Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2647
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: 28602
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Found at i:422 original size:7 final size:7
Alignment explanation
Indices: 412--436 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
402 AAAAATATAT
412 AATTTAA
1 AATTTAA
419 AATTTAA
1 AATTTAA
426 AATTTAA
1 AATTTAA
433 AATT
1 AATT
437 ATTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:427 original size:22 final size:21
Alignment explanation
Indices: 380--420 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
370 CTAACGTAAA
380 AAAAAATTATAATATAAAAAT
1 AAAAAATTATAATATAAAAAT
*
401 AAAAAATATATAATTTAAAA
1 AAAAAAT-TATAATATAAAA
421 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAAATTATAATATAAAAAT
Found at i:1246 original size:5 final size:5
Alignment explanation
Indices: 1236--1300 Score: 55
Period size: 5 Copynumber: 13.2 Consensus size: 5
1226 TATATTTAAA
* * *
1236 TATAT TATAT TATAT T-TAT TATAT TATTTT TATAT T-TAT TA-AA TATCT
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT
*
1284 CATATT TATAT TATAT T
1 TATA-T TATAT TATAT T
1301 TAAAATTATG
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
4 11 0.23
5 28 0.60
6 8 0.17
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:1255 original size:24 final size:24
Alignment explanation
Indices: 1185--1300 Score: 84
Period size: 24 Copynumber: 5.0 Consensus size: 24
1175 TTAAAATTTA
* * *
1185 AAATATA-TAAATGATATATATAAT
1 AAATATATTATATTATAT-TATATT
* *
1209 AAATATGTTATGTTA-ATTATATTT
1 AAATATATTATATTATATTATA-TT
1233 AAATATATTATATTATATT-TATT
1 AAATATATTATATTATATTATATT
*
1256 ATAT-TATT-T-TTATATT-TATT
1 AAATATATTATATTATATTATATT
* *
1276 AAATATCTCATATTTATATTATATT
1 AAATATATTATA-TTATATTATATT
1301 TAAAATTATG
Statistics
Matches: 73, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
20 14 0.19
21 3 0.04
22 5 0.07
23 9 0.12
24 31 0.42
25 11 0.15
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (24 bp):
AAATATATTATATTATATTATATT
Found at i:1257 original size:14 final size:14
Alignment explanation
Indices: 1224--1268 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1214 TGTTATGTTA
* *
1224 ATTATATTTAAATAT
1 ATTATA-TTATATTT
1239 ATTATATTATATTT
1 ATTATATTATATTT
*
1253 ATTATATTATTTTT
1 ATTATATTATATTT
1267 AT
1 AT
1269 ATTTATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 21 0.78
15 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATATTATATTT
Found at i:1274 original size:20 final size:19
Alignment explanation
Indices: 1224--1276 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
1214 TGTTATGTTA
*
1224 ATTATATTTAAATATATTAT
1 ATTATATTT-ATTATATTAT
1244 ATTATATTTATTATATTATT
1 ATTATATTTATTATATTA-T
*
1264 TTTATATTTATTA
1 ATTATATTTATTA
1277 AATATCTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATATTTATTATATTAT
Found at i:1299 original size:11 final size:11
Alignment explanation
Indices: 1236--1302 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
1226 TATATTTAAA
1236 TATATTATA-T
1 TATATTATATT
1246 TATATT-TA-T
1 TATATTATATT
*
1255 TATATTATTTT
1 TATATTATATT
1266 TATATT-TATT
1 TATATTATATT
*
1276 AAATATCTCATATT
1 -TATAT-T-ATATT
1290 TATATTATATT
1 TATATTATATT
1301 TA
1 TA
1303 AAATTATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
9 9 0.19
10 10 0.21
11 18 0.38
12 2 0.04
13 4 0.09
14 4 0.09
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTATATT
Found at i:1721 original size:20 final size:20
Alignment explanation
Indices: 1682--1721 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1672 AATAATTTTT
*
1682 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
1702 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
1722 TCTAACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:1815 original size:11 final size:11
Alignment explanation
Indices: 1779--1839 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
1769 TATTACGTTA
*
1779 TTATATCATAT
1 TTATATTATAT
*
1790 TT-TAATTAATTT
1 TTAT-ATT-ATAT
1802 TTATATTATAT
1 TTATATTATAT
1813 TTATATTATAT
1 TTATATTATAT
*
1824 AATAATATTATAT
1 --TTATATTATAT
1837 TTA
1 TTA
1840 AAATTAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
10 1 0.03
11 20 0.50
12 8 0.20
13 11 0.28
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTATATTATAT
Found at i:1849 original size:24 final size:24
Alignment explanation
Indices: 1804--1849 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1794 ATTAATTTTT
*
1804 ATATTATATTTATATTATATAATA
1 ATATTATATTTAAATTATATAATA
1828 ATATTATATTTAAAATTA-ATAA
1 ATATTATATTT-AAATTATATAA
1850 ATTTATCGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATTATATTTAAATTATATAATA
Found at i:2211 original size:20 final size:21
Alignment explanation
Indices: 2175--2213 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2165 AGCTAATTTC
2175 CATATTCTATGGCTAATTAAG
1 CATATTCTATGGCTAATTAAG
2196 CATATT-TAT-GCTTAATTA
1 CATATTCTATGGC-TAATTA
2214 GTAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (21 bp):
CATATTCTATGGCTAATTAAG
Found at i:2933 original size:3 final size:3
Alignment explanation
Indices: 2925--2962 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2915 GAAGGGAAGA
2925 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2963 AAAGAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3245 original size:18 final size:19
Alignment explanation
Indices: 3202--3246 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
3192 ATTATTATTA
3202 TTATATT-AA-TAATAAGT
1 TTATATTAAATTAATAAGT
*
3219 TT-TAATAAATTAATAA-T
1 TTATATTAAATTAATAAGT
3236 TTATATTAAAT
1 TTATATTAAAT
3247 ATATATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 3 0.13
17 7 0.30
18 13 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TTATATTAAATTAATAAGT
Found at i:3256 original size:21 final size:23
Alignment explanation
Indices: 3220--3278 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 23
3210 ATAATAAGTT
*
3220 TTAATAA-AT-TAATAATTTATA
1 TTAATAATATATATTAATTTATA
3241 TT-A-AATATATATTAA--TATA
1 TTAATAATATATATTAATTTATA
*
3260 TTAATAATATATTTTAATT
1 TTAATAATATATATTAATT
3279 ATTTTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
19 8 0.27
20 4 0.13
21 18 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATAATATATATTAATTTATA
Found at i:4709 original size:29 final size:29
Alignment explanation
Indices: 4652--4739 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
4642 CAAATTATTA
* * *
4652 TTAAATAATAAAAATAT-TTTTATTTAAAT
1 TTAAAT-ATAAAAATATATATTAATAAAAT
*
4681 TTAATTATAAAAATATATATTAATAAAAT
1 TTAAATATAAAAATATATATTAATAAAAT
* *
4710 TTAAATATATTAAATA-ATA-AAATAAAAT
1 TTAAATATA-AAAATATATATTAATAAAAT
4738 TT
1 TT
4740 TAAACTCAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
28 20 0.40
29 25 0.50
30 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAAATATAAAAATATATATTAATAAAAT
Found at i:4714 original size:23 final size:24
Alignment explanation
Indices: 4683--4732 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
4673 ATTTAAATTT
*
4683 AATTATAAAAATA-TATATTAATAA
1 AATTATAAAAATATTA-AATAATAA
*
4707 AATT-TAAATATATTAAATAATAA
1 AATTATAAAAATATTAAATAATAA
4730 AAT
1 AAT
4733 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATTATAAAAATATTAAATAATAA
Found at i:4900 original size:2 final size:2
Alignment explanation
Indices: 4895--4919 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4885 TCTCTCTCTC
4895 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 T
4920 CTGTTATTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5223 original size:2 final size:2
Alignment explanation
Indices: 5218--5246 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5208 CTTATTTGTG
5218 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 T
5247 GATCTTCATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8586 original size:20 final size:22
Alignment explanation
Indices: 8561--8607 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
8551 GTAATATTAA
8561 ATTTATTT-AA-AAATTAAATT
1 ATTTATTTAAATAAATTAAATT
8581 ATTTATTTAAATTAAATTAAATT
1 ATTTATTTAAA-TAAATTAAATT
8604 ATTT
1 ATTT
8608 TTATATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.33
21 2 0.08
23 14 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTATTTAAATAAATTAAATT
Found at i:8594 original size:18 final size:19
Alignment explanation
Indices: 8561--8599 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
8551 GTAATATTAA
8561 ATTTATTTAAAAATTAAATT
1 ATTTATTT-AAAATTAAATT
8581 ATTTATTT-AAATTAAATT
1 ATTTATTTAAAATTAAATT
8599 A
1 A
8600 AATTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.58
20 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTATTTAAAATTAAATT
Found at i:8653 original size:27 final size:26
Alignment explanation
Indices: 8582--8656 Score: 75
Period size: 27 Copynumber: 3.0 Consensus size: 26
8572 AATTAAATTA
* *
8582 TTTATTTAAATTAAAT-TAAATTATT
1 TTTATTTAAATTAATTATAAAATATT
* * *
8607 TTTA--TATATTAATAAAAAAATATT
1 TTTATTTAAATTAATTATAAAATATT
8631 TTTATTTAAATTTAATTATAAAATAT
1 TTTATTTAAA-TTAATTATAAAATAT
8657 ATAAATAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
23 7 0.18
24 11 0.29
25 4 0.11
26 3 0.08
27 13 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTATTTAAATTAATTATAAAATATT
Found at i:15804 original size:28 final size:29
Alignment explanation
Indices: 15767--15821 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
15757 ATTATAATTA
15767 TAATTAAAATTAAATAAAAAT-ATTTTTAT
1 TAATTAAAA-TAAATAAAAATAATTTTTAT
* *
15796 TAATT-AAATAATTTAAAATAATTTTT
1 TAATTAAAATAAATAAAAATAATTTTT
15822 TTTTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 9 0.39
29 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAATTAAAATAAATAAAAATAATTTTTAT
Found at i:20900 original size:28 final size:29
Alignment explanation
Indices: 20860--20919 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
20850 TAACATTGTA
* *
20860 TATATTTTTATAT-AAATTT-TAATATATT
1 TATATATTAATATCAAATTTATAATAT-TT
*
20888 TATATATTAATATCATATTTATAATATTT
1 TATATATTAATATCAAATTTATAATATTT
20917 TAT
1 TAT
20920 CTTTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 11 0.41
29 10 0.37
30 6 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TATATATTAATATCAAATTTATAATATTT
Found at i:24980 original size:19 final size:18
Alignment explanation
Indices: 24934--24970 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
24924 AAAACTGTTA
*
24934 ATTAAATATAATAATTTT
1 ATTAAATTTAATAATTTT
24952 ATTAAATTTAAT-ATTTT
1 ATTAAATTTAATAATTTT
24969 AT
1 AT
24971 ATTATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTAAATTTAATAATTTT
Found at i:25537 original size:17 final size:16
Alignment explanation
Indices: 25512--25546 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
25502 ATTAAAAATT
*
25512 AAAATATAATATAATAA
1 AAAAAATAATATAA-AA
25529 AAAAAATAATATAAAA
1 AAAAAATAATATAAAA
25545 AA
1 AA
25547 TATAAAAAAC
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAATAATATAAAA
Found at i:25539 original size:12 final size:12
Alignment explanation
Indices: 25522--25560 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
25512 AAAATATAAT
25522 ATAATAAAAAAA
1 ATAATAAAAAAA
*
25534 ATAATATAAAAA
1 ATAATAAAAAAA
*
25546 AT-ATAAAAAAC
1 ATAATAAAAAAA
25557 ATAA
1 ATAA
25561 ATGAATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (12 bp):
ATAATAAAAAAA
Found at i:26876 original size:37 final size:35
Alignment explanation
Indices: 26829--26902 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 35
26819 ATACTTTTTG
* *
26829 TAAATTTAAATGAAATAA-AAAATATAATTTTTAATA
1 TAAATTTAAAT--AATAAGAAAATAAAATTTATAATA
26865 TAAATTTTAAATAATAAGTAAAATAAAATTTATAATA
1 TAAA-TTTAAATAATAAG-AAAATAAAATTTATAATA
26902 T
1 T
26903 CAACGTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 5 0.15
36 4 0.12
37 24 0.73
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (35 bp):
TAAATTTAAATAATAAGAAAATAAAATTTATAATA
Found at i:28181 original size:11 final size:11
Alignment explanation
Indices: 28165--28227 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 11
28155 AAATAATTGA
28165 ATTTTATTAAT
1 ATTTTATTAAT
*
28176 ATTTTATTAAAA
1 ATTTTATT-AAT
28188 ATTTTATTTAAT
1 ATTTTA-TTAAT
*
28200 -TTTTAATAAT
1 ATTTTATTAAT
28210 ATTTTAATTAAT
1 ATTTT-ATTAAT
*
28222 TTTTTA
1 ATTTTA
28228 AATATAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
10 4 0.09
11 18 0.42
12 19 0.44
13 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTTATTAAT
Found at i:28221 original size:12 final size:12
Alignment explanation
Indices: 28165--28228 Score: 64
Period size: 11 Copynumber: 5.6 Consensus size: 12
28155 AAATAATTGA
28165 ATTTT-ATTAAT
1 ATTTTAATTAAT
*
28176 ATTTT-ATTAAAA
1 ATTTTAATT-AAT
*
28188 ATTTTATTTAAT
1 ATTTTAATTAAT
28200 -TTTTAA-TAAT
1 ATTTTAATTAAT
28210 ATTTTAATTAAT
1 ATTTTAATTAAT
*
28222 TTTTTAA
1 ATTTTAA
28229 ATATAATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.09
11 19 0.43
12 19 0.43
13 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTTAATTAAT
Found at i:28226 original size:23 final size:24
Alignment explanation
Indices: 28164--28228 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
28154 TAAATAATTG
* *
28164 AATTTT-ATTAATATTTTATTAAA
1 AATTTTAATTAATTTTTTAATAAA
*
28187 AATTTTATTTAA-TTTTTAAT-AA
1 AATTTTAATTAATTTTTTAATAAA
*
28209 TATTTTAATTAATTTTTTAA
1 AATTTTAATTAATTTTTTAA
28229 ATATAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 12 0.34
23 19 0.54
24 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
AATTTTAATTAATTTTTTAATAAA
Found at i:28266 original size:14 final size:16
Alignment explanation
Indices: 28251--28307 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
28241 AGTTTTTTTA
*
28251 ATATTTATATTATAAT
1 ATATATATATTATAAT
28267 AT-TATATATT-TAAT
1 ATATATATATTATAAT
28281 ATAATATATATATATAAT
1 AT-ATATATAT-TATAAT
28299 ATAT-TATAT
1 ATATATATAT
28308 AAAATTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 6 0.17
15 7 0.19
16 14 0.39
17 3 0.08
18 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATATATTATAAT
Found at i:28294 original size:22 final size:21
Alignment explanation
Indices: 28251--28309 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 21
28241 AGTTTTTTTA
*
28251 ATATTTATATTATAATATTAT
1 ATATTTATATAATAATATTAT
28272 ATATTTAATATAATATATATATAT
1 ATATTT-ATATAATA-ATAT-TAT
28296 AATATATTATATAA
1 -ATAT-TTATATAA
28310 AATTTAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.19
22 7 0.22
23 4 0.12
24 3 0.09
25 10 0.31
26 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTTATATAATAATATTAT
Done.