Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 62 of 204
Found at i:19742717 original size:13 final size:13
Alignment explanation
Indices: 19742699--19742729 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19742689 CTTGGGTTAT
*
19742699 TTTGGGTTTGCTG
1 TTTGGGTTGGCTG
19742712 TTTGGGTTGGCTG
1 TTTGGGTTGGCTG
19742725 TTTGG
1 TTTGG
19742730 TGAGGCCCGG
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:0.00, C:0.06, G:0.42, T:0.52
Consensus pattern (13 bp):
TTTGGGTTGGCTG
Found at i:19743116 original size:20 final size:20
Alignment explanation
Indices: 19743082--19743123 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19743072 AACTATTTAA
** *
19743082 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
19743102 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
19743122 AT
1 AT
19743124 GTGTTTATTT
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:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:19743245 original size:21 final size:21
Alignment explanation
Indices: 19743221--19743265 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
19743211 ATGGGATTTC
* *
19743221 ATTTGGAAATCATACCAACAA
1 ATTTGGAAACCACACCAACAA
19743242 ATTTGGAAACCACACCAACAA
1 ATTTGGAAACCACACCAACAA
19743263 ATT
1 ATT
19743266 CTAATATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (21 bp):
ATTTGGAAACCACACCAACAA
Found at i:19749675 original size:23 final size:25
Alignment explanation
Indices: 19749616--19749677 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 25
19749606 TTATGTATTC
*
19749616 AAATTAA--ATTTTATAAATAATTA
1 AAATTAATTATTTTATAAAAAATTA
*
19749639 ATATTAATTA-TTTA-AAAAAATTA
1 AAATTAATTATTTTATAAAAAATTA
*
19749662 AAATT-TTTATTTTATA
1 AAATTAATTATTTTATA
19749678 TATCAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
22 3 0.10
23 22 0.71
24 5 0.16
25 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATTAATTATTTTATAAAAAATTA
Found at i:19750046 original size:2 final size:2
Alignment explanation
Indices: 19750041--19750068 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19750031 CGAAAAAACA
19750041 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
19750069 CTAACTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19752901 original size:22 final size:22
Alignment explanation
Indices: 19752866--19752910 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19752856 GGAGAGCTCA
19752866 ATCGCAATACTATAGTGGAATG
1 ATCGCAATACTATAGTGGAATG
* *
19752888 ATCGCTATATTATAGTGGAATG
1 ATCGCAATACTATAGTGGAATG
19752910 A
1 A
19752911 CTTCGTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (22 bp):
ATCGCAATACTATAGTGGAATG
Found at i:19753162 original size:4 final size:4
Alignment explanation
Indices: 19753149--19753177 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
19753139 AGTTTTTTTG
19753149 AATT -ATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
19753178 AGTTTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:19753324 original size:16 final size:17
Alignment explanation
Indices: 19753298--19753332 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
19753288 TAGAATTGGG
*
19753298 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
19753315 TTGA-AAAATTAATTAA
1 TTGAGAAAATTAATTAA
19753331 TT
1 TT
19753333 AATTAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:19756198 original size:37 final size:35
Alignment explanation
Indices: 19756105--19756198 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 35
19756095 GTCTCCAAAT
* *
19756105 TCACATTTCAATTCAATTTCACTTTTTCACTTTCAA
1 TCACAATTCAATTCAA-TTCACTTTTCCACTTTCAA
*
19756141 TCACAATTCAATTCAAAATTCACTTTTCCATTTTTCAA
1 TCACAATTCAATTC--AATTCACTTTTCCA-CTTTCAA
19756179 GTCA-ATATTCAATTCAATTC
1 -TCACA-ATTCAATTCAATTC
19756199 CACACATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
36 13 0.26
37 16 0.32
38 9 0.18
39 12 0.24
ACGTcount: A:0.32, C:0.23, G:0.01, T:0.44
Consensus pattern (35 bp):
TCACAATTCAATTCAATTCACTTTTCCACTTTCAA
Found at i:19761441 original size:8 final size:8
Alignment explanation
Indices: 19761428--19761490 Score: 65
Period size: 8 Copynumber: 7.8 Consensus size: 8
19761418 GTTTAATTAA
19761428 AATATAAT
1 AATATAAT
*
19761436 AATATAAC
1 AATATAAT
19761444 AATATAAT
1 AATATAAT
19761452 AATATAAT
1 AATATAAT
* *
19761460 -ATAATTTAC
1 AAT-A-TAAT
19761469 AATATAAT
1 AATATAAT
*
19761477 AAAATAAT
1 AATATAAT
19761485 AATATA
1 AATATA
19761491 CTTCAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
7 2 0.05
8 37 0.84
9 3 0.07
10 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (8 bp):
AATATAAT
Found at i:19766544 original size:31 final size:31
Alignment explanation
Indices: 19766509--19766569 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
19766499 TAAAAGAATC
*
19766509 ATTAAACTATTTAAAAATTTTTATTTAAGTT
1 ATTAAACTATTCAAAAATTTTTATTTAAGTT
19766540 ATTAAACTATTCAAAAATTTTTATTTAAGT
1 ATTAAACTATTCAAAAATTTTTATTTAAGT
19766570 CATTGGTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTAAACTATTCAAAAATTTTTATTTAAGTT
Found at i:19766582 original size:26 final size:26
Alignment explanation
Indices: 19766553--19766604 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
19766543 AAACTATTCA
19766553 AAAATTTTTATTTAAGTCATTGGTTG
1 AAAATTTTTATTTAAGTCATTGGTTG
19766579 AAAATTTTTATTTAAGTCATTGGTTG
1 AAAATTTTTATTTAAGTCATTGGTTG
19766605 TTAGGTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (26 bp):
AAAATTTTTATTTAAGTCATTGGTTG
Found at i:19771790 original size:21 final size:21
Alignment explanation
Indices: 19771766--19771809 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
19771756 ATGTTTAACC
19771766 TAATTTTATCTTGTTTTACAT
1 TAATTTTATCTTGTTTTACAT
*
19771787 TAATTTTGTCTTGTTTTACAT
1 TAATTTTATCTTGTTTTACAT
19771808 TA
1 TA
19771810 TTTCAATCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (21 bp):
TAATTTTATCTTGTTTTACAT
Found at i:19775782 original size:23 final size:23
Alignment explanation
Indices: 19775755--19775800 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
19775745 TAATTTGTTA
19775755 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
19775778 TATTAATTTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
19775801 TACTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:19781181 original size:25 final size:20
Alignment explanation
Indices: 19781124--19781165 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
19781114 TATATTAAAC
19781124 ATATATTAACCTTATTATTA
1 ATATATTAACCTTATTATTA
19781144 ATATATTAACCTTATTATTA
1 ATATATTAACCTTATTATTA
19781164 AT
1 AT
19781166 TTACTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAACCTTATTATTA
Found at i:19781971 original size:17 final size:17
Alignment explanation
Indices: 19781945--19781977 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19781935 CATTGTTTAT
*
19781945 TTTTCTTTATTTATTTC
1 TTTTCGTTATTTATTTC
19781962 TTTTCGTTATTTATTT
1 TTTTCGTTATTTATTT
19781978 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTCGTTATTTATTTC
Found at i:19786797 original size:102 final size:102
Alignment explanation
Indices: 19786621--19786824 Score: 372
Period size: 102 Copynumber: 2.0 Consensus size: 102
19786611 AATATAAGTA
*
19786621 AAAAAATCCAGTATAGTAGCAGGTGCGGTTGTGTGGCCACCTCCGAGTCTCTCGCAGCACCGGTC
1 AAAAAATCCAGTATAGTAGCAGGTGCGGTTGTGTGGCCACCTCCGAGTCTCTCACAGCACCGGTC
*
19786686 CTTAAGACTGGGGATTACCTGTAAGAAAAACAGAGGG
66 ATTAAGACTGGGGATTACCTGTAAGAAAAACAGAGGG
*
19786723 AAAAAATCCAGTATAGTAGCAGGTGCGGTTGTGTGGCCACTTCCGAGTCTCTCACAGCACCGGTC
1 AAAAAATCCAGTATAGTAGCAGGTGCGGTTGTGTGGCCACCTCCGAGTCTCTCACAGCACCGGTC
*
19786788 ATTAAGACTGGGGATTACCTGTAAGAAAAATAGAGGG
66 ATTAAGACTGGGGATTACCTGTAAGAAAAACAGAGGG
19786825 GGTAACTTTA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (102 bp):
AAAAAATCCAGTATAGTAGCAGGTGCGGTTGTGTGGCCACCTCCGAGTCTCTCACAGCACCGGTC
ATTAAGACTGGGGATTACCTGTAAGAAAAACAGAGGG
Found at i:19787691 original size:49 final size:49
Alignment explanation
Indices: 19787619--19787717 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
19787609 CTCATGGTGA
19787619 CCACAACAGTCTAATACCCACGTTTTATGCATTCGGTTTACTACACGAG
1 CCACAACAGTCTAATACCCACGTTTTATGCATTCGGTTTACTACACGAG
19787668 CCACAACAGTCTAATACCCACGTTTTATGCATTCGGTTTACTACACGAG
1 CCACAACAGTCTAATACCCACGTTTTATGCATTCGGTTTACTACACGAG
19787717 C
1 C
19787718 AAGCGCACGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.28
Consensus pattern (49 bp):
CCACAACAGTCTAATACCCACGTTTTATGCATTCGGTTTACTACACGAG
Found at i:19793158 original size:4 final size:4
Alignment explanation
Indices: 19793149--19793416 Score: 365
Period size: 4 Copynumber: 66.8 Consensus size: 4
19793139 ATTTAGGTGA
19793149 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * * * * *
19793197 GTAT GCAT GGAT GCAT GGAT GCAT GTAT GCAT GGAT GCAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * * *
19793245 ATAT GCATT GTAT GCAT GTAT GCAT GCAT GCAT GCAT GTAT GTAT GTAT
1 GTAT GTA-T GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
19793294 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
19793342 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAC GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
19793390 GTAT GTAT GTAC GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTA
19793417 CGGTAATAAA
Statistics
Matches: 239, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
4 236 0.99
5 3 0.01
ACGTcount: A:0.25, C:0.05, G:0.26, T:0.44
Consensus pattern (4 bp):
GTAT
Found at i:19794929 original size:27 final size:27
Alignment explanation
Indices: 19794893--19794947 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
19794883 CAGAATTAGA
19794893 AGATAGATAGAAAGAAAAACATTTCTT
1 AGATAGATAGAAAGAAAAACATTTCTT
*
19794920 AGATAGATAGAAAGAAAAACCTTTCTT
1 AGATAGATAGAAAGAAAAACATTTCTT
19794947 A
1 A
19794948 ATGGTTACAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (27 bp):
AGATAGATAGAAAGAAAAACATTTCTT
Found at i:19800706 original size:57 final size:59
Alignment explanation
Indices: 19800617--19800727 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 59
19800607 GAATAGAAAT
* * * * *
19800617 AGAGAAATGGGAAACGTTTGGAAATGAAATGTGGTTTTCTCCTAAATGAAAATGAAAAA
1 AGAGAAATGAGAAACATTTAGAAATGAAATGTGGCTTTCTCCAAAATGAAAATGAAAAA
19800676 AGAGAAAT-AGAAACATTTAGAAATG-AATGTGGCTTTCTCCAAAATGAAAATG
1 AGAGAAATGAGAAACATTTAGAAATGAAATGTGGCTTTCTCCAAAATGAAAATG
19800728 GCTTGGAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 25 0.53
58 14 0.30
59 8 0.17
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (59 bp):
AGAGAAATGAGAAACATTTAGAAATGAAATGTGGCTTTCTCCAAAATGAAAATGAAAAA
Found at i:19816986 original size:31 final size:31
Alignment explanation
Indices: 19816951--19817021 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
19816941 AATTTTCAAC
*
19816951 TTAGTCACTAACATTTTAGATAATTTCTATT
1 TTAGTCACTAACATTTTAAATAATTTCTATT
* * * **
19816982 TTAGTCCCTCACGTTTTAAATTGTTTCTATT
1 TTAGTCACTAACATTTTAAATAATTTCTATT
*
19817013 TTGGTCACT
1 TTAGTCACT
19817022 CTCCATTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (31 bp):
TTAGTCACTAACATTTTAAATAATTTCTATT
Found at i:19820254 original size:16 final size:16
Alignment explanation
Indices: 19820202--19820255 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
19820192 ATCAAGGTGA
19820202 CTAAAATAAAAATAAT
1 CTAAAATAAAAATAAT
* * * *
19820218 TTAAAATATAAGTGA-
1 CTAAAATAAAAATAAT
*
19820233 CTAAAATACAAATAAT
1 CTAAAATAAAAATAAT
19820249 CTAAAAT
1 CTAAAAT
19820256 GTTAGTAGCT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (16 bp):
CTAAAATAAAAATAAT
Found at i:19827549 original size:39 final size:39
Alignment explanation
Indices: 19827492--19827687 Score: 284
Period size: 39 Copynumber: 5.0 Consensus size: 39
19827482 CCAAGGCACC
* *
19827492 GTGATTTTCAGGGAAGAGATTCAAGTTCTGCGGGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
* *
19827531 GTGATTTTCATGGCAGAGATTCAAGTTCTGCTAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
* * *
19827570 GTGATTTTCAGGGCAAAGATTCAAGTTCAGCTAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
19827609 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
* * * * *
19827648 GTGACTTCCTGGGCAGAGATTCAAGTTTTGCAAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
19827687 G
1 G
19827688 GTCCTCATCG
Statistics
Matches: 142, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 142 1.00
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (39 bp):
GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
Found at i:19830704 original size:9 final size:9
Alignment explanation
Indices: 19830651--19830705 Score: 76
Period size: 9 Copynumber: 6.2 Consensus size: 9
19830641 TTTGGTTAAA
*
19830651 AATTACCTG
1 AATTACCCG
19830660 AATTACCCG
1 AATTACCCG
19830669 AATTACCCG
1 AATTACCCG
*
19830678 -ATTAACCG
1 AATTACCCG
*
19830686 AATTAACCG
1 AATTACCCG
19830695 AATTACCCG
1 AATTACCCG
19830704 AA
1 AA
19830706 AATTACCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
8 7 0.17
9 35 0.83
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:19831357 original size:23 final size:23
Alignment explanation
Indices: 19831308--19831358 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
19831298 TCTCTTCCAC
* *
19831308 AATCCTTCAAGAATTGAAGCAAA
1 AATCCTTCAAGAATAGAAACAAA
*
19831331 AATCCTATCAAGAA-AGAAACAAG
1 AATCCT-TCAAGAATAGAAACAAA
19831354 AATCC
1 AATCC
19831359 AGTCTCTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.18
Consensus pattern (23 bp):
AATCCTTCAAGAATAGAAACAAA
Found at i:19831809 original size:13 final size:14
Alignment explanation
Indices: 19831788--19831825 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
19831778 ATATTTGAAT
19831788 TAAATATTTAATA-A
1 TAAA-ATTTAATAGA
19831802 TAAAATTTAATAGA
1 TAAAATTTAATAGA
19831816 TAAAATTTAA
1 TAAAATTTAA
19831826 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
TAAAATTTAATAGA
Found at i:19836350 original size:21 final size:21
Alignment explanation
Indices: 19836326--19836365 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19836316 TATGATTTAA
*
19836326 GTCTAAAATGTTGTTATAGGT
1 GTCTAAAATGTTATTATAGGT
**
19836347 GTCTCGAATGTTATTATAG
1 GTCTAAAATGTTATTATAG
19836366 ATATATATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (21 bp):
GTCTAAAATGTTATTATAGGT
Found at i:19838464 original size:11 final size:11
Alignment explanation
Indices: 19838450--19838483 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19838440 GTGTGTAAAG
19838450 AAAAAAAGAAT
1 AAAAAAAGAAT
19838461 AAAAAAAGAAT
1 AAAAAAAGAAT
**
19838472 AGTAAAAGAAT
1 AAAAAAAGAAT
19838483 A
1 A
19838484 TCCTATCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (11 bp):
AAAAAAAGAAT
Found at i:19839512 original size:15 final size:14
Alignment explanation
Indices: 19839491--19839526 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
19839481 ATAATCCTTA
*
19839491 ATAATTATCTTAAT
1 ATAATTATCCTAAT
19839505 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
19839520 ATAATTA
1 ATAATTA
19839527 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:19842977 original size:5 final size:5
Alignment explanation
Indices: 19842967--19842997 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
19842957 TTAAACTATA
*
19842967 CTCTC CTCTC CCCTC CTCTC CTCTC CTCTC C
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC C
19842998 AAATAAGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (5 bp):
CTCTC
Found at i:19847012 original size:29 final size:27
Alignment explanation
Indices: 19846953--19847015 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 27
19846943 ACACATTGGG
*
19846953 TTTTTAAGAATTAAAGCAACCACAGGG
1 TTTTTAAGAATTAAAGCAACCACAGGA
* * *
19846980 TTTTTAAGTAAATTAAAGCAGCGATAGGA
1 TTTTTAAG--AATTAAAGCAACCACAGGA
19847009 TTTTTAA
1 TTTTTAA
19847016 AAATGTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 8 0.27
29 22 0.73
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (27 bp):
TTTTTAAGAATTAAAGCAACCACAGGA
Found at i:19848962 original size:49 final size:47
Alignment explanation
Indices: 19848899--19849005 Score: 144
Period size: 49 Copynumber: 2.2 Consensus size: 47
19848889 AAAGAAGAGC
* *
19848899 AAAGGAAATTGGGAA-GAAGAAACATCACCATGAAAAAGAAAAAAAAAA
1 AAAGGAAATAGGGAAGGAA-AAACATCACCAAGAAAAAG-AAAAAAAAA
* *
19848947 AGAAGGAAATAGGGAAGGAAAAACATCACCAAGAAAAAGAAAGACAAA
1 A-AAGGAAATAGGGAAGGAAAAACATCACCAAGAAAAAGAAAAAAAAA
19848995 AAAGGAAATAG
1 AAAGGAAATAG
19849006 TTTTAAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
47 10 0.19
48 9 0.17
49 31 0.58
50 3 0.06
ACGTcount: A:0.64, C:0.08, G:0.21, T:0.07
Consensus pattern (47 bp):
AAAGGAAATAGGGAAGGAAAAACATCACCAAGAAAAAGAAAAAAAAA
Found at i:19862627 original size:17 final size:18
Alignment explanation
Indices: 19862593--19862633 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
19862583 TTTCTGCTTC
19862593 TTCTTCTCGTACGCTTCTT
1 TTCTTCTCG-ACGCTTCTT
*
19862612 TTCTTCTC-ACGTTTCTT
1 TTCTTCTCGACGCTTCTT
19862629 TTCTT
1 TTCTT
19862634 TTCTCCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.62
19 8 0.38
ACGTcount: A:0.05, C:0.29, G:0.07, T:0.59
Consensus pattern (18 bp):
TTCTTCTCGACGCTTCTT
Found at i:19862690 original size:5 final size:5
Alignment explanation
Indices: 19862680--19862705 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19862670 CTTTCCTTGT
19862680 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
19862706 GTAAAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:19864012 original size:23 final size:23
Alignment explanation
Indices: 19863985--19864178 Score: 184
Period size: 23 Copynumber: 8.5 Consensus size: 23
19863975 GTGTTATAAT
19863985 GTTCATGTTTTGGTTTCTGTTAA
1 GTTCATGTTTTGGTTTCTGTTAA
* *
19864008 GTTCATGTTTTGGTTTATGTGTTA
1 GTTCATGTTTTGGTTTCTGT-TAA
* *
19864032 --TAATGTTCAT-GTTTCTGTTAA
1 GTTCATGTT-TTGGTTTCTGTTAA
19864053 GTTCATGTTTTGGTTTCTGTTAA
1 GTTCATGTTTTGGTTTCTGTTAA
* * *
19864076 GTTCATGTTTAGGTTTATGTGTTA
1 GTTCATGTTTTGGTTTCTGT-TAA
* *
19864100 --TAATGTTCAT-GTTTCTGTTAA
1 GTTCATGTT-TTGGTTTCTGTTAA
* **
19864121 GTTCATGTTTTGGTTTATGTTTTG
1 GTTCATGTTTTGGTTTCTG-TTAA
19864145 GTTCATGTTTTGGTTTCTGTTAA
1 GTTCATGTTTTGGTTTCTGTTAA
*
19864168 GTTGATGTTTT
1 GTTCATGTTTT
19864179 TCTGTATTAA
Statistics
Matches: 135, Mismatches: 25, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
21 4 0.03
22 28 0.21
23 79 0.59
24 24 0.18
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.57
Consensus pattern (23 bp):
GTTCATGTTTTGGTTTCTGTTAA
Found at i:19864106 original size:45 final size:46
Alignment explanation
Indices: 19864057--19864177 Score: 156
Period size: 45 Copynumber: 2.6 Consensus size: 46
19864047 TGTTAAGTTC
19864057 ATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTT-ATA
1 ATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTTGATA
* * * * *
19864102 ATGTTCAT-GTTTCTGTTAAGTTCATGTTTTGGTTTATGTTTTGGTTC
1 ATGTT-TTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTT-GATA
*
19864149 ATGTTTTGGTTTCTGTTAAGTTGATGTTT
1 ATGTTTTGGTTTCTGTTAAGTTCATGTTT
19864178 TTCTGTATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
45 37 0.57
46 2 0.03
47 26 0.40
ACGTcount: A:0.15, C:0.06, G:0.22, T:0.57
Consensus pattern (46 bp):
ATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTTGATA
Found at i:19864142 original size:12 final size:12
Alignment explanation
Indices: 19864125--19864165 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
19864115 TGTTAAGTTC
19864125 ATGTTTTGGTTT
1 ATGTTTTGGTTT
*
19864137 ATGTTTTGGTTC
1 ATGTTTTGGTTT
19864149 ATGTTTTGGTTT
1 ATGTTTTGGTTT
*
19864161 CTGTT
1 ATGTT
19864166 AAGTTGATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.05, G:0.24, T:0.63
Consensus pattern (12 bp):
ATGTTTTGGTTT
Found at i:19864191 original size:68 final size:68
Alignment explanation
Indices: 19863985--19864160 Score: 307
Period size: 68 Copynumber: 2.6 Consensus size: 68
19863975 GTGTTATAAT
19863985 GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTTGGTTTATGTGTTATAATGTTCATGTTTCTGT
1 GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTTGGTTTATGTGTTATAATGTTCATGTTTCTGT
19864050 TAA
66 TAA
*
19864053 GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTTATAATGTTCATGTTTCTGT
1 GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTTGGTTTATGTGTTATAATGTTCATGTTTCTGT
19864118 TAA
66 TAA
* **
19864121 GTTCATGTTTTGGTTTATGTTTTGGTTCATGTTTTGGTTT
1 GTTCATGTTTTGGTTTCTG-TTAAGTTCATGTTTTGGTTT
19864161 CTGTTAAGTT
Statistics
Matches: 102, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
68 85 0.83
69 17 0.17
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.57
Consensus pattern (68 bp):
GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTTGGTTTATGTGTTATAATGTTCATGTTTCTGT
TAA
Found at i:19864201 original size:20 final size:21
Alignment explanation
Indices: 19864164--19864203 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19864154 TTGGTTTCTG
19864164 TTAAGTTGATGTTTTTCTGTA
1 TTAAGTTGATGTTTTTCTGTA
19864185 TTAAGTTGATG-TTTTCTGT
1 TTAAGTTGATGTTTTTCTGT
19864204 TTCTGTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.57
Consensus pattern (21 bp):
TTAAGTTGATGTTTTTCTGTA
Found at i:19864270 original size:19 final size:20
Alignment explanation
Indices: 19864246--19864287 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
19864236 TATGTTTTGG
19864246 TTTCTG-TTAAGTTGATGTT
1 TTTCTGATTAAGTTGATGTT
*
19864265 TTTCTGTATTAATTTGATGTT
1 TTTCTG-ATTAAGTTGATGTT
19864286 TT
1 TT
19864288 CCCATACCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
21 14 0.70
ACGTcount: A:0.17, C:0.05, G:0.17, T:0.62
Consensus pattern (20 bp):
TTTCTGATTAAGTTGATGTT
Found at i:19865181 original size:16 final size:16
Alignment explanation
Indices: 19865160--19865193 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
19865150 TATTATATAT
19865160 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
19865176 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
19865192 TT
1 TT
19865194 CCAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTTTAATA
Found at i:19865246 original size:18 final size:18
Alignment explanation
Indices: 19865223--19865257 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19865213 ATCTGTTAAA
19865223 ATAAAAATAATTAAATTC
1 ATAAAAATAATTAAATTC
*
19865241 ATAAAACTAATTAAATT
1 ATAAAAATAATTAAATT
19865258 ATATATTTAC
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:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAAATAATTAAATTC
Found at i:19865313 original size:16 final size:16
Alignment explanation
Indices: 19865292--19865325 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
19865282 AAATTAAATT
19865292 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
19865308 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
19865324 TT
1 TT
19865326 GCAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTTTAATA
Found at i:19865342 original size:133 final size:133
Alignment explanation
Indices: 19865040--19865338 Score: 546
Period size: 133 Copynumber: 2.3 Consensus size: 133
19865030 TAAAGTTTGG
19865040 ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAA
1 ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAA
* *
19865105 TGCATAAAACTAATCAAATTATATATTTACAAATTAATTAAATTATATTATATATTTTTTTATTT
66 TGCATAAAACTAATCAAATTATATATTTACAAATTAATTAAATTAAATTAAATATTTTTTTATTT
19865170 TTA
131 TTA
19865173 ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAA
1 ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAA
* *
19865238 TTCATAAAACTAATTAAATTATATATTTACAAATTAATTAAATTAAATTAAAT-TTTTTTTATTT
66 TGCATAAAACTAATCAAATTATATATTTACAAATTAATTAAATTAAATTAAATATTTTTTTATTT
19865302 TTA
131 TTA
*
19865305 ATATTTTTTATTTTTAATATTGCAATTTATTAAA
1 ATATTTTTTATTTTTAATATTCCAATTTATTAAA
19865339 ATAAAAATAA
Statistics
Matches: 161, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
132 47 0.29
133 114 0.71
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.49
Consensus pattern (133 bp):
ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAA
TGCATAAAACTAATCAAATTATATATTTACAAATTAATTAAATTAAATTAAATATTTTTTTATTT
TTA
Found at i:19867719 original size:49 final size:49
Alignment explanation
Indices: 19867662--19867765 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
19867652 TCATGTGTTA
* * * *
19867662 TAATTTTATACAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
19867711 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
19867760 TAATTT
1 TAATTT
19867766 GTTTTTTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:19869279 original size:120 final size:120
Alignment explanation
Indices: 19869152--19870233 Score: 1798
Period size: 120 Copynumber: 9.0 Consensus size: 120
19869142 AAGTAGATTA
** *
19869152 TAAATTATATTTTATAGTACCATATATTAAGATTTTAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
19869217 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
* * * * *
19869272 TAGATTATATTTTATAATATTATATATCATGATTATAGTAAATTCATGTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
19869337 AAGAATTTTATTAAATTATATACTTTTAATAAATTATATTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
19869392 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* * *
19869457 AAGAATTTTATTAAATTATATCTTTTTATTAAATTATATTTAAAAATAATTAATT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
19869512 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* **
19869574 AAGAATTTTATTAAATTATATATTTTTACTAAATTATATTTTTAATAATTGTTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTT
* * *
19869631 TAAATTATATTTTATAGTGTTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATCTT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
19869696 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAAAAATAATTAATT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
19869751 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* * *
19869813 AAGAATTTTATTAAATTATATAGTTTTACTAAATTATATTTTTAATAATTATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTT
*
19869870 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
19869935 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
*
19869990 TAAATTATATTTTATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* * *
19870055 AAGAATTTTATTAAATTATATGTTTTTATGAAATTATATTTAATAATAATTATGT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
* *
19870110 TAAATTATATTTTATAGTATTATATATTATGATTTAAGAAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
19870175 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
19870230 TAAA
1 TAAA
19870234 ATATGATTAA
Statistics
Matches: 899, Mismatches: 53, Indels: 20
0.92 0.05 0.02
Matches are distributed among these distances:
117 105 0.12
119 116 0.13
120 572 0.64
122 106 0.12
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (120 bp):
TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
Found at i:19869600 original size:18 final size:17
Alignment explanation
Indices: 19869579--19869616 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
19869569 ATATTAAGAA
*
19869579 TTTTATTAAATTATATAT
1 TTTTACTAAATTATAT-T
19869597 TTTTACTAAATTATATT
1 TTTTACTAAATTATATT
19869614 TTT
1 TTT
19869617 AATAATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTACTAAATTATATT
Found at i:19869724 original size:239 final size:238
Alignment explanation
Indices: 19869152--19870226 Score: 1805
Period size: 239 Copynumber: 4.5 Consensus size: 238
19869142 AAGTAGATTA
** *
19869152 TAAATTATATTTTATAGTACCATATATTAAGATTTTAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
19869217 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAGATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
* * *
19869282 TTTATAATATTATATATCATGATTATAGTAAATTCATGTAAGAATATTTAATATTAAGAATTTTA
131 TTTATAGTATTATATATTATGATTTTAGTAAATTCA--TAAGAATATTTAATATTAAGAATTTTA
* *
19869347 TTAAATTATATACTTTTAATAAATTATATTTAATAATAATTATTT
194 TTAAATTATATATTTTTACTAAATTATATTTAATAATAATTATTT
19869392 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
19869457 AAGAATTTTATTAAATTATATCTTTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
19869522 TTTATAGTATTATATATTATGATTTTAGTAAATTC-TAAGAATATTTAATATTAAGAATTTTATT
131 TTTATAGTATTATATATTATGATTTTAGTAAATTCATAAGAATATTTAATATTAAGAATTTTATT
**
19869586 AAATTATATATTTTTACTAAATTATATTTTTAATAATTGTTATTT
196 AAATTATATATTTTTACTAAATTATA--TTTAATAATAATTATTT
* * *
19869631 TAAATTATATTTTATAGTGTTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATCTT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
19869696 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
19869761 TTTATAGTATTATATATTATGATTTTAGTAAATTC-TAAGAATATTTAATATTAAGAATTTTATT
131 TTTATAGTATTATATATTATGATTTTAGTAAATTCATAAGAATATTTAATATTAAGAATTTTATT
* *
19869825 AAATTATATAGTTTTACTAAATTATATTTTTAATAATTATTATTT
196 AAATTATATATTTTTACTAAATTATA--TTTAATAATAATTATTT
*
19869870 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
19869935 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
*
19870000 TTTATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTA
131 TTTATAGTATTATATATTATGATTTTAGTAAATTC--ATAAGAATATTTAATATTAAGAATTTTA
* *
19870065 TTAAATTATATGTTTTTA-TGAAATTATATTTAATAATAATTATGT
194 TTAAATTATATATTTTTACT-AAATTATATTTAATAATAATTATTT
* *
19870110 TAAATTATATTTTATAGTATTATATATTATGATTTAAGAAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
19870175 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTA
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTA
19870227 TGTTAAAATA
Statistics
Matches: 797, Mismatches: 32, Indels: 12
0.95 0.04 0.01
Matches are distributed among these distances:
237 53 0.07
239 408 0.51
240 284 0.36
241 1 0.00
242 51 0.06
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (238 bp):
TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
TTTATAGTATTATATATTATGATTTTAGTAAATTCATAAGAATATTTAATATTAAGAATTTTATT
AAATTATATATTTTTACTAAATTATATTTAATAATAATTATTT
Found at i:19869855 original size:16 final size:15
Alignment explanation
Indices: 19869818--19869882 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 15
19869808 ATATTAAGAA
19869818 TTTTATTAAATTATAT
1 TTTTA-TAAATTATAT
19869834 AGTTTTACTAAATTATAT
1 --TTTTA-TAAATTATAT
19869852 TTTTA-ATAATTAT-T
1 TTTTATA-AATTATAT
*
19869866 ATTT-TAAATTATAT
1 TTTTATAAATTATAT
19869880 TTT
1 TTT
19869883 ATAGTATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
13 6 0.15
14 9 0.22
15 6 0.15
16 5 0.12
18 15 0.37
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTTATAAATTATAT
Found at i:19869891 original size:28 final size:29
Alignment explanation
Indices: 19869842--19869897 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
19869832 ATAGTTTTAC
19869842 TAAATTATATTTTTAATAATTAT-TATTT
1 TAAATTATATTTTTAATAATTATATATTT
*
19869870 TAAATTATATTTTATAGT-ATTATATATT
1 TAAATTATATTTT-TAATAATTATATATT
19869898 ATGATTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TAAATTATATTTTTAATAATTATATATTT
Found at i:19870454 original size:45 final size:44
Alignment explanation
Indices: 19870371--19870466 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 44
19870361 ATTACAATAT
*
19870371 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
1 CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
*
19870415 CATTACATTCAACCAAACA-ATTGAATTACTATTACGCCTCTATTC
1 CATTACATTCAACCAAACACA-AGAA-TACTATTACGCCTCTATTC
19870460 CATTACA
1 CATTACA
19870467 GCTCTATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.44
45 26 0.54
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.30
Consensus pattern (44 bp):
CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
Found at i:19870471 original size:16 final size:16
Alignment explanation
Indices: 19870452--19870484 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19870442 ACTATTACGC
19870452 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
19870468 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
19870484 C
1 C
19870485 GAACCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:19877079 original size:2 final size:2
Alignment explanation
Indices: 19877072--19877113 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19877062 AGCACATAAC
19877072 AT AT 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 AT AT
19877114 CAAAATAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19887137 original size:22 final size:22
Alignment explanation
Indices: 19887109--19887191 Score: 121
Period size: 22 Copynumber: 3.8 Consensus size: 22
19887099 GTCAGTGATT
19887109 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
19887131 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
19887153 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
19887175 CATGAGAGCTTAGTACG
1 CATGAGAGCTTAGTACG
19887192 ACCGAGAATC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:19888594 original size:22 final size:22
Alignment explanation
Indices: 19888569--19888612 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19888559 TAACGTCATA
*
19888569 CTAGAATCCTTGACTAAAAGGG
1 CTAGAATCCTCGACTAAAAGGG
19888591 CTAGAATCCTCGACTAAAAGGG
1 CTAGAATCCTCGACTAAAAGGG
19888613 GAAAGGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (22 bp):
CTAGAATCCTCGACTAAAAGGG
Found at i:19891940 original size:38 final size:37
Alignment explanation
Indices: 19891897--19891991 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 37
19891887 AAAATTTATT
19891897 TTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAA
1 TTAAAAATTAAAA-AAAAATTAAAAAAA-TATTTTAAAA
* ** **
19891936 TAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
1 T-TAAAAATTAAAAAAAAATTAAAAAAATATTTTAAAA
19891974 TTAAAAAAATTAAAAAAA
1 TT--AAAAATTAAAAAAA
19891992 GTATTTTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
38 11 0.24
39 24 0.52
40 11 0.24
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (37 bp):
TTAAAAATTAAAAAAAAATTAAAAAAATATTTTAAAA
Found at i:19891950 original size:9 final size:9
Alignment explanation
Indices: 19891932--19892022 Score: 60
Period size: 9 Copynumber: 9.7 Consensus size: 9
19891922 AAAGTATTTT
19891932 AAAA-TAAA
1 AAAATTAAA
19891940 AAAATTAAA
1 AAAATTAAA
19891949 AAAGTATTTTAAA
1 AAA--A--TTAAA
* **
19891962 AATATTTTA
1 AAAATTAAA
19891971 -AAATTAAA
1 AAAATTAAA
19891979 AAAATTAAA
1 AAAATTAAA
***
19891988 AAAAGTATTTT
1 AAAA-T-TAAA
19891999 AAAATTAAA
1 AAAATTAAA
19892008 AAAATTAAA
1 AAAATTAAA
19892017 AAAATT
1 AAAATT
19892023 TATTATATTC
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
8 9 0.14
9 38 0.60
10 2 0.03
11 7 0.11
13 7 0.11
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATTAAA
Found at i:19891963 original size:28 final size:30
Alignment explanation
Indices: 19891893--19891965 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 30
19891883 ACCAAAAATT
19891893 TATTTTAAAAATTAAAACAAAAATTAAAAAAAG
1 TATTTTAAAAA-T--AACAAAAATTAAAAAAAG
19891926 TATTTT-AAAATAA-AAAAATT-AAAAAAG
1 TATTTTAAAAATAACAAAAATTAAAAAAAG
19891953 TATTTTAAAAATA
1 TATTTTAAAAATA
19891966 TTTTAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
27 13 0.33
28 13 0.33
29 2 0.05
31 1 0.03
32 4 0.10
33 6 0.15
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (30 bp):
TATTTTAAAAATAACAAAAATTAAAAAAAG
Found at i:19891963 original size:39 final size:40
Alignment explanation
Indices: 19891920--19892002 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
19891910 CAAAAATTAA
19891920 AAAAAGTATTTTAAAA-TAAAAAAATT-AAAAAAGTATTTT
1 AAAAA-TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
19891959 AAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
19891999 AAAA
1 AAAA
19892003 TTAAAAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
38 10 0.24
39 15 0.36
40 17 0.40
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (40 bp):
AAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
Found at i:19891988 original size:8 final size:9
Alignment explanation
Indices: 19891970--19892022 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
19891960 AAAATATTTT
19891970 AAAATTAAA
1 AAAATTAAA
19891979 AAAATTAAA
1 AAAATTAAA
***
19891988 AAAAGTATTTT
1 AAAA-T-TAAA
19891999 AAAATTAAA
1 AAAATTAAA
19892008 AAAATTAAA
1 AAAATTAAA
19892017 AAAATT
1 AAAATT
19892023 TATTATATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 29 0.81
10 2 0.06
11 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAATTAAA
Found at i:19892020 original size:40 final size:39
Alignment explanation
Indices: 19891932--19892022 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 39
19891922 AAAGTATTTT
***
19891932 AAAA-TAAAAAAATTAAAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATAAA
19891970 AAAATTAAAAAAATTAAAAAAAGTATTTT-AAAAT-TAAA
1 AAAATTAAAAAAATT-AAAAAAGTATTTTAAAAATATAAA
19892008 AAAATTAAAAAAATT
1 AAAATTAAAAAAATT
19892023 TATTATATTC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
38 20 0.42
39 15 0.31
40 13 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (39 bp):
AAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATAAA
Found at i:19892040 original size:5 final size:5
Alignment explanation
Indices: 19892032--19892063 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
19892022 TTATTATATT
19892032 CGGGC CGGGC CGGGC CGGGC CGGGCC CGGGC C
1 CGGGC CGGGC CGGGC CGGGC CGGG-C CGGGC C
19892064 AAAAAAGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.44, G:0.56, T:0.00
Consensus pattern (5 bp):
CGGGC
Found at i:19897427 original size:3 final size:3
Alignment explanation
Indices: 19897419--19897447 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19897409 AATAGCTCTT
19897419 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19897448 TTAATATACA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19898439 original size:16 final size:17
Alignment explanation
Indices: 19898406--19898446 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
19898396 ACCTTCCAAG
19898406 GTTATTCTCAACATGAT
1 GTTATTCTCAACATGAT
*
19898423 GTTATTCT-AATATGAT
1 GTTATTCTCAACATGAT
*
19898439 GATATTCT
1 GTTATTCT
19898447 TAAAAATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (17 bp):
GTTATTCTCAACATGAT
Found at i:19908942 original size:7 final size:7
Alignment explanation
Indices: 19908930--19908962 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
19908920 TAGTCGATTC
19908930 GTATTTA
1 GTATTTA
19908937 GTATTTA
1 GTATTTA
19908944 GTATTTA
1 GTATTTA
19908951 GTATTTA
1 GTATTTA
19908958 GTATT
1 GTATT
19908963 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:19909615 original size:18 final size:18
Alignment explanation
Indices: 19909592--19909634 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
19909582 TGCCAAGTGC
* *
19909592 GTATCCTATCCCTTTTAT
1 GTATCCTAACCCTTATAT
19909610 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
19909628 GTTTCCT
1 GTATCCT
19909635 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.07, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:19909901 original size:21 final size:21
Alignment explanation
Indices: 19909877--19909923 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
19909867 CAACATTGAT
*
19909877 AACCA-AATCCCCTACCGGAGG
1 AACCAGAATCCCC-ACCGGAGC
*
19909898 AACCAGAATCCTCACCGGAGC
1 AACCAGAATCCCCACCGGAGC
19909919 AACCA
1 AACCA
19909924 CAACCCTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.36, C:0.38, G:0.17, T:0.09
Consensus pattern (21 bp):
AACCAGAATCCCCACCGGAGC
Found at i:19909931 original size:21 final size:21
Alignment explanation
Indices: 19909886--19909932 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
19909876 TAACCAAATC
* *
19909886 CCCT-ACCGGAGGAACCAGAA
1 CCCTCACCGGAGCAACCACAA
*
19909906 TCCTCACCGGAGCAACCACAA
1 CCCTCACCGGAGCAACCACAA
19909927 CCCTCA
1 CCCTCA
19909933 TCGAAAGCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.32, C:0.43, G:0.17, T:0.09
Consensus pattern (21 bp):
CCCTCACCGGAGCAACCACAA
Found at i:19912729 original size:243 final size:243
Alignment explanation
Indices: 19912322--19912780 Score: 756
Period size: 243 Copynumber: 1.9 Consensus size: 243
19912312 CATTGGGGCT
* * *
19912322 GGGCTCTCGAGGTGGATCCACATCGAACTCATCTTCTAACCCACCATCATCTGTAACGTACAAGG
1 GGGCTCTCGAGGTGGATCCACATCGAACTCATATTCTAACCCACCATCATATGCAACGTACAAGG
* * *
19912387 TCCCCTCACCGGTGGACGTCCTAGGGAATACATTATCCCTTCTTCTGGGCGTTTCATAACGTCCC
66 TCCCCTCACCGGTAGACGTCCTAGGGAATACATCATCCCTTCTTCTGGGCGTTTCATAACATCCC
* *
19912452 CATTTGGACGTAGATTGCCAACCACTAGAAGTTGATGTCGTTCCCCAGTACGTATTTTCAGCATC
131 CAATTAGACGTAGATTGCCAACCACTAGAAGTTGATGTCGTTCCCCAGTACGTATTTTCAGCATC
*
19912517 AAACATCAACCCACCGAGGTGTTGTGTAACTTCTGCACCATCAGGTTC
196 AAACACCAACCCACCGAGGTGTTGTGTAACTTCTGCACCATCAGGTTC
* * *
19912565 GGGCTCTTGAGGTGGATCCACATCGGACTCATATTCTAACCCACCATCATATGCAACGTACGAGG
1 GGGCTCTCGAGGTGGATCCACATCGAACTCATATTCTAACCCACCATCATATGCAACGTACAAGG
** *
19912630 TCCCCTCACCGGTAGACGTTGTAGGGAATACATCATCCCTTCTTCTGGGCGTTTCATAACATCTC
66 TCCCCTCACCGGTAGACGTCCTAGGGAATACATCATCCCTTCTTCTGGGCGTTTCATAACATCCC
* *
19912695 CAATTAGATGTAGATTGCCAACTACTAGAAGTTGATGTCGTTCCCCAGTACGTATTTTCAGCATC
131 CAATTAGACGTAGATTGCCAACCACTAGAAGTTGATGTCGTTCCCCAGTACGTATTTTCAGCATC
*
19912760 AAACACCGACCCACCGAGGTG
196 AAACACCAACCCACCGAGGTG
19912781 CATGTCTCAT
Statistics
Matches: 198, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
243 198 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (243 bp):
GGGCTCTCGAGGTGGATCCACATCGAACTCATATTCTAACCCACCATCATATGCAACGTACAAGG
TCCCCTCACCGGTAGACGTCCTAGGGAATACATCATCCCTTCTTCTGGGCGTTTCATAACATCCC
CAATTAGACGTAGATTGCCAACCACTAGAAGTTGATGTCGTTCCCCAGTACGTATTTTCAGCATC
AAACACCAACCCACCGAGGTGTTGTGTAACTTCTGCACCATCAGGTTC
Found at i:19913590 original size:126 final size:126
Alignment explanation
Indices: 19913358--19913769 Score: 639
Period size: 126 Copynumber: 3.3 Consensus size: 126
19913348 CAGGCCAAAT
*
19913358 AGGAACTACTATAGCAAAAGAGCGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
1 AGGAACTACTATAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
* * *
19913423 TCCTGCTTGAAGTGTTTTTGACACTATTTGCTCAGAAACATCTTATCAAAATTATTTTTTC
66 TCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTC
* *
19913484 AGGAACTACTATAGTAAAAGAGCGTCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
1 AGGAACTACTATAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
* * *
19913549 TCCTGCTTAAAGCGTTTTTTACACTATTTGCTTAGACACATCTTCTCAAAATTATTTTTTC
66 TCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTC
* * * * *
19913610 AGAAACTACTGTAGCAAAAGAGCATCCACGTGGGAGTTTCTTTCAGTACTTTTGCTGACAATGCA
1 AGGAACTACTATAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
* * * *
19913675 TCCTACTTAAAGCGTTTTTGACACTATTT-CTCATAAACCTCTTCCCAAAATTA-TTTTTC
66 TCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTC
*
19913734 AGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAG
1 AGGAACTACTATAGCAAAAGAGCGTCCACGTGGGAG
19913770 TTTTTTTAAA
Statistics
Matches: 261, Mismatches: 25, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
124 40 0.15
125 19 0.07
126 202 0.77
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (126 bp):
AGGAACTACTATAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
TCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTC
Found at i:19913944 original size:7 final size:7
Alignment explanation
Indices: 19913932--19913961 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
19913922 TTTTCCTTAA
19913932 AAACCCT
1 AAACCCT
19913939 AAACCCT
1 AAACCCT
*
19913946 AAACACT
1 AAACCCT
19913953 AAACCCT
1 AAACCCT
19913960 AA
1 AA
19913962 TCTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:19913985 original size:100 final size:102
Alignment explanation
Indices: 19913843--19914230 Score: 469
Period size: 100 Copynumber: 4.0 Consensus size: 102
19913833 TTTTTCTTTA
* * *
19913843 AAACCCTAAACCCTAATCTAATTTTTTTTAAATTTATAATTAATTTACTCAAGTAATCAC-AAAC
1 AAACACTAAACCCTAATCTAA-TTTTTTAAAATTTATAATTAATTTACTCAAGTAA-CCCTAAAC
* *
19913907 CTTAATTTATTT-ATTTTTTCCTTAAAAACCCTAAACCCT
64 CCTAATTTATTTAATTTTTTTCTTAAAAACCCTAAA-CCT
19913946 AAACACTAAACCCTAATCT-ATTTTTT-AAATTTATAATTAATTTACTCAAGTAACCCTAAACCC
1 AAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCC
*
19914009 TAATTTATTTGATTTTTTTCTTAAAAACCCTAAACACT
66 TAATTTATTTAATTTTTTTCTTAAAAACCCTAAAC-CT
* * *
19914047 AAACCCT-AA-TCTAAT-T-TTTTTTTCAAAATTTATAATTAATTTACTCAAGTAACCCTAAACC
1 AAACACTAAACCCTAATCTAATTTTTT-AAAATTTATAATTAATTTACTCAAGTAACCCTAAACC
19914108 CTAATTTATTTAATTTTTTTCTTAAAAA-CC---A--T
65 CTAATTTATTTAATTTTTTTCTTAAAAACCCTAAACCT
*
19914140 AAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATT-A---AC-CTA--AACCCTAAACCC
1 AAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCC
* *
19914198 TTATTTATTTAATTTTTTCCTT-AAAACCCTAAA
66 TAATTTATTTAATTTTTTTCTTAAAAACCCTAAA
19914231 ATCTAAAAAT
Statistics
Matches: 258, Mismatches: 14, Indels: 37
0.83 0.05 0.12
Matches are distributed among these distances:
88 4 0.02
89 34 0.13
91 2 0.01
92 3 0.01
93 7 0.03
94 2 0.01
95 6 0.02
96 15 0.06
97 6 0.02
98 7 0.03
99 9 0.03
100 108 0.42
101 36 0.14
102 1 0.00
103 18 0.07
ACGTcount: A:0.39, C:0.20, G:0.01, T:0.41
Consensus pattern (102 bp):
AAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCC
TAATTTATTTAATTTTTTTCTTAAAAACCCTAAACCT
Found at i:19914005 original size:50 final size:50
Alignment explanation
Indices: 19913951--19914118 Score: 136
Period size: 50 Copynumber: 3.4 Consensus size: 50
19913941 ACCCTAAACA
19913951 CTAAACCCTAATCTATTTTTTAAATTTATAATTAATTTACTCAAGTAACC
1 CTAAACCCTAATCTATTTTTTAAATTTATAATTAATTTACTCAAGTAACC
* * ** * * *
19914001 CTAAACCCTAATTTATTTGATTT---TTT-T-CTTAA-AAACCCTA--AACA
1 CTAAACCCTAATCTATTT--TTTAAATTTATAATTAATTTACTCAAGTAACC
19914045 CTAAACCCTAATCTAATTTTTTTTTCAAAATTTATAATTAATTTACTCAAGTAACC
1 CTAAACCCTAATCT-A---TTTTTT--AAATTTATAATTAATTTACTCAAGTAACC
*
19914101 CTAAACCCTAATTTATTT
1 CTAAACCCTAATCTATTT
19914119 AATTTTTTTC
Statistics
Matches: 87, Mismatches: 15, Indels: 30
0.66 0.11 0.23
Matches are distributed among these distances:
44 16 0.18
45 1 0.01
46 7 0.08
47 4 0.05
48 4 0.05
49 3 0.03
50 17 0.20
51 3 0.03
52 7 0.08
53 4 0.05
54 4 0.05
55 1 0.01
56 16 0.18
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (50 bp):
CTAAACCCTAATCTATTTTTTAAATTTATAATTAATTTACTCAAGTAACC
Found at i:19915580 original size:18 final size:20
Alignment explanation
Indices: 19915559--19915600 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
19915549 TATTTAAGGA
*
19915559 ATTTTTTTAA-TTTTA-AAT
1 ATTTTTATAATTTTTATAAT
19915577 ATTTTTATAATTTTTATAAT
1 ATTTTTATAATTTTTATAAT
19915597 ATTT
1 ATTT
19915601 ATATTTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 5 0.24
20 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTTATAATTTTTATAAT
Found at i:19916703 original size:17 final size:17
Alignment explanation
Indices: 19916681--19916731 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
19916671 AAAAATTAAA
*
19916681 AAAATTATAATATTTTT
1 AAAATTATAATATTTTG
*
19916698 AAAATTCAAAATATTTATG
1 AAAATT-ATAATATTT-TG
*
19916717 AAAATT-TAAAATTTT
1 AAAATTATAATATTTT
19916732 ATATTTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 1 0.04
17 12 0.43
18 8 0.29
19 7 0.25
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
AAAATTATAATATTTTG
Found at i:19916720 original size:19 final size:19
Alignment explanation
Indices: 19916689--19916733 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
19916679 AAAAAATTAT
*
19916689 AATATTT-TTAAAATTCAA
1 AATATTTATGAAAATTCAA
*
19916707 AATATTTATGAAAATTTAA
1 AATATTTATGAAAATTCAA
19916726 AAT-TTTAT
1 AATATTTAT
19916734 ATTTTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
AATATTTATGAAAATTCAA
Found at i:19916746 original size:19 final size:19
Alignment explanation
Indices: 19916724--19916768 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
19916714 ATGAAAATTT
* **
19916724 AAAATTTTATATTTTTCAA
1 AAAATTTTAAATTTTAAAA
*
19916743 AAAATTCTAAATTTTAAAA
1 AAAATTTTAAATTTTAAAA
19916762 AAAATTT
1 AAAATTT
19916769 GAAAAATATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATTTTAAATTTTAAAA
Found at i:19918233 original size:15 final size:15
Alignment explanation
Indices: 19918194--19918233 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
19918184 CCAGAACAGG
19918194 GCAAAGTAGAACATA
1 GCAAAGTAGAACATA
*
19918209 ACAGAA-TAGAACATA
1 GCA-AAGTAGAACATA
19918224 GCAAAGTAGA
1 GCAAAGTAGA
19918234 GCATGTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 2 0.10
15 17 0.81
16 2 0.10
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.12
Consensus pattern (15 bp):
GCAAAGTAGAACATA
Found at i:19920511 original size:58 final size:58
Alignment explanation
Indices: 19920439--19920574 Score: 236
Period size: 58 Copynumber: 2.3 Consensus size: 58
19920429 TGTAATAGCC
* *
19920439 TCTTTCATCTATGGTCTTACACCGTATACCTTATACCTTTTACCATGTTGTCATGACA
1 TCTTTCATCCATGGTCTTACACCGTATACCTTATACATTTTACCATGTTGTCATGACA
* *
19920497 TCTTTCATCCATGGTCTTACACTGTATACCTTATACATTTTACCATGTTGTCATGGCA
1 TCTTTCATCCATGGTCTTACACCGTATACCTTATACATTTTACCATGTTGTCATGACA
19920555 TCTTTCATCCATGGTCTTAC
1 TCTTTCATCCATGGTCTTAC
19920575 GCAACGTACC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 74 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (58 bp):
TCTTTCATCCATGGTCTTACACCGTATACCTTATACATTTTACCATGTTGTCATGACA
Found at i:19921942 original size:86 final size:86
Alignment explanation
Indices: 19921788--19921947 Score: 214
Period size: 86 Copynumber: 1.9 Consensus size: 86
19921778 GTACTTGCAT
* * ** * *
19921788 AAAATGTCTAATGTGGTACTTGTACTTTGAAAATGTTTATTATGGTATATGAACTATTAATAGAT
1 AAAATGTCCAATGTGGTACATGTACTTTGAAAATGTCCAATATGGTATACGAACTATTAATAGAT
19921853 GTTTTATTATGCTCTTTCATC
66 GTTTTATTATGCTCTTTCATC
* * * *
19921874 AAAATGTCCAATGTGGTACATGTAGTTTGAAAATGTCCAATGTGGTATCCGAACTATTTATATG-
1 AAAATGTCCAATGTGGTACATGTACTTTGAAAATGTCCAATATGGTATACGAACTATTAATA-GA
19921938 TGTTTTATTA
65 TGTTTTATTA
19921948 CGGTACTTGT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
86 62 0.98
87 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (86 bp):
AAAATGTCCAATGTGGTACATGTACTTTGAAAATGTCCAATATGGTATACGAACTATTAATAGAT
GTTTTATTATGCTCTTTCATC
Found at i:19931072 original size:13 final size:13
Alignment explanation
Indices: 19931054--19931081 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19931044 ATAAAATTGG
19931054 AAAGATGAAAAAT
1 AAAGATGAAAAAT
19931067 AAAGATGAAAAAT
1 AAAGATGAAAAAT
19931080 AA
1 AA
19931082 TAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAGATGAAAAAT
Found at i:19932978 original size:15 final size:15
Alignment explanation
Indices: 19932958--19932988 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19932948 ATAAAACTTG
19932958 AAAATAGTGAAATAT
1 AAAATAGTGAAATAT
19932973 AAAATAGTGAAATAT
1 AAAATAGTGAAATAT
19932988 A
1 A
19932989 CAAAGTAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (15 bp):
AAAATAGTGAAATAT
Found at i:19939501 original size:13 final size:13
Alignment explanation
Indices: 19939485--19939509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19939475 TTAAGAAAAA
19939485 AAATATCAAATTC
1 AAATATCAAATTC
19939498 AAATATCAAATT
1 AAATATCAAATT
19939510 AGATGAAAAA
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:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATCAAATTC
Found at i:19943649 original size:15 final size:15
Alignment explanation
Indices: 19943629--19943659 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19943619 TCCTTAATCA
19943629 AATTAGGGAACGATT
1 AATTAGGGAACGATT
19943644 AATTAGGGAACGATT
1 AATTAGGGAACGATT
19943659 A
1 A
19943660 TGGAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (15 bp):
AATTAGGGAACGATT
Found at i:19943830 original size:7 final size:7
Alignment explanation
Indices: 19943814--19943845 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
19943804 CTAAAGCTAC
*
19943814 CACTTAT
1 CACTTGT
19943821 CACTTGT
1 CACTTGT
19943828 CACTTGT
1 CACTTGT
19943835 CACTTGT
1 CACTTGT
19943842 CACT
1 CACT
19943846 GATCAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.09, T:0.41
Consensus pattern (7 bp):
CACTTGT
Found at i:19943835 original size:51 final size:51
Alignment explanation
Indices: 19943738--19943991 Score: 348
Period size: 51 Copynumber: 4.9 Consensus size: 51
19943728 ATTTGTCCCC
* *
19943738 GATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGCCATTTGTCATT
1 GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTGTCACT
19943788 GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACTTGTCACT
1 GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG---C----CACTTGTCACT
*
19943846 GATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTGCCACTTGTCACT
1 GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTGTCACT
* * * * *
19943897 GATTAGATAAGTATAGCTGAAGCTATCACTTATCACTTGCCATTTGTCACT
1 GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTGTCACT
* *
19943948 GATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACT
1 GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACT
19943992 GATCAGAAGT
Statistics
Matches: 182, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
50 18 0.10
51 115 0.63
54 1 0.01
55 1 0.01
58 47 0.26
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (51 bp):
GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTGTCACT
Found at i:19943837 original size:14 final size:14
Alignment explanation
Indices: 19943814--19943850 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
19943804 CTAAAGCTAC
19943814 CACTTATCACTTGT
1 CACTTATCACTTGT
*
19943828 CACTTGTCACTTGT
1 CACTTATCACTTGT
*
19943842 CACTGATCA
1 CACTTATCA
19943851 GATAAGTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.38
Consensus pattern (14 bp):
CACTTATCACTTGT
Found at i:19943914 original size:109 final size:108
Alignment explanation
Indices: 19943719--19943991 Score: 371
Period size: 109 Copynumber: 2.6 Consensus size: 108
19943709 TTGCGTATGA
* * *
19943719 TCACTTATCATTTGTCCCCGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGCCATTTG
1 TCACTT-TCATTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTG
* *
19943783 TCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
65 TCACTGATCAGATAAGTATAGCTAAAGCTACCACTTATCACTTG
* *
19943827 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTGCCACTTG
1 TCACTT-TCATTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTG
* * *
19943892 TCACTGATTAGATAAGTATAGCTGAAGCTATCACTTATCACTTG
65 TCACTGATCAGATAAGTATAGCTAAAGCTACCACTTATCACTTG
* *
19943936 ---C---CATTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACT
1 TCACTTTCATTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACT
19943992 GATCAGAAGT
Statistics
Matches: 149, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
102 51 0.34
106 1 0.01
108 33 0.22
109 64 0.43
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (108 bp):
TCACTTTCATTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTGT
CACTGATCAGATAAGTATAGCTAAAGCTACCACTTATCACTTG
Found at i:19952381 original size:3 final size:3
Alignment explanation
Indices: 19952306--19952365 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
19952296 GAGGAGGAAA
* * *
19952306 TGG TGG TGG AGG TGG AGG TGG AGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
19952354 TGG TGG TGG TGG
1 TGG TGG TGG TGG
19952366 AGGAGGAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.05, C:0.00, G:0.67, T:0.28
Consensus pattern (3 bp):
TGG
Found at i:19952484 original size:3 final size:3
Alignment explanation
Indices: 19952476--19952532 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
19952466 CACTGTAGTT
* * * *
19952476 GTG GTG GTG G-G GGG GTG GGG GTG GTG GTG GTG GTG GAG GTG GTG GAG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
*
19952523 GTG GAG GTG G
1 GTG GTG GTG G
19952533 AAATGGAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.05, C:0.00, G:0.72, T:0.23
Consensus pattern (3 bp):
GTG
Found at i:19957509 original size:15 final size:15
Alignment explanation
Indices: 19957489--19957518 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19957479 AGCTGGTACT
*
19957489 TCTTCTTCCTCCTCA
1 TCTTCTTCATCCTCA
19957504 TCTTCTTCATCCTCA
1 TCTTCTTCATCCTCA
19957519 CGTTTCTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTTCTTCATCCTCA
Found at i:19962285 original size:131 final size:131
Alignment explanation
Indices: 19961920--19962317 Score: 487
Period size: 131 Copynumber: 3.0 Consensus size: 131
19961910 GATGAGATCG
* * * *
19961920 TTCATGATGTTAAATCGAATGAACTTAGGCTATAATATTAAATTAATGAGCCTTAACATTATTAG
1 TTCATGATATTAAATCGAATGAACTTAGGCTGTGATATTAAATTAGTGAGCCTTAACATTATTAG
* * * * *
19961985 TTGCGATCTTATATCAGTGAGCTATTTAGAGTAGCAATATTAAATCAAATAACTCAAATAAAATT
66 TTGCGATATTAAATCAGTGAGCTATTTAGAGTAGCGATATTAAATCAGATAACTCAAAGAAAATT
19962050 AT
131 -T
** * * * * * *
19962052 TT-ATGATATTAAATTAAATAAACTT-GGCTGCGATATTAAA-TCGACGAGCTTTAACATTATCA
1 TTCATGATATTAAATCGAATGAACTTAGGCTGTGATATTAAATTAG-TGAGCCTTAACATTATTA
* * * * * * * *
19962114 GCTGCAATATTAAATCAGTAAGTTATTTAAAGTAGTGATATTAAATCGGGTAACTCAAAGAAAAT
65 GTTGCGATATTAAATCAGTGAGCTATTTAGAGTAGCGATATTAAATCAGATAACTCAAAGAAAAT
19962179 TT
130 TT
*
19962181 TTCATGATATTAAATCGAATGAACTTAGGCTGTGATTTTAAATTAGTGAGCCTTAACATTATTAG
1 TTCATGATATTAAATCGAATGAACTTAGGCTGTGATATTAAATTAGTGAGCCTTAACATTATTAG
* * * *
19962246 TTGTGATATTAAATCAGCGAGCTATTTAGAGTAACGATATTAAATCAGCTAACTCAAAGAAAATT
66 TTGCGATATTAAATCAGTGAGCTATTTAGAGTAGCGATATTAAATCAGATAACTCAAAGAAAATT
19962311 T
131 T
19962312 TTCATG
1 TTCATG
19962318 TTAGATAAAC
Statistics
Matches: 217, Mismatches: 45, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
129 4 0.02
130 100 0.46
131 109 0.50
132 4 0.02
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (131 bp):
TTCATGATATTAAATCGAATGAACTTAGGCTGTGATATTAAATTAGTGAGCCTTAACATTATTAG
TTGCGATATTAAATCAGTGAGCTATTTAGAGTAGCGATATTAAATCAGATAACTCAAAGAAAATT
T
Found at i:19969888 original size:17 final size:16
Alignment explanation
Indices: 19969868--19969927 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
19969858 TGTTTAAACC
19969868 TATTTTTAATATAA-T
1 TATTTTTAATATAATT
* *
19969883 TATATTTAGT-TAATT
1 TATTTTTAATATAATT
19969898 CTCATTTTTAAATATAATT
1 -T-ATTTTT-AATATAATT
19969917 TATTTCTTAAT
1 TATTT-TTAAT
19969928 TTTTATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 3 0.09
15 9 0.26
16 1 0.03
17 12 0.34
18 5 0.14
19 5 0.14
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (16 bp):
TATTTTTAATATAATT
Found at i:19969936 original size:31 final size:32
Alignment explanation
Indices: 19969868--19969936 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
19969858 TGTTTAAACC
*
19969868 TATTTTTAATATAATTATATTTAGTTAATTCT
1 TATTTTTAATATAATTATATTTACTTAATTCT
* *
19969900 CATTTTTAAATATAATT-TATTT-CTTAATTTT
1 TATTTTT-AATATAATTATATTTACTTAATTCT
19969931 TATTTT
1 TATTTT
19969937 ATATTTCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 12 0.38
32 11 0.34
33 9 0.28
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (32 bp):
TATTTTTAATATAATTATATTTACTTAATTCT
Found at i:19972967 original size:29 final size:31
Alignment explanation
Indices: 19972904--19972970 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
19972894 AAAATACAAT
* *
19972904 GACTAAAATTAATCAATATGTAAAGTACAGA
1 GACTAAAATTAATCAATATGCAAAGTAAAGA
*
19972935 GACTAAAATTGATCAA-AT-CAAAGTATAAG-
1 GACTAAAATTAATCAATATGCAAAGTA-AAGA
19972964 GACTAAA
1 GACTAAA
19972971 CTCACAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 13 0.41
30 4 0.12
31 15 0.47
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.24
Consensus pattern (31 bp):
GACTAAAATTAATCAATATGCAAAGTAAAGA
Found at i:19978818 original size:22 final size:21
Alignment explanation
Indices: 19978793--19978836 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
19978783 TCTATCTATT
*
19978793 TTCTCTCAATCTCTCTTTCAAA
1 TTCTCTCAAACT-TCTTTCAAA
*
19978815 TTCTCTCAAACTTCTTTGAAA
1 TTCTCTCAAACTTCTTTCAAA
19978836 T
1 T
19978837 ATTTGGTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.45
Consensus pattern (21 bp):
TTCTCTCAAACTTCTTTCAAA
Found at i:19997025 original size:10 final size:10
Alignment explanation
Indices: 19997010--19997034 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19997000 ATTGCTACCC
19997010 AAGTTACAAG
1 AAGTTACAAG
19997020 AAGTTACAAG
1 AAGTTACAAG
19997030 AAGTT
1 AAGTT
19997035 GTGATTCGAC
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:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (10 bp):
AAGTTACAAG
Found at i:20013116 original size:9 final size:9
Alignment explanation
Indices: 20013099--20013130 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
20013089 GCGAAAGAAC
*
20013099 AAAAGAAAG
1 AAAAAAAAG
20013108 AAAAAAAAG
1 AAAAAAAAG
20013117 AAAAAAAAG
1 AAAAAAAAG
20013126 AAAAA
1 AAAAA
20013131 TCAAATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:20022341 original size:18 final size:17
Alignment explanation
Indices: 20022318--20022351 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20022308 TTTAATTTCC
20022318 TAATTTTGAAATTTAGCA
1 TAATTTT-AAATTTAGCA
*
20022336 TAATTTTCAATTTAGC
1 TAATTTTAAATTTAGC
20022352 CTATATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (17 bp):
TAATTTTAAATTTAGCA
Found at i:20026002 original size:51 final size:52
Alignment explanation
Indices: 20025943--20026050 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 52
20025933 ATATTATTCT
* * *
20025943 AATATTTGGCAAT-ACAAAATTAGTTGAAAGCTCCAGAAGAGTTAATATATC
1 AATATTTGGCAATAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATC
* * *
20025994 AATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATT
1 AATATTTGGCAATAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATC
20026046 AATAT
1 AATAT
20026051 CTAAAAAGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
51 11 0.22
52 39 0.78
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (52 bp):
AATATTTGGCAATAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATC
Found at i:20026066 original size:52 final size:52
Alignment explanation
Indices: 20025956--20026067 Score: 136
Period size: 52 Copynumber: 2.2 Consensus size: 52
20025946 ATTTGGCAAT
* * ****
20025956 ACAAAATTAGTTGAAAGCTCCAGAAGAGTTAATATATCAATATTTGGTAGTA
1 ACAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATCAATATTAAAAAGTA
* *
20026008 AAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATCTAAAAAG-A
1 ACAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATCAATAT-TAAAAAGTA
20026060 ACAAAATT
1 ACAAAATT
20026068 TGTGATGGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 47 0.94
53 3 0.06
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (52 bp):
ACAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATCAATATTAAAAAGTA
Found at i:20035667 original size:53 final size:53
Alignment explanation
Indices: 20035586--20035744 Score: 221
Period size: 53 Copynumber: 3.0 Consensus size: 53
20035576 TTTTTTAATT
* * *
20035586 TTTCCATATGATGCCATAACCCATCAGTTACGATCTTACATGATATGGTCTTC
1 TTTCCATATGATGTCATAACCCACCAGTTACGATCTTACACGATATGGTCTTC
* * * * *
20035639 TTTCCATATGATTTCATGACCCACCAGTTA-TAGTCTTACACAATATGGTATTC
1 TTTCCATATGATGTCATAACCCACCAGTTACGA-TCTTACACGATATGGTCTTC
*
20035692 TTTCCATATGATGTCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
1 TTTCCATATGATGTCATAACCCACCAGTTACGATCTTACACGATATGGTCTTC
20035745 AATGCCATGG
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.01
53 89 0.99
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (53 bp):
TTTCCATATGATGTCATAACCCACCAGTTACGATCTTACACGATATGGTCTTC
Found at i:20055377 original size:20 final size:22
Alignment explanation
Indices: 20055349--20055388 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20055339 TTGTTTTTAC
*
20055349 TTCTCTTTTACAT-TTTTTTGT
1 TTCTCTTTTAAATATTTTTTGT
20055370 TTCT-TTTTAAATATTTTTT
1 TTCTCTTTTAAATATTTTTT
20055389 TATGTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (22 bp):
TTCTCTTTTAAATATTTTTTGT
Found at i:20055603 original size:17 final size:17
Alignment explanation
Indices: 20055571--20055604 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20055561 TCTCAATGTT
*
20055571 AATATAAAATTGAAATA
1 AATATAAAATTAAAATA
*
20055588 AATATAAATTTAAAATA
1 AATATAAAATTAAAATA
20055605 CTTCATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AATATAAAATTAAAATA
Found at i:20060467 original size:132 final size:132
Alignment explanation
Indices: 20060261--20060633 Score: 532
Period size: 132 Copynumber: 2.8 Consensus size: 132
20060251 TTTAGGTTCG
* * * *
20060261 ATTCTTCTCTTACTCACATTTGTA-TTTTTTCATTTCATGTTGCTTCAAACTTTTTAAAATTTTA
1 ATTCTTCTCCTACTCACATTTGTATTTTTTTTATTTCATGTTGCTTCAAACTTTTTTAATTTTTA
* *
20060325 ATTAATTTTTTGAACATATTAGTTCTTTGGTTAGATGGTTGCAATTATATCCTTGAGTCTCAAGT
66 ATTAATTTTTT-AACATATTAGTTCTTTGGTTAGATGGTTGCAATTACATCCTTAAGTCTCAAGT
20060390 TTA
130 TTA
20060393 ATTCTTCTCCTACTCACATTTGTATTTTTTTTATTTCATGTTGCTTCAAACTTTTTTAATTTTTA
1 ATTCTTCTCCTACTCACATTTGTATTTTTTTTATTTCATGTTGCTTCAAACTTTTTTAATTTTTA
* **
20060458 ATTAATTTTTTAACATATTAGTTCTTTGGTTAGATAGTTGCAATTACATCCTTAAGTCTTGAGTT
66 ATTAATTTTTTAACATATTAGTTCTTTGGTTAGATGGTTGCAATTACATCCTTAAGTCTCAAGTT
20060523 TA
131 TA
* * * * *
20060525 ATTCCTCTCCTACTCACATTTGCATTTTGTTTTATTTCATATTGCTTCAAGCTTTTCTTTTATTT
1 ATTCTTCTCCTACTCACATTTGTATTTT-TTTTATTTCATGTTGCTTCAAAC-TTT-TTTAATTT
* * *
20060590 TTAATTAATATTTTTAACATATTAGCTTGTTTTGTTAAATGGTT
63 TTAATTAAT-TTTTTAACATATTAG-TTCTTTGGTTAGATGGTT
20060634 AGATAATTGC
Statistics
Matches: 217, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
132 100 0.46
133 69 0.32
134 3 0.01
135 16 0.07
136 15 0.07
137 14 0.06
ACGTcount: A:0.24, C:0.14, G:0.09, T:0.53
Consensus pattern (132 bp):
ATTCTTCTCCTACTCACATTTGTATTTTTTTTATTTCATGTTGCTTCAAACTTTTTTAATTTTTA
ATTAATTTTTTAACATATTAGTTCTTTGGTTAGATGGTTGCAATTACATCCTTAAGTCTCAAGTT
TA
Found at i:20060787 original size:16 final size:16
Alignment explanation
Indices: 20060750--20060788 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20060740 GTTTTGATGA
*
20060750 TATTTTTAATTACTTT
1 TATTTTTAATTAATTT
*
20060766 TATTTTTAATTAATAT
1 TATTTTTAATTAATTT
20060782 T-TTTTTA
1 TATTTTTA
20060789 TTTTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTTAATTAATTT
Found at i:20060789 original size:21 final size:21
Alignment explanation
Indices: 20060721--20060816 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
20060711 TGTTTCAAGC
*
20060721 TTTTTTATTTTTAATTAATGT
1 TTTTTTATTTTTAATTAATAT
* * *
20060742 TTTGATGATATTT--TTAAT-T
1 TTT-TTTATTTTTAATTAATAT
**
20060761 ACTTTTATTTTTAATTAATAT
1 TTTTTTATTTTTAATTAATAT
20060782 TTTTTTATTTTTAATTAATAT
1 TTTTTTATTTTTAATTAATAT
20060803 TTTTTTATTTTTAA
1 TTTTTTATTTTTAA
20060817 CTCTTAACCA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
18 6 0.10
19 2 0.03
20 10 0.16
21 37 0.61
22 6 0.10
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (21 bp):
TTTTTTATTTTTAATTAATAT
Found at i:20070057 original size:3 final size:3
Alignment explanation
Indices: 20070049--20070075 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20070039 GAATTTAGTA
20070049 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
20070076 ATATAGCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20073291 original size:18 final size:18
Alignment explanation
Indices: 20073268--20073307 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
20073258 TTTGAATTTT
20073268 ATAATTCGAATAACTCAA
1 ATAATTCGAATAACTCAA
* *
20073286 ATAATTTGAATAACTCGA
1 ATAATTCGAATAACTCAA
20073304 ATAA
1 ATAA
20073308 CAGATTGGTG
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:0.50, C:0.12, G:0.07, T:0.30
Consensus pattern (18 bp):
ATAATTCGAATAACTCAA
Found at i:20073745 original size:5 final size:5
Alignment explanation
Indices: 20073705--20073743 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
20073695 ATAATTTCTG
*
20073705 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGAC TCGA
1 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGA
20073744 CTTGAATTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (5 bp):
TCGAT
Found at i:20078192 original size:26 final size:26
Alignment explanation
Indices: 20078135--20078213 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
20078125 AGTGATCCAT
*
20078135 ATCGGGAAGCTC-CAGAGAG-CATTA
1 ATCGGGAAGCTCACAAAGAGCCATTA
** *
20078159 ATTAGGAAGCTCACAAAGAGCCTTTA
1 ATCGGGAAGCTCACAAAGAGCCATTA
* *
20078185 ATCGGGAAGCTAACGAAGAGCCATATA
1 ATCGGGAAGCTCACAAAGAGCCAT-TA
20078212 AT
1 AT
20078214 GGAAAACTCG
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
24 10 0.23
25 6 0.14
26 23 0.53
27 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (26 bp):
ATCGGGAAGCTCACAAAGAGCCATTA
Found at i:20084457 original size:7 final size:7
Alignment explanation
Indices: 20084445--20084476 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
20084435 ATCAACATTA
20084445 AAAAAAT
1 AAAAAAT
20084452 AAAAAAT
1 AAAAAAT
20084459 AAAAAAT
1 AAAAAAT
20084466 AAAAAAAT
1 -AAAAAAT
20084474 AAA
1 AAA
20084477 CTAAAATGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:20084464 original size:14 final size:15
Alignment explanation
Indices: 20084445--20084476 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
20084435 ATCAACATTA
20084445 AAAAAAT-AAAAAAT
1 AAAAAATAAAAAAAT
20084459 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
20084474 AAA
1 AAA
20084477 CTAAAATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:20097724 original size:21 final size:21
Alignment explanation
Indices: 20097698--20097739 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20097688 GGAGTTGTTT
20097698 CTCACATGATAATGGTTCATG
1 CTCACATGATAATGGTTCATG
20097719 CTCACATGATAATGGTTCATG
1 CTCACATGATAATGGTTCATG
20097740 AGTTGCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (21 bp):
CTCACATGATAATGGTTCATG
Found at i:20100038 original size:23 final size:23
Alignment explanation
Indices: 20099964--20100038 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
20099954 TTCGAGAACG
* ** *
20099964 TAAACAAACATATTCACAAATGT
1 TAAACAAACATGTTTGCAAATGC
* ** *
20099987 TAAAAAGAACATGTTTGTGAATAC
1 TAAACA-AACATGTTTGCAAATGC
*
20100011 CAAACAAACATGTTTGCAAATGC
1 TAAACAAACATGTTTGCAAATGC
20100034 TAAAC
1 TAAAC
20100039 GAATTGATCC
Statistics
Matches: 37, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
23 23 0.62
24 14 0.38
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (23 bp):
TAAACAAACATGTTTGCAAATGC
Found at i:20106676 original size:15 final size:15
Alignment explanation
Indices: 20106656--20106687 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20106646 TCACTTATCA
*
20106656 AATGGAACCTTTTAC
1 AATGGAACCTCTTAC
20106671 AATGGAACCTCTTAC
1 AATGGAACCTCTTAC
20106686 AA
1 AA
20106688 CCTTAGCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (15 bp):
AATGGAACCTCTTAC
Found at i:20114563 original size:40 final size:40
Alignment explanation
Indices: 20114495--20114588 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
20114485 AGGGGTACAA
*
20114495 AAGTACAAATA-GGGCACGTATGGTCAATCAAGGGTACTG
1 AAGTACAAACAGGGGCACGTATGGTCAATCAAGGGTACTG
*
20114534 AAGTACAAACAGGGGCACGTAT-GTGCAATCAGGGGTACTG
1 AAGTACAAACAGGGGCACGTATGGT-CAATCAAGGGTACTG
20114574 AAGTACAAACAGGGG
1 AAGTACAAACAGGGG
20114589 AAATTATGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 12 0.24
40 39 0.76
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.17
Consensus pattern (40 bp):
AAGTACAAACAGGGGCACGTATGGTCAATCAAGGGTACTG
Found at i:20114586 original size:20 final size:20
Alignment explanation
Indices: 20114526--20114588 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
20114516 GGTCAATCAA
20114526 GGGTACTGAAGTACAAACAG
1 GGGTACTGAAGTACAAACAG
* * * *
20114546 GGGCAC-GTATGTGCAATCAG
1 GGGTACTG-AAGTACAAACAG
20114566 GGGTACTGAAGTACAAACAG
1 GGGTACTGAAGTACAAACAG
20114586 GGG
1 GGG
20114589 AAATTATGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.35, T:0.16
Consensus pattern (20 bp):
GGGTACTGAAGTACAAACAG
Found at i:20114602 original size:40 final size:40
Alignment explanation
Indices: 20114519--20114602 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
20114509 CACGTATGGT
* * *
20114519 CAATCAAGGGTACTGAAGTACAAACAGGGGCACGTATGTG
1 CAATCAAGGGTACTGAAGTACAAACAGGGGAAAGTATGAG
* *
20114559 CAATCAGGGGTACTGAAGTACAAACAGGGGAAATTATGAG
1 CAATCAAGGGTACTGAAGTACAAACAGGGGAAAGTATGAG
20114599 CAAT
1 CAAT
20114603 AATTTAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.18
Consensus pattern (40 bp):
CAATCAAGGGTACTGAAGTACAAACAGGGGAAAGTATGAG
Done.