Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013580.1 Kokia drynarioides strain JFW-HI SEQ_128606, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 246016
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:624 original size:4 final size:4
Alignment explanation
Indices: 604--670 Score: 55
Period size: 4 Copynumber: 16.2 Consensus size: 4
594 AACACATTAC
* * * * *
604 CTTT CTTT CATT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT ATTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT -CTTT CTTT
653 CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT C
671 CCGTTTATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
3 3 0.06
4 37 0.74
5 10 0.20
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:666 original size:17 final size:18
Alignment explanation
Indices: 604--670 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 18
594 AACACATTAC
604 CTTTCTTTCATTCTTCTTT
1 CTTTCTTTC-TTCTTCTTT
*
623 CTTTCCTCTCCTTCTTCCTTT
1 CTTT-CT-TTCTTCTT-CTTT
*
644 ATTTTCTTTCTT-TTCTTT
1 -CTTTCTTTCTTCTTCTTT
662 CTTTCTTTC
1 CTTTCTTTC
671 CCGTTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
17 8 0.20
18 4 0.10
19 6 0.15
20 11 0.28
21 8 0.20
22 3 0.08
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (18 bp):
CTTTCTTTCTTCTTCTTT
Found at i:1724 original size:6 final size:6
Alignment explanation
Indices: 1713--1740 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1703 ACGGGTATGG
1713 GGGAGA GGGAGA GGGAGA GGGAGA GGGA
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGA
1741 CAGTGGTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:2089 original size:26 final size:26
Alignment explanation
Indices: 2040--2089 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2030 GTTAGTTATT
2040 ATTATTTGATGTTCAATAATTTTTCA
1 ATTATTTGATGTTCAATAATTTTTCA
* *
2066 ATTATTTTAT-TTTAATAATATTTT
1 ATTATTTGATGTTCAATAAT-TTTT
2090 ATATAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (26 bp):
ATTATTTGATGTTCAATAATTTTTCA
Found at i:3989 original size:5 final size:5
Alignment explanation
Indices: 3981--4177 Score: 107
Period size: 5 Copynumber: 39.6 Consensus size: 5
3971 GAGTCTAATT
* * *
3981 GAATC GAATC -AAGTC GAATC GAAAT- GAATC AAATC GAATT GAATT GAATC
1 GAATC GAATC GAA-TC GAATC G-AATC GAATC GAATC GAATC GAATC GAATC
* * * * * *
4031 GAGT- GAGTA GAATC AAATC GAATA GAGTC -AAGTC -AAGTC GAATC GAATC
1 GAATC GAATC GAATC GAATC GAATC GAATC GAA-TC GAA-TC GAATC GAATC
* * * * * * * *
4080 GAGTC GAATC TAGTC GAATT GAATC GAGTC GAATC AAATT GAATC GGATC
1 GAATC GAATC GAATC GAATC GAATC GAATC GAATC GAATC GAATC GAATC
* * * * * * *
4130 GAATA AAATC GAACC GAATC GAGTT GAGTC GAATC GAATC AAATC GAA
1 GAATC GAATC GAATC GAATC GAATC GAATC GAATC GAATC GAATC GAA
4178 GTGAGTGAAA
Statistics
Matches: 144, Mismatches: 41, Indels: 14
0.72 0.21 0.07
Matches are distributed among these distances:
4 10 0.07
5 127 0.88
6 7 0.05
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (5 bp):
GAATC
Found at i:4257 original size:15 final size:15
Alignment explanation
Indices: 4195--4273 Score: 50
Period size: 15 Copynumber: 5.3 Consensus size: 15
4185 AAAGTGTTAA
* *
4195 AATCGAATCGAATTG
1 AATCGAGTCAAATTG
* * *
4210 AGTCGAGTCCAATAG
1 AATCGAGTCAAATTG
** * *
4225 AATCGAGTTGAGTCG
1 AATCGAGTCAAATTG
*
4240 AATCTAGTCAAATTG
1 AATCGAGTCAAATTG
**
4255 AATCGAGTTGAATTG
1 AATCGAGTCAAATTG
4270 AATC
1 AATC
4274 AAATTGAATC
Statistics
Matches: 47, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (15 bp):
AATCGAGTCAAATTG
Found at i:4262 original size:25 final size:25
Alignment explanation
Indices: 4234--4283 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4224 GAATCGAGTT
*
4234 GAGTCGAATCT-AGTCAAATTGAATC
1 GAGTCGAAT-TGAATCAAATTGAATC
*
4259 GAGTTGAATTGAATCAAATTGAATC
1 GAGTCGAATTGAATCAAATTGAATC
4284 AAATGAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (25 bp):
GAGTCGAATTGAATCAAATTGAATC
Found at i:7335 original size:43 final size:43
Alignment explanation
Indices: 7274--7405 Score: 169
Period size: 43 Copynumber: 3.1 Consensus size: 43
7264 GAATCACCTA
**
7274 ATGTATAAATAAAAGACTCATGTCTCAGGATGAGCATGAGATT
1 ATGTATAAATGGAAGACTCATGTCTCAGGATGAGCATGAGATT
* * *
7317 ATGTATAAATGGAAGACTCGTGACTC-GAGATGAGCATGATATT
1 ATGTATAAATGGAAGACTCATGTCTCAG-GATGAGCATGAGATT
* * *
7360 ATGTTTAAA-GGAAGACTCATGTCTCAAGATGAGTATGAGATT
1 ATGTATAAATGGAAGACTCATGTCTCAGGATGAGCATGAGATT
7402 ATGT
1 ATGT
7406 TTATAGGAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.42
43 44 0.58
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (43 bp):
ATGTATAAATGGAAGACTCATGTCTCAGGATGAGCATGAGATT
Found at i:7390 original size:42 final size:42
Alignment explanation
Indices: 7286--7426 Score: 183
Period size: 42 Copynumber: 3.3 Consensus size: 42
7276 GTATAAATAA
* *
7286 AAGACTCATGTCTCAGGATGAGCATGAGATTATGTATAAATGG
1 AAGACTCATGTCTCAAGATGAGCATGAGATTATGTTTAAA-GG
* * * *
7329 AAGACTCGTGACTCGAGATGAGCATGATATTATGTTTAAAGG
1 AAGACTCATGTCTCAAGATGAGCATGAGATTATGTTTAAAGG
* *
7371 AAGACTCATGTCTCAAGATGAGTATGAGATTATGTTTATAGG
1 AAGACTCATGTCTCAAGATGAGCATGAGATTATGTTTAAAGG
* *
7413 AAGATTTATGTCTC
1 AAGACTCATGTCTC
7427 GGTAGAGCAT
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 50 0.60
43 34 0.40
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (42 bp):
AAGACTCATGTCTCAAGATGAGCATGAGATTATGTTTAAAGG
Found at i:11141 original size:15 final size:16
Alignment explanation
Indices: 11123--11157 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11113 GGGTTTGGAC
11123 TTGGTTCA-ATTGGGT
1 TTGGTTCACATTGGGT
*
11138 TTGGTTCACTTTGGGT
1 TTGGTTCACATTGGGT
11154 TTGG
1 TTGG
11158 GTTATTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.09, C:0.09, G:0.34, T:0.49
Consensus pattern (16 bp):
TTGGTTCACATTGGGT
Found at i:17260 original size:20 final size:22
Alignment explanation
Indices: 17221--17260 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17211 CTTTTGTAAC
*
17221 TACCGATACTCAAGAAAGGTTT
1 TACCAATACTCAAGAAAGGTTT
17243 TACCAATACT-AA-AAAGGT
1 TACCAATACTCAAGAAAGGT
17261 CAGTAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (22 bp):
TACCAATACTCAAGAAAGGTTT
Found at i:20952 original size:26 final size:26
Alignment explanation
Indices: 20922--20976 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
20912 TGGGAATAGA
* *
20922 TAATTGTAAATAAAATTATTGTATTC
1 TAATTGTAAAAAAAAATATTGTATTC
20948 TAATTGTAAAAAAAAATATTGTATTC
1 TAATTGTAAAAAAAAATATTGTATTC
20974 TAA
1 TAA
20977 AAACAAATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (26 bp):
TAATTGTAAAAAAAAATATTGTATTC
Found at i:21744 original size:15 final size:15
Alignment explanation
Indices: 21704--21735 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
21694 AAATTTTTTA
21704 TTTTAATTAAT--CT
1 TTTTAATTAATAACT
21717 TTTTAATTAATAACT
1 TTTTAATTAATAACT
21732 TTTT
1 TTTT
21736 TATTCATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.65
15 6 0.35
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAATTAATAACT
Found at i:21892 original size:13 final size:14
Alignment explanation
Indices: 21876--21908 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
21866 TATATTTTTC
21876 TTTATATAT-AATA
1 TTTATATATAAATA
21889 TTTATATATCAAATA
1 TTTATATAT-AAATA
21904 TTTAT
1 TTTAT
21909 TTTCTCCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
15 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTATATATAAATA
Found at i:25583 original size:17 final size:16
Alignment explanation
Indices: 25550--25593 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
25540 TAGTAATAAA
*
25550 AATAA-AAATAAATGT
1 AATAATAAATAAAGGT
25565 AATAATAAACTAAAGGT
1 AATAATAAA-TAAAGGT
25582 AATAAATAAATA
1 AAT-AATAAATA
25594 TATGGATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 5 0.20
16 3 0.12
17 11 0.44
18 6 0.24
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (16 bp):
AATAATAAATAAAGGT
Found at i:41854 original size:35 final size:35
Alignment explanation
Indices: 41808--41878 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
41798 TGACCTAAAT
41808 TCTAAGAGATTGCTTGCAAGTCAAGTTAAACAAAA
1 TCTAAGAGATTGCTTGCAAGTCAAGTTAAACAAAA
*
41843 TCTAAGAGATTGTTTGCAAGTCAAGTTAAACAAAA
1 TCTAAGAGATTGCTTGCAAGTCAAGTTAAACAAAA
41878 T
1 T
41879 ATATTTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (35 bp):
TCTAAGAGATTGCTTGCAAGTCAAGTTAAACAAAA
Found at i:43678 original size:21 final size:19
Alignment explanation
Indices: 43652--43703 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
43642 TTTAATTTTC
43652 ATATAATATAAATTACAAAAT
1 ATATAATATAAA--ACAAAAT
* *
43673 ATATAAAATAAAATAAAAT
1 ATATAATATAAAACAAAAT
*
43692 ATATATTATAAA
1 ATATAATATAAA
43704 CTTGAGAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.59
21 11 0.41
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATAATATAAAACAAAAT
Found at i:46640 original size:16 final size:16
Alignment explanation
Indices: 46624--46679 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 16
46614 TTTTTTCATA
46624 AAAATATTTAAAAATAAT
1 AAAA-ATTTAAAAAT-AT
46642 AAAAAATTATAAAAATAT
1 -AAAAATT-TAAAAATAT
*
46660 AAAAATAT-AAAATAT
1 AAAAATTTAAAAATAT
46675 AAAAA
1 AAAAA
46680 AGAAATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
15 12 0.34
16 1 0.03
17 6 0.17
18 5 0.14
19 11 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATTTAAAAATAT
Found at i:46680 original size:9 final size:9
Alignment explanation
Indices: 46623--46680 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
46613 ATTTTTTCAT
*
46623 AAAAATATTT
1 AAAAATA-TA
46633 AAAAATAATA
1 AAAAAT-ATA
46643 AAAAAT-TA
1 AAAAATATA
46651 TAAAAATAT-
1 -AAAAATATA
46660 AAAAATAT-
1 AAAAATATA
46668 -AAAATATA
1 AAAAATATA
46676 AAAAA
1 AAAAA
46681 GAAATATTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
7 7 0.17
8 10 0.24
9 10 0.24
10 14 0.33
11 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAAATATA
Found at i:46680 original size:16 final size:17
Alignment explanation
Indices: 46621--46800 Score: 84
Period size: 19 Copynumber: 9.9 Consensus size: 17
46611 ATATTTTTTC
46621 ATAAAAATATT-TAAAAAT
1 ATAAAAA-ATTAT-AAAAT
46639 AATAAAAAATTATAAAA-
1 -ATAAAAAATTATAAAAT
46656 ATATAAAAA-TATAAAAT
1 ATA-AAAAATTATAAAAT
*
46673 ATAAAAAAGAAATATTAAAAT
1 AT--AAAA-AATTA-TAAAAT
* *
46694 ATTAAAATTATTATAAACT
1 A-TAAAA-AATTATAAAAT
* *
46713 -TACTAAAACTATAAAATT
1 ATA-AAAAATTATAAAA-T
46731 ATAAAATAATTATCAAAAGT
1 ATAAAA-AATTAT-AAAA-T
*
46751 -TATAAATATTATAAAAT
1 ATA-AAAAATTATAAAAT
*
46768 AT-AAAAATTAACAAAAT
1 ATAAAAAATT-ATAAAAT
* *
46785 CTAATAAATTATAAAA
1 ATAAAAAATTATAAAA
46801 AATTATAACA
Statistics
Matches: 126, Mismatches: 17, Indels: 38
0.70 0.09 0.21
Matches are distributed among these distances:
16 16 0.13
17 29 0.23
18 26 0.21
19 30 0.24
20 17 0.13
21 7 0.06
22 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (17 bp):
ATAAAAAATTATAAAAT
Found at i:46764 original size:9 final size:8
Alignment explanation
Indices: 46644--46800 Score: 74
Period size: 8 Copynumber: 18.5 Consensus size: 8
46634 AAAATAATAA
46644 AAAATTAT
1 AAAATTAT
*
46652 AAAAATAT
1 AAAATTAT
*
46660 AAAAATAT
1 AAAATTAT
46668 AAAA-TAT
1 AAAATTAT
* *
46675 AAAA-AAG
1 AAAATTAT
46682 AAATATTA-
1 AAA-ATTAT
46690 AAATATTA-
1 AAA-ATTAT
46698 AAATTATTAT
1 AAA--ATTAT
*
46708 AAACTTACT
1 AAAATTA-T
*
46717 AAAACTAT
1 AAAATTAT
46725 AAAATTAT
1 AAAATTAT
46733 AAAATAATTAT
1 --AA-AATTAT
46744 CAAAAGTTAT
1 -AAAA-TTAT
46754 AAATATTAT
1 AAA-ATTAT
46763 AAAA-TAT
1 AAAATTAT
*
46770 AAAAATTAAC
1 -AAAATT-AT
46780 AAAATCTA-
1 AAAAT-TAT
46788 ATAAATTAT
1 A-AAATTAT
46797 AAAA
1 AAAA
46801 AATTATAACA
Statistics
Matches: 123, Mismatches: 10, Indels: 32
0.75 0.06 0.19
Matches are distributed among these distances:
7 14 0.11
8 53 0.43
9 36 0.29
10 14 0.11
11 6 0.05
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (8 bp):
AAAATTAT
Found at i:46805 original size:10 final size:10
Alignment explanation
Indices: 46725--46808 Score: 56
Period size: 10 Copynumber: 9.0 Consensus size: 10
46715 CTAAAACTAT
46725 AAAATTATAA
1 AAAATTATAA
*
46735 AATAATTATCA
1 AA-AATTATAA
*
46746 AAAGTTAT-A
1 AAAATTATAA
*
46755 AATATTAT--
1 AAAATTATAA
46763 AAAA-TAT-A
1 AAAATTATAA
*
46771 AAAATTA-AC
1 AAAATTATAA
*
46780 AAAA-TCTAA
1 AAAATTATAA
*
46789 TAAATTATAA
1 AAAATTATAA
46799 AAAATTATAA
1 AAAATTATAA
46809 CATTAATATA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
7 3 0.05
8 8 0.14
9 17 0.30
10 20 0.35
11 9 0.16
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (10 bp):
AAAATTATAA
Found at i:61005 original size:21 final size:22
Alignment explanation
Indices: 60967--61009 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
60957 AAAATATTAA
* *
60967 AATTAATAAAGCTTATAAAAAT
1 AATTAATAAAGATCATAAAAAT
60989 AATTAA-AAAGATCATAAAAAT
1 AATTAATAAAGATCATAAAAAT
61010 TTGAATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (22 bp):
AATTAATAAAGATCATAAAAAT
Found at i:61536 original size:12 final size:12
Alignment explanation
Indices: 61518--61547 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
61508 AAATGAACTT
61518 AAAATGGAAATG
1 AAAATGGAAATG
*
61530 GAAATGGAAATG
1 AAAATGGAAATG
61542 AAAATG
1 AAAATG
61548 AAAAATGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:65543 original size:42 final size:42
Alignment explanation
Indices: 65480--65563 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
65470 CTTACTTAGC
*
65480 CTATGCTTGCCCTCAAGCATAATGTTTATTCTATATTAATGT
1 CTATGCTTGCCCTCAAACATAATGTTTATTCTATATTAATGT
65522 CTATGCTTGCCCTCAAACATAATGTTTATTCTATATTAATGT
1 CTATGCTTGCCCTCAAACATAATGTTTATTCTATATTAATGT
65564 TATTCGATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (42 bp):
CTATGCTTGCCCTCAAACATAATGTTTATTCTATATTAATGT
Found at i:71273 original size:20 final size:21
Alignment explanation
Indices: 71235--71274 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
71225 TAAACCAACC
*
71235 ATCACTGAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
71256 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
71275 TAAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:84597 original size:33 final size:33
Alignment explanation
Indices: 84557--84623 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
84547 AGCAACAGTA
84557 AAAGTTAGATATATATGTCATAAACTATGCTGT
1 AAAGTTAGATATATATGTCATAAACTATGCTGT
84590 AAAGTTAGATATATATGTCATAAACTATGCTGT
1 AAAGTTAGATATATATGTCATAAACTATGCTGT
84623 A
1 A
84624 CCCTTGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (33 bp):
AAAGTTAGATATATATGTCATAAACTATGCTGT
Found at i:87281 original size:6 final size:6
Alignment explanation
Indices: 87270--87305 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
87260 TATAAGAAAC
* *
87270 ATCATT ATCATT ATCATT ATCATT AGCATT AGCATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
87306 TTTCTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (6 bp):
ATCATT
Found at i:96539 original size:26 final size:26
Alignment explanation
Indices: 96510--96574 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
96500 AACGAGTTCC
* *
96510 TGCAGCGACAATTCTGGGCATGC-TCA
1 TGCAGCGACAATTCTAGACAT-CATCA
* *
96536 TGCAGCTACATTTCTAGACATCATCA
1 TGCAGCGACAATTCTAGACATCATCA
*
96562 TGCAGTGACAATT
1 TGCAGCGACAATT
96575 TTGAGCGCAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 1 0.03
26 30 0.97
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (26 bp):
TGCAGCGACAATTCTAGACATCATCA
Found at i:97808 original size:9 final size:9
Alignment explanation
Indices: 97794--97822 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
97784 GTATGGTGTT
97794 TTTTCTTCC
1 TTTTCTTCC
97803 TTTTCTT-C
1 TTTTCTTCC
97811 TTTTCTTCC
1 TTTTCTTCC
97820 TTT
1 TTT
97823 CTGTGCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTCTTCC
Found at i:98985 original size:17 final size:17
Alignment explanation
Indices: 98963--99088 Score: 155
Period size: 17 Copynumber: 7.3 Consensus size: 17
98953 CAAACTCATC
98963 TTAAATTTATTTTAAGA-
1 TTAAATTTATTTTAA-AT
* *
98980 TTAAATTTGTTTAAAAAT
1 TTAAATTTATTT-TAAAT
98998 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
*
99015 TTAAATTTATTTCAAAT
1 TTAAATTTATTTTAAAT
* *
99032 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAT
99049 TTAAATTTATTTTCAAAT
1 TTAAATTTATTTT-AAAT
* *
99067 TTAAAATTATTATAAAT
1 TTAAATTTATTTTAAAT
99084 TTAAA
1 TTAAA
99089 ATAAATAAAG
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
17 67 0.71
18 27 0.29
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:99002 original size:35 final size:34
Alignment explanation
Indices: 98963--99077 Score: 151
Period size: 35 Copynumber: 3.3 Consensus size: 34
98953 CAAACTCATC
* *
98963 TTAAATTTATTTTAAGATTAAATTTGTTTAAAAAT
1 TTAAATTTATTTTAAGATTAAATTTATTT-CAAAT
98998 TTAAATTTATTTTAA-ATTTAAATTTATTTCAAAT
1 TTAAATTTATTTTAAGA-TTAAATTTATTTCAAAT
* *
99032 TTAAATTTAATTTAAGTTTAAATTTATTTTCAAAT
1 TTAAATTTATTTTAAGATTAAATTTA-TTTCAAAT
*
99067 TTAAAATTATT
1 TTAAATTTATT
99078 ATAAATTTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
34 28 0.39
35 43 0.61
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (34 bp):
TTAAATTTATTTTAAGATTAAATTTATTTCAAAT
Found at i:99005 original size:6 final size:6
Alignment explanation
Indices: 98994--99088 Score: 78
Period size: 6 Copynumber: 16.5 Consensus size: 6
98984 ATTTGTTTAA
*
98994 AAATTT AAATTT -ATTTT AAATTT AAATTT --ATTT CAAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
* * *
99040 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAAATT --ATTAT AAATTT
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT AAATT-T AAATTT
99086 AAA
1 AAA
99089 ATAAATAAAG
Statistics
Matches: 71, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
4 6 0.08
5 14 0.20
6 40 0.56
7 11 0.15
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:99013 original size:11 final size:11
Alignment explanation
Indices: 99014--99069 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
99004 TTATTTTAAA
99014 TTTAAATTTAT
1 TTTAAATTTAT
* *
99025 TTCAAATTTAAA
1 TTTAAATTT-AT
*
99037 TTT-AATTTAAG
1 TTTAAATTT-AT
99048 TTTAAATTTAT
1 TTTAAATTTAT
99059 TTTCAAATTTA
1 TTT-AAATTTA
99070 AAATTATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 22 0.59
12 15 0.41
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:99779 original size:19 final size:18
Alignment explanation
Indices: 99738--99782 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
99728 AATAATATCT
*
99738 ATAATAATATCAATGGTA
1 ATAATAATAACAATGGTA
* *
99756 TTAATAATAAACAGTGGTA
1 ATAATAAT-AACAATGGTA
99775 ATAATAAT
1 ATAATAAT
99783 GATGTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.33
Consensus pattern (18 bp):
ATAATAATAACAATGGTA
Found at i:100858 original size:29 final size:29
Alignment explanation
Indices: 100816--101107 Score: 333
Period size: 29 Copynumber: 9.9 Consensus size: 29
100806 CCCTGGAGGT
* *
100816 CCCT-AAACCTTCCAAACATTCCATTTTTA
1 CCCTCAAA-CTTCCAAAAATCCCATTTTTA
*
100845 CCCTCGAACTTCCAAAAATCCCATTTTTA
1 CCCTCAAACTTCCAAAAATCCCATTTTTA
* * *
100874 CCCTCGAACTTCAAAAAATCCCGTTTTTGA
1 CCCTCAAACTTCCAAAAATCCCATTTTT-A
*
100904 CCC-CGAAACTTCCAAAAATTCCATTTTTA
1 CCCTC-AAACTTCCAAAAATCCCATTTTTA
*
100933 TCCTCAAACTTCCAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATCCCATTTTT-A
*
100963 CCCTAAAACTTCCAAAAATTCCC-TTTTTA
1 CCCTCAAACTTCCAAAAA-TCCCATTTTTA
*
100992 CCCCCAAACTTCCAAAAATCCCATTTTTAA
1 CCCTCAAACTTCCAAAAATCCCATTTTT-A
* *
101022 CCCTAAAACTTCCAAAAATTCCA-TTTTA
1 CCCTCAAACTTCCAAAAATCCCATTTTTA
*
101050 CCCCCCAAACTTCCAAAAATCCCATTTTTTA
1 -CCCTCAAACTTCCAAAAATCCCA-TTTTTA
* *
101081 CACTCGAACTTCC-AAAATCTCCATTTT
1 CCCTCAAACTTCCAAAAATC-CCATTTT
101108 CGACTTCGAA
Statistics
Matches: 227, Mismatches: 24, Indels: 24
0.83 0.09 0.09
Matches are distributed among these distances:
28 5 0.02
29 131 0.58
30 82 0.36
31 9 0.04
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.32
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATCCCATTTTTA
Found at i:100943 original size:59 final size:59
Alignment explanation
Indices: 100824--101107 Score: 344
Period size: 59 Copynumber: 4.8 Consensus size: 59
100814 GTCCCTAAAC
* * * * *
100824 CTTCCAAACATTCCATTTTT-ACCCTCG-AACTTCCAAAAATCCCATTTTTACCCTCGAA
1 CTTCCAAAAATCCCATTTTTGACCC-CGAAACTTCCAAAAATTCCATTTTTACCCCCAAA
* * * *
100882 CTTCAAAAAATCCCGTTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTATCCTCAAA
1 CTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCCCAAA
** *
100941 CTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCCTTTTTACCCCCAAA
1 CTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCCCAAA
* **
101000 CTTCCAAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCCA-TTTTACCCCCCAAA
1 CTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTA-CCCCCAAA
* *
101059 CTTCCAAAAATCCCATTTTTTACACTCG-AACTTCC-AAAATCTCCATTTT
1 CTTCCAAAAATCCCATTTTTGAC-CCCGAAACTTCCAAAAAT-TCCATTTT
101108 CGACTTCGAA
Statistics
Matches: 200, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
58 28 0.14
59 168 0.84
60 4 0.02
ACGTcount: A:0.33, C:0.32, G:0.02, T:0.32
Consensus pattern (59 bp):
CTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCCCAAA
Found at i:103273 original size:26 final size:26
Alignment explanation
Indices: 103244--103314 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
103234 AACGAGTTCC
103244 TGCAGCGACAATTCTGGGCATGC-TCA
1 TGCAGCGACAATTCTGGGCAT-CATCA
* *
103270 TGCAGCGACATTTCTGGACATCATCA
1 TGCAGCGACAATTCTGGGCATCATCA
* *
103296 TGCAGTGACAATTTTGGGC
1 TGCAGCGACAATTCTGGGC
103315 GCAATTCTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (26 bp):
TGCAGCGACAATTCTGGGCATCATCA
Found at i:109969 original size:51 final size:51
Alignment explanation
Indices: 109789--109968 Score: 299
Period size: 51 Copynumber: 3.5 Consensus size: 51
109779 TAAACGAAAG
*
109789 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCTTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAA
*
109840 GGTTCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAA
* *
109891 AGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTCA-GGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTT-ATGGATTAAA
*
109942 GGTCCGATGACTAAGTGTTATCGTGAG
1 GGTCCGATGACTAAGTGTCATCGTGAG
109969 TTTATGGATT
Statistics
Matches: 121, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
51 120 0.99
52 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAA
Found at i:117162 original size:50 final size:51
Alignment explanation
Indices: 117022--117193 Score: 249
Period size: 51 Copynumber: 3.4 Consensus size: 51
117012 TAAACGAAAG
* ** *
117022 GGTCCGATGACTAAGTGTCATCATGAGCAAATGAATCCTTTGTGGATTAAA
1 GGTCTGATGACTAAGTGTCATTGTGAGCAAATGAATCCTTTATGGATTAAA
*
117073 GGT-TCGATGACTAAGTGTCATTGTGAGCAAATGAATCCTTTACGGATTAAA
1 GGTCT-GATGACTAAGTGTCATTGTGAGCAAATGAATCCTTTATGGATTAAA
* * *
117124 GGTCTGAT-ACTAAGTGTCATTGTGTGTAAATGAGTCCTTTATGGATTAAA
1 GGTCTGATGACTAAGTGTCATTGTGAGCAAATGAATCCTTTATGGATTAAA
117174 GGTCTGATGACTAAGTGTCA
1 GGTCTGATGACTAAGTGTCA
117194 CCGTGAGTTT
Statistics
Matches: 109, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
50 46 0.42
51 62 0.57
52 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (51 bp):
GGTCTGATGACTAAGTGTCATTGTGAGCAAATGAATCCTTTATGGATTAAA
Found at i:126148 original size:23 final size:24
Alignment explanation
Indices: 126109--126163 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
126099 GGAGAGTTCT
*
126109 CAAGAGGAAAAAGAAAAAGAAAAA
1 CAAGAAGAAAAAGAAAAAGAAAAA
*
126133 CAAGAAGAAAAA-AAAATGAAAAA
1 CAAGAAGAAAAAGAAAAAGAAAAA
126156 CAAGAAGA
1 CAAGAAGA
126164 TACCCATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.75, C:0.05, G:0.18, T:0.02
Consensus pattern (24 bp):
CAAGAAGAAAAAGAAAAAGAAAAA
Found at i:140267 original size:14 final size:14
Alignment explanation
Indices: 140250--140285 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
140240 TTAATACTTG
*
140250 TATATATATATAAA
1 TATATATATACAAA
*
140264 TATATATATACCAA
1 TATATATATACAAA
140278 TATATATA
1 TATATATA
140286 CGTTTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATATATACAAA
Found at i:140268 original size:12 final size:13
Alignment explanation
Indices: 140251--140285 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
140241 TAATACTTGT
140251 ATATATATATA-A
1 ATATATATATACA
140263 ATATATATATACCA
1 ATATATATATA-CA
140277 ATATATATA
1 ATATATATA
140286 CGTTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.52
14 10 0.48
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATATATACA
Found at i:141152 original size:30 final size:30
Alignment explanation
Indices: 141118--141273 Score: 144
Period size: 29 Copynumber: 5.3 Consensus size: 30
141108 AAAAATTTAG
*
141118 TTTTGACCCTCGAACTTTCCTAAAATCACA
1 TTTTGACCCTCAAACTTTCCTAAAATCACA
*
141148 TTTTGATCC-CAAACTTT-CTCAAAATCACA
1 TTTTGACCCTCAAACTTTCCT-AAAATCACA
* *
141177 TTTTGACCC-CTAAACTTTCCCAAAATCAAA
1 TTTTGACCCTC-AAACTTTCCTAAAATCACA
* *
141207 TTTTGA-CCTCTAACTTTCC-AAAATTACA
1 TTTTGACCCTCAAACTTTCCTAAAATCACA
* * * ** *
141235 CTTTAACCCTTAAA-TTTTATAAAATTACA
1 TTTTGACCCTCAAACTTTCCTAAAATCACA
141264 TTTTGACCCT
1 TTTTGACCCT
141274 AAATTCTCTA
Statistics
Matches: 104, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
28 16 0.15
29 57 0.55
30 30 0.29
31 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (30 bp):
TTTTGACCCTCAAACTTTCCTAAAATCACA
Found at i:141172 original size:59 final size:60
Alignment explanation
Indices: 141130--141248 Score: 147
Period size: 59 Copynumber: 2.0 Consensus size: 60
141120 TTGACCCTCG
* *
141130 AACTTTCCTAAAATCACATTTTGATCC-CAAACTTTCTCAAAA-TCACATTTTGACCCCTA
1 AACTTTCCCAAAATCAAATTTTGA-CCTCAAACTTTCTCAAAATTCACATTTTGACCCCTA
* * * *
141189 AACTTTCCCAAAATCAAATTTTGACCTCTAACTTTC-CAAAATT-ACACTTTAACCCTTA
1 AACTTTCCCAAAATCAAATTTTGACCTCAAACTTTCTCAAAATTCACATTTTGACCCCTA
141247 AA
1 AA
141249 TTTTATAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
58 21 0.40
59 31 0.60
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (60 bp):
AACTTTCCCAAAATCAAATTTTGACCTCAAACTTTCTCAAAATTCACATTTTGACCCCTA
Found at i:141273 original size:29 final size:28
Alignment explanation
Indices: 141226--141295 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
141216 CTAACTTTCC
* *
141226 AAAATTACACTTTAACCCTTAAATTTTAT
1 AAAATTACATTTTAACCC-TAAATTCTAT
* *
141255 AAAATTACATTTTGACCCTAAATTCTCT
1 AAAATTACATTTTAACCCTAAATTCTAT
141283 AAAACTT-CATTTT
1 AAAA-TTACATTTT
141296 TCGACCCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 18 0.50
29 18 0.50
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (28 bp):
AAAATTACATTTTAACCCTAAATTCTAT
Found at i:141293 original size:28 final size:27
Alignment explanation
Indices: 141118--141295 Score: 117
Period size: 29 Copynumber: 6.1 Consensus size: 27
141108 AAAAATTTAG
* *
141118 TTTTGACCCTCGAACTTTCCTAAAATCACA
1 TTTTGACCCT--AAATTT-CTAAAATTACA
*
141148 TTTTGATCCC-AAACTTTCTCAAAATCACA
1 TTTTGA-CCCTAAA-TTTCT-AAAATTACA
* * *
141177 TTTTGACCCCTAAACTTTCCCAAAATCAAA
1 TTTTGA-CCCTAAA-TTT-CTAAAATTACA
* *
141207 TTTTGACCTCTAACTTTCCAAAATTACA
1 TTTTGACC-CTAAATTTCTAAAATTACA
* * *
141235 CTTTAACCCTTAAATTTTATAAAATTACA
1 TTTTGACCC-TAAA-TTTCTAAAATTACA
141264 TTTTGACCCTAAATTCTCTAAAACTT-CA
1 TTTTGACCCTAAATT-TCTAAAA-TTACA
141292 TTTT
1 TTTT
141296 TCGACCCCTT
Statistics
Matches: 123, Mismatches: 15, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
27 3 0.02
28 38 0.31
29 47 0.38
30 31 0.25
31 4 0.03
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (27 bp):
TTTTGACCCTAAATTTCTAAAATTACA
Found at i:150014 original size:2 final size:2
Alignment explanation
Indices: 150007--150036 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
149997 AGAGTGATGT
150007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
150037 GTGGCATTAG
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):
TA
Found at i:155527 original size:25 final size:24
Alignment explanation
Indices: 155499--155551 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
155489 TTCTCCCCCT
155499 TTATGTCTCACTCTATCTCACC-TCC
1 TTATGTCTC-CT-TATCTCACCTTCC
* *
155524 TTATTTCTCCTTCTCTCACCTTCC
1 TTATGTCTCCTTATCTCACCTTCC
155548 TTAT
1 TTAT
155552 CTCTTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 9 0.36
25 8 0.32
ACGTcount: A:0.13, C:0.38, G:0.02, T:0.47
Consensus pattern (24 bp):
TTATGTCTCCTTATCTCACCTTCC
Found at i:162683 original size:35 final size:35
Alignment explanation
Indices: 162642--162711 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
162632 CATAGAAAAA
162642 GTAGGACTGATTTTTAGTATTTTTTTTAAATTAAG
1 GTAGGACTGATTTTTAGTATTTTTTTTAAATTAAG
162677 GTAGGACTGATTTTTAGTATTTTTTTTAAATTAAG
1 GTAGGACTGATTTTTAGTATTTTTTTTAAATTAAG
162712 TCTTTCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (35 bp):
GTAGGACTGATTTTTAGTATTTTTTTTAAATTAAG
Found at i:170185 original size:8 final size:9
Alignment explanation
Indices: 170152--170183 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
170142 AAGAAATTTG
170152 AAAAAATAA
1 AAAAAATAA
170161 AAAAAATAA
1 AAAAAATAA
170170 AAAAAATAA
1 AAAAAATAA
170179 AAAAA
1 AAAAA
170184 TATAGGCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAATAA
Found at i:176680 original size:15 final size:15
Alignment explanation
Indices: 176662--176717 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
176652 ACATGAAAGA
* *
176662 TGCGAGCACTAGTGT
1 TGCGAGCACTAATGC
176677 TGCGAGCACTAATGC
1 TGCGAGCACTAATGC
* *
176692 TACGAACACTAATGC
1 TGCGAGCACTAATGC
*
176707 AGCGAGCACTA
1 TGCGAGCACTA
176718 CTGTTGTGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (15 bp):
TGCGAGCACTAATGC
Found at i:178065 original size:13 final size:13
Alignment explanation
Indices: 178047--178071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
178037 CCCATTTTAT
178047 CATTTTTAGCATG
1 CATTTTTAGCATG
178060 CATTTTTAGCAT
1 CATTTTTAGCAT
178072 TTTTAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:187192 original size:23 final size:23
Alignment explanation
Indices: 187173--187332 Score: 221
Period size: 23 Copynumber: 7.0 Consensus size: 23
187163 TCCATTTACA
187173 CATAAATCATATTAATATTTAAG
1 CATAAATCATATTAATATTTAAG
*
187196 CATAAATCACATTAATATTTAAG
1 CATAAATCATATTAATATTTAAG
**
187219 CATAAATCATATTAGCATTTAAG
1 CATAAATCATATTAATATTTAAG
* *
187242 CAAAAATCATGTTAATATTTAAG
1 CATAAATCATATTAATATTTAAG
* * *
187265 CACAACTCACATTAATATTTAAG
1 CATAAATCATATTAATATTTAAG
*
187288 CATAAATCATATTAACATTTAAG
1 CATAAATCATATTAATATTTAAG
* *
187311 CATAAATTACATTAATATTTAA
1 CATAAATCATATTAATATTTAA
187333 CACATTTAAT
Statistics
Matches: 118, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 118 1.00
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (23 bp):
CATAAATCATATTAATATTTAAG
Found at i:187238 original size:69 final size:69
Alignment explanation
Indices: 187165--187336 Score: 258
Period size: 69 Copynumber: 2.5 Consensus size: 69
187155 TTCATGAGTC
*
187165 CATTTACA-CATAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAATCAT
1 CATTTA-AGCATAAATCATATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATCAT
*
187229 ATTAG
65 ATTAA
* * *
187234 CATTTAAGCAAAAATCATGTTAATATTTAAGCACAACTCACATTAATATTTAAGCATAAATCATA
1 CATTTAAGCATAAATCATATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATCATA
187299 TTAA
66 TTAA
* *
187303 CATTTAAGCATAAATTACATTAATATTTAA-CACA
1 CATTTAAGCATAAATCATATTAATATTTAAGCACA
187337 TTTAATGATA
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
68 5 0.05
69 88 0.95
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (69 bp):
CATTTAAGCATAAATCATATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATCATA
TTAA
Found at i:189872 original size:6 final size:6
Alignment explanation
Indices: 189861--189916 Score: 71
Period size: 6 Copynumber: 9.5 Consensus size: 6
189851 CAGCAATTTA
*
189861 TTCTTT TTCTTT TTCTTT TTCTTT CTTCTTT TTCTCT TT-TTT TT-TTT
1 TTCTTT TTCTTT TTCTTT TTCTTT -TTCTTT TTCTTT TTCTTT TTCTTT
*
189908 TTGTTT TTC
1 TTCTTT TTC
189917 AAGTGACTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
5 9 0.20
6 30 0.67
7 6 0.13
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:214027 original size:3 final size:3
Alignment explanation
Indices: 214019--214056 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
214009 TTTATTTCTT
214019 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
214057 TCACTTTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:220662 original size:41 final size:41
Alignment explanation
Indices: 220589--220824 Score: 346
Period size: 41 Copynumber: 5.7 Consensus size: 41
220579 TCAAGTCATA
** * * * * *
220589 AGTCTTCCTTTAACCATATTCTCAGTCCCATCTCGATACATG
1 AGTCTTCC-TTATTCATAATCTCATTCTCATCTCGAGATATG
* * *
220631 AGTCTTCCTTAATCTTAATCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGATATG
220672 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGATATG
1 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGATATG
220713 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGATATG
1 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGATATG
*
220754 AGTCTTCTTTATTCATAATCTCATTCTCATCTCGAGATATG
1 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGATATG
* *
220795 AGTCTTTCTTATTCATAATCTCATGCTCAT
1 AGTCTTCCTTATTCATAATCTCATTCTCAT
220825 TTCTAAGTCA
Statistics
Matches: 181, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
41 173 0.96
42 8 0.04
ACGTcount: A:0.24, C:0.25, G:0.09, T:0.41
Consensus pattern (41 bp):
AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGATATG
Found at i:221733 original size:22 final size:22
Alignment explanation
Indices: 221692--221733 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
221682 CATAATTAAG
* *
221692 TTAATTAATCATCTTTTTAACC
1 TTAATTAATCATATTATTAACC
*
221714 TTAATTAATCTTATTATTAA
1 TTAATTAATCATATTATTAA
221734 TCAATATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATTAATCATATTATTAACC
Found at i:229439 original size:17 final size:19
Alignment explanation
Indices: 229417--229453 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
229407 TATAGCAATA
229417 TTTC-TTTT-TTTTCTTTT
1 TTTCTTTTTCTTTTCTTTT
229434 TTTCTTTTTCTTTTCTTTT
1 TTTCTTTTTCTTTTCTTTT
229453 T
1 T
229454 CTCATTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 4 0.22
19 10 0.56
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTCTTTTTCTTTTCTTTT
Found at i:229447 original size:11 final size:11
Alignment explanation
Indices: 229417--229455 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
229407 TATAGCAATA
*
229417 TTTCTTTTTTT
1 TTTCTTTTCTT
*
229428 TCTTTTTTTCTT
1 T-TTCTTTTCTT
229440 TTTCTTTTCTT
1 TTTCTTTTCTT
229451 TTTCT
1 TTTCT
229456 CATTCAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:229454 original size:17 final size:17
Alignment explanation
Indices: 229417--229455 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
229407 TATAGCAATA
*
229417 TTTCTTTTTTTTCTTTT
1 TTTCTTTTTTTTCTCTT
229434 TTTCTTTTTCTTT-TCTT
1 TTTCTTTTT-TTTCTCTT
229451 TTTCT
1 TTTCT
229456 CATTCAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTCTTTTTTTTCTCTT
Found at i:230204 original size:21 final size:21
Alignment explanation
Indices: 230178--230224 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
230168 CTCTCATTCC
* *
230178 TCCTTGTGCTTCTTCTT-TTAG
1 TCCTTGCGCTTCCTCTTCTT-G
230199 TCCTTGCGCTTCCTCTTCTTG
1 TCCTTGCGCTTCCTCTTCTTG
230220 TCCTT
1 TCCTT
230225 CGAACCAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.02, C:0.32, G:0.13, T:0.53
Consensus pattern (21 bp):
TCCTTGCGCTTCCTCTTCTTG
Found at i:238920 original size:133 final size:133
Alignment explanation
Indices: 238641--238908 Score: 491
Period size: 133 Copynumber: 2.0 Consensus size: 133
238631 TACCTACAAT
238641 TACCCCATCTCTCGATGTTGGCAACTCTATTCACTTAAGAACAAGTGATAAAATCTCTTCTAATC
1 TACCCCATCTCTCGATGTTGGCAACTCTATTCACTTAAGAACAAGTGATAAAATCTCTTCTAATC
**
238706 CCAAGAAGATCTCACTGACTTGCTTGTTAATCTAACTTGTCACCGTATCTCTTGATGTTTGTAGA
66 CCAAGAAGATCTCACTGACTTGCTTGTTAATCTAACTTGTCACCGTATCTCTTGATGTCGGTAGA
238771 CTG
131 CTG
* *
238774 TACCCCATTTCTCGATGTTGGCAACTCTATTCACTTAAGAACAAGTGATAGAATCTCTTCTAATC
1 TACCCCATCTCTCGATGTTGGCAACTCTATTCACTTAAGAACAAGTGATAAAATCTCTTCTAATC
*
238839 CCAAGAAGCTCTCACTGACTTGCTTGTTAATCTAACTTGTCACCGTATCTCTTGATGTCGGTAGA
66 CCAAGAAGATCTCACTGACTTGCTTGTTAATCTAACTTGTCACCGTATCTCTTGATGTCGGTAGA
238904 CTG
131 CTG
238907 TA
1 TA
238909 ATTCCACTCT
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 130 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Consensus pattern (133 bp):
TACCCCATCTCTCGATGTTGGCAACTCTATTCACTTAAGAACAAGTGATAAAATCTCTTCTAATC
CCAAGAAGATCTCACTGACTTGCTTGTTAATCTAACTTGTCACCGTATCTCTTGATGTCGGTAGA
CTG
Found at i:240005 original size:41 final size:41
Alignment explanation
Indices: 239922--240190 Score: 297
Period size: 41 Copynumber: 6.5 Consensus size: 41
239912 TATGCTCTAC
* * * * *
239922 CGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTAATCT
1 CGAGACATGAGTCTTCC-TTAATCATAATCTCATTCTCATCT
* *
239964 CGAGACATGAGTCTTCCTTAATCTTAATCTTATTCTCATCT
1 CGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATCT
*
240005 CGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATCT
* * *
240046 CGAGATATAAGTCTTCCTTATTCATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATCT
* * * *
240087 CTAGATATGAGTCTTCCTTATTCATAATCTCATTCTCATTCC
1 CGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCA-TCT
* * * * * *
240129 CGAGTCACGAGTCTTCCACTAATACA-AATTCTCATGCTCAACC
1 CGAGACATGAGTCTTCC-TTAAT-CATAA-TCTCATTCTCATCT
240172 CGAGACATGAGTCTTCCTT
1 CGAGACATGAGTCTTCCTT
240191 TTTATACACC
Statistics
Matches: 197, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
41 132 0.67
42 31 0.16
43 22 0.11
44 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.38
Consensus pattern (41 bp):
CGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATCT
Found at i:242210 original size:11 final size:11
Alignment explanation
Indices: 242194--242218 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
242184 AAGTTGATGC
242194 ATAATCTATGG
1 ATAATCTATGG
242205 ATAATCTATGG
1 ATAATCTATGG
242216 ATA
1 ATA
242219 GTGGATTTAG
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:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
ATAATCTATGG
Done.