Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1531
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: 66980
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:2468 original size:25 final size:22
Alignment explanation
Indices: 2411--2459 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
2401 TGGACATGTT
2411 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
2433 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
2455 AAAAA
1 AAAAA
2460 AAATGCATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:3426 original size:20 final size:20
Alignment explanation
Indices: 3379--3453 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
3369 AAAAAGACAT
*
3379 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
3398 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
3419 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
3439 AATGTATCGATACAT
1 AATGTATCGATACAT
3454 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:3447 original size:40 final size:39
Alignment explanation
Indices: 3376--3453 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3366 GGTAAAAAGA
* *
3376 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
3415 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3454 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3680 original size:2 final size:2
Alignment explanation
Indices: 3673--3702 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
3663 TTAAAGTAAC
3673 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
3703 AATAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4323 original size:183 final size:183
Alignment explanation
Indices: 4015--4348 Score: 598
Period size: 183 Copynumber: 1.8 Consensus size: 183
4005 AAAATTTTTT
*
4015 TTTTATGATTTTCTTACCAATTTTGCTATGCCAAATTGCATTTCCGCCATTGCAGCTGTTTCCTT
1 TTTTATGATTTTCTTACCAATTTTGCTATGCCAAATTGCATTTCCGCCATTGCAGCTCTTTCCTT
4080 TACCTTCACCGACCGTTAGTTTCACTCACATTGCATCGGTATCGGCGCATTGTTTTGCGAACTAA
66 TACCTTCACCGACCGTTAGTTTCACTCACATTGCATCGGTATCGGCGCATTGTTTTGCGAACTAA
4145 TTCGAATTCTTAAATTTGGTCGGCTTGCTTTTTTTTTTTTTTTTTTTTTTTAA
131 TTCGAATTCTTAAATTTGGTCGGCTTGCTTTTTTTTTTTTTTTTTTTTTTTAA
* *
4198 TTTTATGATTTTCTTCCCAATTTTGCTCTGCCAAATTGCATTTCCGCCATTGCAGCTCTTTCCTT
1 TTTTATGATTTTCTTACCAATTTTGCTATGCCAAATTGCATTTCCGCCATTGCAGCTCTTTCCTT
4263 TACCTTCACCGACC-TTAGTTTTCACTCACATTGCATCGGTATCGGCGCATTGTTTTGCGAACTA
66 TACCTTCACCGACCGTTAG-TTTCACTCACATTGCATCGGTATCGGCGCATTGTTTTGCGAACTA
* * *
4327 ATTCGATTTGTTCAATTTGGTC
130 ATTCGAATTCTTAAATTTGGTC
4349 CACATTTTTA
Statistics
Matches: 144, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 4 0.03
183 140 0.97
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.45
Consensus pattern (183 bp):
TTTTATGATTTTCTTACCAATTTTGCTATGCCAAATTGCATTTCCGCCATTGCAGCTCTTTCCTT
TACCTTCACCGACCGTTAGTTTCACTCACATTGCATCGGTATCGGCGCATTGTTTTGCGAACTAA
TTCGAATTCTTAAATTTGGTCGGCTTGCTTTTTTTTTTTTTTTTTTTTTTTAA
Found at i:8722 original size:22 final size:23
Alignment explanation
Indices: 8685--8728 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
8675 ATTATTATTT
8685 AATAATAATTATAAAAATATATA
1 AATAATAATTATAAAAATATATA
* *
8708 AATATTAA-TATAAAATTATAT
1 AATAATAATTATAAAAATATAT
8729 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAATAATTATAAAAATATATA
Found at i:10351 original size:13 final size:13
Alignment explanation
Indices: 10335--10359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10325 TTACTGGTAC
10335 TCGGATATAAGTG
1 TCGGATATAAGTG
10348 TCGGATATAAGT
1 TCGGATATAAGT
10360 ATGTGTTTGA
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:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (13 bp):
TCGGATATAAGTG
Found at i:11951 original size:3 final size:3
Alignment explanation
Indices: 11943--11971 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11933 TATATGAAAA
11943 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11972 AACAGAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12114 original size:17 final size:17
Alignment explanation
Indices: 12080--12115 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12070 TTACTTATAA
**
12080 ATATTAAATATATGTAT
1 ATATTAAATATAAATAT
12097 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
12114 AT
1 AT
12116 TTATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATTAAATATAAATAT
Found at i:12617 original size:19 final size:18
Alignment explanation
Indices: 12593--12631 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
12583 GGATTTAATA
12593 ATTTATATATTTGTATTAT
1 ATTTATATATTT-TATTAT
*
12612 ATTTATTTATTTTATTAT
1 ATTTATATATTTTATTAT
12630 AT
1 AT
12632 CATAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:13089 original size:27 final size:26
Alignment explanation
Indices: 13059--13111 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
13049 AAAATATATT
13059 AAAAT-ATTTTTATAATTAATTTAAATAA
1 AAAATAATTTTT-T-ATTAA-TTAAATAA
13087 AAAATAATTTTTTATTAATTAAATA
1 AAAATAATTTTTTATTAATTAAATA
13112 GTAATTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.29
27 5 0.21
28 6 0.25
29 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AAAATAATTTTTTATTAATTAAATAA
Found at i:15207 original size:17 final size:18
Alignment explanation
Indices: 15150--15206 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
15140 TATATGAATG
15150 TATTAAAATTTATAT-AA
1 TATTAAAATTTATATAAA
*
15167 TA-T-AAA-TTAT-TAATT
1 TATTAAAATTTATATAA-A
15182 TATTAAAATTTATATAAA
1 TATTAAAATTTATATAAA
15200 TATTAAA
1 TATTAAA
15207 TAATTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 5 0.16
16 2 0.06
17 5 0.16
18 11 0.34
19 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAAATTTATATAAA
Found at i:15216 original size:26 final size:27
Alignment explanation
Indices: 15166--15216 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
15156 AATTTATATA
* *
15166 ATATAAATTATTAATTTATTAAAATTT
1 ATATAAATTATTAAATAATTAAAATTT
*
15193 ATATAAA-TATTAAATAATTTAAAT
1 ATATAAATTATTAAATAATTAAAAT
15217 ACGATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATAAATTATTAAATAATTAAAATTT
Found at i:15447 original size:4 final size:4
Alignment explanation
Indices: 15438--15465 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
15428 ATTGTGACCT
15438 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
15466 GTTCTTATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:15578 original size:3 final size:3
Alignment explanation
Indices: 15570--15610 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
15560 TTGTTTTCTT
15570 TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T
15611 GTCATGTGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:15802 original size:29 final size:29
Alignment explanation
Indices: 15701--15804 Score: 72
Period size: 29 Copynumber: 3.5 Consensus size: 29
15691 ATGAAAATTT
*
15701 TTAAAATATTTTTACTTA-TTATTTTATTA
1 TTAAAATATTTTTA-TTATTTATTATATTA
** *
15730 TTTAAAA-ATTTTTAAAATTT-TTAAATTCGA
1 -TTAAAATATTTTTATTATTTATTATATT--A
* *
15760 -AAAAAAATTATTTTATTATTTATTATATTA
1 TTAAAATA-T-TTTTATTATTTATTATATTA
15790 TTAAAATATTTTTAT
1 TTAAAATATTTTTAT
15805 ATTAATATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 17
0.67 0.12 0.20
Matches are distributed among these distances:
28 10 0.18
29 16 0.29
30 10 0.18
31 14 0.25
32 6 0.11
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (29 bp):
TTAAAATATTTTTATTATTTATTATATTA
Found at i:15811 original size:14 final size:14
Alignment explanation
Indices: 15794--15821 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15784 ATATTATTAA
15794 AATATTTTTATATT
1 AATATTTTTATATT
15808 AATATTTTTATATT
1 AATATTTTTATATT
15822 TATAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:16736 original size:2 final size:2
Alignment explanation
Indices: 16729--16758 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16719 CATCTCACAA
16729 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
16759 TAATAGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20139 original size:10 final size:10
Alignment explanation
Indices: 20108--20151 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
20098 ATTATACCAA
20108 AAAAAATAATT
1 AAAAAATAA-T
20119 AAAAAATTAAT
1 AAAAAA-TAAT
*
20130 ATAAAATAAT
1 AAAAAATAAT
20140 AAAAAAT-AT
1 AAAAAATAAT
20149 AAA
1 AAA
20152 TAGCATATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 5 0.17
10 10 0.33
11 12 0.40
12 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:21571 original size:22 final size:23
Alignment explanation
Indices: 21546--21599 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
21536 AATATAATAA
*
21546 AATATTAAAATTATTTT-TAATT
1 AATATTTAAATTATTTTATAATT
*
21568 AATATTTATA-TATTTTATAATT
1 AATATTTAAATTATTTTATAATT
21590 AA-ATTTAAAT
1 AATATTTAAAT
21600 AAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTAAATTATTTTATAATT
Found at i:21583 original size:21 final size:21
Alignment explanation
Indices: 21557--21596 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
21547 ATATTAAAAT
21557 TATTTT-TAATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
21578 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
21597 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:22568 original size:22 final size:21
Alignment explanation
Indices: 22529--22569 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
22519 TTAAAAAAAT
* *
22529 TATTTTTAATTTATATTTATA
1 TATTTTTAAATTAAATTTATA
22550 TATTTTTATAATTAAATTTA
1 TATTTTTA-AATTAAATTTA
22570 AATAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTTAAATTAAATTTATA
Found at i:28619 original size:22 final size:22
Alignment explanation
Indices: 28567--28619 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
28557 ATAATATTTT
28567 TATTTAAAT-TTAATTATAAAA
1 TATTTAAATATTAATTATAAAA
*
28588 TATATAAATATTAATGTA-AAAA
1 TATTTAAATATTAAT-TATAAAA
*
28610 TATTTTAATA
1 TATTTAAATA
28620 AATATAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 17 0.63
23 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTTAAATATTAATTATAAAA
Found at i:29594 original size:36 final size:36
Alignment explanation
Indices: 29540--29750 Score: 223
Period size: 36 Copynumber: 5.9 Consensus size: 36
29530 TATGTACTCC
*
29540 TTGGCCTTGCTACTTTGTGCCCTAGCGGAAT-GATCA
1 TTGGCCTTGCTACCTTGTGCCCTAGCGG-ATGGATCA
* *
29576 TTGGCCTTGCTGCCTTGTGCTCC-AGCAGATGGATCA
1 TTGGCCTTGCTACCTTGTGC-CCTAGCGGATGGATCA
* * *
29612 TTGGCCTTGCTACCTTGTGCTCTGGCGGATGGATCT
1 TTGGCCTTGCTACCTTGTGCCCTAGCGGATGGATCA
* *
29648 TTGGCCATGCTACCTTGTG-CTTGAGCGGATGGATCA
1 TTGGCCTTGCTACCTTGTGCCCT-AGCGGATGGATCA
* * * *
29684 TTGGCATTGCTACCTTGTG-CTTGAGCGGATGAATCT
1 TTGGCCTTGCTACCTTGTGCCCT-AGCGGATGGATCA
* * *
29720 TTGGCCTTGCTACCGTGTGCCCCAGGGGATG
1 TTGGCCTTGCTACCTTGTGCCCTAGCGGATG
29751 AATCTGTTTT
Statistics
Matches: 148, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
35 4 0.03
36 141 0.95
37 3 0.02
ACGTcount: A:0.14, C:0.25, G:0.29, T:0.32
Consensus pattern (36 bp):
TTGGCCTTGCTACCTTGTGCCCTAGCGGATGGATCA
Found at i:29664 original size:72 final size:72
Alignment explanation
Indices: 29540--29744 Score: 261
Period size: 72 Copynumber: 2.8 Consensus size: 72
29530 TATGTACTCC
* * * * *
29540 TTGGCCTTGCTACTTTGTGCCCTAGCGGAAT-GATCATTGGCCTTGCTGCCTTGTGCTCCAGCAG
1 TTGGCCTTGCTACCTTGTGCTCTGGCGG-ATGGATCTTTGGCCTTGCTACCTTGTGCTCCAGCAG
29604 ATGGATCA
65 ATGGATCA
* ** *
29612 TTGGCCTTGCTACCTTGTGCTCTGGCGGATGGATCTTTGGCCATGCTACCTTGTGCTTGAGCGGA
1 TTGGCCTTGCTACCTTGTGCTCTGGCGGATGGATCTTTGGCCTTGCTACCTTGTGCTCCAGCAGA
29677 TGGATCA
66 TGGATCA
* * * *
29684 TTGGCATTGCTACCTTGTGCT-TGAGCGGATGAATCTTTGGCCTTGCTACCGTGTGCCCCAG
1 TTGGCCTTGCTACCTTGTGCTCTG-GCGGATGGATCTTTGGCCTTGCTACCTTGTGCTCCAG
29745 GGGATGAATC
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
71 4 0.03
72 111 0.97
ACGTcount: A:0.14, C:0.25, G:0.28, T:0.33
Consensus pattern (72 bp):
TTGGCCTTGCTACCTTGTGCTCTGGCGGATGGATCTTTGGCCTTGCTACCTTGTGCTCCAGCAGA
TGGATCA
Found at i:29729 original size:108 final size:108
Alignment explanation
Indices: 29540--29739 Score: 269
Period size: 108 Copynumber: 1.9 Consensus size: 108
29530 TATGTACTCC
* * * *
29540 TTGGCCTTGCTACTTTGTGCCCTAGCGGAATGATCATTGGCCTTGCTGCCTTGTGCTCCAGCAGA
1 TTGGCCATGCTACCTTGTGCCCTAGCGGAATGATCATTGGCATTGCTACCTTGTGCTCCAGCAGA
* *
29605 TGGATCATTGGCCTTGCTACCTTGTGCTCTGGCGGATGGATCT
66 TGAATCATTGGCCTTGCTACCGTGTGCTCTGGCGGATGGATCT
* ** *
29648 TTGGCCATGCTACCTTGTG-CTTGAGCGG-ATGGATCATTGGCATTGCTACCTTGTGCTTGAGCG
1 TTGGCCATGCTACCTTGTGCCCT-AGCGGAAT-GATCATTGGCATTGCTACCTTGTGCTCCAGCA
*
29711 GATGAATCTTTGGCCTTGCTACCGTGTGC
64 GATGAATCATTGGCCTTGCTACCGTGTGC
29740 CCCAGGGGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
107 4 0.05
108 75 0.95
ACGTcount: A:0.14, C:0.24, G:0.28, T:0.34
Consensus pattern (108 bp):
TTGGCCATGCTACCTTGTGCCCTAGCGGAATGATCATTGGCATTGCTACCTTGTGCTCCAGCAGA
TGAATCATTGGCCTTGCTACCGTGTGCTCTGGCGGATGGATCT
Found at i:32565 original size:24 final size:23
Alignment explanation
Indices: 32516--32565 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
32506 CTTCTTTATC
* * *
32516 TTATTCCTTCCTCTCTTTTCTGT
1 TTATTCCTTCCTCTCTATCCTCT
*
32539 TTATTCTTTGCCTCTCTATCCTCT
1 TTATTCCTT-CCTCTCTATCCTCT
32563 TTA
1 TTA
32566 CGTAATCTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.08, C:0.30, G:0.04, T:0.58
Consensus pattern (23 bp):
TTATTCCTTCCTCTCTATCCTCT
Found at i:33750 original size:32 final size:33
Alignment explanation
Indices: 33709--33779 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
33699 AGATATGTGT
**
33709 TTATATAAATTTTGACATATTAATA-ATTTATA
1 TTATATAAATTTCAACATATTAATATATTTATA
* * *
33741 TTATATAAATTTCAATATATTTATATATTTTTA
1 TTATATAAATTTCAACATATTAATATATTTATA
33774 TTATAT
1 TTATAT
33780 CATATTTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (33 bp):
TTATATAAATTTCAACATATTAATATATTTATA
Found at i:34838 original size:21 final size:21
Alignment explanation
Indices: 34814--34854 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34804 TCCTGGAGGG
*
34814 CCACCGGGAGGTCCAGGTGGA
1 CCACCAGGAGGTCCAGGTGGA
* *
34835 CCACCAGGCGGTCCGGGTGG
1 CCACCAGGAGGTCCAGGTGG
34855 TCCTGGTGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.32, G:0.44, T:0.10
Consensus pattern (21 bp):
CCACCAGGAGGTCCAGGTGGA
Found at i:34887 original size:33 final size:33
Alignment explanation
Indices: 34850--34929 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
34840 AGGCGGTCCG
* *
34850 GGTGGTCCTGGTGGTGGGGCAGCATAAGGAAAA
1 GGTGGGCCGGGTGGTGGGGCAGCATAAGGAAAA
34883 GGTGGGCCGGGTGGTGGGGCAGCATAAGGAAAA
1 GGTGGGCCGGGTGGTGGGGCAGCATAAGGAAAA
34916 GGTGGGCCGGGTGG
1 GGTGGGCCGGGTGG
34930 AGGTGGAGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.20, C:0.12, G:0.53, T:0.15
Consensus pattern (33 bp):
GGTGGGCCGGGTGGTGGGGCAGCATAAGGAAAA
Found at i:34976 original size:24 final size:24
Alignment explanation
Indices: 34923--34986 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
34913 AAAGGTGGGC
34923 CGGGTGGAGGTGGAGCAAGTGCGA
1 CGGGTGGAGGTGGAGCAAGTGCGA
** *
34947 TAGGTGGAGGTGGAGCAGGTGCGA
1 CGGGTGGAGGTGGAGCAAGTGCGA
* *
34971 CGGGTGGTGGAGGAGC
1 CGGGTGGAGGTGGAGC
34987 TGGAGCAGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.11, G:0.56, T:0.14
Consensus pattern (24 bp):
CGGGTGGAGGTGGAGCAAGTGCGA
Found at i:35137 original size:4 final size:4
Alignment explanation
Indices: 35128--35153 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
35118 ATGTAAAAGT
35128 TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA
35154 GCACTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:35337 original size:24 final size:22
Alignment explanation
Indices: 35305--35358 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
35295 ACTTTAGTTA
*
35305 AATTATTATTAAATTAATGAAAAAT
1 AATTTTTATTAAA-T-AT-AAAAAT
*
35330 -ATTTTTATTTAATATAAAAAT
1 AATTTTTATTAAATATAAAAAT
35351 AATTTTTA
1 AATTTTTA
35359 AATATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.23
22 9 0.35
23 1 0.04
24 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATTTTTATTAAATATAAAAAT
Found at i:36202 original size:45 final size:45
Alignment explanation
Indices: 36138--36227 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
36128 GAGCTCCAGG
*
36138 TCCAGGACCGCCTGGTCCAGGAGGACCCCAACCACCAGGACCTCC
1 TCCAGGACCGCCAGGTCCAGGAGGACCCCAACCACCAGGACCTCC
*
36183 TCCAGGACCGCCAGGTCCAGGAGGACCCCAACCACCAGGTCCTCC
1 TCCAGGACCGCCAGGTCCAGGAGGACCCCAACCACCAGGACCTCC
36228 AGGTCCCGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.22, C:0.44, G:0.24, T:0.09
Consensus pattern (45 bp):
TCCAGGACCGCCAGGTCCAGGAGGACCCCAACCACCAGGACCTCC
Found at i:38672 original size:34 final size:36
Alignment explanation
Indices: 38618--38691 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 36
38608 TATTTTTTTA
*
38618 ATTTTTA--AAATTAAATATTT-AATGATTTAATAT
1 ATTTTTATTAAATTAAATATTTAAATAATTTAATAT
38651 -TTTTTATTAAATTCAAA-ATTTAAATAATTTAATAT
1 ATTTTTATTAAATT-AAATATTTAAATAATTTAATAT
38686 ATTTTT
1 ATTTTT
38692 TAATGTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
32 6 0.17
34 9 0.26
35 15 0.43
36 5 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (36 bp):
ATTTTTATTAAATTAAATATTTAAATAATTTAATAT
Found at i:43538 original size:56 final size:56
Alignment explanation
Indices: 43443--43578 Score: 220
Period size: 56 Copynumber: 2.4 Consensus size: 56
43433 TTCACACCCG
* *
43443 AGTCCGAGTAACTTAA-ATGCCATGTGTCATTTTTTCTGGTCAAAGAACAATTCCCA
1 AGTCTGAGTAAC-TAAGATGCCATGTGTCATTTTTACTGGTCAAAGAACAATTCCCA
*
43499 AGTCTGATTAACTAAGATGCCATGTGTCATTTTTACTGGTCAAAGAACAATTCCCA
1 AGTCTGAGTAACTAAGATGCCATGTGTCATTTTTACTGGTCAAAGAACAATTCCCA
*
43555 AGTTTGAGTAACTAAGATGCCATG
1 AGTCTGAGTAACTAAGATGCCATG
43579 ATGGTTAAGT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
55 3 0.04
56 71 0.96
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (56 bp):
AGTCTGAGTAACTAAGATGCCATGTGTCATTTTTACTGGTCAAAGAACAATTCCCA
Found at i:43945 original size:170 final size:166
Alignment explanation
Indices: 43658--43997 Score: 468
Period size: 170 Copynumber: 2.0 Consensus size: 166
43648 GAGCAGAAGA
* *
43658 CAAGCCACAAAGACATTACACACCTTTGTGCAAATCTTCAAGAGAAAACATTATTTATTAACAAG
1 CAAGCCACAAAGACATTACACACCTTTGTACAAATCTTCAAGAGAAAACATTAATTATTAACAAG
* * *
43723 GTAAAACTATATCATCAAGATTTTATGAGTTTCAGTAATCCAAACCGGATAAACTATGGTCTTAG
66 GT--AACTATATCATCAAAATTTTATGAGTTTCAGTAATCCAAACCGGATAAACTATGCTCTTAA
* * *
43788 AAACAAGCCCCGAACAATGTTTATTTGACCATTGAAAC
129 AAACAAGCCCCAAACAATATTAATTTGACCATTGAAAC
*
43826 CAAGCCACAAAGACATTACACGCCATTT-TACAAATCTTCAAGAGAAAACATAACTAAAATTATT
1 CAAGCCACAAAGACATTACACACC-TTTGTACAAATCTTCAAGAGAAAACAT---T--AATTATT
** * *
43890 AATGAGGT-ACTATATCATCAAAATTTTATGAGTTTCAGTAATCCGAACTGGATAAACTATGCTC
60 AACAAGGTAACTATATCATCAAAATTTTATGAGTTTCAGTAATCCAAACCGGATAAACTATGCTC
*
43954 TTAAAAACAAGCCCTAAACAATATTAATTTGACCATTGAAAC
125 TTAAAAACAAGCCCCAAACAATATTAATTTGACCATTGAAAC
43996 CA
1 CA
43998 GACTGAAAAC
Statistics
Matches: 152, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
168 45 0.30
169 3 0.02
170 91 0.60
171 1 0.01
173 12 0.08
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (166 bp):
CAAGCCACAAAGACATTACACACCTTTGTACAAATCTTCAAGAGAAAACATTAATTATTAACAAG
GTAACTATATCATCAAAATTTTATGAGTTTCAGTAATCCAAACCGGATAAACTATGCTCTTAAAA
ACAAGCCCCAAACAATATTAATTTGACCATTGAAAC
Found at i:52465 original size:26 final size:25
Alignment explanation
Indices: 52436--52485 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
52426 TTCAAATTAA
52436 ATTATTTTAAATTTT-TATTTATTTTT
1 ATTATTTT-AATTTTATA-TTATTTTT
*
52462 ATTATTTTGATTTTATATTATTTT
1 ATTATTTTAATTTTATATTATTTT
52486 AAATTTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (25 bp):
ATTATTTTAATTTTATATTATTTTT
Found at i:52482 original size:16 final size:15
Alignment explanation
Indices: 52456--52485 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
52446 ATTTTTATTT
52456 ATTTTTATTATTTTG
1 ATTTTTATTATTTTG
52471 ATTTTATATTATTTT
1 ATTTT-TATTATTTT
52486 AAATTTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
ATTTTTATTATTTTG
Found at i:52569 original size:22 final size:21
Alignment explanation
Indices: 52538--52579 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
52528 TTCATATTAT
52538 TTTAAATTTGAGTCAATTAAG
1 TTTAAATTTGAGTCAATTAAG
*
52559 TTTAACATTTGAGTTAATTAA
1 TTTAA-ATTTGAGTCAATTAA
52580 TCTTGAGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (21 bp):
TTTAAATTTGAGTCAATTAAG
Found at i:53107 original size:24 final size:23
Alignment explanation
Indices: 53066--53116 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
53056 TAAATTTTGA
*
53066 TATATTGATAATTCATATTACAT
1 TATATTGATAATTCATATAACAT
* * *
53089 TATATTTATATATTTATATAATAT
1 TATATTGATA-ATTCATATAACAT
53113 TATA
1 TATA
53117 AATATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTGATAATTCATATAACAT
Found at i:53284 original size:18 final size:18
Alignment explanation
Indices: 53222--53284 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
53212 TTTATATTCG
**
53222 ATTAAATTTTATTTTTAAA
1 ATTAAATTTT-TAATTAAA
53241 AGTTAAA--TTTAATTAAA
1 A-TTAAATTTTTAATTAAA
*
53258 A-TATTATTTTTAATTAAA
1 ATTA-AATTTTTAATTAAA
53276 ATTAAATTT
1 ATTAAATTT
53285 AAAATATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
15 2 0.06
16 1 0.03
17 7 0.20
18 17 0.49
19 3 0.09
20 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTAAATTTTTAATTAAA
Found at i:59296 original size:2 final size:2
Alignment explanation
Indices: 59289--59317 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59279 GAAAAACAAA
59289 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
59318 ATCTGTGTTC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:60366 original size:24 final size:23
Alignment explanation
Indices: 60339--60422 Score: 75
Period size: 24 Copynumber: 3.6 Consensus size: 23
60329 AATATGATAC
60339 AAAAATTA-AAATATAAAGTAATAT
1 AAAAATTATAAATATAAA-TAAT-T
* *
60363 AAAAA-TATGAATATAAATATTTT
1 AAAAATTATAAATATAAATA-ATT
*
60386 AAAATTTATATAATATAAATAATT
1 AAAAATTATA-AATATAAATAATT
60410 AAAATATTA-AAAT
1 AAAA-ATTATAAAT
60423 TTATTATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
23 12 0.24
24 24 0.49
25 13 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAAATTATAAATATAAATAATT
Found at i:60403 original size:25 final size:25
Alignment explanation
Indices: 60367--60414 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
60357 TAATATAAAA
*
60367 ATATGAATATAAATATTTTAAAATTT
1 ATATGAATATAAATA-ATTAAAATTT
60393 ATAT-AATATAAATAATTAAAAT
1 ATATGAATATAAATAATTAAAAT
60415 ATTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 10 0.48
26 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
ATATGAATATAAATAATTAAAATTT
Found at i:60601 original size:3 final size:3
Alignment explanation
Indices: 60593--60621 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
60583 AATTCATTAT
60593 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
60622 TTAGGTCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:61161 original size:23 final size:23
Alignment explanation
Indices: 61135--61180 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
61125 ATTTGTAATC
61135 GTTTAATAATATGAATTAAAGTG
1 GTTTAATAATATGAATTAAAGTG
61158 GTTTAATAATATGAATTAAAGTG
1 GTTTAATAATATGAATTAAAGTG
61181 ATATTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.39
Consensus pattern (23 bp):
GTTTAATAATATGAATTAAAGTG
Found at i:61703 original size:19 final size:20
Alignment explanation
Indices: 61676--61714 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61666 TATTTAAATA
61676 TAATAAAAA-TATAAAATTT
1 TAATAAAAATTATAAAATTT
*
61695 TAATTAAAATTATAAAATTT
1 TAATAAAAATTATAAAATTT
61715 AAAGACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATAAAAATTATAAAATTT
Found at i:62884 original size:22 final size:21
Alignment explanation
Indices: 62855--62895 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
62845 ATATTTTTTA
62855 AAATTTAATTAT-AAAATATAT
1 AAATTTAA-TATGAAAATATAT
62876 AAATATTAATATGAAAATAT
1 AAAT-TTAATATGAAAATAT
62896 CTTTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTTAATATGAAAATATAT
Found at i:63607 original size:29 final size:30
Alignment explanation
Indices: 63546--63612 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
63536 AAATATATAA
*
63546 AAATATAAA-A-ATTTTTATAATTAAATTT
1 AAATATAAATATATTTTTATAATTAAATAT
*
63574 AAATA-AAATATATTTTTATATTTAAATA-
1 AAATATAAATATATTTTTATAATTAAATAT
63602 ATAATATAAAT
1 A-AATATAAAT
63613 TGAATTAGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 3 0.09
28 7 0.21
29 19 0.58
30 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AAATATAAATATATTTTTATAATTAAATAT
Found at i:63657 original size:2 final size:2
Alignment explanation
Indices: 63650--63697 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
63640 CGAAGAAATT
63650 TA TA TA TA TA TA 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 TA TA TA TA TA TA
63692 TA TA TA
1 TA TA TA
63698 GGAAGGATCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66117 original size:22 final size:22
Alignment explanation
Indices: 66068--66117 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
66058 ATTTTAATTT
*
66068 AAAATT-TTATTTATATAATAT
1 AAAATTATTATTTATATAATAA
*
66089 AAAATTATTAATTT-TATTATAA
1 AAAATTATT-ATTTATATAATAA
66111 AAAATTA
1 AAAATTA
66118 ATTTTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.24
22 15 0.60
23 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATTATTATTTATATAATAA
Done.