Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold232
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: 2516017
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.33
Warning! 28201 characters in sequence are not A, C, G, or T
File 4 of 16
Found at i:470483 original size:47 final size:47
Alignment explanation
Indices: 470432--470692 Score: 240
Period size: 47 Copynumber: 5.6 Consensus size: 47
470422 CAATATAATT
* * * *
470432 AAACGAGGGTAAAAAGAGTTTAACCAAGTACTAACGCTAATACAGTC
1 AAACAAGGGTAAAAAGAGTTTGACCAAGTCCTAACGCCAATACAGTC
* ** *
470479 AAACGAGGGTGGAAAGAGTTTGACCAACTCCTAACGCCAATACAGTC
1 AAACAAGGGTAAAAAGAGTTTGACCAAGTCCTAACGCCAATACAGTC
* * * *
470526 AAACAAAGGTAAAAATAGTTTGACCATGTCCTAACGCCAATACAATC
1 AAACAAGGGTAAAAAGAGTTTGACCAAGTCCTAACGCCAATACAGTC
* *
470573 AAACAAGGGTAAAAAGAGTTTGACCAGATGT--TAACACCAATACAGTT
1 AAACAAGGGTAAAAAGAGTTTGACCA-A-GTCCTAACGCCAATACAGTC
* * ** * * * *
470620 AGACAACGGTGGAAAGAGTTTGACTAGGTCCTAATGCTAATGA-AGTC
1 AAACAAGGGTAAAAAGAGTTTGACCAAGTCCTAACGCCAAT-ACAGTC
* ** *
470667 AAACGATAGTAAAAAAAGTTTGACCA
1 AAACAAGGGTAAAAAGAGTTTGACCA
470693 TATACAGTCA
Statistics
Matches: 171, Mismatches: 38, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
45 2 0.01
47 166 0.97
48 1 0.01
49 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (47 bp):
AAACAAGGGTAAAAAGAGTTTGACCAAGTCCTAACGCCAATACAGTC
Found at i:470669 original size:94 final size:94
Alignment explanation
Indices: 470439--470692 Score: 269
Period size: 94 Copynumber: 2.7 Consensus size: 94
470429 ATTAAACGAG
* * **
470439 GGTAAAAAGAGTTTAACCAAGTACTAACGCTAATACAGTCAAACGAGGGTGGAAAGAGTTTGACC
1 GGTAAAAAGAGTTTGACCAAGTCCTAACGCTAATACAGTCAAACGAGGGTAAAAAGAGTTTGACC
*
470504 AACTCCTAACGCCAATACAGTCAAACAAA
66 AACTCCTAACACCAATACAGTCAAACAAA
* * * * *
470533 GGTAAAAATAGTTTGACCATGTCCTAACGCCAATACAATCAAACAAGGGTAAAAAGAGTTTGACC
1 GGTAAAAAGAGTTTGACCAAGTCCTAACGCTAATACAGTCAAACGAGGGTAAAAAGAGTTTGACC
** * * *
470598 AGA-TGTTAACACCAATACAGTTAGACAAC
66 A-ACTCCTAACACCAATACAGTCAAACAAA
** * * * ** *
470627 GGTGGAAAGAGTTTGACTAGGTCCTAATGCTAATGA-AGTCAAACGATAGTAAAAAAAGTTTGAC
1 GGTAAAAAGAGTTTGACCAAGTCCTAACGCTAAT-ACAGTCAAACGAGGGTAAAAAGAGTTTGAC
470691 CA
65 CA
470693 TATACAGTCA
Statistics
Matches: 131, Mismatches: 27, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
94 129 0.98
95 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.21
Consensus pattern (94 bp):
GGTAAAAAGAGTTTGACCAAGTCCTAACGCTAATACAGTCAAACGAGGGTAAAAAGAGTTTGACC
AACTCCTAACACCAATACAGTCAAACAAA
Found at i:470679 original size:141 final size:140
Alignment explanation
Indices: 470415--470693 Score: 330
Period size: 141 Copynumber: 2.0 Consensus size: 140
470405 GTTTGAAGGA
* * * * * *
470415 CTAATGCCAATATAATTAAACGAGGGTAAAAAGAGTTTAACCAAGTACTAACGCTAATACAGTCA
1 CTAACGCCAATACAATCAAACAAGGGTAAAAAGAGTTTAACCAAGTA-TAACACCAATACAGTCA
* * *
470480 AACGAGGGTGGAAAGAGTTTGACCAACTCCTAACGCCAATACAGTCAAACAAAGGTAAAAATAGT
65 AACAACGGTGGAAAGAGTTTGACCAACTCCTAACGCCAATACAGTCAAACAAAGGTAAAAAAAGT
470545 TTGACCATGTC
130 TTGACCATGTC
* *
470556 CTAACGCCAATACAATCAAACAAGGGTAAAAAGAGTTTGACCAGATGT-TAACACCAATACAGTT
1 CTAACGCCAATACAATCAAACAAGGGTAAAAAGAGTTTAACCA-A-GTATAACACCAATACAGTC
* * ** * * *
470620 AGACAACGGTGGAAAGAGTTTGACTAGGTCCTAATGCTAATGA-AGTCAAACGATA-GTAAAAAA
64 AAACAACGGTGGAAAGAGTTTGACCAACTCCTAACGCCAAT-ACAGTCAAAC-AAAGGTAAAAAA
470683 AGTTTGACCAT
127 AGTTTGACCAT
470694 ATACAGTCAA
Statistics
Matches: 116, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
141 110 0.95
142 4 0.03
143 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.22
Consensus pattern (140 bp):
CTAACGCCAATACAATCAAACAAGGGTAAAAAGAGTTTAACCAAGTATAACACCAATACAGTCAA
ACAACGGTGGAAAGAGTTTGACCAACTCCTAACGCCAATACAGTCAAACAAAGGTAAAAAAAGTT
TGACCATGTC
Found at i:470722 original size:35 final size:35
Alignment explanation
Indices: 470663--470774 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 35
470653 ATGCTAATGA
* ** * *
470663 AGTCAAACGATAGTAAAAAAAGTTTGACCATATAC
1 AGTCAAACGATAATGGAAAGAGTTTGACCAGATAC
*
470698 AGTCAAACGATAATGGAAAGAGTTTAACCAGATAC
1 AGTCAAACGATAATGGAAAGAGTTTGACCAGATAC
* * * *
470733 ATTCAAATGATGATGGAAAGATTTTGACCAGATAC
1 AGTCAAACGATAATGGAAAGAGTTTGACCAGATAC
*
470768 TGTCAAA
1 AGTCAAA
470775 TAAGGATGAA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (35 bp):
AGTCAAACGATAATGGAAAGAGTTTGACCAGATAC
Found at i:470775 original size:35 final size:35
Alignment explanation
Indices: 470683--470794 Score: 127
Period size: 35 Copynumber: 3.2 Consensus size: 35
470673 TAGTAAAAAA
* * * *
470683 AGTTTGACCATATACAGTCAAACGATAATGGAAAG
1 AGTTTGACCAGATACTGTCAAATGATGATGGAAAG
*
470718 AGTTTAACCAGATACAT-TCAAATGATGATGGAAAG
1 AGTTTGACCAGATAC-TGTCAAATGATGATGGAAAG
* * * *
470753 ATTTTGACCAGATACTGTCAAATAAGGATGAAAAG
1 AGTTTGACCAGATACTGTCAAATGATGATGGAAAG
470788 AGTTTGA
1 AGTTTGA
470795 TGAAGAGCGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.02
35 63 0.98
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.26
Consensus pattern (35 bp):
AGTTTGACCAGATACTGTCAAATGATGATGGAAAG
Found at i:472145 original size:19 final size:18
Alignment explanation
Indices: 472064--472141 Score: 77
Period size: 18 Copynumber: 4.2 Consensus size: 18
472054 TTTTCATGAT
*
472064 TTTTCATTCTTTTTTTTGC
1 TTTTC-TTCTTTTTTTTTC
* **
472083 TTGT-TTCTATTTTCATTC
1 TTTTCTTCT-TTTTTTTTC
*
472101 CTTTCATTCTTTTTTTTTC
1 TTTTC-TTCTTTTTTTTTC
472120 TTTTCTTCTTTTTTTTTC
1 TTTTCTTCTTTTTTTTTC
472138 TTTT
1 TTTT
472142 TCTTTTCACA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
17 4 0.09
18 25 0.53
19 14 0.30
20 4 0.09
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTCTTCTTTTTTTTTC
Found at i:478183 original size:155 final size:153
Alignment explanation
Indices: 477815--478185 Score: 429
Period size: 155 Copynumber: 2.4 Consensus size: 153
477805 CTCGATTCTG
* * * *
477815 AAATTACAAAAATAGCCTTAGGGGATACCTTTGACATAGAAGTACTCGGCACCTTTAAAGGACTC
1 AAATTACGAAAATA-CCTTAGGGGATACCTTTGACTTAGAAGTACTC-GCACCTCTAAAAGACTC
* * *
477880 AAAAAGGTAAAAAGATGGGATGAACCTATCCTTAATACCCACCTTCAACATAAAAGCAGACTCGA
64 AAAAAGGTAAAAAGATGGGATGAACCCATCCTAAATACCCACCTTCAACATAAAAGCAAACTCGA
* *
477945 TGACAACTTAGGACTCGATTATAAA
129 TGACAACCTAAGACTCGATTATAAA
* * * * * * * * *
477970 AAATTATGAAAATACCCCTAGGGGATACTTTTGACTTAAAAATGCTCGATACCCCTAAAAGACTT
1 AAATTACGAAAATA-CCTTAGGGGATACCTTTGACTTAGAAGTACTCG-CACCTCTAAAAGACTC
* * * *
478035 AAAAAGG-ATTATAGATGGGATGAACCCATCCTAAATGCCCACTTTCAACATAAAAGCAAACTCG
64 AAAAAGGTA-AAAAGATGGGATGAACCCATCCTAAATACCCACCTTCAACATAAAAGCAAACTCG
* *
478099 GTGACAACCTAAGACTCGATTTTAAA
128 ATGACAACCTAAGACTCGATTATAAA
* **
478125 AAATTACGAAAATACCTTTAGAGGATACCTTCAACTTAGAAGTACTCAGCACCTCTAAAAG
1 AAATTACGAAAATACC-TTAGGGGATACCTTTGACTTAGAAGTACTC-GCACCTCTAAAAG
478186 GGCTCGAAAA
Statistics
Matches: 176, Mismatches: 36, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
154 4 0.02
155 171 0.97
156 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.24
Consensus pattern (153 bp):
AAATTACGAAAATACCTTAGGGGATACCTTTGACTTAGAAGTACTCGCACCTCTAAAAGACTCAA
AAAGGTAAAAAGATGGGATGAACCCATCCTAAATACCCACCTTCAACATAAAAGCAAACTCGATG
ACAACCTAAGACTCGATTATAAA
Found at i:478643 original size:138 final size:139
Alignment explanation
Indices: 478381--478643 Score: 354
Period size: 138 Copynumber: 1.9 Consensus size: 139
478371 AAACCTTAGG
* * * *
478381 AATATTAAAAATATTGAAAAATTAAGACAATAATTTTTGTTTAATTTTTATTTTAAAAAATTTAT
1 AATATTAAAAATATGGAAAAATTAAGAAAATAATTTTTGTTTAATTTTTATATTAAAAAAATTAT
* * *
478446 TTCATACTTTAATAGAGAACTGAAAAGATACAAAAAGTTTTGAAAATTTTCATACCCCTATAGAT
66 TTCATACCTTAATAGAGAACTGAAAAGACACAAAAAGTGTTGAAAATTTTCATACCCCTATAGAT
478511 ACCCATGAA
131 ACCCATGAA
* * *
478520 AATATTAGAAATATGGAGAAATTAAGAAAATAATTTTTTTTTAATTTTTA-ATTAAAAAAATTAT
1 AATATTAAAAATATGGAAAAATTAAGAAAATAATTTTTGTTTAATTTTTATATTAAAAAAATTAT
** *
478584 TTCATACCTTAAT-GAAGAA-TCGAAAAGACAGGAAAAGTGTTGAAGA-TTTCTATACCCCTA
66 TTCATACCTTAATAG-AGAACT-GAAAAGACACAAAAAGTGTTGAAAATTTTC-ATACCCCTA
478644 CGGATAAACA
Statistics
Matches: 108, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
137 6 0.06
138 57 0.53
139 45 0.42
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (139 bp):
AATATTAAAAATATGGAAAAATTAAGAAAATAATTTTTGTTTAATTTTTATATTAAAAAAATTAT
TTCATACCTTAATAGAGAACTGAAAAGACACAAAAAGTGTTGAAAATTTTCATACCCCTATAGAT
ACCCATGAA
Found at i:478667 original size:138 final size:138
Alignment explanation
Indices: 478314--478671 Score: 393
Period size: 139 Copynumber: 2.6 Consensus size: 138
478304 CATTTTGTAT
* * * * * *
478314 CTTAATGGAGAAGCGAAAAGATACAAAAAGTTTTGAAGATTGCTATAACTCTACCGA-AAACCTT
1 CTTAATGAAGAA-CGAAAAGATACAAAAAGTTTTGAAGATTTCTATACCCCTACAGATAAA-CAT
* * * * * *
478378 AGGAATATTAAAAATATTGAAAAATTAAGACAATAATTTTTGTTTAATTTTTATTTTAAAAAATT
64 AAGAATATTAGAAATATGGAAAAATTAAGAAAATAATTTTTGTTTAATTTTTATATTAAAAAAAT
478443 TATTTCATAC
129 TATTTCATAC
* * * **
478453 TTTAAT-AGAGAACTGAAAAGATACAAAAAGTTTTGAAAATTT-TCATACCCCTATAGATACCCA
1 CTTAATGA-AGAAC-GAAAAGATACAAAAAGTTTTGAAGATTTCT-ATACCCCTACAGATAAACA
* *
478516 TGAA-AATATTAGAAATATGGAGAAATTAAGAAAATAATTTTTTTTTAATTTTTA-ATTAAAAAA
63 T-AAGAATATTAGAAATATGGAAAAATTAAGAAAATAATTTTTGTTTAATTTTTATATTAAAAAA
478579 ATTATTTCATAC
127 ATTATTTCATAC
* ** * *
478591 CTTAATGAAGAATCGAAAAGACAGGAAAAGTGTTGAAGATTTCTATACCCCTACGGATAAACATA
1 CTTAATGAAGAA-CGAAAAGATACAAAAAGTTTTGAAGATTTCTATACCCCTACAGATAAACATA
*
478656 AGAATAATAGAAATAT
65 AGAATATTAGAAATAT
478672 ATAAAAATGA
Statistics
Matches: 180, Mismatches: 30, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
137 2 0.01
138 82 0.46
139 94 0.52
140 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.33
Consensus pattern (138 bp):
CTTAATGAAGAACGAAAAGATACAAAAAGTTTTGAAGATTTCTATACCCCTACAGATAAACATAA
GAATATTAGAAATATGGAAAAATTAAGAAAATAATTTTTGTTTAATTTTTATATTAAAAAAATTA
TTTCATAC
Found at i:479762 original size:21 final size:20
Alignment explanation
Indices: 479718--479762 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
479708 CCATTTAAAA
*
479718 TTTCATGTCCTTTTGTTTTT
1 TTTCATGTCCTTTTGTTATT
479738 TTTCATGTCATCTTTT-TTATT
1 TTTCATGTC--CTTTTGTTATT
479759 TTTC
1 TTTC
479763 CAAGCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 8 0.36
22 5 0.23
ACGTcount: A:0.09, C:0.16, G:0.07, T:0.69
Consensus pattern (20 bp):
TTTCATGTCCTTTTGTTATT
Found at i:480562 original size:33 final size:33
Alignment explanation
Indices: 480520--480582 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
480510 TCATTGTTTG
*
480520 TATCGATACATGGT-ACATTGTATCGATACAATA
1 TATCGATACATGATGA-ATTGTATCGATACAATA
480553 TATCGATACATGATGAATTGTATCGATACA
1 TATCGATACATGATGAATTGTATCGATACA
480583 TTGCTTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (33 bp):
TATCGATACATGATGAATTGTATCGATACAATA
Found at i:484673 original size:15 final size:16
Alignment explanation
Indices: 484647--484676 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
484637 GATGAAAGTA
484647 TCCAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
484663 TCCAAAA-GAAGAAG
1 TCCAAAATGAAGAAG
484677 TTGATGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.17, G:0.20, T:0.10
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:486775 original size:13 final size:13
Alignment explanation
Indices: 486757--486783 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
486747 ATAATATTCC
486757 TTGTATCGATACA
1 TTGTATCGATACA
486770 TTGTATCGATACA
1 TTGTATCGATACA
486783 T
1 T
486784 AGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:489156 original size:20 final size:20
Alignment explanation
Indices: 489114--489170 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
489104 CACACCCAGA
*
489114 TGTATCGATACA-TGTTCAT
1 TGTATCGATACATTGTACAT
489133 TGTATCGATACATTG-ACAAT
1 TGTATCGATACATTGTAC-AT
*
489153 TGTATCGACACATTGTAC
1 TGTATCGATACATTGTAC
489171 CGATACATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
20 18 0.55
21 2 0.06
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTGTACAT
Found at i:498233 original size:20 final size:20
Alignment explanation
Indices: 498188--498263 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 20
498178 GACATGGTTT
* **
498188 TGTATCGATACATTTAAGACA
1 TGTATCGATACATTCACCA-A
* **
498209 TGTATCAATACATTCATTAA
1 TGTATCGATACATTCACCAA
498229 TGTATCGATACATTCACCAA
1 TGTATCGATACATTCACCAA
498249 TTGTATCGATACATT
1 -TGTATCGATACATT
498264 TTGTCAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 18 0.38
21 29 0.62
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTCACCAA
Found at i:498698 original size:20 final size:17
Alignment explanation
Indices: 498659--498709 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
498649 CAAAATAGAA
*
498659 AAAATTATAAAAAATTT
1 AAAATTTTAAAAAATTT
*
498676 AAATTTTTGAAAAAATTCAT
1 AAAATTTT-AAAAAATT--T
498696 AAAATTTTAAAAAA
1 AAAATTTTAAAAAA
498710 GTAATAGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.21
18 8 0.29
19 6 0.21
20 8 0.29
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAATTTTAAAAAATTT
Found at i:498775 original size:24 final size:24
Alignment explanation
Indices: 498717--498766 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
498707 AAAGTAATAG
* *
498717 AAGTAAAATAT-AGCTTTTTTAAAA
1 AAGTAAAAAATGA-CTTTTTCAAAA
498741 AAGTAAAAAATGACTTTTTCAAAA
1 AAGTAAAAAATGACTTTTTCAAAA
498765 AA
1 AA
498767 TATGAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (24 bp):
AAGTAAAAAATGACTTTTTCAAAA
Found at i:498920 original size:16 final size:18
Alignment explanation
Indices: 498899--498935 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
498889 CTCACATATT
498899 TCTTTC-CCT-TTCTTTC
1 TCTTTCTCCTCTTCTTTC
*
498915 TCTTTCTCCTCTTTTTTC
1 TCTTTCTCCTCTTCTTTC
498933 TCT
1 TCT
498936 CTCCTGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 3 0.17
18 9 0.50
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (18 bp):
TCTTTCTCCTCTTCTTTC
Found at i:499116 original size:16 final size:15
Alignment explanation
Indices: 499091--499120 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
499081 TTCTTTCTAG
499091 ATTTATTTTTTTAAT
1 ATTTATTTTTTTAAT
499106 ATTTAATTTTTTTAA
1 ATTT-ATTTTTTTAA
499121 AAGATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTATTTTTTTAAT
Found at i:499274 original size:64 final size:64
Alignment explanation
Indices: 499145--499274 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 64
499135 ATATTTTTAG
* * **
499145 TTTTTTAAATTTTAATTTTTTTATATTTTTTATTATTGTATTCATTTTAAAAATTTTAAGATTT
1 TTTTTTAAATTTTAATCTTTTTATATTTTTTAATATTGTATGAATTTTAAAAATTTTAAGATTT
* * * *
499209 TTTTTTCAATTTTAAGTACTTTTTAT-TTTTTTAATATT-TA-GAATTTTAATATTTTTATGATT
1 TTTTTTAAATTTTAA-T-CTTTTTATATTTTTTAATATTGTATGAATTTTAAAAATTTTAAGATT
499271 T
64 T
499272 TTT
1 TTT
499275 GAATTTTTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
63 21 0.38
64 16 0.29
65 12 0.21
66 7 0.12
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (64 bp):
TTTTTTAAATTTTAATCTTTTTATATTTTTTAATATTGTATGAATTTTAAAAATTTTAAGATTT
Found at i:500391 original size:26 final size:29
Alignment explanation
Indices: 500339--500392 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 29
500329 TCTCTTACTT
*
500339 TTTAAGATAATTATAAAATATTTTTATTA
1 TTTAAGATAATTATAAAATATTATTATTA
500368 TTTAA-ATAATTA-AAAAT-TTATTATT
1 TTTAAGATAATTATAAAATATTATTATT
500393 TCACTTACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 5 0.21
28 7 0.29
29 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTAAGATAATTATAAAATATTATTATTA
Found at i:501514 original size:19 final size:19
Alignment explanation
Indices: 501446--501535 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
501436 TACCAGTCTT
* *
501446 ATGTATC-AAACAATTGAGT
1 ATGTATCGATACAA-TGAGC
501465 ATGTATCGATACAATGAGC
1 ATGTATCGATACAATGAGC
*
501484 ATGTATCAATACAATGAGC
1 ATGTATCGATACAATGAGC
* **
501503 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAATG-AGC
501523 ATGTATCGATACA
1 ATGTATCGATACA
501536 TCTGGATATG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
19 43 0.69
20 19 0.31
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (19 bp):
ATGTATCGATACAATGAGC
Found at i:503053 original size:15 final size:15
Alignment explanation
Indices: 503033--503065 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
503023 CAATAATCGA
*
503033 AGTTACTGATGATGG
1 AGTTACTGATAATGG
503048 AGTTACTGATAATGG
1 AGTTACTGATAATGG
503063 AGT
1 AGT
503066 ATTAGGTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (15 bp):
AGTTACTGATAATGG
Found at i:509867 original size:23 final size:23
Alignment explanation
Indices: 509837--509883 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
509827 CAAGGCTTAG
509837 ATAAGAATCTCACAATCTCTTTA
1 ATAAGAATCTCACAATCTCTTTA
509860 ATAAGAATCTCACAATCTCTTTA
1 ATAAGAATCTCACAATCTCTTTA
509883 A
1 A
509884 GAATTATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.34
Consensus pattern (23 bp):
ATAAGAATCTCACAATCTCTTTA
Found at i:510428 original size:20 final size:18
Alignment explanation
Indices: 510403--510451 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
510393 CAGTCTCATG
*
510403 TATCGATACAATTGAGTATA
1 TATCGATACAA-TGAGCA-A
*
510423 TATCGATACAATGAGCAG
1 TATCGATACAATGAGCAA
510441 TATCGATACAA
1 TATCGATACAA
510452 AGCATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 11 0.41
19 5 0.19
20 11 0.41
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (18 bp):
TATCGATACAATGAGCAA
Found at i:510446 original size:18 final size:20
Alignment explanation
Indices: 510399--510451 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
510389 CTACCAGTCT
510399 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
* *
510419 TATATATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
510438 CA-GTATCGATACAA
1 CATGTATCGATACAA
510452 AGCATAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 11 0.38
19 5 0.17
20 13 0.45
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:523678 original size:20 final size:20
Alignment explanation
Indices: 523653--523696 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
523643 TCAATATATC
523653 GATACAAATACTGAATGTAT-
1 GATACAAA-ACTGAATGTATA
* *
523673 GATACATAAGTGAATGTATA
1 GATACAAAACTGAATGTATA
523693 GATA
1 GATA
523697 TATGTCTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (20 bp):
GATACAAAACTGAATGTATA
Found at i:523835 original size:50 final size:52
Alignment explanation
Indices: 523781--523890 Score: 152
Period size: 52 Copynumber: 2.2 Consensus size: 52
523771 ACAAATAATG
* *
523781 TATCGATATATTCT-GG-GTTTAACCTAAATGTATCGATACATTATTCATTA
1 TATCGATATATTCTAGGTGTTTAACCTAAATATATCGATACATTATTCAATA
* * * *
523831 TATCGATATATTCTAGGTTTTTGACCTAAATATATTGATACATTCTTCAATA
1 TATCGATATATTCTAGGTGTTTAACCTAAATATATCGATACATTATTCAATA
523883 TATCGATA
1 TATCGATA
523891 CATGCAGATA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 14 0.27
51 2 0.04
52 36 0.69
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (52 bp):
TATCGATATATTCTAGGTGTTTAACCTAAATATATCGATACATTATTCAATA
Found at i:525744 original size:20 final size:20
Alignment explanation
Indices: 525702--525755 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
525692 TTTTACCCAG
* *
525702 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATATATCA
*
525722 ATGTATCGATACATATATGA
1 ATGTATCGATACATATATCA
* *
525742 ATGCATTGATACAT
1 ATGTATCGATACAT
525756 TCTATCTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATATATCA
Found at i:525751 original size:72 final size:71
Alignment explanation
Indices: 525621--525787 Score: 264
Period size: 71 Copynumber: 2.4 Consensus size: 71
525611 AAAGTCACAG
* * *
525621 TTTTACCCAGATGTATTGATACA-TTTTCAATGTATCGATACATGGATAAATGTATTGATACATT
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATAGATAAATGCATTGATACATT
*
525685 CTGTCTT
66 CTATC-T
* *
525692 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATATATGAATGCATTGATACATT
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATAGATAAATGCATTGATACATT
525757 CTATCT
66 CTATCT
525763 TTTTACCCAGATGTATCGATACATT
1 TTTTACCCAGATGTATCGATACATT
525788 GAATAATGTA
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
71 48 0.54
72 41 0.46
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (71 bp):
TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATAGATAAATGCATTGATACATT
CTATCT
Found at i:531709 original size:15 final size:15
Alignment explanation
Indices: 531689--531723 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
531679 AGAAAAAAGT
531689 TATTCATGGCTACTC
1 TATTCATGGCTACTC
*
531704 TATTCATGGCTACTT
1 TATTCATGGCTACTC
531719 TATTC
1 TATTC
531724 TTCTTCATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.46
Consensus pattern (15 bp):
TATTCATGGCTACTC
Found at i:531980 original size:15 final size:16
Alignment explanation
Indices: 531971--532000 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
531961 AATTTTAAAT
531971 TCATAAATTTAAAAAA
1 TCATAAATTTAAAAAA
531987 TCATAAA-TTAAAAA
1 TCATAAATTTAAAAA
532001 TATAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
TCATAAATTTAAAAAA
Found at i:532722 original size:2 final size:2
Alignment explanation
Indices: 532715--532742 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
532705 TAATATAAGC
532715 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
532743 CAATAAAAAA
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:533132 original size:96 final size:96
Alignment explanation
Indices: 532968--533160 Score: 262
Period size: 96 Copynumber: 2.0 Consensus size: 96
532958 CAAAGTTTGG
* * *
532968 ACCTTTATATCTTAGCACTAACGTTAAACCCGCAAAAAAAAAAAGTGGATGACAAGGCAAATATT
1 ACCTTTATATCTTAGCACAAACGTTAAACCCACAAAAAAAAAAAGTGGATGACAAGGCAAATAAT
* *
533033 GTACCAATCCTTTGCACGATCCGTCGACAAC
66 GTACCAATCCCTTGCACGATCCATCGACAAC
* * * * * *
533064 ACCTTTATATCTTAGCACAAATGTTAAATCTAC-AAAAGAAATAGTGGATGACAAGGGCACATAA
1 ACCTTTATATCTTAGCACAAACGTTAAACCCACAAAAAAAAAAAGTGGATGACAA-GGCAAATAA
*
533128 TGTACCAATCCCTTGTACGATCCATCGACAAC
65 TGTACCAATCCCTTGCACGATCCATCGACAAC
533160 A
1 A
533161 AAAAATGGCC
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 19 0.23
96 65 0.77
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.24
Consensus pattern (96 bp):
ACCTTTATATCTTAGCACAAACGTTAAACCCACAAAAAAAAAAAGTGGATGACAAGGCAAATAAT
GTACCAATCCCTTGCACGATCCATCGACAAC
Found at i:533702 original size:28 final size:28
Alignment explanation
Indices: 533661--533723 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
533651 ATCACCACAA
533661 TATTCATAAACTGATATCTTTTAATCACT
1 TATT-ATAAACTGATATCTTTTAATCACT
533690 TATTATAAACTGATATCTTTTAATCACT
1 TATTATAAACTGATATCTTTTAATCACT
533718 TATTAT
1 TATTAT
533724 CCTAAATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 30 0.88
29 4 0.12
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.48
Consensus pattern (28 bp):
TATTATAAACTGATATCTTTTAATCACT
Found at i:534518 original size:17 final size:17
Alignment explanation
Indices: 534496--534529 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
534486 GAGTTCTTTG
534496 TTTTTTAAAAAATGACA
1 TTTTTTAAAAAATGACA
534513 TTTTTTAAAAAATGACA
1 TTTTTTAAAAAATGACA
534530 ATATTTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
TTTTTTAAAAAATGACA
Found at i:534536 original size:17 final size:17
Alignment explanation
Indices: 534499--534536 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
534489 TTCTTTGTTT
* *
534499 TTTAAAAAATGACATTT
1 TTTAAAAAATGACAATA
534516 TTTAAAAAATGACAATA
1 TTTAAAAAATGACAATA
534533 TTTA
1 TTTA
534537 GAAAGGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (17 bp):
TTTAAAAAATGACAATA
Found at i:538398 original size:62 final size:61
Alignment explanation
Indices: 538288--538467 Score: 161
Period size: 61 Copynumber: 3.0 Consensus size: 61
538278 AAATAGGTTA
* * * ** *
538288 AACTTAAAAA-AAAGA-CCT--CGACTAACTCAAGGTTTAACCTATATCTTGAAAACAAGTTC
1 AACTTAAAAAGAAAGACCCTGAC-ACAAACTCGAGGCTTAACCTATCCCTTGAAAA-AAGGTC
* * *
538347 AATTTAAAAAGAAAGACCCTGACACAAACTCGAGGCTTAACCTTTCCCTTGAAAATAGGTC
1 AACTTAAAAAGAAAGACCCTGACACAAACTCGAGGCTTAACCTATCCCTTGAAAAAAGGTC
* * * * * * * *
538408 GACTTAAAATGAATGAGCTTGACACTAACTCGAGGCTTGACCTATCCCTTGAAAATAGGT
1 AACTTAAAAAGAAAGACCCTGACACAAACTCGAGGCTTAACCTATCCCTTGAAAAAAGGT
538468 TCGACATAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
59 9 0.09
60 5 0.05
61 58 0.59
62 26 0.26
63 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (61 bp):
AACTTAAAAAGAAAGACCCTGACACAAACTCGAGGCTTAACCTATCCCTTGAAAAAAGGTC
Found at i:542670 original size:25 final size:27
Alignment explanation
Indices: 542633--542683 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
542623 TTAAAACGTA
**
542633 ATCTATAATTTTTTTAAAAAAATCAAG
1 ATCTATAATTTTTAAAAAAAAATCAAG
542660 ATCT-TAA-TTTTAAAAAAAAATCAA
1 ATCTATAATTTTTAAAAAAAAATCAA
542684 ATCAAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 3 0.14
27 4 0.18
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (27 bp):
ATCTATAATTTTTAAAAAAAAATCAAG
Found at i:546592 original size:29 final size:29
Alignment explanation
Indices: 546559--546617 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
546549 TCTTGGAAGT
*
546559 AAGAAATTAAGTAAAATTTAAGTGCAAAA
1 AAGAAATTAAATAAAATTTAAGTGCAAAA
546588 AAGAAATTAAATAAAATTTAAGTGCAAAA
1 AAGAAATTAAATAAAATTTAAGTGCAAAA
546617 A
1 A
546618 TCCTAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (29 bp):
AAGAAATTAAATAAAATTTAAGTGCAAAA
Found at i:549532 original size:21 final size:21
Alignment explanation
Indices: 549503--549542 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
549493 AAAAGCTATT
*
549503 TTTTCAATTTTAATGTTTTAC
1 TTTTAAATTTTAATGTTTTAC
*
549524 TTTTAAATTTTTATGTTTT
1 TTTTAAATTTTAATGTTTT
549543 TAGATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTAAATTTTAATGTTTTAC
Found at i:550936 original size:20 final size:20
Alignment explanation
Indices: 550902--550951 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
550892 ATATTTTTTA
** *
550902 ATATTAATAGTAAATATATT
1 ATATTAATAAAAAATAAATT
550922 ATATTAATAAAAAATAAATT
1 ATATTAATAAAAAATAAATT
550942 -TA-TAATAAAA
1 ATATTAATAAAA
550952 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 8 0.30
19 2 0.07
20 17 0.63
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATATTAATAAAAAATAAATT
Found at i:551830 original size:436 final size:438
Alignment explanation
Indices: 550745--551938 Score: 1185
Period size: 436 Copynumber: 2.7 Consensus size: 438
550735 AAATATAATG
*
550745 TATTTATGTAAAATATTTTTTCAAGAAAATTAAATATAATATTTACAAAATAATTTTGT-ATTTT
1 TATTTATGTAAAATATTTTTTCAAGAAAATTAAATATAATTTTTAC-AAATAATTTT-TAATTTT
* * * * *
550809 TATTAAACATATTATATGT-AGGAAATTATTTTTTTTAATAATTTTTGAAGTAAAAGAATTTTAT
64 TATTAAATACATTATATATGAGGAAATTA-ATTTTTT-ATAATTTTTGAAGTAAAAAAATTTT-T
* *
550873 ATAGTTTTATCTTACTAATATATTTTTTAATATTA-ATAGTAAATATATTATATTAATAAAAAAT
126 ATA-TTTTATCTTATTAATATA-TTTTTAATATTAGATA-TAAATATATTATATTAATAAAAATT
* * * *
550937 AAATTTATAATAAAA-TTTTATTTTTTTATTAGTTAAAAAGAATTACTACTGAAGATTACTGAAA
188 AATTTTATAATAAAATTTTTA-TTTTTTATTAGTTAAAAA-AATTACTATTAAAGATTAC-AAAA
* * * * *
551001 TTATACATACACATTAGAATTTA-ATTAAATCATTAGAA-TGTAAATAATGTCTGTATGTAATAT
250 TTATACATAAACATTAGAATTTACA-TAAATCATTA-AAGTGTAGAT-ATTTTTGTATATAATAT
* *** * *
551064 GTGTTATGGGTAATGTGTTTGTATAAATAATTTTTGAAGATAACGTTTATATGTAAAAAAATTAC
312 GAGTTATACATAATGTGTTTGTAT-AATAA--TATGAAGATAAC-TTTATATATAAAAAAATTAC
* * * * *
551129 ATAAAATAGTATCGAGTTACATACAAATATTCTAAAGGTACATAAAACATTACCAAAACTATAAT
373 ATAAAACAGTATCAAGTTACATACAAATATTATAAAGGTACATAAAACATTACCAAAACTACAAC
*
551194 G
438 A
*
551195 TATTTATGTAAAATATTTTTTCAAGAAAATTAAATATAATTTTTTTC-AA-AA----TAA--TTT
1 TATTTATGTAAAATATTTTTTCAAGAAAATTAAATATAA-TTTTTACAAATAATTTTTAATTTTT
* * *
551252 ATTAAATATTATATATATAT-AGAAAATTAATTTTTT-TCAATTTTTGAAGT-AAAAAA-TTATA
65 ATTAAATA-CAT-TATATATGAGGAAATTAATTTTTTAT-AATTTTTGAAGTAAAAAAATTTTTA
* *
551313 T-TTTTATTTTATTAATATAAATTTTGTAATATTAGCA-ATAAATATATTATTTTAATAAAAATT
127 TATTTTATCTTATTAATAT--ATTTT-TAATATTAG-ATATAAATATATTATATTAATAAAAA-T
*
551376 TAATTTTATAATAAAATTTTTACTTTTTTACTT-GTTAAAAAAACTACTATTAAAGATTATCAAA
187 TAATTTTATAATAAAATTTTTA-TTTTTTA-TTAGTTAAAAAAATTACTATTAAAGATTA-CAAA
* * * * * *
551440 ATTATGCATAAATATTACAGTTTACATAAATCATTAAAGTGTAGGTATTTTTGTATATACTATGC
249 ATTATACATAAACATTAGAATTTACATAAATCATTAAAGTGTAGATATTTTTGTATATAATATG-
* * * *
551505 AGTTATACATAAT-T-TATT-TAT-GTAA-AT-AA-AT-A-TTTGTATAT-AACAAATTATATAA
313 AGTTATACATAATGTGT-TTGTATAATAATATGAAGATAACTTTATATATAAAAAAATTACAT-A
* * * * * *
551560 AAACATTATCAAGTTATATACAAATATTATAGAGTTGCATAAAACATTATTCAAAACTACAACA
376 AAACAGTATCAAGTTACATACAAATATTATAAAGGTACATAAAACATTA-CCAAAACTACAACA
* * *
551624 TATTTATGTTAAATATTCTTTC-AGAAAAATTAAATGTAATTTTTACAAATAATTTTTAATTTTT
1 TATTTATGTAAAATATTTTTTCAAG-AAAATTAAATATAATTTTTACAAATAATTTTTAATTTTT
*
551688 ATTAAATACATTATATATGCAGGAAATTAATTTTTTAGTAA-TTTTCAAGTAAACAAAATTTTTA
65 ATTAAATACATTATATATG-AGGAAATTAATTTTTTA-TAATTTTTGAAGTAAA-AAAATTTTTA
* *
551752 TATTTTATGTTATTAATATATTTTTAATATTAGATATAAATATATTATATTGATAAAAATTAATT
127 TATTTTATCTTATTAATATATTTTTAATATTAGATATAAATATATTATATTAATAAAAATTAATT
* * * *
551817 TTATAATAAAATTTTTATTTTTTATTAATTGAAAAGAATTGCTATTAAAGATTACCAAAATTACA
192 TTATAATAAAATTTTTATTTTTTATTAGTT-AAAAAAATTACTATTAAAGATTA-CAAAATTATA
* * * * * *
551882 CATATACATTAGAATTTACATGAAGCATTAGAGTGTAGATAATTTTGTATGTAATAT
255 CATAAACATTAGAATTTACATAAATCATTAAAGTGTAGATATTTTTGTATATAATAT
551939 ATGTTATGAG
Statistics
Matches: 624, Mismatches: 80, Indels: 94
0.78 0.10 0.12
Matches are distributed among these distances:
427 10 0.02
428 57 0.09
429 45 0.07
430 3 0.00
431 2 0.00
432 2 0.00
433 1 0.00
434 12 0.02
435 11 0.02
436 135 0.22
437 50 0.08
438 18 0.03
439 58 0.09
440 94 0.15
441 29 0.05
442 24 0.04
443 10 0.02
444 15 0.02
448 2 0.00
449 2 0.00
450 39 0.06
451 5 0.01
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.44
Consensus pattern (438 bp):
TATTTATGTAAAATATTTTTTCAAGAAAATTAAATATAATTTTTACAAATAATTTTTAATTTTTA
TTAAATACATTATATATGAGGAAATTAATTTTTTATAATTTTTGAAGTAAAAAAATTTTTATATT
TTATCTTATTAATATATTTTTAATATTAGATATAAATATATTATATTAATAAAAATTAATTTTAT
AATAAAATTTTTATTTTTTATTAGTTAAAAAAATTACTATTAAAGATTACAAAATTATACATAAA
CATTAGAATTTACATAAATCATTAAAGTGTAGATATTTTTGTATATAATATGAGTTATACATAAT
GTGTTTGTATAATAATATGAAGATAACTTTATATATAAAAAAATTACATAAAACAGTATCAAGTT
ACATACAAATATTATAAAGGTACATAAAACATTACCAAAACTACAACA
Found at i:552024 original size:21 final size:21
Alignment explanation
Indices: 551973--552028 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
551963 TGAATGTAAC
* *
551973 AAATTATATAAAAACATTATT
1 AAATTACATAAAAACATTATA
* * *
551994 AAGTTCCATACAAACATTATA
1 AAATTACATAAAAACATTATA
552015 AAATTACATAAAAA
1 AAATTACATAAAAA
552029 AATATTTTGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATTACATAAAAACATTATA
Found at i:553882 original size:29 final size:27
Alignment explanation
Indices: 553838--553891 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 27
553828 ATATGATAAA
553838 ATTATATAATAAAAAATTAAT-TAAAAT
1 ATTATATAATAAAAAA-TAATATAAAAT
553865 ATTATATAATATAAAAAATAATATAAA
1 ATTATAT-A-ATAAAAAATAATATAAA
553892 TATAATACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 7 0.29
28 5 0.21
29 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
ATTATATAATAAAAAATAATATAAAAT
Found at i:553898 original size:11 final size:11
Alignment explanation
Indices: 553868--553995 Score: 63
Period size: 11 Copynumber: 11.5 Consensus size: 11
553858 TTAAAATATT
553868 ATATAATATAAA
1 ATATAATAT-AA
*
553880 AAATAATATAA
1 ATATAATATAA
*
553891 ATATAATACGAA
1 ATATAATA-TAA
*
553903 TATATATATGTTAA
1 -ATATA-AT-ATAA
*
553917 A-AT-TTATATA
1 ATATAATATA-A
*
553927 ATATTAATTATTA
1 ATA-TAA-TATAA
553940 ATAT-AT-TAA
1 ATATAATATAA
*
553949 AT-TTATATAA
1 ATATAATATAA
*
553959 ATATAATATTA
1 ATATAATATAA
553970 A-A-AATATAA
1 ATATAATATAA
*
553979 TTATAATATAA
1 ATATAATATAA
553990 ATATAA
1 ATATAA
553996 GATGCCCGGT
Statistics
Matches: 87, Mismatches: 15, Indels: 29
0.66 0.11 0.22
Matches are distributed among these distances:
8 1 0.01
9 14 0.16
10 11 0.13
11 30 0.34
12 14 0.16
13 10 0.11
14 7 0.08
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.41
Consensus pattern (11 bp):
ATATAATATAA
Found at i:553904 original size:29 final size:29
Alignment explanation
Indices: 553846--553906 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
553836 AAATTATATA
* *
553846 ATAAAAAATTAATTAAAATATTATATAAT
1 ATAAAAAATTAATTAAAATATAATAGAAT
553875 ATAAAAAA-TAA-TATAAATATAATACGAAT
1 ATAAAAAATTAATTA-AAATATAATA-GAAT
553904 ATA
1 ATA
553907 TATATGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 12 0.43
29 14 0.50
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
ATAAAAAATTAATTAAAATATAATAGAAT
Found at i:553969 original size:22 final size:21
Alignment explanation
Indices: 553942--553992 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
553932 AATTATTAAT
*
553942 ATATTAAATTTATATAAATATA
1 ATATTAAA-TAATATAAATATA
*
553964 ATATTAAA-AATATAATTATA
1 ATATTAAATAATATAAATATA
553984 ATA-TAAATA
1 ATATTAAATA
553993 TAAGATGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 14 0.54
22 8 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATTAAATAATATAAATATA
Found at i:555809 original size:20 final size:21
Alignment explanation
Indices: 555762--555806 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
555752 ATTATTTTTT
555762 AAAAATTATACTTATTTACTA
1 AAAAATTATACTTATTTACTA
* *
555783 ATAAATTATCCTT-TTTA-TA
1 AAAAATTATACTTATTTACTA
555802 AAAAA
1 AAAAA
555807 ATTTTACCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 6 0.29
20 4 0.19
21 11 0.52
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAATTATACTTATTTACTA
Found at i:556077 original size:13 final size:14
Alignment explanation
Indices: 556059--556091 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
556049 GTTTCACCTA
556059 TTTTTCTTTTCT-T
1 TTTTTCTTTTCTAT
*
556072 TTTTTCTTTTTTAT
1 TTTTTCTTTTCTAT
556086 TTTTTC
1 TTTTTC
556092 ACTTATACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTCTTTTCTAT
Found at i:556272 original size:22 final size:23
Alignment explanation
Indices: 556244--556287 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
556234 AGGAATAAAT
556244 TTATTTA-TAAA-CTATTTAAAAC
1 TTATTTATTAAATC-ATTTAAAAC
556266 TTATTTATTAAATCATTTAAAA
1 TTATTTATTAAATCATTTAAAA
556288 TTTACTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 12 0.60
24 1 0.05
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
TTATTTATTAAATCATTTAAAAC
Found at i:556423 original size:16 final size:15
Alignment explanation
Indices: 556398--556429 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
556388 TAAATTTAAA
556398 TTATTTTTTGTTTAT
1 TTATTTTTTGTTTAT
556413 TTATTTGTTTGTTTAT
1 TTATTT-TTTGTTTAT
556429 T
1 T
556430 GTGCATGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (15 bp):
TTATTTTTTGTTTAT
Found at i:559869 original size:24 final size:22
Alignment explanation
Indices: 559831--559876 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
559821 TTAAATAAAA
559831 TAAATAAAATAAATTATTCAATTT
1 TAAATAAAATAAATT-TT-AATTT
* *
559855 TAAATAAATTTAATTTTAATTT
1 TAAATAAAATAAATTTTAATTT
559877 AAGAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 2 0.10
24 13 0.65
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATAAAATAAATTTTAATTT
Found at i:563773 original size:21 final size:21
Alignment explanation
Indices: 563733--563805 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
563723 TAGTACAATT
* *
563733 TGTATAGATACAACAAGTGAAA
1 TGTATCGATAC-ATAAGTGAAA
563755 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAGTGAAA
***
563775 TGTAAT-GATACATGTTTGAAA
1 TGT-ATCGATACATAAGTGAAA
563796 TGTATCGATA
1 TGTATCGATA
563806 AAAGAACATG
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 16 0.37
21 17 0.40
22 10 0.23
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (21 bp):
TGTATCGATACATAAGTGAAA
Found at i:563778 original size:20 final size:20
Alignment explanation
Indices: 563733--563787 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
563723 TAGTACAATT
*
563733 TGTATAGATACAACAAGTGAAA
1 TGTAT-GATAC-ATAAGTGAAA
563755 TGTATCGATACATAAGTG-AA
1 TGTAT-GATACATAAGTGAAA
563775 TGTAATGATACAT
1 TGT-ATGATACAT
563788 GTTTGAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.40
21 8 0.27
22 10 0.33
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (20 bp):
TGTATGATACATAAGTGAAA
Found at i:563974 original size:52 final size:52
Alignment explanation
Indices: 563844--564031 Score: 206
Period size: 52 Copynumber: 3.7 Consensus size: 52
563834 CCTAGAAAGA
**
563844 AAATGTATTC-ATACATT-TT-ATTGTATCGATACATTCTGAG--TTTGGTCC
1 AAATGTA-TCGATACATTCTTCATTGTATCGATACATTCTGAGTTTTTGAACC
* * * *
563892 AAATGTATCAATACATTTTTCATTGCATCGATACATTCTGAGTTTTTGACCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGAGTTTTTGAACC
* * * * **
563944 GAATATATCGATACATTCTTCATTGTATCGATACATTTTGGGTTTTTGAATT
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGAGTTTTTGAACC
* *
563996 AAATGTATTGATACATTCTTCAATGTATCGATACAT
1 AAATGTATCGATACATTCTTCATTGTATCGATACAT
564032 CTAGTTAAAT
Statistics
Matches: 118, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
47 2 0.02
48 14 0.12
49 2 0.02
50 20 0.17
52 80 0.68
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGAGTTTTTGAACC
Found at i:564133 original size:40 final size:40
Alignment explanation
Indices: 564078--564159 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
564068 TTTACTCATT
564078 GGACCTAATGTTTGGTGTAAACACGTTTTCTCACACCGTA
1 GGACCTAATGTTTGGTGTAAACACGTTTTCTCACACCGTA
564118 GGACCTAATGTTTGGTGTAAACACGTTTTCTCACACCGTA
1 GGACCTAATGTTTGGTGTAAACACGTTTTCTCACACCGTA
564158 GG
1 GG
564160 TTACCAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (40 bp):
GGACCTAATGTTTGGTGTAAACACGTTTTCTCACACCGTA
Found at i:567530 original size:23 final size:24
Alignment explanation
Indices: 567489--567539 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
567479 TTACTAAAAT
* * *
567489 TTTAAATAATAGTAATTT-ATTAA
1 TTTAAATAAAAATAATTTAATAAA
*
567512 TTTAAATAAAAATATTTTAATAAA
1 TTTAAATAAAAATAATTTAATAAA
567536 TTTA
1 TTTA
567540 TTTCAAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTAAATAAAAATAATTTAATAAA
Found at i:567977 original size:12 final size:11
Alignment explanation
Indices: 567962--568006 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
567952 AATTTAGAAT
567962 AAATAATTATA
1 AAATAATTATA
567973 TAAATAA-TA-A
1 -AAATAATTATA
*
567983 AAATAAATATA
1 AAATAATTATA
567994 AAATAATT-TA
1 AAATAATTATA
568004 AAA
1 AAA
568007 GTTTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 6 0.20
10 8 0.27
11 10 0.33
12 6 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATAATTATA
Found at i:567999 original size:36 final size:35
Alignment explanation
Indices: 567932--567999 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 35
567922 AGATTTCATT
** * * *
567932 ATTATATAATAATATGAATTAATTTAGAATAAATA
1 ATTATATAATAATAAAAATAAATATAAAATAAATA
567967 ATTATATAAATAATAAAAATAAATATAAAATAA
1 ATTATAT-AATAATAAAAATAAATATAAAATAA
568000 TTTAAAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 7 0.26
36 20 0.74
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (35 bp):
ATTATATAATAATAAAAATAAATATAAAATAAATA
Found at i:568006 original size:21 final size:21
Alignment explanation
Indices: 567962--568000 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
567952 AATTTAGAAT
*
567962 AAATAATTATATAAATAATAA
1 AAATAAATATATAAATAATAA
567983 AAATAAATATA-AAATAAT
1 AAATAAATATATAAATAAT
568001 TTAAAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAATATATAAATAATAA
Found at i:569505 original size:25 final size:24
Alignment explanation
Indices: 569477--569523 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
569467 TCATGAACTG
*
569477 TTAAAATTATACTTATAAATAATTA
1 TTAAAATTATA-TTAAAAATAATTA
569502 TTAAAATTATATTAAAAATAAT
1 TTAAAATTATATTAAAAATAAT
569524 GAATAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAAAATTATATTAAAAATAATTA
Found at i:569645 original size:16 final size:15
Alignment explanation
Indices: 569622--569655 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
569612 GTTTTCTCAA
569622 AAATT-TTTTTAAAC
1 AAATTATTTTTAAAC
*
569636 AAATTATTTTTAATC
1 AAATTATTTTTAAAC
569651 AAATT
1 AAATT
569656 GCTAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATTATTTTTAAAC
Found at i:571413 original size:2 final size:2
Alignment explanation
Indices: 571406--571432 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
571396 AGATTTCAAA
571406 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
571433 CACATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:571827 original size:10 final size:10
Alignment explanation
Indices: 571812--571844 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
571802 CTATTTCATA
571812 TTTTTTTCTT
1 TTTTTTTCTT
571822 TTTTTTTC-T
1 TTTTTTTCTT
*
571831 TTTCTTTCTT
1 TTTTTTTCTT
571841 TTTT
1 TTTT
571845 CTCCATCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:571835 original size:15 final size:16
Alignment explanation
Indices: 571815--571846 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
571805 TTTCATATTT
571815 TTTTCTTT-TTTTTTC
1 TTTTCTTTCTTTTTTC
571830 TTTTCTTTCTTTTTTC
1 TTTTCTTTCTTTTTTC
571846 T
1 T
571847 CCATCTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTCTTTTTTC
Found at i:572559 original size:3 final size:3
Alignment explanation
Indices: 572551--572576 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
572541 TTTCTTTCCT
572551 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
572577 TAAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:572740 original size:35 final size:34
Alignment explanation
Indices: 572660--572740 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 34
572650 TATAAACATT
* *
572660 AAAAAATATTAAATTATTTAAATTTTAAAATTCA
1 AAAAAATATTAAATTAGTTAAATCTTAAAATTCA
572694 ATACAAAATATTAAATT-GTTAAATCTTAAAATTTCA
1 A-A-AAAATATTAAATTAGTTAAATCTTAAAA-TTCA
572730 AAAAATATATT
1 AAAAA-ATATT
572741 TTTTAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
34 4 0.10
35 19 0.46
36 18 0.44
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (34 bp):
AAAAAATATTAAATTAGTTAAATCTTAAAATTCA
Found at i:574993 original size:29 final size:29
Alignment explanation
Indices: 574951--575008 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
574941 ACACATTCAA
574951 TGCTTGAAGCATAAAAAGTAAATTTATCC
1 TGCTTGAAGCATAAAAAGTAAATTTATCC
* *
574980 TGCTTGAAGCATAAACATTAAATTTATCC
1 TGCTTGAAGCATAAAAAGTAAATTTATCC
575009 CAGCATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (29 bp):
TGCTTGAAGCATAAAAAGTAAATTTATCC
Found at i:578799 original size:3 final size:3
Alignment explanation
Indices: 578791--578838 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
578781 AATGTTTTTA
* *
578791 ATT ATT ATT ATT ATT ATT ATT ATT ATT CTT ATT CTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
578839 TGCTATTCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:580629 original size:3 final size:3
Alignment explanation
Indices: 580621--580658 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
580611 TACAAGTGTA
* *
580621 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
580659 CAAGAACAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:583244 original size:3 final size:3
Alignment explanation
Indices: 583236--583296 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
583226 TAGAGCCCAC
* **
583236 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA GCA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
583284 ATA AGA ATA ATA A
1 ATA ATA ATA ATA A
583297 ATTTTAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:583354 original size:27 final size:26
Alignment explanation
Indices: 583292--583373 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 26
583282 TAATAAGAAT
*
583292 AATAAATTTTAAAAATA-TTTAATAA
1 AATAATTTTTAAAAATATTTTAATAA
*
583317 AA-ATTTATTTAAAAATATTTTGAATAA
1 AATAATT-TTTAAAAATATTTT-AATAA
* * *
583344 AATAATTTTTATAAATTTTTTTAAAAA
1 AATAATTTTTA-AAAATATTTTAATAA
583371 AAT
1 AAT
583374 TCTGCCAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
24 2 0.04
25 12 0.26
26 3 0.07
27 18 0.39
28 11 0.24
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
AATAATTTTTAAAAATATTTTAATAA
Found at i:583690 original size:20 final size:21
Alignment explanation
Indices: 583654--583708 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
583644 ATAAGTAGTA
583654 ATGTGATATTATAATTTTTATT
1 ATGTGATATT-TAATTTTTATT
*
583676 TTGTGAT-TTTAATTTTTATT
1 ATGTGATATTTAATTTTTATT
583696 AT-TGATATTTAAT
1 ATGTGATATTTAAT
583709 GTAATTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.13
20 18 0.60
21 2 0.07
22 6 0.20
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (21 bp):
ATGTGATATTTAATTTTTATT
Found at i:584046 original size:14 final size:14
Alignment explanation
Indices: 584027--584058 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
584017 TAATAAATTT
584027 AATAATTATAAAAA
1 AATAATTATAAAAA
584041 AATAATTATAAAAA
1 AATAATTATAAAAA
584055 AATA
1 AATA
584059 GTATCTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAATTATAAAAA
Found at i:584118 original size:113 final size:113
Alignment explanation
Indices: 583984--584210 Score: 418
Period size: 113 Copynumber: 2.0 Consensus size: 113
583974 TAGTACAAAA
583984 AGTTTGACACTTAGTAAATAATTGATAATATATTAATAAATTTAATAATTATAAAAAAATAATTA
1 AGTTTGACACTTAGTAAATAATTGATAATATATTAATAAATTTAATAATTATAAAAAAATAATTA
584049 TAAAAAAATAGTATCTGATGTATAATATAATAGTAACCGATTAATAAC
66 TAAAAAAATAGTATCTGATGTATAATATAATAGTAACCGATTAATAAC
* *
584097 AGTTTGACACTTAGTAAATAATTGATAATATATTAATAAATTTAATAATTTTTAAAAAATAATTA
1 AGTTTGACACTTAGTAAATAATTGATAATATATTAATAAATTTAATAATTATAAAAAAATAATTA
* *
584162 TAAAAGAATAGTATCTGATGTATAATATAGTAGTAACCGATTAATAAC
66 TAAAAAAATAGTATCTGATGTATAATATAATAGTAACCGATTAATAAC
584210 A
1 A
584211 TAGTAGTAAA
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (113 bp):
AGTTTGACACTTAGTAAATAATTGATAATATATTAATAAATTTAATAATTATAAAAAAATAATTA
TAAAAAAATAGTATCTGATGTATAATATAATAGTAACCGATTAATAAC
Found at i:584664 original size:2 final size:2
Alignment explanation
Indices: 584659--584701 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
584649 CTAACACGTG
584659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
584701 T
1 T
584702 TACAGCTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:584842 original size:28 final size:26
Alignment explanation
Indices: 584770--584842 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 26
584760 TCAAGTCAAT
584770 TCAATTAAA--AATTAAAAATTAAAA
1 TCAATTAAATTAATTAAAAATTAAAA
*
584794 T-AATTTAATATTATATAAAAAATTAAAAA
1 TCAA-TTAA-ATTA-ATTAAAAATT-AAAA
584823 TCAATTAAATTAACTTAAAA
1 TCAATTAAATTAA-TTAAAA
584843 TCACTTCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
23 2 0.05
24 5 0.13
25 1 0.03
27 2 0.05
28 18 0.46
29 9 0.23
30 2 0.05
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (26 bp):
TCAATTAAATTAATTAAAAATTAAAA
Found at i:585059 original size:18 final size:19
Alignment explanation
Indices: 585028--585066 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
585018 TTATCATTTA
585028 TTTAACATTAAAAA-TATT
1 TTTAACATTAAAAATTATT
* *
585046 TTTAATATTTAAAATTATT
1 TTTAACATTAAAAATTATT
585065 TT
1 TT
585067 AATTAGATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAACATTAAAAATTATT
Found at i:585502 original size:13 final size:13
Alignment explanation
Indices: 585484--585509 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
585474 GTTATGATTA
585484 ATATTTTATATTT
1 ATATTTTATATTT
585497 ATATTTTATATTT
1 ATATTTTATATTT
585510 TTAATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTTTATATTT
Found at i:585529 original size:22 final size:21
Alignment explanation
Indices: 585487--585537 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
585477 ATGATTAATA
*
585487 TTTTATATTTATATTTTATAT
1 TTTTATATTTATATTTGATAT
585508 TTTTAATATTTAT-TATTGATAT
1 TTTT-ATATTTATAT-TTGATAT
585530 TTATTATA
1 TT-TTATA
585538 ATTAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.19
22 19 0.73
23 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATATTTATATTTGATAT
Found at i:585542 original size:29 final size:28
Alignment explanation
Indices: 585475--585543 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
585465 CAGATTTATG
* *
585475 TTATGATTAATATTTTATATTTATATTT
1 TTATAATTAATATTTTATATTGATATTT
**
585503 TATATTTTTAATA-TTTATTATTGATATTT
1 T-TATAATTAATATTTTA-TATTGATATTT
585532 ATTATAATTAAT
1 -TTATAATTAAT
585544 TATAATAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 5 0.15
29 27 0.82
30 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (28 bp):
TTATAATTAATATTTTATATTGATATTT
Found at i:586505 original size:14 final size:14
Alignment explanation
Indices: 586483--586517 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
586473 GATCATAATC
*
586483 TAATATTATAATTT
1 TAATTTTATAATTT
*
586497 TTATTTTATAATTT
1 TAATTTTATAATTT
586511 TAATTTT
1 TAATTTT
586518 TTTCATCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TAATTTTATAATTT
Found at i:586864 original size:36 final size:37
Alignment explanation
Indices: 586777--586873 Score: 133
Period size: 36 Copynumber: 2.6 Consensus size: 37
586767 TTTCAAGTAA
*
586777 TTACTTAAAAAATTAATCTTGCAGATGAAACTAAAAAC
1 TTACTT-AAAAATTAATCTTGCATATGAAACTAAAAAC
* * * *
586815 TCACTTAAAAATTAATCTTGCATATG-CACTAGAAAT
1 TTACTTAAAAATTAATCTTGCATATGAAACTAAAAAC
586851 TTACTTAAAAATTAATCTTGCAT
1 TTACTTAAAAATTAATCTTGCAT
586874 GATCGGTGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 29 0.55
37 19 0.36
38 5 0.09
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.34
Consensus pattern (37 bp):
TTACTTAAAAATTAATCTTGCATATGAAACTAAAAAC
Found at i:592232 original size:33 final size:32
Alignment explanation
Indices: 592191--592255 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
592181 AACTCTTGTA
* *
592191 TGTATCAATACATTATGCTTTGTATCAATACAT
1 TGTATCAATACATGAT-CATTGTATCAATACAT
* *
592224 TGTATCAATATATGATCATTGTATCGATACAT
1 TGTATCAATACATGATCATTGTATCAATACAT
592256 ACACAATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (32 bp):
TGTATCAATACATGATCATTGTATCAATACAT
Found at i:594564 original size:20 final size:21
Alignment explanation
Indices: 594539--594593 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
594529 ACAATAAGGC
594539 AATGTATCGATACAT-ATGTG-
1 AATGTATCGATACATGAT-TGA
* *
594559 AATGTATCGATACCTGCTTGA
1 AATGTATCGATACATGATTGA
594580 AATGTATCGATACA
1 AATGTATCGATACA
594594 GTACTATGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (21 bp):
AATGTATCGATACATGATTGA
Found at i:595183 original size:13 final size:13
Alignment explanation
Indices: 595165--595190 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
595155 TACACAAAGT
595165 ATGTATCGATACA
1 ATGTATCGATACA
595178 ATGTATCGATACA
1 ATGTATCGATACA
595191 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:595188 original size:32 final size:33
Alignment explanation
Indices: 595147--595210 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
595137 TAGCCAAACG
**
595147 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
595179 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
595211 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:597427 original size:22 final size:22
Alignment explanation
Indices: 597400--597455 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
597390 TTGCAAGTTG
597400 AAATAAAGAACTTGGCTAATG-A
1 AAATAAAGAACTTGGCTAA-GAA
* *
597422 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAACTTGGCTAAGAA
597443 AAATAAA-AACTTG
1 AAATAAAGAACTTG
597456 CATGATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
AAATAAAGAACTTGGCTAAGAA
Found at i:601360 original size:13 final size:13
Alignment explanation
Indices: 601342--601380 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
601332 ATTTTTTTCT
601342 TTGTATCGATACA
1 TTGTATCGATACA
601355 TTGTATCGATACA
1 TTGTATCGATACA
*
601368 CTGTATCGATACA
1 TTGTATCGATACA
601381 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:605683 original size:10 final size:10
Alignment explanation
Indices: 605668--605700 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
605658 CTATTTCATA
605668 TTTTTTTCTT
1 TTTTTTTCTT
605678 TTTTTTTC-T
1 TTTTTTTCTT
*
605687 TTTCTTTCTT
1 TTTTTTTCTT
605697 TTTT
1 TTTT
605701 CTCCTCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:605696 original size:19 final size:19
Alignment explanation
Indices: 605668--605722 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
605658 CTATTTCATA
605668 TTTT-TTTCTTTTTTTTTC
1 TTTTCTTTCTTTTTTTTTC
* *
605686 TTTTCTTTCTTTTTTCTCC
1 TTTTCTTTCTTTTTTTTTC
*
605705 TCTTC-TTCTTTTTCTTTT
1 TTTTCTTTCTTTTT-TTTT
605723 ACCTAACTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTTTCTTTTTTTTTC
Found at i:606579 original size:35 final size:35
Alignment explanation
Indices: 606499--606579 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
606489 GTATAAACAT
* *
606499 TAAAAATATTAAATTATTTAAATTTTAAAATTCAA
1 TAAAAATATTAAATTAGTTAAATCTTAAAATTCAA
606534 TACAAAATATTAAATT-GTTAAATCTTAAAATTTCAA
1 TA-AAAATATTAAATTAGTTAAATCTTAAAA-TTCAA
606570 -AAAATATATT
1 TAAAA-ATATT
606580 TTTTAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 3 0.07
35 20 0.49
36 18 0.44
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (35 bp):
TAAAAATATTAAATTAGTTAAATCTTAAAATTCAA
Found at i:608821 original size:29 final size:29
Alignment explanation
Indices: 608779--608836 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
608769 ACACATTCAA
608779 TGCTTGAAGCATAAAAAGTAAATTTATCC
1 TGCTTGAAGCATAAAAAGTAAATTTATCC
* *
608808 TGCTTGAAGCATAAACATTAAATTTATCC
1 TGCTTGAAGCATAAAAAGTAAATTTATCC
608837 CAGCATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (29 bp):
TGCTTGAAGCATAAAAAGTAAATTTATCC
Found at i:612622 original size:3 final size:3
Alignment explanation
Indices: 612614--612661 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
612604 AATGTTTTTA
* *
612614 ATT ATT ATT ATT ATT ATT ATT ATT ATT CTT ATT CTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
612662 TGCTATTCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:617012 original size:3 final size:3
Alignment explanation
Indices: 617004--617064 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
616994 TAGAGCCCAC
* **
617004 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA GCA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
617052 ATA AGA ATA ATA A
1 ATA ATA ATA ATA A
617065 ATTTTAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:617117 original size:24 final size:24
Alignment explanation
Indices: 617067--617117 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
617057 AATAATAAAT
*
617067 TTTAAAAATATTTAATAAAATTTA
1 TTTAAAAATATTTAATAAAATTAA
617091 TTTAAAAATATTTGAATAAAA-TAA
1 TTTAAAAATATTT-AATAAAATTAA
617115 TTT
1 TTT
617118 TATAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTAAAAATATTTAATAAAATTAA
Found at i:617119 original size:25 final size:25
Alignment explanation
Indices: 617056--617124 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
617046 GCAATAATAA
*
617056 GAATAATA-AATTTTAAAAATATTT
1 GAATAAAATAATTTTAAAAATATTT
*
617080 -AATAAAAT-TTATTTAAAAATATTT
1 GAATAAAATAAT-TTTAAAAATATTT
*
617104 GAATAAAATAATTTTATAAAT
1 GAATAAAATAATTTTAAAAAT
617125 TTTTTTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 7 0.19
24 13 0.35
25 16 0.43
26 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
GAATAAAATAATTTTAAAAATATTT
Found at i:617451 original size:19 final size:20
Alignment explanation
Indices: 617419--617469 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
617409 AGTAGTAATG
617419 TGATATTATAATTTTTATT-T
1 TGATATT-TAATTTTTATTAT
617439 TG-TGATTTAATTTTTATTAT
1 TGAT-ATTTAATTTTTATTAT
617459 TGATATTTAAT
1 TGATATTTAAT
617470 GTAATTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 12 0.43
20 15 0.54
21 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
TGATATTTAATTTTTATTAT
Found at i:617822 original size:15 final size:14
Alignment explanation
Indices: 617790--617819 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
617780 TAATAAATTT
617790 AATAATTATAAAAA
1 AATAATTATAAAAA
617804 AATAATTATAAAAA
1 AATAATTATAAAAA
617818 AA
1 AA
617820 ATAGTATCTG
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAATTATAAAAA
Found at i:617959 original size:112 final size:115
Alignment explanation
Indices: 617747--617972 Score: 395
Period size: 112 Copynumber: 2.0 Consensus size: 115
617737 TAGTACAAAA
617747 AGTTTGACACTTAGTAAATAATTGATAATATATTAATAAATTTAATAATTATAAAAAAATAATTA
1 AGTTTGACACTTAGTAAATAATTGATAATATATTAATAAATTTAATAATTATAAAAAAATAATTA
617812 TAAAAAAAATAGTATCTGATGTATAATATAATAGTAACCGATTAATAACC
66 TAAAAAAAATAGTATCTGATGTATAATATAATAGTAACCGATTAATAACC
*
617862 AGTTTGACACTTAGTAAATAATTGATAATATATTAATAAA-TTAATAATT-T-TAAAAATAATTA
1 AGTTTGACACTTAGTAAATAATTGATAATATATTAATAAATTTAATAATTATAAAAAAATAATTA
* * *
617924 TAACAAGAATAGTATCTGATGTATAATATAGTAGTAACCGATTAATAAC
66 TAAAAAAAATAGTATCTGATGTATAATATAATAGTAACCGATTAATAAC
617973 ATAGTAGTAA
Statistics
Matches: 107, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
112 57 0.53
113 1 0.01
114 9 0.08
115 40 0.37
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (115 bp):
AGTTTGACACTTAGTAAATAATTGATAATATATTAATAAATTTAATAATTATAAAAAAATAATTA
TAAAAAAAATAGTATCTGATGTATAATATAATAGTAACCGATTAATAACC
Found at i:618426 original size:2 final size:2
Alignment explanation
Indices: 618421--618463 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
618411 CTAACACGTG
618421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
618463 T
1 T
618464 TACAGCTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:618605 original size:28 final size:26
Alignment explanation
Indices: 618533--618605 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 26
618523 TCAAGTCAAT
618533 TCAATTAAA--AATTAAAAATTAAAA
1 TCAATTAAATTAATTAAAAATTAAAA
*
618557 T-AATTTAATATTATATAAAAAATTAAAAA
1 TCAA-TTAA-ATTA-ATTAAAAATT-AAAA
618586 TCAATTAAATTAACTTAAAA
1 TCAATTAAATTAA-TTAAAA
618606 TCACTTCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
23 2 0.05
24 5 0.13
25 1 0.03
27 2 0.05
28 18 0.46
29 9 0.23
30 2 0.05
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (26 bp):
TCAATTAAATTAATTAAAAATTAAAA
Found at i:618812 original size:17 final size:19
Alignment explanation
Indices: 618792--618829 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
618782 TTATCATTTA
618792 TTTAACA-TTAAAA-TATT
1 TTTAACATTTAAAATTATT
*
618809 TTTAATATTTAAAATTATT
1 TTTAACATTTAAAATTATT
618828 TT
1 TT
618830 AATTAGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 6 0.33
19 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAACATTTAAAATTATT
Found at i:619263 original size:13 final size:13
Alignment explanation
Indices: 619245--619270 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
619235 GTTATGATTA
619245 ATATTTTATATTT
1 ATATTTTATATTT
619258 ATATTTTATATTT
1 ATATTTTATATTT
619271 TTAATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTTTATATTT
Found at i:619290 original size:22 final size:21
Alignment explanation
Indices: 619248--619298 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
619238 ATGATTAATA
*
619248 TTTTATATTTATATTTTATAT
1 TTTTATATTTATATTTGATAT
619269 TTTTAATATTTAT-TATTGATAT
1 TTTT-ATATTTATAT-TTGATAT
619291 TTATTATA
1 TT-TTATA
619299 ATTAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.19
22 19 0.73
23 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATATTTATATTTGATAT
Found at i:619303 original size:29 final size:28
Alignment explanation
Indices: 619236--619304 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
619226 CAGATTTATG
* *
619236 TTATGATTAATATTTTATATTTATATTT
1 TTATAATTAATATTTTATATTGATATTT
**
619264 TATATTTTTAATA-TTTATTATTGATATTT
1 T-TATAATTAATATTTTA-TATTGATATTT
619293 ATTATAATTAAT
1 -TTATAATTAAT
619305 TATAATAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 5 0.15
29 27 0.82
30 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (28 bp):
TTATAATTAATATTTTATATTGATATTT
Found at i:620266 original size:14 final size:14
Alignment explanation
Indices: 620244--620278 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
620234 GATCATAATC
*
620244 TAATATTATAATTT
1 TAATTTTATAATTT
*
620258 TTATTTTATAATTT
1 TAATTTTATAATTT
620272 TAATTTT
1 TAATTTT
620279 TTTCATCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TAATTTTATAATTT
Found at i:620624 original size:36 final size:37
Alignment explanation
Indices: 620537--620633 Score: 133
Period size: 36 Copynumber: 2.6 Consensus size: 37
620527 TTTCAAGTAA
*
620537 TTACTTAAAAAATTAATCTTGCAGATGAAACTAAAAAC
1 TTACTT-AAAAATTAATCTTGCATATGAAACTAAAAAC
* * * *
620575 TCACTTAAAAATTAATCTTGCATATG-CACTAGAAAT
1 TTACTTAAAAATTAATCTTGCATATGAAACTAAAAAC
620611 TTACTTAAAAATTAATCTTGCAT
1 TTACTTAAAAATTAATCTTGCAT
620634 GATCGGTGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 29 0.55
37 19 0.36
38 5 0.09
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.34
Consensus pattern (37 bp):
TTACTTAAAAATTAATCTTGCATATGAAACTAAAAAC
Found at i:625981 original size:33 final size:32
Alignment explanation
Indices: 625940--626004 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
625930 AACTCTTGTA
* *
625940 TGTATCAATACATTATGCTTTGTATCAATACAT
1 TGTATCAATACATGAT-CATTGTATCAATACAT
* *
625973 TGTATCAATATATGATCATTGTATCGATACAT
1 TGTATCAATACATGATCATTGTATCAATACAT
626005 ACACAATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (32 bp):
TGTATCAATACATGATCATTGTATCAATACAT
Found at i:628313 original size:20 final size:21
Alignment explanation
Indices: 628288--628342 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
628278 ACAATAAGGC
628288 AATGTATCGATACAT-ATGTG-
1 AATGTATCGATACATGAT-TGA
* *
628308 AATGTATCGATACCTGCTTGA
1 AATGTATCGATACATGATTGA
628329 AATGTATCGATACA
1 AATGTATCGATACA
628343 GTACTATGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (21 bp):
AATGTATCGATACATGATTGA
Found at i:628932 original size:13 final size:13
Alignment explanation
Indices: 628914--628939 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
628904 TACACAAAGT
628914 ATGTATCGATACA
1 ATGTATCGATACA
628927 ATGTATCGATACA
1 ATGTATCGATACA
628940 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:628937 original size:32 final size:33
Alignment explanation
Indices: 628896--628959 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
628886 TAGCCAAACG
**
628896 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
628928 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
628960 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:631177 original size:22 final size:22
Alignment explanation
Indices: 631150--631205 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
631140 TTGCAAGTTG
631150 AAATAAAGAACTTGGCTAATG-A
1 AAATAAAGAACTTGGCTAA-GAA
* *
631172 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAACTTGGCTAAGAA
631193 AAATAAA-AACTTG
1 AAATAAAGAACTTG
631206 CATGATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
AAATAAAGAACTTGGCTAAGAA
Found at i:635108 original size:13 final size:13
Alignment explanation
Indices: 635090--635128 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
635080 ACATTTTTCT
635090 TTGTATCGATACA
1 TTGTATCGATACA
635103 TTGTATCGATACA
1 TTGTATCGATACA
*
635116 CTGTATCGATACA
1 TTGTATCGATACA
635129 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:635292 original size:20 final size:19
Alignment explanation
Indices: 635251--635293 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
635241 ATCTTTTACA
635251 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
635271 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
635291 AAA
1 AAA
635294 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:637712 original size:21 final size:20
Alignment explanation
Indices: 637666--637718 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
637656 GTAGCCAAAC
**
637666 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
637686 -TGTATCGATACACAAAAAAA
1 TTGTATCGATACAC-AAAAAA
637706 TTGTATCGATACA
1 TTGTATCGATACA
637719 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:644397 original size:151 final size:151
Alignment explanation
Indices: 644134--644516 Score: 341
Period size: 151 Copynumber: 2.5 Consensus size: 151
644124 TTCCGAATTT
* *
644134 ATAATTTTCAAAATTCATAAAATATTATTGTTTATTTCAAATTAAATCAATTTAAAAAATTTAAT
1 ATAATTTTC-AAATTCATCAAATATTATTGTTTAATTCAAATTAAATCAATTTAAAAAATTTAAT
* ** *
644199 TTATTTTATGAGTTTTAAAAATATTTTTTGTTATTGAAATAAAAGTTTTCTA-T-GGTAAATTTT
65 TTATTTTATAAGTTTTAAAAATATTTTTTGTTATCCAAATAAAAGTTTTCTACTCCG-AAATTTT
644262 TTCAGTAT-GATTTTTCTAAGTTC
129 TTCAGT-TGGATTTTTCTAAGTTC
* * ** * * *
644285 ATAATTTTCAGAATTCTTCAAATATTATTTTTTAATTCGTATTAAATTAGTTTTAAAAATTTTAA
1 ATAATTTTCA-AATTCATCAAATATTATTGTTTAATTCAAATTAAATCA-ATTTAAAAAATTTAA
*** * *
644350 TTTATTTTATAAG-TTTCGTAAT-TTTTTTGTT-TCCAAAGTGTATAGTTTTCTACTCCGAAATT
64 TTTATTTTATAAGTTTTAAAAATATTTTTTGTTATCCAAA-T-AAAAGTTTTCTACTCCGAAATT
** *
644412 TTTTTGGTTGGATTTTTCTCAGTTC
127 TTTTCAGTTGGATTTTTCTAAGTTC
* * ** * * * * *
644437 AAAATTTT-AAATTTCATCAAATATTTTTACTAAATTC-AATTAAACCATTTTTATAAAATTCAA
1 ATAATTTTCAAA-TTCATCAAATATTATTGTTTAATTCAAATTAAATCA-ATTTAAAAAATTTAA
* *
644500 TCTATTTTATGAGTTTT
64 TTTATTTTATAAGTTTT
644517 GAATTTTTTT
Statistics
Matches: 187, Mismatches: 36, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
149 4 0.02
150 43 0.23
151 81 0.43
152 58 0.31
153 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (151 bp):
ATAATTTTCAAATTCATCAAATATTATTGTTTAATTCAAATTAAATCAATTTAAAAAATTTAATT
TATTTTATAAGTTTTAAAAATATTTTTTGTTATCCAAATAAAAGTTTTCTACTCCGAAATTTTTT
CAGTTGGATTTTTCTAAGTTC
Found at i:646152 original size:166 final size:166
Alignment explanation
Indices: 645928--646355 Score: 517
Period size: 166 Copynumber: 2.6 Consensus size: 166
645918 GCATTTTTAA
*
645928 AAATTTCTATTATTCCTATGGTCTTCTATAGGGGTATAGAAAATTTTAAAACTTTTCATATCCTC
1 AAATTTCTATTATTCCTATGGTCTTCTATAGAGGTATAGAAAATTTTAAAACTTTTCATATCCT-
** * * *
645993 TT-GATTTTTCGTTGGGTACGAAATGAAATTTTTAAAAGTTTAGGGACTAAATAGCAAATTTAGT
65 TTCGATTTTTCACTGGATACGAAATGAAATTTTTAAAAGTTTAGAGACTAAATAGCAAATTTAGA
* *
646057 TTTTAGAAG-AAAATTAGCTATCTTAGTCATTTTATTT
130 TTTTAGAAGAAAAATAATC-ATCTTAGTCATTTTATTT
* * * * *
646094 AAATTTTTATTATTTCTATGGTCTTCTGTAGAGGTATAGAAACTTTTAAAATTTTTCATATCCTT
1 AAATTTCTATTATTCCTATGGTCTTCTATAGAGGTATAGAAAATTTTAAAACTTTTCATATCCTT
* * * *
646159 TCGGTTTTTCACTGGATATGAAATGAAATTTTTAAAAGTTTAGAGACTAAGTAGCAAATTTGGAT
66 TCGATTTTTCACTGGATACGAAATGAAATTTTTAAAAGTTTAGAGACTAAATAGCAAATTTAGAT
*
646224 TTTAGAAGAAAAATAATCATCTTAGTCATTTTCTTT
131 TTTAGAAGAAAAATAATCATCTTAGTCATTTTATTT
* * * * **
646260 AGATTTCTATTATTCCTATGGCCTTCCATAG-GAATATA-AAAATTTTTAAAACTTTTTGTATCC
1 AAATTTCTATTATTCCTATGGTCTTCTATAGAG-GTATAGAAAA-TTTTAAAACTTTTCATATCC
* * *
646323 TCTC-AGTTTTCCATCTGG-TACGAAATGTAATTT
64 TTTCGA-TTTTTCA-CTGGATACGAAATGAAATTT
646356 CAAAAATTTA
Statistics
Matches: 222, Mismatches: 34, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
165 6 0.03
166 205 0.92
167 11 0.05
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (166 bp):
AAATTTCTATTATTCCTATGGTCTTCTATAGAGGTATAGAAAATTTTAAAACTTTTCATATCCTT
TCGATTTTTCACTGGATACGAAATGAAATTTTTAAAAGTTTAGAGACTAAATAGCAAATTTAGAT
TTTAGAAGAAAAATAATCATCTTAGTCATTTTATTT
Found at i:652101 original size:19 final size:19
Alignment explanation
Indices: 652077--652159 Score: 124
Period size: 19 Copynumber: 4.7 Consensus size: 19
652067 CAATAGCTAA
652077 TTATGTATCGATACAACAC
1 TTATGTATCGATACAACAC
652096 TTATGTATCGATACAACAC
1 TTATGTATCGATACAACAC
652115 TTATGTATCGAT---ACA-
1 TTATGTATCGATACAACAC
652130 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAACAC
652147 TTATGTATCGATA
1 TTATGTATCGATA
652160 TAAATCGTTG
Statistics
Matches: 58, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 6 0.10
18 1 0.02
19 41 0.71
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAACAC
Done.