Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold156
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: 2697547
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 13 of 14
Found at i:2420642 original size:31 final size:30
Alignment explanation
Indices: 2420550--2420645 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 30
2420540 CGGCATCTCT
2420550 TATAATT-ATATTTATATAAATTTTAATATTT-
1 TATAATTAATATTT-TAT-AATTTT-ATATTTA
* *
2420581 TAATAATTTATATTATATAATTTTA-A--TA
1 T-ATAATTAATATTTTATAATTTTATATTTA
*
2420609 TATTATTAATATTTTATATATTTTATATTTA
1 TATAATTAATATTTTATA-ATTTTATATTTA
2420640 TATAAT
1 TATAAT
2420646 CATATCTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
27 15 0.28
28 7 0.13
29 2 0.04
30 1 0.02
31 14 0.26
32 9 0.17
33 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TATAATTAATATTTTATAATTTTATATTTA
Found at i:2420645 original size:27 final size:28
Alignment explanation
Indices: 2420557--2420645 Score: 85
Period size: 31 Copynumber: 3.1 Consensus size: 28
2420547 TCTTATAATT
*
2420557 ATATTTATATAAATTTTAATATTT-TAATA
1 ATATTT-TATATATTTTAATATTTAT-ATA
*
2420586 ATTTATATTATATAATTTTAATATATTAT-TA
1 A--TATTTTATAT-ATTTTAATAT-TTATATA
2420617 ATATTTTATATATTTT-ATATTTATATA
1 ATATTTTATATATTTTAATATTTATATA
2420644 AT
1 AT
2420646 CATATCTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
26 4 0.08
27 8 0.16
28 5 0.10
29 10 0.20
30 4 0.08
31 17 0.33
32 2 0.04
33 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATATTTTATATATTTTAATATTTATATA
Found at i:2421339 original size:28 final size:27
Alignment explanation
Indices: 2421307--2421396 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 27
2421297 TTTATCTTAT
2421307 ATTTTATATAAATTTTTTATATAATTAA
1 ATTTTATATAAATTTTTTAT-TAATTAA
* *
2421335 ATTTTAACTTTAAATTTATTTATTAAAT-A
1 ATTTT-A-TATAAATTT-TTTATTAATTAA
* *
2421364 TTTTTAAATAAA--TTTTATTAATTATA
1 ATTTTATATAAATTTTTTATTAATTA-A
2421390 ATTTTAT
1 ATTTTAT
2421397 TTAATTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 9 0.18
25 1 0.02
26 6 0.12
27 4 0.08
28 6 0.12
29 6 0.12
30 12 0.24
31 5 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTATATAAATTTTTTATTAATTAA
Found at i:2421462 original size:3 final size:3
Alignment explanation
Indices: 2421454--2421480 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2421444 GAATAACTAG
2421454 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2421481 CTACTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2421679 original size:8 final size:8
Alignment explanation
Indices: 2421668--2421745 Score: 54
Period size: 8 Copynumber: 9.5 Consensus size: 8
2421658 ATTTATATAA
2421668 ATTTTAAT
1 ATTTTAAT
2421676 ATTTTAAT
1 ATTTTAAT
*
2421684 AATTT-AT
1 ATTTTAAT
*
2421691 ATTAT-AT
1 ATTTTAAT
2421698 AATTTTAAT
1 -ATTTTAAT
*
2421707 ATATTATTAT
1 AT-TT-TAAT
*
2421717 ATTATAAAT
1 ATT-TTAAT
2421726 ATTTTATAT
1 ATTTTA-AT
2421735 ATTTT-AT
1 ATTTTAAT
2421742 ATTT
1 ATTT
2421746 ATATAATCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
7 13 0.23
8 20 0.36
9 17 0.30
10 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTAAT
Found at i:2421679 original size:18 final size:18
Alignment explanation
Indices: 2421656--2421751 Score: 75
Period size: 18 Copynumber: 5.7 Consensus size: 18
2421646 TCTTATAATT
2421656 ATATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
2421674 ATATTT-TA-ATAA-TTT-
1 ATATTTATATA-AATTTTA
2421689 ATA-TTATAT-AATTTTA
1 ATATTTATATAAATTTTA
* *
2421705 ATATATTAT-TATATTATAA
1 ATAT-TTATATAAATT-TTA
*
2421724 ATATTT-TATATATTTT-
1 ATATTTATATAAATTTTA
2421740 ATATTTATATAA
1 ATATTTATATAA
2421752 TCATATCTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 23
0.70 0.04 0.26
Matches are distributed among these distances:
14 4 0.06
15 8 0.13
16 13 0.21
17 11 0.17
18 21 0.33
19 6 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTATATAAATTTTA
Found at i:2421722 original size:31 final size:32
Alignment explanation
Indices: 2421648--2421749 Score: 103
Period size: 31 Copynumber: 3.4 Consensus size: 32
2421638 ATAGAATCTC
* *
2421648 TTATAATTATATTTATATAAATTTTAATATTTTA
1 TTATATTTATA-TTATAT-AATTTTAATATATTA
*
2421682 ATA-ATTTATATTATATAATTTTAATATATTA
1 TTATATTTATATTATATAATTTTAATATATTA
2421713 TTATA-TTATA--A-AT-ATTTT-ATATATT-
1 TTATATTTATATTATATAATTTTAATATATTA
2421738 TTATATTTATAT
1 TTATATTTATAT
2421750 AATCATATCT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
25 5 0.08
26 12 0.20
27 5 0.08
28 2 0.03
29 1 0.02
31 21 0.34
32 7 0.11
33 6 0.10
34 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TTATATTTATATTATATAATTTTAATATATTA
Found at i:2421736 original size:9 final size:9
Alignment explanation
Indices: 2421655--2421743 Score: 64
Period size: 9 Copynumber: 10.3 Consensus size: 9
2421645 CTCTTATAAT
2421655 TATATTTATA
1 TATATTT-TA
*
2421665 TAAATTTTA
1 TATATTTTA
2421674 -ATATTTTA
1 TATATTTTA
*
2421682 -ATA-ATT-
1 TATATTTTA
*
2421688 TATATTATA
1 TATATTTTA
2421697 TA-ATTTTA
1 TATATTTTA
*
2421705 -ATATATTA
1 TATATTTTA
*
2421713 TTATATTATA
1 -TATATTTTA
*
2421723 AATATTTTA
1 TATATTTTA
2421732 TATATTTTA
1 TATATTTTA
2421741 TAT
1 TAT
2421744 TTATATAATC
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
7 6 0.10
8 21 0.34
9 22 0.36
10 12 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATATTTTA
Found at i:2421747 original size:26 final size:26
Alignment explanation
Indices: 2421672--2421752 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 26
2421662 ATATAAATTT
*
2421672 TAATATTTTA-ATAATTTATATTATA
1 TAATATTTTATATATTTTATATTATA
*
2421697 TAAT-TTTAATATATTATTATATTATA
1 TAATATTTTATATATT-TTATATTATA
2421723 -AATATTTTATATATTTTATATTTATA
1 TAATATTTTATATATTTTATA-TTATA
2421749 TAAT
1 TAAT
2421753 CATATCTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.08
25 16 0.33
26 25 0.52
27 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TAATATTTTATATATTTTATATTATA
Found at i:2421750 original size:28 final size:27
Alignment explanation
Indices: 2421673--2421751 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 27
2421663 TATAAATTTT
*
2421673 AATATTTTA-ATAATTTATATTATAT-
1 AATATTTTATATATTTTATATTATATA
*
2421698 AAT-TTTAATATATTATTATA-T-TATA
1 AATATTTTATATATT-TTATATTATATA
2421723 AATATTTTATATATTTTATATTTATATA
1 AATATTTTATATATTTTATA-TTATATA
2421751 A
1 A
2421752 TCATATCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
24 7 0.16
25 16 0.36
26 15 0.34
27 1 0.02
28 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
AATATTTTATATATTTTATATTATATA
Found at i:2422170 original size:36 final size:36
Alignment explanation
Indices: 2422130--2422198 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
2422120 AATTTTTATT
** *
2422130 TTTTATCCAAATAGTTTTTTTTTTTGAAAAAATAGC
1 TTTTATCCAAATAGTTAATTTTTTTAAAAAAATAGC
*
2422166 TTTTATCCAACTAGTTAATTTTTTTAAAAAAAT
1 TTTTATCCAAATAGTTAATTTTTTTAAAAAAAT
2422199 TTTAACTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (36 bp):
TTTTATCCAAATAGTTAATTTTTTTAAAAAAATAGC
Found at i:2422748 original size:27 final size:28
Alignment explanation
Indices: 2422718--2422827 Score: 93
Period size: 27 Copynumber: 4.0 Consensus size: 28
2422708 TTGAAATATA
2422718 TATATTAAATTTAATA-ATTTAATAATT
1 TATATTAAATTTAATATATTTAATAATT
* * *
2422745 TATATTATA-TTCATATATTTTATAATAT
1 TATATTAAATTTAATATATTTAATAAT-T
* * * *
2422773 TATAATTATATTTAAAATATTTTAT-ATG
1 TAT-ATTAAATTTAATATATTTAATAATT
*
2422801 TATA-TAAATTTTAATATATATAATAAT
1 TATATTAAA-TTTAATATATTTAATAAT
2422828 ATTTAAAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
26 8 0.12
27 30 0.45
28 9 0.13
29 8 0.12
30 12 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (28 bp):
TATATTAAATTTAATATATTTAATAATT
Found at i:2422822 original size:16 final size:17
Alignment explanation
Indices: 2422791--2422823 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2422781 TATTTAAAAT
*
2422791 ATTTTATATGTATATAA
1 ATTTTATATATATATAA
2422808 ATTTTA-ATATATATAA
1 ATTTTATATATATATAA
2422824 TAATATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
ATTTTATATATATATAA
Found at i:2422831 original size:20 final size:20
Alignment explanation
Indices: 2422766--2422831 Score: 68
Period size: 18 Copynumber: 3.5 Consensus size: 20
2422756 CATATATTTT
* *
2422766 ATAATATTATAATTATATTTA
1 ATAATATTTTAA-TATATATA
*
2422787 A-AATATTTT-ATATGTAT-
1 ATAATATTTTAATATATATA
2422804 ATAA-ATTTTAATATATATA
1 ATAATATTTTAATATATATA
2422823 ATAATATTT
1 ATAATATTT
2422832 AAAATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
17 6 0.16
18 14 0.38
19 5 0.14
20 11 0.30
21 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAATATTTTAATATATATA
Found at i:2423769 original size:11 final size:11
Alignment explanation
Indices: 2423753--2423806 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
2423743 AATATATTCA
2423753 TATATTTTTAT
1 TATATTTTTAT
**
2423764 TATATTCATAT
1 TATATTTTTAT
*
2423775 TATTTTTTTAT
1 TATATTTTTAT
*
2423786 CATATTTTTATAT
1 TATA-TTTT-TAT
2423799 TATATTTT
1 TATATTTT
2423807 AAGTAATTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
11 19 0.58
12 8 0.24
13 6 0.18
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:2423785 original size:22 final size:19
Alignment explanation
Indices: 2423737--2423804 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
2423727 TGTTATATAG
*
2423737 ATTTTTAATATATTCATAT
1 ATTTTTATTATATTCATAT
2423756 ATTTTTATTATATTCATAT
1 ATTTTTATTATATTCATAT
2423775 -TATTTT-TT-TA-TCATAT
1 AT-TTTTATTATATTCATAT
2423791 -TTTTATATTATATT
1 ATTTT-TATTATATT
2423805 TTAAGTAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
15 3 0.07
16 8 0.19
17 4 0.09
18 5 0.12
19 23 0.53
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTATTATATTCATAT
Found at i:2423969 original size:25 final size:24
Alignment explanation
Indices: 2423941--2423992 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
2423931 AATTTATATA
2423941 ATATAAAT-TATTAATTTATTAAAAT
1 ATATAAATATA-TAATTT-TTAAAAT
*
2423966 ATATAAATATATAATTTTTTAAAT
1 ATATAAATATATAATTTTTAAAAT
2423990 ATA
1 ATA
2423993 ATTATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 14 0.56
26 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATAAATATATAATTTTTAAAAT
Found at i:2425500 original size:21 final size:21
Alignment explanation
Indices: 2425458--2425503 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2425448 TGAATTGTTA
2425458 TTTATTAATTAAAAATTAATT
1 TTTATTAATTAAAAATTAATT
2425479 TTTAGTTAATATAAAAA-T-ATT
1 TTTA-TTAAT-TAAAAATTAATT
2425500 TTTA
1 TTTA
2425504 ATATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.48
22 6 0.26
23 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTATTAATTAAAAATTAATT
Found at i:2425749 original size:21 final size:21
Alignment explanation
Indices: 2425710--2425768 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
2425700 ATATTTTTAA
2425710 AATT-ATAATAA-ATAAAAAAT
1 AATTAATAATAATA-AAAAAAT
2425730 AATTAATAATAATAAAAAAAT
1 AATTAATAATAATAAAAAAAT
* *
2425751 ATTTAAATATTAATAAAA
1 AATT-AATAATAATAAAA
2425769 TTTTGACGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.12
21 17 0.50
22 13 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTAATAATAATAAAAAAAT
Found at i:2425961 original size:15 final size:15
Alignment explanation
Indices: 2425943--2425992 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
2425933 TATCATAATT
2425943 TTAAAAATATAAAAA
1 TTAAAAATATAAAAA
* *
2425958 TT-AAAATATTAAAT
1 TTAAAAATATAAAAA
*
2425972 TTAATAATATAAAAA
1 TTAAAAATATAAAAA
*
2425987 CTAAAA
1 TTAAAA
2425993 TATTTTATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAAAATATAAAAA
Found at i:2425963 original size:14 final size:14
Alignment explanation
Indices: 2425946--2425995 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
2425936 CATAATTTTA
2425946 AAAATATAAAAATT
1 AAAATATAAAAATT
* *
2425960 AAAATATTAAATTT
1 AAAATATAAAAATT
*
2425974 AATAATATAAAAACT
1 AA-AATATAAAAATT
2425989 AAAATAT
1 AAAATAT
2425996 TTTATTTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:2438154 original size:3 final size:3
Alignment explanation
Indices: 2438141--2438174 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
2438131 GATGGATTCA
2438141 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2438175 TTGGAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2439501 original size:21 final size:22
Alignment explanation
Indices: 2439475--2439515 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2439465 TTTGAAGCTC
2439475 TTAAAAATTAAAT-TTTTATTA
1 TTAAAAATTAAATATTTTATTA
* *
2439496 TTAAAATTTTAATATTTTAT
1 TTAAAAATTAAATATTTTAT
2439516 CTATAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAAAAATTAAATATTTTATTA
Found at i:2439955 original size:15 final size:15
Alignment explanation
Indices: 2439912--2439959 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
2439902 TAATGTAAAT
*
2439912 TAAATTTTTA-TATA
1 TAAAATTTTATTATA
2439926 TTAATAATTTATATTATA
1 -TAA-AATTT-TATTATA
2439944 TAAAATTTTATTATA
1 TAAAATTTTATTATA
2439959 T
1 T
2439960 TTAAATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 11 0.38
16 9 0.31
17 5 0.17
18 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAAAATTTTATTATA
Found at i:2439964 original size:17 final size:16
Alignment explanation
Indices: 2439910--2439966 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
2439900 TATAATGTAA
*
2439910 ATTAAATTTTTA-TAT
1 ATTAAAATTTTATTAT
2439925 ATTAATAATTTATATTAT
1 ATTAA-AATTT-TATTAT
2439943 A-TAAAATTTTATTAT
1 ATTAAAATTTTATTAT
*
2439958 ATTTAAATT
1 ATTAAAATT
2439967 ATAATAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
15 12 0.33
16 15 0.42
17 5 0.14
18 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTAAAATTTTATTAT
Found at i:2439967 original size:26 final size:25
Alignment explanation
Indices: 2439923--2439994 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
2439913 AAATTTTTAT
* * *
2439923 ATATTAATAATTTATATTATATAAA
1 ATATTATTTATTTAAATTATATAAA
* *
2439948 ATTTTATTATATTTAAATTATA-ATA
1 ATATTATT-TATTTAAATTATATAAA
* *
2439973 ATATTATTTTTTTACATTATAT
1 ATATTATTTATTTAAATTATAT
2439995 CATGTTTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 11 0.30
25 15 0.41
26 11 0.30
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (25 bp):
ATATTATTTATTTAAATTATATAAA
Found at i:2439986 original size:24 final size:24
Alignment explanation
Indices: 2439942--2439993 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2439932 ATTTATATTA
*
2439942 TATAAAATTTTATTATATTTAAAT
1 TATAAAATATTATTATATTTAAAT
* *
2439966 TATAATAATATTATT-TTTTTACAT
1 TATAA-AATATTATTATATTTAAAT
2439990 TATA
1 TATA
2439994 TCATGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TATAAAATATTATTATATTTAAAT
Found at i:2452302 original size:90 final size:89
Alignment explanation
Indices: 2452189--2452365 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
2452179 TAATTAAATC
* *
2452189 CAAGTAAACTATAAAAAAAATTTTAAAAATAAATCATTTTATTCTAAAGTTTTTAATTATCTATT
1 CAAGTAAAATATAAAAAAAATTTTAAAAATAAATCATTTTATTCCAAAGTTTTTAATTATCTATT
2452254 TTAATAAATTTTAATTAAATCTTTT
66 TTAATAAATTTTAATT-AATCTTTT
* ** *
2452279 CAAGTAAAATATACAAAGCATTTTAAAAATAAATCATTTTATTCCAAAGTTTTTAATTATCTGTT
1 CAAGTAAAATATAAAAAAAATTTTAAAAATAAATCATTTTATTCCAAAGTTTTTAATTATCTATT
2452344 TTAATAAATTTTAATTAATCTT
66 TTAATAAATTTTAATTAATCTT
2452366 AAAAAAAGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 6 0.07
90 75 0.93
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (89 bp):
CAAGTAAAATATAAAAAAAATTTTAAAAATAAATCATTTTATTCCAAAGTTTTTAATTATCTATT
TTAATAAATTTTAATTAATCTTTT
Found at i:2452482 original size:24 final size:23
Alignment explanation
Indices: 2452455--2452515 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
2452445 TTATCCAAAC
*
2452455 AAAAAATTTTAAATTTATGAATTT
1 AAAAAATTTTAAATTTA-AAATTT
**
2452479 AAAAAATGATAAATTTAAAATTT
1 AAAAAATTTTAAATTTAAAATTT
*
2452502 -TAAAA-TTTAAATTT
1 AAAAAATTTTAAATTT
2452516 TCAAATGCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 7 0.23
22 4 0.13
23 5 0.16
24 15 0.48
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (23 bp):
AAAAAATTTTAAATTTAAAATTT
Found at i:2452768 original size:82 final size:82
Alignment explanation
Indices: 2452674--2452828 Score: 292
Period size: 82 Copynumber: 1.9 Consensus size: 82
2452664 TTACTAATAA
2452674 ATATAGATATGCATGTAATTTAGAAATGCTTGTACATGCTATAATACATACTTTATTAAAAAACT
1 ATATAGATATGCATGTAATTTAGAAATGCTTGTACATGCTATAATACATACTTTATTAAAAAACT
2452739 TGTAAATATATATATTT
66 TGTAAATATATATATTT
* *
2452756 ATATAGGTATGCATGTAATTTAGAAATGCTTGTACATGCTATAATATATACTTTATTAAAAAACT
1 ATATAGATATGCATGTAATTTAGAAATGCTTGTACATGCTATAATACATACTTTATTAAAAAACT
2452821 TGTAAATA
66 TGTAAATA
2452829 AGTTTTATAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.39
Consensus pattern (82 bp):
ATATAGATATGCATGTAATTTAGAAATGCTTGTACATGCTATAATACATACTTTATTAAAAAACT
TGTAAATATATATATTT
Found at i:2453205 original size:4 final size:4
Alignment explanation
Indices: 2453196--2453224 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2453186 TGTGGACATG
2453196 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
2453225 GGATTACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:2453476 original size:24 final size:24
Alignment explanation
Indices: 2453448--2453498 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2453438 AAATTTAACT
*
2453448 TATTTAATTATTAATAT-ATTTATA
1 TATTTAATT-GTAATATCATTTATA
* *
2453472 TATTTTATTGTATTATCATTTATA
1 TATTTAATTGTAATATCATTTATA
2453496 TAT
1 TAT
2453499 ATATAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TATTTAATTGTAATATCATTTATA
Found at i:2453480 original size:21 final size:21
Alignment explanation
Indices: 2453455--2453583 Score: 56
Period size: 23 Copynumber: 6.1 Consensus size: 21
2453445 ACTTATTTAA
2453455 TTATTAATATATTTATATATT
1 TTATTAATATATTTATATATT
*
2453476 TTATTGTATTATCATTTATATA-T
1 TTA-T-TAATAT-ATTTATATATT
* *
2453499 ATA-TAA-AT-TTTAT-TATA
1 TTATTAATATATTTATATATT
* * * *
2453516 TTAATAATTTATTTTTTTTAAATT
1 TTATTAA--TA-TATTTATATATT
*
2453540 TTAAT-ATATATTTATATTATT
1 TTATTAATATATTTATA-TATT
*
2453561 TTATATTATATATTTA-ATATT
1 TTAT-TAATATATTTATATATT
2453582 TT
1 TT
2453584 TTATCGATCA
Statistics
Matches: 82, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
16 2 0.02
17 7 0.09
18 3 0.04
19 2 0.02
20 8 0.10
21 18 0.22
22 4 0.05
23 22 0.27
24 16 0.20
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (21 bp):
TTATTAATATATTTATATATT
Found at i:2453509 original size:32 final size:33
Alignment explanation
Indices: 2453437--2453527 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 33
2453427 GTTTTAAATT
* * * *
2453437 TAAATTTAACTTAT-TTAATTATTAATATATTTA
1 TAAATTTTA-TTATATTAATAATTTATATATATA
* * *
2453470 TATATTTTATTGTATT-ATCATTTATATATATA
1 TAAATTTTATTATATTAATAATTTATATATATA
2453502 TAAATTTTATTATATTAATAATTTAT
1 TAAATTTTATTATATTAATAATTTAT
2453528 TTTTTTTAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
32 30 0.64
33 17 0.36
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (33 bp):
TAAATTTTATTATATTAATAATTTATATATATA
Found at i:2453570 original size:23 final size:23
Alignment explanation
Indices: 2453537--2453587 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2453527 TTTTTTTTAA
2453537 ATTTTA-ATATATATTT-ATATT
1 ATTTTATATATATATTTAATATT
2453558 ATTTTATATTATATATTTAATATT
1 ATTTTATA-TATATATTTAATATT
2453582 -TTTTAT
1 ATTTTAT
2453588 CGATCATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.22
22 1 0.04
23 15 0.56
24 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTATATATATATTTAATATT
Found at i:2453580 original size:7 final size:8
Alignment explanation
Indices: 2453456--2453582 Score: 60
Period size: 8 Copynumber: 16.6 Consensus size: 8
2453446 CTTATTTAAT
*
2453456 TATTAATA
1 TATTTATA
2453464 TATTTATA
1 TATTTATA
2453472 TATTT-TA
1 TATTTATA
*
2453479 T-TGTATTA
1 TATTTA-TA
2453487 TCATTTATA
1 T-ATTTATA
*
2453496 TATATATA
1 TATTTATA
*
2453504 AATTTTATTA
1 TA-TTTA-TA
*
2453514 TATTAATA
1 TATTTATA
2453522 -ATTTAT-
1 TATTTATA
* *
2453528 TTTTTTTA
1 TATTTATA
*
2453536 AATTT-TA
1 TATTTATA
2453543 -A--TATA
1 TATTTATA
2453548 TATTTATA
1 TATTTATA
2453556 TTATTT-TA
1 -TATTTATA
2453564 TA-TTATA
1 TATTTATA
2453571 TATTTA-A
1 TATTTATA
2453578 TATTT
1 TATTT
2453583 TTTATCGATC
Statistics
Matches: 91, Mismatches: 13, Indels: 31
0.67 0.10 0.23
Matches are distributed among these distances:
4 1 0.01
5 2 0.02
6 6 0.07
7 26 0.29
8 36 0.40
9 14 0.15
10 6 0.07
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (8 bp):
TATTTATA
Found at i:2453920 original size:17 final size:18
Alignment explanation
Indices: 2453900--2453933 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2453890 TTTATTTTAA
2453900 TAATATAAAA-TTAATAT
1 TAATATAAAATTTAATAT
2453917 TAATATAAAATTTAATA
1 TAATATAAAATTTAATA
2453934 ATTTAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATATAAAATTTAATAT
Found at i:2455004 original size:2 final size:2
Alignment explanation
Indices: 2454997--2455046 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
2454987 CATCTTTAAA
* *
2454997 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2455039 AT AT AT AT
1 AT AT AT AT
2455047 CAATTTATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2455913 original size:29 final size:27
Alignment explanation
Indices: 2455880--2455946 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
2455870 TGATAATTAA
*
2455880 TATATTTATATTATATTT-ATATATTT
1 TATATTTATATTATATTTAAGATATTT
* *
2455906 TATTATATCATGATTGTATTTAAGATATTT
1 TA-TAT-TTAT-ATTATATTTAAGATATTT
2455936 TATATTTATAT
1 TATATTTATAT
2455947 AAATGTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
26 2 0.06
27 5 0.15
28 6 0.18
29 11 0.33
30 9 0.27
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (27 bp):
TATATTTATATTATATTTAAGATATTT
Found at i:2461796 original size:13 final size:13
Alignment explanation
Indices: 2461778--2461806 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2461768 ACCTCTAGTG
2461778 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
2461791 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
2461804 AAA
1 AAA
2461807 CATCAACACT
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:2462666 original size:27 final size:27
Alignment explanation
Indices: 2462636--2462713 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
2462626 TATTTTATGT
2462636 TATATAA-ATATAATGTATA-TATTTTAA
1 TATATAATAT-TAAT-TATATTATTTTAA
*
2462663 TATATTATATTAATTATATTATTTT--
1 TATATAATATTAATTATATTATTTTAA
* *
2462688 TATAT-TTATTAAATATATTATATTTA
1 TATATAATATTAATTATATTAT-TTTA
2462714 TATTTTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
24 14 0.32
25 8 0.18
26 4 0.09
27 16 0.36
28 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (27 bp):
TATATAATATTAATTATATTATTTTAA
Found at i:2462680 original size:24 final size:24
Alignment explanation
Indices: 2462652--2462708 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2462642 AATATAATGT
2462652 ATATATT-TTAATATATTATATTAA
1 ATATATTATTAATATATT-TATTAA
* **
2462676 TTATATTATTTTTATATTTATTAA
1 ATATATTATTAATATATTTATTAA
2462700 ATATATTAT
1 ATATATTAT
2462709 ATTTATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATATTATTAATATATTTATTAA
Found at i:2462713 original size:24 final size:24
Alignment explanation
Indices: 2462663--2462718 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
2462653 TATATTTTAA
* *
2462663 TATATTATATTAATTATATTATTTT
1 TATATT-TATTAAATATATTATATT
2462688 TATATTTATTAAATATATTATATT
1 TATATTTATTAAATATATTATATT
2462712 TATATTT
1 TATATTT
2462719 TATTTTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 23 0.79
25 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATATTTATTAAATATATTATATT
Found at i:2462744 original size:37 final size:36
Alignment explanation
Indices: 2462653--2462754 Score: 104
Period size: 37 Copynumber: 2.8 Consensus size: 36
2462643 ATATAATGTA
* *
2462653 TATAT-TTTAATA-TATTATATTAATTATATTATTTT
1 TATATGTTTAATATTATTATATTTA-TATTTTATTTT
*
2462688 TATATTTATTAA-ATATATTATATTTATATTTTATTTT
1 TATATGT-TTAATAT-TATTATATTTATATTTTATTTT
*
2462725 TATCATGTTTAATATTATTAAATTTA-ATTT
1 TAT-ATGTTTAATATTATTATATTTATATTT
2462755 AATGAAACAG
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
35 5 0.09
36 6 0.11
37 31 0.54
38 15 0.26
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (36 bp):
TATATGTTTAATATTATTATATTTATATTTTATTTT
Found at i:2463297 original size:2 final size:2
Alignment explanation
Indices: 2463292--2463323 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2463282 ATGATTTGAA
2463292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2463324 GAAACCCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2464232 original size:2 final size:2
Alignment explanation
Indices: 2464225--2464259 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2464215 CTGAAAACTA
2464225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2464260 GATGGAATAG
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2464505 original size:42 final size:41
Alignment explanation
Indices: 2464415--2464505 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 41
2464405 TAAATACGAT
*
2464415 TTGATATATTTAAATTTGATATTATATTTATATTTAAAATA
1 TTGATATATTTAAATTTGATATTACATTTATATTTAAAATA
* * *
2464456 TTAATATATTTAATAATTT-ATATTACGTTTATATTT-ATATAA
1 TTGATATATTT-A-AATTTGATATTACATTTATATTTAAAAT-A
2464498 TTGATATA
1 TTGATATA
2464506 AAAAAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
41 13 0.31
42 24 0.57
43 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (41 bp):
TTGATATATTTAAATTTGATATTACATTTATATTTAAAATA
Found at i:2464565 original size:17 final size:18
Alignment explanation
Indices: 2464543--2464581 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2464533 TATCAAATTT
* *
2464543 AATTA-TAATCAATTAAA
1 AATTATTAAGCAAATAAA
2464560 AATTATTAAGCAAATAAA
1 AATTATTAAGCAAATAAA
2464578 AATT
1 AATT
2464582 TACTAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (18 bp):
AATTATTAAGCAAATAAA
Found at i:2464644 original size:3 final size:3
Alignment explanation
Indices: 2464636--2464675 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2464626 TTTTCTCTAT
2464636 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2464676 GAGATTGAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2466314 original size:16 final size:16
Alignment explanation
Indices: 2466274--2466308 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2466264 AAAACTCGAA
2466274 TTAAAA-AATTTAAAT
1 TTAAAATAATTTAAAT
2466289 TTAAAATAATTT-AAT
1 TTAAAATAATTTAAAT
2466304 TTAAA
1 TTAAA
2466309 CTTAATCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAATAATTTAAAT
Found at i:2466415 original size:18 final size:17
Alignment explanation
Indices: 2466392--2466436 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2466382 TCGATTCGAA
*
2466392 TTAAAAAAAAATTAAAAT
1 TTAAAAAAAAA-TAAAAC
*
2466410 TTAAAATAAAATAAAAC
1 TTAAAAAAAAATAAAAC
2466427 TTAAAAAAAA
1 TTAAAAAAAA
2466437 TATTCTAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
TTAAAAAAAAATAAAAC
Found at i:2467018 original size:13 final size:15
Alignment explanation
Indices: 2466988--2467033 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
2466978 TTAAATTTTA
2466988 AATTTATTAAATAAT
1 AATTTATTAAATAAT
2467003 AATTT-TTAAA-AAT
1 AATTTATTAAATAAT
2467016 AA-TTATATAAACTAAT
1 AATTTAT-TAAA-TAAT
2467032 AA
1 AA
2467034 AGTTAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.07
13 6 0.22
14 9 0.33
15 5 0.19
16 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTATTAAATAAT
Found at i:2468256 original size:12 final size:13
Alignment explanation
Indices: 2468234--2468262 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2468224 AAAGTGATTG
2468234 AAATAAAAAATAA
1 AAATAAAAAATAA
2468247 AAAT-AAAAATAA
1 AAATAAAAAATAA
2468259 AAAT
1 AAAT
2468263 TATTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:2469067 original size:34 final size:34
Alignment explanation
Indices: 2469023--2469089 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
2469013 ATATAATATA
* *
2469023 TATTGAATATATTATTA-TTATTATTTTTATATTT
1 TATTAAATATATT-TTATTTATAATTTTTATATTT
*
2469057 TATTAAATATATTTTATTTATAATTTTTTTATT
1 TATTAAATATATTTTATTTATAATTTTTATATT
2469090 GTAAGTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 3 0.10
34 26 0.90
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (34 bp):
TATTAAATATATTTTATTTATAATTTTTATATTT
Found at i:2472209 original size:42 final size:43
Alignment explanation
Indices: 2472162--2472246 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
2472152 GGTAGGCAAT
*
2472162 CATGCAAGTTTGGGTTTTT-ATTTTTTTCTCCTTCTATGTATA
1 CATGCAAGTTTGGGTTTTTAATTTTTTTCTCCTTCTATATATA
*
2472204 CATGCAAGTTTGGGTTTTTAATTTTTTTCTCTTTCTATATATA
1 CATGCAAGTTTGGGTTTTTAATTTTTTTCTCCTTCTATATATA
2472247 TATATATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 19 0.47
43 21 0.52
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (43 bp):
CATGCAAGTTTGGGTTTTTAATTTTTTTCTCCTTCTATATATA
Found at i:2485962 original size:22 final size:22
Alignment explanation
Indices: 2485934--2485977 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2485924 AAAAATTATT
2485934 TTTATTTTAAT-ATTAATATTTA
1 TTTATTTTAATAATTAA-ATTTA
*
2485956 TTTATTTTTATAATTAAATTTA
1 TTTATTTTAATAATTAAATTTA
2485978 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATTTTAATAATTAAATTTA
Found at i:2494262 original size:31 final size:29
Alignment explanation
Indices: 2494201--2494264 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
2494191 GAGGTGAGAG
* * * *
2494201 GGAAGGAAGAGAAAAAGAGAGATAAGAAA
1 GGAAGGAAGAGAAAAAGAAAAAAAAAAAA
2494230 GGAAGGAAGAGAAAAAAAGAAAAAAAAAAAA
1 GGAAGGAAGAG--AAAAAGAAAAAAAAAAAA
2494261 GGAA
1 GGAA
2494265 AGACGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 11 0.38
31 18 0.62
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.02
Consensus pattern (29 bp):
GGAAGGAAGAGAAAAAGAAAAAAAAAAAA
Found at i:2495483 original size:36 final size:36
Alignment explanation
Indices: 2495443--2495555 Score: 108
Period size: 36 Copynumber: 3.1 Consensus size: 36
2495433 ATTTTATATG
2495443 TATTTATTATCAAATTAAACCAACTAAATGTCAAAT
1 TATTTATTATCAAATTAAACCAACTAAATGTCAAAT
** * * * *
2495479 TATTTCGTA-AATAATTAAA-AAAC-AATTAT-TTATAT
1 TATTTATTATCA-AATTAAACCAACTAA--ATGTCAAAT
2495514 GTATTTATTATCAAATTAAACCAACTAAATGTCAAAT
1 -TATTTATTATCAAATTAAACCAACTAAATGTCAAAT
2495551 TATTT
1 TATTT
2495556 CGTAAATAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
34 2 0.04
35 8 0.14
36 37 0.65
37 8 0.14
38 2 0.04
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (36 bp):
TATTTATTATCAAATTAAACCAACTAAATGTCAAAT
Found at i:2495552 original size:72 final size:73
Alignment explanation
Indices: 2495435--2495580 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 73
2495425 TTATGTTTAT
2495435 TTTATATGTATTTATTATCAAATTAAACCAACTAAATGTCAAATTATTTCGTAAATAATT-AAAA
1 TTTATATGTATTTATTATCAAATTAAACCAACTAAATGTCAAATTATTTCGTAAATAATTAAAAA
2495499 AACAATTA
66 AACAATTA
2495507 TTTATATGTATTTATTATCAAATTAAACCAACTAAATGTCAAATTATTTCGTAAATAATTAAAAA
1 TTTATATGTATTTATTATCAAATTAAACCAACTAAATGTCAAATTATTTCGTAAATAATTAAAAA
2495572 AACAATTA
66 AACAATTA
2495580 T
1 T
2495581 CTTGAGAGTT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 60 0.82
73 13 0.18
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (73 bp):
TTTATATGTATTTATTATCAAATTAAACCAACTAAATGTCAAATTATTTCGTAAATAATTAAAAA
AACAATTA
Found at i:2495567 original size:36 final size:36
Alignment explanation
Indices: 2495455--2495569 Score: 112
Period size: 36 Copynumber: 3.2 Consensus size: 36
2495445 TTTATTATCA
2495455 AATTAAACCAACTAAATGTCAAATTATTTCGTAAAT
1 AATTAAACCAACTAAATGTCAAATTATTTCGTAAAT
* * * ** *
2495491 AATTAAA-AAAC-AATTAT-TTATATGTATTTATTATCA-
1 AATTAAACCAACTAA--ATGTCAAAT-TATTTCGTA-AAT
2495527 AATTAAACCAACTAAATGTCAAATTATTTCGTAAAT
1 AATTAAACCAACTAAATGTCAAATTATTTCGTAAAT
2495563 AATTAAA
1 AATTAAA
2495570 AAAACAATTA
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
34 2 0.03
35 8 0.14
36 39 0.66
37 8 0.14
38 2 0.03
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (36 bp):
AATTAAACCAACTAAATGTCAAATTATTTCGTAAAT
Found at i:2498365 original size:22 final size:20
Alignment explanation
Indices: 2498309--2498366 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 20
2498299 ATATTTTTTT
*
2498309 ATAATTAAATTTAAA-TAAAA
1 ATAATTTAA-TTAAATTAAAA
*
2498329 ATAATTTTATT--ATTAAATA
1 ATAATTTAATTAAATTAAA-A
2498348 ATAATTTAAGTTAAATTAA
1 ATAATTTAA-TTAAATTAA
2498367 CTAAATCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
17 1 0.03
18 4 0.13
19 11 0.37
20 9 0.30
22 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATTTAATTAAATTAAAA
Found at i:2498536 original size:15 final size:16
Alignment explanation
Indices: 2498504--2498539 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
2498494 AGTTTCTAGT
2498504 GAATTTTGTTACCCTTG
1 GAATTTTGTTA-CCTTG
2498521 GAATTTTGTT-CCTTG
1 GAATTTTGTTACCTTG
2498536 GAAT
1 GAAT
2498540 AGATCTTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
17 10 0.53
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.47
Consensus pattern (16 bp):
GAATTTTGTTACCTTG
Found at i:2499233 original size:29 final size:29
Alignment explanation
Indices: 2499205--2499260 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
2499195 AATATTAATA
* * *
2499205 AAAAATAT-ATTTTAATATTATTTTAAAT
1 AAAAATATAAATTTAAAATTAATTTAAAT
*
2499233 AATAATATAAATTTAAAATTAATTTAAA
1 AAAAATATAAATTTAAAATTAATTTAAA
2499261 CTTAATCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAAATATAAATTTAAAATTAATTTAAAT
Found at i:2507371 original size:22 final size:22
Alignment explanation
Indices: 2507306--2507372 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
2507296 AAAGAACAGG
2507306 ATAATATATTAAAAATTACAAAATT
1 ATAA-ATATTAAAAA-TA-AAAATT
* * *
2507331 TTATATCATTAATAA-AAAAATT
1 ATAAAT-ATTAAAAATAAAAATT
2507353 ATAAATATTAAAAATAAAAA
1 ATAAATATTAAAAATAAAAA
2507373 ATATTATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
21 7 0.21
22 15 0.44
23 1 0.03
24 2 0.06
25 9 0.26
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAATATTAAAAATAAAAATT
Found at i:2513065 original size:23 final size:22
Alignment explanation
Indices: 2513039--2513083 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2513029 GATTTAATTT
2513039 ATTAATAATATATAAAATTATAA
1 ATTAATAATATATAAAA-TATAA
* * *
2513062 ATTATTTATATATCAAATATAA
1 ATTAATAATATATAAAATATAA
2513084 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTAATAATATATAAAATATAA
Found at i:2513339 original size:14 final size:15
Alignment explanation
Indices: 2513320--2513353 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2513310 TAATTTTTAA
2513320 TTAAATTT-TATTTT
1 TTAAATTTATATTTT
2513334 TTAAATTTAATATTTT
1 TTAAATTT-ATATTTT
2513350 TTAA
1 TTAA
2513354 TAATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
16 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTAAATTTATATTTT
Found at i:2519882 original size:17 final size:17
Alignment explanation
Indices: 2519856--2519897 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2519846 CACTTTAAAT
2519856 AATAAAATAAATTTT-TA
1 AATAAAAT-AATTTTATA
*
2519873 AATAACATAATTTTATA
1 AATAAAATAATTTTATA
*
2519890 AAAAAAAT
1 AATAAAAT
2519898 TAAACTGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAAAATAATTTTATA
Found at i:2525927 original size:2 final size:2
Alignment explanation
Indices: 2525920--2525955 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2525910 ACCAAACGAG
2525920 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2525956 AAAAAAAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2526743 original size:5 final size:5
Alignment explanation
Indices: 2526724--2526812 Score: 55
Period size: 5 Copynumber: 18.4 Consensus size: 5
2526714 CTCTAAATAC
* * *
2526724 ATAAT ATAAAC ATAAT ATAA- AAAAT AAAAAT ATAAT ATAAT ATAAT ATAA-
1 ATAAT AT-AAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT
* * *
2526774 AT-AT ATAATT ATATT AAAAT -TTAT ATAA- A-AAT ATAAT AT
1 ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
2526813 TTTAAATATA
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
3 3 0.05
4 11 0.17
5 38 0.58
6 13 0.20
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:2526816 original size:20 final size:20
Alignment explanation
Indices: 2526793--2526832 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2526783 TATATTAAAA
* *
2526793 TTTATATAAAAATATAATAT
1 TTTAAATAAAAATAAAATAT
*
2526813 TTTAAATATAAATAAAATAT
1 TTTAAATAAAAATAAAATAT
2526833 ATAAAAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAATAAAAATAAAATAT
Found at i:2526832 original size:11 final size:11
Alignment explanation
Indices: 2526726--2526861 Score: 57
Period size: 11 Copynumber: 11.9 Consensus size: 11
2526716 CTAAATACAT
* *
2526726 AATATAAACAT
1 AATATAAATAA
2526737 AATAT-AA-AA
1 AATATAAATAA
* *
2526746 AATAAAAATAT
1 AATATAAATAA
*
2526757 AATAT-AATAT
1 AATATAAATAA
2526767 AATATAAATATA
1 AATATAAATA-A
*
2526779 TAAT-TATATTAA
1 -AATATA-AATAA
* *
2526791 AATTTATATAAA
1 AATATAAAT-AA
*
2526803 AATATAATATTTTA
1 AATATAA-A--TAA
2526817 AATATAAATAA
1 AATATAAATAA
2526828 AATATATAA-AA
1 AATATA-AATAA
2526839 AATATACAAATAA
1 AATAT--AAATAA
*
2526852 GATATAAATA
1 AATATAAATA
2526862 TTAAATTACT
Statistics
Matches: 97, Mismatches: 13, Indels: 30
0.69 0.09 0.21
Matches are distributed among these distances:
9 5 0.05
10 14 0.14
11 38 0.39
12 16 0.16
13 15 0.15
14 8 0.08
15 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (11 bp):
AATATAAATAA
Found at i:2527037 original size:20 final size:20
Alignment explanation
Indices: 2526999--2527044 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2526989 ATATATTAAA
2526999 TATATT-TTATTACATTTAT
1 TATATTATTATTACATTTAT
* *
2527018 TATATTATTTTTATATTTAT
1 TATATTATTATTACATTTAT
*
2527038 TAAATTA
1 TATATTA
2527045 ACATATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATTATTATTACATTTAT
Found at i:2527727 original size:21 final size:19
Alignment explanation
Indices: 2527703--2527749 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
2527693 TATAAATATT
2527703 AATTTAATTAATATTATTTAA
1 AATTTAATTAAT-TT-TTTAA
2527724 AATTAATAATTAATTTTTTAA
1 AATT--TAATTAATTTTTTAA
2527745 AATTT
1 AATTT
2527750 TACAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 1 0.04
21 13 0.54
22 2 0.08
23 8 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTTAATTAATTTTTTAA
Found at i:2527896 original size:2 final size:2
Alignment explanation
Indices: 2527889--2527921 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2527879 GGATTTCATG
2527889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2527922 ATTTTTCCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2528626 original size:17 final size:15
Alignment explanation
Indices: 2528604--2528637 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
2528594 TTGTTAAGTT
2528604 TAAATTGAAATATTAAA
1 TAAATT-AAA-ATTAAA
2528621 TAAATTAAAATTAAA
1 TAAATTAAAATTAAA
2528636 TA
1 TA
2528638 TTTTAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
TAAATTAAAATTAAA
Found at i:2528735 original size:25 final size:25
Alignment explanation
Indices: 2528707--2528778 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
2528697 AAAATCTTAC
2528707 TTTATATAAATAATTAAATTTAAAA
1 TTTATATAAATAATTAAATTTAAAA
* * ***
2528732 TTTA-ATAATAAAATTAAGTTTATTT
1 TTTATATAA-ATAATTAAATTTAAAA
*
2528757 TTTAT-TAAATAAATAAATTTAA
1 TTTATATAAATAATTAAATTTAA
2528779 TCAAATCTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
24 14 0.39
25 22 0.61
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (25 bp):
TTTATATAAATAATTAAATTTAAAA
Found at i:2528888 original size:17 final size:17
Alignment explanation
Indices: 2528855--2528890 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2528845 TAAAATTTAA
*
2528855 TTAAATTAAATTAAATT
1 TTAAATTAAACTAAATT
*
2528872 TTAAATTAAACTCAATT
1 TTAAATTAAACTAAATT
2528889 TT
1 TT
2528891 TTTTTCTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATTAAACTAAATT
Found at i:2530705 original size:14 final size:13
Alignment explanation
Indices: 2530688--2530734 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2530678 TATTTATAAA
2530688 AATATATTAATATT
1 AATAT-TTAATATT
* *
2530702 AATATTT-TTTTT
1 AATATTTAATATT
2530714 AATATTTAATAATT
1 AATATTTAAT-ATT
2530728 AATATTT
1 AATATTT
2530735 TTTAAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 10 0.37
13 3 0.11
14 14 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATATTTAATATT
Found at i:2530707 original size:26 final size:26
Alignment explanation
Indices: 2530678--2530734 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
2530668 TTTTTAAATT
2530678 TATTTATAAAAATATATTAAT-ATTAA
1 TATTTATAAAAATAT-TTAATAATTAA
* ***
2530704 TATTTTTTTTAATATTTAATAATTAA
1 TATTTATAAAAATATTTAATAATTAA
2530730 TATTT
1 TATTT
2530735 TTTAAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTTATAAAAATATTTAATAATTAA
Found at i:2530735 original size:25 final size:26
Alignment explanation
Indices: 2530687--2530742 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
2530677 TTATTTATAA
2530687 AAATATATTAATATTAATATTTTTTT
1 AAATATATTAATATTAATATTTTTTT
*
2530713 TAATAT-TTAATAATTAATA-TTTTTT
1 AAATATATTAAT-ATTAATATTTTTTT
2530738 AAATA
1 AAATA
2530743 ATAAAATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AAATATATTAATATTAATATTTTTTT
Found at i:2530735 original size:26 final size:26
Alignment explanation
Indices: 2530688--2530737 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
2530678 TATTTATAAA
2530688 AATATATTAATATTAATATTTTTTTT
1 AATATATTAATATTAATATTTTTTTT
2530714 AATAT-TTAATAATTAATATTTTTT
1 AATATATTAAT-ATTAATATTTTTT
2530738 AAATAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
AATATATTAATATTAATATTTTTTTT
Found at i:2530744 original size:14 final size:14
Alignment explanation
Indices: 2530699--2530745 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
2530689 ATATATTAAT
2530699 ATTAATATTTTTT-
1 ATTAATATTTTTTA
**
2530712 -TTAATATTTAATA
1 ATTAATATTTTTTA
2530725 ATTAATATTTTTTA
1 ATTAATATTTTTTA
*
2530739 AATAATA
1 ATTAATA
2530746 AAATGAGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
12 10 0.37
14 17 0.63
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTAATATTTTTTA
Found at i:2530744 original size:28 final size:28
Alignment explanation
Indices: 2530684--2530745 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 28
2530674 AATTTATTTA
2530684 TAAA-AATATATTAATATTAATATTTTT
1 TAAATAATATATTAATATTAATATTTTT
*
2530711 T--TTAATAT-TTAATAATTAATATTTTT
1 TAAATAATATATTAAT-ATTAATATTTTT
2530737 TAAATAATA
1 TAAATAATA
2530746 AAATGAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
25 5 0.17
26 18 0.62
27 1 0.03
28 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TAAATAATATATTAATATTAATATTTTT
Found at i:2531473 original size:11 final size:11
Alignment explanation
Indices: 2531457--2531488 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2531447 AATTTGTATG
2531457 ATATATATATA
1 ATATATATATA
2531468 ATATATATAT-
1 ATATATATATA
2531478 ATAT-TATATA
1 ATATATATATA
2531488 A
1 A
2531489 ACTAGATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.25
10 5 0.25
11 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATATATATA
Found at i:2531475 original size:13 final size:13
Alignment explanation
Indices: 2531457--2531487 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2531447 AATTTGTATG
2531457 ATATATATATAAT
1 ATATATATATAAT
*
2531470 ATATATATATATT
1 ATATATATATAAT
2531483 ATATA
1 ATATA
2531488 AACTAGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATAAT
Found at i:2532249 original size:2 final size:2
Alignment explanation
Indices: 2532242--2532268 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2532232 GGATTAAAAT
2532242 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2532269 TGCCTAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2533693 original size:3 final size:3
Alignment explanation
Indices: 2533687--2533717 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2533677 TTAAATGTTG
2533687 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2533718 CCCCTTCAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2534089 original size:21 final size:22
Alignment explanation
Indices: 2534039--2534089 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
2534029 TGAATAATTT
* *
2534039 TAAATTTTTTATATTTTTGTTA
1 TAAAATTTTTAAATTTTTGTTA
2534061 -AAAA-TTTTAAATTTTT-TTA
1 TAAAATTTTTAAATTTTTGTTA
2534080 TAAAATTTTT
1 TAAAATTTTT
2534090 GCTATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 15 0.60
21 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TAAAATTTTTAAATTTTTGTTA
Found at i:2534325 original size:2 final size:2
Alignment explanation
Indices: 2534318--2534348 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2534308 CAAATAAGAA
2534318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2534349 ACTTAGCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2534630 original size:2 final size:2
Alignment explanation
Indices: 2534617--2534689 Score: 55
Period size: 2 Copynumber: 38.0 Consensus size: 2
2534607 TTAATTTTAA
* * * * *
2534617 AT AT AA AT AT AT AT AT AT AT A- AT AT AT AT GT AT CT -T GT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2534657 -T AT AT AT -T AA AT AT AT CAT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
2534690 TGCATTCAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
1 4 0.07
2 52 0.90
3 2 0.03
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2537063 original size:2 final size:2
Alignment explanation
Indices: 2537056--2537106 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2537046 ATCATTGCAC
2537056 AG AG 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 AG AG
2537098 AG AG AG AG A
1 AG AG AG AG A
2537107 AGATTCAGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2544387 original size:86 final size:86
Alignment explanation
Indices: 2544265--2544427 Score: 229
Period size: 86 Copynumber: 1.9 Consensus size: 86
2544255 ACCAGACGGT
* * *
2544265 TCTGAAATCTTGTCATGTAATGCAGATGGCAAAGCCAAACATCACGCGATCTCAATCC-GACTTG
1 TCTGAAATCTTCTCATGTAACGCAGATGGCAAAGCCAAACATCACACGATCTCAA-CCTGACTTG
2544329 AAGGAAAAATGTGCCAAACCAA
65 AAGGAAAAATGTGCCAAACCAA
* * ** *
2544351 TCTGAAATCTTCTCATTTAACGCAGATGGCAAAGCCAAACGTTGCACGATCTCAACCTGGCTTGA
1 TCTGAAATCTTCTCATGTAACGCAGATGGCAAAGCCAAACATCACACGATCTCAACCTGACTTGA
*
2544416 AGGAAACATGTG
66 AGGAAAAATGTG
2544428 AGATTGAATT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
85 2 0.03
86 65 0.97
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (86 bp):
TCTGAAATCTTCTCATGTAACGCAGATGGCAAAGCCAAACATCACACGATCTCAACCTGACTTGA
AGGAAAAATGTGCCAAACCAA
Found at i:2545138 original size:30 final size:28
Alignment explanation
Indices: 2545103--2545193 Score: 75
Period size: 30 Copynumber: 3.3 Consensus size: 28
2545093 TATATAAATA
2545103 TAAAATATTTTAAAAATGATCATTATACGG
1 TAAAATATTTTAAAAAT-AT-ATTATACGG
* * * *
2545133 TAAAATA-TATGAATATATA-AATA---
1 TAAAATATTTTAAAAATATATTATACGG
2545156 TAAAATATTTTAAAAATAATTATTATACGG
1 TAAAATATTTTAAAAAT-A-TATTATACGG
2545186 TAAAATAT
1 TAAAATAT
2545194 ATGAATATGA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
23 7 0.15
24 6 0.13
25 1 0.02
26 5 0.11
27 4 0.09
28 2 0.04
29 6 0.13
30 15 0.33
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (28 bp):
TAAAATATTTTAAAAATATATTATACGG
Found at i:2545155 original size:53 final size:53
Alignment explanation
Indices: 2545093--2545201 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
2545083 TATTAAAATT
*
2545093 TATATAAATATAAAATATTTTAAAAATGATCATTATACGGTAAAATATATGAA
1 TATATAAATATAAAATATTTTAAAAATAATCATTATACGGTAAAATATATGAA
*
2545146 TATATAAATATAAAATATTTTAAAAATAATTATTATACGGTAAAATATATGAA
1 TATATAAATATAAAATATTTTAAAAATAATCATTATACGGTAAAATATATGAA
2545199 TAT
1 TAT
2545202 GATATGATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (53 bp):
TATATAAATATAAAATATTTTAAAAATAATCATTATACGGTAAAATATATGAA
Found at i:2547022 original size:2 final size:2
Alignment explanation
Indices: 2547015--2547041 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2547005 TTTTATTATC
2547015 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2547042 TACTTAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2552036 original size:27 final size:28
Alignment explanation
Indices: 2552000--2552073 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 28
2551990 TTAATGTTTG
2552000 ATATTATAAATATATTTAATTTGTT-TA-T
1 ATATT-TAAATATATTTAATTT-TTATATT
*
2552028 ATATTTAAA-A-AATTATATTTTTATATT
1 ATATTTAAATATATTTA-ATTTTTATATT
*
2552055 ATATTTAAATATATATAAT
1 ATATTTAAATATATTTAAT
2552074 ACGTAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
25 6 0.16
26 7 0.18
27 14 0.37
28 8 0.21
29 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
ATATTTAAATATATTTAATTTTTATATT
Found at i:2558129 original size:22 final size:22
Alignment explanation
Indices: 2558101--2558149 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2558091 TTATTACATT
*
2558101 ATTTCTTAGATTTTGTACAGAC
1 ATTTCTTAGATTATGTACAGAC
2558123 ATTTCTTAGATTATGTACAGAC
1 ATTTCTTAGATTATGTACAGAC
2558145 ATTTC
1 ATTTC
2558150 ACCTGCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (22 bp):
ATTTCTTAGATTATGTACAGAC
Found at i:2561929 original size:2 final size:2
Alignment explanation
Indices: 2561922--2561958 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2561912 TTGATGTACC
2561922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2561959 TGGAGTAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2565689 original size:28 final size:27
Alignment explanation
Indices: 2565604--2565689 Score: 68
Period size: 28 Copynumber: 3.2 Consensus size: 27
2565594 TTTTAATGTA
* **
2565604 TATATATATATATAAAAGAAA--GATT
1 TATATATTTATATAAATTAAATTGATT
*
2565629 TATATATTTATATAAATTAAATTAATT
1 TATATATTTATATAAATTAAATTGATT
* * **
2565656 TAATATATTTTTATAATTTTTATATGATT
1 T-ATATATTTATATAAATTAAAT-TGATT
2565685 TATAT
1 TATAT
2565690 TTATTTAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
25 18 0.38
27 4 0.08
28 21 0.44
29 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (27 bp):
TATATATTTATATAAATTAAATTGATT
Found at i:2566235 original size:16 final size:16
Alignment explanation
Indices: 2566210--2566241 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2566200 ATTAAAAAAA
*
2566210 TTAAAGATATTTTTAT
1 TTAAAAATATTTTTAT
2566226 TTAAAAATATTTTTAT
1 TTAAAAATATTTTTAT
2566242 AATCTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTAAAAATATTTTTAT
Found at i:2566698 original size:17 final size:16
Alignment explanation
Indices: 2566647--2566698 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
2566637 TGTATGTACG
*
2566647 TTATAATATATTTAAATT
1 TTATAAT-T-TTTTAATT
2566665 ATTAT-ATTTTTTAATT
1 -TTATAATTTTTTAATT
2566681 TTATAATTTTTTATATT
1 TTATAATTTTTTA-ATT
2566698 T
1 T
2566699 ATGTTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.13
16 15 0.50
17 5 0.17
18 2 0.07
19 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATAATTTTTTAATT
Found at i:2575746 original size:18 final size:18
Alignment explanation
Indices: 2575713--2575747 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2575703 TATGATGAGA
* *
2575713 GGCGGAGGGGGGGAGGGG
1 GGCGGAGGGAGAGAGGGG
2575731 GGCGGAGGGAGAGAGGG
1 GGCGGAGGGAGAGAGGG
2575748 TGATTGGATG
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:0.17, C:0.06, G:0.77, T:0.00
Consensus pattern (18 bp):
GGCGGAGGGAGAGAGGGG
Found at i:2576571 original size:19 final size:19
Alignment explanation
Indices: 2576516--2576572 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
2576506 AAGATTTATA
*
2576516 TAAAAATATATATAATATCT
1 TAAAAATA-ATATAATATCG
*
2576536 TAAATATAATTATAATAT-G
1 TAAAAATAA-TATAATATCG
2576555 TAAAAATAATATGAATAT
1 TAAAAATAATAT-AATAT
2576573 AATATACATG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.09
19 14 0.44
20 15 0.47
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (19 bp):
TAAAAATAATATAATATCG
Found at i:2576653 original size:26 final size:28
Alignment explanation
Indices: 2576616--2576680 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
2576606 ATTAACTAAA
* *
2576616 ATTTAT-TAAAATATT-AAAATTAAACT
1 ATTTATATAAATTATTAAAAATTAAAAT
2576642 ATTTATATAAATTTTATTAAAAATTAAAAT
1 ATTTATATAAA--TTATTAAAAATTAAAAT
2576672 ATTTATATA
1 ATTTATATA
2576681 CTATTTTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 6 0.18
27 4 0.12
29 4 0.12
30 19 0.58
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTATATAAATTATTAAAAATTAAAAT
Found at i:2576667 original size:30 final size:31
Alignment explanation
Indices: 2576627--2576695 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
2576617 TTTATTAAAA
*
2576627 TATT-AAAATTAAACTATTTATATA-AATTT
1 TATTAAAAATTAAAATATTTATATACAATTT
*
2576656 TATTAAAAATTAAAATATTTATATACTATTT
1 TATTAAAAATTAAAATATTTATATACAATTT
*
2576687 TATCAAAAA
1 TATTAAAAA
2576696 ATATTTATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 4 0.11
30 19 0.54
31 12 0.34
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (31 bp):
TATTAAAAATTAAAATATTTATATACAATTT
Found at i:2578136 original size:19 final size:19
Alignment explanation
Indices: 2578114--2578175 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
2578104 AAAATAATAT
2578114 ATTTTTATAAATAAATTTA
1 ATTTTTATAAATAAATTTA
* *
2578133 ATTTTTTTATCA-AAATTT-
1 ATTTTTATA-AATAAATTTA
2578151 ATTTTTA-AAATATAA--TA
1 ATTTTTATAAATA-AATTTA
2578168 ATTTTTAT
1 ATTTTTAT
2578176 TTAAATTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
16 2 0.06
17 9 0.26
18 8 0.24
19 14 0.41
20 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTATAAATAAATTTA
Found at i:2580181 original size:4 final size:4
Alignment explanation
Indices: 2580172--2580196 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2580162 TCAAGCAATC
2580172 CCAT CCAT CCAT CCAT CCAT CCAT C
1 CCAT CCAT CCAT CCAT CCAT CCAT C
2580197 GATCACCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.52, G:0.00, T:0.24
Consensus pattern (4 bp):
CCAT
Found at i:2581015 original size:19 final size:20
Alignment explanation
Indices: 2580978--2581017 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2580968 AATATGAATA
2580978 TCAATATCTATATCTTTTTT
1 TCAATATCTATATCTTTTTT
2580998 TCAATAT-TATAGTCTTTTTT
1 TCAATATCTATA-TCTTTTTT
2581018 ATCTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.60
Consensus pattern (20 bp):
TCAATATCTATATCTTTTTT
Found at i:2581769 original size:14 final size:14
Alignment explanation
Indices: 2581745--2581778 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2581735 TGAAAAATAT
2581745 TATTATAAATTTTAA
1 TATT-TAAATTTTAA
2581760 TATTTAAATTTTAA
1 TATTTAAATTTTAA
2581774 -ATTTA
1 TATTTA
2581779 TTTACTGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 10 0.53
15 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTTAAATTTTAA
Found at i:2584958 original size:13 final size:14
Alignment explanation
Indices: 2584932--2584962 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2584922 TTCAAAAACT
2584932 TTTTAAAAACATAA
1 TTTTAAAAACATAA
2584946 TTTTAAAAA-ATAA
1 TTTTAAAAACATAA
2584959 TTTT
1 TTTT
2584963 TTATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTTAAAAACATAA
Found at i:2585815 original size:20 final size:21
Alignment explanation
Indices: 2585790--2585829 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2585780 GAATATAATT
*
2585790 TAATTTAATAAT-AATTAAAA
1 TAATTTAAAAATAAATTAAAA
2585810 TAATTTAAAAATAAATTAAA
1 TAATTTAAAAATAAATTAAA
2585830 TTTTTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATTTAAAAATAAATTAAAA
Found at i:2587491 original size:11 final size:11
Alignment explanation
Indices: 2587475--2587499 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2587465 CAAGTGTAGT
2587475 AAGTATGATGG
1 AAGTATGATGG
2587486 AAGTATGATGG
1 AAGTATGATGG
2587497 AAG
1 AAG
2587500 GCAAGGTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (11 bp):
AAGTATGATGG
Found at i:2588211 original size:24 final size:24
Alignment explanation
Indices: 2588165--2588224 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 24
2588155 ATTAAATAAA
*
2588165 TTTTA-ATAA-ATTATA--TTATT
1 TTTTATATAATATTATATTTTAAT
2588185 TTTTATATAATATTATATTTTAAT
1 TTTTATATAATATTATATTTTAAT
2588209 TTTT-T-T-ATATTATATT
1 TTTTATATAATATTATATT
2588225 CATATATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 5 0.14
21 14 0.40
22 7 0.20
23 1 0.03
24 8 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTATATAATATTATATTTTAAT
Found at i:2588245 original size:24 final size:23
Alignment explanation
Indices: 2588144--2588245 Score: 70
Period size: 24 Copynumber: 4.5 Consensus size: 23
2588134 TTTAATATAT
* *
2588144 TAATAAT-TTATATTAAATAAATTT
1 TAATAATATTATATT--ATATATTA
* *
2588168 TAATAA-ATTATATTATTTTTTA
1 TAATAATATTATATTATATATTA
*
2588190 T-ATAATATTATATTTTA-ATT-
1 TAATAATATTATATTATATATTA
** *
2588210 TTTTTATATTATATTCATATATTA
1 TAATAATATTATATT-ATATATTA
2588234 TAATAATATTAT
1 TAATAATATTAT
2588246 GTCCAACGCT
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
20 1 0.02
21 17 0.29
22 16 0.27
23 3 0.05
24 22 0.37
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (23 bp):
TAATAATATTATATTATATATTA
Found at i:2593369 original size:2 final size:2
Alignment explanation
Indices: 2593362--2593390 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2593352 CTGGTGTCAG
2593362 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
2593391 AAGTAGTCTT
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:2597267 original size:9 final size:10
Alignment explanation
Indices: 2597246--2597270 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2597236 TTGGATTATC
2597246 AAAATTTTAA
1 AAAATTTTAA
2597256 AAAATTTTAA
1 AAAATTTTAA
2597266 AAAAT
1 AAAAT
2597271 AAATGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:2598933 original size:18 final size:18
Alignment explanation
Indices: 2598910--2598945 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2598900 TTCAGTCCTT
2598910 ATCTATTAATGGTTTTTC
1 ATCTATTAATGGTTTTTC
*
2598928 ATCTATTGATGGTTTTTC
1 ATCTATTAATGGTTTTTC
2598946 TACTCGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (18 bp):
ATCTATTAATGGTTTTTC
Found at i:2616336 original size:20 final size:20
Alignment explanation
Indices: 2616303--2616341 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2616293 ATTTGCCACC
2616303 TTATTTAAAACCATGTTTCCT
1 TTATTTAAAACCAT-TTTCCT
*
2616324 TTATTT-AAGCCATTTTCC
1 TTATTTAAAACCATTTTCC
2616342 AGAAGATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (20 bp):
TTATTTAAAACCATTTTCCT
Found at i:2618383 original size:2 final size:2
Alignment explanation
Indices: 2618378--2618402 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2618368 TACATATATA
2618378 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2618403 CTGTCGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2618589 original size:15 final size:15
Alignment explanation
Indices: 2618569--2618604 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2618559 GAATATTGTA
* *
2618569 TTTAATTTTTTTTTG
1 TTTAATTTATCTTTG
2618584 TTTAATTTATCTTTG
1 TTTAATTTATCTTTG
2618599 TTTAAT
1 TTTAAT
2618605 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (15 bp):
TTTAATTTATCTTTG
Done.