Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 9 of 325
Found at i:2596533 original size:61 final size:62
Alignment explanation
Indices: 2596441--2596560 Score: 136
Period size: 61 Copynumber: 2.0 Consensus size: 62
2596431 TTTTTCTCAA
* * * * * ** *
2596441 TTTTTAAAGTTAGGACTAAATTGATAGATTTTGTAAATGTTGAG-GACTAAGTTTATTAATTT
1 TTTTTAAAGTTAGAACTAAAATAATAAATTTTATAAACATTGAGCG-CTAAATTTATTAATTT
*
2596503 TTTTTGAA-TTAGAACTAAAATAATAAATTTTATAAACATTGAGCGCTAAATTTATTAA
1 TTTTTAAAGTTAGAACTAAAATAATAAATTTTATAAACATTGAGCGCTAAATTTATTAA
2596561 ACATTTTATA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
61 40 0.83
62 8 0.17
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (62 bp):
TTTTTAAAGTTAGAACTAAAATAATAAATTTTATAAACATTGAGCGCTAAATTTATTAATTT
Found at i:2601867 original size:11 final size:11
Alignment explanation
Indices: 2601849--2601884 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2601839 GAAGGGAAGG
2601849 AAAGAAAGAAA
1 AAAGAAAGAAA
*
2601860 AGAGAAAGAAA
1 AAAGAAAGAAA
2601871 AAAGAAAGGAAA
1 AAAGAAA-GAAA
2601883 AA
1 AA
2601885 TAGGGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:2602567 original size:17 final size:16
Alignment explanation
Indices: 2602536--2602579 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
2602526 TTAAAAATGT
2602536 ATTG-AATTGATATTG
1 ATTGAAATTGATATTG
2602551 ATTGAAATTGTATATTG
1 ATTGAAATTG-ATATTG
2602568 ATTGGAAATTGA
1 ATT-GAAATTGA
2602580 ATTATGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 10 0.38
18 7 0.27
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
ATTGAAATTGATATTG
Found at i:2602593 original size:18 final size:17
Alignment explanation
Indices: 2602536--2602594 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
2602526 TTAAAAATGT
2602536 ATTG-AATTG-ATATTG
1 ATTGAAATTGAATATTG
*
2602551 ATTGAAATTGTATATTG
1 ATTGAAATTGAATATTG
2602568 ATTGGAAATTGAAT-TATG
1 ATT-GAAATTGAATAT-TG
2602586 AATTGAAAT
1 -ATTGAAAT
2602595 ACCCTATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
15 4 0.11
16 5 0.13
17 10 0.26
18 16 0.42
19 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (17 bp):
ATTGAAATTGAATATTG
Found at i:2604811 original size:16 final size:16
Alignment explanation
Indices: 2604770--2604816 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2604760 GGATCTAAGT
2604770 TTTCTTGTTTATTTCAG
1 TTTCTT-TTTATTTCAG
2604787 TTT-TGTTTTATTTCA-
1 TTTCT-TTTTATTTCAG
2604802 TCTTCTTTTTATTTC
1 T-TTCTTTTTATTTC
2604817 TATTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 21 0.78
17 5 0.19
ACGTcount: A:0.11, C:0.13, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTCTTTTTATTTCAG
Found at i:2604826 original size:16 final size:15
Alignment explanation
Indices: 2604777--2604826 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
2604767 AGTTTTCTTG
*
2604777 TTTATTTCAGTTTTGT
1 TTTATTTCA-TTTTTT
*
2604793 TTTATTTCATCTTCTT
1 TTTATTTCAT-TTTTT
2604809 TTTATTTCTATTTTTT
1 TTTATTTC-ATTTTTT
2604825 TT
1 TT
2604827 CTTACTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 26 0.90
17 2 0.07
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.74
Consensus pattern (15 bp):
TTTATTTCATTTTTT
Found at i:2605700 original size:26 final size:26
Alignment explanation
Indices: 2605671--2605952 Score: 113
Period size: 26 Copynumber: 11.0 Consensus size: 26
2605661 TTAGATACCT
2605671 TTTATTTTAAACTATTTTATATATTA
1 TTTATTTTAAACTATTTTATATATTA
* *
2605697 TTTA-TTTAAAAT-TTTTATATGTTA
1 TTTATTTTAAACTATTTTATATATTA
** * * * *
2605721 TTTA-GATATATTATTCTATATGTTA
1 TTTATTTTAAACTATTTTATATATTA
* * * *
2605746 ATCACTTTAAGTTCCT-TTTTAT-TATT-
1 TTTATTTTAA---ACTATTTTATATATTA
* **
2605772 TTTATTTTGAACT-TTCCATATATTA
1 TTTATTTTAAACTATTTTATATATTA
* *
2605797 TTTATTTTTAAA-TATTTTTATATACTC
1 TTTA-TTTTAAACTA-TTTTATATATTA
* *
2605824 TTTATTTTAAACTACTTTATGTATTA
1 TTTATTTTAAACTATTTTATATATTA
*
2605850 TTATCTATTTAAA--ATTTTCATATATAGTA
1 TT-TAT-TTTAAACTATTTT-ATATAT--TA
* * * * *
2605879 TTTAGTTTAAATTGTTTTATATGTTC
1 TTTATTTTAAACTATTTTATATATTA
* * *
2605905 CTCATTTTAAA--ACTTT-TATATTA
1 TTTATTTTAAACTATTTTATATATTA
* *
2605928 TTTATTTTAAGCTCTTTTATATATT
1 TTTATTTTAAACTATTTTATATATT
2605953 TTCAAAGGGT
Statistics
Matches: 183, Mismatches: 52, Indels: 42
0.66 0.19 0.15
Matches are distributed among these distances:
23 19 0.10
24 26 0.14
25 28 0.15
26 54 0.30
27 30 0.16
28 17 0.09
29 9 0.05
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTATTTTAAACTATTTTATATATTA
Found at i:2606158 original size:22 final size:24
Alignment explanation
Indices: 2606086--2606163 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 24
2606076 CTTTTTTTGC
* * *
2606086 ATATTGTTTATTCTGAATCATTTCAT
1 ATATTATTTATTTTAAATC-TTT-AT
*
2606112 ATATTATTTATTTTAAATTTTTTTAT
1 ATATTATTTATTTTAAA--TCTTTAT
2606138 ATATTATTT-TTTTAAA-CTTTAT
1 ATATTATTTATTTTAAATCTTTAT
2606160 ATAT
1 ATAT
2606164 CTTTTTACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
22 9 0.20
25 7 0.16
26 25 0.56
27 3 0.07
28 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (24 bp):
ATATTATTTATTTTAAATCTTTAT
Found at i:2606162 original size:24 final size:26
Alignment explanation
Indices: 2606110--2606176 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 26
2606100 GAATCATTTC
* *
2606110 ATATATTATTTATTTTAAATTTTTTT
1 ATATATTATTTATTTTAAATCTTTAT
2606136 ATATATTATTT-TTTTAAA-CTTTAT
1 ATATATTATTTATTTTAAATCTTTAT
* *
2606160 ATATCTT-TTTACTTTAA
1 ATATATTATTTATTTTAA
2606177 TTGGTTTCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.08
24 15 0.42
25 7 0.19
26 11 0.31
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
ATATATTATTTATTTTAAATCTTTAT
Found at i:2606323 original size:13 final size:13
Alignment explanation
Indices: 2606305--2606329 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2606295 TTTTTTTCAT
2606305 ATTATTTCATATA
1 ATTATTTCATATA
2606318 ATTATTTCATAT
1 ATTATTTCATAT
2606330 TGTCCATTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATTTCATATA
Found at i:2611496 original size:17 final size:17
Alignment explanation
Indices: 2611464--2611501 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2611454 TTTATAACTT
2611464 TATTTATTTAATTTTAA
1 TATTTATTTAATTTTAA
*
2611481 GTATTT-TTTTATTTTAA
1 -TATTTATTTAATTTTAA
2611498 TATT
1 TATT
2611502 AATACTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 10 0.53
18 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TATTTATTTAATTTTAA
Found at i:2618379 original size:24 final size:24
Alignment explanation
Indices: 2618352--2618398 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2618342 AAATATTATA
*
2618352 TAAAAAAGTAAAA-AAAACTAAAAT
1 TAAAAAACTAAAATAAAA-TAAAAT
*
2618376 TAAAAATCTAAAATAAAATAAAA
1 TAAAAAACTAAAATAAAATAAAA
2618399 AAAGCACGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (24 bp):
TAAAAAACTAAAATAAAATAAAAT
Found at i:2618501 original size:13 final size:13
Alignment explanation
Indices: 2618469--2618510 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2618459 TTTTAGAAAT
2618469 AAAAAAAAT-TAA
1 AAAAAAAATCTAA
*
2618481 AATTAAAAATCTAA
1 AA-AAAAAATCTAA
*
2618495 AAAAAAAAACTAA
1 AAAAAAAATCTAA
2618508 AAA
1 AAA
2618511 TTAGTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 2 0.08
13 18 0.72
14 5 0.20
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAAAAATCTAA
Found at i:2629051 original size:28 final size:28
Alignment explanation
Indices: 2629002--2629065 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
2628992 TGGATTCTCT
* * *
2629002 AAGGCTTGTGTGCGTCATTTCATTACAG
1 AAGGCTTGTGTGCGCCAATTCATAACAG
*
2629030 AAGGCTTGTGTGAC-CCAATTCATAACGG
1 AAGGCTTGTGTG-CGCCAATTCATAACAG
2629058 AAGGCTTG
1 AAGGCTTG
2629066 CTGAGTCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (28 bp):
AAGGCTTGTGTGCGCCAATTCATAACAG
Found at i:2642299 original size:21 final size:21
Alignment explanation
Indices: 2642274--2642327 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
2642264 TGCAAGGCAT
2642274 ACACGCCCGTGTGGCCAAGGG
1 ACACGCCCGTGTGGCCAAGGG
* * *
2642295 ACACGCCCGTGAGGTCATGGG
1 ACACGCCCGTGTGGCCAAGGG
*
2642316 ACACACCCGTGT
1 ACACGCCCGTGT
2642328 CTCAGGCCGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.13
Consensus pattern (21 bp):
ACACGCCCGTGTGGCCAAGGG
Found at i:2644425 original size:12 final size:12
Alignment explanation
Indices: 2644408--2644435 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2644398 ATAAAATTTA
2644408 ATAATATAATAT
1 ATAATATAATAT
2644420 ATAATATAATAT
1 ATAATATAATAT
2644432 ATAA
1 ATAA
2644436 AACATAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:2647147 original size:91 final size:91
Alignment explanation
Indices: 2647039--2647205 Score: 237
Period size: 91 Copynumber: 1.8 Consensus size: 91
2647029 AATAGACAAT
* * * *
2647039 AAAAATAGAAATTGAAAATAGCTCAGCGTGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGA-CCTAAGGCTCAACTCACCTCTCACAATACGA
2647103 GTCGATTTTTTTGAAAGGAAAAAATTG
65 GTCGATTTTTTTGAAAGGAAAAAATTG
* * **
2647130 AAAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGTCTCTCACAATACGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCTAAGGCTCAACTCACCTCTCACAATACGAG
*
2647195 TTGATTTTTTT
66 TCGATTTTTTT
2647206 TTTGACAACA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
90 2 0.03
91 64 0.97
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (91 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCTAAGGCTCAACTCACCTCTCACAATACGAG
TCGATTTTTTTGAAAGGAAAAAATTG
Found at i:2647267 original size:77 final size:78
Alignment explanation
Indices: 2647133--2648860 Score: 462
Period size: 75 Copynumber: 21.9 Consensus size: 78
2647123 AAAATTGAAA
** * **
2647133 AACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGTCTCTCACAATACGAGTTG
1 AACAGAAATTGAAAATACCTCAACATGT-ACCTGAGGCTCAACTCACCTCTCACAATACGAGTTG
*
2647198 ATTTTTTTTTTGAC
65 AATTTTTTTTTGAC
* * *
2647212 AACAGAAATTGAAATTACCTCAACATGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTGA
*
2647276 A---TTTTTTGAA
66 ATTTTTTTTTGAC
* * * * ** * * * * * * *
2647286 AATATAAATTTAAAAGCAGAAATTGAA-AT-TAACTCAACGTGCCTTGAGGCTCAACT-T-AC-C
1 AACAGAAA-TTGAAA--A-TACCTCAACATGTACCT-GA-G-G-C-TCA-ACTCACCTCTCACAA
* * * *
2647346 TCTCGTAGTATGAGTTGATTTTTTGAA
56 T-ACG-AGT-TGAATT-TTTTTTTGAC
* * * * * ** * *
2647373 AGATAAAAATTGAAAATACCTCAGCATGT-CTTAAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 A-ACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTG
2647437 -A-TTTTTTTTGAC
65 AATTTTTTTTTGAC
* * * * *
2647449 AACAGAAATTGAAATTACCTCAGCGTGT-CTTGAGGCTCAACTCACCTCTCACAATATGAGTTGA
1 AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTGA
*
2647513 A-TTTTTTTTGAAA
66 ATTTTTTTTTG-AC
* * ** ** * * *
2647526 AATATAAATTGAAAAGCAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCG
1 AACAGAAATT-----G-A-AAA-T--ACCT-CAAC-ATGTACC-TGAGGCTCAACTCACCTCTCA
* *
2647591 CAATATGAGTTG-A---TTTTTTGAA
53 CAATACGAGTTGAATTTTTTTTTGAC
* * * * ** * *
2647613 AGACAAAAATTGAAAATACCTCAGCATGT-CTTAAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 A-ACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTG
2647677 -A--TTTTTTTGAC
65 AATTTTTTTTTGAC
* * * * * * *
2647688 AACAGAAATTGAAATTACCTCAGCGTGT-CTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGA
1 AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTGA
*
2647752 A--TTTTTTTGAAA
66 ATTTTTTTTTG-AC
* * ** ** * * *
2647764 AATATAAATTGAAAAGCAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCG
1 AACAGAAATT-----G-A-AAA-T--ACCT-CAAC-ATGTACC-TGAGGCTCAACTCACCTCTCA
* *
2647829 CAATATGAGTTG-A----TTTTTGAAA
53 CAATACGAGTTGAATTTTTTTTTG-AC
* * * *
2647851 AACAGAAATTGAAAATACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-
1 AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTGA
** ** *
2647914 ATTTTTGAAAAACATAAATTG
66 ATTTTT------TTTTGA--C
* * * ** * *
2647935 AACAGAAATTGAAACTACCTCAACGTGT-CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-
1 AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTGA
*
2647998 ATTTTTTTTTGAA
66 ATTTTTTTTTGAC
* * * * ** * *
2648011 AGACAAAAATTGAAAATATCTCAGCATGT-CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 A-ACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTG
*
2648075 -A--TTTTTTTGAA
65 AATTTTTTTTTGAC
* * * * ** * *
2648086 AGACAAAAATTGAAAATACCTCAGCGTGT-CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 A-ACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTG
2648150 -A-TTTTTTTT-AC
65 AATTTTTTTTTGAC
* * * * *
2648161 AACAGAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTGA
*
2648225 ATTTTTTTTTTATAAATTGAA
66 A----TTTTTT-T---TTGAC
* * * *
2648246 AAGCGGAAATTGAAATTACCTCAAC--GTGCCTTGAGGCTCAACTCACCTCTCACAATATGAGTT
1 AA-CAGAAATTGAAAATACCTCAACATGTACC-TGAGGCTCAACTCACCTCTCACAATACGAGTT
2648309 G-A----TTTTTGAC
64 GAATTTTTTTTTGAC
* * * ** ** *
2648319 AAACAGAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCATTTCTCGTAATATGAGTTG
1 -AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTG
***** *
2648383 -ATTTTTGAAAAAT
65 AATTTTTTTTTGAC
** *** * ** * * *
2648396 AGATTGAAACACAAAAATTGACAATACCTCAGTGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
1 A-ACAGAAA-TTGAAAA-T-AC-CT-CAACA-TGT-ACCTGAGGCTCAACTCACCTCTCACAATA
* *
2648461 TGAGTTG-A----TTTTTGAAA
58 CGAGTTGAATTTTTTTTTG-AC
* * * * *
2648478 AAAAGAAATTGAAAATACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-
1 AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTGA
** ** *
2648541 ATTTTTGAAAAACATAAATTG
66 ATTTTT------TTTTGA--C
* * * ** * *
2648562 AACAGAAATTGAAACTACCTCAACGTGT-CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-
1 AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTGA
* *
2648625 ATTTTTTTTTTAA
66 ATTTTTTTTTGAC
* * * * ** * *
2648638 AGACAAAAATTGAAAATACATCAGCATGT-CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 A-ACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTG
*
2648702 -A--TTTTTTTGAA
65 AATTTTTTTTTGAC
* * * ** * *
2648713 AGACAAAAATTGAAAATACCTCAGCATGT-CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 A-ACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTG
2648777 -ATTTTTTTTT-AC
65 AATTTTTTTTTGAC
* * * * * * *
2648789 AACAGAAATTGAAATTACCTCAGCGTGT-CTTGAGGCTCAACTCACCTCTCGCAATATGAATTGA
1 AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTGA
2648853 ATTTTTTT
66 ATTTTTTT
2648861 GAAAAATATA
Statistics
Matches: 1320, Mismatches: 210, Indels: 241
0.75 0.12 0.14
Matches are distributed among these distances:
73 123 0.09
74 165 0.12
75 290 0.22
76 57 0.04
77 185 0.14
78 16 0.01
79 35 0.03
80 23 0.02
81 19 0.01
82 18 0.01
83 19 0.01
84 139 0.11
85 43 0.03
86 55 0.04
87 39 0.03
88 24 0.02
89 4 0.00
90 34 0.03
91 32 0.02
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (78 bp):
AACAGAAATTGAAAATACCTCAACATGTACCTGAGGCTCAACTCACCTCTCACAATACGAGTTGA
ATTTTTTTTTGAC
Found at i:2647363 original size:88 final size:88
Alignment explanation
Indices: 2647214--2647388 Score: 255
Period size: 88 Copynumber: 2.0 Consensus size: 88
2647204 TTTTTGACAA
*
2647214 CAGAAATTGAAATTACCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAATTAACTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATT
* *
2647279 TTTTGAAA-ATATAAATTTAAAAG
65 TTTTGAAAGATAAAAATTGAAAAG
* * * *
2647302 CAGAAATTGAAATTAACTCAACGTG-CCTTGAGGCTCAACTTACCTCTCGTAGTATGAGTTGATT
1 CAGAAATTGAAATTAACTCAACATGTCC-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
2647366 TTTTGAAAGATAAAAATTGAAAA
65 TTTTGAAAGATAAAAATTGAAAA
2647389 TACCTCAGCA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
87 13 0.17
88 65 0.83
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (88 bp):
CAGAAATTGAAATTAACTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTTGAAAGATAAAAATTGAAAAG
Found at i:2647859 original size:73 final size:74
Alignment explanation
Indices: 2647772--2648866 Score: 884
Period size: 75 Copynumber: 14.1 Consensus size: 74
2647762 AAAATATAAA
* * *
2647772 TTGAAAAGCAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGA
2647837 GTTGA-TTT
66 GTTGATTTT
* *
2647845 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTG-CCTTGAGGCTCAACTCATCTCTCGCAATATG
2647909 AGTTGA-TTT
65 AGTTGATTTT
* * * *
2647918 TTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAACTCATTTC
1 TTG--------AAA---AACAGAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCATCTC
2647983 TCGCAATATGAGTTGATTTTTTT
55 TCGCAATATGAGTTGA---TTTT
* * * * * * *
2648006 TTGAAAGACAAAAATTGAAAATATCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGA
2648071 GTTGATTTTT
66 GTTGA-TTTT
* * * * *
2648081 TTGAAAGACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGA
2648146 GTTGATTTT
66 GTTGATTTT
** * *
2648155 TTTTACAACAGAAATTGAAATTACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTG-CCTTGAGGCTCAACTCATCTCTCGCAATATG
2648219 AGTTGAATTTTTTTTTTAT
65 AGTTG-A-------TTT-T
* * * * *
2648238 AAATTGAAAAGCGGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCACAATA
1 ---TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATA
2648303 TGAGTTGA-TTT
63 TGAGTTGATTTT
* * *
2648314 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCC-TGAGGCTCAACTCATTTCTCGTAATATG
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTG-CCTTGAGGCTCAACTCATCTCTCGCAATATG
2648378 AGTTGA-TTT
65 AGTTGATTTT
* * *** * * * * * *
2648387 TTGAAAAATAG--ATTGAAA-CACAAAAATTGACAATACCTCAGTGTGCCCCGAGGCTCAACTCA
1 TTGAAAAACAGAAATTGAAATTAC-CTCA--G-C-GTGCCT---TGAGGCTC-A-ACTC-A-T--
2648449 CCTCTCGCAATATGAGTTGA-TTT
52 -CTCTCGCAATATGAGTTGATTTT
* * *
2648472 TTGAAAAAAAGAAATTGAAAATACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTG-CCTTGAGGCTCAACTCATCTCTCGCAATATG
2648536 AGTTGA-TTT
65 AGTTGATTTT
* * * *
2648545 TTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAACTCATTTC
1 TTG--------AAA---AACAGAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCATCTC
2648610 TCGCAATATGAGTTGATTTTTTT
55 TCGCAATATGAGTTGA---TTTT
* * * * * * * *
2648633 TTTAAAGACAAAAATTGAAAATACATCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGA
2648698 GTTGATTTTT
66 GTTGA-TTTT
* * * * * *
2648708 TTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGA
2648773 GTTGATTTTT
66 GTTGA-TTTT
** * * *
2648783 TTTTACAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGA
*
2648848 ATTGAATTTTT
66 GTTG-A-TTTT
2648859 TTGAAAAA
1 TTGAAAAA
2648867 TATAAATTTA
Statistics
Matches: 859, Mismatches: 94, Indels: 135
0.79 0.09 0.12
Matches are distributed among these distances:
70 2 0.00
71 8 0.01
73 167 0.19
74 69 0.08
75 213 0.25
76 12 0.01
77 119 0.14
78 8 0.01
79 2 0.00
80 14 0.02
81 7 0.01
82 4 0.00
83 4 0.00
84 116 0.14
85 34 0.04
86 59 0.07
87 8 0.01
88 13 0.02
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGA
GTTGATTTT
Found at i:2648558 original size:627 final size:626
Alignment explanation
Indices: 2647045--2649030 Score: 2616
Period size: 627 Copynumber: 3.1 Consensus size: 626
2647035 CAATAAAAAT
* * *
2647045 AGAAATTGAAAATAGCTCAGCGTGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
1 AGAAATTGAAAATACCTCAGCGTGT---CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
* * *
2647109 TTTTTTGAAAGGAAAAAATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCA
62 TTTTTTGAAA--AATAAATTG-AAAACAGAAATTG-AAATACCTC--AGTGTGCCCTGAGGCTCA
** * * * * * *
2647174 ACTCGTCTCTCACAATACGAGTTGATTTTTTTTTTG-ACAACAGAAATTGAAATTACCTCAACAT
121 ACTCACCTCTCGCAATATGAGTTGA-----TTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
* *
2647238 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTG-AAAATATAAATTTAAAAG
181 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTTTGAAAAACATAAA-TT-GAA-
* * * * ** * *
2647302 CAGAAATTGAAATTAACTCAACGTGCCTTGAGGCTCAACTTACCTCTCGTAGTATGAGTTGA---
241 CAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
* *
2647364 TTTTTTGAAAGATAAAAATTGAAAATACCTCAGCATGTCTTAAGGCTCAACTCATTTCTCGCAAT
306 TTTTTTGAAAGACAAAAATTGAAAATA-CTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAT
* * *
2647429 ATGAGTTGATTTTTTTTGACA-ACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCA
370 ATGAGTTGA-TTTTTTTGAAAGACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCA
** * *
2647493 CCTCTCACAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCAGAAATTGAAATTAC
434 TTTCTCGCAATATGAGTTG-A---TTTTT------T-T---TT-ACAA-CAGAAATTGAAATTAC
* *
2647558 CTCAACGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A----TTTTTT-GAAA--
483 CTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTTTATAAATT
* * * * * * **
2647614 GACAA---AAATTGAAAATACCTCAGCATGTCTTAAGGCTCAACTCATTTCTCGCAATATGAGTT
547 GAAAAGCGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTT
2647676 GATTTTTTTGAC-AAC
612 GA-TTTTTTGACAAAC
* * *
2647691 AGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTT
1 AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TT
** *
2647756 TTTTGAAAAATATAAATTGAAAAGCAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTC
64 TTTTG-AAAA-ATAAATTGAAAA-CAGAAATTGAAA-TACCTCAGTGTGCCCTGAGGCTCAACTC
2647821 ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGG
125 ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGG
2647886 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGAAATTGAAACT
190 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGAAATTGAAACT
2647951 ACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACA
255 ACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACA
2648016 AAAATTGAAAATATCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
320 AAAATTGAAAATA-CTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
2648081 TTGAAAGACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
384 TTGAAAGACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
2648146 GTTGA-TTTTTTTTACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
449 GTTGATTTTTTTTTACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
2648210 CGCAATATGAGTTGAATTTTTTTTTTATAAATTGAAAAGCGGAAATTGAAATTACCTCAACGTGC
514 CGCAATATGAGTTGAATTTTTTTTTTATAAATTGAAAAGC-GAAATTGAAATTACCTCAACGTGC
*
2648275 CTTGAGGCTCAACTCACCTCTCACAATATGAGTTGA-TTTTTGACAAAC
578 CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAAC
* ** *
2648323 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGA-TTT
1 AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* * *
2648387 TTGAAAAATAGATTGAAACACAAAAATTGACAATACCTCAGTGTGCCCCGAGGCTCAACTCACCT
66 TTGAAAAATAAATTGAAA-ACAGAAATTGA-AATACCTCAGTGTGCCCTGAGGCTCAACTCACCT
*
2648452 CTCGCAATATGAGTTGATTTTTGAAAAAAAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCA
129 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCA
2648517 ACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCT
194 ACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCT
*
2648582 CAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTAAAGACAAAAA
259 CAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAAAAA
2648647 TTGAAAATACATCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGA
324 TTGAAAATAC-TCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGA
*
2648712 AAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
388 AAGACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
*
2648777 ATTTTTTTTTACAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCA
453 ATTTTTTTTTACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
* ** *
2648842 ATATGAATTGAATTTTTTTGAAAAATATAAATTTAAAAGCAGAAATTGAAATTACCTCAACGTGC
518 ATATGAGTTGAATTTTTTT----TTTATAAATTGAAAAGC-GAAATTGAAATTACCTCAACGTGC
* *
2648907 CTTGAGGCTCAACTTACCTCTCGCAGTATGAGTTGATTTTTTTTTGA-AAAGC
578 CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTGACAAA-C
** * *
2648959 AGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTT
1 AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT
2649024 TTTGAAA
65 TTTGAAA
2649031 CAGAAATAAA
Statistics
Matches: 1221, Mismatches: 78, Indels: 90
0.88 0.06 0.06
Matches are distributed among these distances:
621 57 0.05
622 6 0.00
623 2 0.00
626 8 0.01
627 372 0.30
628 87 0.07
629 10 0.01
631 9 0.01
632 131 0.11
633 55 0.05
635 57 0.05
636 65 0.05
637 19 0.02
638 153 0.13
639 61 0.05
643 35 0.03
644 37 0.03
645 31 0.03
646 26 0.02
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (626 bp):
AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TTGAAAAATAAATTGAAAACAGAAATTGAAATACCTCAGTGTGCCCTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAAC
TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCA
ACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAAAAATT
GAAAATACTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGAAAG
ACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATT
TTTTTTTACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGAATTTTTTTTTTATAAATTGAAAAGCGAAATTGAAATTACCTCAACGTGCCTTGAGGC
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAAC
Found at i:2648948 original size:90 final size:91
Alignment explanation
Indices: 2648791--2648956 Score: 271
Period size: 90 Copynumber: 1.8 Consensus size: 91
2648781 TTTTTTACAA
* *
2648791 CAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAATTGA-AT
1 CAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAATTGATAT
2648855 TTTTTTGAAAAATATAAATTTAAAAG
66 TTTTTTGAAAAATATAAATTTAAAAG
* * * *
2648881 CAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTTACCTCTCGCAGTATGAGTTGATTT
1 CAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAATTGATAT
2648946 TTTTTTGAAAA
66 TTTTTTGAAAA
2648957 GCAGAAATTG
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 57 0.83
91 12 0.17
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (91 bp):
CAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAATTGATAT
TTTTTTGAAAAATATAAATTTAAAAG
Found at i:2648967 original size:77 final size:77
Alignment explanation
Indices: 2648876--2649026 Score: 248
Period size: 77 Copynumber: 2.0 Consensus size: 77
2648866 ATATAAATTT
* * *
2648876 AAAAGCAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTTACCTCTCGCAGTATGAGTT
1 AAAAGCAGAAATTGAAAATACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTT
2648941 GATTTTTTTTTG
66 GATTTTTTTTTG
* * *
2648953 AAAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGTAATATGAGTT
1 AAAAGCAGAAATTGAAAATACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTT
2649018 GATTTTTTT
66 GATTTTTTT
2649027 GAAACAGAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (77 bp):
AAAAGCAGAAATTGAAAATACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTTTTTG
Found at i:2649014 original size:167 final size:164
Alignment explanation
Indices: 2648719--2649030 Score: 471
Period size: 165 Copynumber: 1.9 Consensus size: 164
2648709 TGAAAGACAA
* * **
2648719 AAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACATGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* * *
2648784 TTTACAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAA
66 TTTAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAA
2648849 TTGAATTTTTTTGAAAAATATAAATTTAAAAGCAG
131 TTG-ATTTTTTTGAAAAATATAAATTTAAAAGCAG
* * * *
2648884 AAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTTACCTCTCGCAGTATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACATGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* *
2648949 TTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGTAATATG
66 TTT-AAAA-CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
*
2649014 AGTTGATTTTTTTGAAA
129 AATTGATTTTTTTGAAA
2649031 CAGAAATAAA
Statistics
Matches: 131, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
165 60 0.46
166 15 0.11
167 56 0.43
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (164 bp):
AAATTGAAAATACCTCAACATGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
TTTAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAA
TTGATTTTTTTGAAAAATATAAATTTAAAAGCAG
Found at i:2657397 original size:12 final size:12
Alignment explanation
Indices: 2657377--2657412 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2657367 TGGGATATGC
*
2657377 AATGTATGAATG
1 AATGCATGAATG
2657389 AATGCATGAATG
1 AATGCATGAATG
2657401 AATGCATGAATG
1 AATGCATGAATG
2657413 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:2661952 original size:33 final size:31
Alignment explanation
Indices: 2661915--2661983 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 31
2661905 AGTACACTTG
*
2661915 TATTATTTATGTA-TAATTATTGAAAAGATATTT
1 TATTATTTAT-TATTAATTAGT-AAAAGATA-TT
2661948 TATTATTTATTATTAATTAGTAAAAGATATT
1 TATTATTTATTATTAATTAGTAAAAGATATT
2661979 TATTA
1 TATTA
2661984 GATGTTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.21
32 10 0.29
33 17 0.50
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (31 bp):
TATTATTTATTATTAATTAGTAAAAGATATT
Found at i:2662003 original size:31 final size:32
Alignment explanation
Indices: 2661915--2662003 Score: 87
Period size: 33 Copynumber: 2.8 Consensus size: 32
2661905 AGTACACTTG
*
2661915 TATTATTTATGTA-TAATTATTGAAAAGATATTT
1 TATTATGTAT-TATTAATTATT-AAAAGATATTT
* *
2661948 TATTATTTATTATTAATTAGTAAAAGATA-TT
1 TATTATGTATTATTAATTATTAAAAGATATTT
2661979 TATTAGATGT-TTATT-ATTATTAAAA
1 TATT--ATGTATTATTAATTATTAAAA
2662004 TTATTAATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
31 15 0.30
32 15 0.30
33 20 0.40
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (32 bp):
TATTATGTATTATTAATTATTAAAAGATATTT
Found at i:2663105 original size:18 final size:18
Alignment explanation
Indices: 2663082--2663118 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2663072 ATGGACTAGG
2663082 TAGTATTTAATACTAAGA
1 TAGTATTTAATACTAAGA
2663100 TAGTATTTAATACTAAGA
1 TAGTATTTAATACTAAGA
2663118 T
1 T
2663119 TCTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (18 bp):
TAGTATTTAATACTAAGA
Found at i:2665639 original size:11 final size:11
Alignment explanation
Indices: 2665623--2665651 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2665613 ACAAACAAAT
2665623 AGAATTCCTTA
1 AGAATTCCTTA
2665634 AGAATTCCTTA
1 AGAATTCCTTA
2665645 AGAATTC
1 AGAATTC
2665652 TCAAATGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (11 bp):
AGAATTCCTTA
Found at i:2670107 original size:3 final size:3
Alignment explanation
Indices: 2670093--2670146 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
2670083 GACAATAAAG
* *
2670093 AAT AAT AGT AAT AAT AAT AAT -AT AGAT AAT AAT ATAT ACAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT A-AT AAT AAT
2670140 AAT AAT A
1 AAT AAT A
2670147 GTTAGAGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
2 2 0.05
3 33 0.77
4 8 0.19
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2670361 original size:3 final size:3
Alignment explanation
Indices: 2670353--2670403 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
2670343 TATAAATATG
* * * *
2670353 ATA ATA ATA ATA ATA ATG ATA ATG ATA ATA ATA AT- ATA GTA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2670400 ATA A
1 ATA A
2670404 AAGTAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2670778 original size:35 final size:32
Alignment explanation
Indices: 2670736--2670829 Score: 100
Period size: 37 Copynumber: 2.8 Consensus size: 32
2670726 TATGCATAAC
2670736 AATAAAAATACAATATTAAAATATATATACGAGT
1 AATAAAAATACAATATTAAAATATATATAC-A-T
**
2670770 AATAAAAAATGTATCCGTATTAAAA-ATATATACAT
1 AAT-AAAAA--TA-CAATATTAAAATATATATACAT
2670805 AATAAAAATACAATATTTAAAATAT
1 AATAAAAATACAATA-TTAAAATAT
2670830 GTACACAGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
31 3 0.06
32 8 0.16
33 2 0.04
34 8 0.16
35 9 0.18
36 1 0.02
37 10 0.20
38 9 0.18
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (32 bp):
AATAAAAATACAATATTAAAATATATATACAT
Found at i:2670810 original size:17 final size:17
Alignment explanation
Indices: 2670752--2670814 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
2670742 AATACAATAT
2670752 TAAAATATATATACGAGTAA
1 TAAAA-ATATATAC-A-TAA
* * * *
2670772 TAAAAAATGTATCCGTAT
1 T-AAAAATATATACATAA
2670790 TAAAAATATATACATAA
1 TAAAAATATATACATAA
2670807 TAAAAATA
1 TAAAAATA
2670815 CAATATTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 20 0.59
18 3 0.09
20 7 0.21
21 4 0.12
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAAAATATATACATAA
Found at i:2670976 original size:23 final size:23
Alignment explanation
Indices: 2670940--2670984 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2670930 GTACATAACA
2670940 TAAATATCATACATATA-ATATC
1 TAAATATCATACATATATATATC
2670962 TAAATATACATACATATATATAT
1 TAAATAT-CATACATATATATAT
2670985 AGTATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATATCATACATATATATATC
Found at i:2671737 original size:18 final size:18
Alignment explanation
Indices: 2671716--2671756 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2671706 TCGAAAATAA
2671716 AATAAAAAGGAAA-AAAAT
1 AATAAAAA-GAAAGAAAAT
*
2671734 AATAAATAGAAAGAAAAT
1 AATAAAAAGAAAGAAAAT
2671752 AATAA
1 AATAA
2671757 TGTGATATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (18 bp):
AATAAAAAGAAAGAAAAT
Found at i:2671755 original size:21 final size:22
Alignment explanation
Indices: 2671715--2671757 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2671705 TTCGAAAATA
2671715 AAATAAAAAGGAAAAAAATAAT
1 AAATAAAAAGGAAAAAAATAAT
* *
2671737 AAATAGAAA-GAAAATAATAAT
1 AAATAAAAAGGAAAAAAATAAT
2671758 GTGATATCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.16
Consensus pattern (22 bp):
AAATAAAAAGGAAAAAAATAAT
Found at i:2674771 original size:32 final size:32
Alignment explanation
Indices: 2674723--2674813 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 32
2674713 ATATTCAAGT
* * *
2674723 AATATTACTTG-A-AGTTATATTTATTTATGA
1 AATATTAATTGAATAGTTATATCTATTTAGGA
* *
2674753 AATGTTATTTGAATAGTTATATCTATTTAGGA
1 AATATTAATTGAATAGTTATATCTATTTAGGA
* *
2674785 TATATTAATTGAATAATTATATCTATTTA
1 AATATTAATTGAATAGTTATATCTATTTA
2674814 AAAGGTATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 9 0.18
31 1 0.02
32 41 0.80
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.49
Consensus pattern (32 bp):
AATATTAATTGAATAGTTATATCTATTTAGGA
Found at i:2685677 original size:14 final size:14
Alignment explanation
Indices: 2685653--2685686 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2685643 TAGATTGGGT
2685653 TTCTT-TTGTATTC
1 TTCTTGTTGTATTC
*
2685666 TTTTTGTTGTATTC
1 TTCTTGTTGTATTC
2685680 TTCTTGT
1 TTCTTGT
2685687 AGTGTATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.71
Consensus pattern (14 bp):
TTCTTGTTGTATTC
Found at i:2703238 original size:35 final size:35
Alignment explanation
Indices: 2703192--2703264 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
2703182 GCTACAGTAT
*
2703192 TTTATTAATAAAAAACAGCATCGCTTTATTTGTCC
1 TTTATTAATAAAAAACAGCATCACTTTATTTGTCC
*
2703227 TTTATTAATAAAAAATAGCATCACTTTATTTGTCC
1 TTTATTAATAAAAAACAGCATCACTTTATTTGTCC
2703262 TTT
1 TTT
2703265 TTTACTCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTATTAATAAAAAACAGCATCACTTTATTTGTCC
Found at i:2703992 original size:19 final size:20
Alignment explanation
Indices: 2703956--2703994 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2703946 TTCAACCAAA
**
2703956 ATATCATTTAATTTATATAT
1 ATATCATTTAATAAATATAT
2703976 ATAT-ATTTAATAAATATAT
1 ATATCATTTAATAAATATAT
2703995 GTATTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATCATTTAATAAATATAT
Found at i:2706006 original size:31 final size:32
Alignment explanation
Indices: 2705971--2706039 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
2705961 TTATAAAATG
2705971 GTCACTA-AACTATTC-AAATGTTTTCATTCAA
1 GTCACTATAACTATTCGAAA-GTTTTCATTCAA
** *
2706002 GTCAC-ATAACTATTCGAAAGTTTTTGTTTAA
1 GTCACTATAACTATTCGAAAGTTTTCATTCAA
2706033 GTCACTA
1 GTCACTA
2706040 GACAATGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.03
31 27 0.84
32 4 0.12
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.39
Consensus pattern (32 bp):
GTCACTATAACTATTCGAAAGTTTTCATTCAA
Found at i:2708338 original size:33 final size:33
Alignment explanation
Indices: 2708296--2708362 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
2708286 TTTATGTTTA
** *
2708296 TCTAAAGTAACCCTAATGATTTTGTATGACTTT
1 TCTAAAGTAACCAAAATGACTTTGTATGACTTT
2708329 TCTAAAGTAACCAAAATGACTTTGTATGACTTT
1 TCTAAAGTAACCAAAATGACTTTGTATGACTTT
2708362 T
1 T
2708363 TATGGAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (33 bp):
TCTAAAGTAACCAAAATGACTTTGTATGACTTT
Found at i:2711588 original size:18 final size:19
Alignment explanation
Indices: 2711547--2711588 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
2711537 CTTTATCATG
* *
2711547 CATTTTTTCCTTTTATCTC
1 CATTTTTTCCTTATATCCC
*
2711566 TATTTTTT-CTTATATCCC
1 CATTTTTTCCTTATATCCC
2711584 CATTT
1 CATTT
2711589 CTATGCAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (19 bp):
CATTTTTTCCTTATATCCC
Found at i:2712369 original size:29 final size:31
Alignment explanation
Indices: 2712332--2712391 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2712322 TGTGTATGTA
* *
2712332 TAAAATTTTAATA-AA-TAAAAAATATATAT
1 TAAAATTTTAAAAGAATTAAAAAATAGATAT
2712361 TAAAATTTTAAAAGAATTAAAAAATAGATAT
1 TAAAATTTTAAAAGAATTAAAAAATAGATAT
2712392 AAATTAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 12 0.44
30 2 0.07
31 13 0.48
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (31 bp):
TAAAATTTTAAAAGAATTAAAAAATAGATAT
Found at i:2722280 original size:30 final size:30
Alignment explanation
Indices: 2722245--2722301 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
2722235 CGTAATGAAA
2722245 AAAAGGATATTCATATATGATAGTACGTAG
1 AAAAGGATATTCATATATGATAGTACGTAG
2722275 AAAAGGATATTCATATATGATAGTACG
1 AAAAGGATATTCATATATGATAGTACG
2722302 CATACGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (30 bp):
AAAAGGATATTCATATATGATAGTACGTAG
Found at i:2726231 original size:55 final size:55
Alignment explanation
Indices: 2726137--2726345 Score: 193
Period size: 55 Copynumber: 3.7 Consensus size: 55
2726127 TGCTAGAATA
* * * ** * * *
2726137 TTCTTTTCAATCGATTGTTTTTTATGTTTAAATAAATTGTCATGTTGAAATGTTAT
1 TTCTTTTAAATAGATTG-TTTATATGTTTAAATCGATTGTTATGTTGGAATATTAT
* * *
2726193 TTCTTTTAAATAGATTATTTATATGTTTAAATCGATTGTTATGATGGAATACTACT
1 TTCTTTTAAATAGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATATTA-T
* * * * * **
2726249 TCCTTTTTTAATTGATTGTTTATATATTTAAATGGATTGTTATGTTGGAATATTGC
1 TTC-TTTTAAATAGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATATTAT
* * * *
2726305 TTATTTTGAATAAATTGTTTATATGTTCAAATCGATTGTTA
1 TTCTTTTAAATAGATTGTTTATATGTTTAAATCGATTGTTA
2726346 CATAACAAGT
Statistics
Matches: 122, Mismatches: 29, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
55 61 0.50
56 18 0.15
57 43 0.35
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (55 bp):
TTCTTTTAAATAGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATATTAT
Found at i:2726279 original size:57 final size:55
Alignment explanation
Indices: 2726196--2726345 Score: 174
Period size: 57 Copynumber: 2.7 Consensus size: 55
2726186 ATGTTATTTC
* *
2726196 TTTTAAATAGATTATTTATATGTTTAAATCGATTGTTATGATGGAATACTACTTCCT
1 TTTTAAATAGATTGTTTATATGTTTAAATCGATTGTTATGATGGAATACTACTT--A
* * * * * * *
2726253 TTTTTAATTGATTGTTTATATATTTAAATGGATTGTTATGTTGGAATATTGCTTA
1 TTTTAAATAGATTGTTTATATGTTTAAATCGATTGTTATGATGGAATACTACTTA
* * *
2726308 TTTTGAATAAATTGTTTATATGTTCAAATCGATTGTTA
1 TTTTAAATAGATTGTTTATATGTTTAAATCGATTGTTA
2726346 CATAACAAGT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
55 32 0.41
57 46 0.59
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (55 bp):
TTTTAAATAGATTGTTTATATGTTTAAATCGATTGTTATGATGGAATACTACTTA
Found at i:2726294 original size:112 final size:113
Alignment explanation
Indices: 2726140--2726345 Score: 261
Period size: 112 Copynumber: 1.8 Consensus size: 113
2726130 TAGAATATTC
* * * * *
2726140 TTTTCAATCGATTGTTTTTTATGTTTAAATAAATTGTCATGTTGAAATGTTATTTCTTTTAAATA
1 TTTTCAATCGATTGTTTTATATATTTAAATAAATTGTCATGTTGAAATATTACTTATTTTAAATA
* *
2726205 GATTATTTATATGTTTAAATCGATTGTTATGATGGAATACTACTTCCT
66 AATTATTTATATGTTCAAATCGATTGTTATGATGGAATACTACTTCCT
* * ** * * * *
2726253 TTTTTAATTGATTG-TTTATATATTTAAATGGATTGTTATGTTGGAATATTGCTTATTTTGAATA
1 TTTTCAATCGATTGTTTTATATATTTAAATAAATTGTCATGTTGAAATATTACTTATTTTAAATA
*
2726317 AATTGTTTATATGTTCAAATCGATTGTTA
66 AATTATTTATATGTTCAAATCGATTGTTA
2726346 CATAACAAGT
Statistics
Matches: 77, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
112 65 0.84
113 12 0.16
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (113 bp):
TTTTCAATCGATTGTTTTATATATTTAAATAAATTGTCATGTTGAAATATTACTTATTTTAAATA
AATTATTTATATGTTCAAATCGATTGTTATGATGGAATACTACTTCCT
Found at i:2726838 original size:190 final size:189
Alignment explanation
Indices: 2726515--2726895 Score: 654
Period size: 190 Copynumber: 2.0 Consensus size: 189
2726505 ATCTCACCCC
*
2726515 TTCAATATGCTTTTCCACGTCCAAGAGTCGGGTGATCATCTCTGCACGTCTAGAAATTTTTTATT
1 TTCAATATGCTTTTCCACGTCCAAGAGTCGGGTGATCATCTCTGCACATCTAGAAATTTTTTATT
* * *
2726580 AGAGCAGTATTTAGTTAAGAACGTAGCATGGGCCACAGCATGTAGCCTTGTGAGTATTCATCAGG
66 AGAGCAGTATTTAGTTAAGAACGTAGCATGAGCCACAGCATGCAACCTTGTGAGTATTCATCAGG
2726645 CTTGTTTGCAAAGAACTGCATCGTTCATTACTTCAGCTTAACGGATGTCCAATCCATCCT
131 CTTGTTTGCAAAGAACTGCATCGTTCATTA-TTCAGCTTAACGGATGTCCAATCCATCCT
* *
2726705 TTCAATATGCTTTTCCACGTTCAAGAGTCGGGTGATCATCTCTGTACATCTAGAAATTTTTTATT
1 TTCAATATGCTTTTCCACGTCCAAGAGTCGGGTGATCATCTCTGCACATCTAGAAATTTTTTATT
*
2726770 AGAGTAGTATTTAGTTAAGAACGTAGCATGAGCCACAGCATGCAACCTTGTGAGTATTCATCAGG
66 AGAGCAGTATTTAGTTAAGAACGTAGCATGAGCCACAGCATGCAACCTTGTGAGTATTCATCAGG
* * * *
2726835 CTTGTTTGCAAAGAAGTGCATCGTTCATTATTTAGCTTAACGGATGTCGAATCTATCCT
131 CTTGTTTGCAAAGAACTGCATCGTTCATTATTCAGCTTAACGGATGTCCAATCCATCCT
2726894 TT
1 TT
2726896 TGTTTTCACC
Statistics
Matches: 180, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
189 28 0.16
190 152 0.84
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (189 bp):
TTCAATATGCTTTTCCACGTCCAAGAGTCGGGTGATCATCTCTGCACATCTAGAAATTTTTTATT
AGAGCAGTATTTAGTTAAGAACGTAGCATGAGCCACAGCATGCAACCTTGTGAGTATTCATCAGG
CTTGTTTGCAAAGAACTGCATCGTTCATTATTCAGCTTAACGGATGTCCAATCCATCCT
Found at i:2736110 original size:14 final size:14
Alignment explanation
Indices: 2736086--2736119 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
2736076 TCTCTACTTC
2736086 GTTTCTGTTTCTTTT
1 GTTTCTGTTTC-TTT
2736101 GTTT-TGTTTCTTT
1 GTTTCTGTTTCTTT
2736114 GTTTCT
1 GTTTCT
2736120 TTAATTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.39
14 7 0.39
15 4 0.22
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.74
Consensus pattern (14 bp):
GTTTCTGTTTCTTT
Found at i:2744518 original size:21 final size:22
Alignment explanation
Indices: 2744492--2744538 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
2744482 CTCTGCTCAA
*
2744492 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
2744513 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
2744535 ACTC
1 ACTC
2744539 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:2750174 original size:15 final size:15
Alignment explanation
Indices: 2750145--2750183 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2750135 AAATATAATT
2750145 ATTTTTAGTAAATATA
1 ATTTTTA-TAAATATA
*
2750161 ATTTTTATATATATA
1 ATTTTTATAAATATA
*
2750176 ATATTTAT
1 ATTTTTAT
2750184 TTTTCAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
ATTTTTATAAATATA
Found at i:2750181 original size:17 final size:18
Alignment explanation
Indices: 2750135--2750181 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
2750125 TAATTATTGC
2750135 AAATATAATTATTTTTAGT
1 AAATATAA-TATTTTTAGT
2750154 AAATAT-A-ATTTTTA-T
1 AAATATAATATTTTTAGT
*
2750169 ATATATAATATTT
1 AAATATAATATTT
2750182 ATTTTTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 6 0.24
16 8 0.32
17 4 0.16
18 1 0.04
19 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AAATATAATATTTTTAGT
Found at i:2750444 original size:22 final size:22
Alignment explanation
Indices: 2750414--2750455 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2750404 AATACTTTAT
*
2750414 TAATGATATAATTATTATTAAA
1 TAATAATATAATTATTATTAAA
**
2750436 TAATAATATTTTTATTATTA
1 TAATAATATAATTATTATTA
2750456 TGTAGGTTGT
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:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TAATAATATAATTATTATTAAA
Found at i:2752123 original size:23 final size:23
Alignment explanation
Indices: 2752079--2752123 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2752069 ATTAATATTT
* *
2752079 ATATTATTAAACTATATTTAATA
1 ATATTACTAAACTATATATAATA
2752102 ATATTACT-AACTATAATATAAT
1 ATATTACTAAACTAT-ATATAAT
2752124 TGAATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTACTAAACTATATATAATA
Found at i:2755063 original size:32 final size:32
Alignment explanation
Indices: 2755017--2755079 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2755007 TCAACTTTGT
*
2755017 ATACTAATTTTAATTAAATTATATAATATTTC
1 ATACCAATTTTAATTAAATTATATAATATTTC
2755049 ATACCAATTTTAATTAAATTATATAATATTT
1 ATACCAATTTTAATTAAATTATATAATATTT
2755080 ATTATTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.49
Consensus pattern (32 bp):
ATACCAATTTTAATTAAATTATATAATATTTC
Found at i:2755415 original size:11 final size:11
Alignment explanation
Indices: 2755401--2755441 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
2755391 TGTTTTCTCC
2755401 CTATTTTGCTA
1 CTATTTTGCTA
*
2755412 CTATTTTACTA
1 CTATTTTGCTA
* *
2755423 TTATGTTGCTA
1 CTATTTTGCTA
2755434 CTATTTTG
1 CTATTTTG
2755442 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:2755685 original size:12 final size:12
Alignment explanation
Indices: 2755664--2755697 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2755654 TATATATTTT
*
2755664 AAAATTATATAA
1 AAAATAATATAA
2755676 AAAATAATATAA
1 AAAATAATATAA
*
2755688 AAATTAATAT
1 AAAATAATAT
2755698 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:2758804 original size:22 final size:22
Alignment explanation
Indices: 2758779--2758875 Score: 97
Period size: 22 Copynumber: 4.5 Consensus size: 22
2758769 AGAGCATTAT
*
2758779 AGTGCTAAACAGAGAGTACCGA
1 AGTGCTAAACAGAGAGCACCGA
* *
2758801 AGTGCCAAGCAGAGAGCACC-A
1 AGTGCTAAACAGAGAGCACCGA
* * * *
2758822 AATGCTAAGCAAACAGCACCGA
1 AGTGCTAAACAGAGAGCACCGA
* *
2758844 AGTGCTAAATAGAGAGCACCAA
1 AGTGCTAAACAGAGAGCACCGA
*
2758866 AGTGCAAAAC
1 AGTGCTAAAC
2758876 TCGTACAAGC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
21 17 0.29
22 42 0.71
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.10
Consensus pattern (22 bp):
AGTGCTAAACAGAGAGCACCGA
Found at i:2758829 original size:43 final size:44
Alignment explanation
Indices: 2758779--2758875 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 44
2758769 AGAGCATTAT
* * * *
2758779 AGTGCTAAACAGAGAGTACCGAAGTGCCAAGCAGAGAGCACCAA
1 AGTGCTAAACAAACAGCACCGAAGTGCCAAACAGAGAGCACCAA
* * *
2758823 A-TGCTAAGCAAACAGCACCGAAGTGCTAAATAGAGAGCACCAA
1 AGTGCTAAACAAACAGCACCGAAGTGCCAAACAGAGAGCACCAA
*
2758866 AGTGCAAAAC
1 AGTGCTAAAC
2758876 TCGTACAAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
43 36 0.84
44 7 0.16
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.10
Consensus pattern (44 bp):
AGTGCTAAACAAACAGCACCGAAGTGCCAAACAGAGAGCACCAA
Found at i:2765106 original size:17 final size:17
Alignment explanation
Indices: 2765084--2765117 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2765074 CTTCCTTTTT
2765084 GACTCTTTAATAAACGA
1 GACTCTTTAATAAACGA
2765101 GACTCTTTAATAAACGA
1 GACTCTTTAATAAACGA
2765118 AGTTGTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
GACTCTTTAATAAACGA
Found at i:2765597 original size:23 final size:24
Alignment explanation
Indices: 2765552--2765602 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2765542 ATTTTAGCCC
* *
2765552 TTAACTTTTATATTTTTTGTTAAT
1 TTAACCTTTATATTTTTTGTTAAG
2765576 TTAACCTTTAT-TATTTTT-TTAAG
1 TTAACCTTTATAT-TTTTTGTTAAG
2765599 TTAA
1 TTAA
2765603 ATTTAGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (24 bp):
TTAACCTTTATATTTTTTGTTAAG
Found at i:2770914 original size:16 final size:16
Alignment explanation
Indices: 2770893--2770927 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2770883 TAAAGTGAAA
*
2770893 AGAAAATAGGAAGGAT
1 AGAAAATAGGAAGAAT
*
2770909 AGAAAATTGGAAGAAT
1 AGAAAATAGGAAGAAT
2770925 AGA
1 AGA
2770928 TCAATAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (16 bp):
AGAAAATAGGAAGAAT
Found at i:2773773 original size:21 final size:21
Alignment explanation
Indices: 2773748--2773787 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2773738 TTTTCATTTA
2773748 TTTGTTTTATTTATATTTAAT
1 TTTGTTTTATTTATATTTAAT
* *
2773769 TTTGTTTTCTTTATTTTTA
1 TTTGTTTTATTTATATTTA
2773788 TTTCATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (21 bp):
TTTGTTTTATTTATATTTAAT
Found at i:2792228 original size:3 final size:3
Alignment explanation
Indices: 2792220--2792245 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2792210 CTGTGCTGTT
2792220 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2792246 TCTGTAGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2805667 original size:25 final size:27
Alignment explanation
Indices: 2805619--2805669 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2805609 TAAATAAAAA
* *
2805619 ATTTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAAACATAATAAATCAAATAT
2805646 ATTTAAAAAACATAA-AAA-CAAATA
1 ATTTAAAAAACATAATAAATCAAATA
2805670 CTAAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (27 bp):
ATTTAAAAAACATAATAAATCAAATAT
Found at i:2805677 original size:12 final size:12
Alignment explanation
Indices: 2805660--2805699 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2805650 AAAAAACATA
2805660 AAAACAAATACT
1 AAAACAAATACT
2805672 AAAACAAATA--
1 AAAACAAATACT
*
2805682 AAAA-TAATACT
1 AAAACAAATACT
2805693 AAAACAA
1 AAAACAA
2805700 TTTTTAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
9 4 0.17
10 4 0.17
11 4 0.17
12 11 0.48
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAACAAATACT
Found at i:2805682 original size:22 final size:22
Alignment explanation
Indices: 2805649--2805699 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
2805639 CAAATATATT
2805649 TAAAA-AACATAAAAACAAATAC
1 TAAAACAACATAAAAA-AAATAC
*
2805671 TAAAACAA-ATAAAAATAATAC
1 TAAAACAACATAAAAAAAATAC
2805692 TAAAACAA
1 TAAAACAA
2805700 TTTTTAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 13 0.48
22 12 0.44
23 2 0.07
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.16
Consensus pattern (22 bp):
TAAAACAACATAAAAAAAATAC
Found at i:2808751 original size:21 final size:20
Alignment explanation
Indices: 2808727--2808766 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2808717 TAGTTGTTAG
*
2808727 GAAGCTAAGTTTCAAGACTTA
1 GAAGCTAAGTCTCAA-ACTTA
2808748 GAAGCTAAGTCTCAAACTT
1 GAAGCTAAGTCTCAAACTT
2808767 GGAGGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (20 bp):
GAAGCTAAGTCTCAAACTTA
Found at i:2815046 original size:8 final size:9
Alignment explanation
Indices: 2815025--2815050 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2815015 TAAATTTTAA
2815025 AAAAAATTC
1 AAAAAATTC
2815034 AAAAAATTC
1 AAAAAATTC
2815043 AAAAAATT
1 AAAAAATT
2815051 ATTCTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAAATTC
Found at i:2815054 original size:21 final size:19
Alignment explanation
Indices: 2815022--2815080 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 19
2815012 TTTTAAATTT
2815022 TAAAAAAA-ATTCAAAAAA
1 TAAAAAAATATTCAAAAAA
*
2815040 TTCAAAAAATTATTCTTAAAAAA
1 -T-AAAAAAATATTC--AAAAAA
*
2815063 TAAAAAAATATTTAAAAA
1 TAAAAAAATATTCAAAAA
2815081 GTCTAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 6 0.18
20 6 0.18
21 14 0.42
22 1 0.03
23 6 0.18
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAAAAAATATTCAAAAAA
Found at i:2820094 original size:20 final size:19
Alignment explanation
Indices: 2820069--2820112 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2820059 GGACTAAATT
2820069 AAAAATATATAAATTTATG-G
1 AAAAAT-TATAAATTT-TGTG
*
2820089 AAAAATTCTAAATTTTGTG
1 AAAAATTATAAATTTTGTG
2820108 AAAAA
1 AAAAA
2820113 CATGGGCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 14 0.64
20 6 0.27
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (19 bp):
AAAAATTATAAATTTTGTG
Found at i:2820636 original size:24 final size:24
Alignment explanation
Indices: 2820609--2820658 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2820599 AGCGTCTCAT
2820609 TATTAGCTCT-TATGAGC-ATCCCGA
1 TATTAGCTCTCT-TGAGCTA-CCCGA
*
2820633 TATTGGCTCTCTTGAGCTACCCGA
1 TATTAGCTCTCTTGAGCTACCCGA
2820657 TA
1 TA
2820659 CATGACTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (24 bp):
TATTAGCTCTCTTGAGCTACCCGA
Found at i:2820868 original size:25 final size:25
Alignment explanation
Indices: 2820786--2820868 Score: 64
Period size: 25 Copynumber: 3.4 Consensus size: 25
2820776 TAAGCTTTCG
* **
2820786 ATATGGCTCACATGAGCTT-CT-CA
1 ATATGGCTCTCATGAGCTTCCTGTT
**
2820809 ATTATGGCTCTTTTGAGCTTTCC-GTT
1 A-TATGGCTCTCATGAGC-TTCCTGTT
* *
2820835 ACATAGCTCTCATGAGCTTCCTGTT
1 ATATGGCTCTCATGAGCTTCCTGTT
2820860 ATATGGCTC
1 ATATGGCTC
2820869 GAAAGAGCTA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
23 1 0.02
24 17 0.39
25 24 0.55
26 2 0.05
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (25 bp):
ATATGGCTCTCATGAGCTTCCTGTT
Found at i:2823522 original size:31 final size:31
Alignment explanation
Indices: 2823444--2823533 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 31
2823434 TCAAATGAAT
*
2823444 GCCAAACC-TTTCAAAA-TAGTCAAATAAGG
1 GCCAAACCTTTTCAAAAGTACTCAAATAAGG
* * ** * *
2823473 GCCTAACATTTTTGAAAGTACTCAGATAGGG
1 GCCAAACCTTTTCAAAAGTACTCAAATAAGG
*
2823504 GCCAAACCTTTTCAAAAGTGCTCAAA-AAGG
1 GCCAAACCTTTTCAAAAGTACTCAAATAAGG
2823534 ACTTCTCAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
29 6 0.13
30 9 0.20
31 30 0.67
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (31 bp):
GCCAAACCTTTTCAAAAGTACTCAAATAAGG
Found at i:2825331 original size:23 final size:23
Alignment explanation
Indices: 2825296--2825365 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
2825286 AAAATTACGA
** *
2825296 ATTTAAATTTTAAAGATAATATT
1 ATTTAAAAATTAAAAATAATATT
*
2825319 ATTTAAAAATTAATAAAT-TTATT
1 ATTTAAAAATTAA-AAATAATATT
*
2825342 TTTTATAAAA-TAAAAATAATATT
1 ATTTA-AAAATTAAAAATAATATT
2825365 A
1 A
2825366 GAAACAGTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
22 4 0.11
23 26 0.70
24 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
ATTTAAAAATTAAAAATAATATT
Found at i:2826481 original size:30 final size:31
Alignment explanation
Indices: 2826416--2826474 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
2826406 CCTAAAATGG
* *
2826416 TAAAAATTTAAAAAATTACACTTTAACCTCC
1 TAAAAATATAAAAAATTACACTTTAACATCC
2826447 TAAAAATGATAAAAAATTA-A-TTTAACAT
1 TAAAAAT-ATAAAAAATTACACTTTAACAT
2826475 TTTAAAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 8 0.32
32 10 0.40
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (31 bp):
TAAAAATATAAAAAATTACACTTTAACATCC
Found at i:2826954 original size:22 final size:22
Alignment explanation
Indices: 2826911--2826953 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2826901 GGTCGAAATC
2826911 AAAAAATTAAATTATAATTTTT
1 AAAAAATTAAATTATAATTTTT
*
2826933 AAAAGATTAAATTA-AATTTTT
1 AAAAAATTAAATTATAATTTTT
2826954 TTTATTTTAA
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:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAAAATTAAATTATAATTTTT
Found at i:2826973 original size:30 final size:31
Alignment explanation
Indices: 2826929--2826988 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
2826919 AAATTATAAT
*
2826929 TTTTAAAAGATTAAATTA-AATTTT-TTTTA
1 TTTTAAAAGATTAAAGTACAATTTTATTTTA
*
2826958 TTTTAAAGGAGTTAAAGTACAATTTTATTTT
1 TTTTAAAAGA-TTAAAGTACAATTTTATTTT
2826989 TACTAGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 7 0.27
31 6 0.23
32 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (31 bp):
TTTTAAAAGATTAAAGTACAATTTTATTTTA
Found at i:2829630 original size:12 final size:12
Alignment explanation
Indices: 2829613--2829637 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2829603 AATTTTTATA
2829613 AATTATTAATAT
1 AATTATTAATAT
2829625 AATTATTAATAT
1 AATTATTAATAT
2829637 A
1 A
2829638 GCGTCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATTAATAT
Found at i:2835028 original size:17 final size:17
Alignment explanation
Indices: 2835003--2835041 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2834993 AGAAACAATT
*
2835003 GAAATAGAAAAAAAAAG
1 GAAAAAGAAAAAAAAAG
* *
2835020 GAAAAAGAAAATAAAGG
1 GAAAAAGAAAAAAAAAG
2835037 GAAAA
1 GAAAA
2835042 CCCGTGATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (17 bp):
GAAAAAGAAAAAAAAAG
Found at i:2836065 original size:34 final size:34
Alignment explanation
Indices: 2836019--2836085 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
2836009 GTGTGAGTGT
* ** *
2836019 GGGTGTTTATATATAGTTTATGTATATATAATGC
1 GGGTGTTCATATATAACTTATGTACATATAATGC
2836053 GGGTGTTCATATATAACTTATGTACATATAATG
1 GGGTGTTCATATATAACTTATGTACATATAATG
2836086 ACAGAGTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.43
Consensus pattern (34 bp):
GGGTGTTCATATATAACTTATGTACATATAATGC
Found at i:2840391 original size:27 final size:28
Alignment explanation
Indices: 2840344--2840400 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
2840334 TGTAATTTAA
**
2840344 ATTAAGTTTTAATTAAGTATTGTTTATT
1 ATTAAGTTTTAATTAAGTATTAATTATT
*
2840372 ATTAAGTTTT-A-TATGATATTAATTATT
1 ATTAAGTTTTAATTAAG-TATTAATTATT
2840399 AT
1 AT
2840401 AAAATATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 3 0.12
27 12 0.48
28 10 0.40
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (28 bp):
ATTAAGTTTTAATTAAGTATTAATTATT
Found at i:2840407 original size:17 final size:18
Alignment explanation
Indices: 2840387--2840424 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2840377 GTTTTATATG
*
2840387 ATATTA-ATTATTATAAA
1 ATATTATATTATTAGAAA
*
2840404 ATATTATTTTATTAGAAA
1 ATATTATATTATTAGAAA
2840422 ATA
1 ATA
2840425 AATTTCCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATTATATTATTAGAAA
Found at i:2845167 original size:29 final size:30
Alignment explanation
Indices: 2845134--2845215 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 30
2845124 GCAATTAATT
* *
2845134 AATTATTTTTAAATTTAAAAAATT-TTAAA
1 AATTATTTTAAAAATTAAAAAATTATTAAA
*
2845163 AATTATTTTAAAAATTAAAAAGTTATTAAA
1 AATTATTTTAAAAATTAAAAAATTATTAAA
* *
2845193 AAGTA---TAAATATTAAAAAATTAT
1 AATTATTTTAAAAATTAAAAAATTAT
2845216 AAATATAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.35
29 21 0.46
30 9 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
AATTATTTTAAAAATTAAAAAATTATTAAA
Found at i:2845172 original size:12 final size:12
Alignment explanation
Indices: 2845147--2845179 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2845137 TATTTTTAAA
2845147 TTTAAAAA--AT
1 TTTAAAAATTAT
2845157 TTTAAAAATTAT
1 TTTAAAAATTAT
2845169 TTTAAAAATTA
1 TTTAAAAATTA
2845180 AAAAGTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
12 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TTTAAAAATTAT
Found at i:2845207 original size:16 final size:17
Alignment explanation
Indices: 2845186--2845221 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2845176 ATTAAAAAGT
2845186 TATT-AAAAAGTATAAA
1 TATTAAAAAAGTATAAA
*
2845202 TATTAAAAAATTATAAA
1 TATTAAAAAAGTATAAA
2845219 TAT
1 TAT
2845222 AAGATGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TATTAAAAAAGTATAAA
Found at i:2846347 original size:38 final size:41
Alignment explanation
Indices: 2846285--2846373 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 41
2846275 TAAAAAGTAT
*
2846285 TTATATTAAAAAATACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAATACTACAATAAATATAATAAATATTTTA
* *
2846326 TTATATTAAAAAA-AC-A-AATAAATGTAATAAGTATTTTA
1 TTATATTAAAAAATACTACAATAAATATAATAAATATTTTA
*
2846364 TTGTATTAAA
1 TTATATTAAA
2846374 TATAATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 28 0.64
39 1 0.02
40 2 0.05
41 13 0.30
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (41 bp):
TTATATTAAAAAATACTACAATAAATATAATAAATATTTTA
Found at i:2846546 original size:17 final size:16
Alignment explanation
Indices: 2846519--2846550 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2846509 TTTTTTAACA
2846519 TATAAAATTAATATAT
1 TATAAAATTAATATAT
2846535 TATAAGAATTAATATA
1 TATAA-AATTAATATA
2846551 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TATAAAATTAATATAT
Found at i:2847311 original size:24 final size:24
Alignment explanation
Indices: 2847282--2847333 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
2847272 AGAATAAAGT
2847282 GAAGTTGTTGATTGTTTGGCAAAA
1 GAAGTTGTTGATTGTTTGGCAAAA
2847306 GAAGTTGTTGATTGTTTGGCAAAA
1 GAAGTTGTTGATTGTTTGGCAAAA
2847330 GAAG
1 GAAG
2847334 CGTTGCCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (24 bp):
GAAGTTGTTGATTGTTTGGCAAAA
Found at i:2855666 original size:14 final size:14
Alignment explanation
Indices: 2855647--2855689 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2855637 GATGTTTGGC
2855647 AAAAAGAAAGGAAA
1 AAAAAGAAAGGAAA
*
2855661 AAAAAGAAA-AAAA
1 AAAAAGAAAGGAAA
*
2855674 AAAAAAAGAAGGAAA
1 AAAAAGA-AAGGAAA
2855689 A
1 A
2855690 TATACAAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.38
14 11 0.46
15 4 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGGAAA
Found at i:2856764 original size:40 final size:41
Alignment explanation
Indices: 2856692--2856782 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 41
2856682 AAAAAAATAT
* *
2856692 TTATATTAAAAAACACTACCATAAATACAATAAGTATTTTA
1 TTATATTAAAAAACACTACAATAAATACAATAAATATTTTA
**
2856733 TTATATTAAAAGAACAC-A-AATAAATGTAATAAATATTTTA
1 TTATATTAAAA-AACACTACAATAAATACAATAAATATTTTA
*
2856773 TTGTATTAAA
1 TTATATTAAA
2856783 TATATTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
40 27 0.61
41 12 0.27
42 5 0.11
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (41 bp):
TTATATTAAAAAACACTACAATAAATACAATAAATATTTTA
Found at i:2857989 original size:6 final size:6
Alignment explanation
Indices: 2857971--2858011 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
2857961 CAAAATACTA
*
2857971 TAATAA TAA-AT TAATAT TAATAT TAATAT TAATAT TGAATA
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT T-AATA
2858012 AAATAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
5 4 0.12
6 24 0.75
7 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (6 bp):
TAATAT
Found at i:2863297 original size:29 final size:29
Alignment explanation
Indices: 2863265--2863328 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
2863255 TAGTCCCTTT
* *
2863265 TATTTTAT-TTTTCTTTCAATTTCGCCCTA
1 TATTTTATGTTTTATTTCAATTTAGCCC-A
*
2863294 TATTTT-TGTTTTATTTCGATTTAGCCCA
1 TATTTTATGTTTTATTTCAATTTAGCCCA
2863322 TATTTTA
1 TATTTTA
2863329 GCAATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.59
Consensus pattern (29 bp):
TATTTTATGTTTTATTTCAATTTAGCCCA
Found at i:2863348 original size:3 final size:3
Alignment explanation
Indices: 2863340--2863411 Score: 67
Period size: 3 Copynumber: 24.3 Consensus size: 3
2863330 CAATTTTATG
* * *
2863340 TTA TTA TTA TTA TTA TT- TTAA ATA TTA TTA TTA GT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
** *
2863384 TTA TTA TGG TTA TTA TTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2863412 CGTTAGTATT
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 3 0.06
3 50 0.93
4 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2876117 original size:44 final size:43
Alignment explanation
Indices: 2876009--2876522 Score: 247
Period size: 44 Copynumber: 11.9 Consensus size: 43
2875999 ATTATACAGG
* * * **
2876009 TCTTATTTCCCTGAGACTACAGTAGAACAGACCGAAGAATTTCAG-A
1 TCTTATCTCCCTGAGATTACAGTAGAGCAGATTGAAG-A--T-AGAA
**
2876055 TCTTAT-TCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTAGAGCAGATTGAAGATAG-AA
* * * * *
2876098 TCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAACGA-AGAA
1 TCTTATCTCCCTGAGATTACAGTAGAGCAGATT-GAA-GATAGAA
* * * *
2876142 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG-TG-TCAG-A
1 TCTTATCTCCCTGAGA-TTACAGTAGAGCAGATTGAAGAT-AGAA
* *
2876183 TCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTAGAGCAGATTGAAGATAG-AA
* * * * *
2876227 TCCTATCT-CCTGAGATTACAGTGGAGCGGATTAAAACGA-AGGA
1 TCTTATCTCCCTGAGATTACAGTAGAGCAGATT-GAA-GATAGAA
* * *
2876270 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATTG-TG-TCAG-A
1 TCTTATCTCCCTGAGA-TTACAGTAGAGCAGATTGAAGAT-AGAA
** *
2876311 TCTTATCTCCCTGAGATTACAAAAGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTAGAGCAGATTGAAGATAG-AA
* * * * *
2876355 TCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATGAAGGA
1 TCTTATCTCCCTGAGATTACAGTAGAGCAGATTGAAGAT--AGAA
* * * * * *
2876399 TCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCG-TG-TCAG-G
1 TCTTATCTCCCTGAGA-TTACAGTAGAGCAGATTGAAGAT-AGAA
* * ** **
2876440 TCTTATTTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAG-A
1 TCTTATCTCCCTGAGATTACAGTAGAGCAGATTGAAG-A--T-AGAA
* **
2876486 TCTTATCTCCCTGAGATTATAGCGGAGCAGATTGAAG
1 TCTTATCTCCCTGAGATTACAGTAGAGCAGATTGAAG
2876523 CCGATAATCC
Statistics
Matches: 357, Mismatches: 77, Indels: 68
0.71 0.15 0.14
Matches are distributed among these distances:
41 88 0.25
42 17 0.05
43 44 0.12
44 135 0.38
45 31 0.09
46 42 0.12
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGTAGAGCAGATTGAAGATAGAA
Found at i:2876429 original size:129 final size:129
Alignment explanation
Indices: 2876050--2876461 Score: 711
Period size: 128 Copynumber: 3.2 Consensus size: 129
2876040 CCGAAGAATT
** * *
2876050 TCAGATCTTAT-TCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGATA
1 TCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
2876114 TTACAGTGGAGCGGATTAAAACGAAGAATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
66 TTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
2876178 TCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAATCCTATCT-CCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
2876242 TTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTGTG
66 TTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
*
2876306 TCAGATCTTATCTCCCTGAGATTACAAAAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
2876371 TTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGTG
66 TTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
* *
2876435 TCAGGTCTTATTTCCCTGAGATTACAG
1 TCAGATCTTATCTCCCTGAGATTACAG
2876462 TGGAATAGAC
Statistics
Matches: 269, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
128 135 0.50
129 134 0.50
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (129 bp):
TCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
Found at i:2877954 original size:29 final size:29
Alignment explanation
Indices: 2877921--2877984 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
2877911 TAGTCCCTTT
* *
2877921 TATTTTAT-TTTTCTTTCAATTTCGCCCTA
1 TATTTTATGTTTTATTTCAATTTAGCCC-A
*
2877950 TATTTT-TGTTTTATTTCGATTTAGCCCA
1 TATTTTATGTTTTATTTCAATTTAGCCCA
2877978 TATTTTA
1 TATTTTA
2877985 GCAATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.59
Consensus pattern (29 bp):
TATTTTATGTTTTATTTCAATTTAGCCCA
Found at i:2878004 original size:3 final size:3
Alignment explanation
Indices: 2877996--2878070 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
2877986 CAATTTTATG
* * *
2877996 TTA TTA TTA TTA TTA TTA TT- TTAA ATA TTA TTA TTA GT- TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
** *
2878040 TTA TTA TTA TGG TTA TTA TTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2878071 CGTTAGTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.05
3 53 0.93
4 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2885251 original size:20 final size:21
Alignment explanation
Indices: 2885226--2885267 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2885216 AGTTAATTTT
*
2885226 TTTATTTTA-TTTTACTATTA
1 TTTATTATATTTTTACTATTA
2885246 TTTATTATATTTTTACTATTA
1 TTTATTATATTTTTACTATTA
2885267 T
1 T
2885268 AGTTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTATTATATTTTTACTATTA
Found at i:2885265 original size:18 final size:19
Alignment explanation
Indices: 2885235--2885279 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
2885225 TTTTATTTTA
2885235 TTTTACTATTATTTA-TTATAT
1 TTTTACTATTA--TAGTTAT-T
2885256 TTTTACTATTATAGTTATT
1 TTTTACTATTATAGTTATT
2885275 TTTTA
1 TTTTA
2885280 TTTTCATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.35
20 4 0.17
21 11 0.48
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTACTATTATAGTTATT
Found at i:2885300 original size:27 final size:26
Alignment explanation
Indices: 2885241--2885301 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
2885231 TTTATTTTAC
2885241 TATTATTTATTATATTTTTACTATTA
1 TATTATTTATTATATTTTTACTATTA
*
2885267 TAGTTATTTTTTAT-TTTCATTACTACTT-
1 TA-TTATTTATTATATTT--TTACTA-TTA
2885295 TATTATT
1 TATTATT
2885302 ATTGTAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 5 0.17
27 15 0.50
28 8 0.27
29 2 0.07
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (26 bp):
TATTATTTATTATATTTTTACTATTA
Found at i:2885413 original size:3 final size:3
Alignment explanation
Indices: 2885394--2885450 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
2885384 TTTTGAATTG
* * *
2885394 TTA TCA TTA TTA CTA TTA TTA -TA TTA -TA TTTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
2885438 TTA TTA CTA TTA T
1 TTA TTA TTA TTA T
2885451 ATTTTAATCT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2885413 original size:9 final size:9
Alignment explanation
Indices: 2885399--2885450 Score: 61
Period size: 9 Copynumber: 5.6 Consensus size: 9
2885389 AATTGTTATC
2885399 ATTATTACT
1 ATTATTACT
2885408 ATTATTA-T
1 ATTATTACT
*
2885416 ATTATATTTATT
1 A-T-TA-TTACT
2885428 ATTATTACT
1 ATTATTACT
2885437 ATTATTACT
1 ATTATTACT
2885446 ATTAT
1 ATTAT
2885451 ATTTTAATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 2 0.05
9 26 0.68
10 4 0.11
11 4 0.11
12 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTATTACT
Found at i:2885462 original size:15 final size:14
Alignment explanation
Indices: 2885415--2885527 Score: 72
Period size: 15 Copynumber: 7.5 Consensus size: 14
2885405 ACTATTATTA
2885415 TATTATATTTATTAT-
1 TATTATA-TT-TTATC
2885430 TATTACTATTATTA-C
1 TATTA-TATT-TTATC
2885445 TATTATATTTTAATC
1 TATTATATTTT-ATC
*
2885460 TATATTTATTTTATC
1 TAT-TATATTTTATC
2885475 TAATT-TATTTTATC
1 T-ATTATATTTTATC
2885489 TATTTATATCTCTGTTAT-
1 TA-TTATA--T-T-TTATC
*
2885507 TATTATATTTTATG
1 TATTATATTTTATC
2885521 TATTATA
1 TATTATA
2885528 CCTATATTTA
Statistics
Matches: 84, Mismatches: 1, Indels: 27
0.75 0.01 0.24
Matches are distributed among these distances:
13 7 0.08
14 25 0.30
15 28 0.33
16 11 0.13
17 6 0.07
18 3 0.04
19 4 0.05
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (14 bp):
TATTATATTTTATC
Found at i:2885484 original size:14 final size:14
Alignment explanation
Indices: 2885450--2885495 Score: 67
Period size: 14 Copynumber: 3.2 Consensus size: 14
2885440 ATTACTATTA
2885450 TATTTTAATCTATATT
1 TATTTT-ATCTA-ATT
2885466 TATTTTATCTAATT
1 TATTTTATCTAATT
2885480 TATTTTATCT-ATT
1 TATTTTATCTAATT
2885493 TAT
1 TAT
2885496 ATCTCTGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.20
14 13 0.43
15 5 0.17
16 6 0.20
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTTATCTAATT
Found at i:2885639 original size:3 final size:3
Alignment explanation
Indices: 2885633--2886058 Score: 217
Period size: 3 Copynumber: 144.7 Consensus size: 3
2885623 TTTTGTGTCT
2885633 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2885679 TTA TTA TTA TTA TTA TTA TTA TT- TT- TTA GTTA -TA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * ** * * *
2885722 TTT TTA -TA TTTA TTC TTA CTA TTA TTA TTA TTA CCA CTA CTA TGA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * **
2885767 TTT TTA TTA ACA -TA TTA TTG TTA TT- TT- TTA CCA -TA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** *
2885810 TCCTA TCTT TTA TATA TTA TTG TTA TTA ACA TATA TTA TTA TTA AT-
1 T--TA T-TA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* * * *
2885856 TTA CTA TTA TTT TTA CTT- TTA TTA TTA TTA CTA -TA TTA TTA TTG
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * ** * *
2885900 TTA TTA TTG TT- TTC TATA GTA TTA ATA CAA ATA TTAA TT- TTC TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* * * *
2885945 TTA TTA CTA TTA TTA GTA TCA -TA GGTA TTA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* ** *
2885989 TTA TTA TCA TTA TTA TT- TT- TTA -TA TTA TCC TT- TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
2886033 TTA TTA TCA ATA TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2886059 GTTTTCATTA
Statistics
Matches: 323, Mismatches: 72, Indels: 56
0.72 0.16 0.12
Matches are distributed among these distances:
2 35 0.11
3 262 0.81
4 25 0.08
5 1 0.00
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2885877 original size:29 final size:26
Alignment explanation
Indices: 2885845--2885907 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 26
2885835 TTAACATATA
*
2885845 TTATTATTAATTTACTATTATTTTTACTT-
1 TTATTATT-A-TTACTA-TATTATTA-TTG
2885874 TTATTATTATTACTATATTATTATTG
1 TTATTATTATTACTATATTATTATTG
2885900 TTATTATT
1 TTATTATT
2885908 GTTTTCTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 2 0.06
26 15 0.47
27 6 0.19
28 1 0.03
29 8 0.25
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (26 bp):
TTATTATTATTACTATATTATTATTG
Found at i:2888935 original size:18 final size:18
Alignment explanation
Indices: 2888914--2888948 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2888904 AAATATGTTG
*
2888914 AATTGAAAAAAAATTAAA
1 AATTAAAAAAAAATTAAA
2888932 AATTAAAAAAAAATTAA
1 AATTAAAAAAAAATTAA
2888949 TTCGTAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AATTAAAAAAAAATTAAA
Found at i:2894791 original size:17 final size:18
Alignment explanation
Indices: 2894766--2894799 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2894756 AAATATGTTG
2894766 AATTGAAAAAAAATTAAA
1 AATTGAAAAAAAATTAAA
2894784 AATT-AAAAAAAATTAA
1 AATTGAAAAAAAATTAA
2894800 TTCGTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTGAAAAAAAATTAAA
Found at i:2897563 original size:23 final size:23
Alignment explanation
Indices: 2897518--2897566 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
2897508 TTTAATATTT
* *
2897518 ATATGATTATATTAATATTTATA
1 ATATGATTAAATTAATATATATA
2897541 ATATGATTAAATTAAATAATATATA
1 ATATGATTAAATT-AAT-ATATATA
2897566 A
1 A
2897567 AAAGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 3 0.14
25 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
ATATGATTAAATTAATATATATA
Found at i:2900851 original size:9 final size:10
Alignment explanation
Indices: 2900831--2900855 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2900821 ATTTTTGGAA
2900831 TTATTCATTT
1 TTATTCATTT
2900841 TTATTCATTT
1 TTATTCATTT
2900851 TTATT
1 TTATT
2900856 TTATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (10 bp):
TTATTCATTT
Found at i:2928489 original size:28 final size:28
Alignment explanation
Indices: 2928449--2928505 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2928439 ATCTGGATTC
* *
2928449 TAAACCCTAGACCATAGACCTTAAACTT
1 TAAACCATAGACCATAGACCTCAAACTT
* *
2928477 TAAACCATCGACCTTAGACCTCAAACTT
1 TAAACCATAGACCATAGACCTCAAACTT
2928505 T
1 T
2928506 GGACCCCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.26
Consensus pattern (28 bp):
TAAACCATAGACCATAGACCTCAAACTT
Found at i:2928502 original size:21 final size:21
Alignment explanation
Indices: 2928459--2928502 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2928449 TAAACCCTAG
* *
2928459 ACCATAGACCTTAAACTTTAA
1 ACCATAGACCTTAAACCTCAA
* *
2928480 ACCATCGACCTTAGACCTCAA
1 ACCATAGACCTTAAACCTCAA
2928501 AC
1 AC
2928503 TTTGGACCCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.23
Consensus pattern (21 bp):
ACCATAGACCTTAAACCTCAA
Found at i:2929334 original size:21 final size:21
Alignment explanation
Indices: 2929308--2929348 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2929298 AGACTTCACA
* *
2929308 TATTTTTTTCACTCTCTCTTT
1 TATTTTCTTCACACTCTCTTT
2929329 TATTTTCTTCACACTCTCTT
1 TATTTTCTTCACACTCTCTT
2929349 ATTTTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTCTTCACACTCTCTTT
Found at i:2933145 original size:39 final size:39
Alignment explanation
Indices: 2933097--2933179 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
2933087 ATCATGGCGG
* * *
2933097 TCGGTTTGGTGCGTACTGTTTCAGTACTAACATGGAACA
1 TCGGCTTGGTGCGCACTGTTTCAGTACTAAAATGGAACA
2933136 TCGGCTTGGTGCGCACTGTTTCAGTACTAAAATGGAACA
1 TCGGCTTGGTGCGCACTGTTTCAGTACTAAAATGGAACA
2933175 TCGGC
1 TCGGC
2933180 CGTTTTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (39 bp):
TCGGCTTGGTGCGCACTGTTTCAGTACTAAAATGGAACA
Found at i:2940215 original size:45 final size:45
Alignment explanation
Indices: 2940151--2940243 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
2940141 AATCCGAGAA
2940151 CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
1 CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
* *
2940196 CTGTGATTGCTTACAAGGTATGCCGTTCCTTTTAGAGAGTTAGCT
1 CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
2940241 CTG
1 CTG
2940244 GTTTATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (45 bp):
CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
Found at i:2944582 original size:3 final size:3
Alignment explanation
Indices: 2944561--2944624 Score: 92
Period size: 3 Copynumber: 20.7 Consensus size: 3
2944551 CGTCTGATAC
* *
2944561 TAT TAT TTT TAT TCCT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2944607 TAT TAT TAT TAT GTAT TA
1 TAT TAT TAT TAT -TAT TA
2944625 GTGTATACTT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
3 50 0.91
4 5 0.09
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2944766 original size:21 final size:20
Alignment explanation
Indices: 2944720--2944788 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 20
2944710 ATTTCAATAT
2944720 TATTATTATTAT-TA-GTATA
1 TATT-TTATTATATATGTATA
*
2944739 TGTTTTATTATATATGTATA
1 TATTTTATTATATATGTATA
2944759 TATCTTTAATATATATATACGTATA
1 TAT-TTT-AT-TATATAT--GTATA
2944784 TATTT
1 TATTT
2944789 ATGTAGTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 7 0.17
19 5 0.12
20 7 0.17
21 3 0.07
22 2 0.05
23 7 0.17
24 2 0.05
25 8 0.20
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.57
Consensus pattern (20 bp):
TATTTTATTATATATGTATA
Found at i:2945162 original size:3 final size:3
Alignment explanation
Indices: 2945154--2945182 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2945144 TAATTTACTG
2945154 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2945183 CACTATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.