Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1699
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: 127455
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Found at i:418 original size:9 final size:9
Alignment explanation
Indices: 404--445 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
394 TAAGAATGAT
404 ATATATATA
1 ATATATATA
413 ATATATATA
1 ATATATATA
422 AT-TATAT-
1 ATATATATA
429 ATAT-TATA
1 ATATATATA
*
437 ATAGATATA
1 ATATATATA
446 CATTTAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
7 5 0.17
8 9 0.31
9 15 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (9 bp):
ATATATATA
Found at i:444 original size:12 final size:12
Alignment explanation
Indices: 402--444 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
392 ATTAAGAATG
402 ATATATA-TATA
1 ATATATATTATA
* *
413 ATATATATAATT
1 ATATATATTATA
425 ATATATATTATA
1 ATATATATTATA
*
437 ATAGATAT
1 ATATATAT
445 ACATTTAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
ATATATATTATA
Found at i:3957 original size:27 final size:27
Alignment explanation
Indices: 3922--3991 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
3912 CACCCCTTGT
* *
3922 TTGTAAAAAATGGTGGTTACTTTGTGC
1 TTGTCAAAAATGGTGGTTACTTTGTAC
* * *
3949 TTGTCAAAAATGGTGGTTTCTTTTTAT
1 TTGTCAAAAATGGTGGTTACTTTGTAC
3976 TTGTCAAAAATGGTGG
1 TTGTCAAAAATGGTGG
3992 CATGTTGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (27 bp):
TTGTCAAAAATGGTGGTTACTTTGTAC
Found at i:10511 original size:18 final size:18
Alignment explanation
Indices: 10488--10522 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
10478 TTTGGCATTG
10488 ATTATTATTGCATTAATA
1 ATTATTATTGCATTAATA
10506 ATTATTATTGCATTAAT
1 ATTATTATTGCATTAAT
10523 TACATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
ATTATTATTGCATTAATA
Found at i:10522 original size:15 final size:15
Alignment explanation
Indices: 10482--10524 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
10472 CTTGACTTTG
*
10482 GCATTGATTATTATT
1 GCATTAATTATTATT
10497 GCATTAATAATTATTATT
1 GCA-T--TAATTATTATT
10515 GCATTAATTA
1 GCATTAATTA
10525 CATTAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 9 0.38
16 1 0.04
17 1 0.04
18 13 0.54
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (15 bp):
GCATTAATTATTATT
Found at i:12496 original size:17 final size:18
Alignment explanation
Indices: 12464--12499 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
12454 TTAGAATTGT
12464 TAATAATTTAAATAAATA
1 TAATAATTTAAATAAATA
*
12482 TAATCATTT-AATAAATA
1 TAATAATTTAAATAAATA
12499 T
1 T
12500 TTAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATTTAAATAAATA
Found at i:17656 original size:121 final size:122
Alignment explanation
Indices: 17435--17658 Score: 351
Period size: 121 Copynumber: 1.8 Consensus size: 122
17425 ATGTTAAGTC
* * *
17435 CAATATTCCATAACACATTTATATATTTCATTTTTTTTATGTTTATTAATATTGAATTAAGATTT
1 CAATATTCCATAACACATTTATATATTTCA-TTTTTTTATGTTTATTAAAATTAAATTAAGATTC
**
17500 TTTGTCAATTAATTAATTGAGTTGGTGTCTTTTGACTAGTGATATCACAAGGAGCATG
65 TTTGTCAATTAATTAATTGAGTTGGTGTCCATTGACTAGTGATATCACAAGGAGCATG
* *
17558 CAATATTCCCTAACATATTTATATATTTCA-TTTTTTATGTTTATTAAAATTAAATTAAGATTCT
1 CAATATTCCATAACACATTTATATATTTCATTTTTTTATGTTTATTAAAATTAAATTAAGATTCT
**
17622 TTGTCAATTCTTTAATTGAGTTGGTGTCCATTGACTA
66 TTGTCAATTAATTAATTGAGTTGGTGTCCATTGACTA
17659 ATAATATTGT
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
121 64 0.70
123 28 0.30
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (122 bp):
CAATATTCCATAACACATTTATATATTTCATTTTTTTATGTTTATTAAAATTAAATTAAGATTCT
TTGTCAATTAATTAATTGAGTTGGTGTCCATTGACTAGTGATATCACAAGGAGCATG
Found at i:20604 original size:20 final size:20
Alignment explanation
Indices: 20579--20705 Score: 76
Period size: 20 Copynumber: 5.8 Consensus size: 20
20569 ATTTGCCTGC
20579 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
20599 ATGTATCGATACATCTGGGTAAAAAAATA
1 ATGTATCGATACAT-T--G------AATA
*
20628 GATGTATCGATACAATG-ATAA
1 -ATGTATCGATACATTGAAT-A
**
20649 ATGTATCGATACAATTTGAAGC
1 ATGTATCGATAC-A-TTGAATA
* * *
20671 ATGGATCGATACATTTATTA
1 ATGTATCGATACATTGAATA
20691 ATGTATCGATACATT
1 ATGTATCGATACATT
20706 TCCTTGGCAG
Statistics
Matches: 83, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
20 45 0.54
21 4 0.05
22 13 0.16
23 2 0.02
27 1 0.01
29 5 0.06
30 13 0.16
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:20706 original size:20 final size:20
Alignment explanation
Indices: 20629--20706 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
20619 AAAAAAATAG
* *
20629 ATGTATCGATACAATGATAA
1 ATGTATCGATACATTTATAA
*
20649 ATGTATCGATACAATTTGA-AGC
1 ATGTATCGATAC-ATTT-ATA-A
* *
20671 ATGGATCGATACATTTATTA
1 ATGTATCGATACATTTATAA
20691 ATGTATCGATACATTT
1 ATGTATCGATACATTT
20707 CCTTGGCAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
20 28 0.60
21 7 0.15
22 12 0.26
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTTATAA
Found at i:21538 original size:22 final size:21
Alignment explanation
Indices: 21513--21579 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
21503 CTTTGATTAT
* *
21513 AAAAGTTACATTTTTTTCATCC
1 AAAAATTACA-TTCTTTCATCC
*
21535 AAAAATTGCATTCTTTCATCC
1 AAAAATTACATTCTTTCATCC
** *
21556 AACCATTGCA-TCATTTCATCC
1 AAAAATTACATTC-TTTCATCC
21577 AAA
1 AAA
21580 TACACATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.05
21 28 0.74
22 8 0.21
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.37
Consensus pattern (21 bp):
AAAAATTACATTCTTTCATCC
Found at i:21553 original size:21 final size:21
Alignment explanation
Indices: 21527--21579 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
21517 GTTACATTTT
21527 TTTCATCCAAAAATTGCATTC-
1 TTTCATCCAAAAATTGCA-TCA
**
21548 TTTCATCCAACCATTGCATCA
1 TTTCATCCAAAAATTGCATCA
21569 TTTCATCCAAA
1 TTTCATCCAAA
21580 TACACATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (21 bp):
TTTCATCCAAAAATTGCATCA
Found at i:24813 original size:21 final size:21
Alignment explanation
Indices: 24787--24839 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
24777 AGTTATATTT
24787 TTTCATCCAAAAATTACATTC-
1 TTTCATCCAAAAATTACA-TCA
* ** *
24808 TTTCATTCAACCATTGCATCA
1 TTTCATCCAAAAATTACATCA
24829 TTTCATCCAAA
1 TTTCATCCAAA
24840 TACATATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTCATCCAAAAATTACATCA
Found at i:25757 original size:3 final size:3
Alignment explanation
Indices: 25751--25787 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
25741 GATGATGATG
* *
25751 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ACA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
25788 AAAGAAGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:25768 original size:12 final size:12
Alignment explanation
Indices: 25751--25787 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
25741 GATGATGATG
*
25751 ATAATAATAATA
1 ATAATAACAATA
25763 ATAATAACAATA
1 ATAATAACAATA
25775 ATAATAACAATA
1 ATAATAACAATA
25787 A
1 A
25788 AAAGAAGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAATAACAATA
Found at i:30913 original size:22 final size:21
Alignment explanation
Indices: 30871--30930 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
30861 ATTCAAAATG
*
30871 ATTTT-AAATTAAATTAATTAA
1 ATTTTAAAATTTAA-TAATTAA
30892 ATTTTAAAATTTAATAATTTAA
1 ATTTTAAAATTTAATAA-TTAA
*
30914 A-TTCAAAATTTTAATAA
1 ATTTTAAAA-TTTAATAA
30931 AATAATTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 14 0.41
22 20 0.59
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTAAAATTTAATAATTAA
Found at i:32075 original size:13 final size:11
Alignment explanation
Indices: 32046--32111 Score: 53
Period size: 13 Copynumber: 5.5 Consensus size: 11
32036 TTGTTTATAG
32046 ATTTTTTTATCT
1 ATTTTTTTAT-T
32058 AATTTTTAATTATT
1 -ATTTTT--TTATT
32072 ATTTTTGTTATTT
1 ATTTTT-TTA-TT
32085 ATTTATTTTATT
1 ATTT-TTTTATT
*
32097 ATTTTTAT-TT
1 ATTTTTTTATT
32107 ATTTT
1 ATTTT
32112 ATATAGTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
10 7 0.15
11 3 0.06
12 9 0.19
13 21 0.45
14 3 0.06
15 4 0.09
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (11 bp):
ATTTTTTTATT
Found at i:32126 original size:22 final size:20
Alignment explanation
Indices: 32077--32132 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 20
32067 TTATTATTTT
32077 TGTTATTTATTTATTTTATTA
1 TGTTA-TTATTTATTTTATTA
32098 T-TT-TTATTTATTTTATATA
1 TGTTATTATTTATTTTAT-TA
32117 GTGTTATTA-TTATTTT
1 -TGTTATTATTTATTTT
32133 GATGCTTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 13 0.42
19 2 0.06
20 3 0.10
21 10 0.32
22 3 0.10
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
TGTTATTATTTATTTTATTA
Found at i:33989 original size:549 final size:548
Alignment explanation
Indices: 33049--34139 Score: 1437
Period size: 549 Copynumber: 2.0 Consensus size: 548
33039 TCAGCTCCAA
* * * * * *
33049 TTGTTTGTCATTAGCTACAAAAGATTTAGCGTAATTCATCACTAAATAAGATTTGCATAATATTT
1 TTGTTTGCCATTAGCTACAAAAGATTTAGCATAATTCATCACTAAAAAAAATTTACATAATATCT
*
33114 AAATAATCAAATGTAAGAACCTATATTAACTAATTGATCAAATATAAATCCATACCTTTGAAGGA
66 AAATAATCAAATGTAAGAA-CTATATTAACTAATTGATCAAATATAAATCCATACCTTTAAAGGA
*** * *
33179 TCGAAAGCTTTCAATTTGATTGTGGCTTAAATCCAATGTCTTCAAGTTTATCAAATTATTGAATT
130 TCGAAAGCTTTCAATTTGATTCCCGCTTAAATCCAATATCTTCAAGTTTATAAAATTATTGAATT
* * * * *
33244 CTATATATTCAAAGTTTCAATTCAAACAATGATTATATATGTTAGTCTTATTAATAATAGTCATA
195 CTATATATCCAAAGTTTCAATTCAAACAACGATTATATATGTCAGTCTGATTAATAATAATCATA
* * * * * *
33309 CATAATGTACATAAAGATGAAAAACTATTTACTTAATATTTTTAATGGTTTTAATGAAATAAAAA
260 AATAATGTACATAAAGATGAAAAACCATTTAATCAATATTTTTAATGGATGTAATGAAATAAAAA
* * * ** * *
33374 TAGCAAAGCAAATTTAAAACTTTAACTACAGATAAAACTCTTAAATGTTGGATGTAAACGTAATC
325 TAACAAAGCAAATCTAAAACTTTAACTACAGAAAAAACTCCAAAATGATGGATGTAAACATAATC
* *
33439 ATTTGAAATAATTTTACTTTTAATATCTATTGAGCCTTGCAATTGGTTGTCACTCATATG-TAAG
390 ATTTGAAATAATTTTACCTTTAATATCTATTGAGCCTTGCAATTGGTTGTCACTCATA-GACAAG
* * * * *
33503 GACTTTAGACTTGAAAGGCCTGAAGGGAATGCCAATGTGTTATTCCCGAAGAGATTATCATTCAA
454 GACTTTAGACTTGAAAAGCCTGAAGGGAATACCAATGTGTTATTCCCGAAAAGATTATAACTCAA
33568 ATAAAGTTCCTCCAAATTGGTCAATTTTAG
519 ATAAAGTTCCTCCAAATTGGTCAATTTTAG
* *
33598 TTGTTTGCCATTAGCTACAGAAGATTTA-TATAATTCATCA-TAAAAAAAATTTACATAATATCT
1 TTGTTTGCCATTAGCTACAAAAGATTTAGCATAATTCATCACTAAAAAAAATTTACATAATATCT
* * * * * * *
33661 AAATAATTATATGTAAGAA-TTTATTAATTAATTGATCAAATATAATTGCATGCCTTTAAAGGAT
66 AAATAATCAAATGTAAGAACTATATTAACTAATTGATCAAATATAAATCCATACCTTTAAAGGAT
* * *
33725 TGAAAGCTTTCAATTTGATTCCCTCTTAAATCCAATATCTTTAAGTTTGA-AAAATTATTGAATT
131 CGAAAGCTTTCAATTTGATTCCCGCTTAAATCCAATATCTTCAAGTTT-ATAAAATTATTGAATT
* *
33789 CTATATATCCAAAG-TTCAATTCAGATAACCG-TTATATATGTCAGTCTGATTAATAATAATCAT
195 CTATATATCCAAAGTTTCAATTCAAACAA-CGATTATATATGTCAGTCTGATTAATAATAATCAT
*
33852 AAATAATGT-CAATAAAGATGAAAAACCGTTTAATCAATATTTTTAATAATGGATGTAATGAAAT
259 AAATAATGTAC-ATAAAGATGAAAAACCATTTAATCAATA-TTTT--TAATGGATGTAATGAAAT
* ** *
33916 AAAAATAACAAAGTAAATCTAAAGTTTTAACTGA-AGACAAAAACTCCCAAAAT-ATGAGATGTG
320 AAAAATAACAAAGCAAATCTAAAACTTTAACT-ACAGA-AAAAACT-CCAAAATGATG-GATGTA
* * * *
33979 AATATAATCATTTGAAATAATTTTACCTTTAATATCTATTGAGCCTTGTAATTTGTTGTTACTCA
381 AACATAATCATTTGAAATAATTTTACCTTTAATATCTATTGAGCCTTGCAATTGGTTGTCACTCA
**
34044 TAGACAAGGACTTTAGACTTGAAAAGCCTGAAGGGAATACCAATGTGTTATTCTTGAAAAGATTA
446 TAGACAAGGACTTTAGACTTGAAAAGCCTGAAGGGAATACCAATGTGTTATTCCCGAAAAGATTA
*
34109 TAACTCAAATCAAGTTCCTCCAAATTGGTCA
511 TAACTCAAATAAAGTTCCTCCAAATTGGTCA
34140 GCTTCAGTTT
Statistics
Matches: 468, Mismatches: 63, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
543 1 0.00
544 73 0.16
545 111 0.24
546 1 0.00
547 82 0.18
548 20 0.04
549 180 0.38
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (548 bp):
TTGTTTGCCATTAGCTACAAAAGATTTAGCATAATTCATCACTAAAAAAAATTTACATAATATCT
AAATAATCAAATGTAAGAACTATATTAACTAATTGATCAAATATAAATCCATACCTTTAAAGGAT
CGAAAGCTTTCAATTTGATTCCCGCTTAAATCCAATATCTTCAAGTTTATAAAATTATTGAATTC
TATATATCCAAAGTTTCAATTCAAACAACGATTATATATGTCAGTCTGATTAATAATAATCATAA
ATAATGTACATAAAGATGAAAAACCATTTAATCAATATTTTTAATGGATGTAATGAAATAAAAAT
AACAAAGCAAATCTAAAACTTTAACTACAGAAAAAACTCCAAAATGATGGATGTAAACATAATCA
TTTGAAATAATTTTACCTTTAATATCTATTGAGCCTTGCAATTGGTTGTCACTCATAGACAAGGA
CTTTAGACTTGAAAAGCCTGAAGGGAATACCAATGTGTTATTCCCGAAAAGATTATAACTCAAAT
AAAGTTCCTCCAAATTGGTCAATTTTAG
Found at i:37772 original size:2 final size:2
Alignment explanation
Indices: 37759--37804 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
37749 GAATAGCCAA
* *
37759 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37801 -G AG A
1 AG AG A
37805 CTTGTCATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38359 original size:20 final size:19
Alignment explanation
Indices: 38322--38384 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
38312 AACCGATAAA
* *
38322 ATAAAATTATAACTATTATT
1 ATAAAAATATAA-AATTATT
*
38342 ATAAAATATATATAATTATGT
1 ATAAAA-ATATAAAATTAT-T
*
38363 GTAAAAATATAAAATTA-T
1 ATAAAAATATAAAATTATT
38381 ATAA
1 ATAA
38385 TAGCAAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.11
20 21 0.60
21 10 0.29
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (19 bp):
ATAAAAATATAAAATTATT
Found at i:39640 original size:23 final size:23
Alignment explanation
Indices: 39605--39668 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
39595 AATTATTTAT
39605 ATTTA-ATATTTAATAATATATAA
1 ATTTATATA-TTAATAATATATAA
39628 ATTTATATATTAATAATATATAA
1 ATTTATATATTAATAATATATAA
* *
39651 ATTTATATAATATTAATA
1 ATTTATATATTAATAATA
39669 AATCAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 35 0.92
24 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTATATATTAATAATATATAA
Found at i:39679 original size:34 final size:34
Alignment explanation
Indices: 39621--39708 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 34
39611 TATTTAATAA
* * *
39621 TATATAA-ATTTATATATTAATAATATATAAATT
1 TATATAATATTAATAAATCAATAATATATAAATT
39654 TATATAATATTAATAAATCAATAATATATAAATT
1 TATATAATATTAATAAATCAATAATATATAAATT
* * *
39688 TATTTATTATCAATAAATCAA
1 TATATAATATTAATAAATCAA
39709 ATAAAATCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 7 0.15
34 41 0.85
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (34 bp):
TATATAATATTAATAAATCAATAATATATAAATT
Found at i:39686 original size:15 final size:15
Alignment explanation
Indices: 39639--39686 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
39629 TTTATATATT
*
39639 AATAATATATAAATTT
1 AATAATATATAAA-TC
39655 ATATAATATTAATAAATC
1 A-ATAATA-T-ATAAATC
39673 AATAATATATAAAT
1 AATAATATATAAAT
39687 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 6 0.21
16 2 0.07
17 12 0.43
18 3 0.11
19 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAATATATAAATC
Found at i:39732 original size:20 final size:21
Alignment explanation
Indices: 39707--39745 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
39697 TCAATAAATC
39707 AAATAAAATCATTT-TATTAA
1 AAATAAAATCATTTATATTAA
*
39727 AAATAAAATTATTTATATT
1 AAATAAAATCATTTATATT
39746 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATAAAATCATTTATATTAA
Found at i:40212 original size:16 final size:17
Alignment explanation
Indices: 40193--40225 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40183 GAAAAAGTAG
*
40193 AAAAATAATTT-TTTAA
1 AAAAAGAATTTATTTAA
40209 AAAAAGAATTTATTTAA
1 AAAAAGAATTTATTTAA
40226 CTGTACATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAAAAGAATTTATTTAA
Found at i:40970 original size:27 final size:27
Alignment explanation
Indices: 40940--40999 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
40930 TAACTTATAA
*
40940 TTATTTAATATAAAT-TAATTTTAATTT
1 TTATTTAACATAAATATAATTTT-ATTT
40967 TTATTTAACATAAATATAATTTTATTT
1 TTATTTAACATAAATATAATTTTATTT
*
40994 ATATTT
1 TTATTT
41000 TATTATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
TTATTTAACATAAATATAATTTTATTT
Found at i:41015 original size:35 final size:35
Alignment explanation
Indices: 40946--41037 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
40936 ATAATTATTT
* * *
40946 AATATAAATTAATTT-TAATTT-TTATTTAACATA
1 AATATAATTTTATTTATATTTTATTATTTAACATA
*
40979 AATATAATTTTATTTATATTTTATTATTTAATATA
1 AATATAATTTTATTTATATTTTATTATTTAACATA
*
41014 AATAT-ATTTTATTTTATATATTAT
1 AATATAATTTTA-TTTATATTTTAT
41038 ATATATACAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
33 13 0.25
34 11 0.22
35 27 0.53
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (35 bp):
AATATAATTTTATTTATATTTTATTATTTAACATA
Found at i:41021 original size:29 final size:31
Alignment explanation
Indices: 40979--41053 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
40969 ATTTAACATA
* *
40979 AATATAATTTTATTTATATTTTAT-TATT-T
1 AATATAAATATATTTATATTTTATATATTAT
41008 AATATAAATATATTT-TATTTTATATATTAT
1 AATATAAATATATTTATATTTTATATATTAT
*
41038 ATATATACATAT-TTTA
1 A-ATATAAATATATTTA
41054 ATCTAATACT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 8 0.21
29 17 0.44
30 5 0.13
31 9 0.23
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
AATATAAATATATTTATATTTTATATATTAT
Found at i:41041 original size:23 final size:22
Alignment explanation
Indices: 40988--41043 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
40978 AAATATAATT
*
40988 TTATTTATATTTTATTATTTAA
1 TTATATATATTTTATTATTTAA
*
41010 TATAAATATATTTTATT-TTATATA
1 T-TATATATATTTTATTATT-TA-A
41034 TTATATATAT
1 TTATATATAT
41044 ACATATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.11
23 23 0.82
24 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATATATTTTATTATTTAA
Found at i:42624 original size:21 final size:21
Alignment explanation
Indices: 42595--42636 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42585 ACTAATTTTC
42595 TTTTATTTTATTTCAAA-AAAT
1 TTTTATTTTATTT-AAATAAAT
*
42616 TTTTCTTTTATTTAAATAAAT
1 TTTTATTTTATTTAAATAAAT
42637 ATATATGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATTTTATTTAAATAAAT
Found at i:43198 original size:56 final size:56
Alignment explanation
Indices: 43131--43238 Score: 189
Period size: 56 Copynumber: 1.9 Consensus size: 56
43121 TTTGGCCAAA
* * *
43131 AAACCAGTTATTGGAAGACCTTGACTTGTACTAAACGAATAGCCAAAGAAAGAAAG
1 AAACCACTTATTGGAAGACCTTGACTTGTAATAAACAAATAGCCAAAGAAAGAAAG
43187 AAACCACTTATTGGAAGACCTTGACTTGTAATAAACAAATAGCCAAAGAAAG
1 AAACCACTTATTGGAAGACCTTGACTTGTAATAAACAAATAGCCAAAGAAAG
43239 TAGGAAAGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.20
Consensus pattern (56 bp):
AAACCACTTATTGGAAGACCTTGACTTGTAATAAACAAATAGCCAAAGAAAGAAAG
Found at i:43387 original size:38 final size:38
Alignment explanation
Indices: 43318--43390 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
43308 ATTTTATAAA
*
43318 TTTATTTAAATTAGTTTAATTTAAAATATAAATAATTT
1 TTTATTTAAATTAGTTCAATTTAAAATATAAATAATTT
*
43356 TTTATTTAAATCTA-TTCATATTTATAA-ATAAATAA
1 TTTATTTAAAT-TAGTTCA-ATTTAAAATATAAATAA
43391 ATAATCTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 22 0.71
39 9 0.29
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (38 bp):
TTTATTTAAATTAGTTCAATTTAAAATATAAATAATTT
Found at i:43832 original size:18 final size:18
Alignment explanation
Indices: 43809--43870 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
43799 CTAAAATAAA
*
43809 ATTATAATAAT-TATTATT
1 ATTATAA-AATATATAATT
43827 ATTATAAAATATATAATT
1 ATTATAAAATATATAATT
*
43845 ATATATAAAAATATAAAATT
1 AT-TAT-AAAATATATAATT
43865 -TTATAA
1 ATTATAA
43871 TGGACAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.13
18 18 0.46
19 4 0.10
20 12 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTATAAAATATATAATT
Found at i:43855 original size:20 final size:20
Alignment explanation
Indices: 43811--43869 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
43801 AAAATAAAAT
* *
43811 TATAATAAT-TATTATTAT-
1 TATAAAAATATATAATTATA
43829 TAT-AAAATATATAATTATA
1 TATAAAAATATATAATTATA
* *
43848 TATAAAAATATAAAATTTTA
1 TATAAAAATATATAATTATA
43868 TA
1 TA
43870 ATGGACAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 4 0.12
18 11 0.32
19 3 0.09
20 16 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAAAAATATATAATTATA
Found at i:45119 original size:19 final size:19
Alignment explanation
Indices: 45084--45162 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
45074 AGATTTTTTA
* *
45084 ATTATTTATAT-TTAATTT
1 ATTATTAATATATAAATTT
45102 ATTATTAATATATAAATTT
1 ATTATTAATATATAAATTT
*
45121 ATATATT-ATAAATAAA-TT
1 AT-TATTAATATATAAATTT
45139 A--A-TAATATATAAATTT
1 ATTATTAATATATAAATTT
45155 ATGTATTA
1 AT-TATTA
45163 TTAAAAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
14 1 0.02
15 9 0.18
16 3 0.06
18 13 0.27
19 17 0.35
20 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (19 bp):
ATTATTAATATATAAATTT
Found at i:45150 original size:15 final size:15
Alignment explanation
Indices: 45102--45153 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
45092 TATTTAATTT
*
45102 ATTATTAATATATAA
1 ATTAATAATATATAA
*
45117 ATTTATATATTATAAATAA
1 A-TTA-ATA--ATATATAA
45136 ATTAATAATATATAA
1 ATTAATAATATATAA
45151 ATT
1 ATT
45154 TATGTATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 11 0.37
16 3 0.10
17 5 0.17
18 3 0.10
19 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAATAATATATAA
Found at i:45150 original size:34 final size:33
Alignment explanation
Indices: 45102--45180 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 33
45092 TATTTAATTT
*
45102 ATTATTAATATATAAATTTATATATTATAAATAA
1 ATTAATAATATATAAATTTATATATTATAAA-AA
* *
45136 ATTAATAATATATAAATTTATGTATTATTAAAA
1 ATTAATAATATATAAATTTATATATTATAAAAA
45169 ATTAAATAATAT
1 ATT-AATAATAT
45181 TATTTTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 5 0.12
34 36 0.88
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
ATTAATAATATATAAATTTATATATTATAAAAA
Found at i:45193 original size:25 final size:24
Alignment explanation
Indices: 45136--45213 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 24
45126 TTATAAATAA
* * *
45136 ATTAATAATATATAAATTTATGTATT
1 ATTAAAAATAAAT-AATTTATAT-TT
45162 ATTAAAAATTAAATAATATTAT-TTT
1 ATTAAAAA-TAAATAAT-TTATATTT
*
45187 ATTAAAAATAAATTATTTATATTT
1 ATTAAAAATAAATAATTTATATTT
45211 ATT
1 ATT
45214 TTAAAAGATT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 4 0.09
24 13 0.28
25 10 0.22
26 11 0.24
27 8 0.17
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (24 bp):
ATTAAAAATAAATAATTTATATTT
Found at i:45195 original size:20 final size:20
Alignment explanation
Indices: 45172--45209 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
45162 ATTAAAAATT
45172 AAATAATATTATTT-TATTAA
1 AAATAA-ATTATTTATATTAA
45192 AAATAAATTATTTATATT
1 AAATAAATTATTTATATT
45210 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATAAATTATTTATATTAA
Found at i:45198 original size:24 final size:25
Alignment explanation
Indices: 45150--45213 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
45140 ATAATATATA
*
45150 AATTTATGTATTATTAAAAATTAAAT
1 AATTTATAT-TTATTAAAAATTAAAT
45176 AATATTAT-TTTATTAAAAA-TAAAT
1 AAT-TTATATTTATTAAAAATTAAAT
*
45200 TATTTATATTTATT
1 AATTTATATTTATT
45214 TTAAAAGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
23 4 0.11
24 13 0.37
25 10 0.29
26 4 0.11
27 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
AATTTATATTTATTAAAAATTAAAT
Found at i:45621 original size:7 final size:7
Alignment explanation
Indices: 45609--45642 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
45599 AAAAGTGGGT
45609 AAAATAA
1 AAAATAA
45616 AAAATAA
1 AAAATAA
45623 AAAATATA
1 AAAATA-A
*
45631 TAAATAA
1 AAAATAA
45638 AAAAT
1 AAAAT
45643 TTATTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAATAA
Found at i:46344 original size:14 final size:15
Alignment explanation
Indices: 46327--46367 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
46317 TTTCTTTTTC
46327 TTTATTTTTAATT-A
1 TTTATTTTTAATTAA
*
46341 TTTA-TTTGATATTAA
1 TTTATTTTTA-ATTAA
46356 TTTATTTTTAAT
1 TTTATTTTTAAT
46368 ATAAATACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
13 4 0.18
14 7 0.32
15 7 0.32
16 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTATTTTTAATTAA
Found at i:46703 original size:20 final size:21
Alignment explanation
Indices: 46665--46703 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46655 ATTAATTAAA
*
46665 AATTTTAAATATTAAATAATT
1 AATTTTAAATATAAAATAATT
46686 AATTTTAAA-ATAAAATAA
1 AATTTTAAATATAAAATAA
46704 ATATTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTTTAAATATAAAATAATT
Found at i:46720 original size:16 final size:15
Alignment explanation
Indices: 46670--46724 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 15
46660 TTAAAAATTT
46670 TAAATATT-AAATAA
1 TAAATATTAAAATAA
* *
46684 TTAATTTTAAAATAAAA
1 TAAATATTAAAAT--AA
46701 TAAATATTAAACATAA
1 TAAATATTAAA-ATAA
46717 TAAATATT
1 TAAATATT
46725 TATAAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.18
15 4 0.12
16 10 0.30
17 11 0.33
18 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAATATTAAAATAA
Found at i:47046 original size:30 final size:27
Alignment explanation
Indices: 47002--47073 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
46992 CGTTAATATC
* *
47002 ATATTAT-TTTTTAACAAAATTAATGATT
1 ATATTATATATTTAACAAAATT-AT-AAT
47030 AGTATTATATATTTAACAAAATTATAAT
1 A-TATTATATATTTAACAAAATTATAAT
47058 ATATGTATATATTTAA
1 ATAT-TATATATTTAA
47074 ATATTTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 3 0.08
28 15 0.38
29 8 0.21
30 13 0.33
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (27 bp):
ATATTATATATTTAACAAAATTATAAT
Found at i:47443 original size:16 final size:16
Alignment explanation
Indices: 47404--47453 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
47394 ATTTTAATTT
47404 TATTAAATATTAATTA-A
1 TATTAAA-A-TAATTATA
*
47421 TTATTAAAATATTTATA
1 -TATTAAAATAATTATA
47438 TATTAAAATAATTATA
1 TATTAAAATAATTATA
47454 ATTTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 20 0.69
17 2 0.07
18 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTAAAATAATTATA
Found at i:47451 original size:25 final size:23
Alignment explanation
Indices: 47423--47469 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
47413 TTAATTAATT
*
47423 ATTAAAATATTTATATATTAAAATA
1 ATTAAAAT-TTTA-ATATAAAAATA
*
47448 ATTATAATTTTAATATAAAAAT
1 ATTAAAATTTTAATATAAAAAT
47470 TAAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTAAAATTTTAATATAAAAATA
Found at i:47465 original size:17 final size:17
Alignment explanation
Indices: 47418--47465 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
47408 AAATATTAAT
*
47418 TAATTATTAAAATATTTA
1 TAATT-TTAAAATAATTA
*
47436 T-ATATTAAAATAATTA
1 TAATTTTAAAATAATTA
*
47452 TAATTTTAATATAA
1 TAATTTTAAAATAA
47466 AAATTAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 12 0.48
17 12 0.48
18 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTTTAAAATAATTA
Found at i:48302 original size:28 final size:31
Alignment explanation
Indices: 48237--48302 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
48227 TAACTGATAT
* *
48237 TTAAAAATTTACATTTGATACAAATAATAAA
1 TTAAATATTTAAATTTGATACAAATAATAAA
*
48268 TTCAATATTTAAATTT-ATA-AAA-AATAAA
1 TTAAATATTTAAATTTGATACAAATAATAAA
48296 TTAAATA
1 TTAAATA
48303 GTGTCAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 12 0.39
29 3 0.10
30 3 0.10
31 13 0.42
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (31 bp):
TTAAATATTTAAATTTGATACAAATAATAAA
Found at i:48605 original size:6 final size:6
Alignment explanation
Indices: 48594--48634 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
48584 TAATAAAAAA
*
48594 ATATTT ATATTT ATATTT ATATTT AATATTT TTATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT -ATATTT ATATTT ATAT
48635 AAAATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:48640 original size:19 final size:19
Alignment explanation
Indices: 48600--48646 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
48590 AAAAATATTT
* **
48600 ATATTTATATTTATATTTA
1 ATATTTTTATTTATATAAA
48619 ATATTTTTATTTATATAAA
1 ATATTTTTATTTATATAAA
48638 ATATATTTT
1 ATAT-TTTT
48647 TACTAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTTTTATTTATATAAA
Found at i:48857 original size:21 final size:22
Alignment explanation
Indices: 48831--48872 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
48821 TAGAAAGAAT
48831 ATTTAAT-TTTT-ATATTAATAA
1 ATTTAATATTTTAAT-TTAATAA
48852 ATTTAATATTTTAATTTAATA
1 ATTTAATATTTTAATTTAATA
48873 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTAATATTTTAATTTAATAA
Found at i:48869 original size:13 final size:13
Alignment explanation
Indices: 48851--48876 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48841 TATATTAATA
48851 AATTTAATATTTT
1 AATTTAATATTTT
48864 AATTTAATATTTT
1 AATTTAATATTTT
48877 TTAAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATTTAATATTTT
Found at i:48911 original size:22 final size:21
Alignment explanation
Indices: 48886--48939 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
48876 TTTAAATTAT
*
48886 AATAAATAAAAAAATAGTTTA
1 AATAAATAAAAAAATAGTATA
* *
48907 CAAT-ATTAAAAAAATTGTATA
1 -AATAAATAAAAAAATAGTATA
48928 AATATAATAAAA
1 AATA-AATAAAA
48940 TATTAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 14 0.54
22 9 0.35
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
AATAAATAAAAAAATAGTATA
Found at i:48931 original size:20 final size:21
Alignment explanation
Indices: 48892--48941 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
48882 TTATAATAAA
*
48892 TAAAAAAATAGTTTACAATAT
1 TAAAAAAATAGTATACAATAT
*
48913 TAAAAAAATTGTATA-AATA-
1 TAAAAAAATAGTATACAATAT
*
48932 TAATAAAATA
1 TAAAAAAATA
48942 TTAATAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 8 0.32
20 4 0.16
21 13 0.52
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (21 bp):
TAAAAAAATAGTATACAATAT
Found at i:51737 original size:9 final size:9
Alignment explanation
Indices: 51716--51748 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
51706 AATTTAAAAT
51716 TTAAATT-A
1 TTAAATTAA
51724 TTAAATTAA
1 TTAAATTAA
51733 TTAAATTAA
1 TTAAATTAA
51742 TTAAATT
1 TTAAATT
51749 TAAATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAATTAA
Found at i:52211 original size:25 final size:25
Alignment explanation
Indices: 52181--52259 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
52171 TCATTAAATT
52181 TAATATTAATTTTTATATAAATTAA
1 TAATATTAATTTTTATATAAATTAA
*
52206 TAATATTTAA-TTATATA-AAATT-A
1 TAATA-TTAATTTTTATATAAATTAA
*
52229 TATTATTAAATTTTTAT-T--ATTAA
1 TAATATT-AATTTTTATATAAATTAA
52252 TAA-ATTAA
1 TAATATTAA
52260 ATCATTTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
21 2 0.04
22 8 0.18
23 10 0.22
24 10 0.22
25 11 0.24
26 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TAATATTAATTTTTATATAAATTAA
Found at i:52235 original size:23 final size:23
Alignment explanation
Indices: 52193--52261 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
52183 ATATTAATTT
*
52193 TTATATAAATTAATAATATTTAA
1 TTATATAAATTAATAATATTAAA
*
52216 TTATATAAAATT-ATATTATTAAA
1 TTATAT-AAATTAATAATATTAAA
* *
52239 TT-TTTATTATTAATAA-ATTAAA
1 TTATATA-AATTAATAATATTAAA
52261 T
1 T
52262 CATTTATGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 1 0.03
22 12 0.32
23 20 0.53
24 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATATAAATTAATAATATTAAA
Found at i:52462 original size:41 final size:41
Alignment explanation
Indices: 52416--52501 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
52406 AGAGCTAATG
* *
52416 TAAATAAATTATAATAAAAATTTGATATGATTTGATAAAAT
1 TAAATAAATTATAATAAAAATTTGATAAGATTTAATAAAAT
52457 TAAATAAATTATAATAAAAATTTGATAAGATTTAATAAAAT
1 TAAATAAATTATAATAAAAATTTGATAAGATTTAATAAAAT
52498 TAAA
1 TAAA
52502 AGTTTATGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (41 bp):
TAAATAAATTATAATAAAAATTTGATAAGATTTAATAAAAT
Found at i:57097 original size:31 final size:30
Alignment explanation
Indices: 57025--57114 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 30
57015 ATAAAATTTT
*
57025 ATAAAAATATATTAATCTTTTTAA-TATTA
1 ATAAAAATATATTTATCTTTTTAAGTATTA
*
57054 A-AAAAATTTATTTATCTTTTTAAGGT-TTA
1 ATAAAAATATATTTATCTTTTTAA-GTATTA
57083 GATAAAAATATATTTAT-TTTCTTAAGTTATTA
1 -ATAAAAATATATTTATCTTT-TTAAG-TATTA
57115 TTTATAGGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
28 20 0.39
29 4 0.08
30 6 0.12
31 18 0.35
32 3 0.06
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (30 bp):
ATAAAAATATATTTATCTTTTTAAGTATTA
Found at i:57637 original size:25 final size:27
Alignment explanation
Indices: 57594--57648 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
57584 TATCTTTAAA
** *
57594 ATTTTTAAAATAATGATAAT-TAATTT
1 ATTTTTAAAATAAAAATAATATAATAT
57620 ATTTTT-AAATAAAAATAATATAATAT
1 ATTTTTAAAATAAAAATAATATAATAT
57646 ATT
1 ATT
57649 AATATCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTTTTAAAATAAAAATAATATAATAT
Found at i:58920 original size:2 final size:2
Alignment explanation
Indices: 58913--58938 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58903 TAAACAAGTT
58913 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
58939 AACTATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59445 original size:42 final size:43
Alignment explanation
Indices: 59348--59439 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 43
59338 ATCTAAGGAC
*
59348 TCTTTTGAGTCTTAATAATGCCTTCAAGCCATAATTAAGATTA
1 TCTTTTGAGTCTTAAAAATGCCTTCAAGCCATAATTAAGATTA
59391 TC-TTTGAGTCTTAAAAATGCCTTCAAGCCATAATTAAGATTA
1 TCTTTTGAGTCTTAAAAATGCCTTCAAGCCATAATTAAGATTA
59433 TCTTTTG
1 TCTTTTG
59440 CTCTTATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 41 0.87
43 6 0.13
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (43 bp):
TCTTTTGAGTCTTAAAAATGCCTTCAAGCCATAATTAAGATTA
Found at i:60456 original size:21 final size:21
Alignment explanation
Indices: 60404--60456 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
60394 ATTATATATA
* *
60404 ACATGAAAAAATAACACGAAC
1 ACATGAAAAAAAAACAAGAAC
* * * *
60425 ACGTCACAAAAAAACAAGAAT
1 ACATGAAAAAAAAACAAGAAC
60446 ACATGAAAAAA
1 ACATGAAAAAA
60457 TAAGACGACC
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.64, C:0.17, G:0.09, T:0.09
Consensus pattern (21 bp):
ACATGAAAAAAAAACAAGAAC
Found at i:61313 original size:29 final size:29
Alignment explanation
Indices: 61271--61333 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
61261 ATCACACGAG
*
61271 AAAATAATTATATTTTTATTAA-TAATTTT
1 AAAATAATTATATTTTGA-TAATTAATTTT
*
61300 AAAATAA-TATTATTTTGATAATTTATTTT
1 AAAATAATTA-TATTTTGATAATTAATTTT
61329 AAAAT
1 AAAAT
61334 TAAAAGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
AAAATAATTATATTTTGATAATTAATTTT
Found at i:61883 original size:40 final size:39
Alignment explanation
Indices: 61823--61900 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
61813 TTTTATCCAG
*
61823 ATGTATCGATATATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATATATTCTTCAATATATCGATACAT-TATGA
* *
61863 ATGTATCGATATATTCTTCAATGTATTGATACATTATG
1 ATGTATCGATATATTCTTCAATATATCGATACATTATG
61901 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (39 bp):
ATGTATCGATATATTCTTCAATATATCGATACATTATGA
Found at i:61885 original size:20 final size:19
Alignment explanation
Indices: 61823--61893 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
61813 TTTTATCCAG
61823 ATGTATCGATATATTTTTCA
1 ATGTATCGATATA-TTTTCA
* * * *
61843 ATATATCGATACATGTATGA
1 ATGTATCGATATAT-TTTCA
61863 ATGTATCGATATATTCTTCA
1 ATGTATCGATATATT-TTCA
*
61883 ATGTATTGATA
1 ATGTATCGATA
61894 CATTATGTCT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.05
20 38 0.95
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.44
Consensus pattern (19 bp):
ATGTATCGATATATTTTCA
Found at i:70882 original size:57 final size:57
Alignment explanation
Indices: 70783--70892 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
70773 TTTAACATGT
* * * *
70783 TGATGACACTTGGGCATGCTGATGAATCTGGTAATTGCCCGGATCCCTATATCTTGC
1 TGATGACACTTGAGCATGCTGATGAACCTGGCAATTACCCGGATCCCTATATCTTGC
* *
70840 TGATGACACTTGAGCATGCTGATGAACCTGGCAATTATCCGGATCCCTCTATC
1 TGATGACACTTGAGCATGCTGATGAACCTGGCAATTACCCGGATCCCTATATC
70893 ACCCCAGACA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (57 bp):
TGATGACACTTGAGCATGCTGATGAACCTGGCAATTACCCGGATCCCTATATCTTGC
Found at i:73667 original size:21 final size:21
Alignment explanation
Indices: 73637--73685 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
73627 TTAAAAATGA
73637 AAAACTTGTTAATTCAATGGCT
1 AAAA-TTGTTAATTCAATGGCT
73659 AAAATTGTTAATTCAATGGCT
1 AAAATTGTTAATTCAATGGCT
73680 AAAATT
1 AAAATT
73686 CATAAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAATTGTTAATTCAATGGCT
Found at i:76378 original size:42 final size:42
Alignment explanation
Indices: 76319--76405 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
76309 CGGCTAATAT
76319 ACCCACGGGTAACTCCAATATCCCACTATCTATACTATCTTG
1 ACCCACGGGTAACTCCAATATCCCACTATCTATACTATCTTG
*
76361 ACCCACGGGTAACTCCAATATCCCACTATCTATAGTATCTTG
1 ACCCACGGGTAACTCCAATATCCCACTATCTATACTATCTTG
76403 ACC
1 ACC
76406 GTTGGATGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.28
Consensus pattern (42 bp):
ACCCACGGGTAACTCCAATATCCCACTATCTATACTATCTTG
Found at i:76839 original size:27 final size:28
Alignment explanation
Indices: 76809--76870 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
76799 GTCATATTAT
76809 TATAATATTTAAA-ATATTTAAT-ATTTA
1 TATAATATTTAAATATA-TTAATAATTTA
* *
76836 TATAA-ATTTTAATATATTATTAATTTA
1 TATAATATTTAAATATATTAATAATTTA
*
76863 TATTATAT
1 TATAATAT
76871 AAATTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 10 0.34
27 17 0.59
28 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TATAATATTTAAATATATTAATAATTTA
Found at i:76848 original size:18 final size:18
Alignment explanation
Indices: 76820--76883 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
76810 ATAATATTTA
76820 AAATATTTAATATTTATAT
1 AAAT-TTTAATATTTATAT
76839 AAATTTTAATATATTAT-T
1 AAATTTTAATAT-TTATAT
76857 -AA-TTT-ATA-TTATAT
1 AAATTTTAATATTTATAT
*
76871 AAATTTTTATATT
1 AAATTTTAATATT
76884 GTTATTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 4 0.10
14 1 0.03
15 5 0.13
16 6 0.15
17 5 0.13
18 10 0.26
19 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTTTAATATTTATAT
Found at i:76874 original size:32 final size:34
Alignment explanation
Indices: 76824--76918 Score: 101
Period size: 32 Copynumber: 2.9 Consensus size: 34
76814 TATTTAAAAT
76824 ATTTAATATTTATATAAATTTTAATA-TATTATTA
1 ATTT-ATATTTATATAAATTTTAATATTATTATTA
* *
76858 ATTTATA-TTATATAAATTTTTATATTGTTATT-
1 ATTTATATTTATATAAATTTTAATATTATTATTA
*
76890 ATTT-TATTCT-TATCAAATATTAATATTAT
1 ATTTATATT-TATAT-AAATTTTAATATTAT
76919 ATTTACTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
31 2 0.04
32 24 0.46
33 22 0.42
34 4 0.08
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (34 bp):
ATTTATATTTATATAAATTTTAATATTATTATTA
Found at i:76879 original size:17 final size:17
Alignment explanation
Indices: 76833--76883 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
76823 TATTTAATAT
76833 TTATATAAATTTTAATATA
1 TTATATAAATTTT--TATA
76852 TTAT-T-AA--TTTATA
1 TTATATAAATTTTTATA
76865 TTATATAAATTTTTATA
1 TTATATAAATTTTTATA
76882 TT
1 TT
76884 GTTATTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 8 0.29
14 1 0.04
15 4 0.14
17 10 0.36
18 1 0.04
19 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATAAATTTTTATA
Found at i:76879 original size:33 final size:33
Alignment explanation
Indices: 76824--76896 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
76814 TATTTAAAAT
76824 ATTTAATATTTATATAAATTTTA-ATATATTATTA
1 ATTT-ATATTTATATAAATTTTATAT-TATTATTA
*
76858 ATTTATA-TTATATAAATTTTTATATTGTTATTA
1 ATTTATATTTATATAAA-TTTTATATTATTATTA
*
76891 TTTTAT
1 ATTTAT
76897 TCTTATCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 9 0.26
33 20 0.57
34 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
ATTTATATTTATATAAATTTTATATTATTATTA
Found at i:78383 original size:25 final size:24
Alignment explanation
Indices: 78318--78383 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
78308 TTTGTTAAAG
** *
78318 TTTAATTTTTATTATTTTAAATAT
1 TTTAATTAATATTATTTAAAATAT
*
78342 TTTAATTAAT-TAAATTTAAAATAT
1 TTTAATTAATAT-TATTTAAAATAT
*
78366 ATTTATTTAATATTATTT
1 -TTTAATTAATATTATTT
78384 TATTTAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.03
24 18 0.55
25 13 0.39
26 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTAATTAATATTATTTAAAATAT
Found at i:80438 original size:19 final size:21
Alignment explanation
Indices: 80409--80454 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
80399 TTTATTCTTT
80409 ATATGATATAAAT-TAA-AAAA
1 ATAT-ATATAAATATAATAAAA
*
80429 ATATATATAAATATAATAATA
1 ATATATATAAATATAATAAAA
80450 ATATA
1 ATATA
80455 ACCGAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATATATAAATATAATAAAA
Found at i:88759 original size:18 final size:17
Alignment explanation
Indices: 88738--88771 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
88728 CAATATAAAA
*
88738 TTATTATTTAATAAAATT
1 TTATAATTTAA-AAAATT
88756 TTATAATTTAAAAAAT
1 TTATAATTTAAAAAAT
88772 AATTTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATAATTTAAAAAATT
Found at i:89203 original size:17 final size:17
Alignment explanation
Indices: 89171--89204 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
89161 AATTTATTAA
*
89171 AATTTTAAATATAAACT
1 AATTTTAAATAAAAACT
*
89188 AATTTTAATTAAAAACT
1 AATTTTAAATAAAAACT
89205 TACATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTTAAATAAAAACT
Found at i:90814 original size:18 final size:19
Alignment explanation
Indices: 90785--90820 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
90775 GAAAAAGTTA
*
90785 TCTTTCTCCAACGAAAATC
1 TCTTTCTCCAACCAAAATC
90804 TCTTT-TCCAACCAAAAT
1 TCTTTCTCCAACCAAAAT
90821 AAAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (19 bp):
TCTTTCTCCAACCAAAATC
Found at i:96805 original size:21 final size:22
Alignment explanation
Indices: 96775--96819 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
96765 AATTCCAAAC
*
96775 TATATATTT-ATATCATATTTA
1 TATATATTTAATATCATAATTA
*
96796 TATATTTTTACATATCATAATTA
1 TATATATTTA-ATATCATAATTA
96819 T
1 T
96820 GTTTACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATATTTAATATCATAATTA
Found at i:96868 original size:19 final size:19
Alignment explanation
Indices: 96844--96883 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
96834 AATTTTGATA
96844 TGTTAATAATTTAT-TAAAT
1 TGTTAATAATTT-TGTAAAT
96863 TGTTAATAATTTTGTAAAT
1 TGTTAATAATTTTGTAAAT
96882 TG
1 TG
96884 CATATTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (19 bp):
TGTTAATAATTTTGTAAAT
Found at i:99074 original size:2 final size:2
Alignment explanation
Indices: 99067--99092 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
99057 TTCAAAAGCA
99067 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
99093 CCATCGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99494 original size:2 final size:2
Alignment explanation
Indices: 99489--99524 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
99479 ATATTACGTT
*
99489 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
99525 AGGTTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:99573 original size:13 final size:13
Alignment explanation
Indices: 99555--99583 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
99545 CTCCTCACTG
99555 AAATTAAAAATTC
1 AAATTAAAAATTC
99568 AAATTAAAAATTC
1 AAATTAAAAATTC
99581 AAA
1 AAA
99584 AATATATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTAAAAATTC
Found at i:100044 original size:6 final size:7
Alignment explanation
Indices: 100017--100045 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
100007 GAAAATATTA
100017 TAAAATT
1 TAAAATT
100024 TAAAATT
1 TAAAATT
100031 TAAAATT
1 TAAAATT
100038 T-AAATT
1 TAAAATT
100044 TA
1 TA
100046 TTAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAAAATT
Found at i:101161 original size:18 final size:17
Alignment explanation
Indices: 101121--101187 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
101111 TATATAACTC
101121 AAAATTTATAT-AATAT
1 AAAATTTATATAAATAT
*
101137 -TAA-TTAT-TAATATATT
1 AAAATTTATATAA-ATA-T
101153 AAAATTTATATAAATAT
1 AAAATTTATATAAATAT
101170 AAAATATT-T-TAAATAT
1 AAAAT-TTATATAAATAT
101186 AA
1 AA
101188 TTATAACGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 5 0.12
16 10 0.24
17 9 0.21
18 9 0.21
19 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTTATATAAATAT
Found at i:101451 original size:21 final size:22
Alignment explanation
Indices: 101427--101474 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
101417 TTTTACCGTG
101427 TTTATATTAAAA-TTATATTCA
1 TTTATATTAAAATTTATATTCA
*
101448 TTTA-CTTAAAATTTATATTCA
1 TTTATATTAAAATTTATATTCA
101469 TATTAT
1 T-TTAT
101475 TACTATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 14 0.61
22 3 0.13
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTATATTAAAATTTATATTCA
Found at i:101721 original size:22 final size:22
Alignment explanation
Indices: 101683--101725 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
101673 ATATATTTTT
*
101683 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTAAAAAAATATA
101705 TAAATATTAA-TAAAAAAATAT
1 TAAAT-TTAATTAAAAAAATAT
101726 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATTTAATTAAAAAAATATA
Found at i:102330 original size:20 final size:20
Alignment explanation
Indices: 102305--102345 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
102295 TTAATATTTA
*
102305 AAATATATTTAATCAAATAT
1 AAATATATTTAATAAAATAT
102325 AAATATATTTAATAAAATAT
1 AAATATATTTAATAAAATAT
102345 A
1 A
102346 TTTAAAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATATATTTAATAAAATAT
Found at i:102470 original size:16 final size:17
Alignment explanation
Indices: 102449--102481 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
102439 TAACACTAAA
*
102449 TTCGA-TTAAATCAATT
1 TTCGATTTAAATAAATT
102465 TTCGATTTAAATAAATT
1 TTCGATTTAAATAAATT
102482 AAACTGACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TTCGATTTAAATAAATT
Found at i:103530 original size:38 final size:36
Alignment explanation
Indices: 103488--103563 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 36
103478 TCTCATGCTT
103488 AAATTTAAATTTAAAAAATTT-AAAAATAAATTCATTCA
1 AAATTTAAATTT-AAAAATTTCAAAAA-AAATT-ATTCA
* *
103526 AAATTTTAATTTAAAATTTTCAAAAAAAATTATTCA
1 AAATTTAAATTTAAAAATTTCAAAAAAAATTATTCA
103562 AA
1 AA
103564 TATGGATAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 7 0.20
37 12 0.34
38 16 0.46
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (36 bp):
AAATTTAAATTTAAAAATTTCAAAAAAAATTATTCA
Found at i:104611 original size:34 final size:32
Alignment explanation
Indices: 104545--104616 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
104535 TATAATTATC
* * *
104545 TTAATATATTTTAGTAACCAGAAAATTAGTTA
1 TTAAAATATTTTAATAACAAGAAAATTAGTTA
104577 -TAAAATATTTTACATAACAAGAATAATTTAGTTA
1 TTAAAATATTTTA-ATAACAAGAA-AA-TTAGTTA
104611 TTAAAA
1 TTAAAA
104617 CTTTAAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 11 0.33
32 8 0.24
33 2 0.06
34 7 0.21
35 5 0.15
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.39
Consensus pattern (32 bp):
TTAAAATATTTTAATAACAAGAAAATTAGTTA
Found at i:106309 original size:14 final size:13
Alignment explanation
Indices: 106286--106320 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
106276 TGGTATTACC
106286 TTTT-AAAAATAA
1 TTTTAAAAAATAA
106298 TTTTTAAAAAATAA
1 -TTTTAAAAAATAA
106312 TTTTAAAAA
1 TTTTAAAAA
106321 TCAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTTAAAAAATAA
Found at i:109099 original size:27 final size:29
Alignment explanation
Indices: 109069--109137 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
109059 TAAATCAATA
*
109069 ATTGAATTTTTCCACT-AATGTT-TTTTT
1 ATTGAATTTTACCACTAAATGTTATTTTT
** *
109096 ATTGAATTCAACCACTAAATTTTGATTTTT
1 ATTGAATTTTACCACTAAATGTT-ATTTTT
109126 ATTGAATTTTAC
1 ATTGAATTTTAC
109138 TGCTCCAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 13 0.39
28 5 0.15
30 15 0.45
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (29 bp):
ATTGAATTTTACCACTAAATGTTATTTTT
Found at i:109648 original size:14 final size:12
Alignment explanation
Indices: 109627--109662 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
109617 CTTAAAGTAC
109627 AATAATAAATATT
1 AATAATAAATA-T
109640 AATTAATAAATAT
1 AA-TAATAAATAT
109653 AATAATAAAT
1 AATAATAAAT
109663 TTCAATAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.36
13 5 0.23
14 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:109669 original size:13 final size:12
Alignment explanation
Indices: 109627--109671 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
109617 CTTAAAGTAC
109627 AATAATAAATATT
1 AATAATAAAT-TT
*
109640 AATTAATAAATAT
1 AA-TAATAAATTT
109653 AATAATAAATTT
1 AATAATAAATTT
109665 CAATAAT
1 -AATAAT
109672 CCGCCAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 9 0.32
13 11 0.39
14 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
AATAATAAATTT
Found at i:110359 original size:21 final size:22
Alignment explanation
Indices: 110320--110360 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
110310 TATTATATTT
110320 TTAAAAGAAAAATAAATTAAAA
1 TTAAAAGAAAAATAAATTAAAA
110342 TTAAAA-AATAAA-AAATTAA
1 TTAAAAGAA-AAATAAATTAA
110361 TTTTTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
TTAAAAGAAAAATAAATTAAAA
Found at i:112381 original size:19 final size:19
Alignment explanation
Indices: 112349--112397 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
112339 AAACAACTAA
* * *
112349 AAATTGAAAGATCAAGGTG
1 AAATTAAAATATCAAAGTG
112368 AAATTAAAATATCAAAGTG
1 AAATTAAAATATCAAAGTG
112387 AAATTAAAATA
1 AAATTAAAATA
112398 ATATGTTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.57, C:0.04, G:0.14, T:0.24
Consensus pattern (19 bp):
AAATTAAAATATCAAAGTG
Done.