Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold488
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: 2093548
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 1 of 14
Found at i:919 original size:17 final size:17
Alignment explanation
Indices: 897--950 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
887 AAACTTGACC
897 TAATTATATAATAAAAA
1 TAATTATATAATAAAAA
*
914 TAATTATAAAATAATAAA
1 TAATTATATAATAA-AAA
* *
932 -ATATAATATAATATAAA
1 TA-ATTATATAATAAAAA
949 TA
1 TA
951 TAATACGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATTATATAATAAAAA
Found at i:926 original size:11 final size:10
Alignment explanation
Indices: 904--953 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
894 ACCTAATTAT
904 ATAATA-AAA
1 ATAATATAAA
913 ATAATTATAAA
1 ATAA-TATAAA
924 ATAATA-AAA
1 ATAATATAAA
*
933 TATAATATAAT
1 -ATAATATAAA
944 ATAAATATAA
1 AT-AATATAA
954 TACGAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
9 7 0.20
10 12 0.34
11 16 0.46
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAATATAAA
Found at i:929 original size:20 final size:20
Alignment explanation
Indices: 904--966 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
894 ACCTAATTAT
904 ATAATAAAA-ATAATTATAAA
1 ATAATAAAATATAA-TATAAA
*
924 ATAATAAAATATAATATAAT
1 ATAATAAAATATAATATAAA
* *
944 ATAAATATAATACGAATATAAA
1 AT-AATAAAATA-TAATATAAA
966 A
1 A
967 ATATATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.44
21 12 0.33
22 8 0.22
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
ATAATAAAATATAATATAAA
Found at i:934 original size:5 final size:5
Alignment explanation
Indices: 902--955 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
892 TGACCTAATT
* * *
902 ATATA ATA-A AAATA ATTATA AAATA ATAAA ATATA ATATA ATATAA ATATA
1 ATATA ATATA ATATA A-TATA ATATA ATATA ATATA ATATA ATAT-A ATATA
953 ATA
1 ATA
956 CGAATATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 28 0.70
6 9 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
ATATA
Found at i:961 original size:17 final size:16
Alignment explanation
Indices: 902--965 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 16
892 TGACCTAATT
*
902 ATATAATA-AAAATAA
1 ATATAATAGAATATAA
* * *
917 TTATAAAATAATA-AA
1 ATATAATAGAATATAA
*
932 ATATAATATAATATAA
1 ATATAATAGAATATAA
948 ATATAATACGAATATAA
1 ATATAATA-GAATATAA
965 A
1 A
966 AATATATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 19 0.47
16 13 0.32
17 8 0.20
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
ATATAATAGAATATAA
Found at i:1008 original size:8 final size:8
Alignment explanation
Indices: 913--1041 Score: 52
Period size: 8 Copynumber: 15.1 Consensus size: 8
903 TATAATAAAA
*
913 ATAATTAT
1 ATAAATAT
921 A-AAATA-
1 ATAAATAT
927 ATAAA-AT
1 ATAAATAT
934 ATAATATAAT
1 ATAA-AT-AT
944 ATAAATAT
1 ATAAATAT
952 AATACGAATAT
1 -ATA--AATAT
*
963 AAAAATAT
1 ATAAATAT
*
971 ATTAAAATTT
1 A-T-AAATAT
*
981 ATAAA-AC
1 ATAAATAT
988 ATAAATTTAT
1 ATAAA--TAT
998 ATAAATAT
1 ATAAATAT
1006 AT-AATACT
1 ATAAATA-T
*
1014 TTAAATATT
1 ATAAATA-T
*
1023 ATTATAACAT
1 A-TA-AATAT
1033 ATAAATAT
1 ATAAATAT
1041 A
1 A
1042 CATAAATATG
Statistics
Matches: 92, Mismatches: 12, Indels: 34
0.67 0.09 0.25
Matches are distributed among these distances:
6 2 0.02
7 20 0.22
8 25 0.27
9 13 0.14
10 24 0.26
11 8 0.09
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (8 bp):
ATAAATAT
Found at i:4148 original size:14 final size:14
Alignment explanation
Indices: 4129--4157 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4119 TTGAATCGAT
4129 AAAAAAAC-TTAAA
1 AAAAAAACTTTAAA
4142 AAAAAAACTTTAAA
1 AAAAAAACTTTAAA
4156 AA
1 AA
4158 CTGGTTTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAAACTTTAAA
Found at i:4516 original size:32 final size:31
Alignment explanation
Indices: 4424--4518 Score: 100
Period size: 32 Copynumber: 3.0 Consensus size: 31
4414 TGAATTATGC
* * *
4424 ATAATTACTTATAAATTTAATAAAAATAAAAT
1 ATAATTACTCATAAATTTAA-AAATATTAAAT
* * * *
4456 AAAATTATTCATAAATTTGATAAATATTATAT
1 ATAATTACTCATAAATTT-AAAAATATTAAAT
4488 ATAATTACTCATAAATTTAAAAATTATTAAA
1 ATAATTACTCATAAATTTAAAAA-TATTAAA
4519 AAATTTCAGT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
31 4 0.08
32 45 0.90
33 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
ATAATTACTCATAAATTTAAAAATATTAAAT
Found at i:4634 original size:14 final size:15
Alignment explanation
Indices: 4617--4646 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4607 GATATATAAA
4617 ATTTATTTTAT-TTT
1 ATTTATTTTATATTT
4631 ATTTATTTTATATTT
1 ATTTATTTTATATTT
4646 A
1 A
4647 AAAATATTTT
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTATTTTATATTT
Found at i:5820 original size:16 final size:18
Alignment explanation
Indices: 5795--5831 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
5785 TGTATTTATA
5795 TTATGTTCATATTAT-TT
1 TTATGTTCATATTATATT
5812 TTATG-TCATATTATATT
1 TTATGTTCATATTATATT
5829 TTA
1 TTA
5832 ATTATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (18 bp):
TTATGTTCATATTATATT
Found at i:5931 original size:13 final size:14
Alignment explanation
Indices: 5901--5970 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
5891 TTTTTATACA
*
5901 ATTAAATTTTAATT
1 ATTAAATTTTATTT
5915 -TTAAA-TTTATTT
1 ATTAAATTTTATTT
*
5927 ATTAAATATTT-TTA
1 ATTAAAT-TTTATTT
* *
5941 AATAAATTTTATTA
1 ATTAAATTTTATTT
5955 ATTATAATTTTATTT
1 ATTA-AATTTTATTT
5970 A
1 A
5971 ATCAAAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
12 6 0.13
13 13 0.28
14 14 0.30
15 13 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTAAATTTTATTT
Found at i:6894 original size:28 final size:27
Alignment explanation
Indices: 6842--6894 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
6832 AGTTTATATT
**
6842 AATATTTTTATAATTAAATTTAAATAA
1 AATATTTTTATAATTAAATAAAAATAA
*
6869 AATATTTTTATTTATTAAATAAAAAT
1 AATATTTTTA-TAATTAAATAAAAAT
6895 TTTAACCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATATTTTTATAATTAAATAAAAATAA
Found at i:7088 original size:222 final size:222
Alignment explanation
Indices: 6702--7150 Score: 871
Period size: 222 Copynumber: 2.0 Consensus size: 222
6692 GTAACTCTGA
6702 ATTTAAATTAAAAATATTTTTGGATCAAATTGTTTTAAGATAATAATTTTTTATTTATTTAAAGT
1 ATTTAAATTAAAAATATTTTTGGATCAAATTGTTTTAAGATAATAATTTTTTATTTATTTAAAGT
*
6767 TTGATAAATTTAACTCATTATTAAATTTAAAAAATATTTGATTGTTTAAAATATCTTAAAATGTT
66 TTGATAAATTTAACTCATTATTAAATTAAAAAAATATTTGATTGTTTAAAATATCTTAAAATGTT
6832 AGTTTATATTAATATTTTTATAATTAAATTTAAATAAAATATTTTTATTTATTAAATAAAAATTT
131 AGTTTATATTAATATTTTTATAATTAAATTTAAATAAAATATTTTTATTTATTAAATAAAAATTT
*
6897 TAACCAAGTTAAAATAATTCTACTTAT
196 TAACCAAATTAAAATAATTCTACTTAT
6924 ATTTAAATTAAAAATATTTTTGGATCAAATTGTTTTAAGATAATAATTTTTTATTTATTTAAAGT
1 ATTTAAATTAAAAATATTTTTGGATCAAATTGTTTTAAGATAATAATTTTTTATTTATTTAAAGT
6989 TTGATAAATTTAACTCATTATTAAATTAAAAAAATATTTGATTGTTTAAAATATCTTAAAATGTT
66 TTGATAAATTTAACTCATTATTAAATTAAAAAAATATTTGATTGTTTAAAATATCTTAAAATGTT
7054 AGTTTATATTAATATTTTTATAATTAAATTTAAATAAAATATTTTTATTTATTAAATAAAAATTT
131 AGTTTATATTAATATTTTTATAATTAAATTTAAATAAAATATTTTTATTTATTAAATAAAAATTT
*
7119 TAACCAAATTAAAATAATTTTACTTAT
196 TAACCAAATTAAAATAATTCTACTTAT
7146 ATTTA
1 ATTTA
7151 TAAAATCTTA
Statistics
Matches: 224, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
222 224 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (222 bp):
ATTTAAATTAAAAATATTTTTGGATCAAATTGTTTTAAGATAATAATTTTTTATTTATTTAAAGT
TTGATAAATTTAACTCATTATTAAATTAAAAAAATATTTGATTGTTTAAAATATCTTAAAATGTT
AGTTTATATTAATATTTTTATAATTAAATTTAAATAAAATATTTTTATTTATTAAATAAAAATTT
TAACCAAATTAAAATAATTCTACTTAT
Found at i:7116 original size:28 final size:27
Alignment explanation
Indices: 7064--7116 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
7054 AGTTTATATT
**
7064 AATATTTTTATAATTAAATTTAAATAA
1 AATATTTTTATAATTAAATAAAAATAA
*
7091 AATATTTTTATTTATTAAATAAAAAT
1 AATATTTTTA-TAATTAAATAAAAAT
7117 TTTAACCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATATTTTTATAATTAAATAAAAATAA
Found at i:7944 original size:21 final size:21
Alignment explanation
Indices: 7920--7960 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7910 TAAGTCTTGG
7920 TAAA-AAATTTTATTCACCATA
1 TAAATAAA-TTTATTCACCATA
*
7941 TAAATAAATTTATTTACCAT
1 TAAATAAATTTATTCACCAT
7961 TTTAATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATAAATTTATTCACCATA
Found at i:8113 original size:21 final size:21
Alignment explanation
Indices: 8056--8124 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 21
8046 CAAAATTCTT
8056 TAAATTTAAATTA-AAAAAAT-
1 TAAATTT-AATTATAAAAAATA
*
8076 TATTATTTAATTAATAAAAAATA
1 TA-AATTTAATT-ATAAAAAATA
*
8099 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAAAATA
8120 TAAAT
1 TAAAT
8125 AATAATATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.14
21 19 0.45
22 15 0.36
23 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTTAATTATAAAAAATA
Found at i:8127 original size:19 final size:21
Alignment explanation
Indices: 8064--8131 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
8054 TTTAAATTTA
* * *
8064 AATTAA-AAAAATTATTATTT
1 AATTAATAAAAAATATAAATT
8084 AATTAATAAAAAATATAAATTT
1 AATTAATAAAAAATATAAA-TT
*
8106 AATT-ATAAAATATATAAA-T
1 AATTAATAAAAAATATAAATT
8125 AA-TAATA
1 AATTAATA
8132 TAAAGATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
19 6 0.15
20 6 0.15
21 22 0.54
22 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAATAAAAAATATAAATT
Found at i:10846 original size:20 final size:20
Alignment explanation
Indices: 10809--10845 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10799 AAATTTTAAG
*
10809 AAAAATAAAAGATTAAAAGC
1 AAAAATAAAAGATAAAAAGC
10829 AAAAATAAAA-ATAAAAA
1 AAAAATAAAAGATAAAAA
10846 ATAGAGTTTT
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:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (20 bp):
AAAAATAAAAGATAAAAAGC
Found at i:11345 original size:30 final size:30
Alignment explanation
Indices: 11309--11366 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11299 TTTTCTTAAT
*
11309 TACATTTGATTTGGCACATGGCTTTAGGAA
1 TACATTTCATTTGGCACATGGCTTTAGGAA
* *
11339 TACATTTCATTTTGCACATGGTTTTAGG
1 TACATTTCATTTGGCACATGGCTTTAGG
11367 CATTATCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (30 bp):
TACATTTCATTTGGCACATGGCTTTAGGAA
Found at i:11489 original size:12 final size:14
Alignment explanation
Indices: 11468--11545 Score: 60
Period size: 14 Copynumber: 5.8 Consensus size: 14
11458 TTATATACTC
11468 AATA-AATATAA-A
1 AATATAATATAATA
11480 AA-ATAATATAATA
1 AATATAATATAATA
*
11493 AATATAATATATTTA
1 AATATAATATA-ATA
11508 TAATATAAT-TAATA
1 -AATATAATATAATA
**
11522 TAAT-TAATACGATA
1 -AATATAATATAATA
11536 AA-ATAATATA
1 AATATAATATA
11546 TTTAATATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
11 1 0.02
12 9 0.17
13 14 0.26
14 17 0.32
15 4 0.08
16 8 0.15
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (14 bp):
AATATAATATAATA
Found at i:11529 original size:4 final size:5
Alignment explanation
Indices: 11482--11530 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
11472 AATATAAAAA
*
11482 ATAAT ATAAT A-AAT ATAAT ATATTT ATAAT ATAAT -TAAT ATAAT -TAAT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT
11530 A
1 A
11531 CGATAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 12 0.32
5 22 0.58
6 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATAAT
Found at i:11604 original size:16 final size:17
Alignment explanation
Indices: 11583--11622 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
11573 AAAATTTTAA
11583 TATATTTATAATA-ATT
1 TATATTTATAATATATT
*
11599 TATA-TTATATTATATT
1 TATATTTATAATATATT
11615 TATATTTA
1 TATATTTA
11623 CATAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 7 0.33
16 11 0.52
17 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTATAATATATT
Found at i:13409 original size:14 final size:14
Alignment explanation
Indices: 13390--13420 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
13380 GATATATAGA
13390 ACTTGAAAAGCTGG
1 ACTTGAAAAGCTGG
13404 ACTTGAAAAGCTGG
1 ACTTGAAAAGCTGG
13418 ACT
1 ACT
13421 GCTTCAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (14 bp):
ACTTGAAAAGCTGG
Found at i:13561 original size:4 final size:4
Alignment explanation
Indices: 13552--13581 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
13542 TAATAATAAT
13552 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
13582 ATTTAAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:15725 original size:104 final size:104
Alignment explanation
Indices: 15540--15745 Score: 342
Period size: 104 Copynumber: 2.0 Consensus size: 104
15530 TTGGCCTATG
*
15540 CCTCTAACTCTTTAGTTAGTTGTAGAAGCTGCATAGATGTTTATATTAGCGAATCACTAATGTTT
1 CCTCTAACTCTTTAGTTAGTTATAGAAGCTGCATAGATGTTTATATTAGCGAATCACTAATGTTT
15605 ACTATGTCATAATTTGAGAACATTTGTGCTCTCCAATCT
66 ACTATGTCATAATTTGAGAACATTTGTGCTCTCCAATCT
* *
15644 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCATAGATGTTTATATCT-GCGAATCCCTAATGTT
1 CCTCTAACTCTTTAGTTAGTTATAGAAGCTGCATAGATGTTTATAT-TAGCGAATCACTAATGTT
* * *
15708 TACTATGTCATAGTTTGAGAATATTTGTGTTCTCCAAT
65 TACTATGTCATAATTTGAGAACATTTGTGCTCTCCAAT
15746 TTGCTTGTTG
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
104 94 0.99
105 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (104 bp):
CCTCTAACTCTTTAGTTAGTTATAGAAGCTGCATAGATGTTTATATTAGCGAATCACTAATGTTT
ACTATGTCATAATTTGAGAACATTTGTGCTCTCCAATCT
Found at i:15824 original size:223 final size:222
Alignment explanation
Indices: 15431--15842 Score: 630
Period size: 223 Copynumber: 1.9 Consensus size: 222
15421 TGGCCTATGC
* * * * *
15431 CTTTAGTTAGTCATAGAAGCTGCGTAGATGTTTCTATTTGTGGATCACTAATTTTACTATGTCAT
1 CTTTAGTTAGTCATAGAAGCTGCATAGATGTTTATATCTGCGAATCACTAATTTTACTATGTCAT
*
15496 AGTTTGAGAATATTTGTGCTCTCCAATCTGCTATTTGGCCTATGCCTCTAACTCTTTAGTTAGTT
66 AGTTTGAGAATATTTGTGCTCTCCAATCTGCTATTTGGCCTATGCATCTAACTCTTTAGTTAGTT
* *
15561 GTAGAAGCTGCATAGATGTTTATATTAGCGAATCACTAATGTTTACTATGTCATAATTTGAGAAC
131 ATAGAAGCTGCATAGATGTTTATATTAGCAAATCACTAATGTTTACTATGTCATAATTTGAGAAC
15626 ATTTGTGCTCTCCAATCTCCTCTAATT
196 ATTTGTGCTCTCCAATCTCCTCTAATT
* *
15653 CTTTAGTTAGTTATAGAAGCTGCATAGATGTTTATATCTGCGAATCCCTAATGTTTACTATGTCA
1 CTTTAGTTAGTCATAGAAGCTGCATAGATGTTTATATCTGCGAATCACTAAT-TTTACTATGTCA
* *
15718 TAGTTTGAGAATATTTGTGTTCTCCAATTTGCT-TGTTGGCCTATGCATCTAA-TACTTTAGTTA
65 TAGTTTGAGAATATTTGTGCTCTCCAATCTGCTAT-TTGGCCTATGCATCTAACT-CTTTAGTTA
* * * * *
15781 GTTATAGAAGCTGCGTTGATTTTTATATTTGCAAATTACTAATGTTTACTATGTCATAATTT
128 GTTATAGAAGCTGCATAGATGTTTATATTAGCAAATCACTAATGTTTACTATGTCATAATTT
15843 AAAAGGATTT
Statistics
Matches: 170, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
222 47 0.28
223 123 0.72
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (222 bp):
CTTTAGTTAGTCATAGAAGCTGCATAGATGTTTATATCTGCGAATCACTAATTTTACTATGTCAT
AGTTTGAGAATATTTGTGCTCTCCAATCTGCTATTTGGCCTATGCATCTAACTCTTTAGTTAGTT
ATAGAAGCTGCATAGATGTTTATATTAGCAAATCACTAATGTTTACTATGTCATAATTTGAGAAC
ATTTGTGCTCTCCAATCTCCTCTAATT
Found at i:15857 original size:119 final size:119
Alignment explanation
Indices: 15644--16262 Score: 661
Period size: 119 Copynumber: 5.2 Consensus size: 119
15634 TCTCCAATCT
* * *
15644 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCATAGATGTTTATATCTGCGAATCCCTAATGTTT
1 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCATTGATGTTTATATTTGCGAATCACTAATGTTT
* * *
15709 ACTATGTCATAGTTTGAGAATATTTGTGTTCTCCAATTTGCTTGTTGGCCTATG
66 ACTATGTCATAATTTGAGAAGATTTGTGTTCTCCAATCTGCTTGTTGGCCTATG
* * * * * *
15763 CATCTAATACTTTAGTTAGTTATAGAAGCTGCGTTGATTTTTATATTTGCAAATTACTAATGTTT
1 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCATTGATGTTTATATTTGCGAATCACTAATGTTT
* ** *
15828 ACTATGTCATAATTT-AAAAGGATTTGTGTTCTCCCCTCCGTTCTGCTTGTTGGCCTGTG
66 ACTATGTCATAATTTGAGAA-GATTTGTG-T-T---CTCCAATCTGCTTGTTGGCCTATG
* * ** * * *
15887 CCTCTAATTCTTTAGTTAGTTATAGAAGTTGCGTCAATTTTTATAATTGTGAATCACTAATGTTT
1 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCATTGATGTTTATATTTGCGAATCACTAATGTTT
* * **
15952 ACTATATCATAATTTGAAAAGA-TT-TGTTC-CC--TC--C--AAT-GCCTATG
66 ACTATGTCATAATTTGAGAAGATTTGTGTTCTCCAATCTGCTTGTTGGCCTATG
* * * *
15996 CCTCTAATTCTTTAGTTAGTTATATAAGCTGCATGGATGTTTATATTTGTGTGAATCTCTAATGT
1 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCATTGATGTTTATA-TT-TGCGAATCACTAATGT
* * * * *
16061 TTACTATGTCATAATTTTGAGAAGATATCTGCTCTCCAATCTGCTTCTTGGTCTATG
64 TTACTATGTCATAA-TTTGAGAAGATTTGTGTTCTCCAATCTGCTTGTTGGCCTATG
* *
16118 CCTCTAATTCTTTAGTTAGTTATAGAAACT-CTATTGATGTTTCTATTTGCGAATCACTAATGTT
1 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGC-ATTGATGTTTATATTTGCGAATCACTAATGTT
* *
16182 TACTATGTCATAATTTGAGAAGATTTGTG-CCTTCCAATCTGCTTGTTGGTCTATG
65 TACTATGTCATAATTTGAGAAGATTTGTGTTC-TCCAATCTGCTTGTTGGCCTATG
* **
16237 CCTTTAATTCTTTAGACAGTTATAGA
1 CCTCTAATTCTTTAGTTAGTTATAGA
16263 TTTGGTTTTC
Statistics
Matches: 421, Mismatches: 57, Indels: 44
0.81 0.11 0.08
Matches are distributed among these distances:
109 45 0.11
110 2 0.00
111 28 0.07
112 10 0.02
113 1 0.00
114 6 0.01
115 2 0.00
116 2 0.00
117 3 0.01
118 4 0.01
119 137 0.33
120 30 0.07
121 6 0.01
122 47 0.11
123 2 0.00
124 92 0.22
125 4 0.01
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (119 bp):
CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCATTGATGTTTATATTTGCGAATCACTAATGTTT
ACTATGTCATAATTTGAGAAGATTTGTGTTCTCCAATCTGCTTGTTGGCCTATG
Found at i:16174 original size:231 final size:231
Alignment explanation
Indices: 15644--16219 Score: 619
Period size: 231 Copynumber: 2.4 Consensus size: 231
15634 TCTCCAATCT
* *
15644 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCATAGATGTTTATATCTGCGAATCCCTAATGTTT
1 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCATAGATGTTTATATTTGCGAATCACTAATGTTT
* * *
15709 ACTATGTCATAGTTTGAGAATATTTGTGT-TCTCCAATTTGCTTGTTGGCCTATGCATCTAATAC
66 ACTATGTCATAATTTGAGAAGATTTGT-TCCCTCCAA---------TGGCCTATGCATCTAATAC
* * *
15773 TTTAGTTAGTTATAGAAGCTGCGTTGATTTTTATATTTGCAAATTACTAATGTTTACTATGTCAT
121 TTTAGTTAGTTATAGAAGCTGCATGGATGTTTATATTTGCAAATTACTAATGTTTACTATGTCAT
* * ** * *
15838 AATTTAAAAGGATTTGTGTTCTCCCCTCCGTTCTGCTTGTTGGCCTGTG
186 AATTTAAAAGGATATCTG-TCT--CCTCCAATCTGCTTCTTGGCCTATG
* * * * *
15887 CCTCTAATTCTTTAGTTAGTTATAGAAGTTGCGTCA-ATTTTTATAATTGTGAATCACTAATGTT
1 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCAT-AGATGTTTATATTTGCGAATCACTAATGTT
* * * *
15951 TACTATATCATAATTTGAAAAGATTTGTTCCCTCCAAT-GCCTATGCCTCTAATTCTTTAGTTAG
65 TACTATGTCATAATTTGAGAAGATTTGTTCCCTCCAATGGCCTATGCATCTAATACTTTAGTTAG
* **
16015 TTATATAAGCTGCATGGATGTTTATATTTGTGTGAATCT-CTAATGTTTACTATGTCATAATTTT
130 TTATAGAAGCTGCATGGATGTTTATA-TT-TGCAAAT-TACTAATGTTTACTATGTCATAA-TTT
* *
16079 GAGAA-GATATCTG-CT-CTCCAATCTGCTTCTTGGTCTATG
191 -AAAAGGATATCTGTCTCCTCCAATCTGCTTCTTGGCCTATG
* * *
16118 CCTCTAATTCTTTAGTTAGTTATAGAAACT-CTATTGATGTTTCTATTTGCGAATCACTAATGTT
1 CCTCTAATTCTTTAGTTAGTTATAGAAGCTGC-ATAGATGTTTATATTTGCGAATCACTAATGTT
* *
16182 TACTATGTCATAATTTGAGAAGATTTGTGCCTTCCAAT
65 TACTATGTCATAATTTGAGAAGATTTGTTCCCTCCAAT
16220 CTGCTTGTTG
Statistics
Matches: 284, Mismatches: 40, Indels: 30
0.80 0.11 0.08
Matches are distributed among these distances:
230 1 0.00
231 106 0.37
233 46 0.16
234 5 0.02
235 26 0.09
236 10 0.04
237 3 0.01
242 1 0.00
243 85 0.30
244 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (231 bp):
CCTCTAATTCTTTAGTTAGTTATAGAAGCTGCATAGATGTTTATATTTGCGAATCACTAATGTTT
ACTATGTCATAATTTGAGAAGATTTGTTCCCTCCAATGGCCTATGCATCTAATACTTTAGTTAGT
TATAGAAGCTGCATGGATGTTTATATTTGCAAATTACTAATGTTTACTATGTCATAATTTAAAAG
GATATCTGTCTCCTCCAATCTGCTTCTTGGCCTATG
Found at i:16283 original size:32 final size:32
Alignment explanation
Indices: 16241--16301 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
16231 TCTATGCCTT
*
16241 TAATTCTTTAGACAGTTATAGATTTGGTTTTC
1 TAATTCTTTAGACAGTTATAAATTTGGTTTTC
* *
16273 TAATTGTTTAGATAGTTATAAATTTGGTT
1 TAATTCTTTAGACAGTTATAAATTTGGTT
16302 CATTAAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.51
Consensus pattern (32 bp):
TAATTCTTTAGACAGTTATAAATTTGGTTTTC
Found at i:17076 original size:2 final size:2
Alignment explanation
Indices: 17069--17098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17059 CAAGATTCTG
17069 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
17099 TTTTCATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23590 original size:15 final size:15
Alignment explanation
Indices: 23550--23607 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
23540 TTTAGACTCA
23550 TTTAAGTTTATTTATAT
1 TTTAA-TTT-TTTATAT
*
23567 TAT-ATTTTTTATAT
1 TTTAATTTTTTATAT
* *
23581 TTTAATTTTTTTTAAA
1 TTTAATTTTTTAT-AT
23597 TTTAATTTTTT
1 TTTAATTTTTT
23608 TAAGGTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 9 0.26
15 11 0.31
16 13 0.37
17 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTAATTTTTTATAT
Found at i:23618 original size:17 final size:16
Alignment explanation
Indices: 23571--23608 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
23561 TTATATTATA
23571 TTTTTTATATTTTAATT
1 TTTTTTA-ATTTTAATT
*
23588 TTTTTTAAATTTAATT
1 TTTTTTAATTTTAATT
23604 TTTTT
1 TTTTT
23609 AAGGTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTAATTTTAATT
Found at i:23836 original size:2 final size:2
Alignment explanation
Indices: 23829--23873 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
23819 AACCCTTACA
23829 AT AT AT AT AT 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 AT AT AT AT AT
23871 AT A
1 AT A
23874 AAATTACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24797 original size:21 final size:20
Alignment explanation
Indices: 24750--24797 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
24740 TATAATTAAA
* *
24750 TTTAAATAAAAATATATTAT
1 TTTAATTAAAAAAATATTAT
24770 TTTAATTAAAAAAATATTAT
1 TTTAATTAAAAAAATATTAT
24790 TTTGAATT
1 TTT-AATT
24798 GAACGGGACG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTAATTAAAAAAATATTAT
Found at i:25444 original size:17 final size:18
Alignment explanation
Indices: 25412--25455 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
25402 AAATTTTAAC
25412 ATATTTATATATTCATATT
1 ATATTT-TATATTCATATT
*
25431 ATTTTTTATA-TCATATT
1 ATATTTTATATTCATATT
25448 ATATTTTA
1 ATATTTTA
25456 CTTTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 14 0.61
18 4 0.17
19 5 0.22
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTTATATTCATATT
Found at i:25660 original size:24 final size:28
Alignment explanation
Indices: 25632--25690 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 28
25622 AATTTTAAAT
25632 ATAATAT-AATTATA-T-AATA-AAAAA
1 ATAATATAAATTATAGTAAATATAAAAA
25656 ATAAT-TAAATTATAGTAAAATATAAAAA
1 ATAATATAAATTATAGT-AAATATAAAAA
25684 ATAATAT
1 ATAATAT
25691 GAACATGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 1 0.03
24 12 0.41
25 1 0.03
27 4 0.14
28 10 0.34
29 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (28 bp):
ATAATATAAATTATAGTAAATATAAAAA
Found at i:29835 original size:18 final size:20
Alignment explanation
Indices: 29792--29836 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
29782 ATCAAATAAC
* *
29792 AATATTAAAGATAATTATAT
1 AATATAAAAAATAATTATAT
29812 AATATAAAAAATAATTA-A-
1 AATATAAAAAATAATTATAT
29830 AATATAA
1 AATATAA
29837 TATGAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 1 0.04
20 15 0.65
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AATATAAAAAATAATTATAT
Found at i:30272 original size:3 final size:3
Alignment explanation
Indices: 30264--30295 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30254 TAAACATATG
30264 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
30296 AGTAAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34499 original size:2 final size:2
Alignment explanation
Indices: 34494--34520 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34484 TTTTTTGCAT
34494 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
34521 TCAATGGAAC
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:34737 original size:2 final size:2
Alignment explanation
Indices: 34730--34756 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34720 CGTATAAATC
34730 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
34757 GATAGTAAAT
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:35184 original size:2 final size:2
Alignment explanation
Indices: 35179--35203 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35169 AAAAAGTACC
35179 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 A
35204 CAAACCCAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36132 original size:21 final size:20
Alignment explanation
Indices: 36111--36148 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36101 ATATTTTTAT
36111 TTAAAT-TTAATTATAAAATA
1 TTAAATATTAA-TATAAAATA
*
36131 TTAAGTATTAATATAAAA
1 TTAAATATTAATATAAAA
36149 ATAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TTAAATATTAATATAAAATA
Found at i:37074 original size:3 final size:3
Alignment explanation
Indices: 37066--37104 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
37056 TTGCAACCAC
37066 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
37105 TATTATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:37159 original size:18 final size:18
Alignment explanation
Indices: 37132--37167 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
37122 TTATTTTTAT
*
37132 AAAGTAAAAGTAAAAGGA
1 AAAGTAAAAGAAAAAGGA
*
37150 AAAGTGAAAGAAAAAGGA
1 AAAGTAAAAGAAAAAGGA
37168 TGTGTTTGGA
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:0.67, C:0.00, G:0.25, T:0.08
Consensus pattern (18 bp):
AAAGTAAAAGAAAAAGGA
Found at i:37480 original size:2 final size:2
Alignment explanation
Indices: 37473--37509 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
37463 TAGTTAATAA
37473 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37510 GAATCCTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37996 original size:2 final size:2
Alignment explanation
Indices: 37984--38020 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
37974 TCATTTAAAC
*
37984 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38021 AAACTAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38092 original size:2 final size:2
Alignment explanation
Indices: 38085--38114 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38075 AATTAAGTAG
38085 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
38115 TAAGTAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38537 original size:2 final size:2
Alignment explanation
Indices: 38530--38563 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38520 TAGTGAAATA
38530 AT 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 AT
38564 GCAAATACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38988 original size:2 final size:2
Alignment explanation
Indices: 38981--39037 Score: 80
Period size: 2 Copynumber: 28.5 Consensus size: 2
38971 TTCACGTAGT
* *
38981 TA TA TA TA TA TT TG TA -A GTA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
39023 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
39038 TAGTTTGTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39252 original size:21 final size:21
Alignment explanation
Indices: 39217--39257 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
39207 ATGTTTTATT
39217 TAAGTTTAATGATAAAATATA
1 TAAGTTTAATGATAAAATATA
39238 TAAGTATTAAT-ATAAAATAT
1 TAAGT-TTAATGATAAAATAT
39258 TTTTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
TAAGTTTAATGATAAAATATA
Found at i:39605 original size:19 final size:19
Alignment explanation
Indices: 39564--39612 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
39554 AGGTTTAAGA
*
39564 TTCTTTCTTTCTTTCATTCT
1 TTCTTT-TTTTTTTCATTCT
39584 TTCTTTTTTTTTTC-TTCTT
1 TTCTTTTTTTTTTCATTC-T
39603 TTCTTTTTTT
1 TTCTTTTTTT
39613 GTATTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.11
19 18 0.67
20 6 0.22
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (19 bp):
TTCTTTTTTTTTTCATTCT
Found at i:40426 original size:20 final size:20
Alignment explanation
Indices: 40388--40438 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
40378 TTCTCCCATG
*
40388 TAAATATAAATTA-GATAATTT
1 TAAATAT-AA-TACGATAATTA
*
40409 TAGATATAATACGATAATTA
1 TAAATATAATACGATAATTA
40429 TAAATATAAT
1 TAAATATAAT
40439 GTAAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.08
20 18 0.69
21 6 0.23
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (20 bp):
TAAATATAATACGATAATTA
Found at i:40483 original size:11 final size:11
Alignment explanation
Indices: 40457--40492 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
40447 TATGATACAA
*
40457 ATAAAATATTAT
1 ATAAAA-ATAAT
40469 ATAAAAATAAT
1 ATAAAAATAAT
40480 ATAAAAATAAT
1 ATAAAAATAAT
40491 AT
1 AT
40493 TAATATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:40520 original size:28 final size:27
Alignment explanation
Indices: 40461--40513 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
40451 ATACAAATAA
40461 AATATTATATAAAAATAATATAAAAAT
1 AATATTATATAAAAATAATATAAAAAT
*
40488 AATATTAATATATAAATAGAT-TAAAA
1 AATATT-ATATAAAAATA-ATATAAAA
40514 TTTATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 15 0.65
29 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
AATATTATATAAAAATAATATAAAAAT
Found at i:40583 original size:27 final size:27
Alignment explanation
Indices: 40549--40616 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
40539 ATTAAAACTT
* *
40549 ATATAAATATATAATATTTTAAATATA
1 ATATAAATATATAATAATATAAATATA
* * *
40576 AT-TAAAATAAAAAATAATATAAATATG
1 ATAT-AAATATATAATAATATAAATATA
40603 ATATAAATATATAA
1 ATATAAATATATAA
40617 ATTACTAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
26 1 0.03
27 30 0.94
28 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (27 bp):
ATATAAATATATAATAATATAAATATA
Found at i:40625 original size:27 final size:26
Alignment explanation
Indices: 40549--40626 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 26
40539 ATTAAAACTT
*
40549 ATATAAATATATAATATTTTAAATATA
1 ATATAAATATATAA-ATTATAAATATA
* *
40576 AT-TAAA-ATAAAAAATAATATAAATATG
1 ATATAAATAT-ATAAAT--TATAAATATA
40603 ATATAAATATATAAATTACTAAAT
1 ATATAAATATATAAATTA-TAAAT
40627 TTAAATCAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
25 4 0.10
26 9 0.22
27 17 0.41
28 9 0.22
29 2 0.05
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (26 bp):
ATATAAATATATAAATTATAAATATA
Found at i:41175 original size:2 final size:2
Alignment explanation
Indices: 41168--41205 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
41158 GTTTAATTTA
41168 AT AT AT 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 AT AT AT
41206 GACATGGGTC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41463 original size:2 final size:2
Alignment explanation
Indices: 41456--41488 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41446 TTTCTTTTAC
41456 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
41489 AATTTAAGCA
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:42253 original size:20 final size:21
Alignment explanation
Indices: 42214--42263 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
42204 CAATGTTATC
*
42214 AAAATTTTAAAAATTAAAATAT
1 AAAAATTT-AAAATTAAAATAT
* *
42236 ATAAATTTAAAA-TAAAATCT
1 AAAAATTTAAAATTAAAATAT
42256 AAAAATTT
1 AAAAATTT
42264 TAATCAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 14 0.58
21 4 0.17
22 6 0.25
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAATTTAAAATTAAAATAT
Found at i:43721 original size:23 final size:23
Alignment explanation
Indices: 43666--43731 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
43656 ACATAATACG
*
43666 AACATAATATGAAAAA-AATCTA
1 AACATAATATGAAAAATAATATA
43688 AA-ATACGATATGAAAAATAATATA
1 AACATA--ATATGAAAAATAATATA
*
43712 AACATAATATTAAAACATAA
1 AACATAATATGAAAA-ATAA
43732 ATATCTCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 3 0.08
22 2 0.05
23 18 0.49
24 11 0.30
25 3 0.08
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.24
Consensus pattern (23 bp):
AACATAATATGAAAAATAATATA
Found at i:44030 original size:2 final size:2
Alignment explanation
Indices: 44023--44053 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44013 GAGAGTTAAT
44023 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 T
44054 GATTAATTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44113 original size:2 final size:2
Alignment explanation
Indices: 44106--44138 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
44096 CTTTGAGTTT
*
44106 TA TA TA TA TA CA 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 T
44139 GATTAATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:44114 original size:85 final size:85
Alignment explanation
Indices: 44023--44183 Score: 304
Period size: 85 Copynumber: 1.9 Consensus size: 85
44013 GAGAGTTAAT
* *
44023 TATATATATATATATATATATATATATATATGATTAATTAGGTCTTAAACTTATGGCCATGTTTT
1 TATATATACATATATATATATATATATATATGATTAATTAGGTCTTAAACTTATGGCCATGTTTC
44088 AAATTAAACTTTGAGTTTTA
66 AAATTAAACTTTGAGTTTTA
44108 TATATATACATATATATATATATATATATATGATTAATTAGGTCTTAAACTTATGGCCATGTTTC
1 TATATATACATATATATATATATATATATATGATTAATTAGGTCTTAAACTTATGGCCATGTTTC
44173 AAATTAAACTT
66 AAATTAAACTT
44184 CAAAACATGT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 74 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (85 bp):
TATATATACATATATATATATATATATATATGATTAATTAGGTCTTAAACTTATGGCCATGTTTC
AAATTAAACTTTGAGTTTTA
Found at i:45179 original size:15 final size:17
Alignment explanation
Indices: 45145--45181 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 17
45135 AATATTTTAT
45145 ATTTTTAGTAAATTAATA
1 ATTTTTAGTAAA-TAATA
45163 ATTTTTA-TAAA-AATA
1 ATTTTTAGTAAATAATA
45178 ATTT
1 ATTT
45182 AAATTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
17 4 0.21
18 7 0.37
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTTTAGTAAATAATA
Found at i:45404 original size:16 final size:16
Alignment explanation
Indices: 45383--45415 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45373 ATGAAAAAAA
*
45383 AGAAAGAAAATATTAT
1 AGAAAGAAAATAATAT
45399 AGAAAGAAAATAATAT
1 AGAAAGAAAATAATAT
45415 A
1 A
45416 AAATTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (16 bp):
AGAAAGAAAATAATAT
Found at i:50005 original size:15 final size:15
Alignment explanation
Indices: 49985--50017 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
49975 TTTACAAAAA
49985 TATCATAGAAAATGG
1 TATCATAGAAAATGG
50000 TATCATAGAAAATGG
1 TATCATAGAAAATGG
50015 TAT
1 TAT
50018 ACAAAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (15 bp):
TATCATAGAAAATGG
Found at i:50187 original size:2 final size:2
Alignment explanation
Indices: 50182--50209 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
50172 ACACACACAA
50182 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
50210 TTGGAGTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59002 original size:4 final size:4
Alignment explanation
Indices: 58993--59017 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
58983 ATGAAAAGTC
58993 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
59018 ATTTGATAAA
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:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:60102 original size:25 final size:27
Alignment explanation
Indices: 60074--60129 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 27
60064 TTTTATATGC
60074 TAAAAATTACATA-ATA-TATAAAATA-
1 TAAAAATTA-ATATATATTATAAAATAG
*
60099 T-AAAATTAATATATATTATATAATAG
1 TAAAAATTAATATATATTATAAAATAG
60125 TAAAA
1 TAAAA
60130 CAAGCTAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.12
24 10 0.38
25 9 0.35
26 1 0.04
27 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
TAAAAATTAATATATATTATAAAATAG
Found at i:61599 original size:18 final size:18
Alignment explanation
Indices: 61576--61613 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
61566 CTTCTTTTTC
61576 TTTATTAATGAACAGTGG
1 TTTATTAATGAACAGTGG
*
61594 TTTATTAATGAGCAGTGG
1 TTTATTAATGAACAGTGG
61612 TT
1 TT
61614 GGCAGAGGAG
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:0.29, C:0.05, G:0.24, T:0.42
Consensus pattern (18 bp):
TTTATTAATGAACAGTGG
Found at i:64877 original size:17 final size:17
Alignment explanation
Indices: 64851--64884 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
64841 TGAATTACAA
64851 ATATTGAATATATATAT
1 ATATTGAATATATATAT
* *
64868 ATATTTAATATTTATAT
1 ATATTGAATATATATAT
64885 GAGAGTATAT
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATTGAATATATATAT
Found at i:65385 original size:17 final size:17
Alignment explanation
Indices: 65354--65392 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
65344 AAAAAAAATC
65354 AAAAACTTAACTTATGAT
1 AAAAACTTAACTTATG-T
*
65372 AAAATCTTAA-TTATGT
1 AAAAACTTAACTTATGT
65388 AAAAA
1 AAAAA
65393 ATCAGTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (17 bp):
AAAAACTTAACTTATGT
Found at i:66366 original size:23 final size:22
Alignment explanation
Indices: 66334--66379 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
66324 TTTTAAATGT
* *
66334 TATTTTTATATATTATAATTATA
1 TATTTATATAAATTATAA-TATA
*
66357 TATTTATATAAATTTTAATATA
1 TATTTATATAAATTATAATATA
66379 T
1 T
66380 TAATAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTATATAAATTATAATATA
Found at i:66423 original size:33 final size:31
Alignment explanation
Indices: 66335--66430 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 31
66325 TTTAAATGTT
*
66335 ATTTTTATATATTATAATTATATATTTATATAA
1 ATTTTAATATATTATAATTA-ATA-TTATATAA
66368 ATTTTAATATATTAATAATTAATATTATATAA
1 ATTTTAATATATT-ATAATTAATATTATATAA
* *
66400 ATTTTAATATATTCGTAATTTAATAATATAT
1 ATTTTAATATATT-ATAA-TTAATATTATAT
66431 TTATAATAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
32 24 0.42
33 26 0.46
34 7 0.12
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
ATTTTAATATATTATAATTAATATTATATAA
Found at i:66549 original size:25 final size:25
Alignment explanation
Indices: 66516--66565 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
66506 GAAGGAAATG
*
66516 CTAAGTTGGTGTACTGTAAATGCAA
1 CTAAATTGGTGTACTGTAAATGCAA
66541 CTAAATTGGTGTACTGTAAATGCAA
1 CTAAATTGGTGTACTGTAAATGCAA
66566 TCATAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (25 bp):
CTAAATTGGTGTACTGTAAATGCAA
Found at i:66736 original size:11 final size:11
Alignment explanation
Indices: 66720--66744 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
66710 TAGAAACATC
66720 AAATTAATTAA
1 AAATTAATTAA
66731 AAATTAATTAA
1 AAATTAATTAA
66742 AAA
1 AAA
66745 CAAAATATTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTAATTAA
Found at i:67295 original size:23 final size:21
Alignment explanation
Indices: 67247--67295 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
67237 ATTTACTCAA
67247 ATATT-TTTATTAAAATATAT
1 ATATTATTTATTAAAATATAT
* *
67267 AAATTATTTATTAATACATATTT
1 ATATTATTTATTAA-A-ATATAT
67290 ATATTA
1 ATATTA
67296 ATATTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 8 0.35
22 1 0.04
23 10 0.43
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTATTTATTAAAATATAT
Found at i:67510 original size:16 final size:16
Alignment explanation
Indices: 67489--67529 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 16
67479 TCTTAAACTT
67489 AAACTATTGCATTATA
1 AAACTATTGCATTATA
67505 AAACTACGATTGCATTATA
1 AAACT---ATTGCATTATA
67524 AAACTA
1 AAACTA
67530 CGGTAGAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.27
19 16 0.73
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (16 bp):
AAACTATTGCATTATA
Found at i:67518 original size:19 final size:19
Alignment explanation
Indices: 67494--67531 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
67484 AACTTAAACT
67494 ATTGCATTATAAAACTACG
1 ATTGCATTATAAAACTACG
67513 ATTGCATTATAAAACTACG
1 ATTGCATTATAAAACTACG
67532 GTAGAAGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (19 bp):
ATTGCATTATAAAACTACG
Found at i:67835 original size:10 final size:10
Alignment explanation
Indices: 67817--67866 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
67807 TTTAAAATAT
67817 TATATATTTA
1 TATATATTTA
*
67827 TATAAATTT-
1 TATATATTTA
67836 TAATATATTTA
1 T-ATATATTTA
67847 TATAT-TTT-
1 TATATATTTA
67855 TATCATATTTA
1 TAT-ATATTTA
67866 T
1 T
67867 GTTATCCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
8 3 0.09
9 6 0.18
10 22 0.67
11 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATATTTA
Found at i:68871 original size:32 final size:32
Alignment explanation
Indices: 68830--68937 Score: 171
Period size: 32 Copynumber: 3.4 Consensus size: 32
68820 AAACAGCAAC
* * *
68830 TGTATCGATACATAAGTGATGTATTGTTACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
68862 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
68894 TGTATCGCTACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
68926 TGTATCGCTACA
1 TGTATCGATACA
68938 AAGCTACTGC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:68886 original size:19 final size:19
Alignment explanation
Indices: 68862--68924 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
68852 ATTGTTACAA
68862 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
68881 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
*
68894 TGTATCGCTACATAAGTGT
1 TGTATCGATACATAAGTGT
68913 TGTATCGATACA
1 TGTATCGATACA
68925 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:74331 original size:18 final size:18
Alignment explanation
Indices: 74308--74346 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
74298 ATTAATTATT
74308 TATATAATTAAT-TTAATA
1 TATATAA-TAATGTTAATA
*
74326 TATATAATAATGTTTATA
1 TATATAATAATGTTAATA
74344 TAT
1 TAT
74347 TTATTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TATATAATAATGTTAATA
Found at i:74576 original size:23 final size:24
Alignment explanation
Indices: 74550--74598 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
74540 TTATCTAGAT
*
74550 AAATAAAATTAACAGTT-TAATTA
1 AAATAAAATTAACAATTCTAATTA
* *
74573 AAATAGAATTAAGAATTCTAATTA
1 AAATAAAATTAACAATTCTAATTA
74597 AA
1 AA
74599 CTCTCTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAAAATTAACAATTCTAATTA
Found at i:78456 original size:2 final size:2
Alignment explanation
Indices: 78449--78474 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78439 GCTTATAATC
78449 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
78475 TTGTTGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79561 original size:14 final size:15
Alignment explanation
Indices: 79542--79570 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
79532 TTTAGTAAAT
79542 ATAAAAAT-AATATA
1 ATAAAAATGAATATA
79556 ATAAAAATGAATATA
1 ATAAAAATGAATATA
79571 GCATGTATTT
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:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
ATAAAAATGAATATA
Found at i:79804 original size:27 final size:26
Alignment explanation
Indices: 79753--79805 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
79743 AAATAAAAAT
79753 CTTATAAAATATATAAATTTTATCAA
1 CTTATAAAATATATAAATTTTATCAA
*
79779 CTTAT-AAATTTATAAATCTTTGATCAA
1 CTTATAAAATATATAAAT-TTT-ATCAA
79806 TTTAATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 11 0.46
26 8 0.33
27 5 0.21
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
CTTATAAAATATATAAATTTTATCAA
Found at i:80762 original size:96 final size:96
Alignment explanation
Indices: 80598--80784 Score: 293
Period size: 96 Copynumber: 1.9 Consensus size: 96
80588 CAAGCAAAAC
* ** * * * *
80598 TAAATAATATAAATAGTTAGATCTAATTATTTTGTATTTGTATTATATTTAATTGTTTATATATT
1 TAAATAATATAAATAGTTAGATCTAATCATTTTACATTTGTATCATAGTTAATTATTCATATATT
80663 TTATATATTATAATTATATTTAAAATGTTAT
66 TTATATATTATAATTATATTTAAAATGTTAT
* *
80694 TAAATAATATGAATAGTTAGATTTAATCATTTTACATTTGTATCATAGTTAATTATTCATATATT
1 TAAATAATATAAATAGTTAGATCTAATCATTTTACATTTGTATCATAGTTAATTATTCATATATT
80759 TTATATATTATAATTATATTTAAAAT
66 TTATATATTATAATTATATTTAAAAT
80785 ATTACATAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.52
Consensus pattern (96 bp):
TAAATAATATAAATAGTTAGATCTAATCATTTTACATTTGTATCATAGTTAATTATTCATATATT
TTATATATTATAATTATATTTAAAATGTTAT
Found at i:80853 original size:18 final size:18
Alignment explanation
Indices: 80811--80882 Score: 55
Period size: 17 Copynumber: 4.2 Consensus size: 18
80801 TATATTAATA
* *
80811 ATTTAT-TTTATTTAAAT
1 ATTTATATTAATTTATAT
*
80828 -TTTTTATTAATTTATAT
1 ATTTATATTAATTTATAT
*
80845 ATTTATATT-ATAT-TAT
1 ATTTATATTAATTTATAT
*
80861 A-TTATATTATATTTTTAT
1 ATTTATATTA-ATTTATAT
80879 ATTT
1 ATTT
80883 TAATTATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
15 7 0.16
16 8 0.19
17 15 0.35
18 11 0.26
19 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTATATTAATTTATAT
Found at i:80857 original size:5 final size:5
Alignment explanation
Indices: 80839--80881 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
80829 TTTTATTAAT
80839 TTATA -TAT- TTATA TTATA TTATA TTATA TTATA TT-T- TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
80882 TTAATTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.06
4 8 0.24
5 24 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:80862 original size:10 final size:9
Alignment explanation
Indices: 80811--80881 Score: 69
Period size: 10 Copynumber: 8.0 Consensus size: 9
80801 TATATTAATA
*
80811 ATTTATTTT
1 ATTTATATT
*
80820 ATTTAAATT
1 ATTTATATT
80829 -TTT-TATT
1 ATTTATATT
80836 AATTTATA-T
1 -ATTTATATT
80845 ATTTATATT
1 ATTTATATT
80854 ATATTATATT
1 AT-TTATATT
80864 ATATTATATT
1 AT-TTATATT
80874 -TTTATATT
1 ATTTATATT
80882 TTAATTATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
7 3 0.06
8 17 0.31
9 15 0.28
10 19 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTATATT
Found at i:80893 original size:18 final size:18
Alignment explanation
Indices: 80795--80895 Score: 57
Period size: 18 Copynumber: 5.3 Consensus size: 18
80785 ATTACATAAA
* *
80795 TTTTTATATATTAATAAT
1 TTTTTATATTTTAATTAT
*
80813 TTATTT-TATTTAAATT-T
1 TT-TTTATATTTTAATTAT
80830 TTTATTA-ATTTATATATTTAT
1 TTT-TTATATTT-TA-A-TTAT
*
80851 ATTATATTATATTAT-ATTAT
1 -TT-T-TTATATTTTAATTAT
80871 ATTTTTATATTTTAATTAT
1 -TTTTTATATTTTAATTAT
80890 TTTTTA
1 TTTTTA
80896 AAATCATATT
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
16 1 0.02
17 9 0.14
18 24 0.36
19 10 0.15
20 9 0.14
21 2 0.03
22 2 0.03
23 6 0.09
24 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTATATTTTAATTAT
Found at i:85212 original size:12 final size:12
Alignment explanation
Indices: 85195--85241 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
85185 AAAAAATATT
85195 TTTATATTAATA
1 TTTATATTAATA
85207 TTTATAGTTAA-A
1 TTTATA-TTAATA
85219 -TT-TA--AATA
1 TTTATATTAATA
85227 TTTATATTAATA
1 TTTATATTAATA
85239 TTT
1 TTT
85242 TTATAAATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 2 0.07
8 1 0.03
9 2 0.07
10 4 0.14
11 2 0.07
12 14 0.48
13 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
TTTATATTAATA
Found at i:85228 original size:20 final size:20
Alignment explanation
Indices: 85203--85241 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
85193 TTTTTATATT
85203 AATATTTATAGTTAA-ATTTA
1 AATATTTATA-TTAATATTTA
85223 AATATTTATATTAATATTT
1 AATATTTATATTAATATTT
85242 TTATAAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
AATATTTATATTAATATTTA
Found at i:90346 original size:20 final size:20
Alignment explanation
Indices: 90318--90358 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
90308 TATTGTTTAT
*
90318 TGATTTGATGTTAATTTTTG
1 TGATATGATGTTAATTTTTG
* *
90338 TGATATGATTTTGATTTTTG
1 TGATATGATGTTAATTTTTG
90358 T
1 T
90359 CACATATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.61
Consensus pattern (20 bp):
TGATATGATGTTAATTTTTG
Found at i:92045 original size:311 final size:307
Alignment explanation
Indices: 91356--92079 Score: 660
Period size: 311 Copynumber: 2.3 Consensus size: 307
91346 TTTATGACCG
* * * * * * *
91356 TTTTCAAGCTCTTTAAGGTTATCGAA-ATACTTTCATATTGAAGGTATAC-CTTAAAGGTATGTT
1 TTTTCAAGTTTTTTAGGGTTATC-AAGATACTTTTATATTAAAGGTATACTC-TAAGGGTATTTT
* * * * *
91419 AATAATTTTGCATTAGAATCAAGTCTTATGTGATTACTTGGATACTTTCATGTCGAAGATACAGA
64 AATAATTTTGCATTAAAACCAAGTCTTATGTGATTACTTGGATACTTTCATATCAAAGATACACA
* * * *
91484 TTATGATAGATTATTTTAGACTATTTTCAAATCCTTTAAAGTTATCGGGATGCATTCAAGACGAA
129 TTAAGATAGATTATTTTAGACTATTTTCAAATCATTTAAAGTTATCGGGATGCATTCAAAACAAA
* * * * * * ** *
91549 AGTAGTCCCTAAGTGCATTTTAGTAATTTCTATTAGAACCAAGTTTGATCTAGTCACTAAGATAC
194 AATAATCCCTAAGAGCATTTTAGTAATTTCTACTAGAACCAAGTCTAAAATAGTCAATAAGATAC
* * * * *
91614 TTTTATGGCAAAGGTGTACATTTAGGATAGGTTCATCTTTTATTGATCG
259 TTTTATGCCAAAGGTGTACATATAGGATAGCTTCATCTTTTAGTGATCA
* * * * * * **
91663 TTTTCAAGTCTTTTAGGGTTAT-GAGCTACTTCTATGTTGAAA-GTATA-TCCCAAGGTGCCTTT
1 TTTTCAAGTTTTTTAGGGTTATCAAGATACTTTTATATT-AAAGGTATACT-CTAAGG-GTATTT
** * *
91725 TGTTAATTTTGCATTAAAACCAAGTCTTATGTGGTTACTTGGATACTTTCATATCAAAGGTACAC
63 TAATAATTTTGCATTAAAACCAAGTCTTATGTGATTACTTGGATACTTTCATATCAAAGATACAC
* ** *
91790 ATTAGAGATTGATTCGTTATTTTA-AGCTATTTTCAAATCATTTAGGGTT-TCGGGATG-TTATC
128 ATTA-AGATAGA----TTATTTTAGA-CTATTTTCAAATCATTTAAAGTTATCGGGATGCAT-TC
** * ** * *
91852 AAAACAAAAATAATTTCTAAGAGCATTTTAGTAATTT-TCCCTAGAGTCAAGTCTAAAATTGTTA
186 AAAACAAAAATAATCCCTAAGAGCATTTTAGTAATTTCT-ACTAGAACCAAGTCTAAAATAGTCA
* * *
91916 ATAGGATGCTTTTATGCCAAAGGTGTACATATAGGATAGCTTTATCTTTCT-GTGA-CTA
250 ATAAGATACTTTTATGCCAAAGGTGTACATATAGGATAGCTTCATCTTT-TAGTGATC-A
*
91974 TTTTCAAGTTTTTTAGGGTTATCAAGATACTTTTACATTAAAGGTATACTCTAAGGGTATTTTAA
1 TTTTCAAGTTTTTTAGGGTTATCAAGATACTTTTATATTAAAGGTATACTCTAAGGGTATTTTAA
* ** * * * *
92039 TAATTTTACACGAGAAGCAAGTCCTATGTGACTACTTGGAT
66 TAATTTTGCATTAAAACCAAGTCTTATGTGATTACTTGGAT
92080 TTCTGGAAAC
Statistics
Matches: 324, Mismatches: 75, Indels: 32
0.75 0.17 0.07
Matches are distributed among these distances:
305 1 0.00
306 17 0.05
307 84 0.26
308 5 0.02
310 3 0.01
311 163 0.50
312 50 0.15
313 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (307 bp):
TTTTCAAGTTTTTTAGGGTTATCAAGATACTTTTATATTAAAGGTATACTCTAAGGGTATTTTAA
TAATTTTGCATTAAAACCAAGTCTTATGTGATTACTTGGATACTTTCATATCAAAGATACACATT
AAGATAGATTATTTTAGACTATTTTCAAATCATTTAAAGTTATCGGGATGCATTCAAAACAAAAA
TAATCCCTAAGAGCATTTTAGTAATTTCTACTAGAACCAAGTCTAAAATAGTCAATAAGATACTT
TTATGCCAAAGGTGTACATATAGGATAGCTTCATCTTTTAGTGATCA
Found at i:95516 original size:2 final size:2
Alignment explanation
Indices: 95476--95504 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
95466 AAAAATAGAA
95476 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
95505 ATAACGATAT
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:97008 original size:21 final size:21
Alignment explanation
Indices: 96984--97031 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
96974 ATACTAAATT
** *
96984 AAGATAAAATGGAGAATGAAA
1 AAGATAAAATAAAAAATGAAA
*
97005 AAGATAATATAAAAAATGAAA
1 AAGATAAAATAAAAAATGAAA
97026 AAGATA
1 AAGATA
97032 CATCTCTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (21 bp):
AAGATAAAATAAAAAATGAAA
Found at i:100582 original size:63 final size:64
Alignment explanation
Indices: 100494--100629 Score: 166
Period size: 65 Copynumber: 2.1 Consensus size: 64
100484 TACACTTTTA
* * *
100494 TCAAATTATATTTGGATTCAATTTATTTCAAACTT-TATTTCTTTTAGATTTGAATAATTTTATA
1 TCAAATT-T-TTTGAATTCAATTTATTTCAAACTTCTATTTCTTTTAAATTTAAATAATTTTATA
100558 T
64 T
* * * * *
100559 TTAAATTTTTTGAATTTAATTTATTTGAAATTTCGTATTTTTTTTAAATTTAAATAATTTTATAT
1 TCAAATTTTTTGAATTCAATTTATTTCAAACTTC-TATTTCTTTTAAATTTAAATAATTTTATAT
100624 TCAAAT
1 TCAAAT
100630 CAATTTTTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
63 21 0.35
64 1 0.02
65 38 0.63
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (64 bp):
TCAAATTTTTTGAATTCAATTTATTTCAAACTTCTATTTCTTTTAAATTTAAATAATTTTATAT
Found at i:101866 original size:21 final size:21
Alignment explanation
Indices: 101842--101888 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
101832 ATACTAAATT
** *
101842 AAGATAAAATGGAGAATGAAA
1 AAGATAAAATAAAAAATGAAA
*
101863 AAGATAATATAAAAAATGAAA
1 AAGATAAAATAAAAAATGAAA
101884 AAGAT
1 AAGAT
101889 GCATCTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (21 bp):
AAGATAAAATAAAAAATGAAA
Found at i:105434 original size:63 final size:64
Alignment explanation
Indices: 105346--105481 Score: 166
Period size: 65 Copynumber: 2.1 Consensus size: 64
105336 TACACTTTTA
* * *
105346 TCAAATTATATTTGGATTCAATTTATTTCAAACTT-TATTTCTTTTAGATTTGAATAATTTTATA
1 TCAAATT-T-TTTGAATTCAATTTATTTCAAACTTCTATTTCTTTTAAATTTAAATAATTTTATA
105410 T
64 T
* * * * *
105411 TTAAATTTTTTGAATTTAATTTATTTGAAATTTCGTATTTTTTTTAAATTTAAATAATTTTATAT
1 TCAAATTTTTTGAATTCAATTTATTTCAAACTTC-TATTTCTTTTAAATTTAAATAATTTTATAT
105476 TCAAAT
1 TCAAAT
105482 CAATTTTTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
63 21 0.35
64 1 0.02
65 38 0.63
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (64 bp):
TCAAATTTTTTGAATTCAATTTATTTCAAACTTCTATTTCTTTTAAATTTAAATAATTTTATAT
Found at i:106718 original size:21 final size:21
Alignment explanation
Indices: 106694--106740 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
106684 ATACTAAATT
** *
106694 AAGATAAAATGGAGAATGAAA
1 AAGATAAAATAAAAAATGAAA
*
106715 AAGATAATATAAAAAATGAAA
1 AAGATAAAATAAAAAATGAAA
106736 AAGAT
1 AAGAT
106741 GCATCTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (21 bp):
AAGATAAAATAAAAAATGAAA
Found at i:112930 original size:19 final size:19
Alignment explanation
Indices: 112889--112931 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
112879 TTCAAAACTT
*
112889 AAAAGCATAACAAAACTGC
1 AAAAGCATAACAAAACTGA
*
112908 AAAAGCA-AACAAAGATTGA
1 AAAAGCATAACAAA-ACTGA
112927 AAAAG
1 AAAAG
112932 TATGACGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.63, C:0.14, G:0.14, T:0.09
Consensus pattern (19 bp):
AAAAGCATAACAAAACTGA
Found at i:113584 original size:20 final size:19
Alignment explanation
Indices: 113557--113595 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
113547 ATTTATTTTA
113557 TTATTTTATAA-TTTATAAT
1 TTATTTTA-AATTTTATAAT
113576 TTATATTTAAATTTTATAAT
1 TTAT-TTTAAATTTTATAAT
113596 AATTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTTAAATTTTATAAT
Found at i:113589 original size:27 final size:28
Alignment explanation
Indices: 113541--113595 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
113531 TATTTAATTA
*
113541 TTATACATTTATTTTATTATTTTATAAT
1 TTATACATTTATTTTATAATTTTATAAT
113569 TTATA-ATTTATATTTA-AATTTTATAAT
1 TTATACATTTAT-TTTATAATTTTATAAT
113596 AATTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
TTATACATTTATTTTATAATTTTATAAT
Found at i:114547 original size:6 final size:6
Alignment explanation
Indices: 114536--114565 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
114526 TTTCATCTAT
114536 CCAGCA CCAGCA CCAGCA CCAGCA CCAGCA
1 CCAGCA CCAGCA CCAGCA CCAGCA CCAGCA
114566 GCAACATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
CCAGCA
Found at i:129176 original size:178 final size:178
Alignment explanation
Indices: 128877--129201 Score: 596
Period size: 178 Copynumber: 1.8 Consensus size: 178
128867 CCCATGGACT
*
128877 TTCAAGCAGCTTCCTCCTGTGGGTAAACAATCAAGACATCTATTTGCATCCAGAAATGACTAGTC
1 TTCAAGCAGCTTCCTCCTGTGGGTAAACAATCAAGACATCTAGTTGCATCCAGAAATGACTAGTC
* *
128942 TAGCATGCTACAATTTATCAACTTAAAAGACATATGAACTCGAATGGGAATAACTTCACTGCTAC
66 TAGCATGCTACAATTTATCAACCTAAAAGACATATGAACTCGAATGGGAATAACTTCACCGCTAC
*
129007 CAAAGCGCAACTATTTGTGATATACATGAATTTCTGGATGGGAATAAC
131 AAAAGCGCAACTATTTGTGATATACATGAATTTCTGGATGGGAATAAC
*
129055 TTCAAGCAGCTTCCTCCTGTTGGTAAACAATCAAGACATCTAGTTGCATCCAGAAATGACTAGTC
1 TTCAAGCAGCTTCCTCCTGTGGGTAAACAATCAAGACATCTAGTTGCATCCAGAAATGACTAGTC
*
129120 TAGCATGCTACAATTTATCAACCTATAAGACATATGAACTCGAATGGGAATAACTTCACCGCTAC
66 TAGCATGCTACAATTTATCAACCTAAAAGACATATGAACTCGAATGGGAATAACTTCACCGCTAC
129185 AAAAGCGCAACTATTTG
131 AAAAGCGCAACTATTTG
129202 AAATATAAAG
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
178 141 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (178 bp):
TTCAAGCAGCTTCCTCCTGTGGGTAAACAATCAAGACATCTAGTTGCATCCAGAAATGACTAGTC
TAGCATGCTACAATTTATCAACCTAAAAGACATATGAACTCGAATGGGAATAACTTCACCGCTAC
AAAAGCGCAACTATTTGTGATATACATGAATTTCTGGATGGGAATAAC
Found at i:131362 original size:26 final size:27
Alignment explanation
Indices: 131290--131363 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 27
131280 AAATTATTAA
*
131290 AATATTAAAAATTTTATTT-TT-ACTTT
1 AATATTAAAAA-TTTATTTATTAAATTT
* * *
131316 AATATTAATATTTTA-TAATTAAATTT
1 AATATTAAAAATTTATTTATTAAATTT
131342 AA-ATTAAAAATTTATTTATTAA
1 AATATTAAAAATTTATTTATTAA
131364 TTAAAAAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
24 1 0.03
25 16 0.42
26 21 0.55
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (27 bp):
AATATTAAAAATTTATTTATTAAATTT
Found at i:131365 original size:25 final size:26
Alignment explanation
Indices: 131290--131365 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 26
131280 AAATTATTAA
*
131290 AATATTAAAAATTTTATTT-TTACTTT
1 AATATTAAAAA-TTTATTTATTAATTT
* * *
131316 AATATTAATATTTTA-TAATTAAATTT
1 AATATTAAAAATTTATTTATT-AATTT
131342 AA-ATTAAAAATTTATTTATTAATT
1 AATATTAAAAATTTATTTATTAATT
131366 AAAAAATGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
24 1 0.03
25 20 0.50
26 19 0.47
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
AATATTAAAAATTTATTTATTAATTT
Found at i:132427 original size:23 final size:23
Alignment explanation
Indices: 132399--132446 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
132389 TAGAAAATGT
* *
132399 TTAATTTAAAGATTTTGTAACAA
1 TTAATTAAAAGATTTTGCAACAA
*
132422 TTAATTAAAATATTTTGCAACAA
1 TTAATTAAAAGATTTTGCAACAA
132445 TT
1 TT
132447 GTTTTAAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (23 bp):
TTAATTAAAAGATTTTGCAACAA
Found at i:132874 original size:33 final size:33
Alignment explanation
Indices: 132832--132901 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
132822 ATCTTTGGTC
* *
132832 ATAATAATAAAGATACATTAGAGCTAGAACATG
1 ATAATAATAAAGACACATTAGAACTAGAACATG
* *
132865 ATAATAATAAAGGCACATTAGAACTAGAACATT
1 ATAATAATAAAGACACATTAGAACTAGAACATG
132898 ATAA
1 ATAA
132902 AGCTAGAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.24
Consensus pattern (33 bp):
ATAATAATAAAGACACATTAGAACTAGAACATG
Found at i:133866 original size:14 final size:15
Alignment explanation
Indices: 133844--133879 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
133834 AAAGCAAAAA
133844 TATATATTAATAAA-T
1 TATA-ATTAATAAATT
133859 TATAATTAATAAATT
1 TATAATTAATAAATT
133874 TATAAT
1 TATAAT
133880 AAAAAGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATTAATAAATT
Found at i:135784 original size:2 final size:2
Alignment explanation
Indices: 135777--135806 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
135767 TTTTATTAGG
135777 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
135807 CTTTACAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:136049 original size:11 final size:11
Alignment explanation
Indices: 136021--136050 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
136011 AAAAAAAAAA
*
136021 AAAGAAAAAAG
1 AAAGAAGAAAG
136032 AAAGAAGAAAG
1 AAAGAAGAAAG
136043 AAAGAAGA
1 AAAGAAGA
136051 GTAAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAAG
Found at i:138747 original size:14 final size:13
Alignment explanation
Indices: 138730--138760 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
138720 ACAAATAAAA
138730 TTCTTTTATTTTAT
1 TTCTTTTATTTT-T
138744 TTCTTTTATTTTT
1 TTCTTTTATTTTT
138757 TTCT
1 TTCT
138761 AAATAAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (13 bp):
TTCTTTTATTTTT
Found at i:139203 original size:17 final size:19
Alignment explanation
Indices: 139169--139205 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
139159 TTTTATATTT
*
139169 TATTCATATTGTATAATTA
1 TATTCATATTGTAAAATTA
139188 TATT-ATATT-TAAAATTA
1 TATTCATATTGTAAAATTA
139205 T
1 T
139206 CAAATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
TATTCATATTGTAAAATTA
Found at i:140163 original size:26 final size:26
Alignment explanation
Indices: 140129--140178 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
140119 TACATGCCGT
* *
140129 ATAATGGTTAGTTTTTATTTTTTTAAA
1 ATAATGGTTA-TATTAATTTTTTTAAA
140156 ATAA-GGTTATATTAATTTTTTTA
1 ATAATGGTTATATTAATTTTTTTA
140179 CATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 5 0.24
27 4 0.19
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (26 bp):
ATAATGGTTATATTAATTTTTTTAAA
Found at i:143329 original size:22 final size:22
Alignment explanation
Indices: 143288--143330 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
143278 GAAACAGCCC
* *
143288 TTTCTTTTTTTTTATTTTTTTA
1 TTTCTTTTTTTCTATGTTTTTA
*
143310 TTTCTTTTTTTCTCTGTTTTT
1 TTTCTTTTTTTCTATGTTTTT
143331 TCCTTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTCTTTTTTTCTATGTTTTTA
Found at i:143594 original size:70 final size:66
Alignment explanation
Indices: 143411--143597 Score: 180
Period size: 70 Copynumber: 2.7 Consensus size: 66
143401 TTTAAGTTCT
* * * *
143411 ATAATCAAATAAAAAAATTTTAAATTTCTATAAATAAAAATAAATTTTATCATCAAAAATTTAAA
1 ATAATCAAATAAAAAAAATTTAAATTT-TACAAAT-AAAATAAATTATACCATCAAAAATTTAAA
143476 CTC
64 CTC
* *
143479 AT-ATCATACCTAAAAAAACACATTTGAAATTTTACAAATCAAAATAAATTATACCCT-AAAAAT
1 ATAATCA-A-AT-AAAAAA-A-ATTT-AAATTTTACAAAT-AAAATAAATTATACCATCAAAAAT
143542 TTAAACTCGC
59 TTAAACT--C
143552 ATAATCAAATAAAAATAAATTTAAACTTTTACAAATAGAAATAAAT
1 ATAATCAAATAAAAA-AAATTTAAA-TTTTACAAATA-AAATAAAT
143598 AATATTTTTA
Statistics
Matches: 99, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
67 4 0.04
68 3 0.03
69 5 0.05
70 28 0.28
71 20 0.20
72 25 0.25
73 10 0.10
74 4 0.04
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.32
Consensus pattern (66 bp):
ATAATCAAATAAAAAAAATTTAAATTTTACAAATAAAATAAATTATACCATCAAAAATTTAAACT
C
Found at i:145043 original size:22 final size:21
Alignment explanation
Indices: 145018--145086 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 21
145008 TATAACATTT
145018 ATATTAATATTTAATAAATATA
1 ATATTAA-ATTTAATAAATATA
145040 ATATTTAAATTTTAAGTAAATA-A
1 ATA-TTAAA-TTTAA-TAAATATA
*
145063 AT-TTAAAATT-A-AAATATA
1 ATATTAAATTTAATAAATATA
145081 ATATTA
1 ATATTA
145087 TATAATATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
17 5 0.12
18 3 0.07
19 4 0.10
20 2 0.05
21 5 0.12
22 4 0.10
23 12 0.29
24 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
ATATTAAATTTAATAAATATA
Done.