Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 8 of 221
Found at i:2671436 original size:22 final size:22
Alignment explanation
Indices: 2671408--2671763 Score: 271
Period size: 22 Copynumber: 15.9 Consensus size: 22
2671398 TAGATTATAA
*
2671408 TTTTGTATGAATATTCTAATTT
1 TTTTGTATGAATATTGTAATTT
2671430 TTTTGTATGAATATTGTAA--T
1 TTTTGTATGAATATTGTAATTT
2671450 TTTT-TATGAATATTGTAA---
1 TTTTGTATGAATATTGTAATTT
* *
2671468 TGTTGTATGAATATTGTAATTA
1 TTTTGTATGAATATTGTAATTT
* *
2671490 TTTTATAATTAA-ATTTGT-ATTT
1 TTTTGT-ATGAATA-TTGTAATTT
* * *
2671512 ATAGTT-T-TGGAT-TAGTAA---
1 -T-TTTGTATGAATATTGTAATTT
2671530 -TTTGTATGAATATTGTAA--T
1 TTTTGTATGAATATTGTAATTT
2671549 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATATTGTAATTT
2671571 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-ATT-T
*
2671596 AGTTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAATTT
2671620 TTTTGTATGAATATTGTAATTTTGT
1 TTTTGTATGAATATTGTAA--TT-T
2671645 AATTTTGTATGAATATTGTAA-TT
1 --TTTTGTATGAATATTGTAATTT
2671668 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-ATT-T
*
2671693 AATTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAATTT
*
2671717 TTTTGTATGAATTTTGTAATTTTGT
1 TTTTGTATGAATATTGTAA--TT-T
2671742 AATTTTGTATGAATATTGTAAT
1 --TTTTGTATGAATATTGTAAT
2671764 GTCGGGATAT
Statistics
Matches: 277, Mismatches: 19, Indels: 73
0.75 0.05 0.20
Matches are distributed among these distances:
15 2 0.01
16 1 0.00
17 4 0.01
18 8 0.03
19 28 0.10
20 26 0.09
21 20 0.07
22 80 0.29
23 13 0.05
24 13 0.05
25 11 0.04
26 2 0.01
27 69 0.25
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (22 bp):
TTTTGTATGAATATTGTAATTT
Found at i:2671444 original size:61 final size:60
Alignment explanation
Indices: 2671379--2671728 Score: 173
Period size: 48 Copynumber: 6.0 Consensus size: 60
2671369 TAAATTATCT
*
2671379 ATATTTAGTGTTTATAGTTTAGATTATAATTTTGTATGAATATTCTAATTTTTTTGTATGA
1 ATATTTAGT-TTTATAGTTTAGATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGA
* * ** * * * * * *
2671440 ATATTGTAATTTTTTA-TGAATATTGTAATGTTGTATGAATATTGTAATTATTTTATAATTA
1 ATATT-TAGTTTTATAGTTTAGATTATAATTTTGTATGAATATTGTAATTTTTTTGT-ATGA
*
2671501 A-ATTT-GTATTTATAGTTTTGGATTAGTAA-TTTGTATGAATATTGTAA--TTTTTGTATGA
1 ATATTTAGT-TTTATAG-TTTAGATTA-TAATTTTGTATGAATATTGTAATTTTTTTGTATGA
* * * * *
2671559 ATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGCAATTTTTTT
1 ATATT-T-A---GTTT-TAT--A-GTT-T-AGATTATAATTTTGTATGAATATTGTAATTTTTTT
2671624 GTATGA
55 GTATGA
*
2671630 ATA-TT-G---TA-A--TT---TTGTAATTTTGTATGAATATTGTAATTTTTT-GTATGA
1 ATATTTAGTTTTATAGTTTAGATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGA
*
2671678 ATA-TT-G---TA-A---T--ATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGA
1 ATATTTAGTTTTATAGTTTAGATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGA
2671727 AT
1 AT
2671729 TTTGTAATTT
Statistics
Matches: 231, Mismatches: 34, Indels: 60
0.71 0.10 0.18
Matches are distributed among these distances:
47 1 0.00
48 44 0.19
49 36 0.16
53 1 0.00
54 1 0.00
57 1 0.00
58 5 0.02
59 14 0.06
60 38 0.16
61 35 0.15
62 6 0.03
64 2 0.01
65 4 0.02
67 3 0.01
68 3 0.01
69 22 0.10
70 1 0.00
71 14 0.06
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (60 bp):
ATATTTAGTTTTATAGTTTAGATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGA
Found at i:2671499 original size:49 final size:49
Alignment explanation
Indices: 2671446--2671811 Score: 271
Period size: 49 Copynumber: 7.5 Consensus size: 49
2671436 ATGAATATTG
* *
2671446 TAATTTTTTATGAATATTGTAA-TGTTGTATGAATATTGTAATTATTTTA
1 TAATTTTGTATGAATATTGTAATTTTTGTATGAATATTGTAA-TATTTTA
*** * * * *
2671495 TAATTAAATTTG--TATT-TATAGTTTTGGATTAGTAAT-TTGTATGAATATTGTA
1 TAATTTTGTATGAATATTGTA-ATTTTTGTA-T-G-AATATTG--T-AATATTTTA
*
2671547 -ATTTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATA--TTA
1 TAATTTTGTATGAATATTGTAA--TTTTTGTATGAATATTGTAATATTTTA
* * *
2671595 TAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT-A-ATTTTG
1 TAATTTTGTATGAATATTGTAA--TTTTTGTATGAATATTGTAATATTTTA
2671644 TAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATA--TTA
1 TAATTTTGTATGAATATTGTAA-TTTTTGTATGAATATTGTAATATTTTA
* * *
2671692 TAATTTTGTATGAATATTGCAATTTTTTTGTATGAATTTTGT-A-ATTTTG
1 TAATTTTGTATGAATATTGTAA--TTTTTGTATGAATATTGTAATATTTTA
* ** * *
2671741 TAATTTTGTATGAATATTGTAATGTCGGGAT--ATATTGTAATATTGTA
1 TAATTTTGTATGAATATTGTAATTTTTGTATGAATATTGTAATATTTTA
*
2671788 -ATTTTTTGTATGAATATTGTAATT
1 TA-ATTTTGTATGAATATTGTAATT
2671812 ATTTTATAAT
Statistics
Matches: 258, Mismatches: 34, Indels: 52
0.75 0.10 0.15
Matches are distributed among these distances:
45 6 0.02
46 4 0.02
47 36 0.14
48 51 0.20
49 112 0.43
50 9 0.03
51 10 0.04
52 10 0.04
53 11 0.04
54 3 0.01
55 6 0.02
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (49 bp):
TAATTTTGTATGAATATTGTAATTTTTGTATGAATATTGTAATATTTTA
Found at i:2671578 original size:69 final size:70
Alignment explanation
Indices: 2671521--2671809 Score: 211
Period size: 76 Copynumber: 4.0 Consensus size: 70
2671511 TATAGTTTTG
*
2671521 GATTAGTA-ATTTGTATGAATATTGTAA-TTTTTGTATGAATATTGTAATTTTTTTGTATGAATA
1 GATTA-TAGATTTGTATGAATATTGCAATTTTTTGTATGAATATTGTAATTTTTTTGTATGAATA
2671584 TTGTAA
65 TTGTAA
* *
2671590 TATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTTGTAATTTTGTAT
1 GATTATAGATTTGTATGAATATTGCAA-TTTTTTGTATGAATATTGTAA--TT-T--TTTTGTAT
2671655 GAATATTGT-A
60 GAATATTGTAA
* *
2671665 -ATT-T---TTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTAT
1 GATTATAGATTTGTATGAATATTG-CA-A-T-T--TTTTGTATGAATATTGTAATTTTTTTGTAT
*
2671725 GAATTTTGTAA
60 GAATATTGTAA
** * * *** *
2671736 TTTTGTA-ATTTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTGTAA-TTTTTTGTAT
1 GATTATAGA-TTTGTATGAATATTGCAAT-T--TTTTGTA-TG-AATATTGTAATTTTTTTGTAT
2671799 GAATATTGTAA
60 GAATATTGTAA
2671810 TTATTTTATA
Statistics
Matches: 182, Mismatches: 17, Indels: 37
0.77 0.07 0.16
Matches are distributed among these distances:
68 2 0.01
69 21 0.12
70 31 0.17
71 22 0.12
72 6 0.03
73 12 0.07
74 27 0.15
75 29 0.16
76 32 0.18
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.53
Consensus pattern (70 bp):
GATTATAGATTTGTATGAATATTGCAATTTTTTGTATGAATATTGTAATTTTTTTGTATGAATAT
TGTAA
Found at i:2671603 original size:27 final size:24
Alignment explanation
Indices: 2671530--2671763 Score: 224
Period size: 27 Copynumber: 9.8 Consensus size: 24
2671520 GGATTAGTAA
2671530 TTTGTATGAATATTGT-A-A--TT
1 TTTGTATGAATATTGTAATATTTT
2671550 TTTGTATGAATATTGT-A-ATTTT
1 TTTGTATGAATATTGTAATATTTT
2671572 TTTGTATGAATATTGTAATATTATAGT
1 TTTGTATGAATATTGTAATATT-T--T
*
2671599 TTTGTATGAATATTG-CA-ATTTT
1 TTTGTATGAATATTGTAATATTTT
*
2671621 TTTGTATGAATATTGTAATTTTGTAAT
1 TTTGTATGAATATTGTAATATT-T--T
2671648 TTTGTATGAATATTGT-A-A-TTT
1 TTTGTATGAATATTGTAATATTTT
2671669 TTTGTATGAATATTGTAATATTATAAT
1 TTTGTATGAATATTGTAATATT-T--T
*
2671696 TTTGTATGAATATTG-CA-ATTTT
1 TTTGTATGAATATTGTAATATTTT
* *
2671718 TTTGTATGAATTTTGTAATTTTGTAAT
1 TTTGTATGAATATTGTAATATT-T--T
2671745 TTTGTATGAATATTGTAAT
1 TTTGTATGAATATTGTAAT
2671764 GTCGGGATAT
Statistics
Matches: 182, Mismatches: 9, Indels: 39
0.79 0.04 0.17
Matches are distributed among these distances:
20 18 0.10
21 17 0.09
22 50 0.27
23 5 0.03
24 11 0.06
25 10 0.05
26 3 0.02
27 68 0.37
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (24 bp):
TTTGTATGAATATTGTAATATTTT
Found at i:2671690 original size:97 final size:97
Alignment explanation
Indices: 2671542--2671816 Score: 412
Period size: 97 Copynumber: 2.8 Consensus size: 97
2671532 TGTATGAATA
*
2671542 TTGTAATTTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATG
1 TTGTAA-TTTTGTATGAATATTGTAA-TTTTTTGTATGAATATTGTAATATTATAATTTTGTATG
2671607 AATATTGCAATTTTTTTGTATGAATATTGTAATT
64 AATATTGCAATTTTTTTGTATGAATATTGTAATT
2671641 TTGTAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
1 TTGTAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
*
2671706 TATTGCAATTTTTTTGTATGAATTTTGTAATT
66 TATTGCAATTTTTTTGTATGAATATTGTAATT
* ** * *
2671738 TTGTAATTTTGTATGAATATTGTAA-TGTCGGGAT--ATATTGTAATATTGTAATTTTTTGTATG
1 TTGTAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAA--TTTTGTATG
* *
2671800 AATATTGTAATTATTTT
64 AATATTGCAATTTTTTT
2671817 ATAATTAATT
Statistics
Matches: 165, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
94 16 0.10
96 29 0.18
97 95 0.58
98 19 0.12
99 6 0.04
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.55
Consensus pattern (97 bp):
TTGTAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
TATTGCAATTTTTTTGTATGAATATTGTAATT
Found at i:2671739 original size:8 final size:8
Alignment explanation
Indices: 2671726--2671750 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2671716 TTTTTGTATG
2671726 AATTTTGT
1 AATTTTGT
2671734 AATTTTGT
1 AATTTTGT
2671742 AATTTTGT
1 AATTTTGT
2671750 A
1 A
2671751 TGAATATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (8 bp):
AATTTTGT
Found at i:2671885 original size:60 final size:60
Alignment explanation
Indices: 2671804--2671925 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
2671794 TGTATGAATA
* * ** * * *
2671804 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTGGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTCAGGATTAAGCTATAAATTGTTGTGT
*
2671864 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTCAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGTAATTCAGGATTAAGCTATAAATTGTTGTGT
2671924 TT
1 TT
2671926 AGTTTAGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 6 0.11
60 47 0.89
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTCAGGATTAAGCTATAAATTGTTGTGT
Found at i:2672004 original size:38 final size:38
Alignment explanation
Indices: 2671959--2672040 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
2671949 CATATAAAGT
2671959 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
2671997 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
2672035 TTATAA
1 TTATAA
2672041 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:2672118 original size:15 final size:16
Alignment explanation
Indices: 2672077--2672118 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2672067 GTTAACTCAT
*
2672077 TTAATTTTTATATAAG
1 TTAAATTTTATATAAG
* *
2672093 GTAACTTTTATATAA-
1 TTAAATTTTATATAAG
2672108 TTAAATTTTAT
1 TTAAATTTTAT
2672119 TTGATTTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (16 bp):
TTAAATTTTATATAAG
Found at i:2673758 original size:12 final size:12
Alignment explanation
Indices: 2673741--2673779 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
2673731 GCATCATGCA
2673741 CCAGAGCCAAAG
1 CCAGAGCCAAAG
2673753 CCAGAGCCAAAG
1 CCAGAGCCAAAG
*
2673765 CCAGAGCCAGAG
1 CCAGAGCCAAAG
2673777 CCA
1 CCA
2673780 AAACTACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.38, C:0.36, G:0.26, T:0.00
Consensus pattern (12 bp):
CCAGAGCCAAAG
Found at i:2673760 original size:6 final size:6
Alignment explanation
Indices: 2673741--2673779 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
2673731 GCATCATGCA
* *
2673741 CCAGAG CCAAAG CCAGAG CCAAAG CCAGAG CCAGAG CCA
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCA
2673780 AAACTACATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.38, C:0.36, G:0.26, T:0.00
Consensus pattern (6 bp):
CCAGAG
Found at i:2677117 original size:21 final size:21
Alignment explanation
Indices: 2677093--2677145 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2677083 ATACCTTATT
2677093 TTTTCTTCTTTTCCTTCCTTC
1 TTTTCTTCTTTTCCTTCCTTC
* *
2677114 TTTTCTTCTGCTTCCTTCTTTC
1 TTTTCTTCT-TTTCCTTCCTTC
*
2677136 TTAT-TTCTTT
1 TTTTCTTCTTT
2677146 CGTTTCTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 13 0.48
22 13 0.48
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTCTTCTTTTCCTTCCTTC
Found at i:2684518 original size:14 final size:14
Alignment explanation
Indices: 2684499--2684527 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2684489 AATGAAGCTT
2684499 ACTTCATACATTGA
1 ACTTCATACATTGA
2684513 ACTTCATACATTGA
1 ACTTCATACATTGA
2684527 A
1 A
2684528 AAGGGAGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (14 bp):
ACTTCATACATTGA
Found at i:2684689 original size:13 final size:14
Alignment explanation
Indices: 2684658--2684690 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2684648 GTCAAATATT
*
2684658 AATATTTTATGTCA
1 AATATTTTATGTAA
2684672 AATATTTTAT-TAA
1 AATATTTTATGTAA
2684685 AATATT
1 AATATT
2684691 CTTAAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (14 bp):
AATATTTTATGTAA
Found at i:2686473 original size:18 final size:19
Alignment explanation
Indices: 2686435--2686473 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2686425 TTAATAATGA
2686435 TTGAAACTAGACGTTCAAT
1 TTGAAACTAGACGTTCAAT
2686454 TTGAAACT-GA-GTTACAAT
1 TTGAAACTAGACGTT-CAAT
2686472 TT
1 TT
2686474 ATTTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (19 bp):
TTGAAACTAGACGTTCAAT
Found at i:2693810 original size:25 final size:25
Alignment explanation
Indices: 2693776--2693827 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2693766 CGAGTGATTC
2693776 AAAGTGCATTTCGAAGCTAAGAGAT
1 AAAGTGCATTTCGAAGCTAAGAGAT
2693801 AAAGTGCATTTCGAAGCTAAGAGAT
1 AAAGTGCATTTCGAAGCTAAGAGAT
2693826 AA
1 AA
2693828 CTCTTCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (25 bp):
AAAGTGCATTTCGAAGCTAAGAGAT
Found at i:2696175 original size:27 final size:28
Alignment explanation
Indices: 2696140--2696193 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
2696130 TAAATATATA
2696140 TTTTTTAA-TTTTTAATTTTAAAATACT
1 TTTTTTAATTTTTTAATTTTAAAATACT
*
2696167 TTTTTTAATTTTTTTATTTTTAAAATA
1 TTTTTTAA-TTTTTTAATTTTAAAATA
2696194 AATTTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.33
29 16 0.67
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTTTAATTTTTTAATTTTAAAATACT
Found at i:2696199 original size:29 final size:27
Alignment explanation
Indices: 2696130--2696201 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 27
2696120 TCGAATATAA
*
2696130 TAAATATATATTTTTTAATTTTTAATTT
1 TAAA-ATAAATTTTTTAATTTTTAATTT
** *
2696158 TAAAATACTTTTTTTAATTTTTTTATTTT
1 TAAAATAAATTTTTTAA--TTTTTAATTT
2696187 TAAAATAAATTTTTT
1 TAAAATAAATTTTTT
2696202 GTGTTTATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 11 0.30
28 4 0.11
29 22 0.59
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (27 bp):
TAAAATAAATTTTTTAATTTTTAATTT
Found at i:2697096 original size:43 final size:43
Alignment explanation
Indices: 2697042--2697127 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
2697032 GAAATAAATG
* *
2697042 AAAATTTTAAGAACATGATATACATGTGGATTATTATATGGAC
1 AAAAATTTAAGAACATGACATACATGTGGATTATTATATGGAC
2697085 AAAAATTTAAGAACATGACATACATGTGGATTATTATATGGAC
1 AAAAATTTAAGAACATGACATACATGTGGATTATTATATGGAC
2697128 CACATGTTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (43 bp):
AAAAATTTAAGAACATGACATACATGTGGATTATTATATGGAC
Found at i:2698997 original size:19 final size:20
Alignment explanation
Indices: 2698964--2699002 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2698954 TTAAGTTGTA
2698964 TTATTTTAAAAAAT-ATTTT
1 TTATTTTAAAAAATAATTTT
**
2698983 TTATTTTAATTAATAATTTT
1 TTATTTTAAAAAATAATTTT
2699003 AACATATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTTAAAAAATAATTTT
Found at i:2701428 original size:12 final size:12
Alignment explanation
Indices: 2701405--2701439 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2701395 TATATATATT
2701405 TAAAAATT-ATA
1 TAAAAATTAATA
2701416 TAAAAATTAATA
1 TAAAAATTAATA
2701428 TAAAAATTAATA
1 TAAAAATTAATA
2701440 CGGCCGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAAAATTAATA
Found at i:2706290 original size:23 final size:22
Alignment explanation
Indices: 2706261--2706307 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
2706251 CAAAGAAAAC
* *
2706261 AATATGAATATACAAATATATAT
1 AATATGAATAAAAAAATATA-AT
2706284 AATATGAATAAAAAAATATAAT
1 AATATGAATAAAAAAATATAAT
2706306 AA
1 AA
2706308 AATAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AATATGAATAAAAAAATATAAT
Found at i:2706308 original size:13 final size:15
Alignment explanation
Indices: 2706284--2706315 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2706274 AAATATATAT
2706284 AATATGAATAAAA-A
1 AATATGAATAAAATA
2706298 AATAT-AATAAAATA
1 AATATGAATAAAATA
2706312 AATA
1 AATA
2706316 CATGATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
AATATGAATAAAATA
Found at i:2708147 original size:18 final size:18
Alignment explanation
Indices: 2708126--2708163 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2708116 GTAATTTTAT
2708126 TTTTATATAAAAATTAAA
1 TTTTATATAAAAATTAAA
*
2708144 TTTTATATATAAATTAAA
1 TTTTATATAAAAATTAAA
2708162 TT
1 TT
2708164 AAATCAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTATATAAAAATTAAA
Found at i:2708315 original size:16 final size:17
Alignment explanation
Indices: 2708279--2708315 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2708269 AATTTTATTT
2708279 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
2708296 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
2708311 TAATA
1 TAATA
2708316 TTCAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:2710087 original size:21 final size:23
Alignment explanation
Indices: 2710042--2710091 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2710032 GATTTATAAA
2710042 AATATATATTGATAAATATTGAT
1 AATATATATTGATAAATATTGAT
*
2710065 AATATATATTTATAAAT-TT-AT
1 AATATATATTGATAAATATTGAT
2710086 AATATA
1 AATATA
2710092 AAAATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 8 0.31
22 2 0.08
23 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
AATATATATTGATAAATATTGAT
Found at i:2710142 original size:14 final size:14
Alignment explanation
Indices: 2710123--2710163 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2710113 GTAAGCCATT
2710123 ATAATATTTTTATA
1 ATAATATTTTTATA
*
2710137 ATAATA--TATATA
1 ATAATATTTTTATA
*
2710149 ATATTATTTTTATA
1 ATAATATTTTTATA
2710163 A
1 A
2710164 ATGTACTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATAATATTTTTATA
Found at i:2717871 original size:20 final size:21
Alignment explanation
Indices: 2717846--2717889 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2717836 ATTTTTCACC
*
2717846 ATCTAGGA-AAAAGTATCGAT
1 ATCTAGGACAAAAATATCGAT
2717866 ATCTAGGACCAAAAATATCGAT
1 ATCTAGGA-CAAAAATATCGAT
2717888 AT
1 AT
2717890 TTTTACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (21 bp):
ATCTAGGACAAAAATATCGAT
Found at i:2723822 original size:20 final size:20
Alignment explanation
Indices: 2723797--2723837 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2723787 AAAATATTTA
2723797 AATGCTGAATATTTATTGAT
1 AATGCTGAATATTTATTGAT
2723817 AATGCTGAATATTTATTGAT
1 AATGCTGAATATTTATTGAT
2723837 A
1 A
2723838 TGTAGAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (20 bp):
AATGCTGAATATTTATTGAT
Found at i:2723861 original size:22 final size:22
Alignment explanation
Indices: 2723835--2723877 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2723825 ATATTTATTG
*
2723835 ATAT-GTAGAGTATTTTAGATTA
1 ATATGGTAGAG-ATGTTAGATTA
2723857 ATATGGTAGAGATGTTAGATT
1 ATATGGTAGAGATGTTAGATT
2723878 GATTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (22 bp):
ATATGGTAGAGATGTTAGATTA
Found at i:2730702 original size:20 final size:20
Alignment explanation
Indices: 2730678--2730716 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2730668 TCCTTTTTTT
*
2730678 GTTTTTTT-TTTCTAAATTC
1 GTTTTTTTGTTTTTAAATTC
2730697 GTTTTTTTGTTTTTAAATTC
1 GTTTTTTTGTTTTTAAATTC
2730717 AATTCAGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (20 bp):
GTTTTTTTGTTTTTAAATTC
Found at i:2733088 original size:6 final size:7
Alignment explanation
Indices: 2733072--2733097 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2733062 TATAAAACCC
2733072 AAAAATA
1 AAAAATA
2733079 AAAAATA
1 AAAAATA
2733086 AAAAATA
1 AAAAATA
2733093 AAAAA
1 AAAAA
2733098 CAGTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2734672 original size:18 final size:18
Alignment explanation
Indices: 2734634--2734669 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2734624 TTATTATTTT
*
2734634 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
2734652 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
2734670 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:2734784 original size:21 final size:22
Alignment explanation
Indices: 2734758--2734801 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2734748 ATATTTAATA
2734758 ATATTAAAAATTT-AATATTTT
1 ATATTAAAAATTTAAATATTTT
* *
2734779 ATATTAATATTTTAAATATTTT
1 ATATTAAAAATTTAAATATTTT
2734801 A
1 A
2734802 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTAAAAATTTAAATATTTT
Found at i:2751873 original size:21 final size:20
Alignment explanation
Indices: 2751821--2751863 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2751811 TAATTATTAT
2751821 AATAAGTAAAAAAAAAGATA
1 AATAAGTAAAAAAAAAGATA
2751841 AATAAGTAAAAAAAAAGATA
1 AATAAGTAAAAAAAAAGATA
2751861 AAT
1 AAT
2751864 TATGGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.16
Consensus pattern (20 bp):
AATAAGTAAAAAAAAAGATA
Found at i:2751915 original size:4 final size:4
Alignment explanation
Indices: 2751906--2751933 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2751896 TTCAAAAGCT
2751906 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
2751934 TACTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:2755092 original size:14 final size:15
Alignment explanation
Indices: 2755048--2755098 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
2755038 TTACCTTAGA
2755048 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAC
* * **
2755063 TTATGTTTGAAACA-
1 TTACGTTTTAGTCAC
*
2755077 TTACGTTTTAGTCAT
1 TTACGTTTTAGTCAC
2755092 TTACGTT
1 TTACGTT
2755099 ATCATGTTGT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (15 bp):
TTACGTTTTAGTCAC
Found at i:2781519 original size:14 final size:15
Alignment explanation
Indices: 2781495--2781523 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2781485 AGGTATTTTA
2781495 ATTTTTCTAAAAAAT
1 ATTTTTCTAAAAAAT
2781510 ATTTTT-TAAAAAAT
1 ATTTTTCTAAAAAAT
2781524 TAATTTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTTTCTAAAAAAT
Found at i:2782532 original size:30 final size:30
Alignment explanation
Indices: 2782475--2782533 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
2782465 TTATAAACTT
* * * *
2782475 ATAAATTGATTATTTGAATTCAGTAACTCG
1 ATAAATTAATTAATTAAATTCAATAACTCG
*
2782505 ATAAATTAATTAATTAAATTTAATAACTC
1 ATAAATTAATTAATTAAATTCAATAACTC
2782534 ATACTGATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (30 bp):
ATAAATTAATTAATTAAATTCAATAACTCG
Found at i:2783200 original size:21 final size:22
Alignment explanation
Indices: 2783159--2783208 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2783149 GAAATGACAA
*
2783159 CAAAACAGTGAGAAAATAACAG
1 CAAAACAGTGAGAAAACAACAG
* *
2783181 TAAAATAGTG-GAAAACAACAG
1 CAAAACAGTGAGAAAACAACAG
2783202 CAAAACA
1 CAAAACA
2783209 ACAATTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.10
Consensus pattern (22 bp):
CAAAACAGTGAGAAAACAACAG
Found at i:2784453 original size:116 final size:116
Alignment explanation
Indices: 2784249--2784481 Score: 466
Period size: 116 Copynumber: 2.0 Consensus size: 116
2784239 CTTCTTCTTT
2784249 TATGTTTATTAATAGACTAACAGTCTAAACCGGTATAAGATAGGGTTAATTTTTGTTTTAATGTA
1 TATGTTTATTAATAGACTAACAGTCTAAACCGGTATAAGATAGGGTTAATTTTTGTTTTAATGTA
2784314 TTTTTTTACTTTCTAATCTAAACTTTCCCACCTCTTTTATCGTGAAAATCA
66 TTTTTTTACTTTCTAATCTAAACTTTCCCACCTCTTTTATCGTGAAAATCA
2784365 TATGTTTATTAATAGACTAACAGTCTAAACCGGTATAAGATAGGGTTAATTTTTGTTTTAATGTA
1 TATGTTTATTAATAGACTAACAGTCTAAACCGGTATAAGATAGGGTTAATTTTTGTTTTAATGTA
2784430 TTTTTTTACTTTCTAATCTAAACTTTCCCACCTCTTTTATCGTGAAAATCA
66 TTTTTTTACTTTCTAATCTAAACTTTCCCACCTCTTTTATCGTGAAAATCA
2784481 T
1 T
2784482 GTTGTTGAGG
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (116 bp):
TATGTTTATTAATAGACTAACAGTCTAAACCGGTATAAGATAGGGTTAATTTTTGTTTTAATGTA
TTTTTTTACTTTCTAATCTAAACTTTCCCACCTCTTTTATCGTGAAAATCA
Found at i:2789741 original size:12 final size:11
Alignment explanation
Indices: 2789683--2789752 Score: 60
Period size: 11 Copynumber: 6.7 Consensus size: 11
2789673 ATTAAATTTT
*
2789683 TTTTAAAAA-G
1 TTTTAAAAATA
2789693 TTTTAAAAATA
1 TTTTAAAAATA
2789704 TTTT--AAA-A
1 TTTTAAAAATA
*
2789712 -TTTAAAAAAA
1 TTTTAAAAATA
* *
2789722 ATTAAAAAAGTA
1 TTTTAAAAA-TA
2789734 TTTTAAAAATA
1 TTTTAAAAATA
2789745 TTTTAAAA
1 TTTTAAAA
2789753 TTAAAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 3 0.06
8 1 0.02
9 6 0.12
10 10 0.20
11 21 0.43
12 8 0.16
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:2789759 original size:39 final size:39
Alignment explanation
Indices: 2789693--2789801 Score: 173
Period size: 39 Copynumber: 2.7 Consensus size: 39
2789683 TTTTAAAAAG
2789693 TTTTAAAAATATTTTAAAATTTAAAAAAAATTAAAAAAGTA
1 TTTTAAAAATATTTTAAAA-TT-AAAAAAATTAAAAAAGTA
*
2789734 TTTTAAAAATATTTTAAAATTAAAAAAATTAAAACAGTA
1 TTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAGTA
* *
2789773 TGTAAAAAATATTTTAAAATTAAAAAAAT
1 TTTTAAAAATATTTTAAAATTAAAAAAAT
2789802 AAATATATTT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
39 44 0.68
40 2 0.03
41 19 0.29
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.36
Consensus pattern (39 bp):
TTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAGTA
Found at i:2790070 original size:28 final size:26
Alignment explanation
Indices: 2789994--2790072 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 26
2789984 CATATACATA
2789994 TATATATACATATCTATATTTTATAATC
1 TATATATACATA-C-ATATTTTATAATC
* * * *
2790022 TATGTATATATGCATGCATTTTATTATC
1 TATATATACATACAT--ATTTTATAATC
2790050 TGAATATATACATACATATTTTA
1 T--ATATATACATACATATTTTA
2790073 GGATATATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
26 2 0.05
27 1 0.03
28 26 0.65
30 11 0.28
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (26 bp):
TATATATACATACATATTTTATAATC
Found at i:2790840 original size:14 final size:15
Alignment explanation
Indices: 2790821--2790850 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2790811 AATGAAATGA
2790821 TTAATATATTA-TAT
1 TTAATATATTACTAT
2790835 TTAATATATTACTAT
1 TTAATATATTACTAT
2790850 T
1 T
2790851 ACTTATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATATATTACTAT
Found at i:2799862 original size:22 final size:24
Alignment explanation
Indices: 2799831--2799875 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2799821 ATTTTAAATA
2799831 ATTTAATAAATTTA-ATCCTTCAC
1 ATTTAATAAATTTATATCCTTCAC
*
2799854 ATTT-ATAAATTTATTTCCTTCA
1 ATTTAATAAATTTATATCCTTCA
2799876 AGGTACATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTAATAAATTTATATCCTTCAC
Found at i:2801419 original size:5 final size:5
Alignment explanation
Indices: 2801409--2801440 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2801399 TATATATATG
2801409 TATAA TATAA TA-AA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TAT
2801441 CTAGATTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:2801428 original size:14 final size:15
Alignment explanation
Indices: 2801409--2801440 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
2801399 TATATATATG
2801409 TATAATATAATA-AA
1 TATAATATAATATAA
2801423 TATAATATAATATAA
1 TATAATATAATATAA
2801438 TAT
1 TAT
2801441 CTAGATTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATAATATAATATAA
Found at i:2802904 original size:13 final size:13
Alignment explanation
Indices: 2802886--2802914 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2802876 TAAGTTGCTT
2802886 CCATTGTGATGGA
1 CCATTGTGATGGA
2802899 CCATTGTGATGGA
1 CCATTGTGATGGA
2802912 CCA
1 CCA
2802915 CATATGATCA
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:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (13 bp):
CCATTGTGATGGA
Found at i:2808290 original size:29 final size:30
Alignment explanation
Indices: 2808257--2808324 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
2808247 ATTATGGGAC
2808257 TAGATCAAATTAGTACCTT-CATTA-TTAAA
1 TAGATCAAATTAGT-CCTTGCATTATTTAAA
* *
2808286 TAGATCAATTTAGTCTTTGCATTATTTAAA
1 TAGATCAAATTAGTCCTTGCATTATTTAAA
2808316 -AGAATCAAA
1 TAG-ATCAAA
2808325 CAAGGTCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 3 0.09
29 20 0.61
30 10 0.30
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (30 bp):
TAGATCAAATTAGTCCTTGCATTATTTAAA
Found at i:2809990 original size:20 final size:20
Alignment explanation
Indices: 2809965--2810025 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2809955 TATTTTGAAG
2809965 TTGTAAAAATTCTAAAAAAT
1 TTGTAAAAATTCTAAAAAAT
* * *
2809985 TTGTAAAAATTATAATAATT
1 TTGTAAAAATTCTAAAAAAT
* *
2810005 TTTTAAAAATTACAAAAAAAT
1 TTGTAAAAATT-CTAAAAAAT
2810026 ATTAAAACTA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TTGTAAAAATTCTAAAAAAT
Found at i:2810635 original size:20 final size:20
Alignment explanation
Indices: 2810598--2810634 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2810588 TTCTAAATAA
*
2810598 ATTTTTAAACTAATTTTTAT
1 ATTTTTAAAATAATTTTTAT
2810618 ATTTTTAAAAT-ATTTTT
1 ATTTTTAAAATAATTTTT
2810635 TGCAAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTAAAATAATTTTTAT
Found at i:2828277 original size:77 final size:77
Alignment explanation
Indices: 2828150--2828304 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
2828140 GATTAGCAGG
2828150 GGCAGTATTAGCCTACTGTTACAGTATGGTCAGTTGACCAGTCAACGGTTAGTTGTTAGTGGTTA
1 GGCAGTATTAGCCTACTGTTACAGTATGGTCAGTTGACCAGTCAACGGTTAGTTGTTAGTGGTTA
2828215 ATAAGATGGTTA
66 ATAAGATGGTTA
2828227 GGCAGTATTAGCCTACTGTTACAGTATGGTCAGTTGACCAGTCAACGGTTAGTTGTTAGTGGTTA
1 GGCAGTATTAGCCTACTGTTACAGTATGGTCAGTTGACCAGTCAACGGTTAGTTGTTAGTGGTTA
2828292 ATAAGATGGTTA
66 ATAAGATGGTTA
2828304 G
1 G
2828305 CTCATAACCG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.34
Consensus pattern (77 bp):
GGCAGTATTAGCCTACTGTTACAGTATGGTCAGTTGACCAGTCAACGGTTAGTTGTTAGTGGTTA
ATAAGATGGTTA
Found at i:2828330 original size:19 final size:19
Alignment explanation
Indices: 2828300--2828345 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2828290 TAATAAGATG
2828300 GTTAGCTCATAACCGTTTTA
1 GTTAG-TCATAACCGTTTTA
*
2828320 GTTAGTCATAACTGTTTTA
1 GTTAGTCATAACCGTTTTA
2828339 GTTAGTC
1 GTTAGTC
2828346 GGTTGAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.43
Consensus pattern (19 bp):
GTTAGTCATAACCGTTTTA
Found at i:2828801 original size:19 final size:19
Alignment explanation
Indices: 2828777--2828847 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
2828767 AATCTTGTAA
2828777 TATAATATATATGTAAATT
1 TATAATATATATGTAAATT
* * **
2828796 TATAATTTATAATGTGAACA
1 TATAATATAT-ATGTAAATT
* *
2828816 TA-AATATCTATTTACAACTT
1 TATAATATATATGTA-AA-TT
2828836 TATAATATATAT
1 TATAATATATAT
2828848 AAATATATTC
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
18 3 0.08
19 16 0.43
20 10 0.27
21 8 0.22
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (19 bp):
TATAATATATATGTAAATT
Found at i:2830586 original size:43 final size:42
Alignment explanation
Indices: 2830524--2830713 Score: 263
Period size: 43 Copynumber: 4.5 Consensus size: 42
2830514 AGAAATAAAT
*
2830524 GCCGCTATAGATCATGACCTTTAGCGGCGCCTTTTCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCG-CTTTTCCACAAAC
* * * *
2830567 GCCGCTATAAATCAGGACCTTTAGCAGCGCTTTTACACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCACAAAC
* * * *
2830609 GCCGCTATAGCTCAAGATCTTTAGCGACGCTTTTTCCACAAAT
1 GCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTTCCACAAAC
2830652 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-CCACAAAC
*
2830695 GCCGCTATAGCTCAAGACC
1 GCCGCTATAGATCAAGACC
2830714 CTAACAAACG
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 40 0.31
43 88 0.69
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (42 bp):
GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCACAAAC
Found at i:2830632 original size:85 final size:86
Alignment explanation
Indices: 2830524--2830713 Score: 283
Period size: 85 Copynumber: 2.2 Consensus size: 86
2830514 AGAAATAAAT
* * * *
2830524 GCCGCTATAGATCATGACCTTTAGCGGCGCCTTTTCCACAAACGCCGCTATAAATCAGGACCTTT
1 GCCGCTATAGCTCAAGACCTTTAGCGACGCCTTTTCCACAAACGCCGCTATAAATCAAGACCTTT
2830589 AGCAGCGCTTTT-ACACAAAC
66 AGCAGCGCTTTTCACACAAAC
* * * *
2830609 GCCGCTATAGCTCAAGATCTTTAGCGACGCTTTTTCCACAAATGCCGCTATAGATCAAGACCTTT
1 GCCGCTATAGCTCAAGACCTTTAGCGACGCCTTTTCCACAAACGCCGCTATAAATCAAGACCTTT
* *
2830674 AGCGGCGCTTTTCCCACAAAC
66 AGCAGCGCTTTTCACACAAAC
2830695 GCCGCTATAGCTCAAGACC
1 GCCGCTATAGCTCAAGACC
2830714 CTAACAAACG
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 68 0.73
86 25 0.27
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (86 bp):
GCCGCTATAGCTCAAGACCTTTAGCGACGCCTTTTCCACAAACGCCGCTATAAATCAAGACCTTT
AGCAGCGCTTTTCACACAAAC
Found at i:2830867 original size:16 final size:16
Alignment explanation
Indices: 2830846--2830879 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2830836 GTTTATTAAA
*
2830846 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
2830862 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
2830878 TA
1 TA
2830880 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:2843393 original size:12 final size:13
Alignment explanation
Indices: 2843376--2843412 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2843366 GAACCGGACA
2843376 CGAACCGAA-CTC
1 CGAACCGAAGCTC
2843388 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
2843400 CGAACCGTAGCTC
1 CGAACCGAAGCTC
2843413 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:2848387 original size:18 final size:17
Alignment explanation
Indices: 2848366--2848403 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2848356 TTATTTTTAA
2848366 TTTTTAAAATGTTCTAAT
1 TTTTTAAAATGTTC-AAT
*
2848384 TTTTTAAAATTTTCAAT
1 TTTTTAAAATGTTCAAT
2848401 TTT
1 TTT
2848404 CATCATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTTAAAATGTTCAAT
Found at i:2854097 original size:31 final size:31
Alignment explanation
Indices: 2854062--2854128 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2854052 GTTACAAAAT
* ** *
2854062 AGTCATTGAATTATTTGAGAGTTTTCATTTA
1 AGTCATTGAACTATTCAAAAGTTTTCATTTA
*
2854093 AGTCATTGAACTATTCAAAAGTTTTTATTTA
1 AGTCATTGAACTATTCAAAAGTTTTCATTTA
2854124 AGTCA
1 AGTCA
2854129 CTGGGATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (31 bp):
AGTCATTGAACTATTCAAAAGTTTTCATTTA
Found at i:2857211 original size:20 final size:20
Alignment explanation
Indices: 2857186--2857229 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2857176 CATGATTGTT
2857186 TATAATTTCCTCTATTTTTG
1 TATAATTTCCTCTATTTTTG
2857206 TATAATTTCCTCTATTTTTG
1 TATAATTTCCTCTATTTTTG
2857226 TATA
1 TATA
2857230 CTTTTTAAGA
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:0.23, C:0.14, G:0.05, T:0.59
Consensus pattern (20 bp):
TATAATTTCCTCTATTTTTG
Found at i:2858463 original size:31 final size:29
Alignment explanation
Indices: 2858428--2858504 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
2858418 TTAATAGCTC
*
2858428 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
2858459 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
2858488 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
2858505 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:2863618 original size:25 final size:25
Alignment explanation
Indices: 2863584--2863632 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2863574 ATTTATTTTT
* *
2863584 TATAATTTTTATAATTTTTTTAAAA
1 TATAATTTTTATAATATTTATAAAA
*
2863609 TATAATTTTTTTAATATTTATAAA
1 TATAATTTTTATAATATTTATAAA
2863633 TATTTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TATAATTTTTATAATATTTATAAAA
Found at i:2863625 original size:14 final size:15
Alignment explanation
Indices: 2863593--2863622 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2863583 TTATAATTTT
2863593 TATAATTTTTTTAAAA
1 TATAATTTTTTT-AAA
2863609 TATAATTTTTTTAA
1 TATAATTTTTTTAA
2863623 TATTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 2 0.14
16 12 0.86
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATAATTTTTTTAAA
Found at i:2864980 original size:25 final size:26
Alignment explanation
Indices: 2864947--2865000 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
2864937 CTAAATTTTG
*
2864947 AATTACTTT-TAATTTTAATATGGAAC
1 AATTACTTTCTAATTATAA-ATGGAAC
*
2864973 AATT-CTTTCTAATTATAAATTGAAC
1 AATTACTTTCTAATTATAAATGGAAC
2864998 AAT
1 AAT
2865001 GGTAGCAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (26 bp):
AATTACTTTCTAATTATAAATGGAAC
Found at i:2872988 original size:21 final size:21
Alignment explanation
Indices: 2872936--2872988 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
2872926 AATACTAAAA
* *
2872936 ATAATATTATATAATTAATAT
1 ATAATATTTTATAATAAATAT
* *
2872957 ATTAA-AATTTATTATAAATAT
1 A-TAATATTTTATAATAAATAT
2872978 ATAATATTTTA
1 ATAATATTTTA
2872989 AATTATTACA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAATATTTTATAATAAATAT
Found at i:2875262 original size:16 final size:18
Alignment explanation
Indices: 2875228--2875270 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
2875218 TTTAGACGAA
*
2875228 TTTTTAATTAATTTGATT
1 TTTTTATTTAATTTGATT
2875246 TTTTTATTTAA-TT-ATT
1 TTTTTATTTAATTTGATT
*
2875262 TTTTGATTT
1 TTTTTATTT
2875271 TATAATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
17 2 0.09
18 10 0.43
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (18 bp):
TTTTTATTTAATTTGATT
Found at i:2876492 original size:17 final size:18
Alignment explanation
Indices: 2876460--2876495 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2876450 AAAAAAATTG
*
2876460 AAAATAAAATTGTTTTAT
1 AAAATAAAATTATTTTAT
2876478 AAAAT-AAATTATTTTAT
1 AAAATAAAATTATTTTAT
2876495 A
1 A
2876496 TAAAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AAAATAAAATTATTTTAT
Found at i:2882603 original size:74 final size:74
Alignment explanation
Indices: 2882457--2882592 Score: 233
Period size: 71 Copynumber: 1.9 Consensus size: 74
2882447 TCATGATTAA
*
2882457 ATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTCTAAA
1 ATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATAATAATTATTCTAAA
2882522 AGAAAATTT
66 AGAAAATTT
*
2882531 ATTATCAAGAATTTTATGAAA-T-TATAT-ATTATTAAATTATATTTAATAATAATTATTTTAAA
1 ATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATAATAATTATTCTAAA
2882593 TTATACAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
71 33 0.55
72 5 0.08
73 1 0.02
74 21 0.35
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (74 bp):
ATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATAATAATTATTCTAAA
AGAAAATTT
Found at i:2882862 original size:120 final size:120
Alignment explanation
Indices: 2882638--2883648 Score: 1776
Period size: 120 Copynumber: 8.4 Consensus size: 120
2882628 AATTATTTTA
* * *
2882638 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
* * * * *
2882702 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAA
66 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
* * * *
2882757 AATTTTATTAAATCATATATTTTAATTAAATTTTATTTAATAATAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AATTTATATTT
* *
2882821 TATAGTATCATATATTATGATTTTAGTAAATTAATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
* *
2882877 AATTTCATTAAATTATATATTTTAATTAAAATATATTTAATAATAAATATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
2882942 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
*
2882997 AATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
2883062 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
*
2883117 AATTTCATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
2883182 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
*
2883237 AATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
2883302 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
*
2883357 AATTTCATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
2883422 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
*
2883477 AATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
2883542 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
2883597 AATTTTATTAAATTATATA-TTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
2883649 TAAATATGAT
Statistics
Matches: 862, Mismatches: 28, Indels: 4
0.96 0.03 0.00
Matches are distributed among these distances:
119 82 0.10
120 778 0.90
121 2 0.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
Found at i:2883618 original size:17 final size:17
Alignment explanation
Indices: 2883598--2883631 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2883588 ATTATTAAGA
* *
2883598 ATTTTATTAAATTATAT
1 ATTTAATTAAAATATAT
2883615 ATTTAATTAAAATATAT
1 ATTTAATTAAAATATAT
2883632 TTAATAATAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAATTAAAATATAT
Found at i:2883888 original size:16 final size:16
Alignment explanation
Indices: 2883867--2883935 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
2883857 GATTAGCTAT
*
2883867 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
2883883 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
2883900 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2883916 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2883932 TACA
1 TACA
2883936 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 36 0.71
17 15 0.29
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2883909 original size:33 final size:32
Alignment explanation
Indices: 2883867--2883935 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
2883857 GATTAGCTAT
*
2883867 TACACCTCTAATCTAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
2883900 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
2883932 TACA
1 TACA
2883936 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:2885151 original size:14 final size:14
Alignment explanation
Indices: 2885118--2885157 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2885108 CTATCTTTTT
2885118 ATATTTTTA-AAAA
1 ATATTTTTATAAAA
*
2885131 ATATTTTTATAAGA
1 ATATTTTTATAAAA
*
2885145 ATTTTTTTATAAA
1 ATATTTTTATAAA
2885158 TTTGTTACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
ATATTTTTATAAAA
Found at i:2894201 original size:18 final size:18
Alignment explanation
Indices: 2894180--2894214 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2894170 ATTTTACTAA
2894180 AAATATTTTTT-TTAAATG
1 AAAT-TTTTTTATTAAATG
2894198 AAATTTTTTTATTAAAT
1 AAATTTTTTTATTAAAT
2894215 AACACAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AAATTTTTTTATTAAATG
Found at i:2894271 original size:18 final size:18
Alignment explanation
Indices: 2894248--2894283 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2894238 CCATCCAACA
*
2894248 CAAAAAAAAATTATTTTT
1 CAAAAAAAAATAATTTTT
*
2894266 CAAAAATAAATAATTTTT
1 CAAAAAAAAATAATTTTT
2894284 AATGAAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
CAAAAAAAAATAATTTTT
Found at i:2898895 original size:16 final size:16
Alignment explanation
Indices: 2898874--2898907 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2898864 TACTTCATGC
*
2898874 TAAATTCTTTTTTTTT
1 TAAATTCTTTTCTTTT
2898890 TAAATTCTTTTCTTTT
1 TAAATTCTTTTCTTTT
2898906 TA
1 TA
2898908 TTTTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TAAATTCTTTTCTTTT
Found at i:2901610 original size:18 final size:18
Alignment explanation
Indices: 2901589--2901628 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2901579 TTAAAATTAA
2901589 AAATATATAAAAAAATAG
1 AAATATATAAAAAAATAG
* * *
2901607 AAATTTATAAAATATTAG
1 AAATATATAAAAAAATAG
2901625 AAAT
1 AAAT
2901629 GTTATTTCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AAATATATAAAAAAATAG
Found at i:2902206 original size:68 final size:68
Alignment explanation
Indices: 2902097--2902306 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
2902087 TCAAGTTTAT
* *
2902097 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAGTTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
2902162 AAA
66 AAA
*
2902165 TTTACTAATCAAATTTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
2902230 AAA
66 AAA
2902233 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
2902296 AAT
66 AAA
2902299 TTTACTAA
1 TTTACTAA
2902307 CAATTAATTT
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
66 27 0.20
67 1 0.01
68 109 0.80
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:2902207 original size:9 final size:9
Alignment explanation
Indices: 2902195--2902222 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2902185 TTTTATTACA
2902195 ACAATTAAT
1 ACAATTAAT
2902204 ACAATTAAT
1 ACAATTAAT
2902213 ACAATTAAT
1 ACAATTAAT
2902222 A
1 A
2902223 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:2902316 original size:16 final size:16
Alignment explanation
Indices: 2902295--2902336 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2902285 AATAATTTGA
*
2902295 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
2902311 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
2902327 TAGTTTTAAT
1 TAATTTTAAT
2902337 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:2904673 original size:13 final size:13
Alignment explanation
Indices: 2904655--2904679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2904645 AATCGACATG
2904655 TTTATTTTATTTA
1 TTTATTTTATTTA
2904668 TTTATTTTATTT
1 TTTATTTTATTT
2904680 GGTGAATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:2907076 original size:26 final size:28
Alignment explanation
Indices: 2907046--2907100 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
2907036 ATTAGCCGTA
2907046 ACTTTTATAA-ATAAATA-TATTATAAT
1 ACTTTTATAACATAAATATTATTATAAT
* *
2907072 ACTTTTATAACATATATATTTTTATAAT
1 ACTTTTATAACATAAATATTATTATAAT
2907100 A
1 A
2907101 AGCTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
27 6 0.24
28 9 0.36
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.49
Consensus pattern (28 bp):
ACTTTTATAACATAAATATTATTATAAT
Found at i:2929205 original size:18 final size:18
Alignment explanation
Indices: 2929179--2929213 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2929169 TATTTTACTA
*
2929179 AAATATTTTTTTTAAATG
1 AAATATTTTTATTAAATG
*
2929197 AAATTTTTTTATTAAAT
1 AAATATTTTTATTAAAT
2929214 AACACAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AAATATTTTTATTAAATG
Found at i:2929269 original size:18 final size:18
Alignment explanation
Indices: 2929246--2929281 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2929236 CCATCCAACA
*
2929246 CAAAAAAAAATTATTTTT
1 CAAAAAAAAATAATTTTT
*
2929264 CAAAAATAAATAATTTTT
1 CAAAAAAAAATAATTTTT
2929282 AATGAAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
CAAAAAAAAATAATTTTT
Found at i:2933852 original size:15 final size:16
Alignment explanation
Indices: 2933832--2933864 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2933822 TACTTCATGC
2933832 TAAATTCTTTT-TTTT
1 TAAATTCTTTTCTTTT
2933847 TAAATTCTTTTCTTTT
1 TAAATTCTTTTCTTTT
2933863 TA
1 TA
2933865 TTTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (16 bp):
TAAATTCTTTTCTTTT
Found at i:2936538 original size:18 final size:18
Alignment explanation
Indices: 2936517--2936556 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2936507 TTAAAATTAA
2936517 AAATATATAAAAAAATAG
1 AAATATATAAAAAAATAG
* * *
2936535 AAATTTATAAAATATTAG
1 AAATATATAAAAAAATAG
2936553 AAAT
1 AAAT
2936557 GTTATTTCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AAATATATAAAAAAATAG
Found at i:2937138 original size:68 final size:68
Alignment explanation
Indices: 2937029--2937238 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
2937019 TCAAGTTTAT
* *
2937029 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAGTTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
2937094 AAA
66 AAA
*
2937097 TTTACTAATCAAATTTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
2937162 AAA
66 AAA
2937165 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
2937228 AAT
66 AAA
2937231 TTTACTAA
1 TTTACTAA
2937239 CAATTAATTT
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
66 27 0.20
67 1 0.01
68 109 0.80
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:2937139 original size:9 final size:9
Alignment explanation
Indices: 2937127--2937154 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2937117 TTTTATTACA
2937127 ACAATTAAT
1 ACAATTAAT
2937136 ACAATTAAT
1 ACAATTAAT
2937145 ACAATTAAT
1 ACAATTAAT
2937154 A
1 A
2937155 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:2937248 original size:16 final size:16
Alignment explanation
Indices: 2937227--2937268 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2937217 AATAATTTGA
*
2937227 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
2937243 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
2937259 TAGTTTTAAT
1 TAATTTTAAT
2937269 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:2939606 original size:13 final size:13
Alignment explanation
Indices: 2939588--2939612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2939578 AATCGACATG
2939588 TTTATTTTATTTA
1 TTTATTTTATTTA
2939601 TTTATTTTATTT
1 TTTATTTTATTT
2939613 GGTGAATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:2941207 original size:19 final size:18
Alignment explanation
Indices: 2941183--2941227 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2941173 AATTCATATT
* *
2941183 TAAAAAATATTAATTACTA
1 TAAAAAATATT-ATCACGA
*
2941202 TAAAAATTATTATCACGA
1 TAAAAAATATTATCACGA
2941220 TAAAAAAT
1 TAAAAAAT
2941228 TTCTAAATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (18 bp):
TAAAAAATATTATCACGA
Found at i:2942011 original size:27 final size:28
Alignment explanation
Indices: 2941983--2942035 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2941973 AGCCGTAACT
2941983 TTTTATAA-ATAAATA-TATTATAATAC
1 TTTTATAACATAAATATTATTATAATAC
* *
2942009 TTTTATAACATATATATTTTTATAATA
1 TTTTATAACATAAATATTATTATAATA
2942036 AGCTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 6 0.26
28 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTATAACATAAATATTATTATAATAC
Found at i:2949834 original size:18 final size:18
Alignment explanation
Indices: 2949813--2949875 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 18
2949803 AGAAGAATGG
2949813 TGGAAACAGGGAGTAGCA
1 TGGAAACAGGGAGTAGCA
* *
2949831 TGG----AGGG-TTATCA
1 TGGAAACAGGGAGTAGCA
* *
2949844 GGGAAACGGGGAGTAGCA
1 TGGAAACAGGGAGTAGCA
2949862 TGGAAACAGGGAGT
1 TGGAAACAGGGAGT
2949876 TGATTTCTTG
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
13 6 0.19
14 4 0.12
17 3 0.09
18 19 0.59
ACGTcount: A:0.33, C:0.10, G:0.43, T:0.14
Consensus pattern (18 bp):
TGGAAACAGGGAGTAGCA
Found at i:2963712 original size:19 final size:20
Alignment explanation
Indices: 2963685--2963735 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2963675 CAAATAATTT
* **
2963685 AAAATTTATAAAAATAT-CC
1 AAAAATTATAAAAATATAAA
*
2963704 AAAAATTATAAAATTATAAA
1 AAAAATTATAAAAATATAAA
2963724 AAAAATTATAAA
1 AAAAATTATAAA
2963736 CATCCGCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAATATAAA
Found at i:2964903 original size:29 final size:27
Alignment explanation
Indices: 2964871--2964930 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 27
2964861 TGTCAACATA
2964871 CTTTTCATAATATAATTAATATAAATATG
1 CTTTT-ATAA-ATAATTAATATAAATATG
*
2964900 CTTTTTTAAATAATTAATATAAATATG
1 CTTTTATAAATAATTAATATAAATATG
2964927 CTTT
1 CTTT
2964931 CCAATAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 22 0.73
28 3 0.10
29 5 0.17
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (27 bp):
CTTTTATAAATAATTAATATAAATATG
Found at i:2964941 original size:27 final size:28
Alignment explanation
Indices: 2964879--2964941 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
2964869 TACTTTTCAT
**
2964879 AATATAATTAATATAAATATGCTTTTTT
1 AATATAATTAATATAAATATGCTTTTCC
2964907 AA-ATAATTAATATAAATATGC-TTTCC
1 AATATAATTAATATAAATATGCTTTTCC
*
2964933 AATAAAATT
1 AATATAATT
2964942 GCAATTGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 5 0.16
27 24 0.77
28 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (28 bp):
AATATAATTAATATAAATATGCTTTTCC
Found at i:2967588 original size:22 final size:23
Alignment explanation
Indices: 2967561--2967603 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2967551 AAACATATGA
**
2967561 AATAACTTTAAAT-TTTAAAAAT
1 AATAACTACAAATATTTAAAAAT
2967583 AATAACTACAAATATTTAAAA
1 AATAACTACAAATATTTAAAA
2967604 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAACTACAAATATTTAAAAAT
Found at i:2972645 original size:139 final size:138
Alignment explanation
Indices: 2972458--2972843 Score: 469
Period size: 139 Copynumber: 2.8 Consensus size: 138
2972448 TCTTCTACTG
* *
2972458 ACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATCTTTAATTAATTTTTTTAACAT
1 ACATTTGTATTTTTTATTTCATGTTGCTTCAAGCATTTTAAAT-TTTAATTAATATTTTTAACAT
* * * * *
2972523 ATTAGTTCTTTGGTTAGATGGTTAAATAGTTACAATTACATCCTTGAGTCTCAAGTTTAATTCAT
65 ATTAATTCTTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGTCTCAAGTTCAATTCAT
*
2972588 CTCCGACTC
130 CTACGACTC
* * * *
2972597 ATATTTGTATTTTCTATTTCATGTTACTTCAAGCATTTTCAAATTTTAATTAATATTTTTAACTT
1 ACATTTGTATTTTTTATTTCATGTTGCTTCAAGCATTTT-AAATTTTAATTAATATTTTTAACAT
* * * * * * * *
2972662 TTTAATTCTTTCGTTAGATGGTTAGATAGTCGTAAGTACATTCTTGAGTCTCGAGTTCGATTCCT
65 ATTAATTCTTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGTCTCAAGTTCAATTCAT
*
2972727 CTACTACTC
130 CTACGACTC
*
2972736 ACATTTGTATTTTTTATTTCATGTTGCTTC-A--ATTTT---TTTTAATTAATATTTCTAACATA
1 ACATTTGTATTTTTTATTTCATGTTGCTTCAAGCATTTTAAATTTTAATTAATATTTTTAACATA
** * *
2972795 TTACCTCTTTTCGTTAGATGGTTAGATAATTGCTATTACATCCTTGAGT
66 TTAATTC-TTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGT
2972844 ATGAGGTTTC
Statistics
Matches: 210, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
132 25 0.12
133 35 0.17
136 5 0.02
138 1 0.00
139 140 0.67
140 4 0.02
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (138 bp):
ACATTTGTATTTTTTATTTCATGTTGCTTCAAGCATTTTAAATTTTAATTAATATTTTTAACATA
TTAATTCTTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGTCTCAAGTTCAATTCATC
TACGACTC
Found at i:2976084 original size:30 final size:29
Alignment explanation
Indices: 2976049--2976115 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
2976039 TAACCAACCA
*
2976049 AATCGATTTAATTCGGTTA-ATTGGTCGGTT
1 AATCGATTTAATTCAGTTAGA--GGTCGGTT
2976079 AATCGATTTAATTCAGTTAGAGGTCGGTT
1 AATCGATTTAATTCAGTTAGAGGTCGGTT
2976108 AAT-GATTT
1 AATCGATTT
2976116 TTTAGAAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 5 0.14
29 11 0.31
30 18 0.51
31 1 0.03
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (29 bp):
AATCGATTTAATTCAGTTAGAGGTCGGTT
Found at i:2995908 original size:2 final size:2
Alignment explanation
Indices: 2995901--2995938 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2995891 AACAAGTATC
2995901 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2995939 GAATGCCGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3009373 original size:28 final size:28
Alignment explanation
Indices: 3009281--3009374 Score: 66
Period size: 28 Copynumber: 3.2 Consensus size: 28
3009271 AATTGAACCT
*
3009281 AAAAAAAAACTTAGGTACCAAATTA-GG
1 AAAAAAAAATTTAGGTACCAAATTAGGG
** * *
3009308 AAAAAATGTCAGGTTCAGGTGCCAAATT-GGG
1 AAAAAA----AAATTTAGGTACCAAATTAGGG
**
3009339 CCCAAAAAAATTTAGGTACCAAATTAGGG
1 -AAAAAAAAATTTAGGTACCAAATTAGGG
3009368 AAAAAAA
1 AAAAAAA
3009375 TGTAAAATTT
Statistics
Matches: 47, Mismatches: 13, Indels: 13
0.64 0.18 0.18
Matches are distributed among these distances:
27 6 0.13
28 19 0.40
29 3 0.06
31 15 0.32
32 4 0.09
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (28 bp):
AAAAAAAAATTTAGGTACCAAATTAGGG
Found at i:3009394 original size:61 final size:59
Alignment explanation
Indices: 3009283--3009395 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
3009273 TTGAACCTAA
* **
3009283 AAAAAAACTTAGGTACCAAATTAGGAAAAAATGTCAGGTTCAGGTGCCAAATTGGGCCC
1 AAAAAAACTTAGGTACCAAATTAGGAAAAAATGTAAAATTCAGGTGCCAAATTGGGCCC
* * *
3009342 AAAAAAATTTAGGTACCAAATTAGGGAAAAAAATGTAAAATTTAGGTTCCAAAT
1 AAAAAAACTTAGGTACCAAATTA-GG-AAAAAATGTAAAATTCAGGTGCCAAAT
3009396 GTTACATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 22 0.48
60 2 0.04
61 22 0.48
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (59 bp):
AAAAAAACTTAGGTACCAAATTAGGAAAAAATGTAAAATTCAGGTGCCAAATTGGGCCC
Found at i:3019056 original size:9 final size:9
Alignment explanation
Indices: 3019042--3019087 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
3019032 TTTCATTTTC
3019042 TTATAATTT
1 TTATAATTT
3019051 TTATAATGTT
1 TTATAAT-TT
*
3019061 TTACAATTT
1 TTATAATTT
* *
3019070 TTAAAAGTT
1 TTATAATTT
3019079 TTATAATTT
1 TTATAATTT
3019088 AAAAATTACA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (9 bp):
TTATAATTT
Found at i:3019699 original size:51 final size:51
Alignment explanation
Indices: 3019604--3019701 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
3019594 ATTTTTTGAT
* * * *
3019604 TTTTTTAGAATTAGGATTAAATTGATATCATTTGCAAATCTTGAGGGTTAA
1 TTTTTTAAAATTAGGATTAAATTGATATAATATGCAAAACTTGAGGGTTAA
* * * *
3019655 TTTTTTAAAATTATGATTCAATTGATATAATATGTAAAAGTTGAGGG
1 TTTTTTAAAATTAGGATTAAATTGATATAATATGCAAAACTTGAGGG
3019702 CTAAATTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (51 bp):
TTTTTTAAAATTAGGATTAAATTGATATAATATGCAAAACTTGAGGGTTAA
Found at i:3020179 original size:13 final size:11
Alignment explanation
Indices: 3020152--3020233 Score: 54
Period size: 11 Copynumber: 7.9 Consensus size: 11
3020142 ATTTTTTTAA
3020152 TTTTAAAATAT
1 TTTTAAAATAT
3020163 TTTTAAAATACAT
1 TTTTAAAAT--AT
3020176 TTTT--AAT-T
1 TTTTAAAATAT
* *
3020184 TTTT---TTAA
1 TTTTAAAATAT
3020192 TTTTAAAATAT
1 TTTTAAAATAT
3020203 TTTTAAAATAAT
1 TTTTAAAAT-AT
*
3020215 TTTT-TAA-AT
1 TTTTAAAATAT
3020224 TTTTAAAATA
1 TTTTAAAATA
3020234 AATTTTTGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
7 1 0.02
8 9 0.16
9 6 0.11
10 2 0.04
11 26 0.46
12 6 0.11
13 6 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3020190 original size:40 final size:40
Alignment explanation
Indices: 3020128--3020227 Score: 148
Period size: 40 Copynumber: 2.5 Consensus size: 40
3020118 GCCCGAATAT
**
3020128 AATAGATTTTTTTTATTTTTTTAATTTTAAAATATTTTTAA
1 AATA-ATTTTTTAAATTTTTTTAATTTTAAAATATTTTTAA
*
3020169 AATACA-TTTTTAATTTTTTTTAATTTTAAAATATTTTTAA
1 AATA-ATTTTTTAAATTTTTTTAATTTTAAAATATTTTTAA
3020209 AATAATTTTTTAAATTTTT
1 AATAATTTTTTAAATTTTT
3020228 AAAATAAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.02
40 47 0.89
41 5 0.09
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (40 bp):
AATAATTTTTTAAATTTTTTTAATTTTAAAATATTTTTAA
Found at i:3020225 original size:21 final size:21
Alignment explanation
Indices: 3020201--3020240 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3020191 ATTTTAAAAT
*
3020201 ATTTTTAAAATAATTTTTTAA
1 ATTTTTAAAATAAATTTTTAA
3020222 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
3020241 GGTATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTAA
Found at i:3020247 original size:22 final size:21
Alignment explanation
Indices: 3020199--3020247 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3020189 TAATTTTAAA
*
3020199 ATATTTTTAAAATAATTTTTT
1 ATATTTTTAAAATAATTTTTG
*
3020220 AAATTTTTAAAATAAATTTTTG
1 ATATTTTTAAAAT-AATTTTTG
*
3020242 GTATTT
1 ATATTT
3020248 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
ATATTTTTAAAATAATTTTTG
Found at i:3038544 original size:16 final size:14
Alignment explanation
Indices: 3038518--3038557 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
3038508 ACTATTATAA
3038518 TTATT-TATATATC
1 TTATTATATATATC
3038531 TTTATATATATATATC
1 -TTAT-TATATATATC
3038547 TTATTATATAT
1 TTATTATATAT
3038558 GTGTATACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.46
15 5 0.21
16 8 0.33
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTATATATATC
Found at i:3047130 original size:13 final size:13
Alignment explanation
Indices: 3047091--3047181 Score: 57
Period size: 13 Copynumber: 7.2 Consensus size: 13
3047081 GAGAAATTTC
3047091 AACATTTATTTAA
1 AACATTTATTTAA
** *
3047104 AACAAATATCTAA
1 AACATTTATTTAA
3047117 AACATTTATTT-A
1 AACATTTATTTAA
* *
3047129 AATATTTAAATATT-T
1 AACATTT--AT-TTAA
3047144 AA-A--TATTTAA
1 AACATTTATTTAA
**
3047154 AACAAATATTTAA
1 AACATTTATTTAA
3047167 AACATTTATTTAA
1 AACATTTATTTAA
3047180 AA
1 AA
3047182 TTTCTTAGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
9 2 0.03
10 4 0.07
11 1 0.02
12 8 0.13
13 38 0.63
14 3 0.05
15 4 0.07
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (13 bp):
AACATTTATTTAA
Found at i:3047136 original size:8 final size:8
Alignment explanation
Indices: 3047123--3047154 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
3047113 CTAAAACATT
3047123 TATTTAAA
1 TATTTAAA
3047131 TATTTAAA
1 TATTTAAA
3047139 TATTTAAA
1 TATTTAAA
3047147 TATTTAAA
1 TATTTAAA
3047155 ACAAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TATTTAAA
Found at i:3054421 original size:13 final size:12
Alignment explanation
Indices: 3054403--3054441 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
3054393 AGAGTTATTG
3054403 ATATTTATTTATA
1 ATATTTA-TTATA
3054416 ATATTTATTATTA
1 ATATTTATTA-TA
3054429 ATATTTAATTATA
1 ATATTT-ATTATA
3054442 TTTAAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 17 0.71
14 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATATTTATTATA
Found at i:3063329 original size:20 final size:20
Alignment explanation
Indices: 3063293--3063330 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3063283 ACAACACACG
*
3063293 GCCATGAAGAAGGAAAAGAA
1 GCCATGAAGAAGAAAAAGAA
3063313 GCCAT-AAGAGAGAAAAAG
1 GCCATGAAGA-AGAAAAAG
3063331 GAATATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.55, C:0.11, G:0.29, T:0.05
Consensus pattern (20 bp):
GCCATGAAGAAGAAAAAGAA
Found at i:3070083 original size:27 final size:27
Alignment explanation
Indices: 3070018--3070093 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
3070008 GTAGTGATTC
*
3070018 AATTTGGTTAATTCGGGTAATTCGGTT
1 AATTTGGTTAATTCGGTTAATTCGGTT
*
3070045 AATTCAGG-TAATTCGGTTAATTCGGTT
1 AATT-TGGTTAATTCGGTTAATTCGGTT
* *
3070072 AATTTGGTTAATTTGATTAATT
1 AATTTGGTTAATTCGGTTAATT
3070094 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
27 38 0.90
28 2 0.05
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.46
Consensus pattern (27 bp):
AATTTGGTTAATTCGGTTAATTCGGTT
Found at i:3070086 original size:9 final size:9
Alignment explanation
Indices: 3070018--3070084 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
3070008 GTAGTGATTC
*
3070018 AATTTGGTT
1 AATTCGGTT
*
3070027 AATTCGGGT
1 AATTCGGTT
3070036 AATTCGGTT
1 AATTCGGTT
3070045 AATTCAGG-T
1 AATTC-GGTT
3070054 AATTCGGTT
1 AATTCGGTT
3070063 AATTCGGTT
1 AATTCGGTT
*
3070072 AATTTGGTT
1 AATTCGGTT
3070081 AATT
1 AATT
3070085 TGATTAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
8 2 0.04
9 48 0.92
10 2 0.04
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:3070091 original size:18 final size:18
Alignment explanation
Indices: 3070012--3070094 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 18
3070002 AATTATGTAG
3070012 TGATTCAATTTGGTTAATT
1 TGATT-AATTTGGTTAATT
* ** *
3070031 CGGGTAATTCGGTTAA-T
1 TGATTAATTTGGTTAATT
* * *
3070048 TCAGGTAATTCGGTTAATT
1 TGA-TTAATTTGGTTAATT
* *
3070067 CGGTTAATTTGGTTAATT
1 TGATTAATTTGGTTAATT
3070085 TGATTAATTT
1 TGATTAATTT
3070095 TTAACCAAAA
Statistics
Matches: 48, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
17 1 0.02
18 44 0.92
19 3 0.06
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (18 bp):
TGATTAATTTGGTTAATT
Found at i:3071510 original size:2 final size:2
Alignment explanation
Indices: 3071503--3071528 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3071493 AAAGAGAAAA
3071503 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3071529 GTGACAGGTA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.