Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 8 of 425
Found at i:2104661 original size:72 final size:72
Alignment explanation
Indices: 2104524--2104662 Score: 174
Period size: 72 Copynumber: 1.9 Consensus size: 72
2104514 TGATCACACT
* * * * **
2104524 ACTCAAGTTGTTTGATGACAAATCGAGTACAGTAAGGTACACAAGATCAAAAATGGAATCTGGTA
1 ACTCAAGTTGTTGGAGGACAAATCGAGTACAGTAAGGTACACAAGATAAAAAATAGAATAGGGTA
2104589 TTAGACC
66 TTAGACC
* *
2104596 ACTCAAGTTGTTGGAGGACAAAT-GAAGCT-CAGTAAGGTTCATAAGATAAAAAATAGAATAGGG
1 ACTCAAGTTGTTGGAGGACAAATCG-AG-TACAGTAAGGTACACAAGATAAAAAATAGAATAGGG
2104659 TATT
64 TATT
2104663 GAATCACTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
71 1 0.02
72 55 0.96
73 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.25
Consensus pattern (72 bp):
ACTCAAGTTGTTGGAGGACAAATCGAGTACAGTAAGGTACACAAGATAAAAAATAGAATAGGGTA
TTAGACC
Found at i:2110447 original size:18 final size:18
Alignment explanation
Indices: 2110428--2110520 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
2110418 CCCAACTACT
* *
2110428 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTACC
*
2110446 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
2110464 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
2110482 ATATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
2110500 GTATATGTGAATAGTACC
1 GTATACGTGAATAGTACC
2110518 GTA
1 GTA
2110521 AACGGTCGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:2111609 original size:7 final size:7
Alignment explanation
Indices: 2111597--2111622 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2111587 CCTTTATATT
2111597 TTCAAAA
1 TTCAAAA
2111604 TTCAAAA
1 TTCAAAA
2111611 TTCAAAA
1 TTCAAAA
2111618 TTCAA
1 TTCAA
2111623 TTCCAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (7 bp):
TTCAAAA
Found at i:2125856 original size:20 final size:22
Alignment explanation
Indices: 2125831--2125873 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
2125821 TTTAATTTTA
2125831 TTAAAATA-ATTTAT-CATATT
1 TTAAAATACATTTATGCATATT
*
2125851 TTAAAATACTTTTATGCATATT
1 TTAAAATACATTTATGCATATT
2125873 T
1 T
2125874 ATTTATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 5 0.25
22 7 0.35
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAAATACATTTATGCATATT
Found at i:2130341 original size:72 final size:72
Alignment explanation
Indices: 2130251--2130391 Score: 223
Period size: 72 Copynumber: 2.0 Consensus size: 72
2130241 TTGATGACAC
* * *
2130251 CACTCAAGTTGTTTGATGACAAATCAAG-ATAATTAATGTTCACAAGATCAAAAATGGAAT-CGG
1 CACTCAAGTTGTTTGATGACAAATCAAGTA-AAGTAAGGTTCACAAGATAAAAAATGGAATAC-G
2130314 GTATTGGAT
64 GTATTGGAT
2130323 CACTCAAGTTGTTTGATGACAAATCAAGTAAAGTAAGGTTCACAAGATAAAAAATGGAATACGGT
1 CACTCAAGTTGTTTGATGACAAATCAAGTAAAGTAAGGTTCACAAGATAAAAAATGGAATACGGT
2130388 ATTG
66 ATTG
2130392 AACCACCAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
72 62 0.97
73 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (72 bp):
CACTCAAGTTGTTTGATGACAAATCAAGTAAAGTAAGGTTCACAAGATAAAAAATGGAATACGGT
ATTGGAT
Found at i:2152667 original size:72 final size:72
Alignment explanation
Indices: 2152586--2152733 Score: 205
Period size: 72 Copynumber: 2.1 Consensus size: 72
2152576 ACTTGATCAC
*
2152586 ACCACTCAAGTTGTTTGATGACAAATAAAGAT-AA-TTAGCGTTCACAAGATGAAAA-ATGGAAT
1 ACCACTCAAGTTGTTTGATGACAAATAAAG-TGAAGTAAG-GTTCACAAGAT-AAAATATGGAAT
*
2152648 -CTGGTATTGG
63 AC-GGTATTGA
*
2152658 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATAAAATATGGAATACG
1 ACCACTCAAGTTGTTTGATGACAAATAAAGTGAAGTAAGGTTCACAAGATAAAATATGGAATACG
2152723 GTATTGA
66 GTATTGA
2152730 ACCA
1 ACCA
2152734 ATTATAACTC
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
71 5 0.07
72 60 0.87
73 4 0.06
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (72 bp):
ACCACTCAAGTTGTTTGATGACAAATAAAGTGAAGTAAGGTTCACAAGATAAAATATGGAATACG
GTATTGA
Found at i:2156409 original size:23 final size:22
Alignment explanation
Indices: 2156345--2156409 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
2156335 ATCTTACGTA
2156345 AAAATATATACAT--ATATATT
1 AAAATATATACATACATATATT
* *
2156365 AAAA-ATAAACATACGGTAATATT
1 AAAATATATACATAC-AT-ATATT
2156388 AAAAGTATATACATACATATAT
1 AAAA-TATATACATACATATAT
2156410 ACATAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
19 7 0.20
20 4 0.11
22 1 0.03
23 13 0.37
24 1 0.03
25 9 0.26
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (22 bp):
AAAATATATACATACATATATT
Found at i:2156851 original size:18 final size:18
Alignment explanation
Indices: 2156804--2156862 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
2156794 GAAAATGAAT
* *
2156804 ATAATAATACAATAATAA
1 ATAATGATATAATAATAA
*
2156822 ATAGTGATATAATAATAA
1 ATAATGATATAATAATAA
*
2156840 A-AATGATGATAATGATAA
1 ATAATGAT-ATAATAATAA
2156858 TATAA
1 -ATAA
2156863 GTAATAAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 5 0.15
18 25 0.76
19 1 0.03
20 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (18 bp):
ATAATGATATAATAATAA
Found at i:2158548 original size:45 final size:45
Alignment explanation
Indices: 2158503--2158669 Score: 182
Period size: 45 Copynumber: 3.8 Consensus size: 45
2158493 ATTTGTAATT
*
2158503 TTCAGCCTATTACCCTACTGCTTAGGGGGTTAAGGTCTGTAAAT-
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTAAATC
* * * *
2158547 TT-GGCTTGTTACCCTACTGCTTAGGGGGTTAAAG-CT-TATCATC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTA-AATC
* * * *
2158590 TTC-GATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAGATC
1 TTCAG-CCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTAAATC
* *
2158635 TTCAGCCTGTTACCCTACTACTTAGGGGATTAAGG
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
2158670 CTTGGTGGTT
Statistics
Matches: 100, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
43 31 0.31
44 27 0.27
45 33 0.33
46 3 0.03
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.35
Consensus pattern (45 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTAAATC
Found at i:2158621 original size:44 final size:43
Alignment explanation
Indices: 2158512--2158667 Score: 147
Period size: 43 Copynumber: 3.6 Consensus size: 43
2158502 TTTCAGCCTA
* * *
2158512 TTACCCTACTGCTTAGGGGGTTAAGGTCTGTAAATTTGGCTTG
1 TTACCCTACTGCTTAGGGGGTTAAAGTCTGTAAATTTCGATTG
*
2158555 TTACCCTACTGCTTAGGGGGTTAAAG-CT-TATCATCTTCGATCTG
1 TTACCCTACTGCTTAGGGGGTTAAAGTCTGTA-AAT-TTCGAT-TG
* * **
2158599 TTTCCCTACTGCTTAGGGGGTT-AAGATCTGTAGATCTTCAGCCTG
1 TTACCCTACTGCTTAGGGGGTTAAAG-TCTGTAAAT-TTC-GATTG
* *
2158644 TTACCCTACTACTTAGGGGATTAA
1 TTACCCTACTGCTTAGGGGGTTAA
2158668 GGCTTGGTGG
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
43 32 0.34
44 23 0.24
45 29 0.31
46 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (43 bp):
TTACCCTACTGCTTAGGGGGTTAAAGTCTGTAAATTTCGATTG
Found at i:2158787 original size:44 final size:45
Alignment explanation
Indices: 2158737--2158906 Score: 163
Period size: 44 Copynumber: 3.8 Consensus size: 45
2158727 TGATCTGCTT
2158737 CCCTACTGCTTAGGGTGATAAGATCTATAAA-CTTCAGCTTGTTA
1 CCCTACTGCTTAGGGTGATAAGATCTATAAATCTTCAGCTTGTTA
* * * ** * *
2158781 CCCTACTGCTTAGGGGGTTGAAGCTCGT-T--GCCTTC-GATCTGTTT
1 CCCTACTGCTTAGGGTGAT-AAGATC-TATAAATCTTCAGCT-TGTTA
* * *
2158825 CCCTACTGCTTAGGGTGATGAGATCTACAAATCTTCAGCCTGTTA
1 CCCTACTGCTTAGGGTGATAAGATCTATAAATCTTCAGCTTGTTA
* *
2158870 CCCTACTGCTTAGGG-GGTAAGATCTGTAAATCTTCAG
1 CCCTACTGCTTAGGGTGATAAGATCTATAAATCTTCAG
2158907 TCTGCTTCAC
Statistics
Matches: 98, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
42 1 0.01
43 6 0.06
44 60 0.61
45 29 0.30
46 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (45 bp):
CCCTACTGCTTAGGGTGATAAGATCTATAAATCTTCAGCTTGTTA
Found at i:2158939 original size:223 final size:222
Alignment explanation
Indices: 2158515--2158940 Score: 552
Period size: 223 Copynumber: 1.9 Consensus size: 222
2158505 CAGCCTATTA
* * * **
2158515 CCCTACTGCTTAGGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAA
1 CCCTACTGCTTAGGGGGATAAGATCTATAAATTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAA
* * * ** *
2158580 GCTTATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAGATCTTCAGCCTGT
66 GCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTACAAATCTTCAGCCTGT
* ** * * *
2158645 TACCCTACTACTTAGGGGATTAAGGCTTGGTGGTTTGAATCTGCTTCACTGCAACTTCAGGAGGG
131 TACCCTACTACTTAGGGGAGTAAGGCTTGGTAATTTCAATCTGCTTCACTGCAACTTCAGGAAGA
2158710 CAAGATTCACCGTCTTTTGATCTGCTT
196 CAAGATTCACCGTCTTTTGATCTGCTT
* *
2158737 CCCTACTGCTTAGGGTGATAAGATCTATAAACTTCAGCTTGTTACCCTACTGCTTAGGGGGTTGA
1 CCCTACTGCTTAGGGGGATAAGATCTATAAA-TTCAGCTTGTTACCCTACTGCTTAGGGGGTTAA
* ** * *
2158802 AGCTCGTTGCCTTCGATCTGTTTCCCTACTGCTTAGGGTGATGAGATCTACAAATCTTCAGCCTG
65 AGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTACAAATCTTCAGCCTG
* * *
2158867 TTACCCTACTGCTTAGGGG-GTAA-GATCT-GTAAATCTTCAGTCTGCTTCACTGCAACTTCAGG
130 TTACCCTACTACTTAGGGGAGTAAGGCT-TGGT-AAT-TTCAATCTGCTTCACTGCAACTTCAGG
2158929 AAGACAAGATTC
192 AAGACAAGATTC
2158941 GCTCCAACCT
Statistics
Matches: 173, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
221 4 0.02
222 32 0.18
223 137 0.79
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (222 bp):
CCCTACTGCTTAGGGGGATAAGATCTATAAATTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAA
GCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTACAAATCTTCAGCCTGT
TACCCTACTACTTAGGGGAGTAAGGCTTGGTAATTTCAATCTGCTTCACTGCAACTTCAGGAAGA
CAAGATTCACCGTCTTTTGATCTGCTT
Found at i:2159157 original size:44 final size:44
Alignment explanation
Indices: 2159080--2159564 Score: 307
Period size: 44 Copynumber: 10.8 Consensus size: 44
2159070 GACTTGCTGT
* * * *
2159080 CTTCAGTCTACTCCACTGCAACTTCGGGGAGATAAGGCTTGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAA
* * *
2159124 CTCCAATCTGCTCTACTGCAACTTTAGGGAGATAAGGTTTGT--
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAA
** * * *
2159166 -TTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTTTATTCATA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG----GTTT-GT-A-A
* * * * * ** *
2159216 GCTTCAGTCTGTTCCACTGCAACTTTAGGGAAACAAGACTTGCTAT
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-TAA
* * * *
2159262 TTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCTTGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAA
* *
2159306 CTCCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGT--
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAA
** * * *
2159348 -TTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTTTATTCATA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG----GTTT-GT-A-A
* * * * ** *
2159398 GCTTCAATCTGTTCCACTGTAACTTCAGGGAAACAAGACTTGCTAT
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-TAA
* * *
2159444 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATCTGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAA
* * * * *
2159488 CTTCAACCTGCTCCTCTGTAACTTTAGGGAGATAAGGTTTGTGA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAA
* * * * *
2159532 CTTCAATCTACTCCGCTGAAAATTCAAGGAGAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGAT
2159565 CTGCTATGGC
Statistics
Matches: 335, Mismatches: 82, Indels: 48
0.72 0.18 0.10
Matches are distributed among these distances:
41 59 0.18
44 137 0.41
45 76 0.23
46 2 0.01
47 2 0.01
48 6 0.02
52 53 0.16
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAA
Found at i:2159204 original size:182 final size:182
Alignment explanation
Indices: 2158899--2159529 Score: 941
Period size: 182 Copynumber: 3.5 Consensus size: 182
2158889 AGATCTGTAA
* * * * *
2158899 ATCTTCAGTCTGCTTCACTGCAACTTCAGGAAGACAA-GATTCG---CTCCAACCTGCTCCACTG
1 ATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCTT-GTAACTCCAACCTGCTCCACTG
* * * * * * *
2158960 TAACTTCAAGGAGATAAGGTTTATTCTGATATGCTCTACTACAACTTCAGAGAGATAAGATCTAT
65 CAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGT
*
2159025 TTATTCATAGCTTCAGTCTATTCCACTGCAATTTCAGGGAAACAAGACTTGCT
130 TTATTCATAGCTTCAGTCTGTTCCACTGCAATTTCAGGGAAACAAGACTTGCT
* * * *
2159078 GTCTTCAGTCTACTCCACTGCAACTTCGGGGAGATAAGGCTTGTAACTCCAATCTGCTCTACTGC
1 ATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCTTGTAACTCCAACCTGCTCCACTGC
*
2159143 AACTTTAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTT
66 AACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTT
2159208 TATTCATAGCTTCAGTCTGTTCCACTGCAACTTT-AGGGAAACAAGACTTGCT
131 TATTCATAGCTTCAGTCTGTTCCACTGCAA-TTTCAGGGAAACAAGACTTGCT
*
2159260 ATTTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCTTGTAACTCCAACCTGCTCCACTGC
1 ATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCTTGTAACTCCAACCTGCTCCACTGC
2159325 AACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTT
66 AACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTT
* * *
2159390 TATTCATAGCTTCAATCTGTTCCACTGTAACTTCAGGGAAACAAGACTTGCT
131 TATTCATAGCTTCAGTCTGTTCCACTGCAATTTCAGGGAAACAAGACTTGCT
* * * *
2159442 ATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAA-GATCTGTAACTTCAACCTGCTCCTCTG
1 ATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCT-TGTAACTCCAACCTGCTCCACTG
* *
2159506 TAACTTTAGGGAGATAAGGTTTGT
65 CAACTTCAGGGAGATAAGGTTTGT
2159530 GACTTCAATC
Statistics
Matches: 411, Mismatches: 34, Indels: 11
0.90 0.07 0.02
Matches are distributed among these distances:
179 32 0.08
180 3 0.01
181 4 0.01
182 369 0.90
183 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (182 bp):
ATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCTTGTAACTCCAACCTGCTCCACTGC
AACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTT
TATTCATAGCTTCAGTCTGTTCCACTGCAATTTCAGGGAAACAAGACTTGCT
Found at i:2159390 original size:41 final size:41
Alignment explanation
Indices: 2159313--2159390 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
2159303 TAACTCCAAC
* * *
2159313 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTTTGAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTTTTGAT
*
2159354 CTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTTT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTTT
2159391 ATTCATAGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTTTTGAT
Found at i:2159726 original size:43 final size:44
Alignment explanation
Indices: 2159667--2160128 Score: 320
Period size: 43 Copynumber: 10.7 Consensus size: 44
2159657 TCATCTTCGA
* * *
2159667 TCTGTTTCCCTACTACTTAGGGGTTTAAGATCTGCAAATTCAGC
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGCAAATTCAGC
* *
2159711 T-TGTTACCCTACTACTTAGGGGTTTAAGATCTGCAAATTCAGC
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGCAAATTCAGC
* * * * * *
2159754 T-TGTTACCCTACTACTTAGGGGGTTAA-AGCCTATCACATT-TGA
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGA-TCT-GCAAATTCAGC
* * * * *
2159797 TCTATTTCCCTACTGCTTAGGGGGTTAATATCTGTAAATTTAGC
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGCAAATTCAGC
* ** * *** * *
2159841 -CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTT-GGA
1 TCTGTTACCCTACTGCTTAGGGGGTTAA-GATCTGCAAATTCAGC
* * * * * * *
2159884 TCTGCTT-CACTGCTGTTTAGGGAGATAAGATCTGC-AATT-TGG
1 TCTG-TTACCCTACTGCTTAGGGGGTTAAGATCTGCAAATTCAGC
* * * *** *
2159926 TCTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTC-GA
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGA-TCTGCAAATTCAGC
* *
2159970 TCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGC
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGCAAATTCAGC
* * * * ** *
2160014 -CTGTTACCCTACTGCTTAGGGAGTTAAGGCTTTTCATTTTC-GA
1 TCTGTTACCCTACTGCTTAGGGGGTTAA-GATCTGCAAATTCAGC
* *
2160057 TCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGC
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGCAAATTCAGC
*
2160101 -CTGTTACCCTACTGCTTAGGGAGTTAAG
1 TCTGTTACCCTACTGCTTAGGGGGTTAAG
2160129 GCTTGTGAAT
Statistics
Matches: 320, Mismatches: 82, Indels: 33
0.74 0.19 0.08
Matches are distributed among these distances:
41 2 0.01
42 25 0.08
43 171 0.53
44 119 0.37
45 3 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (44 bp):
TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGCAAATTCAGC
Found at i:2159866 original size:173 final size:172
Alignment explanation
Indices: 2159668--2160128 Score: 495
Period size: 173 Copynumber: 2.7 Consensus size: 172
2159658 CATCTTCGAT
* * * * * * *
2159668 CTGTTTCCCTACTACTTAGGGGTTTAA-GATCTGCAAATTC-AGCTTGTTACCCTACTACTTAGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCTCTTCATATTCGATC-TGTT-CCCTACTGCTTAGG
* *
2159731 GGTTTAAGATCTGCAAATTCAGCTTGTTACCCTACTACTTAGGGGGTTAA-AGCCTATC-ACATT
64 GG-TTAAGATCTGCAAATTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAGACCCT-TCGAC-TT
* * * *
2159794 TGATCTATTTCCCTACTGCTTAGGGGGTTAATATCTGTAAATTTAGC
126 CGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGC
* * * * * * *
2159841 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTGGATCTGCTTCACTGCTGTTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCTCTTCATATTCGATCTG-TTCCCTACTGCTTAGGG
* * * * *
2159906 AGATAAGATCTGC-AATT-TGGTCTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCG
65 -GTTAAGATCTGCAAATTCAGCT-TGTTACCCTACTGCTTAGGGGGTTAAGACCCTTCGACTTCG
*
2159969 ATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGC
128 ATCTATTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGC
* *
2160014 CTGTTACCCTACTGCTTAGGGAG-TTAAGGCTTTTCATTTTCGATCTGTTTCCCTACTGCTTAGG
1 CTGTTACCCTACTGCTTAGGG-GTTTAAGGCTCTTCATATTCGATCTG-TTCCCTACTGCTTA-G
* * *
2160078 GGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGAGTTAAG
63 GGGTTAAGATCTGCAAATTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAG
2160129 GCTTGTGAAT
Statistics
Matches: 235, Mismatches: 42, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
172 2 0.01
173 160 0.68
174 67 0.29
175 6 0.03
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (172 bp):
CTGTTACCCTACTGCTTAGGGGTTTAAGGCTCTTCATATTCGATCTGTTCCCTACTGCTTAGGGG
TTAAGATCTGCAAATTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAGACCCTTCGACTTCGATC
TATTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGC
Found at i:2159940 original size:86 final size:87
Alignment explanation
Indices: 2159712--2160130 Score: 497
Period size: 87 Copynumber: 4.8 Consensus size: 87
2159702 AAATTCAGCT
* * * * * * *
2159712 TGTTACCCTACTACTTAGGGGTTTAAGATCTGCAAATTCAGCTTGTTACCCTACTACTTAGGGGG
1 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGAG
* * *
2159777 TTAAAG-CCTATC-ACATTTGATC
66 TTAAGGCCCT-TCGTC-TTCGATC
* * * *
2159799 TATTTCCCTACTGCTTAGGGGGTTAATATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGG-G
1 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGAG
*
2159863 TTTAAGGCCCTTCGTCTTGGATC
66 -TTAAGGCCCTTCGTCTTCGATC
* * * * * * * ** *
2159886 TGCTTCACTGCTGTTTAGGGAGATAAGATCT-GCAATTTGGTCTGTTACCCTACTGCTTAGGG-G
1 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGAG
*
2159949 TTTAAGACCCTTCGTCTTCGATC
66 -TTAAGGCCCTTCGTCTTCGATC
2159972 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGAG
1 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGAG
** * *
2160037 TTAAGGCTTTTCATTTTCGATC
66 TTAAGGCCCTTCGTCTTCGATC
2160059 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGAG
1 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGAG
2160124 TTAAGGC
66 TTAAGGC
2160131 TTGTGAATTC
Statistics
Matches: 286, Mismatches: 41, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
86 75 0.26
87 206 0.72
88 5 0.02
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (87 bp):
TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGAG
TTAAGGCCCTTCGTCTTCGATC
Found at i:2160127 original size:130 final size:129
Alignment explanation
Indices: 2159618--2160121 Score: 448
Period size: 130 Copynumber: 3.9 Consensus size: 129
2159608 ATATTTGATT
* * *
2159618 TTCAACCTGTTACCCTACTGCTTAGAGAGTTAAGGCCCATC-ATCTTCGATCTGTTTCCCTACTA
1 TTCAGCCTGTTACCCTACTGCTTAGGGAGTTAAGGCCCATCAAT-TT-GATCTGTTTCCCTACTG
* * * * *
2159682 CTTAGGGGTTTAAGATCTGCAAATTCAGCTTGTTACCCTACTACTTAGGGGTTTAAGATCTGCAA
64 CTTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGATCTGGAA
2159747 A
129 A
* * * * * *
2159748 TTCAGCTTGTTACCCTACTACTTAGGGGGTTAAAGCCTATCACATTTGATCTATTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGAGTTAAGGCCCATCA-ATTTGATCTGTTTCCCTACTGC
* * * ** *
2159813 TTAGGGGGTTAATATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCG-
65 TTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAA-GATC-TGGA
**
2159877 TC
128 AA
* * * * * * ** * *
2159879 TT-GGATCTGCTT-CACTGCTGTTTAGGGAGATAA-GATC-TGCAATTTGGTCTGTTACCCTACT
1 TTCAG-CCTG-TTACCCTACTGCTTAGGGAGTTAAGGCCCAT-CAATTTGATCTGTTTCCCTACT
* * * ** * * *
2159940 GCTTAGGGGTTTAAGACCCTTCG-TCTTC-GATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT
63 GCTTAGGGGGTTAAGA-TC-TGGAAATTCAG-CCTGTTACCCTACTGCTTAGGGGTTTAAGATCT
2160003 GGAAA
125 GGAAA
*** *
2160008 TTCAGCCTGTTACCCTACTGCTTAGGGAGTTAAGGCTTTTCATTTTCGATCTGTTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGAGTTAAGGCCCATCAATTT-GATCTGTTTCCCTACTGC
2160073 TTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGG
65 TTAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGG
2160122 AGTTAAGGCT
Statistics
Matches: 286, Mismatches: 70, Indels: 36
0.73 0.18 0.09
Matches are distributed among these distances:
128 4 0.01
129 59 0.21
130 163 0.57
131 55 0.19
132 5 0.02
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (129 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGAGTTAAGGCCCATCAATTTGATCTGTTTCCCTACTGCT
TAGGGGGTTAAGATCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGATCTGGAAA
Found at i:2161532 original size:15 final size:16
Alignment explanation
Indices: 2161512--2161541 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2161502 CTTTTTCCTT
2161512 TTTCTTTT-TCTTTTC
1 TTTCTTTTCTCTTTTC
2161527 TTTCTTTTCTCTTTT
1 TTTCTTTTCTCTTTT
2161542 TTGTTTCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTCTTTTCTCTTTTC
Found at i:2161557 original size:77 final size:76
Alignment explanation
Indices: 2161439--2161590 Score: 234
Period size: 77 Copynumber: 2.0 Consensus size: 76
2161429 TTGCCCTCTC
* * * *
2161439 CTTTTTCTTTTTTCTTTTCTTTTTTTTTGTTTCAAGGTGCCCTTTGTGGGTTTTCACATTGGCCT
1 CTTTTTCTTTTTTCTTTTCTTCTTTTTTGTTTCAAGGTGCCCTTTGCGAGTTTTCACATCGGCCT
*
2161504 TTTTCCTTTTT
66 CTTTCCTTTTT
2161515 CTTTTTCTTTTCTTTCTTTTC-TCTTTTTTGTTTCAAGGTGCCCTTTGCGAGTTTTCACATCGGC
1 CTTTTTC-TTT-TTTCTTTTCTTCTTTTTTGTTTCAAGGTGCCCTTTGCGAGTTTTCACATCGGC
2161579 CTCTTTCCTTTT
64 CTCTTTCCTTTT
2161591 AGGTAGAATG
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
76 7 0.10
77 53 0.77
78 9 0.13
ACGTcount: A:0.06, C:0.22, G:0.12, T:0.60
Consensus pattern (76 bp):
CTTTTTCTTTTTTCTTTTCTTCTTTTTTGTTTCAAGGTGCCCTTTGCGAGTTTTCACATCGGCCT
CTTTCCTTTTT
Found at i:2161606 original size:77 final size:78
Alignment explanation
Indices: 2161449--2161606 Score: 183
Period size: 77 Copynumber: 2.0 Consensus size: 78
2161439 CTTTTTCTTT
* * * * *
2161449 TTTCTTTTCTTTTTTTTTGTTTCAAGGTGCCCTTTGTGGGTTTTCACATTGGCCTTTTTCCTTTT
1 TTTCTTTTCTTCTTTTTTGTTTCAAGGTGCCCTTTGCGAGTTTTCACATCGGCCTCTTTCCTTTT
* * **** **
2161514 TCTTTTTCTTTTC
66 ACGTAGAATGCTC
2161527 TTTCTTTTC-TCTTTTTTGTTTCAAGGTGCCCTTTGCGAGTTTTCACATCGGCCTCTTTCCTTTT
1 TTTCTTTTCTTCTTTTTTGTTTCAAGGTGCCCTTTGCGAGTTTTCACATCGGCCTCTTTCCTTTT
*
2161591 AGGTAGAATGCTC
66 ACGTAGAATGCTC
2161604 TTT
1 TTT
2161607 GATTGGATTT
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
77 57 0.86
78 9 0.14
ACGTcount: A:0.08, C:0.21, G:0.15, T:0.56
Consensus pattern (78 bp):
TTTCTTTTCTTCTTTTTTGTTTCAAGGTGCCCTTTGCGAGTTTTCACATCGGCCTCTTTCCTTTT
ACGTAGAATGCTC
Found at i:2162101 original size:3 final size:3
Alignment explanation
Indices: 2162093--2162117 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2162083 CTTTCCATGA
2162093 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
2162118 TTTTTATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:2170385 original size:22 final size:22
Alignment explanation
Indices: 2170360--2170401 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2170350 TATTAAGTAC
*
2170360 AATAATATATGATA-TATATAGA
1 AATAATA-ATAATACTATATAGA
2170382 AATAATAATAATACTATATA
1 AATAATAATAATACTATATA
2170402 AAGAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (22 bp):
AATAATAATAATACTATATAGA
Found at i:2170502 original size:13 final size:13
Alignment explanation
Indices: 2170484--2170512 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2170474 TTAAAAGATG
2170484 TATGCATAGTATA
1 TATGCATAGTATA
2170497 TATGCATAGTATA
1 TATGCATAGTATA
2170510 TAT
1 TAT
2170513 TAGGAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (13 bp):
TATGCATAGTATA
Found at i:2170772 original size:11 final size:13
Alignment explanation
Indices: 2170746--2170776 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2170736 ATATTAAAAG
2170746 TATATACATAACA
1 TATATACATAACA
*
2170759 TATATACATAATA
1 TATATACATAACA
2170772 TATAT
1 TATAT
2170777 TTAGATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (13 bp):
TATATACATAACA
Found at i:2184421 original size:14 final size:15
Alignment explanation
Indices: 2184389--2184422 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2184379 ATATTATTAT
*
2184389 TATTTATCTAATTTT
1 TATTTATCTAATTTA
2184404 TATTTATC-AATTTA
1 TATTTATCTAATTTA
2184418 TATTT
1 TATTT
2184423 CTACTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTATCTAATTTA
Found at i:2184431 original size:44 final size:44
Alignment explanation
Indices: 2184339--2184469 Score: 119
Period size: 44 Copynumber: 3.0 Consensus size: 44
2184329 TTGTTATTAT
* * * *
2184339 TATTATTATGTTTCTATTTA-TATTTAT--TTTTTTGA-TTCTAA
1 TATTATTATATTTCTATTTATTATTTATCAATTTAT-ATTTCTAC
2184380 TATTATTATTATTTATCTAATTT-TTATTTATCAATTTATATTTCTAC
1 TATTATTA-TA-TT-TCT-ATTTATTATTTATCAATTTATATTTCTAC
* * *
2184427 TATTATTATATTTCTATTTATTATTTTTCTATTTCTATTTCTA
1 TATTATTATATTTCTATTTATTATTTATCAATTTATATTTCTA
2184470 TTTATATACT
Statistics
Matches: 74, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
41 8 0.11
42 1 0.01
43 6 0.08
44 26 0.35
45 13 0.18
46 3 0.04
47 17 0.23
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.65
Consensus pattern (44 bp):
TATTATTATATTTCTATTTATTATTTATCAATTTATATTTCTAC
Found at i:2184447 original size:12 final size:12
Alignment explanation
Indices: 2184432--2184476 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
2184422 TCTACTATTA
2184432 TTATATTTCTAT
1 TTATATTTCTAT
2184444 TTATTATTTTTCTAT
1 TTA-TA--TTTCTAT
*
2184459 TTCTATTTCTAT
1 TTATATTTCTAT
2184471 TTATAT
1 TTATAT
2184477 ACTAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 15 0.54
13 2 0.07
14 2 0.07
15 9 0.32
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTTCTAT
Found at i:2184449 original size:15 final size:15
Alignment explanation
Indices: 2184415--2184460 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
2184405 ATTTATCAAT
2184415 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
2184432 TTATATTTCTATTTA
1 TTATATTTCTATTTA
*
2184447 TTATTTTTCTATTT
1 TTATATTTCTATTT
2184461 CTATTTCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:2184749 original size:22 final size:22
Alignment explanation
Indices: 2184724--2184767 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2184714 TTCCAACTCT
2184724 TATACAAATTATTTATTTTAAA
1 TATACAAATTATTTATTTTAAA
*** *
2184746 TATATTTATTGTTTATTTTAAA
1 TATACAAATTATTTATTTTAAA
2184768 CTTTTCTTCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATACAAATTATTTATTTTAAA
Found at i:2190466 original size:18 final size:18
Alignment explanation
Indices: 2190443--2190494 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
2190433 CTCTTATGCG
2190443 ATTAAATTTTACTATTAA
1 ATTAAATTTTACTATTAA
2190461 ATTAAATTTTACTATTAA
1 ATTAAATTTTACTATTAA
*
2190479 ACTTTAAATTTAACTA
1 A--TTAAATTTTACTA
2190495 AATTTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 19 0.61
20 12 0.39
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTAAATTTTACTATTAA
Found at i:2200371 original size:11 final size:11
Alignment explanation
Indices: 2200351--2200404 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
2200341 TTAGAATATA
*
2200351 CCCATTCCTTG
1 CCCATACCTTG
2200362 CCCATACCTTG
1 CCCATACCTTG
*
2200373 CCCATACCTTT
1 CCCATACCTTG
*
2200384 CCCATACC-TA
1 CCCATACCTTG
2200394 CCCATACCTTG
1 CCCATACCTTG
2200405 GAAAGGTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.19, C:0.46, G:0.06, T:0.30
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:2202478 original size:31 final size:31
Alignment explanation
Indices: 2202438--2202506 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
2202428 GTTAACAGTC
*
2202438 TAGTAACTTAAATAAAAACTTTTCAATAATT
1 TAGTGACTTAAATAAAAACTTTTCAATAATT
* * *
2202469 TAGTGACTTAAATGAAAACTTTTGAATAGTT
1 TAGTGACTTAAATAAAAACTTTTCAATAATT
*
2202500 TAATGAC
1 TAGTGAC
2202507 CAAATTATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTTTCAATAATT
Found at i:2205261 original size:72 final size:72
Alignment explanation
Indices: 2205181--2205339 Score: 243
Period size: 72 Copynumber: 2.2 Consensus size: 72
2205171 ACTTGATCAC
*
2205181 ACCACTCAAGTTGTTTGATGACAAATCAAG-TGAAGTAATG-TTCACAAGATCAAAAATGGAATC
1 ACCACTCAAGTTGTTTGATGACAAATCAAGAT-AAGTAA-GCTTCACAAGATCAAAAATGAAATC
*
2205244 TGGTATTGG
64 TGGTATTGA
*
2205253 ACCACTCAAGTTGTTTGATGACAAATCAAGATAAGTAAGCTTCACAAGATCAAAATTGAAATCTG
1 ACCACTCAAGTTGTTTGATGACAAATCAAGATAAGTAAGCTTCACAAGATCAAAAATGAAATCTG
2205318 GTATTGA
66 GTATTGA
2205325 ACCAC-CAATGTTGTT
1 ACCACTCAA-GTTGTT
2205340 ATAACTCAGG
Statistics
Matches: 81, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
71 4 0.05
72 76 0.94
73 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (72 bp):
ACCACTCAAGTTGTTTGATGACAAATCAAGATAAGTAAGCTTCACAAGATCAAAAATGAAATCTG
GTATTGA
Found at i:2206755 original size:20 final size:20
Alignment explanation
Indices: 2206718--2206755 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2206708 TCAATCAAGT
*
2206718 AAATAATTTATCATATTTCA
1 AAATAATTTATCACATTTCA
2206738 AAATAATTTTAT-ACATTT
1 AAATAA-TTTATCACATTT
2206756 TTATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAATTTATCACATTTCA
Found at i:2207579 original size:17 final size:16
Alignment explanation
Indices: 2207545--2207595 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2207535 TATATAATTT
*
2207545 AAAAATATAAAAATAA
1 AAAAATTTAAAAATAA
*
2207561 AAAAATTTAAAATTCAA
1 AAAAATTTAAAAAT-AA
* *
2207578 AAAGATTTATAAA-AA
1 AAAAATTTAAAAATAA
2207593 AAA
1 AAA
2207596 TTAACATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 5 0.17
16 12 0.41
17 12 0.41
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAATTTAAAAATAA
Found at i:2210809 original size:26 final size:26
Alignment explanation
Indices: 2210780--2210941 Score: 243
Period size: 26 Copynumber: 6.2 Consensus size: 26
2210770 TGGTACAAAT
* *
2210780 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
2210806 TGATAATGGATTAGGTAAATATTCAA
1 TGATAATGGGTTAGGTAAATATTCCA
*
2210832 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
2210858 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
2210884 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
2210910 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATATTCCA
2210936 TGATAA
1 TGATAA
2210942 GAATTTCATG
Statistics
Matches: 123, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 123 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:2210845 original size:52 final size:51
Alignment explanation
Indices: 2210780--2210941 Score: 270
Period size: 52 Copynumber: 3.1 Consensus size: 51
2210770 TGGTACAAAT
*
2210780 TGATAATGTGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCAA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTC-A
2210832 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT-CA
* *
2210884 TGATAATGGGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATA-TTCA
2210936 TGATAA
1 TGATAA
2210942 GAATTTCATG
Statistics
Matches: 105, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
52 102 0.97
53 3 0.03
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (51 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCA
Found at i:2216882 original size:3 final size:3
Alignment explanation
Indices: 2216874--2217077 Score: 64
Period size: 3 Copynumber: 67.3 Consensus size: 3
2216864 TTAATATGTC
* * * * *
2216874 ATT ATT ATT ATT ATT ATT -TT GTT AAT ATT AAT ATT ATA ATT A-T ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
2216920 -TT ATT TTT ATTT ATTT ATG GTT -TT ATT ATT AATT CATT AAT -TT ACT
1 ATT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT -ATT -ATT ATT ATT ATT
** * * *
2216966 ATT ATT AAC A-T ATT ATT ATT ATT AAGGT ATT AAT ACT ATCT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -A-TT ATT ATT ATT AT-T A-TT ATT
** * * * *
2217014 ATT ATT ACC ATT -TT CATT ACT ATT ATT TTT ATT TTT ATT ACT ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
2217059 ATCT -TT TTT ATT ATT ATT A
1 AT-T ATT ATT ATT ATT ATT A
2217078 CCTTTTTGCT
Statistics
Matches: 146, Mismatches: 39, Indels: 32
0.67 0.18 0.15
Matches are distributed among these distances:
2 12 0.08
3 110 0.75
4 22 0.15
5 2 0.01
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:2217353 original size:3 final size:3
Alignment explanation
Indices: 2217345--2217445 Score: 57
Period size: 3 Copynumber: 34.0 Consensus size: 3
2217335 CATTATTTTC
* * * * * *
2217345 TAT TAT TAT TAT TAA TAT CAC TAT TAT CAT CAG TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
2217392 TA- TAA TACCT CT-T TAT TAT TAT TAC TAT T-G TAT TAT TAC TAT TAT
1 TAT TAT TA--T -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2217437 TAT TAT TAT
1 TAT TAT TAT
2217446 ATTTTCCCTT
Statistics
Matches: 74, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
2 6 0.08
3 67 0.91
6 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:2217427 original size:14 final size:15
Alignment explanation
Indices: 2217408--2217448 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
2217398 ACCTCTTTAT
2217408 TATTATTACTATT-G
1 TATTATTACTATTAG
*
2217422 TATTATTACTATTAT
1 TATTATTACTATTAG
2217437 TATTATTA-TATT
1 TATTATTACTATT
2217449 TTCCCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (15 bp):
TATTATTACTATTAG
Found at i:2217540 original size:20 final size:22
Alignment explanation
Indices: 2217515--2217577 Score: 58
Period size: 26 Copynumber: 2.8 Consensus size: 22
2217505 TGTATTAGCA
2217515 CATTTATTTTATTTATA-T-AT
1 CATTTATTTTATTTATATTCAT
*
2217535 CATTTACTCTTATTTTATTATTTCAT
1 CATTTA-TTTTA-TTTA-TA-TTCAT
*
2217561 CATCTATTTTATTTATA
1 CATTTATTTTATTTATA
2217578 GTTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
20 6 0.18
21 4 0.12
22 4 0.12
23 4 0.12
24 4 0.12
25 5 0.15
26 7 0.21
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (22 bp):
CATTTATTTTATTTATATTCAT
Found at i:2219304 original size:46 final size:44
Alignment explanation
Indices: 2219245--2219359 Score: 140
Period size: 44 Copynumber: 2.6 Consensus size: 44
2219235 ACAGGACAGA
* *
2219245 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* * *
2219291 ATAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
2219335 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2219360 GTCAAAGACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 34 0.58
46 25 0.42
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:2219351 original size:44 final size:45
Alignment explanation
Indices: 2219245--2219378 Score: 135
Period size: 46 Copynumber: 3.0 Consensus size: 45
2219235 ACAGGACAGA
* * *
2219245 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * * *
2219291 ATAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * * *
2219335 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2219379 CAGGATATTG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
44 35 0.49
45 1 0.01
46 36 0.50
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2222088 original size:72 final size:72
Alignment explanation
Indices: 2221966--2222124 Score: 232
Period size: 72 Copynumber: 2.2 Consensus size: 72
2221956 ACTTGATCAC
* * *
2221966 ACCATTCAAGTTGTTTGATGACAAATAAAGTGAAGTAAGGTTCACAAGATCAAAAATGGAATCTG
1 ACCACTCAAGTTGTTTGATGACAAATAAAGTGAAGTAAGCTTCACAAGATCAAAAATGAAATCTG
*
2222031 GTATTGG
66 GTATTGA
* *
2222038 ACCACTCAAGTTGTTTGATGACAAATCAAGAT-AAGTAAGCTTCACAAGATCAAAATTGAAATCT
1 ACCACTCAAGTTGTTTGATGACAAATAAAG-TGAAGTAAGCTTCACAAGATCAAAAATGAAATCT
2222102 GGTATTGA
65 GGTATTGA
2222110 ACCAC-CAATGTTGTT
1 ACCACTCAA-GTTGTT
2222125 ATAACTCAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 3 0.04
72 75 0.95
73 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (72 bp):
ACCACTCAAGTTGTTTGATGACAAATAAAGTGAAGTAAGCTTCACAAGATCAAAAATGAAATCTG
GTATTGA
Found at i:2224538 original size:2 final size:2
Alignment explanation
Indices: 2224531--2224561 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2224521 GGCCATTGAC
*
2224531 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2224562 GGTTTCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2224717 original size:6 final size:6
Alignment explanation
Indices: 2224683--2224729 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
2224673 ATTCGATTTA
*
2224683 ATTTTT ATATTTT -TTATTAT ATTTTT ATTTGT ATTTTT ATTTTT ATT
1 ATTTTT AT-TTTT ATT-TT-T ATTTTT ATTTTT ATTTTT ATTTTT ATT
2224730 GTAATATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 1 0.03
6 25 0.71
7 7 0.20
8 2 0.06
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:2224722 original size:20 final size:19
Alignment explanation
Indices: 2224679--2224728 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
2224669 TTCGATTCGA
2224679 TTTA-ATTTTTATATTTTT
1 TTTATATTTTTATATTTTT
*
2224697 TATTATATTTTTAT-TTGTAT
1 T-TTATATTTTTATATT-TTT
2224717 TTT-TATTTTTAT
1 TTTATATTTTTAT
2224729 TGTAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.36
19 7 0.25
20 11 0.39
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTATATTTTTATATTTTT
Found at i:2228505 original size:39 final size:39
Alignment explanation
Indices: 2228456--2228535 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
2228446 AGCACTGGCA
* *
2228456 GTCATTGAATTTATACCGA-AGGCCTATCCATCATAACAT
1 GTCATAGAATTTATACC-ATAGGCCCATCCATCATAACAT
*
2228495 GTCATAGAATTTATACCATAGGCCCATGCATCATAACAT
1 GTCATAGAATTTATACCATAGGCCCATCCATCATAACAT
2228534 GT
1 GT
2228536 TTGCAATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (39 bp):
GTCATAGAATTTATACCATAGGCCCATCCATCATAACAT
Found at i:2230957 original size:24 final size:24
Alignment explanation
Indices: 2230930--2230978 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2230920 AATTTTCCTC
2230930 ACAACAATATTAAGATTTGAACCT
1 ACAACAATATTAAGATTTGAACCT
2230954 ACAACAATATTAAGATTTGAACCT
1 ACAACAATATTAAGATTTGAACCT
2230978 A
1 A
2230979 AATTCCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (24 bp):
ACAACAATATTAAGATTTGAACCT
Found at i:2235426 original size:7 final size:7
Alignment explanation
Indices: 2235416--2235468 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
2235406 AGGTTTAAGG
2235416 TTTAAAA
1 TTTAAAA
2235423 TTTAAAA
1 TTTAAAA
2235430 TTTAAAA
1 TTTAAAA
2235437 TTTAAAA
1 TTTAAAA
* *
2235444 TTCAAGA
1 TTTAAAA
**
2235451 TTTATGA
1 TTTAAAA
*
2235458 TTTGAAA
1 TTTAAAA
2235465 TTTA
1 TTTA
2235469 GAGTTTGATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (7 bp):
TTTAAAA
Found at i:2235503 original size:14 final size:14
Alignment explanation
Indices: 2235479--2235521 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
2235469 GAGTTTGATG
*
2235479 TTCATGATTTAAGA
1 TTCAAGATTTAAGA
*
2235493 TTCGAGATTTAAGA
1 TTCAAGATTTAAGA
2235507 TTCAAGATTTAAGA
1 TTCAAGATTTAAGA
2235521 T
1 T
2235522 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (14 bp):
TTCAAGATTTAAGA
Found at i:2243919 original size:8 final size:8
Alignment explanation
Indices: 2243904--2243953 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
2243894 TCAACCAAAT
2243904 TTAA-AAA
1 TTAATAAA
2243911 TTAATAAA
1 TTAATAAA
2243919 TTAATAAA
1 TTAATAAA
2243927 --AA-AAA
1 TTAATAAA
*
2243932 TTGAAAAAA
1 TT-AATAAA
2243941 TTAATAAA
1 TTAATAAA
2243949 TTAAT
1 TTAAT
2243954 CAGTAGCTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
5 3 0.08
6 2 0.05
7 4 0.11
8 23 0.62
9 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (8 bp):
TTAATAAA
Found at i:2243931 original size:22 final size:22
Alignment explanation
Indices: 2243906--2243948 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2243896 AACCAAATTT
*
2243906 AAAAATT-AATAAATTAATAAA
1 AAAAATTGAAAAAATTAATAAA
2243927 AAAAATTGAAAAAATTAATAAA
1 AAAAATTGAAAAAATTAATAAA
2243949 TTAATCAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAATTGAAAAAATTAATAAA
Found at i:2260897 original size:18 final size:18
Alignment explanation
Indices: 2260874--2260914 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
2260864 ACTGTAATTA
2260874 TATTTTTTTATTATTCTT
1 TATTTTTTTATTATTCTT
2260892 TATTTTTTTATTATTCTT
1 TATTTTTTTATTATTCTT
2260910 TATTT
1 TATTT
2260915 ATATATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTTTTTTATTATTCTT
Found at i:2260921 original size:18 final size:18
Alignment explanation
Indices: 2260882--2260921 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2260872 TATATTTTTT
* *
2260882 TATTATTCTTTATTTTTT
1 TATTATTCTTTATTTATA
2260900 TATTATTCTTTATTTATA
1 TATTATTCTTTATTTATA
2260918 TATT
1 TATT
2260922 TATTTTGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTATTCTTTATTTATA
Found at i:2261354 original size:31 final size:31
Alignment explanation
Indices: 2261316--2261376 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2261306 GCAAGTTTGA
*
2261316 AGGAATATAATGAATTGTATAATAAATAAAG
1 AGGAATATAATCAATTGTATAATAAATAAAG
*
2261347 AGGAATATAATCAATTGTATGATAAATAAA
1 AGGAATATAATCAATTGTATAATAAATAAA
2261377 ATATCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.30
Consensus pattern (31 bp):
AGGAATATAATCAATTGTATAATAAATAAAG
Found at i:2261419 original size:2 final size:2
Alignment explanation
Indices: 2261412--2261444 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2261402 TTAGAATCTC
2261412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2261445 ATTACACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2262164 original size:33 final size:35
Alignment explanation
Indices: 2262108--2262172 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 35
2262098 AAATTAACAT
* *
2262108 TATTTATTACAAAATTTGAAAAAATTGTAAAAAAA
1 TATTTATTACAAAATTTAAAAAAATTATAAAAAAA
*
2262143 TATTT-TTA-AAAGTTTAAAAAAATTATAAAA
1 TATTTATTACAAAATTTAAAAAAATTATAAAA
2262173 TTCTAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 19 0.70
34 3 0.11
35 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (35 bp):
TATTTATTACAAAATTTAAAAAAATTATAAAAAAA
Found at i:2262172 original size:8 final size:8
Alignment explanation
Indices: 2262161--2262208 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
2262151 AAAGTTTAAA
2262161 AAAATTAT
1 AAAATTAT
*
2262169 AAAATTCT
1 AAAATTAT
2262177 AAAA-TAT
1 AAAATTAT
*
2262184 ATAATTAT
1 AAAATTAT
*
2262192 AAAATTCT
1 AAAATTAT
2262200 AAAAATTAT
1 -AAAATTAT
2262209 TTAAATTTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
7 5 0.16
8 20 0.62
9 7 0.22
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (8 bp):
AAAATTAT
Found at i:2263259 original size:51 final size:53
Alignment explanation
Indices: 2263162--2263267 Score: 153
Period size: 51 Copynumber: 2.0 Consensus size: 53
2263152 TTTTAATAGA
*
2263162 AATGACCAATTTACATTTTAATTAATCTAACGTACAGGAACTAATTTACTTATTT
1 AATGACCAATTTACA-TTT-ATTAATCTAACGTACAAGAACTAATTTACTTATTT
* *
2263217 AATGACCAATTTAC-TTT-TTAATCTAACGTATAAGAATTAATTTACTTATTT
1 AATGACCAATTTACATTTATTAATCTAACGTACAAGAACTAATTTACTTATTT
2263268 TTTAAATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
51 31 0.65
53 3 0.06
55 14 0.29
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (53 bp):
AATGACCAATTTACATTTATTAATCTAACGTACAAGAACTAATTTACTTATTT
Found at i:2263853 original size:18 final size:19
Alignment explanation
Indices: 2263818--2263855 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2263808 TCTCTCACAA
2263818 AAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
*
2263837 AAAAATTTCAAAT-TTTAT
1 AAAAATTTAAAATATTTAT
2263855 A
1 A
2263856 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:2264156 original size:26 final size:26
Alignment explanation
Indices: 2264138--2264200 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
2264128 ATTTCACTTG
2264138 ATTCGATTCGACTCGAATTACATTTC
1 ATTCGATTCGACTCGAATTACATTTC
*
2264164 ACTCGATTCGACTCGAATTACATTTC
1 ATTCGATTCGACTCGAATTACATTTC
2264190 ATTCGATTCGA
1 ATTCGATTCGA
2264201 TTCAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (26 bp):
ATTCGATTCGACTCGAATTACATTTC
Found at i:2264163 original size:31 final size:31
Alignment explanation
Indices: 2264128--2264203 Score: 101
Period size: 26 Copynumber: 2.6 Consensus size: 31
2264118 AACTCAAATA
2264128 ATTTCACTTGATTCGATTCGACTCGAATTAC
1 ATTTCACTTGATTCGATTCGACTCGAATTAC
2264159 ATTTCAC-----TCGATTCGACTCGAATTAC
1 ATTTCACTTGATTCGATTCGACTCGAATTAC
2264185 ATTTCA-TTCGATTCGATTC
1 ATTTCACTT-GATTCGATTC
2264204 AAAAAAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
26 25 0.64
31 14 0.36
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (31 bp):
ATTTCACTTGATTCGATTCGACTCGAATTAC
Found at i:2264952 original size:53 final size:53
Alignment explanation
Indices: 2264894--2264994 Score: 175
Period size: 53 Copynumber: 1.9 Consensus size: 53
2264884 ATAAATGTTA
2264894 AATCAACATTCATTCCAGAATAATAAACCCTAAATCTTAAACTATACCGAGCC
1 AATCAACATTCATTCCAGAATAATAAACCCTAAATCTTAAACTATACCGAGCC
* * *
2264947 AATCAACATTCATTCGAGAATTATAAACCCTAAATCTTAAATTATACC
1 AATCAACATTCATTCCAGAATAATAAACCCTAAATCTTAAACTATACC
2264995 AAACTAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.28
Consensus pattern (53 bp):
AATCAACATTCATTCCAGAATAATAAACCCTAAATCTTAAACTATACCGAGCC
Found at i:2267351 original size:22 final size:23
Alignment explanation
Indices: 2267298--2267358 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
2267288 CATACTATAA
* * *
2267298 TATTATTACAGTATCTAATTTTAC
1 TATTATTACATTA-ATATTTTTAC
2267322 TATTATTA-ATTAATATTTTTAC
1 TATTATTACATTAATATTTTTAC
2267344 -ATTAATTACATTAAT
1 TATT-ATTACATTAAT
2267359 GTATAGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 3 0.09
22 12 0.38
23 9 0.28
24 8 0.25
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTATTACATTAATATTTTTAC
Found at i:2274663 original size:13 final size:13
Alignment explanation
Indices: 2274645--2274671 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2274635 TGACATGCCC
2274645 CATGTACTTTATT
1 CATGTACTTTATT
2274658 CATGTACTTTATT
1 CATGTACTTTATT
2274671 C
1 C
2274672 CGACATACAA
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:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (13 bp):
CATGTACTTTATT
Found at i:2275934 original size:20 final size:20
Alignment explanation
Indices: 2275909--2275950 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2275899 GGGAGGGAGT
*
2275909 AAAAATTATGGGAAAAAATA
1 AAAAATTATGAGAAAAAATA
* *
2275929 AAAAATTTTGAGAAAAAGTA
1 AAAAATTATGAGAAAAAATA
2275949 AA
1 AA
2275951 TGGGAGAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (20 bp):
AAAAATTATGAGAAAAAATA
Found at i:2276130 original size:9 final size:9
Alignment explanation
Indices: 2276116--2276152 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
2276106 TATAATTTAA
2276116 TATTCGAAT
1 TATTCGAAT
2276125 TATTCGAAT
1 TATTCGAAT
2276134 TATTC-AAGT
1 TATTCGAA-T
2276143 TATTCGAAT
1 TATTCGAAT
2276152 T
1 T
2276153 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:2289412 original size:120 final size:119
Alignment explanation
Indices: 2289184--2289400 Score: 260
Period size: 120 Copynumber: 1.8 Consensus size: 119
2289174 AACATGAGAG
* * * *
2289184 CAAGCCACCGAAACAATTAAGCACTGCTCTATGATTCAAGACAGGTGAGACCAATCTATCCTTTC
1 CAAGCCACCGAAACAATTAAACACTGCTCTATAATTCAAGACAGGTGAGACCAATCTATCATTTA
** * * * * * *
2289249 CTTCTGCTTTTTGTAAAACGTTATCACTAAGCAAGAAAAAAGCACAAAGCAAAT
66 CTTCTGCTTTAGGAAAAAAGTAAACACAAAGAAAGAAAAAAGCACAAAGCAAAT
*
2289303 CAAGCCAGCGAAACAATTAAA-ACATAGCTCTATAATTCAAGACAGGTGAGACCAATCTATCATT
1 CAAGCCACCGAAACAATTAAACAC-T-GCTCTATAATTCAAGACAGGTGAGACCAATCTATCATT
* *
2289367 TACTTTTGC-TTAGGAAAAAAG-AAACAGAAAGAAA
64 TACTTCTGCTTTAGGAAAAAAGTAAACACAAAGAAA
2289401 ATAGAAAAAG
Statistics
Matches: 81, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
118 10 0.12
119 28 0.35
120 43 0.53
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (119 bp):
CAAGCCACCGAAACAATTAAACACTGCTCTATAATTCAAGACAGGTGAGACCAATCTATCATTTA
CTTCTGCTTTAGGAAAAAAGTAAACACAAAGAAAGAAAAAAGCACAAAGCAAAT
Found at i:2293433 original size:39 final size:39
Alignment explanation
Indices: 2293389--2293467 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
2293379 AAATACATAG
2293389 CACCGATAAAGCTAGATATACAATTTGAAGGTATTGTTA
1 CACCGATAAAGCTAGATATACAATTTGAAGGTATTGTTA
2293428 CACCGATAAAGCTAGATATACAATTTGAAGGTATTGTTA
1 CACCGATAAAGCTAGATATACAATTTGAAGGTATTGTTA
2293467 C
1 C
2293468 TCTGCCCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (39 bp):
CACCGATAAAGCTAGATATACAATTTGAAGGTATTGTTA
Found at i:2297121 original size:21 final size:22
Alignment explanation
Indices: 2297088--2297130 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2297078 ATTAAAATTG
2297088 TTAATACAATTAATCAAT-TTGT
1 TTAATACAATTAA-CAATGTTGT
*
2297110 TTAAT-CACTTAACAATGTTGT
1 TTAATACAATTAACAATGTTGT
2297131 AATTTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (22 bp):
TTAATACAATTAACAATGTTGT
Found at i:2298402 original size:22 final size:22
Alignment explanation
Indices: 2298368--2298409 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2298358 AAATAAAGTT
** *
2298368 TAGATTTTCTTAATTTTTGGAA
1 TAGATTTGATTAATATTTGGAA
2298390 TAGATTTGATTAATATTTGG
1 TAGATTTGATTAATATTTGG
2298410 GTAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (22 bp):
TAGATTTGATTAATATTTGGAA
Found at i:2299498 original size:30 final size:31
Alignment explanation
Indices: 2299435--2299498 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
2299425 GAGTCCGATT
2299435 ATAAGGTTTGAAATAGAGGGTAAAAATTTAA
1 ATAAGGTTTGAAATAGAGGGTAAAAATTTAA
2299466 ATAAGGTTTGAAATAGAGGGTAAAAA-TTAA
1 ATAAGGTTTGAAATAGAGGGTAAAAATTTAA
2299496 ATA
1 ATA
2299499 GTATATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (31 bp):
ATAAGGTTTGAAATAGAGGGTAAAAATTTAA
Found at i:2299554 original size:24 final size:24
Alignment explanation
Indices: 2299522--2299569 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2299512 ATAATAAAAA
* * *
2299522 TATAATTTTGTTATTTTAATAATT
1 TATAATTTTATAATTTTAAAAATT
*
2299546 TATATTTTTATAATTTTAAAAATT
1 TATAATTTTATAATTTTAAAAATT
2299570 AAATCAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TATAATTTTATAATTTTAAAAATT
Found at i:2305048 original size:26 final size:26
Alignment explanation
Indices: 2304992--2305051 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
2304982 ATATTAAATT
2304992 TATTTTAATGTGTAATTTAATACATA
1 TATTTTAATGTGTAATTTAATACATA
* * **
2305018 AATTTTAAT-TTTAATTTAATTATGTA
1 TATTTTAATGTGTAATTTAA-TACATA
2305044 TATTTTAA
1 TATTTTAA
2305052 GAAATAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (26 bp):
TATTTTAATGTGTAATTTAATACATA
Found at i:2311542 original size:16 final size:15
Alignment explanation
Indices: 2311516--2311547 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
2311506 CGTGCGTTTA
2311516 CTGAAAAGAACAATG
1 CTGAAAAGAACAATG
2311531 CTGAAGAAGAACAATG
1 CTGAA-AAGAACAATG
2311547 C
1 C
2311548 AATGAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (15 bp):
CTGAAAAGAACAATG
Found at i:2311620 original size:6 final size:6
Alignment explanation
Indices: 2311609--2311644 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
2311599 AGAATCGTCC
2311609 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG
2311645 TTAAGGGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
ATTTGG
Found at i:2312826 original size:15 final size:15
Alignment explanation
Indices: 2312802--2312834 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2312792 TCTACAAAAC
2312802 TTAAAAAAATCATGT
1 TTAAAAAAATCATGT
*
2312817 TTAAATAAATCATGT
1 TTAAAAAAATCATGT
2312832 TTA
1 TTA
2312835 GTAAATAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
TTAAAAAAATCATGT
Found at i:2316708 original size:18 final size:19
Alignment explanation
Indices: 2316664--2316710 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
2316654 ATATGTCATT
2316664 TTAACAAATA-ATTTAAAAG
1 TTAA-AAATATATTTAAAAG
* *
2316683 TTATAAATATATTTTAAA-
1 TTAAAAATATATTTAAAAG
2316701 TTAAAAATAT
1 TTAAAAATAT
2316711 CAAACTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAAAAATATATTTAAAAG
Found at i:2317741 original size:2 final size:2
Alignment explanation
Indices: 2317734--2317771 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2317724 TCAAATGCAA
2317734 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2317772 TTTAATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2319647 original size:31 final size:31
Alignment explanation
Indices: 2319612--2319672 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
2319602 CATTACCGCA
*
2319612 ACTTAACTAAAAAAGTTCAAATAGTTCAATG
1 ACTTAAATAAAAAAGTTCAAATAGTTCAATG
* ** *
2319643 ACTTAAATGAAAACTTTCATATAGTTCAAT
1 ACTTAAATAAAAAAGTTCAAATAGTTCAAT
2319673 TATTGTTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (31 bp):
ACTTAAATAAAAAAGTTCAAATAGTTCAATG
Found at i:2331558 original size:22 final size:22
Alignment explanation
Indices: 2331520--2331563 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2331510 TTTATTAATT
2331520 AAATTTAATTATGAAAATATATA
1 AAATTTAATTA-GAAAATATATA
2331543 AAATATTAATTA-AAAATATAT
1 AAAT-TTAATTAGAAAATATAT
2331564 TTTTTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
24 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATTTAATTAGAAAATATATA
Found at i:2335779 original size:32 final size:32
Alignment explanation
Indices: 2335730--2335796 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
2335720 AACTTTTATG
*
2335730 AAATATTTTCAGAAAATTGA-TCAAACAACCAA
1 AAATATTTTCAGAAAATTCATTCAAA-AACCAA
* *
2335762 AAATATTTTACA-TAAATTCATTCAAATACCAA
1 AAATATTTT-CAGAAAATTCATTCAAAAACCAA
2335794 AAA
1 AAA
2335797 ATTATTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.28
Consensus pattern (32 bp):
AAATATTTTCAGAAAATTCATTCAAAAACCAA
Found at i:2338836 original size:59 final size:61
Alignment explanation
Indices: 2338760--2338897 Score: 169
Period size: 59 Copynumber: 2.3 Consensus size: 61
2338750 TTTTTTCTTT
* * * * * *
2338760 ATCCAATTATG-AAAGTTACT-AAATGGTTACTTAATTA-CTAGTATATTTTTTTTTTG-TC
1 ATCCAAATATGAAAAGTTACTAAAATGGTCACTCAACTATC-AGTAAATTTCTTTTTTGATC
*
2338818 ATTCAAATATGAAAAGTTA-TAAAATGGTCACTCAACTATCAGTAAATTTCTTTTTTGATC
1 ATCCAAATATGAAAAGTTACTAAAATGGTCACTCAACTATCAGTAAATTTCTTTTTTGATC
2338878 ATCCAAATATGAAAAGTTAC
1 ATCCAAATATGAAAAGTTAC
2338898 AACATAGCTA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
58 10 0.15
59 36 0.54
60 21 0.31
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (61 bp):
ATCCAAATATGAAAAGTTACTAAAATGGTCACTCAACTATCAGTAAATTTCTTTTTTGATC
Found at i:2341120 original size:25 final size:22
Alignment explanation
Indices: 2341084--2341130 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
2341074 ATATTAATGC
*
2341084 AAATTTAGATTAATTTTTATAAAA
1 AAATTTAAATT-ATTTTT-TAAAA
2341108 AAATATTAAATTATTTTTTAAAA
1 AAAT-TTAAATTATTTTTTAAAA
2341131 GGTAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 10 0.48
25 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATTTAAATTATTTTTTAAAA
Found at i:2345607 original size:2 final size:2
Alignment explanation
Indices: 2345595--2345626 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2345585 ATATTTTCTC
*
2345595 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2345627 TATTATACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2350468 original size:3 final size:3
Alignment explanation
Indices: 2350454--2350529 Score: 61
Period size: 3 Copynumber: 26.0 Consensus size: 3
2350444 ATATAGATAT
* * *
2350454 TTA TTAA TTA TTA TTA TTA TTA TT- CTA TTA -AA TTA TAA TT- TATA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
2350498 TTA TTA -AA TTA TGA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2350530 AAAATAAATT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
2 4 0.07
3 49 0.86
4 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2350483 original size:20 final size:19
Alignment explanation
Indices: 2350454--2350529 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 19
2350444 ATATAGATAT
*
2350454 TTATTAATTATTATTATTA
1 TTATTTATTATTATTATTA
* *
2350473 TTATTCTATTA-AATTATAA
1 TTATT-TATTATTATTATTA
* *
2350492 TT-TATATTATTA-AATTA
1 TTATTTATTATTATTATTA
*
2350509 TGA-TTATTATTATTATTA
1 TTATTTATTATTATTATTA
2350527 TTA
1 TTA
2350530 AAAATAAATT
Statistics
Matches: 42, Mismatches: 11, Indels: 9
0.68 0.18 0.15
Matches are distributed among these distances:
17 17 0.40
18 8 0.19
19 13 0.31
20 4 0.10
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (19 bp):
TTATTTATTATTATTATTA
Found at i:2350499 original size:25 final size:23
Alignment explanation
Indices: 2350451--2350526 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
2350441 AGTATATAGA
*
2350451 TATTTATTAATTATTATTATTAT
1 TATTTATTAATTATAATTATTAT
2350474 TATTCTATTAAATTATAA-T-TTA-
1 TATT-TATT-AATTATAATTATTAT
*
2350496 TA-TTATTAAATTATGATTATTAT
1 TATTTATT-AATTATAATTATTAT
2350519 TA-TTATTA
1 TATTTATTA
2350527 TTAAAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
20 12 0.26
21 2 0.04
22 6 0.13
23 14 0.30
24 5 0.11
25 7 0.15
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (23 bp):
TATTTATTAATTATAATTATTAT
Found at i:2350825 original size:13 final size:13
Alignment explanation
Indices: 2350807--2350858 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
2350797 TTATAAAGTT
2350807 AATAAAATGAAAG-
1 AATAAAAT-AAAGA
2350820 AATAAAATAAATGA
1 AATAAAATAAA-GA
2350834 AATAAAATAAAGA
1 AATAAAATAAAGA
*
2350847 AATAAAACAAAG
1 AATAAAATAAAG
2350859 TAAAGAAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 3 0.08
13 22 0.61
14 11 0.31
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:2351246 original size:40 final size:40
Alignment explanation
Indices: 2351184--2351264 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
2351174 AATTATGGGA
* ** *
2351184 TACTGAATATTGTTTTGAATACTGAATTGAACTGTGAAAT
1 TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
* * *
2351224 TACTGAATAATGTTACGTATACTGCATTGAATTGTAAAAT
1 TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
2351264 T
1 T
2351265 TTTAATGAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (40 bp):
TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
Found at i:2351527 original size:45 final size:45
Alignment explanation
Indices: 2351477--2351575 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 45
2351467 CGACTACTAT
*
2351477 TACTGTTACCGTTACTGTTACCGATCC-GACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATCCAG-CACTTTGTGTGTCGAA
* *
2351522 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATCCAGCACTTTGTGTGTCGAA
2351567 TACTGTTAC
1 TACTGTTAC
2351576 TAATTACTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
45 49 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATCCAGCACTTTGTGTGTCGAA
Found at i:2367241 original size:50 final size:50
Alignment explanation
Indices: 2367182--2367281 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
2367172 ACATAGCCAT
2367182 TAGGTAATGTAAAGTCTACCTACTTTAATTGAAGCAATTAAATAGTTTGG
1 TAGGTAATGTAAAGTCTACCTACTTTAATTGAAGCAATTAAATAGTTTGG
2367232 TAGGTAATGTAAAGTCTACCTACTTTAATTGAAGCAATTAAATAGTTTGG
1 TAGGTAATGTAAAGTCTACCTACTTTAATTGAAGCAATTAAATAGTTTGG
2367282 ATCCTTTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (50 bp):
TAGGTAATGTAAAGTCTACCTACTTTAATTGAAGCAATTAAATAGTTTGG
Found at i:2373507 original size:14 final size:14
Alignment explanation
Indices: 2373488--2373515 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2373478 TGAAAGATCC
2373488 AAAAAAAACAAAAA
1 AAAAAAAACAAAAA
2373502 AAAAAAAACAAAAA
1 AAAAAAAACAAAAA
2373516 TGGCAATGAA
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:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAAA
Found at i:2376234 original size:32 final size:33
Alignment explanation
Indices: 2376190--2376251 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
2376180 CAAAAGTTCC
* *
2376190 TAGTTGGTACCTGAA-TTGTCTAAACAAATACG
1 TAGTTGGCACCTGAACTTGTCTAAAAAAATACG
2376222 TAGTTGGCACCTGAACTTGTCTAAAAAAAT
1 TAGTTGGCACCTGAACTTGTCTAAAAAAAT
2376252 TGTACTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (33 bp):
TAGTTGGCACCTGAACTTGTCTAAAAAAATACG
Found at i:2379420 original size:38 final size:38
Alignment explanation
Indices: 2379331--2379419 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
2379321 AACAATAATA
* * **
2379331 TTTAATACAATGAAATATTTATTATATTTATTTGTATT
1 TTTAATATAATAAAATATTTATTATATTTATAAGTATT
*
2379369 TTTAATATAATAAAATATTTATTATATTTATGGAAGTGTTT
1 TTTAATATAATAAAATATTTATTATATTTAT--AAGT-ATT
2379410 TTTAATATAA
1 TTTAATATAA
2379420 ATACTTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 29 0.67
40 2 0.05
41 12 0.28
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (38 bp):
TTTAATATAATAAAATATTTATTATATTTATAAGTATT
Found at i:2380085 original size:19 final size:19
Alignment explanation
Indices: 2380049--2380086 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2380039 TAATGACAAT
*
2380049 AAAATAATTTAATAATATA
1 AAAATAATTTAAAAATATA
2380068 AAAAT-ATTTAAAACATATA
1 AAAATAATTTAAAA-ATATA
2380087 TTAAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATAATTTAAAAATATA
Found at i:2380621 original size:3 final size:3
Alignment explanation
Indices: 2380613--2380645 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2380603 TTAGACTTCT
2380613 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2380646 TGAACTTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2380671 original size:3 final size:3
Alignment explanation
Indices: 2380663--2380701 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2380653 TCGAGATTCA
2380663 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2380702 TACCTTTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2383133 original size:15 final size:15
Alignment explanation
Indices: 2383113--2383142 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2383103 AAACCAACAA
2383113 AGCAAAGTAATTGTT
1 AGCAAAGTAATTGTT
2383128 AGCAAAGTAATTGTT
1 AGCAAAGTAATTGTT
2383143 GGAATTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (15 bp):
AGCAAAGTAATTGTT
Found at i:2385942 original size:69 final size:69
Alignment explanation
Indices: 2385831--2385969 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
2385821 CAAGACTCTA
*
2385831 TCAGCCCTACCACCACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
1 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
2385896 CCTG
66 CCTG
2385900 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
1 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
2385965 CCTG
66 CCTG
2385969 T
1 T
2385970 TTTTCCTATC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.27
Consensus pattern (69 bp):
TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
CCTG
Found at i:2392492 original size:71 final size:71
Alignment explanation
Indices: 2392406--2392546 Score: 264
Period size: 71 Copynumber: 2.0 Consensus size: 71
2392396 GAAAATAACT
*
2392406 CTTAAATTTTATCAAACTGTCCATGCCGTAAGTACACAAGTACTTAAGACTTCAGAGTTTGATTC
1 CTTAAATTTTATCAAACTGTCCATGCCATAAGTACACAAGTACTTAAGACTTCAGAGTTTGATTC
2392471 ACGTGA
66 ACGTGA
*
2392477 CTTAAATTTTATCAAACTGTCCATGCCATAAGTACACAAGTACTTAAGACTTTAGAGTTTGATTC
1 CTTAAATTTTATCAAACTGTCCATGCCATAAGTACACAAGTACTTAAGACTTCAGAGTTTGATTC
2392542 ACGTG
66 ACGTG
2392547 CTTCAAGTTC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (71 bp):
CTTAAATTTTATCAAACTGTCCATGCCATAAGTACACAAGTACTTAAGACTTCAGAGTTTGATTC
ACGTGA
Found at i:2392927 original size:53 final size:53
Alignment explanation
Indices: 2392865--2392970 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
2392855 AAGAAAAGTG
*
2392865 TAATGCCATCCAAATTATCACTCGAATCAAGAAACTCAAAAGGGAGGGGTTAA
1 TAATGCCATCCAAATTATCACTCGAATCAAGAAACTCAAAAGGGAGGAGTTAA
*
2392918 TAATGCCATCCAAATTATCATTCGAATCAAGAAACTCAAAAGGGAGGAGTTAA
1 TAATGCCATCCAAATTATCACTCGAATCAAGAAACTCAAAAGGGAGGAGTTAA
2392971 CCTTACTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (53 bp):
TAATGCCATCCAAATTATCACTCGAATCAAGAAACTCAAAAGGGAGGAGTTAA
Found at i:2398768 original size:36 final size:36
Alignment explanation
Indices: 2398726--2398797 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
2398716 AACCATAAAG
2398726 ATGTTATATTTGCAGAGCAAATCAATAGCTCCATCT
1 ATGTTATATTTGCAGAGCAAATCAATAGCTCCATCT
2398762 ATGTTATATTTGCAGAGCAAATCAATAGCTCCATCT
1 ATGTTATATTTGCAGAGCAAATCAATAGCTCCATCT
2398798 TAATTTCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (36 bp):
ATGTTATATTTGCAGAGCAAATCAATAGCTCCATCT
Found at i:2400271 original size:20 final size:20
Alignment explanation
Indices: 2400246--2400285 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2400236 AATTTAATCC
*
2400246 AAAAAAATTACAA-GAAATGA
1 AAAAAAAAT-CAATGAAATGA
2400266 AAAAAAAATCAATGAAATGA
1 AAAAAAAATCAATGAAATGA
2400286 GAGAATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.70, C:0.05, G:0.10, T:0.15
Consensus pattern (20 bp):
AAAAAAAATCAATGAAATGA
Found at i:2401646 original size:5 final size:5
Alignment explanation
Indices: 2401636--2401677 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
2401626 ACATATAATA
2401636 ATATT ATATT ATATT ATATT ATATT ATA-T ATATT -T-TT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
2401678 TTTTAGTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 2 0.06
4 6 0.18
5 26 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATATT
Found at i:2403974 original size:17 final size:17
Alignment explanation
Indices: 2403952--2403986 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2403942 TCCATTGCCT
2403952 CTGAATAAACGAGACTG
1 CTGAATAAACGAGACTG
2403969 CTGAATAAACGAGACTG
1 CTGAATAAACGAGACTG
2403986 C
1 C
2403987 AAATCTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (17 bp):
CTGAATAAACGAGACTG
Found at i:2411508 original size:28 final size:28
Alignment explanation
Indices: 2411477--2411547 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
2411467 ATATTGATTT
* * * *
2411477 TTAAATCTATTAAGTCAAATTAGTTCAA
1 TTAAATCTATTAAATCAAAATAATTAAA
2411505 TTAAATCTATTAAATCAAAATAATTAAA
1 TTAAATCTATTAAATCAAAATAATTAAA
*
2411533 TTAAATCTATAAAAT
1 TTAAATCTATTAAAT
2411548 AGGTTTAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (28 bp):
TTAAATCTATTAAATCAAAATAATTAAA
Found at i:2411547 original size:14 final size:14
Alignment explanation
Indices: 2411477--2411547 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
2411467 ATATTGATTT
*
2411477 TTAAATCTATTAAG
1 TTAAATCTATTAAA
* *
2411491 TCAAAT-TAGTTCAA
1 TTAAATCTA-TTAAA
2411505 TTAAATCTATTAAA
1 TTAAATCTATTAAA
* *
2411519 TCAAAAT-AATTAAA
1 T-TAAATCTATTAAA
*
2411533 TTAAATCTATAAAA
1 TTAAATCTATTAAA
2411547 T
1 T
2411548 AGGTTTAAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
13 6 0.14
14 31 0.72
15 6 0.14
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (14 bp):
TTAAATCTATTAAA
Found at i:2414192 original size:15 final size:16
Alignment explanation
Indices: 2414161--2414192 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2414151 TCTTTCGAAA
2414161 TTTCTTTTTTTTCTTT
1 TTTCTTTTTTTTCTTT
2414177 TTTC-TTTTTTTCTTT
1 TTTCTTTTTTTTCTTT
2414192 T
1 T
2414193 ATTTTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTCTTTTTTTTCTTT
Found at i:2415109 original size:14 final size:11
Alignment explanation
Indices: 2415055--2415115 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 11
2415045 CGTGTGCGTA
2415055 TATATATATTT
1 TATATATATTT
*
2415066 GTA-ACTATATTG
1 -TATA-TATATTT
*
2415078 TGTATATATTT
1 TATATATATTT
2415089 TATATATATTAT
1 TATATATATT-T
2415101 TATGCATATATTT
1 TAT--ATATATTT
2415114 TA
1 TA
2415116 GCATCATTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
11 17 0.43
12 13 0.32
13 3 0.08
14 7 0.17
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (11 bp):
TATATATATTT
Found at i:2416676 original size:3 final size:3
Alignment explanation
Indices: 2416662--2416724 Score: 108
Period size: 3 Copynumber: 20.7 Consensus size: 3
2416652 ATTTTTATAA
*
2416662 TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2416710 TAT TAT TAT GTAT TA
1 TAT TAT TAT -TAT TA
2416725 GCTTATGTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2417394 original size:2 final size:2
Alignment explanation
Indices: 2417389--2417417 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2417379 TATATTGTCT
2417389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2417418 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2418778 original size:15 final size:16
Alignment explanation
Indices: 2418753--2418783 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2418743 ATGTATATAT
2418753 TATGTTTTTTTAATAC
1 TATGTTTTTTTAATAC
2418769 TATG-TTTTTTAATAC
1 TATGTTTTTTTAATAC
2418784 CATATGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TATGTTTTTTTAATAC
Found at i:2418815 original size:27 final size:27
Alignment explanation
Indices: 2418777--2418852 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
2418767 ACTATGTTTT
*
2418777 TTAATACCATATGTAT-TGTGTATATTC
1 TTAATACTATAT-TATATGTGTATATTC
* *
2418804 TTAATACTATA-TATTATATGTATTTTC
1 TTAATACTATATTA-TATGTGTATATTC
*
2418831 TTAATAACTATATTATGTGTGT
1 TTAAT-ACTATATTATATGTGT
2418853 TATAGGCCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
25 2 0.05
26 1 0.03
27 24 0.60
28 11 0.28
29 2 0.05
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (27 bp):
TTAATACTATATTATATGTGTATATTC
Found at i:2419572 original size:21 final size:20
Alignment explanation
Indices: 2419547--2419586 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2419537 ATAAACATAA
*
2419547 AGAAATAAAAAGCAAAAAAAG
1 AGAAA-AAAAAGAAAAAAAAG
*
2419568 AGAAAAAAAATAAAAAAAA
1 AGAAAAAAAAGAAAAAAAA
2419587 TTACCTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (20 bp):
AGAAAAAAAAGAAAAAAAAG
Found at i:2420534 original size:2 final size:2
Alignment explanation
Indices: 2420518--2420556 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
2420508 ATTTGAGTGT
2420518 TA TA T- TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2420557 TTCCAATGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2433424 original size:71 final size:71
Alignment explanation
Indices: 2433303--2433436 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
2433293 GTTTTCCAAG
* * *
2433303 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
2433368 GTTTCA
66 GTTTCA
* * *
2433374 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
2433437 CTACTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Done.