Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 111 of 235
Found at i:38193450 original size:25 final size:25
Alignment explanation
Indices: 38193317--38193550 Score: 139
Period size: 25 Copynumber: 9.2 Consensus size: 25
38193307 CAAGATATAC
*
38193317 ATTATGTAAGTTATGTAAGTTATGT
1 ATTATGAAAGTTATGTAAGTTATGT
* * ** * *
38193342 AAGTTGTGTAAGTTGCGTAAGATGTGT
1 -A-TTATGAAAGTTATGTAAGTTATGT
*
38193369 ATTATGAAACTTATGTAAGTTATGT
1 ATTATGAAAGTTATGTAAGTTATGT
* * ** * *
38193394 AAGTTGTGTAAGTTGCGTAAGATGTGT
1 -A-TTATGAAAGTTATGTAAGTTATGT
*
38193421 ATTATGAAACTTATGTAAGTTATGT
1 ATTATGAAAGTTATGTAAGTTATGT
* ** * *
38193446 CTTATGTTAGTTATGTAATTTTTGT
1 ATTATGAAAGTTATGTAAGTTATGT
* * *
38193471 ATTATTTACA--CATGTAAGTTATGT
1 ATTA-TGAAAGTTATGTAAGTTATGT
* * * ** *
38193495 CTTATGTAAGATGCGTAAGTTGTGT
1 ATTATGAAAGTTATGTAAGTTATGT
38193520 ATTATGAAAGTTATGTAAGTTATGT
1 ATTATGAAAGTTATGTAAGTTATGT
*
38193545 GTTATG
1 ATTATG
38193551 TAAATGAATA
Statistics
Matches: 148, Mismatches: 54, Indels: 13
0.69 0.25 0.06
Matches are distributed among these distances:
23 2 0.01
24 14 0.09
25 90 0.61
26 6 0.04
27 36 0.24
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.44
Consensus pattern (25 bp):
ATTATGAAAGTTATGTAAGTTATGT
Found at i:38193928 original size:29 final size:31
Alignment explanation
Indices: 38193886--38193963 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
38193876 TTATTAATAA
*
38193886 AATTTAATAAAATTTAAATAATTG-T-TAAAT
1 AATTT-ATTAAATTTAAATAATTGTTATAAAT
*
38193916 TATTTATTAAATTTAAATAATTGTTATAAAT
1 AATTTATTAAATTTAAATAATTGTTATAAAT
38193947 AATTTATTAAATTTAAA
1 AATTTATTAAATTTAAA
38193964 ATTTAAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.40
30 5 0.12
31 21 0.49
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (31 bp):
AATTTATTAAATTTAAATAATTGTTATAAAT
Found at i:38194662 original size:14 final size:14
Alignment explanation
Indices: 38194643--38194672 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38194633 CACGAACAGC
38194643 AAGATGATTAACTA
1 AAGATGATTAACTA
38194657 AAGATGATTAACTA
1 AAGATGATTAACTA
38194671 AA
1 AA
38194673 AACCTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (14 bp):
AAGATGATTAACTA
Found at i:38196018 original size:27 final size:27
Alignment explanation
Indices: 38195986--38196037 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
38195976 TCTTACTTTT
* *
38195986 AAATAATTAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
*
38196013 AAATAAATAATTACTAACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
38196038 TTTGTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:38196128 original size:8 final size:10
Alignment explanation
Indices: 38196105--38196141 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
38196095 TAATAACTAT
38196105 ATATATATCC
1 ATATATATCC
*
38196115 ATATATATTC
1 ATATATATCC
38196125 ATATATATCC
1 ATATATATCC
38196135 ATATATA
1 ATATATA
38196142 AGTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATCC
Found at i:38197160 original size:82 final size:82
Alignment explanation
Indices: 38197041--38197217 Score: 336
Period size: 82 Copynumber: 2.2 Consensus size: 82
38197031 GCTACCGGAA
*
38197041 AAAACGCCACTAACTTTTCAATTACAGAAAGAAACGGTGACGTTTTCACAAAATTGTAGACATAT
1 AAAACGCCACTAAATTTTCAATTACAGAAAGAAACGGTGACGTTTTCACAAAATTGTAGACATAT
38197106 TTGCGGCGTTTTACCTT
66 TTGCGGCGTTTTACCTT
38197123 AAAACGCCACTAAATTTTCAATTACAGAAAGAAACGGTGACGTTTTCACAAAATTGTAGACATAT
1 AAAACGCCACTAAATTTTCAATTACAGAAAGAAACGGTGACGTTTTCACAAAATTGTAGACATAT
*
38197188 TTGCGGCGTTTTCCCTT
66 TTGCGGCGTTTTACCTT
38197205 AAAACGCCACTAA
1 AAAACGCCACTAA
38197218 TAGAGTACAC
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 93 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (82 bp):
AAAACGCCACTAAATTTTCAATTACAGAAAGAAACGGTGACGTTTTCACAAAATTGTAGACATAT
TTGCGGCGTTTTACCTT
Found at i:38204832 original size:37 final size:37
Alignment explanation
Indices: 38204786--38204860 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
38204776 GGATTTAAGG
38204786 AGACAACAGAACCTTCAGTTTGTTTAAGTGCAGGTAC
1 AGACAACAGAACCTTCAGTTTGTTTAAGTGCAGGTAC
*
38204823 AGACCACAGAACCTTCAGTTTGTTTAAGTGCAGGTAC
1 AGACAACAGAACCTTCAGTTTGTTTAAGTGCAGGTAC
38204860 A
1 A
38204861 CGGGAGCGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (37 bp):
AGACAACAGAACCTTCAGTTTGTTTAAGTGCAGGTAC
Found at i:38213162 original size:16 final size:15
Alignment explanation
Indices: 38213142--38213193 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
38213132 GGGAGGAATG
38213142 GAATAGAGCTGTAAT
1 GAATAGAGCTGTAAT
*
38213157 GTAATAGAGTTGTAAT
1 G-AATAGAGCTGTAAT
38213173 AGAATAGA-CTTGTAAT
1 -GAATAGAGC-TGTAAT
38213189 GAATA
1 GAATA
38213194 ATTCAGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 6 0.19
16 25 0.78
17 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (15 bp):
GAATAGAGCTGTAAT
Found at i:38213409 original size:26 final size:26
Alignment explanation
Indices: 38213354--38213409 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
38213344 TTTTAAATTT
* * * *
38213354 TAATAAAATTATTATTAAATATAATT
1 TAATAAAAATAATAATAAATATAATA
38213380 TAATAAAAATAATAATAAATAATAA-A
1 TAATAAAAATAATAATAAAT-ATAATA
38213406 TAAT
1 TAAT
38213410 TTAATCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATAAAAATAATAATAAATATAATA
Found at i:38219740 original size:25 final size:25
Alignment explanation
Indices: 38219684--38219741 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
38219674 AAGTGTTATA
* **
38219684 CAGAGAGCATTAATGTGCTAATAAT
1 CAGAGAGCACTAACATGCTAATAAT
38219709 C-GAAGAGCACTAACATGCTAATAAT
1 CAG-AGAGCACTAACATGCTAATAAT
38219734 CAGAGAGC
1 CAGAGAGC
38219742 GCGCTAGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.04
25 26 0.93
26 1 0.04
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (25 bp):
CAGAGAGCACTAACATGCTAATAAT
Found at i:38220122 original size:25 final size:25
Alignment explanation
Indices: 38220100--38220148 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
38220090 CGCACTCTTT
38220100 GATTATTAGCACA-TTACTGCTCTCC
1 GATTATTAGCACATTTA-TGCTCTCC
38220125 GATTATTAGCACATTTATGCTCTC
1 GATTATTAGCACATTTATGCTCTC
38220149 TGTATAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (25 bp):
GATTATTAGCACATTTATGCTCTCC
Found at i:38225031 original size:18 final size:18
Alignment explanation
Indices: 38225004--38225047 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
38224994 AATATTCCTA
38225004 AAAAACTAAATATTAA-TTT
1 AAAAA-TAAA-ATTAACTTT
*
38225023 AACAATAAAATTAACTTT
1 AAAAATAAAATTAACTTT
38225041 AAAAATA
1 AAAAATA
38225048 TGGGTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 13 0.59
19 4 0.18
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATAAAATTAACTTT
Found at i:38226403 original size:5 final size:5
Alignment explanation
Indices: 38226393--38226424 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
38226383 GAAGTGTGAA
38226393 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
38226425 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:38226418 original size:9 final size:9
Alignment explanation
Indices: 38226394--38226424 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
38226384 AAGTGTGAAA
38226394 AAATAAAAT
1 AAATAAAAT
38226403 AAAATAAAAT
1 -AAATAAAAT
38226413 AAATAAAAT
1 AAATAAAAT
38226422 AAA
1 AAA
38226425 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:38230077 original size:5 final size:5
Alignment explanation
Indices: 38230067--38230098 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
38230057 CAATTTGTGA
38230067 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
38230099 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:38230092 original size:9 final size:9
Alignment explanation
Indices: 38230068--38230098 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
38230058 AATTTGTGAA
38230068 AAATAAAAT
1 AAATAAAAT
38230077 AAAATAAAAT
1 -AAATAAAAT
38230087 AAATAAAAT
1 AAATAAAAT
38230096 AAA
1 AAA
38230099 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:38235204 original size:62 final size:62
Alignment explanation
Indices: 38235107--38235224 Score: 218
Period size: 62 Copynumber: 1.9 Consensus size: 62
38235097 GTCACCTCGT
* *
38235107 TTAATTAGGCTTGACAAAGAGTGGTATCAAAGCCAGGTTTTGTGATTCTATGTTTCTTAGGA
1 TTAATGAGGCTTGACAAAGAGTGGTATCAAAGCCAGGTTTAGTGATTCTATGTTTCTTAGGA
38235169 TTAATGAGGCTTGACAAAGAGTGGTATCAAAGCCAGGTTTAGTGATTCTATGTTTC
1 TTAATGAGGCTTGACAAAGAGTGGTATCAAAGCCAGGTTTAGTGATTCTATGTTTC
38235225 CTGGGATTCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.36
Consensus pattern (62 bp):
TTAATGAGGCTTGACAAAGAGTGGTATCAAAGCCAGGTTTAGTGATTCTATGTTTCTTAGGA
Found at i:38244534 original size:30 final size:30
Alignment explanation
Indices: 38244490--38244547 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
38244480 CTGGGCATTT
*
38244490 CCACACGGGATGGCCACACGCCCATGTGAG
1 CCACACAGGATGGCCACACGCCCATGTGAG
*
38244520 CCACACAGGTTGGCCACACGCCCATGTG
1 CCACACAGGATGGCCACACGCCCATGTG
38244548 CCAGTCCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.38, G:0.28, T:0.12
Consensus pattern (30 bp):
CCACACAGGATGGCCACACGCCCATGTGAG
Found at i:38247573 original size:13 final size:13
Alignment explanation
Indices: 38247555--38247579 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38247545 TAATGGTATA
38247555 TTGAATCCATGAT
1 TTGAATCCATGAT
38247568 TTGAATCCATGA
1 TTGAATCCATGA
38247580 AAATTTAGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:38249531 original size:47 final size:47
Alignment explanation
Indices: 38249480--38249890 Score: 716
Period size: 47 Copynumber: 8.7 Consensus size: 47
38249470 TTAGGATTCT
* * *
38249480 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
38249527 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
38249574 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
38249621 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
38249668 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
38249715 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
38249762 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * *
38249809 ATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
38249856 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
38249891 TCCCGAAGGG
Statistics
Matches: 352, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
46 1 0.00
47 351 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:38250065 original size:37 final size:37
Alignment explanation
Indices: 38250009--38250087 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
38249999 CCGAGCTCTA
* * *
38250009 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
38250046 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
38250083 AAGAC
1 AAGAC
38250088 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:38255070 original size:62 final size:62
Alignment explanation
Indices: 38254993--38255284 Score: 478
Period size: 62 Copynumber: 4.7 Consensus size: 62
38254983 CAATGTACCT
*
38254993 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATAACAA
* **
38255055 AATTTCTATTACAAAGTTTGTTCCAATTTTTAATGCCGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATAACAA
*
38255117 AATTTCTATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATAACAA
* * *
38255179 AATTTATATTAGAAAGTTTGTTCTAATTTTTAATATTGTAATGTATTTAATTTATATTAA-AA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATA-TAACAA
* *
38255241 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTATAATGT
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGT
38255285 TGTAATGTTG
Statistics
Matches: 214, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
62 211 0.99
63 3 0.01
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATAACAA
Found at i:38255284 original size:8 final size:8
Alignment explanation
Indices: 38255271--38255302 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
38255261 TTCCAAGTTT
*
38255271 TAATGTTA
1 TAATGTTG
38255279 TAATGTTG
1 TAATGTTG
38255287 TAATGTTG
1 TAATGTTG
38255295 TAATGTTG
1 TAATGTTG
38255303 CAATTAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (8 bp):
TAATGTTG
Found at i:38258789 original size:31 final size:30
Alignment explanation
Indices: 38258739--38258839 Score: 132
Period size: 31 Copynumber: 3.3 Consensus size: 30
38258729 CTACGGAGAT
* *
38258739 GGCGTCACCAGTGGTGCCGCCT-TTGCCCTA
1 GGCGTGACCAGGGGTGCCGCCTCTT-CCCTA
38258769 GGCGTGACCAGGAGGTGCCGCCTCTTCCCTA
1 GGCGTGACCAGG-GGTGCCGCCTCTTCCCTA
* *
38258800 GGTGTGACTAGGGGATGCCGCCTCTTCCCTA
1 GGCGTGACCAGGGG-TGCCGCCTCTTCCCTA
38258831 GGCGTGACC
1 GGCGTGACC
38258840 CCTTGTGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
30 12 0.19
31 48 0.77
32 2 0.03
ACGTcount: A:0.12, C:0.34, G:0.33, T:0.22
Consensus pattern (30 bp):
GGCGTGACCAGGGGTGCCGCCTCTTCCCTA
Found at i:38259406 original size:12 final size:12
Alignment explanation
Indices: 38259389--38259422 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
38259379 TAATTTGTGT
38259389 ATTGTTTTAAGA
1 ATTGTTTTAAGA
38259401 ATTGTTTTAAGA
1 ATTGTTTTAAGA
38259413 ATTGTTTTAA
1 ATTGTTTTAA
38259423 TATATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (12 bp):
ATTGTTTTAAGA
Found at i:38266490 original size:44 final size:43
Alignment explanation
Indices: 38266344--38266497 Score: 172
Period size: 42 Copynumber: 3.6 Consensus size: 43
38266334 CATACAATGT
*
38266344 CAACGTCCCAAACGTGGTCTTACATGTAATCAAATATCGATGC
1 CAACGTCCCAAACGTGGTCTTACACGTAATCAAATATCGATGC
** * **
38266387 CATTGT-CCAGACAG-GGTCTTACACAAAATCAAATA-CGATGC
1 CAACGTCCCAAAC-GTGGTCTTACACGTAATCAAATATCGATGC
* * *
38266428 CAATGTCCCAAACATGGTCTTACACGTAATCACAATATCTATGC
1 CAACGTCCCAAACGTGGTCTTACACGTAATCA-AATATCGATGC
38266472 CAACGTCCCAGAA-GTGGTCTTACACG
1 CAACGTCCCA-AACGTGGTCTTACACG
38266498 AAAACACATA
Statistics
Matches: 91, Mismatches: 14, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
41 11 0.12
42 43 0.47
43 9 0.10
44 26 0.29
45 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
CAACGTCCCAAACGTGGTCTTACACGTAATCAAATATCGATGC
Found at i:38275116 original size:36 final size:36
Alignment explanation
Indices: 38275055--38275168 Score: 90
Period size: 36 Copynumber: 3.2 Consensus size: 36
38275045 TGACCTTTGG
* *
38275055 TTTTCTAATAGTCCGCTAATTTACGATCACGATTGTCA
1 TTTT-TAA-AGTCCACTGATTTACGATCACGATTGTCA
** * **
38275093 TTTTTAAAG-CTCGTTGATTTACGACCACGGCT-T-A
1 TTTTTAAAGTC-CACTGATTTACGATCACGATTGTCA
* * *
38275127 TTCTTACAGTCCACTGATTTACGATCACAATTGTCA
1 TTTTTAAAGTCCACTGATTTACGATCACGATTGTCA
38275163 TTTTTA
1 TTTTTA
38275169 CGATCATGGC
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
34 23 0.40
35 4 0.07
36 24 0.41
37 3 0.05
38 4 0.07
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTTTAAAGTCCACTGATTTACGATCACGATTGTCA
Found at i:38275272 original size:164 final size:164
Alignment explanation
Indices: 38275001--38275318 Score: 429
Period size: 164 Copynumber: 1.9 Consensus size: 164
38274991 GGCTTGCTGA
* * ** ** *
38275001 TTTACGATCACGACTTATTCTTACGATCCAATGATTTATGATCATGACCTTTGGTTTTCTAATAG
1 TTTACGATCACGACTTATTCTTACGATCCAATAATTTACGATCACAACCTTCAGTTTTCTAACAG
* * * *
38275066 TCCGCTAATTTACGATCACGATTGTCATTTTTAAAGCTCGTTGATTTACGACCACGGCTTATTCT
66 TCCACTAATTTACGATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAACCACGGCTTATTCT
* *
38275131 TACAGTCCACTGATTTACGATCACAATTGTCATT
131 TACAGTCCACTAATTTACAATCACAATTGTCATT
* * * *
38275165 TTTACGATCATGGCTTATTCTTACGGTCCACTAATTTACGATCACAACCTTCAGTTTTCTAACAG
1 TTTACGATCACGACTTATTCTTACGATCCAATAATTTACGATCACAACCTTCAGTTTTCTAACAG
* * * *
38275230 TTCATTAATTTACGATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAATCATGGCTTATTCT
66 TCCACTAATTTACGATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAACCACGGCTTATTCT
* *
38275295 TACAGTTCGCTAATTTACAATCAC
131 TACAGTCCACTAATTTACAATCAC
38275319 GAACTTCGGT
Statistics
Matches: 131, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
164 131 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (164 bp):
TTTACGATCACGACTTATTCTTACGATCCAATAATTTACGATCACAACCTTCAGTTTTCTAACAG
TCCACTAATTTACGATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAACCACGGCTTATTCT
TACAGTCCACTAATTTACAATCACAATTGTCATT
Found at i:38275356 original size:109 final size:108
Alignment explanation
Indices: 38275178--38275577 Score: 469
Period size: 109 Copynumber: 3.7 Consensus size: 108
38275168 ACGATCATGG
* * * * * *
38275178 CTTATTCTTACGGTCCACTAATTTACGATCACAACCTTCAGTTTTCTAACAGTTCATTAATTTAC
1 CTTATTCTTAC-GTTCGCTAATTTACAATCACAACCTTCGGTTTTCTAACAGTTCGTTGATTTAC
* *
38275243 GATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAATCATGG
65 GATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGA
* *
38275287 CTTATTCTTACAGTTCGCTAATTTACAATCACGAA-CTTCGGTTTTCTAATAGTTCGCTGATTTA
1 CTTATTCTTAC-GTTCGCTAATTTACAATCAC-AACCTTCGGTTTTCTAACAGTTCGTTGATTTA
* *
38275351 TGATCACAACTGTCATTTTTAAAGCTCATTGATTTACAATCACGA
64 CGATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGA
* * *** ** *
38275396 CTTATTCTTACGGTCTGCTGATTTATGGTCATGACCTTCGGTTTTATAACAGTTCGTTGATTTAC
1 CTTATTCTTACGTTC-GCTAATTTACAATCACAACCTTCGGTTTTCTAACAGTTCGTTGATTTAC
* * * * *
38275461 TATCACAATTATCATTTTTAAAGCTCGTTAATTTACGATCACGA
65 GATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGA
* * * * * *
38275505 TTTATTCTTACGATTCGTTGATTTACAATCACAACCTTTGATTTTCTAACAATTCGTTGATTTAC
1 CTTATTCTTACG-TTCGCTAATTTACAATCACAACCTTCGGTTTTCTAACAGTTCGTTGATTTAC
38275570 GATCACAA
65 GATCACAA
38275578 TTTATTCTTA
Statistics
Matches: 244, Mismatches: 43, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
108 4 0.02
109 236 0.97
110 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (108 bp):
CTTATTCTTACGTTCGCTAATTTACAATCACAACCTTCGGTTTTCTAACAGTTCGTTGATTTACG
ATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGA
Found at i:38275480 original size:39 final size:35
Alignment explanation
Indices: 38275437--38275677 Score: 150
Period size: 34 Copynumber: 6.6 Consensus size: 35
38275427 TGACCTTCGG
*
38275437 TTTTATAACAGTTCGTTGATTTACTATCACAATTATCA
1 TTTT-TAACAGTTCGTTGATTTACGATCACAATT-T-A
* * *
38275475 TTTTTAA-AGCTCGTTAATTTACGATCACGATTTA
1 TTTTTAACAGTTCGTTGATTTACGATCACAATTTA
* *
38275509 TTCTT-AC-GATTCGTTGATTTACAATCACAACCTTTGA
1 TTTTTAACAG-TTCGTTGATTTACGATCACAA--TTT-A
*
38275546 TTTTCTAACAATTCGTTGATTTACGATCACAATTTA
1 TTTT-TAACAGTTCGTTGATTTACGATCACAATTTA
* * * * * *
38275582 TTCTT-ACAATTCGTTTATTTACAACCACAACTTTCGC
1 TTTTTAACAGTTCGTTGATTTACGATCACAA-TTT--A
* ** *
38275619 TTTTCTAACAATTCACTGATTTACGATCACGAATGTCA
1 TTTT-TAACAGTTCGTTGATTTACGATCAC-AAT-TTA
* *
38275657 TTTTTAA-AGCTCCTTGATTTA
1 TTTTTAACAGTTCGTTGATTTA
38275678 TTATCACGGC
Statistics
Matches: 159, Mismatches: 29, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
33 2 0.01
34 44 0.28
35 5 0.03
36 38 0.24
37 16 0.10
38 10 0.06
39 41 0.26
40 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (35 bp):
TTTTTAACAGTTCGTTGATTTACGATCACAATTTA
Found at i:38275529 original size:34 final size:34
Alignment explanation
Indices: 38275448--38275603 Score: 152
Period size: 34 Copynumber: 4.4 Consensus size: 34
38275438 TTTATAACAG
* *
38275448 TTCGTTGATTTACTATCACAATTATCATTTTTA-AA
1 TTCGTTGATTTACGATCACAATT-T-ATTCTTACAA
* * * *
38275483 GCTCGTTAATTTACGATCACGATTTATTCTTACGA
1 -TTCGTTGATTTACGATCACAATTTATTCTTACAA
* *
38275518 TTCGTTGATTTACAATCACAACCTTTGATTTTCTAACAA
1 TTCGTTGATTTACGATCACAA--TTT-A--TTCTTACAA
38275557 TTCGTTGATTTACGATCACAATTTATTCTTACAA
1 TTCGTTGATTTACGATCACAATTTATTCTTACAA
*
38275591 TTCGTTTATTTAC
1 TTCGTTGATTTAC
38275604 AACCACAACT
Statistics
Matches: 99, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
34 43 0.43
35 2 0.02
36 23 0.23
37 4 0.04
39 27 0.27
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (34 bp):
TTCGTTGATTTACGATCACAATTTATTCTTACAA
Found at i:38275568 original size:218 final size:218
Alignment explanation
Indices: 38275178--38275577 Score: 525
Period size: 218 Copynumber: 1.8 Consensus size: 218
38275168 ACGATCATGG
*
38275178 CTTATTCTTACGGTCCACTAATTTACGATCACAACCTTCAGTTTTCTAACAGTTCATTAATTTAC
1 CTTATTCTTACGGTCCACTAATTTACGATCACAACCTTCAGTTTTATAACAGTTCATTAATTTAC
* * * *
38275243 GATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAATCATGGCTTATTCTTACAGTTCGCTAA
66 GATCACAACTATCATTTTTAAAGCTCGTTAATTTACAATCACGACTTATTCTTACAGTTCGCTAA
* * * *
38275308 TTTACAATCACGAACTTCGGTTTTCTAATAGTTCGCTGATTTATGATCACAACTGTCATTTTTAA
131 TTTACAATCACGAACTTCGATTTTCTAACAATTCGCTGATTTACGATCACAACTGTCATTTTTAA
38275373 AGCTCATTGATTTACAATCACGA
196 AGCTCATTGATTTACAATCACGA
** * * * ** * * *
38275396 CTTATTCTTACGGTCTGCTGATTTATGGTCATGACCTTCGGTTTTATAACAGTTCGTTGATTTAC
1 CTTATTCTTACGGTCCACTAATTTACGATCACAACCTTCAGTTTTATAACAGTTCATTAATTTAC
* * * * * *
38275461 TATCACAATTATCATTTTTAAAGCTCGTTAATTTACGATCACGATTTATTCTTAC-GATTCGTTG
66 GATCACAACTATCATTTTTAAAGCTCGTTAATTTACAATCACGACTTATTCTTACAG-TTCGCTA
* *
38275525 ATTTACAATCAC-AACCTTTGATTTTCTAACAATTCGTTGATTTACGATCACAA
130 ATTTACAATCACGAA-CTTCGATTTTCTAACAATTCGCTGATTTACGATCACAA
38275578 TTTATTCTTA
Statistics
Matches: 153, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
217 3 0.02
218 150 0.98
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (218 bp):
CTTATTCTTACGGTCCACTAATTTACGATCACAACCTTCAGTTTTATAACAGTTCATTAATTTAC
GATCACAACTATCATTTTTAAAGCTCGTTAATTTACAATCACGACTTATTCTTACAGTTCGCTAA
TTTACAATCACGAACTTCGATTTTCTAACAATTCGCTGATTTACGATCACAACTGTCATTTTTAA
AGCTCATTGATTTACAATCACGA
Found at i:38275581 original size:73 final size:72
Alignment explanation
Indices: 38275448--38275648 Score: 246
Period size: 73 Copynumber: 2.8 Consensus size: 72
38275438 TTTATAACAG
* * ** * *
38275448 TTCGTTGATTTACTATCACAA-TTATCATTTT-TAA-AGCTCGTTAATTTACGATCACGATTTAT
1 TTCGTTGATTTACAATCACAACTT-TGATTTTCTAACAATTCGTTGATTTACGATCACAATTTAT
*
38275510 TCTTACGA
65 TCTTACAA
38275518 TTCGTTGATTTACAATCACAACCTTTGATTTTCTAACAATTCGTTGATTTACGATCACAATTTAT
1 TTCGTTGATTTACAATCACAA-CTTTGATTTTCTAACAATTCGTTGATTTACGATCACAATTTAT
38275583 TCTTACAA
65 TCTTACAA
* * * **
38275591 TTCGTTTATTTACAACCACAACTTTCGCTTTTCTAACAATTCACTGATTTACGATCAC
1 TTCGTTGATTTACAATCACAACTTT-GATTTTCTAACAATTCGTTGATTTACGATCAC
38275649 GAATGTCATT
Statistics
Matches: 114, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
70 20 0.18
71 6 0.05
72 9 0.08
73 79 0.69
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.42
Consensus pattern (72 bp):
TTCGTTGATTTACAATCACAACTTTGATTTTCTAACAATTCGTTGATTTACGATCACAATTTATT
CTTACAA
Found at i:38275585 original size:182 final size:182
Alignment explanation
Indices: 38275379--38275757 Score: 433
Period size: 182 Copynumber: 2.1 Consensus size: 182
38275369 TTAAAGCTCA
* ** **** ** *
38275379 TTGATTTACAATCACGACTTATTCTTAC-GGTCTGCTGATTTATGGTCATGACCTTCGGTTTTAT
1 TTGATTTACAATCACAACTTATTCTTACAATTC-GCTGATTTACAACCACAACCTTCGCTTTTAT
* ** * * *
38275443 AACAGTTCGTTGATTTACTATCAC-AATTATCATTTTTAAAGCTCGTTAATTTACGATCACGATT
65 AACAATTCACTGATTTACGATCACGAA-TATCATTTTTAAAGCTCCTTAATTTACGATCACGACT
38275507 TATTCTTACGAT-TCGTTGATTTACAATCACAACCTTT-GATTTTCTAACAATTCG
129 TATTCTTACGATAT-GTTGATTTACAATCACAA-CTTTCGATTTTCTAACAATTCG
* * * * * *
38275561 TTGATTTACGATCACAATTTATTCTTACAATTCGTTTATTTACAACCACAACTTTCGCTTTTCTA
1 TTGATTTACAATCACAACTTATTCTTACAATTCGCTGATTTACAACCACAACCTTCGCTTTTATA
* * ** *
38275626 ACAATTCACTGATTTACGATCACGAATGTCATTTTTAAAGCTCCTTGATTTATTATCACGGCTTA
66 ACAATTCACTGATTTACGATCACGAATATCATTTTTAAAGCTCCTTAATTTACGATCACGACTTA
*
38275691 TTCTTATGATATGTTGATTTACAATCACAACTTTCGATTTTCTAACAATTCG
131 TTCTTACGATATGTTGATTTACAATCACAACTTTCGATTTTCTAACAATTCG
*
38275743 CTGATTTACAATCAC
1 TTGATTTACAATCAC
38275758 GACTGTCATT
Statistics
Matches: 163, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
181 4 0.02
182 154 0.94
183 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.42
Consensus pattern (182 bp):
TTGATTTACAATCACAACTTATTCTTACAATTCGCTGATTTACAACCACAACCTTCGCTTTTATA
ACAATTCACTGATTTACGATCACGAATATCATTTTTAAAGCTCCTTAATTTACGATCACGACTTA
TTCTTACGATATGTTGATTTACAATCACAACTTTCGATTTTCTAACAATTCG
Found at i:38275674 original size:109 final size:109
Alignment explanation
Indices: 38275561--38275785 Score: 299
Period size: 109 Copynumber: 2.1 Consensus size: 109
38275551 TAACAATTCG
* * *
38275561 TTGATTTACGATCACAATTTATTCTTACAAT-TCGTTTATTTACAACCACAACTTTCGCTTTTCT
1 TTGATTTACGATCACAACTTATTCTTACAATAT-GTTGATTTACAACCACAACTTTCGATTTTCT
* *
38275625 AACAATTCACTGATTTACGATCACGAATGTCATTTTTAAAGCTCC
65 AACAATTCACTGATTTACAATCACGAATGTCATTTTTAAAGCTAC
** ** ** *
38275670 TTGATTTATTATCACGGCTTATTCTTATGATATGTTGATTTACAATCACAACTTTCGATTTTCTA
1 TTGATTTACGATCACAACTTATTCTTACAATATGTTGATTTACAACCACAACTTTCGATTTTCTA
* * *
38275735 ACAATTCGCTGATTTACAATCACGACTGTCATTTTTAAAGCTAG
66 ACAATTCACTGATTTACAATCACGAATGTCATTTTTAAAGCTAC
38275779 TTGATTT
1 TTGATTT
38275786 CTTCGACAAG
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 99 0.99
110 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.42
Consensus pattern (109 bp):
TTGATTTACGATCACAACTTATTCTTACAATATGTTGATTTACAACCACAACTTTCGATTTTCTA
ACAATTCACTGATTTACAATCACGAATGTCATTTTTAAAGCTAC
Found at i:38277389 original size:4 final size:4
Alignment explanation
Indices: 38277382--38277425 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
38277372 ATATTTATAC
* *
38277382 ATGT ATGT ATGC ATGT ATGT ATGT AAGT ATGT ATG- -TGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
38277426 TTTTTATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
4 32 0.94
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:38277982 original size:67 final size:67
Alignment explanation
Indices: 38277874--38278008 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
38277864 TAGCTATCAA
*
38277874 ATTTCAATGCTTGATCAATATGGTATAAGTTTTAAGTGTTGTAGATATGATATAATTATTCTCAC
1 ATTTCAATGCTTGATCAATATGGTATAAGTTCTAAGTGTTGTAGATATGATATAATTATTCTCAC
38277939 GC
66 GC
38277941 ATTTCAATGCTTGATCAATATGGTATAAGTTCTAAGTGTTGTAGATATGATATAATTATTCTCAC
1 ATTTCAATGCTTGATCAATATGGTATAAGTTCTAAGTGTTGTAGATATGATATAATTATTCTCAC
38278006 GC
66 GC
38278008 A
1 A
38278009 CGATCCAATA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (67 bp):
ATTTCAATGCTTGATCAATATGGTATAAGTTCTAAGTGTTGTAGATATGATATAATTATTCTCAC
GC
Found at i:38280092 original size:7 final size:7
Alignment explanation
Indices: 38280080--38280139 Score: 120
Period size: 7 Copynumber: 8.6 Consensus size: 7
38280070 GCTGATGGCC
38280080 TGATGCT
1 TGATGCT
38280087 TGATGCT
1 TGATGCT
38280094 TGATGCT
1 TGATGCT
38280101 TGATGCT
1 TGATGCT
38280108 TGATGCT
1 TGATGCT
38280115 TGATGCT
1 TGATGCT
38280122 TGATGCT
1 TGATGCT
38280129 TGATGCT
1 TGATGCT
38280136 TGAT
1 TGAT
38280140 TTTTTTTTCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.15, C:0.13, G:0.28, T:0.43
Consensus pattern (7 bp):
TGATGCT
Found at i:38280194 original size:6 final size:7
Alignment explanation
Indices: 38280179--38280203 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38280169 TATTATTAGA
38280179 TTTTATT
1 TTTTATT
38280186 TTTTATT
1 TTTTATT
38280193 TTTTATT
1 TTTTATT
38280200 TTTT
1 TTTT
38280204 TGGGTTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:38282728 original size:4 final size:4
Alignment explanation
Indices: 38282719--38282769 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
38282709 AGGAATCATG
* * *
38282719 TACA TACA TACA TGCA TACC TACA TGCA TACA TACA -AGCA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA-CA TACA TACA
38282767 TAC
1 TAC
38282770 TCTGTTCTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 1 0.03
4 37 0.95
5 1 0.03
ACGTcount: A:0.43, C:0.27, G:0.06, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:38282742 original size:12 final size:12
Alignment explanation
Indices: 38282721--38282767 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
38282711 GAATCATGTA
38282721 CATACATACATG
1 CATACATACATG
*
38282733 CATACCTACATG
1 CATACATACATG
*
38282745 CATACATACAAG
1 CATACATACATG
38282757 CATACATACAT
1 CATACATACAT
38282768 ACTCTGTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.43, C:0.28, G:0.06, T:0.23
Consensus pattern (12 bp):
CATACATACATG
Found at i:38284668 original size:25 final size:25
Alignment explanation
Indices: 38284640--38284690 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
38284630 AAAAACGTGC
38284640 ATTCCTATTCAACTTTAAAATGCAT
1 ATTCCTATTCAACTTTAAAATGCAT
38284665 ATTCCTATTCAACTTTAAAATGCAT
1 ATTCCTATTCAACTTTAAAATGCAT
38284690 A
1 A
38284691 CTTGATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (25 bp):
ATTCCTATTCAACTTTAAAATGCAT
Found at i:38293157 original size:6 final size:6
Alignment explanation
Indices: 38293146--38293172 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38293136 AAAGAAAGAT
38293146 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
38293173 TAGATGGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:38293173 original size:11 final size:11
Alignment explanation
Indices: 38293131--38293174 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
38293121 CTTCAAAAAT
*
38293131 AAATAAAAGAA
1 AAATAAAATAA
*
38293142 AGATAAAATAA
1 AAATAAAATAA
38293153 AAATAAAAATAA
1 AAAT-AAAATAA
38293165 AAATAAAATA
1 AAATAAAATA
38293175 GATGGACTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:38295027 original size:15 final size:14
Alignment explanation
Indices: 38295009--38295053 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
38294999 GAGGAAAGAG
38295009 AGAAAGAAGAGATAA
1 AGAAAGAAGAGA-AA
*
38295024 AGAAAGAAAAAGAAA
1 AGAAAG-AAGAGAAA
38295039 AGAAGAGAAGAGAAA
1 AGAA-AGAAGAGAAA
38295054 GGGAGAGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (14 bp):
AGAAAGAAGAGAAA
Found at i:38306924 original size:15 final size:15
Alignment explanation
Indices: 38306888--38306926 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
38306878 CTGCAAGTTT
*
38306888 CAAGAATATAATCAA
1 CAAGAATATCATCAA
*
38306903 C-AGAATATCATGAA
1 CAAGAATATCATCAA
38306917 CAAGAATATC
1 CAAGAATATC
38306927 CTCCAAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (15 bp):
CAAGAATATCATCAA
Found at i:38309094 original size:17 final size:18
Alignment explanation
Indices: 38309074--38309114 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38309064 AATAAAAAAT
*
38309074 ATAATAT-AATACCATTC
1 ATAATATAAAAACCATTC
*
38309091 ATAATATAAAAACCTTTC
1 ATAATATAAAAACCATTC
38309109 ATAATA
1 ATAATA
38309115 ATTATAAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATATAAAAACCATTC
Found at i:38309338 original size:12 final size:11
Alignment explanation
Indices: 38309317--38309344 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
38309307 TAATTATCCC
38309317 TTTTTATTTTT
1 TTTTTATTTTT
38309328 TTTTTATTTTT
1 TTTTTATTTTT
38309339 TTTTTA
1 TTTTTA
38309345 CCAAATCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTATTTTT
Found at i:38315599 original size:16 final size:16
Alignment explanation
Indices: 38315578--38315608 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38315568 TTCACTATTA
*
38315578 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
38315594 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
38315609 GTATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:38323334 original size:17 final size:17
Alignment explanation
Indices: 38323312--38323345 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38323302 TTGAGTAATA
*
38323312 TTTAAATGTTTTAAAAG
1 TTTAAATGTTCTAAAAG
38323329 TTTAAATGTTCTAAAAG
1 TTTAAATGTTCTAAAAG
38323346 ATGAGGGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTAAATGTTCTAAAAG
Found at i:38323510 original size:26 final size:26
Alignment explanation
Indices: 38323481--38323533 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
38323471 ATAACAAAAG
38323481 TATGGTTAATGGTTGTAGTAAAGGTT
1 TATGGTTAATGGTTGTAGTAAAGGTT
38323507 TATGGTTAATGGTTGTAGTAAAGGTT
1 TATGGTTAATGGTTGTAGTAAAGGTT
38323533 T
1 T
38323534 GGTAATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.43
Consensus pattern (26 bp):
TATGGTTAATGGTTGTAGTAAAGGTT
Found at i:38325945 original size:28 final size:29
Alignment explanation
Indices: 38325907--38325961 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
38325897 GTCGCAAAGC
38325907 TCATTCTTTAGATGG-T-GCCACAAAGGCAT
1 TCATTCTTTAG--GGATAGCCACAAAGGCAT
38325936 TCATT-TTTAGGGATAGCCACAAAGGC
1 TCATTCTTTAGGGATAGCCACAAAGGC
38325962 TTCCATATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 2 0.08
27 1 0.04
28 16 0.67
29 5 0.21
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (29 bp):
TCATTCTTTAGGGATAGCCACAAAGGCAT
Found at i:38326018 original size:31 final size:27
Alignment explanation
Indices: 38325980--38326055 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 27
38325970 CCATAAATTG
38325980 CCACAAAGGTGTCCTTTTCATCAAGTACTCA
1 CCACAAAGGTGTCCTTTT-A--AAGT-CTCA
* *
38326011 CCACAAAGGTTTTCCTTTTAGAGTCTCA
1 CCACAAAGG-TGTCCTTTTAAAGTCTCA
*
38326039 CCACAAAGGCGTCCTTT
1 CCACAAAGGTGTCCTTT
38326056 AAGAGGTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 6 0.15
28 13 0.32
29 3 0.08
31 10 0.25
32 8 0.20
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.30
Consensus pattern (27 bp):
CCACAAAGGTGTCCTTTTAAAGTCTCA
Found at i:38326066 original size:27 final size:28
Alignment explanation
Indices: 38326007--38326074 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
38325997 TCATCAAGTA
** *
38326007 CTCACCACAAAGGTTTTCCTTTTAGAGT
1 CTCACCACAAAGGTCGTCCTTTAAGAGT
38326035 CTCACCACAAAGG-CGTCCTTTAAGAGGT
1 CTCACCACAAAGGTCGTCCTTTAAGA-GT
*
38326063 -TCACAACAAAGG
1 CTCACCACAAAGG
38326075 ATTACCCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.57
28 15 0.43
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (28 bp):
CTCACCACAAAGGTCGTCCTTTAAGAGT
Found at i:38328187 original size:25 final size:23
Alignment explanation
Indices: 38328152--38328219 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 23
38328142 AAACATAACA
38328152 TAAACACTTAATTCATATCCTTCAT
1 TAAACACTTAATTCATAT-C-TCAT
*
38328177 TAAACAATTAATTCATAAATCTCAT
1 TAAACACTTAATTCAT--ATCTCAT
*
38328202 TTAACACTTAATTCATAT
1 TAAACACTTAATTCATAT
38328220 GTATTACTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 2 0.05
25 33 0.87
26 1 0.03
27 2 0.05
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAACACTTAATTCATATCTCAT
Found at i:38331739 original size:21 final size:21
Alignment explanation
Indices: 38331713--38331758 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
38331703 CACACGGGCA
38331713 TGTGGTAACTGGGCCAGGCCG
1 TGTGGTAACTGGGCCAGGCCG
*
38331734 TGTGGTAAGTGGGCCAGGCCG
1 TGTGGTAACTGGGCCAGGCCG
38331755 TGTG
1 TGTG
38331759 ATCCACACGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.20, G:0.46, T:0.22
Consensus pattern (21 bp):
TGTGGTAACTGGGCCAGGCCG
Found at i:38341106 original size:13 final size:13
Alignment explanation
Indices: 38341078--38341111 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
38341068 AATCTAATAT
*
38341078 ATATGTA-TATAT
1 ATATGTATTATAA
38341090 ATATGTATTATAA
1 ATATGTATTATAA
38341103 ATATGTATT
1 ATATGTATT
38341112 CATTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (13 bp):
ATATGTATTATAA
Found at i:38341202 original size:19 final size:15
Alignment explanation
Indices: 38341164--38341192 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38341154 TAATTATTAT
38341164 TATAATAAAATAAAG
1 TATAATAAAATAAAG
38341179 TATAATAAAATAAA
1 TATAATAAAATAAA
38341193 TAGGTGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
TATAATAAAATAAAG
Found at i:38341248 original size:10 final size:10
Alignment explanation
Indices: 38341227--38341255 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
38341217 CTTCCAAACT
38341227 AAGAAA-AAA
1 AAGAAAGAAA
38341236 AAGAAAGAAA
1 AAGAAAGAAA
38341246 AAGAAAGAAA
1 AAGAAAGAAA
38341256 TGGGAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:38342632 original size:26 final size:27
Alignment explanation
Indices: 38342569--38342635 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
38342559 TAAGGTTGCA
38342569 AATTTTCATTTCCATTTTTGTAAACCT
1 AATTTTCATTTCCATTTTTGTAAACCT
38342596 AATTTTCATTTCCATTTTTGTAAACCT
1 AATTTTCATTTCCATTTTTGTAAACCT
38342623 ACA-TTT-ATTTCCA
1 A-ATTTTCATTTCCA
38342636 AATTATTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
26 7 0.18
27 31 0.79
28 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.03, T:0.51
Consensus pattern (27 bp):
AATTTTCATTTCCATTTTTGTAAACCT
Found at i:38345366 original size:19 final size:18
Alignment explanation
Indices: 38345335--38345378 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
38345325 TTTACTTTTT
*
38345335 CCCCAAAACTTTTACTTC
1 CCCCAAAAATTTTACTTC
38345353 CCCTCAAAAATTTTACTTC
1 CCC-CAAAAATTTTACTTC
38345372 CCCCAAA
1 CCCCAAA
38345379 TCCCAAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.30
Consensus pattern (18 bp):
CCCCAAAAATTTTACTTC
Found at i:38345672 original size:36 final size:38
Alignment explanation
Indices: 38345630--38345700 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
38345620 TGTATCAATT
38345630 TCACATTTTAT-C-TTTAAAATA-AATTTTATTAATAAA
1 TCACATTTTATACATTTAAAATATAATTTT-TTAATAAA
* *
38345666 TCACATTTTTTACATTTAATATATAATTTTTTAAT
1 TCACATTTTATACATTTAAAATATAATTTTTTAAT
38345701 TTCAAAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 10 0.33
37 1 0.03
38 13 0.43
39 6 0.20
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.52
Consensus pattern (38 bp):
TCACATTTTATACATTTAAAATATAATTTTTTAATAAA
Found at i:38345685 original size:23 final size:20
Alignment explanation
Indices: 38345658--38345702 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
38345648 ATAAATTTTA
38345658 TTAATAAATCACATTTTTTACAT
1 TTAATAAAT-A-ATTTTTTA-AT
*
38345681 TTAATATATAATTTTTTAAT
1 TTAATAAATAATTTTTTAAT
38345701 TT
1 TT
38345703 CAAAATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 8 0.38
22 1 0.05
23 8 0.38
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATAAATAATTTTTTAAT
Found at i:38345840 original size:19 final size:19
Alignment explanation
Indices: 38345816--38345853 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38345806 AAGTTAATAA
38345816 CAAATTAGATTACGGTAGG
1 CAAATTAGATTACGGTAGG
* *
38345835 CAAATTTGATTATGGTAGG
1 CAAATTAGATTACGGTAGG
38345854 TAGTAGTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (19 bp):
CAAATTAGATTACGGTAGG
Found at i:38346350 original size:12 final size:13
Alignment explanation
Indices: 38346327--38346356 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38346317 TTAGCTTTCC
38346327 AAAAACACTTTTG
1 AAAAACACTTTTG
*
38346340 AAAAACATTTTTG
1 AAAAACACTTTTG
38346353 AAAA
1 AAAA
38346357 GAAAAAGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (13 bp):
AAAAACACTTTTG
Found at i:38346603 original size:33 final size:34
Alignment explanation
Indices: 38346566--38346663 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 34
38346556 ATGGTTATAT
38346566 TTAAATATTTAAAATATAATTTATATATT-CTGA
1 TTAAATATTTAAAATATAATTTATATATTACTGA
* * * *
38346599 TTAAAT-TTTATAA-ATAATTAATAT-TTATTGT
1 TTAAATATTTAAAATATAATTTATATATTACTGA
*
38346630 TTAAAAATATTTAAAATTTATATTTCATATATTA
1 TT--AAATATTTAAAATATA-ATTT-ATATATTA
38346664 AAATATTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
30 2 0.04
31 14 0.28
32 6 0.12
33 10 0.20
34 6 0.12
35 2 0.04
36 3 0.06
37 4 0.08
38 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (34 bp):
TTAAATATTTAAAATATAATTTATATATTACTGA
Found at i:38346637 original size:24 final size:24
Alignment explanation
Indices: 38346605--38346650 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
38346595 CTGATTAAAT
* *
38346605 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAATTTATTG
*
38346629 TTTAAAAATATTTAAAATTTAT
1 TTTAAAAATAATTAAAATTTAT
38346651 ATTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTTATTG
Found at i:38346757 original size:19 final size:22
Alignment explanation
Indices: 38346735--38346776 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38346725 TAATTTGAAC
38346735 ATTATTT-A-AAT-ACATATTT
1 ATTATTTGATAATAACATATTT
38346754 ATTATTTGATAATAACATATTT
1 ATTATTTGATAATAACATATTT
38346776 A
1 A
38346777 AAATGGACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 3 0.15
22 9 0.45
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATTTGATAATAACATATTT
Found at i:38348974 original size:3 final size:3
Alignment explanation
Indices: 38348966--38348995 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
38348956 CAATTCAGGC
38348966 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
38348996 GGTTGTGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:38355105 original size:28 final size:28
Alignment explanation
Indices: 38355051--38355105 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
38355041 ACAAATAATT
* *
38355051 TAAAAAAAACCTAATTTAATATCAAAAG
1 TAAAAAAAACATAATTTAATATAAAAAG
*
38355079 TAAAAAAAATATAATTATAA-ATAAAAA
1 TAAAAAAAACATAATT-TAATATAAAAA
38355106 AAATACCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.25
Consensus pattern (28 bp):
TAAAAAAAACATAATTTAATATAAAAAG
Found at i:38355560 original size:4 final size:4
Alignment explanation
Indices: 38355551--38355580 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
38355541 GCATCCCCTC
38355551 TTAT TTAT TTAT TTAT TTAT TTAT TT-T TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
38355581 CTTTCAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:38359946 original size:46 final size:46
Alignment explanation
Indices: 38359894--38359987 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
38359884 AAGATAATAT
38359894 CAATACCTATTGCTCCTATTTTGCATAGTGATCCCTTCTAGTGGTA
1 CAATACCTATTGCTCCTATTTTGCATAGTGATCCCTTCTAGTGGTA
*
38359940 CAATACCTATTGCTTCTATTTTGCATAGTGATCCCTTCTAGTGGTA
1 CAATACCTATTGCTCCTATTTTGCATAGTGATCCCTTCTAGTGGTA
38359986 CA
1 CA
38359988 TACTTTTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (46 bp):
CAATACCTATTGCTCCTATTTTGCATAGTGATCCCTTCTAGTGGTA
Found at i:38361297 original size:10 final size:11
Alignment explanation
Indices: 38361272--38361296 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38361262 CAGTCAAGAT
38361272 AAAACGTTACA
1 AAAACGTTACA
38361283 AAAACGTTACA
1 AAAACGTTACA
38361294 AAA
1 AAA
38361297 CCCCTTGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAACGTTACA
Found at i:38362011 original size:13 final size:13
Alignment explanation
Indices: 38361993--38362021 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38361983 TCAATCCTTT
38361993 TTTGAAAAGGGAC
1 TTTGAAAAGGGAC
38362006 TTTGAAAAGGGAC
1 TTTGAAAAGGGAC
38362019 TTT
1 TTT
38362022 TAAATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (13 bp):
TTTGAAAAGGGAC
Found at i:38364206 original size:23 final size:23
Alignment explanation
Indices: 38364180--38364239 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
38364170 ACTTATATAT
38364180 ATATATATTTAGAATTTTTTACA
1 ATATATATTTAGAATTTTTTACA
* * *
38364203 ATATAAATTTTGAATTTTTTATA
1 ATATATATTTAGAATTTTTTACA
38364226 A-ATAT-TTTA-AATTT
1 ATATATATTTAGAATTT
38364240 AAAAAATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 5 0.16
21 3 0.09
22 3 0.09
23 21 0.66
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (23 bp):
ATATATATTTAGAATTTTTTACA
Found at i:38364761 original size:22 final size:24
Alignment explanation
Indices: 38364735--38364796 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 24
38364725 GAAATTAAAT
38364735 TATATATTTTTATAATAGTAA-AA
1 TATATATTTTTATAATAGTAATAA
* * **
38364758 -ATATAATTTTATTATTTTAATAA
1 TATATATTTTTATAATAGTAATAA
*
38364781 TTTATATTTTTATAAT
1 TATATATTTTTATAAT
38364797 TTTTAAAAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 16 0.53
23 2 0.07
24 12 0.40
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATATATTTTTATAATAGTAATAA
Found at i:38364790 original size:15 final size:16
Alignment explanation
Indices: 38364760--38364798 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
38364750 TAGTAAAAAT
38364760 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
38364777 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
38364792 ATAATTT
1 ATAATTT
38364799 TTAAAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:38370535 original size:18 final size:18
Alignment explanation
Indices: 38370465--38370528 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
38370455 GAACAATTAT
* *
38370465 TTATTTAGTAATAGTCAG
1 TTATTCAGTAATAATCAG
*
38370483 TTATTCAGTAATAATCAA
1 TTATTCAGTAATAATCAG
*
38370501 TTATTCAATAATAATCAG
1 TTATTCAGTAATAATCAG
38370519 TTATTCAGTA
1 TTATTCAGTA
38370529 TCAATCAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (18 bp):
TTATTCAGTAATAATCAG
Found at i:38370853 original size:6 final size:6
Alignment explanation
Indices: 38370842--38370868 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38370832 TACCGAATCG
38370842 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
38370869 GTCGACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:38378194 original size:20 final size:20
Alignment explanation
Indices: 38378151--38378194 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
38378141 CACATGTATT
* * * *
38378151 CATTAAATTTTAGAATTTTT
1 CATTAAATTTCACAACTTTA
38378171 CATTAAATTTCACAACTTTA
1 CATTAAATTTCACAACTTTA
38378191 CATT
1 CATT
38378195 TTAGTCCCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (20 bp):
CATTAAATTTCACAACTTTA
Found at i:38379663 original size:9 final size:9
Alignment explanation
Indices: 38379651--38379697 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
38379641 CTAATTCTCC
38379651 TTCTTTTAT
1 TTCTTTTAT
*
38379660 TTCTCTT-T
1 TTCTTTTAT
*
38379668 TTCTTTCTTT
1 TTCTTT-TAT
*
38379678 TTCTTTTGT
1 TTCTTTTAT
38379687 TTCTTTTAT
1 TTCTTTTAT
38379696 TT
1 TT
38379698 GTTCTTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.19
9 19 0.59
10 7 0.22
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (9 bp):
TTCTTTTAT
Found at i:38379727 original size:8 final size:8
Alignment explanation
Indices: 38379714--38379749 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
38379704 TATATTTTAT
38379714 ATAATATA
1 ATAATATA
38379722 ATAATATA
1 ATAATATA
*
38379730 GTAATATA
1 ATAATATA
38379738 ATAATATA
1 ATAATATA
38379746 ATAA
1 ATAA
38379750 CATTTACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (8 bp):
ATAATATA
Found at i:38379791 original size:17 final size:18
Alignment explanation
Indices: 38379769--38379804 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38379759 AAATAATAAG
38379769 TAAATATA-ATTTATTAT
1 TAAATATATATTTATTAT
*
38379786 TAAATATATGTTTATTAT
1 TAAATATATATTTATTAT
38379804 T
1 T
38379805 TACACACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TAAATATATATTTATTAT
Found at i:38386565 original size:36 final size:39
Alignment explanation
Indices: 38386516--38386607 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 39
38386506 GTGTAGGCAT
* *
38386516 TAAAGCAAGCATGCATGACCGAA-TTAATGTGCAAGTAC
1 TAAAGAAAGCATGCATGACCAAATTTAATGTGCAAGTAC
* *
38386554 T-AA-AAAGCATGCATGACCAAATTTAATGTGCAGGTAT
1 TAAAGAAAGCATGCATGACCAAATTTAATGTGCAAGTAC
38386591 TAAAGAAAGCATGCATG
1 TAAAGAAAGCATGCATG
38386608 GGACAGCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
36 16 0.34
37 16 0.34
38 3 0.06
39 12 0.26
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (39 bp):
TAAAGAAAGCATGCATGACCAAATTTAATGTGCAAGTAC
Found at i:38386651 original size:30 final size:30
Alignment explanation
Indices: 38386604--38386692 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 30
38386594 AGAAAGCATG
* * *
38386604 CATGGGACAGCATTAAAGGAGCTGCTGGTG
1 CATGGAACAACATTAAAGGAGCTGCTGGTA
* * *
38386634 CTTGGAACAATATTAAAGGAGTTGCTGGTA
1 CATGGAACAACATTAAAGGAGCTGCTGGTA
***
38386664 CATGGAATGGCATTAAAGGAGCTGCTGGT
1 CATGGAACAACATTAAAGGAGCTGCTGGT
38386693 TCCTCTTTTC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (30 bp):
CATGGAACAACATTAAAGGAGCTGCTGGTA
Found at i:38387812 original size:21 final size:20
Alignment explanation
Indices: 38387775--38387813 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
38387765 TAGCAACTCC
* *
38387775 AGAATAGGTTCGTAAAAAAA
1 AGAAGAGGTTCGGAAAAAAA
38387795 AGAAGAGGTTTCGGAAAAA
1 AGAAGAGG-TTCGGAAAAA
38387814 TAATATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.51, C:0.05, G:0.26, T:0.18
Consensus pattern (20 bp):
AGAAGAGGTTCGGAAAAAAA
Found at i:38391024 original size:39 final size:39
Alignment explanation
Indices: 38390928--38391038 Score: 125
Period size: 38 Copynumber: 2.9 Consensus size: 39
38390918 TTTGTTGATT
* * * *
38390928 TTTAATGTGTAGGCATTAAAACAAGCATGCATGACCGAA
1 TTTAATGTGCAGGTATTAAAAAAAGCATGCATGGCCGAA
* * * * *
38390967 -TTAATGTGCAAGTGTTAAAAAAAACATGTATGGCTGAA
1 TTTAATGTGCAGGTATTAAAAAAAGCATGCATGGCCGAA
*
38391005 TTTAATGTGCAGGTATTAAAGAAAGCATGCATGG
1 TTTAATGTGCAGGTATTAAAAAAAGCATGCATGG
38391039 GACAACATTA
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
38 29 0.51
39 28 0.49
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28
Consensus pattern (39 bp):
TTTAATGTGCAGGTATTAAAAAAAGCATGCATGGCCGAA
Found at i:38391086 original size:27 final size:30
Alignment explanation
Indices: 38391032--38391122 Score: 119
Period size: 30 Copynumber: 3.0 Consensus size: 30
38391022 AAAGAAAGCA
*
38391032 TGCATGGGACAACATTAAAGGTGCTGCTGG
1 TGCATGGAACAACATTAAAGGTGCTGCTGG
*
38391062 TGCATGGAACAATATTAAAGGTGCTGCTGG
1 TGCATGGAACAACATTAAAGGTGCTGCTGG
* ** * *
38391092 TGTATGGAACGGCATTAAAGGAGCTACTGG
1 TGCATGGAACAACATTAAAGGTGCTGCTGG
38391122 T
1 T
38391123 TCCTCTTTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (30 bp):
TGCATGGAACAACATTAAAGGTGCTGCTGG
Found at i:38392368 original size:50 final size:49
Alignment explanation
Indices: 38392314--38392431 Score: 173
Period size: 50 Copynumber: 2.4 Consensus size: 49
38392304 TCCCGATCTA
** *
38392314 TGGCTCTTTGGAGCTTCCAGATAAAAAGCTCTTTGTGAGCTTTCCGATTG
1 TGGCTCTCCGGAGCTTCC-GATAAAAAGCACTTTGTGAGCTTTCCGATTG
* *
38392364 TGGCTCTCCGAAGCTTTCCGATAAAAGGCACTTTGTGAGCTTTCCGATTG
1 TGGCTCTCCGGAGC-TTCCGATAAAAAGCACTTTGTGAGCTTTCCGATTG
38392414 TGGCTCTCCGGAGCTTCC
1 TGGCTCTCCGGAGCTTCC
38392432 TAATATTGGC
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
49 4 0.07
50 53 0.87
51 4 0.07
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (49 bp):
TGGCTCTCCGGAGCTTCCGATAAAAAGCACTTTGTGAGCTTTCCGATTG
Found at i:38392369 original size:25 final size:25
Alignment explanation
Indices: 38392341--38392420 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
38392331 CAGATAAAAA
38392341 GCTCTTTGTGAGCTTTCCGATTGTG
1 GCTCTTTGTGAGCTTTCCGATTGTG
** * ***
38392366 GCTCTCCG-AAGCTTTCCGATAAAAG
1 GCTCTTTGTGAGCTTTCCGAT-TGTG
*
38392391 GCACTTTGTGAGCTTTCCGATTGTG
1 GCTCTTTGTGAGCTTTCCGATTGTG
38392416 GCTCT
1 GCTCT
38392421 CCGGAGCTTC
Statistics
Matches: 39, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
24 11 0.28
25 17 0.44
26 11 0.28
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (25 bp):
GCTCTTTGTGAGCTTTCCGATTGTG
Found at i:38393279 original size:73 final size:73
Alignment explanation
Indices: 38393155--38393327 Score: 220
Period size: 73 Copynumber: 2.4 Consensus size: 73
38393145 ATTTTCACAT
* * * * * * **
38393155 GGCCTAGCACACGAGCGTGTGACTTGGCCGTGCGTCCCCTGCACCTCAATAATATAAGTCAAATT
1 GGCCTAGCACACGGGCGTGTGGCTTGGCCATGCATCCCCTGCACCTAAATAATACAACCCAAATT
38393220 GCTAACAC
66 GCTAACAC
* * * * *
38393228 GGCCTAACACACGGGCATGTGGCTTGGCCATGTATCCCTTGCACCTAAATAATGCAACCCAAATT
1 GGCCTAGCACACGGGCGTGTGGCTTGGCCATGCATCCCCTGCACCTAAATAATACAACCCAAATT
*
38393293 GCTCACAC
66 GCTAACAC
38393301 GGCCTAGCACACGGGCGTGTGGCTTGG
1 GGCCTAGCACACGGGCGTGTGGCTTGG
38393328 TCGTGTGACC
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.21
Consensus pattern (73 bp):
GGCCTAGCACACGGGCGTGTGGCTTGGCCATGCATCCCCTGCACCTAAATAATACAACCCAAATT
GCTAACAC
Found at i:38393827 original size:53 final size:52
Alignment explanation
Indices: 38393748--38393854 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 52
38393738 GGCTATGTGT
* *
38393748 CTATACATATATCTATGTACTGATACCTTAGATAAGGTACTGACACATAGGC
1 CTATACATATATCTATGTACTGATACCTTAGATAAGATACTAACACATAGGC
*
38393800 CTATACATATATTCTATGTACTGATACCTTAGGTAAGATACTAACACATAGGC
1 CTATACATATA-TCTATGTACTGATACCTTAGATAAGATACTAACACATAGGC
38393853 CT
1 CT
38393855 TATATATTGA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 11 0.22
53 40 0.78
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (52 bp):
CTATACATATATCTATGTACTGATACCTTAGATAAGATACTAACACATAGGC
Found at i:38394700 original size:18 final size:18
Alignment explanation
Indices: 38394665--38394700 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38394655 CTTTTCAAAA
*
38394665 TATATCGATACCATTTTT
1 TATATCGATACCACTTTT
*
38394683 TATATCGATATCACTTTT
1 TATATCGATACCACTTTT
38394701 GCATTCTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (18 bp):
TATATCGATACCACTTTT
Found at i:38397340 original size:848 final size:848
Alignment explanation
Indices: 38395681--38398301 Score: 4136
Period size: 848 Copynumber: 3.0 Consensus size: 848
38395671 GGTATTTAGG
*
38395681 GGTTTTAGTTCATAACTAAAT-AAGAAAACATCTCAGAAGAATAAAGAATACAAAACATAAAGAA
1 GGTTTTAGTTCATAACTAAATAAAAAAAACATCTCAGAAGAATAAAGAATACAAAACATAAAGAA
38395745 AACCCAAAACTTCTGAAGGGAAATTGAGGAGAGATCTTCAGTCTTGATGATAAATCTGGCTTCTA
66 AACCCAAAACTTCTGAAGGGAAATTGAGGAGAGATCTTCAGTCTTGATGATAAATCTGGCTTCTA
38395810 AGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTCCGTCTCCCTTTTCTTCCT
131 AGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTCCGTCTCCCTTTTCTTCCT
38395875 TCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAAATTAGCCTTTTCCGAATA
196 TCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAAATTAGCCTTTTCCGAATA
38395940 TGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGTGTTCGATTACTTCAGGCC
261 TGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGTGTTCGATTACTTCAGGCC
38396005 GTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTGAGGAGGTCCAGGCTGTGT
326 GTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTGAGGAGGTCCAGGCTGTGT
38396070 TGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCGTTCCTTTCACTCTCCTAT
391 TGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCGTTCCTTTCACTCTCCTAT
38396135 GCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAATTCACCAATTCTAATGAG
456 GCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAATTCACCAATTCTAATGAG
38396200 AAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAATTTACGGTTTATCAAGTCG
521 AAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAATTTACGGTTTATCAAGTCG
38396265 CCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAATCATTCTAATAAAGCATT
586 CCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAATCATTCTAATAAAGCATT
38396330 TTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACGAGTTCGGAAGTCAGTTAC
651 TTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACGAGTTCGGAAGTCAGTTAC
38396395 GCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGTATTGATCAATTAACGTCC
716 GCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGTATTGATCAATTAACGTCC
38396460 TAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAAACGTTTAGATAACTTGAA
781 TAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAAACGTTTAGATAACTTGAA
38396525 TTT
846 TTT
38396528 GGTTTTAGTTCATAACTAAATAAAAAAAACATCTCAGAAGAATAAAGAATACAAAACATAAAGAA
1 GGTTTTAGTTCATAACTAAATAAAAAAAACATCTCAGAAGAATAAAGAATACAAAACATAAAGAA
38396593 AACCCAAAACTTCTGAAGGGAAATTGAGGAGAGATCTTCAGTCTTGATGATAAATCTGGCTTCTA
66 AACCCAAAACTTCTGAAGGGAAATTGAGGAGAGATCTTCAGTCTTGATGATAAATCTGGCTTCTA
38396658 AGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTCCGTCTCCCTTTTCTTCCT
131 AGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTCCGTCTCCCTTTTCTTCCT
38396723 TCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAAATTAGCCTTTTCCGAATA
196 TCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAAATTAGCCTTTTCCGAATA
38396788 TGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGTGTTCGATTACTTCAGGCC
261 TGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGTGTTCGATTACTTCAGGCC
38396853 GTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTGAGGAGGTCCAGGCTGTGT
326 GTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTGAGGAGGTCCAGGCTGTGT
38396918 TGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCGTTCCTTTCACTCTCCTAT
391 TGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCGTTCCTTTCACTCTCCTAT
38396983 GCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAATTCACCAATTCTAATGAG
456 GCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAATTCACCAATTCTAATGAG
38397048 AAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAATTTACGGTTTATCAAGTCG
521 AAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAATTTACGGTTTATCAAGTCG
38397113 CCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAATCATTCTAATAAAGCATT
586 CCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAATCATTCTAATAAAGCATT
38397178 TTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACGAGTTCGGAAGTCAGTTAC
651 TTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACGAGTTCGGAAGTCAGTTAC
38397243 GCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGTATTGATCAATTAACGTCC
716 GCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGTATTGATCAATTAACGTCC
38397308 TAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAAACGTTTAGATAACTTGAA
781 TAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAAACGTTTAGATAACTTGAA
38397373 -TT
846 TTT
** * * * * * * * * * *
38397375 GGATGTCGAGATTC-T-CCCAGAAGGAGTAAAATATCATGTCCAGCACGATTGGATACAACATTT
1 GG-T-TTTAG-TTCATAACTA-AA-TA--AAAAAAACATCT-CAG-A--A--GAATA-AAGAATA
* * * ** * ** *
38397438 CAAACCCTCAATACGAGATCATCCCATAATTTTCAAAACTCATACATTTGAAATTTCAAAAAGGA
52 CAAAACAT-AA-A-GA-A--AACCCA-AAACTT-----CT--GA-A-GGGAAA-TT----GAGGA
* ** ** ** * * * * ** *
38397503 TATTTGGCTATTCGGCCAAACGGTAAATCGAAACCCAACACGATTGGGC-ACGATTTATCGAACT
96 GA----G--A-TC-TTCAGTC--TTGAT-GATA---AA-TC---T-GGCTTCTA-AGAT-GGA--
38397567 TCCAAAATCTGGCTTCTAAGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTC
138 T-------------------------CAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTC
38397632 CGTCTCCCTTTTCTTCCTTCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAA
178 CGTCTCCCTTTTCTTCCTTCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAA
38397697 ATTAGCCTTTTCCGAATATGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGT
243 ATTAGCCTTTTCCGAATATGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGT
38397762 GTTCGATTACTTCAGGCCGTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTG
308 GTTCGATTACTTCAGGCCGTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTG
38397827 AGGAGGTCCAGGCTGTGTTGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCG
373 AGGAGGTCCAGGCTGTGTTGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCG
38397892 TTCCTTTCACTCTCCTATGCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAA
438 TTCCTTTCACTCTCCTATGCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAA
38397957 TTCACCAATTCTAATGAGAAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAAT
503 TTCACCAATTCTAATGAGAAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAAT
38398022 TTACGGTTTATCAAGTCGCCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAA
568 TTACGGTTTATCAAGTCGCCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAA
38398087 TCATTCTAATAAAGCATTTTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACG
633 TCATTCTAATAAAGCATTTTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACG
38398152 AGTTCGGAAGTCAGTTACGCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGT
698 AGTTCGGAAGTCAGTTACGCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGT
38398217 ATTGATCAATTAACGTCCTAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAA
763 ATTGATCAATTAACGTCCTAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAA
38398282 ACGTTTAGATAACTTGAATT
828 ACGTTTAGATAACTTGAATT
38398302 GGATGTCGAG
Statistics
Matches: 1653, Mismatches: 36, Indels: 89
0.93 0.02 0.05
Matches are distributed among these distances:
847 25 0.02
848 825 0.50
849 6 0.00
850 4 0.00
852 9 0.01
853 3 0.00
854 1 0.00
856 1 0.00
858 4 0.00
859 10 0.01
860 2 0.00
861 1 0.00
862 2 0.00
863 1 0.00
865 5 0.00
866 4 0.00
871 2 0.00
873 1 0.00
874 1 0.00
875 4 0.00
876 2 0.00
880 5 0.00
884 1 0.00
886 1 0.00
887 2 0.00
888 3 0.00
890 3 0.00
891 3 0.00
894 2 0.00
895 1 0.00
898 3 0.00
899 5 0.00
900 2 0.00
902 1 0.00
927 707 0.43
928 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (848 bp):
GGTTTTAGTTCATAACTAAATAAAAAAAACATCTCAGAAGAATAAAGAATACAAAACATAAAGAA
AACCCAAAACTTCTGAAGGGAAATTGAGGAGAGATCTTCAGTCTTGATGATAAATCTGGCTTCTA
AGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTCCGTCTCCCTTTTCTTCCT
TCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAAATTAGCCTTTTCCGAATA
TGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGTGTTCGATTACTTCAGGCC
GTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTGAGGAGGTCCAGGCTGTGT
TGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCGTTCCTTTCACTCTCCTAT
GCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAATTCACCAATTCTAATGAG
AAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAATTTACGGTTTATCAAGTCG
CCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAATCATTCTAATAAAGCATT
TTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACGAGTTCGGAAGTCAGTTAC
GCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGTATTGATCAATTAACGTCC
TAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAAACGTTTAGATAACTTGAA
TTT
Found at i:38398437 original size:927 final size:927
Alignment explanation
Indices: 38396644--38398497 Score: 3699
Period size: 927 Copynumber: 2.0 Consensus size: 927
38396634 TCTTGATGAT
38396644 AAATCTGGCTTCTAAGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTCCGTC
1 AAATCTGGCTTCTAAGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTCCGTC
38396709 TCCCTTTTCTTCCTTCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAAATTA
66 TCCCTTTTCTTCCTTCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAAATTA
38396774 GCCTTTTCCGAATATGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGTGTTC
131 GCCTTTTCCGAATATGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGTGTTC
38396839 GATTACTTCAGGCCGTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTGAGGA
196 GATTACTTCAGGCCGTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTGAGGA
38396904 GGTCCAGGCTGTGTTGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCGTTCC
261 GGTCCAGGCTGTGTTGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCGTTCC
38396969 TTTCACTCTCCTATGCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAATTCA
326 TTTCACTCTCCTATGCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAATTCA
38397034 CCAATTCTAATGAGAAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAATTTAC
391 CCAATTCTAATGAGAAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAATTTAC
38397099 GGTTTATCAAGTCGCCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAATCAT
456 GGTTTATCAAGTCGCCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAATCAT
38397164 TCTAATAAAGCATTTTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACGAGTT
521 TCTAATAAAGCATTTTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACGAGTT
38397229 CGGAAGTCAGTTACGCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGTATTG
586 CGGAAGTCAGTTACGCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGTATTG
38397294 ATCAATTAACGTCCTAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAAACGT
651 ATCAATTAACGTCCTAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAAACGT
38397359 TTAGATAACTTGAATTGGATGTCGAGATTCTCCCAGAAGGAGTAAAATATCATGTCCAGCACGAT
716 TTAGATAACTTGAATTGGATGTCGAGATTCTCCCAGAAGGAGTAAAATATCATGTCCAGCACGAT
38397424 TGGATACAACATTTCAAACCCTCAATACGAGATCATCCCATAATTTTCAAAACTCATACATTTGA
781 TGGATACAACATTTCAAACCCTCAATACGAGATCATCCCATAATTTTCAAAACTCATACATTTGA
38397489 AATTTCAAAAAGGATATTTGGCTATTCGGCCAAACGGTAAATCGAAACCCAACACGATTGGGCAC
846 AATTTCAAAAAGGATATTTGGCTATTCGGCCAAACGGTAAATCGAAACCCAACACGATTGGGCAC
38397554 GATTTATCGAACTTCCA
911 GATTTATCGAACTTCCA
38397571 AAATCTGGCTTCTAAGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTCCGTC
1 AAATCTGGCTTCTAAGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTCCGTC
38397636 TCCCTTTTCTTCCTTCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAAATTA
66 TCCCTTTTCTTCCTTCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAAATTA
38397701 GCCTTTTCCGAATATGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGTGTTC
131 GCCTTTTCCGAATATGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGTGTTC
38397766 GATTACTTCAGGCCGTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTGAGGA
196 GATTACTTCAGGCCGTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTGAGGA
38397831 GGTCCAGGCTGTGTTGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCGTTCC
261 GGTCCAGGCTGTGTTGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCGTTCC
38397896 TTTCACTCTCCTATGCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAATTCA
326 TTTCACTCTCCTATGCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAATTCA
38397961 CCAATTCTAATGAGAAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAATTTAC
391 CCAATTCTAATGAGAAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAATTTAC
38398026 GGTTTATCAAGTCGCCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAATCAT
456 GGTTTATCAAGTCGCCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAATCAT
38398091 TCTAATAAAGCATTTTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACGAGTT
521 TCTAATAAAGCATTTTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACGAGTT
38398156 CGGAAGTCAGTTACGCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGTATTG
586 CGGAAGTCAGTTACGCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGTATTG
38398221 ATCAATTAACGTCCTAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAAACGT
651 ATCAATTAACGTCCTAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAAACGT
38398286 TTAGATAACTTGAATTGGATGTCGAGATTCTCCCAGAAGGAGTAAAATATCATGTCCAGCACGAT
716 TTAGATAACTTGAATTGGATGTCGAGATTCTCCCAGAAGGAGTAAAATATCATGTCCAGCACGAT
38398351 TGGATACAACATTTCAAACCCTCAATACGAGATCATCCCATAATTTTCAAAACTCATACATTTGA
781 TGGATACAACATTTCAAACCCTCAATACGAGATCATCCCATAATTTTCAAAACTCATACATTTGA
*
38398416 AATTTCAAAAAGGATATTTGGCTATTTGGCCAAACGGTAAATCGAAACCCAACACGATTGGGCAC
846 AATTTCAAAAAGGATATTTGGCTATTCGGCCAAACGGTAAATCGAAACCCAACACGATTGGGCAC
38398481 GATTTATCGAACTTCCA
911 GATTTATCGAACTTCCA
38398498 TATACGAAAT
Statistics
Matches: 926, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
927 926 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (927 bp):
AAATCTGGCTTCTAAGATGGATCAATCGGCTTCCTTGGAGTAATCCCTTACTCCTTATCTCCGTC
TCCCTTTTCTTCCTTCTCTCGGGTGTATTTATAGGCTTTGGAATGGCTAGAAGCCCTCAAAATTA
GCCTTTTCCGAATATGACTCAACTTGGGCTTGACAGGGACATGCCCGTGGCACACGCCCGTGTTC
GATTACTTCAGGCCGTGCTCGAGCTTGTCAAATTGACACGACCGTGTGGTCTGCACGTGTGAGGA
GGTCCAGGCTGTGTTGATTTCGTACTTTGGCCCATTTTCTCCGTTTTTGGCCCGTTTCTCGTTCC
TTTCACTCTCCTATGCTCTCCTAAGTATAAAACATGAAATCAAAGCATTAGGAGCATCGAATTCA
CCAATTCTAATGAGAAATCATCCATAAAATGCATTAAACATGGGGTAAAAATATGTATAATTTAC
GGTTTATCAAGTCGCCACCAATCCTTTTTGTTTAGGTGTGATCGGGTCACCTTGTGATCAATCAT
TCTAATAAAGCATTTTGGTTTATTAAAACAATATTTTTGGTCTATGAAAGACTAGAAAACGAGTT
CGGAAGTCAGTTACGCGCGAGGAAGGATTATCACCCTCGCAACGCCCAAAATCGGTACCGTATTG
ATCAATTAACGTCCTAATGTTGAAAATTTGAAAAAGATTTTAAAATACAATTCCTTTAAAAACGT
TTAGATAACTTGAATTGGATGTCGAGATTCTCCCAGAAGGAGTAAAATATCATGTCCAGCACGAT
TGGATACAACATTTCAAACCCTCAATACGAGATCATCCCATAATTTTCAAAACTCATACATTTGA
AATTTCAAAAAGGATATTTGGCTATTCGGCCAAACGGTAAATCGAAACCCAACACGATTGGGCAC
GATTTATCGAACTTCCA
Found at i:38398749 original size:125 final size:124
Alignment explanation
Indices: 38398454--38398732 Score: 405
Period size: 125 Copynumber: 2.2 Consensus size: 124
38398444 GCCAAACGGT
* * *
38398454 AAATCGAAACCCAACACGATTGGGCACGATTTATCGAACTTCCATATACGAAATATTGCCTCATT
1 AAATCGAAACCCAGCACGATTGGGCACGA-TTATCGAACTTCCAAATACGAAATATTGCCTCACT
* **
38398519 TTAATTTAAGAAAACATGGATGAAATTCCAAAAGGATATTTCATATTTTAATCGAATGAA
65 TTAATTTAAGAAAACATAGAAAAAATTCCAAAAGGATATTTCATATTTTAATCGAATGAA
* * *
38398579 AAATCGAAACCCAGCACCATTGGGCACGATTTATCGAACTTCCAAATATGAAATATTGCCTCGCT
1 AAATCGAAACCCAGCACGATTGGGCACGA-TTATCGAACTTCCAAATACGAAATATTGCCTCACT
* * ** *
38398644 TTAATTTAAGAGAACATAGAAAAAATTTCAAAAGGATATTTTGTATTTTAGTCGAATGAA
65 TTAATTTAAGAAAACATAGAAAAAATTCCAAAAGGATATTTCATATTTTAATCGAATGAA
*
38398704 AAATCGAAACCTAGCACGATTGGGCACGA
1 AAATCGAAACCCAGCACGATTGGGCACGA
38398733 CCTCGTAAAC
Statistics
Matches: 138, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
125 138 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (124 bp):
AAATCGAAACCCAGCACGATTGGGCACGATTATCGAACTTCCAAATACGAAATATTGCCTCACTT
TAATTTAAGAAAACATAGAAAAAATTCCAAAAGGATATTTCATATTTTAATCGAATGAA
Found at i:38399335 original size:25 final size:26
Alignment explanation
Indices: 38399295--38399362 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 26
38399285 AGAACCAAAT
38399295 TATACATAAATAAATTTAA-A-AGAA
1 TATACATAAATAAATTTAAGAGAGAA
*
38399319 TATATATATAATAAATTTAAGAGAGAA
1 TATACATA-AATAAATTTAAGAGAGAA
38399346 TATTTACATAAAATAAA
1 TA--TACAT-AAATAAA
38399363 AGGAAGTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
24 7 0.19
25 11 0.31
26 1 0.03
27 6 0.17
29 10 0.28
30 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (26 bp):
TATACATAAATAAATTTAAGAGAGAA
Found at i:38401691 original size:17 final size:18
Alignment explanation
Indices: 38401669--38401702 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38401659 AATTGAGTTA
38401669 AGAAAA-TAATCTAATTG
1 AGAAAATTAATCTAATTG
*
38401686 AGAAAATTAATTTAATT
1 AGAAAATTAATCTAATT
38401703 AATTAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (18 bp):
AGAAAATTAATCTAATTG
Found at i:38402282 original size:17 final size:16
Alignment explanation
Indices: 38402260--38402291 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38402250 TTATAAATAT
*
38402260 AAAAAAATTAATTTTA
1 AAAAAAATTAAATTTA
38402276 AAAAAAATTAAATTTA
1 AAAAAAATTAAATTTA
38402292 TGTCTAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAAAAATTAAATTTA
Found at i:38404148 original size:24 final size:25
Alignment explanation
Indices: 38404074--38404151 Score: 79
Period size: 24 Copynumber: 3.1 Consensus size: 25
38404064 TTAAAAATGT
*
38404074 AAAAATGTATATAATATATAATTTTA
1 AAAAATGTATAAAATATATAA-TTTA
* **
38404100 AAAAATGTTTAAAA-ATTATTTTTTA
1 AAAAATGTATAAAATA-TATAATTTA
*
38404125 TAAAAT-TATAAAATATATAATTTA
1 AAAAATGTATAAAATATATAATTTA
38404149 AAA
1 AAA
38404152 TTTTAAAAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
24 15 0.37
25 11 0.27
26 15 0.37
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
AAAAATGTATAAAATATATAATTTA
Found at i:38404443 original size:10 final size:10
Alignment explanation
Indices: 38404421--38404514 Score: 56
Period size: 10 Copynumber: 9.5 Consensus size: 10
38404411 TAAATTTTAT
38404421 TTTTATAATTA
1 TTTTAT-ATTA
38404432 TTTTATATTA
1 TTTTATATTA
38404442 TTTTATATGT-
1 TTTTATAT-TA
* *
38404452 TTTTTTA-GA
1 TTTTATATTA
38404461 TTTTATA-TA
1 TTTTATATTA
* *
38404470 TTTTTTAATTT
1 TTTTAT-ATTA
38404481 TTTTATA-TA
1 TTTTATATTA
*
38404490 -TTTATTTCTA
1 TTTTATAT-TA
38404500 TTTTTATATT-
1 -TTTTATATTA
38404510 TTTTA
1 TTTTA
38404515 ATGTGTATAC
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
8 5 0.08
9 18 0.28
10 22 0.34
11 14 0.22
12 6 0.09
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTATATTA
Found at i:38404466 original size:29 final size:28
Alignment explanation
Indices: 38404431--38404513 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 28
38404421 TTTTATAATT
*
38404431 ATTTTATATTATTTTATATGTTTTTTTAG
1 ATTTTATATTATTTT-TATATTTTTTTAG
*
38404460 ATTTTATA-TATTTTT-TAATTTTTTTAT
1 ATTTTATATTATTTTTAT-ATTTTTTTAG
*
38404487 ATATTTATTTCTATTTTTATATTTTTT
1 AT-TTTATAT-TATTTTTATATTTTTT
38404514 AATGTGTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
26 1 0.02
27 11 0.24
28 11 0.24
29 8 0.17
30 14 0.30
31 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.02, T:0.72
Consensus pattern (28 bp):
ATTTTATATTATTTTTATATTTTTTTAG
Found at i:38404475 original size:18 final size:17
Alignment explanation
Indices: 38404441--38404516 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 17
38404431 ATTTTATATT
*
38404441 ATTTTATATGTTTTTTTA
1 ATTTTATAT-ATTTTTTA
38404459 GATTTTATATATTTTTTA
1 -ATTTTATATATTTTTTA
*
38404477 ATTTTTTTATATATTTATTTCT
1 A---TTTTATATATTT-TTT-A
38404499 ATTTT-TATATTTTTTA
1 ATTTTATATATTTTTTA
38404515 AT
1 AT
38404517 GTGTATACAC
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
16 2 0.04
17 4 0.08
18 14 0.29
19 13 0.27
20 12 0.24
21 3 0.06
22 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTTATATATTTTTTA
Found at i:38404502 original size:22 final size:20
Alignment explanation
Indices: 38404401--38404513 Score: 70
Period size: 20 Copynumber: 5.5 Consensus size: 20
38404391 TTCAATTATC
*
38404401 ATATTTTTTTTAAATTTTATTT
1 ATATATTTTTT-AATTTT-TTT
* *
38404423 TTATAATTATTTTATATTATTTT
1 ATAT-ATT-TTTTA-ATTTTTTT
* * **
38404446 ATATGTTTTTTTA-GATTTT
1 ATATATTTTTTAATTTTTTT
38404465 ATATATTTTTTAATTTTTTT
1 ATATATTTTTTAATTTTTTT
* *
38404485 ATATATTTATTT-CTATTTTT
1 ATATATTT-TTTAATTTTTTT
38404505 ATAT-TTTTT
1 ATATATTTTT
38404514 AATGTGTATA
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
18 2 0.03
19 19 0.26
20 23 0.32
21 7 0.10
22 5 0.07
23 9 0.12
24 8 0.11
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.72
Consensus pattern (20 bp):
ATATATTTTTTAATTTTTTT
Found at i:38405044 original size:20 final size:21
Alignment explanation
Indices: 38405019--38405058 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
38405009 GTTGACTAGT
38405019 TAAAATTTA-TTTAAAAATTG
1 TAAAATTTATTTTAAAAATTG
38405039 TAAAATTTATTTTAAAAATT
1 TAAAATTTATTTTAAAAATT
38405059 CTAATTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
TAAAATTTATTTTAAAAATTG
Found at i:38405149 original size:10 final size:9
Alignment explanation
Indices: 38405095--38405179 Score: 55
Period size: 9 Copynumber: 9.2 Consensus size: 9
38405085 ATATAAAGTT
38405095 TTTTTAAAA
1 TTTTTAAAA
*
38405104 -TATTAAAA
1 TTTTTAAAA
*
38405112 TGTTATAAAA
1 T-TTTTAAAA
* *
38405122 ATTGTAAAA
1 TTTTTAAAA
*
38405131 ATTTTAAAA
1 TTTTTAAAA
38405140 TTTTTGAAAA
1 TTTTT-AAAA
**
38405150 TCATTAAAA
1 TTTTTAAAA
38405159 TTTTTTAAAA
1 -TTTTTAAAA
**
38405169 TGATTAAAA
1 TTTTTAAAA
38405178 TT
1 TT
38405180 ATAAAAATTA
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
8 7 0.12
9 31 0.53
10 20 0.34
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:38405149 original size:19 final size:19
Alignment explanation
Indices: 38405134--38405206 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
38405124 TGTAAAAATT
*
38405134 TTAAAATTTTTGAAAATCA
1 TTAAAATTTTTAAAAATCA
* *
38405153 TTAAAATTTTTTAAAATGA
1 TTAAAATTTTTAAAAATCA
* *
38405172 TTAAAA-TTATAAAAATTA
1 TTAAAATTTTTAAAAATCA
38405190 -TAAGAATTTTTTAAAAA
1 TTAA-AA-TTTTTAAAAA
38405207 ATTATTATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
17 3 0.07
18 11 0.24
19 23 0.51
20 8 0.18
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (19 bp):
TTAAAATTTTTAAAAATCA
Found at i:38405186 original size:9 final size:9
Alignment explanation
Indices: 38405114--38405197 Score: 51
Period size: 9 Copynumber: 9.2 Consensus size: 9
38405104 TATTAAAATG
38405114 TTATAAAAA
1 TTATAAAAA
*
38405123 TTGTAAAAA
1 TTATAAAAA
* *
38405132 TTTTAAAAT
1 TTATAAAAA
* *
38405141 TTTTGAAAA
1 TTATAAAAA
* *
38405150 TCATTAAAAT
1 TTA-TAAAAA
* *
38405160 TTTTTAAAA
1 TTATAAAAA
* *
38405169 TGATTAAAA
1 TTATAAAAA
38405178 TTATAAAAA
1 TTATAAAAA
*
38405187 TTATAAGAA
1 TTATAAAAA
38405196 TT
1 TT
38405198 TTTTAAAAAA
Statistics
Matches: 56, Mismatches: 18, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
9 51 0.91
10 5 0.09
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (9 bp):
TTATAAAAA
Found at i:38405463 original size:23 final size:23
Alignment explanation
Indices: 38405416--38405464 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
38405406 TTTTATAATT
**
38405416 TTTAAAATTCTTATTTTTTTTAA
1 TTTAAAATTCTTATTTTTTAAAA
38405439 TTTAAAATT-TTATTTTTTCAAAA
1 TTTAAAATTCTTATTTTTT-AAAA
38405462 TTT
1 TTT
38405465 TCTTATCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTAAAATTCTTATTTTTTAAAA
Found at i:38405546 original size:11 final size:11
Alignment explanation
Indices: 38405530--38405599 Score: 62
Period size: 11 Copynumber: 6.7 Consensus size: 11
38405520 ACTTCTTAAT
38405530 ATTTTTAAATA
1 ATTTTTAAATA
38405541 ATTTTT--AT-
1 ATTTTTAAATA
38405549 ATTTTTAAATA
1 ATTTTTAAATA
38405560 ATTTTT-AA-A
1 ATTTTTAAATA
*
38405569 ATTTGGTAAATA
1 ATTT-TTAAATA
*
38405581 ATATTTT-TATA
1 AT-TTTTAAATA
38405592 ATTTTTAA
1 ATTTTTAA
38405600 TATTTTTGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
8 6 0.13
9 7 0.15
10 9 0.19
11 19 0.40
12 4 0.09
13 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAAATA
Found at i:38405550 original size:19 final size:19
Alignment explanation
Indices: 38405528--38405599 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 19
38405518 CAACTTCTTA
38405528 ATATTTTTAAATAATTTTT
1 ATATTTTTAAATAATTTTT
38405547 ATATTTTTAAATAATTTTT
1 ATATTTTTAAATAATTTTT
* *
38405566 AAAATTTGGTAAATAATATTTTT
1 -ATATTT-TTAAAT-A-ATTTTT
38405589 ATAATTTTTAA
1 AT-ATTTTTAA
38405600 TATTTTTGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 19 0.43
20 5 0.11
21 5 0.11
22 5 0.11
23 10 0.23
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
ATATTTTTAAATAATTTTT
Found at i:38405604 original size:9 final size:9
Alignment explanation
Indices: 38405525--38405606 Score: 51
Period size: 9 Copynumber: 8.2 Consensus size: 9
38405515 GTACAACTTC
38405525 TTAATATTT
1 TTAATATTT
38405534 TTAAATAATTT
1 TT-AAT-ATTT
38405545 TT-ATATTT
1 TTAATATTT
38405553 TTAAATAATTT
1 TT-AAT-ATTT
*
38405564 TTAAAATTT
1 TTAATATTT
38405573 GGTAAATAATATTT
1 --T---TAATATTT
38405587 TT-ATAATTT
1 TTAAT-ATTT
38405596 TTAATATTT
1 TTAATATTT
38405605 TT
1 TT
38405607 GGACCAATCA
Statistics
Matches: 59, Mismatches: 2, Indels: 24
0.69 0.02 0.28
Matches are distributed among these distances:
8 8 0.14
9 21 0.36
10 9 0.15
11 13 0.22
12 1 0.02
14 7 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (9 bp):
TTAATATTT
Found at i:38408498 original size:20 final size:20
Alignment explanation
Indices: 38408462--38408499 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38408452 TTTGTAACTT
*
38408462 AAAATTTATTTATTAAAAGA
1 AAAATTTATATATTAAAAGA
38408482 AAAATTT-TATATATAAAA
1 AAAATTTATATAT-TAAAA
38408500 TATTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
AAAATTTATATATTAAAAGA
Found at i:38409367 original size:18 final size:18
Alignment explanation
Indices: 38409344--38409380 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
38409334 ATGGTGAGAA
38409344 TACCTTTTTGACTCTTTG
1 TACCTTTTTGACTCTTTG
38409362 TACCTTTTTGACTCTTTG
1 TACCTTTTTGACTCTTTG
38409380 T
1 T
38409381 TTTCGGTCGT
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:0.11, C:0.22, G:0.11, T:0.57
Consensus pattern (18 bp):
TACCTTTTTGACTCTTTG
Found at i:38410635 original size:41 final size:42
Alignment explanation
Indices: 38410589--38410667 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
38410579 CACTTTGATA
*
38410589 TGATATTTGCATAT-GTGTACGTTATAAG-CAAAATTCTATTT
1 TGATATTTGCAT-TCGCGTACGTTATAAGTCAAAATTCTATTT
* *
38410630 TGATATTTGCATTCGCGTATGTTATAAGTTAAAATTCT
1 TGATATTTGCATTCGCGTACGTTATAAGTCAAAATTCT
38410668 GTATATAGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 1 0.03
41 24 0.73
42 8 0.24
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (42 bp):
TGATATTTGCATTCGCGTACGTTATAAGTCAAAATTCTATTT
Found at i:38412012 original size:20 final size:18
Alignment explanation
Indices: 38411974--38412025 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
38411964 TCTCGCTTAA
*
38411974 ATTGTTTTATATAAGATT
1 ATTGTTTTATATAAAATT
38411992 ATTGTTTTATTTATAAAATT
1 ATTGTTTTA--TATAAAATT
*
38412012 ATTATTTTA-ATAAA
1 ATTGTTTTATATAAA
38412026 TAAATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 5 0.17
18 9 0.30
20 16 0.53
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTGTTTTATATAAAATT
Found at i:38423517 original size:19 final size:19
Alignment explanation
Indices: 38423493--38423536 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
38423483 GTCCAATATC
38423493 TAAAATCAAAA-TACAAAAA
1 TAAAAT-AAAATTACAAAAA
*
38423512 TAAAATAAAATTATAAAAA
1 TAAAATAAAATTACAAAAA
38423531 TAAAAT
1 TAAAAT
38423537 TTAAGCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAAATAAAATTACAAAAA
Found at i:38429494 original size:50 final size:51
Alignment explanation
Indices: 38429403--38429502 Score: 123
Period size: 50 Copynumber: 2.0 Consensus size: 51
38429393 ATTCCATGGC
*
38429403 ACCATATCGTGTAAAGACCATATCTAGTGGGCTATGACATCATATCGAAAT
1 ACCATATCGTATAAAGACCATATCTAGTGGGCTATGACATCATATCGAAAT
* * * * *
38429454 ACCATATCGTAT-AAGATCATAAT-TGGTGGGTTATGGCATCATATGGAAA
1 ACCATATCGTATAAAGACCAT-ATCTAGTGGGCTATGACATCATATCGAAA
38429503 GAACTGAAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 29 0.69
51 13 0.31
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (51 bp):
ACCATATCGTATAAAGACCATATCTAGTGGGCTATGACATCATATCGAAAT
Found at i:38429635 original size:27 final size:28
Alignment explanation
Indices: 38429594--38429655 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
38429584 CACACCAGAA
* *
38429594 AAATGGAAGCTTTTGTGGTAATCTAT-G
1 AAATGGAAGCCTTTGTGGCAATCTATGG
*
38429621 AAATGGAAGCCTTTGTGGCGATCTATGG
1 AAATGGAAGCCTTTGTGGCAATCTATGG
38429649 AAA-GGAA
1 AAATGGAA
38429656 CTCCTTCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (28 bp):
AAATGGAAGCCTTTGTGGCAATCTATGG
Found at i:38429784 original size:27 final size:27
Alignment explanation
Indices: 38429754--38429821 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
38429744 AAATATGACA
* * *
38429754 AACTTTGAAGGAATAGTACATATGGCG
1 AACTCTGAAGAAAAAGTACATATGGCG
* *
38429781 AACTCTGAAGAAAAAGTGCGTATGGCG
1 AACTCTGAAGAAAAAGTACATATGGCG
*
38429808 AACACTGAGAGAAA
1 AACTCTGA-AGAAA
38429822 TAGTTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.19
Consensus pattern (27 bp):
AACTCTGAAGAAAAAGTACATATGGCG
Done.