Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1915
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: 67281
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:936 original size:19 final size:19
Alignment explanation
Indices: 912--948 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
902 ATGGATGAGA
*
912 GGGAGGTGGAGGAAGGGGG
1 GGGAGGGGGAGGAAGGGGG
*
931 GGGAGGGGGAGGGAGGGG
1 GGGAGGGGGAGGAAGGGG
949 AAGAGAGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.78, T:0.03
Consensus pattern (19 bp):
GGGAGGGGGAGGAAGGGGG
Found at i:939 original size:10 final size:10
Alignment explanation
Indices: 910--948 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
900 GGATGGATGA
*
910 GAGGGAGGTG
1 GAGGGAGGGG
*
920 GAGGAAGGGG
1 GAGGGAGGGG
930 G-GGGAGGGG
1 GAGGGAGGGG
939 GAGGGAGGGG
1 GAGGGAGGGG
949 AAGAGAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.21, C:0.00, G:0.77, T:0.03
Consensus pattern (10 bp):
GAGGGAGGGG
Found at i:3215 original size:43 final size:44
Alignment explanation
Indices: 3153--3275 Score: 187
Period size: 43 Copynumber: 2.8 Consensus size: 44
3143 AGTATTTTTA
* * *
3153 TTATTTATTTTTCCGTGGATTAGCATAGCCACCCAATTGCA-AT
1 TTATTTATTTTTTCATGGATTGGCATAGCCACCCAATTGCATAT
3196 TTATTTATTTTTTCATGGATTGGCATAGCCACCCAATTGCATAT
1 TTATTTATTTTTTCATGGATTGGCATAGCCACCCAATTGCATAT
*
3240 TTATTTA-TTTTTAAGTGGATTGGCATAGCCACCCAA
1 TTATTTATTTTTTCA-TGGATTGGCATAGCCACCCAA
3276 ATTCTAACAA
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 44 0.59
44 30 0.41
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (44 bp):
TTATTTATTTTTTCATGGATTGGCATAGCCACCCAATTGCATAT
Found at i:4234 original size:1 final size:1
Alignment explanation
Indices: 4228--4282 Score: 83
Period size: 1 Copynumber: 55.0 Consensus size: 1
4218 AAAGTGTTTG
***
4228 AAAAAAAAAAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4283 TTTAAATGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.95, C:0.00, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:4267 original size:29 final size:29
Alignment explanation
Indices: 4225--4284 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
4215 GATAAAGTGT
4225 TTGAAAAAAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAAAAAAA
4254 TTGAAAAAAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAAAAAAA
4283 TT
1 TT
4285 TAAATGTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (29 bp):
TTGAAAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:4381 original size:19 final size:19
Alignment explanation
Indices: 4357--4424 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
4347 AATTCAACAA
4357 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
4376 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
4391 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
4408 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
4425 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:4396 original size:13 final size:13
Alignment explanation
Indices: 4378--4402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4368 ACATAAGTTT
4378 TGTATCGATACAA
1 TGTATCGATACAA
4391 TGTATCGATACA
1 TGTATCGATACA
4403 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4400 original size:32 final size:32
Alignment explanation
Indices: 4359--4421 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4349 TTCAACAATT
*
4359 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
4391 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
4422 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:4482 original size:13 final size:13
Alignment explanation
Indices: 4464--4489 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4454 CATTTTTCTG
4464 TGTATCGATACAT
1 TGTATCGATACAT
4477 TGTATCGATACAT
1 TGTATCGATACAT
4490 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4486 original size:33 final size:33
Alignment explanation
Indices: 4444--4510 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4434 GCCAAGGAAA
***
4444 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
4477 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
4510 T
1 T
4511 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:7017 original size:27 final size:28
Alignment explanation
Indices: 6978--7053 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 28
6968 TTTCTTCACA
* *
6978 ATCGAGGACACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
7005 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
7033 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
7054 ACTTTATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 23 0.53
28 20 0.47
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:7048 original size:28 final size:27
Alignment explanation
Indices: 6987--7053 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 27
6977 AATCGAGGAC
*
6987 ACTCCAACCCCGTTAATCATCGGGGAT
1 ACTCCAACCCCGTTAATCATAGGGGAT
*
7014 ACTCCAACCCCGTTATTTC-TGAGGGGAT
1 ACTCCAACCCCGTTA-ATCAT-AGGGGAT
7042 ACTCCAACCCCG
1 ACTCCAACCCCG
7054 ACTTTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 16 0.44
28 20 0.56
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (27 bp):
ACTCCAACCCCGTTAATCATAGGGGAT
Found at i:7098 original size:51 final size:51
Alignment explanation
Indices: 7036--7206 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
7026 TTATTTCTGA
* * *
7036 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
7087 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
7140 GGGGATACTCCAATTCCGATTTTATTTCCCAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTT-TCAAAATACCAATTTTTCATAATC
*
7192 GAGGATACTCCAACC
1 GGGGATACTCCAACC
7207 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 31 0.32
54 12 0.12
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:7225 original size:28 final size:28
Alignment explanation
Indices: 7189--7270 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
7179 ATTTTTCACA
*
7189 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
7217 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
7245 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
7271 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:12173 original size:44 final size:44
Alignment explanation
Indices: 12112--12232 Score: 224
Period size: 44 Copynumber: 2.8 Consensus size: 44
12102 GGTGTTTTTA
*
12112 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
1 TTATTTATTTTTTCGTGGATTGGCATAGCCACCCAATTGCATAT
12156 TTATTTATTTTTTCGTGGATTGGCATAGCCACCCAATTGCATAT
1 TTATTTATTTTTTCGTGGATTGGCATAGCCACCCAATTGCATAT
*
12200 TTATTTATTTTTTCGTGGATTGACATAGCCACC
1 TTATTTATTTTTTCGTGGATTGGCATAGCCACC
12233 AAAATTCTAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 75 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (44 bp):
TTATTTATTTTTTCGTGGATTGGCATAGCCACCCAATTGCATAT
Found at i:12934 original size:13 final size:13
Alignment explanation
Indices: 12916--12942 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12906 TGCATCTCAT
12916 ATAAAATTAATTA
1 ATAAAATTAATTA
12929 ATAAAATTAATTA
1 ATAAAATTAATTA
12942 A
1 A
12943 ATATATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAAAATTAATTA
Found at i:14080 original size:16 final size:16
Alignment explanation
Indices: 14045--14091 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
14035 AAATAAATTT
14045 TTATAT-TTAAATATC
1 TTATATATTAAATATC
* *
14060 ATATATATTAAATATG
1 TTATATATTAAATATC
14076 TTATATTAATTAAATA
1 TTATA-T-ATTAAATA
14092 AATTATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 5 0.19
16 12 0.46
17 1 0.04
18 8 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
TTATATATTAAATATC
Found at i:14097 original size:18 final size:18
Alignment explanation
Indices: 14066--14100 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14056 TATCATATAT
**
14066 ATTAAATATGTTATATTA
1 ATTAAATAAATTATATTA
14084 ATTAAATAAATTATATT
1 ATTAAATAAATTATATT
14101 TATATATATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTAAATAAATTATATTA
Found at i:14130 original size:14 final size:16
Alignment explanation
Indices: 14097--14137 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
14087 AAATAAATTA
*
14097 TATTTATATATATCAT
1 TATTTTTATATATCAT
14113 TATTTTTAT-TAT-AT
1 TATTTTTATATATCAT
14127 TATTTTTATAT
1 TATTTTTATAT
14138 TTATTATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 11 0.48
15 4 0.17
16 8 0.35
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTTTATATATCAT
Found at i:14140 original size:20 final size:20
Alignment explanation
Indices: 14094--14156 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
14084 ATTAAATAAA
14094 TTATATTTA-TATA-TATCA-
1 TTATATTTATTATATTAT-AT
* *
14112 TTATTTTTATTATATTATTT
1 TTATATTTATTATATTATAT
*
14132 TTATATTTATTATGTTATAT
1 TTATATTTATTATATTATAT
14152 TTATA
1 TTATA
14157 CCATATGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 8 0.22
19 4 0.11
20 25 0.68
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TTATATTTATTATATTATAT
Found at i:14149 original size:14 final size:12
Alignment explanation
Indices: 14094--14155 Score: 54
Period size: 14 Copynumber: 4.8 Consensus size: 12
14084 ATTAAATAAA
*
14094 TTATATTTATAT
1 TTATATTTATTT
*
14106 ATATCA-TTATTT
1 TTAT-ATTTATTT
14118 TTATTATATTATTT
1 TTA-TAT-TTATTT
14132 TTATATTTATTAT
1 TTATATTTATT-T
14145 GTTATATTTAT
1 -TTATATTTAT
14156 ACCATATGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
12 16 0.39
13 6 0.15
14 19 0.46
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (12 bp):
TTATATTTATTT
Found at i:15378 original size:9 final size:10
Alignment explanation
Indices: 15340--15427 Score: 56
Period size: 10 Copynumber: 8.6 Consensus size: 10
15330 ATTTGACGTC
15340 AATATATTTA
1 AATATATTTA
*
15350 ATTAT-TTTA
1 AATATATTTA
*
15359 AATTTTATTTA
1 AA-TATATTTA
15370 AATAT-TTTA
1 AATATATTTA
*
15379 AAAATTATATTA
1 AATA-TAT-TTA
*
15391 TATATATTTA
1 AATATATTTA
* *
15401 AAAATATATA
1 AATATATTTA
15411 GAATAT-TATTA
1 -AATATAT-TTA
15422 AATATA
1 AATATA
15428 AATATTTTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
9 12 0.21
10 25 0.43
11 16 0.28
12 5 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (10 bp):
AATATATTTA
Found at i:15389 original size:22 final size:22
Alignment explanation
Indices: 15342--15410 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
15332 TTGACGTCAA
*
15342 TATATTTAATTATTTT--AAAT
1 TATATTTAAATATTTTAAAAAT
*
15362 TTTATTTAAATATTTTAAAAAT
1 TATATTTAAATATTTTAAAAAT
*
15384 TATA-TTATATATATTTAAAAAT
1 TATATTTAAATAT-TTTAAAAAT
15406 ATATA
1 -TATA
15411 GAATATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.34
21 7 0.17
22 16 0.39
23 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATATTTAAATATTTTAAAAAT
Found at i:15403 original size:21 final size:20
Alignment explanation
Indices: 15342--15409 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
15332 TTGACGTCAA
* *
15342 TATATTTAATTATTTTAAAT
1 TATATTTAAATATTTAAAAT
*
15362 TTTATTTAAATATTTTAAAAAT
1 TATATTTAAATA-TTT-AAAAT
* *
15384 TATATTATATATATTTAAAAA
1 TATATT-TAAATATTTAAAAT
15405 TATAT
1 TATAT
15410 AGAATATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 10 0.26
21 12 0.31
22 12 0.31
23 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTTAAATATTTAAAAT
Found at i:15416 original size:21 final size:21
Alignment explanation
Indices: 15342--15423 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 21
15332 TTGACGTCAA
* **
15342 TATATTTAATTATTTTAAATTT
1 TATA-TTAAATATTTTAAAAAT
15364 TAT-TTAAATATTTTAAAAAT
1 TATATTAAATATTTTAAAAAT
*
15384 TATATTATATATATTTAAAAA-
1 TATATTAAATAT-TTTAAAAAT
15405 TATA-TAGAATATTATTAAA
1 TATATTA-AATATT-TTAAA
15424 TATAAATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 20 0.39
21 20 0.39
22 11 0.22
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
TATATTAAATATTTTAAAAAT
Found at i:15420 original size:22 final size:22
Alignment explanation
Indices: 15371--15420 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
15361 TTTTATTTAA
**
15371 ATAT-TTTAAAAATTATATTAT
1 ATATATTTAAAAATTATAGAAT
15392 ATATATTTAAAAATATATAGAAT
1 ATATATTTAAAAAT-TATAGAAT
15415 AT-TATT
1 ATATATT
15421 AAATATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 13 0.52
23 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATATTTAAAAATTATAGAAT
Found at i:16754 original size:15 final size:15
Alignment explanation
Indices: 16745--16780 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
16735 GAATTTTTTA
16745 AATTTAAATTGATTT
1 AATTTAAATTGATTT
16760 AATTTAAATT-A-TT
1 AATTTAAATTGATTT
16773 -ATTTAAAT
1 AATTTAAAT
16781 AATAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.38
13 2 0.10
14 1 0.05
15 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
AATTTAAATTGATTT
Found at i:17255 original size:2 final size:2
Alignment explanation
Indices: 17248--17273 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17238 TTATATGGTG
17248 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
17274 TACTATGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17566 original size:3 final size:3
Alignment explanation
Indices: 17558--17584 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17548 AGGTACTTAA
17558 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
17585 TTTTTTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:18044 original size:6 final size:7
Alignment explanation
Indices: 18023--18047 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18013 TAGCCCCTTG
18023 AAATAAA
1 AAATAAA
18030 AAATAAA
1 AAATAAA
18037 AAATAAA
1 AAATAAA
18044 AAAT
1 AAAT
18048 GGCCCGTCTA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:18204 original size:9 final size:9
Alignment explanation
Indices: 18190--18219 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
18180 TAACATTTAA
18190 ATTTTAAAT
1 ATTTTAAAT
18199 ATTTTAAAT
1 ATTTTAAAT
*
18208 ATGTTAAAT
1 ATTTTAAAT
18217 ATT
1 ATT
18220 ATTTATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:18216 original size:18 final size:16
Alignment explanation
Indices: 18185--18219 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
18175 AACGTTAACA
18185 TTTAAATTTTAAATAT
1 TTTAAATTTTAAATAT
18201 TTTAAATATGTTAAATAT
1 TTTAAAT-T-TTAAATAT
18219 T
1 T
18220 ATTTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAAATTTTAAATAT
Found at i:19749 original size:22 final size:23
Alignment explanation
Indices: 19724--19777 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
19714 AAAATATCAA
19724 AATA-TTAAAGAATATTTAT-ATT
1 AATATTTAAA-AATATTTATAATT
*
19746 AATATTTAAAAATTTTTATAATT
1 AATATTTAAAAATATTTATAATT
19769 AA-ATTTAAA
1 AATATTTAAA
19778 TAAAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 19 0.66
23 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AATATTTAAAAATATTTATAATT
Found at i:26939 original size:11 final size:11
Alignment explanation
Indices: 26923--26956 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
26913 AGGTTAGTTA
26923 TCGATTTGGAT
1 TCGATTTGGAT
26934 TCGATTTGGAT
1 TCGATTTGGAT
26945 TCGATTTGGAT
1 TCGATTTGGAT
26956 T
1 T
26957 GAATCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.26, T:0.47
Consensus pattern (11 bp):
TCGATTTGGAT
Found at i:33557 original size:20 final size:19
Alignment explanation
Indices: 33518--33569 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
33508 AATCGATGAG
*
33518 TAAATAATTTAAATATTAAA
1 TAAATAA-TTAAATAATAAA
33538 TAAATAATTAATATAATAAA
1 TAAATAATTAA-ATAATAAA
* *
33558 TCATTAATTAAA
1 TAAATAATTAAA
33570 GTATATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATAATTAAATAATAAA
Found at i:36847 original size:3 final size:3
Alignment explanation
Indices: 36839--36876 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
36829 ATTAATACAT
36839 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
36877 TAACCTAAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39468 original size:22 final size:22
Alignment explanation
Indices: 39426--39470 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39416 ATAATGAATG
*
39426 TGTTTAATTTGATTTGATTATT
1 TGTTTAATTTGATTTAATTATT
*
39448 TGTTTATTTTGA-TTAACTTATT
1 TGTTTAATTTGATTTAA-TTATT
39470 T
1 T
39471 ATATTTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.64
Consensus pattern (22 bp):
TGTTTAATTTGATTTAATTATT
Found at i:40362 original size:20 final size:18
Alignment explanation
Indices: 40334--40376 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
40324 TATTTGATCA
*
40334 TTTTTTATTTTTAATTTT
1 TTTTTTATTCTTAATTTT
*
40352 GTTTTTCTATTCTTGATTTT
1 -TTTTT-TATTCTTAATTTT
40372 TTTTT
1 TTTTT
40377 GTCTGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTTTATTCTTAATTTT
Found at i:41249 original size:24 final size:22
Alignment explanation
Indices: 41221--41283 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
41211 TTAAGTTATT
*
41221 TTAAATATAATATATTTATATAA
1 TTAAATATAATATAATTA-ATAA
* *
41244 TATAAATATGATAAAAATTAATAA
1 T-TAAATATAAT-ATAATTAATAA
41268 TTAAAATATAATATAA
1 TT-AAATATAATATAA
41284 AATATAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 5 0.16
24 22 0.69
25 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAATATAATATAATTAATAA
Found at i:41308 original size:41 final size:41
Alignment explanation
Indices: 41224--41322 Score: 98
Period size: 41 Copynumber: 2.4 Consensus size: 41
41214 AGTTATTTTA
* *
41224 AATAT-AATATATTTATATAATATAAATATGATAAAAATTAAT
1 AATATAAATATA-ATATAAAATATAAATATGATAAAAA-TAAT
41266 AAT-TAAAATATAATATAAAATATAATATTAT-ATAAAAA-AAT
1 AATAT-AAATATAATATAAAATATAA-A-TATGATAAAAATAAT
*
41307 AATATAAATATGATAT
1 AATATAAATATAATAT
41323 TTAATAGTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
41 17 0.35
42 15 0.31
43 14 0.29
44 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (41 bp):
AATATAAATATAATATAAAATATAAATATGATAAAAATAAT
Found at i:41399 original size:20 final size:20
Alignment explanation
Indices: 41311--41412 Score: 64
Period size: 20 Copynumber: 4.8 Consensus size: 20
41301 AAAAATAATA
* * * *
41311 TAAATATGATATTTAATAGT
1 TAAATATAATATATAAAATT
*
41331 TAGATATGAATATATTAAAATTT
1 TAAATAT-AATATA-TAAAA-TT
41354 GTAAATTATGAATATATCAAAATT
1 -TAAA-TAT-AATATAT-AAAATT
*
41378 TATATA-AATATATAAAATTT
1 TAAATATAATATATAAAA-TT
41398 TAAATATAAT-TATAA
1 TAAATATAATATATAA
41413 TATGTCAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
19 4 0.06
20 25 0.38
21 7 0.11
22 6 0.09
23 4 0.06
24 6 0.09
25 14 0.21
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (20 bp):
TAAATATAATATATAAAATT
Found at i:41553 original size:3 final size:3
Alignment explanation
Indices: 41545--41583 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
41535 AGAAGCTCAC
41545 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41584 TTGTACAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46202 original size:20 final size:20
Alignment explanation
Indices: 46163--46200 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
46153 TAAGATAAAT
46163 TATAAATATATTAATATTTA
1 TATAAATATATTAATATTTA
46183 TATAAATATA-TAATATTT
1 TATAAATATATTAATATTT
46201 TAAACATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAAATATATTAATATTTA
Found at i:46486 original size:22 final size:21
Alignment explanation
Indices: 46450--46491 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
46440 ATAATAAAAA
*
46450 TTTAATTAATTTTAAAATTATT
1 TTTAATTAATATT-AAATTATT
*
46472 TTTAATTACTATTAAATTAT
1 TTTAATTAATATTAAATTAT
46492 AATCTAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAATTAATATTAAATTATT
Found at i:47306 original size:95 final size:99
Alignment explanation
Indices: 47131--47319 Score: 253
Period size: 95 Copynumber: 1.9 Consensus size: 99
47121 GTTAAGAATG
**
47131 GTATCAAATTATTTATAACTTGATTTTGACACATCAAAAAAAAAATTAATTTCTTAAAGTTAAAA
1 GTATCAAATTATTTATAACTAAATTTTGACACAT----AAAAAAA-TAATTTCTTAAAGTTAAAA
47196 TGATAGCTAA-TTTTTTTAAAATTTTTATGGGTGAAATA
61 TGATAGCTAATTTTTTTTAAAATTTTTATGGGTGAAATA
*
47234 GTATCAAATTATTT-TAACTAAATTTTGACACAT-AAAAAA-AA-TTCTTAAAAGTTAAAGTGAT
1 GTATCAAATTATTTATAACTAAATTTTGACACATAAAAAAATAATTTCTT-AAAGTTAAAATGAT
*
47295 AGCTAGTTTTTTTTAAAATTTTTAT
65 AGCTAATTTTTTTTAAAATTTTTAT
47320 AGGTTAATAT
Statistics
Matches: 80, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
94 5 0.06
95 20 0.25
96 18 0.22
97 6 0.08
102 17 0.21
103 14 0.17
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (99 bp):
GTATCAAATTATTTATAACTAAATTTTGACACATAAAAAAATAATTTCTTAAAGTTAAAATGATA
GCTAATTTTTTTTAAAATTTTTATGGGTGAAATA
Found at i:47947 original size:2 final size:2
Alignment explanation
Indices: 47940--47972 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
47930 TAAACGTATG
47940 AT AT AT AT 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 AT AT AT AT A
47973 CGATTTATCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48521 original size:3 final size:3
Alignment explanation
Indices: 48515--48558 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
48505 CTTTTTTTAG
48515 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
48559 TCATACAGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:49168 original size:20 final size:21
Alignment explanation
Indices: 49130--49168 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49120 GTAAATTATT
49130 AAAAAATAAAGATAATAAAAG
1 AAAAAATAAAGATAATAAAAG
*
49151 AAAAAATAAA-ATATTAAA
1 AAAAAATAAAGATAATAAA
49169 GATTTAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (21 bp):
AAAAAATAAAGATAATAAAAG
Found at i:49405 original size:27 final size:27
Alignment explanation
Indices: 49366--49436 Score: 117
Period size: 27 Copynumber: 2.6 Consensus size: 27
49356 ACAACAAGTT
49366 ACTATTTTTTACAAACAAAAATAAATC
1 ACTATTTTTTACAAACAAAAATAAATC
49393 A-TCATTTTTTACAAACAAAAATAAATC
1 ACT-ATTTTTTACAAACAAAAATAAATC
*
49420 ACTATTTTTAACAAACA
1 ACTATTTTTTACAAACA
49437 CAAAGGGTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (27 bp):
ACTATTTTTTACAAACAAAAATAAATC
Found at i:54194 original size:26 final size:27
Alignment explanation
Indices: 54157--54215 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
54147 TTTATCTTAT
54157 TTTTATTATATCTAAATAAATTTTTAA
1 TTTTATTATATCTAAATAAATTTTTAA
*
54184 TTTT-TTATATCTAAATAAGTTTTTAA
1 TTTTATTATATCTAAATAAATTTTTAA
54210 TCTTTA
1 T-TTTA
54216 AATTGTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTATTATATCTAAATAAATTTTTAA
Found at i:55565 original size:17 final size:17
Alignment explanation
Indices: 55543--55582 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
55533 TAATAAAGTC
55543 GAAATTAATTATTTTAT
1 GAAATTAATTATTTTAT
55560 GAAATT-ATTATTTTAT
1 GAAATTAATTATTTTAT
55576 -AAATTAA
1 GAAATTAA
55583 ATGATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 11 0.50
17 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
GAAATTAATTATTTTAT
Found at i:57405 original size:15 final size:15
Alignment explanation
Indices: 57365--57405 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
57355 AATTTTAAAA
57365 ATATTAAATATACCT
1 ATATTAAATATACCT
* *
57380 ATTTTAAATATACTT
1 ATATTAAATATACCT
*
57395 ATATTATATAT
1 ATATTAAATAT
57406 TCACTTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTAAATATACCT
Found at i:60017 original size:28 final size:27
Alignment explanation
Indices: 59962--60027 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
59952 ACCACCCATT
*
59962 TGTTTGTTAAAAATGATAGTTATTTTG
1 TGTTTGTCAAAAATGATAGTTATTTTG
*
59989 TGTTTGTCAAAAATGATGGTT-TCCTTTG
1 TGTTTGTCAAAAATGATAGTTAT--TTTG
*
60017 TATTTGTCAAA
1 TGTTTGTCAAA
60028 TATGGAGGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.56
28 14 0.41
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATGATAGTTATTTTG
Found at i:60134 original size:20 final size:20
Alignment explanation
Indices: 60109--60154 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
60099 AAATAGAGGC
*
60109 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
60129 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
60149 TCCCTC
1 TCCCTC
60155 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:64591 original size:28 final size:27
Alignment explanation
Indices: 64536--64616 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 27
64526 GCCACCCATT
64536 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
64563 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* * *
64591 TATTTGTCAAATATGGAGGCTTATTT
1 TGTTTGTCAAAAATGGTGG-TTATTT
64617 ATTTGTCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
26 1 0.02
27 21 0.45
28 22 0.47
29 2 0.04
30 1 0.02
ACGTcount: A:0.22, C:0.07, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Done.