Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1648
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: 63207
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:96 original size:17 final size:17
Alignment explanation
Indices: 72--128 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
62 TTGTAATTTT
72 TATTTAATAATAAATTAG
1 TATTTAATAATAAATT-G
*
90 T-TTTAAT--TAAATTT
1 TATTTAATAATAAATTG
* *
104 TATTTAATAATAATTTT
1 TATTTAATAATAAATTG
121 TATTTAAT
1 TATTTAAT
129 TTTTGTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 1 0.03
15 12 0.35
17 20 0.59
18 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTAATAATAAATTG
Found at i:826 original size:16 final size:15
Alignment explanation
Indices: 807--840 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
797 TTTATCATTT
807 AAAAAATAAAAATTAA
1 AAAAAATAAAAA-TAA
*
823 AAAAAATTAAAATAA
1 AAAAAATAAAAATAA
838 AAA
1 AAA
841 TTAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAATAAAAATAA
Found at i:829 original size:10 final size:11
Alignment explanation
Indices: 810--850 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
800 ATCATTTAAA
810 AAATAAAAATT
1 AAATAAAAATT
821 AAA-AAAAATT
1 AAATAAAAATT
831 AAAATAAAAATT
1 -AAATAAAAATT
*
843 AATTAAAA
1 AAATAAAA
851 TACTTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 7 0.26
11 13 0.48
12 7 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAAAATT
Found at i:839 original size:12 final size:12
Alignment explanation
Indices: 809--844 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
799 TATCATTTAA
809 AAAATAAAAATT
1 AAAATAAAAATT
821 -AAA-AAAAATT
1 AAAATAAAAATT
831 AAAATAAAAATT
1 AAAATAAAAATT
843 AA
1 AA
845 TTAAAATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 7 0.32
11 6 0.27
12 9 0.41
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:1069 original size:23 final size:23
Alignment explanation
Indices: 1025--1077 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1015 TAATATTTAA
*
1025 AATTAAAAAAATAAATTAAAAAT
1 AATTAATAAAATAAATTAAAAAT
1048 AATTAATAAAAT-AATTAAAAAAT
1 AATTAATAAAATAAATT-AAAAAT
*
1071 ATTTAAT
1 AATTAAT
1078 TAATCTGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATTAATAAAATAAATTAAAAAT
Found at i:1071 original size:11 final size:11
Alignment explanation
Indices: 1025--1076 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
1015 TAATATTTAA
1025 AATTAAAAAAAT
1 AATT-AAAAAAT
1037 AAATT-AAAAAT
1 -AATTAAAAAAT
1048 AATTAATAAAAT
1 AATTAA-AAAAT
1060 AATTAAAAAAT
1 AATTAAAAAAT
*
1071 ATTTAA
1 AATTAA
1077 TTAATCTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
10 4 0.11
11 17 0.47
12 11 0.31
13 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATTAAAAAAT
Found at i:2847 original size:9 final size:9
Alignment explanation
Indices: 2833--2865 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2823 TTTCCCACAG
2833 CAACAAGTC
1 CAACAAGTC
2842 CAACAAGTC
1 CAACAAGTC
*
2851 CATCAAGTC
1 CAACAAGTC
2860 CAACAA
1 CAACAA
2866 TAGCTCGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.45, C:0.33, G:0.09, T:0.12
Consensus pattern (9 bp):
CAACAAGTC
Found at i:4151 original size:14 final size:14
Alignment explanation
Indices: 4132--4170 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
4122 AAAGCATATG
4132 TTTCTTTTTTTCT-T
1 TTTCTTTTTTT-TGT
4146 TTTCTTTTTTTTGT
1 TTTCTTTTTTTTGT
*
4160 TTCCTTTTTTT
1 TTTCTTTTTTT
4171 GTATCAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.04
14 22 0.96
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (14 bp):
TTTCTTTTTTTTGT
Found at i:4155 original size:13 final size:13
Alignment explanation
Indices: 4130--4172 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
4120 TGAAAGCATA
4130 TGTTTCTTTTTTT
1 TGTTTCTTTTTTT
*
4143 CTTTTTCTTTTTTT
1 -TGTTTCTTTTTTT
*
4157 TGTTTCCTTTTTT
1 TGTTTCTTTTTTT
4170 TGT
1 TGT
4173 ATCAAGTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (13 bp):
TGTTTCTTTTTTT
Found at i:6227 original size:19 final size:19
Alignment explanation
Indices: 6187--6229 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
6177 CTACTAATTT
*
6187 TAATTATCTAATATTAAAA
1 TAATTATCTAACATTAAAA
*
6206 TAATTATTTAACA-TAAATA
1 TAATTATCTAACATTAAA-A
6225 TAATT
1 TAATT
6230 TTATTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATTATCTAACATTAAAA
Found at i:6246 original size:17 final size:17
Alignment explanation
Indices: 6226--6310 Score: 59
Period size: 17 Copynumber: 4.8 Consensus size: 17
6216 ACATAAATAT
6226 AATTTT-ATTAATTATCA
1 AATTTTAATTAA-TATCA
6243 AATTTTAATTAATATCATA
1 AATTTTAATTAATATC--A
* * *
6262 AATATTAAATAA-ATTTA
1 AATTTTAATTAATA-TCA
*
6279 AATTTTTATTATATAT-A
1 AATTTTAATTA-ATATCA
6296 AATTTTAATTTAATA
1 AATTTTAA-TTAATA
6311 ATTTTTTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
17 30 0.56
18 11 0.20
19 13 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTTAATTAATATCA
Found at i:7887 original size:26 final size:25
Alignment explanation
Indices: 7858--7927 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 25
7848 GTCAGATTTG
7858 TTTTTTAGTTATATAATATATATTAA
1 TTTTTTA-TTATATAATATATATTAA
*
7884 TTTTATATT-TAT-ATAT-TATATAA
1 TTTTTTATTATATAATATATAT-TAA
*
7907 -TTTTTATTGTATAATATATAT
1 TTTTTTATTATATAATATATAT
7928 ATATATAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 10 0.26
23 10 0.26
24 7 0.18
25 5 0.13
26 6 0.16
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
TTTTTTATTATATAATATATATTAA
Found at i:7899 original size:21 final size:22
Alignment explanation
Indices: 7873--7928 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
7863 TAGTTATATA
7873 ATATATAT-TAATTTTATATT-T
1 ATATATATATAATTTT-TATTGT
7894 ATATATTATATAATTTTTATTGT
1 ATATA-TATATAATTTTTATTGT
7917 ATAATATATATA
1 AT-ATATATATA
7929 TATATAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.16
22 7 0.23
23 16 0.52
24 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATATATATAATTTTTATTGT
Found at i:7941 original size:28 final size:28
Alignment explanation
Indices: 7893--7948 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
7883 ATTTTATATT
* *
7893 TATATATTATATAATTTTTATTGTATAA
1 TATATATTATATAATTGTTATAGTATAA
7921 TATATATATATATAA-TGTTATAGTATAA
1 TATATAT-TATATAATTGTTATAGTATAA
7949 ACATTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (28 bp):
TATATATTATATAATTGTTATAGTATAA
Found at i:8214 original size:19 final size:20
Alignment explanation
Indices: 8187--8228 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
8177 TAAACACCTA
8187 TTATAATTTTATAAAAT-TAT
1 TTATAATTTTA-AAAATATAT
8207 TTAT-ATTTTAAAAATATAT
1 TTATAATTTTAAAAATATAT
8226 TTA
1 TTA
8229 AAGTACTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATAATTTTAAAAATATAT
Found at i:9521 original size:16 final size:16
Alignment explanation
Indices: 9502--9541 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
9492 TTTGATATTC
9502 AAGTTATTTAAAGTTT
1 AAGTTATTTAAAGTTT
**
9518 AAGTTATTTCGAGTTT
1 AAGTTATTTAAAGTTT
*
9534 GAGTTATT
1 AAGTTATT
9542 CTGATTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (16 bp):
AAGTTATTTAAAGTTT
Found at i:9566 original size:16 final size:17
Alignment explanation
Indices: 9547--9581 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9537 TTATTCTGAT
9547 TTTAGATT-ATTTCAAA
1 TTTAGATTGATTTCAAA
*
9563 TTTAGATTGTTTTCAAA
1 TTTAGATTGATTTCAAA
9580 TT
1 TT
9582 GATCAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (17 bp):
TTTAGATTGATTTCAAA
Found at i:11501 original size:11 final size:11
Alignment explanation
Indices: 11477--11563 Score: 52
Period size: 12 Copynumber: 7.2 Consensus size: 11
11467 ATGTGAGTAC
*
11477 AAATACATAAAA
1 AAATA-ATATAA
11489 AATATAAT-TAA
1 AA-ATAATATAA
11500 AACATAATATAA
1 AA-ATAATATAA
11512 AAATAATATGAA
1 AAATAATAT-AA
*
11524 TACAATATAAATAA
1 -A-AATA-ATATAA
11538 ATAA-ACATATAA
1 A-AATA-ATATAA
11550 AAATATATATAA
1 AAATA-ATATAA
11562 AA
1 AA
11564 TAAATTATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
11 18 0.30
12 27 0.44
13 7 0.11
14 6 0.10
15 3 0.05
ACGTcount: A:0.68, C:0.05, G:0.01, T:0.26
Consensus pattern (11 bp):
AAATAATATAA
Found at i:11528 original size:50 final size:51
Alignment explanation
Indices: 11459--11563 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 51
11449 TTTAAGCACA
* * * * * *
11459 AAAAATTAATGTGAGTACAA-ATACATAAA-AAATATAATTAAAACATAATAT
1 AAAAATTAATATGAATACAATATAAATAAATAAACAT-ATAAAAATAT-ATAT
11510 AAAAA-TAATATGAATACAATATAAATAAATAAACATATAAAAATATATAT
1 AAAAATTAATATGAATACAATATAAATAAATAAACATATAAAAATATATAT
11560 AAAA
1 AAAA
11564 TAAATTATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
50 20 0.43
51 21 0.46
52 5 0.11
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.27
Consensus pattern (51 bp):
AAAAATTAATATGAATACAATATAAATAAATAAACATATAAAAATATATAT
Found at i:11545 original size:157 final size:155
Alignment explanation
Indices: 11325--11642 Score: 421
Period size: 155 Copynumber: 2.0 Consensus size: 155
11315 TTAATACAAT
* ** * *
11325 ATAAGAAAAATAATTAAAACATAATATGAAAAATAACTTTAATATGACAAGAATAAATCAACATG
1 ATAA-AAAAATAATTAAAACATAATATGAAAAATAACTTGAATACAACAAGAATAAATAAACATA
11390 TCAAAAAATATATATAAAATAAATTATTAACATATAAAAATTTATAAAAAATT-AAAAC-CTTTA
65 T--AAAAATATATATAAAATAAATTATTAACATATAAAAATTTATAAAAAATTCAAAACTCTTTA
*
11453 AGCACAAAAAATTAATGTGAGTACAAATAC
128 AACACAAAAAA--AATGTGAGTACAAATAC
*
11483 ATAAAAAATATAATTAAAACATAATAT-AAAAATAA-TATGAATACAATATA-AATAAATAAACA
1 ATAAAAAA-ATAATTAAAACATAATATGAAAAATAACT-TGAATACAACA-AGAATAAATAAACA
* * * *
11545 TATAAAAATATATATAAAATAAATTATTAATATATAAAAATTTATATAAATTTCAAAACTTTTTA
63 TATAAAAATATATATAAAATAAATTATTAACATATAAAAATTTATAAAAAATTCAAAACTCTTTA
*
11610 AACACAAAAAAATTGTGAGTACAAATAC
128 AACACAAAAAAAATGTGAGTACAAATAC
11638 ATAAA
1 ATAAA
11643 CTTTGTTTCT
Statistics
Matches: 143, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
155 68 0.48
156 6 0.04
157 46 0.32
158 23 0.16
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (155 bp):
ATAAAAAAATAATTAAAACATAATATGAAAAATAACTTGAATACAACAAGAATAAATAAACATAT
AAAAATATATATAAAATAAATTATTAACATATAAAAATTTATAAAAAATTCAAAACTCTTTAAAC
ACAAAAAAAATGTGAGTACAAATAC
Found at i:11822 original size:13 final size:13
Alignment explanation
Indices: 11804--11828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11794 TAATTGTGTA
11804 CCTACTTTATCTG
1 CCTACTTTATCTG
11817 CCTACTTTATCT
1 CCTACTTTATCT
11829 TTTCATATTC
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:0.16, C:0.32, G:0.04, T:0.48
Consensus pattern (13 bp):
CCTACTTTATCTG
Found at i:15056 original size:2 final size:2
Alignment explanation
Indices: 15018--15046 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15008 AATTGATCTG
15018 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
15047 GACTTATATA
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:16307 original size:16 final size:15
Alignment explanation
Indices: 16286--16335 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
16276 AAAAAGTAAA
16286 AAAAAAATTAAATTT
1 AAAAAAATTAAATTT
* *
16301 TAAAAAATTAAATAT
1 AAAAAAATTAAATTT
*
16316 AAAATAATTTAAATTT
1 AAAA-AAATTAAATTT
16332 AAAA
1 AAAA
16336 TTATCTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAAAATTAAATTT
Found at i:16331 original size:31 final size:26
Alignment explanation
Indices: 16274--16335 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 26
16264 CTTAATTTGA
16274 TAAAAAAGTAAAAAAAAAATTAAATTT
1 TAAAAAAGTAAAAAAAAAATTAAA-TT
*
16301 TAAAAAATTAAATATAAAATAATTTAAATT
1 TAAAAAAGTAAA-A-AAAA-AA-TTAAATT
16331 TAAAA
1 TAAAA
16336 TTATCTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 11 0.37
28 1 0.03
29 4 0.13
30 9 0.30
31 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (26 bp):
TAAAAAAGTAAAAAAAAAATTAAATT
Found at i:16336 original size:16 final size:16
Alignment explanation
Indices: 16293--16352 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
16283 AAAAAAAAAA
16293 TTAAATTTTAAAA-AA-
1 TTAAA-TTTAAAATAAT
*
16308 TTAAATATAAAATAAT
1 TTAAATTTAAAATAAT
*
16324 TTAAATTTAAAATTAT
1 TTAAATTTAAAATAAT
*
16340 CTAAATCTTAAAA
1 TTAAAT-TTAAAA
16353 ACTTCAACCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.16
15 7 0.18
16 19 0.50
17 6 0.16
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATTTAAAATAAT
Found at i:16478 original size:15 final size:17
Alignment explanation
Indices: 16460--16500 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
16450 AATTTATTCG
16460 AATTTAAAATGA-TTT-
1 AATTTAAAATGAGTTTA
16475 AA-TTAAAAT-AGTTTA
1 AATTTAAAATGAGTTTA
16490 AATTTAAAATG
1 AATTTAAAATG
16501 TTCAAACCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.05
14 10 0.45
15 4 0.18
16 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (17 bp):
AATTTAAAATGAGTTTA
Found at i:17044 original size:5 final size:5
Alignment explanation
Indices: 17036--17134 Score: 51
Period size: 5 Copynumber: 19.4 Consensus size: 5
17026 TTTTATGAAG
* * ** * * *
17036 AAAGA AAAGA AAAGA AAAAA AAAGG GGA-A AAAGT AAAGA TAATAGA GAGGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA -AA-AGA AAAGA
* *
17087 AAAG- AAAGA GAATGA GAAAGA AAAGA AAGGA AAA-A AAAGA AGAAGA
1 AAAGA AAAGA -AAAGA -AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA
17133 AA
1 AA
17135 GATTCATAAG
Statistics
Matches: 69, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
4 9 0.13
5 40 0.58
6 17 0.25
7 3 0.04
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:17145 original size:29 final size:29
Alignment explanation
Indices: 17113--17171 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
17103 AAAGAAAAGA
17113 AAGGAAAAAAAAGAAGAAGAAAGATTCAT
1 AAGGAAAAAAAAGAAGAAGAAAGATTCAT
17142 AAGGAAAAAAAAGAAGAAGAAAGATTCAT
1 AAGGAAAAAAAAGAAGAAGAAAGATTCAT
17171 A
1 A
17172 TATTTGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.20, T:0.10
Consensus pattern (29 bp):
AAGGAAAAAAAAGAAGAAGAAAGATTCAT
Found at i:17951 original size:13 final size:13
Alignment explanation
Indices: 17933--17958 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17923 CTGTGGCAGA
17933 TTAAAACAATTAT
1 TTAAAACAATTAT
17946 TTAAAACAATTAT
1 TTAAAACAATTAT
17959 AGAGTACAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAACAATTAT
Found at i:18186 original size:16 final size:16
Alignment explanation
Indices: 18167--18197 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18157 AAATAAACTT
*
18167 TTATTTATTAAAAATG
1 TTATTTATCAAAAATG
18183 TTATTTATCAAAAAT
1 TTATTTATCAAAAAT
18198 AATTTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
TTATTTATCAAAAATG
Found at i:18286 original size:18 final size:19
Alignment explanation
Indices: 18265--18302 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
18255 ATATTTCATT
18265 AATAACGATAATTTT-GTA
1 AATAACGATAATTTTAGTA
*
18283 AATAATGATAATTTTAGTA
1 AATAACGATAATTTTAGTA
18302 A
1 A
18303 TAAAGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (19 bp):
AATAACGATAATTTTAGTA
Found at i:18601 original size:23 final size:24
Alignment explanation
Indices: 18574--18619 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
18564 CTAATAATTA
*
18574 ATATTAATTGTA-TATTTTTATTC
1 ATATTAATTGTATTATTATTATTC
18597 ATATTAATTGTATTATTATTATT
1 ATATTAATTGTATTATTATTATT
18620 TGTATGGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (24 bp):
ATATTAATTGTATTATTATTATTC
Found at i:19653 original size:20 final size:20
Alignment explanation
Indices: 19579--19653 Score: 50
Period size: 20 Copynumber: 3.8 Consensus size: 20
19569 TTAAATTATC
19579 ATTATAAATA-TTTT-ATTATT
1 ATTA-AAATATTTTTAATT-TT
*
19599 AATAAAAT-TTATTTAA-TTT
1 ATTAAAATATT-TTTAATTTT
* **
19618 ATAAATAATAAATTTAATTTT
1 ATTAA-AATATTTTTAATTTT
19639 ATTAAAATATTTTTA
1 ATTAAAATATTTTTA
19654 TTAAATAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
19 10 0.24
20 23 0.56
21 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAAAATATTTTTAATTTT
Found at i:24394 original size:11 final size:11
Alignment explanation
Indices: 24378--24402 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24368 GTCGTCTTAT
24378 AATTTATTTTA
1 AATTTATTTTA
24389 AATTTATTTTA
1 AATTTATTTTA
24400 AAT
1 AAT
24403 AAAATATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:25468 original size:17 final size:17
Alignment explanation
Indices: 25446--25478 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25436 TTAATGATTT
*
25446 TAAATTAAATATAAAAA
1 TAAATTAAAAATAAAAA
25463 TAAATTAAAAATAAAA
1 TAAATTAAAAATAAAA
25479 TCATTTGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATTAAAAATAAAAA
Found at i:28621 original size:2 final size:2
Alignment explanation
Indices: 28609--28639 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
28599 ATTATTTAAA
28609 AT AT A- 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
28640 GTCTGCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31170 original size:18 final size:19
Alignment explanation
Indices: 31144--31180 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
31134 AATTTTTTTA
31144 AAATATTAAATAAATAATT
1 AAATATTAAATAAATAATT
31163 AAAT-TTAAATAAATAATT
1 AAATATTAAATAAATAATT
31181 TAATCCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATATTAAATAAATAATT
Found at i:31607 original size:15 final size:15
Alignment explanation
Indices: 31583--31612 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31573 AAAAATCCAG
*
31583 ATATTTTATTTTAAA
1 ATATTATATTTTAAA
31598 ATATTATATTTTAAA
1 ATATTATATTTTAAA
31613 TTAAAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTATATTTTAAA
Found at i:31608 original size:20 final size:20
Alignment explanation
Indices: 31583--31623 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
31573 AAAAATCCAG
**
31583 ATATTTTATTTTAAAATATT
1 ATATTTTAAATTAAAATATT
31603 ATATTTTAAATTAAAATATT
1 ATATTTTAAATTAAAATATT
31623 A
1 A
31624 AAATTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTTTAAATTAAAATATT
Found at i:31630 original size:20 final size:19
Alignment explanation
Indices: 31593--31635 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
31583 ATATTTTATT
* *
31593 TTAAAATATTATATTTTAAA
1 TTAAAATATTAAAATTT-AA
31613 TTAAAATATTAAAATTTAA
1 TTAAAATATTAAAATTTAA
31632 TTAA
1 TTAA
31636 TTAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAATATTAAAATTTAA
Found at i:32083 original size:11 final size:11
Alignment explanation
Indices: 32062--32112 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
32052 GTATTTTTGT
32062 TATTATATTTA
1 TATTATATTTA
* *
32073 TGTTATTTTTA
1 TATTATATTTA
*
32084 TATTATAATTA
1 TATTATATTTA
* *
32095 TATTAAATATA
1 TATTATATTTA
32106 T-TTATAT
1 TATTATAT
32113 AAATTATAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
10 5 0.16
11 26 0.84
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
TATTATATTTA
Found at i:32144 original size:31 final size:29
Alignment explanation
Indices: 32094--32169 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
32084 TATTATAATT
*
32094 ATATTA-AATATA-TTTATATAAATTATAA
1 ATATTATAATTTATTTTATATAAA-TATAA
*
32122 ATATTAATAATTTATTTTATATAAATATTA
1 ATATT-ATAATTTATTTTATATAAATATAA
* *
32152 ATATTTTTATTTATTTTA
1 ATATTATAATTTATTTTA
32170 ATTATTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 5 0.12
29 12 0.29
30 14 0.34
31 10 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATTATAATTTATTTTATATAAATATAA
Found at i:32146 original size:24 final size:25
Alignment explanation
Indices: 32094--32163 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 25
32084 TATTATAATT
**
32094 ATATTAAATATATTTATATAAATTATAA
1 ATATT-AATATATTTAT-TTTA-TATAA
32122 ATATTAATA-ATTTATTTTATATAA
1 ATATTAATATATTTATTTTATATAA
*
32146 ATATTAATATTTTTATTT
1 ATATTAATATATTTATTT
32164 ATTTTAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 14 0.37
25 9 0.24
26 6 0.16
27 4 0.11
28 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATTAATATATTTATTTTATATAA
Found at i:32619 original size:22 final size:23
Alignment explanation
Indices: 32589--32635 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
32579 ATATTTAAAA
*
32589 TATTGTAATTATTAT-TAAATAT
1 TATTGTAATTAATATATAAATAT
* *
32611 TATTTTAATTAATATATAATTAT
1 TATTGTAATTAATATATAAATAT
32634 TA
1 TA
32636 AAATATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATTGTAATTAATATATAAATAT
Found at i:32793 original size:15 final size:15
Alignment explanation
Indices: 32749--32793 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
32739 TGTTATTAAT
*
32749 TATTATTAAAATAAA
1 TATTATTAAAATATA
* * *
32764 TAATATTACATTATA
1 TATTATTAAAATATA
32779 TATTATTAAAATATA
1 TATTATTAAAATATA
32794 GATAGGTATG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTATTAAAATATA
Found at i:34995 original size:10 final size:10
Alignment explanation
Indices: 34982--35029 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
34972 AAGTATAATT
34982 AAAATAAATAAA
1 AAAATAAAT--A
34994 AAAATAATATA
1 AAAATAA-ATA
*
35005 AACAT-AATA
1 AAAATAAATA
35014 AAAATAAATA
1 AAAATAAATA
35024 AAAATA
1 AAAATA
35030 TCAAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 7 0.22
10 11 0.34
11 5 0.16
12 7 0.22
13 2 0.06
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAATAAATA
Found at i:35035 original size:19 final size:20
Alignment explanation
Indices: 34987--35029 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
34977 TAATTAAAAT
34987 AAATAA-AAAAATAATATAA
1 AAATAATAAAAATAATATAA
*
35006 ACATAATAAAAATAA-ATAA
1 AAATAATAAAAATAATATAA
35025 AAATA
1 AAATA
35030 TCAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAATAAAAATAATATAA
Found at i:35254 original size:15 final size:14
Alignment explanation
Indices: 35234--35277 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
35224 TATTTTCATT
35234 TTATAAAAATATATA
1 TTAT-AAAATATATA
*
35249 TTATAAATTATAATA
1 TTATAAAATAT-ATA
*
35264 TAATAAAATATATA
1 TTATAAAATATATA
35278 AATATAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTATAAAATATATA
Found at i:37927 original size:4 final size:4
Alignment explanation
Indices: 37920--37944 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
37910 TAAATATATT
37920 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
37945 ATATGCTTTA
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:38314 original size:2 final size:2
Alignment explanation
Indices: 38307--38348 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
38297 CTATATCCAA
38307 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
38349 GTTCTTTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39802 original size:22 final size:21
Alignment explanation
Indices: 39775--39815 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
39765 TATTAAAAAT
*
39775 TATTTTTATATTAATATTTATA
1 TATTTTAATATTAA-ATTTATA
39797 TATTTTAATATTAAATTTA
1 TATTTTAATATTAAATTTA
39816 AATAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTAATATTAAATTTATA
Found at i:41037 original size:27 final size:25
Alignment explanation
Indices: 41005--41094 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 25
40995 CACCCATTTG
41005 TTTGTCAAAAATGGTGGTTATTTTGTA
1 TTTGTCAAAAATGGTGGTT-TTTT-TA
41032 TTTGTCAAAAATGGTGGTTTCCTTTATA
1 TTTGTCAAAAATGGTGGTTT--TTT-TA
* * * *
41060 TTTGTCAAATATGGAGGCTTGTTTA
1 TTTGTCAAAAATGGTGGTTTTTTTA
41085 TTTGTCAAAA
1 TTTGTCAAAA
41095 TTTGTGGCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 19 0.35
28 22 0.40
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.46
Consensus pattern (25 bp):
TTTGTCAAAAATGGTGGTTTTTTTA
Found at i:41175 original size:20 final size:20
Alignment explanation
Indices: 41150--41198 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
41140 AAATAGAGGC
41150 TCCCTCTTCCCTCTCAAGTA
1 TCCCTCTTCCCTCTCAAGTA
* * **
41170 TCCCTCATCCTTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGTA
41190 TCCCTCTTC
1 TCCCTCTTC
41199 AATTTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.45, G:0.04, T:0.41
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGTA
Found at i:45637 original size:28 final size:27
Alignment explanation
Indices: 45578--45667 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 27
45568 CACCCATTTG
* *
45578 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
45605 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
45633 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
45658 TTTGTCAAAA
1 TTTGTCAAAA
45668 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.06
27 19 0.35
28 21 0.39
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:45748 original size:20 final size:20
Alignment explanation
Indices: 45723--45768 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
45713 AAATAGAGGC
*
45723 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
* **
45743 TCCCTCATCCTTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
45763 TCCCTC
1 TCCCTC
45769 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.48, G:0.04, T:0.37
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:46022 original size:13 final size:13
Alignment explanation
Indices: 46004--46030 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
45994 AGGGTGTAAA
46004 CTCAAATTCTAAT
1 CTCAAATTCTAAT
46017 CTCAAATTCTAAT
1 CTCAAATTCTAAT
46030 C
1 C
46031 ATTGAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (13 bp):
CTCAAATTCTAAT
Found at i:51502 original size:21 final size:21
Alignment explanation
Indices: 51452--51504 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
51442 ATTTATAATA
51452 TAATAATTATATTTAAAATATT
1 TAATAATT-TATTTAAAATATT
* *
51474 TTAT-ATTTATTT-TAATATGT
1 TAATAATTTATTTAAAATAT-T
51494 TAATAATTTAT
1 TAATAATTTAT
51505 ATTATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 5 0.19
20 9 0.35
21 9 0.35
22 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TAATAATTTATTTAAAATATT
Found at i:51973 original size:14 final size:14
Alignment explanation
Indices: 51954--51985 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
51944 ATTTATATAG
51954 TAAAAAGTCATGAC
1 TAAAAAGTCATGAC
*
51968 TAAAAAGTCCTGAC
1 TAAAAAGTCATGAC
51982 TAAA
1 TAAA
51986 TTTATGTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (14 bp):
TAAAAAGTCATGAC
Found at i:53145 original size:2 final size:2
Alignment explanation
Indices: 53138--53168 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
53128 TATCTAACTC
53138 TA TA TA TA TA T- 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
53169 AACAATGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54235 original size:39 final size:38
Alignment explanation
Indices: 54162--54237 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
54152 TTTAAGATTT
*
54162 TATATATAAATTTAATAAAATAATACATATTTTTTAAA
1 TATATATAAATTTAATAAAATAATACATAATTTTTAAA
*
54200 TATATTTAAATTTAA-AAAA-AATACGTGATAATTTTTAA
1 TATATATAAATTTAATAAAATAATAC---ATAATTTTTAA
54238 TCTTCCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
36 5 0.15
37 4 0.12
38 14 0.42
39 10 0.30
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (38 bp):
TATATATAAATTTAATAAAATAATACATAATTTTTAAA
Found at i:56074 original size:2 final size:2
Alignment explanation
Indices: 56069--56106 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
56059 ACACACACAC
*
56069 AT AT AT AT AT AT AT AT AT AT AT AT AT TT 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
56107 TTGAGACCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:56554 original size:28 final size:25
Alignment explanation
Indices: 56509--56564 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
56499 TAGTAAAAAT
* *
56509 AAATATAATTTATTTTTATTTTTAA
1 AAATATAATTTATTTTTAATTTAAA
56534 AAATAATAATATTATTATTTAATTTAAA
1 AAAT-ATAAT-TTATT-TTTAATTTAAA
56562 AAA
1 AAA
56565 AATTATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 5 0.19
27 5 0.19
28 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AAATATAATTTATTTTTAATTTAAA
Found at i:56564 original size:29 final size:28
Alignment explanation
Indices: 56502--56579 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
56492 TGTTCTCTAG
56502 TAAAAATAAATATAAT-TTATT-TTTATT
1 TAAAAA-AAATATAATATTATTATTTATT
**
56529 T-TTAAAAATAATAATATTATTATTTAATT
1 TAAAAAAAAT-ATAATATTATTATTT-ATT
56558 TAAAAAAAATTATAA-ATTATTA
1 TAAAAAAAA-TATAATATTATTA
56580 GTGTAACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
25 4 0.10
26 7 0.17
27 6 0.15
28 3 0.07
29 11 0.27
30 9 0.22
31 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAAAAAAATATAATATTATTATTTATT
Found at i:56722 original size:16 final size:16
Alignment explanation
Indices: 56678--56716 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
56668 ATGAGATTTG
*
56678 TAAATATTAAA-AT-T
1 TAAATATTAAATTTAT
56692 TAAATATTAAATTTAT
1 TAAATATTAAATTTAT
56708 TAAATATTA
1 TAAATATTA
56717 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 1 0.05
16 10 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATATTAAATTTAT
Found at i:56723 original size:13 final size:14
Alignment explanation
Indices: 56673--56724 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
56663 TTGACATGAG
*
56673 ATTTGTAAATATTA
1 ATTTTTAAATATTA
**
56687 AAATTTAAATATTAA
1 ATTTTTAAATATT-A
56702 ATTTATTAAATATT-
1 ATTT-TTAAATATTA
56716 ATTTTTAAA
1 ATTTTTAAA
56725 AATAATTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 5 0.16
14 14 0.45
15 3 0.10
16 9 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
ATTTTTAAATATTA
Found at i:57819 original size:15 final size:15
Alignment explanation
Indices: 57787--57836 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
57777 AATTTAATAT
57787 TATAAAATTATATTA
1 TATAAAATTATATTA
*
57802 TATAAAATT-TTTTA
1 TATAAAATTATATTA
*
57816 -ATATAATTATA-TA
1 TATAAAATTATATTA
57829 TATTAAAA
1 TA-TAAAA
57837 ATGTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 9 0.32
14 6 0.21
15 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAAAATTATATTA
Found at i:57930 original size:20 final size:18
Alignment explanation
Indices: 57894--57940 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
57884 ATATTAAAAT
*
57894 AAAAATAAAATATTTTTA
1 AAAAATAAAATAATTTTA
57912 AAAATATAATAATAATTTTA
1 AAAA-ATAA-AATAATTTTA
57932 AAAAATAAA
1 AAAAATAAA
57941 TATACTTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 5 0.19
19 8 0.31
20 13 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATAAAATAATTTTA
Found at i:57942 original size:20 final size:21
Alignment explanation
Indices: 57880--57942 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
57870 TTAATATATT
*
57880 AAATATATTAAAATAA-AAATA
1 AAATATTTTAAAA-AATAAATA
*
57901 AAATATTTTTAAAAATATAATA
1 AAATATTTTAAAAAATA-AATA
*
57923 ATA-ATTTTAAAAAATAAATA
1 AAATATTTTAAAAAATAAATA
57943 TACTTGACGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.17
21 24 0.67
22 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATTTTAAAAAATAAATA
Found at i:58982 original size:2 final size:2
Alignment explanation
Indices: 58975--59010 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
58965 GTTGTTTGTG
58975 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
59011 TCATTTTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60459 original size:25 final size:27
Alignment explanation
Indices: 60430--60484 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
60420 TCAATCAATT
60430 TAATATTTATTATA-AT-TAATTATAA
1 TAATATTTATTATATATATAATTATAA
*
60455 TAATATTTATTATATTTATAATTATAA
1 TAATATTTATTATATATATAATTATAA
60482 TAA
1 TAA
60485 ATACGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 14 0.52
26 1 0.04
27 12 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TAATATTTATTATATATATAATTATAA
Done.