Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008005.1 Hibiscus syriacus cultivar Beakdansim tig00110467_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: 1778185
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 7
Found at i:16510 original size:25 final size:26
Alignment explanation
Indices: 16464--16516 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
16454 TTTTTAACTT
*
16464 AAAATATATTAAATTATAAGATATATA
1 AAAATATATTAAA-TATAAGATAAATA
*
16491 AAAATATATTAAA-ATTAGATAAATA
1 AAAATATATTAAATATAAGATAAATA
16516 A
1 A
16517 TCATACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.46
27 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (26 bp):
AAAATATATTAAATATAAGATAAATA
Found at i:16549 original size:20 final size:20
Alignment explanation
Indices: 16526--16571 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
16516 ATCATACTAT
*
16526 TTTTTTTGTAATTTTTC-GTA
1 TTTTTTTATAATTTTTCTG-A
*
16546 TTTTTTTATATTTTTTCTGA
1 TTTTTTTATAATTTTTCTGA
16566 TTTTTT
1 TTTTTT
16572 ATCCGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (20 bp):
TTTTTTTATAATTTTTCTGA
Found at i:23608 original size:16 final size:16
Alignment explanation
Indices: 23587--23621 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
23577 TTTTATATAA
23587 TTTTCTGTGTTCTTGT
1 TTTTCTGTGTTCTTGT
*
23603 TTTTCTTTGTTCTTGT
1 TTTTCTGTGTTCTTGT
23619 TTT
1 TTT
23622 GCAATAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.14, T:0.74
Consensus pattern (16 bp):
TTTTCTGTGTTCTTGT
Found at i:26020 original size:10 final size:10
Alignment explanation
Indices: 25996--26042 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
25986 ACCTGACATC
25996 TGCAGCA-GG
1 TGCAGCATGG
26005 -GCAGCATGG
1 TGCAGCATGG
26014 TGCAGCATGG
1 TGCAGCATGG
*
26024 -GCGGCATGG
1 TGCAGCATGG
26033 TGCAGCATGG
1 TGCAGCATGG
26043 CATTTGCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 6 0.18
9 10 0.30
10 17 0.52
ACGTcount: A:0.19, C:0.21, G:0.45, T:0.15
Consensus pattern (10 bp):
TGCAGCATGG
Found at i:26030 original size:19 final size:19
Alignment explanation
Indices: 25996--26042 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
25986 ACCTGACATC
25996 TGCAGCA-GGGCAGCATGG
1 TGCAGCATGGGCAGCATGG
*
26014 TGCAGCATGGGCGGCATGG
1 TGCAGCATGGGCAGCATGG
26033 TGCAGCATGG
1 TGCAGCATGG
26043 CATTTGCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.19, C:0.21, G:0.45, T:0.15
Consensus pattern (19 bp):
TGCAGCATGGGCAGCATGG
Found at i:29837 original size:13 final size:14
Alignment explanation
Indices: 29809--29841 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
29799 TCCTGGTAAT
*
29809 TTTAAAAAATTTTA
1 TTTAAAAAATTATA
29823 TTTAAAAAA-TATA
1 TTTAAAAAATTATA
29836 TTTAAA
1 TTTAAA
29842 CAAAACCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAAAAATTATA
Found at i:33143 original size:14 final size:14
Alignment explanation
Indices: 33095--33147 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
33085 AAGTGGTATA
33095 TATAAAATAAATATT
1 TATAAAAT-AATATT
33110 TA-AAAA-AAGTAATT
1 TATAAAATAA-T-ATT
33124 TAATAAAATAATATT
1 T-ATAAAATAATATT
33139 TATAAAATA
1 TATAAAATA
33148 TGAAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
12 2 0.06
13 1 0.03
14 16 0.48
15 7 0.21
16 5 0.15
17 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TATAAAATAATATT
Found at i:37310 original size:3 final size:3
Alignment explanation
Indices: 37295--37535 Score: 207
Period size: 3 Copynumber: 82.3 Consensus size: 3
37285 ATTTTTACCA
* * * * * *
37295 TAT TAT TAA TAT TAT TTT TAT TAT TTT TAT TAT TAT TAT T-C TAC TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
37342 TAT TAT TAT TAT TAT TAT TAT CT-T T-T TCAT CAT CAT AAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT T-AT TAT TAT TAT TAT TAT
** * *
37387 TAT TAT TAT T-T TAT T-T TGC TAT TAT TAT T-T TGT TAT TAT TAT T-C
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
37431 TAT T-T TAT TAT TAT TAT TAT T-C TAT TAT TAT TAT TAT TAGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
37475 T-T TAT TAT TAT TAT TAT TAT T-T TAC TAT TAT TATT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT
*
37520 TAT TAT TGT TAT TAT T
1 TAT TAT TAT TAT TAT T
37536 GTTGTTGTTG
Statistics
Matches: 199, Mismatches: 25, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
2 18 0.09
3 169 0.85
4 12 0.06
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:37416 original size:14 final size:14
Alignment explanation
Indices: 37392--37550 Score: 116
Period size: 14 Copynumber: 11.6 Consensus size: 14
37382 ATCATTATTA
37392 TTATT-TTATTTTG
1 TTATTATTATTTTG
*
37405 CTATTATTATTTTG
1 TTATTATTATTTTG
* *
37419 TTATTATTATTCTA
1 TTATTATTATTTTG
*
37433 TT-TTATTA--TTA
1 TTATTATTATTTTG
* * *
37444 TTATTATTCTATTA
1 TTATTATTATTTTG
*
37458 TTATTATTA-TTAG
1 TTATTATTATTTTG
*
37471 TTATT-TTATTATTA
1 TTATTATTATT-TTG
*
37485 TTATTATTATTTTA
1 TTATTATTATTTTG
*
37499 CTATTATTATTTAT-
1 TTATTATTATTT-TG
37513 TTATTATTATTATTG
1 TTATTATTATT-TTG
*
37528 TTATTATTGTTGTTG
1 TTATTATTATT-TTG
*
37543 TTGTTATT
1 TTATTATT
37551 TCAAAAAAAA
Statistics
Matches: 119, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
11 4 0.03
12 8 0.07
13 17 0.14
14 63 0.53
15 27 0.23
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (14 bp):
TTATTATTATTTTG
Found at i:37423 original size:33 final size:32
Alignment explanation
Indices: 37304--37535 Score: 162
Period size: 32 Copynumber: 7.2 Consensus size: 32
37294 ATATTATTAA
* * *
37304 TATTATTTTTATTATTTTTATTATTATTA-TTC
1 TATTATTATT-TTATTATTATTATTATTATTTT
* *
37336 TACTACTATTATTATTATTATTATTATCT-TTTT
1 TATTATTATT-TTATTATTATTATTAT-TATTTT
* * *
37369 CATCATCATAATTATCATTATTATTATT-TTATTTT
1 --T-ATTATTATT-TTATTATTATTATTATTATTTT
* *
37404 GCTATTATTATTTTGTTATTATTATT-CTA-TTT
1 --TATTATTATTTTATTATTATTATTATTATTTT
* *
37436 TATTATTA--TTATTATT-CTATTATTATTAT
1 TATTATTATTTTATTATTATTATTATTATTTT
37465 TATTAGTTATTTTATTATTATTATTATTATTTT
1 TATTA-TTATTTTATTATTATTATTATTATTTT
*
37498 ACTATTATTA-TTTA-T-TTATTATTATTATTGT
1 --TATTATTATTTTATTATTATTATTATTATTTT
37529 TATTATT
1 TATTATT
37536 GTTGTTGTTG
Statistics
Matches: 162, Mismatches: 24, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
27 4 0.02
28 9 0.06
29 14 0.09
30 11 0.07
31 15 0.09
32 35 0.22
33 32 0.20
34 11 0.07
35 12 0.07
36 19 0.12
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (32 bp):
TATTATTATTTTATTATTATTATTATTATTTT
Found at i:37441 original size:58 final size:60
Alignment explanation
Indices: 37379--37550 Score: 195
Period size: 64 Copynumber: 2.8 Consensus size: 60
37369 CATCATCATA
* *
37379 ATTATCATTATTATTATTTTATT-TTGCTATTATTATTTTGTTATTATTATT-CTATTTT
1 ATTATTATTATTATTATTTTATTATTGTTATTATTATTTTGTTATTATTATTACTATTTT
* * * * *
37437 ATTATTATTATTATTCTATTATTATTATTATTAGTTATTTTATTATTATTATTATTATTTT
1 ATTATTATTATTATTATTTTATTATTGTTATTA-TTATTTTGTTATTATTATTACTATTTT
* * *
37498 ACTATTATTATTTATTTATTATTATTATTGTTATTATTGTTGTTGTTGTTATT
1 ATTATTATTA-TTA-TTATT-TTATTATTGTTATTATTATT-TTGTTATTATT
37551 TCAAAAAAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
58 20 0.22
59 7 0.08
60 18 0.19
61 15 0.16
62 3 0.03
63 7 0.08
64 23 0.25
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (60 bp):
ATTATTATTATTATTATTTTATTATTGTTATTATTATTTTGTTATTATTATTACTATTTT
Found at i:38049 original size:14 final size:14
Alignment explanation
Indices: 38001--38053 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
37991 AAGTGGTATA
38001 TATAAAATAAATATT
1 TATAAAAT-AATATT
38016 TA-AAAA-AAGTAATT
1 TATAAAATAA-T-ATT
38030 TAATAAAATAATATT
1 T-ATAAAATAATATT
38045 TATAAAATA
1 TATAAAATA
38054 TGAAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
12 2 0.06
13 1 0.03
14 16 0.48
15 7 0.21
16 5 0.15
17 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TATAAAATAATATT
Found at i:42192 original size:3 final size:3
Alignment explanation
Indices: 42184--42395 Score: 167
Period size: 3 Copynumber: 72.7 Consensus size: 3
42174 ATCACCATTT
* * *
42184 TTA TTA TTA TTA TT- CTA CTA CTA TTA TTA TTA TTA TCT- TT- TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TT-A
* * * * * * *
42228 TCA TCA TAA TTA TCA TTA TTA TTA TT- TTA TT- TTG CTA TTA TTC TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
42273 TTG TTA TTA TTA TT- CTA TT- TTA TTA TTA TTA TTA TT- CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
42318 TTA TTA TTA GTTA TT- TTA TTA TTA TTA TTA TTA TTA TT- TTA CTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
42362 TTA TTA TTTA TTTA TTA TTA TTA TTG TTA TTA TT
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TT
42396 GTTGTTGTTG
Statistics
Matches: 175, Mismatches: 20, Indels: 28
0.78 0.09 0.13
Matches are distributed among these distances:
2 18 0.10
3 145 0.83
4 12 0.07
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:42285 original size:17 final size:17
Alignment explanation
Indices: 42182--42386 Score: 152
Period size: 17 Copynumber: 11.9 Consensus size: 17
42172 CAATCACCAT
*
42182 TTTTATTATTATTATTC
1 TTTTATTATTATTATTA
** *
42199 TACTACTATTATTATTA
1 TTTTATTATTATTATTA
* * * * *
42216 TTATCTTTTTCATCATCA
1 TTTTATTATT-ATTATTA
* *
42234 TAATTATCATTATTATTA
1 T-TTTATTATTATTATTA
* *
42252 TTTTATTTTGCTATTATTC
1 TTTTATTAT--TATTATTA
*
42271 TTTTGTTATTATTATTCTA
1 TTTTATTATTATTA-T-TA
42290 TTTTATTATTATTATTA
1 TTTTATTATTATTATTA
*
42307 TTCTATTATTATTATTA
1 TTTTATTATTATTATTA
42324 --TTAGTTATT-TTATTA
1 TTTTA-TTATTATTATTA
42339 --TTATTATTATTATTA
1 TTTTATTATTATTATTA
*
42354 TTTTACTATTATTATT-
1 TTTTATTATTATTATTA
42370 TATTTATTATTATTATT
1 T-TTTATTATTATTATT
42387 GTTATTATTG
Statistics
Matches: 147, Mismatches: 30, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
14 5 0.03
15 17 0.12
16 6 0.04
17 73 0.50
18 14 0.10
19 32 0.22
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.65
Consensus pattern (17 bp):
TTTTATTATTATTATTA
Found at i:42354 original size:108 final size:111
Alignment explanation
Indices: 42182--42395 Score: 260
Period size: 108 Copynumber: 1.9 Consensus size: 111
42172 CAATCACCAT
*
42182 TTTTATTATTATTATTCTACTACTATTATTATTATTATCTTTTTCATCATCATAATTATCATTA-
1 TTTTATTATTATTATTATACTACTATTATTATTATTATCTTTTTCATCATCATAATTATCATTAT
* *
42246 TTATTATT-TTATTT-TGCTATTATTCTT-TTGTTATTATTATTCTA
66 TTACTATTATTATTTAT-CTATTATTATTATTGTTATTATTATTCTA
* * * * * *
42290 TTTTATTATTATTATTATTCTATTATTATTATTATTAGT-TATTTT-ATTATTATTATTATTATT
1 TTTTATTATTATTATTATACTACTATTATTATTATTA-TCT-TTTTCATCATCATAATTATCATT
*
42353 ATTTTACTATTATTATTTATTTATTATTATTATTGTTATTATT
64 A-TTTACTATTATTATTTATCTATTATTATTATTGTTATTATT
42396 GTTGTTGTTG
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
108 50 0.56
109 5 0.06
110 7 0.08
111 15 0.17
112 12 0.13
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (111 bp):
TTTTATTATTATTATTATACTACTATTATTATTATTATCTTTTTCATCATCATAATTATCATTAT
TTACTATTATTATTTATCTATTATTATTATTGTTATTATTATTCTA
Found at i:43491 original size:194 final size:194
Alignment explanation
Indices: 43162--43554 Score: 786
Period size: 194 Copynumber: 2.0 Consensus size: 194
43152 AATGAAGATG
43162 TAAATCTTGTAAGTCTTGGTGCTCTTCCTGATCTTCTTCTTCCCTAAACGAAATCAAGGATTTGA
1 TAAATCTTGTAAGTCTTGGTGCTCTTCCTGATCTTCTTCTTCCCTAAACGAAATCAAGGATTTGA
43227 AAGAAGGCGAGTTGAATCAGGAGATAAGGAATTGAGGGGGTTCGGCGGGGGCAGCTTTTGGTGGC
66 AAGAAGGCGAGTTGAATCAGGAGATAAGGAATTGAGGGGGTTCGGCGGGGGCAGCTTTTGGTGGC
43292 GTTGATGGAAGCAGTAGCGGCGGAGGCATCTACGGGGAGGAAATGGCGTCGGAGATTCGAAGGC
131 GTTGATGGAAGCAGTAGCGGCGGAGGCATCTACGGGGAGGAAATGGCGTCGGAGATTCGAAGGC
43356 TAAATCTTGTAAGTCTTGGTGCTCTTCCTGATCTTCTTCTTCCCTAAACGAAATCAAGGATTTGA
1 TAAATCTTGTAAGTCTTGGTGCTCTTCCTGATCTTCTTCTTCCCTAAACGAAATCAAGGATTTGA
43421 AAGAAGGCGAGTTGAATCAGGAGATAAGGAATTGAGGGGGTTCGGCGGGGGCAGCTTTTGGTGGC
66 AAGAAGGCGAGTTGAATCAGGAGATAAGGAATTGAGGGGGTTCGGCGGGGGCAGCTTTTGGTGGC
43486 GTTGATGGAAGCAGTAGCGGCGGAGGCATCTACGGGGAGGAAATGGCGTCGGAGATTCGAAGGC
131 GTTGATGGAAGCAGTAGCGGCGGAGGCATCTACGGGGAGGAAATGGCGTCGGAGATTCGAAGGC
43550 TAAAT
1 TAAAT
43555 TGGAAGCGGC
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
194 199 1.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (194 bp):
TAAATCTTGTAAGTCTTGGTGCTCTTCCTGATCTTCTTCTTCCCTAAACGAAATCAAGGATTTGA
AAGAAGGCGAGTTGAATCAGGAGATAAGGAATTGAGGGGGTTCGGCGGGGGCAGCTTTTGGTGGC
GTTGATGGAAGCAGTAGCGGCGGAGGCATCTACGGGGAGGAAATGGCGTCGGAGATTCGAAGGC
Found at i:46238 original size:309 final size:309
Alignment explanation
Indices: 45679--46297 Score: 1229
Period size: 309 Copynumber: 2.0 Consensus size: 309
45669 GTATTGCTTT
45679 TATTTTTTGTATTTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATAAA
1 TATTTTTTGTATTTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATAAA
45744 CTGATACTATTATTTTTCATGTTTGCTCGGTTGTCAAAGTGAAGCATGCAGGGCTTTGGGGATCA
66 CTGATACTATTATTTTTCATGTTTGCTCGGTTGTCAAAGTGAAGCATGCAGGGCTTTGGGGATCA
45809 TATGGTGTTCAAATCAATCACTTCCATAATGAATTCTGGTTTGCTAAAGCACCTTGACTTTGATG
131 TATGGTGTTCAAATCAATCACTTCCATAATGAATTCTGGTTTGCTAAAGCACCTTGACTTTGATG
*
45874 ATTTGCTTTTGCTTCTGGCTGATATGGATCCTTCTACATGTCATGAAAAATTATTAAGTTGCTGG
196 ATTTGCTTTTGATTCTGGCTGATATGGATCCTTCTACATGTCATGAAAAATTATTAAGTTGCTGG
45939 CAAGATCAGCAAAATAATTCTTGCTTAAAATCATCATTGTTTAGAGCAA
261 CAAGATCAGCAAAATAATTCTTGCTTAAAATCATCATTGTTTAGAGCAA
45988 TATTTTTTGTATTTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATAAA
1 TATTTTTTGTATTTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATAAA
46053 CTGATACTATTATTTTTCATGTTTGCTCGGTTGTCAAAGTGAAGCATGCAGGGCTTTGGGGATCA
66 CTGATACTATTATTTTTCATGTTTGCTCGGTTGTCAAAGTGAAGCATGCAGGGCTTTGGGGATCA
46118 TATGGTGTTCAAATCAATCACTTCCATAATGAATTCTGGTTTGCTAAAGCACCTTGACTTTGATG
131 TATGGTGTTCAAATCAATCACTTCCATAATGAATTCTGGTTTGCTAAAGCACCTTGACTTTGATG
46183 ATTTGCTTTTGATTCTGGCTGATATGGATCCTTCTACATGTCATGAAAAATTATTAAGTTGCTGG
196 ATTTGCTTTTGATTCTGGCTGATATGGATCCTTCTACATGTCATGAAAAATTATTAAGTTGCTGG
46248 CAAGATCAGCAAAATAATTCTTGCTTAAAATCATCATTGTTTAGAGCAA
261 CAAGATCAGCAAAATAATTCTTGCTTAAAATCATCATTGTTTAGAGCAA
46297 T
1 T
46298 CTTCTATGCT
Statistics
Matches: 309, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
309 309 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (309 bp):
TATTTTTTGTATTTCAGTACAAAATGTGTCTTGTTTTCCCTTTTTTATTTTCTAAATTAAATAAA
CTGATACTATTATTTTTCATGTTTGCTCGGTTGTCAAAGTGAAGCATGCAGGGCTTTGGGGATCA
TATGGTGTTCAAATCAATCACTTCCATAATGAATTCTGGTTTGCTAAAGCACCTTGACTTTGATG
ATTTGCTTTTGATTCTGGCTGATATGGATCCTTCTACATGTCATGAAAAATTATTAAGTTGCTGG
CAAGATCAGCAAAATAATTCTTGCTTAAAATCATCATTGTTTAGAGCAA
Found at i:47133 original size:122 final size:122
Alignment explanation
Indices: 46916--47162 Score: 449
Period size: 122 Copynumber: 2.0 Consensus size: 122
46906 CATATGAGAT
46916 GATAAAGAAAGTTTAACAAAAGGTTTCTTAGTATACTAAGATTTTGGGTTCCTACCAGTTTCTAA
1 GATAAAGAAAGTTTAACAAAAGGTTTCTTAGTATACTAAGATTTTGGGTTCCTACCAGTTTCTAA
46981 AGGAAGAACTGGTGTTCCTGATCGCCTCTCAAGAAAAAACATCCTTGTCATTAGCAG
66 AGGAAGAACTGGTGTTCCTGATCGCCTCTCAAGAAAAAACATCCTTGTCATTAGCAG
* * *
47038 GATAAAGAAAGTTTAACAAAATGTTTCTTAGTATATTAGGATTTTGGGTTCCTACCAGTTTCTAA
1 GATAAAGAAAGTTTAACAAAAGGTTTCTTAGTATACTAAGATTTTGGGTTCCTACCAGTTTCTAA
* *
47103 AGGAAGAACTTGTGTTCCTGATCGCCTCTCAAGAAAAAGCATCCTTGTCATTAGCAG
66 AGGAAGAACTGGTGTTCCTGATCGCCTCTCAAGAAAAAACATCCTTGTCATTAGCAG
47160 GAT
1 GAT
47163 TTGATGGGAT
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 120 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (122 bp):
GATAAAGAAAGTTTAACAAAAGGTTTCTTAGTATACTAAGATTTTGGGTTCCTACCAGTTTCTAA
AGGAAGAACTGGTGTTCCTGATCGCCTCTCAAGAAAAAACATCCTTGTCATTAGCAG
Found at i:50100 original size:306 final size:298
Alignment explanation
Indices: 49590--50153 Score: 862
Period size: 306 Copynumber: 1.9 Consensus size: 298
49580 TGGGCCCTGA
* *
49590 CTGATGAACCACTCTGCAAATTCTCCCAAAAACCATGCGAGTAAGAACGAATTACTCTTTTCCTT
1 CTGATGAACCACTCTGCAAACTCTCCCAAAAACCATGCGAGTAAGAACGAATTACTCTTTTCCTG
* *
49655 TACCATTTGTCACTGGCTTTCTTAATGTCTTCAGAGGGAGCAATGCCAAGATTCCTCAATATTTT
66 TACCATTTGTCACTGGCTTTCTT-ATGTCTTCAGAGGGAGAAATGCCAAGATTCATCAATATTTT
* *
49720 GAGGATCTTTTTTGTAATATTGGCTGCTGCGAAGAATACGGCCTAAGAACTAGTAACAAATTCCT
130 GAGGATCTTTTTTGTAATATTGGCTGCTGCGAAAAATACGGCCTAAGAACTAGCAACAAATTCCT
* * * *
49785 CCGTGAGGTTTGGTCACAATGTTTCTTTACTACTAGACCATTTTTTTCGTCTTTCAAGTTTTCCT
195 CCCTGAGGTTTGGTCACAATGTTTCTTTACTACTAGACCATTTTATCCATCTTTCAAGTTTTCCT
49850 CTTTGAAGAGCATGCTTTATATTTTCAGGGACTTTTTCG
260 CTTTGAAGAGCATGCTTTATATTTTCAGGGACTTTTTCG
* **
49889 CTGATGAACCACTCTGCAAACTCTCCCATAAACCATGCGAGTAAGAATTAATTACTCTTTTCCTG
1 CTGATGAACCACTCTGCAAACTCTCCCAAAAACCATGCGAGTAAGAACGAATTACTCTTTTCCTG
* *
49954 TACCATTTGTCACATATGTCACTGGCTTTCTT-TGTCTTCAGGGGGAGAAATGCCAATATTCATC
66 TACCA----T----T-TGTCACTGGCTTTCTTATGTCTTCAGAGGGAGAAATGCCAAGATTCATC
*
50018 AGTATTTTGAGGATCTTTTTTTGTAATATTGGCTGCTGC-AAAAATACGGCCTAAGAACTAGCAA
122 AATATTTTGAGGATC-TTTTTTGTAATATTGGCTGCTGCGAAAAATACGGCCTAAGAACTAGCAA
*
50082 CAAATTCCTCCCTGAGGTTTGGTCACAATGTTTCTTTACTACTTGACCATTTTATCCATCTTTCA
186 CAAATTCCTCCCTGAGGTTTGGTCACAATGTTTCTTTACTACTAGACCATTTTATCCATCTTTCA
50147 AGTTTTC
251 AGTTTTC
50154 ACCTTTTAAG
Statistics
Matches: 238, Mismatches: 17, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
299 65 0.27
303 1 0.00
306 132 0.55
307 24 0.10
308 16 0.07
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (298 bp):
CTGATGAACCACTCTGCAAACTCTCCCAAAAACCATGCGAGTAAGAACGAATTACTCTTTTCCTG
TACCATTTGTCACTGGCTTTCTTATGTCTTCAGAGGGAGAAATGCCAAGATTCATCAATATTTTG
AGGATCTTTTTTGTAATATTGGCTGCTGCGAAAAATACGGCCTAAGAACTAGCAACAAATTCCTC
CCTGAGGTTTGGTCACAATGTTTCTTTACTACTAGACCATTTTATCCATCTTTCAAGTTTTCCTC
TTTGAAGAGCATGCTTTATATTTTCAGGGACTTTTTCG
Found at i:56175 original size:13 final size:13
Alignment explanation
Indices: 56157--56182 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56147 TTGGTAGTTA
56157 CCGAGGAAAAGGG
1 CCGAGGAAAAGGG
56170 CCGAGGAAAAGGG
1 CCGAGGAAAAGGG
56183 GAAACCCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.46, T:0.00
Consensus pattern (13 bp):
CCGAGGAAAAGGG
Found at i:61372 original size:17 final size:17
Alignment explanation
Indices: 61350--61382 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
61340 GATATCTTCT
61350 TTCTTTCATTATAAATC
1 TTCTTTCATTATAAATC
61367 TTCTTTCATTATAAAT
1 TTCTTTCATTATAAAT
61383 GACTTCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (17 bp):
TTCTTTCATTATAAATC
Found at i:71022 original size:207 final size:207
Alignment explanation
Indices: 70770--71179 Score: 802
Period size: 207 Copynumber: 2.0 Consensus size: 207
70760 AATGAAAGAG
*
70770 ATAGAAGTATCTACTCTATCTCTGCTCCTTCTAATACCCAAAAAAAGTGGCAACTTACTATTTAT
1 ATAGAAGTATCTACTCTATCTCTGCTCCTTCCAATACCCAAAAAAAGTGGCAACTTACTATTTAT
70835 GGACTGCTCTTTTTATTAAAAACATAGTTTTACTGTATTTTTGTGTGTGGGATGTGTAGGGAAGA
66 GGACTGCTCTTTTTATTAAAAACATAGTTTTACTGTATTTTTGTGTGTGGGATGTGTAGGGAAGA
*
70900 GTTTAGATTCTTTCTAAAAATGAGAATGGCAAAGATGCAGGTGTAATTGGCATTGTCTACATACA
131 GTTTAGATTCTTTCTAAAAATGAGAATGGCAAAGATGCAGGTGTAATTGGCATTGGCTACATACA
70965 CTTTTTAAAAAC
196 CTTTTTAAAAAC
70977 ATAGAAGTATCTACTCTATCTCTGCTCCTTCCAATACCCAAAAAAAGTGGCAACTTACTATTTAT
1 ATAGAAGTATCTACTCTATCTCTGCTCCTTCCAATACCCAAAAAAAGTGGCAACTTACTATTTAT
71042 GGACTGCTCTTTTTATTAAAAACATAGTTTTACTGTATTTTTGTGTGTGGGATGTGTAGGGAAGA
66 GGACTGCTCTTTTTATTAAAAACATAGTTTTACTGTATTTTTGTGTGTGGGATGTGTAGGGAAGA
71107 GTTTAGATTCTTTCTAAAAATGAGAATGGCAAAGATGCAGGTGTAATTGGCATTGGCTACATACA
131 GTTTAGATTCTTTCTAAAAATGAGAATGGCAAAGATGCAGGTGTAATTGGCATTGGCTACATACA
71172 CTTTTTAA
196 CTTTTTAA
71180 GTTTTTTTTT
Statistics
Matches: 201, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
207 201 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (207 bp):
ATAGAAGTATCTACTCTATCTCTGCTCCTTCCAATACCCAAAAAAAGTGGCAACTTACTATTTAT
GGACTGCTCTTTTTATTAAAAACATAGTTTTACTGTATTTTTGTGTGTGGGATGTGTAGGGAAGA
GTTTAGATTCTTTCTAAAAATGAGAATGGCAAAGATGCAGGTGTAATTGGCATTGGCTACATACA
CTTTTTAAAAAC
Found at i:76517 original size:103 final size:103
Alignment explanation
Indices: 76348--76562 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
76338 TGTCCATAAG
* * * *
76348 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGAAACAAGTATGTGTCTCACCAGAC
76413 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
76451 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGAAACAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGAAACAAGTATGTGTCTCACCAGAC
*
76516 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
76554 GACCACATA
1 GACCACATA
76563 GACCCTCGAC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGAAACAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:77358 original size:23 final size:23
Alignment explanation
Indices: 77328--77401 Score: 93
Period size: 23 Copynumber: 3.4 Consensus size: 23
77318 TACACAGTGT
77328 ATCGATGCATTCCCTATCGGTGC
1 ATCGATGCATTCCCTATCGGTGC
* * *
77351 ATCGATGCA----CTACCTGTGT
1 ATCGATGCATTCCCTATCGGTGC
77370 ATCGATGCATTCCCTATCGGTGC
1 ATCGATGCATTCCCTATCGGTGC
77393 ATCGATGCA
1 ATCGATGCA
77402 CTACCTGTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 16 0.39
23 25 0.61
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (23 bp):
ATCGATGCATTCCCTATCGGTGC
Found at i:77375 original size:19 final size:19
Alignment explanation
Indices: 77307--77420 Score: 75
Period size: 19 Copynumber: 5.5 Consensus size: 19
77297 TGAAGGTATA
*
77307 CATCGATGCACTACACAGTG
1 CATCGATGCACTAC-CGGTG
* *
77327 TATCGATGCATTCCCTATCGGTG
1 CATCGATGCA----CTACCGGTG
*
77350 CATCGATGCACTACCTGTG
1 CATCGATGCACTACCGGTG
* *
77369 TATCGATGCATTCCCTATCGGTG
1 CATCGATGCA----CTACCGGTG
*
77392 CATCGATGCACTACCTGTG
1 CATCGATGCACTACCGGTG
*
77411 CATCGGTGCA
1 CATCGATGCA
77421 TAAAATACAT
Statistics
Matches: 73, Mismatches: 13, Indels: 17
0.71 0.13 0.17
Matches are distributed among these distances:
19 32 0.44
20 9 0.12
23 29 0.40
24 3 0.04
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (19 bp):
CATCGATGCACTACCGGTG
Found at i:77379 original size:42 final size:42
Alignment explanation
Indices: 77307--77421 Score: 194
Period size: 42 Copynumber: 2.7 Consensus size: 42
77297 TGAAGGTATA
*
77307 CATCGATGCACTACACAGTGTATCGATGCATTCCCTATCGGTG
1 CATCGATGCACTAC-CTGTGTATCGATGCATTCCCTATCGGTG
77350 CATCGATGCACTACCTGTGTATCGATGCATTCCCTATCGGTG
1 CATCGATGCACTACCTGTGTATCGATGCATTCCCTATCGGTG
* *
77392 CATCGATGCACTACCTGTGCATCGGTGCAT
1 CATCGATGCACTACCTGTGTATCGATGCAT
77422 AAAATACATT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 55 0.80
43 14 0.20
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29
Consensus pattern (42 bp):
CATCGATGCACTACCTGTGTATCGATGCATTCCCTATCGGTG
Found at i:77522 original size:19 final size:19
Alignment explanation
Indices: 77498--77561 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
77488 TTTTAAAAGA
77498 GTGCATCGATGCACTACCT
1 GTGCATCGATGCACTACCT
*
77517 GTGCATCGATGCACTATCT
1 GTGCATCGATGCACTACCT
*
77536 GTGCATCTATGCACTACCT
1 GTGCATCGATGCACTACCT
77555 GTGCATC
1 GTGCATC
77562 AATACACCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCACTACCT
Found at i:82347 original size:23 final size:23
Alignment explanation
Indices: 82321--82389 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
82311 CACCACAGCT
82321 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
82344 CATATAATTGCATCGAAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
82367 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
82390 TATAATACTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:82562 original size:96 final size:96
Alignment explanation
Indices: 82408--82587 Score: 324
Period size: 96 Copynumber: 1.9 Consensus size: 96
82398 TGTCCATAAG
* * *
82408 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAACCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
82473 TTCACACATGTTCCAAAGATATGTCCCGAAA
66 TTCACACATGTTCCAAAGATATGTCCCGAAA
*
82504 GACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAACCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
82569 TTCACACATGTTCCAAAGA
66 TTCACACATGTTCCAAAGA
82588 ATACATATAT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 80 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (96 bp):
GACCACATATCATTCCTTAAGAACCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGATATGTCCCGAAA
Found at i:84591 original size:37 final size:34
Alignment explanation
Indices: 84550--84632 Score: 94
Period size: 37 Copynumber: 2.3 Consensus size: 34
84540 TGGTAATTCG
84550 ATAATAAAAAATACAATAATAATGTATTAATATGAAA
1 ATAATAAAAAATACAAT--TAATGTATTAATAT-AAA
* *
84587 ATAATTATAAAATTACAGTTAATGTATTAATATAAA
1 ATAA-TA-AAAAATACAATTAATGTATTAATATAAA
*
84623 GTAATAAAAA
1 ATAATAAAAA
84633 TAATCATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
34 4 0.10
35 2 0.05
36 6 0.15
37 18 0.44
38 2 0.05
39 9 0.22
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (34 bp):
ATAATAAAAAATACAATTAATGTATTAATATAAA
Found at i:85271 original size:74 final size:76
Alignment explanation
Indices: 85139--85290 Score: 191
Period size: 74 Copynumber: 2.0 Consensus size: 76
85129 TTTTATAAAC
* * * * * **
85139 TTGACTCGACTTAAAAAATTTTCAAATAAAGTTTTAGTTATAAAATAGGACCCGTCAACTCGAAT
1 TTGACTCGACTCAAAAAACTTTCAAATAAAATTTTAATTATAAAATAAGACAAGTCAACTCGAAT
85204 AACTC-AAATT
66 AACTCAAAATT
* * * *
85214 TTGACTCGACTCGAAAAACTTT-AAATAAAATTTTAATTATAAAATAAGATAATTCAACTTGAAT
1 TTGACTCGACTCAAAAAACTTTCAAATAAAATTTTAATTATAAAATAAGACAAGTCAACTCGAAT
85278 AACTCAAAATT
66 AACTCAAAATT
85289 TT
1 TT
85291 TTGACTTAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 39 0.60
75 26 0.40
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.34
Consensus pattern (76 bp):
TTGACTCGACTCAAAAAACTTTCAAATAAAATTTTAATTATAAAATAAGACAAGTCAACTCGAAT
AACTCAAAATT
Found at i:85677 original size:17 final size:17
Alignment explanation
Indices: 85655--85696 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
85645 CATTAAAATT
85655 AAAATTTTAAACGCCTC
1 AAAATTTTAAACGCCTC
85672 AAAATTTTAAACGCCTC
1 AAAATTTTAAACGCCTC
*
85689 AAAGTTTT
1 AAAATTTT
85697 TAGAATACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (17 bp):
AAAATTTTAAACGCCTC
Found at i:87921 original size:4 final size:4
Alignment explanation
Indices: 87914--87939 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
87904 TTTATTTAAT
87914 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
87940 TGAAATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:92291 original size:12 final size:12
Alignment explanation
Indices: 92276--92301 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
92266 GAATAATTCA
92276 GTGAACCAGTAT
1 GTGAACCAGTAT
92288 GTGAACCAGTAT
1 GTGAACCAGTAT
92300 GT
1 GT
92302 CCGAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (12 bp):
GTGAACCAGTAT
Found at i:97720 original size:28 final size:26
Alignment explanation
Indices: 97660--97720 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
97650 TTGAATTATT
* * *
97660 ATATTAAAATGATTTTTAGTTTACAA
1 ATATTAAAATAATTTTAAATTTACAA
97686 ATTATTAAAATAATTATTAAATTTATCAA
1 A-TATTAAAATAATT-TTAAATTTA-CAA
97715 ATATTA
1 ATATTA
97721 TAAAATGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 12 0.41
28 12 0.41
29 4 0.14
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (26 bp):
ATATTAAAATAATTTTAAATTTACAA
Found at i:97876 original size:19 final size:19
Alignment explanation
Indices: 97818--97877 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
97808 TGCTCACTCT
97818 ATAATTTTAT-ATATTCTAA
1 ATAATTTTATAATATT-TAA
*
97837 TGATGATTTTATAA-ATATTAA
1 --ATAATTTTATAATAT-TTAA
97858 ATAATTTTATAATATTTAA
1 ATAATTTTATAATATTTAA
97877 A
1 A
97878 ATATTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 16 0.47
20 2 0.06
21 14 0.41
22 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (19 bp):
ATAATTTTATAATATTTAA
Found at i:109346 original size:5 final size:5
Alignment explanation
Indices: 109336--109368 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
109326 ATATTTGAAG
*
109336 TTTGA TTTGA TTTGA TTTGA TTTAA TTTGA TTT
1 TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTT
109369 TTACAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (5 bp):
TTTGA
Found at i:109914 original size:15 final size:15
Alignment explanation
Indices: 109890--109926 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
109880 GCAACATTAA
*
109890 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
109905 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
*
109920 ACTAAAT
1 ATTAAAT
109927 GAATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:111604 original size:16 final size:16
Alignment explanation
Indices: 111575--111605 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
111565 TTTTATAAAT
*
111575 ATTACATTTTAATTAA
1 ATTACATTTAAATTAA
111591 ATTACATTTAAATTA
1 ATTACATTTAAATTA
111606 TTAAATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTACATTTAAATTAA
Found at i:132901 original size:61 final size:61
Alignment explanation
Indices: 132831--132952 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
132821 CAAAGATCAC
132831 GTAAGCAAAAAATTAAAAACCTAATTAAAAACTCGTATAAAGATAAATGTCAATACATCTT
1 GTAAGCAAAAAATTAAAAACCTAATTAAAAACTCGTATAAAGATAAATGTCAATACATCTT
*
132892 GTAAGCAAAAAATTAAAAACCTAATTAAAAACTCGTATAAAGATAAATGTCAATATATCTT
1 GTAAGCAAAAAATTAAAAACCTAATTAAAAACTCGTATAAAGATAAATGTCAATACATCTT
132953 ATTACATCAC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.27
Consensus pattern (61 bp):
GTAAGCAAAAAATTAAAAACCTAATTAAAAACTCGTATAAAGATAAATGTCAATACATCTT
Found at i:133217 original size:25 final size:25
Alignment explanation
Indices: 133189--133247 Score: 102
Period size: 24 Copynumber: 2.4 Consensus size: 25
133179 AAAGAAGATA
*
133189 AAAAAAACGTACTGAAATATAGGGG
1 AAAAAAACGTACCGAAATATAGGGG
133214 -AAAAAACGTACCGAAATATAGGGG
1 AAAAAAACGTACCGAAATATAGGGG
133238 AAAAAAACGT
1 AAAAAAACGT
133248 GCCAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.54, C:0.10, G:0.22, T:0.14
Consensus pattern (25 bp):
AAAAAAACGTACCGAAATATAGGGG
Found at i:149886 original size:32 final size:31
Alignment explanation
Indices: 149781--149883 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
149771 ATTAGTTTGG
* * *
149781 TCATGAAATTTGTCAAAC-ATTACAAAAT-A
1 TCATTAAATTTATCAAACTATTATAAAATGA
* *
149810 GTCATTAAATTTATCAAA-TGTTATAAGATGA
1 -TCATTAAATTTATCAAACTATTATAAAATGA
149841 TCATTACAATTTATCAAACTATTATAAAATGA
1 TCATTA-AATTTATCAAACTATTATAAAATGA
149873 TCATTAAATTT
1 TCATTAAATTT
149884 TATTGAACTG
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
30 28 0.45
31 17 0.27
32 17 0.27
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.38
Consensus pattern (31 bp):
TCATTAAATTTATCAAACTATTATAAAATGA
Found at i:164333 original size:60 final size:60
Alignment explanation
Indices: 164253--164401 Score: 176
Period size: 60 Copynumber: 2.5 Consensus size: 60
164243 AGTTTGTAAA
* * * *
164253 GAAATTAAAATGTTCAAAAGTTTAAGGACCAATCTAGAATGAGAGTCATAGT-TTGATGAT
1 GAAATTAAAACGTTCAAAAGTTTAAGGACCAATCTAGAACGAGAGACATAGTATGGA-GAT
* * *
164313 GAAATTAAAACGTTCAAAAGTTTAAGAACTAATTTAGAACGAGAGACATAGTATGGAGAT
1 GAAATTAAAACGTTCAAAAGTTTAAGGACCAATCTAGAACGAGAGACATAGTATGGAGAT
* * *
164373 -AGAATTAAAACATTCAAAAATTTATGGAC
1 GA-AATTAAAACGTTCAAAAGTTTAAGGAC
164402 TATTTTTTTA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.01
60 72 0.95
61 3 0.04
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.28
Consensus pattern (60 bp):
GAAATTAAAACGTTCAAAAGTTTAAGGACCAATCTAGAACGAGAGACATAGTATGGAGAT
Found at i:166656 original size:19 final size:20
Alignment explanation
Indices: 166619--166656 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
166609 TAAAATCGTA
*
166619 AAAAATAATGATTAAATAAT
1 AAAAATAATGATCAAATAAT
*
166639 AAAAATAA-GATCATATAA
1 AAAAATAATGATCAAATAA
166657 AGAAAACAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAAATAATGATCAAATAAT
Found at i:169183 original size:23 final size:22
Alignment explanation
Indices: 169157--169207 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
169147 TTCTTAACAA
*
169157 TTCTGCCTTTTTGACACGTATTT
1 TTCTGCCTTTATGACACGT-TTT
*
169180 TTCTACCTTTATGACACGTTTT
1 TTCTGCCTTTATGACACGTTTT
169202 TCTCTG
1 T-TCTG
169208 TCTCTATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.14, C:0.24, G:0.12, T:0.51
Consensus pattern (22 bp):
TTCTGCCTTTATGACACGTTTT
Found at i:170090 original size:259 final size:252
Alignment explanation
Indices: 169487--170095 Score: 788
Period size: 259 Copynumber: 2.4 Consensus size: 252
169477 CTTATTCATA
*
169487 TATTGAATAAAAATATTTTTTTTATAATTTCGGGTC-GG--GTTTCTAATTCATATATTCGGGTC
1 TATTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTCGTTTCTAATTCATATATTCGGGTC
* * *
169549 GGGTCGGGTGAAACTTTATTTTGGTCGGGTTGGGTAGGTTTTTTAAAAGTGTGATATTCGGGTCG
66 GGGTCGGGTGAAACTTTATTTTGGTCGGG-TCGGTAGATTTTTTAAAAGTGTGATATTAGGGTCG
* * *
169614 GGTCGGGTCGGGTTTAGGGTGAAAATACCCGACCCGAAAATATATATAATTTCAACTTATATATT
130 GGTCGGGT--GGTTTAGGATGAAAATACCCGACCCAAAAAAATATATAATTTCAACTTATATATT
* *
169679 TAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTCCAATTAAGTCATTGCTTT
193 TAGGAATAATTACAATAATACCCCTCTATATATAATATTTTCCAATTAAGTCACTGCTTT
* *
169739 TATTGAATAAAAATA-ATTTTTTATTATTTCGTGTCGGGTCGGGTTTCTAATTCATATATTCGGG
1 TATTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTC--GTTTCTAATTCATATATTCGGG
* *
169803 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTCGATTTTTT-TAAGTGTGATATTAGGGTC
64 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTAGATTTTTTAAAAGTGTGATATTAGGGTC
** * *
169867 GGGTTTGGT-GTTTAGGATGAAAAATACCCTACCCGACTCGACCCAAAAAAATATATAATTTTAC
129 GGGTCGGGTGGTTTAGGATG--AAA-A---TA--C--C-CGACCCAAAAAAATATATAATTTCAA
169931 CTTATATATTTAGGAATAATTACAATAATA-CCC-CTATATAT-ATATTTT-CAATTAAGTCACT
183 CTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATATTTTCCAATTAAGTCACT
*
169992 GTTTT
248 GCTTT
* * *
169997 TGTTGCATAAAAATATTTTTTTTATTATTTCGGGTCGGGTCAAGTTTCTAATTCATATATTTGGG
1 TATTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTC--GTTTCTAATTCATATATTCGGG
*
170062 TTGGGTCGGGTGAAACTTTATTTTGGTCGGGTCG
64 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCG
170096 AGTCTCGGAT
Statistics
Matches: 314, Mismatches: 26, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
251 26 0.08
252 17 0.05
253 3 0.01
254 25 0.08
255 11 0.04
256 53 0.17
257 2 0.01
258 29 0.09
259 84 0.27
260 8 0.03
261 4 0.01
262 52 0.17
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (252 bp):
TATTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTCGTTTCTAATTCATATATTCGGGTC
GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTAGATTTTTTAAAAGTGTGATATTAGGGTCGG
GTCGGGTGGTTTAGGATGAAAATACCCGACCCAAAAAAATATATAATTTCAACTTATATATTTAG
GAATAATTACAATAATACCCCTCTATATATAATATTTTCCAATTAAGTCACTGCTTT
Found at i:171219 original size:25 final size:25
Alignment explanation
Indices: 171163--171219 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
171153 TTATTATAAT
* *
171163 TTAAATATTTTCTATTTTTAATAAAA
1 TTAAATATTTTCTA-TTTAAAGAAAA
171189 TT-AATATTTTCTA-TTAAAGAAAA
1 TTAAATATTTTCTATTTAAAGAAAA
171212 TGTAAATA
1 T-TAAATA
171220 AATATGTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 9 0.33
24 1 0.04
25 15 0.56
26 2 0.07
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
TTAAATATTTTCTATTTAAAGAAAA
Found at i:171565 original size:21 final size:21
Alignment explanation
Indices: 171531--171635 Score: 122
Period size: 21 Copynumber: 4.8 Consensus size: 21
171521 ATTGCGATAG
*
171531 TCTAAGTTCACGTTGCGATATAT
1 TCTAAGTT--CGTTGCGATTTAT
171554 TCTAAGTTCGTTGCGATTTAT
1 TCTAAGTTCGTTGCGATTTAT
* *
171575 TCTAAATTCGTTGTGATTTAT
1 TCTAAGTTCGTTGCGATTTAT
171596 T-TCAAGTTCGCGTTGCGATTTAT
1 TCT-AAGTT--CGTTGCGATTTAT
*
171619 TCCAAGTTCGTTGCGAT
1 TCTAAGTTCGTTGCGAT
171636 AGTCGTTGCG
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.01
21 45 0.62
23 26 0.36
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (21 bp):
TCTAAGTTCGTTGCGATTTAT
Found at i:171587 original size:42 final size:41
Alignment explanation
Indices: 171557--171843 Score: 333
Period size: 42 Copynumber: 7.0 Consensus size: 41
171547 GATATATTCT
* * * *
171557 AAGTT-CGTTGCGATTTATTCTAAATTCGTTGTGATTTATTTC
1 AAGTTCCGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCC
*
171599 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCG--A-T--
1 AAGTTC-CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCC
* *
171636 -AG-T-CGTTGCGATTTATTCCAAATTCATTGCGATAGTCG
1 AAGTTCCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCC
* *
171674 AAGTTCGCGTTGCGATGTATTCTAAATTCGTTGCGATAGTCC
1 AAGTTC-CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCC
171716 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCC
1 AAGTTC-CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCC
*
171758 AAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTCC
1 AAGTTC-CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCC
*
171800 AAGTTCGCGTTGCGTTTTATT-CAAAGTTCGTTGCGATAGTCC
1 AAGTTC-CGTTGCGATTTATTCCAAA-TTCGTTGCGATAGTCC
171842 AA
1 AA
171844 AATCGCAACG
Statistics
Matches: 219, Mismatches: 14, Indels: 24
0.85 0.05 0.09
Matches are distributed among these distances:
33 26 0.12
35 2 0.01
36 3 0.01
39 3 0.01
40 2 0.01
41 4 0.02
42 154 0.70
44 25 0.11
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (41 bp):
AAGTTCCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCC
Found at i:171648 original size:33 final size:33
Alignment explanation
Indices: 171606--171673 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
171596 TTCAAGTTCG
* *
171606 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGT
1 CGTTGCGATTTATTCCAAATTCATTGCGATAGT
171639 CGTTGCGATTTATTCCAAATTCATTGCGATAGT
1 CGTTGCGATTTATTCCAAATTCATTGCGATAGT
171672 CG
1 CG
171674 AAGTTCGCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (33 bp):
CGTTGCGATTTATTCCAAATTCATTGCGATAGT
Found at i:171667 original size:21 final size:20
Alignment explanation
Indices: 171638--171836 Score: 120
Period size: 21 Copynumber: 9.5 Consensus size: 20
171628 GTTGCGATAG
171638 TCGTTGCGATTTATTCCAAAT
1 TCGTTGCGA-TTATTCCAAAT
* * * *
171659 TCATTGCGA-TAGTCGAAGT
1 TCGTTGCGATTATTCCAAAT
*
171678 TCGCGTTGCGATGTATTCTAAAT
1 T--CGTTGCGAT-TATTCCAAAT
* *
171701 TCGTTGCGA-TAGTCCAAGT
1 TCGTTGCGATTATTCCAAAT
171720 TCGCGTTGCGATTTATTCCAAAT
1 T--CGTTGCGA-TTATTCCAAAT
* *
171743 TCGTTGCGA-TAGTCCAAGT
1 TCGTTGCGATTATTCCAAAT
*
171762 TCGCGTTGTGATTTATTCCAAAT
1 T--CGTTGCGA-TTATTCCAAAT
* *
171785 TCGTTGCGA-TAGTCCAAGT
1 TCGTTGCGATTATTCCAAAT
*
171804 TCGCGTTGCGTTTTATT-CAAAGT
1 T--CGTTGCG-ATTATTCCAAA-T
171827 TCGTTGCGAT
1 TCGTTGCGAT
171837 AGTCCAAAAT
Statistics
Matches: 136, Mismatches: 25, Indels: 35
0.69 0.13 0.18
Matches are distributed among these distances:
19 34 0.25
20 1 0.01
21 67 0.49
22 3 0.02
23 31 0.23
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGTTGCGATTATTCCAAAT
Found at i:172450 original size:11 final size:11
Alignment explanation
Indices: 172434--172460 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
172424 GTCCGCCTCG
172434 GGTCGGGTCGT
1 GGTCGGGTCGT
172445 GGTCGGGTCGT
1 GGTCGGGTCGT
172456 GGTCG
1 GGTCG
172461 TGGTAGTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.26
Consensus pattern (11 bp):
GGTCGGGTCGT
Found at i:172461 original size:17 final size:16
Alignment explanation
Indices: 172431--172464 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
172421 GCCGTCCGCC
172431 TCGGGTCGGGTCGTGG
1 TCGGGTCGGGTCGTGG
172447 TCGGGTCGTGGTCGTGG
1 TCGGGTCG-GGTCGTGG
172464 T
1 T
172465 AGTTCGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (16 bp):
TCGGGTCGGGTCGTGG
Found at i:172583 original size:21 final size:21
Alignment explanation
Indices: 172559--172627 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
172549 TTTGGAATAA
172559 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
172580 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
**
172599 AAATTACAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
172622 ATCGCA
1 ATCGCA
172628 TTGCGATTTA
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
19 9 0.26
21 16 0.47
23 9 0.26
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:172724 original size:21 final size:21
Alignment explanation
Indices: 172698--172772 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
172688 TATTCACATT
*
172698 TTCGCATTGCGATAATCTAAG
1 TTCGCATTGCGATAGTCTAAG
172719 TTCGCATTGCGATAGTCTAAG
1 TTCGCATTGCGATAGTCTAAG
*
172740 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCTAAG
*
172761 TTCGCGTTGCGA
1 TTCGCATTGCGA
172773 ATCTGAAAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCTAAG
Found at i:172851 original size:46 final size:46
Alignment explanation
Indices: 172784--172880 Score: 167
Period size: 46 Copynumber: 2.1 Consensus size: 46
172774 TCTGAAAACT
*
172784 GATTTGCGATACTGGAGATCGCATTACGAATTATCGATCGCATTGC
1 GATTTGCGATACTGGAGATCGCATTACGAATTATCAATCGCATTGC
* *
172830 GATTTGCGATACTGGAGATCGCATTGCGAATTATCAATCGCATTGT
1 GATTTGCGATACTGGAGATCGCATTACGAATTATCAATCGCATTGC
172876 GATTT
1 GATTT
172881 AGTTGGTCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (46 bp):
GATTTGCGATACTGGAGATCGCATTACGAATTATCAATCGCATTGC
Found at i:173640 original size:23 final size:23
Alignment explanation
Indices: 173614--173657 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
173604 CATTTTTGGC
173614 ACGTATTAT-TCTGTCTTTATAAT
1 ACGT-TTATCTCTGTCTTTATAAT
*
173637 ACGTTTTTCTCTGTCTTTATA
1 ACGTTTATCTCTGTCTTTATA
173658 GTAGTTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (23 bp):
ACGTTTATCTCTGTCTTTATAAT
Found at i:173666 original size:21 final size:23
Alignment explanation
Indices: 173623--173665 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
173613 CACGTATTAT
173623 TCTGTCTTTATAATACGTTTTTC
1 TCTGTCTTTATAATACGTTTTTC
*
173646 TCTGTCTTTATAGTA-GTTTT
1 TCTGTCTTTATAATACGTTTT
173666 CGGTTATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (23 bp):
TCTGTCTTTATAATACGTTTTTC
Found at i:182433 original size:21 final size:21
Alignment explanation
Indices: 182391--182433 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
182381 TTTCTGGGCT
* * *
182391 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
182412 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
182433 A
1 A
182434 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:184073 original size:23 final size:23
Alignment explanation
Indices: 184040--184107 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
184030 ATTATTATAT
*
184040 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
184063 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
184086 GGCACTTCGGTGCAATTTTACG
1 GGCACTACGGTGCAATTCTACG
184108 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:184896 original size:16 final size:16
Alignment explanation
Indices: 184849--184901 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
184839 TCATGTTTCC
184849 TTAGTAATTTAATTTT
1 TTAGTAATTTAATTTT
*
184865 TTAAATATATATTTAATTTT
1 TT--A-GTA-ATTTAATTTT
184885 TTAGTAATTTAATTTT
1 TTAGTAATTTAATTTT
184901 T
1 T
184902 AATTTTAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 13 0.42
17 2 0.06
18 2 0.06
19 2 0.06
20 12 0.39
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (16 bp):
TTAGTAATTTAATTTT
Found at i:185169 original size:24 final size:24
Alignment explanation
Indices: 185136--185183 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
185126 CAAAGGGATA
*
185136 CATTGTGTTTGTTTTCTAAGTTTG
1 CATTGAGTTTGTTTTCTAAGTTTG
185160 CATTGAGTTTGTTTTCTAAGTTTG
1 CATTGAGTTTGTTTTCTAAGTTTG
185184 AGGCCACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.08, G:0.21, T:0.56
Consensus pattern (24 bp):
CATTGAGTTTGTTTTCTAAGTTTG
Found at i:187722 original size:14 final size:14
Alignment explanation
Indices: 187705--187735 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
187695 ATTTACGTTG
*
187705 TCTGTGATATCTTT
1 TCTGTAATATCTTT
187719 TCTGTAATATCTTT
1 TCTGTAATATCTTT
187733 TCT
1 TCT
187736 TTTGGGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.58
Consensus pattern (14 bp):
TCTGTAATATCTTT
Found at i:191887 original size:42 final size:42
Alignment explanation
Indices: 191811--191905 Score: 124
Period size: 42 Copynumber: 2.2 Consensus size: 42
191801 ATTAATATTT
191811 AAATCTAAATTTTAAAAAATTATTTAACTTTTTAACTTAAC-A
1 AAATCTAAA-TTTAAAAAATTATTTAACTTTTTAACTTAACAA
*
191853 AAATCTAAATTT-AAATATTA-TTAACTAATATTTAACTTAACAA
1 AAATCTAAATTTAAAAAATTATTTAACT--T-TTTAACTTAACAA
191896 AAATCTAAAT
1 AAATCTAAAT
191906 ACTATCTATC
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
39 6 0.12
40 7 0.15
41 4 0.08
42 20 0.42
43 11 0.23
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (42 bp):
AAATCTAAATTTAAAAAATTATTTAACTTTTTAACTTAACAA
Found at i:199909 original size:96 final size:97
Alignment explanation
Indices: 199739--199913 Score: 280
Period size: 96 Copynumber: 1.8 Consensus size: 97
199729 TCTTGATGGC
* * * *
199739 TTTTCTTTCACATGTGTATTTTTTGGGCTGCTGGTGATTTCGCCCACTACATCTATTAAAGGAGA
1 TTTTCTTTCACATGTGTATTATTTGGGCTGCTGGCGATTTCGCCCACTACATCCACTAAAGGAGA
*
199804 GGTTGAGTTTTGATCAAAGAACGTCAAGATGT
66 GGTTAAGTTTTGATCAAAGAACGTCAAGATGT
* *
199836 TTTTCTTTCACATGTGTA-TATTTGGGCTGCTGGCGATTTCGCCCACTGCATCCACTGAAGGAGA
1 TTTTCTTTCACATGTGTATTATTTGGGCTGCTGGCGATTTCGCCCACTACATCCACTAAAGGAGA
199900 GGTTAAGTTTTGAT
66 GGTTAAGTTTTGAT
199914 GAGATGAACT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
96 53 0.75
97 18 0.25
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (97 bp):
TTTTCTTTCACATGTGTATTATTTGGGCTGCTGGCGATTTCGCCCACTACATCCACTAAAGGAGA
GGTTAAGTTTTGATCAAAGAACGTCAAGATGT
Found at i:200937 original size:23 final size:23
Alignment explanation
Indices: 200894--200937 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
200884 CGAAGATATT
200894 AATAAAAATATATATTATAATAC
1 AATAAAAATATATATTATAATAC
*
200917 AATAAATAATATA-ATTTTAAT
1 AATAAA-AATATATATTATAAT
200938 TTTATGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAAAAATATATATTATAATAC
Found at i:208986 original size:15 final size:15
Alignment explanation
Indices: 208966--208996 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
208956 TTGCTCAAAT
208966 TTCTTAACCTTGAGG
1 TTCTTAACCTTGAGG
208981 TTCTTAACCTTGAGG
1 TTCTTAACCTTGAGG
208996 T
1 T
208997 CGTGGGATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (15 bp):
TTCTTAACCTTGAGG
Found at i:212451 original size:71 final size:71
Alignment explanation
Indices: 212335--212476 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
212325 TAACTCTCTG
*
212335 CTTGTGTTAACCTTTAGAAGGATCATGTGTGATCATATGATAATGTGTAAAAGGTTTACACTTGT
1 CTTGTGTTAACCTTTAGAAGGATCATGTGTGATAATATGATAATGTGTAAAAGGTTTACACTTGT
212400 ATTTAT
66 ATTTAT
*
212406 CTTGTGTTAACCTTTAGAAGGATCATGTGTGATAATATGATAATGTGTCAAAGGTTTACACTTGT
1 CTTGTGTTAACCTTTAGAAGGATCATGTGTGATAATATGATAATGTGTAAAAGGTTTACACTTGT
212471 ATTTAT
66 ATTTAT
212477 ACATGTTGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.41
Consensus pattern (71 bp):
CTTGTGTTAACCTTTAGAAGGATCATGTGTGATAATATGATAATGTGTAAAAGGTTTACACTTGT
ATTTAT
Found at i:217520 original size:42 final size:40
Alignment explanation
Indices: 217472--217572 Score: 166
Period size: 40 Copynumber: 2.5 Consensus size: 40
217462 TCGCAACGTT
217472 AACTTCGACTATCGCAACGAATTTGAAATAAATCGCAAAGCA
1 AACTTCGACTATCGCAACGAATTTG-AA-AAATCGCAAAGCA
* *
217514 AACTTCGACTATCGCAACGAATTTGAAAAATCGCAACGCG
1 AACTTCGACTATCGCAACGAATTTGAAAAATCGCAAAGCA
217554 AACTTCGACTATCGCAACG
1 AACTTCGACTATCGCAACG
217573 CGAACTTGGA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
40 30 0.53
41 2 0.04
42 25 0.44
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.21
Consensus pattern (40 bp):
AACTTCGACTATCGCAACGAATTTGAAAAATCGCAAAGCA
Found at i:217596 original size:21 final size:21
Alignment explanation
Indices: 217454--217597 Score: 111
Period size: 21 Copynumber: 7.0 Consensus size: 21
217444 CAGATTCGCA
**
217454 TTCGACTATCGCAACGTTAAC
1 TTCGACTATCGCAACGCGAAC
217475 TTCGACTATCGCAA--CGAA-
1 TTCGACTATCGCAACGCGAAC
* * * *
217493 TTTGAAATAAATCGCAAAGCAAAC
1 TTCG-ACT--ATCGCAACGCGAAC
217517 TTCGACTATCGCAA--CGAA-
1 TTCGACTATCGCAACGCGAAC
* **
217535 TTTGAAAAATCGCAACGCGAAC
1 TTCG-ACTATCGCAACGCGAAC
217557 TTCGACTATCGCAACGCGAAC
1 TTCGACTATCGCAACGCGAAC
* *
217578 TTGGACTATCGCAATGCGAA
1 TTCGACTATCGCAACGCGAA
217598 TATGTAAATC
Statistics
Matches: 97, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
18 6 0.06
19 15 0.15
21 65 0.67
22 3 0.03
23 5 0.05
24 3 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (21 bp):
TTCGACTATCGCAACGCGAAC
Found at i:220507 original size:94 final size:95
Alignment explanation
Indices: 220339--220510 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 95
220329 CTTATTTTTC
* * * * *
220339 AATTAAGATCATTTTTTATGATTTAATAATAAAATAGTCAAAAATAAGAACAAGTTAAAGTTAAG
1 AATTAAGATCACTTTTAAAGATTTAATAACAAAATAGTCAAAAATAAGAACAAGTTAAAGTTAAC
* *
220404 TTTCGATTAAGTTTATTTACTTTTAATGAT
66 TCTCAATTAAGTTTATTTACTTTTAATGAT
* * *
220434 AATTAAGATCACTTTTAAAGATTT-ATGACAAAATAGTC-AAAATAAGAACAATTTAAAAGTTTA
1 AATTAAGATCACTTTTAAAGATTTAATAACAAAATAGTCAAAAATAAGAACAAGTT-AAAGTTAA
220497 CTCTCAATTAAGTT
65 CTCTCAATTAAGTT
220511 CACTTTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
93 15 0.23
94 30 0.45
95 21 0.32
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.38
Consensus pattern (95 bp):
AATTAAGATCACTTTTAAAGATTTAATAACAAAATAGTCAAAAATAAGAACAAGTTAAAGTTAAC
TCTCAATTAAGTTTATTTACTTTTAATGAT
Found at i:222051 original size:17 final size:17
Alignment explanation
Indices: 222026--222067 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
222016 CAACCAATCA
* *
222026 TCAACATCTTACCTTGG
1 TCAATATCTTACCTAGG
222043 TCAATATCTTACCTAGG
1 TCAATATCTTACCTAGG
222060 TCAATATC
1 TCAATATC
222068 CTAAACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.36
Consensus pattern (17 bp):
TCAATATCTTACCTAGG
Found at i:222520 original size:12 final size:12
Alignment explanation
Indices: 222503--222527 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
222493 CCCCTTACCC
222503 ATTACATATTGA
1 ATTACATATTGA
222515 ATTACATATTGA
1 ATTACATATTGA
222527 A
1 A
222528 ATAAGGGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTACATATTGA
Found at i:226962 original size:22 final size:24
Alignment explanation
Indices: 226937--226993 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 24
226927 GTATCATTAT
226937 TAAAATATTTTAA-ATAT-TTAAA
1 TAAAATATTTTAATATATGTTAAA
*
226959 TAAAA-A-ATTAATATATGTTAAA
1 TAAAATATTTTAATATATGTTAAA
*
226981 T-AATTATTTTAAT
1 TAAAATATTTTAAT
226994 TAAAATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 4 0.14
21 7 0.25
22 12 0.43
23 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
TAAAATATTTTAATATATGTTAAA
Found at i:231802 original size:18 final size:18
Alignment explanation
Indices: 231779--231826 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
231769 AATTTGTTAG
231779 TTAATTATTAATTAT-AGT
1 TTAATT-TTAATTATAAGT
* *
231797 TTAATTTTAATTTTAATT
1 TTAATTTTAATTATAAGT
231815 TTAATTTTAATT
1 TTAATTTTAATT
231827 TTTTCATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTAATTTTAATTATAAGT
Found at i:231807 original size:6 final size:6
Alignment explanation
Indices: 231796--231828 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
231786 TTAATTATAG
231796 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTT
231829 TTCATCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:245256 original size:20 final size:20
Alignment explanation
Indices: 245127--245313 Score: 208
Period size: 20 Copynumber: 9.6 Consensus size: 20
245117 CGATTTCAAT
* * *
245127 AATCGCAACGCGAAT-AGAA
1 AATCGCAACGCGTATCCGTA
* *
245146 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
245166 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
245186 AATCGCAACG-GTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
245205 AATCGCAACGC-TAT-GGTA
1 AATCGCAACGCGTATCCGTA
*
245223 AATCGC-ATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
245242 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
245262 AATCGCAACG-ATAATACATA
1 AATCGCAACGCGT-ATCCGTA
245282 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
245302 AATCGCAACGCG
1 AATCGCAACGCG
245314 ATATTAAAGC
Statistics
Matches: 141, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.02
18 13 0.09
19 43 0.30
20 79 0.56
21 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:245706 original size:32 final size:32
Alignment explanation
Indices: 245668--245736 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
245658 ATTTCACTTA
*
245668 GATTTCATTTCGCGTTACGATTCTGTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
245700 GATTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
245732 GATTT
1 GATTT
245737 TCAAGTTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:245717 original size:18 final size:18
Alignment explanation
Indices: 245668--245717 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
245658 ATTTCACTTA
*
245668 GATTTCATTTCGCGTTAC
1 GATTTCATTTCGCGTTGC
*
245686 GA-TTC-TGT--CGTTGC
1 GATTTCATTTCGCGTTGC
245700 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
245718 TATTCTCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 3 0.12
16 4 0.16
17 3 0.12
18 8 0.32
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:245876 original size:31 final size:33
Alignment explanation
Indices: 245838--245927 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 33
245828 GATAAATGAA
***
245838 AATCGCAACGAG-AATGACTGTCGC-ACGAGAG
1 AATCGCAACGAGAAATGAAAATCGCAACGAGAG
*
245869 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGAGAAATGAAAATCGCAACGAGAG
* **
245902 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGAGAAATGAAAATCGCA
245928 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
31 11 0.22
32 9 0.18
33 31 0.61
ACGTcount: A:0.42, C:0.24, G:0.23, T:0.10
Consensus pattern (33 bp):
AATCGCAACGAGAAATGAAAATCGCAACGAGAG
Found at i:245904 original size:33 final size:33
Alignment explanation
Indices: 245858--245927 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
245848 AGAATGACTG
**
245858 TCGC-ACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
245890 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
245923 TCGCA
1 TCGCA
245928 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 4 0.11
33 31 0.89
ACGTcount: A:0.43, C:0.26, G:0.23, T:0.09
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:245945 original size:19 final size:18
Alignment explanation
Indices: 245923--246019 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
245913 GAAACCAAAA
*
245923 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
245942 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
245956 TCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
245974 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
* *
245988 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATT
246007 TCGCGTTGCGATT
1 TCGCGTTGCGATT
246020 CTCGTTGCGA
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
14 20 0.31
15 4 0.06
16 2 0.03
17 6 0.09
18 10 0.16
19 22 0.34
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:245964 original size:14 final size:14
Alignment explanation
Indices: 245945--246031 Score: 70
Period size: 14 Copynumber: 5.7 Consensus size: 14
245935 TTTCATTTCG
245945 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
245959 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
245977 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
245991 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
246008 CGCGTTGCGA-T-TCT
1 --CGTTGCGATTCTCT
246022 CGTTGCGATT
1 CGTTGCGATT
246032 TTCATTTCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 21
0.73 0.02 0.25
Matches are distributed among these distances:
12 8 0.13
13 1 0.02
14 21 0.34
15 4 0.07
16 3 0.05
17 6 0.10
18 10 0.16
19 8 0.13
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:245975 original size:32 final size:33
Alignment explanation
Indices: 245928--246039 Score: 185
Period size: 32 Copynumber: 3.5 Consensus size: 33
245918 CAAAATCGCA
245928 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
245961 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
245993 TTGCGATTGTCATCTCGCGTTGCGA-T-TCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
246024 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
246040 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
31 19 0.26
32 33 0.45
33 22 0.30
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:247991 original size:183 final size:178
Alignment explanation
Indices: 247688--248059 Score: 649
Period size: 183 Copynumber: 2.1 Consensus size: 178
247678 TAGATTGCTT
247688 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTCTTTAACACTGTGAAATAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTCTTTAACACTGTGAAATAGTATTT
247753 GTCTTTTTTGTCTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTAT
66 GTCTTTTTTGTCTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTAT
247818 TCTTTAACACTGTGAA-AATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TC-TTAACACTGTGAATAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
247866 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTG---TCTTTAACACTGTGAAATAGTA
247930 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
63 TTTGTC-TT-TTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
247995 GTGTATTCTTAACACTGTGAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
125 GTGTATTCTTAACACTGTGAATAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
248049 AGTAAATTTAT
1 AGTAAATTTAT
248060 CCATTCAAGT
Statistics
Matches: 184, Mismatches: 3, Indels: 9
0.94 0.02 0.05
Matches are distributed among these distances:
178 39 0.21
180 8 0.04
181 21 0.11
182 20 0.11
183 96 0.52
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (178 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTCTTTAACACTGTGAAATAGTATTT
GTCTTTTTTGTCTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTAT
TCTTAACACTGTGAATAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:248076 original size:92 final size:93
Alignment explanation
Indices: 247688--248057 Score: 654
Period size: 91 Copynumber: 4.1 Consensus size: 93
247678 TAGATTGCTT
*
247688 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTG---TCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
247750 TTTGTC-TT-TTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
247775 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
247838 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
247866 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
247930 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
247958 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
248021 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
248049 AGTAAATTT
1 AGTAAATTT
248058 ATCCATTCAA
Statistics
Matches: 274, Mismatches: 1, Indels: 12
0.95 0.00 0.04
Matches are distributed among these distances:
87 39 0.14
88 8 0.03
89 3 0.01
90 28 0.10
91 120 0.44
92 76 0.28
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:248160 original size:19 final size:18
Alignment explanation
Indices: 248101--248228 Score: 110
Period size: 19 Copynumber: 7.3 Consensus size: 18
248091 TAGTTTACTT
*
248101 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC--AAAA
*
248121 TCGCAACGCGAAACCAAA
1 TCGCAACGCGAAACAAAA
*
248139 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
248158 TCGCAA--CG--ACAGAA
1 TCGCAACGCGAAACAAAA
248172 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
*
248191 TCGCAA--CG--ACAAGA
1 TCGCAACGCGAAACAAAA
248205 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
248224 TCGCA
1 TCGCA
248229 TTGCGATTTC
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 18 0.20
19 28 0.32
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:248179 original size:33 final size:32
Alignment explanation
Indices: 248135--248228 Score: 152
Period size: 33 Copynumber: 2.9 Consensus size: 32
248125 AACGCGAAAC
**
248135 CAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAATCGCAACGCGAAACCAAAATCGCAACGA
248167 CAGAATCGCAACGCGAAACCAAAATCGCAACGA
1 CA-AATCGCAACGCGAAACCAAAATCGCAACGA
248200 CAAGATCGCAACGCGAAACCAAAATCGCA
1 CAA-ATCGCAACGCGAAACCAAAATCGCA
248229 TTGCGATTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 3 0.05
33 55 0.95
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.07
Consensus pattern (32 bp):
CAAATCGCAACGCGAAACCAAAATCGCAACGA
Found at i:248250 original size:18 final size:18
Alignment explanation
Indices: 248224--248337 Score: 95
Period size: 18 Copynumber: 6.8 Consensus size: 18
248214 GAAACCAAAA
*
248224 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
248242 TCGCGTTGCGA--T--TT
1 TCGCGTTGCGATTTCATT
248256 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
* *
248273 TCGCATTGCGA-TTC-TG
1 TCGCGTTGCGATTTCATT
248289 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
**
248306 TCGCGTTGCGATTTGGTT
1 TCGCGTTGCGATTTCATT
248324 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
248338 TAAGTTTCGT
Statistics
Matches: 77, Mismatches: 7, Indels: 24
0.71 0.06 0.22
Matches are distributed among these distances:
12 8 0.10
14 10 0.13
15 1 0.01
16 6 0.08
17 8 0.10
18 29 0.38
19 15 0.19
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.46
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:248262 original size:12 final size:12
Alignment explanation
Indices: 248245--248269 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
248235 TTTCATTTCG
248245 CGTTGCGATTTT
1 CGTTGCGATTTT
248257 CGTTGCGATTTT
1 CGTTGCGATTTT
248269 C
1 C
248270 ATTTCGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.48
Consensus pattern (12 bp):
CGTTGCGATTTT
Found at i:248298 original size:33 final size:31
Alignment explanation
Indices: 248229--248319 Score: 148
Period size: 33 Copynumber: 2.9 Consensus size: 31
248219 CAAAATCGCA
248229 TTGCGA-TTTCATTTCGCGTTGCGATTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCG
*
248259 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-T-TCG
248292 TTGCGATTTTCATTTCGCGTTGCGATTT
1 TTGCGATTTTCATTTCGCGTTGCGATTT
248320 GGTTTCGCGT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
30 6 0.11
31 19 0.34
32 2 0.04
33 29 0.52
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (31 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCG
Found at i:250231 original size:13 final size:14
Alignment explanation
Indices: 250215--250249 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
250205 ATTGTTTAAT
250215 TGATTTGT-AAAGA
1 TGATTTGTAAAAGA
*
250228 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
250242 TGATTTGT
1 TGATTTGT
250250 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:250422 original size:20 final size:19
Alignment explanation
Indices: 250355--250436 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
250345 AAAAATGACT
250355 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
250374 ATCGCAA--CG-AA-G--A
1 ATCGCAATGCGAAATGAAA
250387 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
250406 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
250426 ATCGCAATGCG
1 ATCGCAATGCG
250437 TTTATAATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
13 8 0.14
15 3 0.05
16 4 0.07
17 3 0.05
19 19 0.34
20 19 0.34
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:250483 original size:52 final size:52
Alignment explanation
Indices: 250443--250708 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
250433 TGCGTTTATA
*
250443 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
250494 ATTTCGCATTGCG-TTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
250545 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
250602 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
250654 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
250707 AT
1 AT
250709 GTTGGGATTT
Statistics
Matches: 204, Mismatches: 3, Indels: 14
0.92 0.01 0.06
Matches are distributed among these distances:
50 31 0.15
51 30 0.15
52 67 0.33
53 19 0.09
54 5 0.02
55 6 0.03
56 2 0.01
57 44 0.22
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:250489 original size:19 final size:19
Alignment explanation
Indices: 250465--250736 Score: 336
Period size: 19 Copynumber: 15.4 Consensus size: 19
250455 GATTATCTCG
250465 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
250484 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
250502 TTGCG---TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
250515 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
250534 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
250553 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
250572 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
250591 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
250610 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
250624 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
250643 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
250662 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
250676 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
250696 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
250710 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
250729 TTGCGATT
1 TTGCGATT
250737 GTATTTTCCG
Statistics
Matches: 223, Mismatches: 8, Indels: 44
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.02
14 23 0.10
15 5 0.02
16 22 0.10
17 18 0.08
18 20 0.09
19 118 0.53
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:250557 original size:38 final size:38
Alignment explanation
Indices: 250443--250736 Score: 336
Period size: 33 Copynumber: 8.4 Consensus size: 38
250433 TGCGTTTATA
*
250443 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
250476 ATTTCGCATTGCGA-TTTCATTTCGCATTGCG---TTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
250510 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
*
250545 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
250583 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
*
250619 -TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
*
250654 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
*
250687 ATTTCCGCATTGCGATTTTCA--T-G--TTGGGATTTTC
1 ATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTC
*
250721 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
250737 GTATTTTCCG
Statistics
Matches: 233, Mismatches: 8, Indels: 40
0.83 0.03 0.14
Matches are distributed among these distances:
31 6 0.03
32 17 0.07
33 70 0.30
34 30 0.13
35 20 0.09
36 18 0.08
37 5 0.02
38 67 0.29
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (38 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:253028 original size:12 final size:12
Alignment explanation
Indices: 253011--253035 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
253001 TCTTCGGGGA
253011 CTTTTTCTTCTT
1 CTTTTTCTTCTT
253023 CTTTTTCTTCTT
1 CTTTTTCTTCTT
253035 C
1 C
253036 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:253960 original size:20 final size:20
Alignment explanation
Indices: 253932--254321 Score: 450
Period size: 20 Copynumber: 19.4 Consensus size: 20
253922 AAATTTCAGT
* * * *
253932 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
253952 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* *
253972 GTTGCGATTTACAGATTA-TC
1 GTTGCGATTTACGGA-TACGC
*
253992 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
254012 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
254032 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
254052 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
254072 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
254092 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
254112 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
254132 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
254152 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
254173 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
254193 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
254213 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
254233 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
254253 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
254273 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
254293 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
254313 GTTGCGATT
1 GTTGCGATT
254322 ATTGAAAATC
Statistics
Matches: 327, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.02
20 301 0.92
21 18 0.06
22 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:257095 original size:3 final size:3
Alignment explanation
Indices: 257087--257158 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
257077 TTTTTATTTG
257087 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
257135 TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
257159 CAAATATTCG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:263108 original size:21 final size:21
Alignment explanation
Indices: 263082--263134 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
263072 GTTTCCATAT
*
263082 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCAACTA
*
263103 TCGCAACGCGAACTTCAACTA
1 TCGCAACGCGAACATCAACTA
*
263124 TCGCAATGCGA
1 TCGCAACGCGA
263135 TTTTCCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCAACTA
Found at i:263201 original size:44 final size:40
Alignment explanation
Indices: 263130--263210 Score: 126
Period size: 44 Copynumber: 1.9 Consensus size: 40
263120 ACTATCGCAA
263130 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
263170 TGCGATTTATTCCAAATTCGAGTTGCGATAGTCCAAGTTCG
1 TGCGA-TT-TTCCAAATTC--GTTGCGATAGTCCAAGTTCG
263211 TTGAGATAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
40 5 0.14
41 2 0.05
42 10 0.27
44 20 0.54
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (40 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:263229 original size:63 final size:62
Alignment explanation
Indices: 263138--263392 Score: 245
Period size: 63 Copynumber: 4.1 Consensus size: 62
263128 AATGCGATTT
*
263138 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGAGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC-AGTTGCGATAG
* * * *
263201 TCCAAGTTCGTTGAGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAGTTCA-TTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCAGTTGCGATAG
** * * *
263262 TAGAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGT-CAAAGTTCGCGTTGCGA
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAA-TTC-AGTTGCGA
*
263322 TTTAT
60 --TAG
* * * *
263327 TCCAAGTTCATTGCGATAATCGAAGTTCGCGTTGCGATTTATTCCAAGTTC-GTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCAGTTGCGATAG
263388 TCCAA
1 TCCAA
263393 AATCGCAACG
Statistics
Matches: 155, Mismatches: 23, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
60 3 0.02
61 37 0.24
62 1 0.01
63 88 0.57
65 23 0.15
66 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (62 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCAGTTGCGATAG
Found at i:263248 original size:42 final size:42
Alignment explanation
Indices: 263201--263389 Score: 315
Period size: 42 Copynumber: 4.5 Consensus size: 42
263191 GTTGCGATAG
* *
263201 TCCAAGTTCGTTGAGATAGTCGAAGTTCGCGTTGTGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
263243 TCCAAGTTCATTGCGATAGTAGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
263285 TCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
263327 TCCAAGTTCATTGCGATAATCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
263369 TCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
263390 CAAAATCGCA
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 135 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:264297 original size:21 final size:21
Alignment explanation
Indices: 264272--264343 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
264262 ATTTTGGACT
264272 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
264293 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
264314 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
264335 ATCGCAACG
1 ATCGCAACG
264344 CGAACTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 9 0.21
21 23 0.55
23 10 0.24
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:264330 original size:42 final size:42
Alignment explanation
Indices: 264268--264362 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
264258 TGCAATTTTG
264268 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
264310 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
264352 GACTATCGCAA
1 GACTATCGCAA
264363 ATCAGTTTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:264359 original size:21 final size:19
Alignment explanation
Indices: 264268--264362 Score: 66
Period size: 21 Copynumber: 4.6 Consensus size: 19
264258 TGCAATTTTG
*
264268 GACTATCGCAACGAACTTG
1 GACTATCGCAACGAACTTT
* *
264287 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAA--CGAACTTT
264310 GACTATCGCAACGAA-TTT
1 GACTATCGCAACGAACTTT
*
264328 GGAATAAATCGCAACGCGAACTTT
1 -GACT--ATCGCAA--CGAACTTT
264352 GACTATCGCAA
1 GACTATCGCAA
264363 ATCAGTTTCC
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
18 2 0.03
19 10 0.17
21 28 0.47
23 17 0.28
24 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (19 bp):
GACTATCGCAACGAACTTT
Found at i:266498 original size:35 final size:35
Alignment explanation
Indices: 266445--266515 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
266435 CCCAATTAAA
* * *
266445 ACATGAAAAGAATAGAAATTTAATTGAAGTTTATT
1 ACATGAAAAGAATAGAAATGTAATTAAAGTTAATT
* * *
266480 ACATGAAAATACTGGAAATGTAATTAAAGTTAATT
1 ACATGAAAAGAATAGAAATGTAATTAAAGTTAATT
266515 A
1 A
266516 AATTAAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.32
Consensus pattern (35 bp):
ACATGAAAAGAATAGAAATGTAATTAAAGTTAATT
Found at i:270555 original size:2 final size:2
Alignment explanation
Indices: 270550--270597 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
270540 ATTTCAATTC
270550 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
270592 CT CT CT
1 CT CT CT
270598 TTGTTCTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:272460 original size:77 final size:77
Alignment explanation
Indices: 272374--272528 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
272364 CGATAACGTA
*
272374 ACGGATCAATCATGTTAGTTTTTAAATCGTTGTCGTAATCGGTTTTCGTCCGGGCATGAATTTTT
1 ACGGATCAATCATGTTAGTTTTTAAATCGCTGTCGTAATCGGTTTTCGTCCGGGCATGAATTTTT
272439 TTACTTAACGGG
66 TTACTTAACGGG
272451 ACGGATCAATCATGTTAGTTTTTAAATCGCTGTCGTAATCGGTTTTCGTCCGGGCATGAATTTTT
1 ACGGATCAATCATGTTAGTTTTTAAATCGCTGTCGTAATCGGTTTTCGTCCGGGCATGAATTTTT
272516 TTACTTAACGGG
66 TTACTTAACGGG
272528 A
1 A
272529 AAATTGATGT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (77 bp):
ACGGATCAATCATGTTAGTTTTTAAATCGCTGTCGTAATCGGTTTTCGTCCGGGCATGAATTTTT
TTACTTAACGGG
Found at i:272883 original size:26 final size:27
Alignment explanation
Indices: 272849--272902 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
272839 ATTTCGAAAT
272849 TATAATTATAAA-AAAATATTAATTTA
1 TATAATTATAAATAAAATATTAATTTA
* *
272875 TATATTTATAAATAAAATATTTATTTA
1 TATAATTATAAATAAAATATTAATTTA
272902 T
1 T
272903 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TATAATTATAAATAAAATATTAATTTA
Found at i:273090 original size:2 final size:2
Alignment explanation
Indices: 273083--273146 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
273073 ATTATTTAAA
* *
273083 AT AT AT AT AT AT AT AT AT AT AT AA AT AA AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
273125 AT AT AT AT AT TT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
273147 TTATTTATGT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273147 original size:12 final size:12
Alignment explanation
Indices: 273116--273154 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
273106 AATAAATATA
* *
273116 TATATATATATA
1 TATATATTTATT
273128 TATATATTTATT
1 TATATATTTATT
273140 TATATATTTATT
1 TATATATTTATT
273152 TAT
1 TAT
273155 GTGATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATATTTATT
Found at i:273151 original size:16 final size:16
Alignment explanation
Indices: 273092--273154 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
273082 AATATATATA
* **
273092 TATATATATATATAAA
1 TATATATATATTTATT
* * *
273108 TAAATATATATATATA
1 TATATATATATTTATT
273124 TATATATATATTTATT
1 TATATATATATTTATT
*
273140 TATATATTTATTTAT
1 TATATATATATTTAT
273155 GTGATTAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATATATATTTATT
Found at i:273182 original size:17 final size:17
Alignment explanation
Indices: 273160--273193 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
273150 TTTATGTGAT
273160 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
273177 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
273194 CAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:273218 original size:16 final size:16
Alignment explanation
Indices: 273199--273231 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
273189 AATAACAAAT
273199 TAATA-TTATAAATAAA
1 TAATATTTA-AAATAAA
273215 TAATATTTAAAATAAA
1 TAATATTTAAAATAAA
273231 T
1 T
273232 TTAAAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATTTAAAATAAA
Found at i:274889 original size:113 final size:113
Alignment explanation
Indices: 274664--275639 Score: 1575
Period size: 113 Copynumber: 8.7 Consensus size: 113
274654 ATAGAGTCAT
* *
274664 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * **
274728 ATTATGAA--ATCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
* * * *
274774 GCAAAAGGTTAAACAAATTCTTCTCATTCTGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
274839 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTTAA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
* * * * *
274887 GCAAAAAGTTGAACAAGTTCTTCTCATTCTGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
274952 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
*
275000 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTTTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
275065 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
*
275113 GCAAAAGGTTGAAAAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
275178 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGAT-AGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGA-ATTTGA
275226 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
275291 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
275339 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
275404 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
275452 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * **
275517 ATTATGAACTTTCTCTGGCAAAGCTGATCCATCGAA-TGATGAATTCAA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATC-AAGTGATGAATTTGA
* * * * * *
275565 GTAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
275630 ATTATGAACT
66 ATTATGAACT
275640 CTAACTGACA
Statistics
Matches: 822, Mismatches: 38, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
110 40 0.05
111 28 0.03
113 752 0.91
114 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
Found at i:276096 original size:22 final size:22
Alignment explanation
Indices: 276070--276124 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
276060 GATAAAACTT
*
276070 TCATCTTTGAAAAGAGAATATG
1 TCATCTTTGAAAAGAGAATATA
* * * *
276092 TCATCTTTAAAAAGGGATTCTA
1 TCATCTTTGAAAAGAGAATATA
276114 TCATCTTTGAA
1 TCATCTTTGAA
276125 GAGTGTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:276566 original size:54 final size:54
Alignment explanation
Indices: 276484--276649 Score: 278
Period size: 54 Copynumber: 3.1 Consensus size: 54
276474 AGAATAGCAG
** * *
276484 GTTCGTAAAACATTTGACGGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
*
276538 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTAGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
*
276592 GTTCGTAAAACATTTGACAACACATTCATTCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
276646 GTTC
1 GTTC
276650 TCAATCATTG
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 105 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
Found at i:278914 original size:114 final size:115
Alignment explanation
Indices: 278714--278938 Score: 362
Period size: 114 Copynumber: 2.0 Consensus size: 115
278704 GATCATGCAG
* * * *
278714 TTCATCTTTCAATTCCAATGATTGGTTCTGGGACTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGACTCATACCAAACCAAATCAGATAACTCAAAGA
278779 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTAC-TATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTTATGAGCAAA
* * * **
278828 TTCATCTTTTAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGACTCATACCAAACCAAATCAGATAACTCAAAGA
278893 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTTATGAG
278939 AACGTGGCAC
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
114 95 0.94
115 6 0.06
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGACTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTTATGAGCAAA
Found at i:282625 original size:30 final size:30
Alignment explanation
Indices: 282359--282608 Score: 482
Period size: 30 Copynumber: 8.3 Consensus size: 30
282349 GAAGGACCTA
282359 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
282389 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
282419 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
282449 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
282479 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
282509 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
282539 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
282569 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
282599 TCCATAGGTC
1 TCCAGAGGTC
282609 CCGAAGAACC
Statistics
Matches: 217, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 217 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Done.