Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001577.1 Hibiscus syriacus cultivar Beakdansim tig00003137_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: 426047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:213 original size:13 final size:14
Alignment explanation
Indices: 190--241 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
180 AAAAGAAAAA
*
190 CAAAGAGAAAAGAAG
1 CAAAGAAAAAAG-AG
205 CAAAGAAAAAAAGAG
1 CAAAG-AAAAAAGAG
220 CAAAGAAAAAA-A-
1 CAAAGAAAAAAGAG
232 -AAAGAAAAAA
1 CAAAGAAAAAA
242 AAAGAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
11 10 0.29
13 1 0.03
14 6 0.17
15 12 0.34
16 6 0.17
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (14 bp):
CAAAGAAAAAAGAG
Found at i:218 original size:16 final size:16
Alignment explanation
Indices: 197--244 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 16
187 AAACAAAGAG
197 AAAAGAAGCAAAGAAA
1 AAAAGAAGCAAAGAAA
213 AAAAG-AGCAAAGAAA
1 AAAAGAAGCAAAGAAA
*
228 AAAAAAAG-AAA-AAA
1 AAAAGAAGCAAAGAAA
242 AAA
1 AAA
245 GAAAAAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 6 0.20
15 17 0.57
16 7 0.23
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAGAAGCAAAGAAA
Found at i:219 original size:40 final size:36
Alignment explanation
Indices: 175--252 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 36
165 AATTAAAGCG
*
175 AAGAGAAAAGAAAAACAAAGAGAAAAGAAGCAAAGAAAAA
1 AAGAGAAAAGAAAAA-AAAAAGAAAA-AA--AAAGAAAAA
*
215 AAGAGCAAAGAAAAAAAAAAGAAAAAAAAAGAAAAA
1 AAGAGAAAAGAAAAAAAAAAGAAAAAAAAAGAAAAA
251 AA
1 AA
253 ACCAAAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 11 0.31
38 2 0.06
39 9 0.25
40 14 0.39
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (36 bp):
AAGAGAAAAGAAAAAAAAAAGAAAAAAAAAGAAAAA
Found at i:224 original size:23 final size:25
Alignment explanation
Indices: 181--226 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
171 AGCGAAGAGA
181 AAAGAAAAACAAAGAGAAAAGAAGC
1 AAAGAAAAACAAAGAGAAAAGAAGC
*
206 AAAG-AAAA-AAAGAGCAAAGAA
1 AAAGAAAAACAAAGAGAAAAGAA
227 AAAAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 4 0.20
25 4 0.20
ACGTcount: A:0.74, C:0.07, G:0.20, T:0.00
Consensus pattern (25 bp):
AAAGAAAAACAAAGAGAAAAGAAGC
Found at i:238 original size:51 final size:50
Alignment explanation
Indices: 180--306 Score: 125
Period size: 51 Copynumber: 2.5 Consensus size: 50
170 AAGCGAAGAG
180 AAAAGAAAAACAAAGAGAAAAGAAGCAAAGA-AA-AAAAGAGCAAAGAAAAAA
1 AAAAGAAAAA-AAAGAGAAAAGAAGCAAA-ACAAGAAAA-AGCAAAGAAAAAA
* * *
231 AAAAGAAAAAAAA-AGAAAAAAAACCAAAACAAGGAAAAAGCAAAGAAAAAG
1 AAAAGAAAAAAAAGAG-AAAAGAAGCAAAACAA-GAAAAAGCAAAGAAAAAA
* * *
282 CAAAGAGAAAAAAGAAGACAAGAAG
1 AAAAGAAAAAAAAG-AGAAAAGAAG
307 TACATGCAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
49 3 0.05
50 15 0.24
51 33 0.53
52 9 0.15
53 2 0.03
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (50 bp):
AAAAGAAAAAAAAGAGAAAAGAAGCAAAACAAGAAAAAGCAAAGAAAAAA
Found at i:243 original size:15 final size:16
Alignment explanation
Indices: 180--281 Score: 50
Period size: 17 Copynumber: 6.3 Consensus size: 16
170 AAGCGAAGAG
*
180 AAAAGAAAAACAAAGAG
1 AAAAGAAAAACAAA-AA
*
197 AAAAGAAGCAAAGAAAAA
1 AAAAGAA--AAACAAAAA
* *
215 AAGAGCAAAGA-AAAAA
1 AAAAG-AAAAACAAAAA
231 AAAAG-AAAA-AAAAA
1 AAAAGAAAAACAAAAA
* *
245 GAAA-AAAAACCAAAA
1 AAAAGAAAAACAAAAA
* * *
260 CAAGGAAAAAGCAAAGA
1 AAAAGAAAAA-CAAAAA
277 AAAAG
1 AAAAG
282 CAAAGAGAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
14 15 0.23
15 6 0.09
16 14 0.22
17 16 0.25
18 5 0.08
19 8 0.12
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAACAAAAA
Found at i:259 original size:10 final size:10
Alignment explanation
Indices: 180--253 Score: 60
Period size: 10 Copynumber: 7.3 Consensus size: 10
170 AAGCGAAGAG
180 AAAAGAAAAA
1 AAAAGAAAAA
* *
190 CAAAGAGAAA
1 AAAAGAAAAA
* *
200 AGAAGCAAAGA
1 AAAAG-AAAAA
* *
211 AAAA-AAGAG
1 AAAAGAAAAA
*
220 CAAAGAAAAAA
1 AAAAG-AAAAA
231 AAAAGAAAAA
1 AAAAGAAAAA
241 AAAAGAAAAA
1 AAAAGAAAAA
251 AAA
1 AAA
254 CCAAAACAAG
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
9 5 0.11
10 29 0.62
11 13 0.28
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:259 original size:18 final size:17
Alignment explanation
Indices: 206--269 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 17
196 GAAAAGAAGC
206 AAAGAAAAAAAGAGCAAAGA
1 AAAGAAAAAAA-A-CAAA-A
226 AAA-AAAAAAGAA-AAAA
1 AAAGAAAAAA-AACAAAA
242 AAAGAAAAAAAACCAAAA
1 AAAGAAAAAAAA-CAAAA
*
260 CAAGGAAAAA
1 -AAAGAAAAA
270 GCAAAGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
16 6 0.16
17 9 0.24
18 4 0.11
19 15 0.39
20 4 0.11
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAACAAAA
Found at i:280 original size:11 final size:11
Alignment explanation
Indices: 181--292 Score: 64
Period size: 11 Copynumber: 10.8 Consensus size: 11
171 AGCGAAGAGA
181 AAAGAAAAA-C
1 AAAGAAAAAGC
191 AAAGAGAAAAG-
1 AAAGA-AAAAGC
*
202 -AAG-CAAAG-
1 AAAGAAAAAGC
210 AAA-AAAAGAGC
1 AAAGAAAA-AGC
**
221 AAAGAAAAAAA
1 AAAGAAAAAGC
*
232 AAAGAAAAA-A
1 AAAGAAAAAGC
242 AAAGAAAAA--
1 AAAGAAAAAGC
**
251 AAACCAAAA-C
1 AAAGAAAAAGC
*
261 AAGGAAAAAGC
1 AAAGAAAAAGC
272 AAAGAAAAAGC
1 AAAGAAAAAGC
283 AAAGAGAAAA
1 AAAGA-AAAA
293 AAGAAGACAA
Statistics
Matches: 82, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
8 4 0.05
9 11 0.13
10 26 0.32
11 33 0.40
12 8 0.10
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGC
Found at i:303 original size:40 final size:38
Alignment explanation
Indices: 184--303 Score: 91
Period size: 40 Copynumber: 3.0 Consensus size: 38
174 GAAGAGAAAA
* * *
184 GAAAAACAAAGAGAAAAGAAGCAAAGAAAAAAAG-AGCAAA
1 GAAAAA-AAAAAG-AAA-AAGCAAAGAAAAAAAGAAACAAG
* *
224 GAAAAAAAAAAGAAAAA-AAAAGAAAAAAAACCAAAACAAG
1 GAAAAAAAAAAGAAAAAGCAAAG-AAAAAAA--GAAACAAG
**
264 GAAAAAGCAAAGAAAAAGCAAAGAGAAAAAAGAAGACAAG
1 GAAAAAAAAAAGAAAAAGCAAAGA-AAAAAAGAA-ACAAG
304 AAGTACATGC
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
36 4 0.06
37 9 0.14
38 3 0.05
39 7 0.11
40 31 0.48
41 10 0.16
ACGTcount: A:0.75, C:0.07, G:0.17, T:0.00
Consensus pattern (38 bp):
GAAAAAAAAAAGAAAAAGCAAAGAAAAAAAGAAACAAG
Found at i:1627 original size:38 final size:39
Alignment explanation
Indices: 1550--1629 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
1540 TAAACCAGAT
* * *
1550 TTTATCTCGCTTGAGATGGTTTCACATCGAAATAGAAGA
1 TTTATCTCGCTTGAGATAGTTTCACATCGAAACAAAAGA
**
1589 TTTATCTCGCTTGAGATAGTTTTGC-TCGAAACAAAAGA
1 TTTATCTCGCTTGAGATAGTTTCACATCGAAACAAAAGA
1627 TTT
1 TTT
1630 TAAGAAACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 14 0.39
39 22 0.61
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (39 bp):
TTTATCTCGCTTGAGATAGTTTCACATCGAAACAAAAGA
Found at i:1722 original size:42 final size:40
Alignment explanation
Indices: 1662--1785 Score: 133
Period size: 42 Copynumber: 3.0 Consensus size: 40
1652 AAGGGTTTCT
* * *
1662 TGATGAGTAAGTCATTCGGGCCATCAATAAGTCTTTTGAGCG
1 TGATG-GTAAGTCCTTCGGGCCATC-ATAAGTCTTTCGAGCA
1704 TGATGCGTAAGTCCTTCGGGCCATC-TAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATCATAAGTCTTTCGAGCA
* * * * *
1744 AGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGAGCA
1 TGATGGTAAGTCCTTCGGGCCAT-CATAAGTCTTTCGAGCA
1785 T
1 T
1786 AATGTTTTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 16 0.23
40 18 0.26
41 13 0.19
42 23 0.33
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (40 bp):
TGATGGTAAGTCCTTCGGGCCATCATAAGTCTTTCGAGCA
Found at i:2311 original size:30 final size:30
Alignment explanation
Indices: 2272--2452 Score: 90
Period size: 30 Copynumber: 5.8 Consensus size: 30
2262 CTTGAGACAG
2272 TTCCTCTTGAAACACAAATCTTTGAGATCGT
1 TTCC-CTTGAAACACAAATCTTTGAGATCGT
*
2303 TTCCCTTGAAACGA-ATTTTATCTCCTTGAGA-CGGT
1 TTCCCTTGAAAC-ACA---AATCT--TTGAGATC-GT
* * **
2338 TTCCCTTGGAACACCAATCTTTGA-ATATAT
1 TTCCCTTGAAACACAAATCTTTGAGAT-CGT
*
2368 TTCCCTTGAAACA-AATTTTGTCTCTCTGAGA-CAGT
1 TTCCCTTGAAACACAA----ATCT-T-TGAGATC-GT
* *
2403 TTCTCTTGAAATACAAATCTTTGAGATCGT
1 TTCCCTTGAAACACAAATCTTTGAGATCGT
2433 TTCCCTT-AAA-ACAAAT-TTTG
1 TTCCCTTGAAACACAAATCTTTG
2453 CCTCTCTTAA
Statistics
Matches: 115, Mismatches: 15, Indels: 44
0.66 0.09 0.25
Matches are distributed among these distances:
27 4 0.03
28 6 0.05
29 5 0.04
30 39 0.34
31 7 0.06
32 7 0.06
33 7 0.06
34 3 0.03
35 34 0.30
36 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (30 bp):
TTCCCTTGAAACACAAATCTTTGAGATCGT
Found at i:2351 original size:65 final size:65
Alignment explanation
Indices: 2131--2481 Score: 369
Period size: 65 Copynumber: 5.4 Consensus size: 65
2121 CAAATTTTAT
* * * *
2131 CTTGAGACAGTTTCTCTTGAAACA-AAAGTCTTT-AAATCTATTTCCCTTGAAACAAAATTTAGT
1 CTTGAGACAGTTTCCCTTGAAACACAAA-TCTTTGAGATC-GTTTCCCTTGAAAC-AAATTTTGT
2194 CTCC
63 CT-C
* * *
2198 CTTGAGACAGTTTCTCTTGAAACAC-AA--TTTAAGTAT-GTTTCCCTTGGAACAAAATTTTGTC
1 CTTGAGACAGTTTCCCTTGAAACACAAATCTTTGAG-ATCGTTTCCCTTGAAAC-AAATTTTGTC
2259 TCC
64 T-C
* *
2262 CTTGAGACAG-TTCCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACGAATTTTATCT
1 CTTGAGACAGTTTCC-CTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCT
2326 C
65 C
* * * **
2327 CTTGAGACGGTTTCCCTTGGAACACCAATCTTTGA-ATATATTTCCCTTGAAACAAATTTTGTCT
1 CTTGAGACAGTTTCCCTTGAAACACAAATCTTTGAGAT-CGTTTCCCTTGAAACAAATTTTGTCT
2391 -
65 C
* * * *
2391 CTCTGAGACAGTTTCTCTTGAAATACAAATCTTTGAGATCGTTTCCCTTAAAACAAATTTTGCCT
1 CT-TGAGACAGTTTCCCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCT
2456 C
65 C
*
2457 TCTTAAGACAGTTTCCCTTGAAACA
1 -CTTGAGACAGTTTCCCTTGAAACA
2482 ATTTTGTTTC
Statistics
Matches: 242, Mismatches: 28, Indels: 29
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.01
64 52 0.21
65 103 0.43
66 38 0.16
67 46 0.19
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (65 bp):
CTTGAGACAGTTTCCCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTC
Found at i:2384 original size:131 final size:129
Alignment explanation
Indices: 2131--2481 Score: 442
Period size: 131 Copynumber: 2.7 Consensus size: 129
2121 CAAATTTTAT
* * *
2131 CTTGAGACAGTTTCTCTTGAAACA-AAAGTCTTT-AAATCTATTTCCCTTGAAACAAAATTTAGT
1 CTTGAGACAGTTTCTCTTGAAACACAAA-TCTTTGAGATC-GTTTCCCTTGAAACAAATTTTA-T
* * *
2194 CTCCCTTGAGACAGTTTCTCTTGAAACACAATTTAAGTATGTTTCCCTTGGAACAAAATTTTGTC
63 CT-CCTTGAGACAGTTTCCCTTGAAACACAATTTAAGTATATTTCCCTTGAAACAAAATTTTGTC
2259 TCC
127 TCC
* *
2262 CTTGAGACAGTTCCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACGAATTTTATCTC
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTATCTC
* *
2327 CTTGAGACGGTTTCCCTTGGAACACCAATCTTTGAA-TATATTTCCCTTGAAAC-AAATTTTGTC
66 CTTGAGACAGTTTCCCTTGAAACA-CAA--TTT-AAGTATATTTCCCTTGAAACAAAATTTTGTC
*
2390 TCT
127 TCC
* * **
2393 C-TGAGACAGTTTCTCTTGAAATACAAATCTTTGAGATCGTTTCCCTTAAAACAAATTTTGCCTC
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTATCTC
*
2457 TCTTAAGACAGTTTCCCTTGAAACA
66 -CTTGAGACAGTTTCCCTTGAAACA
2482 ATTTTGTTTC
Statistics
Matches: 193, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
129 22 0.11
130 63 0.33
131 81 0.42
132 25 0.13
133 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (129 bp):
CTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTATCTC
CTTGAGACAGTTTCCCTTGAAACACAATTTAAGTATATTTCCCTTGAAACAAAATTTTGTCTCC
Found at i:2481 original size:36 final size:36
Alignment explanation
Indices: 2367--2623 Score: 214
Period size: 35 Copynumber: 7.4 Consensus size: 36
2357 TTTGAATATA
*
2367 TTTCCCTTGAAACAAATTTTGTCTCTC-TGAGACAG
1 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
*
2402 TTTCTCTTGAAATACAAA-------TCT-TTGAGATC-G
1 TTTCCCTT-AAA-ACAAATTTTGTCTCTCTTGAGA-CAG
* *
2432 TTTCCCTTAAAACAAATTTTGCCTCTCTTAAGACAG
1 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2468 TTTCCCTTGAAAC-AATTTTGTTTCCCTTGAGACAG
1 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
2503 TTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGACGG
1 TTTCCCTTAAAACAAA-TTTTGTCTCTCTTGAGACAG
** * *
2540 TTTCTTTTAAAAAAAATTTTGTCTGTCTTGAGACAG
1 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2576 TTTCCCTTAAAAC-AAGTTTGTCTCTCTTGATACGG
1 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
2611 TTTCTCTTGAAAC
1 TTTCCCTTAAAAC
2624 CATCATACCC
Statistics
Matches: 180, Mismatches: 27, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
28 5 0.03
29 3 0.02
30 16 0.09
31 1 0.01
35 70 0.39
36 49 0.27
37 36 0.20
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:3373 original size:16 final size:18
Alignment explanation
Indices: 3336--3379 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 18
3326 AAAAATGAGG
3336 AAGAAAAAGAGAACACAA
1 AAGAAAAAGAGAACACAA
*
3354 AAGAATAAGAG-ACA-AA
1 AAGAAAAAGAGAACACAA
3370 AAGAAAAAGA
1 AAGAAAAAGA
3380 AAGCAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.46
17 3 0.12
18 10 0.42
ACGTcount: A:0.73, C:0.07, G:0.18, T:0.02
Consensus pattern (18 bp):
AAGAAAAAGAGAACACAA
Found at i:4193 original size:60 final size:60
Alignment explanation
Indices: 4124--4256 Score: 194
Period size: 60 Copynumber: 2.2 Consensus size: 60
4114 GTAATTACTA
* * *
4124 TTTACTCCCTTAAGTTTCTATTTTTACTATTTTGGCCCTTTAAATTTATATTTTTGTTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTACTATTTTAGCCCTTTAAATTTATATTCTTGTTAT
* * * * *
4184 TTTAGTCCCTTAAGTTTTTGTTTTTTCTATTTTAGTCCTTTAAATTTCTATTCTTGTTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTACTATTTTAGCCCTTTAAATTTATATTCTTGTTAT
4244 TTTAGTCCCTTAA
1 TTTAGTCCCTTAA
4257 ATGTTTATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.59
Consensus pattern (60 bp):
TTTAGTCCCTTAAGTTTCTATTTTTACTATTTTAGCCCTTTAAATTTATATTCTTGTTAT
Found at i:4245 original size:30 final size:30
Alignment explanation
Indices: 4124--4275 Score: 148
Period size: 30 Copynumber: 5.1 Consensus size: 30
4114 GTAATTACTA
* * **
4124 TTTACTCCCTTAAGTTTCTATTTTTACTAT
1 TTTAGTCCCTTAAATTTCTATTTTTGTTAT
* *
4154 TTT-GGCCCTTTAAATTTATATTTTTGTTAT
1 TTTAGTCCC-TTAAATTTCTATTTTTGTTAT
* * *
4184 TTTAGTCCCTTAAGTTTTTGTTTTT-TCTAT
1 TTTAGTCCCTTAAATTTCTATTTTTGT-TAT
* *
4214 TTTAGTCCTTTAAATTTCTATTCTTGTTAT
1 TTTAGTCCCTTAAATTTCTATTTTTGTTAT
*
4244 TTTAGTCCCTTAAATGTT-TATTTTTGGTAT
1 TTTAGTCCCTTAAAT-TTCTATTTTTGTTAT
4274 TT
1 TT
4276 AATTTTATCT
Statistics
Matches: 99, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
29 4 0.04
30 88 0.89
31 7 0.07
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (30 bp):
TTTAGTCCCTTAAATTTCTATTTTTGTTAT
Found at i:6709 original size:38 final size:37
Alignment explanation
Indices: 6635--6989 Score: 106
Period size: 34 Copynumber: 9.9 Consensus size: 37
6625 ATAGTTTACG
6635 AATGATTTTTGAAATATATAATATATATAGTTTTGAA
1 AATGATTTTTGAAATATATAATATATATAGTTTTGAA
*
6672 AATGATTTTTGAAA-ATGGAT-ATATTATATTGTTTTG-A
1 AATGATTTTTGAAATAT--ATAATA-TATATAGTTTTGAA
* ** *
6709 AATCATTTTAAAAATTTATATAATAT-T-TGGGTTTT-AA
1 AATGATTTTTGAAA--TATATAATATATAT-AGTTTTGAA
* * *
6746 AA-AATATTTTGAAA-AT-TATATAATATATGGTTTTTAA
1 AATGAT-TTTTGAAATATATA-AT-ATATATAGTTTTGAA
** *
6783 AA--A-AATTGAAA-ATAT-ATAATATATAGTTTTTAA
1 AATGATTTTTGAAATATATAAT-ATATATAGTTTTGAA
* * * *
6816 AA-CA-TGTTGAAA-ATA-AAAATATATAGTTTTAAA
1 AATGATTTTTGAAATATATAATATATATAGTTTTGAA
* * *
6849 ACAT-TTTTAATTAATATATATATATATATATATAGTTTTTAA
1 A-ATGATTT--TTGA-A-ATATATA-ATATATATAGTTTTGAA
* * *
6891 AA-CA-TTTTGAAA-ATATTATATAATATA-TTTTTAA
1 AATGATTTTTGAAATATATAATAT-ATATAGTTTTGAA
*
6925 AA-CA--TTTGAAATATAT-ATAATATATAGTTTT-AA
1 AATGATTTTTGAAATATATAAT-ATATATAGTTTTGAA
* *
6958 AA-CA-TTTTGAAA-ATATATTAATATATAGTTTT
1 AATGATTTTTGAAATATATAAT-ATATATAGTTTT
6990 TTAAACATTT
Statistics
Matches: 259, Mismatches: 24, Indels: 73
0.73 0.07 0.21
Matches are distributed among these distances:
33 60 0.23
34 70 0.27
35 13 0.05
36 14 0.05
37 53 0.20
38 20 0.08
39 4 0.02
40 7 0.03
41 2 0.01
42 16 0.06
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (37 bp):
AATGATTTTTGAAATATATAATATATATAGTTTTGAA
Found at i:6984 original size:67 final size:71
Alignment explanation
Indices: 6641--7004 Score: 276
Period size: 75 Copynumber: 5.1 Consensus size: 71
6631 TACGAATGAT
* * * *
6641 TTTTGAAATATATA-ATATATATAGTTTTGAAAATGATTTTTGAAAATGGA-TATATTATATTGT
1 TTTTGAAATATATATATATATATAGTTTTTAAAA-CA-TTTTGAAAAT--ATTATATAATATAGT
* *
6704 TTTGAAATCA
62 TTTTAAAACA
* * * * * *
6714 TTTT-AAAAATTTATATAATATTTGGGTTTTAAAAAATATTTTG-AAA-ATTATATAATATATGG
1 TTTTGAAATATATATAT-ATATAT-AGTTTT-TAAAACATTTTGAAAATATTATATAATATA--G
6776 TTTTTAAAA-A
61 TTTTTAAAACA
** * * *
6786 AATTGAAA-ATATATA-ATATATAGTTTTTAAAACATGTTGAAAATA-AAAAT-ATATAG-TTTT
1 TTTTGAAATATATATATATATATAGTTTTTAAAACATTTTGAAAATATTATATAATATAGTTTTT
6846 AAAACA
66 AAAACA
*
6852 TTTTTAATTAATATATATATATATATATATAGTTTTTAAAACATTTTGAAAATATTATATAATAT
1 ---TT--TTGA-A-ATATATATATATATATAGTTTTTAAAACATTTTGAAAATATTATATAATAT
6917 A-TTTTTAAAACA
59 AGTTTTTAAAACA
6929 -TTTGAAATATATATA-ATATATAG-TTTTAAAACATTTTGAAAATA-TAT-TAATATATAGTTT
1 TTTTGAAATATATATATATATATAGTTTTTAAAACATTTTGAAAATATTATAT-A-ATATAGTTT
*
6989 TTTAAACA
64 TTAAAACA
6997 TTTTGAAA
1 TTTTGAAA
7005 ATTTAATTTT
Statistics
Matches: 236, Mismatches: 28, Indels: 58
0.73 0.09 0.18
Matches are distributed among these distances:
65 9 0.04
66 6 0.03
67 26 0.11
68 32 0.14
69 27 0.11
70 8 0.03
71 15 0.06
72 17 0.07
73 22 0.09
74 17 0.07
75 35 0.15
76 7 0.03
77 15 0.06
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (71 bp):
TTTTGAAATATATATATATATATAGTTTTTAAAACATTTTGAAAATATTATATAATATAGTTTTT
AAAACA
Found at i:7019 original size:35 final size:34
Alignment explanation
Indices: 6641--7006 Score: 298
Period size: 33 Copynumber: 10.3 Consensus size: 34
6631 TACGAATGAT
* *
6641 TTTTG-AAATATATAATATATATAGTTTTGAAAATGA
1 TTTTGAAAATATAT-A-ATATATAGTTTTTAAAA-CA
* * * *
6677 TTTTTGAAAATGGATATATTATATTGTTTTGAAATCA
1 -TTTTGAAAAT--ATATAATATATAGTTTTTAAAACA
* * * * *
6714 TTTTAAAAATTTATATAATATTTGGGTTTTAAAAAATA
1 TTTTGAAAA--TATATAATATAT-AGTTTT-TAAAACA
*
6752 TTTTGAAAATTATATAATATATGGTTTTTAAAA-A
1 TTTTGAAAA-TATATAATATATAGTTTTTAAAACA
**
6786 AATTGAAAATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATAATATATAGTTTTTAAAACA
* *
6820 TGTTGAAAATA-AAAATATATAG-TTTTAAAACA
1 TTTTGAAAATATATAATATATAGTTTTTAAAACA
*
6852 TTTTTAATTAATATATATATATATATATATAGTTTTTAAAACA
1 ---TT--TTGA-A-A-ATATATA-ATATATAGTTTTTAAAACA
6895 TTTTGAAAATAT-TATATAATATA-TTTTTAAAACA
1 TTTTGAAAATATATA-AT-ATATAGTTTTTAAAACA
6929 -TTTGAAATATATATAATATATAG-TTTTAAAACA
1 TTTTGAAA-ATATATAATATATAGTTTTTAAAACA
*
6962 TTTTGAAAATATATTAATATATAGTTTTTTAAACA
1 TTTTGAAAATATA-TAATATATAGTTTTTAAAACA
6997 TTTTGAAAAT
1 TTTTGAAAAT
7007 TTAATTTTAT
Statistics
Matches: 278, Mismatches: 25, Indels: 54
0.78 0.07 0.15
Matches are distributed among these distances:
32 10 0.04
33 59 0.21
34 57 0.21
35 35 0.13
36 24 0.09
37 27 0.10
38 35 0.13
39 2 0.01
40 9 0.03
41 2 0.01
42 8 0.03
43 10 0.04
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (34 bp):
TTTTGAAAATATATAATATATAGTTTTTAAAACA
Found at i:8973 original size:64 final size:64
Alignment explanation
Indices: 8905--9069 Score: 160
Period size: 64 Copynumber: 2.6 Consensus size: 64
8895 ATAAATATGC
* * *
8905 TTCGATGTTTTGAA-AAAGCCTAG-GTGCATCGATGCATGGCT-TGTGCATCGGTGCATAAAATC
1 TTCGATGTTTT-AATAAA-CATAGAGTGCATCGATGCATGG-TATGTGCATCGGTACACAAAATC
8967 AA
63 AA
* * * * *
8969 TTCGATATTTTAATATATATGGAGTGCATCGATGCATGGTATGTGCATCGGTACACAAAATCCA
1 TTCGATGTTTTAATAAACATAGAGTGCATCGATGCATGGTATGTGCATCGGTACACAAAATCAA
* *
9033 TTCGATG-TTCAATTAAAACA-AGGGTGCATCGATGCAT
1 TTCGATGTTTTAA-T-AAACATAGAGTGCATCGATGCAT
9070 TGATTCATGC
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
63 9 0.11
64 70 0.85
65 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (64 bp):
TTCGATGTTTTAATAAACATAGAGTGCATCGATGCATGGTATGTGCATCGGTACACAAAATCAA
Found at i:9438 original size:16 final size:17
Alignment explanation
Indices: 9417--9453 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
9407 CTCCCCCTTA
9417 CTTTAAC-ACTTC-CCCC
1 CTTTAACGA-TTCTCCCC
9433 CTTTAACGATTCTCCCC
1 CTTTAACGATTCTCCCC
9450 CTTT
1 CTTT
9454 TTGTTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.16, C:0.43, G:0.03, T:0.38
Consensus pattern (17 bp):
CTTTAACGATTCTCCCC
Found at i:10140 original size:21 final size:21
Alignment explanation
Indices: 10104--10150 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
10094 CCGGAAGAGG
** * *
10104 AGGAGGAGCATGAGAAGCGGT
1 AGGAGGAGCACAAGAAGAGCT
10125 AGGAGGAGCACAAGAAGAGCT
1 AGGAGGAGCACAAGAAGAGCT
10146 AGGAG
1 AGGAG
10151 CAGCTCGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.45, T:0.06
Consensus pattern (21 bp):
AGGAGGAGCACAAGAAGAGCT
Found at i:10713 original size:19 final size:18
Alignment explanation
Indices: 10677--10713 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
10667 TCAGAGAAAA
*
10677 TTTTGAAAAAATGTTTGT
1 TTTTGAAAAAATGATTGT
10695 TTTTGAAAAAATTGATTGT
1 TTTTGAAAAAA-TGATTGT
10714 AAAATATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (18 bp):
TTTTGAAAAAATGATTGT
Found at i:11133 original size:21 final size:21
Alignment explanation
Indices: 11109--11172 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 21
11099 TCGGTGCATC
11109 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* * *
11130 TTCAAAGGGATGCATCGATGCACT
1 TTC--A-TGATGTATCGATGCACA
11154 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
11173 TTATGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 1 0.03
23 1 0.03
24 17 0.50
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:11158 original size:45 final size:44
Alignment explanation
Indices: 11079--11172 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 44
11069 TTGTGCATCA
*
11079 ATGCACATTCAAGGAGTGCATCGGTGCATCTTCAT-GATGTATCG
1 ATGCACATTCAAGGAGTGCATCGATGCATCTTCATAG-TGTATCG
11123 ATGCACATTCAAAGG-GATGCATCGATGCA-CTTTCATAGTGTATCG
1 ATGCACATTC-AAGGAG-TGCATCGATGCATC-TTCATAGTGTATCG
11168 ATGCA
1 ATGCA
11173 TTATGCACAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
44 12 0.27
45 32 0.71
46 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (44 bp):
ATGCACATTCAAGGAGTGCATCGATGCATCTTCATAGTGTATCG
Found at i:17439 original size:3 final size:3
Alignment explanation
Indices: 17431--17472 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
17421 TTTATTTTCT
17431 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA -TA TATA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TT
17473 TTTTATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.17
3 26 0.74
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17489 original size:22 final size:22
Alignment explanation
Indices: 17437--17522 Score: 68
Period size: 23 Copynumber: 3.6 Consensus size: 22
17427 TTCTTTATTA
17437 TTATTATTATTATTATTATTTT-AT
1 TTATT-TTATT-TT-TTATTTTGAT
17461 ATATATTTTATTTTTTATTTTGAT
1 -T-TATTTTATTTTTTATTTTGAT
*
17485 TTATTTAATATTTTTT-CTTTGAT
1 TTATTT--TATTTTTTATTTTGAT
*
17508 TTATTTAATATTTTT
1 TTATTTTAT-TTTTT
17523 CGAATTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.04
22 10 0.19
23 20 0.37
24 12 0.22
25 6 0.11
26 4 0.07
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.71
Consensus pattern (22 bp):
TTATTTTATTTTTTATTTTGAT
Found at i:17498 original size:23 final size:23
Alignment explanation
Indices: 17447--17522 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
17437 TTATTATTAT
* *
17447 TATTATTATTTT-ATATATATTTTA
1 TATTTTTATTTTGAT-T-TATTTAA
17471 T-TTTTTATTTTGATTTATTTAA
1 TATTTTTATTTTGATTTATTTAA
17493 TATTTTT-TCTTTGATTTATTTAA
1 TATTTTTAT-TTTGATTTATTTAA
17516 TATTTTT
1 TATTTTT
17523 CGAATTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.17
23 36 0.77
24 3 0.06
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (23 bp):
TATTTTTATTTTGATTTATTTAA
Found at i:17522 original size:24 final size:24
Alignment explanation
Indices: 17469--17522 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
17459 ATATATATTT
17469 TATTTTTTATTTTGATTTATTTAA
1 TATTTTTTATTTTGATTTATTTAA
*
17493 TATTTTTT-CTTTGATTTATTTAA
1 TATTTTTTATTTTGATTTATTTAA
17516 TATTTTT
1 TATTTTT
17523 CGAATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (24 bp):
TATTTTTTATTTTGATTTATTTAA
Found at i:19120 original size:17 final size:17
Alignment explanation
Indices: 19100--19132 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19090 TTACCTTACA
19100 TATTTGTATAT-CTTATT
1 TATTT-TATATACTTATT
19117 TATTTTATATACTTAT
1 TATTTTATATACTTAT
19133 GTTGCATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTTTATATACTTATT
Found at i:20250 original size:14 final size:15
Alignment explanation
Indices: 20220--20251 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20210 TTCTCGATCC
20220 TTAAGATTAATTTTT
1 TTAAGATTAATTTTT
*
20235 TTAATATTAATTTTT
1 TTAAGATTAATTTTT
20250 TT
1 TT
20252 GTTGCCTCTA
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:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TTAAGATTAATTTTT
Found at i:20467 original size:26 final size:26
Alignment explanation
Indices: 20427--20479 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
20417 TTCGAGAAGT
*
20427 GAAATTGAATAATAATTGAATAGACA
1 GAAATTGAATAATAATTAAATAGACA
*
20453 GAAATTGAATGATAATTAAATAGACA
1 GAAATTGAATAATAATTAAATAGACA
20479 G
1 G
20480 GCGGAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (26 bp):
GAAATTGAATAATAATTAAATAGACA
Found at i:21189 original size:7 final size:7
Alignment explanation
Indices: 21177--21226 Score: 57
Period size: 7 Copynumber: 6.7 Consensus size: 7
21167 AACAAGTCCC
21177 TTTTGTT
1 TTTTGTT
21184 TTTTGTCTTT
1 TTTTG---TT
21194 TTTTGTT
1 TTTTGTT
21201 TTTTGTT
1 TTTTGTT
21208 TTTTCGTT
1 TTTT-GTT
21216 TTTT-TT
1 TTTTGTT
21222 TTTTG
1 TTTTG
21227 GTGACAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.16
7 18 0.47
8 7 0.18
10 7 0.18
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (7 bp):
TTTTGTT
Found at i:21199 original size:17 final size:16
Alignment explanation
Indices: 21177--21225 Score: 66
Period size: 15 Copynumber: 3.1 Consensus size: 16
21167 AACAAGTCCC
21177 TTTTGTTTTTTGTCTTT
1 TTTTGTTTTTTGT-TTT
21194 TTTTGTTTTTTG-TTT
1 TTTTGTTTTTTGTTTT
*
21209 TTTCGTTTTTT-TTTT
1 TTTTGTTTTTTGTTTT
21224 TT
1 TT
21226 GGTGACAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 18 0.60
17 12 0.40
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (16 bp):
TTTTGTTTTTTGTTTT
Found at i:21207 original size:24 final size:23
Alignment explanation
Indices: 21177--21225 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
21167 AACAAGTCCC
21177 TTTTGTTTTTT-GTCTTTTTTTGTT
1 TTTTGTTTTTTCGT-TTTTTTT-TT
21201 TTTTGTTTTTTCGTTTTTTTTTT
1 TTTTGTTTTTTCGTTTTTTTTTT
21224 TT
1 TT
21226 GGTGACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 4 0.17
24 18 0.75
25 2 0.08
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (23 bp):
TTTTGTTTTTTCGTTTTTTTTTT
Found at i:24740 original size:29 final size:29
Alignment explanation
Indices: 24670--24740 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
24660 TGCGTTCTGG
24670 ATTATTTGTATTTACTATTTAGCCCTTTAA
1 ATTATTTGT-TTTACTATTTAGCCCTTTAA
* *
24700 ATTAATTT-TTTTCCTATTTTAGTCCTTTAA
1 ATT-ATTTGTTTTACTA-TTTAGCCCTTTAA
*
24730 GTT-TTTGTTTT
1 ATTATTTGTTTT
24741 TGCATTTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
28 3 0.09
29 10 0.29
30 18 0.51
31 4 0.11
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (29 bp):
ATTATTTGTTTTACTATTTAGCCCTTTAA
Found at i:28999 original size:14 final size:14
Alignment explanation
Indices: 28989--29038 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
28979 AGCAAAAGTC
28989 AAGAAAAAAAAGAA
1 AAGAAAAAAAAGAA
29003 AAG-AAAAAAAGAAA
1 AAGAAAAAAAAG-AA
29017 AAGAAAAACAAAG-A
1 AAGAAAAA-AAAGAA
29031 AAGAAAAA
1 AAGAAAAA
29039 GACAAGAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.24
14 17 0.52
15 4 0.12
16 4 0.12
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:29024 original size:20 final size:20
Alignment explanation
Indices: 28995--29040 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
28985 AGTCAAGAAA
*
28995 AAAAAG-AAAAGAAAAAAAG
1 AAAAAGAAAAACAAAAAAAG
*
29014 AAAAAGAAAAACAAAGAAAG
1 AAAAAGAAAAACAAAAAAAG
29034 AAAAAGA
1 AAAAAGA
29041 CAAGAAGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAACAAAAAAAG
Found at i:29043 original size:16 final size:16
Alignment explanation
Indices: 28989--29032 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 16
28979 AGCAAAAGTC
28989 AAGAAAAA-AAAG-AA
1 AAGAAAAACAAAGAAA
29003 AAG-AAAA-AAAGAAA
1 AAGAAAAACAAAGAAA
29017 AAGAAAAACAAAGAAA
1 AAGAAAAACAAAGAAA
29033 GAAAAAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.30
14 8 0.30
15 4 0.15
16 7 0.26
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (16 bp):
AAGAAAAACAAAGAAA
Found at i:31640 original size:81 final size:81
Alignment explanation
Indices: 31495--32179 Score: 1022
Period size: 81 Copynumber: 8.5 Consensus size: 81
31485 GTATTAATGG
* * * * * * * *
31495 CACCTTTCTGCCAAAAAGCACAGTTAGGTATTTAGTCATTCATCACAAAGGTATTTAACCTTTCA
1 CACCTTTCTGTC-AAATGCACAGCTAGGCATTTAATCTTTTA-CTCAAAGGTATTTAACCTTTCA
*
31560 TCTAACTTGCATGATTGA
64 TCTAACTGGCATGATTGA
* * * *
31578 CACATTTCTGTCAAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTTAACATTTCATC
1 CACCTTTCTGTCAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATC
31643 TAACTGGCATGATTGA
66 TAACTGGCATGATTGA
* *
31659 CACCTTTCTGTCAAATGAACAGCTAGGCATTTAATCTTTTACTCAAAGGAATTTAACCTTTCATC
1 CACCTTTCTGTCAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATC
*
31724 TAACTGGCATGATTAA
66 TAACTGGCATGATTGA
* * * *
31740 CACATTTCAGTCAAATGCACAGCTAGGCATTTAATCTTTTACTTAAAGGAATTTAACCTTTCATC
1 CACCTTTCTGTCAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATC
31805 TAACTGGCATGATTGA
66 TAACTGGCATGATTGA
*
31821 CACCTTTCTTTCAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATC
1 CACCTTTCTGTCAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATC
31886 TAACTGGCATGATTGA
66 TAACTGGCATGATTGA
* * *
31902 CACCTTTCTGTCAAATGCAAAGTTAGGCATTTAATCTTTTACTCAAATGTATTTAA-----CATC
1 CACCTTTCTGTCAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATC
31962 TAACTGGCATGATTGA
66 TAACTGGCATGATTGA
* * *
31978 CACCTTTCTGTCAAATGCAAAGTTAGGCATTTAATCTTTTACTCAAATGTATTTAACCTTTCATC
1 CACCTTTCTGTCAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATC
32043 TAACTGGCATGATTGA
66 TAACTGGCATGATTGA
* * *
32059 CACCTTTCTGTCAAATGCACAACTAGGCATTTAATATTTTACTCAAAGGAATTTAACCTTTCATC
1 CACCTTTCTGTCAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATC
32124 TAACTGGCATGATTGA
66 TAACTGGCATGATTGA
* *
32140 CACATTTCTTTCAAA-GCACAGCTAGGCATTTAATCTTTTA
1 CACCTTTCTGTCAAATGCACAGCTAGGCATTTAATCTTTTA
32180 TTTTAAAATG
Statistics
Matches: 555, Mismatches: 42, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
76 76 0.14
80 23 0.04
81 423 0.76
82 23 0.04
83 10 0.02
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (81 bp):
CACCTTTCTGTCAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATC
TAACTGGCATGATTGA
Found at i:32593 original size:20 final size:20
Alignment explanation
Indices: 32568--32617 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
32558 TGGCTCAATA
*
32568 GTATCGGTACCCCTACCTTG
1 GTATCGATACCCCTACCTTG
32588 GTATCGATACCCCTACCTTG
1 GTATCGATACCCCTACCTTG
32608 GTATCGATAC
1 GTATCGATAC
32618 TTTTATATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.32, G:0.18, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCCTACCTTG
Found at i:33853 original size:131 final size:131
Alignment explanation
Indices: 33618--34039 Score: 566
Period size: 131 Copynumber: 3.3 Consensus size: 131
33608 GGGTATGACA
* *
33618 ACGTAGGAACTGTGTTATCAT-CCTAAAGATGGCATATCGTCCTCATCGCGTAGAAACCATGTCA
1 ACGTAGGAACCGTGTTATCATCCCTAAAGATGGCATATCGTCCTCATCGCGTAGGAACCATGTCA
**
33682 T-CCCTCGACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGTTATCCTCA
66 TCCCCT-GACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCA
*
33746 TG
130 TC
* * * ** * *
33748 ATGTAGGAACAGTGTTATCATCACTAAAGATGGCATGCCGTCCTCATCGCATAGGAACCGTGTCA
1 ACGTAGGAACCGTGTTATCATCCCTAAAGATGGCATATCGTCCTCATCGCGTAGGAACCATGTCA
* * * * * *
33813 TCCCCTGATCAGATCTCCTCTTCACGTAGGAGACGTGTCACCCTTAGATAATCAGCCGTCCTCAT
66 TCCCCTGACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCAT
33878 C
131 C
* * * * * *
33879 ACATAGGAACCGTGTTATCATCCCTAAATATGGCCTATCATCCTCATCACGTAGGAACCTTGTCA
1 ACGTAGGAACCGTGTTATCATCCCTAAAGATGGCATATCGTCCTCATCGCGTAGGAACCATGTCA
* *
33944 TCTCCT-ACCAGACCT-C-CATCATGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCAT
66 TCCCCTGACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCAT
34006 C
131 C
34007 ACGTAGGAACCGTGTTATCATCCCTAAAGATGG
1 ACGTAGGAACCGTGTTATCATCCCTAAAGATGG
34040 TCATTGTTTG
Statistics
Matches: 251, Mismatches: 39, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
128 73 0.29
129 1 0.00
130 26 0.10
131 147 0.59
132 4 0.02
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (131 bp):
ACGTAGGAACCGTGTTATCATCCCTAAAGATGGCATATCGTCCTCATCGCGTAGGAACCATGTCA
TCCCCTGACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCAT
C
Found at i:33893 original size:43 final size:40
Alignment explanation
Indices: 33784--33893 Score: 100
Period size: 43 Copynumber: 2.7 Consensus size: 40
33774 AAGATGGCAT
*
33784 GCCGTCCTCATCGCATAGGAACCGTGTCATCCCCTGATCA
1 GCCGTCCTCATCACATAGGAACCGTGTCATCCCCTGATCA
* * * *
33824 GATC-TCCTCTTCACGTAGGAGA-CGTGTCA-CCCTTAGATAATCA
1 G-CCGTCCTCATCACATAGGA-ACCGTGTCATCCCCT-G---ATCA
33867 GCCGTCCTCATCACATAGGAACCGTGT
1 GCCGTCCTCATCACATAGGAACCGTGT
33894 TATCATCCCT
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
39 4 0.07
40 22 0.41
41 2 0.04
42 2 0.04
43 24 0.44
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.25
Consensus pattern (40 bp):
GCCGTCCTCATCACATAGGAACCGTGTCATCCCCTGATCA
Found at i:34251 original size:30 final size:30
Alignment explanation
Indices: 34194--34256 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
34184 ATATTTACTG
*
34194 TTTAGCCCTTTAAATTTCTATTTTTTTCTAT
1 TTTAGCCCTTTAAATTTCTAGTTTTTTC-AT
* *
34225 TTTAGTCCTTTAAGTTTCT-GTTTTTTCAT
1 TTTAGCCCTTTAAATTTCTAGTTTTTTCAT
34254 TTT
1 TTT
34257 GGTCTTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.17
30 7 0.24
31 17 0.59
ACGTcount: A:0.16, C:0.14, G:0.06, T:0.63
Consensus pattern (30 bp):
TTTAGCCCTTTAAATTTCTAGTTTTTTCAT
Found at i:41688 original size:19 final size:19
Alignment explanation
Indices: 41661--41706 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41651 TGAAAAGATT
* *
41661 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAAAAGAAAA
41681 TAATAAATAAAAAAGAAAA
1 TAATAAATAAAAAAGAAAA
*
41700 AAATAAA
1 TAATAAA
41707 ATAATAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (19 bp):
TAATAAATAAAAAAGAAAA
Found at i:41779 original size:18 final size:17
Alignment explanation
Indices: 41761--41802 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
41751 GTTGTTTTTA
*
41761 AAATAAAGATAACAATT
1 AAATAAAGAAAACAATT
*
41778 AAATAAAAGAAAATAATT
1 AAAT-AAAGAAAACAATT
41796 AAATAAA
1 AAATAAA
41803 TAATTTAAAT
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:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (17 bp):
AAATAAAGAAAACAATT
Found at i:42479 original size:24 final size:24
Alignment explanation
Indices: 42451--42552 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 24
42441 AAGATAAATA
42451 TAAAATAATATCCTAAAACTTAAT
1 TAAAATAATATCCTAAAACTTAAT
* *
42475 T--AA-AATA--CTAAAACCTATT
1 TAAAATAATATCCTAAAACTTAAT
* * *
42494 TAAACTAAAATACCTAAAA-TAAAGAT
1 TAAAATAATAT-CCTAAAACT-TA-AT
*
42520 AAAAAAATAATATCCTAAAACTTAAT
1 --TAAAATAATATCCTAAAACTTAAT
42546 TAAAATA
1 TAAAATA
42553 CTAAAACCTA
Statistics
Matches: 55, Mismatches: 12, Indels: 22
0.62 0.13 0.25
Matches are distributed among these distances:
19 11 0.20
21 5 0.09
22 5 0.09
24 7 0.13
25 7 0.13
26 3 0.05
27 8 0.15
28 9 0.16
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.28
Consensus pattern (24 bp):
TAAAATAATATCCTAAAACTTAAT
Found at i:42536 original size:71 final size:71
Alignment explanation
Indices: 42401--42602 Score: 306
Period size: 71 Copynumber: 2.9 Consensus size: 71
42391 TCTTAAATCC
* *
42401 TAATT-AAACACTTAAA-CTATTTAAACT-AAATACC-AAAACAAAGATAAATATAAAATAATAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGAT-AA-A-AAAATAATAT
42462 CCTAAAACT
63 CCTAAAACT
*
42471 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAAGATAAAAAAATAATATCCT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAAAATAATATCCT
42536 AAAACT
66 AAAACT
*
42542 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGAT-AAAATATAATAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAAAATAATAT
42603 TTAAAATATT
Statistics
Matches: 123, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
70 16 0.13
71 76 0.62
72 12 0.10
73 9 0.07
74 10 0.08
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.27
Consensus pattern (71 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAAAATAATATCCT
AAAACT
Found at i:44561 original size:10 final size:11
Alignment explanation
Indices: 44547--44576 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
44537 CTGTTCAGAG
44547 AAAAATAAAAT
1 AAAAATAAAAT
44558 -AAAATAAAAT
1 AAAAATAAAAT
44568 AAAAATAAA
1 AAAAATAAA
44577 TAGAAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:50196 original size:20 final size:21
Alignment explanation
Indices: 50171--50221 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
50161 TGAAAAGATT
* *
50171 TAATAAAATAAAATAG-ATAA
1 TAATAAAATAAAAAAGAAAAA
50191 TAAT-AAATAAAAAAGAAAAA
1 TAATAAAATAAAAAAGAAAAA
50211 TAATAAAATAA
1 TAATAAAATAA
50222 TAAATTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 10 0.37
20 11 0.41
21 6 0.22
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (21 bp):
TAATAAAATAAAAAAGAAAAA
Found at i:50291 original size:18 final size:18
Alignment explanation
Indices: 50270--50312 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
50260 GTTGTTTTTA
*
50270 AAATAAAATAAAATAATT
1 AAATAAAAGAAAATAATT
50288 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
50306 AAATAAA
1 AAATAAA
50313 TAATTTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:50791 original size:12 final size:12
Alignment explanation
Indices: 50776--50805 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
50766 AAAAGTATAC
50776 GAAAAATAGAGA
1 GAAAAATAGAGA
*
50788 GAAAACTAGAGA
1 GAAAAATAGAGA
50800 GAAAAA
1 GAAAAA
50806 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:53417 original size:78 final size:79
Alignment explanation
Indices: 53270--53568 Score: 438
Period size: 79 Copynumber: 3.8 Consensus size: 79
53260 TATAATTGGG
* * * * *
53270 TCACCACTTTCATACTTAGATGTGTACTCTGTACGATACATCATCTTGCTTGTAGTGGGTGTGTT
1 TCACCACTTTCATATTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAGTGGGTGTGTA
53335 TCCCGTACAATACA
66 TCCCGTACAATACA
* * * * *
53349 TCACCACTTTCATTTTTAGATGTGTACCCCATATGAT-CATCATCTTGCTTACAGTAGGTGTGTA
1 TCACCACTTTCATATTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAGTGGGTGTGTA
*
53413 TCCCGTACAATGCA
66 TCCCGTACAATACA
* * *
53427 TCATCAGTTTCATATTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAATGGGTGTGTA
1 TCACCACTTTCATATTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAGTGGGTGTGTA
*
53492 TCCCATACAATACA
66 TCCCGTACAATACA
*
53506 TCACCACTTTCATATTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAACTGGGTGT
1 TCACCACTTTCATATTTAGATGTGTACCCCGTACGATACATCATCTTGCTTAT-AGTGGGTGT
53569 ATACCCCATG
Statistics
Matches: 194, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
78 68 0.35
79 118 0.61
80 8 0.04
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (79 bp):
TCACCACTTTCATATTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAGTGGGTGTGTA
TCCCGTACAATACA
Found at i:53458 original size:40 final size:39
Alignment explanation
Indices: 53336--53550 Score: 166
Period size: 40 Copynumber: 5.5 Consensus size: 39
53326 GGGTGTGTTT
* *
53336 CCCGTACAATACATCACCACTTTCATTTTTAGATGTGTAC
1 CCCGTACAATACATCATCA-TTTCATATTTAGATGTGTAC
* ** * * ** * *
53376 CCCATATGAT-CATCATC-TTGCTTACAGTAGGTGTGTAT
1 CCCGTACAATACATCATCATTTCATA-TTTAGATGTGTAC
*
53414 CCCGTACAATGCATCATCAGTTTCATATTTAGATGTGTAC
1 CCCGTACAATACATCATCA-TTTCATATTTAGATGTGTAC
* * * * * * *
53454 CCCGTACGATACATCATC-TTGCTTATAATGGGTGTGTAT
1 CCCGTACAATACATCATCATTTCATAT-TTAGATGTGTAC
* *
53493 CCCATACAATACATCACCACTTTCATATTTAGATGTGTAC
1 CCCGTACAATACATCATCA-TTTCATATTTAGATGTGTAC
*
53533 CCCGTACGATACATCATC
1 CCCGTACAATACATCATC
53551 TTGCTTATAA
Statistics
Matches: 128, Mismatches: 40, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
37 4 0.03
38 22 0.17
39 36 0.28
40 55 0.43
41 11 0.09
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (39 bp):
CCCGTACAATACATCATCATTTCATATTTAGATGTGTAC
Found at i:53570 original size:157 final size:157
Alignment explanation
Indices: 53277--53568 Score: 449
Period size: 157 Copynumber: 1.8 Consensus size: 157
53267 GGGTCACCAC
* * * * * *
53277 TTTCATACTTAGATGTGTACTCTGTACGATACATCATCTTGCTTGTAGTGGGTGTGTTTCCCGTA
1 TTTCATACTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAATGGGTGTGTATCCCATA
* * * *
53342 CAATACATCACCACTTTCATTTTTAGATGTGTACCCCATATGATCATCATCTTGCTTACAGTAGG
66 CAATACATCACCACTTTCATATTTAGATGTGTACCCCATACGATCATCATCTTGCTTAAACTAGG
53407 TGTGTATCCCGTACAATGCATCATCAG
131 TGTGTATCCCGTACAATGCATCATCAG
*
53434 TTTCATATTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAATGGGTGTGTATCCCATA
1 TTTCATACTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAATGGGTGTGTATCCCATA
* *
53499 CAATACATCACCACTTTCATATTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAACTG
66 CAATACATCACCACTTTCATATTTAGATGTGTACCCCATACGAT-CATCATCTTGCTTA-AACTA
53564 GGTGT
129 GGTGT
53569 ATACCCCATG
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
157 99 0.82
158 14 0.12
159 7 0.06
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (157 bp):
TTTCATACTTAGATGTGTACCCCGTACGATACATCATCTTGCTTATAATGGGTGTGTATCCCATA
CAATACATCACCACTTTCATATTTAGATGTGTACCCCATACGATCATCATCTTGCTTAAACTAGG
TGTGTATCCCGTACAATGCATCATCAG
Found at i:53574 original size:40 final size:39
Alignment explanation
Indices: 53290--53575 Score: 150
Period size: 40 Copynumber: 7.3 Consensus size: 39
53280 CATACTTAGA
* * * *
53290 TGTGTACTCTGTACGATACATCATCTTGCTTGTAGTGGG
1 TGTGTACCCCGTACGATACATCATCTTGCTTATAATGGG
** * * * * * *
53329 TGTGTTTCCCGTACAATACATCACCACTTTCATT-T-TTAGA
1 TGTGTACCCCGTACGATACATCA--TCTTGC-TTATAATGGG
* * * * *
53369 TGTGTACCCCATATGAT-CATCATCTTGCTTACAGTAGG
1 TGTGTACCCCGTACGATACATCATCTTGCTTATAATGGG
* * * * * * * *
53407 TGTGTATCCCGTACAATGCATCATC-AGTTTCATATTTAGA
1 TGTGTACCCCGTACGATACATCATCTTGCTT-ATA-ATGGG
53447 TGTGTACCCCGTACGATACATCATCTTGCTTATAATGGG
1 TGTGTACCCCGTACGATACATCATCTTGCTTATAATGGG
* * * * * * * * *
53486 TGTGTATCCCATACAATACATCACCACTTTCATAT-TTAGA
1 TGTGTACCCCGTACGATACATCA--TCTTGCTTATAATGGG
53526 TGTGTACCCCGTACGATACATCATCTTGCTTATAACTGGG
1 TGTGTACCCCGTACGATACATCATCTTGCTTATAA-TGGG
*
53566 TGTATACCCC
1 TGTGTACCCC
53576 ATGCTCTGAA
Statistics
Matches: 178, Mismatches: 56, Indels: 25
0.69 0.22 0.10
Matches are distributed among these distances:
36 2 0.01
37 4 0.02
38 26 0.15
39 54 0.30
40 75 0.42
41 15 0.08
42 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (39 bp):
TGTGTACCCCGTACGATACATCATCTTGCTTATAATGGG
Found at i:53949 original size:17 final size:17
Alignment explanation
Indices: 53927--54006 Score: 79
Period size: 17 Copynumber: 4.5 Consensus size: 17
53917 AAACAAGTTT
53927 CAACCTAAATATGGTTG
1 CAACCTAAATATGGTTG
*
53944 CAACCTAATTATGGTTG
1 CAACCTAAATATGGTTG
* ** *
53961 CAACCTAAAAACAAGTTC
1 CAACCTAAATA-TGGTTG
*
53979 CAACTTAAAATATGGATTG
1 CAACCT-AAATATGG-TTG
53998 CAACCTAAA
1 CAACCTAAA
54007 AACAAGCATG
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
17 25 0.52
18 12 0.25
19 11 0.23
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.26
Consensus pattern (17 bp):
CAACCTAAATATGGTTG
Found at i:54126 original size:25 final size:25
Alignment explanation
Indices: 54076--54127 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
54066 TAAAAATCAG
* *
54076 TTCATCACATACTACCAATATTGAA
1 TTCATCACAAACTACCAATATCGAA
*
54101 TTCATCATAAACTA-CAACTATCGAA
1 TTCATCACAAACTACCAA-TATCGAA
54126 TT
1 TT
54128 TATTAAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (25 bp):
TTCATCACAAACTACCAATATCGAA
Found at i:54793 original size:23 final size:23
Alignment explanation
Indices: 54749--54794 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54739 ATGATAACCC
* *
54749 ATTTTTATCTTTTCTCCCTTTTT
1 ATTTTTATCTTCTCTCACTTTTT
* *
54772 ATTTTTTTCTTCTCTCATTTTTT
1 ATTTTTATCTTCTCTCACTTTTT
54795 TAGAAACCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.72
Consensus pattern (23 bp):
ATTTTTATCTTCTCTCACTTTTT
Found at i:61122 original size:136 final size:136
Alignment explanation
Indices: 60872--61139 Score: 464
Period size: 136 Copynumber: 2.0 Consensus size: 136
60862 TTGAAGCCAC
* *
60872 TGATCTCTTTAGAGCTCAACTTTTAGACTTCAATCCTTAATCTAAATTCAATTTAGTCCTTAATA
1 TGATATCTTTAGAGCTCAACTTTTAGACTTCAAGCCTTAATCTAAATTCAATTTAGTCCTTAATA
* * *
60937 TGGCGAAAACTTCTAACCCCAAAATCAAGGTGTAACATAATAAGGGACTAGATCCCAGATGTCGT
66 TGGCGAAAAATTCTAACCCCAAAATCAAGGTGTAACAGAATAAGAGACTAGATCCCAGATGTCGT
61002 GGTCAT
131 GGTCAT
61008 TGATATCTTTAGAGCTCAACTTTTAGACTTCAAGCCTTAATCTAAATTCAATTTAGTCCTTAATA
1 TGATATCTTTAGAGCTCAACTTTTAGACTTCAAGCCTTAATCTAAATTCAATTTAGTCCTTAATA
* * *
61073 TGGCGAAAAATTCTAACCCCAAAATCAGGGTGTAACAGAATGAGAGACTAGATCCTAGATGTCGT
66 TGGCGAAAAATTCTAACCCCAAAATCAAGGTGTAACAGAATAAGAGACTAGATCCCAGATGTCGT
61138 GG
131 GG
61140 CCTTTAGACG
Statistics
Matches: 124, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
136 124 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (136 bp):
TGATATCTTTAGAGCTCAACTTTTAGACTTCAAGCCTTAATCTAAATTCAATTTAGTCCTTAATA
TGGCGAAAAATTCTAACCCCAAAATCAAGGTGTAACAGAATAAGAGACTAGATCCCAGATGTCGT
GGTCAT
Found at i:63661 original size:19 final size:18
Alignment explanation
Indices: 63618--63667 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
63608 TTTCATATAA
*
63618 TTTAGATATTTTTTATTTT
1 TTTA-ATATTTTTTATTCT
63637 TATTAATATTTTTTATCTCT
1 T-TTAATATTTTTTAT-TCT
*
63657 TTTAAAATTTT
1 TTTAATATTTT
63668 ATAAGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTAATATTTTTTATTCT
Found at i:63677 original size:25 final size:26
Alignment explanation
Indices: 63648--63708 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
63638 ATTAATATTT
* *
63648 TTTATCTCTTT-TAAAATTTTATAAG
1 TTTATCTCTTTCTAAAATATTATAAA
63673 TTTATCT-TATTCTAAAATATTATAAA
1 TTTATCTCT-TTCTAAAATATTATAAA
*
63699 TTCATCTCTT
1 TTTATCTCTT
63709 AATATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 1 0.03
25 9 0.30
26 19 0.63
27 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTATCTCTTTCTAAAATATTATAAA
Found at i:77560 original size:19 final size:19
Alignment explanation
Indices: 77538--77580 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
77528 ATTACCCTTT
77538 CAAATGTATATATTCATTC
1 CAAATGTATATATTCATTC
77557 CAAATGTATATATTCATTC
1 CAAATGTATATATTCATTC
77576 CAAAT
1 CAAAT
77581 TTTCTTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (19 bp):
CAAATGTATATATTCATTC
Found at i:79146 original size:11 final size:10
Alignment explanation
Indices: 79130--79246 Score: 78
Period size: 11 Copynumber: 11.5 Consensus size: 10
79120 GAATAATAAT
*
79130 AAAAATAAAG
1 AAAAAAAAAG
79140 AAAAAATAAAG
1 AAAAAA-AAAG
*
79151 AAAAAATGAA-
1 AAAAAA-AAAG
* *
79161 AAAAGAAAAT
1 AAAAAAAAAG
*
79171 AAAAGAAAAG
1 AAAAAAAAAG
*
79181 --GAAAAAAG
1 AAAAAAAAAG
**
79189 AAGGAAAAAG
1 AAAAAAAAAG
*
79199 AAGGAAAAAAG
1 AA-AAAAAAAG
79210 AAGAAAAAAAG
1 AA-AAAAAAAG
79221 AAGAAAAAAAG
1 AA-AAAAAAAG
*
79232 AAAAAAGAAG
1 AAAAAAAAAG
79242 AAAAA
1 AAAAA
79247 GGAAAAAAGA
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
8 6 0.07
9 2 0.02
10 40 0.44
11 43 0.47
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:79163 original size:8 final size:7
Alignment explanation
Indices: 79147--79267 Score: 86
Period size: 8 Copynumber: 16.1 Consensus size: 7
79137 AAGAAAAAAT
79147 AAAGAAA
1 AAAGAAA
79154 AAATGAAA
1 AAA-GAAA
79162 AAAGAAA
1 AAAGAAA
79169 ATAA-AAGA
1 A-AAGAA-A
79177 AAAGGAAA
1 AAA-GAAA
*
79185 AAAGAAGG
1 AAAGAA-A
*
79193 AAA-AAG
1 AAAGAAA
*
79199 AAGGAAA
1 AAAGAAA
79206 AAAGAAGA
1 AAAGAA-A
79214 AAA-AAA
1 AAAGAAA
*
79220 GAAGAAAA
1 AAAG-AAA
79228 AAAGAAA
1 AAAGAAA
79235 AAAGAAGAA
1 AAAG-A-AA
79244 AAAGGAAA
1 AAA-GAAA
79252 AAAGAAA
1 AAAGAAA
79259 AAGAGAAA
1 AA-AGAAA
79267 A
1 A
79268 TAAAATTGAA
Statistics
Matches: 94, Mismatches: 6, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
6 6 0.06
7 39 0.41
8 40 0.43
9 8 0.09
10 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:79202 original size:21 final size:22
Alignment explanation
Indices: 79158--79257 Score: 105
Period size: 22 Copynumber: 4.5 Consensus size: 22
79148 AAGAAAAAAT
*
79158 GAAAAAAGAA-AATAAAAGAAAAG
1 GAAAAAAGAAGAA-AAAA-AGAAG
*
79181 GAAAAAAGAAG-GAAAAAGAAG
1 GAAAAAAGAAGAAAAAAAGAAG
79202 GAAAAAAGAAGAAAAAAAGAAG
1 GAAAAAAGAAGAAAAAAAGAAG
* * *
79224 AAAAAAAGAAAAAAGAAGAAAAAG
1 GAAAAAAGAAGAAA-AA-AAGAAG
79248 GAAAAAAGAA
1 GAAAAAAGAA
79258 AAAGAGAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.23
22 25 0.38
23 12 0.18
24 14 0.21
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (22 bp):
GAAAAAAGAAGAAAAAAAGAAG
Found at i:80978 original size:28 final size:28
Alignment explanation
Indices: 80947--81014 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
80937 TACCTTGAGA
80947 AGAGAAAATCATAATTCAAACCTCAAAT
1 AGAGAAAATCATAATTCAAACCTCAAAT
*
80975 AGAGAAAATCACAATTCAAACCTCAAAT
1 AGAGAAAATCATAATTCAAACCTCAAAT
81003 AGAGAAAATCAT
1 AGAGAAAATCAT
81015 GTTTGGAGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.19
Consensus pattern (28 bp):
AGAGAAAATCATAATTCAAACCTCAAAT
Found at i:81510 original size:101 final size:101
Alignment explanation
Indices: 81332--81671 Score: 361
Period size: 101 Copynumber: 3.4 Consensus size: 101
81322 ACGATAAAAA
** * * *
81332 TTATCTCACTTGAGATCCTTTTTCTTAAAATCAATTTCGTCTCACTTGAGACAGATTCCTTTGAA
1 TTATCTCACTTGAGATTATTTTTCTTAAAATCAATTTCGTCTCGCTTGAGATAGTTTCCTTTGAA
*
81397 GCACAAAATTTGGAATTGCTTCACTTGAAACAAGAT
66 ACACAAAATTTGGAATTGCTTCACTTGAAACAAGAT
* * *
81433 TTATCTCACTCGATATTGTTTTTCTTAAAATCAATTTCGTCTCGCTTGAGATAGTTTCCTTTGAA
1 TTATCTCACTTGAGATTATTTTTCTTAAAATCAATTTCGTCTCGCTTGAGATAGTTTCCTTTGAA
**
81498 ACACAAGTTTTGGGAA-TGCTTCA-TTCGAAACAAGAT
66 ACACAAAATTT-GGAATTGCTTCACTT-GAAACAAGAT
* * * * * *
81534 TTATCTGACTTGAGATTATTTTTCTTAAAGTCAATTTCATATTGCTTGA-ATCATTTTCCTCTT-
1 TTATCTCACTTGAGATTATTTTTCTTAAAATCAATTTCGTCTCGCTTGAGAT-AGTTTCCT-TTG
* *
81597 AAACATAAAATTTGGAATTGTTTCACTTGAAA-AATG-T
64 AAACACAAAATTTGGAATTGCTTCACTTGAAACAA-GAT
* * * * *
81634 TTATCCCATTTGAGA-TATCTTTTATTGAAATAAATTTC
1 TTATCTCACTTGAGATTAT-TTTTCTTAAAATCAATTTC
81672 TTTTCTTTCA
Statistics
Matches: 201, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
99 3 0.01
100 38 0.19
101 152 0.76
102 8 0.04
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (101 bp):
TTATCTCACTTGAGATTATTTTTCTTAAAATCAATTTCGTCTCGCTTGAGATAGTTTCCTTTGAA
ACACAAAATTTGGAATTGCTTCACTTGAAACAAGAT
Found at i:82013 original size:45 final size:43
Alignment explanation
Indices: 81891--82019 Score: 141
Period size: 45 Copynumber: 2.9 Consensus size: 43
81881 TTGTTCGTCC
* ** *
81891 TTTTGCTCGATTCTATCACAGAAGAAGGTATATCATCATCAACA
1 TTTTGCTCGATTCTATCACAGAAGGAGGTGGATCAT-ATTAACA
* * * **
81935 TTTTGTTCAATTCCATCACAGAAGGAGGTGGATCAATATTGTCA
1 TTTTGCTCGATTCTATCACAGAAGGAGGTGGATC-ATATTAACA
81979 TTCTTGCTCGATTCTATCACAGAAGGAGGTGGATCGATATT
1 TT-TTGCTCGATTCTATCACAGAAGGAGGTGGATC-ATATT
82020 TACAATGGAA
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
44 34 0.49
45 36 0.51
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (43 bp):
TTTTGCTCGATTCTATCACAGAAGGAGGTGGATCATATTAACA
Found at i:82149 original size:208 final size:208
Alignment explanation
Indices: 81783--82387 Score: 808
Period size: 208 Copynumber: 2.9 Consensus size: 208
81773 TTCAATTCAA
* * * * *
81783 TCCATCAAAGAAGGAGATGGATC-ATCATTTCCAATGGAAAGGTTCATAATGAGAATAACTCATC
1 TCCATCACAGAAGGAGGTGGATCGATCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATA
* *
81847 CGAAGAGGGAGAAGAAATTCATAATAAGAAGAACTTGTTCG-TCCTTTTGCTCGATTCTATCACA
66 CGAAGAGGGAGAA-TAGTTCATAATAAGAAGAACTTGTTCGCT-CTTTTGCTCGATTCTATCACA
* * * * *
81911 GAAGAAGGTATATCATCATCAACATTTTGTTCAATTCCATCACAGAAGGAGGTGGATCAATATTG
129 GAATAAGGTAGATCAACACCAACATTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAATATTG
81976 TCATTCTTG-CTCGAT
194 TCATTCTTGCCT-GAT
* * *
81991 TCTATCACAGAAGGAGGTGGATCGAT-ATTTACAATGGAAGGGTTCATAATGAAAAGAACTCATA
1 TCCATCACAGAAGGAGGTGGATCGATCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATA
* *
82055 CGAAGAGGGAGAATTAGTTCATAATGAGAAGAACATGTTCGCTCTTTTGCTCGATTCTATCACAG
66 CGAAGAGGGAGAA-TAGTTCATAATAAGAAGAACTTGTTCGCTCTTTTGCTCGATTCTATCACAG
* *
82120 AATAAGGTAGATCAACACCAACATTTTGTTCGATTCCATCATAGAAGGAGGTGGATAAATATTGT
130 AATAAGGTAGATCAACACCAACATTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAATATTGT
82185 CATTCTTGCCTGAT
195 CATTCTTGCCTGAT
* * * *
82199 TCCATCACAGAAAGAAGTGGAACG-TCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCGTC
1 TCCATCACAGAAGGAGGTGGATCGATCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCAT-
* * * * *
82263 TCGAAGAGGGAGAATAGGTTCATAATAAGAAGAACTTGTCCACCCTTTTGTTCGATTCTATCACA
65 ACGAAGAGGGAGAATA-GTTCATAATAAGAAGAACTTGTTCGCTCTTTTGCTCGATTCTATCACA
* * * **
82328 GAATGAGGTAGATCAAC-CTCAACATTTCGTTCGATCCCATCACAGAATAAGGTGGATCAA
129 GAATAAGGTAGATCAACAC-CAACATTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAA
82388 CATTTCCAAT
Statistics
Matches: 349, Mismatches: 41, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
207 1 0.00
208 237 0.68
209 111 0.32
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (208 bp):
TCCATCACAGAAGGAGGTGGATCGATCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATA
CGAAGAGGGAGAATAGTTCATAATAAGAAGAACTTGTTCGCTCTTTTGCTCGATTCTATCACAGA
ATAAGGTAGATCAACACCAACATTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAATATTGTC
ATTCTTGCCTGAT
Found at i:83746 original size:14 final size:14
Alignment explanation
Indices: 83657--83748 Score: 53
Period size: 14 Copynumber: 6.5 Consensus size: 14
83647 TTTTTATTTA
83657 TTTAATTTTAGTCC
1 TTTAATTTTAGTCC
* * *
83671 TTTAATTTCATTAC
1 TTTAATTTTAGTCC
*
83685 TTTAATTTTCTA-T-T
1 TTTAA-TTT-TAGTCC
* * *
83699 TTTTATTTTTGCCC
1 TTTAATTTTAGTCC
* * *
83713 TTCATTTTTCAGTAC
1 TTTAATTTT-AGTCC
83728 TTTAATTTTAGTCC
1 TTTAATTTTAGTCC
83742 TTTAATT
1 TTTAATT
83749 ATTGCGCTTT
Statistics
Matches: 55, Mismatches: 18, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
12 1 0.02
13 3 0.05
14 37 0.67
15 13 0.24
16 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.04, T:0.61
Consensus pattern (14 bp):
TTTAATTTTAGTCC
Found at i:83797 original size:2 final size:2
Alignment explanation
Indices: 83790--83831 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
83780 AGTCCCATGA
*
83790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
83832 TATCACATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:106298 original size:8 final size:8
Alignment explanation
Indices: 106266--106329 Score: 57
Period size: 8 Copynumber: 8.5 Consensus size: 8
106256 CTTGAAGAAA
*
106266 AAAAAAGG
1 AAAAAATG
*
106274 AACAAAT-
1 AAAAAATG
106281 AAAAAGATG
1 AAAAA-ATG
106290 AAAAAATG
1 AAAAAATG
106298 -AAAAATG
1 AAAAAATG
106305 -AAAAA--
1 AAAAAATG
*
106310 AAGAAATG
1 AAAAAATG
106318 AAAAAATG
1 AAAAAATG
106326 AAAA
1 AAAA
106330 GAGAAAAAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
6 4 0.09
7 16 0.35
8 21 0.46
9 5 0.11
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:106316 original size:13 final size:13
Alignment explanation
Indices: 106300--106338 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
106290 AAAAAATGAA
106300 AAATGAAAAAAAG
1 AAATGAAAAAAAG
*
106313 AAATGAAAAAATG
1 AAATGAAAAAAAG
* *
106326 AAAAGAGAAAAAG
1 AAATGAAAAAAAG
106339 GAGGGTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
AAATGAAAAAAAG
Found at i:107820 original size:334 final size:334
Alignment explanation
Indices: 107211--107853 Score: 1020
Period size: 334 Copynumber: 1.9 Consensus size: 334
107201 TTGATCAACA
*
107211 TTTCCAATGAAGAGTTTATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
* * *
107276 AAGAGCCTATTCGACCTATCACTTGATTCATGGCGTTTCGAATCAGTGACACCTCGCTTGAGGGA
66 AAGAGCCTATTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGA
*
107341 TCAACATTTCCAGAGAATAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGA
131 TCAACATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGA
* *
107406 GAAGAACTTGTTCCTTTCAAATCCATCACAGAAAGAGATGGATTAAAATTTCCAATGGAGAGTTC
196 GAAGAACTTGTTCCTTTCAAATCCATCACAGAAAGAGATGGATCAAAATTTCCAATGAAGAGTTC
* * *
107471 ATAATAAGAAGAACTCATCCAACGA-GAGAGAATAATTTCATAATGAGAAAAATTTGTCCAACTT
261 ATAATAAGAAGAACTCATCCAAAGAGGA-AGAAGAAGTTCATAATGAGAAAAATTTGTCCAACTT
107535 CGCATTAGTG
325 CGCATTAGTG
*
107545 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
** * *
107610 AAGAGTTTGTTCGACCTATCACTCGATTCACGGCATTTTGAATCAGTGACACCTCGCTTGAGGGA
66 AAGAGCCTATTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGA
** * * * *
107675 TTGACATTTCTA-ATTAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGGGAAAGTTCATAATG
131 TCAACATTTCCAGA-GAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATG
* * * *
107739 AGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTGAAGAGTT
195 AGAAGAACTTGTTCCTTTCAAATCCATCACAGAAAGAGATGGATCAAAATTTCCAATGAAGAGTT
*
107804 CATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAA
260 CATAATAAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAA
107854 GAACTTGTTC
Statistics
Matches: 281, Mismatches: 26, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
333 1 0.00
334 278 0.99
335 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (334 bp):
TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
AAGAGCCTATTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGA
TCAACATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGA
GAAGAACTTGTTCCTTTCAAATCCATCACAGAAAGAGATGGATCAAAATTTCCAATGAAGAGTTC
ATAATAAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAAAATTTGTCCAACTTC
GCATTAGTG
Found at i:107863 original size:20 final size:20
Alignment explanation
Indices: 107800--107864 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
107790 TTCAGTGAAG
107800 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
107820 CA-TCCA-AA-GAGGAAGAAGA
1 -AGTTCATAATGA-GAAGAACT
107839 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
107859 TGTTCA
1 AGTTCA
107865 ACCTTGGTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:107927 original size:117 final size:114
Alignment explanation
Indices: 107690--107982 Score: 408
Period size: 117 Copynumber: 2.6 Consensus size: 114
107680 ATTTCTAATT
*
107690 AAGAGTTCATAATGAGAAGAACTCGTCCTAAAG-GG--G-A-AAGTTCATAATGAGAAGAACTTG
1 AAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
107750 TT---CCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
65 TTCAACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
107797 AAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * *
107862 TCAACCTTGGTTCGATTTCATCACAGAAGGAGGTGGATCAACATTTTCAGTG
66 TCAACC-T--TTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
107914 AAGAGTTCATAATGAGAAGAACTCATCCAACA-A-GAGAGAAGAAGTTCATAATGAGAAGAACTT
1 AAGAGTTCATAATGAGAAGAACTCATCCAA-AGAGGA-AGAAGAAGTTCATAATGAGAAGAACTT
107977 GTTCAA
64 GTTCAA
107983 TCCAACGCTT
Statistics
Matches: 167, Mismatches: 6, Indels: 16
0.88 0.03 0.08
Matches are distributed among these distances:
106 4 0.02
107 29 0.17
109 1 0.01
110 1 0.01
111 25 0.15
114 2 0.01
115 1 0.01
116 2 0.01
117 101 0.60
118 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (114 bp):
AAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
Found at i:115543 original size:12 final size:12
Alignment explanation
Indices: 115527--115559 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
115517 CATTTTTTTA
115527 TTTTTATCTTCAC
1 TTTTTAT-TTCAC
115540 TTTTTATTTCA-
1 TTTTTATTTCAC
115551 TTTTTATTT
1 TTTTTATTT
115560 GATCAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 4 0.20
13 7 0.35
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATTTCAC
Found at i:118394 original size:18 final size:19
Alignment explanation
Indices: 118364--118406 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
118354 TATTCTATTA
*
118364 TTTT-TTTACTTTAATTGC
1 TTTTATTTACTTTAATCGC
*
118382 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGC
118400 TTTTATT
1 TTTTATT
118407 ACTACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGC
Found at i:120857 original size:31 final size:31
Alignment explanation
Indices: 120811--120883 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
120801 ATAAAAAGAT
* * *
120811 AGAGAGAAAATATAGAAAAATAAGGAAA-AAA
1 AGAGATAAAAGATAGAAAAAGAA-GAAACAAA
120842 AGAGATAAAAGATAGAAAAAGAAGAAACAAA
1 AGAGATAAAAGATAGAAAAAGAAGAAACAAA
*
120873 A-AAATAAAAGA
1 AGAGATAAAAGA
120884 GAAATGATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 13 0.35
31 24 0.65
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.08
Consensus pattern (31 bp):
AGAGATAAAAGATAGAAAAAGAAGAAACAAA
Found at i:125348 original size:26 final size:26
Alignment explanation
Indices: 125319--125370 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
125309 GGATCAATTT
125319 TTTGAAGAGAAGCTCGAAATATTGGG
1 TTTGAAGAGAAGCTCGAAATATTGGG
125345 TTTGAAGAGAAGCTCGAAATATTGGG
1 TTTGAAGAGAAGCTCGAAATATTGGG
125371 GCATGCTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (26 bp):
TTTGAAGAGAAGCTCGAAATATTGGG
Found at i:125938 original size:7 final size:7
Alignment explanation
Indices: 125928--125964 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
125918 AACAAAAACA
125928 AAAAGAT
1 AAAAGAT
125935 AAAAGAT
1 AAAAGAT
125942 AAAAGAT
1 AAAAGAT
125949 AAAAGAT
1 AAAAGAT
125956 AAAAGAT
1 AAAAGAT
125963 AA
1 AA
125965 TAAAAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAGAT
Found at i:125938 original size:14 final size:13
Alignment explanation
Indices: 125901--125975 Score: 62
Period size: 14 Copynumber: 5.5 Consensus size: 13
125891 AAAAATATAT
125901 AAAAAGATAGAAAA
1 AAAAAGATA-AAAA
* * *
125915 CAAAACA-AAAAC
1 AAAAAGATAAAAA
125927 AAAAAGATAAAAGA
1 AAAAAGATAAAA-A
*
125941 TAAAAGATAAAAGA
1 AAAAAGATAAAA-A
*
125955 TAAAAGATAATAAA
1 AAAAAGATAA-AAA
125969 AAAAAGA
1 AAAAAGA
125976 AGAATAAGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
12 8 0.16
13 5 0.10
14 35 0.70
15 2 0.04
ACGTcount: A:0.76, C:0.04, G:0.11, T:0.09
Consensus pattern (13 bp):
AAAAAGATAAAAA
Found at i:125945 original size:21 final size:20
Alignment explanation
Indices: 125921--125975 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
125911 AAAACAAAAC
125921 AAAAACAAAAAGATAAAAGAT
1 AAAAA-AAAAAGATAAAAGAT
*
125942 AAAAGATAAAAGATAAAAGAT
1 AAAA-AAAAAAGATAAAAGAT
125963 AATAAAAAAAAGA
1 AA-AAAAAAAAGA
125976 AGAATAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.76, C:0.02, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAAAAAAAAGATAAAAGAT
Found at i:128513 original size:133 final size:134
Alignment explanation
Indices: 128309--128867 Score: 669
Period size: 134 Copynumber: 4.2 Consensus size: 134
128299 GTGAGTCAAA
* * * *
128309 CTCGATTCAATCTTCCCTGAAGAACAATAGAATGAATCAACATCCCCAGATATGATTTTCCTTCA
1 CTCGATTCAATCTTCCCTGAGGAACAATAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
** *
128374 AGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
66 AGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
128439 CTAC
131 CTAC
* * * * *
128443 CTTGATTCAATCTTCCATGAGGAACAATGGAATGAATTAACGT-CTCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGGAACAATAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * ** * * *
128507 AAAAGAAGCATAACAGATCTTTGTTTTTCAAGATTTGATATTCCCTGAGTAATA-TAGGAACAAG
66 AGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGT-GGAACAAG
* *
128571 TATGC
130 TCTAC
* * * * *
128576 CTCGATTCAATCTTCCATGAGTAACAATAGAATGAATCAATG-CCTCCAGATCTGATATTCCCTT
1 CTCGATTCAATCTTCCCTGAGGAACAATAGAATGAATCAACGTCC-CCAGATCTGATTTTCCCTC
* * *
128640 AAGAAGAAGCAAAACTGAT-CC-CTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAG
65 AAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
128703 TCTAC
130 TCTAC
* ** * * *
128708 CTCGATTCAATCTTCCCTGAGTAACGGTGGAATAAATCAAAGTCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGGAACAATAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * ***
128773 AGAAGAAGTAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGGTAGTGGAACAAGT
66 AGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
128838 CTAC
131 CTAC
** * *
128842 CTTAATTCAATTTTCCCTGAAGAACA
1 CTCGATTCAATCTTCCCTGAGGAACA
128868 GAGAAATAAG
Statistics
Matches: 356, Mismatches: 62, Indels: 14
0.82 0.14 0.03
Matches are distributed among these distances:
132 108 0.30
133 116 0.33
134 132 0.37
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAGGAACAATAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
AGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTAC
Found at i:129068 original size:3 final size:3
Alignment explanation
Indices: 129060--129101 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
129050 CGTTTTAATT
* *
129060 TTA TTA TTA TTA TTT TTC TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
129102 ACATTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:133800 original size:2 final size:2
Alignment explanation
Indices: 133793--133819 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
133783 CCATTTTTAT
133793 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
133820 TTGGTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:133841 original size:187 final size:188
Alignment explanation
Indices: 133617--133993 Score: 702
Period size: 187 Copynumber: 2.0 Consensus size: 188
133607 TGTGTATGTG
133617 TATATATATATATATGTTGGTTTATAGATTAAGTCTTATGGATTCTTTTATTTTTCCACGATAGA
1 TATATATATATATATGTTGGTTTATAGATTAAGTCTTATGGATTCTTTTATTTTTCCACGATAGA
*
133682 GGTAAATGTCCTATAGTATTTTTTTATGGGATTCTATTGTACAAAGAAATGTGAGTGCATAGCTT
66 GGTAAATGTCCTATAGTATTTTTTTATGGGATTCTATTGTACAAAGAAATATGAGTGCATAGCTT
*
133747 TTGCTTCGACAATTATTAAGTTTGGTTTTTTGTTCCCCATTTTTATTATATATATATA
131 TTGCTTCGACAATTATTAAGTTTGGTTTTATGTTCCCCATTTTTATTATATATATATA
* *
133805 TATATATATATATAT-TTGGTTTATAGATTAAGTCTTATGGATTCTTTTATTTTTCCTCGATTGA
1 TATATATATATATATGTTGGTTTATAGATTAAGTCTTATGGATTCTTTTATTTTTCCACGATAGA
133869 GGTAAATGTCCTATAGTATTTTTTTATGGGATTCTATTGTACAAAGAAATATGAGTGCATAGCTT
66 GGTAAATGTCCTATAGTATTTTTTTATGGGATTCTATTGTACAAAGAAATATGAGTGCATAGCTT
*
133934 TTGCTTCGATAATTATTAAGTTTGGTTTTATGTTCCCCATTTTTATTATATATATATA
131 TTGCTTCGACAATTATTAAGTTTGGTTTTATGTTCCCCATTTTTATTATATATATATA
133992 TA
1 TA
133994 CATACATAAA
Statistics
Matches: 184, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
187 169 0.92
188 15 0.08
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (188 bp):
TATATATATATATATGTTGGTTTATAGATTAAGTCTTATGGATTCTTTTATTTTTCCACGATAGA
GGTAAATGTCCTATAGTATTTTTTTATGGGATTCTATTGTACAAAGAAATATGAGTGCATAGCTT
TTGCTTCGACAATTATTAAGTTTGGTTTTATGTTCCCCATTTTTATTATATATATATA
Found at i:137945 original size:38 final size:38
Alignment explanation
Indices: 137901--137976 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
137891 TGATATAAGT
137901 TATATGATATG-GACATAAAGAATAATATGA-ACATGTGA
1 TATATGATATGAG-C-TAAAGAATAATATGATACATGTGA
* *
137939 TATATGATATGAGCTAAAGAATTATATGATATATGTGA
1 TATATGATATGAGCTAAAGAATAATATGATACATGTGA
137977 ACATAGTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 14 0.41
38 19 0.56
39 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (38 bp):
TATATGATATGAGCTAAAGAATAATATGATACATGTGA
Found at i:138336 original size:21 final size:21
Alignment explanation
Indices: 138310--138399 Score: 110
Period size: 21 Copynumber: 4.3 Consensus size: 21
138300 TCCCTAAGGA
*
138310 GTGGTCCTTTGGGACATCTAT
1 GTGGTCCTTTGGGACATATAT
*
138331 GTGGT-CTTTCGGGACATCTAT
1 GTGGTCCTTT-GGGACATATAT
* *
138352 CTGGTCCTTCGGGACATATAT
1 GTGGTCCTTTGGGACATATAT
* *
138373 GTGGTCCTTTAGGACAAATAT
1 GTGGTCCTTTGGGACATATAT
138394 GTGGTC
1 GTGGTC
138400 TTTCGAGACA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
20 4 0.07
21 53 0.88
22 3 0.05
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.36
Consensus pattern (21 bp):
GTGGTCCTTTGGGACATATAT
Found at i:138409 original size:21 final size:21
Alignment explanation
Indices: 138310--138412 Score: 93
Period size: 21 Copynumber: 4.9 Consensus size: 21
138300 TCCCTAAGGA
**
138310 GTGGTCCTTT-GGGACATCTAT
1 GTGGT-CTTTCGGGACAAATAT
**
138331 GTGGTCTTTCGGGACATCTAT
1 GTGGTCTTTCGGGACAAATAT
* * *
138352 CTGGTCCTTCGGGACATATAT
1 GTGGTCTTTCGGGACAAATAT
*
138373 GTGGTCCTTT-AGGACAAATAT
1 GTGGT-CTTTCGGGACAAATAT
*
138394 GTGGTCTTTCGAGACAAAT
1 GTGGTCTTTCGGGACAAAT
138413 TCTATGTGCC
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
20 8 0.11
21 59 0.84
22 3 0.04
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (21 bp):
GTGGTCTTTCGGGACAAATAT
Found at i:150764 original size:30 final size:30
Alignment explanation
Indices: 150728--150785 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
150718 ATTGTATTTG
*
150728 TTGTATTTATTATTTATCTAAATTATTTAT
1 TTGTATTTATCATTTATCTAAATTATTTAT
* * *
150758 TTGTATTTATCGTTTATTTGAATTATTT
1 TTGTATTTATCATTTATCTAAATTATTT
150786 GATTATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.03, G:0.07, T:0.64
Consensus pattern (30 bp):
TTGTATTTATCATTTATCTAAATTATTTAT
Found at i:163380 original size:8 final size:8
Alignment explanation
Indices: 163367--163396 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
163357 CCTAAGTTGA
163367 AAAAAAAG
1 AAAAAAAG
163375 AAAAAAAG
1 AAAAAAAG
163383 AAAAAAGAG
1 AAAAAA-AG
163392 AAAAA
1 AAAAA
163397 CATTTAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:163472 original size:14 final size:14
Alignment explanation
Indices: 163433--163481 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
163423 GCCCTAAATT
163433 GAAA-AAAG-AAAA
1 GAAAGAAAGAAAAA
163445 GAAA-AAGAGAAAAAA
1 GAAAGAA-AG-AAAAA
*
163460 GAACGAAAGAAAAA
1 GAAAGAAAGAAAAA
163474 GAAAGAAA
1 GAAAGAAA
163482 ACAAGGTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 6 0.19
13 2 0.06
14 12 0.39
15 9 0.29
16 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (14 bp):
GAAAGAAAGAAAAA
Found at i:164394 original size:105 final size:105
Alignment explanation
Indices: 164212--164473 Score: 452
Period size: 105 Copynumber: 2.5 Consensus size: 105
164202 GGTTTTACCT
164212 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
164277 TGAAGGGACCGCTGGTTGTCAACAATAGCTTCCCAAATTC
66 CGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAAATTC
* * *
164317 AGAGCCAATTTTAACTTAACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
164382 CGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAAATTC
*
164422 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
164474 GACCGCTGGT
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
105 146 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.21
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAAATTC
Found at i:164532 original size:86 final size:86
Alignment explanation
Indices: 164387--164559 Score: 303
Period size: 86 Copynumber: 2.0 Consensus size: 86
164377 CACGACGAAG
164387 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
1 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
164452 ATTGGACT-CAAGACAACGCAA
66 ATTGGACTCCAA-ACAACGCAA
* *
164473 GGACCGCTGGTTGTCAATAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAATGAT
1 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
*
164538 ATTGGACTCCAAACAATGCAA
66 ATTGGACTCCAAACAACGCAA
164559 G
1 G
164560 TTCAACTTCA
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
86 80 0.96
87 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (86 bp):
GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
ATTGGACTCCAAACAACGCAA
Found at i:164604 original size:105 final size:105
Alignment explanation
Indices: 164473--165182 Score: 917
Period size: 105 Copynumber: 6.7 Consensus size: 105
164463 GACAACGCAA
* *
164473 GGACCGCTGGTTGTCAATAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAATGAT
1 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
*
164538 ATTGGACTCCAAACAATGCAAGTTCAACTTCACGACGAAG
66 ATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAAG
* *
164578 GGACCGCTGGTTGTCAACAACAACTTCCCAAATTCAGATCCAATTTCAACTTCACAGCGAAGGAT
1 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
* *
164643 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAG
66 ATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAAG
*
164683 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCACAGCGAAGGAT
1 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
*
164748 ATTGGACT-CAAGACAACGCAAGTTCAACTTCACGACAAAG
66 ATTGGACTCCAA-ACAACGCAAGTTCAACTTCACGACGAAG
* *
164788 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCACAGGGAAGGAT
1 GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
*
164853 ATTGGACT-CAAGACAACGCAAGTTCAACTTCACAACGAAG
66 ATTGGACTCCAA-ACAACGCAAGTTCAACTTCACGACGAAG
* * * * * *
164893 GGACGGCTGGTTGTCAAAAAACAATTTCCCAATTTTAGGGCCAATTTCAACTTCACAGCGAAGAA
1 GGACCGCTGGTTGTC-AACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGA
* * *
164958 TATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAG
65 TATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAAG
* ** * * * * *
164999 GGACGGCTGGTTGTCAACAAACAACTTTTC-AGTT-ACACCCACGATTTCAA-TTCCACAACGGA
1 GGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA--ATTTCAACTT-CACAGCGAA
* * * * *
165061 GGATATCGTGCCACTCGAGACAACACAAGTTAAACTTCACGACGAAG
62 GGATAT--TG-GACTCCAAACAACGCAAGTTCAACTTCACGACGAAG
** * * * * *
165108 GGATGGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGA
1 GGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGA
165173 TATTGGACTC
65 TATTGGACTC
165183 AGAAGGGGCC
Statistics
Matches: 542, Mismatches: 50, Indels: 25
0.88 0.08 0.04
Matches are distributed among these distances:
104 6 0.01
105 317 0.58
106 127 0.23
107 3 0.01
108 2 0.00
109 79 0.15
110 3 0.01
111 5 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
GGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
ATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAAG
Found at i:164746 original size:296 final size:305
Alignment explanation
Indices: 164212--165025 Score: 1207
Period size: 296 Copynumber: 2.7 Consensus size: 305
164202 GGTTTTACCT
*
164212 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGA
* * * * * *
164277 TGAAGGGACCGCTGGTTGTCAACAATAGCTTCCCAAATTCAGAGCCAATTTTAACTTAACAACGA
66 CGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAAATTCAGAGCCAATTTCAACTTCACAGCGA
164342 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
131 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
164407 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT-CAA-G-A-C-A
196 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTACAACGAATCAA
*
164467 -ACG-C-AA-GGACCGCTGGTTGTCAATAACAACTTCCCAATTTC
261 CACGACAAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTC
* *
164508 AGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAAACAATGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGA
*
164573 CGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAAATTCAGATCCAATTTCAACTTCACAGCGA
66 CGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAAATTCAGAGCCAATTTCAACTTCACAGCGA
*
164638 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAA
131 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
164703 CAACTTCCCAATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCA
196 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT----ACAACG-A
*
164768 AGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTT
256 A--TCAA---CACGACAAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTC
* *
164823 AGAGCCAATTTCAACTTCACAGGGAAGGATATTGGACT-CAAGACAACGCAAGTTCAACTTCACA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA-ACAACGCAAGTTCAACTTCACG
* * * * * *
164887 ACGAAGGGACGGCTGGTTGTCAAAAAACAATTTCCCAATTTTAGGGCCAATTTCAACTTCACAGC
65 ACGAAGGGACCGCTGGTTGTC-AACAACAACTTCCCAAATTCAGAGCCAATTTCAACTTCACAGC
* * * *
164952 GAAGAATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
129 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
165017 AAACAACTT
194 -AACAACTT
165026 TTCAGTTACA
Statistics
Matches: 466, Mismatches: 30, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
296 236 0.51
301 3 0.01
302 1 0.00
304 1 0.00
307 1 0.00
308 1 0.00
312 3 0.01
313 1 0.00
314 5 0.01
315 109 0.23
316 97 0.21
317 8 0.02
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (305 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAAATTCAGAGCCAATTTCAACTTCACAGCGA
AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTACAACGAATCAA
CACGACAAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTC
Found at i:165853 original size:26 final size:25
Alignment explanation
Indices: 165791--165853 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
165781 TCAACTGTAG
*
165791 ATATTATTTATATAATATATATTTC
1 ATATTATTTATATAATATATATTAC
* *
165816 TTATTATATTATATTATATA-ATATAC
1 ATATTAT-TTATATAATATATAT-TAC
165842 ATATTCATTTAT
1 ATATT-ATTTAT
165854 TTGTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 8 0.26
26 21 0.68
27 2 0.06
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (25 bp):
ATATTATTTATATAATATATATTAC
Found at i:167210 original size:22 final size:22
Alignment explanation
Indices: 167174--167228 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
167164 GTAAGTATTA
* * *
167174 TTATTATCTTACTATTTTTTGAT
1 TTATTTTCTTTCTATATTTT-AT
167197 TT-TTTTCTTTCTATATTTTAT
1 TTATTTTCTTTCTATATTTTAT
167218 TTATTTTCTTT
1 TTATTTTCTTT
167229 TCTTTCCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.14
22 22 0.79
23 2 0.07
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (22 bp):
TTATTTTCTTTCTATATTTTAT
Found at i:167357 original size:17 final size:16
Alignment explanation
Indices: 167326--167375 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
167316 TTTGTATATA
*
167326 TATTATTATTTATTTATT
1 TATT-TTATTCATTT-TT
167344 TATTTTATTCATTTTT
1 TATTTTATTCATTTTT
*
167360 TATCTTACTTCATTTT
1 TATTTTA-TTCATTTT
167376 CGTTTCTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.28
17 17 0.59
18 4 0.14
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTATTCATTTTT
Found at i:172888 original size:22 final size:23
Alignment explanation
Indices: 172842--172896 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
172832 ATGACACAAT
172842 AAAGCCTCAAAGAGCCACCCCCA
1 AAAGCCTCAAAGAGCCACCCCCA
172865 AAAGCCTCAAAGAGCCA-CCCCA
1 AAAGCCTCAAAGAGCCACCCCCA
172887 AAAGCCTCAA
1 AAAGCCTCAA
172897 CTGCCTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.42, C:0.40, G:0.13, T:0.05
Consensus pattern (23 bp):
AAAGCCTCAAAGAGCCACCCCCA
Found at i:191800 original size:14 final size:14
Alignment explanation
Indices: 191783--191811 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
191773 GAAATCAATT
191783 TTGTAAAATTACTC
1 TTGTAAAATTACTC
191797 TTGTAAAATTACTC
1 TTGTAAAATTACTC
191811 T
1 T
191812 CCCTTACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (14 bp):
TTGTAAAATTACTC
Found at i:192876 original size:44 final size:44
Alignment explanation
Indices: 192811--192898 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
192801 TCTAAACCAC
*
192811 CAAGAGATCATCAAATAAAGGAATCGCTCGTGATGAGTTCTTAA
1 CAAGAGATCATCAAATAAAGGAATCACTCGTGATGAGTTCTTAA
*
192855 CAAGAGATCATCAAATGAAGGAATCACTCGTGATGAGTTCTTAA
1 CAAGAGATCATCAAATAAAGGAATCACTCGTGATGAGTTCTTAA
192899 GGTACTTACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (44 bp):
CAAGAGATCATCAAATAAAGGAATCACTCGTGATGAGTTCTTAA
Found at i:194175 original size:43 final size:43
Alignment explanation
Indices: 194084--194183 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
194074 TGCATAGCAG
* * *
194084 AGTGCATCAATGCACATTCAAGGAATGCATCGTGTATCTTTAT
1 AGTGTATCAATGCACATTCAAGGAATGCATCGTGTAACTCTAT
* * *
194127 GGTGTATCAATGCACATTCAAGGGATGCATCG-GTACACTCTCT
1 AGTGTATCAATGCACATTCAAGGAATGCATCGTGTA-ACTCTAT
*
194170 AGTGTATCGATGCA
1 AGTGTATCAATGCA
194184 TTATGCACAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 3 0.06
43 45 0.94
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (43 bp):
AGTGTATCAATGCACATTCAAGGAATGCATCGTGTAACTCTAT
Found at i:198011 original size:19 final size:21
Alignment explanation
Indices: 197971--198016 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
197961 GAGATTATTT
197971 TCATTTTTCAGTTTTGAAAAA
1 TCATTTTTCAGTTTTGAAAAA
*
197992 TCATTTTTTA-TTTT-AAAAA
1 TCATTTTTCAGTTTTGAAAAA
*
198011 TAATTT
1 TCATTT
198017 CTCATAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 4 0.17
21 9 0.39
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (21 bp):
TCATTTTTCAGTTTTGAAAAA
Found at i:201174 original size:12 final size:11
Alignment explanation
Indices: 201157--201228 Score: 81
Period size: 12 Copynumber: 6.1 Consensus size: 11
201147 CATATTGAAT
201157 TTTCTTTTAAA
1 TTTCTTTTAAA
201168 CTTTCTTTTTAAA
1 -TTTC-TTTTAAA
201181 TTTCTTTTAAA
1 TTTCTTTTAAA
201192 CTTTCTTTTTAAA
1 -TTTC-TTTTAAA
*
201205 TTTCTTTTTAA
1 TTTCTTTTAAA
*
201216 TCTTCTTTGAAA
1 T-TTCTTTTAAA
201228 T
1 T
201229 ATTTTTATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
11 14 0.26
12 25 0.47
13 14 0.26
ACGTcount: A:0.24, C:0.12, G:0.01, T:0.62
Consensus pattern (11 bp):
TTTCTTTTAAA
Found at i:201223 original size:24 final size:24
Alignment explanation
Indices: 201157--201212 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
201147 CATATTGAAT
201157 TTTCTTTTAAACTTTCTTTTTAAA
1 TTTCTTTTAAACTTTCTTTTTAAA
201181 TTTCTTTTAAACTTTCTTTTTAAA
1 TTTCTTTTAAACTTTCTTTTTAAA
201205 TTTCTTTT
1 TTTCTTTT
201213 TAATCTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTCTTTTAAACTTTCTTTTTAAA
Found at i:202131 original size:34 final size:34
Alignment explanation
Indices: 202036--202134 Score: 121
Period size: 32 Copynumber: 3.0 Consensus size: 34
202026 TGCACTATTC
*
202036 GAACATTAAAAAAATAGCAGTACAATTTTGGTTT
1 GAACAATAAAAAAATAGCAGTACAATTTTGGTTT
* * *
202070 GAACAGT--GAAAACAGCAGTACAATTTTGGTTT
1 GAACAATAAAAAAATAGCAGTACAATTTTGGTTT
** *
202102 GAACAATAAAAAAATAATAGTACAGTTTTGGTT
1 GAACAATAAAAAAATAGCAGTACAATTTTGGTT
202135 CAAACAGTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
32 29 0.54
34 25 0.46
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (34 bp):
GAACAATAAAAAAATAGCAGTACAATTTTGGTTT
Found at i:204698 original size:12 final size:11
Alignment explanation
Indices: 204681--204728 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
204671 CATATTGAAT
204681 TTTCTTTTAAA
1 TTTCTTTTAAA
204692 CTTTCTTTTTAAA
1 -TTTC-TTTTAAA
*
204705 TTTCTTTTTAA
1 TTTCTTTTAAA
*
204716 TCTTCTTTGAAA
1 T-TTCTTTTAAA
204728 T
1 T
204729 CTTTTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 7 0.23
12 17 0.55
13 7 0.23
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.62
Consensus pattern (11 bp):
TTTCTTTTAAA
Found at i:204703 original size:13 final size:12
Alignment explanation
Indices: 204681--204715 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
204671 CATATTGAAT
204681 TTTC-TTTTAAA
1 TTTCTTTTTAAA
204692 CTTTCTTTTTAAA
1 -TTTCTTTTTAAA
204705 TTTCTTTTTAA
1 TTTCTTTTTAA
204716 TCTTCTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTCTTTTTAAA
Found at i:204769 original size:19 final size:20
Alignment explanation
Indices: 204727--204770 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
204717 CTTCTTTGAA
204727 ATCT-TTTTATTTTTCTGTC
1 ATCTATTTTATTTTTCTGTC
*
204746 TTCTATTTTATTTTTCT-TC
1 ATCTATTTTATTTTTCTGTC
204765 ATCTAT
1 ATCTAT
204771 AAATCCCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.14, C:0.16, G:0.02, T:0.68
Consensus pattern (20 bp):
ATCTATTTTATTTTTCTGTC
Found at i:212417 original size:22 final size:22
Alignment explanation
Indices: 212389--212432 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
212379 AGCCTGTGAT
212389 GGGCCAGGATTGAGGGTTTGAC
1 GGGCCAGGATTGAGGGTTTGAC
212411 GGGCCAGGATTGAGGGTTTGAC
1 GGGCCAGGATTGAGGGTTTGAC
212433 AGCCCAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GGGCCAGGATTGAGGGTTTGAC
Found at i:212704 original size:47 final size:48
Alignment explanation
Indices: 212613--212710 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 48
212603 GAATAAATGT
* * *
212613 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTCTCGAAC-AAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATATGTCTCAAACAAAGC
* *
212660 ATGCGAATTAGATATCATGCGGTTAGGGTTT-TAATGT-TCAAACAAAGC
1 ATGCGAACTAGAAATCATGCGGTTA-GGTTTAT-ATGTCTCAAACAAAGC
212708 ATG
1 ATG
212711 GGGTTAGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
47 29 0.67
48 14 0.33
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (48 bp):
ATGCGAACTAGAAATCATGCGGTTAGGTTTATATGTCTCAAACAAAGC
Found at i:219452 original size:44 final size:44
Alignment explanation
Indices: 219404--219487 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
219394 TCCTTCGGGC
219404 CATCAGTAAGTCTTTCGAGCATGATGATTAAAAATCCTTCAAGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAAAATCCTTCAAGT
219448 CATCAGTAAGTCTTTCGAGCATGATGATTAAAAATCCTTC
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAAAATCCTTC
219488 GGGCCATCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (44 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAAAATCCTTCAAGT
Found at i:219877 original size:42 final size:42
Alignment explanation
Indices: 219740--219866 Score: 191
Period size: 42 Copynumber: 3.0 Consensus size: 42
219730 TGAAGCAAGT
* *
219740 CATCAGTAAGTCTTTCGATCATGATGCTTAAAAATCCTTCAGGC
1 CATCAGTAAGTCTTTCGAGCATGATGCTT--AAATCCTTCGGGC
* *
219784 CATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGC
*
219826 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
219867 TAATTTGTAA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
42 49 0.64
44 27 0.36
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGC
Found at i:220003 original size:93 final size:93
Alignment explanation
Indices: 219826--220009 Score: 287
Period size: 93 Copynumber: 2.0 Consensus size: 93
219816 TCCTTAGGGC
* * * **
219826 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTAATTTGTAAGACTTCACCAAAGA
* *
219891 GTAGTGAAGCAAACCCATCAGTAAGTGT
66 GTAGTGAAGAAAACCCATCAATAAGTGT
219919 CATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTAATTTGTAAGACTTCACCAAAGA
1 CATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTAATTTGTAAGACTTCACCAAAGA
**
219984 GTAGTGAAGAAAATTCATCAATAAGT
66 GTAGTGAAGAAAACCCATCAATAAGT
220010 CTTTCGAGCA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (93 bp):
CATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCAGGTAATTTGTAAGACTTCACCAAAGA
GTAGTGAAGAAAACCCATCAATAAGTGT
Done.