Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2548
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: 42255
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:1471 original size:16 final size:18
Alignment explanation
Indices: 1452--1484 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1442 CTTAATAATT
1452 TTAAGA-AGA-AATATTA
1 TTAAGATAGATAATATTA
1468 TTAAGATAGATAATATT
1 TTAAGATAGATAATATT
1485 CCTTTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (18 bp):
TTAAGATAGATAATATTA
Found at i:3613 original size:3 final size:3
Alignment explanation
Indices: 3605--3635 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3595 TCAAAAGAAT
3605 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3636 AGATTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4742 original size:22 final size:22
Alignment explanation
Indices: 4714--4755 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
4704 ATTAAAAAAT
4714 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
4736 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
4756 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:6370 original size:11 final size:11
Alignment explanation
Indices: 6347--6380 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6337 AAATTATTTA
6347 TTAAATT-AAT
1 TTAAATTAAAT
6357 TTAAATTAAAT
1 TTAAATTAAAT
*
6368 TTAAATAAAAT
1 TTAAATTAAAT
6379 TT
1 TT
6381 TTTATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:6768 original size:20 final size:18
Alignment explanation
Indices: 6731--6769 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
6721 CCTTATTTTA
*
6731 TTTTTTTATTTTATTAAT
1 TTTTTTTATTTCATTAAT
6749 TTTTTCTTACTTTCATTAAT
1 TTTTT-TTA-TTTCATTAAT
6769 T
1 T
6770 AAATTGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 10 0.56
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTTATTTCATTAAT
Found at i:7097 original size:17 final size:16
Alignment explanation
Indices: 7075--7108 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7065 TTTCTTGCCT
7075 TAAAAGAGATTTTTTTA
1 TAAAAG-GATTTTTTTA
*
7092 TAAAAGGTTTTTTTTA
1 TAAAAGGATTTTTTTA
7108 T
1 T
7109 CAATTGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TAAAAGGATTTTTTTA
Found at i:11477 original size:18 final size:18
Alignment explanation
Indices: 11443--11479 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11433 CGTGATAACT
11443 AAAATATTTAAATAATTA
1 AAAATATTTAAATAATTA
11461 AAAAT-TTTAAATAAATTA
1 AAAATATTTAAAT-AATTA
11479 A
1 A
11480 CATCATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATTTAAATAATTA
Found at i:13205 original size:15 final size:15
Alignment explanation
Indices: 13185--13230 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
13175 GAAGGGTTAA
13185 TATTTATAAAATTTT
1 TATTTATAAAATTTT
13200 TATTTAAATAAAATTTT
1 TATTT--ATAAAATTTT
* *
13217 AATTAATAAAATTT
1 TATTTATAAAATTT
13231 ATTTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 14 0.52
17 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTATAAAATTTT
Found at i:13212 original size:17 final size:16
Alignment explanation
Indices: 13190--13230 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
13180 GTTAATATTT
*
13190 ATAAAATTTTTATTTAA
1 ATAAAATTTTTAATT-A
13207 ATAAAA-TTTTAATTA
1 ATAAAATTTTTAATTA
13222 ATAAAATTT
1 ATAAAATTT
13231 ATTTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 9 0.41
17 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAAATTTTTAATTA
Found at i:13289 original size:13 final size:13
Alignment explanation
Indices: 13224--13391 Score: 62
Period size: 13 Copynumber: 12.2 Consensus size: 13
13214 TTTAATTAAT
*
13224 AAAATTTATTTAA
1 AAAATTTATATAA
13237 AAATATTTA-ATAA
1 AAA-ATTTATATAA
*
13250 ATAAATTTAAAGTTAA
1 A-AAATTTATA--TAA
13266 AATTTAA-TTATATAA
1 AA---AATTTATATAA
13281 AAAATTTATAT--
1 AAAATTTATATAA
* * *
13292 AAAATATA-AGAT
1 AAAATTTATATAA
*
13304 AAATTTTAATATAAA
1 AAAATTT-ATAT-AA
*
13319 TAAAATTTATTTAA
1 -AAAATTTATATAA
13333 AAATATTTA-ATAA
1 AAA-ATTTATATAA
*
13346 ATAAATTTAAAGTTAA
1 A-AAATTTATA--TAA
13362 AATTTAA-TTATATAA
1 AA---AATTTATATAA
13377 AAAATTTATATAA
1 AAAATTTATATAA
13390 AA
1 AA
13392 TATAAGATAA
Statistics
Matches: 119, Mismatches: 12, Indels: 48
0.66 0.07 0.27
Matches are distributed among these distances:
10 1 0.01
11 7 0.06
12 9 0.08
13 41 0.34
14 19 0.16
15 16 0.13
16 14 0.12
17 8 0.07
18 4 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
AAAATTTATATAA
Found at i:13294 original size:28 final size:27
Alignment explanation
Indices: 13201--13296 Score: 81
Period size: 30 Copynumber: 3.5 Consensus size: 27
13191 TAAAATTTTT
13201 ATTTAAATAAAATTTTAATTAAT--AAA
1 ATTTAAATAAAA-TTTAATTAATAAAAA
** * *
13227 ATTTATTTAAAA-ATATTTAATAAATAA
1 ATTTAAATAAAATTTAATTAATAAA-AA
13254 ATTTAAAGTTAAAATTTAATTATATAAAAA
1 ATTTAAA--TAAAATTTAATTA-ATAAAAA
*
13284 ATTTATATAAAAT
1 ATTTAAATAAAAT
13297 ATAAGATAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
24 7 0.13
26 11 0.20
27 7 0.13
28 6 0.11
29 5 0.09
30 13 0.24
31 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
ATTTAAATAAAATTTAATTAATAAAAA
Found at i:13307 original size:22 final size:22
Alignment explanation
Indices: 13275--13318 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
13265 AAATTTAATT
13275 ATATAAAAAA-TTT-ATATAAA
1 ATATAAAAAATTTTAATATAAA
13295 ATATAAGATAAATTTTAATATAAA
1 ATATAA-A-AAATTTTAATATAAA
13319 TAAAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 3 0.15
23 3 0.15
24 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATAAAAAATTTTAATATAAA
Found at i:13341 original size:96 final size:96
Alignment explanation
Indices: 13210--13413 Score: 394
Period size: 96 Copynumber: 2.1 Consensus size: 96
13200 TATTTAAATA
13210 AAATTTTAAT-T-AATAAAATTTATTTAAAAATATTTAATAAATAAATTTAAAGTTAAAATTTAA
1 AAATTTTAATATAAATAAAATTTATTTAAAAATATTTAATAAATAAATTTAAAGTTAAAATTTAA
13273 TTATATAAAAAATTTATATAAAATATAAGAT
66 TTATATAAAAAATTTATATAAAATATAAGAT
13304 AAATTTTAATATAAATAAAATTTATTTAAAAATATTTAATAAATAAATTTAAAGTTAAAATTTAA
1 AAATTTTAATATAAATAAAATTTATTTAAAAATATTTAATAAATAAATTTAAAGTTAAAATTTAA
13369 TTATATAAAAAATTTATATAAAATATAAGAT
66 TTATATAAAAAATTTATATAAAATATAAGAT
13400 AAATTTTAATATAA
1 AAATTTTAATATAA
13414 CACAAATATA
Statistics
Matches: 108, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
94 10 0.09
95 1 0.01
96 97 0.90
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (96 bp):
AAATTTTAATATAAATAAAATTTATTTAAAAATATTTAATAAATAAATTTAAAGTTAAAATTTAA
TTATATAAAAAATTTATATAAAATATAAGAT
Found at i:13738 original size:22 final size:22
Alignment explanation
Indices: 13712--13753 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
13702 AACACGACAT
13712 AAACACAATATAAAAATAATTA
1 AAACACAATATAAAAATAATTA
*
13734 AAACACAGTATAAAAATAAT
1 AAACACAATATAAAAATAAT
13754 ATGAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (22 bp):
AAACACAATATAAAAATAATTA
Found at i:14651 original size:16 final size:16
Alignment explanation
Indices: 14619--14939 Score: 131
Period size: 16 Copynumber: 19.7 Consensus size: 16
14609 AAAAAATGAA
*
14619 AAATTAATTTTAGATTT
1 AAATT-ATTTTAAATTT
*
14636 AAATTATTTCAAATTT
1 AAATTATTTTAAATTT
* *
14652 AAATTATTTTGATTTT
1 AAATTATTTTAAATTT
* * *
14668 AATTTATTTTGATTTT
1 AAATTATTTTAAATTT
* *
14684 AATTTATTTTAAATTA
1 AAATTATTTTAAATTT
*
14700 AAATTATTTTAATTTT
1 AAATTATTTTAAATTT
* * *
14716 TAATTA-ATTAGATTT
1 AAATTATTTTAAATTT
** * *
14731 AATATTATGGTGAATTG
1 AA-ATTATTTTAAATTT
*
14748 AAGTTTAATATTTAAA--T
1 AA-ATT-AT-TTTAAATTT
*
14765 AAATTAAATTTAAA--T
1 AAATT-ATTTTAAATTT
* * *
14780 CAATCAAATTTAATATTT
1 AAAT-TATTTTAA-ATTT
**
14798 AAA-T-TTACAGAATTT
1 AAATTATTTTA-AATTT
*
14813 -AATTTTTTTAAATTT
1 AAATTATTTTAAATTT
*
14828 AACTTATTTCAAATTAATTATTT
1 AAATTA-TT----TTAA--ATTT
**
14851 AGTTTATTTTAAATTT
1 AAATTATTTTAAATTT
*
14867 AAATT-TTTT-ATTTT
1 AAATTATTTTAAATTT
*
14881 AAATTATTTTATATTT
1 AAATTATTTTAAATTT
*
14897 AATTTATTTTAAATTT
1 AAATTATTTTAAATTT
*
14913 AAATTATTTTGAATTT
1 AAATTATTTTAAATTT
*
14929 ATATTATTTTA
1 AAATTATTTTA
14940 CGTTATTTTT
Statistics
Matches: 229, Mismatches: 54, Indels: 43
0.70 0.17 0.13
Matches are distributed among these distances:
14 11 0.05
15 44 0.19
16 131 0.57
17 17 0.07
18 9 0.04
19 3 0.01
21 4 0.02
22 2 0.01
23 8 0.03
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (16 bp):
AAATTATTTTAAATTT
Found at i:14691 original size:48 final size:49
Alignment explanation
Indices: 14620--14738 Score: 147
Period size: 48 Copynumber: 2.5 Consensus size: 49
14610 AAAAATGAAA
* *
14620 AATTAATTTTAGATTTAAATTATTTCAAATTTAAATTATTTTGA-TTTT
1 AATTAATTTTAGATTTAAATTATTTCAAATTAAAATTATTTTAATTTTT
* * *
14668 AATTTATTTT-GATTTTAATTTATTTTAAATTAAAATTATTTTAATTTTT
1 AATTAATTTTAGA-TTTAAATTATTTCAAATTAAAATTATTTTAATTTTT
14717 AATTAA--TTAGATTTAATATTAT
1 AATTAATTTTAGATTTAA-ATTAT
14739 GGTGAATTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
47 9 0.15
48 42 0.70
49 9 0.15
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (49 bp):
AATTAATTTTAGATTTAAATTATTTCAAATTAAAATTATTTTAATTTTT
Found at i:14777 original size:15 final size:14
Alignment explanation
Indices: 14752--14804 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
14742 GAATTGAAGT
14752 TTAATATTTAAATAAA
1 TTAA-ATTTAAAT-AA
14768 TTAAATTTAAATCAA
1 TTAAATTTAAAT-AA
* *
14783 TCAAATTT-AATAT
1 TTAAATTTAAATAA
14796 TTAAATTTA
1 TTAAATTTA
14805 CAGAATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 8 0.25
14 3 0.09
15 17 0.53
16 4 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAATTTAAATAA
Found at i:14886 original size:39 final size:38
Alignment explanation
Indices: 14809--14921 Score: 109
Period size: 46 Copynumber: 2.7 Consensus size: 38
14799 AATTTACAGA
*
14809 ATTTAATTTTTTTAAATTTAACTTATTTCAAATTAATT
1 ATTTAATTTTTTTAAATTTAAATTATTTCAAATTAATT
* * *
14847 ATTTAGTTTATTTTAAATTTAAATTTTTTATTTTAAATTATTTTAT
1 ATTTAATTT-TTTTAAATTTAAA----TTATTTCAAATTA--AT-T
14893 ATTTAATTTATTTTAAATTTAAATTATTT
1 ATTTAATTT-TTTTAAATTTAAATTATTT
14922 TGAATTTATA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
38 8 0.13
39 12 0.19
42 6 0.10
43 12 0.19
45 1 0.02
46 23 0.37
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (38 bp):
ATTTAATTTTTTTAAATTTAAATTATTTCAAATTAATT
Found at i:14904 original size:46 final size:48
Alignment explanation
Indices: 14846--14939 Score: 147
Period size: 46 Copynumber: 2.0 Consensus size: 48
14836 TCAAATTAAT
* *
14846 TATTTAGTTTATTTTAAATTTAAATT-TTTT-ATTTTAAATTATTTTA
1 TATTTAATTTATTTTAAATTTAAATTATTTTGAATTTAAATTATTTTA
*
14892 TATTTAATTTATTTTAAATTTAAATTATTTTGAATTTATATTATTTTA
1 TATTTAATTTATTTTAAATTTAAATTATTTTGAATTTAAATTATTTTA
14940 CGTTATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 25 0.58
47 4 0.09
48 14 0.33
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (48 bp):
TATTTAATTTATTTTAAATTTAAATTATTTTGAATTTAAATTATTTTA
Found at i:15954 original size:25 final size:25
Alignment explanation
Indices: 15913--15970 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
15903 ATAATTTAAA
**
15913 TTATTA-TTTAATTAATAAAAATAT
1 TTATTATTTTAAAAAATAAAAATAT
* *
15937 TTATTATTTTAAAAAATATAGATAT
1 TTATTATTTTAAAAAATAAAAATAT
15962 TTATTATTT
1 TTATTATTT
15971 AAATTTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 6 0.21
25 23 0.79
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TTATTATTTTAAAAAATAAAAATAT
Found at i:15991 original size:27 final size:27
Alignment explanation
Indices: 15918--16005 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
15908 TTAAATTATT
15918 ATTTAATTAATAAAAATATTTATTATTTTAA
1 ATTTAATT-AT-AAAA-ATTTATTA-TTTAA
* * *
15949 A---AAATATAGATATTTATTATTTAA
1 ATTTAATTATAAAAATTTATTATTTAA
*
15973 ATTTAATTATAAAAATTTATAAATTT-A
1 ATTTAATTATAAAAATTTAT-TATTTAA
16000 ATTTAA
1 ATTTAA
16006 ATTTTATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
24 6 0.13
25 8 0.17
26 2 0.04
27 22 0.48
28 7 0.15
31 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
ATTTAATTATAAAAATTTATTATTTAA
Found at i:16016 original size:16 final size:16
Alignment explanation
Indices: 15995--16025 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
15985 AAATTTATAA
15995 ATTTAATTTAAATTTT
1 ATTTAATTTAAATTTT
16011 ATTTAATTTAAATTT
1 ATTTAATTTAAATTT
16026 ATATAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTAATTTAAATTTT
Found at i:17034 original size:16 final size:16
Alignment explanation
Indices: 17008--17055 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
16998 CAAACTATAT
17008 AACAA-CTAAATTCAA
1 AACAATCTAAATTCAA
*
17023 AACAATCTAAATTGAA
1 AACAATCTAAATTCAA
* * *
17039 AATAATTTAAATCCAA
1 AACAATCTAAATTCAA
17055 A
1 A
17056 CTTATCTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (16 bp):
AACAATCTAAATTCAA
Found at i:17732 original size:30 final size:29
Alignment explanation
Indices: 17698--17785 Score: 70
Period size: 30 Copynumber: 2.8 Consensus size: 29
17688 ACTCGATAAA
*
17698 AAATAATTATAATATAATATAATATTATAT
1 AAATAATTATAATATAA-AAAATATTATAT
* *
17728 AAATATATAAATAA-ATAAAAAATTTTATAT
1 AAATA-AT-TATAATATAAAAAATATTATAT
17758 AACATTAATTATTAATATATTAAAAATA
1 AA-A-TAATTA-TAATATA--AAAAATA
17786 AATAATAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
30 18 0.40
31 12 0.27
32 9 0.20
34 6 0.13
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
AAATAATTATAATATAAAAAATATTATAT
Found at i:17758 original size:45 final size:45
Alignment explanation
Indices: 17709--17795 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
17699 AATAATTATA
* *
17709 ATATAATATAATATTATATAA-ATA-TATAAATAAATAAAAAATTTT
1 ATATAACATAA-ATTAT-TAATATATTAAAAATAAATAAAAAATTTT
* *
17754 ATATAACATTAATTATTAATATATTAAAAATAAATAATAAAT
1 ATATAACATAAATTATTAATATATTAAAAATAAATAAAAAAT
17796 ATATAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 3 0.08
44 8 0.22
45 25 0.69
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (45 bp):
ATATAACATAAATTATTAATATATTAAAAATAAATAAAAAATTTT
Found at i:17798 original size:40 final size:38
Alignment explanation
Indices: 17693--17798 Score: 95
Period size: 40 Copynumber: 2.6 Consensus size: 38
17683 ACAGAACTCG
*
17693 ATAAAAAATAATTATAATATAATATAATATTATATAAATAT
1 ATAAAAAATAA--ATAATA-AATATAACATTATATAAATAT
* ** *
17734 ATAAATAAATAAAAAATTTTATATAACATTAATTATTAATAT
1 ATAAA-AAATAAATAA-TAAATATAACATT-A-TATAAATAT
*
17776 ATTAAAAATAAATAATAAATATA
1 ATAAAAAATAAATAATAAATATA
17799 TAATTTTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
40 18 0.35
41 16 0.31
42 18 0.35
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (38 bp):
ATAAAAAATAAATAATAAATATAACATTATATAAATAT
Found at i:18119 original size:2 final size:2
Alignment explanation
Indices: 18112--18142 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18102 TTCAATGATC
18112 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
18143 GAAAAACTGT
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:18398 original size:19 final size:19
Alignment explanation
Indices: 18374--18412 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
18364 AAATCTATAA
*
18374 CTATAACAAAGAGAAGAGT
1 CTATAAAAAAGAGAAGAGT
18393 CTATAAAAAAGAGAAGAGT
1 CTATAAAAAAGAGAAGAGT
18412 C
1 C
18413 GTGGTGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.21, T:0.15
Consensus pattern (19 bp):
CTATAAAAAAGAGAAGAGT
Found at i:20642 original size:23 final size:22
Alignment explanation
Indices: 20601--20646 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
20591 AATTTTTGAC
* * *
20601 AAAATTTTTGTTGATAATAGTTT
1 AAAATTTTTATCGAAAATA-TTT
20624 AAAATTTTTATCGAAAATATTT
1 AAAATTTTTATCGAAAATATTT
20646 A
1 A
20647 TTTATAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (22 bp):
AAAATTTTTATCGAAAATATTT
Found at i:24014 original size:19 final size:20
Alignment explanation
Indices: 23982--24022 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
23972 AAACTCCCTC
23982 TTAATAAAATTTTCTCT-TT
1 TTAATAAAATTTTCTCTCTT
24001 TTAA-AAAATATTTCTCTCTT
1 TTAATAAAAT-TTTCTCTCTT
24021 TT
1 TT
24023 TTTGTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 11 0.55
20 4 0.20
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATAAAATTTTCTCTCTT
Found at i:24931 original size:22 final size:23
Alignment explanation
Indices: 24888--24931 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
24878 AGAATGTGGG
*
24888 TTATAAAGAGATGAAGATAGTGA
1 TTATAAAGAGAGGAAGATAGTGA
*
24911 TTATAAAGA-AGGAGGATAGTG
1 TTATAAAGAGAGGAAGATAGTG
24932 GCTTTGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (23 bp):
TTATAAAGAGAGGAAGATAGTGA
Found at i:26000 original size:20 final size:21
Alignment explanation
Indices: 25972--26010 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
25962 TCTCAGTTTT
25972 TTCAGATGTATCGATACATCA
1 TTCAGATGTATCGATACATCA
25993 TTCA-ATGTATCGATACAT
1 TTCAGATGTATCGATACAT
26011 TCTGAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (21 bp):
TTCAGATGTATCGATACATCA
Found at i:26167 original size:26 final size:26
Alignment explanation
Indices: 26116--26170 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
26106 AATCATTATG
*
26116 ATTAAACATCAAAAACAAACACAATC
1 ATTAAACATCAAAAACAAACAAAATC
**
26142 ATTAAACATCACAAAA-ACTCAAAATC
1 ATTAAACATCA-AAAACAAACAAAATC
26168 ATT
1 ATT
26171 CAATCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.20
Consensus pattern (26 bp):
ATTAAACATCAAAAACAAACAAAATC
Found at i:30494 original size:3 final size:3
Alignment explanation
Indices: 30486--30516 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
30476 CGAGTCAACT
*
30486 TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
30517 TATCTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:30521 original size:9 final size:9
Alignment explanation
Indices: 30484--30522 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
30474 TCCGAGTCAA
30484 CTTCATCAT
1 CTTCATCAT
*
30493 CATCATCAT
1 CTTCATCAT
*
30502 CATCATCAT
1 CTTCATCAT
*
30511 CTTCATTAT
1 CTTCATCAT
30520 CTT
1 CTT
30523 TGATAGTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTCATCAT
Found at i:32212 original size:20 final size:20
Alignment explanation
Indices: 32187--32233 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
32177 TTTATATATA
*
32187 GATACAATTCTTCATTTATC
1 GATACAATTCTTCATGTATC
32207 GATACAATTCTTCATGTATC
1 GATACAATTCTTCATGTATC
32227 GATACAA
1 GATACAA
32234 AGCAATATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (20 bp):
GATACAATTCTTCATGTATC
Found at i:32264 original size:20 final size:21
Alignment explanation
Indices: 32241--32279 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
32231 CAAAGCAATA
32241 TGTATCGATAC-TTCTAGGCT
1 TGTATCGATACTTTCTAGGCT
32261 TGTATCGATACTTTCTAGG
1 TGTATCGATACTTTCTAGG
32280 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (21 bp):
TGTATCGATACTTTCTAGGCT
Found at i:33166 original size:36 final size:36
Alignment explanation
Indices: 33119--33190 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
33109 GCAATGGATT
33119 CTCCTGTTGCAACAGCAGATACAGGAAACACAAGAA
1 CTCCTGTTGCAACAGCAGATACAGGAAACACAAGAA
*
33155 CTCCTGTTGCAACAGCAGATACAGGAAACGCAAGAA
1 CTCCTGTTGCAACAGCAGATACAGGAAACACAAGAA
33191 TAACTAAAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.14
Consensus pattern (36 bp):
CTCCTGTTGCAACAGCAGATACAGGAAACACAAGAA
Found at i:37365 original size:22 final size:22
Alignment explanation
Indices: 37337--37389 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
37327 TTAAACATCA
*
37337 AATTTAAAATTAATTGATAAAT
1 AATTTAAAAATAATTGATAAAT
*
37359 AATTTAAAAATAATTGGTAAAT
1 AATTTAAAAATAATTGATAAAT
37381 AATTTAAAA
1 AATTTAAAA
37390 GACTTACGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (22 bp):
AATTTAAAAATAATTGATAAAT
Found at i:37721 original size:32 final size:32
Alignment explanation
Indices: 37680--37797 Score: 94
Period size: 34 Copynumber: 3.3 Consensus size: 32
37670 AGTTAAATTT
37680 AAATTATTTTTTATAAATTAATAAAAATTTAA
1 AAATTATTTTTTATAAATTAATAAAAATTTAA
*
37712 AAATTA-TTTTTATTAATATTTATATAATTTATAATTAAA
1 AAATTATTTTTTA-TAA-A-TTA-ATAA---A-AATTTAA
**
37751 TTAAATTATTACTTATAAATTAATAAAAATTTAAAA
1 --AAATTATTTTTTATAAATTAATAAAAATTT--AA
37787 AAATTATTTTT
1 AAATTATTTTT
37798 ATATTAATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 24
0.69 0.06 0.25
Matches are distributed among these distances:
31 6 0.09
32 9 0.13
33 1 0.01
34 16 0.24
35 5 0.07
36 2 0.03
38 5 0.07
39 9 0.13
40 1 0.01
41 9 0.13
42 4 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
AAATTATTTTTTATAAATTAATAAAAATTTAA
Found at i:37767 original size:73 final size:74
Alignment explanation
Indices: 37672--37835 Score: 244
Period size: 73 Copynumber: 2.2 Consensus size: 74
37662 TCGAGTTAAG
**
37672 TTAAATTTAAATTATTTTTTATAAATTAATAAAAATTT-AAAAATTA-TTTT-TATTAATATTTA
1 TTAAA-TTAAATTATTACTTATAAATTAATAAAAATTTAAAAAATTATTTTTATATTAATATTTA
37734 TATAATTTATAA
65 TAT--TTTATAA
37746 TTAAATTAAATTATTACTTATAAATTAATAAAAATTTAAAAAAATTATTTTTATATTAATATTTA
1 TTAAATTAAATTATTACTTATAAATTAATAAAAATTT-AAAAAATTATTTTTATATTAATATTTA
37811 TATTTTATAA
65 TATTTTATAA
37821 TTAAATTAAAATTAT
1 TTAAATT-AAATTAT
37836 ATTCGAAATT
Statistics
Matches: 83, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
73 30 0.36
74 5 0.06
75 22 0.27
76 11 0.13
77 15 0.18
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.51
Consensus pattern (74 bp):
TTAAATTAAATTATTACTTATAAATTAATAAAAATTTAAAAAATTATTTTTATATTAATATTTAT
ATTTTATAA
Found at i:38245 original size:23 final size:22
Alignment explanation
Indices: 38201--38245 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
38191 TTGATTAACA
*
38201 TAAAATTTTTTGATTTATAATT
1 TAAAATTTTTTGATTTAAAATT
38223 TAAAATTAATTTT-ATTTAAAATT
1 TAAAATT--TTTTGATTTAAAATT
38246 CGTGATTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TAAAATTTTTTGATTTAAAATT
Found at i:39118 original size:20 final size:20
Alignment explanation
Indices: 39093--39155 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
39083 ATGGTGAACA
39093 ATTTTTATTATTAAAAAAAT
1 ATTTTTATTATTAAAAAAAT
39113 ATTTTTATTTATTAAATAAAAT
1 ATTTTTA-TTATTAAA-AAAAT
*
39135 AATATTT-TT-TT-AAAAAAT
1 -ATTTTTATTATTAAAAAAAT
39153 ATT
1 ATT
39156 AATTAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 2 0.05
18 5 0.13
19 2 0.05
20 9 0.24
21 10 0.26
22 5 0.13
23 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTTTATTATTAAAAAAAT
Found at i:39123 original size:24 final size:25
Alignment explanation
Indices: 39096--39143 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39086 GTGAACAATT
*
39096 TTTATT-ATTAAAAAAATATTTTTA
1 TTTATTAAATAAAAAAATATTTTTA
*
39120 TTTATTAAATAAAATAATATTTTT
1 TTTATTAAATAAAAAAATATTTTT
39144 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTATTAAATAAAAAAATATTTTTA
Found at i:39190 original size:28 final size:28
Alignment explanation
Indices: 39122--39191 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
39112 TATTTTTATT
* *
39122 TATTAAATAAAATAATATTTTTTTAAAAAA
1 TATTAAATATAAT--TATTTTATTAAAAAA
39152 TATT-AAT-TAATTATTATTATTAAAAAA
1 TATTAAATATAATTATT-TTATTAAAAAA
39179 -ATTAAATATAATT
1 TATTAAATATAATT
39192 TATCTAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
26 7 0.20
27 13 0.37
28 8 0.23
29 3 0.09
30 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TATTAAATATAATTATTTTATTAAAAAA
Found at i:39493 original size:15 final size:15
Alignment explanation
Indices: 39475--39531 Score: 71
Period size: 15 Copynumber: 3.6 Consensus size: 15
39465 AGTAATTAAA
39475 AAATATTTATTAAT-T
1 AAAT-TTTATTAATAT
39490 AAATTTTAAATTAAATAT
1 AAATTTT--ATT-AATAT
39508 AAATTTTATTAATAT
1 AAATTTTATTAATAT
39523 AAATTTTAT
1 AAATTTTAT
39532 ATTAAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.08
15 18 0.47
16 6 0.16
17 3 0.08
18 8 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATTTTATTAATAT
Found at i:39525 original size:21 final size:18
Alignment explanation
Indices: 39489--39537 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 18
39479 ATTTATTAAT
39489 TAAATTTTAAATTAAATA
1 TAAATTTTAAATTAAATA
39507 TAAATTTT--ATT-AATA
1 TAAATTTTAAATTAAATA
*
39522 TAAATTTTATATTAAA
1 TAAATTTTAAATTAAA
39538 ATTATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 12 0.43
16 3 0.11
17 3 0.11
18 10 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATTTTAAATTAAATA
Found at i:39530 original size:33 final size:33
Alignment explanation
Indices: 39475--39537 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
39465 AGTAATTAAA
39475 AAATATTTATTAATTAAATTTTAAATTAAATAT
1 AAATATTTATTAATTAAATTTTAAATTAAATAT
*
39508 AAAT-TTTATTAATATAAATTTTATATTAAA
1 AAATATTTATTAAT-TAAATTTTAAATTAAA
39538 ATTATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 9 0.32
33 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
AAATATTTATTAATTAAATTTTAAATTAAATAT
Found at i:39836 original size:15 final size:15
Alignment explanation
Indices: 39811--39850 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
39801 AGCTTTTCTT
39811 TTTCTTTTTCTTTTCC
1 TTTC-TTTTCTTTTCC
39827 TTTCTTTTCTTTTCC
1 TTTCTTTTCTTTTCC
*
39842 TTTCATTTC
1 TTTCTTTTC
39851 CCTCTCGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTCTTTTCTTTTCC
Found at i:39844 original size:6 final size:5
Alignment explanation
Indices: 39803--39850 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
39793 CTAACCCCAG
* * *
39803 CTTTT CTTTTT CTTTTT CTTTT CCTTT CTTTT CTTTT CCTTT CATTT C
1 CTTTT C-TTTT C-TTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT C
39851 CCTCTCGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 27 0.71
6 11 0.29
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (5 bp):
CTTTT
Done.