Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2723
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: 62340
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:198 original size:12 final size:12
Alignment explanation
Indices: 176--210 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
166 ATATTAAAAA
176 AATTATATATTT
1 AATTATATATTT
188 ATATT-TATATTT
1 A-ATTATATATTT
200 AATTATATATT
1 AATTATATATT
211 AAATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
AATTATATATTT
Found at i:687 original size:24 final size:24
Alignment explanation
Indices: 629--688 Score: 79
Period size: 22 Copynumber: 2.6 Consensus size: 24
619 ACAGTAAATA
* *
629 AATATGTTTATAAACATATAATTG
1 AATATATTTATAAACATATAATCG
*
653 -A-ATATTCATAAACATATAATCG
1 AATATATTTATAAACATATAATCG
675 AATATATTTATAAA
1 AATATATTTATAAA
689 TAAATTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 18 0.60
23 2 0.07
24 10 0.33
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (24 bp):
AATATATTTATAAACATATAATCG
Found at i:1360 original size:10 final size:9
Alignment explanation
Indices: 1344--1407 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
1334 AATATTTTTT
1344 TAATAAATA
1 TAATAAATA
1353 TAAATAAATA
1 T-AATAAATA
1363 TAATAAATA
1 TAATAAATA
1372 TGACAT-AATA
1 T-A-ATAAATA
**
1382 TTTTTAAATA
1 -TAATAAATA
*
1392 TAATTAATA
1 TAATAAATA
1401 TAA-AAAT
1 TAATAAAT
1408 TTTAATATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
8 3 0.07
9 20 0.45
10 18 0.41
11 3 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (9 bp):
TAATAAATA
Found at i:1983 original size:21 final size:20
Alignment explanation
Indices: 1950--2002 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
1940 TTTTAAGTTG
1950 ATTAT-TTATAAAAATAAAAT
1 ATTATATTA-AAAAATAAAAT
*
1970 ATTTATATTAAAAAATTAAAT
1 A-TTATATTAAAAAATAAAAT
1991 ATTATATGTAAA
1 ATTATAT-TAAA
2003 TCTAACGCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.24
21 19 0.66
22 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTATATTAAAAAATAAAAT
Found at i:2291 original size:59 final size:63
Alignment explanation
Indices: 2228--2376 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 63
2218 ATATATAGAA
*
2228 TAAATAATTAAAATTATTAAAATTATATTT-TA-AATAATAA-AATTAAAATTTTATTTAT-T
1 TAAATAATTAAAATTATTAAAATTATATTTATACAATAATAAGAATTAAAATTATATTTATAT
2287 TAAATAA-T---A--ATTAAAATTATATTTATACTAATAATAAGTAATTAAAATTATATTTATAT
1 TAAATAATTAAAATTATTAAAATTATATTTATAC-AATAATAAG-AATTAAAATTATATTTATAT
*
2346 TAAATAATAAAATATATATTAAAATTATATT
1 TAAATAATTAAA-AT-TATTAAAATTATATT
2377 ATGTAAAAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
53 15 0.20
54 2 0.03
55 1 0.01
56 8 0.11
58 18 0.24
59 15 0.20
64 1 0.01
67 14 0.19
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.45
Consensus pattern (63 bp):
TAAATAATTAAAATTATTAAAATTATATTTATACAATAATAAGAATTAAAATTATATTTATAT
Found at i:2306 original size:21 final size:21
Alignment explanation
Indices: 2230--2306 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
2220 ATATAGAATA
2230 AATAATTAAAATTATTAAAAT
1 AATAATTAAAATTATTAAAAT
* * * *
2251 TATATTTTAAA-TAATAAAATT
1 AATAATTAAAATTATTAAAA-T
** * *
2272 AA-AATTTTATTTATTTAAAT
1 AATAATTAAAATTATTAAAAT
2292 AATAATTAAAATTAT
1 AATAATTAAAATTAT
2307 ATTTATACTA
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
20 15 0.38
21 25 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATTAAAATTATTAAAAT
Found at i:2329 original size:31 final size:29
Alignment explanation
Indices: 2243--2407 Score: 146
Period size: 27 Copynumber: 5.6 Consensus size: 29
2233 AATTAAAATT
2243 ATTAAAATTATATTT-TA-AATAATAA-A
1 ATTAAAATTATATTTATATAATAATAATA
* *
2269 ATTAAAATTTTATTTAT-TTA-AATAATA
1 ATTAAAATTATATTTATATAATAATAATA
2296 ATTAAAATTATATTTATACTAATAATAAGTA
1 ATTAAAATTATATTTATA-TAATAATAA-TA
2327 ATTAAAATTATATTTATATTAAATAATAAAATATA
1 ATTAAAATTATATTTATA-T-AATAAT---A-ATA
* *
2362 TATTAAAATTATA-TTATGTAA-AAAAATA
1 -ATTAAAATTATATTTATATAATAATAATA
*
2390 TTTAAAAATTATATTTAT
1 ATT-AAAATTATATTTAT
2408 TTTAAAAATA
Statistics
Matches: 116, Mismatches: 8, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
26 19 0.16
27 21 0.18
28 12 0.10
29 7 0.06
30 5 0.04
31 21 0.18
32 8 0.07
33 2 0.02
34 1 0.01
35 7 0.06
36 13 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (29 bp):
ATTAAAATTATATTTATATAATAATAATA
Found at i:2352 original size:56 final size:51
Alignment explanation
Indices: 2235--2365 Score: 149
Period size: 56 Copynumber: 2.4 Consensus size: 51
2225 GAATAAATAA
* *
2235 TTAAAATTATTAAAATTATATTTTAAATAATAAAATTAAAATTTTATTTAT
1 TTAAAATAATTAAAATTATATTTTAAATAATAAAATTAAAATTATATTTAT
2286 TTAAATAATAATTAAAATTATATTTATACTAATAATAAGTAATTAAAATTATATTTAT
1 TT-AA-AATAATTAAAATTATATTT-TA--AATAATAA--AATTAAAATTATATTTAT
2344 ATT-AAATAA-TAAAATATATATT
1 -TTAAAATAATTAAAAT-TATATT
2366 AAAATTATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
51 2 0.03
52 2 0.03
53 18 0.26
54 2 0.03
55 6 0.09
56 19 0.28
57 1 0.01
58 17 0.25
59 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (51 bp):
TTAAAATAATTAAAATTATATTTTAAATAATAAAATTAAAATTATATTTAT
Found at i:2368 original size:67 final size:63
Alignment explanation
Indices: 2288--2433 Score: 170
Period size: 64 Copynumber: 2.3 Consensus size: 63
2278 TTATTTATTT
*
2288 AAATAATAATTAAAATTATATTTATACTAATAATAAGTAATT-AAAATTATATTTATATTAAATA
1 AAATAATAATTAAAATTATA-TTAT-CTAA-AA-AAATAATTAAAAATTATATTTATATTAAA-A
2352 ATA
61 ATA
* * *
2355 AAAT-ATATATTAAAATTATATTATGTAAAAAAATATTTAAAAATTATATTTATTTTAAAAATA
1 AAATAATA-ATTAAAATTATATTATCTAAAAAAATAATTAAAAATTATATTTATATTAAAAATA
* *
2418 AATTAATAATAAAAAT
1 AAATAATAATTAAAAT
2434 ATTAAAATAT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
63 20 0.29
64 24 0.34
65 3 0.04
66 7 0.10
67 16 0.23
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (63 bp):
AAATAATAATTAAAATTATATTATCTAAAAAAATAATTAAAAATTATATTTATATTAAAAATA
Found at i:2397 original size:28 final size:30
Alignment explanation
Indices: 2340--2404 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
2330 AAAATTATAT
2340 TTATATTAAATAATAAAATATATATTAAAA
1 TTATATTAAATAATAAAATATATATTAAAA
**
2370 TTATATTATGTAA-AAAA-ATAT-TTAAAAA
1 TTATATTAAATAATAAAATATATATT-AAAA
2398 TTATATT
1 TTATATT
2405 TATTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.06
28 15 0.47
29 4 0.12
30 11 0.34
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
TTATATTAAATAATAAAATATATATTAAAA
Found at i:2414 original size:28 final size:28
Alignment explanation
Indices: 2352--2423 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
2342 ATATTAAATA
2352 ATAAAATATATATTAAAATTATATTATGT
1 ATAAAA-ATATATTAAAATTATATTATGT
*
2381 AAAAAAATAT-TTAAAAATTATATTTAT-T
1 ATAAAAATATATT-AAAATTATA-TTATGT
* *
2409 TTAAAAATAAATTAA
1 ATAAAAATATATTAA
2424 TAATAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
27 2 0.06
28 23 0.64
29 11 0.31
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
ATAAAAATATATTAAAATTATATTATGT
Found at i:2414 original size:30 final size:29
Alignment explanation
Indices: 2253--2423 Score: 120
Period size: 31 Copynumber: 5.7 Consensus size: 29
2243 ATTAAAATTA
*
2253 TATTTTAAATAATAA-AATTAAAATTTTATT
1 TATTTTAAA-AA-AATAATTAAAATTATATT
*
2283 TA-TTT-AAATAATAATTAAAATTATATT
1 TATTTTAAAAAAATAATTAAAATTATATT
** *
2310 TATACTAATAATAAGTAATTAAAATTATATT
1 TATTTTAA-AA-AAATAATTAAAATTATATT
2341 TATATTAAATAATAAAATATATATTAAAATTATA-T
1 TAT-TT---TAA-AAAA-ATA-ATTAAAATTATATT
* *
2376 TA-TGTAAAAAAATATTTAAAAATTATATT
1 TATTTTAAAAAAATAATT-AAAATTATATT
*
2405 TATTTTAAAAATA-AATTAA
1 TATTTTAAAAAAATAATTAA
2424 TAATAAAAAT
Statistics
Matches: 113, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
26 2 0.02
27 19 0.17
28 17 0.15
29 14 0.12
30 15 0.13
31 20 0.18
33 1 0.01
34 2 0.02
35 11 0.10
36 12 0.11
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
TATTTTAAAAAAATAATTAAAATTATATT
Found at i:2448 original size:64 final size:64
Alignment explanation
Indices: 2330--2450 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 64
2320 ATAAGTAATT
* * *
2330 AAAATTATATTTATATTAAATAATAAAATATATATTAAAATTATATTATGTAAAAAAATATTTA
1 AAAATTATATTTATATTAAATAATAAAATATATATAAAAATTAAAATATGTAAAAAAATATTTA
* *
2394 AAAATTATATTTATTTTAAA-AATAAATTA-ATAATAAAAATATTAAAATAT-TAAAAAA
1 AAAATTATATTTATATTAAATAATAAAATATAT-AT-AAAA-ATTAAAATATGTAAAAAA
2451 TAGAAAGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 2 0.04
63 10 0.20
64 29 0.59
65 8 0.16
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.40
Consensus pattern (64 bp):
AAAATTATATTTATATTAAATAATAAAATATATATAAAAATTAAAATATGTAAAAAAATATTTA
Found at i:4029 original size:26 final size:25
Alignment explanation
Indices: 3981--4029 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3971 GAAATCAAAT
** *
3981 AAAAATTATGTTCTAAAATTTAAAA
1 AAAAATTATGTGATAAAAGTTAAAA
4006 AAAAATTATGTGATAATAAGTTAA
1 AAAAATTATGTGATAA-AAGTTAA
4030 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (25 bp):
AAAAATTATGTGATAAAAGTTAAAA
Found at i:7501 original size:45 final size:44
Alignment explanation
Indices: 7438--7527 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 44
7428 TACCAGACAC
7438 TTAATTTACTGGGAAATACTGTTTCTTTGAAGATAGACAAGACT
1 TTAATTTACTGGGAAATACTGTTTCTTTGAAGATAGACAAGACT
7482 TTAATTTTACTGGGAAATACTGTTTCTTTGAAGATAGACAAGACT
1 TTAA-TTTACTGGGAAATACTGTTTCTTTGAAGATAGACAAGACT
7527 T
1 T
7528 ATCGCTCTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 4 0.09
45 41 0.91
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (44 bp):
TTAATTTACTGGGAAATACTGTTTCTTTGAAGATAGACAAGACT
Found at i:9219 original size:2 final size:2
Alignment explanation
Indices: 9214--9251 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
9204 ATTTTTTTAA
*
9214 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9252 CCAATACTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11586 original size:19 final size:16
Alignment explanation
Indices: 11553--11584 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11543 TCATTATTAA
11553 TTTTTTTTTTAATATT
1 TTTTTTTTTTAATATT
11569 TTTTTATTTTTAATAT
1 TTTTT-TTTTTAATAT
11585 ATATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTTTTAATATT
Found at i:15712 original size:16 final size:16
Alignment explanation
Indices: 15665--15717 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
15655 AACATGGTTA
*
15665 AAATAA-ATACAAATAT
1 AAATAATATA-AAATTT
15681 AAATATATATTAAAATTT
1 AAATA-ATA-TAAAATTT
15699 AAATAATATAAAATATT
1 AAATAATATAAAAT-TT
15716 AA
1 AA
15718 TTTATGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 11 0.34
17 8 0.25
18 11 0.34
19 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAATATAAAATTT
Found at i:22173 original size:26 final size:27
Alignment explanation
Indices: 22136--22201 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
22126 ATAAATTAAA
* *
22136 ATAAATTAATTTAATTAAAAAATTAT-T
1 ATAAATAAATTTAA-TAAAAAAGTATAT
*
22163 A-AAATAAATTTTATAAAAAAGTATAT
1 ATAAATAAATTTAATAAAAAAGTATAT
*
22189 ATTAATAAATTTA
1 ATAAATAAATTTA
22202 TATATATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
25 10 0.31
26 12 0.38
27 10 0.31
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
ATAAATAAATTTAATAAAAAAGTATAT
Found at i:22175 original size:27 final size:25
Alignment explanation
Indices: 22151--22205 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
22141 TTAATTTAAT
*
22151 TAAAAAATTATTAAAATAAATTTTA
1 TAAAAAAGTATTAAAATAAATTTTA
*
22176 TAAAAAAGTATATATTAATAAATTTATA
1 TAAAAAAGTAT-TA-AAATAAATTT-TA
22204 TA
1 TA
22206 TATAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.40
26 2 0.08
27 9 0.36
28 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TAAAAAAGTATTAAAATAAATTTTA
Found at i:25853 original size:2 final size:2
Alignment explanation
Indices: 25846--25876 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
25836 TATATCTGTT
25846 TA TA TA TA -A 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
25877 GGGTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:25951 original size:13 final size:13
Alignment explanation
Indices: 25916--25964 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
25906 AAGGTACAAA
25916 TATT-ATAAATTAT
1 TATTAATAAATT-T
*
25929 TA-TAAAAAATTT
1 TATTAATAAATTT
25941 TATTAATAAATTT
1 TATTAATAAATTT
*
25954 T-TTAATTAATT
1 TATTAATAAATT
25965 AATTTGATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 13 0.42
13 18 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTAATAAATTT
Found at i:25996 original size:36 final size:39
Alignment explanation
Indices: 25956--26027 Score: 89
Period size: 36 Copynumber: 1.9 Consensus size: 39
25946 ATAAATTTTT
*
25956 TAATTAATTAATTTGA-TGT-AA-TAA-TTTTAAAATATA
1 TAATTAATT-ATTTAATTGTAAATTAATTTTTAAAATATA
*
25992 TAATTGATTATTTAATTGTAAATTAATTTTTAAAAT
1 TAATTAATTATTTAATTGTAAATTAATTTTTAAAAT
26028 TATTGTATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
35 5 0.17
36 11 0.37
37 2 0.07
38 3 0.10
39 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (39 bp):
TAATTAATTATTTAATTGTAAATTAATTTTTAAAATATA
Found at i:37964 original size:22 final size:22
Alignment explanation
Indices: 37930--37984 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
37920 TATTTTAAAA
* *
37930 AATATTAAAATATTTTTATAT-T
1 AATATTTAAATA-TATTATATGT
*
37952 AATATTTATATATATTATATGT
1 AATATTTAAATATATTATATGT
37974 AA-ATTTAAATA
1 AATATTTAAATA
37985 AAAATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AATATTTAAATATATTATATGT
Found at i:40501 original size:2 final size:2
Alignment explanation
Indices: 40494--40537 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
40484 GGGAGAAATA
40494 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
40536 CT
1 CT
40538 TTAGCTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:41276 original size:25 final size:24
Alignment explanation
Indices: 41216--41277 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 24
41206 ATAAAATATA
41216 AATT-AATTTAAAAATTATTATTT
1 AATTAAATTTAAAAATTATTATTT
*
41239 -ATTATAATATT-AAAATATATTTTTAT
1 AATTA-AAT-TTAAAAAT-TATTATT-T
41265 AATTAAATTTAAA
1 AATTAAATTTAAA
41278 TAAAAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
22 3 0.10
24 8 0.26
25 10 0.32
26 6 0.19
27 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTAAATTTAAAAATTATTATTT
Found at i:41278 original size:24 final size:26
Alignment explanation
Indices: 41216--41279 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 26
41206 ATAAAATATA
*
41216 AATT-AATTTAAAAATTATTATTTAT
1 AATTAAATTTAAATATTATTATTTAT
* *
41241 TA-TAATATTAAAATA-TATT-TTTAT
1 AATTAA-ATTTAAATATTATTATTTAT
41265 AATTAAATTTAAATA
1 AATTAAATTTAAATA
41280 AAAATATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
24 15 0.48
25 9 0.29
26 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AATTAAATTTAAATATTATTATTTAT
Found at i:41303 original size:25 final size:25
Alignment explanation
Indices: 41224--41305 Score: 62
Period size: 25 Copynumber: 3.1 Consensus size: 25
41214 TAAATTAATT
*
41224 TAAAAATTATTA-TTTATTA-TAATAT
1 TAAAAA-TATTATTTTATTATTAA-AA
*
41249 TAAAATATATT-TTTATAATTAAATTTAAA
1 TAAAA-ATATTATTT-T-ATT--ATTAAAA
41278 TAAAAATATTATTTTATTATTAAAA
1 TAAAAATATTATTTTATTATTAAAA
41303 TAA
1 TAA
41306 TAATTAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
25 20 0.43
26 2 0.04
27 6 0.13
28 6 0.13
29 10 0.22
30 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAAAATATTATTTTATTATTAAAA
Found at i:48249 original size:30 final size:30
Alignment explanation
Indices: 48189--48277 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 30
48179 ATAAAAAATT
* *
48189 ATTAAAATTATTATCAATCTTAATTTTTTAATA
1 ATTAAAATTGTTA-AAAT-TTAA-TTTTTAATA
*
48222 ATTAAAATTGTTAAAATTTAATTTTTAATT
1 ATTAAAATTGTTAAAATTTAATTTTTAATA
*
48252 ATTAAAA--GTAAAAATTTAATATTTTA
1 ATTAAAATTGTTAAAATTTAAT-TTTTA
48278 TCAATTTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
28 12 0.24
29 5 0.10
30 15 0.29
31 4 0.08
32 3 0.06
33 12 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
ATTAAAATTGTTAAAATTTAATTTTTAATA
Found at i:50152 original size:15 final size:15
Alignment explanation
Indices: 50132--50161 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
50122 CATATTGTAT
50132 CATATTAACATAAAC
1 CATATTAACATAAAC
50147 CATATTAACATAAAC
1 CATATTAACATAAAC
50162 AGATCAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (15 bp):
CATATTAACATAAAC
Found at i:53812 original size:37 final size:38
Alignment explanation
Indices: 53770--53873 Score: 96
Period size: 37 Copynumber: 2.8 Consensus size: 38
53760 GATTAATTTA
53770 ATTTAAATTATTATTTATATAATAAAATAAT-ATTTTT
1 ATTTAAATTATTATTTATATAATAAAATAATAATTTTT
**
53807 ATTTAAATGTAATTATAAATATTAATATAAA-AATAATTTTT
1 ATTTAAAT-T-ATTATTTATA-TAATA-AAATAATAATTTTT
53848 A---AATATTATT-TTTA-ATAATAAAATAA
1 ATTTAA-ATTATTATTTATATAATAAAATAA
53874 GTTTCGGATT
Statistics
Matches: 56, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
33 3 0.05
34 7 0.12
35 1 0.02
36 2 0.04
37 11 0.20
38 4 0.07
39 10 0.18
40 8 0.14
41 10 0.18
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (38 bp):
ATTTAAATTATTATTTATATAATAAAATAATAATTTTT
Found at i:53989 original size:18 final size:18
Alignment explanation
Indices: 53934--53991 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 18
53924 CTATTTTAAA
*
53934 ATAACATATCAAA-TTTAT
1 ATAA-ATATTAAATTTTAT
*
53952 AT-AATA-TAAATTAT-T
1 ATAAATATTAAATTTTAT
53967 A-AAATATTAAATTTTAT
1 ATAAATATTAAATTTTAT
53984 ATAAATAT
1 ATAAATAT
53992 AATTAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
15 9 0.28
16 12 0.38
17 3 0.09
18 8 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAAATATTAAATTTTAT
Found at i:54029 original size:38 final size:38
Alignment explanation
Indices: 53927--54036 Score: 102
Period size: 38 Copynumber: 2.9 Consensus size: 38
53917 AATATCTCTA
* * *
53927 TTTTAAAATA-ACATATCAAAT-TTATATAATATAAAT
1 TTTTAAAATATATATATTAAATATAATATAATATAAAT
* * **
53963 TATTAAAATAT-TAAATTTTATATAAATATAAT-TAAAAT
1 TTTTAAAATATATATATTAAATAT-AATATAATAT-AAAT
54001 TTTTAAAATATATATATTAAATATAATATAAATATA
1 TTTTAAAATATATATATTAAATATAATAT-AATATA
54037 TAAATCATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
36 14 0.25
37 2 0.04
38 26 0.46
39 13 0.23
40 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (38 bp):
TTTTAAAATATATATATTAAATATAATATAATATAAAT
Found at i:54037 original size:20 final size:20
Alignment explanation
Indices: 53966--54046 Score: 58
Period size: 20 Copynumber: 3.9 Consensus size: 20
53956 TATAAATTAT
* *
53966 TAAA-ATATTAAATTTTATA
1 TAAATATATTAAATATAATA
* *
53985 TAAATATAATTAAAATTTTTAAAA
1 TAAATAT-ATT-AAA--TATAATA
*
54009 TATATATATTAAATATAATA
1 TAAATATATTAAATATAATA
54029 TAAATATA-TAAATCATAA
1 TAAATATATTAAAT-ATAA
54047 AATTTAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
19 9 0.18
20 18 0.36
21 3 0.06
22 6 0.12
23 3 0.06
24 11 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATATATTAAATATAATA
Found at i:54550 original size:14 final size:13
Alignment explanation
Indices: 54531--54590 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 13
54521 TATAATGGTG
54531 TTATAATTATTATT
1 TTATAATT-TTATT
54545 TTATAATTTTATT
1 TTATAATTTTATT
* *
54558 TT-TTATTTTAAAAT
1 TTATAATTTT--ATT
54572 TTA-AA-TTTATT
1 TTATAATTTTATT
54583 TTATAATT
1 TTATAATT
54591 AAATCATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
11 5 0.14
12 8 0.22
13 11 0.30
14 13 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATAATTTTATT
Found at i:54565 original size:20 final size:19
Alignment explanation
Indices: 54540--54590 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
54530 GTTATAATTA
**
54540 TTATTTTATAATTTTATTTT
1 TTATTTTATAATTTTA-AAT
*
54560 TTATTTTA-AAATTTAAAT
1 TTATTTTATAATTTTAAAT
54578 TTATTTTATAATT
1 TTATTTTATAATT
54591 AAATCATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 9 0.35
19 9 0.35
20 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTATAATTTTAAAT
Found at i:54582 original size:18 final size:17
Alignment explanation
Indices: 54559--54594 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
54549 AATTTTATTT
54559 TTTATTTTAAAATTTAAA
1 TTTATTTTAAAA-TTAAA
*
54577 TTTATTTTATAATTAAA
1 TTTATTTTAAAATTAAA
54594 T
1 T
54595 CATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTATTTTAAAATTAAA
Found at i:62294 original size:16 final size:17
Alignment explanation
Indices: 62273--62305 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62263 TTTATGCAAA
62273 TAATTT-AAAAATAAAT
1 TAATTTAAAAAATAAAT
62289 TAATTTAAAAAATAAAT
1 TAATTTAAAAAATAAAT
62306 AAAAAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATTTAAAAAATAAAT
Done.