Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2288
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: 23753
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Found at i:1358 original size:2 final size:2
Alignment explanation
Indices: 1351--1375 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1341 TTAGAAGCAA
1351 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1376 ATAAAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3278 original size:22 final size:22
Alignment explanation
Indices: 3253--3302 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
3243 AATAAGTTTA
* * *
3253 TTTATGAATTATTTAAAGCTCG
1 TTTATAAATCATTTAAAACTCG
3275 TTTAATAAATCATTTAAAACTCG
1 TTT-ATAAATCATTTAAAACTCG
3298 TTTAT
1 TTTAT
3303 TATTTGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (22 bp):
TTTATAAATCATTTAAAACTCG
Found at i:3489 original size:23 final size:23
Alignment explanation
Indices: 3447--3503 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
3437 TTTGTTTATC
* *
3447 ATTCATAAATA-ATTTTTTAATT
1 ATTCATAAATATATTTATTAAAT
*
3469 ATTCATGAATATATTTATTAAAT
1 ATTCATAAATATATTTATTAAAT
*
3492 GTTCATAAATAT
1 ATTCATAAATAT
3504 GATCATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTCATAAATATATTTATTAAAT
Found at i:4149 original size:12 final size:13
Alignment explanation
Indices: 4130--4166 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
4120 ATATAAATAT
4130 ATAAATATATTAA
1 ATAAATATATTAA
*
4143 A-AAATATATAAA
1 ATAAATATATTAA
4155 ATAAAT-TATTAA
1 ATAAATATATTAA
4167 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAATATATTAA
Found at i:5092 original size:9 final size:9
Alignment explanation
Indices: 5074--5143 Score: 76
Period size: 9 Copynumber: 7.9 Consensus size: 9
5064 TTAAAATTAA
5074 ATTT-TAAT
1 ATTTATAAT
5082 ATTTATAAT
1 ATTTATAAT
5091 ATTTAT-AT
1 ATTTATAAT
*
5099 ATTTTATAAAA
1 A-TTTAT-AAT
5110 ATTT-TAAT
1 ATTTATAAT
5118 ATTTATAAT
1 ATTTATAAT
5127 ATTTAT-AT
1 ATTTATAAT
5135 ATTTTATAA
1 A-TTTATAA
5144 AAATTTTACA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
8 16 0.30
9 31 0.58
10 4 0.08
11 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTTATAAT
Found at i:5112 original size:36 final size:36
Alignment explanation
Indices: 5072--5151 Score: 160
Period size: 36 Copynumber: 2.2 Consensus size: 36
5062 ATTTAAAATT
5072 AAATTTTAATATTTATAATATTTATATATTTTATAA
1 AAATTTTAATATTTATAATATTTATATATTTTATAA
5108 AAATTTTAATATTTATAATATTTATATATTTTATAA
1 AAATTTTAATATTTATAATATTTATATATTTTATAA
5144 AAATTTTA
1 AAATTTTA
5152 CAAAAAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (36 bp):
AAATTTTAATATTTATAATATTTATATATTTTATAA
Found at i:5297 original size:16 final size:16
Alignment explanation
Indices: 5276--5314 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5266 AATTTTATAA
5276 ATATATTTTTTAAAAT
1 ATATATTTTTTAAAAT
*
5292 ATATATTTTTTAAATT
1 ATATATTTTTTAAAAT
5308 AT-TATTT
1 ATATATTT
5315 AAAAATTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATATTTTTTAAAAT
Found at i:5300 original size:15 final size:14
Alignment explanation
Indices: 5268--5318 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
5258 AATTTTTTAA
5268 TTTTATAAATATATT
1 TTTTA-AAATATATT
5283 TTTTAAAATATATAT
1 TTTTAAAATATAT-T
*
5298 TTTTTAAAT-TATT
1 TTTTAAAATATATT
*
5311 ATTTAAAA
1 TTTTAAAA
5319 ATTATCACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 7 0.22
14 11 0.34
15 14 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAAAATATATT
Found at i:5462 original size:14 final size:16
Alignment explanation
Indices: 5443--5479 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5433 TATTTATAAA
5443 AAAAAATAAA-T-TTT
1 AAAAAATAAATTATTT
*
5457 AAAAAAAAAATTATTT
1 AAAAAATAAATTATTT
5473 AAAAAAT
1 AAAAAAT
5480 TAAAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 9 0.47
15 1 0.05
16 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAAATAAATTATTT
Found at i:5462 original size:16 final size:16
Alignment explanation
Indices: 5441--5478 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5431 TTTATTTATA
5441 AAAAAAAATAAAT-TTT
1 AAAAAAAA-AAATATTT
*
5457 AAAAAAAAAATTATTT
1 AAAAAAAAAAATATTT
5473 AAAAAA
1 AAAAAA
5479 TTAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAAAAAAATATTT
Found at i:5472 original size:17 final size:17
Alignment explanation
Indices: 5434--5478 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
5424 TTTTTATTTT
5434 ATTTATAAAAAAAAATAA
1 ATTTA-AAAAAAAAATAA
*
5452 ATTTTAAAAAAAAAAT-T
1 A-TTTAAAAAAAAAATAA
5469 ATTTAAAAAA
1 ATTTAAAAAA
5479 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 9 0.36
17 1 0.04
18 11 0.44
19 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTTAAAAAAAAAATAA
Found at i:5982 original size:23 final size:25
Alignment explanation
Indices: 5935--5989 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
5925 ACTTAAAATT
5935 ATTTT-TATGAATATAAATTTATAA
1 ATTTTATATGAATATAAATTTATAA
5959 ATTTTATATG-ATA-AAACTTT-TAA
1 ATTTTATATGAATATAAA-TTTATAA
5982 ATTTTATA
1 ATTTTATA
5990 AATAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 14 0.48
24 11 0.38
25 4 0.14
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
ATTTTATATGAATATAAATTTATAA
Found at i:5994 original size:22 final size:22
Alignment explanation
Indices: 5937--5998 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
5927 TTAAAATTAT
*
5937 TTTTATGAATATAAATTTATAAA
1 TTTTATAAATA-AAATTTATAAA
*
5960 TTTTATATGATAAAACTTT-TAAA
1 TTTTATA-AATAAAA-TTTATAAA
5983 TTTTATAAATAAAATT
1 TTTTATAAATAAAATT
5999 AAAAAATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.06
22 6 0.18
23 20 0.59
24 6 0.18
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (22 bp):
TTTTATAAATAAAATTTATAAA
Found at i:6538 original size:17 final size:16
Alignment explanation
Indices: 6512--6546 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
6502 TTAAAAAATT
6512 AATATTTTTTAAAGTA
1 AATATTTTTTAAAGTA
*
6528 AATAGTTTTTTTAAGTA
1 AATA-TTTTTTAAAGTA
6545 AA
1 AA
6547 AAGTGACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (16 bp):
AATATTTTTTAAAGTA
Found at i:7636 original size:21 final size:21
Alignment explanation
Indices: 7612--7659 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
7602 AAAATGTTAT
* *
7612 TATTTATATTATTTTTATATA
1 TATTTATATCATTTTTAAATA
**
7633 TATTCGTATCATTTTTAAATA
1 TATTTATATCATTTTTAAATA
7654 T-TTTAT
1 TATTTAT
7660 CATATCATAA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TATTTATATCATTTTTAAATA
Found at i:7737 original size:16 final size:16
Alignment explanation
Indices: 7670--7737 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
7660 CATATCATAA
*
7670 TTATATT-TAAAATATT
1 TTATATTATATAA-ATT
7686 TTATATTTATATAAATT
1 TTATA-TTATATAAATT
* *
7703 TTA-A-TAAATTAATCAT
1 TTATATTATATAAAT--T
7719 TTATATTATATAAATT
1 TTATATTATATAAATT
7735 TTA
1 TTA
7738 AAATAAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
14 7 0.17
16 14 0.34
17 9 0.22
18 11 0.27
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATTATATAAATT
Found at i:8204 original size:2 final size:2
Alignment explanation
Indices: 8199--8241 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
8189 ATATTGTGTG
*
8199 TA TA TA TA TA TA TA TA T- TA TA TG TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8239 TA T
1 TA T
8242 CCACATGCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8219 original size:17 final size:17
Alignment explanation
Indices: 8199--8241 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
8189 ATATTGTGTG
8199 TATATATATATATATAT
1 TATATATATATATATAT
*
8216 TATATGTATATATATAT
1 TATATATATATATATAT
*
8233 AATATATAT
1 TATATATAT
8242 CCACATGCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:8225 original size:19 final size:19
Alignment explanation
Indices: 8203--8239 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8193 TGTGTGTATA
*
8203 TATATATATATATTATATG
1 TATATATATATAATATATG
8222 TATATATATATAATATAT
1 TATATATATATAATATAT
8240 ATCCACATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATATATATAATATATG
Found at i:9399 original size:28 final size:29
Alignment explanation
Indices: 9361--9450 Score: 73
Period size: 28 Copynumber: 3.1 Consensus size: 29
9351 TATTAAAAAT
*
9361 AAATATTATATTTAATTTAATAATATTAA
1 AAATATAATATTTAATTTAATAATATTAA
* *
9390 AAATA-AATA-TCACTTTTAA-AATATTTAAA
1 AAATATAATATTTA-ATTTAATAATA-TT-AA
*
9419 AAATATAAT-TTTAA-TAAATAATTATTAA
1 AAATATAATATTTAATTTAATAA-TATTAA
9447 AAAT
1 AAAT
9451 TATTTTTCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
27 6 0.12
28 19 0.40
29 16 0.33
30 7 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
AAATATAATATTTAATTTAATAATATTAA
Found at i:9661 original size:17 final size:17
Alignment explanation
Indices: 9641--9685 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
9631 TTAAAAAAAA
9641 TAATTTTTAATAA-TTTT
1 TAATTTTTAA-AATTTTT
9658 TAATTTTTAAAATTTTT
1 TAATTTTTAAAATTTTT
*
9675 TTATTTTTAAA
1 TAATTTTTAAA
9686 CTATGAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 2 0.08
17 24 0.92
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TAATTTTTAAAATTTTT
Found at i:10292 original size:8 final size:8
Alignment explanation
Indices: 10279--10368 Score: 56
Period size: 8 Copynumber: 10.1 Consensus size: 8
10269 TAAATATAAC
10279 ATAAATAT
1 ATAAATAT
10287 ATAAATAT
1 ATAAATAT
10295 ATCAAAATTTAT
1 AT--AAA--TAT
10307 ATAAATAT
1 ATAAATAT
10315 ATTAAATAT
1 A-TAAATAT
10324 ATAACAT-T
1 ATAA-ATAT
*
10332 TTAAATATT
1 ATAAATA-T
*
10341 ATTTTAATAT
1 A--TAAATAT
*
10351 AAAAATAAT
1 ATAAAT-AT
10360 ATAAATAT
1 ATAAATAT
10368 A
1 A
10369 ATATAAATAC
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
7 2 0.03
8 27 0.42
9 18 0.28
10 8 0.12
11 5 0.08
12 5 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (8 bp):
ATAAATAT
Found at i:10302 original size:29 final size:29
Alignment explanation
Indices: 10270--10325 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
10260 AAAATAAAAT
10270 AAATATAACATAAATATA-TAAATATATCA
1 AAAT-TAACATAAATATATTAAATATATCA
* *
10299 AAATTTATATAAATATATTAAATATAT
1 AAATTAACATAAATATATTAAATATAT
10326 AACATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATTAACATAAATATATTAAATATATCA
Found at i:10376 original size:11 final size:11
Alignment explanation
Indices: 10224--10377 Score: 62
Period size: 11 Copynumber: 14.7 Consensus size: 11
10214 GCTGTGCATT
10224 TATAAATA-AA
1 TATAAATATAA
* *
10234 -ATAATTAAAA
1 TATAAATATAA
*
10244 TATAATATATTA
1 TATAA-ATATAA
* *
10256 TACAAAAATAA
1 TATAAATATAA
*
10267 AATAAATATAA
1 TATAAATATAA
*
10278 CAT-AA-AT-A
1 TATAAATATAA
10286 TATAAATAT-A
1 TATAAATATAA
*
10296 TCA-AAAT-TTA
1 T-ATAAATATAA
10306 TATAAATAT-A
1 TATAAATATAA
10316 T-TAAATAT-A
1 TATAAATATAA
* *
10325 TA-ACATTTTAAA
1 TATA-AATAT-AA
* * *
10337 TATTATTTTAA
1 TATAAATATAA
*
10348 TATAAAAATAA
1 TATAAATATAA
10359 TATAAATATAA
1 TATAAATATAA
10370 TATAAATA
1 TATAAATA
10378 CATAAAATAT
Statistics
Matches: 110, Mismatches: 20, Indels: 27
0.70 0.13 0.17
Matches are distributed among these distances:
8 3 0.03
9 22 0.20
10 23 0.21
11 47 0.43
12 15 0.14
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAAATATAA
Found at i:10385 original size:20 final size:20
Alignment explanation
Indices: 10261--10392 Score: 58
Period size: 20 Copynumber: 7.0 Consensus size: 20
10251 TATTATACAA
* *
10261 AAATAAAATAAATATAACAT
1 AAATAATATAAATATAATAT
10281 AAAT-ATATAAATAT-ATCA-
1 AAATAATATAAATATAAT-AT
*
10299 AAATTTATATAAATAT-AT-T
1 AAA-TAATATAAATATAATAT
10318 AAAT-ATATAACAT-T--T-T
1 AAATAATATAA-ATATAATAT
* *
10334 AAAT-AT-T-ATTTTAATAT
1 AAATAATATAAATATAATAT
10351 AAAAATAATATAAATATAATAT
1 --AAATAATATAAATATAATAT
*
10373 AAATACATA-AAATATTATAT
1 AAATA-ATATAAATATAATAT
10393 TTATATATTA
Statistics
Matches: 91, Mismatches: 6, Indels: 30
0.72 0.05 0.24
Matches are distributed among these distances:
13 1 0.01
14 2 0.02
15 1 0.01
16 9 0.10
17 8 0.09
18 7 0.08
19 18 0.20
20 33 0.36
21 4 0.04
22 8 0.09
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATAATATAAATATAATAT
Found at i:10805 original size:23 final size:25
Alignment explanation
Indices: 10757--10821 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 25
10747 AATTTTTAAT
*
10757 TATTATTT-TAA-AATTAATTAATA
1 TATTATTTATAATAATTAATTAAAA
10780 TATTATTTATAATAA-TAA-TAAAA
1 TATTATTTATAATAATTAATTAAAA
** *
10803 TATTAAATATAATACTTAA
1 TATTATTTATAATAATTAA
10822 CAACTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 24 0.69
24 9 0.26
25 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATTATTTATAATAATTAATTAAAA
Found at i:11172 original size:21 final size:20
Alignment explanation
Indices: 11136--11180 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
11126 CAAGATTATT
**
11136 AAATTAAAAATTTTAAATATA
1 AAATTAAAAAAATT-AATATA
*
11157 AAATTAAAAAAATTAATATT
1 AAATTAAAAAAATTAATATA
11177 AAAT
1 AAAT
11181 AAGTATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTAAAAAAATTAATATA
Found at i:11201 original size:27 final size:27
Alignment explanation
Indices: 11132--11219 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 27
11122 TAAACAAGAT
*
11132 TATTAAAT-TAA-AAATTTTAAATATAA
1 TATTAAATATAATAAATATTAAATA-AA
* * * *
11158 AATTAAA-AAAATTAATATTAAATAAG
1 TATTAAATATAATAAATATTAAATAAA
*
11184 TATTAAATATAATAAATATTTAATAAA
1 TATTAAATATAATAAATATTAAATAAA
*
11211 -ATTATATAT
1 TATTAAATAT
11220 TTAACTAAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
26 23 0.48
27 25 0.52
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (27 bp):
TATTAAATATAATAAATATTAAATAAA
Found at i:11497 original size:18 final size:19
Alignment explanation
Indices: 11454--11499 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
11444 CATGGTTAAC
11454 TATTATATT-TAATATAATA
1 TATTA-ATTATAATATAATA
11473 T-TATAATTATAA-ATAATA
1 TAT-TAATTATAATATAATA
11491 TATTAATTA
1 TATTAATTA
11500 ATTTTAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTAATTATAATATAATA
Found at i:14139 original size:35 final size:35
Alignment explanation
Indices: 14075--14154 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
14065 GTACTTATTA
* * *
14075 TATTAATATTATTTTAAATATAATAATTAATAATTT
1 TATT-ATATAATTTTAAATATAATAATTAAAAATAT
* *
14111 TATT-TATAATTTTTAATATATTATATTAAAAATAT
1 TATTATATAATTTTAAATATAATA-ATTAAAAATAT
14146 TATTATATA
1 TATTATATA
14155 TAATAATCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 16 0.43
35 13 0.35
36 8 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
TATTATATAATTTTAAATATAATAATTAAAAATAT
Found at i:14542 original size:21 final size:20
Alignment explanation
Indices: 14518--14577 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
14508 TCAATTTGAG
14518 ATATAATTTTTTAAATTTAAA
1 ATAT-ATTTTTTAAATTTAAA
**
14539 ATATTATTTAATAAA--TAAA
1 ATA-TATTTTTTAAATTTAAA
*
14558 ATATTTTTATTTAAATTTAA
1 ATATATTT-TTTAAATTTAA
14578 TTATAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
18 4 0.13
19 11 0.37
21 14 0.47
22 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATATTTTTTAAATTTAAA
Found at i:15675 original size:20 final size:20
Alignment explanation
Indices: 15635--15695 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
15625 ATATAGGTTG
*
15635 AAAAATAAATATTTAATATATT
1 AAAAATTAATA-TT-ATATATT
*
15657 TAAAATTAATATTATATATT
1 AAAAATTAATATTATATATT
*
15677 AAAAATTAAAATTATATAT
1 AAAAATTAATATTATATAT
15696 GGTTATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 24 0.69
21 2 0.06
22 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAAATTAATATTATATATT
Found at i:15773 original size:22 final size:21
Alignment explanation
Indices: 15748--15788 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
15738 AATATAAACA
15748 ATTATCGTTAATCATATTTTAT
1 ATTATCGTTAAT-ATATTTTAT
**
15770 ATTATTTTTAATATATTTT
1 ATTATCGTTAATATATTTT
15789 TAAATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTATCGTTAATATATTTTAT
Found at i:15786 original size:11 final size:11
Alignment explanation
Indices: 15755--15813 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
15745 ACAATTATCG
15755 TTAATCATA-TT
1 TTAAT-ATATTT
15766 TT-ATATTATTT
1 TTAATA-TATTT
15777 TTAATATATTT
1 TTAATATATTT
15788 TTAAATATAATTT
1 TT-AATAT-ATTT
*
15801 ATTAAAATATTT
1 -TTAATATATTT
15813 T
1 T
15814 AAAATAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
9 1 0.02
10 4 0.10
11 14 0.34
12 12 0.29
13 8 0.20
14 2 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTAATATATTT
Found at i:15810 original size:15 final size:12
Alignment explanation
Indices: 15772--15823 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 12
15762 TATTTTATAT
15772 TATTTTT-AATA
1 TATTTTTAAATA
15783 TATTTTTAAATA
1 TATTTTTAAATA
15795 TAATTTATTAAA-A
1 T-ATTT-TTAAATA
*
15808 TATTTTAAAATA
1 TATTTTTAAATA
15820 -ATTT
1 TATTT
15824 ATTTTATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
11 15 0.42
12 10 0.28
13 6 0.17
14 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTTTTAAATA
Found at i:15824 original size:23 final size:25
Alignment explanation
Indices: 15768--15826 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
15758 ATCATATTTT
* *
15768 ATATTATTT-TTAATATATTTTTAA
1 ATATAATTTATTAAAATATTTTTAA
15792 ATATAATTTATTAAAATA-TTTTAA
1 ATATAATTTATTAAAATATTTTTAA
15816 A-ATAATTTATT
1 ATATAATTTATT
15827 TTATAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 10 0.31
24 15 0.47
25 7 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATATAATTTATTAAAATATTTTTAA
Found at i:15835 original size:23 final size:23
Alignment explanation
Indices: 15781--15840 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
15771 TTATTTTTAA
*
15781 TATATTTTTAAATATAATTTATT
1 TATAATTTTAAATATAATTTATT
* *
15804 AAAATATTTTAAA-ATAATTTATTT
1 TATA-ATTTTAAATATAATTTA-TT
15828 TATAATTTTAAAT
1 TATAATTTTAAAT
15841 TTATTAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATAATTTTAAATATAATTTATT
Found at i:16208 original size:37 final size:37
Alignment explanation
Indices: 16122--16209 Score: 97
Period size: 39 Copynumber: 2.3 Consensus size: 37
16112 TATTATTTTT
** *
16122 TAAATTAATATTTTTATATATTTTATAATTTAATTTAAA
1 TAAATTAA-ATTTTTATATATTAAATAA-TTAATTCAAA
*
16161 TCAAACTAAATTTTTATATATTAAATAA-TAATTCAAA
1 T-AAATTAAATTTTTATATATTAAATAATTAATTCAAA
16198 CTAAATTAAATT
1 -TAAATTAAATT
16210 AACTTGAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
37 17 0.40
38 1 0.02
39 18 0.43
40 6 0.14
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (37 bp):
TAAATTAAATTTTTATATATTAAATAATTAATTCAAA
Found at i:16509 original size:2 final size:2
Alignment explanation
Indices: 16504--16547 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
16494 ACACACACAC
*
16504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
16546 AT
1 AT
16548 GTAAAAAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16725 original size:21 final size:20
Alignment explanation
Indices: 16691--16735 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
16681 ATTTAATAAA
*
16691 TAAATTTAATTAAA-AATATT
1 TAAATTTAAATAAATAAT-TT
16711 TAAATATTAAATAAATAATTT
1 TAAAT-TTAAATAAATAATTT
16732 TAAA
1 TAAA
16736 ATAAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 14 0.64
22 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATTTAAATAAATAATTT
Found at i:18754 original size:16 final size:16
Alignment explanation
Indices: 18735--18786 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
18725 TAAAAATATT
18735 ATATATATAAATTTTA
1 ATATATATAAATTTTA
*
18751 ATATAT-TAATAATTTA
1 ATATATATAA-ATTTTA
*
18767 A-ATTATATATATTTTA
1 ATA-TATATAAATTTTA
18783 ATAT
1 ATAT
18787 CTTCATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
15 4 0.14
16 22 0.76
17 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATATATAAATTTTA
Found at i:18757 original size:34 final size:32
Alignment explanation
Indices: 18717--18786 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
18707 TTATATTTTA
* *
18717 TAATATTTTAAAAATATTATA-TATATAAATTT
1 TAATATATTAAAAAT-TTAAATTATATAAATTT
* *
18749 TAATATATTAATAATTTAAATTATATATATTT
1 TAATATATTAAAAATTTAAATTATATAAATTT
18781 TAATAT
1 TAATAT
18787 CTTCATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 4 0.12
32 29 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TAATATATTAAAAATTTAAATTATATAAATTT
Found at i:19033 original size:20 final size:21
Alignment explanation
Indices: 18986--19033 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
18976 AACGTTGAGA
18986 ATAAAA-AAATTATAAATATT
1 ATAAAATAAATTATAAATATT
*
19006 AAAAAATAAA-TATTAAAT-TT
1 ATAAAATAAATTA-TAAATATT
19026 ATAAAATA
1 ATAAAATA
19034 TTATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAATAAATTATAAATATT
Found at i:23065 original size:2 final size:2
Alignment explanation
Indices: 23058--23091 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23048 CTCAAACACC
23058 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
23092 TTGGATGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.