Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009334.1 Kokia drynarioides strain JFW-HI SEQ_124041, 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: 289732
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:412 original size:62 final size:61
Alignment explanation
Indices: 336--486 Score: 178
Period size: 62 Copynumber: 2.4 Consensus size: 61
326 AATTTTTTTA
** *
336 AAATATTTTAGAATTAAAATTAAATTGACAAATTTTGTAAATGTTGATAACTAAATTTATTG
1 AAAT-TTTTAGAATTAAAATTAAATTGACAAATTTTGTAAACATTAATAACTAAATTTATTG
* * * *
398 AATTTTTTTAGAATT-TAATCTAAATTGATAAATTTTGTAAACATTAATAATTAAATTTATTG
1 AA-ATTTTTAGAATTAAAAT-TAAATTGACAAATTTTGTAAACATTAATAACTAAATTTATTG
* * *
460 AAATTTTTAGATTTAATATCAAATTGA
1 AAATTTTTAGAATTAAAATTAAATTGA
487 TAGTTTACAA
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
61 20 0.27
62 53 0.72
63 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (61 bp):
AAATTTTTAGAATTAAAATTAAATTGACAAATTTTGTAAACATTAATAACTAAATTTATTG
Found at i:453 original size:31 final size:30
Alignment explanation
Indices: 347--488 Score: 78
Period size: 31 Copynumber: 4.7 Consensus size: 30
337 AATATTTTAG
*
347 AATTAA-AATTAAATTGACAAATTTTGTAA
1 AATTAATAATTAAATTGATAAATTTTGTAA
* * * * * * *
376 ATGTTGATAACTAAATTTATTGAATTTTTTTAG
1 A-ATTAATAATTAAATTGA-T-AAATTTTGTAA
409 AATT--TAATCTAAATTGATAAATTTTGTAA
1 AATTAATAAT-TAAATTGATAAATTTTGTAA
* *
438 ACATTAATAATTAAATTTATTGAAATTTT-TAG
1 A-ATTAATAATTAAATTGA-T-AAATTTTGTAA
* *
470 ATTTAAT-ATCAAATTGATA
1 AATTAATAATTAAATTGATA
489 GTTTACAATC
Statistics
Matches: 84, Mismatches: 19, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
28 1 0.01
29 11 0.13
30 18 0.21
31 28 0.33
32 10 0.12
33 16 0.19
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (30 bp):
AATTAATAATTAAATTGATAAATTTTGTAA
Found at i:747 original size:144 final size:144
Alignment explanation
Indices: 487--776 Score: 544
Period size: 144 Copynumber: 2.0 Consensus size: 144
477 ATCAAATTGA
487 TAGTTTACAATCACAAATATAGTGTAATTATAAGTACAATATAATTACACTACAATCACAATCAC
1 TAGTTTACAATCACAAATATAGTGTAATTATAAGTACAATATAATTACACTACAATCACAATCAC
*
552 AAGTGCAAAATATTTTCAAACAACATTTTTGCTTGTTTAGTATTGTTTTTTATTCAAACATGTTT
66 AAGTGCAAAATATTTTCAAACAACATTTTTGCTTGTTTAGTATTGTTTTTTATTCAAACATATTT
617 TTTTACGTCAAAAG
131 TTTTACGTCAAAAG
631 TAGTTTACAATCACAAATATAGTGTAATTATAAGTACAATATAATTACACTACAATCACAATCAC
1 TAGTTTACAATCACAAATATAGTGTAATTATAAGTACAATATAATTACACTACAATCACAATCAC
* *
696 AAGTGCAATATATTTTCAAACAACTTTTTTGCTTGTTTAGTATTGTTTTTTATTCAAACATATTT
66 AAGTGCAAAATATTTTCAAACAACATTTTTGCTTGTTTAGTATTGTTTTTTATTCAAACATATTT
*
761 TTTTACGTGAAAAG
131 TTTTACGTCAAAAG
775 TA
1 TA
777 CTTTTCAAAA
Statistics
Matches: 142, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 142 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (144 bp):
TAGTTTACAATCACAAATATAGTGTAATTATAAGTACAATATAATTACACTACAATCACAATCAC
AAGTGCAAAATATTTTCAAACAACATTTTTGCTTGTTTAGTATTGTTTTTTATTCAAACATATTT
TTTTACGTCAAAAG
Found at i:821 original size:144 final size:144
Alignment explanation
Indices: 524--821 Score: 404
Period size: 144 Copynumber: 2.1 Consensus size: 144
514 TTATAAGTAC
524 AATATAATTACACTACAATCACAATCACAAGTGCAAAATATTTTCAAACAACATTTTTGCTTGTT
1 AATATAATTACACTACAATCACAATCACAAGTGCAAAATATTTTCAAACAACATTTTTGCTTGTT
* * * * *
589 TAGTATTGTTTTTTATTCAAACATGTTTTTTTACGTCAAAAGTAGTTTACAATCACAAATATAGT
66 TAGTATTGTTTTTTATTCAAACATATTTTTTTACGTCAAAAGTACTTTACAATAACAAATAAAAT
** * * *
654 GTAATTATAAGTAC
131 AAAATCATAAATAA
* *
668 AATATAATTACACTACAATCACAATCACAAGTGCAATATATTTTCAAACAACTTTTTTGCTTGTT
1 AATATAATTACACTACAATCACAATCACAAGTGCAAAATATTTTCAAACAACATTTTTGCTTGTT
* * *
733 TAGTATTGTTTTTTATTCAAACATATTTTTTTACGTGAAAAGTACTTTTCAA-AAGC-ATTACCA
66 TAGTATTGTTTTTTATTCAAACATATTTTTTTACGTCAAAAGTACTTTACAATAA-CAAATA--A
796 AATAAAATCA-AAATAA
128 AATAAAATCATAAATAA
*
812 AATAAAATTA
1 AATATAATTA
822 TTACAAAGCA
Statistics
Matches: 135, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
143 4 0.03
144 125 0.93
145 6 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (144 bp):
AATATAATTACACTACAATCACAATCACAAGTGCAAAATATTTTCAAACAACATTTTTGCTTGTT
TAGTATTGTTTTTTATTCAAACATATTTTTTTACGTCAAAAGTACTTTACAATAACAAATAAAAT
AAAATCATAAATAA
Found at i:2838 original size:121 final size:123
Alignment explanation
Indices: 2620--2855 Score: 332
Period size: 121 Copynumber: 1.9 Consensus size: 123
2610 AAGTCATAAT
* *
2620 TTTTATAAATGAACTAAAACGAAAAAGTGAATTTTTTTTAATTGAATGGTTATTTATAGTGATAG
1 TTTTATAAATAAACTAAAACGAAAAAGTGAATATTTTTTAATTGAATGGTTATTTATAGTGATAG
* * *
2685 ATATTTATTACAACTCTTAAATACCTTGGGCAAAAAGGGAAAAGAATCTTTAAAAGGA
66 ATATTTATCACAACTCTTAAATACCTTGGGCAAAAAGGAAAAAAAATCTTTAAAAGGA
* * * * * *
2743 TTTTATAAATAAATTAAAACTAAAAAGT-AA-ATTTTTTATTTGAATGGTTTTTTGTAGTGATTG
1 TTTTATAAATAAACTAAAACGAAAAAGTGAATATTTTTTAATTGAATGGTTATTTATAGTGATAG
* * *
2806 ATATTTATCACAACTCTTAATTACCTTTGGCAACAAGGAAAAAAAATCTT
66 ATATTTATCACAACTCTTAAATACCTTGGGCAAAAAGGAAAAAAAATCTT
2856 AAATGCATTT
Statistics
Matches: 99, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
121 72 0.73
122 2 0.02
123 25 0.25
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (123 bp):
TTTTATAAATAAACTAAAACGAAAAAGTGAATATTTTTTAATTGAATGGTTATTTATAGTGATAG
ATATTTATCACAACTCTTAAATACCTTGGGCAAAAAGGAAAAAAAATCTTTAAAAGGA
Found at i:7743 original size:9 final size:9
Alignment explanation
Indices: 7652--7745 Score: 63
Period size: 9 Copynumber: 10.6 Consensus size: 9
7642 AACGGATACC
*
7652 TTTTTAAAA
1 TTTTTATAA
7661 TTTTTATAA
1 TTTTTATAA
7670 TGTTTTATAAA
1 T-TTTTAT-AA
7681 TCTTTTATAA
1 T-TTTTATAA
**
7691 ACTTTAT-A
1 TTTTTATAA
7699 TTTTTAT-A
1 TTTTTATAA
* **
7707 -TTATATTC
1 TTTTTATAA
7715 TTTCTTA-AA
1 TTT-TTATAA
7724 TTTTTAT-A
1 TTTTTATAA
7732 TTTTTATAA
1 TTTTTATAA
7741 TTTTT
1 TTTTT
7746 TAAATTCTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.07
8 18 0.27
9 25 0.37
10 10 0.15
11 9 0.13
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:7747 original size:10 final size:10
Alignment explanation
Indices: 7652--7774 Score: 53
Period size: 10 Copynumber: 12.1 Consensus size: 10
7642 AACGGATACC
*
7652 TTTTTA-AAA
1 TTTTTATAAT
7661 TTTTTATAAT
1 TTTTTATAAT
*
7671 GTTTTATAAAT
1 TTTTTAT-AAT
*
7682 CTTTTATAA-
1 TTTTTATAAT
**
7691 ACTTTAT-AT
1 TTTTTATAAT
7700 TTTTATATTATAT
1 TTTT-TA-TA-AT
*
7713 TCTTTCT-TAAA
1 T-TTT-TATAAT
7724 TTTTTAT-A-
1 TTTTTATAAT
7732 TTTTTATAAT
1 TTTTTATAAT
7742 TTTTTA-AAT
1 TTTTTATAAT
*
7751 TCTTATATATAT
1 T-TTTTATA-AT
7763 TTTTTACTAAT
1 TTTTTA-TAAT
7774 T
1 T
7775 AAGGGGGAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
8 8 0.09
9 20 0.23
10 26 0.30
11 20 0.23
12 7 0.08
13 3 0.03
14 4 0.05
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:7748 original size:26 final size:26
Alignment explanation
Indices: 7693--7758 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 26
7683 TTTTATAAAC
* **
7693 TTTATATTTTTATA-TTATATTCTTT
1 TTTAAATTTTTATATTTATATAATTT
* *
7718 CTTAAATTTTTATATTTTTATAATTT
1 TTTAAATTTTTATATTTATATAATTT
*
7744 TTTAAATTCTTATAT
1 TTTAAATTTTTATAT
7759 ATATTTTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
25 12 0.36
26 21 0.64
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTAAATTTTTATATTTATATAATTT
Found at i:8249 original size:33 final size:33
Alignment explanation
Indices: 8211--8280 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
8201 AGATTAGTTT
** * *
8211 ATATTTTATGTGTCATTATGTCAAATTATTTAA
1 ATATTTTATGCATCATTATATCAAATTATTGAA
* *
8244 ATATTTTATGCATTATTATATTAAATTATTGAA
1 ATATTTTATGCATCATTATATCAAATTATTGAA
8277 ATAT
1 ATAT
8281 CAAATAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.51
Consensus pattern (33 bp):
ATATTTTATGCATCATTATATCAAATTATTGAA
Found at i:10119 original size:16 final size:15
Alignment explanation
Indices: 10094--10123 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
10084 AAATAAAAAA
10094 AAAAATTTAAAAATT
1 AAAAATTTAAAAATT
10109 AAAAATATTAAAAAT
1 AAAAAT-TTAAAAAT
10124 ATTTTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATTTAAAAATT
Found at i:10171 original size:9 final size:9
Alignment explanation
Indices: 10093--10174 Score: 51
Period size: 9 Copynumber: 9.0 Consensus size: 9
10083 AAAATAAAAA
*
10093 AAAAAATTT
1 AAAAATTTT
10102 AAAAA--TT
1 AAAAATTTT
*
10109 AAAAATATT
1 AAAAATTTT
10118 AAAAATATTT
1 AAAAAT-TTT
**
10128 TCAAATTTT
1 AAAAATTTT
* **
10137 ATATTTTTT
1 AAAAATTTT
*
10146 AAAAAATTATA
1 -AAAAATT-TT
10157 AAAAATTTT
1 AAAAATTTT
10166 AAAAATTTT
1 AAAAATTTT
10175 CTACAGTAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
7 7 0.12
9 31 0.55
10 17 0.30
11 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (9 bp):
AAAAATTTT
Found at i:34096 original size:107 final size:108
Alignment explanation
Indices: 33910--34126 Score: 364
Period size: 107 Copynumber: 2.0 Consensus size: 108
33900 TTTCACACCC
* *
33910 AAAATAAGACTGAATCATTAACCACTGGTTGACATTTTTCCATCATCACATCCTAACGTTTAAAA
1 AAAATAAGACTGAATCATCAACCACTGGTTGACATTTTTCCATCATCACATCCTAACATTTAAAA
33975 CTTTATTACTTTATT-TCTTTTCAGAGTTATGAAATGGAACGA
66 CTTTATTACTTTATTCTCTTTTCAGAGTTATGAAATGGAACGA
* * * *
34017 AAAATAAGATTGAATCCTCAACCATTGGTTGACATTTTTCCATCATCACATCGTAACATTTAAAA
1 AAAATAAGACTGAATCATCAACCACTGGTTGACATTTTTCCATCATCACATCCTAACATTTAAAA
*
34082 CTTTATTACTTTATTCTTTTTTCAGAGTTATGAAATGGAACGA
66 CTTTATTACTTTATTCTCTTTTCAGAGTTATGAAATGGAACGA
34125 AA
1 AA
34127 CATATTTTGA
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
107 74 0.73
108 28 0.27
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (108 bp):
AAAATAAGACTGAATCATCAACCACTGGTTGACATTTTTCCATCATCACATCCTAACATTTAAAA
CTTTATTACTTTATTCTCTTTTCAGAGTTATGAAATGGAACGA
Found at i:42585 original size:11 final size:11
Alignment explanation
Indices: 42568--42631 Score: 67
Period size: 11 Copynumber: 5.7 Consensus size: 11
42558 GGGCCTTTTT
*
42568 TTTAATTT-AT
1 TTTAATTTAAA
*
42578 TTTAAATTTAGA
1 TTT-AATTTAAA
*
42590 TTTATTTTAAA
1 TTTAATTTAAA
*
42601 TTTAAATTTAAT
1 TTT-AATTTAAA
42613 TTTAATTTAAA
1 TTTAATTTAAA
42624 TTTAATTT
1 TTTAATTT
42632 CAAGATTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
10 3 0.07
11 29 0.66
12 12 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:42592 original size:6 final size:5
Alignment explanation
Indices: 42568--42631 Score: 56
Period size: 6 Copynumber: 11.6 Consensus size: 5
42558 GGGCCTTTTT
* *
42568 TTTAA TTTAT TTTAAA TTTAGA TTTAT TTTAAA TTTAAA TTTAA TTTTAA
1 TTTAA TTTAA TTT-AA TTTA-A TTTAA TTT-AA TTT-AA TTTAA -TTTAA
42618 TTTAAA TTTAA TTT
1 TTT-AA TTTAA TTT
42632 CAAGATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
5 21 0.42
6 29 0.58
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:42608 original size:23 final size:23
Alignment explanation
Indices: 42567--42628 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
42557 CGGGCCTTTT
*
42567 TTTTAATTT-ATTTTAAATTTAGA
1 TTTTAATTTAAATTTAAATTTA-A
*
42590 -TTTATTTTAAATTTAAATTTAA
1 TTTTAATTTAAATTTAAATTTAA
42612 TTTTAATTTAAATTTAA
1 TTTTAATTTAAATTTAA
42629 TTTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.24
23 26 0.76
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTAATTTAAATTTAAATTTAA
Found at i:42631 original size:17 final size:17
Alignment explanation
Indices: 42571--42627 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
42561 CCTTTTTTTT
42571 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
42588 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
42605 AATTTAATTTT-AATTTA
1 AATTT-ATTTTAAATTTA
42622 AATTTA
1 AATTTA
42628 ATTTCAAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
16 1 0.03
17 31 0.84
18 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:43341 original size:3 final size:3
Alignment explanation
Indices: 43333--43367 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
43323 CTGATAGCAT
43333 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
43368 TTATTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:43372 original size:3 final size:3
Alignment explanation
Indices: 43366--43394 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
43356 ATAATAATAA
43366 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
43395 ATAAACGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:43683 original size:17 final size:17
Alignment explanation
Indices: 43644--43686 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
43634 CAACACCGAT
43644 TTCTAAAGAGTTTTTCAG
1 TTCTAAA-AGTTTTTCAG
*
43662 ATCTAAAAG-TTTTCATG
1 TTCTAAAAGTTTTTCA-G
43679 TTCTAAAA
1 TTCTAAAA
43687 ACAAGTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 10 0.45
18 6 0.27
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (17 bp):
TTCTAAAAGTTTTTCAG
Found at i:44564 original size:59 final size:60
Alignment explanation
Indices: 44467--44643 Score: 191
Period size: 59 Copynumber: 3.0 Consensus size: 60
44457 CCCTAAACTA
44467 TCCAAAAATTCCATTTTCGACCCCAAAACTTCCAAAAATCCCATTTTT-ACCCTCGAA-CG
1 TCCAAAAATTCCATTTTCGACCCCAAAACTTCCAAAAATCCCATTTTTGA-CCTCGAAGCG
* *** * * *
44526 TCCACAAATTCCATTTTCGACCTTGAAACTTCCAAAAATTCTATTTTTGACCTCGAAGCT
1 TCCAAAAATTCCATTTTCGACCCCAAAACTTCCAAAAATCCCATTTTTGACCTCGAAGCG
* * **
44586 TCCAAAAATTACCATTTTTGCCCCCCGAA-TGTCCAAAAA-CTCCATTTTTGACCTCGAA
1 TCCAAAAATT-CCATTTTCGACCCCAAAACT-TCCAAAAATC-CCATTTTTGACCTCGAA
44644 ACTCTCAAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
59 49 0.51
60 12 0.12
61 36 0.37
ACGTcount: A:0.32, C:0.31, G:0.07, T:0.31
Consensus pattern (60 bp):
TCCAAAAATTCCATTTTCGACCCCAAAACTTCCAAAAATCCCATTTTTGACCTCGAAGCG
Found at i:44653 original size:30 final size:30
Alignment explanation
Indices: 44461--44646 Score: 182
Period size: 30 Copynumber: 6.2 Consensus size: 30
44451 GGAGGTCCCT
* * *
44461 AAACTATCCAAAAATTCCATTTTCGACCCCA
1 AAACT-TCCAAAAATTCCATTTTTGACCTCG
*
44492 AAACTTCCAAAAATCCCATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTGA-CCTCG
* * * *
44522 -AACGTCCACAAATTCCATTTTCGACCTTG
1 AAACTTCCAAAAATTCCATTTTTGACCTCG
*
44551 AAACTTCCAAAAATTCTATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCTCG
* * *
44581 AAGCTTCCAAAAATTACCATTTTTGCCCCCCG
1 AAACTTCCAAAAATT-CCATTTTTG-ACCTCG
*
44613 -AA-TGTCCAAAAACTCCATTTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTGACCTCG
44642 AAACT
1 AAACT
44647 CTCAAAATTA
Statistics
Matches: 125, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
29 27 0.22
30 70 0.56
31 24 0.19
32 4 0.03
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:45690 original size:21 final size:21
Alignment explanation
Indices: 45665--45713 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
45655 AAGTGAGGAA
*
45665 AAAATTTTAGGGGGACAAAAT
1 AAAATTTTAGAGGGACAAAAT
* *
45686 TAAA--TTAGAGGGACAAAGT
1 AAAATTTTAGAGGGACAAAAT
45705 AAAATTTTA
1 AAAATTTTA
45714 TCTTTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
19 16 0.73
21 6 0.27
ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27
Consensus pattern (21 bp):
AAAATTTTAGAGGGACAAAAT
Found at i:48757 original size:38 final size:38
Alignment explanation
Indices: 48704--48792 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 38
48694 CCAAAATGCG
* * *
48704 AAACTCAAACCCAAAACTTGATATATA-TCTTAAATCC-T
1 AAACTTAAACTCAAAACTTGATATAAACT-TTAAA-CCAT
*
48742 AAACTTAAACTCAAAATTTGATATAAACTTTAAACCAT
1 AAACTTAAACTCAAAACTTGATATAAACTTTAAACCAT
48780 AAACTTGAAACTC
1 AAACTT-AAACTC
48793 GAGAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
37 2 0.05
38 35 0.80
39 7 0.16
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.29
Consensus pattern (38 bp):
AAACTTAAACTCAAAACTTGATATAAACTTTAAACCAT
Found at i:48787 original size:25 final size:24
Alignment explanation
Indices: 48741--48787 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
48731 TCTTAAATCC
*
48741 TAAACTTAAACTCAAAATTTGATA
1 TAAACTTAAACTCAAAACTTGATA
48765 TAAACTTTAAAC-CATAAACTTGA
1 TAAAC-TTAAACTCA-AAACTTGA
48788 AACTCGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (24 bp):
TAAACTTAAACTCAAAACTTGATA
Found at i:50506 original size:12 final size:12
Alignment explanation
Indices: 50489--50527 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
50479 GAGTTTTTAT
50489 TTTATTTTAATA
1 TTTATTTTAATA
*
50501 TTTATTTTTAT-
1 TTTATTTTAATA
50512 TTTATTTTAATA
1 TTTATTTTAATA
50524 TTTA
1 TTTA
50528 ATAATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTATTTTAATA
Found at i:50512 original size:23 final size:23
Alignment explanation
Indices: 50482--50527 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
50472 CTCGTATGAG
50482 TTTTTATTTTATTTTAATATTTA
1 TTTTTATTTTATTTTAATATTTA
50505 TTTTTATTTTATTTTAATATTTA
1 TTTTTATTTTATTTTAATATTTA
50528 ATAATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTATTTTATTTTAATATTTA
Found at i:50547 original size:31 final size:28
Alignment explanation
Indices: 50483--50553 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
50473 TCGTATGAGT
**
50483 TTTTATTTTATTTTAATATTTATTTTTA
1 TTTTATTTTATTTTAATATTTATCATTA
50511 TTTTATTTTAATATTTAATAATTTATACATTA
1 TTTTATTTT-AT-TTTAAT-ATTTAT-CATTA
50543 -TTTA-TTTATTT
1 TTTTATTTTATTT
50554 ATATTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 11 0.30
29 4 0.11
30 9 0.24
31 10 0.27
32 3 0.08
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTATTTTATTTTAATATTTATCATTA
Found at i:50581 original size:40 final size:41
Alignment explanation
Indices: 50507--50587 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 41
50497 AATATTTATT
*
50507 TTTATTTTATTTTAATATTTAATAATTTATACATT-ATTTA
1 TTTATTTTATTTTAATATATAATAATTTATACATTAATTTA
* *
50547 TTTATTTATATTTT-TTATATATTAATCTTA-ACATTAATTTA
1 TTTATTT-TATTTTAATATATAATAAT-TTATACATTAATTTA
50588 ATGTTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 21 0.60
41 14 0.40
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (41 bp):
TTTATTTTATTTTAATATATAATAATTTATACATTAATTTA
Found at i:52330 original size:14 final size:14
Alignment explanation
Indices: 52311--52337 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52301 TTTTTGATAT
52311 ATTAAAAGAAATAG
1 ATTAAAAGAAATAG
52325 ATTAAAAGAAATA
1 ATTAAAAGAAATA
52338 TTTTTTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (14 bp):
ATTAAAAGAAATAG
Found at i:55714 original size:2 final size:2
Alignment explanation
Indices: 55709--55741 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
55699 ATACATGAGA
55709 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55742 GAGATTAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:58603 original size:115 final size:113
Alignment explanation
Indices: 58403--58630 Score: 429
Period size: 115 Copynumber: 2.0 Consensus size: 113
58393 ACCTTAAAAG
58403 GTCTTGGTGATATGAATCTTTTATATGCTTTAAAAAATCAGTGTGGGGGAGTAGAGGTGAAGTCA
1 GTCTTGGTGATATGAATCTTTTATATGCTTTAAAAAATCAGTGTGGGGGAGTAGAGGTGAAGTCA
58468 GATTGGTGCTTGTGATAGTCTCTGGTTTTGGGCATTATTTTAGTGTAA
66 GATTGGTGCTTGTGATAGTCTCTGGTTTTGGGCATTATTTTAGTGTAA
*
58516 GTCTTGGTGATATGAATCTTTTATATGCTTTAAAAAATTAGTGTGTGGGGGAGTAGAGGTGAAGT
1 GTCTTGGTGATATGAATCTTTTATATGCTTTAAAAAATCA--GTGTGGGGGAGTAGAGGTGAAGT
58581 CAGATTGGTGCTTGTGATAGTCTCTGGTTTTGGGCATTATTTTAGTGTAA
64 CAGATTGGTGCTTGTGATAGTCTCTGGTTTTGGGCATTATTTTAGTGTAA
58631 AGAGTCAGTT
Statistics
Matches: 112, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
113 39 0.35
115 73 0.65
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.39
Consensus pattern (113 bp):
GTCTTGGTGATATGAATCTTTTATATGCTTTAAAAAATCAGTGTGGGGGAGTAGAGGTGAAGTCA
GATTGGTGCTTGTGATAGTCTCTGGTTTTGGGCATTATTTTAGTGTAA
Found at i:65744 original size:125 final size:125
Alignment explanation
Indices: 65519--65759 Score: 385
Period size: 125 Copynumber: 1.9 Consensus size: 125
65509 ACCAGGTCAT
* *
65519 AGTTTGATGATTTCATTCTCATCATGCTAATTCCTAACAATGTTGTCTATGAAAGCATGGATATG
1 AGTTTGATGATTTCATTCCCATCATACTAATTCCTAACAATGTTGTCTATGAAAGCATGGATATG
* **
65584 ATTTAATAAAAGCGAAGCTAAAACCATGATTAGATAGTTGAAAACAGTTGTCTAGGAACG
66 ATTTAATAAAAGCGAAGCTAAAACCACGACCAGATAGTTGAAAACAGTTGTCTAGGAACG
* *
65644 AGTTTGATGATTTCATTCCCATCATATTAATTCCTAACAATGTTGTCTATGAAAGCATGGCTATG
1 AGTTTGATGATTTCATTCCCATCATACTAATTCCTAACAATGTTGTCTATGAAAGCATGGATATG
* *
65709 ATTTGATAAATA-CGATGCTAAAACCACGACCAGATAGTTGAAAACAGTTGT
66 ATTTAATAAA-AGCGAAGCTAAAACCACGACCAGATAGTTGAAAACAGTTGT
65760 ATGAACGAGT
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
125 105 0.99
126 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (125 bp):
AGTTTGATGATTTCATTCCCATCATACTAATTCCTAACAATGTTGTCTATGAAAGCATGGATATG
ATTTAATAAAAGCGAAGCTAAAACCACGACCAGATAGTTGAAAACAGTTGTCTAGGAACG
Found at i:80249 original size:2 final size:2
Alignment explanation
Indices: 80242--80276 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
80232 GGAGAATAGC
80242 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
80277 TTCAGCTGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:80992 original size:16 final size:17
Alignment explanation
Indices: 80943--80993 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
80933 AGAGAAATTC
*
80943 ATTTATTTTATATATAATA
1 ATTTATTTTA-A-AAAATA
80962 ATTTATTTTAAAAAATA
1 ATTTATTTTAAAAAATA
*
80979 ATTTTTTTTCAAAAA
1 ATTTATTTT-AAAAA
80994 CTTTTGTGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 13 0.45
18 6 0.21
19 10 0.34
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATTTTAAAAAATA
Found at i:89104 original size:22 final size:21
Alignment explanation
Indices: 89068--89109 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
89058 TTTTTTTTTG
*
89068 TTTCAATTCGGTACCTGAGTTT
1 TTTCAATTCGATACCT-AGTTT
*
89090 TTTCAATTTGATACCTAGTT
1 TTTCAATTCGATACCTAGTT
89110 CTATAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (21 bp):
TTTCAATTCGATACCTAGTTT
Found at i:89222 original size:21 final size:21
Alignment explanation
Indices: 89198--89247 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
89188 ATATGCTGTA
*
89198 AATTTTAT-TTAATATTATTAT
1 AATTTTATAGTAATATT-TTAT
89219 AATTTT-TAGTAATATTTTAT
1 AATTTTATAGTAATATTTTAT
*
89239 AAATTTATA
1 AATTTTATA
89248 ATATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
AATTTTATAGTAATATTTTAT
Found at i:89249 original size:18 final size:19
Alignment explanation
Indices: 89207--89258 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
89197 AAATTTTATT
*
89207 TAATATTATTATAATTTTTAG
1 TAATATT-TTATAA-ATTTAG
89228 TAATATTTTATAAATTTA-
1 TAATATTTTATAAATTTAG
89246 TAATATTTT-TAAA
1 TAATATTTTATAAA
89259 AATAATTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 4 0.13
18 9 0.30
19 4 0.13
20 6 0.20
21 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TAATATTTTATAAATTTAG
Found at i:95036 original size:11 final size:11
Alignment explanation
Indices: 95013--95059 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
95003 TATTTATAAA
95013 TTTAATAATTAT
1 TTTAATAA-TAT
95025 TTTAATAATAT
1 TTTAATAATAT
*
95036 TTT-AT--TAA
1 TTTAATAATAT
95044 TTTAATAATAT
1 TTTAATAATAT
95055 TTTAA
1 TTTAA
95060 ATATTATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 5 0.17
9 2 0.07
10 2 0.07
11 13 0.43
12 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTAATAATAT
Found at i:95042 original size:19 final size:19
Alignment explanation
Indices: 95020--95058 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
95010 AAATTTAATA
*
95020 ATTATTTTAATAATATTTT
1 ATTAATTTAATAATATTTT
95039 ATTAATTTAATAATATTTT
1 ATTAATTTAATAATATTTT
95058 A
1 A
95059 AATATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTAATTTAATAATATTTT
Found at i:95046 original size:31 final size:29
Alignment explanation
Indices: 95001--95071 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 29
94991 ATAATTAAAA
95001 AATATTTATAAATTTAATAATTATTTTAAT
1 AATATTTATAAATTTAATAA-TATTTTAAT
*
95031 AATATTTTATTAATTTAATAATATTTT-A-
1 AATA-TTTATAAATTTAATAATATTTTAAT
95059 AATATTATATAAA
1 AATATT-TATAAA
95072 AACTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 2 0.05
28 9 0.24
29 1 0.03
30 10 0.27
31 15 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
AATATTTATAAATTTAATAATATTTTAAT
Found at i:102319 original size:18 final size:19
Alignment explanation
Indices: 102271--102319 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
102261 ATTGAATAAT
*
102271 TTCCGAATAATTTCTAAATGC
1 TTCC-AATAA-TTCTAAATCC
102292 TTCCAA-AATTCTAAATCC
1 TTCCAATAATTCTAAATCC
102310 TT-CAATAATT
1 TTCCAATAATT
102320 TTAATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.12
18 15 0.58
19 2 0.08
20 2 0.08
21 4 0.15
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (19 bp):
TTCCAATAATTCTAAATCC
Found at i:104405 original size:20 final size:21
Alignment explanation
Indices: 104377--104417 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
104367 TTTTTTTTAA
104377 TATTATTTC-CTTTAAAAATT
1 TATTATTTCTCTTTAAAAATT
* *
104397 TATTTTTTCTTTTTAAAAATT
1 TATTATTTCTCTTTAAAAATT
104418 AATATATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATTTCTCTTTAAAAATT
Found at i:104427 original size:21 final size:21
Alignment explanation
Indices: 104387--104427 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
104377 TATTATTTCC
* * *
104387 TTTAAAAATTTATTTTTTCTT
1 TTTAAAAATTAATATATTCTT
104408 TTTAAAAATTAATATATTCT
1 TTTAAAAATTAATATATTCT
104428 GTCAAAATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAAAAATTAATATATTCTT
Found at i:106789 original size:33 final size:34
Alignment explanation
Indices: 106752--106825 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
106742 TATTCTTTAG
**
106752 AATTTTTAT-AATTTTTTAAAATATAAATTTTGA
1 AATTTTTATAAAGATTTTAAAATATAAATTTTGA
* *
106785 AATTTTTATAAAGATTTTAAATTTTAAATTTTGA
1 AATTTTTATAAAGATTTTAAAATATAAATTTTGA
*
106819 ATTTTTT
1 AATTTTT
106826 TTTTTTTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 9 0.26
34 26 0.74
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (34 bp):
AATTTTTATAAAGATTTTAAAATATAAATTTTGA
Found at i:110293 original size:20 final size:22
Alignment explanation
Indices: 110265--110308 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
110255 TTTTTTATTT
110265 TAATAGATG-C-TATAAAAAAA
1 TAATAGATGACTTATAAAAAAA
* *
110285 TAATGGATGACTTATAAATAAA
1 TAATAGATGACTTATAAAAAAA
110307 TA
1 TA
110309 CTAATACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (22 bp):
TAATAGATGACTTATAAAAAAA
Found at i:119019 original size:3 final size:3
Alignment explanation
Indices: 118970--119000 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
118960 AATACATGTT
118970 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
119001 TTATAAGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:120827 original size:55 final size:56
Alignment explanation
Indices: 120768--120874 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 56
120758 AATTTCTCAA
* * * *
120768 AAATATTGTTTCTTTTAGATCGATTATTTTTATGTTTAAATCGATTG-TTATGTCG
1 AAATATTGCTTCTTTTAAATCGATTACTTATATGTTTAAATCGATTGCTTATGTCG
* *
120823 AAATATTGCTTCTTTTAAATCGATTGCTTATATGTTTGAATCGATTGCTTAT
1 AAATATTGCTTCTTTTAAATCGATTACTTATATGTTTAAATCGATTGCTTAT
120875 ATATTTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
55 41 0.91
56 4 0.09
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.50
Consensus pattern (56 bp):
AAATATTGCTTCTTTTAAATCGATTACTTATATGTTTAAATCGATTGCTTATGTCG
Found at i:120866 original size:21 final size:21
Alignment explanation
Indices: 120836--120888 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
120826 TATTGCTTCT
*
120836 TTTAAATCGATTGCTTATATG
1 TTTAAATCGATTGCTTATATA
*
120857 TTTGAATCGATTGCTTATATA
1 TTTAAATCGATTGCTTATATA
120878 TTTAAATCGAT
1 TTTAAATCGAT
120889 GGTTATGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.47
Consensus pattern (21 bp):
TTTAAATCGATTGCTTATATA
Found at i:121466 original size:20 final size:20
Alignment explanation
Indices: 121424--121466 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
121414 AATCTCTCTA
*
121424 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTAT
* *
121444 AAAAAGTTCAAAATACTTAT
1 AAAAAATTCAAAATAATTAT
121464 AAA
1 AAA
121467 GATTCCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTAT
Found at i:122906 original size:2 final size:2
Alignment explanation
Indices: 122899--122948 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
122889 CTTCACCTCT
122899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
122941 TA TA TA TA
1 TA TA TA TA
122949 ATGATTTAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:125889 original size:54 final size:54
Alignment explanation
Indices: 125818--125928 Score: 177
Period size: 54 Copynumber: 2.1 Consensus size: 54
125808 CTTAGGACCT
* * *
125818 CGAACCCCGAATCCAAACCCTAAACCCTAAAACCAAATTTTGGGATTCAAGATC
1 CGAAACCCGAACCCAAACCCTAAACCCTAAAACCAAATTTTGAGATTCAAGATC
**
125872 CGAAACCCGAACCCAAACTTTAAACCCTAAAACCAAATTTTGAGATTCAAGATC
1 CGAAACCCGAACCCAAACCCTAAACCCTAAAACCAAATTTTGAGATTCAAGATC
125926 CGA
1 CGA
125929 GTTCGGAGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (54 bp):
CGAAACCCGAACCCAAACCCTAAACCCTAAAACCAAATTTTGAGATTCAAGATC
Found at i:127268 original size:28 final size:29
Alignment explanation
Indices: 127212--127268 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
127202 CGTGCTTTGG
*
127212 TAAAAAAAAAAAATAATAGGTAATTAATT
1 TAAAAAAAAAAAATAATAGGTAATAAATT
* *
127241 TAAACAAAAAAAA-AATAGGTACTAAATT
1 TAAAAAAAAAAAATAATAGGTAATAAATT
127269 GAACATTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (29 bp):
TAAAAAAAAAAAATAATAGGTAATAAATT
Found at i:127273 original size:27 final size:29
Alignment explanation
Indices: 127212--127273 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
127202 CGTGCTTTGG
* * *
127212 TAAAAAAAAAAAATAATAGGTAATTAATT
1 TAAACAAAAAAAATAATAGGTAACTAAAT
127241 TAAACAAAAAAAA-AATAGGT-ACTAAAT
1 TAAACAAAAAAAATAATAGGTAACTAAAT
*
127268 TGAACA
1 TAAACA
127274 TTGAAGCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 10 0.34
28 7 0.24
29 12 0.41
ACGTcount: A:0.65, C:0.05, G:0.08, T:0.23
Consensus pattern (29 bp):
TAAACAAAAAAAATAATAGGTAACTAAAT
Found at i:129392 original size:15 final size:15
Alignment explanation
Indices: 129374--129447 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
129364 AACTCCCCCA
*
129374 CCGGCTTCTCCACCT
1 CCGGCTACTCCACCT
* *
129389 CCGGCTACCCCACCA
1 CCGGCTACTCCACCT
* * *
129404 CCTGCTTCTCCCCCT
1 CCGGCTACTCCACCT
* *
129419 CCTGCTACTCCTCCT
1 CCGGCTACTCCACCT
* *
129434 CCAGCTACCCCACC
1 CCGGCTACTCCACC
129448 ACCATCTCCT
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.11, C:0.58, G:0.09, T:0.22
Consensus pattern (15 bp):
CCGGCTACTCCACCT
Found at i:135674 original size:16 final size:16
Alignment explanation
Indices: 135655--135693 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
135645 ATTTTGGTTT
*
135655 AGAATAACCATAATTC
1 AGAACAACCATAATTC
*
135671 AGAACAACCATAATTT
1 AGAACAACCATAATTC
135687 AGAACAA
1 AGAACAA
135694 TTGTGGGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.18, G:0.08, T:0.21
Consensus pattern (16 bp):
AGAACAACCATAATTC
Found at i:136907 original size:14 final size:14
Alignment explanation
Indices: 136888--136917 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
136878 TATTTTTAAG
136888 GAGAGAAAGACAAA
1 GAGAGAAAGACAAA
*
136902 GAGAGAGAGACAAA
1 GAGAGAAAGACAAA
136916 GA
1 GA
136918 TCTACATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.33, T:0.00
Consensus pattern (14 bp):
GAGAGAAAGACAAA
Found at i:147157 original size:6 final size:6
Alignment explanation
Indices: 147146--147174 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
147136 CATGTTATAA
147146 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
147175 GAAATGGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:149800 original size:3 final size:3
Alignment explanation
Indices: 149792--149843 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
149782 ATTGCTACAA
149792 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
149840 TAT T
1 TAT T
149844 GTTTGGATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:157503 original size:27 final size:27
Alignment explanation
Indices: 157399--157497 Score: 117
Period size: 27 Copynumber: 3.7 Consensus size: 27
157389 ACAACAAAGA
* *
157399 ACAGTCTTTGTGGCGCACTCTAAATTT
1 ACAGCCTTTGTGGCGCACTCTAAATGT
* *
157426 ACAGCCTTTGTGGCACACTCTAAATGA
1 ACAGCCTTTGTGGCGCACTCTAAATGT
* * * *
157453 ATAGCCTTTGTGGTGCACTTTGAATGT
1 ACAGCCTTTGTGGCGCACTCTAAATGT
*
157480 ACAGCCTTGGTGGCGCAC
1 ACAGCCTTTGTGGCGCAC
157498 ACTGAAAGAA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (27 bp):
ACAGCCTTTGTGGCGCACTCTAAATGT
Found at i:158977 original size:15 final size:15
Alignment explanation
Indices: 158959--158996 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
158949 GTTTGGGATA
*
158959 GATGGGGTAGGATGG
1 GATGGGATAGGATGG
*
158974 GATGGGATGGGATGG
1 GATGGGATAGGATGG
158989 GATGGGAT
1 GATGGGAT
158997 GGGAGAGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.58, T:0.21
Consensus pattern (15 bp):
GATGGGATAGGATGG
Found at i:158978 original size:5 final size:5
Alignment explanation
Indices: 158968--159000 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
158958 AGATGGGGTA
158968 GGATG GGATG GGATG GGATG GGATG GGATG GGA
1 GGATG GGATG GGATG GGATG GGATG GGATG GGA
159001 GAGGAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.61, T:0.18
Consensus pattern (5 bp):
GGATG
Found at i:159055 original size:29 final size:30
Alignment explanation
Indices: 158995--159054 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
158985 ATGGGATGGG
158995 ATGGGAGAGGAGTAAAGTTTTAGGGGAAAA
1 ATGGGAGAGGAGTAAAGTTTTAGGGGAAAA
159025 ATGGGAGA-GAGTAAAAGTTTT-GAGGGAAAA
1 ATGGGAGAGGAGT-AAAGTTTTAG-GGGAAAA
159055 TAAAATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
ATGGGAGAGGAGTAAAGTTTTAGGGGAAAA
Found at i:167469 original size:3 final size:3
Alignment explanation
Indices: 167461--167495 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
167451 CCCTACACTT
* *
167461 GCA GCA GCA GCA GCA GCA GCA GCA TCA GCA ACA GC
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
167496 TCCATCTCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.34, G:0.29, T:0.03
Consensus pattern (3 bp):
GCA
Found at i:170279 original size:37 final size:38
Alignment explanation
Indices: 170227--170300 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
170217 AATTTTAGTA
* *
170227 ATATTTAAATCATTTAATATAATACTGT-TTGTAAATG
1 ATATTTAAATAATTTAATATAATAATGTATTGTAAATG
170264 ATATTTAAATAATTTAATATAATAATGTATTGTAAAT
1 ATATTTAAATAATTTAATATAATAATGTATTGTAAAT
170301 AAGAATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 26 0.76
38 8 0.24
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (38 bp):
ATATTTAAATAATTTAATATAATAATGTATTGTAAATG
Found at i:173799 original size:22 final size:23
Alignment explanation
Indices: 173768--173812 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
173758 TTTTACTATA
*
173768 AATATGATTTTAAT-TATTATTT
1 AATATAATTTTAATATATTATTT
173790 AATATAATTTTAATATATTATTT
1 AATATAATTTTAATATATTATTT
173813 TTTAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
AATATAATTTTAATATATTATTT
Found at i:173830 original size:27 final size:26
Alignment explanation
Indices: 173780--173831 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
173770 TATGATTTTA
**
173780 ATTATTATTTAATATAATTTTAATAT
1 ATTATTATTTAATATAATCCTAATAT
*
173806 ATTATTTTTTAAATATAATCCTAATA
1 ATTATTATTT-AATATAATCCTAATA
173832 CTTTTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTATTATTTAATATAATCCTAATAT
Found at i:179037 original size:20 final size:19
Alignment explanation
Indices: 179002--179039 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
178992 TTTTATTTAT
*
179002 TATATATTACTTCTAAATA
1 TATATATTAATTCTAAATA
179021 TATATATATAATTCTAAAT
1 TATATAT-TAATTCTAAAT
179040 GCATTGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATATTAATTCTAAATA
Found at i:187199 original size:21 final size:21
Alignment explanation
Indices: 187175--187221 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
187165 GCTCAAGCAC
187175 TTTAACTATGAGCACTCAGGT
1 TTTAACTATGAGCACTCAGGT
* *
187196 TTTAATTCTGAGCACTCAGGT
1 TTTAACTATGAGCACTCAGGT
187217 TTTAA
1 TTTAA
187222 TTTCCACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TTTAACTATGAGCACTCAGGT
Found at i:187222 original size:21 final size:21
Alignment explanation
Indices: 187183--187223 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
187173 ACTTTAACTA
187183 TGAGCACTCAGGTTTTAATTC
1 TGAGCACTCAGGTTTTAATTC
187204 TGAGCACTCAGGTTTTAATT
1 TGAGCACTCAGGTTTTAATT
187224 TCCACTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (21 bp):
TGAGCACTCAGGTTTTAATTC
Found at i:194827 original size:3 final size:3
Alignment explanation
Indices: 194815--194862 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
194805 TATGCTCAGC
*
194815 TAT T-T TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
194862 T
1 T
194863 GATTTTGATA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:214659 original size:59 final size:59
Alignment explanation
Indices: 214567--214686 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
214557 AAAGAGAGTA
214567 ACTAAAATATTTAATTTCGAAAAGATTAATATTTGTGTTACCAAAATAGAACCAAAGGC
1 ACTAAAATATTTAATTTCGAAAAGATTAATATTTGTGTTACCAAAATAGAACCAAAGGC
214626 ACTAAAATATTTAATTTCGAAAAGATTAATATTTGTGTTACCAAAATAGAACCAAAGGC
1 ACTAAAATATTTAATTTCGAAAAGATTAATATTTGTGTTACCAAAATAGAACCAAAGGC
214685 AC
1 AC
214687 AATTGGGTGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (59 bp):
ACTAAAATATTTAATTTCGAAAAGATTAATATTTGTGTTACCAAAATAGAACCAAAGGC
Found at i:233898 original size:12 final size:12
Alignment explanation
Indices: 233881--233906 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
233871 ACTGGGCCCA
233881 TCATCGTCGTCG
1 TCATCGTCGTCG
233893 TCATCGTCGTCG
1 TCATCGTCGTCG
233905 TC
1 TC
233907 GCCTTGCCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.35, G:0.23, T:0.35
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:236984 original size:25 final size:23
Alignment explanation
Indices: 236952--237008 Score: 55
Period size: 25 Copynumber: 2.4 Consensus size: 23
236942 TATTGTTCAT
236952 TATT-ATTAAATTGACATAAAA-AA
1 TATTAATTAAATT-A-ATAAAATAA
*
236975 TATTTAATTATATTAATAAAATTAA
1 TA-TTAATTAAATTAATAAAA-TAA
237000 TATTAATTA
1 TATTAATTA
237009 GGAGATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 8 0.28
24 10 0.34
25 11 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TATTAATTAAATTAATAAAATAA
Found at i:238969 original size:2 final size:2
Alignment explanation
Indices: 238964--239002 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
238954 TTCCACTAAA
238964 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
239003 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:241554 original size:23 final size:23
Alignment explanation
Indices: 241531--241672 Score: 155
Period size: 23 Copynumber: 6.1 Consensus size: 23
241521 CTAGCGCGCT
*
241531 CTCTGATTAGCACTGTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCC
*
241554 CTCTGATTAGCATTGTGTGTGCC
1 CTCTGATTAGCACTGTGTGTGCC
* *
241577 CTCTGTTTAGCAC-GTTTCGTGCC
1 CTCTGATTAGCACTGTGT-GTGCC
* *
241600 TTTTG-TTCAGCACTGTGTGTGCC
1 CTCTGATT-AGCACTGTGTGTGCC
241623 CTCTGTTATTAGCACT-TCGTGTGCC
1 CTCTG--ATTAGCACTGT-GTGTGCC
*
241648 CTCTGATTAGCACTTTGTGTGCC
1 CTCTGATTAGCACTGTGTGTGCC
241671 CT
1 CT
241673 TTGTTACCTA
Statistics
Matches: 101, Mismatches: 10, Indels: 16
0.80 0.08 0.13
Matches are distributed among these distances:
22 5 0.05
23 71 0.70
24 5 0.05
25 18 0.18
26 2 0.02
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
CTCTGATTAGCACTGTGTGTGCC
Found at i:241646 original size:71 final size:71
Alignment explanation
Indices: 241538--241703 Score: 191
Period size: 71 Copynumber: 2.4 Consensus size: 71
241528 GCTCTCTGAT
* * * *
241538 TAGCACTGTGTGTGCTCTCTGATTAGCATTGTGTGTGCCCTCTGTTTAGCACGTTT-CGTGCCTT
1 TAGCACTGTGTGTGCCCTCTGATTAGCATTGCGTGTGCCCTCTGATTAGCAC-TTTGCGTGCCCT
241602 TTGTT-C
65 TTGTTAC
*
241608 -AGCACTGTGTGTGCCCTCTGTTATTAGCACTT-CGTGTGCCCTCTGATTAGCACTTTGTGTGCC
1 TAGCACTGTGTGTGCCCTCTG--ATTAGCA-TTGCGTGTGCCCTCTGATTAGCACTTTGCGTGCC
241671 CTTTGTTACC
63 CTTTGTTA-C
*
241681 TAGCACT-TATGTGCCCTCT-ATTA
1 TAGCACTGTGTGTGCCCTCTGATTA
241704 AGTACTTCAG
Statistics
Matches: 83, Mismatches: 6, Indels: 14
0.81 0.06 0.14
Matches are distributed among these distances:
69 19 0.23
70 7 0.08
71 37 0.45
72 2 0.02
73 12 0.14
74 6 0.07
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.40
Consensus pattern (71 bp):
TAGCACTGTGTGTGCCCTCTGATTAGCATTGCGTGTGCCCTCTGATTAGCACTTTGCGTGCCCTT
TGTTAC
Found at i:241647 original size:48 final size:47
Alignment explanation
Indices: 241536--241703 Score: 152
Period size: 48 Copynumber: 3.6 Consensus size: 47
241526 GCGCTCTCTG
* *
241536 ATTAGCACTGTGT-GTGCTCTCTGATTAGCATTGTGTGTGCCCTCTG-T
1 ATTAGCACT-T-TCGTGCCCTCTGATTAGCACTGTGTGTGCCCTCTGTT
* *
241583 -TTAGCACGTTTCGTGCCTTTTG-TTCAGCACTGTGTGTGCCCTCTGTT
1 ATTAGCAC-TTTCGTGCCCTCTGATT-AGCACTGTGTGTGCCCTCTGTT
* *
241630 ATTAGCAC-TTCGTGTGCCCTCTGATTAGCACTTTGTGTGCCCTTTGTT
1 ATTAGCACTTTC--GTGCCCTCTGATTAGCACTGTGTGTGCCCTCTGTT
*
241678 ACCTAGCACTTAT-GTGCCCTCT-ATTA
1 A-TTAGCACTT-TCGTGCCCTCTGATTA
241704 AGTACTTCAG
Statistics
Matches: 101, Mismatches: 9, Indels: 22
0.77 0.07 0.17
Matches are distributed among these distances:
45 3 0.03
46 37 0.37
47 6 0.06
48 45 0.45
49 8 0.08
50 1 0.01
51 1 0.01
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.40
Consensus pattern (47 bp):
ATTAGCACTTTCGTGCCCTCTGATTAGCACTGTGTGTGCCCTCTGTT
Found at i:246683 original size:2 final size:2
Alignment explanation
Indices: 246676--246704 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
246666 TATAATAGCA
246676 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 A
246705 AAGCTTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:256593 original size:18 final size:18
Alignment explanation
Indices: 256570--256612 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
256560 AGAAAGGTTT
256570 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
256588 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
256606 TTAATTA
1 TTAATTA
256613 CACTTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:260675 original size:12 final size:13
Alignment explanation
Indices: 260643--260686 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
260633 AATAAAATAT
260643 TTATATAATTTT-
1 TTATATAATTTTA
260655 TTA-ATAATTTTA
1 TTATATAATTTTA
260667 TTATA-AATTTTGA
1 TTATATAATTTT-A
260680 TTATATA
1 TTATATA
260687 TATATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 8 0.29
12 12 0.43
13 7 0.25
14 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TTATATAATTTTA
Found at i:263294 original size:18 final size:17
Alignment explanation
Indices: 263271--263312 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
263261 TTATTAAAAA
263271 TATTTTATTATATTATAT
1 TATTTTATTATATTA-AT
263289 TATTTTA--ATATTAAT
1 TATTTTATTATATTAAT
*
263304 AATTTTATT
1 TATTTTATT
263313 TTTATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 8 0.38
16 6 0.29
18 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTTATTATATTAAT
Found at i:266314 original size:20 final size:21
Alignment explanation
Indices: 266289--266327 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
266279 ACATGTTTAA
266289 ATTTATA-CTAATTATTTTTT
1 ATTTATATCTAATTATTTTTT
*
266309 ATTTATATCTAATTGTTTT
1 ATTTATATCTAATTATTTT
266328 AAAATATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTTATATCTAATTATTTTTT
Found at i:267663 original size:31 final size:31
Alignment explanation
Indices: 267628--267848 Score: 178
Period size: 31 Copynumber: 7.2 Consensus size: 31
267618 ATCACCTCAC
*
267628 GAGATGGTGAGGCGTGACAGGATCACTTCGT
1 GAGATGGTGAGGCGTGACAGGATCACTTAGT
* * *
267659 GAGATGGTGAGGCGTGATAAGATCACTTAGC
1 GAGATGGTGAGGCGTGACAGGATCACTTAGT
** ** *
267690 GAGATGACGAGGCACGACA-G-TCACTTCGT
1 GAGATGGTGAGGCGTGACAGGATCACTTAGT
* * * ** * *
267719 AAGTTGGTGAGGTGTGATGGGATCAGTTAGC
1 GAGATGGTGAGGCGTGACAGGATCACTTAGT
* * *
267750 GAGATGGTGAGGCATGAGAGGATCACTTAAT
1 GAGATGGTGAGGCGTGACAGGATCACTTAGT
* **
267781 GAGATGGTGAGGCATGATGGGATCAACTTA-T
1 GAGATGGTGAGGCGTGACAGGATC-ACTTAGT
* * * *
267812 GAGATGGTGAGACGTGACGGGATCACTTCGC
1 GAGATGGTGAGGCGTGACAGGATCACTTAGT
267843 GAGATG
1 GAGATG
267849 ATTAGGTGTT
Statistics
Matches: 147, Mismatches: 39, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
29 17 0.12
30 6 0.04
31 119 0.81
32 5 0.03
ACGTcount: A:0.27, C:0.14, G:0.37, T:0.23
Consensus pattern (31 bp):
GAGATGGTGAGGCGTGACAGGATCACTTAGT
Found at i:267865 original size:31 final size:31
Alignment explanation
Indices: 267610--267904 Score: 114
Period size: 31 Copynumber: 9.6 Consensus size: 31
267600 CTCGCAAGGT
* * * *
267610 GTGATGGGATCACCTCACGAGATGGTGAGGC
1 GTGATGGGATCACTTCGCGAGATGATGAAGC
** * * *
267641 GTGACAGGATCACTTCGTGAGATGGTGAGGC
1 GTGATGGGATCACTTCGCGAGATGATGAAGC
** * * *
267672 GTGATAAGATCACTTAGCGAGATGACGAGGC
1 GTGATGGGATCACTTCGCGAGATGATGAAGC
** ** ** * * * *
267703 ACGA-CAG-TCACTTCGTAAGTTGGTGAGGT
1 GTGATGGGATCACTTCGCGAGATGATGAAGC
* * * *
267732 GTGATGGGATCAGTTAGCGAGATGGTGAGGC
1 GTGATGGGATCACTTCGCGAGATGATGAAGC
* *** * *
267763 ATGA-GAGGATCACTTAATGAGATGGTGAGGC
1 GTGATG-GGATCACTTCGCGAGATGATGAAGC
* ** *
267794 ATGATGGGATCAACTT-ATGAGATGGTG-AGAC
1 GTGATGGGATC-ACTTCGCGAGATGATGAAG-C
* * * *
267825 GTGACGGGATCACTTCGCGAGATGATTAGGT
1 GTGATGGGATCACTTCGCGAGATGATGAAGC
* **
267856 GTTATGGGATCACTTAACGAGATGATGAAGC
1 GTGATGGGATCACTTCGCGAGATGATGAAGC
*
267887 GTGATGGAATCACTTCGC
1 GTGATGGGATCACTTCGC
267905 CAAATCGATT
Statistics
Matches: 201, Mismatches: 55, Indels: 16
0.74 0.20 0.06
Matches are distributed among these distances:
29 17 0.08
30 9 0.04
31 169 0.84
32 6 0.03
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.24
Consensus pattern (31 bp):
GTGATGGGATCACTTCGCGAGATGATGAAGC
Found at i:267890 original size:62 final size:62
Alignment explanation
Indices: 267606--267903 Score: 271
Period size: 62 Copynumber: 4.8 Consensus size: 62
267596 CCACCTCGCA
* * *
267606 AGGTGTGATGGGATCACCTCACGAGATGGTGAGGCGTGACAGGATCACTTCGTGAGATGGTG
1 AGGTGTGATGGGATCACTTAACGAGATGGTGAGGCGTGACGGGATCACTTCGTGAGATGGTG
* ** * ** ** * * *
267668 AGGCGTGATAAGATCACTTAGCGAGATGACGAGGCACGAC-AG-TCACTTCGTAAGTTGGTG
1 AGGTGTGATGGGATCACTTAACGAGATGGTGAGGCGTGACGGGATCACTTCGTGAGATGGTG
* * * **
267728 AGGTGTGATGGGATCAGTTAGCGAGATGGTGAGGCATGA-GAGGATCACTTAATGAGATGGTG
1 AGGTGTGATGGGATCACTTAACGAGATGGTGAGGCGTGACG-GGATCACTTCGTGAGATGGTG
** * * * * *
267790 AGGCATGATGGGATCAACTT-ATGAGATGGTGAGACGTGACGGGATCACTTCGCGAGATGATT
1 AGGTGTGATGGGATC-ACTTAACGAGATGGTGAGGCGTGACGGGATCACTTCGTGAGATGGTG
* * * * *
267852 AGGTGTTATGGGATCACTTAACGAGATGATGAAGCGTGATGGAATCACTTCG
1 AGGTGTGATGGGATCACTTAACGAGATGGTGAGGCGTGACGGGATCACTTCG
267904 CCAAATCGAT
Statistics
Matches: 184, Mismatches: 46, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
60 48 0.26
61 6 0.03
62 126 0.68
63 4 0.02
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (62 bp):
AGGTGTGATGGGATCACTTAACGAGATGGTGAGGCGTGACGGGATCACTTCGTGAGATGGTG
Found at i:268561 original size:143 final size:143
Alignment explanation
Indices: 268303--268588 Score: 500
Period size: 143 Copynumber: 2.0 Consensus size: 143
268293 TTTAAATTTG
* * * *
268303 AATATATTTTAAGTACCAAAATGTATATTTACTCTTGTCGTTTATGTATATATTTTTCAACCTAA
1 AATATATTTTAAGTACCAAAATGTATATTTACCCTCGTCGTTTACGTATACATTTTTCAACCTAA
* **
268368 TGCCAAAATTTTAATTCAACAAAAGTCCAAAACACAAGTCTAACAAATGAAGCCATTTGAGTGAT
66 TACCAAAATTTTAAGCCAACAAAAGTCCAAAACACAAGTCTAACAAATGAAGCCATTTGAGTGAT
268433 ATTTTATAGTAAC
131 ATTTTATAGTAAC
268446 AATATATTTTAAGTACCAAAATGTATATTTACCCTCGTCGTTTACGTATACATTTTTCAACCTAA
1 AATATATTTTAAGTACCAAAATGTATATTTACCCTCGTCGTTTACGTATACATTTTTCAACCTAA
*
268511 TACCAAAATTTTAAGCCAACAAAAGTCCAAAACACAAGTCTAACAAATGAAGCCATTTGGGTGAT
66 TACCAAAATTTTAAGCCAACAAAAGTCCAAAACACAAGTCTAACAAATGAAGCCATTTGAGTGAT
268576 ATTTTATAGTAAC
131 ATTTTATAGTAAC
268589 GTGTTGGAAT
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
143 135 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (143 bp):
AATATATTTTAAGTACCAAAATGTATATTTACCCTCGTCGTTTACGTATACATTTTTCAACCTAA
TACCAAAATTTTAAGCCAACAAAAGTCCAAAACACAAGTCTAACAAATGAAGCCATTTGAGTGAT
ATTTTATAGTAAC
Found at i:272010 original size:18 final size:19
Alignment explanation
Indices: 271966--272016 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
271956 GTTTATAATA
*
271966 TTTTATGTTATGTTATTTT
1 TTTTATATTATGTTATTTT
271985 TTTATATATTATGTTATTTT
1 TTT-TATATTATGTTATTTT
272005 TTTATATATTAT
1 TTT-TATATTAT
272017 ATACTTTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (19 bp):
TTTTATATTATGTTATTTT
Found at i:272012 original size:22 final size:20
Alignment explanation
Indices: 271973--272016 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
271963 ATATTTTATG
271973 TTATGTTATTTTTTTATATA
1 TTATGTTATTTTTTTATATA
271993 TTATGTTATTTTTTTATATA
1 TTATGTTATTTTTTTATATA
272013 TTAT
1 TTAT
272017 ATACTTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTATGTTATTTTTTTATATA
Found at i:272018 original size:25 final size:25
Alignment explanation
Indices: 271957--272013 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
271947 TAATTTTAAG
*
271957 TTTATAATATTTTATGTTATGTTATT
1 TTTAT-ATATATTATGTTATGTTATT
*
271983 TTTTTATATATTATGTTA--TT-TT
1 TTTATATATATTATGTTATGTTATT
272005 TTTATATAT
1 TTTATATAT
272014 TATATACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.36
23 2 0.07
25 12 0.43
26 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (25 bp):
TTTATATATATTATGTTATGTTATT
Found at i:276928 original size:6 final size:6
Alignment explanation
Indices: 276917--276945 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
276907 CGTACAACAA
276917 GCCATT GCCATT GCCATT GCCATT GCCAT
1 GCCATT GCCATT GCCATT GCCATT GCCAT
276946 AAATCTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.31
Consensus pattern (6 bp):
GCCATT
Found at i:280834 original size:22 final size:22
Alignment explanation
Indices: 280792--280834 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
280782 TATATTATAA
*
280792 AAAATAAAATAAAAATTAATTG
1 AAAATAAAATAAAAATGAATTG
280814 AAAAT-AAATAAAAATAGAATT
1 AAAATAAAATAAAAAT-GAATT
280835 TGAATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAATAAAATAAAAATGAATTG
Found at i:282049 original size:15 final size:17
Alignment explanation
Indices: 282013--282052 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
282003 TTAATATTAA
282013 TTTTAT-TATAGATTCT
1 TTTTATATATAGATTCT
*
282029 TATTATATAT-GATT-T
1 TTTTATATATAGATTCT
282044 TTTTATATA
1 TTTTATATA
282053 ATATCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 9 0.43
16 9 0.43
17 3 0.14
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTTATATATAGATTCT
Found at i:282050 original size:13 final size:13
Alignment explanation
Indices: 281976--282051 Score: 50
Period size: 13 Copynumber: 5.6 Consensus size: 13
281966 TACATGGGGC
281976 TTTTAT-TGATTT
1 TTTTATATGATTT
281988 ATTTTA-ATGTATTT
1 -TTTTATATG-ATTT
* *
282002 TTTAATATTAATTT
1 TTTTATA-TGATTT
*
282016 TATTATA-GATTCT
1 TTTTATATGATT-T
282029 TATTATATATGATTT
1 T-TT-TATATGATTT
282044 TTTTATAT
1 TTTTATAT
282052 AATATCTATA
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
12 3 0.06
13 18 0.37
14 17 0.35
15 7 0.14
16 4 0.08
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.64
Consensus pattern (13 bp):
TTTTATATGATTT
Found at i:282257 original size:2 final size:2
Alignment explanation
Indices: 282250--282275 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
282240 TATTCCTTTA
282250 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
282276 GGGTGAGTTG
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:285308 original size:14 final size:15
Alignment explanation
Indices: 285285--285315 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
285275 CCCATTGATT
285285 TTTTTATATTATTTA
1 TTTTTATATTATTTA
285300 TTTTT-TATTATTTA
1 TTTTTATATTATTTA
285314 TT
1 TT
285316 ATATAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTATATTATTTA
Found at i:285325 original size:14 final size:14
Alignment explanation
Indices: 285289--285327 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
285279 TTGATTTTTT
*
285289 TATATTATTTATTT
1 TATATTATTTATTA
*
285303 TTTATTATTTATTA
1 TATATTATTTATTA
*
285317 TATAATATTTA
1 TATATTATTTA
285328 AATTTGAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATATTATTTATTA
Done.