Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1482
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: 284187
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:179634 original size:26 final size:26
Alignment explanation
Indices: 179587--179643 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
179577 TAGACTTTGT
* * **
179587 ATCATGCAACCATGATAGCATTCCAC
1 ATCATGCAACCATAATACCATTAAAC
**
179613 ATCATGCATTCATAATACCATTAAAC
1 ATCATGCAACCATAATACCATTAAAC
179639 ATCAT
1 ATCAT
179644 TATTTTTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (26 bp):
ATCATGCAACCATAATACCATTAAAC
Found at i:179866 original size:28 final size:28
Alignment explanation
Indices: 179834--180306 Score: 422
Period size: 28 Copynumber: 16.8 Consensus size: 28
179824 TCATCTCTTG
* *
179834 AAAGCCCACAAGTCATTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
* *
179862 AAAGCCCATAAGTCAGTGGCA-TCTCTTC
1 AAAGCCCACAAGTCAGTGGCACCCT-TTC
* * * *
179890 AATGCCTACAAGTCAATGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
* ***
179918 AAAGTCCACAAGTC-GATGGCATATTTTC
1 AAAGCCCACAAGTCAG-TGGCACCCTTTC
* * *
179946 AAAGCCCATAAGTCCGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
* *
179974 AAAGTCCACAAGTCAGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
* * *
180002 TAAGCCTACAAGTCGGTGGCA-CCTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTT-C
* *
180030 AAAGCCCATAAG-CAAGTGGCACCCTTTT
1 AAAGCCCACAAGTC-AGTGGCACCCTTTC
* * *
180058 TAAGCCCACAAGTCGGTGGCACCCTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
*
180086 AAAGCCCACAAG-CAAGTGGCACCCTTTT
1 AAAGCCCACAAGTC-AGTGGCACCCTTTC
* * *
180114 TAAGCCCACAAGTCAGTGGCACTCTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
*
180142 AAAGCCCACAAG-CAAGTGGCACCCTTTT
1 AAAGCCCACAAGTC-AGTGGCACCCTTTC
* * *
180170 TAAGCCCA-TAGCTCAGTGGCACCCTTCC
1 AAAGCCCACAAG-TCAGTGGCACCCTTTC
*
180198 AAAGCCCACAAG-CAAGTGGCACCCTTTT
1 AAAGCCCACAAGTC-AGTGGCACCCTTTC
* * * *
180226 TAAGCCCATAAGTCAATGGCACCCTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
*
180254 AAAGCCCACAGGTCAGTGGCACCTCTTTTC
1 AAAGCCCACAAGTCAGTGGCACC-C-TTTC
*
180284 AAAGTCCACACAAGTCGGTGGCA
1 AAAG-CC-CACAAGTCAGTGGCA
180307 ACTTTTTTCA
Statistics
Matches: 355, Mismatches: 70, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
27 13 0.04
28 305 0.86
29 15 0.04
30 7 0.02
31 2 0.01
32 13 0.04
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTC
Found at i:179911 original size:56 final size:56
Alignment explanation
Indices: 179835--180306 Score: 499
Period size: 56 Copynumber: 8.4 Consensus size: 56
179825 CATCTCTTGA
* * * * * * *
179835 AAGCCCACAAGTCATTGGCATCCTTTCAAAGCCCATAAGTC-AGTGGCA-TCTCTTC
1 AAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAG-CAAGTGGCACCCTTTTT
* * * * * * ** *
179890 AATGCCTACAAGTCAATGGCATCCTTTCAAAGTCCACAAGTCGA-TGGCA-TATTTTCA
1 AA-GCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAG-CAAGTGGCACCCTTTT-T
* * * * *
179947 AAGCCCATAAGTCCGTGGCATCCTTTCAAAGTCCACAAGTC-AGTGGCACCCTTTTT
1 AAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAG-CAAGTGGCACCCTTTTT
* * * *
180003 AAGCCTACAAGTCGGTGGCACCTTTCCAAAGCCCATAAGCAAGTGGCACCCTTTTT
1 AAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTT
*
180059 AAGCCCACAAGTCGGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTT
1 AAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTT
*
180115 AAGCCCACAAGTCAGTGGCACTCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTT
1 AAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTT
*
180171 AAGCCCA-TAGCTCAGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTT
1 AAGCCCACAAG-TCAGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTT
* * * *
180227 AAGCCCATAAGTCAATGGCACCCTTCCAAAGCCCACAGGTC-AGTGGCACCTCTTTTCA
1 AAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAG-CAAGTGGCACC-CTTTT-T
*
180285 AAGTCCACACAAGTCGGTGGCA
1 AAG-CC-CACAAGTCAGTGGCA
180307 ACTTTTTTCA
Statistics
Matches: 368, Mismatches: 36, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
55 6 0.02
56 330 0.90
57 15 0.04
58 3 0.01
59 2 0.01
60 12 0.03
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (56 bp):
AAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAGCAAGTGGCACCCTTTTT
Found at i:180315 original size:32 final size:32
Alignment explanation
Indices: 180253--180362 Score: 106
Period size: 32 Copynumber: 3.5 Consensus size: 32
180243 GGCACCCTTC
* * * *
180253 CAAAGCC--CACAGGTCAGTGGCACCTCTTTT
1 CAAAGCCTACACAAGTCGGTGGCAACTTTTTT
180283 CAAAGTCC-ACACAAGTCGGTGGCAACTTTTTT
1 CAAAG-CCTACACAAGTCGGTGGCAACTTTTTT
180315 C-AAGCCTACACAAGTCGGTGGC-ACTAATTTTT
1 CAAAGCCTACACAAGTCGGTGGCAACT--TTTTT
180347 -AAAGGCCTACACAAGT
1 CAAA-GCCTACACAAGT
180363 TAGTAGCAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
30 10 0.14
31 20 0.29
32 27 0.39
33 12 0.17
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (32 bp):
CAAAGCCTACACAAGTCGGTGGCAACTTTTTT
Found at i:180355 original size:33 final size:31
Alignment explanation
Indices: 180260--180362 Score: 102
Period size: 31 Copynumber: 3.2 Consensus size: 31
180250 TTCCAAAGCC
* * * *
180260 CACAGGTCAGTGGCACCTCTTTTCAAAGTCC-A
1 CACAAGTCGGTGGCAACT-TTTTTAAAG-CCTA
*
180292 CACAAGTCGGTGGCAACTTTTTTCAAGCCTA
1 CACAAGTCGGTGGCAACTTTTTTAAAGCCTA
180323 CACAAGTCGGTGGC-ACTAATTTTTAAAGGCCTA
1 CACAAGTCGGTGGCAACT--TTTTTAAA-GCCTA
180356 CACAAGT
1 CACAAGT
180363 TAGTAGCAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
30 5 0.08
31 22 0.36
32 22 0.36
33 12 0.20
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (31 bp):
CACAAGTCGGTGGCAACTTTTTTAAAGCCTA
Found at i:185196 original size:96 final size:96
Alignment explanation
Indices: 184978--185202 Score: 229
Period size: 96 Copynumber: 2.3 Consensus size: 96
184968 AAAAATGGGG
* * * ** * * *
184978 AGTATCTCTTCATAAGAATGGGGTTGGATGTCCTTGACGATCATAATTTAGGCAAAACTTAGATT
1 AGTATCCCTTCAAAAGAATGGGGTTGGATATCCTCAACGATCACAATTTAAGCAAAACTAAGATT
* *
185043 CAAATCTTAACAAGTTTAAAAACAGGGTTGG
66 CAAATCTTAACAAGTTTAAAAACAAGGTTGA
* * * * *
185074 AGTATCCCCTT-AGAAGGATGGAGTTGGAGTATCCTCAATGATGACAATTTAAGCAAAA-TAAGA
1 AGTAT-CCCTTCAAAAGAATGGGGTTGGA-TATCCTCAACGATCACAATTTAAGCAAAACTAAGA
* * * * *
185137 TTTAAATCTTGACGAGTTTAAGAATAAGGTTGA
64 TTCAAATCTTAACAAGTTTAAAAACAAGGTTGA
185170 AGTATCCCTTCAAAAGAATGGGGTTGGAATATC
1 AGTATCCCTTCAAAAGAATGGGGTTGG-ATATC
185203 TCGATAAATG
Statistics
Matches: 103, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
95 5 0.05
96 71 0.69
97 27 0.26
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.30
Consensus pattern (96 bp):
AGTATCCCTTCAAAAGAATGGGGTTGGATATCCTCAACGATCACAATTTAAGCAAAACTAAGATT
CAAATCTTAACAAGTTTAAAAACAAGGTTGA
Found at i:186485 original size:21 final size:19
Alignment explanation
Indices: 186452--186491 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
186442 CGGAGATGTT
186452 GAACAAGTCAAAATGCATG
1 GAACAAGTCAAAATGCATG
186471 GAACATAGTACAAAATGCATG
1 GAACA-AGT-CAAAATGCATG
186492 ATCAAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 11 0.58
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.17
Consensus pattern (19 bp):
GAACAAGTCAAAATGCATG
Found at i:187388 original size:52 final size:51
Alignment explanation
Indices: 187331--187470 Score: 181
Period size: 52 Copynumber: 2.7 Consensus size: 51
187321 AATTGCCTGC
* * * *
187331 ATGTATTAATACATTGAAGAATGTATCGATATATTTGGGTTAAAAATCCAAA
1 ATGTATTGATACA-TGAAAAATGTATCGATACATTTGGGTTAAAAACCCAAA
* * *
187383 ATGTATCGATACGATGAAAAATATATCAATACATTTGGGTTAAAAACCCAAA
1 ATGTATTGATAC-ATGAAAAATGTATCGATACATTTGGGTTAAAAACCCAAA
*
187435 ATGTATTGATACAATAAAAAATGTATCGATACATTT
1 ATGTATTGATAC-ATGAAAAATGTATCGATACATTT
187471 TTTTTCTAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
52 74 0.99
53 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (51 bp):
ATGTATTGATACATGAAAAATGTATCGATACATTTGGGTTAAAAACCCAAA
Found at i:189233 original size:6 final size:6
Alignment explanation
Indices: 189205--189283 Score: 54
Period size: 6 Copynumber: 12.5 Consensus size: 6
189195 CCCTTTAAAT
* * *
189205 AAGAAA TAGAAA AA-CAA AA-AAA AAGAAA AAGAAA GAGAAA AATGAAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA-G-AAA
*
189253 AAGAAGA AAGCATAA AATGAAA AAAAAA AAG
1 AAGAA-A AAG-A-AA AA-GAAA AAGAAA AAG
189284 TGCAGATAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
5 8 0.14
6 28 0.48
7 10 0.17
8 10 0.17
9 2 0.03
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:189237 original size:28 final size:29
Alignment explanation
Indices: 189205--189261 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
189195 CCCTTTAAAT
*
189205 AAGAAATAGAAAAA-CAAAAAAAAAGAAA
1 AAGAAAGAGAAAAATCAAAAAAAAAGAAA
* *
189233 AAGAAAGAGAAAAATGAAAAAAGAAGAAA
1 AAGAAAGAGAAAAATCAAAAAAAAAGAAA
189262 GCATAAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (29 bp):
AAGAAAGAGAAAAATCAAAAAAAAAGAAA
Found at i:189259 original size:23 final size:23
Alignment explanation
Indices: 189233--189277 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
189223 AAAAAAGAAA
189233 AAGAAAG-AGAAAAATGAAAAAAG
1 AAGAAAGCA-AAAAATGAAAAAAG
*
189256 AAGAAAGCATAAAATGAAAAAA
1 AAGAAAGCAAAAAATGAAAAAA
189278 AAAAAGTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (23 bp):
AAGAAAGCAAAAAATGAAAAAAG
Found at i:189310 original size:11 final size:12
Alignment explanation
Indices: 189294--189327 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
189284 TGCAGATAGT
189294 AAGAAAAAAT-A
1 AAGAAAAAATGA
189305 AAGAAAAAATGA
1 AAGAAAAAATGA
189317 AA-AAAAAATGA
1 AAGAAAAAATGA
189328 CCAAATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 19 0.86
12 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (12 bp):
AAGAAAAAATGA
Found at i:192816 original size:18 final size:19
Alignment explanation
Indices: 192781--192823 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
192771 AAATGAAGTC
192781 TAATTTGATAAATAATTT-
1 TAATTTGATAAATAATTTG
** *
192799 TAATTTGATACCTGATTTG
1 TAATTTGATAAATAATTTG
192818 TAATTT
1 TAATTT
192824 TTTTTAGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (19 bp):
TAATTTGATAAATAATTTG
Found at i:195378 original size:21 final size:22
Alignment explanation
Indices: 195354--195394 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
195344 TGAAAAAGAT
*
195354 AATATTTTAAA-AATAAAATAA
1 AATATTATAAATAATAAAATAA
*
195375 AATATTATAAATATTAAAAT
1 AATATTATAAATAATAAAAT
195395 TTAAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATTATAAATAATAAAATAA
Found at i:195384 original size:15 final size:15
Alignment explanation
Indices: 195366--195407 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
195356 TATTTTAAAA
195366 ATAAAA-TAAAATATT
1 ATAAAATTAAAAT-TT
195381 ATAAATATTAAAATTT
1 ATAAA-ATTAAAATTT
195397 A-AAAATTAAAA
1 ATAAAATTAAAA
195408 AAAATTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.28
15 8 0.32
16 4 0.16
17 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAAAATTAAAATTT
Found at i:196200 original size:18 final size:18
Alignment explanation
Indices: 196179--196237 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
196169 AAAATAATAA
*
196179 TTATTTTTATTATAATTT
1 TTATTTTTATTATAAATT
196197 TTATTTTTTATTATAAATT
1 TTA-TTTTTATTATAAATT
* *
196216 TTATTATTA--ATAAAAT
1 TTATTTTTATTATAAATT
196232 TTATTT
1 TTATTT
196238 AATTTATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.31
18 8 0.22
19 17 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTTTTATTATAAATT
Found at i:196206 original size:19 final size:19
Alignment explanation
Indices: 196182--196220 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
196172 ATAATAATTA
*
196182 TTTTTATTATAATTTTTAT
1 TTTTTATTATAAATTTTAT
196201 TTTTTATTATAAATTTTAT
1 TTTTTATTATAAATTTTAT
196220 T
1 T
196221 ATTAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTATTATAAATTTTAT
Found at i:197176 original size:22 final size:22
Alignment explanation
Indices: 197140--197180 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
197130 AGCATACTTT
197140 AGTATAAAATATTTTTAAAATA
1 AGTATAAAATATTTTTAAAATA
197162 AGTA-AAAATATTTTTAAAA
1 AGTATAAAATATTTTTAAAA
197181 CCAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (22 bp):
AGTATAAAATATTTTTAAAATA
Found at i:197190 original size:22 final size:21
Alignment explanation
Indices: 197140--197190 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
197130 AGCATACTTT
*
197140 AGTATAAAATATTTTTAAAATA
1 AGTA-AAAATATTTTTAAAACA
197162 AGTAAAAATATTTTTAAAACCA
1 AGTAAAAATATTTTTAAAA-CA
197184 A-TAAAAA
1 AGTAAAAA
197191 CACTTTATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (21 bp):
AGTAAAAATATTTTTAAAACA
Found at i:199763 original size:21 final size:21
Alignment explanation
Indices: 199739--199791 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
199729 TTCAACAATT
*
199739 TGTATTGATACAATAAG-GCAA
1 TGTATCGATACAATAAGTG-AA
199760 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
199780 TGTATCGATACA
1 TGTATCGATACA
199792 TGCCTGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:199781 original size:20 final size:21
Alignment explanation
Indices: 199739--199812 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
199729 TTCAACAATT
* *
199739 TGTATTGATACAATAAG-GCAA
1 TGTATCGATAC-ATAAGTGAAA
199760 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAGTGAAA
***
199780 TGTATCGATACATGCCTGAAA
1 TGTATCGATACATAAGTGAAA
199801 TGTATCGATACA
1 TGTATCGATACA
199813 GGACCATGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.47
21 25 0.53
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATAAGTGAAA
Found at i:199804 original size:21 final size:20
Alignment explanation
Indices: 199758--199812 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
199748 ACAATAAGGC
*
199758 AATGTATCGATACATAAGTG
1 AATGTATCGATACATAACTG
**
199778 AATGTATCGATACATGCCTG
1 AATGTATCGATACATAACTG
199798 AAATGTATCGATACA
1 -AATGTATCGATACA
199813 GGACCATGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACATAACTG
Found at i:199867 original size:20 final size:20
Alignment explanation
Indices: 199842--199913 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
199832 AAGGAAATTC
199842 TATCGATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
* ****
199862 TATCGAAACA-TAAGAAATTG
1 TATCGATACATTTTTCAA-TG
* * *
199882 TATCAATACATTTTTCATTA
1 TATCGATACATTTTTCAATG
199902 TATCGATACATT
1 TATCGATACATT
199914 CTAGGTTTTG
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
19 3 0.08
20 31 0.86
21 2 0.06
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:199891 original size:40 final size:40
Alignment explanation
Indices: 199835--199912 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
199825 ATTTTGGAAG
* *
199835 GAAATTCTATCGATACATTTTTCAATGTATCGAAACATAA
1 GAAATTCTATCAATACATTTTTCAATATATCGAAACATAA
* * *
199875 GAAATTGTATCAATACATTTTTCATTATATCGATACAT
1 GAAATTCTATCAATACATTTTTCAATATATCGAAACAT
199913 TCTAGGTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.38
Consensus pattern (40 bp):
GAAATTCTATCAATACATTTTTCAATATATCGAAACATAA
Found at i:208295 original size:15 final size:17
Alignment explanation
Indices: 208270--208304 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
208260 AAGGTTAGAA
208270 TCAATTTTATTATT-TT
1 TCAATTTTATTATTATT
208286 TCAA-TTTATTATTATT
1 TCAATTTTATTATTATT
208302 TCA
1 TCA
208305 TGCACTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (17 bp):
TCAATTTTATTATTATT
Found at i:215577 original size:15 final size:15
Alignment explanation
Indices: 215533--215579 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 15
215523 TACTTATTCT
*
215533 TATCTTAAATAAATA
1 TATCCTAAATAAATA
*
215548 TATACTCAAATTAAATA
1 TATCCT-AAA-TAAATA
215565 TATCCTAAATAAATA
1 TATCCTAAATAAATA
215580 ATACAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 10 0.37
16 6 0.22
17 11 0.41
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TATCCTAAATAAATA
Found at i:219607 original size:98 final size:95
Alignment explanation
Indices: 219394--219608 Score: 270
Period size: 98 Copynumber: 2.2 Consensus size: 95
219384 TTATTCATTA
*
219394 GGGATACTCTAACCCTATTTTTGAACTTGTCAAGATTTAAATCCTTTTTTTTTTAATTATCATCA
1 GGGATACTCTAACCCTATTTTTGAACTTGTCAAGATTTAAATCCTTTTTTTTTAAATTATCATCA
* * * *
219459 TCAAGGATACTTTAACCCCATTCTTTCGAG
66 TCAAGGATACTTCAACCCCATTCCTCCAAG
* *
219489 GGGATACTCTAACCCCATTTTTGAACTTGTCAAAGATTTAAA-CCTTATTTTTGCTTAAATTGTC
1 GGGATACTCTAACCCTATTTTTGAACTTGTC-AAGATTTAAATCCTT-TTTTT--TTAAATTATC
** *
219553 ATCATCGGGGATACTTCCACCCCATTCCTCCAAG
62 ATCATCAAGGATACTTCAACCCCATTCCTCCAAG
* * *
219587 GGGATAATCCAACTCTATTTTT
1 GGGATACTCTAACCCTATTTTT
219609 AAATCAAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
95 34 0.33
96 15 0.15
98 53 0.52
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (95 bp):
GGGATACTCTAACCCTATTTTTGAACTTGTCAAGATTTAAATCCTTTTTTTTTAAATTATCATCA
TCAAGGATACTTCAACCCCATTCCTCCAAG
Found at i:219840 original size:79 final size:79
Alignment explanation
Indices: 219707--219855 Score: 237
Period size: 79 Copynumber: 1.9 Consensus size: 79
219697 TTAATTCGGT
* * * *
219707 TATCTCTAAATAATCGACCGTAATTATGAGATACGTCATGAATATCACACTTTTCTTTTTCCATT
1 TATCTCCAAATAATCGACCGCAATTACGAGATACATCATGAATATCACACTTTTCTTTTTCCATT
219772 TTGTTCAACTTAGA
66 TTGTTCAACTTAGA
*
219786 TATCTCCAAATAATCGA-CGACAATTACGAGATACATCATGAATATCACATTTTTCTTTTTCCAT
1 TATCTCCAAATAATCGACCG-CAATTACGAGATACATCATGAATATCACACTTTTCTTTTTCCAT
219850 TTTGTT
65 TTTGTT
219856 TAGCTTTGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 2 0.03
79 62 0.97
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.40
Consensus pattern (79 bp):
TATCTCCAAATAATCGACCGCAATTACGAGATACATCATGAATATCACACTTTTCTTTTTCCATT
TTGTTCAACTTAGA
Found at i:220802 original size:16 final size:16
Alignment explanation
Indices: 220781--220814 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
220771 ATATTTATTG
220781 CTAATATGATAAAGGC
1 CTAATATGATAAAGGC
*
220797 CTAATATGATAAATGC
1 CTAATATGATAAAGGC
220813 CT
1 CT
220815 GCTTTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (16 bp):
CTAATATGATAAAGGC
Found at i:226063 original size:17 final size:17
Alignment explanation
Indices: 226041--226074 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
226031 TAGTAATGTA
226041 TCGATACATAGATGTGG
1 TCGATACATAGATGTGG
226058 TCGATACATAGATGTGG
1 TCGATACATAGATGTGG
226075 GAAGGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (17 bp):
TCGATACATAGATGTGG
Found at i:226649 original size:14 final size:15
Alignment explanation
Indices: 226630--226659 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
226620 CTGTGTTTGC
226630 TTCTC-ATTTACATT
1 TTCTCAATTTACATT
226644 TTCTCAATTTACATT
1 TTCTCAATTTACATT
226659 T
1 T
226660 AAATCTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (15 bp):
TTCTCAATTTACATT
Found at i:227251 original size:19 final size:20
Alignment explanation
Indices: 227229--227275 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
227219 ACATTGTATG
*
227229 GATACATGTTC-ATTGCATC
1 GATACATGCTCAATTGCATC
* *
227248 GATACATACTCAATTGTATC
1 GATACATGCTCAATTGCATC
227268 GATACATG
1 GATACATG
227276 AAAGTGGCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (20 bp):
GATACATGCTCAATTGCATC
Found at i:227268 original size:20 final size:19
Alignment explanation
Indices: 227220--227274 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
227210 TGTATCGATA
* **
227220 CATTGTATGGATACATGTT
1 CATTGTATCGATACATACT
*
227239 CATTGCATCGATACATACT
1 CATTGTATCGATACATACT
227258 CAATTGTATCGATACAT
1 C-ATTGTATCGATACAT
227275 GAAAGTGGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:228574 original size:79 final size:79
Alignment explanation
Indices: 228443--228609 Score: 235
Period size: 79 Copynumber: 2.1 Consensus size: 79
228433 GACGGGGCTA
* * * * ***
228443 GAGTAACCCTGATTATGGAAAATCGGTGTTCTGGAAATAAAATCGGGGTTGGAGTATCCCCTTGG
1 GAGTATCCCTAATTATAGAAAATCGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTCAA
228508 AAATAACAGGGTTG
66 AAATAACAGGGTTG
* *
228522 GAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTCAA
1 GAGTATCCCTAATTATAGAAAATCGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTCAA
**
228587 AAATAATGGGGTTG
66 AAATAACAGGGTTG
228601 GAGTATCCC
1 GAGTATCCC
228610 CGCGAAAATA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (79 bp):
GAGTATCCCTAATTATAGAAAATCGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTCAA
AAATAACAGGGTTG
Found at i:228600 original size:28 final size:28
Alignment explanation
Indices: 228565--228639 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
228555 AAAATAAAAT
*
228565 CGGGGTTGGAGTATCCCCTCAAAAATAA
1 CGGGGTTGGAGTATCCCCGCAAAAATAA
* *
228593 TGGGGTTGGAGTATCCCCGCGAAAATAA
1 CGGGGTTGGAGTATCCCCGCAAAAATAA
228621 CGGGGTTGGAGTATCCCCG
1 CGGGGTTGGAGTATCCCCG
228640 ATTGTGAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.21
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGCAAAAATAA
Found at i:228676 original size:107 final size:106
Alignment explanation
Indices: 228565--228757 Score: 280
Period size: 107 Copynumber: 1.8 Consensus size: 106
228555 AAAATAAAAT
* *
228565 CGGGGTTGGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCCGCGA-AAATAACGGGGTTG
1 CGGGGTTGGAGTATCCCATCAAAAATAACGGGGTTGGAGTAT--CCGCGATAAATAACGGGGTTG
* *
228629 GAGTATCCCCGATTGTGAGAAATCAATATTTTAGGAATAAAGC
64 GAGTATCCCCGATTATGAAAAATCAATATTTTAGGAATAAAGC
** * * *
228672 CGGGGTTGGAGTATCCCATCGGAAATAACGGGGTTGGAGTATCCTCGATGATTAACGGGGTTGGA
1 CGGGGTTGGAGTATCCCATCAAAAATAACGGGGTTGGAGTATCCGCGATAAATAACGGGGTTGGA
228737 GTATCCCCGATTATGAAAAAT
66 GTATCCCCGATTATGAAAAAT
228758 TGAGAAACTT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
105 5 0.07
106 33 0.43
107 38 0.50
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.25
Consensus pattern (106 bp):
CGGGGTTGGAGTATCCCATCAAAAATAACGGGGTTGGAGTATCCGCGATAAATAACGGGGTTGGA
GTATCCCCGATTATGAAAAATCAATATTTTAGGAATAAAGC
Found at i:228747 original size:27 final size:29
Alignment explanation
Indices: 228672--228747 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 29
228662 GGAATAAAGC
228672 CGGGGTTGGAGTAT-CCC-ATCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATC-GAAATAA
* *
228700 CGGGGTTGGAGTATCCTCGAT-G-ATTAA
1 CGGGGTTGGAGTATCCCCGATCGAAATAA
228727 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
228748 TATGAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 24 0.56
28 15 0.35
29 2 0.05
30 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.25
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCCCGATCGAAATAA
Found at i:231379 original size:28 final size:28
Alignment explanation
Indices: 231318--231399 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
231308 TTTTGGAGAT
*
231318 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGGGGTTGGAGT-ATCCC-CGATGA
*
231346 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGGGGTTGGAGTATCCCCGATGA
* *
231374 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
231400 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 4 0.09
28 41 0.87
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCCCGATGA
Found at i:231541 original size:51 final size:51
Alignment explanation
Indices: 231379--231551 Score: 204
Period size: 52 Copynumber: 3.4 Consensus size: 51
231369 GATGAAATAA
* *
231379 CGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAAT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAAT
* * * * *
231431 CG-GTGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGAG-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAAT
* *** *
231483 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAAT
231534 CGAGGTTGGAGTATCCCC
1 CGAGGTTGGAGTATCCCC
231552 TCGGAAATAA
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
51 38 0.38
52 52 0.51
53 11 0.11
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAAT
Found at i:231660 original size:54 final size:51
Alignment explanation
Indices: 231593--231727 Score: 150
Period size: 51 Copynumber: 2.6 Consensus size: 51
231583 GATTAACGGG
*
231593 GTTGGAATGTCCCCGATTGTGAAGAAATTGATGTTTTTTGGAAA-TAAAATCGGA
1 GTTGGAATATCCCCGATTGTG-AGAAATTGATG--TTTT-GAAAGTAAAATCGGA
* * *
231647 GTTGGAGTATCCCCGATTAT-AGAAAATTAATGTTTTGAAAGTAAAATCGGA
1 GTTGGAATATCCCCGATTGTGAG-AAATTGATGTTTTGAAAGTAAAATCGGA
*
231698 GTTGGAATATCCTCGATTGTG-GAGAATTGA
1 GTTGGAATATCCCCGATTGTGAGA-AATTGA
231728 GCAAATCAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
50 5 0.07
51 37 0.54
52 2 0.03
53 8 0.12
54 17 0.25
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (51 bp):
GTTGGAATATCCCCGATTGTGAGAAATTGATGTTTTGAAAGTAAAATCGGA
Found at i:231674 original size:211 final size:211
Alignment explanation
Indices: 231326--231715 Score: 579
Period size: 211 Copynumber: 1.8 Consensus size: 211
231316 ATAATAACGG
* * * *
231326 GGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
1 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAAT
* *
231391 ATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATTAAA
66 ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
** * *
231456 GGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATT
131 GGAAAATTAATGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAATATT
231521 TTGGAAATAAAGTCGA
196 TTGGAAATAAAGTCGA
* *
231537 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAAT
1 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAAT
*
231601 GTCCCCGATTGTGAAGAAATTGATGT-TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
66 ATCCCCGATTGTGAA-AAATTG--GTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
* * * *
231665 ATA-GAAAATTAATGTTTTGAAAGTAAAATCGGAGTTGGAATATCCTCGATT
128 AAAGGAAAATTAATGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATT
231716 GTGGAGAATT
Statistics
Matches: 159, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
210 27 0.17
211 91 0.57
212 39 0.25
213 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (211 bp):
GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAAT
ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
GGAAAATTAATGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAATATT
TTGGAAATAAAGTCGA
Found at i:234087 original size:20 final size:20
Alignment explanation
Indices: 234060--234114 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
234050 TAAAATTTCC
*
234060 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
234080 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
234100 AAATGTATCGATACA
1 AAATGTATCGATACA
234115 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:234158 original size:19 final size:18
Alignment explanation
Indices: 234134--234201 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
234124 CAGTAGCTAA
234134 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
234153 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
234168 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
234185 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
234202 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:234174 original size:13 final size:13
Alignment explanation
Indices: 234156--234180 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234146 ACAATACTTA
234156 TGTATCGATACAT
1 TGTATCGATACAT
234169 TGTATCGATACA
1 TGTATCGATACA
234181 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:234178 original size:32 final size:32
Alignment explanation
Indices: 234137--234199 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
234127 TAGCTAATTA
*
234137 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
234169 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
234200 AATCGTTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:235288 original size:13 final size:13
Alignment explanation
Indices: 235270--235294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
235260 ACAAAGATTG
235270 ATGTATCGATACC
1 ATGTATCGATACC
235283 ATGTATCGATAC
1 ATGTATCGATAC
235295 ATTGAATAAT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACC
Found at i:245008 original size:18 final size:18
Alignment explanation
Indices: 244991--245024 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
244981 ATATTTTAAT
244991 TAAATTTTA-TTAAATAA
1 TAAATTTTATTTAAATAA
*
245008 TAATTTTTATTTAAATA
1 TAAATTTTATTTAAATA
245025 TTTATATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAATTTTATTTAAATAA
Found at i:246935 original size:826 final size:828
Alignment explanation
Indices: 244999--247466 Score: 4621
Period size: 834 Copynumber: 3.0 Consensus size: 828
244989 ATTAAATTTT
244999 ATTAAA-T-AATAATTTTTATTTAAATATTTATATAGAATTGGATGCAAATTTTAAATTAATTCG
1 ATTAAATTAAATAATTTTTATTTAAATATTTATATAGAATTGGATGCAAATTTTAAATTAATTCG
*
245062 TGAGTTAATATACAGATCAATTAGTTTAAATTTATCATTTAGAAATAAAGTGAAAATAATTAATC
66 TGAGTTAATATACAGATCAATTAGTTTAAATATATCATTTAGAAATAAAGTGAAAATAATTAATC
245127 AGAGAAATTTATGTTTAAAACCTTTTTCCAAGTGAGTTAAGTATGAATTCTTAATCAATATGCAA
131 AGAGAAATTTATGTTTAAAACCTTTTTCCAAGTGAGTTAAGTATGAATTCTTAATCAATATGCAA
245192 GCTAATATATGTATATCAATCCCTTTAATTAAATCATTTTATTTAAATTTTTTTCAAGCAAGTTG
196 GCTAATATATGTATATCAATCCCTTTAATTAAATCATTTTATTTAAATTTTTTTCAAGCAAGTTG
*
245257 AGTATAGATTTTCTATTGATTCGCGAATCAACTTTTGAATTAACCGTTTTGAATATGTCATTTTA
261 AGTATAGGTTTTCTATTGATTCGCGAATCAACTTTTGAATTAACCGTTTTGAATATGTCATTTTA
245322 AAAAGTAAAATGAAATAATTAATAAAATAATTTCTTAAACTTTTTCTTAAGCATAGATTCTAAAT
326 AAAAGTAAAATGAAATAATTAATAAAATAATTTCTTAAA-TTTTTCTTAAGCATAGATTCTAAAT
245387 CAACCTTTGATTCAATCTCAAGATTAATTTTTTAAATACATTATTTAAAAATTAAATAAAAATAA
390 CAACCTTTGATTCAATCTCAAGATTAATTTTTTAAATACATTATTTAAAAATTAAATAAAAATAA
245452 TTACATAATAAAATAACTTTTTAATTTTTTCTTGTTTGTTAAGTTCGTATCTTAAATGAACCAAC
455 TTACATAATAAAATAACTTTTTAATTTTTTCTTGTTTGTTAAGTTCGTATCTTAAATGAACCAAC
* *
245517 GGATCATATATAAAACAACTCCTTCAAATAAATCATTTAAACATAAAATAAAAAAAAAAGTGAAT
520 AGATCATATATAAAATAACTCCTTCAAATAAATCATTTAAACATAAAAT--AAAAAAAAGTGAAT
245582 ATAAAAAACTAAAAATAATTAATAAAATAATTTTTATTTTTTTGAATAGATTGAGTACAGATTCT
583 ATAAAAAACTAAAAATAATTAATAAAATAA-TTTT-TTTTTTTGAATAGATTGAGTACAGATTCT
245647 AAATCGACTTATAAGTTGTGCAAATCAGCTCCTTTAAATACATTATTGAAAAATAAAATAAAAAT
646 AAATCGACTTATAAGTTGTGCAAATCAGCTCCTTTAAATACATTATTGAAAAATAAAATAAAAAT
245712 TTGAAATCAAAAAAGCTAAAACTAATTAAGTTTTTTTTCTAAGTAAATTGAGTAGAGATTTTAAT
711 TTGAAATC-AAAAAGCTAAAACTAATTAAGTTTTTTTTCTAAGTAAATTGAGTAGAGATTTTAAT
245777 TTGATCGTGAGTTAAATTACAAATCAATTCTTTAAATTAAATTAATTAGTTTAA
775 TTGATCGTGAGTTAAATTACAAATCAATTCTTTAAATTAAATTAATTAGTTTAA
245831 ATTAAATTAAATAATTTTTATTTAAATATTTATATAGAATTGGATGCAAATTTTAAATTAATTCG
1 ATTAAATTAAATAATTTTTATTTAAATATTTATATAGAATTGGATGCAAATTTTAAATTAATTCG
245896 TGAGTTAATATACAGATCAATTAGTTTAAATATATCATTTAGAAATAAAGTGAAAATAATTAATC
66 TGAGTTAATATACAGATCAATTAGTTTAAATATATCATTTAGAAATAAAGTGAAAATAATTAATC
*
245961 AGAGAAATTTATGTTTAAAACCTTTTTCCAAGTGAGTTAAGCATGAATTCTTAATCAATATGCAA
131 AGAGAAATTTATGTTTAAAACCTTTTTCCAAGTGAGTTAAGTATGAATTCTTAATCAATATGCAA
246026 GCTAATATATGTATATCAATCCCTTTAATTAAATCATTTTATTTAAATTTTTTTCAAGCAAGTTG
196 GCTAATATATGTATATCAATCCCTTTAATTAAATCATTTTATTTAAATTTTTTTCAAGCAAGTTG
*
246091 AGTATAGGTTTTCTATTGATTCGCGAATCAATTTTTGAATTAACCGTTTTGAATATGTCATTTTA
261 AGTATAGGTTTTCTATTGATTCGCGAATCAACTTTTGAATTAACCGTTTTGAATATGTCATTTTA
*
246156 AAAAGTAAAATGAAATAATTAATAAAATAATTTCTTAAATTTTTTCTTAAGTATAGATTCTAAAT
326 AAAAGTAAAATGAAATAATTAATAAAATAATTTCTTAAA-TTTTTCTTAAGCATAGATTCTAAAT
246221 CAACCTTTGATTCAATCTCAAGATTAATTTTTTAAATACATTATTTAAAAATTAAATAAAAATAA
390 CAACCTTTGATTCAATCTCAAGATTAATTTTTTAAATACATTATTTAAAAATTAAATAAAAATAA
*
246286 TTAGATAATAAAATAACTTTTTAA-TTTTTCTTGTTTGTTAAGTTCGTATCTTAAATGAACCAAC
455 TTACATAATAAAATAACTTTTTAATTTTTTCTTGTTTGTTAAGTTCGTATCTTAAATGAACCAAC
246350 AGATCATATATAAAATAACTCCTTCAAATAAATCATTTAAACATAAAATAAAAAAAAGTGAATAT
520 AGATCATATATAAAATAACTCCTTCAAATAAATCATTTAAACATAAAATAAAAAAAAGTGAATAT
246415 AAAAAACTAAAAATAATTAATAAAATAA-TTTTTTTTTTGAATAGATTGAGTACAGATTCTAAAT
585 AAAAAACTAAAAATAATTAATAAAATAATTTTTTTTTTTGAATAGATTGAGTACAGATTCTAAAT
246479 CGACTTATAAGTTGTGCAAATCAGCTCCTTTAAATACATTATTGAAAAATAAAATAAAAATTTGA
650 CGACTTATAAGTTGTGCAAATCAGCTCCTTTAAATACATTATTGAAAAATAAAATAAAAATTTGA
246544 AATCAAAAAGCTAAAACTAATTAAGTTTTTTTTCTAAGTAAATTGAGTAGAGATTTTAATTTGAT
715 AATCAAAAAGCTAAAACTAATTAAGTTTTTTTTCTAAGTAAATTGAGTAGAGATTTTAATTTGAT
246609 CGTGAGTTAAATTACAAATCAATTCTTTAAATTAAATTAATTAGTTTAA
780 CGTGAGTTAAATTACAAATCAATTCTTTAAATTAAATTAATTAGTTTAA
246658 ATTAAATTAAATAATTTTTATTTAAATATTTATATAGAATTGGATGCAAATTTTAAATTAATTCG
1 ATTAAATTAAATAATTTTTATTTAAATATTTATATAGAATTGGATGCAAATTTTAAATTAATTCG
246723 TGAGTT-ATATACAGATCAATTAGTTTAAATATATCATTTAGAAATAAAGTGAAAATAATTAATC
66 TGAGTTAATATACAGATCAATTAGTTTAAATATATCATTTAGAAATAAAGTGAAAATAATTAATC
246787 AGAGAAATTTATGTTTAAAACCTTTTTCCAAGTGAGTTAAGTATGAATTCTTAATCAATATGCAA
131 AGAGAAATTTATGTTTAAAACCTTTTTCCAAGTGAGTTAAGTATGAATTCTTAATCAATATGCAA
*
246852 GCTAATATATGTATATCAATCCCTTTAATTAAATCATTTTATTTAAATTTTTTTCAAGCAAGTTA
196 GCTAATATATGTATATCAATCCCTTTAATTAAATCATTTTATTTAAATTTTTTTCAAGCAAGTTG
246917 AGTATAGGTTTTCTATTGATTCGCGAATCAACTTTTGAATTAACCGTTTTGAATATGTCATTTTA
261 AGTATAGGTTTTCTATTGATTCGCGAATCAACTTTTGAATTAACCGTTTTGAATATGTCATTTTA
* *
246982 AAAAGTAAAATGAAATAATTAATAAAATAATTTTTTAAACTTTTCTTAAGCATAGATTCTAAATC
326 AAAAGTAAAATGAAATAATTAATAAAATAATTTCTTAAATTTTTCTTAAGCATAGATTCTAAATC
247047 AACCTTTGATTCAATCTCAAGA-T--TTTTTTAAATACATTATTTAAAAATTAAATAAAAATATA
391 AACCTTTGATTCAATCTCAAGATTAATTTTTTAAATACATTATTTAAAAATTAAATAAAAATA-A
247109 TTACATAATAAAATAACTTTTTAATTTTTTCTTGTTTGTTAAGTTCGTATCTTAAATGAACCAAC
455 TTACATAATAAAATAACTTTTTAATTTTTTCTTGTTTGTTAAGTTCGTATCTTAAATGAACCAAC
*
247174 AGATCATATATAAAATAACTCCTTCAAATAAATTATTTAAACATAAAATAAAAAAAA-TGAATAT
520 AGATCATATATAAAATAACTCCTTCAAATAAATCATTTAAACATAAAATAAAAAAAAGTGAATAT
247238 AAAAAACTAAAAATAATTAATAAAATAATTTTTATTTTTTGAATAGATTGAGTACAGATTCTAAA
585 AAAAAACTAAAAATAATTAATAAAATAATTTTT-TTTTTTGAATAGATTGAGTACAGATTCTAAA
* *
247303 TCGACTTATAAGTTATGCAAATTAGCTCCTTTAAATACATTATTGAAAAATAAAATAAAAATTTG
649 TCGACTTATAAGTTGTGCAAATCAGCTCCTTTAAATACATTATTGAAAAATAAAATAAAAATTTG
* * *
247368 AAATAAAAAAAGCTAAAACTAATTAAGTTTTTTCTCTAAGTAAATTGAGTAAAGATTTTAATTTG
714 AAAT-CAAAAAGCTAAAACTAATTAAGTTTTTTTTCTAAGTAAATTGAGTAGAGATTTTAATTTG
*
247433 ATCGTGAGTTAAATTACAAATCAATTTTTTAAAT
778 ATCGTGAGTTAAATTACAAATCAATTCTTTAAAT
247467 ATATCATTTA
Statistics
Matches: 1606, Mismatches: 23, Indels: 20
0.97 0.01 0.01
Matches are distributed among these distances:
822 37 0.02
823 59 0.04
824 101 0.06
825 144 0.09
826 378 0.24
827 181 0.11
828 102 0.06
829 3 0.00
831 44 0.03
832 6 0.00
833 88 0.05
834 463 0.29
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (828 bp):
ATTAAATTAAATAATTTTTATTTAAATATTTATATAGAATTGGATGCAAATTTTAAATTAATTCG
TGAGTTAATATACAGATCAATTAGTTTAAATATATCATTTAGAAATAAAGTGAAAATAATTAATC
AGAGAAATTTATGTTTAAAACCTTTTTCCAAGTGAGTTAAGTATGAATTCTTAATCAATATGCAA
GCTAATATATGTATATCAATCCCTTTAATTAAATCATTTTATTTAAATTTTTTTCAAGCAAGTTG
AGTATAGGTTTTCTATTGATTCGCGAATCAACTTTTGAATTAACCGTTTTGAATATGTCATTTTA
AAAAGTAAAATGAAATAATTAATAAAATAATTTCTTAAATTTTTCTTAAGCATAGATTCTAAATC
AACCTTTGATTCAATCTCAAGATTAATTTTTTAAATACATTATTTAAAAATTAAATAAAAATAAT
TACATAATAAAATAACTTTTTAATTTTTTCTTGTTTGTTAAGTTCGTATCTTAAATGAACCAACA
GATCATATATAAAATAACTCCTTCAAATAAATCATTTAAACATAAAATAAAAAAAAGTGAATATA
AAAAACTAAAAATAATTAATAAAATAATTTTTTTTTTTGAATAGATTGAGTACAGATTCTAAATC
GACTTATAAGTTGTGCAAATCAGCTCCTTTAAATACATTATTGAAAAATAAAATAAAAATTTGAA
ATCAAAAAGCTAAAACTAATTAAGTTTTTTTTCTAAGTAAATTGAGTAGAGATTTTAATTTGATC
GTGAGTTAAATTACAAATCAATTCTTTAAATTAAATTAATTAGTTTAA
Found at i:247606 original size:14 final size:14
Alignment explanation
Indices: 247582--247621 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
247572 ACATCATCTA
247582 AAAATTTAAAAAATT
1 AAAA-TTAAAAAATT
247597 AAAATTAAAAAATT
1 AAAATTAAAAAATT
*
247611 AAATTTAAAAA
1 AAAATTAAAAA
247622 CTAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATTAAAAAATT
Found at i:247614 original size:13 final size:13
Alignment explanation
Indices: 247587--247626 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
247577 ATCTAAAAAT
247587 TTAAAAAATTAAAA
1 TTAAAAAATT-AAA
247601 TTAAAAAATTAAA
1 TTAAAAAATTAAA
* *
247614 TTTAAAAACTAAA
1 TTAAAAAATTAAA
247627 AAATAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (13 bp):
TTAAAAAATTAAA
Found at i:247753 original size:17 final size:17
Alignment explanation
Indices: 247731--247772 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
247721 CAATGACGAG
*
247731 AAAAATATACAAAATAA
1 AAAAATACACAAAATAA
247748 AAAAATTACACAAAATAA
1 AAAAA-TACACAAAATAA
*
247766 ATAAATA
1 AAAAATA
247773 AAAAGAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAAATACACAAAATAA
Found at i:248915 original size:17 final size:17
Alignment explanation
Indices: 248890--248937 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
248880 ATTTATATTA
* *
248890 ATATATAAAATTTTTTT
1 ATATTTAAAATTTTGTT
*
248907 ATATTTAAAATTATGTT
1 ATATTTAAAATTTTGTT
*
248924 AAATTTAATAATTT
1 ATATTTAA-AATTT
248938 ATATATACGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
ATATTTAAAATTTTGTT
Found at i:249725 original size:20 final size:19
Alignment explanation
Indices: 249693--249748 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
249683 TTAAAATATA
249693 TAAACAGAATAAATTAATTT
1 TAAACA-AATAAATTAATTT
* **
249713 TATATCAAATAAAAAAATTT
1 TA-AACAAATAAATTAATTT
*
249733 TAAACATATAAATTAA
1 TAAACAAATAAATTAA
249749 AAAAATTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 10 0.36
20 15 0.54
21 3 0.11
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAACAAATAAATTAATTT
Found at i:249750 original size:23 final size:23
Alignment explanation
Indices: 249714--249771 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
249704 AATTAATTTT
*
249714 ATATCAAATAAAAAAATTTTAAAC
1 ATAT-AAATAAAAAAAATTTAAAC
* *
249738 ATATAAATTAAAAAAATTTAAAT
1 ATATAAATAAAAAAAATTTAAAC
249761 ATATAAATAAA
1 ATATAAATAAA
249772 TGTAGAAGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (23 bp):
ATATAAATAAAAAAAATTTAAAC
Found at i:254405 original size:31 final size:31
Alignment explanation
Indices: 254367--254438 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
254357 CTAACATTAT
254367 TAAATGAAATGGTCTATTCTTATGATCAGGA
1 TAAATGAAATGGTCTATTCTTATGATCAGGA
254398 TAAATGAAATGGTCTATTCTTATGATCAGGA
1 TAAATGAAATGGTCTATTCTTATGATCAGGA
254429 TAAATGAAAT
1 TAAATGAAAT
254439 ATTTGTGAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (31 bp):
TAAATGAAATGGTCTATTCTTATGATCAGGA
Found at i:259819 original size:9 final size:9
Alignment explanation
Indices: 259796--259824 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
259786 CACATATATT
259796 TAAAATAAA
1 TAAAATAAA
259805 -AAAATAAA
1 TAAAATAAA
259813 TAAAATAAA
1 TAAAATAAA
259822 TAA
1 TAA
259825 TTAAAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
TAAAATAAA
Found at i:259822 original size:13 final size:12
Alignment explanation
Indices: 259798--259836 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
259788 CATATATTTA
259798 AAATAAAAAAAT
1 AAATAAAAAAAT
259810 AAATAAAATAAAT
1 AAATAAAA-AAAT
* *
259823 AATTAAAAAGAT
1 AAATAAAAAAAT
259835 AA
1 AA
259837 TAATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:260181 original size:13 final size:13
Alignment explanation
Indices: 260163--260193 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
260153 GATAAAATCT
*
260163 ATTTAAATTTTAA
1 ATTTAAAATTTAA
260176 ATTTAAAATTTAA
1 ATTTAAAATTTAA
260189 ATTTA
1 ATTTA
260194 GATTCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTAAAATTTAA
Found at i:262667 original size:18 final size:20
Alignment explanation
Indices: 262634--262670 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
262624 TACTTTCAAT
262634 TTAAAAGCATCTCGATAATC
1 TTAAAAGCATCTCGATAATC
262654 TTAAAAG-A-CTCGATAAT
1 TTAAAAGCATCTCGATAAT
262671 ATCATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (20 bp):
TTAAAAGCATCTCGATAATC
Found at i:265427 original size:18 final size:19
Alignment explanation
Indices: 265384--265427 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
265374 TATTTATATT
*
265384 TAAATATATGTAAAGTAAA
1 TAAATATATGTAAAGAAAA
*
265403 TATAATAT-TTTAAAGAAAA
1 TA-AATATATGTAAAGAAAA
265422 TAAATA
1 TAAATA
265428 ATCACAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 13 0.59
20 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (19 bp):
TAAATATATGTAAAGAAAA
Found at i:265695 original size:107 final size:107
Alignment explanation
Indices: 265540--265752 Score: 313
Period size: 107 Copynumber: 2.0 Consensus size: 107
265530 TTGCCATTCC
* * * *
265540 TGTATTTGCTTGCCTTTCCATTACACCTGCCTTTCGTAAGAGACTGCAAATTGA-CATATATATA
1 TGTATTTGCTTGCCTTTCCATCACACCTGCCTTTCGGAAGAGAATGCAAATTGATAATATATATA
* *
265604 TATATATATATTATGCATAAAGACGGATATGATTTTCTTATCA
66 TATATATATATT-TGCAAAAAGACAGATATGATTTTCTTATCA
* * *
265647 TGTATTTTGCTTGCTTTTCCATCACACTTG-CTTTCGGAGGAGAATGCAAATTGATAATATATAT
1 TGTA-TTTGCTTGCCTTTCCATCACACCTGCCTTTCGGAAGAGAATGCAAATTGATAATATATAT
265711 ATATATATATATTTGCAAAAAGACAGATATGATTTTCTTATC
65 ATATATATATATTTGCAAAAAGACAGATATGATTTTCTTATC
265753 TGGTTCCCAA
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 52 0.55
108 43 0.45
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (107 bp):
TGTATTTGCTTGCCTTTCCATCACACCTGCCTTTCGGAAGAGAATGCAAATTGATAATATATATA
TATATATATATTTGCAAAAAGACAGATATGATTTTCTTATCA
Found at i:272495 original size:46 final size:39
Alignment explanation
Indices: 272421--272516 Score: 95
Period size: 45 Copynumber: 2.3 Consensus size: 39
272411 ATAATGAGAA
*
272421 TAAAAAATAAATATTAAAAATATTAAATTAAAATTTATAT
1 TAAATAATAAATATTAAAAATATTAAATT-AAATTTATAT
*
272461 GTATATATAATAAATAATTATAAAA-ACTTAAAATTATATTTATAT
1 -TA-A-ATAATAAAT-ATTA-AAAATA-TT-AAATTAAATTTATAT
272506 TAAATAATAAA
1 TAAATAATAAA
272517 ATATATATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
41 2 0.04
42 9 0.19
43 9 0.19
44 7 0.15
45 15 0.32
46 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (39 bp):
TAAATAATAAATATTAAAAATATTAAATTAAATTTATAT
Found at i:273152 original size:15 final size:15
Alignment explanation
Indices: 273128--273159 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
273118 AGTTAAATAT
*
273128 TTAAATTTAAAAAAA
1 TTAAACTTAAAAAAA
273143 TTAAACTTAAAAAAA
1 TTAAACTTAAAAAAA
273158 TT
1 TT
273160 TAAAATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAACTTAAAAAAA
Found at i:273157 original size:16 final size:16
Alignment explanation
Indices: 273130--273168 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
273120 TTAAATATTT
*
273130 AAATTTAAAAAAATTA
1 AAATTAAAAAAAATTA
* *
273146 AACTTAAAAAAATTTA
1 AAATTAAAAAAAATTA
273162 AAATTAA
1 AAATTAA
273169 TATGACCAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAAAAAAAATTA
Found at i:273277 original size:19 final size:20
Alignment explanation
Indices: 273240--273277 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
273230 CGAAACTTAT
*
273240 AAAAACTCGAATTTATAATA
1 AAAAACTCGAAATTATAATA
*
273260 AAAAACTC-AAATTGTAAT
1 AAAAACTCGAAATTATAAT
273278 TACATGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAACTCGAAATTATAATA
Found at i:274566 original size:20 final size:19
Alignment explanation
Indices: 274501--274588 Score: 53
Period size: 20 Copynumber: 4.7 Consensus size: 19
274491 ACACATGTAG
* *
274501 ATGTATCAATACAAGTTGCA
1 ATGTATCGATACAAATTG-A
274521 ATGTATCGATAC--ATT--
1 ATGTATCGATACAAATTGA
*
274536 A--TATCGTTACAAATTGCA
1 ATGTATCGATACAAATTG-A
*
274554 ATGTATCGATACATTATGTGA
1 ATGTATCGATACA-AAT-TGA
*
274575 AAGTATCGATACAA
1 ATGTATCGATACAA
274589 GTCATTGGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
13 8 0.15
15 4 0.08
18 3 0.06
20 20 0.38
21 15 0.29
22 2 0.04
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAAATTGA
Found at i:274667 original size:21 final size:21
Alignment explanation
Indices: 274635--274692 Score: 84
Period size: 20 Copynumber: 2.8 Consensus size: 21
274625 CATACATAAG
*
274635 ATTGTGTCGATACAATTCCAGA
1 ATTGTATCGATACAATT-CAGA
274657 A-TGTATCGATAC-ATTCAGA
1 ATTGTATCGATACAATTCAGA
274676 ATTGTATCGATACAATT
1 ATTGTATCGATACAATT
274693 AGGCCAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 5 0.15
20 14 0.42
21 13 0.39
22 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (21 bp):
ATTGTATCGATACAATTCAGA
Found at i:274681 original size:20 final size:20
Alignment explanation
Indices: 274615--274689 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
274605 ACCCCTCAAA
* *
274615 TGTATCGATACATACATAAGAT
1 TGTATCGATACATTCA-GA-AT
*
274637 TGTGTCGATACAATTCCAGAA-
1 TGTATCGATAC-ATT-CAGAAT
274658 TGTATCGATACATTCAGAAT
1 TGTATCGATACATTCAGAAT
274678 TGTATCGATACA
1 TGTATCGATACA
274690 ATTAGGCCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.11
20 15 0.33
21 10 0.22
22 11 0.24
23 3 0.07
24 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATTCAGAAT
Found at i:274691 original size:41 final size:43
Alignment explanation
Indices: 274613--274692 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
274603 CTACCCCTCA
*
274613 AATGTATCGATACATACATAAGATTGTGTCGATACAATTCCAG
1 AATGTATCGATACATACATAAGATTGTATCGATACAATTCCAG
* *
274656 AATGTATCGATACATTCA-GA-ATTGTATCGATACAATT
1 AATGTATCGATACATACATAAGATTGTATCGATACAATT
274693 AGGCCAACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 16 0.47
42 1 0.03
43 17 0.50
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (43 bp):
AATGTATCGATACATACATAAGATTGTATCGATACAATTCCAG
Found at i:274743 original size:20 final size:22
Alignment explanation
Indices: 274708--274750 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
274698 AACGGCTATA
274708 ATTTTAAATATAATGTATCGAT
1 ATTTTAAATATAATGTATCGAT
*
274730 ATTTT-AAT-TAATGTATTGAT
1 ATTTTAAATATAATGTATCGAT
274750 A
1 A
274751 CAATGATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 3 0.15
22 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTTTAAATATAATGTATCGAT
Found at i:278444 original size:18 final size:17
Alignment explanation
Indices: 278421--278463 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
278411 AGTTAATTAA
*
278421 ATTAAAACGTATGTAAAT
1 ATTAAAAAGTAT-TAAAT
278439 ATTAAATAAGTATTAAAT
1 ATTAAA-AAGTATTAAAT
278457 A-TAAAAA
1 ATTAAAAA
278464 ATACATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 4 0.17
18 12 0.52
19 5 0.22
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (17 bp):
ATTAAAAAGTATTAAAT
Found at i:279752 original size:13 final size:13
Alignment explanation
Indices: 279734--279758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
279724 TCAAACAATT
279734 TGTATCGATACAA
1 TGTATCGATACAA
279747 TGTATCGATACA
1 TGTATCGATACA
279759 TAAGTGTTGT
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
Done.