Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002537.1 Hibiscus syriacus cultivar Beakdansim tig00005153_pilon, whole genome shotgun sequence
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: 82594
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1378 original size:24 final size:22
Alignment explanation
Indices: 1327--1380 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 22
1317 TAACCCGTTT
*
1327 TCGAGCTTGAAACGAGCTTGAA
1 TCGAGCTTAAAACGAGCTTGAA
*
1349 TCGAGCTTAAAATCGAGCTTTTAA
1 TCGAGCTTAAAA-CGAGC-TTGAA
1373 TCGAGCTT
1 TCGAGCTT
1381 CTCAATCGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 11 0.39
23 5 0.18
24 12 0.43
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (22 bp):
TCGAGCTTAAAACGAGCTTGAA
Found at i:1399 original size:24 final size:23
Alignment explanation
Indices: 1339--1442 Score: 93
Period size: 24 Copynumber: 4.4 Consensus size: 23
1329 GAGCTTGAAA
**
1339 CGAGCTTGAATCGAGCTTAAAAT
1 CGAGCTTGAATCGAGCTTTCAAT
*
1362 CGAGCTTTTAATCGAGCTTCTCAAT
1 CGAGC-TTGAATCGAGCTT-TCAAT
* *
1387 CGAGCTTGCATCGAGTTTTTCAAT
1 CGAGCTTGAATCGAG-CTTTCAAT
* **
1411 CAAGCTCAAAATCGAGCTTT-AAT
1 CGAGCT-TGAATCGAGCTTTCAAT
1434 CGAGCTTGA
1 CGAGCTTGA
1443 GTCTCGAGCT
Statistics
Matches: 63, Mismatches: 14, Indels: 9
0.73 0.16 0.10
Matches are distributed among these distances:
22 1 0.02
23 13 0.21
24 33 0.52
25 16 0.25
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (23 bp):
CGAGCTTGAATCGAGCTTTCAAT
Found at i:1401 original size:11 final size:11
Alignment explanation
Indices: 1327--1463 Score: 85
Period size: 11 Copynumber: 11.6 Consensus size: 11
1317 TAACCCGTTT
1327 TCGAGCTTGAA
1 TCGAGCTTGAA
*
1338 ACGAGCTTGAA
1 TCGAGCTTGAA
*
1349 TCGAGCTTAAAA
1 TCGAGCTT-GAA
*
1361 TCGAGCTTTTAA
1 TCGAGC-TTGAA
*
1373 TCGAGCTTCTCAA
1 TCGAGC-T-TGAA
*
1386 TCGAGCTTGCA
1 TCGAGCTTGAA
* *
1397 TCGAGTTTTTCAA
1 TCGAG--CTTGAA
* **
1410 TCAAGCTCAAAA
1 TCGAGCT-TGAA
*
1422 TCGAGCTTTAA
1 TCGAGCTTGAA
*
1433 TCGAGCTTGAGTC
1 TCGAGCTTGA--A
1446 TCGAGCTTGAA
1 TCGAGCTTGAA
1457 TCGAGCT
1 TCGAGCT
1464 CTTAAAATTT
Statistics
Matches: 98, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
11 43 0.44
12 27 0.28
13 28 0.29
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:1450 original size:60 final size:60
Alignment explanation
Indices: 1347--1461 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
1337 AACGAGCTTG
* * *
1347 AATCGAGCTTAAAATCGAGCTTTTAATCGAGCTTCTCAATCGAGCTTGCATCGAGTTTTTC
1 AATCAAGCTCAAAATCGAGCTTTTAATCGAGCTTCTC-ATCGAGCTTGAATCGAGTTTTTC
*
1408 AATCAAGCTCAAAATCGAGC-TTTAATCGAGCTTGAGTC-TCGAGCTTGAATCGAG
1 AATCAAGCTCAAAATCGAGCTTTTAATCGAGCTT--CTCATCGAGCTTGAATCGAG
1462 CTCTTAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
60 28 0.58
61 18 0.38
62 2 0.04
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (60 bp):
AATCAAGCTCAAAATCGAGCTTTTAATCGAGCTTCTCATCGAGCTTGAATCGAGTTTTTC
Found at i:2411 original size:14 final size:14
Alignment explanation
Indices: 2394--2421 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2384 ATCTTAACAA
2394 AATTATATAACTAT
1 AATTATATAACTAT
2408 AATTATATAACTAT
1 AATTATATAACTAT
2422 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:4346 original size:37 final size:37
Alignment explanation
Indices: 4305--4514 Score: 183
Period size: 37 Copynumber: 5.9 Consensus size: 37
4295 TTTTTTTTTG
* * *
4305 TGTTTCAAGAGAAATTGTCTCAAGGGAGGCAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
4342 TGTTTCAAGAGAAACATAT-TC-A-A-AG-----ATTGG
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT-T
* *
4372 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
4409 TGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
4445 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAA-CT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
4481 AGTTCCAA-AGAAACTATCTCAAGGGAGACAAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
4515 GGCTTCCTTT
Statistics
Matches: 143, Mismatches: 18, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
29 5 0.03
30 16 0.11
31 1 0.01
32 1 0.01
33 2 0.01
34 2 0.01
35 22 0.15
36 43 0.30
37 47 0.33
38 4 0.03
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:4459 original size:36 final size:36
Alignment explanation
Indices: 4372--4514 Score: 189
Period size: 36 Copynumber: 4.0 Consensus size: 36
4362 CAAAGATTGG
* *
4372 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAA-TT
*
4409 TGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATT
*
4445 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATT
* * * **
4481 AGTTCCAA-AGAAACTATCTCAAGGGAGACAAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAAT
4515 GGCTTCCTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
35 22 0.23
36 42 0.44
37 31 0.33
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.23
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATT
Found at i:4466 original size:73 final size:71
Alignment explanation
Indices: 4372--4514 Score: 196
Period size: 73 Copynumber: 2.0 Consensus size: 71
4362 CAAAGATTGG
* * * * * *
4372 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAAAG
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAAC-TAGTTCCAA-AGAAACTATCTCAAGAAAG
4437 ACAAAATT
64 ACAAAATT
**
4445 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTAGTTCCAAAGAAACTATCTCAAGGGAGAC
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTAGTTCCAAAGAAACTATCTCAAGAAAGAC
4510 AAAAT
66 AAAAT
4515 GGCTTCCTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 22 0.35
72 7 0.11
73 33 0.53
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.23
Consensus pattern (71 bp):
TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTAGTTCCAAAGAAACTATCTCAAGAAAGAC
AAAATT
Found at i:5326 original size:93 final size:95
Alignment explanation
Indices: 5134--5355 Score: 274
Period size: 93 Copynumber: 2.3 Consensus size: 95
5124 GGCTAGCTGA
* *
5134 ATCCATAAAG-CAGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTTAATATCATTGTATAGAT
1 ATCCATAAAGCCA-GGGCGTTTAACCAATTGCTCTA-AGGGACAACTTAATATCATTG-ATACAT
*
5198 ATATAATCATCTTTATCAGGCTAGCTGAATATT
63 ATATAATCACCTTTATCAGGCTAGCTGAATATT
* * *
5231 ATCCATAAAGCCAAGGCGTTTAATCAATTGCTCT-AGGGACAACTTAAGCT-TTATTG-TACAT-
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAAGGGACAACTTAA--TATCATTGATACATA
*
5292 TATAATCACCTTTATCAGGCTAGCTGAATCTT
64 TATAATCACCTTTATCAGGCTAGCTGAATATT
* * *
5324 ATCAATAAAGCCGGGGCGTTTAGCCAATTGCT
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCT
5356 TTTGAGGGAT
Statistics
Matches: 110, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
93 57 0.52
94 4 0.04
95 12 0.11
96 5 0.05
97 30 0.27
98 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAAGGGACAACTTAATATCATTGATACATATA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:8233 original size:21 final size:22
Alignment explanation
Indices: 8207--8252 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
8197 AATTTAGTAA
8207 AAAAATGAAAAA-AATAAT-AAT
1 AAAAATGAAAAAGAA-AATAAAT
8228 AAAAATGAAAAAGAAAATAAAT
1 AAAAATGAAAAAGAAAATAAAT
8250 AAA
1 AAA
8253 TAAAATAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (22 bp):
AAAAATGAAAAAGAAAATAAAT
Found at i:12088 original size:80 final size:79
Alignment explanation
Indices: 11991--12152 Score: 306
Period size: 80 Copynumber: 2.0 Consensus size: 79
11981 TATGTCTCTA
11991 ATTAATAAAAAATCATAGATAAGGAAAATAATAATTTATTATAAATGTAGAGAGATTATAAAGAA
1 ATTAATAAAAAATCATAGATAAGGAAAATAATAATTTATTATAAATGTAGAGAGATTATAAAGAA
12056 CACAAATATATAAT
66 CACAAATATATAAT
12070 ATTAATAAAAAAATCATAGATAAGGAAAATAATAATTTATTATAAATGTAGAGAGATTATAAAGA
1 ATTAAT-AAAAAATCATAGATAAGGAAAATAATAATTTATTATAAATGTAGAGAGATTATAAAGA
*
12135 AGACAAATATATAAT
65 ACACAAATATATAAT
12150 ATT
1 ATT
12153 TATGTATCAA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 6 0.07
80 75 0.93
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (79 bp):
ATTAATAAAAAATCATAGATAAGGAAAATAATAATTTATTATAAATGTAGAGAGATTATAAAGAA
CACAAATATATAAT
Found at i:13688 original size:31 final size:31
Alignment explanation
Indices: 13622--13691 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
13612 TGAATGATCG
* *
13622 ATTTGTTATAAACCAATAACGATAGTCATCG
1 ATTTGTTATAAACCAATAACGATAATCATCA
* * * *
13653 ATTTGTTATAAACCAATAATGTTAATGATTA
1 ATTTGTTATAAACCAATAACGATAATCATCA
13684 ATTTGTTA
1 ATTTGTTA
13692 GTTTTAAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (31 bp):
ATTTGTTATAAACCAATAACGATAATCATCA
Found at i:23944 original size:23 final size:23
Alignment explanation
Indices: 23918--23964 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
23908 ATGTGTTTTC
23918 TATTTTTTAAAAATATATAATTT
1 TATTTTTTAAAAATATATAATTT
* *
23941 TATTTTTTAAAATTTTATAATTT
1 TATTTTTTAAAAATATATAATTT
23964 T
1 T
23965 TTTAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTTTTAAAAATATATAATTT
Found at i:29143 original size:12 final size:11
Alignment explanation
Indices: 29128--29363 Score: 53
Period size: 12 Copynumber: 19.1 Consensus size: 11
29118 ATTTTTACTA
29128 TTATTTTCTTTT
1 TTATTTT-TTTT
29140 TTATTTATTTTGT
1 TTATTT-TTTT-T
29153 TTATTATTTTGTT
1 TTATT-TTTT-TT
**
29166 TATATTCATTTT
1 T-TATTTTTTTT
* *
29178 ATATATTTTATT
1 TTAT-TTTTTTT
29190 TTATTTATCTATTT
1 TTATTT-T-T-TTT
**
29204 TTATGTTTTCCT
1 TTAT-TTTTTTT
* *
29216 TTATCTTTATCT
1 TTAT-TTTTTTT
29228 TTATTTTACTTTTT
1 TTA-TTT--TTTTT
*
29242 TTGTATTTTTTT
1 TTAT-TTTTTTT
29254 TTATCTTTATTTAT
1 TTAT-TTT-TTT-T
*
29268 TTATTTTTTGGT
1 TTATTTTTT-TT
*
29280 TTCTTTATCTTTT
1 TTATTT-T-TTTT
*
29293 TT-TTATTTTT
1 TTATTTTTTTT
* * *
29303 TTA-CTTTATC
1 TTATTTTTTTT
29313 TTATTTTCTTTAT
1 TTATTTT-TTT-T
29326 TTCATTTTTTTCCT
1 TT-ATTTTTTT--T
* *
29340 TCATTTTTTCT
1 TTATTTTTTTT
29351 TTATTTTTGTTT
1 TTATTTTT-TTT
29363 T
1 T
29364 CATTATCTAT
Statistics
Matches: 164, Mismatches: 34, Indels: 52
0.66 0.14 0.21
Matches are distributed among these distances:
10 12 0.07
11 16 0.10
12 60 0.37
13 40 0.24
14 34 0.21
15 2 0.01
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (11 bp):
TTATTTTTTTT
Found at i:29147 original size:16 final size:16
Alignment explanation
Indices: 29128--29161 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29118 ATTTTTACTA
*
29128 TTATTTTCTTTTTTAT
1 TTATTTTCTTTATTAT
*
29144 TTATTTTGTTTATTAT
1 TTATTTTCTTTATTAT
29160 TT
1 TT
29162 TGTTTATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TTATTTTCTTTATTAT
Found at i:29155 original size:9 final size:9
Alignment explanation
Indices: 29138--29336 Score: 64
Period size: 9 Copynumber: 22.4 Consensus size: 9
29128 TTATTTTCTT
29138 TTTTATTTA
1 TTTTATTTA
*
29147 TTTTGTTTA
1 TTTTATTTA
* *
29156 TTAT-TTTG
1 TTTTATTTA
*
29164 TTTATATTCA
1 TTT-TATTTA
*
29174 TTTTATATA
1 TTTTATTTA
29183 TTTTATTT-
1 TTTTATTTA
*
29191 TATTTATCTA
1 T-TTTATTTA
*
29201 TTTTTATGT-
1 -TTTTATTTA
**
29210 TTTCCTTTA
1 TTTTATTTA
29219 TCTTTATCTTTA
1 T-TTTA--TTTA
29231 TTTTACTTT-
1 TTTTA-TTTA
*
29240 TTTTGTATT-
1 TTTTAT-TTA
29249 TTTT-TTTA
1 TTTTATTTA
29257 TCTTTATTTA
1 T-TTTATTTA
29267 -TTTATTT-
1 TTTTATTTA
**
29274 TTTGGTTT-
1 TTTTATTTA
* *
29282 CTTTATCT-
1 TTTTATTTA
29290 TTTT-TTTA
1 TTTTATTTA
29298 TTTT-TTTA
1 TTTTATTTA
*
29306 CTTTATCTTA
1 TTTTAT-TTA
*
29316 TTTTCTTTA
1 TTTTATTTA
*
29325 TTTCATTT-
1 TTTTATTTA
29333 TTTT
1 TTTT
29337 CCTTCATTTT
Statistics
Matches: 142, Mismatches: 31, Indels: 35
0.68 0.15 0.17
Matches are distributed among these distances:
7 4 0.03
8 47 0.33
9 53 0.37
10 28 0.20
11 5 0.04
12 5 0.04
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:29157 original size:13 final size:13
Alignment explanation
Indices: 29083--29333 Score: 82
Period size: 12 Copynumber: 19.2 Consensus size: 13
29073 ATCCTTTACA
29083 TTTATTTATTTA-
1 TTTATTTATTTAT
*
29095 TTTATTTATTCAT
1 TTTATTTATTTAT
* * *
29108 TGTATATA-CTATT
1 TTTATTTATTTA-T
29121 TTTACTATTATTT-T
1 TTTA-T-TTATTTAT
29135 CTTT-TTTATTTAT
1 -TTTATTTATTTAT
*
29148 TTTGTTTA-TTAT
1 TTTATTTATTTAT
*
29160 TTTGTTTATATTCAT
1 TTTATTTAT-TT-AT
*
29175 TTTATATATTTTAT
1 TTTATTTA-TTTAT
*
29189 TTTATTTATCTATT
1 TTTATTTATTTA-T
**
29203 TTTATGTT-TTCCT
1 TTTAT-TTATTTAT
*
29216 TTATCTTTATCTTTAT
1 TT-TATTTA--TTTAT
*
29232 TTTACTT-TTT-T
1 TTTATTTATTTAT
*
29243 TGTATTT-TTT-T
1 TTTATTTATTTAT
*
29254 TTATCTTTATTTA-
1 TT-TATTTATTTAT
**
29267 TTTATTT-TTTGG
1 TTTATTTATTTAT
* *
29279 TTTCTTTATCT-T
1 TTTATTTATTTAT
29291 TTT-TTTATTT-T
1 TTTATTTATTTAT
29302 TTTACTTTATCTTAT
1 TTTA-TTTAT-TTAT
*
29317 TTTCTTTATTTCAT
1 TTTATTTATTT-AT
29331 TTT
1 TTT
29334 TTTCCTTCAT
Statistics
Matches: 180, Mismatches: 31, Indels: 54
0.68 0.12 0.20
Matches are distributed among these distances:
11 24 0.13
12 53 0.29
13 38 0.21
14 34 0.19
15 24 0.13
16 7 0.04
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:29184 original size:27 final size:27
Alignment explanation
Indices: 29118--29184 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
29108 TGTATATACT
* * *
29118 ATTTTTACTATTATTTTCTTTTTTATTT
1 ATTTTTA-TATTATTTTCGTTTATATTC
*
29146 ATTTTGTTTATTATTTT-GTTTATATTC
1 ATTTT-TATATTATTTTCGTTTATATTC
29173 ATTTTATATATT
1 ATTTT-TATATT
29185 TTATTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 17 0.53
28 14 0.44
29 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.72
Consensus pattern (27 bp):
ATTTTTATATTATTTTCGTTTATATTC
Found at i:29232 original size:38 final size:36
Alignment explanation
Indices: 29184--29300 Score: 122
Period size: 32 Copynumber: 3.4 Consensus size: 36
29174 TTTTATATAT
29184 TTTAT-TTTATTTATCTATTTTTATGTTTTCCTTTATC
1 TTTATCTTTATTTATCTATTTTT-TGTTTT-CTTTATC
*
29221 TTTATCTTTATTT-TACT-TTTTTTGTATT-TTT-T-
1 TTTATCTTTATTTAT-CTATTTTTTGTTTTCTTTATC
* *
29253 TTTATCTTTATTTATTTATTTTTTGGTTTCTTTATC
1 TTTATCTTTATTTATCTATTTTTTGTTTTCTTTATC
*
29289 TTT-TTTTTATTT
1 TTTATCTTTATTT
29301 TTTTACTTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
32 14 0.21
33 11 0.16
34 6 0.09
35 9 0.13
36 8 0.12
37 11 0.16
38 9 0.13
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (36 bp):
TTTATCTTTATTTATCTATTTTTTGTTTTCTTTATC
Found at i:29240 original size:6 final size:5
Alignment explanation
Indices: 29128--29333 Score: 51
Period size: 5 Copynumber: 40.4 Consensus size: 5
29118 ATTTTTACTA
* * * * *
29128 TTATT TTCTT TTTTAT TTATT TTGTTT ATTATT TT-GT TTATAT TCATT
1 TTATT TTATT TTAT-T TTATT TT-ATT -TTATT TTATT TTAT-T TTATT
* *
29176 TTA-T ATATT TTATT TTA-T TTA-T CTATTT TTATGT TT-TCCT TTATCT
1 TTATT TTATT TTATT TTATT TTATT TTA-TT TTAT-T TTAT--T TTAT-T
*
29222 TTATCT TTATT TTACTT TT-TT TGTATT TTTTT TTATCT TTA-T TTA-T
1 TTAT-T TTATT TTA-TT TTATT T-TATT TTATT TTAT-T TTATT TTATT
* * *
29268 TTATT TT-TT GGTT-TCT TTATCT TTTTT TTA-T TT-TT TTACT TTATC
1 TTATT TTATT --TTAT-T TTAT-T TTATT TTATT TTATT TTATT TTATT
* *
29313 TTATT TT-CT TTATT TCATT TT
1 TTATT TTATT TTATT TTATT TT
29334 TTTCCTTCAT
Statistics
Matches: 152, Mismatches: 26, Indels: 46
0.68 0.12 0.21
Matches are distributed among these distances:
4 35 0.23
5 60 0.39
6 53 0.35
7 4 0.03
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:29304 original size:10 final size:10
Alignment explanation
Indices: 29221--29304 Score: 62
Period size: 10 Copynumber: 8.1 Consensus size: 10
29211 TTCCTTTATC
*
29221 TTTATCTTTAT
1 TTTAT-TTTTT
29232 TTTACTTTTTT
1 TTTA-TTTTTT
*
29243 TGTATTTTTT
1 TTTATTTTTT
* *
29253 TTTATCTTTA
1 TTTATTTTTT
29263 TTTATTTATTT
1 TTTATTT-TTT
** *
29274 TTT-GGTTTC
1 TTTATTTTTT
29283 TTTATCTTTTT
1 TTTAT-TTTTT
29294 TTTATTTTTT
1 TTTATTTTTT
29304 T
1 T
29305 ACTTTATCTT
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
9 5 0.09
10 26 0.46
11 24 0.43
12 1 0.02
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.79
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:29323 original size:62 final size:61
Alignment explanation
Indices: 29219--29336 Score: 145
Period size: 62 Copynumber: 1.9 Consensus size: 61
29209 TTTTCCTTTA
29219 TCTTTATCTTTATTTTACTTTTTTTGTATTTTTTTTTATCTTTATTT-ATTTATTTTTTGGTT
1 TCTTTATCTTTATTTTAC-TTTTTTGTATTTTTTTTTATCTTTATTTCATTT-TTTTTTGGTT
*
29281 TCTTTATCTTTTTTTTA-TTTTTT-TACTTTATCTTATTT-TCTTTATTTCATTTTTTT
1 TCTTTATCTTTATTTTACTTTTTTGTA-TTT-T-TT-TTTATCTTTATTTCATTTTTTT
29337 CCTTCATTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
59 2 0.04
60 9 0.18
61 1 0.02
62 31 0.62
63 7 0.14
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.76
Consensus pattern (61 bp):
TCTTTATCTTTATTTTACTTTTTTGTATTTTTTTTTATCTTTATTTCATTTTTTTTTGGTT
Found at i:29333 original size:32 final size:29
Alignment explanation
Indices: 29287--29356 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 29
29277 GGTTTCTTTA
* * *
29287 TCTTTTTTTTATTTTTTTACTTTATCTTATTT
1 TCTTTATTTCATTTTTTTACTTCA--TT-TTT
*
29319 TCTTTATTTCATTTTTTTCCTTCATTTTT
1 TCTTTATTTCATTTTTTTACTTCATTTTT
29348 TCTTTATTT
1 TCTTTATTT
29357 TTGTTTTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.35
30 2 0.06
32 20 0.59
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (29 bp):
TCTTTATTTCATTTTTTTACTTCATTTTT
Found at i:31592 original size:30 final size:30
Alignment explanation
Indices: 31533--31635 Score: 136
Period size: 30 Copynumber: 3.4 Consensus size: 30
31523 CCCGAAGGAC
* *
31533 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
31562 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
31592 CTGTCCAGAAGTCATAAAGATCCTCGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
* *
31623 CTGTCCATAGGTC
1 CTATCCAGAGGTC
31636 CCGAAGAACC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 19 0.29
30 34 0.52
31 13 0.20
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:31652 original size:31 final size:31
Alignment explanation
Indices: 31608--31685 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
31598 AGAAGTCATA
* *
31608 AAGATCCTCGGTAAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
* *
31639 AAGAACCTAGGTAAACTGTCCATATGTCTCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
*
31670 AA-AGACATAGGTAAAC
1 AAGA-ACCTAGGTAAAC
31686 CCTCGACTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (31 bp):
AAGAACCTAGGTAAACTGTCCATAGGTCCCG
Found at i:32942 original size:21 final size:21
Alignment explanation
Indices: 32912--32956 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32902 ATTCTGTCGT
* *
32912 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
32933 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
32954 TTG
1 TTG
32957 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:36324 original size:30 final size:30
Alignment explanation
Indices: 36265--36367 Score: 154
Period size: 30 Copynumber: 3.4 Consensus size: 30
36255 CCCGAAGGAC
* *
36265 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
36294 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
36324 CTATCCAGAGGTCATAAAGATCCTCGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
* *
36355 CTGTCCATAGGTC
1 CTATCCAGAGGTC
36368 CCGAAGAACC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.28
30 36 0.53
31 13 0.19
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:36384 original size:31 final size:31
Alignment explanation
Indices: 36340--36417 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
36330 AGAGGTCATA
* *
36340 AAGATCCTCGGTAAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
* *
36371 AAGAACCTAGGTAAACTGTCCATATGTCTCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
*
36402 AA-AGACATAGGTAAAC
1 AAGA-ACCTAGGTAAAC
36418 CCTCGACTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (31 bp):
AAGAACCTAGGTAAACTGTCCATAGGTCCCG
Found at i:37671 original size:21 final size:21
Alignment explanation
Indices: 37641--37685 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
37631 ATTCTGTCGT
* *
37641 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
37662 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
37683 TTG
1 TTG
37686 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:42151 original size:23 final size:23
Alignment explanation
Indices: 42068--42143 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
42058 CCTTATTATA
42068 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
42091 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
42114 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
42137 CGGCACT
1 TGGCACT
42144 CCAGTGCATT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:42266 original size:2 final size:2
Alignment explanation
Indices: 42259--42304 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
42249 AACAAATACA
42259 AT AT AT AT AT AT 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 AT AT
42301 AT AT
1 AT AT
42305 GATGGATATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42462 original size:18 final size:18
Alignment explanation
Indices: 42439--42473 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42429 AAATAATTTG
*
42439 ATGATAATGATATAAATA
1 ATGATAATAATATAAATA
42457 ATGATAATAATATAAAT
1 ATGATAATAATATAAAT
42474 GATAATGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (18 bp):
ATGATAATAATATAAATA
Found at i:42476 original size:15 final size:13
Alignment explanation
Indices: 42442--42479 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
42432 TAATTTGATG
42442 ATAATGAT-ATAA
1 ATAATGATAATAA
42454 ATAATGATAATAA
1 ATAATGATAATAA
42467 TATAAATGATAAT
1 -AT-AATGATAAT
42480 GCTAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 2 0.09
15 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (13 bp):
ATAATGATAATAA
Found at i:47029 original size:14 final size:14
Alignment explanation
Indices: 47010--47045 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
47000 AGAGATAAGT
47010 AATATGAATGTGTG
1 AATATGAATGTGTG
47024 AATATGAATGTGTG
1 AATATGAATGTGTG
47038 AATATGAA
1 AATATGAA
47046 ATGAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (14 bp):
AATATGAATGTGTG
Found at i:47281 original size:23 final size:23
Alignment explanation
Indices: 47251--47334 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
47241 CATTATTATA
47251 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
47274 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
47297 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
47320 CGACACTTCGGTGCA
1 TGGCACTACGGTGCA
47335 TTTATACGAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:47449 original size:2 final size:2
Alignment explanation
Indices: 47442--47469 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47432 AACAAATACA
47442 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
47470 GATGGATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47627 original size:18 final size:18
Alignment explanation
Indices: 47604--47638 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47594 AAATAATTTG
*
47604 ATGATAATGATATAAATA
1 ATGATAATAATATAAATA
47622 ATGATAATAATATAAAT
1 ATGATAATAATATAAAT
47639 GATAATGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (18 bp):
ATGATAATAATATAAATA
Found at i:47641 original size:15 final size:13
Alignment explanation
Indices: 47607--47644 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
47597 TAATTTGATG
47607 ATAATGAT-ATAA
1 ATAATGATAATAA
47619 ATAATGATAATAA
1 ATAATGATAATAA
47632 TATAAATGATAAT
1 -AT-AATGATAAT
47645 GCTAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 2 0.09
15 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (13 bp):
ATAATGATAATAA
Found at i:49282 original size:95 final size:95
Alignment explanation
Indices: 49108--49286 Score: 279
Period size: 95 Copynumber: 1.9 Consensus size: 95
49098 TAATATTATT
* * *
49108 TATACAATAAAGCTTGAGTTGTTCCTCTAGAGCAATTGGTTAAAAGCCCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAAAGCCCCGGCTTTATGGATAAG
*
49173 ATTCAACTAGCCTGATAAATGTGATTATAC
66 ATTCAACTAACCTGATAAATGTGATTATAC
*
49203 TATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGA-GCAATTGGTTAAAAGCCCCGGCTTTATGGATAA
* *
49267 GATTGAGCTAACCTGATAAA
65 GATTCAACTAACCTGATAAA
49287 GGTTTTTACA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
94 1 0.01
95 75 0.99
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAAAGCCCCGGCTTTATGGATAAG
ATTCAACTAACCTGATAAATGTGATTATAC
Found at i:50662 original size:36 final size:36
Alignment explanation
Indices: 50611--50712 Score: 113
Period size: 32 Copynumber: 2.9 Consensus size: 36
50601 AAACAAGGGG
*
50611 TTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATT
1 TTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATT
* *
50647 CTGTCTCTCTGGAGACA-TTT-T-TT-AAACAAATT
1 TTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATT
** * *
50679 TTGTCTCTCTTGAGATGGTTTCCCTTGAAACAAA
1 TTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAA
50713 AACTTTGAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
32 22 0.40
33 5 0.09
34 1 0.02
35 5 0.09
36 22 0.40
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATT
Found at i:50684 original size:32 final size:36
Alignment explanation
Indices: 50611--50848 Score: 209
Period size: 36 Copynumber: 6.9 Consensus size: 36
50601 AAACAAGGGG
50611 TTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATT
1 TTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATT
* *
50647 CTGTCTCTCTGGAGACA-TTT-T-TT-AAACAAATT
1 TTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATT
*** * * *
50679 TTGTCTCTCTTGAGATGGTTTCCCTTGAAACAAAAACT
1 TTGTCTCTCTTGAGACATTTTCTCTT-AAA-ACAAATT
**
50717 TTG--AAT-TT--G---TTTTC-C--AAAACAAAGTT
1 TTGTCTCTCTTGAGACATTTTCTCTTAAAACAAA-TT
*
50743 TTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATT
1 TTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATT
50779 TTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATT
1 TTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATT
** * *
50815 TTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAA
1 TTGTCTCTCTTGAGACATTTTCTCTTAAAACAAA
50849 AACTTTGAAT
Statistics
Matches: 162, Mismatches: 22, Indels: 36
0.74 0.10 0.16
Matches are distributed among these distances:
25 4 0.02
26 7 0.04
28 1 0.01
29 3 0.02
30 4 0.02
31 1 0.01
32 22 0.14
33 6 0.04
34 5 0.03
35 8 0.05
36 83 0.51
37 10 0.06
38 8 0.05
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATT
Found at i:50810 original size:100 final size:95
Alignment explanation
Indices: 50637--51269 Score: 413
Period size: 102 Copynumber: 6.3 Consensus size: 95
50627 ATTTTCTCTT
**
50637 AAAACAAATTCTGTCTCTCTGGAGACATTTTTTAAACAAATTTTGTCTCTCTTGAGATGGTTTCC
1 AAAACAAATTCTGTCTCTCTGGAGACATTTTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
*
50702 CTTGAAACAAAAACTTTGAATTTGTTTTCC
66 CTTAAAACAAAAACTTTGAATTTGTTTTCC
* * *
50732 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAT
1 AAAACAAA-TTCTGTCTCTCTGGAGACA-TTT-T-TT-AAACAAATTTTGTCTCTCTTGAGACAG
* ** ** *
50797 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGA-CGGTTTCCC
61 TTTCCCTTAAAACAAA------AACT-TTGA-ATTTGTTTTCC
* ** * **** * *
50839 TTGAAACAAA----AACT-T-TGAATTTGTTTTCCTTGAAACAAAATTTGTCTCTCTTGAGACGG
1 --AAAACAAATTCTGTCTCTCTGGAGACATTTT--TT-AAACAAATTTTGTCTCTCTTGAGACAG
* *
50898 TTTCCCTTGAAACTAAAACTTTGAATTTGTTTTCC
61 TTTCCCTTAAAACAAAAACTTTGAATTTGTTTTCC
* *
50933 TTAAAACAAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGAC
1 --AAAAC-AAATTCTGTCTCTCTGGAGACA-TTT-T-TT-AAACAAATTTTGTCTCTCTTGAGAC
* *
50998 GGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCC
59 AGTTTCCCTTAAAACAAAAACTTTGAATTTGTTTTCC
* * *
51035 TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTTAAACAAATTTTGTCTCTCTTGAGAC
1 --AAAACAAA-TTCTGTCTCTCTGGAGACA--TT-T-TTTAAACAAATTTTGTCTCTCTTGAGAC
** * *
51100 AGTTTCCCTTGCAACAAAATCTTTGAATCTGTTTTCC
59 AGTTTCCCTTAAAACAAAAACTTTGAATTTGTTTTCC
* *
51137 TTAAAACAAATT-TCGTCTCCCTTGAGACAGTTTCTTTCAAAACAAATTTTGTCTCTCTTGAGAC
1 --AAAACAAATTCT-GTCTCTCTGGAGACA-TTT-TTT--AAACAAATTTTGTCTCTCTTGAGAC
* * * * * *
51201 GGTTTTCCTTGAAGCAAAATCTTTGAA-TCGTTTTCC
59 AGTTTCCCTTAAAACAAAAACTTTGAATTTGTTTTCC
* *
51237 TTTAAACAAATT-TCGTCTCTCTTGAGACATTTT
1 --AAAACAAATTCT-GTCTCTCTGGAGACATTTT
51270 CTCTTAAAAT
Statistics
Matches: 445, Mismatches: 61, Indels: 61
0.78 0.11 0.11
Matches are distributed among these distances:
93 1 0.00
94 16 0.04
95 13 0.03
96 17 0.04
97 3 0.01
98 2 0.00
99 12 0.03
100 77 0.17
101 112 0.25
102 160 0.36
103 7 0.02
104 5 0.01
106 2 0.00
107 10 0.02
108 1 0.00
109 7 0.02
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (95 bp):
AAAACAAATTCTGTCTCTCTGGAGACATTTTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
CTTAAAACAAAAACTTTGAATTTGTTTTCC
Found at i:50883 original size:65 final size:65
Alignment explanation
Indices: 50670--50979 Score: 367
Period size: 65 Copynumber: 4.7 Consensus size: 65
50660 GACATTTTTT
*
50670 AAACAAATTTTGTCTCTCTTGAGATGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCC--A
1 AAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTA
* * * * **
50733 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT-AAA-ACAAATTTTGTCTCTCTTGAGACA
1 AAACAAA-TTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAACTTTG--AAT-TT--G---
50796 TTTTCTCTTA
57 TTTTC-CTTA
*
50806 AAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTA
* *
50871 AAACAAAATTTGTCTCTCTTGAGACGGTTTCCCTTGAAACTAAAACTTTGAATTTGTTTTCCTTA
1 AAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTA
** * *
50936 AAACAAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAA
1 AAAC-AAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAA
50980 TTTTGTCTCT
Statistics
Matches: 209, Mismatches: 23, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
62 8 0.04
63 10 0.05
64 26 0.12
65 71 0.34
66 38 0.18
67 1 0.00
69 1 0.00
70 5 0.02
71 3 0.01
72 27 0.13
73 11 0.05
74 8 0.04
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (65 bp):
AAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTA
Found at i:50909 original size:36 final size:36
Alignment explanation
Indices: 50861--51016 Score: 132
Period size: 36 Copynumber: 4.5 Consensus size: 36
50851 CTTTGAATTT
*
50861 GTTTTCCTTGAAACAAAATTTGTCTCTCTTGAGACG
1 GTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACG
**
50897 GTTTCCCTTGAAACTAAAA-------CT-TTGA-ATTT
1 GTTTCCCTTGAAAC-AAAATTTGTCTCTCTTGAGA-CG
* * *
50926 GTTTTCCTTAAAACAAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAA-TTTGTCTCTCTTGAGACG
* * * *
50963 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACG
1 GTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACG
50999 GTTTCCCTTGAAACAAAA
1 GTTTCCCTTGAAACAAAA
51017 ACTTTGAATT
Statistics
Matches: 92, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
28 5 0.05
29 16 0.17
30 2 0.02
36 46 0.50
37 22 0.24
38 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACG
Found at i:51088 original size:36 final size:35
Alignment explanation
Indices: 51030--51210 Score: 153
Period size: 36 Copynumber: 5.2 Consensus size: 35
51020 TTGAATTTGT
*
51030 TTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCTTAAAACAAA-TTTTGTCTCTCTTGAGACAG
*
51066 TTTCTCTTTAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTC-CTTAAAACAAATTTTGTCTCTCTTGAGACAG
** * *
51102 TTTCCCTTGCAACAAA------ATCT-TTGA-ATCTG
1 TTT-CCTTAAAACAAATTTTGTCTCTCTTGAGA-CAG
* *
51131 TTTTCCTTAAAACAAATTTCGTCTCCCTTGAGACAG
1 -TTTCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
51167 TTTCTTTCAAAACAAATTTTGTCTCTCTTGAGACGG
1 TTTCCTT-AAAACAAATTTTGTCTCTCTTGAGACAG
51203 TTTTCCTT
1 -TTTCCTT
51211 GAAGCAAAAT
Statistics
Matches: 116, Mismatches: 15, Indels: 27
0.73 0.09 0.17
Matches are distributed among these distances:
28 1 0.01
29 16 0.14
30 6 0.05
35 8 0.07
36 67 0.58
37 18 0.16
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (35 bp):
TTTCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:51164 original size:167 final size:163
Alignment explanation
Indices: 50758--51078 Score: 446
Period size: 167 Copynumber: 1.9 Consensus size: 163
50748 TCTCTTGAGA
* **
50758 CAGTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTC
1 CAGTTTCCCTTAAAACAAAATTTTG-CAATCTT-AG--ATTTTCTCTTAAAACAAATTTTGTCTC
50822 TCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTGAAACAAAATTTGTCTC
62 TCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTGAAACAAAATTTGTCTC
*
50887 TCTTGAGACGGTTTCCCTTGAAACTAAAACTTTGAAT
127 TCTTGAGACAGTTTCCCTTGAAACTAAAACTTTGAAT
** * **
50924 TTGTTTTCCTTAAAACAAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTC
1 CAGTTTCCCTTAAAACAAAATTTTG-CAATCTT-AG--ATTTTCTCTTAAAACAAATTTTGTCTC
*
50989 TCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTGAAACAAAGTTTTGTCT
62 TCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTGAAACAAA-ATTTGTCT
* *
51054 CTCTTGAGACAGTTTCTCTTTAAAC
126 CTCTTGAGACAGTTTCCCTTGAAAC
51079 AAATTTTGTC
Statistics
Matches: 145, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
166 12 0.08
167 104 0.72
168 29 0.20
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (163 bp):
CAGTTTCCCTTAAAACAAAATTTTGCAATCTTAGATTTTCTCTTAAAACAAATTTTGTCTCTCTT
GAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTGAAACAAAATTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACTAAAACTTTGAAT
Found at i:53002 original size:482 final size:467
Alignment explanation
Indices: 52061--53012 Score: 1607
Period size: 482 Copynumber: 2.0 Consensus size: 467
52051 GTTCGTGTAG
* *
52061 ATTCCTATAGCCGCACATCGCGCACCAACCAACTGCTCGATCAACAAGTCGTCCGAGTTCCCCAC
1 ATTCCTATAGCCGCACATCACGCACCAACCAACTGCCCGATCAACAAGTCGTCCGAGTTCCCCAC
52126 CGGAGCCTCTCCAACAAACGTGCGAACAACCAACAAACACGTTATTAGTGTTCTACTCGGGATTA
66 CGGAGCCTCTCCAACAAACGTGCGAACAACCAACAAACACGTTATTAGTGTTCTACTCGGGATTA
* *
52191 AACTCTAAAAATAGCCAATAGTTTTGGCTATAAAATCAAGTAGAGGGGGGATTTTACACACGAGA
131 AACTCTAAAAATAGCCAATAATTTTGACTATAAAATCAAGTAGAGGGGGGATTTTACACACGAGA
*
52256 AATTTTATTCGAGATCCACACACAGAATACATAAAAAAAGATCGGTAGAAAGATCTAGGGAAAGC
196 AATTTCATTCGAGATCCACACACAGAATACATAAAAAAAGATCGGTAGAAAGATCTAGGGAAAGC
*
52321 CTATTCGAACAGAGAAAAAAACCCAAACAGAAAAAAATCTTACCTCGTCGACTTCACTAGAACTA
261 CCATTCGAACAGAGAAAAAAACCCAAACAGAAAAAAATCTTACCTCGTCGACTTCACTAGAACTA
*
52386 GACGAACTCACTACCGAAAGGATTTAGATACAAGGCGCTATTCTGTTGATTGGGTCCCCTTTGGG
326 GACGAACTCACTACCGAAAGGATTTAGATACAAGGCGCTATTCTATTGATTGGGTCCCCTTTGGG
* *
52451 TTCCTGGTACGGAGAAGGTAGCAATCGAGGACCGGTTAGAAGGATGGATCAAAGACCTGGAAGCA
391 TTCCTAGTACGGAAAAGGTAGCAATCGAGGACCGGTTAGAAGGATGGATCAAAGACCTGGAAGCA
*
52516 AGTGAAGTTGAT
456 AGTGAAGCTGAT
* ** *
52528 ATTCCTATTGCCGCACATCACGCACCAACCAACTGCCCGATCAACAAGTTTTCCGAGTTCCCCGC
1 ATTCCTATAGCCGCACATCACGCACCAACCAACTGCCCGATCAACAAGTCGTCCGAGTTCCCCAC
52593 CGGAGCCTCTCCAACAAACGTGCGAACAACCAACAAACACGTTATTAGTGTTCTACTCGGGATTA
66 CGGAGCCTCTCCAACAAACGTGCGAACAACCAACAAACACGTTATTAGTGTTCTACTCGGGATTA
52658 AACTCTAAAAATAGCCAATAATTTTGACTATAAAATCATGTAATCGAACACAAGTAGAGGGGGGA
131 AACTCTAAAAATAGCCAATAATTTTGACTAT---A--A---AAT------CAAGTAGAGGGGGGA
* *
52723 TTTTACACACGAGAAATTTCATTCGAGATCCACACACATAATACATAAGAAAAGATCGGTAGAAA
182 TTTTACACACGAGAAATTTCATTCGAGATCCACACACAGAATACATAAAAAAAGATCGGTAGAAA
52788 GATCTAGGGAAAGCCCATTCGAACAGAGAAAAAAACCCAAACAGAAAAAAACTCTTACCTCGTCG
247 GATCTAGGGAAAGCCCATTCGAACAGAGAAAAAAACCCAAACAGAAAAAAA-TCTTACCTCGTCG
* *
52853 ACTTCACTAGAACTAGACGAACTCACTACCGAAAGGATTTAGATACAAGGTGTTATTCTATTGAT
311 ACTTCACTAGAACTAGACGAACTCACTACCGAAAGGATTTAGATACAAGGCGCTATTCTATTGAT
52918 TGGGTCCCCTTTGGGTTCCTAGTACGGAAAAGGTAGCAATCGAGGACCGGTTAGAAGGATGGATC
376 TGGGTCCCCTTTGGGTTCCTAGTACGGAAAAGGTAGCAATCGAGGACCGGTTAGAAGGATGGATC
52983 AAAGACCTGGAAGCAAGTGAAGCTGAT
441 AAAGACCTGGAAGCAAGTGAAGCTGAT
53010 ATT
1 ATT
53013 GCAACTTTTG
Statistics
Matches: 452, Mismatches: 18, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
467 153 0.34
470 1 0.00
472 1 0.00
475 3 0.01
481 127 0.28
482 167 0.37
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (467 bp):
ATTCCTATAGCCGCACATCACGCACCAACCAACTGCCCGATCAACAAGTCGTCCGAGTTCCCCAC
CGGAGCCTCTCCAACAAACGTGCGAACAACCAACAAACACGTTATTAGTGTTCTACTCGGGATTA
AACTCTAAAAATAGCCAATAATTTTGACTATAAAATCAAGTAGAGGGGGGATTTTACACACGAGA
AATTTCATTCGAGATCCACACACAGAATACATAAAAAAAGATCGGTAGAAAGATCTAGGGAAAGC
CCATTCGAACAGAGAAAAAAACCCAAACAGAAAAAAATCTTACCTCGTCGACTTCACTAGAACTA
GACGAACTCACTACCGAAAGGATTTAGATACAAGGCGCTATTCTATTGATTGGGTCCCCTTTGGG
TTCCTAGTACGGAAAAGGTAGCAATCGAGGACCGGTTAGAAGGATGGATCAAAGACCTGGAAGCA
AGTGAAGCTGAT
Found at i:53534 original size:4 final size:4
Alignment explanation
Indices: 53525--53765 Score: 65
Period size: 4 Copynumber: 57.2 Consensus size: 4
53515 GATCTTTTAC
* *
53525 ATTT ATTT ATTT ATTT ATTT ATTC ATTGT ATAT ACTATT -TTT ACTATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT-T ATTT A-T-TT ATTT A-T-TT
* * * *
53573 ATTTT CTTT TTTT ATTT ATTTT GTTT A-TT ATTTT CTTT ATATT CATTTT
1 A-TTT ATTT ATTT ATTT A-TTT ATTT ATTT A-TTT ATTT AT-TT -A-TTT
* *
53622 ATTT ATTTT ATTTT ATTTT ATTT ATCT ATTT -TTAT TTTT ATTT -TTT
1 ATTT A-TTT A-TTT A-TTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT
* * * *
53668 CCTTT ATTT -TTT CTTT -TCTT -TTCT -TTT CTTT ATTTT CTTT ATCTTT
1 -ATTT ATTT ATTT ATTT AT-TT ATT-T ATTT ATTT A-TTT ATTT A--TTT
*
53714 ATTTT ACTTT A-TT -TTT ATTT -TTT -TGT ATTT ATTTT ATTT ATTT ATTT
1 A-TTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT
53761 ATTT A
1 ATTT A
53766 ATCTTTATTT
Statistics
Matches: 186, Mismatches: 23, Indels: 56
0.70 0.09 0.21
Matches are distributed among these distances:
3 25 0.13
4 100 0.54
5 48 0.26
6 12 0.06
7 1 0.01
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:53599 original size:9 final size:9
Alignment explanation
Indices: 53526--53854 Score: 129
Period size: 9 Copynumber: 36.3 Consensus size: 9
53516 ATCTTTTACA
53526 TTTATTTA-
1 TTTATTTAT
53534 TTTATTTA-
1 TTTATTTAT
*
53542 TTTATTCAT
1 TTTATTTAT
*
53551 TGTATATACTATT
1 T-T-TAT-TTA-T
53564 TTTACTATTAT
1 TTTA-T-TTAT
*
53575 TTTCTTT-T
1 TTTATTTAT
53583 TTTATTTAT
1 TTTATTTAT
*
53592 TTTGTTTAT
1 TTTATTTAT
* *
53601 TAT-TTTCT
1 TTTATTTAT
*
53609 TTATATTCAT
1 TT-TATTTAT
53619 TTTATTTAT
1 TTTATTTAT
53628 TTTATTTTAT
1 TTTA-TTTAT
53638 TTTATTTAT
1 TTTATTTAT
53647 CTATT-TTTATT
1 -T-TTATTTA-T
53658 TTTATTT-T
1 TTTATTTAT
**
53666 TTCCTTTAT
1 TTTATTTAT
53675 TTT-TTCT-T
1 TTTATT-TAT
*
53683 TTCT-TTTCT
1 TT-TATTTAT
*
53692 TTTCTTTAT
1 TTTATTTAT
*
53701 TTTCTTTAT
1 TTTATTTAT
*
53710 CTTTATTTTAC
1 -TTTA-TTTAT
53721 TTTATTT-T
1 TTTATTTAT
53729 TATT-TTT-T
1 T-TTATTTAT
*
53737 TGTATTTAT
1 TTTATTTAT
53746 TTTATTTA-
1 TTTATTTAT
53754 TTTATTTAT
1 TTTATTTAT
*
53763 TTAATCTT-T
1 TTTAT-TTAT
*
53772 ATT-TTTAT
1 TTTATTTAT
**
53780 TTT-TTTGG
1 TTTATTTAT
*
53788 TTTCTTTAT
1 TTTATTTAT
53797 CTTTATTT-T
1 -TTTATTTAT
*
53806 TTTGGTTTTAT
1 TTT--ATTTAT
*
53817 TTT-TTTAC
1 TTTATTTAT
53825 TTTATCTTAT
1 TTTAT-TTAT
*
53835 TTTCTTTAT
1 TTTATTTAT
*
53844 TTCATTT-T
1 TTTATTTAT
53852 TTT
1 TTT
53855 CCTTCATTTT
Statistics
Matches: 249, Mismatches: 38, Indels: 68
0.70 0.11 0.19
Matches are distributed among these distances:
7 3 0.01
8 80 0.32
9 88 0.35
10 50 0.20
11 20 0.08
12 6 0.02
13 2 0.01
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:53626 original size:27 final size:28
Alignment explanation
Indices: 53569--53665 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 28
53559 CTATTTTTAC
* * *
53569 TATTATTTTCTTTTTTTATTTATTTTGTT
1 TATTATTTTC-TTTTATATTCATTTTATT
53598 TATTATTTTC-TTTATATTCATTTTATT
1 TATTATTTTCTTTTATATTCATTTTATT
* *
53625 TATTTTATTTTATTTTATTTATCTATTTTTATT
1 TA--TTATTTTCTTTTATAT-TC-A-TTTTATT
53658 T-TTATTTT
1 TATTATTTT
53666 TTCCTTTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
27 16 0.28
29 17 0.30
30 13 0.23
31 2 0.04
32 1 0.02
33 8 0.14
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (28 bp):
TATTATTTTCTTTTATATTCATTTTATT
Found at i:53631 original size:5 final size:5
Alignment explanation
Indices: 53582--53851 Score: 88
Period size: 5 Copynumber: 53.8 Consensus size: 5
53572 TATTTTCTTT
* * *
53582 TTTTA -TTTA TTTTGT TTATTA TTTT- CTTTA TATTCA TTTTA -TTTA
1 TTTTA TTTTA TTTT-A TT-TTA TTTTA TTTTA T-TTTA TTTTA TTTTA
* *
53627 TTTTA TTTTA TTTTA -TTTA -TCTA TTTTTA TTTTTA TTTTT TCCTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTTA T--TTTA
* * * * *
53674 TTTTTTC TTTTC TTTTC TTTT- CTTTA TTTT- CTTTA TCTTTA TTTTA
1 --TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA
* *
53720 CTTTA TTTTTA TTTT- TTTGTA -TTTA TTTTA -TTTA -TTTA -TTTA TTTAA
1 TTTTA -TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* **
53767 TCTTTA TTTTTA TTTT- TTTGGTT TCTTTA TCTTTA TTTT- TTTGG TTTTA
1 T-TTTA -TTTTA TTTTA TTT--TA T-TTTA T-TTTA TTTTA TTTTA TTTTA
* * * *
53816 -TTT- TTTTA CTTTA TCTTA TTTT- CTTTA TTTCA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
53852 TTTCCTTCAT
Statistics
Matches: 204, Mismatches: 31, Indels: 60
0.69 0.11 0.20
Matches are distributed among these distances:
4 56 0.27
5 93 0.46
6 42 0.21
7 10 0.05
8 2 0.01
9 1 0.00
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:53665 original size:88 final size:84
Alignment explanation
Indices: 53526--53764 Score: 206
Period size: 83 Copynumber: 2.8 Consensus size: 84
53516 ATCTTTTACA
* * * * * * *
53526 TTTATTTA-TTTATTTA-TTTA-TTCATTGTATATA-CTATTTTTACTATTATTTTCTTTTTTTA
1 TTTATTCATTTTATTTATTTTATTTTATTTTATTTATCTATTTTTATTTTTATTTT-TTTATTTA
*
53587 TTTATTTTGTTTATTATTTTCT
65 TTTATTTT-CTT-TTATTTTCT
**
53609 TTATATTCATTTTATTTATTTTATTTTATTTTATTTATCTATTTTTATTTTTATTTTTTCCTTTA
1 TT-TATTCATTTTATTTATTTTATTTTATTTTATTTATCTATTTTTATTTTTATTTTTTTATTTA
*
53674 -TT-TTTTCTTTTCTTTTCT
65 TTTATTTTCTTTTATTTTCT
* * * * *
53692 TTTCTTTATTTTCTTTATCTTTATTTTACTTTATTT-T-TATTTTTTTGTATTTATTTTATTTAT
1 TTTATTCATTTTATTTAT-TTTATTTTATTTTATTTATCTATTTTTAT-T-TTTATTTT-TTTAT
53755 TTATTTATTT
62 TTATTTATTT
53765 AATCTTTATT
Statistics
Matches: 128, Mismatches: 17, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
81 8 0.06
82 15 0.12
83 36 0.28
84 13 0.10
85 14 0.11
86 9 0.07
87 16 0.12
88 17 0.13
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (84 bp):
TTTATTCATTTTATTTATTTTATTTTATTTTATTTATCTATTTTTATTTTTATTTTTTTATTTAT
TTATTTTCTTTTATTTTCT
Found at i:53771 original size:88 final size:87
Alignment explanation
Indices: 53583--53823 Score: 228
Period size: 88 Copynumber: 2.8 Consensus size: 87
53573 ATTTTCTTTT
* * *
53583 TTTATTT-AT-TTTGTTTATTATTTTCTTTATATTCATTT-TATTTATTTTATTTTATTTTATTT
1 TTTATTTAATCTTTATTT-TTATTTTCTTTATTTTC-TTTATCTTTATTTTA-TTTATTTTATTT
* * * *
53645 ATCTATTTTTATTTTTATTTTTTCC
63 TTTTATATTTATTTTTATTTTTTCA
** *
53670 TTTATTTTTTCTTT-TCTTTTCTTTTCTTTATTTTCTTTATCTTTATTTTACTTTATTTTTATTT
1 TTTATTTAATCTTTAT-TTTTATTTTCTTTATTTTCTTTATCTTTATTTTA-TTTA-TTTTATTT
*
53734 TTTTGTATTTA-TTTTATTTATTT-A
63 TTTTATATTTATTTTTATTT-TTTCA
** *
53758 TTTATTTAATCTTTATTTTTATTTT-TTTGGTTTCTTTATCTTTATTTT-TTTGGTTTTATTTTT
1 TTTATTTAATCTTTATTTTTATTTTCTTTATTTTCTTTATCTTTATTTTATTT-ATTTTATTTTT
53821 TTA
65 TTA
53824 CTTTATCTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
85 15 0.12
87 31 0.24
88 59 0.46
89 24 0.19
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.76
Consensus pattern (87 bp):
TTTATTTAATCTTTATTTTTATTTTCTTTATTTTCTTTATCTTTATTTTATTTATTTTATTTTTT
TATATTTATTTTTATTTTTTCA
Found at i:53772 original size:23 final size:19
Alignment explanation
Indices: 53579--53777 Score: 67
Period size: 19 Copynumber: 10.2 Consensus size: 19
53569 TATTATTTTC
*
53579 TTTTTT-TATTTATTTTGT
1 TTTTTTGTATTTATTTTAT
* * *
53597 TTATTATTTTCTTTATATTCAT
1 TT-TT-TTGTATTTAT-TTTAT
*
53619 TTTATT-TATTTTATTTTAT
1 TTTTTTGTA-TTTATTTTAT
* *
53638 TTTATT-TATCTATTTTTAT
1 TTTTTTGTATTTA-TTTTAT
**
53657 TTTTATT-T-TTTCCTTTA-
1 TTTT-TTGTATTTATTTTAT
* * *
53674 TTTTTTCT-TTTCTTTTCT
1 TTTTTTGTATTTATTTTAT
*
53692 TTTCTT-TATTT-TCTTTAT
1 TTTTTTGTATTTAT-TTTAT
53710 CTTTATTT-TACTTTATTTTTAT
1 -TTT-TTTGTA-TTTA-TTTTAT
53732 TTTTTTGTATTTATTTTAT
1 TTTTTTGTATTTATTTTAT
*
53751 TTATTTATTTATTTAATCTTTAT
1 TT-TTT-TGTATTT-AT-TTTAT
53774 TTTT
1 TTTT
53778 ATTTTTTTGG
Statistics
Matches: 143, Mismatches: 17, Indels: 38
0.72 0.09 0.19
Matches are distributed among these distances:
16 2 0.01
17 14 0.10
18 21 0.15
19 37 0.26
20 26 0.18
21 21 0.15
22 14 0.10
23 8 0.06
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.76
Consensus pattern (19 bp):
TTTTTTGTATTTATTTTAT
Found at i:53777 original size:29 final size:29
Alignment explanation
Indices: 53581--53873 Score: 94
Period size: 28 Copynumber: 10.4 Consensus size: 29
53571 TTATTTTCTT
* *
53581 TTTTTATTTATTTTGTTTATTATTTTCTTTA
1 TTTTTATTTA-TTTATTTATT-TTATCTTTA
* *
53612 TATTCATTTTATTTATTTTATTTTAT-TTTA
1 TTTTTA-TTTATTTA-TTTATTTTATCTTTA
* *
53642 TTTATCTATTT-TTATTTTTATTTTTTCCTTTA
1 TTT-T-TATTTATT-TATTTATTTTAT-CTTTA
* *
53674 TTTTT-TCT-TTTCTTT-TCTTT-TCTTTA
1 TTTTTATTTATTTATTTAT-TTTATCTTTA
* *
53700 -TTTTCTTTA--TCTTTATTTTA-CTTTA
1 TTTTTATTTATTTATTTATTTTATCTTTA
*
53725 TTTTTATTT-TTT-TGTA-TTTAT-TTTA
1 TTTTTATTTATTTATTTATTTTATCTTTA
*
53750 --TTTATTTATTTATTTAATCTTTATTTTTA
1 TTTTTATTTATTTATTT-AT-TTTATCTTTA
** *
53779 TTTTT-TTGGTTTCTTTATCTTTAT-TTT-
1 TTTTTATTTATTTATTTAT-TTTATCTTTA
* * *
53806 TTTGGT-TTTATTTTTTTACTTTATC-TTA
1 TTT-TTATTTATTTATTTATTTTATCTTTA
* * *
53834 -TTTTCTTTATTTCATTT-TTTT-CCTTCA
1 TTTTTATTTATTT-ATTTATTTTATCTTTA
*
53861 TTTTTCTTTATTT
1 TTTTTATTTATTT
53874 TTGTTTTCAT
Statistics
Matches: 204, Mismatches: 27, Indels: 65
0.69 0.09 0.22
Matches are distributed among these distances:
23 7 0.03
24 3 0.01
25 27 0.13
26 21 0.10
27 27 0.13
28 40 0.20
29 16 0.08
30 26 0.13
31 19 0.09
32 18 0.09
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (29 bp):
TTTTTATTTATTTATTTATTTTATCTTTA
Found at i:53793 original size:23 final size:23
Alignment explanation
Indices: 53720--53813 Score: 91
Period size: 23 Copynumber: 4.0 Consensus size: 23
53710 CTTTATTTTA
*
53720 CTTTATTTTTATTTTTTTGTATTT
1 CTTTATTTTTATTTTTTTG-GTTT
* * * **
53744 ATTT-TATTTATTTATTTATTTAAT
1 CTTTATTTTTATTTTTTTGGTT--T
53768 CTTTATTTTTATTTTTTTGGTTT
1 CTTTATTTTTATTTTTTTGGTTT
*
53791 CTTTATCTTTATTTTTTTGGTTT
1 CTTTATTTTTATTTTTTTGGTTT
53814 TATTTTTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.04
23 34 0.61
24 7 0.12
25 13 0.23
ACGTcount: A:0.15, C:0.04, G:0.05, T:0.76
Consensus pattern (23 bp):
CTTTATTTTTATTTTTTTGGTTT
Found at i:53795 original size:71 final size:69
Alignment explanation
Indices: 53720--53854 Score: 186
Period size: 71 Copynumber: 1.9 Consensus size: 69
53710 CTTTATTTTA
* *
53720 CTTTATTTTTATTTTTTT-GTATTTATTTTATTTA-TTTAT-TTATTTAATCTTTATTTTTATTT
1 CTTTATCTTTATTTTTTTGGT-TTTATTTT-TTTACTTTATCTTATTT--TCTTTA-TTTCATTT
53782 TTTTGGTTT
61 TTTTGGTTT
53791 CTTTATCTTTATTTTTTTGGTTTTATTTTTTTACTTTATCTTATTTTCTTTATTTCATTTTTTT
1 CTTTATCTTTATTTTTTTGGTTTTATTTTTTTACTTTATCTTATTTTCTTTATTTCATTTTTTT
53855 CCTTCATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
69 11 0.19
70 10 0.17
71 30 0.51
72 8 0.14
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.76
Consensus pattern (69 bp):
CTTTATCTTTATTTTTTTGGTTTTATTTTTTTACTTTATCTTATTTTCTTTATTTCATTTTTTTG
GTTT
Found at i:53802 original size:48 final size:48
Alignment explanation
Indices: 53692--53804 Score: 133
Period size: 48 Copynumber: 2.3 Consensus size: 48
53682 TTTCTTTTCT
* *
53692 TTTCTTTATTTTCTTTATCTTTATTTTACTTTATTTTTATTTTTTTGTA
1 TTTCTTTATTTTATTTA-CTTTATTTAACTTTATTTTTATTTTTTTGTA
* *
53741 TTTATTT-TATTTATTTA-TTTATTTAATCTTTATTTTTATTTTTTTG-G
1 TTTCTTTAT-TTTATTTACTTTATTTAA-CTTTATTTTTATTTTTTTGTA
53788 TTTCTTTATCTTTATTT
1 TTTCTTTAT-TTTATTT
53805 TTTTGGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
47 14 0.25
48 28 0.51
49 13 0.24
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (48 bp):
TTTCTTTATTTTATTTACTTTATTTAACTTTATTTTTATTTTTTTGTA
Found at i:55441 original size:11 final size:11
Alignment explanation
Indices: 55409--55442 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
55399 AATCCTAGTG
55409 AAAAATATTTA
1 AAAAATATTTA
*
55420 AAAAACA-TTA
1 AAAAATATTTA
55430 AAAAATATTTA
1 AAAAATATTTA
55441 AA
1 AA
55443 TATAATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAATATTTA
Found at i:56128 original size:17 final size:17
Alignment explanation
Indices: 56098--56197 Score: 101
Period size: 17 Copynumber: 5.8 Consensus size: 17
56088 ATGTGTCAGT
*
56098 TAACTGTAAAACATATGA
1 TAACTGT-AAACATCTGA
** *
56116 TATTTGTAAACATTTGA
1 TAACTGTAAACATCTGA
*
56133 TAACTATAAACATCTGA
1 TAACTGTAAACATCTGA
* *
56150 TATCTGTAAATATCTGA
1 TAACTGTAAACATCTGA
*
56167 TAACTGAAAATCATCTGA
1 TAACTGTAAA-CATCTGA
*
56185 TAATTGTAAACAT
1 TAACTGTAAACAT
56198 TTAGAATCCA
Statistics
Matches: 66, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
17 47 0.71
18 19 0.29
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TAACTGTAAACATCTGA
Found at i:56144 original size:34 final size:34
Alignment explanation
Indices: 56098--56199 Score: 125
Period size: 34 Copynumber: 2.9 Consensus size: 34
56088 ATGTGTCAGT
*
56098 TAACTGTAAAACATATGATATTTGTAAACATTTGA
1 TAACTG-AAAACATCTGATATTTGTAAACATTTGA
* * *
56133 TAACT-ATAAACATCTGATATCTGTAAATATCTGA
1 TAACTGA-AAACATCTGATATTTGTAAACATTTGA
*
56167 TAACTGAAAATCATCTGATAATTGTAAACATTT
1 TAACTGAAAA-CATCTGATATTTGTAAACATTT
56200 AGAATCCATC
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
33 1 0.02
34 31 0.55
35 24 0.43
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (34 bp):
TAACTGAAAACATCTGATATTTGTAAACATTTGA
Found at i:68142 original size:13 final size:13
Alignment explanation
Indices: 68120--68169 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
68110 AATGATAAAT
68120 AATAAAAAAATTAC
1 AATAAAAAAA-TAC
*
68134 AATAAAAAAATCC
1 AATAAAAAAATAC
* *
68147 AATAAACAACTAC
1 AATAAAAAAATAC
68160 AATAAAAAAA
1 AATAAAAAAA
68170 ATACTAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (13 bp):
AATAAAAAAATAC
Found at i:68199 original size:21 final size:21
Alignment explanation
Indices: 68157--68199 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
68147 AATAAACAAC
*
68157 TACAATAAAAAAAATACTAAA
1 TACAATAAAAAAAATACAAAA
*
68178 TACAAGTATAAAAAA-ACAAAA
1 TACAA-TAAAAAAAATACAAAA
68199 T
1 T
68200 CTATCGATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (21 bp):
TACAATAAAAAAAATACAAAA
Found at i:74893 original size:28 final size:28
Alignment explanation
Indices: 74858--74917 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
74848 TAGTTGTGTG
*
74858 TTTCATACTCTCGTGCTTTTGTTTTATC
1 TTTCATACTCTCCTGCTTTTGTTTTATC
74886 TTTCATACTCTCCTGCTTTTGTTTTATC
1 TTTCATACTCTCCTGCTTTTGTTTTATC
74914 TTTC
1 TTTC
74918 TCACCAGCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.10, C:0.23, G:0.08, T:0.58
Consensus pattern (28 bp):
TTTCATACTCTCCTGCTTTTGTTTTATC
Found at i:80667 original size:19 final size:19
Alignment explanation
Indices: 80616--80668 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
80606 AAAATCCATT
80616 TAAAGTAGATTTTTTTACA
1 TAAAGTAGATTTTTTTACA
80635 TAAA-T-GATTATTTTATTA-A
1 TAAAGTAGA-T-TTTT-TTACA
80654 TAAAGTAGATTTTTT
1 TAAAGTAGATTTTTT
80669 ACCTATTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
17 2 0.07
18 3 0.10
19 17 0.59
20 5 0.17
21 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (19 bp):
TAAAGTAGATTTTTTTACA
Found at i:82436 original size:74 final size:73
Alignment explanation
Indices: 82271--82594 Score: 390
Period size: 74 Copynumber: 4.5 Consensus size: 73
82261 ATGTAATAGA
* * *
82271 TATTTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTATATTATTAGTAATC-TGTAAAC
1 TATTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTATTAGCAA-CAT-TAAAA
*
82335 AAACCGGTAGT
63 AAACCGGTAGG
* * *
82346 TATTTTGATGTAATAGGTAGCGTCTATTTTTTTTACCGTTTATATTATTAGCAACATTAAAAAAA
1 TATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACATT-AAAAAA
*
82411 ACCAGTAGG
65 ACCGGTAGG
* * * * * *
82420 TAGTTTAATGTTATAGGTAACACCTA-TTTTTTTACCGTTTACATTATTAACAACCTTAGAAAAA
1 TATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACATTA-AAAAA
*
82484 ACCGGTAAG
65 ACCGGTAGG
* *
82493 TATTTTAATGTAACAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTA-CAACA-T-CAAAAA
1 TATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACATTAAAAAAA
82555 CCGGTAGG
66 CCGGTAGG
* *
82563 TATTTTAAAGT-ATAGGTAGCGTCTATTTTTTT
1 TATTTTAATGTAATAGGTAGCGCCTATTTTTTT
Statistics
Matches: 217, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
69 19 0.09
70 22 0.10
72 2 0.01
73 67 0.31
74 79 0.36
75 28 0.13
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (73 bp):
TATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACATTAAAAAAA
CCGGTAGG
Found at i:82490 original size:147 final size:148
Alignment explanation
Indices: 82274--82554 Score: 390
Period size: 147 Copynumber: 1.9 Consensus size: 148
82264 TAATAGATAT
* * * ** * *
82274 TTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTATATTATTAGTAATCTGTAAACAAAC
1 TTTAATGTAATAGGTAACACCTATTTTATTTTACCGTTTACATTATTAACAACCTGTAAAAAAAC
* * * *
82339 CGGT-AGTTATTTTGATGTAATAGGTAGCGTCTATTTTTTTTACCGTTTATATTATTAGCAACAT
66 CGGTAAG-TATTTTAATGTAACAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTA-CAACAT
*
82403 TAAAAAAAACCAGTAGGTAG
129 CAAAAAAAACCAGTAGGTAG
*
82423 TTTAATGTTATAGGTAACACCTA-TTT-TTTTACCGTTTACATTATTAACAACCT-TAGAAAAAA
1 TTTAATGTAATAGGTAACACCTATTTTATTTTACCGTTTACATTATTAACAACCTGTA-AAAAAA
82485 CCGGTAAGTATTTTAATGTAACAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTACAACATC
65 CCGGTAAGTATTTTAATGTAACAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTACAACATC
82550 AAAAA
130 AAAAA
82555 CCGGTAGGTA
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
146 13 0.11
147 79 0.68
148 5 0.04
149 20 0.17
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (148 bp):
TTTAATGTAATAGGTAACACCTATTTTATTTTACCGTTTACATTATTAACAACCTGTAAAAAAAC
CGGTAAGTATTTTAATGTAACAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTACAACATCA
AAAAAAACCAGTAGGTAG
Done.