAAAAATATTAAAAA-TATAT
* *
31509947 AAAAATCGTAAAAATA-TAAAAAAATAT
1 AAAAAT-ATAAAAATATTAAAAATATAT
31509974 -AAAATATAAAA
1 AAAAATATAAAA
31509985 TTGTAAAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 15
0.77 0.09 0.15
Matches are distributed among these distances:
25 5 0.06
26 19 0.24
27 8 0.10
28 30 0.38
29 17 0.22
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAAATATAAAAATATTAAAAATATAT
Found at i:31509966 original size:8 final size:8
Alignment explanation
Indices: 31509917--31509984 Score: 64
Period size: 8 Copynumber: 7.8 Consensus size: 8
31509907 TTAAATTTTA
31509917 ATAAAAAT
1 ATAAAAAT
31509925 ATAAAAAT
1 ATAAAAAT
31509933 ATTAAAAATTAT
1 A-T-AAAA--AT
31509945 ATAAAAAT
1 ATAAAAAT
*
31509953 CGTAAAAAT
1 -ATAAAAAT
*
31509962 ATAAAAAA
1 ATAAAAAT
31509970 ATATAAAAT
1 ATA-AAAAT
31509979 ATAAAA
1 ATAAAA
31509985 TTGTAAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 23 0.46
9 15 0.30
10 8 0.16
11 1 0.02
12 3 0.06
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (8 bp):
ATAAAAAT
Found at i:31509969 original size:9 final size:9
Alignment explanation
Indices: 31509919--31509984 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
31509909 AAATTTTAAT
31509919 AAAAATAT-
1 AAAAATATA
31509927 AAAAATATTA
1 AAAAATA-TA
*
31509937 AAAATTATA
1 AAAAATATA
*
31509946 TAAAAATCGT-
1 -AAAAAT-ATA
31509956 AAAAATATA
1 AAAAATATA
31509965 AAAAA-ATA
1 AAAAATATA
*
31509973 TAAAATATA
1 AAAAATATA
31509982 AAA
1 AAA
31509985 TTGTAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
8 15 0.33
9 19 0.41
10 11 0.24
11 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (9 bp):
AAAAATATA
Found at i:31509977 original size:17 final size:18
Alignment explanation
Indices: 31509917--31509984 Score: 77
Period size: 17 Copynumber: 3.8 Consensus size: 18
31509907 TTAAATTTTA
*
31509917 ATAAAAATATAAAAATAT
1 ATAAAAATATAAAAAAAT
*
31509935 -TAAAAATTATATAAAAAT
1 ATAAAAA-TATAAAAAAAT
*
31509953 CGTAAAAATATAAAAAAAT
1 -ATAAAAATATAAAAAAAT
31509972 AT-AAAATATAAAA
1 ATAAAAATATAAAA
31509985 TTGTAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 17 0.40
18 10 0.23
19 10 0.23
20 6 0.14
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (18 bp):
ATAAAAATATAAAAAAAT
Found at i:31512212 original size:229 final size:228
Alignment explanation
Indices: 31511811--31512260 Score: 846
Period size: 229 Copynumber: 2.0 Consensus size: 228
31511801 AAACACAAGC
31511811 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
1 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
*
31511876 CTAAATTATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
66 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
*
31511941 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTGTTTCT
131 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTA-TTTTATTTCT
31512006 ATATATTCCCTTTTATTCACATTTTATCATTTGA
195 ATATATTCCCTTTTATTCACATTTTATCATTTGA
*
31512040 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGATTTGAATGCCATTGGTGAAAAA
1 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
* *
31512105 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCGAGGTTGTCTTGAAAATTTCC
66 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
31512170 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTATTTCTA
131 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTATTTCTA
31512235 TATATTCCCTTTTATTCACATTTTAT
196 TATATTCCCTTTTATTCACATTTTAT
31512261 TTAAGAAATT
Statistics
Matches: 216, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
228 36 0.17
229 180 0.83
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (228 bp):
ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTATTTCTA
TATATTCCCTTTTATTCACATTTTATCATTTGA
Found at i:31515698 original size:18 final size:18
Alignment explanation
Indices: 31515655--31515700 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
31515645 CTACTAGATC
*
31515655 TTAATTTTTTTTATATAA
1 TTAATTATTTTTATATAA
*
31515673 TTACTTATTTTTAT-TAA
1 TTAATTATTTTTATATAA
31515690 TTTAATTATTT
1 -TTAATTATTT
31515701 ACAAACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAATTATTTTTATATAA
Found at i:31521685 original size:9 final size:9
Alignment explanation
Indices: 31521671--31521699 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
31521661 TTGGTTATAA
31521671 TTACAGTAT
1 TTACAGTAT
31521680 TTACAGTAT
1 TTACAGTAT
31521689 TTACAGTAT
1 TTACAGTAT
31521698 TT
1 TT
31521700 GTGATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTACAGTAT
Found at i:31522352 original size:19 final size:19
Alignment explanation
Indices: 31522328--31522427 Score: 107
Period size: 19 Copynumber: 5.1 Consensus size: 19
31522318 TTTACATTAT
31522328 AATTATAATTAACACTAAA
1 AATTATAATTAACACTAAA
31522347 AATTATAATTAACACTAAA
1 AATTATAATTAACACTAAA
*
31522366 AA-T-TAATCAA-ATGCTACAA
1 AATTATAATTAACA--CTA-AA
*
31522385 CAATTATAATTAACATTACAAA
1 -AATTATAATTAACACT--AAA
31522407 AATTATAATTAACACTAAA
1 AATTATAATTAACACTAAA
31522426 AA
1 AA
31522428 AAGAAAGTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.01
17 6 0.09
18 4 0.06
19 28 0.41
20 2 0.03
21 17 0.25
22 8 0.12
23 2 0.03
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (19 bp):
AATTATAATTAACACTAAA
Found at i:31522429 original size:21 final size:20
Alignment explanation
Indices: 31522328--31522428 Score: 104
Period size: 21 Copynumber: 5.1 Consensus size: 20
31522318 TTTACATTAT
31522328 AATTATAATTAACACT-AAA
1 AATTATAATTAACACTAAAA
31522347 AATTATAATTAACACT-AAA
1 AATTATAATTAACACTAAAA
* *
31522366 AA-T-TAATCAA-ATGCTACAAC
1 AATTATAATTAACA--CTA-AAA
*
31522386 AATTATAATTAACATTACAAA
1 AATTATAATTAACACTA-AAA
31522407 AATTATAATTAACACTAAAA
1 AATTATAATTAACACTAAAA
31522427 AA
1 AA
31522429 AGAAAGTAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.01
17 6 0.09
18 3 0.04
19 21 0.30
20 9 0.13
21 22 0.32
22 6 0.09
23 1 0.01
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (20 bp):
AATTATAATTAACACTAAAA
Found at i:31524480 original size:49 final size:50
Alignment explanation
Indices: 31524423--31524522 Score: 157
Period size: 49 Copynumber: 2.0 Consensus size: 50
31524413 CATGTGTTAT
* ** *
31524423 AATTTTATAAAGTGTTGAGGTTTTGATTCATGATATTGAACTT-AATTTA
1 AATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATTTA
31524472 AATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATTTA
1 AATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATTTA
31524522 A
1 A
31524523 TTTGTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 39 0.85
50 7 0.15
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (50 bp):
AATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATTTA
Found at i:31525211 original size:51 final size:51
Alignment explanation
Indices: 31525151--31525251 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
31525141 AAGGTGGTGA
*
31525151 CATTGGGAGCATGTAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAAGG
1 CATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAAGG
31525202 CATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAAG
1 CATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAAG
31525252 TATCTCATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.33
Consensus pattern (51 bp):
CATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAAGG
Found at i:31527806 original size:29 final size:28
Alignment explanation
Indices: 31527773--31527836 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
31527763 TATTTGTGAG
** *
31527773 AAATTAAGTAAATCAAAATTTCATGTATA
1 AAATTAACAAAATC-AAAGTTCATGTATA
*
31527802 AAATTTCACAAAATCAAAGTTCATGTATA
1 AAA-TTAACAAAATCAAAGTTCATGTATA
31527831 AAATTA
1 AAATTA
31527837 TATATTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.07
29 19 0.66
30 8 0.28
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (28 bp):
AAATTAACAAAATCAAAGTTCATGTATA
Found at i:31527918 original size:20 final size:20
Alignment explanation
Indices: 31527893--31527947 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
31527883 CATAAACATT
*
31527893 AATAATTTTGTAAGAGATTC
1 AATAATTTTGTAAAAGATTC
* *
31527913 AATAATTCTGTAAAAGATTT
1 AATAATTTTGTAAAAGATTC
*
31527933 AGTAATTTTGTAAAA
1 AATAATTTTGTAAAA
31527948 AAAATAGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.40
Consensus pattern (20 bp):
AATAATTTTGTAAAAGATTC
Found at i:31542154 original size:17 final size:17
Alignment explanation
Indices: 31542113--31542156 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
31542103 CTACTAGATC
*
31542113 TTAATTTTTTTATATAA
1 TTAATTATTTTATATAA
*
31542130 TTACTTATTTTAT-TAA
1 TTAATTATTTTATATAA
31542146 TTTAATTATTT
1 -TTAATTATTT
31542157 ACAAACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTATTTTATATAA
Found at i:31548057 original size:9 final size:9
Alignment explanation
Indices: 31548043--31548071 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
31548033 TTGGTTATAA
31548043 TTACAGTAT
1 TTACAGTAT
31548052 TTACAGTAT
1 TTACAGTAT
31548061 TTACAGTAT
1 TTACAGTAT
31548070 TT
1 TT
31548072 GTGATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTACAGTAT
Found at i:31548724 original size:19 final size:19
Alignment explanation
Indices: 31548700--31548799 Score: 107
Period size: 19 Copynumber: 5.1 Consensus size: 19
31548690 TTTACATTAT
31548700 AATTATAATTAACACTAAA
1 AATTATAATTAACACTAAA
31548719 AATTATAATTAACACTAAA
1 AATTATAATTAACACTAAA
*
31548738 AA-T-TAATCAA-ATGCTACAA
1 AATTATAATTAACA--CTA-AA
*
31548757 CAATTATAATTAACATTACAAA
1 -AATTATAATTAACACT--AAA
31548779 AATTATAATTAACACTAAA
1 AATTATAATTAACACTAAA
31548798 AA
1 AA
31548800 AGAAAGTAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.01
17 6 0.09
18 4 0.06
19 28 0.41
20 2 0.03
21 17 0.25
22 8 0.12
23 2 0.03
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (19 bp):
AATTATAATTAACACTAAA
Found at i:31548800 original size:21 final size:20
Alignment explanation
Indices: 31548700--31548800 Score: 104
Period size: 21 Copynumber: 5.1 Consensus size: 20
31548690 TTTACATTAT
31548700 AATTATAATTAACACT-AAA
1 AATTATAATTAACACTAAAA
31548719 AATTATAATTAACACT-AAA
1 AATTATAATTAACACTAAAA
* *
31548738 AA-T-TAATCAA-ATGCTACAAC
1 AATTATAATTAACA--CTA-AAA
*
31548758 AATTATAATTAACATTACAAA
1 AATTATAATTAACACTA-AAA
31548779 AATTATAATTAACACTAAAA
1 AATTATAATTAACACTAAAA
31548799 AA
1 AA
31548801 GAAAGTAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.01
17 6 0.09
18 3 0.04
19 21 0.30
20 9 0.13
21 22 0.32
22 6 0.09
23 1 0.01
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (20 bp):
AATTATAATTAACACTAAAA
Found at i:31550848 original size:49 final size:50
Alignment explanation
Indices: 31550791--31550890 Score: 157
Period size: 49 Copynumber: 2.0 Consensus size: 50
31550781 CATGTGTTAT
* ** *
31550791 AATTTTATAAAGTGTTGAGGTTTTGATTCATGATATTGAACTT-AATTTA
1 AATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATTTA
31550840 AATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATTTA
1 AATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATTTA
31550890 A
1 A
31550891 TTTGTTTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 39 0.85
50 7 0.15
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (50 bp):
AATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAAATTTA
Found at i:31551578 original size:51 final size:51
Alignment explanation
Indices: 31551518--31551618 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
31551508 AAGGTGGTGA
*
31551518 CATTGGGAGCATGTAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAAGG
1 CATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAAGG
31551569 CATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAAG
1 CATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAAG
31551619 TATCTCATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.33
Consensus pattern (51 bp):
CATTGGGAGCATGGAATGCGTGAAGAAATTTCTTCATGTTTCCATTAAAGG
Found at i:31554285 original size:29 final size:28
Alignment explanation
Indices: 31554252--31554315 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
31554242 TATTTGTGAG
** *
31554252 AAATTAAGTAAATCAAAATTTCATGTATA
1 AAATTAACAAAATC-AAAGTTCATGTATA
*
31554281 AAATTTCACAAAATCAAAGTTCATGTATA
1 AAA-TTAACAAAATCAAAGTTCATGTATA
31554310 AAATTA
1 AAATTA
31554316 TATATTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.07
29 19 0.66
30 8 0.28
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (28 bp):
AAATTAACAAAATCAAAGTTCATGTATA
Found at i:31554397 original size:20 final size:20
Alignment explanation
Indices: 31554372--31554426 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
31554362 CATAAACATT
*
31554372 AATAATTTTGTAAGAGATTC
1 AATAATTTTGTAAAAGATTC
* *
31554392 AATAATTCTGTAAAAGATTT
1 AATAATTTTGTAAAAGATTC
*
31554412 AGTAATTTTGTAAAA
1 AATAATTTTGTAAAA
31554427 AAAAATAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.40
Consensus pattern (20 bp):
AATAATTTTGTAAAAGATTC
Found at i:31555742 original size:20 final size:21
Alignment explanation
Indices: 31555704--31555746 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
31555694 TATTATTGTT
*
31555704 ACCCATGATAATTTGGACTTA
1 ACCCATGATAATTTCGACTTA
*
31555725 ACCCATTAT-ATTTCGACTTA
1 ACCCATGATAATTTCGACTTA
31555745 AC
1 AC
31555747 ATGTAATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (21 bp):
ACCCATGATAATTTCGACTTA
Found at i:31556289 original size:13 final size:12
Alignment explanation
Indices: 31556267--31556305 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
31556257 ATTGTTGTTG
31556267 TTTGATTTAAAT
1 TTTGATTTAAAT
31556279 TTTGAATTTAAAT
1 TTTG-ATTTAAAT
31556292 TTT-ATTTAGAAT
1 TTTGATTTA-AAT
31556304 TT
1 TT
31556306 ATTTTCACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.20
12 9 0.36
13 11 0.44
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (12 bp):
TTTGATTTAAAT
Found at i:31557145 original size:22 final size:23
Alignment explanation
Indices: 31557105--31557149 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
31557095 CTTAGGCCCC
31557105 GACTTATTTTTCATTTGTTGAAAAG
1 GACTTATTTTTCA-TTGTT-AAAAG
31557130 GACTT-TTTTTCA-TGTTAAAA
1 GACTTATTTTTCATTGTTAAAA
31557150 CTTATTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
24 7 0.35
25 5 0.25
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (23 bp):
GACTTATTTTTCATTGTTAAAAG
Found at i:31561087 original size:40 final size:41
Alignment explanation
Indices: 31561003--31561110 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 41
31560993 GAGATTGGAG
* *
31561003 GCATGTTAAACATGCTATTGAATT-AAATATGTTACCTTAA
1 GCATGTAAAACATGCCATTGAATTGAAATATGTTACCTTAA
* *
31561043 GCATG-AGATACATGCCATTGAATTGAAAT-TGTTA-CTGTAG
1 GCATGTA-AAACATGCCATTGAATTGAAATATGTTACCT-TAA
* *
31561083 GCATGTAAAACATGCCACTGTATTGAAA
1 GCATGTAAAACATGCCATTGAATTGAAA
31561111 CTGAACTGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 2 0.04
40 50 0.88
41 5 0.09
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (41 bp):
GCATGTAAAACATGCCATTGAATTGAAATATGTTACCTTAA
Found at i:31562661 original size:20 final size:21
Alignment explanation
Indices: 31562623--31562662 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
31562613 TGGCATGCTT
31562623 AGTGATGGTATGAAATGGTTA
1 AGTGATGGTATGAAATGGTTA
31562644 AGTGAGTGGT-TG-AATGGTT
1 AGTGA-TGGTATGAAATGGTT
31562663 TGAGTTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.35
Consensus pattern (21 bp):
AGTGATGGTATGAAATGGTTA
Found at i:31565130 original size:15 final size:15
Alignment explanation
Indices: 31565110--31565138 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31565100 ACATGCCTTT
31565110 AGAAAAGAAAGAAAA
1 AGAAAAGAAAGAAAA
31565125 AGAAAAGAAAGAAA
1 AGAAAAGAAAGAAA
31565139 GACAAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAGAAAA
Found at i:31565853 original size:25 final size:25
Alignment explanation
Indices: 31565805--31565853 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
31565795 CATAATTGAA
* * *
31565805 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
31565830 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
31565854 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:31566360 original size:20 final size:19
Alignment explanation
Indices: 31566321--31566366 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
31566311 GAGAAACGAT
*
31566321 TATGAGATGAGAAATGAGA
1 TATGAAATGAGAAATGAGA
*
31566340 TATGAAATGATGAATTGAGA
1 TATGAAATGA-GAAATGAGA
31566360 TATGAAA
1 TATGAAA
31566367 CTTGAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (19 bp):
TATGAAATGAGAAATGAGA
Found at i:31571240 original size:20 final size:20
Alignment explanation
Indices: 31571215--31571260 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
31571205 GAACTTTTCA
31571215 ATTTTATGAACCGTTAATTT
1 ATTTTATGAACCGTTAATTT
31571235 ATTTTATGAACCGTTAATTT
1 ATTTTATGAACCGTTAATTT
31571255 ATTTTA
1 ATTTTA
31571261 CTTCTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (20 bp):
ATTTTATGAACCGTTAATTT
Found at i:31572520 original size:20 final size:20
Alignment explanation
Indices: 31572495--31572535 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
31572485 TCGAGGAAGG
31572495 AACAAGG-CGATTCAAGCAAA
1 AACAAGGACGA-TCAAGCAAA
*
31572515 AACAAGGACGATGAAGCAAA
1 AACAAGGACGATCAAGCAAA
31572535 A
1 A
31572536 GATGGGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.54, C:0.17, G:0.22, T:0.07
Consensus pattern (20 bp):
AACAAGGACGATCAAGCAAA
Found at i:31577232 original size:37 final size:37
Alignment explanation
Indices: 31577141--31577246 Score: 149
Period size: 37 Copynumber: 2.9 Consensus size: 37
31577131 TTGAAAGTAT
* *
31577141 GCTCAATCGAGCAAATCCTACCGTTATACTGAATGAA
1 GCTCAATCGAGCAAATCTTACTGTTATACTGAATGAA
* *
31577178 TCTCAATCGAGCAAATCTTACTGTTATATTGAATGAA
1 GCTCAATCGAGCAAATCTTACTGTTATACTGAATGAA
* * *
31577215 GCTCAATCAAGCAAATCTTACTTTTACACTGA
1 GCTCAATCGAGCAAATCTTACTGTTATACTGA
31577247 GGGAAACTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (37 bp):
GCTCAATCGAGCAAATCTTACTGTTATACTGAATGAA
Found at i:31587803 original size:25 final size:26
Alignment explanation
Indices: 31587736--31587803 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
31587726 GCCCGACCCA
* *
31587736 TATTAAATATATATAAAAATATATATT
1 TATTAAAAATA-AAAAAAATATATATT
31587763 TGATTAAAAAT--AAAAAATATATA-T
1 T-ATTAAAAATAAAAAAAATATATATT
31587787 TATTAAAAATAAAAAAA
1 TATTAAAAATAAAAAAA
31587804 TTTCCCGGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
23 9 0.25
24 2 0.06
25 16 0.44
27 1 0.03
28 8 0.22
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (26 bp):
TATTAAAAATAAAAAAAATATATATT
Found at i:31588125 original size:14 final size:14
Alignment explanation
Indices: 31588095--31588124 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31588085 GTTCTAAACA
31588095 TTTAATTAATTTAT
1 TTTAATTAATTTAT
31588109 TTTAATTAATTT-T
1 TTTAATTAATTTAT
31588122 TTT
1 TTT
31588125 TCACATATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAATTAATTTAT
Found at i:31589222 original size:29 final size:29
Alignment explanation
Indices: 31589157--31589247 Score: 83
Period size: 30 Copynumber: 3.1 Consensus size: 29
31589147 GGAAGAAAAA
* * * *
31589157 TTTAACAATTTAATGATTTTAAAAAAATTA
1 TTTAATAATTTAATGA-TTTAAATAATTTT
**
31589187 TCAAATAATTTAATGATTTAAATAATTTT
1 TTTAATAATTTAATGATTTAAATAATTTT
* **
31589216 TTTAATAATTAAATGATATTTTATAATTTT
1 TTTAATAATTTAATGAT-TTAAATAATTTT
31589246 TT
1 TT
31589248 AAAATTGAGG
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
29 24 0.49
30 25 0.51
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTAATAATTTAATGATTTAAATAATTTT
Found at i:31589237 original size:20 final size:21
Alignment explanation
Indices: 31589204--31589242 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
31589194 ATTTAATGAT
*
31589204 TTAAATAAT-TTTTTTAATAA
1 TTAAATAATATTTTATAATAA
*
31589224 TTAAATGATATTTTATAAT
1 TTAAATAATATTTTATAAT
31589243 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
TTAAATAATATTTTATAATAA
Found at i:31589249 original size:29 final size:29
Alignment explanation
Indices: 31589190--31589247 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
31589180 AAAATTATCA
*
31589190 AATAATTTAATGATTTAAATAATTTTTTT
1 AATAATTAAATGATTTAAATAATTTTTTT
**
31589219 AATAATTAAATGATATTTTATAATTTTTT
1 AATAATTAAATGAT-TTAAATAATTTTTT
31589248 AAAATTGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
AATAATTAAATGATTTAAATAATTTTTTT
Found at i:31611092 original size:26 final size:26
Alignment explanation
Indices: 31611063--31611122 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
31611053 AATTCTCCAT
*
31611063 AAAGGCTTTCTTTCATATTA-GCCAC
1 AAAGGCTTTCTTTCATATTACACCAC
*
31611088 AAAAGCTTTCTTTCATATTACACCAC
1 AAAGGCTTTCTTTCATATTACACCAC
31611114 AAAGGCTTT
1 AAAGGCTTT
31611123 TCTTACCTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 19 0.61
26 12 0.39
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (26 bp):
AAAGGCTTTCTTTCATATTACACCAC
Found at i:31625975 original size:27 final size:26
Alignment explanation
Indices: 31625944--31626121 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
31625934 TAAATTGTAC
31625944 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
31625971 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
31625997 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
31626025 GGCACTAAGTGTGCGAGGTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
31626053 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
31626080 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
31626107 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31626122 GGCTCAAAAT
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 102 0.80
28 25 0.20
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:31626005 original size:54 final size:54
Alignment explanation
Indices: 31625944--31626121 Score: 200
Period size: 54 Copynumber: 3.3 Consensus size: 54
31625934 TAAATTGTAC
* **
31625944 AGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATT-GACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* ** *
31625999 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGGTTGACTATG-T
1 AGCACTAAGTGTGCG-ATTGACTATGTAGCACTAAGTGTGCGA-GTTGAATATGAT
* * *
31626053 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
*
31626107 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31626122 GGCTCAAAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
54 60 0.57
55 45 0.43
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:31626060 original size:82 final size:81
Alignment explanation
Indices: 31625945--31626100 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 81
31625935 AAATTGTACA
* *
31625945 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31626009 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
31626026 GCACTAAGTGTGCGAGGTT-GACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGT
1 GCACTAAGTGTGCGA--TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGT
*
31626090 GTGCGAGTTGA
64 GTGCGAATTGA
31626101 TTATATAGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 15 0.23
82 48 0.73
83 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:31626112 original size:82 final size:81
Alignment explanation
Indices: 31625941--31626121 Score: 213
Period size: 82 Copynumber: 2.2 Consensus size: 81
31625931 GATTAAATTG
* *
31625941 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31626006 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
31626022 TGCGGCACTAAGTGTGCGAGGTT-GACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGA--TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
31626085 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
31626104 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31626122 GGCTCAAAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 18 0.22
82 63 0.76
83 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:31630437 original size:14 final size:14
Alignment explanation
Indices: 31630418--31630445 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31630408 GTCTCACACT
31630418 AAGCACATGTATTA
1 AAGCACATGTATTA
31630432 AAGCACATGTATTA
1 AAGCACATGTATTA
31630446 TTCTGGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
AAGCACATGTATTA
Found at i:31644334 original size:36 final size:36
Alignment explanation
Indices: 31644287--31644361 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
31644277 GATAACGAGA
31644287 GAGATGAGCTTAGCCTCTAAGATCCACCTTAACCGT
1 GAGATGAGCTTAGCCTCTAAGATCCACCTTAACCGT
*
31644323 GAGATGAGCTTAGGCTCTAAGATCCACCTTAACCGT
1 GAGATGAGCTTAGCCTCTAAGATCCACCTTAACCGT
31644359 GAG
1 GAG
31644362 TTTAAAAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (36 bp):
GAGATGAGCTTAGCCTCTAAGATCCACCTTAACCGT
Found at i:31646276 original size:29 final size:29
Alignment explanation
Indices: 31646243--31646304 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
31646233 CACAAGGTAG
*
31646243 TGTGAGCCACACGGGCTCTCACATGGCCA
1 TGTGAGCCACACGGGCTCTCACAGGGCCA
*
31646272 TGTGAGCCACACGGGCTGTCACAGGGCCA
1 TGTGAGCCACACGGGCTCTCACAGGGCCA
31646301 TGTG
1 TGTG
31646305 CCAAATTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.19, C:0.31, G:0.32, T:0.18
Consensus pattern (29 bp):
TGTGAGCCACACGGGCTCTCACAGGGCCA
Found at i:31651201 original size:53 final size:50
Alignment explanation
Indices: 31651076--31651201 Score: 119
Period size: 50 Copynumber: 2.5 Consensus size: 50
31651066 GGCACTAAAG
** * *
31651076 GACCATATTGTGTAAGACTGTAACTAGTGGTTGATGGCATCATATGGGAA
1 GACCATATAATGTAAGACCGTAACTAGTGGTTGATGACATCATATGGGAA
** * * * *
31651126 GATAATGTCATGTAAGAACGTAACTGGTGGGTT-ATGACATCATATAGGGAGAA
1 GACCATATAATGTAAGACCGTAACTAGT-GGTTGATGACATCATAT--GG-GAA
31651179 GACCATATAATGTAAGACCGTAA
1 GACCATATAATGTAAGACCGTAA
31651202 TTGACAGGTT
Statistics
Matches: 58, Mismatches: 14, Indels: 5
0.75 0.18 0.06
Matches are distributed among these distances:
50 31 0.53
51 4 0.07
52 2 0.03
53 21 0.36
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (50 bp):
GACCATATAATGTAAGACCGTAACTAGTGGTTGATGACATCATATGGGAA
Found at i:31651493 original size:28 final size:28
Alignment explanation
Indices: 31651425--31651497 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
31651415 GAACAATTTT
*
31651425 AAAGGAAAGCCTTCT-TGGCAAACCTCTT
1 AAAGGAAAGCCTT-TGTGGCAAACCTCTG
* * **
31651453 AAGGGACA-CCTTTGTGGCAAGGCTCTG
1 AAAGGAAAGCCTTTGTGGCAAACCTCTG
31651480 AAAGGAAAGCCTTTGTGG
1 AAAGGAAAGCCTTTGTGG
31651498 TTACTGAATG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 1 0.03
27 20 0.56
28 15 0.42
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (28 bp):
AAAGGAAAGCCTTTGTGGCAAACCTCTG
Found at i:31654370 original size:60 final size:60
Alignment explanation
Indices: 31654259--31654387 Score: 161
Period size: 60 Copynumber: 2.1 Consensus size: 60
31654249 ACATAAGCTA
* * * * *
31654259 ACAATATATCAAGGTTGCTCACACAAGCTGACATTATAATAACGCTCCTCACTCAAACTG
1 ACAATATATCAAAGTTGCTCACACAAGCTGACACTATAACAACGCTACTCACACAAACTG
* * *
31654319 ACAATATATCAAAGTTGCTCACACAAG-TAGACACTATAACAAGGGTACTCACACAAGCTG
1 ACAATATATCAAAGTTGCTCACACAAGCT-GACACTATAACAACGCTACTCACACAAACTG
*
31654379 ACATTATAT
1 ACAATATAT
31654388 TGAGGTTACT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.02
60 58 0.98
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (60 bp):
ACAATATATCAAAGTTGCTCACACAAGCTGACACTATAACAACGCTACTCACACAAACTG
Found at i:31654399 original size:30 final size:30
Alignment explanation
Indices: 31654253--31654386 Score: 108
Period size: 30 Copynumber: 4.5 Consensus size: 30
31654243 TTTTGAACAT
* * * *
31654253 AAGCTAACAATATATCAAGGTTGCTCACAC
1 AAGCTGACATTATAACAAGGTTACTCACAC
* * * * *
31654283 AAGCTGACATTATAATAACGCTCCTCACTC
1 AAGCTGACATTATAACAAGGTTACTCACAC
* * * * *
31654313 AAACTGACAATATATCAAAGTTGCTCACAC
1 AAGCTGACATTATAACAAGGTTACTCACAC
* *
31654343 AAG-TAGACACTATAACAAGGGTACTCACAC
1 AAGCT-GACATTATAACAAGGTTACTCACAC
31654373 AAGCTGACATTATA
1 AAGCTGACATTATA
31654387 TTGAGGTTAC
Statistics
Matches: 79, Mismatches: 23, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
29 1 0.01
30 77 0.97
31 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (30 bp):
AAGCTGACATTATAACAAGGTTACTCACAC
Found at i:31670195 original size:22 final size:20
Alignment explanation
Indices: 31670167--31670214 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
31670157 TAAAAACTGG
31670167 TAGAATTGTTATTCCTAGAAAA
1 TAGAATT-TTATT-CTAGAAAA
31670189 TAGAA-TTTATTCTAGAAAA
1 TAGAATTTTATTCTAGAAAA
31670208 TA-AATTT
1 TAGAATTT
31670215 CCACTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 12 0.48
20 5 0.20
21 1 0.04
22 5 0.20
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (20 bp):
TAGAATTTTATTCTAGAAAA
Found at i:31673297 original size:27 final size:26
Alignment explanation
Indices: 31673266--31673443 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 26
31673256 TAAATTGTAC
31673266 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
31673293 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
*
31673319 ATGCACTAAGTGTGCGAATTGAAC-ATGC
1 A-GCACTAAGTGTGCG-ATTG-ACTATGT
*
31673347 GGCACTAAGTGTGCGAGGTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
31673375 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
31673402 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
31673429 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31673444 GGCTCAAAAT
Statistics
Matches: 128, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
26 1 0.01
27 103 0.80
28 24 0.19
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:31673327 original size:54 final size:54
Alignment explanation
Indices: 31673266--31673443 Score: 193
Period size: 54 Copynumber: 3.3 Consensus size: 54
31673256 TAAATTGTAC
* **
31673266 AGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATT-GACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
** *
31673321 -GCACTAAGTGTGCGAATTGAAC-ATGCGGCACTAAGTGTGCGAGGTTGACTATG-T
1 AGCACTAAGTGTGCG-ATTG-ACTATGTAGCACTAAGTGTGCGA-GTTGAATATGAT
* * *
31673375 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
*
31673429 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31673444 GGCTCAAAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 15
0.80 0.08 0.11
Matches are distributed among these distances:
54 59 0.56
55 46 0.44
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:31673382 original size:82 final size:81
Alignment explanation
Indices: 31673267--31673422 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 81
31673257 AAATTGTACA
* *
31673267 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31673331 TGCGAATTGAACATGCG
65 TGCGAATTGAACATGCG
** *
31673348 GCACTAAGTGTGCGAGGTT-GACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGT
1 GCACTAAGTGTGCGA--TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGT
*
31673412 GTGCGAGTTGA
64 GTGCGAATTGA
31673423 TTATATAGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 15 0.23
82 48 0.73
83 3 0.05
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGAACATGCG
Found at i:31673434 original size:82 final size:81
Alignment explanation
Indices: 31673263--31673443 Score: 213
Period size: 82 Copynumber: 2.2 Consensus size: 81
31673253 GATTAAATTG
* *
31673263 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31673328 GTGTGCGAATTGAACA
66 GTGTGCGAATTGAACA
* * ** *
31673344 TGCGGCACTAAGTGTGCGAGGTT-GACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGA--TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
31673407 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGAACA
* *
31673426 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31673444 GGCTCAAAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 18 0.22
82 63 0.76
83 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGAACA
Found at i:31676035 original size:28 final size:28
Alignment explanation
Indices: 31676004--31676059 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
31675994 ACCCATAAAT
31676004 CCTTTTTGAAATTTGATAAAGATGATGG
1 CCTTTTTGAAATTTGATAAAGATGATGG
31676032 CCTTTTTGAAATTTGATAAAGATGATGG
1 CCTTTTTGAAATTTGATAAAGATGATGG
31676060 AGGAAATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (28 bp):
CCTTTTTGAAATTTGATAAAGATGATGG
Found at i:31677272 original size:22 final size:22
Alignment explanation
Indices: 31677229--31677272 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31677219 ATTAACAATA
* **
31677229 TTAATAAATCAATCTATTTTTT
1 TTAAAAAATCAATCTAAATTTT
31677251 TTAAAAAATCAATCTAAATTTT
1 TTAAAAAATCAATCTAAATTTT
31677273 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAAAAATCAATCTAAATTTT
Found at i:31677691 original size:29 final size:30
Alignment explanation
Indices: 31677659--31677715 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
31677649 TGGTTTAATT
*
31677659 TGTAATTGTATATAT-AAATTTTGATTTTA
1 TGTAATTGTATACATGAAATTTTGATTTTA
*
31677688 TGTAATTTTATACATGAAATTTTGATTT
1 TGTAATTGTATACATGAAATTTTGATTT
31677716 GATCCAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (30 bp):
TGTAATTGTATACATGAAATTTTGATTTTA
Found at i:31678612 original size:26 final size:27
Alignment explanation
Indices: 31678576--31678641 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
31678566 ATTTTTTAAT
* *
31678576 GTTAGGGTTTTGTTTT-TTAAAGTA-A
1 GTTAGGATTTTGTTTTCTTAAAATAGA
31678601 GGTTAGGATTTTGTTTTCTTAAAATAGA
1 -GTTAGGATTTTGTTTTCTTAAAATAGA
*
31678629 GTTAAGATTTTGT
1 GTTAGGATTTTGT
31678642 GGATTGTAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.43
27 19 0.54
28 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.50
Consensus pattern (27 bp):
GTTAGGATTTTGTTTTCTTAAAATAGA
Found at i:31678996 original size:32 final size:31
Alignment explanation
Indices: 31678933--31678997 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
31678923 CGTTATTTAT
** *
31678933 AGTGCATTTTTTTTAACATTCAGATAGGTTC
1 AGTGCATTTTTTCGAACATTAAGATAGGTTC
31678964 AGTGCATTATTTTCGAACATTAAGATCA-GTTC
1 AGTGCATT-TTTTCGAACATTAAGAT-AGGTTC
31678996 AG
1 AG
31678998 AAAATATATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 8 0.28
32 20 0.69
33 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (31 bp):
AGTGCATTTTTTCGAACATTAAGATAGGTTC
Found at i:31679274 original size:14 final size:14
Alignment explanation
Indices: 31679255--31679283 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31679245 TACAGAGTTC
31679255 AATAGATCGGACCA
1 AATAGATCGGACCA
31679269 AATAGATCGGACCA
1 AATAGATCGGACCA
31679283 A
1 A
31679284 GGCATTGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
AATAGATCGGACCA
Found at i:31686384 original size:30 final size:30
Alignment explanation
Indices: 31686350--31686411 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
31686340 AAAATGAGTA
31686350 TGTGATTACAATCATCTGATAATTGGTCTT
1 TGTGATTACAATCATCTGATAATTGGTCTT
* *
31686380 TGTGATTACAATCATTTGATGATTGGTCTT
1 TGTGATTACAATCATCTGATAATTGGTCTT
31686410 TG
1 TG
31686412 GGCATACTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.45
Consensus pattern (30 bp):
TGTGATTACAATCATCTGATAATTGGTCTT
Found at i:31686587 original size:35 final size:35
Alignment explanation
Indices: 31686536--31686610 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
31686526 CCCTTTTAGA
*
31686536 CAACTCCGCAGAGACAGAAACAAACTCATCATGCT
1 CAACCCCGCAGAGACAGAAACAAACTCATCATGCT
31686571 CAACCCCGCAGAGACAGAAACAAACTCATCATGCT
1 CAACCCCGCAGAGACAGAAACAAACTCATCATGCT
31686606 CAACC
1 CAACC
31686611 TACTCTCATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.40, C:0.35, G:0.13, T:0.12
Consensus pattern (35 bp):
CAACCCCGCAGAGACAGAAACAAACTCATCATGCT
Found at i:31696560 original size:28 final size:28
Alignment explanation
Indices: 31696521--31696582 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
31696511 AAATAAAATA
**
31696521 AAATAGACGTTGGTCCCAACGGCTAATT
1 AAATAGACGTTGGTCCCAACAACTAATT
*
31696549 AAATAGCCGTTGGTCCCAACAACTAATT
1 AAATAGACGTTGGTCCCAACAACTAATT
31696577 AAATAG
1 AAATAG
31696583 TCATTAGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (28 bp):
AAATAGACGTTGGTCCCAACAACTAATT
Found at i:31696840 original size:28 final size:29
Alignment explanation
Indices: 31696780--31696835 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
31696770 TGTTATTCGC
31696780 TAAAAATAGTCTAATCTCGTAATTTTTCA
1 TAAAAATAGTCTAATCTCGTAATTTTTCA
*
31696809 TAAAAATAGTCTAATCTTGTAATTTTT
1 TAAAAATAGTCTAATCTCGTAATTTTT
31696836 TTAAAATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.45
Consensus pattern (29 bp):
TAAAAATAGTCTAATCTCGTAATTTTTCA
Found at i:31701102 original size:13 final size:13
Alignment explanation
Indices: 31701084--31701110 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31701074 AGCTTTTTTT
31701084 TGTTTTTAATTAA
1 TGTTTTTAATTAA
31701097 TGTTTTTAATTAA
1 TGTTTTTAATTAA
31701110 T
1 T
31701111 AAATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TGTTTTTAATTAA
Found at i:31701204 original size:20 final size:22
Alignment explanation
Indices: 31701164--31701206 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
31701154 TATAAAATCA
*
31701164 AATAATAAATATGTAATTATAT
1 AATAATAAATATATAATTATAT
31701186 AATAA-AAATATAT-ATTATAT
1 AATAATAAATATATAATTATAT
31701206 A
1 A
31701207 TATCATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATAATAAATATATAATTATAT
Found at i:31701238 original size:92 final size:90
Alignment explanation
Indices: 31701139--31701313 Score: 201
Period size: 92 Copynumber: 1.9 Consensus size: 90
31701129 TTTTATTTTT
** *
31701139 AATTAATAAATTTTTTA-TAAAATCAAATAATAAATATGTAATTATATAATAAAAATATATA-TT
1 AATTAATAAATGCTTTATTAAAAT-AAAT-A-AAATA-ATAATTATATAATAAAAATATATATTT
*
31701202 ATATATATCATTATGTTAAAAATATTTGA
62 ATATATACCATTATGTTAAAAATATTTGA
* * * *
31701231 AATTAATAACTGCTTTATTTATATAAATAAAGTAATAATTATATAATAAAAATATATATTTTTAT
1 AATTAATAAATGCTTTATTAAAATAAATAAAATAATAATTATATAATAAAAATATATA--TTTAT
*
31701296 ATTTACCATTATGTTAAA
64 ATATACCATTATGTTAAA
31701314 TATACTTTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
89 23 0.33
90 4 0.06
91 1 0.01
92 38 0.54
93 4 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (90 bp):
AATTAATAAATGCTTTATTAAAATAAATAAAATAATAATTATATAATAAAAATATATATTTATAT
ATACCATTATGTTAAAAATATTTGA
Found at i:31701826 original size:20 final size:21
Alignment explanation
Indices: 31701785--31701826 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
31701775 TCTCTGAATC
*
31701785 TTATTCTTATTCTCTTTGATT
1 TTATTCTTATTCTCTTTAATT
31701806 TTATT-TTATTC-CTTATAATT
1 TTATTCTTATTCTCTT-TAATT
31701826 T
1 T
31701827 GTAAAATGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 3 0.16
20 11 0.58
21 5 0.26
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTCTTATTCTCTTTAATT
Found at i:31703357 original size:33 final size:33
Alignment explanation
Indices: 31703315--31703380 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
31703305 GTCACTTAAG
31703315 TTAGTTTATACAAAATATTCTTTGCGGATACAA
1 TTAGTTTATACAAAATATTCTTTGCGGATACAA
31703348 TTAGTTTATACAAAATATTCTTTGCGGATACAA
1 TTAGTTTATACAAAATATTCTTTGCGGATACAA
31703381 CCAGATTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (33 bp):
TTAGTTTATACAAAATATTCTTTGCGGATACAA
Found at i:31713992 original size:50 final size:50
Alignment explanation
Indices: 31713926--31714109 Score: 280
Period size: 50 Copynumber: 3.7 Consensus size: 50
31713916 AATTATTTGG
* * * *
31713926 AAAGCCTTTGTAGTGTATTGTCTGGAAAGCCTTTGTGGCTAATCTTATGA
1 AAAGCCTTTGTGGTGTATTGTTTGGAAAGCCTTTGTGACTAATCTTGTGA
*
31713976 AAAGTCTTTGTGGTGTATTGTTTGGAAAGCCTTTGTGACTAATCTTGTGA
1 AAAGCCTTTGTGGTGTATTGTTTGGAAAGCCTTTGTGACTAATCTTGTGA
*
31714026 AAAGCCTTTGT-GTCGTATCGTTTGGAAAGCCTTTGTGACTAATCTTGTGA
1 AAAGCCTTTGTGGT-GTATTGTTTGGAAAGCCTTTGTGACTAATCTTGTGA
**
31714076 AAAGCCTTTGTGCCGTATTGTTTGGAAAGCCTTT
1 AAAGCCTTTGTGGTGTATTGTTTGGAAAGCCTTT
31714110 ATGGCATATT
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
49 2 0.02
50 120 0.98
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.39
Consensus pattern (50 bp):
AAAGCCTTTGTGGTGTATTGTTTGGAAAGCCTTTGTGACTAATCTTGTGA
Found at i:31714119 original size:25 final size:25
Alignment explanation
Indices: 31713921--31714119 Score: 161
Period size: 25 Copynumber: 8.0 Consensus size: 25
31713911 AAACGAATTA
* *
31713921 TTTGGAAAGCCTTTGTAGTGTATTG
1 TTTGGAAAGCCTTTGTGGCGTATTG
* * *
31713946 TCTGGAAAGCCTTTGTGGC-TAATC
1 TTTGGAAAGCCTTTGTGGCGTATTG
* * *
31713970 TTATGAAAAGTCTTTGTGGTGTATTG
1 TT-TGGAAAGCCTTTGTGGCGTATTG
* * *
31713996 TTTGGAAAGCCTTTGTGAC-TAATC
1 TTTGGAAAGCCTTTGTGGCGTATTG
* * *
31714020 TTGTGAAAAGCCTTTGTGTCGTATCG
1 TT-TGGAAAGCCTTTGTGGCGTATTG
* * *
31714046 TTTGGAAAGCCTTTGTGAC-TAATC
1 TTTGGAAAGCCTTTGTGGCGTATTG
* *
31714070 TTGTGAAAAGCCTTTGTGCCGTATTG
1 TT-TGGAAAGCCTTTGTGGCGTATTG
* *
31714096 TTTGGAAAGCCTTTATGGCATATT
1 TTTGGAAAGCCTTTGTGGCGTATT
31714120 ATGTGAAAAG
Statistics
Matches: 133, Mismatches: 35, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
24 13 0.10
25 106 0.80
26 14 0.11
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.40
Consensus pattern (25 bp):
TTTGGAAAGCCTTTGTGGCGTATTG
Found at i:31714125 original size:100 final size:100
Alignment explanation
Indices: 31713916--31714129 Score: 281
Period size: 100 Copynumber: 2.1 Consensus size: 100
31713906 AGTAAAAACG
* * * * *
31713916 AATTATTTGGAAAGCCTTTGTAGTGTATTGTCTGGAAAGCCTTTGTGGCTAATCTTATGAAAAGT
1 AATTATGTGAAAAGCCTTTGTAGTGTATCGTCTGGAAAGCCTTTGTGACTAATCTTATGAAAAGC
** *
31713981 CTTTGTGGTGTATTGTTTGGAAAGCCTTTGTGACT
66 CTTTGTGCCGTATTGTTTGGAAAGCCTTTATGACT
* *
31714016 AATCT-TGTGAAAAGCCTTTGT-GTCGTATCGTTTGGAAAGCCTTTGTGACTAATCTTGTGAAAA
1 AAT-TATGTGAAAAGCCTTTGTAGT-GTATCGTCTGGAAAGCCTTTGTGACTAATCTTATGAAAA
*
31714079 GCCTTTGTGCCGTATTGTTTGGAAAGCCTTTATGGC-
64 GCCTTTGTGCCGTATTGTTTGGAAAGCCTTTATGACT
31714115 ATATTATGTGAAAAG
1 A-ATTATGTGAAAAG
31714130 ACTGTAGGAT
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
99 4 0.04
100 94 0.95
101 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (100 bp):
AATTATGTGAAAAGCCTTTGTAGTGTATCGTCTGGAAAGCCTTTGTGACTAATCTTATGAAAAGC
CTTTGTGCCGTATTGTTTGGAAAGCCTTTATGACT
Found at i:31714129 original size:25 final size:25
Alignment explanation
Indices: 31714071--31714129 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
31714061 TGACTAATCT
* * *
31714071 TGTGAAAAGCCTTTGTGCCGTATTG
1 TGTGAAAAGCCTTTATGCCATATTA
* * *
31714096 TTTGGAAAGCCTTTATGGCATATTA
1 TGTGAAAAGCCTTTATGCCATATTA
31714121 TGTGAAAAG
1 TGTGAAAAG
31714130 ACTGTAGGAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (25 bp):
TGTGAAAAGCCTTTATGCCATATTA
Found at i:31717230 original size:47 final size:48
Alignment explanation
Indices: 31717137--31717240 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 48
31717127 TCTGATTTGT
* * *
31717137 AGATAAATTGCCACTGATAACATTTTGTGGACAGGCCACCAATTATGC
1 AGATAAATTGACACTGATAACACTTTGTGGACAAGCCACCAATTATGC
* * *
31717185 AGATAAATTGACACTGA-AACACTTTGTGGACAAGCTACCACTTATGT
1 AGATAAATTGACACTGATAACACTTTGTGGACAAGCCACCAATTATGC
31717232 AGATAAATT
1 AGATAAATT
31717241 TTCACATACT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
47 34 0.68
48 16 0.32
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (48 bp):
AGATAAATTGACACTGATAACACTTTGTGGACAAGCCACCAATTATGC
Found at i:31719245 original size:22 final size:22
Alignment explanation
Indices: 31719201--31719248 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
31719191 CAAGCCACCT
* **
31719201 CATAATTGCCGATAAGTTACCA
1 CATAATTGCAGATAAACTACCA
*
31719223 CATAATTGCAGATAAACTGCCA
1 CATAATTGCAGATAAACTACCA
31719245 CATA
1 CATA
31719249 TCTTCCTCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (22 bp):
CATAATTGCAGATAAACTACCA
Done.