Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, whole genome shotgun sequence
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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 5 of 84
Found at i:424502 original size:29 final size:29
Alignment explanation
Indices: 424446--424502 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
424436 CAATAATATA
* *
424446 AAATAAAATAAAAACTCAAACTATAAAAT
1 AAATAAAATAAAAACTAAAACTAAAAAAT
* * *
424475 AAATAAAATTAAAATTAAAATTAAAAAA
1 AAATAAAATAAAAACTAAAACTAAAAAA
424503 ACCTGCGATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (29 bp):
AAATAAAATAAAAACTAAAACTAAAAAAT
Found at i:425006 original size:21 final size:20
Alignment explanation
Indices: 424982--425024 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
424972 CTTAATCCTC
*
424982 AAAAGCCAAATCTAAACCTAA
1 AAAAGCCAAATC-AAACCCAA
**
425003 AAAATTCAAATCAAACCCAA
1 AAAAGCCAAATCAAACCCAA
425023 AA
1 AA
425025 TTCACAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.60, C:0.23, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAGCCAAATCAAACCCAA
Found at i:425406 original size:5 final size:5
Alignment explanation
Indices: 425382--425586 Score: 108
Period size: 5 Copynumber: 39.4 Consensus size: 5
425372 TATTGTATTG
* *
425382 TATAG TATAA TATAA TATAA TATAA TAATAAA TATAA TATAA TAATGA
1 TATAA TATAA TATAA TATAA TATAA T-AT-AA TATAA TATAA T-ATAA
* * * * * * * *
425430 TATAA CATGA TGTAA TAAAA TATAA TAATAA TATAA TGTAC TATAC CATAA
1 TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA TATAA
* * * * * * * *
425481 TATAC TATCA TACAA TATAC TATAC TATAA TATAC TAT-A TAATAA TACAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA
* * * *
425531 TATAA TACAC TAT-A TAATAA TAGACCA TAATAA TATAC TATAA TAATAA
1 TATAA TATAA TATAA T-ATAA TATA--A T-ATAA TATAA TATAA T-ATAA
425580 TATAA TA
1 TATAA TA
425587 GAAAAATAAA
Statistics
Matches: 149, Mismatches: 39, Indels: 24
0.70 0.18 0.11
Matches are distributed among these distances:
4 2 0.01
5 116 0.78
6 24 0.16
7 5 0.03
8 2 0.01
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (5 bp):
TATAA
Found at i:425979 original size:56 final size:56
Alignment explanation
Indices: 425853--426155 Score: 189
Period size: 56 Copynumber: 5.4 Consensus size: 56
425843 GGACTGAACC
* * * * * * * * *
425853 GCAAGTC-TGGAAAACTAACTTGGACCGAGTCAAGATCAAACAACTGAGACTAAACA
1 GCAAGTCTTGGAAAACGATC-TGGACTGAGCCAAAATCAAACAACTGGGATTGAATA
** * * * * **
425909 GTGAGTCTAGGAAAACGATTTGGACTGAGTCAAGATTGAACAACTGGGGATTGAATA
1 GCAAGTCTTGGAAAACGATCTGGACTGAGCCAAAATCAAACAACT-GGGATTGAATA
* * * *
425966 GCAAGTCTTGAAAAATGATCTAGACTGAGCCAAAATCAAACAACTGGGATTGAATT
1 GCAAGTCTTGGAAAACGATCTGGACTGAGCCAAAATCAAACAACTGGGATTGAATA
* * ** * * *
426022 GTAAGTCTTGGAAAACGATCTGGACAGAGCTGAAATCAAGCGACTGGGATTAAATCA
1 GCAAGTCTTGGAAAACGATCTGGACTGAGCCAAAATCAAACAACTGGGATTGAAT-A
* * * * * ** ** *
426079 -CAAGT-TTGAAAAACTAACTTGGACTGAGTCGAGGTCAAACAACTAAGATTGAATT
1 GCAAGTCTTGGAAAACGATC-TGGACTGAGCCAAAATCAAACAACTGGGATTGAATA
* *
426134 GCGAGTCTTGGAAAATGATCTG
1 GCAAGTCTTGGAAAACGATCTG
426156 AACTAGGCTG
Statistics
Matches: 185, Mismatches: 56, Indels: 12
0.73 0.22 0.05
Matches are distributed among these distances:
55 10 0.05
56 117 0.63
57 58 0.31
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (56 bp):
GCAAGTCTTGGAAAACGATCTGGACTGAGCCAAAATCAAACAACTGGGATTGAATA
Found at i:426213 original size:112 final size:110
Alignment explanation
Indices: 425957--426222 Score: 257
Period size: 112 Copynumber: 2.4 Consensus size: 110
425947 AACAACTGGG
* * **
425957 GATTGAATAGCAAGTCTTGAAAAATGATCTAGACTGAGCCAAAATCAAACAACTGGGATTGAATT
1 GATTGAATA-CAAGTC-TGAAAAATGATTTGGACTGAGCCAAAATCAAACAACTAAGATTGAATT
* * * *
426022 GTAAGTCTTGGAAAACGATCTGGACAGAGCTGAAATCAAGCGACTGG
64 GCAAGTCTTGGAAAACGATCTGAACAGAGCTGAAATCAAGCGAATGA
* * * * * * **
426069 GATTAAATCACAAGTTTGAAAAACTAACTTGGACTGAGTCGAGGTCAAACAACTAAGATTGAATT
1 GATTGAAT-ACAAGTCTGAAAAA-TGATTTGGACTGAGCCAAAATCAAACAACTAAGATTGAATT
* * * *
426134 GCGAGTCTTGGAAAATGATCTGAACTAG-GCTGAGATCGAA-TGAATGA
64 GCAAGTCTTGGAAAACGATCTGAAC-AGAGCTGAAATC-AAGCGAATGA
*
426181 GATTGAACTACAAGTCTGAAAAAGTGATTTGGACAGAGCCAA
1 GATTGAA-TACAAGTCTGAAAAA-TGATTTGGACTGAGCCAA
426223 GATCGAGTAA
Statistics
Matches: 121, Mismatches: 28, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
111 7 0.06
112 108 0.89
113 6 0.05
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (110 bp):
GATTGAATACAAGTCTGAAAAATGATTTGGACTGAGCCAAAATCAAACAACTAAGATTGAATTGC
AAGTCTTGGAAAACGATCTGAACAGAGCTGAAATCAAGCGAATGA
Found at i:436837 original size:4 final size:4
Alignment explanation
Indices: 436830--436862 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
436820 TAATAGATAT
436830 AATA AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA AATA A
436863 GCAAATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:437578 original size:9 final size:10
Alignment explanation
Indices: 437566--437606 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
437556 TTTCTTCTTT
437566 TGTATT-TTA
1 TGTATTATTA
437575 TGTATT-TTA
1 TGTATTATTA
437584 T-TATTATTA
1 TGTATTATTA
437593 T-TATTATTA
1 TGTATTATTA
437602 TGTAT
1 TGTAT
437607 ATCTTTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 4 0.13
9 23 0.77
10 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (10 bp):
TGTATTATTA
Found at i:438329 original size:19 final size:20
Alignment explanation
Indices: 438297--438342 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
438287 TTCGGCCAAC
*
438297 TTCCGGCGAAA-TTTCCAGA
1 TTCCGACGAAATTTTCCAGA
*
438316 TTCCGACGACATTTTCCAGA
1 TTCCGACGAAATTTTCCAGA
*
438336 ATCCGAC
1 TTCCGAC
438343 ACCGGTGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
TTCCGACGAAATTTTCCAGA
Found at i:438886 original size:57 final size:57
Alignment explanation
Indices: 438797--439179 Score: 428
Period size: 57 Copynumber: 6.6 Consensus size: 57
438787 AAAAAATTCC
438797 AAAAAAATATATTTTAGGG-AAAGTTGAAAGTATCAATTT-CTTAGAAAT-AATTTCA
1 AAAAAAATAT-TTTTAGGGAAAAGTTGAAAGTATCAATTTCCTTAGAAATAAATTTCA
* *
438852 AAAAATATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTCCTCAGAAATAAATTCCAAA
1 AAAAA-A-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTCCTTAGAAATAAATTTC--A
* *
438913 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTCCTTAAGGAATAAATTTCC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTCCTT-AGAAATAAATTTCA
* *
438971 AAAAATA-ATTTTTAGGGAAAAGTTGAAA-TATCAATTTTCCTTAAAAGAAAAAATAAATTTCC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA-TTTCCTT---AG---AAATAAATTTCA
439033 AAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTCCTTAGAAATAAATTTTCA
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTCCTTAGAAATAAA-TTTCA
*** * *
439090 AAAAAAGGGTTTTGA-GGAAAA-TTGAAAGTATCAATTTCCTT-GAAAATCGAAATTTCC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTCCTTAG-AAAT--AAATTTCA
*
439147 AAAAAAATA-TTTTGGGGAAAAGTT-AAAGTATCA
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCA
439180 TTCCCTAAAA
Statistics
Matches: 285, Mismatches: 20, Indels: 44
0.82 0.06 0.13
Matches are distributed among these distances:
55 6 0.02
56 49 0.17
57 97 0.34
58 19 0.07
59 46 0.16
60 12 0.04
61 6 0.02
62 38 0.13
63 12 0.04
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (57 bp):
AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTCCTTAGAAATAAATTTCA
Found at i:442996 original size:9 final size:9
Alignment explanation
Indices: 442984--443026 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
442974 GAAAAATGAG
*
442984 AAAAGAGAA
1 AAAAAAGAA
442993 AAAAATA-AA
1 AAAAA-AGAA
443002 AAAAAAGAAA
1 AAAAAAG-AA
443012 AAAAAAGAA
1 AAAAAAGAA
443021 AAAAAA
1 AAAAAA
443027 TGAGAAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.63
10 10 0.33
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.02
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:442998 original size:18 final size:18
Alignment explanation
Indices: 442984--443025 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
442974 GAAAAATGAG
*
442984 AAAAGAGAAAAAAATAAA
1 AAAAAAGAAAAAAATAAA
443002 AAAAAAGAAAAAAA-AAGA
1 AAAAAAGAAAAAAATAA-A
443020 AAAAAA
1 AAAAAA
443026 ATGAGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (18 bp):
AAAAAAGAAAAAAATAAA
Found at i:443004 original size:10 final size:10
Alignment explanation
Indices: 442984--443026 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
442974 GAAAAATGAG
*
442984 AAAAGAGAAA
1 AAAAGAAAAA
*
442994 AAAATAAAAA
1 AAAAGAAAAA
443004 AAAAGAAAAA
1 AAAAGAAAAA
443014 AAAAGAAAAA
1 AAAAGAAAAA
443024 AAA
1 AAA
443027 TGAGAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.02
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:443009 original size:20 final size:20
Alignment explanation
Indices: 442984--443034 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
442974 GAAAAATGAG
*
442984 AAAAGAGAAAAAAATAAAAA
1 AAAAGAGAAAAAAAGAAAAA
*
443004 AAAAGAAAAAAAAAGAAAAA
1 AAAAGAGAAAAAAAGAAAAA
*
443024 AAATGAGAAAA
1 AAAAGAGAAAA
443035 TGAAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (20 bp):
AAAAGAGAAAAAAAGAAAAA
Found at i:443034 original size:10 final size:10
Alignment explanation
Indices: 442991--443042 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
442981 GAGAAAAGAG
442991 AAAAAAAT-A
1 AAAAAAATGA
*
443000 AAAAAAAAGA
1 AAAAAAATGA
*
443010 AAAAAAAAGA
1 AAAAAAATGA
443020 AAAAAAATG-
1 AAAAAAATGA
*
443029 -AGAAAATGA
1 AAAAAAATGA
443038 AAAAA
1 AAAAA
443043 TAAAAAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 7 0.19
9 7 0.19
10 22 0.61
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.06
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:443034 original size:18 final size:16
Alignment explanation
Indices: 442984--443052 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 16
442974 GAAAAATGAG
442984 AAAAGAGAAAAAAAT-A
1 AAAAGA-AAAAAAATAA
*
443000 AAAA-AAAAGAAA-AA
1 AAAAGAAAAAAAATAA
443014 AAAAGAAAAAAAATGAGA
1 AAAAGAAAAAAAAT-A-A
* *
443032 AAATGAAAAAATA-AA
1 AAAAGAAAAAAAATAA
443047 AAAAGA
1 AAAAGA
443053 TATTCAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
14 11 0.26
15 14 0.33
16 5 0.12
17 1 0.02
18 12 0.28
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAAAAATAA
Found at i:444402 original size:41 final size:41
Alignment explanation
Indices: 444295--444419 Score: 218
Period size: 40 Copynumber: 3.1 Consensus size: 41
444285 GTCTAGGAGT
444295 ATTTAC-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
* *
444335 ATTTA-TTTTCCAAAGTTTGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
444375 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
444416 ATTT
1 ATTT
444420 CCAGATTCCG
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
40 42 0.53
41 37 0.47
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.42
Consensus pattern (41 bp):
ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:444439 original size:19 final size:20
Alignment explanation
Indices: 444414--444470 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
444404 TTTAGAGGAG
444414 CAATTTCCAGATTCCGGCGA
1 CAATTTCCAGATTCCGGCGA
*
444434 -AATTTCCAGATTCCGGTGA
1 CAATTTCCAGATTCCGGCGA
* *
444453 CATTTTCCAGAATCCGGC
1 CAATTTCCAGATTCCGGC
444471 ACCGGTGTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (20 bp):
CAATTTCCAGATTCCGGCGA
Found at i:444982 original size:59 final size:58
Alignment explanation
Indices: 444911--445318 Score: 565
Period size: 59 Copynumber: 6.9 Consensus size: 58
444901 TAAAAATAAA
*
444911 AAATTTCAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAATTTCCAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *
444970 AAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
1 AAATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
445028 AAATTTCCAAAAAAAACTATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAAT
1 AAATTTCC-AAAAAAA-TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AAT
* *
445088 AAATTTCCAAAAATA-ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAAT
1 AAATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAAT
*
445150 AAATTTCCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAATTTCC-AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* **
445209 AAATTTTCAAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAAT
1 AAATTTCCAAAAAAA-TATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT
445268 CGAAATTTCCAAAAAAATATTTTTA-GGAAAAGTTGAAAGTATCAATTTTCC
1 --AAATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
445319 CTAAAAAAAA
Statistics
Matches: 316, Mismatches: 16, Indels: 34
0.86 0.04 0.09
Matches are distributed among these distances:
57 35 0.11
58 59 0.19
59 101 0.32
60 53 0.17
61 16 0.05
62 11 0.03
63 7 0.02
64 34 0.11
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.34
Consensus pattern (58 bp):
AAATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:445134 original size:27 final size:27
Alignment explanation
Indices: 445046--445135 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 27
445036 AAAAAAAACT
445046 ATTTTTAGGGAAAAGTTGAAAGTATCA
1 ATTTTTAGGGAAAAGTTGAAAGTATCA
* * * * *
445073 ATTTTCCTTAAGAATAAATTTCCAAA-AAT-A
1 A-TTT--TTAGGGA-AAAGTT-GAAAGTATCA
445103 ATTTTTAGGGAAAAGTTGAAAGTATCA
1 ATTTTTAGGGAAAAGTTGAAAGTATCA
445130 ATTTTT
1 ATTTTT
445136 CTTAAAAGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.07
26 7 0.15
27 13 0.28
28 3 0.07
29 3 0.07
30 7 0.15
31 7 0.15
32 3 0.07
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (27 bp):
ATTTTTAGGGAAAAGTTGAAAGTATCA
Found at i:446168 original size:25 final size:24
Alignment explanation
Indices: 446138--446205 Score: 86
Period size: 23 Copynumber: 2.8 Consensus size: 24
446128 TAAGATTAGT
446138 AATATAAAATAAAATAAAAAGTCAA
1 AATATAAAATAAAATAAAAA-TCAA
*
446163 AATATAAAAT-AAAT-AAAATTAA
1 AATATAAAATAAAATAAAAATCAA
446185 AATTATAAAATAAAAGTAAAA
1 AA-TATAAAATAAAA-TAAAA
446206 TAAAAAAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
22 5 0.13
23 12 0.32
24 7 0.18
25 11 0.29
26 3 0.08
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (24 bp):
AATATAAAATAAAATAAAAATCAA
Found at i:446175 original size:30 final size:29
Alignment explanation
Indices: 446141--446210 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
446131 GATTAGTAAT
446141 ATAAAATAAAATAAAAAGTCA-AAATATAAA
1 ATAAAATAAAATAAAAA-TCATAAA-ATAAA
* *
446171 AT-AAATAAAATTAAAATTATAAAATAAA
1 ATAAAATAAAATAAAAATCATAAAATAAA
446199 AGTAAAATAAAA
1 A-TAAAATAAAA
446211 AAAGGAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.23
29 17 0.49
30 10 0.29
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (29 bp):
ATAAAATAAAATAAAAATCATAAAATAAA
Found at i:446194 original size:14 final size:15
Alignment explanation
Indices: 446161--446210 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
446151 ATAAAAAGTC
446161 AAAATATAAAATAAAT
1 AAAAT-TAAAATAAAT
*
446177 AAAATTAAAAT-TAT
1 AAAATTAAAATAAAT
446191 AAAA-TAAAAGTAAAAT
1 AAAATTAAAA-T-AAAT
446207 AAAA
1 AAAA
446211 AAAGGAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 5 0.17
14 7 0.24
15 6 0.21
16 11 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAATTAAAATAAAT
Found at i:446213 original size:19 final size:19
Alignment explanation
Indices: 446166--446213 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
446156 AAGTCAAAAT
*
446166 ATAAAATAAATAAAATTAAA
1 ATAAAA-AAATAAAAGTAAA
* *
446186 ATTATAAAATAAAAGTAAA
1 ATAAAAAAATAAAAGTAAA
446205 ATAAAAAAA
1 ATAAAAAAA
446214 GGAAAACTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (19 bp):
ATAAAAAAATAAAAGTAAA
Found at i:447110 original size:5 final size:5
Alignment explanation
Indices: 447084--447200 Score: 99
Period size: 5 Copynumber: 22.0 Consensus size: 5
447074 GAAAGAAAAA
* *
447084 ATAAT AATAAT AATAAT ATAGT ATAGT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * * * *
447136 AATAAT AATAAAT ATGAT ATAAT AATGAT ATAAC ATGAT GTAAT AAAAT
1 -ATAAT -AT-AAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT
447185 ATAAT AATAAT ATAAT
1 ATAAT -ATAAT ATAAT
447201 GTACTATACC
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
5 60 0.65
6 30 0.32
7 3 0.03
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:447161 original size:3 final size:3
Alignment explanation
Indices: 447083--447146 Score: 61
Period size: 3 Copynumber: 23.7 Consensus size: 3
447073 AGAAAGAAAA
* *
447083 AAT AAT AAT AAT AAT AAT -AT AGT -AT AGT -AT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
447126 -AT AAT -AT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
447147 ATATGATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
2 12 0.24
3 38 0.76
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:447246 original size:15 final size:15
Alignment explanation
Indices: 447196--447261 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 15
447186 TAATAATAAT
* *
447196 ATAATGTACTATACC
1 ATAATATACTATACA
** * *
447211 ATAATATGTTATCCT
1 ATAATATACTATACA
*
447226 ACAATATACTATACA
1 ATAATATACTATACA
*
447241 ATAATATACTATATA
1 ATAATATACTATACA
447256 ATAATA
1 ATAATA
447262 CATAATAACA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (15 bp):
ATAATATACTATACA
Found at i:447283 original size:15 final size:14
Alignment explanation
Indices: 447231--447284 Score: 53
Period size: 15 Copynumber: 4.0 Consensus size: 14
447221 ATCCTACAAT
*
447231 ATACTATACAATAA
1 ATACTATATAATAA
447245 TATACTATATAAT-A
1 -ATACTATATAATAA
447259 ATAC---ATAATAA
1 ATACTATATAATAA
447270 CATACTATATAATAA
1 -ATACTATATAATAA
447285 TAGACCATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
10 5 0.15
11 1 0.03
12 4 0.12
13 4 0.12
14 1 0.03
15 18 0.55
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (14 bp):
ATACTATATAATAA
Found at i:447285 original size:28 final size:25
Alignment explanation
Indices: 447240--447321 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 25
447230 TATACTATAC
*
447240 AATAATATACTAT-ATAATAATACAT
1 AATAA-ATATTATAATAATAATACAT
*
447265 AATAACATACTATATAATAATAGA-CCAT
1 AATAA-ATA-T-TATAATAATA-ATACAT
*
447293 AATAATTATTATAATAATAAT--AT
1 AATAAATATTATAATAATAATACAT
447316 AATAAA
1 AATAAA
447322 AAAATCAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
23 7 0.15
24 1 0.02
25 18 0.38
26 1 0.02
27 5 0.11
28 14 0.30
29 1 0.02
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.34
Consensus pattern (25 bp):
AATAAATATTATAATAATAATACAT
Found at i:447294 original size:25 final size:25
Alignment explanation
Indices: 447238--447311 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
447228 AATATACTAT
447238 ACAATAATATACTATATAATAATAC
1 ACAATAATATACTATATAATAATAC
* * *
447263 ATAATAACATACTATATAATAATAG
1 ACAATAATATACTATATAATAATAC
* *
447288 ACCATAATA-ATTATTATAATAATA
1 ACAATAATATACTA-TATAATAATA
447312 ATATAATAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 3 0.07
25 38 0.93
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.34
Consensus pattern (25 bp):
ACAATAATATACTATATAATAATAC
Found at i:448169 original size:62 final size:62
Alignment explanation
Indices: 448048--448341 Score: 291
Period size: 62 Copynumber: 4.8 Consensus size: 62
448038 AAAAAATGTA
** * *
448048 TTCAATAATCCCTTTTAAAAAATTAGAGGGGATTATTGAAACCAT-TTTTTTGC-TAAAATGCC
1 TTCAATAATCCCTTTTAAAAAATTAGAGGGGATTATTG-AA-GGTGTTTTTGGCAGAAAATGCC
* * * *
448110 TTCAATATTCCCTTTTAAAAAATTAGAGGGGATTATTGAAGGTGATTTTGGCTTG-AAATGTC
1 TTCAATAATCCCTTTTAAAAAATTAGAGGGGATTATTGAAGGTGTTTTTGGC-AGAAAATGCC
** * * *
448172 TTCAATAATCTCCTCATAAAAAATT------GATTATTGAAGGTATTTTTTGTAGAAAATGCC
1 TTCAATAATC-CCTTTTAAAAAATTAGAGGGGATTATTGAAGGTGTTTTTGGCAGAAAATGCC
* ** *
448229 TTCAATAATCCCCTTTAAAAAATTAGAATGGATTATTGAAGGTGTTTTTAGCAGAAAATGCC
1 TTCAATAATCCCTTTTAAAAAATTAGAGGGGATTATTGAAGGTGTTTTTGGCAGAAAATGCC
* * * * *
448291 TTTAATAATCCCTTCTAAAAAATCAAAGGGGATTATTGAAGGCGTTTTTGG
1 TTCAATAATCCCTTTTAAAAAATTAGAGGGGATTATTGAAGGTGTTTTTGG
448342 TCATCAACTT
Statistics
Matches: 190, Mismatches: 31, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
56 12 0.06
57 34 0.18
60 1 0.01
61 8 0.04
62 123 0.65
63 12 0.06
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (62 bp):
TTCAATAATCCCTTTTAAAAAATTAGAGGGGATTATTGAAGGTGTTTTTGGCAGAAAATGCC
Found at i:449864 original size:61 final size:61
Alignment explanation
Indices: 449790--449966 Score: 162
Period size: 61 Copynumber: 2.9 Consensus size: 61
449780 TTTAGATAGA
* * *
449790 AAACGCCTTCAATAATCCCCTTTAAAAAATTGGAGGGAATTATTGAAGGTTTTTTTCCCCG
1 AAACACCTTCAATAATCCCCTTTAAAAAATTGGAGGGAATTATTGAAGGCTTTTTTCCCAG
* * * * * **
449851 AAACACCTTCAATAAT-CCCTCATAAAAGA-TAGAGGGGATTATTGAAAGCTTTTTTGGCAG
1 AAACACCTTCAATAATCCCCT-TTAAAAAATTGGAGGGAATTATTGAAGGCTTTTTTCCCAG
* *** * *
449911 AAA-ATGCATTCAATAATCTTTTTTAAAAAATTGGAGGAAATTATTGAAGGCATTTT
1 AAACA--CCTTCAATAATCCCCTTTAAAAAATTGGAGGGAATTATTGAAGGCTTTTT
449967 AGCAAAAAAA
Statistics
Matches: 90, Mismatches: 21, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
59 1 0.01
60 31 0.34
61 37 0.41
62 21 0.23
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (61 bp):
AAACACCTTCAATAATCCCCTTTAAAAAATTGGAGGGAATTATTGAAGGCTTTTTTCCCAG
Found at i:449904 original size:60 final size:61
Alignment explanation
Indices: 449790--449905 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 61
449780 TTTAGATAGA
* * * * *
449790 AAACGCCTTCAATAATCCCCTTTAAAAAATTGGAGGGAATTATTGAAGGTTTTTTTCCCCG
1 AAACACCTTCAATAATCCCCTATAAAAAATTAGAGGGAATTATTGAAAGCTTTTTTCCCCG
* *
449851 AAACACCTTCAATAAT-CCCTCATAAAAGA-TAGAGGGGATTATTGAAAGCTTTTTT
1 AAACACCTTCAATAATCCCCT-ATAAAAAATTAGAGGGAATTATTGAAAGCTTTTTT
449906 GGCAGAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
60 26 0.55
61 21 0.45
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (61 bp):
AAACACCTTCAATAATCCCCTATAAAAAATTAGAGGGAATTATTGAAAGCTTTTTTCCCCG
Found at i:455427 original size:52 final size:52
Alignment explanation
Indices: 455340--455498 Score: 194
Period size: 52 Copynumber: 3.0 Consensus size: 52
455330 TGGACAAGAA
* * *
455340 GACTTGCAAAAGAAAAATTCCAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAAAATTCTAAGAGGAAAG-GGATTCTTAATAGGCAAGTTT
* *
455392 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAAAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
* * * * *
455444 GACTTACTAGGAGAATAATTCTAAGAGGAGAGGGATTCTTAATTGAGCAAGTTT
1 GACTTGC-AAGAGAAAAATTCTAAGAGGAAAGGGATTCTTAATAG-GCAAGTTT
455498 G
1 G
455499 TATGGTATAA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
52 47 0.51
53 37 0.40
54 9 0.10
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAAAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:455465 original size:53 final size:52
Alignment explanation
Indices: 455365--455498 Score: 178
Period size: 53 Copynumber: 2.5 Consensus size: 52
455355 AATTCCAAGA
* *
455365 GAAAGAGGATTCTTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAAG
1 GAAAG-GGATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAG
* * *
455418 GAAAGGGATTCTTAATAGGCAAGTTTGACTTACTAGGAGAATAATTCTAAGAG
1 GAAAGGGATTCTTAATAGGCAAGTTTGACTTAC-AAGAGAAGAATTCTAAAAG
* *
455471 GAGAGGGATTCTTAATTGAGCAAGTTTG
1 GAAAGGGATTCTTAATAG-GCAAGTTTG
455499 TATGGTATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
52 26 0.36
53 37 0.51
54 9 0.12
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.28
Consensus pattern (52 bp):
GAAAGGGATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAG
Found at i:456026 original size:31 final size:30
Alignment explanation
Indices: 455982--456125 Score: 189
Period size: 31 Copynumber: 4.7 Consensus size: 30
455972 AGGCTTTTAG
455982 CCCAACAAATGGTATCAGAGCTGTGGTATTT
1 CCCAACAAATGGTATCAGAGCTGTGGTA-TT
* * *
456013 TCCAACAAGTGGTATCAGAGCTGTGGTGATC
1 CCCAACAAATGGTATCAGAGCTGTGGT-ATT
456044 CCCAACAAATGGTATCAGAGCTGTGGTATT
1 CCCAACAAATGGTATCAGAGCTGTGGTATT
* * *
456074 ACTCAACAAATGGTATCAGAGCTGTTGTGTT
1 -CCCAACAAATGGTATCAGAGCTGTGGTATT
*
456105 CCCTAACAAGTGGTATCAGAG
1 CCC-AACAAATGGTATCAGAG
456126 TTGAAGGTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
30 4 0.04
31 94 0.95
32 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (30 bp):
CCCAACAAATGGTATCAGAGCTGTGGTATT
Found at i:456048 original size:62 final size:62
Alignment explanation
Indices: 455982--456125 Score: 218
Period size: 62 Copynumber: 2.3 Consensus size: 62
455972 AGGCTTTTAG
* *
455982 CCCAACAAATGGTATCAGAGCTGTGGTATT-TTCCAACAAGTGGTATCAGAGCTGTGGTGATC
1 CCCAACAAATGGTATCAGAGCTGTGGTATTACT-CAACAAATGGTATCAGAGCTGTGGTGATC
* *
456044 CCCAACAAATGGTATCAGAGCTGTGGTATTACTCAACAAATGGTATCAGAGCTGTTGTGTTC
1 CCCAACAAATGGTATCAGAGCTGTGGTATTACTCAACAAATGGTATCAGAGCTGTGGTGATC
* *
456106 CCTAACAAGTGGTATCAGAG
1 CCCAACAAATGGTATCAGAG
456126 TTGAAGGTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
62 74 0.99
63 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (62 bp):
CCCAACAAATGGTATCAGAGCTGTGGTATTACTCAACAAATGGTATCAGAGCTGTGGTGATC
Found at i:456207 original size:25 final size:25
Alignment explanation
Indices: 456145--456224 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
456135 TGAAATATAA
* * * *
456145 GAAGAGTTGAAGATTCAAGATGTGA
1 GAAGAGCTGAAGGTTCGAGATGTGG
* *
456170 AAAGAGCTTAAGGTTCGAGATGTGG
1 GAAGAGCTGAAGGTTCGAGATGTGG
*
456195 GAAGAGCTGAAGGTTCGAGATATGG
1 GAAGAGCTGAAGGTTCGAGATGTGG
456220 GAAGA
1 GAAGA
456225 ACATGGTTTG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (25 bp):
GAAGAGCTGAAGGTTCGAGATGTGG
Found at i:456598 original size:52 final size:52
Alignment explanation
Indices: 456511--456667 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
456501 TGGACAAGAA
* * *
456511 GACTTGCAAAAGAAAAATTCCAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAAAATTCTAAGAGGAAAG-GGATTCTTAATAGGCAAGTTT
* *
456563 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAAAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
* * * *
456615 GACTTACAGGAGAATAATTCTAAGAGGAGAGGGATTCTTAAT-GAGCAAGTTT
1 GACTTGCAAGAGAAAAATTCTAAGAGGAAAGGGATTCTTAATAG-GCAAGTTT
456667 G
1 G
456668 TATGGTTATA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 1 0.01
52 87 0.94
53 5 0.05
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (52 bp):
GACTTGCAAGAGAAAAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:458252 original size:13 final size:14
Alignment explanation
Indices: 458233--458267 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
458223 AATGATAAAA
458233 ATTTATTAA-TGAT
1 ATTTATTAATTGAT
*
458246 TTTTATTAATTGAT
1 ATTTATTAATTGAT
458260 ATTTATTA
1 ATTTATTA
458268 TTTTCAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (14 bp):
ATTTATTAATTGAT
Found at i:460608 original size:2 final size:2
Alignment explanation
Indices: 460601--460633 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
460591 TCTTACTCTG
*
460601 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
460634 AGTTGAGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:461117 original size:23 final size:23
Alignment explanation
Indices: 461091--461135 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
461081 ACTAAAAATT
* *
461091 ATAATAAAATAACATATAAAAAA
1 ATAAAAAAATAAAATATAAAAAA
*
461114 ATAAAAAAATAAAATTTAAAAA
1 ATAAAAAAATAAAATATAAAAA
461136 TCGATAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (23 bp):
ATAAAAAAATAAAATATAAAAAA
Found at i:462145 original size:23 final size:21
Alignment explanation
Indices: 462103--462149 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
462093 TTATTTCGTG
*
462103 TTTTAACCAATTAAATAAGAAT
1 TTTTAACCAATTAAAAAAG-AT
462125 TTTTAAACC-ATTAAAAAAAGAT
1 TTTT-AACCAATT-AAAAAAGAT
462147 TTT
1 TTT
462150 ATAGAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (21 bp):
TTTTAACCAATTAAAAAAGAT
Found at i:462438 original size:68 final size:65
Alignment explanation
Indices: 462360--462489 Score: 197
Period size: 68 Copynumber: 2.0 Consensus size: 65
462350 AACCAAATTT
* * *
462360 CCAAAGCATATAATTATAAATTATAGTTATATCTTTTTTTTTTATTAAAAGTGTCAACTTAAAAA
1 CCAAAACATATAAGTATAAATTATAGTTATATC--TTTTTCTTA-TAAAAGTGTCAACTTAAAAA
462425 ATG
63 ATG
*
462428 CCAAAACATATAAGTATAAATTATAGTTATATCTTTTTCTTATAAAAGTGTCAACTTCAAAA
1 CCAAAACATATAAGTATAAATTATAGTTATATCTTTTTCTTATAAAAGTGTCAACTTAAAAA
462490 TTTCTAAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
65 19 0.33
66 8 0.14
68 31 0.53
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (65 bp):
CCAAAACATATAAGTATAAATTATAGTTATATCTTTTTCTTATAAAAGTGTCAACTTAAAAAATG
Found at i:463901 original size:14 final size:14
Alignment explanation
Indices: 463882--463912 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
463872 GTGATTTATT
463882 AAATATTTTATAAA
1 AAATATTTTATAAA
*
463896 AAATATTTTCTAAA
1 AAATATTTTATAAA
463910 AAA
1 AAA
463913 AGATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATTTTATAAA
Found at i:463922 original size:13 final size:12
Alignment explanation
Indices: 463906--463941 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
463896 AAATATTTTC
463906 TAAAAAAAGATAA
1 TAAAAAAA-ATAA
463919 TAAAAAATAATAA
1 TAAAAAA-AATAA
463932 TAAAAAAAAT
1 TAAAAAAAAT
463942 CTTTTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 18 0.82
14 1 0.05
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (12 bp):
TAAAAAAAATAA
Found at i:474751 original size:58 final size:57
Alignment explanation
Indices: 474461--475063 Score: 488
Period size: 61 Copynumber: 10.2 Consensus size: 57
474451 TGCCTTTATG
* * * *
474461 CAAGAAAAATTGATACTTTTAACTTTTTCTC-AAAATACCTCTTTTGAAATTTGTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATA-CT-TTTTAAAATTT-TTTTTT
* * *
474520 CAAGGAAAATTGATATTTTTAAC-TTTTCTTCAAAAATATCTTTTTTCAAAATTTTTAATTT
1 CAAGGAAAATTGATACTTTCAACTTTTTC-TCAAAAATA-C-TTTTT-AAAATTTTT-TTTT
* * *
474581 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAATTAATTTTTTTAAAATTTTTTTATT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAAT-A-CTTTTTAAAATTTTTTT-TT
* * *
474641 ACCAAGGAAAATTGATACTTTTAA-TTTCTCCTCAAAAAATGCTTTTTAAAATCTTTTTTTT
1 --CAAGGAAAATTGATACTTTCAACTTT-TTCTC-AAAAATACTTTTTAAAAT-TTTTTTTT
* * * *
474702 CAAGGAGAATTGATA-TCTTCAACTTTTTCTCAAAAATACTTTTTGAAATCTTTGTTTG
1 CAAGGAAAATTGATACT-TTCAACTTTTTCTCAAAAATACTTTTTAAAAT-TTTTTTTT
* * **
474760 CAAGGAAAATTGATACCTTCAATTTTTTCTCAAAAATA-TATTTT-TTATTTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATACT-TTTTAAAATTTTT-TTTT
* * *
474817 CAAGAAAAATTGATCCTTTCAACTTTTTCTCAAAAATGC-TTTTAAAATTTTTTATTTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTTAAAA--TTTT-TTTTT
* * * *
474876 TAA-AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTTTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTT-AAAA---TTTTT-TTTT
** * **
474937 CAAGGAAAATTGATACTTTCAAAATTTTCTCAAAAATGCTTTTTGAATTTTTTTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTT-AA--AATTTTT-TTTT
* * * * * *
474998 CAAGAAAAATTGATACTTTTAACTTTTCCTTAAAAATATTTTTTAAAAATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTT-AAAATTTTTTTTT
475056 -AA-GAAAAT
1 CAAGGAAAAT
475064 CATTAAAAAT
Statistics
Matches: 450, Mismatches: 64, Indels: 63
0.78 0.11 0.11
Matches are distributed among these distances:
56 12 0.03
57 42 0.09
58 102 0.23
59 64 0.14
60 32 0.07
61 118 0.26
62 75 0.17
63 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.47
Consensus pattern (57 bp):
CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTTAAAATTTTTTTTT
Found at i:475148 original size:4 final size:4
Alignment explanation
Indices: 475141--475173 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
475131 CAAAATATAT
475141 ATAA ATAA AT-A ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
475174 TGATAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:475179 original size:12 final size:12
Alignment explanation
Indices: 475141--475182 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
475131 CAAAATATAT
475141 ATAAATAAA-TA
1 ATAAATAAATTA
*
475152 ATAAATAAATAA
1 ATAAATAAATTA
*
475164 ATAAATAAATTG
1 ATAAATAAATTA
475176 ATAAATA
1 ATAAATA
475183 GGATTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (12 bp):
ATAAATAAATTA
Found at i:476354 original size:85 final size:84
Alignment explanation
Indices: 476243--476723 Score: 320
Period size: 85 Copynumber: 5.7 Consensus size: 84
476233 TAGTGCAAGC
* * * * *
476243 CGAAATCCAAAAACATAATGATTTGGATCGAATCGAAGTCTAAAATAAGTAACTTGACTGAA-CT
1 CGAAATCC-AAAACATAATGACTTGGATCGAACCAAAGTCTAAAATAAATAACTTGACTAAATC-
**
476307 GGAGAAGGATCTAGCATAGGT
64 AAAGAAGGATCTAGCATAGGT
* *
476328 CGAAATCCAAAATCATAGTGACTTGGATGGAACCAAAGTCTAAAA-AGAATAACTTAGACTAAAT
1 CGAAATCCAAAA-CATAATGACTTGGATCGAACCAAAGTCTAAAATA-AATAACTT-GACTAAAT
* *
476392 CAAATAAGGATCTGGCATAGGT
63 CAAAGAAGGATCTAGCATAGGT
* * * *
476414 TGAAATCCAAAACAAAATGACCT-GAACTGAACCAAAGTCTAAAATAAATAACTTGGACTAAATC
1 CGAAATCCAAAACATAATGACTTGGATC-GAACCAAAGTCTAAAATAAATAACTT-GACTAAATC
* * *
476478 AAAGAAAGATCTGGCATAGGC
64 AAAGAAGGATCTAGCATAGGT
* * * * * *
476499 CAAAATCCAAAACAAAATGACTTAGGCT-AAATCGAAA-TCTAAAA-AGATTAACTTAGACTAAA
1 CGAAATCCAAAACATAATGACTT-GGATCGAA-CCAAAGTCTAAAATA-AATAACTT-GACTAAA
* * *
476561 CCAAAGAAAGATCT-GACATAGGC
62 TCAAAGAAGGATCTAG-CATAGGT
* * * * * **
476584 CAAAATCCAAAATGA-AATGACCTAGATGGAGTCAAAGTCTAAAA-AGAATAACTTGGACT-AAT
1 CGAAATCCAAAA-CATAATGACTTGGATCGAACCAAAGTCTAAAATA-AATAACTT-GACTAAAT
* * *
476646 CCAATGATGGATCTAGCATAAG-
63 -CAAAGAAGGATCTAGCATAGGT
* * * * * * *
476668 CTGAGATCCAAAACAAAATAACCTAGATAGAACTAAAGTCTAAAAGT-AATAACTTG
1 C-GAAATCCAAAACATAATGACTTGGATCGAACCAAAGTCTAAAA-TAAATAACTTG
476724 GACTGAGCCA
Statistics
Matches: 322, Mismatches: 54, Indels: 41
0.77 0.13 0.10
Matches are distributed among these distances:
84 19 0.06
85 260 0.81
86 41 0.13
87 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.21
Consensus pattern (84 bp):
CGAAATCCAAAACATAATGACTTGGATCGAACCAAAGTCTAAAATAAATAACTTGACTAAATCAA
AGAAGGATCTAGCATAGGT
Found at i:476679 original size:170 final size:170
Alignment explanation
Indices: 476278--476775 Score: 438
Period size: 170 Copynumber: 2.9 Consensus size: 170
476268 GATCGAATCG
* * ** * * * *
476278 AAGTCTAAAATAAGTAACTT-GACTGAA-CTGGAGAAGGATCTAGCATAGGTCGAAATCCAAAAT
1 AAGTCTAAAATAAATAACTTGGACTAAATC-AAAGAAAGATCTAGCATAAGCCAAAATCCAAAA-
* * * * * * * * * *
476341 CATAGTGACTTGGATGGAACCAAAGTCTAAAAAGAATAACTTAGACTAAATCAAATAAGGATCTG
64 CAAAATAACCTAGATAGAACGAAAGTCTAAAAAGAATAACTTAGACTAAACCAAAAAAAGATCTG
* **
476406 GCATAGGTTGAAATCCAAAACAAAATGACCTGAACTGAACCA
129 ACATAGGTCAAAATCCAAAACAAAATGACCTGAACTGAACCA
* *
476448 AAGTCTAAAATAAATAACTTGGACTAAATCAAAGAAAGATCTGGCATAGGCCAAAATCCAAAACA
1 AAGTCTAAAATAAATAACTTGGACTAAATCAAAGAAAGATCTAGCATAAGCCAAAATCCAAAACA
* * * * *
476513 AAATGACTTAGGCTA-AATCGAAA-TCTAAAAAGATTAACTTAGACTAAACCAAAGAAAGATCTG
66 AAATAACCTA-GATAGAA-CGAAAGTCTAAAAAGAATAACTTAGACTAAACCAAAAAAAGATCTG
* ** **
476576 ACATAGGCCAAAATCCAAAATGAAATGACCT-AGA-TGGAGTCA
129 ACATAGGTCAAAATCCAAAACAAAATGACCTGA-ACT-GAACCA
* ** ** *
476618 AAGTCTAAAA-AGAATAACTTGGACT-AATCCAATGATGGATCTAGCATAAGCTGAGATCCAAAA
1 AAGTCTAAAATA-AATAACTTGGACTAAAT-CAAAGAAAGATCTAGCATAAGCCAAAATCCAAAA
* * * *
476681 CAAAATAACCTAGATAGAACTAAAGTCT-AAAAGTAATAACTTGGACTGAGCCAAAAAAAGATCT
64 CAAAATAACCTAGATAGAACGAAAGTCTAAAAAG-AATAACTTAGACTAAACCAAAAAAAGATCT
* *
476745 GACATAAGTCAAAATCTGAAAACAAAATGAC
128 GACATAGGTCAAAATC-CAAAACAAAATGAC
476776 TTGGACTAAA
Statistics
Matches: 268, Mismatches: 48, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
169 18 0.07
170 199 0.74
171 50 0.19
172 1 0.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.20
Consensus pattern (170 bp):
AAGTCTAAAATAAATAACTTGGACTAAATCAAAGAAAGATCTAGCATAAGCCAAAATCCAAAACA
AAATAACCTAGATAGAACGAAAGTCTAAAAAGAATAACTTAGACTAAACCAAAAAAAGATCTGAC
ATAGGTCAAAATCCAAAACAAAATGACCTGAACTGAACCA
Found at i:476724 original size:85 final size:86
Alignment explanation
Indices: 476309--476775 Score: 398
Period size: 85 Copynumber: 5.5 Consensus size: 86
476299 ACTGAACTGG
* * * * * * * * *
476309 AGAAGGATCTAGCATAGGTCGAAATCCAAAATCATAGTGACTTGGATGGAACCAAAGTCTAAAAA
1 AGAAAGATCTGGCATAGGCCAAAATCCAAAA-CAAAATGACCTAGATAGAACCAAAGTCTAAAAA
*
476374 GAATAACTTAGACTAAAT-CAA
65 GAATAACTTGGACTAAATCCAA
* * ***
476395 ATAAGGATCTGGCATAGGTTGAAATCCAAAACAAAATGACCT-GA-ACTGAACCAAAGTCTAAAA
1 AGAAAGATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTAGATA--GAACCAAAGTCTAAAA
476458 TA-AATAACTTGGACTAAAT-CAA
64 -AGAATAACTTGGACTAAATCCAA
* * *
476480 AGAAAGATCTGGCATAGGCCAAAATCCAAAACAAAATGACTTAGGCTA-AATCGAAA-TCTAAAA
1 AGAAAGATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTA-GATAGAA-CCAAAGTCTAAAA
* *
476543 AGATTAACTTAGACTAAA-CCAA
64 AGAATAACTTGGACTAAATCCAA
* ** * **
476565 AGAAAGATCTGACATAGGCCAAAATCCAAAATGAAATGACCTAGATGGAGTCAAAGTCTAAAAAG
1 AGAAAGATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTAGATAGAACCAAAGTCTAAAAAG
476630 AATAACTTGGACT-AATCCAA
66 AATAACTTGGACTAAATCCAA
* ** * * ** * * *
476650 TGATGGATCTAGCATAAGCTGAGATCCAAAACAAAATAACCTAGATAGAACTAAAGTCT-AAAAG
1 AGAAAGATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTAGATAGAACCAAAGTCTAAAAAG
* *
476714 TAATAACTTGGACT-GAGCCAA
66 -AATAACTTGGACTAAATCCAA
* * * * *
476735 AAAAAGATCTGACATAAGTCAAAATCTGAAAACAAAATGAC
1 AGAAAGATCTGGCATAGGCCAAAATC-CAAAACAAAATGAC
476776 TTGGACTAAA
Statistics
Matches: 308, Mismatches: 59, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
84 15 0.05
85 246 0.80
86 45 0.15
87 1 0.00
88 1 0.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (86 bp):
AGAAAGATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTAGATAGAACCAAAGTCTAAAAAG
AATAACTTGGACTAAATCCAA
Found at i:477696 original size:45 final size:46
Alignment explanation
Indices: 477647--477744 Score: 144
Period size: 46 Copynumber: 2.2 Consensus size: 46
477637 TTTTTTTTAT
**
477647 TTTTTTGAAACTTAAATCG-CCTTTACGGGTTTTTAATTTGAGCTC
1 TTTTTTGAAACTTAAATCGCCCTTTACAAGTTTTTAATTTGAGCTC
** *
477692 TTTTTTTTAACTTAAATTGCCCTTTACAAGTTTTTAATTTGAGCTC
1 TTTTTTGAAACTTAAATCGCCCTTTACAAGTTTTTAATTTGAGCTC
477738 TTTTTTG
1 TTTTTTG
477745 TTTTTTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 16 0.35
46 30 0.65
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.52
Consensus pattern (46 bp):
TTTTTTGAAACTTAAATCGCCCTTTACAAGTTTTTAATTTGAGCTC
Found at i:477750 original size:54 final size:54
Alignment explanation
Indices: 477692--477796 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 54
477682 ATTTGAGCTC
* * *
477692 TTTTTTTT-AACTTAAATTGCCCTTTACAAGTTTTTAATTTGAGCTCTTTTTTG
1 TTTTTTTTAAACTTAAACTGCCCTTTACAAGTTTTCAATTTAAGCTCTTTTTTG
* * *
477745 TTTTTTTTAAACTTGAACTGCCTTTTACGAGTTTTCAATTTAAGCTCTTTTT
1 TTTTTTTTAAACTTAAACTGCCCTTTACAAGTTTTCAATTTAAGCTCTTTTT
477797 ATTCCTAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
53 8 0.18
54 37 0.82
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (54 bp):
TTTTTTTTAAACTTAAACTGCCCTTTACAAGTTTTCAATTTAAGCTCTTTTTTG
Found at i:479894 original size:17 final size:17
Alignment explanation
Indices: 479874--479908 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
479864 TAGAATAAGG
479874 ATAAGAATAAAAAAATA
1 ATAAGAATAAAAAAATA
* *
479891 ATAATAATAAATAAATA
1 ATAAGAATAAAAAAATA
479908 A
1 A
479909 AATGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
ATAAGAATAAAAAAATA
Found at i:480774 original size:27 final size:27
Alignment explanation
Indices: 480696--480839 Score: 115
Period size: 27 Copynumber: 5.5 Consensus size: 27
480686 AATTTAGAAC
* *
480696 AGATAAATAAAAAT-AATAATAATAAT
1 AGATAAATAATAATAAATAATATTAAT
*
480722 AGATAAAT-ATAAAAAAT-ATACCTTAAT
1 AGATAAATAATAATAAATAATA--TTAAT
480749 AGATAAATAATAATAAATAATATTAAT
1 AGATAAATAATAATAAATAATATTAAT
* ** *
480776 GGATAACCAATAA-AAATATATATTATT
1 AGATAAATAATAATAAATA-ATATTAAT
*
480803 AGATAAA-AATATATAAA-AATAATAA-
1 AGATAAATAATA-ATAAATAATATTAAT
*
480828 AAATAAA-AATAA
1 AGATAAATAATAA
480840 AATGGGCCAT
Statistics
Matches: 97, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
24 1 0.01
25 16 0.16
26 25 0.26
27 41 0.42
28 11 0.11
29 3 0.03
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (27 bp):
AGATAAATAATAATAAATAATATTAAT
Found at i:480791 original size:54 final size:54
Alignment explanation
Indices: 480696--480841 Score: 151
Period size: 54 Copynumber: 2.8 Consensus size: 54
480686 AATTTAGAAC
* *
480696 AGATAAATAAAAAT-AATAATAATAATAGATAAATATAAAAAATATACCTTAAT
1 AGATAAATAATAATAAATAATAATAATAGATAAATATAAAAAATATACATTAAT
* * * *
480749 AGATAAATAATAATAAATAATATTAATGGATAACCA-AT-AAAAATATATATTATT
1 AGATAAATAATAATAAATAATAATAATAGATAA--ATATAAAAAATATACATTAAT
* *
480803 AGATAAA-AATATATAAA-AATAATAA-AAATAAAAATAAAA
1 AGATAAATAATA-ATAAATAATAATAATAGATAAATATAAAA
480842 TGGGCCATCT
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
50 1 0.01
51 2 0.03
52 7 0.09
53 24 0.31
54 41 0.53
55 2 0.03
56 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (54 bp):
AGATAAATAATAATAAATAATAATAATAGATAAATATAAAAAATATACATTAAT
Found at i:480820 original size:10 final size:10
Alignment explanation
Indices: 480785--480832 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
480775 TGGATAACCA
480785 ATAAAAATAT
1 ATAAAAATAT
** * *
480795 ATATTATTAG
1 ATAAAAATAT
480805 ATAAAAATAT
1 ATAAAAATAT
480815 ATAAAAATA-
1 ATAAAAATAT
480824 ATAAAAATA
1 ATAAAAATA
480833 AAAATAAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 9 0.30
10 21 0.70
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:481101 original size:43 final size:43
Alignment explanation
Indices: 481024--481284 Score: 187
Period size: 43 Copynumber: 6.0 Consensus size: 43
481014 AATTTTGATC
**
481024 AAAGCTCCTCTAAACAAAAGGCTCAGTGACTTTGGAAAATAAAT
1 AAAGCTCCTCTAAAC-AAAGGCTCAACGACTTTGGAAAATAAAT
* *
481068 AAAGCTCCTCTAAACAAAGGCTCAACGACTTTGGAAAATGAAC
1 AAAGCTCCTCTAAACAAAGGCTCAACGACTTTGGAAAATAAAT
* * * * *
481111 AAAACTCCTCTAATCAGAGGCTCAATGAC-TTGAAAGAAAATAAAC
1 AAAGCTCCTCTAAACAAAGGCTCAACGACTTTG---GAAAATAAAT
*
481156 AAAGCTCCTCTAATCAGAA-GCT-AAGCGACTTTGG-AAA-AAAT
1 AAAGCTCCTCTAAACA-AAGGCTCAA-CGACTTTGGAAAATAAAT
* * * * *
481197 AAATTACTCTTCTAAACAGAGGCAACCACGACTTTGGAAAAGTAAAT
1 AAA--GCTCCTCTAAACAAAGGC-TCAACGACTTTGGAAAA-TAAAT
* * * * *
481244 -TA-CTCTTCTAAACAGAGGCAACAACGACTTT-GAAAGTAAAT
1 AAAGCTCCTCTAAACAAAGGC-TCAACGACTTTGGAAAATAAAT
481285 GCTCCTTGAC
Statistics
Matches: 181, Mismatches: 22, Indels: 31
0.77 0.09 0.13
Matches are distributed among these distances:
41 11 0.06
42 11 0.06
43 90 0.50
44 26 0.14
45 34 0.19
46 5 0.03
47 4 0.02
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (43 bp):
AAAGCTCCTCTAAACAAAGGCTCAACGACTTTGGAAAATAAAT
Found at i:481199 original size:45 final size:44
Alignment explanation
Indices: 481023--481193 Score: 190
Period size: 43 Copynumber: 3.9 Consensus size: 44
481013 AAATTTTGAT
* **
481023 CAAAGCTCCTCTAAACAAAAGGCTCAGTGACTTTGGAAAATAAA
1 CAAAGCTCCTCTAAACAGAAGGCTCAACGACTTTGGAAAATAAA
* *
481067 TAAAGCTCCTCTAAACA-AAGGCTCAACGACTTTGGAAAATGAA
1 CAAAGCTCCTCTAAACAGAAGGCTCAACGACTTTGGAAAATAAA
* * *
481110 CAAAACTCCTCTAATCAG-AGGCTCAATGAC-TTGAAAGAAAATAAA
1 CAAAGCTCCTCTAAACAGAAGGCTCAACGACTTTG---GAAAATAAA
*
481155 CAAAGCTCCTCTAATCAGAA-GCT-AAGCGACTTTGGAAAA
1 CAAAGCTCCTCTAAACAGAAGGCTCAA-CGACTTTGGAAAA
481194 AATAAATTAC
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
42 3 0.03
43 53 0.49
44 18 0.17
45 31 0.28
46 4 0.04
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (44 bp):
CAAAGCTCCTCTAAACAGAAGGCTCAACGACTTTGGAAAATAAA
Found at i:481211 original size:88 final size:87
Alignment explanation
Indices: 481023--481219 Score: 217
Period size: 88 Copynumber: 2.3 Consensus size: 87
481013 AAATTTTGAT
* * * *
481023 CAAAGCTCCTCTAAACAAAAGGCTCAGTGACTTTG---GAAAATAAATAAAGCTCCTCTAAACAA
1 CAAAACTCCTCTAAAC-AGAGGCTCAATGAC-TTGAAAGAAAATAAACAAAGCTCCTCTAAACAA
481085 AGGCTCAACGACTTTGGAAAATGAA
64 AGGCTCAACGACTTTGGAAAA-GAA
* *
481110 CAAAACTCCTCTAATCAGAGGCTCAATGACTTGAAAGAAAATAAACAAAGCTCCTCTAATCAGAA
1 CAAAACTCCTCTAAACAGAGGCTCAATGACTTGAAAGAAAATAAACAAAGCTCCTCTAAACA-AA
481175 -GCT-AAGCGACTTTGGAAAA-AA
65 GGCTCAA-CGACTTTGGAAAAGAA
* *
481196 TAAATTACTCTTCTAAACAGAGGC
1 CAAA--ACTCCTCTAAACAGAGGC
481220 AACCACGACT
Statistics
Matches: 94, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
85 3 0.03
86 17 0.18
87 16 0.17
88 56 0.60
89 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (87 bp):
CAAAACTCCTCTAAACAGAGGCTCAATGACTTGAAAGAAAATAAACAAAGCTCCTCTAAACAAAG
GCTCAACGACTTTGGAAAAGAA
Found at i:481273 original size:132 final size:133
Alignment explanation
Indices: 481023--481284 Score: 293
Period size: 131 Copynumber: 2.0 Consensus size: 133
481013 AAATTTTGAT
* * *
481023 CAAAGCTCCTCTAAACAAAAGGCTCAGTGACTTTGGAAAATAAATAAAGCTCCTCTAAACAAAGG
1 CAAAGCTCCTCTAAACAAAAGGCTAAGCGACTTTGGAAAATAAATAAAACTCCTCTAAACAAAGG
* * * *
481088 CTCAACGACTTTGGAAAATGAACAAAACTCCTCTAATCAGAGGCTCAATGAC-TTGAAAGAAAAT
66 CACAACGACTTTGGAAAATGAACAAAACTCCTCTAAACAGAGGCACAACGACTTTGAAAGAAAAT
481152 AAA
131 AAA
* * * *
481155 CAAAGCTCCTCTAATCAGAA-GCTAAGCGACTTTGG-AAA-AAATAAATTACTCTTCTAAACAGA
1 CAAAGCTCCTCTAAACAAAAGGCTAAGCGACTTTGGAAAATAAATAAA--ACTCCTCTAAACAAA
* ** *
481217 GGCAACCACGACTTTGGAAAA-GTAA-ATTACTCTTCTAAACAGAGGCAACAACGACTTTGAAAG
64 GGC-ACAACGACTTTGGAAAATG-AACAAAACTCCTCTAAACAGAGGC-ACAACGACTTTGAAAG
*
481280 TAAAT
126 AAAAT
481285 GCTCCTTGAC
Statistics
Matches: 108, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
129 7 0.06
130 3 0.03
131 46 0.43
132 41 0.38
133 11 0.10
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (133 bp):
CAAAGCTCCTCTAAACAAAAGGCTAAGCGACTTTGGAAAATAAATAAAACTCCTCTAAACAAAGG
CACAACGACTTTGGAAAATGAACAAAACTCCTCTAAACAGAGGCACAACGACTTTGAAAGAAAAT
AAA
Found at i:489472 original size:15 final size:15
Alignment explanation
Indices: 489451--489485 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
489441 TTACTTTGTT
*
489451 AAATGTATTGAATGA
1 AAATGTAATGAATGA
*
489466 GAATGTAATGAATGA
1 AAATGTAATGAATGA
489481 AAATG
1 AAATG
489486 CATGCATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (15 bp):
AAATGTAATGAATGA
Found at i:492858 original size:62 final size:61
Alignment explanation
Indices: 492676--492907 Score: 309
Period size: 62 Copynumber: 3.9 Consensus size: 61
492666 AAATGAAAGT
* * * * *
492676 TTTTA-TTTTAAGAAAAATTGATACTTTCAACTATTCCT-TAAAATATTTTTCTTTGGAAA
1 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTTGAAA
* *
492735 TTTTATTTTTAAGGAAAATTGATACTTCCAACTTTTTCC-C---AA-ATTTTTTTTTTGAAT
1 TTTTATTTTTAAGGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTTTTGAAA
492792 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTTTGAAA
1 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTTTTGAAA
*
492854 TTTTATTTTCAAGGAAAATTGATACTTTCAA-TTTTCTCTCAAAAATATTTTTTT
1 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTC-CTCAAAAATATTTTTTT
492908 ATTTTAAAAA
Statistics
Matches: 154, Mismatches: 9, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
56 6 0.04
57 44 0.29
58 2 0.01
59 5 0.03
60 26 0.17
61 18 0.12
62 53 0.34
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (61 bp):
TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTTGAAA
Found at i:493745 original size:10 final size:10
Alignment explanation
Indices: 493730--493788 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
493720 AAATCAAAAA
493730 AAATAATAAT
1 AAATAATAAT
*
493740 AGATAA-ATAT
1 AAATAATA-AT
493750 AAATAAT-AT
1 AAATAATAAT
*
493759 ACATTAATAGAT
1 A-AATAATA-AT
*
493771 AAATAATAAA
1 AAATAATAAT
493781 AAATAATA
1 AAATAATA
493789 TTAATGGATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
9 4 0.10
10 26 0.67
11 6 0.15
12 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATAATAAT
Found at i:493773 original size:27 final size:28
Alignment explanation
Indices: 493716--493834 Score: 124
Period size: 27 Copynumber: 4.4 Consensus size: 28
493706 AATTCAGAAC
*
493716 AGATAAATCA-AAAAAA-ATA-A-TAAT
1 AGATAAATAATAAAAAATATATATTAAT
* *
493740 AGATAAAT-ATAAATAATATACATTAAT
1 AGATAAATAATAAAAAATATATATTAAT
493767 AGATAAATAATAAAAAATA-ATATTAAT
1 AGATAAATAATAAAAAATATATATTAAT
* * *
493794 GGATAACTAATAAAAATATATATATTATT
1 AGATAAATAATAAAAA-ATATATATTAAT
*
493823 AGATAAAAAATA
1 AGATAAATAATA
493835 TATAAAAAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.01
24 13 0.16
25 3 0.04
26 1 0.01
27 33 0.42
28 12 0.15
29 16 0.20
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (28 bp):
AGATAAATAATAAAAAATATATATTAAT
Found at i:502966 original size:58 final size:58
Alignment explanation
Indices: 502625--503140 Score: 430
Period size: 60 Copynumber: 8.8 Consensus size: 58
502615 ATGCTTTATG
* * * * **
502625 CAAGAAAAATTGATATTTTTC-ACTTTTCCT--TAAA-GCATTTTTGAAATTTTTATCGT
1 CAAGAAAAATTGATA-CTTTCAACTTTTCCTCAAAAATTC-TTTTTGAAATCTTTATTTT
* * * *
502681 CAAGGAAAATTGATGCTTTTAACTTTTCCTC-AAAATATCTCTTTTGAAAT-TTGTATTTG
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TCT-TTTTGAAATCTT-TATTTT
* * *
502740 CAAGAAAAATTGATACTGTCAACTTTTCCTCAAAAATACCTTTTTTGAAAAT-TTTAATTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TC-TTTTTG-AAATCTTTATTTT
* * * * * *
502800 CAAGAAAATTTGATACATTCAACTTTTTCTCAAAATACTT-TTTTT-AATTTTTTTTATTTC
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAA-A-TTCTTTTTGAA--ATCTTTATTTT
* * * *
502860 CAAGGAAAATTGATACTTTCAATTTTTTCTCAAAAACTTCTTTTTGAAATCTTCATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAA-TTCTTTTTGAAATCTTTATTTT
* * * * *
502919 CAAGGAGAATT-ACTACCTTCAACTTTTCTTCAAAAATTCTTTTTGAAATCTTTATTTG
1 CAAGAAAAATTGA-TACTTTCAACTTTTCCTCAAAAATTCTTTTTGAAATCTTTATTTT
* * ** * *
502977 CAAGGAAAATTGATA-TATTCAATTTTTCCAAAAAAATAT-TTTTTAAAATTTTTATTTT
1 CAAGAAAAATTGATACT-TTCAACTTTTCCTCAAAAAT-TCTTTTTGAAATCTTTATTTT
* *
503035 CAAGAAAAATTAATA-TTTCAACTTTTCCTCAAAAATAT-TTTTTGAAATTTTTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TCTTTTTGAAA--TCTTTATTTT
*
503094 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATGCTTTTTGAA
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATTCTTTTTGAA
503141 TTTTTTTTTT
Statistics
Matches: 380, Mismatches: 56, Indels: 44
0.79 0.12 0.09
Matches are distributed among these distances:
55 3 0.01
56 22 0.06
57 32 0.08
58 82 0.22
59 112 0.29
60 118 0.31
61 10 0.03
62 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (58 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATTCTTTTTGAAATCTTTATTTT
Found at i:503012 original size:117 final size:116
Alignment explanation
Indices: 502701--503140 Score: 419
Period size: 117 Copynumber: 3.7 Consensus size: 116
502691 TGATGCTTTT
* * * * *
502701 AACTTTTCCTC-AAAATATCTCTTTTGAAATT-TGTATTTGCAAGAAAAATTGATACTGTCAACT
1 AACTTTTCCTCAAAAATAT-T-TTTTGAAATTCTTTATTTCCAAGGAAAATTGATACTTTCAATT
* * * * *
502764 TTTCCTCAAAAATACCTTTTTTGAAAAT-TTTAATTTCAAGAAAATTTGATACATTC
64 TTTCCTCAAAAAT-TC-TTTTTG-AAATCTTCATTTTCAAGAAAAATTAATAC-TTC
* * * *
502820 AACTTTTTCTC-AAAATACTTTTTTTAATTTTTTTTATTTCCAAGGAAAATTGATACTTTCAATT
1 AACTTTTCCTCAAAAATA-TTTTTTGAA-ATTCTTTATTTCCAAGGAAAATTGATACTTTCAATT
* * * *
502884 TTTTCTCAAAAACTTCTTTTTGAAATCTTCATTTTCAAGGAGAATTACTACCTTC
64 TTTCCTCAAAAA-TTCTTTTTGAAATCTTCATTTTCAAGAAAAATTAATA-CTTC
* *
502939 AACTTTTCTTCAAAAAT-TCTTTTTGAAA-TCTTTATTTGCAAGGAAAATTGATA-TATTCAATT
1 AACTTTTCCTCAAAAATAT-TTTTTGAAATTCTTTATTTCCAAGGAAAATTGATACT-TTCAATT
** * * * *
503001 TTTCCAAAAAAATAT-TTTTTAAAATTTTTATTTTCAAGAAAAATTAATATTTC
64 TTTCCTCAAAAAT-TCTTTTTGAAATCTTCATTTTCAAGAAAAATTAATACTTC
* * * *
503054 AACTTTTCCTCAAAAATATTTTTTGAAATTTTTTTATTTTCAAGAAAAATTGATACTTTCAACTT
1 AACTTTTCCTCAAAAATATTTTTTGAAA-TTCTTTATTTCCAAGGAAAATTGATACTTTCAATTT
*
503119 TTCCTCAAAAATGCTTTTTGAA
65 TTCCTCAAAAATTCTTTTTGAA
503141 TTTTTTTTTT
Statistics
Matches: 264, Mismatches: 42, Indels: 32
0.78 0.12 0.09
Matches are distributed among these distances:
115 28 0.11
116 31 0.12
117 86 0.33
118 12 0.05
119 60 0.23
120 46 0.17
121 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (116 bp):
AACTTTTCCTCAAAAATATTTTTTGAAATTCTTTATTTCCAAGGAAAATTGATACTTTCAATTTT
TCCTCAAAAATTCTTTTTGAAATCTTCATTTTCAAGAAAAATTAATACTTC
Found at i:503147 original size:59 final size:57
Alignment explanation
Indices: 502625--503220 Score: 465
Period size: 59 Copynumber: 10.1 Consensus size: 57
502615 ATGCTTTATG
* * * **
502625 CAAGAAAAATTGATATTTTTC-ACTTTTCCT--TAAAGCATTTTTGAAATTTTTATCGT
1 CAAGAAAAATTGATA-CTTTCAACTTTTCCTCAAAAATC-TTTTTGAAATTTTTATTTT
* * * * *
502681 CAAGGAAAATTGATGCTTTTAACTTTTCCTCAAAATATCTCTTTTGAAATTTGTATTTG
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAA-ATCT-TTTTGAAATTTTTATTTT
* * *
502740 CAAGAAAAATTGATACTGTCAACTTTTCCTCAAAAATACCTTTTTTGAAAATTTTAATTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT--C-TTTTTGAAATTTTTATTTT
* * * * * *
502800 CAAGAAAATTTGATACATTCAACTTTTTCTC-AAAATACTTTTTTTAATTTTTTTTATTTC
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-C-TTTTTGAA--ATTTTTATTTT
* * * * *
502860 CAAGGAAAATTGATACTTTCAATTTTTTCTCAAAAACTTCTTTTTGAAATCTTCATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAA--TCTTTTTGAAATTTTTATTTT
* * * * * *
502919 CAAGGAGAATT-ACTACCTTCAACTTTTCTTCAAAAATTCTTTTTGAAATCTTTATTTG
1 CAAGAAAAATTGA-TACTTTCAACTTTTCCTCAAAAA-TCTTTTTGAAATTTTTATTTT
* * ** * *
502977 CAAGGAAAATTGATA-TATTCAATTTTTCCAAAAAAATATTTTTTAAAATTTTTATTTT
1 CAAGAAAAATTGATACT-TTCAACTTTTCCTCAAAAAT-CTTTTTGAAATTTTTATTTT
* *
503035 CAAGAAAAATTAATA-TTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTTGAAA--TTTTTATTTT
*
503094 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATGCTTTTTGAATTTTTTTTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTTGAA----ATTTTTATTTT
* * * * * *
503156 -AAAAAAAAGTTGATACTTT-AACTTTTCTTTAAAAATATTTTTTAAAAAATTTTATTTT
1 CAAGAAAAA-TTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTT-GAAATTTTTATTTT
503214 -AAGAAAA
1 CAAGAAAA
503221 TCATTGGAAA
Statistics
Matches: 441, Mismatches: 73, Indels: 50
0.78 0.13 0.09
Matches are distributed among these distances:
55 3 0.01
56 22 0.05
57 28 0.06
58 107 0.24
59 113 0.26
60 105 0.24
61 39 0.09
62 23 0.05
63 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (57 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTGAAATTTTTATTTT
Found at i:503269 original size:22 final size:21
Alignment explanation
Indices: 503240--503280 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
503230 ATTAAAGAAT
503240 ATTTAATTAAATAAATAAATG
1 ATTTAATTAAATAAATAAATG
* *
503261 ATTTCAATTTAATCAATAAA
1 ATTT-AATTAAATAAATAAA
503281 CAAATAAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTTAATTAAATAAATAAATG
Found at i:504839 original size:56 final size:56
Alignment explanation
Indices: 504779--504905 Score: 148
Period size: 56 Copynumber: 2.3 Consensus size: 56
504769 ACTTCTTTAG
* * *
504779 ACTTGCAATTCAATTCCAATCGTTTGACCTCAACTCAATCCAGGTCAGCTT-TCCAA
1 ACTTGTAATTCAATTCCAATCATTTGACCTCAACTCAATCCAGATC-GCTTCTCCAA
* * * * * *
504835 ACTTGTAGTTCAATCCCAGTCATTTGATCTCAACTCCATCCAGATCGTTTCTCCAA
1 ACTTGTAATTCAATTCCAATCATTTGACCTCAACTCAATCCAGATCGCTTCTCCAA
*
504891 ACTTGTGATTCAATT
1 ACTTGTAATTCAATT
504906 TTGATCATTC
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
55 3 0.05
56 55 0.95
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (56 bp):
ACTTGTAATTCAATTCCAATCATTTGACCTCAACTCAATCCAGATCGCTTCTCCAA
Found at i:505328 original size:5 final size:5
Alignment explanation
Indices: 505314--505418 Score: 103
Period size: 5 Copynumber: 21.6 Consensus size: 5
505304 ATTACATTAC
* * *
505314 TATAC TATAT TATAT TATTAT TATAT TGTTAT TATAT TATAA TATAT TATAT
1 TATAT TATAT TATAT TA-TAT TATAT T-ATAT TATAT TATAT TATAT TATAT
* * *
505366 TATAT TATA- T-TAT TATAG TACAT T-TAT TATA- T-TAT TATAG TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
505411 TATAT TAT
1 TATAT TAT
505419 GACAACTATT
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
3 4 0.05
4 7 0.09
5 62 0.76
6 9 0.11
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:505334 original size:3 final size:3
Alignment explanation
Indices: 505321--505474 Score: 84
Period size: 3 Copynumber: 55.3 Consensus size: 3
505311 TACTATACTA
* *
505321 TAT TA- TAT TAT TAT TA- TAT TGT TAT TA- TAT TAT AAT ATAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* *
505363 TAT TA- TAT TA- TAT TAT TA- TAG TA- CATT TAT TA- TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * * * * *
505403 TAG TA- TAT TA- TAT TAT GAC AAC TAT TAT TAC TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
505449 TAT T-T TAT GAT TAT TA- TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
505475 CTTCTTTCCT
Statistics
Matches: 118, Mismatches: 17, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
2 27 0.23
3 88 0.75
4 3 0.03
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:505371 original size:47 final size:45
Alignment explanation
Indices: 505314--505418 Score: 133
Period size: 47 Copynumber: 2.3 Consensus size: 45
505304 ATTACATTAC
* * *
505314 TATACTATATTATATTATTATTA-TA-TTGTTATTATATTATAATATAT
1 TATATTATATTATATTATTA-TAGTACAT-TTATTATATTAT--TATAG
505361 TATATTATATTATATTATTATAGTACATTTATTATATTATTATAG
1 TATATTATATTATATTATTATAGTACATTTATTATATTATTATAG
505406 TATATTATATTAT
1 TATATTATATTAT
505419 GACAACTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
45 17 0.32
46 2 0.04
47 33 0.62
48 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (45 bp):
TATATTATATTATATTATTATAGTACATTTATTATATTATTATAG
Found at i:505473 original size:17 final size:17
Alignment explanation
Indices: 505425--505470 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
505415 TTATGACAAC
* *
505425 TATTATTACTATTATTAT
1 TATTATTA-TTTTATGAT
505443 TATTATTATTTTATGAT
1 TATTATTATTTTATGAT
505460 TATTA-TATTTT
1 TATTATTATTTT
505471 TATTCTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 6 0.23
17 12 0.46
18 8 0.31
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTATTATTTTATGAT
Found at i:507016 original size:74 final size:75
Alignment explanation
Indices: 506889--507053 Score: 233
Period size: 74 Copynumber: 2.2 Consensus size: 75
506879 ACACAAATTT
* *
506889 GCAAGAACTCAAATTCACAAAAATTTTCAGTTTTGCATTTGAGAGATTCACATCCAAAGTTTAAT
1 GCAAGAACTCAAATTCACAAAAATTTTCAATTTCGCATTTGAGAGATTCACATCCAAAGTTTAAT
506954 TTAGAGATTC
66 TTAGAGATTC
* * * * * **
506964 GCAATAACTCATATTCAC-AAGATTTTTAATTTCGCATTTGCGAGATTCACATCCATTGTTTAAT
1 GCAAGAACTCAAATTCACAAAAATTTTCAATTTCGCATTTGAGAGATTCACATCCAAAGTTTAAT
*
507028 TTAGATATTC
66 TTAGAGATTC
507038 GCAAGAACTCAAATTC
1 GCAAGAACTCAAATTC
507054 GCATCAAAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 62 0.79
75 16 0.21
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (75 bp):
GCAAGAACTCAAATTCACAAAAATTTTCAATTTCGCATTTGAGAGATTCACATCCAAAGTTTAAT
TTAGAGATTC
Found at i:507363 original size:22 final size:23
Alignment explanation
Indices: 507317--507370 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
507307 TTTCACATCT
* *
507317 AAATTCAAAGGTTCATATTCGAA
1 AAATTCAAAGGTTCACATTCCAA
*
507340 AAATTCAAGGGTTCACA-TCCAA
1 AAATTCAAAGGTTCACATTCCAA
*
507362 AATTTCAAA
1 AAATTCAAA
507371 AATTCTCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (23 bp):
AAATTCAAAGGTTCACATTCCAA
Found at i:508704 original size:16 final size:17
Alignment explanation
Indices: 508685--508725 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
508675 TTTTTCACCC
*
508685 TTTTCACTTTTTTATTT
1 TTTTCACTTTTTCATTT
508702 TTTTCA-TTTTTCATTT
1 TTTTCACTTTTTCATTT
508718 TTTT-ACTT
1 TTTTCACTT
508726 CATTTGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 15 0.68
17 6 0.27
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCACTTTTTCATTT
Found at i:512821 original size:132 final size:129
Alignment explanation
Indices: 512647--512904 Score: 399
Period size: 132 Copynumber: 2.0 Consensus size: 129
512637 GCCTAATTAA
* * * * **
512647 AAATATTTTTTCACCTAGAAATGTCTTAGATAATCATTCATTTGTAATTGTTAAGAATTTCATCC
1 AAATATTTTCTCACCTAAAAATGTCTTAGATAATCATCCATTTGCAATTACTAAGAATTTCATCC
*
512712 TTGAAATTTATTCTTTTTATTTTACAAATTTTATTTCTAAATTTTCTACCATTTAGGTTAAATTG
66 TTGAAATTTA-T-TTTTTATTTTACAAATTTTA-TTCTAAATTTTCCACCATTTAGGTTAAATTG
512777 AG
128 AG
* *
512779 AAATATTTTCTCATCTAAAAATGTCTTAGATAATCATCCATTTGCGATTACTAAGAATTTCATCC
1 AAATATTTTCTCACCTAAAAATGTCTTAGATAATCATCCATTTGCAATTACTAAGAATTTCATCC
*
512844 TTGAGATTTATTTTTTATTTTACAAATTTTATTCTAAATTTTCCACCATTTAGGTTAAATT
66 TTGAAATTTATTTTTTATTTTACAAATTTTATTCTAAATTTTCCACCATTTAGGTTAAATT
512905 TTAAAAAATC
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
129 29 0.25
130 20 0.17
131 1 0.01
132 66 0.57
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (129 bp):
AAATATTTTCTCACCTAAAAATGTCTTAGATAATCATCCATTTGCAATTACTAAGAATTTCATCC
TTGAAATTTATTTTTTATTTTACAAATTTTATTCTAAATTTTCCACCATTTAGGTTAAATTGAG
Found at i:512989 original size:129 final size:130
Alignment explanation
Indices: 512665--512947 Score: 349
Period size: 132 Copynumber: 2.2 Consensus size: 130
512655 TTTCACCTAG
* ** ** ** * *
512665 AAATGTCTTAGATAATCATTCATTTGTAATTGTTAAGAATTTCATCCTTGAAATTTATTCTTTTT
1 AAATGTCTTAGAAAATCACCCATTTGCGATTACTAAGAATTTCATCATTGAGATTTA-T-TTTTT
* * * *
512730 ATTTTACAAATTTTATTTCTAAATTTTCTACCATTTAGGTTAAATTGAGAAATATTTTCTCATCT
64 ATTTTACAAATTTTATTTCTAAATTTTCCACCATTTAGGTTAAATTGAGAAAAATCTCCTCATCT
512795 AA
129 AA
* * *
512797 AAATGTCTTAGATAATCATCCATTTGCGATTACTAAGAATTTCATCCTTGAGATTTATTTTTTAT
1 AAATGTCTTAGAAAATCACCCATTTGCGATTACTAAGAATTTCATCATTGAGATTTATTTTTTAT
*
512862 TTTACAAATTTTA-TTCTAAATTTTCCACCATTTAGGTTAAATTTTA-AAAAATCTCCT-ATCTA
66 TTTACAAATTTTATTTCTAAATTTTCCACCATTTAGGTTAAA-TTGAGAAAAATCTCCTCATCTA
512924 A
130 A
*
512925 AAATTTC-TAGAAAATCACCCATT
1 AAATGTCTTAGAAAATCACCCATT
512948 CTTGATTTTA
Statistics
Matches: 136, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
127 14 0.10
128 12 0.09
129 35 0.26
130 23 0.17
131 1 0.01
132 51 0.38
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (130 bp):
AAATGTCTTAGAAAATCACCCATTTGCGATTACTAAGAATTTCATCATTGAGATTTATTTTTTAT
TTTACAAATTTTATTTCTAAATTTTCCACCATTTAGGTTAAATTGAGAAAAATCTCCTCATCTAA
Found at i:516014 original size:30 final size:30
Alignment explanation
Indices: 515980--516041 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
515970 TACAATTCAC
515980 TCAATGATTTCATTCCTTTGACTCACAAAT
1 TCAATGATTTCATTCCTTTGACTCACAAAT
516010 TCAATGATTTCATTCCTTTGACTCACAAAT
1 TCAATGATTTCATTCCTTTGACTCACAAAT
516040 TC
1 TC
516042 CTTGTAGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.40
Consensus pattern (30 bp):
TCAATGATTTCATTCCTTTGACTCACAAAT
Found at i:517393 original size:2 final size:2
Alignment explanation
Indices: 517380--517417 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
517370 CTTTAAATAC
* *
517380 AT AT AC AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
517418 CCCAGGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:519898 original size:243 final size:243
Alignment explanation
Indices: 519414--519909 Score: 545
Period size: 243 Copynumber: 2.0 Consensus size: 243
519404 CTTGCATTCT
*
519414 ATAATCCAATCAATAAATTTTTAGTTAGAATTATTAAAGACGATTTTTGTCAAAAACACATTCAA
1 ATAATCCATTCAATAAATTTTTAGTTAGAATTATTAAAGACGATTTTTGTCAAAAACACATTCAA
* * * * * * *
519479 TAATCTATAGACAAAAGTTGGAACAGATTCTTGAAGGCGTTTTTGGCTCAAAACGCCTTTAATAT
66 TAATCCATACAAAAAAGTTGAAACAGAATCTTAAAGGCGTTTTTGGCCCAAAACGCCTTTAATAT
* * ** * * *
519544 TCCAGACGATAAATTTGAATGGTTGAATTATTGAAGGTAATTTTTTCCAAAAATACCTTTAATAA
131 TCCACACAATAAATTTGAATGGAGGAATTATTGAAGGTAATTTTGTCAAAAAATACCTTCAATAA
*
519609 TACTTTGTTATGAATTATTCAAGGCATTACTGATAGGAAAATGCCCTTA
196 TACTTTGTTAGGAATTATTCAAGGCATTACTGATA-GAAAATGCCCTTA
* * * * ** ** * *
519658 ATAATCCATTCAATTAATTTTTAGTTGGTATTATTGAAGGTGATTTTT-TTTAAAACACCTTTAA
1 ATAATCCATTCAATAAATTTTTAGTTAGAATTATTAAAGACGATTTTTGTCAAAAACACATTCAA
*
519722 TAATCCATACAAAAAAGTTGAAA-ACGAAATCTTAAAGGCGTTTTTTGCCCAAAACGCCTTTAAT
66 TAATCCATACAAAAAAGTTGAAACA-G-AATCTTAAAGGCGTTTTTGGCCCAAAACGCCTTTAAT
* * * * * *
519786 ATTTCACACAATAAAATTT-TA-GGAGGGATTATTTAAGGTAGTTTTGGT-AAAAAATGCCTTCA
129 ATTCCACACAAT-AAATTTGAATGGAGGAATTATTGAAGGTAATTTT-GTCAAAAAATACCTTCA
* * * * *
519848 ATAATATTTTGTTAGGGATTATTCAAGGCATTTTCTTGCTA-AATATGCCCTTA
192 ATAATACTTTGTTAGGAATTATTCAAGGCA-TTAC-TGATAGAAAATGCCCTTA
519901 ATAATCCAT
1 ATAATCCAT
519910 AAAAAAAATA
Statistics
Matches: 208, Mismatches: 38, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
242 1 0.00
243 109 0.52
244 88 0.42
245 10 0.05
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (243 bp):
ATAATCCATTCAATAAATTTTTAGTTAGAATTATTAAAGACGATTTTTGTCAAAAACACATTCAA
TAATCCATACAAAAAAGTTGAAACAGAATCTTAAAGGCGTTTTTGGCCCAAAACGCCTTTAATAT
TCCACACAATAAATTTGAATGGAGGAATTATTGAAGGTAATTTTGTCAAAAAATACCTTCAATAA
TACTTTGTTAGGAATTATTCAAGGCATTACTGATAGAAAATGCCCTTA
Found at i:520290 original size:35 final size:34
Alignment explanation
Indices: 520244--520312 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
520234 TGTATATGTC
* *
520244 AAGTCAATTGTAGGTTTATGTCCAGAAAATGTTTG
1 AAGTCAATTGTAGATTTATGTCCA-AAAATATTTG
*
520279 AAGTCAATTGTATATTTATGTCCAAAAATATTTG
1 AAGTCAATTGTAGATTTATGTCCAAAAATATTTG
520313 GTTTATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (34 bp):
AAGTCAATTGTAGATTTATGTCCAAAAATATTTG
Found at i:523529 original size:25 final size:25
Alignment explanation
Indices: 523476--523604 Score: 116
Period size: 25 Copynumber: 5.2 Consensus size: 25
523466 AATAATGTGC
* * * * *
523476 TCAGACACACCCTTCAGTAAATCAC
1 TCAGAAACACCATTCAGCAAACCAT
* *
523501 TCAGAAACACCATTCATCAAACTAT
1 TCAGAAACACCATTCAGCAAACCAT
*
523526 TCAGAAATACCATTCAGCAAACCACT
1 TCAGAAACACCATTCAGCAAACCA-T
* *
523552 T-AGAAAAACTATTCAGCAAACCAT
1 TCAGAAACACCATTCAGCAAACCAT
* * * *
523576 TCAAAAACACTATTCAGCATACGAT
1 TCAGAAACACCATTCAGCAAACCAT
523601 TCAG
1 TCAG
523605 CATACCAATA
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
24 2 0.02
25 81 0.95
26 2 0.02
ACGTcount: A:0.43, C:0.28, G:0.08, T:0.22
Consensus pattern (25 bp):
TCAGAAACACCATTCAGCAAACCAT
Found at i:523577 original size:12 final size:12
Alignment explanation
Indices: 523509--523611 Score: 66
Period size: 12 Copynumber: 8.3 Consensus size: 12
523499 ACTCAGAAAC
*
523509 ACCATTCATCAA
1 ACCATTCAGCAA
* *
523521 ACTATTCAGAAA
1 ACCATTCAGCAA
523533 TACCATTCAGCAA
1 -ACCATTCAGCAA
*
523546 ACCACTT-AGAAAA
1 ACCA-TTCAG-CAA
*
523559 ACTATTCAGCAA
1 ACCATTCAGCAA
*
523571 ACCATTCA-AAA
1 ACCATTCAGCAA
*
523582 ACACTATTCAGCAT
1 AC-C-ATTCAGCAA
* *
523596 ACGATTCAGCAT
1 ACCATTCAGCAA
523608 ACCA
1 ACCA
523612 ATATCATACA
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
11 4 0.06
12 39 0.56
13 24 0.34
14 3 0.04
ACGTcount: A:0.44, C:0.27, G:0.07, T:0.22
Consensus pattern (12 bp):
ACCATTCAGCAA
Found at i:524239 original size:62 final size:60
Alignment explanation
Indices: 524114--524241 Score: 161
Period size: 62 Copynumber: 2.1 Consensus size: 60
524104 TAGAAAATTG
* * * *
524114 CCTTTAATAATTATGTATAAAAATTAAGGAATTAGTGAAGGCGTTTGTTCTCAAAAAATA
1 CCTTCAATAATTATGTACAAAAATTAAGGAATTAGTGAAGGCATTTGTTCTCAAAAAACA
*
524174 CCTTCAATAATTATGTACATAAATTAGAAGGAATTAGTGAAGGCATTT-TTCT-AGAATAAACA
1 CCTTCAATAATTATGTACAAAAATT--AAGGAATTAGTGAAGGCATTTGTTCTCA-AA-AAACA
524236 CCTTCA
1 CCTTCA
524242 CTAACCATCT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
60 23 0.39
61 6 0.10
62 30 0.51
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.34
Consensus pattern (60 bp):
CCTTCAATAATTATGTACAAAAATTAAGGAATTAGTGAAGGCATTTGTTCTCAAAAAACA
Found at i:524282 original size:63 final size:63
Alignment explanation
Indices: 524211--524525 Score: 178
Period size: 63 Copynumber: 5.1 Consensus size: 63
524201 AAGGAATTAG
**
524211 TGAAGGCATTTTTCTAGAATAAACACCTTCACTAACCATCTTAAAATTTGAGTTATGAAAAAT
1 TGAAGGCATTTTTCTAGAATAAACACCTTCACTAATAATCTTAAAATTTGAGTTATGAAAAAT
* * * * **
524274 TGAAGGCATTTTTC-ACTGGA-AGACATCTT---TAATAATCTCAAAATTT---TTAAAAAAAAA
1 TGAAGGCATTTTTCTA--GAATAAACACCTTCACTAATAATCTTAAAATTTGAGTT-ATGAAAAA
524331 TT
63 -T
** ** *
524333 AGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAATCGTCTTAAAATTTGAGTTGTGAAAAAT
1 --TGAAGGCATTTTTCTAGAATAAACACCTTCACTAATAATCTTAAAATTTGAGTTATGAAAAAT
* * * * * * *
524398 TGAATGCATTTTTCACTTG-A-AGACGCCTT---TAATAATCCTAAAAATT---TTAAGAGAAAA
1 TGAAGGCATTTTT--CTAGAATAAACACCTTCACTAATAATCTTAAAATTTGAGTTATGA-AAAA
524455 T
63 T
* * * *
524456 TAGTAAAGCCATTTTTCTGGAATAAACACCTTCACTAACT-ATCTTAAAATTTGAGTTGTGGAAA
1 T-G--AAGGCATTTTTCTAGAATAAACACCTTCACTAA-TAATCTTAAAATTTGAGTTATGAAAA
524520 AT
62 AT
524522 TGAA
1 TGAA
524526 AACGTTTTTC
Statistics
Matches: 184, Mismatches: 39, Indels: 58
0.65 0.14 0.21
Matches are distributed among these distances:
57 6 0.03
58 12 0.07
59 5 0.03
60 30 0.16
61 35 0.19
62 2 0.01
63 42 0.23
64 30 0.16
65 6 0.03
66 11 0.06
67 5 0.03
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Consensus pattern (63 bp):
TGAAGGCATTTTTCTAGAATAAACACCTTCACTAATAATCTTAAAATTTGAGTTATGAAAAAT
Found at i:524341 original size:124 final size:123
Alignment explanation
Indices: 524205--524598 Score: 545
Period size: 124 Copynumber: 3.2 Consensus size: 123
524195 AATTAGAAGG
*
524205 AATTAGTGAAGGCATTTTTCTAGAATAAACACCTTCACTAACCATCTTAAAATTTGAGTTATGAA
1 AATTAGTGAAGGCATTTTTCTAGAATAAACACCTTCACTAACCATCTTAAAATTTGAGTTGTGAA
* * * * *
524270 AAATTGAAGGCATTTTTCACTGGAAGACATCTTTAATAATCTCAAAATTTTTAAAAAAA
66 AAATTGAAAGCATTTTTCACTGGAAGACACCTTTAATAATC-CAAAAATTTTAAGAGAA
** * *
524329 AATTAGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAATCGTCTTAAAATTTGAGTTGTGAA
1 AATTAGTGAAGGCATTTTTCTAGAATAAACACCTTCACTAACCATCTTAAAATTTGAGTTGTGAA
* * *
524394 AAATTGAATGCATTTTTCACTTGAAGACGCCTTTAATAATCCTAAAAATTTTAAGAGAA
66 AAATTGAAAGCATTTTTCACTGGAAGACACCTTTAATAATCC-AAAAATTTTAAGAGAA
* * * * *
524453 AATTAGTAAAGCCATTTTTCTGGAATAAACACCTTCACTAACTATCTTAAAATTTGAGTTGTGGA
1 AATTAGTGAAGGCATTTTTCTAGAATAAACACCTTCACTAACCATCTTAAAATTTGAGTTGTGAA
* * *
524518 AAATTGAAAACGTTTTTCACTGGAAGACACCTTTAATAATCCCAAAAAATTTAAGAGAA
66 AAATTGAAAGCATTTTTCACTGGAAGACACCTTTAATAAT-CCAAAAATTTTAAGAGAA
* *
524577 AATTATTGAAGGCGTTTGTTCT
1 AATTAGTGAAGGCATTT-TTCT
524599 CAAAAAACGC
Statistics
Matches: 236, Mismatches: 31, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
123 1 0.00
124 229 0.97
125 6 0.03
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (123 bp):
AATTAGTGAAGGCATTTTTCTAGAATAAACACCTTCACTAACCATCTTAAAATTTGAGTTGTGAA
AAATTGAAAGCATTTTTCACTGGAAGACACCTTTAATAATCCAAAAATTTTAAGAGAA
Found at i:524690 original size:185 final size:185
Alignment explanation
Indices: 524453--524896 Score: 599
Period size: 185 Copynumber: 2.4 Consensus size: 185
524443 TTTAAGAGAA
* * *
524453 AATTAGTAAAGCCATTTTTCTGGAATAAACACCTTCACTAACTATCTTAAAATTTGAGTTGTGGA
1 AATTAGTAAAGGCATTTTTCT-GAATAAACGCCTTCACTAACCATCTTAAAATTTGAGTTGTGGA
524518 AAATTGAAAACGTTTTTCACTGGAAGACACCTTTAATAATCCCAAAAAA-TTTAAG-AGAAAATT
65 AAATTGAAAACGTTTTTCACTGGAAGACACCTTTAATAAT-CCAAAAAATTTTAAGAAG-AAATT
* * *
524581 ATTGAAGGCGTTTGTTCTCAAAAAACGCTTTCAATAATTATGTACGTAAATTAAAAAG
128 ATTGAAGGCATTTGTTCTCAAAAAACGCCTTCAATAATTATGTACATAAATTAAAAAG
* **
524639 AATTAGTAAAGGCA-TTTTCTAGAATAAACGCATTCACTAACCATCTTAAAATTTTG-GTTGTAA
1 AATTAGTAAAGGCATTTTTCT-GAATAAACGCCTTCACTAACCATCTTAAAA-TTTGAGTTGTGG
** **
524702 AAAATTGAAGGCGTTTTTCACTGGAAGATGCCTTTAATAATCCAAAAAATTTTAAGAAGAAATTA
64 AAAATTGAAAACGTTTTTCACTGGAAGACACCTTTAATAATCCAAAAAATTTTAAGAAGAAATTA
* * * *
524767 TTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATTATTATGTACATAAATTAGAAGG
129 TTGAAGGCATTTGTTCTCAAAAAACGCCTTCAATAATTATGTACATAAATTAAAAAG
* * * * *
524824 AATTAGTGAAGGCATTTATTCTGAAAAAATGCCTTCACTAACCGTTTTAAAATTTGAGTTGTGGA
1 AATTAGTAAAGGCATTT-TTCTGAATAAACGCCTTCACTAACCATCTTAAAATTTGAGTTGTGGA
*
524889 ATATTGAA
65 AAATTGAA
524897 GGCATTTGTT
Statistics
Matches: 225, Mismatches: 27, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
184 8 0.04
185 154 0.68
186 59 0.26
187 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (185 bp):
AATTAGTAAAGGCATTTTTCTGAATAAACGCCTTCACTAACCATCTTAAAATTTGAGTTGTGGAA
AATTGAAAACGTTTTTCACTGGAAGACACCTTTAATAATCCAAAAAATTTTAAGAAGAAATTATT
GAAGGCATTTGTTCTCAAAAAACGCCTTCAATAATTATGTACATAAATTAAAAAG
Found at i:524835 original size:62 final size:61
Alignment explanation
Indices: 524756--524985 Score: 202
Period size: 62 Copynumber: 3.7 Consensus size: 61
524746 AAAAATTTTA
* *
524756 AGAAGAAATTATTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATTATTATGTACATAAATT
1 AGAAGAAATTAGTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATAATTAT-TACATAAATT
* * * * *
524818 AGAAGGAATTAGTGAAGGCATTTATTCTGAAAAAATGCCTTCACTAACCGTT-TTA-A-AATTT
1 AGAAGAAATTAGTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATAA---TTATTACATAAATT
** * * *
524879 GAGTTGTGGAA-TATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATT
1 -AG--AAGAAATTAGTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATAATTAT-TACATAAATT
* *
524943 ATAAGAAATTAGTAAAGGCATTT-TTCT-AGAATAAATGCCTTCA
1 AGAAGAAATTAGTGAAGGCATTTGTTCTCA-AA-AAATGCCTTCA
524986 CTAAATATCT
Statistics
Matches: 133, Mismatches: 22, Indels: 26
0.73 0.12 0.14
Matches are distributed among these distances:
60 3 0.02
61 13 0.10
62 69 0.52
63 37 0.28
64 9 0.07
65 2 0.02
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (61 bp):
AGAAGAAATTAGTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATAATTATTACATAAATT
Found at i:524979 original size:125 final size:125
Alignment explanation
Indices: 524760--525028 Score: 378
Period size: 125 Copynumber: 2.1 Consensus size: 125
524750 ATTTTAAGAA
* * * *
524760 GAAATTATTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATTATTATGTACATAAATTAGAAGGA
1 GAAA-TATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTAGAAGAA
* * * * *
524825 ATTAGTGAAGGCATTTATTCTGAAAAAATGCCTTCACTAACCGTTTTAAAATTTGAGTTGT
65 ATTAGTAAAGGCATTTATTCTGAAAAAATGCCTTCACTAAACATCTTAAAAATTGAGTTGT
* *
524886 GGAATATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTATAAGAAA
1 GAAATATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTAGAAGAAA
* * *
524951 TTAGTAAAGGCATTT-TTCTAGAATAAATGCCTTCACTAAATATCTTAAAAATTGATTTGT
66 TTAGTAAAGGCATTTATTCT-GAAAAAATGCCTTCACTAAACATCTTAAAAATTGAGTTGT
*
525011 GAAAAATTGAAGGCATTT
1 GAAATATTGAAGGCATTT
525029 TTCATTAGAA
Statistics
Matches: 126, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
124 4 0.03
125 119 0.94
126 3 0.02
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (125 bp):
GAAATATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTAGAAGAAA
TTAGTAAAGGCATTTATTCTGAAAAAATGCCTTCACTAAACATCTTAAAAATTGAGTTGT
Found at i:525042 original size:311 final size:308
Alignment explanation
Indices: 524143--525214 Score: 1027
Period size: 311 Copynumber: 3.5 Consensus size: 308
524133 AAAATTAAGG
* *
524143 AATTAGTGAAGGCGTTTGTTCTCAAAAAATACCTTCAATAATTATGTACATAAATTAGAAGGAAT
1 AATTAGTAAAGGCATTTGTTCTCAAAAAATACCTTCAATAATTATGTACATAAATTAGAAGGAAT
* *
524208 TAGTGAAGGCATTTTTCTAGAATAAACA-CCTTCACTAACCATCTTAAAATTTGAGTTATGAAAA
66 TAGTGAAGGCATTTTTCTAGAA-AAA-ATCCTTCACTAACCATCTTAAAATTTGAGTTGTGAAAT
* * * * **
524272 ATTGAAGGCATTT-TTCACTGGAAGACAT--CTTTAATAATCTCA-A-A-AT-TTTTAAAAAAAA
129 ATTGAAGGCATTTGTT-A-T-CAAAAAATGCCTTCAATAAT-T-ATATACATAAATT--AAAAAA
* *
524330 ATTAGTGAAGGCATTTTTCTAGAATAAATGCCTTCACT-AATCGTCTTAAAATTTGAGTTGTGAA
187 ATTAGTAAAGGCATTTTTCTAGAATAAATGCCTTCACTAAAT-ATCTTAAAATTTGAGTTGTGAA
* *
524394 AAATTGAATGCATTTTTCACTTGAAGACGCCTTTAATAATCCTAAAAATTTTAAGAGAA
251 AAATTGAAGGCATTTTTCA-TTGAAGATGCCTTTAATAATCCTAAAAATTTTAAGAGAA
* * * * * * * * **
524453 AATTAGTAAAGCCATTT-TTCTGGAATAAACACCTTCACTAACTATCTTA-A-AATTTGAGTTGT
1 AATTAGTAAAGGCATTTGTTCT-CAAAAAATACCTTCAATAATTAT-GTACATAAATT-AG--AA
* * ** * * * * * * ** * *
524515 GGAA-AATTGAAAACGTTTTTCACTGGAAGACA-CCTTTAATAATCC--CAAAAAATTTAAG-AG
61 GGAATTAGTGAAGGCATTTTT--CTAGAAAAAATCCTTCACTAA-CCATCTTAAAATTTGAGTTG
* * * * * * *
524575 -AAAATTATTGAAGGCGTTTGTTCTCAAAAAACGCTTTCAATAATTATGTACGTAAATTAAAAAG
123 TGAAA-TATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTAAAAA-
* * ** *
524639 AATTAGTAAAGGCA-TTTTCTAGAATAAACGCATTCACTAACCATCTTAAAATTTTG-GTTGTAA
186 AATTAGTAAAGGCATTTTTCTAGAATAAATGCCTTCACTAAATATCTTAAAA-TTTGAGTTGTGA
* * *
524702 AAAATTGAAGGCGTTTTTCACTGGAAGATGCCTTTAATAATCCAAAAAATTTTAAGA-AGA
250 AAAATTGAAGGCATTTTTCA-TTGAAGATGCCTTTAATAATCCTAAAAATTTTAAGAGA-A
* * * *
524762 AATTATTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATTATTATGTACATAAATTAGAAGGAAT
1 AATTAGTAAAGGCATTTGTTCTCAAAAAATACCTTCAATAATTATGTACATAAATTAGAAGGAAT
* * *
524827 TAGTGAAGGCATTTATTCT-GAAAAAATGCCTTCACTAACCGTTTTAAAATTTGAGTTGTGGAAT
66 TAGTGAAGGCATTT-TTCTAGAAAAAAT-CCTTCACTAACCATCTTAAAATTTGAGTTGTGAAAT
*
524891 ATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTATAAGAAATTAGT
129 ATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTA-AAAAAATTAGT
* *
524956 AAAGGCATTTTTCTAGAATAAATGCCTTCACTAAATATCTTAAAAATTGATTTGTGAAAAATTGA
193 AAAGGCATTTTTCTAGAATAAATGCCTTCACTAAATATCTTAAAATTTGAGTTGTGAAAAATTGA
* *
525021 AGGCATTTTTCATTAGAAGATGCCTTTAATAATCTTAAAAATTTAAAGAGAA
258 AGGCATTTTTCATT-GAAGATGCCTTTAATAATCCTAAAAATTTTAAGAGAA
* ** * * * *
525073 AATTATTAAAGGCGCTTATTCTAAAAAAATACCTTCAATAATTATGTACGTAAATTAGAAGAAAT
1 AATTAGTAAAGGCATTTGTTCTCAAAAAATACCTTCAATAATTATGTACATAAATTAGAAGGAAT
* * * *
525138 TAATGAAGGTATTTTTCTAGAATAAACTCCTTCACTAACCATCTTAAAATTTGAGTTGTGGAATA
66 TAGTGAAGGCATTTTTCTAGAA-AAAATCCTTCACTAACCATCTTAAAATTTGAGTTGTGAAATA
* *
525203 TTCAAGGTATTT
130 TTGAAGGCATTT
525215 TTCACTGGAA
Statistics
Matches: 606, Mismatches: 118, Indels: 75
0.76 0.15 0.09
Matches are distributed among these distances:
306 5 0.01
307 13 0.02
308 25 0.04
309 167 0.28
310 145 0.24
311 234 0.39
312 12 0.02
313 5 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (308 bp):
AATTAGTAAAGGCATTTGTTCTCAAAAAATACCTTCAATAATTATGTACATAAATTAGAAGGAAT
TAGTGAAGGCATTTTTCTAGAAAAAATCCTTCACTAACCATCTTAAAATTTGAGTTGTGAAATAT
TGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTAAAAAAATTAGTAAA
GGCATTTTTCTAGAATAAATGCCTTCACTAAATATCTTAAAATTTGAGTTGTGAAAAATTGAAGG
CATTTTTCATTGAAGATGCCTTTAATAATCCTAAAAATTTTAAGAGAA
Found at i:525095 original size:125 final size:125
Alignment explanation
Indices: 524766--525109 Score: 360
Period size: 125 Copynumber: 2.8 Consensus size: 125
524756 AGAAGAAATT
* * * * *
524766 ATTGAAGGCATTTGTTCTCAAAAAATGCCTTCAATTATTATGTACATAAATTAGAAGGAATTAGT
1 ATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTAAAAGAAATTAGT
* * * * * * *
524831 GAAGGCATTTATTCT-GAAAAAATGCCTTCACTAACCGTTTTAAAATTTGAGTTGTGGAAT
66 AAAGGCA-TTATTCTAGAAAAAATGCCTTCACTAAACATCTTAAAAATTGAGTTGTGAAAA
*
524891 ATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTATAAGAAATTAGT
1 ATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTAAAAGAAATTAGT
* * * *
524956 AAAGGCATTTTTCTAGAATAAATGCCTTCACTAAATATCTTAAAAATTGATTTGTGAAAA
66 AAAGGCATTATTCTAGAAAAAATGCCTTCACTAAACATCTTAAAAATTGAGTTGTGAAAA
* * * * *
525016 ATTGAAGGCATTT-TTCATTAGAAGATGCCTTTAATAATCT-TA-A-A-AATTTAAAGAGAAAAT
1 ATTGAAGGCATTTGTT-ATCAAAAAATGCCTTCAATAAT-TATATACATAAATTAAA-AG-AAAT
* * *
525076 TATTAAAGGCGCTTATTCTA-AAAAAATACCTTCA
62 TAGTAAAGGC-ATTATTCTAGAAAAAATGCCTTCA
525110 ATAATTATGT
Statistics
Matches: 186, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
122 6 0.03
123 3 0.02
124 34 0.18
125 142 0.76
126 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (125 bp):
ATTGAAGGCATTTGTTATCAAAAAATGCCTTCAATAATTATATACATAAATTAAAAGAAATTAGT
AAAGGCATTATTCTAGAAAAAATGCCTTCACTAAACATCTTAAAAATTGAGTTGTGAAAA
Found at i:534705 original size:2 final size:2
Alignment explanation
Indices: 534700--534736 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
534690 ACAGTTACAA
534700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
534737 GACTCACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:539518 original size:10 final size:10
Alignment explanation
Indices: 539475--539521 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
539465 AATTTTTCTA
*
539475 TTTCCATTACT
1 TTTCCTTTA-T
539486 TTT-CTTTAT
1 TTTCCTTTAT
*
539495 TTTTCTTTAT
1 TTTCCTTTAT
539505 TTTCCTTTAT
1 TTTCCTTTAT
539515 TTTCCTT
1 TTTCCTT
539522 CGCTTCCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 4 0.12
10 26 0.79
11 3 0.09
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTCCTTTAT
Found at i:539974 original size:19 final size:19
Alignment explanation
Indices: 539935--539984 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
539925 ATTATAATTT
* *
539935 ATTAATTATTTATTCAGTA
1 ATTAATTAATTATTCAATA
*
539954 ATTAATTAATTATTTAATA
1 ATTAATTAATTATTCAATA
539973 ATATAA-TAATTA
1 AT-TAATTAATTA
539985 ATTATATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 24 0.89
20 3 0.11
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATTAATTAATTATTCAATA
Found at i:539982 original size:23 final size:23
Alignment explanation
Indices: 539916--539989 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
539906 ATTTGGTTTT
*
539916 TTATTTAA-AATTATAATTTATTAA
1 TTATTTAATAA-TATAA-TAATTAA
* * *
539940 TTATTTATTCAGTA-ATTAATTAA
1 TTATTTAAT-AATATAATAATTAA
539963 TTATTTAATAATATAATAATTAA
1 TTATTTAATAATATAATAATTAA
539986 TTAT
1 TTAT
539990 ATGAATATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
22 3 0.08
23 26 0.65
24 8 0.20
25 2 0.05
26 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
TTATTTAATAATATAATAATTAA
Found at i:539998 original size:21 final size:19
Alignment explanation
Indices: 539960--540001 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
539950 AGTAATTAAT
*
539960 TAATTATTTAATAATATAA
1 TAATTAATTAATAATATAA
539979 TAATTAATTATATGAATATAA
1 TAATTAATTA-AT-AATATAA
540000 TA
1 TA
540002 CGTGATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TAATTAATTAATAATATAA
Found at i:543732 original size:3 final size:3
Alignment explanation
Indices: 543726--543773 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
543716 AACCCTCCTC
543726 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
543774 TTTAGCAGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:545730 original size:31 final size:31
Alignment explanation
Indices: 545689--545752 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
545679 TCATGCCAAG
**
545689 AAATGGTGAATGAAGCAAGATGAGGCTGTCT
1 AAATGGTGAATGAAGCAAGAAAAGGCTGTCT
* *
545720 AAATGTTGAATGGAGCAAGAAAAGGCTGTCT
1 AAATGGTGAATGAAGCAAGAAAAGGCTGTCT
545751 AA
1 AA
545753 TTTGGGAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (31 bp):
AAATGGTGAATGAAGCAAGAAAAGGCTGTCT
Found at i:553082 original size:22 final size:22
Alignment explanation
Indices: 553058--553100 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
553048 CTTTTTCCTT
*
553058 TTTTTTTACCA-TTTTTTTTAA
1 TTTTTTTACCACTCTTTTTTAA
553079 TTTTTTTACCACTCTTTTTTAA
1 TTTTTTTACCACTCTTTTTTAA
553101 ACTTTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTTTACCACTCTTTTTTAA
Found at i:553288 original size:16 final size:16
Alignment explanation
Indices: 553255--553287 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
553245 TTTAATTAAA
553255 TTATTTTAAATTATTT
1 TTATTTTAAATTATTT
*
553271 TTATTTTCAA-TATTT
1 TTATTTTAAATTATTT
553286 TT
1 TT
553288 TTCTCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAAATTATTT
Found at i:553635 original size:29 final size:28
Alignment explanation
Indices: 553581--553636 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
553571 AATTAAAAAA
** *
553581 TTATTTATAATTTAAATTTGATCAATAT
1 TTATTTATAATAAAAATTTGAACAATAT
*
553609 TTATTTAATAATAAAAATTTTAACAATA
1 TTATTT-ATAATAAAAATTTGAACAATA
553637 ATTTTATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (28 bp):
TTATTTATAATAAAAATTTGAACAATAT
Found at i:562195 original size:22 final size:22
Alignment explanation
Indices: 562169--562212 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
562159 TGTATATTTA
*
562169 TATTTGTATCTCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
*
562191 TATTTGTATCCCTATAATTAAG
1 TATTTGTATCCCTAAAATTAAG
562213 GATAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:568421 original size:16 final size:16
Alignment explanation
Indices: 568402--568438 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
568392 TATTAAAATC
568402 ATCATAAATCATCATT
1 ATCATAAATCATCATT
568418 ATCATAAATCATCATT
1 ATCATAAATCATCATT
568434 ATCAT
1 ATCAT
568439 TGGTTTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATAAATCATCATT
Found at i:572693 original size:23 final size:23
Alignment explanation
Indices: 572666--572713 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
572656 AAATTTGAAT
572666 TCAAATTTTATGCAAAAATTCAA
1 TCAAATTTTATGCAAAAATTCAA
572689 TCAAATTTTATGCAAAAATTCAA
1 TCAAATTTTATGCAAAAATTCAA
572712 TC
1 TC
572714 TCTATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (23 bp):
TCAAATTTTATGCAAAAATTCAA
Found at i:573033 original size:17 final size:18
Alignment explanation
Indices: 573000--573036 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
572990 TTCAAATCTT
573000 TAAAATTTATAATATATA
1 TAAAATTTATAATATATA
573018 TAAAATTTAT-ATATATA
1 TAAAATTTATAATATATA
573035 TA
1 TA
573037 CTTATCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATTTATAATATATA
Found at i:580025 original size:22 final size:23
Alignment explanation
Indices: 579984--580053 Score: 115
Period size: 23 Copynumber: 3.1 Consensus size: 23
579974 ACTACCTATC
*
579984 GCTGTGTATAGAATGATATCAGA
1 GCTGTGTATAGAATGGTATCAGA
580007 GCTGTGTAT-GAATGGTATCAGA
1 GCTGTGTATAGAATGGTATCAGA
*
580029 ACTGTGTATAGAATGGTATCAGA
1 GCTGTGTATAGAATGGTATCAGA
580052 GC
1 GC
580054 GTCAGAGTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 20 0.47
23 23 0.53
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.30
Consensus pattern (23 bp):
GCTGTGTATAGAATGGTATCAGA
Found at i:589612 original size:23 final size:23
Alignment explanation
Indices: 589582--589626 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
589572 GTTGCAAGGC
589582 CTGATACCATTCTATACACAGCT
1 CTGATACCATTCTATACACAGCT
589605 CTGATACCATTCTATACACAGC
1 CTGATACCATTCTATACACAGC
589627 AGCAGGTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.29
Consensus pattern (23 bp):
CTGATACCATTCTATACACAGCT
Found at i:590359 original size:15 final size:15
Alignment explanation
Indices: 590341--590370 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
590331 TCAAAGGTAT
590341 CTCCTTTCCCTTTCA
1 CTCCTTTCCCTTTCA
590356 CTCCTTTCCCTTTCA
1 CTCCTTTCCCTTTCA
590371 AACATTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.47, G:0.00, T:0.47
Consensus pattern (15 bp):
CTCCTTTCCCTTTCA
Found at i:605404 original size:25 final size:25
Alignment explanation
Indices: 605384--605446 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
605374 ATGATTTTCT
605384 TACATTAGTGCAAATCCGATTCTCC
1 TACATTAGTGCAAATCCGATTCTCC
*
605409 TACATTAGTGCAAATCCAATTCTCC
1 TACATTAGTGCAAATCCGATTCTCC
605434 TACATTAGTGCAA
1 TACATTAGTGCAA
605447 CTTGATTTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (25 bp):
TACATTAGTGCAAATCCGATTCTCC
Found at i:614145 original size:17 final size:16
Alignment explanation
Indices: 614107--614173 Score: 55
Period size: 17 Copynumber: 4.0 Consensus size: 16
614097 TCTATTTTTT
*
614107 CTTTTATTATTTCATTC
1 CTTTTATT-TTTCTTTC
*
614124 TTTTTATTTTTCTTTCC
1 CTTTTATTTTTCTTT-C
614141 CTTTTACTTTTTC-TTC
1 CTTTTA-TTTTTCTTTC
* *
614157 CTCTTCATCTTTCTTTC
1 CT-TTTATTTTTCTTTC
614174 TTTGCCAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 14 0.34
17 21 0.51
18 6 0.15
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (16 bp):
CTTTTATTTTTCTTTC
Found at i:617546 original size:2 final size:2
Alignment explanation
Indices: 617539--617571 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
617529 TTTTCTTTTA
*
617539 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
617572 CTCCTTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:623219 original size:2 final size:2
Alignment explanation
Indices: 623212--623241 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
623202 AATTATAAAA
623212 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
623242 AAGCCTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:623598 original size:1 final size:1
Alignment explanation
Indices: 623592--623618 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
623582 AGTATTTAAG
623592 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
623619 GCGATTTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:624575 original size:12 final size:12
Alignment explanation
Indices: 624536--624581 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 12
624526 GATTTATTAG
624536 ATTAATTTTTTCT
1 ATTAATTTTTT-T
624549 ATTAAGTTTTATTT
1 ATTAA-TTTT-TTT
*
624563 ATTAATATTTTT
1 ATTAATTTTTTT
624575 ATTAATT
1 ATTAATT
624582 AATAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 9 0.31
13 8 0.28
14 10 0.34
15 2 0.07
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (12 bp):
ATTAATTTTTTT
Found at i:624576 original size:16 final size:16
Alignment explanation
Indices: 624555--624585 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
624545 TTCTATTAAG
*
624555 TTTTATTTATTAATAT
1 TTTTATTAATTAATAT
624571 TTTTATTAATTAATA
1 TTTTATTAATTAATA
624586 ATTAAATATA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATTAATTAATAT
Found at i:625780 original size:14 final size:13
Alignment explanation
Indices: 625761--625806 Score: 69
Period size: 14 Copynumber: 3.6 Consensus size: 13
625751 ATTTGTTTTT
625761 AATAATAATAATAA
1 AATAATAATAAT-A
625775 AATAATAATAATA
1 AATAATAATAATA
625788 AATAATAAT-A-A
1 AATAATAATAATA
625799 AATAATAA
1 AATAATAA
625807 AAATTGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.28
12 1 0.03
13 10 0.31
14 12 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:625796 original size:24 final size:23
Alignment explanation
Indices: 625760--625806 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
625750 TATTTGTTTT
625760 TAATAATAATAATAAAATAATAA
1 TAATAATAATAATAAAATAATAA
625783 TAATAAATAATAATAAAATAATAA
1 TAAT-AATAATAATAAAATAATAA
625807 AAATTGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TAATAATAATAATAAAATAATAA
Found at i:625819 original size:3 final size:3
Alignment explanation
Indices: 625760--625806 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
625750 TATTTGTTTT
625760 TAA TAA TAA TAA TAA -AA TAA TAA TAA TAAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
625804 TAA
1 TAA
625807 AAATTGAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Done.