Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007987.1 Hibiscus syriacus cultivar Beakdansim tig00110432_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: 872063
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:318372 original size:47 final size:47
Alignment explanation
Indices: 318318--318437 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
318308 CCTTATGGAC
*
318318 ATTATTATATGGCACTACGGTGTAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
*
318365 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTTCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
318412 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
318438 ATATGAGCTG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
46 20 0.29
47 49 0.71
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
Found at i:318438 original size:23 final size:23
Alignment explanation
Indices: 318318--318442 Score: 124
Period size: 23 Copynumber: 5.3 Consensus size: 23
318308 CCTTATGGAC
* *
318318 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
318342 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
318365 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
318389 ATTCTACGCGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
318412 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
318435 ATTATATG
1 ATTATATG
318443 AGCTGTGGTG
Statistics
Matches: 81, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
23 60 0.74
24 21 0.26
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:323186 original size:23 final size:22
Alignment explanation
Indices: 323138--323186 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
323128 CCAGAATGTC
323138 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* * *
323159 CAGGAGGGAATCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
323182 AAGGA
1 AAGGA
323187 AAATTGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.33, C:0.29, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:324008 original size:18 final size:18
Alignment explanation
Indices: 323985--324020 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
323975 AGGAATGATA
323985 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
324003 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
324021 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:324096 original size:121 final size:121
Alignment explanation
Indices: 323882--324245 Score: 692
Period size: 121 Copynumber: 3.0 Consensus size: 121
323872 CGAGGGTCTA
323882 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
323947 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
324003 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* *
324068 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGAAAA
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
324124 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
324189 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
324245 T
1 T
324246 ATTATATGGC
Statistics
Matches: 237, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 237 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:324297 original size:47 final size:47
Alignment explanation
Indices: 324243--324362 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
324233 CCTTATGGAC
324243 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
324290 ATTATTATATGGCTCTACGGTGCAATTCTACGCGGCACTTCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
324337 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
324363 ATATGAGCTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 19 0.28
47 49 0.72
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
Found at i:324363 original size:23 final size:23
Alignment explanation
Indices: 324243--324367 Score: 124
Period size: 23 Copynumber: 5.3 Consensus size: 23
324233 CCTTATGGAC
*
324243 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
324267 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
324290 ATTATTATATGGCTCTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
324314 ATTCTACGCGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
324337 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
324360 ATTATATG
1 ATTATATG
324368 AGCTGTGGTG
Statistics
Matches: 80, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
23 60 0.75
24 20 0.25
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:326212 original size:20 final size:20
Alignment explanation
Indices: 326187--326253 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
326177 GAAATTCAGT
326187 GTTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAAAATCGC
* * *
326207 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAAAATCGC
*
326227 ATTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAAAATCGC
326247 GTTGCGA
1 GTTGCGA
326254 ATCTGGAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (20 bp):
GTTGCGATAGTCAAAATCGC
Found at i:326272 original size:40 final size:39
Alignment explanation
Indices: 326166--326275 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 39
326156 ACTAAAATCT
* *
326166 GTTGCGAATTTGAAATTCAGTGTTGCGATAGTCAAAATCGC
1 GTTGCGAATTAGAAATTGA-T-TTGCGATAGTCAAAATCGC
* * *
326207 GTTGCGATTTACATATTCGCA-TTGCGATAGTCAAAATCGC
1 GTTGCGAATTAGAAATT-G-ATTTGCGATAGTCAAAATCGC
*
326247 GTTGCGAATCTGGAAATTGATTTGCGATA
1 GTTGCGAAT-TAGAAATTGATTTGCGATA
326276 CTGGAGATCG
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
39 1 0.02
40 36 0.64
41 18 0.32
43 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (39 bp):
GTTGCGAATTAGAAATTGATTTGCGATAGTCAAAATCGC
Found at i:327348 original size:83 final size:83
Alignment explanation
Indices: 327227--327384 Score: 253
Period size: 83 Copynumber: 1.9 Consensus size: 83
327217 GTCTTGGCCA
* * * *
327227 TTCTTATCTAGATTAAATTTCTCGAAACTCCTTTTATCACCAGTAGTCTATAGCGAATAGCCTCC
1 TTCTTAGCTAGATTAAATTTCTCGAAACTCCTTGTATCACCAGTAGTATATAGCAAATAGCCTCC
327292 TTACAAATGTTTTGGTTG
66 TTACAAATGTTTTGGTTG
* * *
327310 TTCTTAGCTAGCTTATATTTCTCGAAACTCCTTGTATCACCAGTAGTATATAGCAAATGGCCTCC
1 TTCTTAGCTAGATTAAATTTCTCGAAACTCCTTGTATCACCAGTAGTATATAGCAAATAGCCTCC
327375 TTACAAATGT
66 TTACAAATGT
327385 CTTGAAAATT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (83 bp):
TTCTTAGCTAGATTAAATTTCTCGAAACTCCTTGTATCACCAGTAGTATATAGCAAATAGCCTCC
TTACAAATGTTTTGGTTG
Found at i:327412 original size:83 final size:83
Alignment explanation
Indices: 327243--327450 Score: 245
Period size: 83 Copynumber: 2.5 Consensus size: 83
327233 TCTAGATTAA
* * * * **
327243 ATTTCTCGAAACTCCTTTTATCACCAGTAGTCTATAGCGAATAGCCTCCTTACAAATGTTTTGGT
1 ATTTCTCGAAACTCCTTGTATCACCAGTAGTATATAGCAAATAGCCTCCTTACAAATGTCTTGAA
** * *
327308 TGTTCTTAGCTAGCTTAT
66 AATTATTAGCCAGCTTAT
*
327326 ATTTCTCGAAACTCCTTGTATCACCAGTAGTATATAGCAAATGGCCTCCTTACAAATGTCTTGAA
1 ATTTCTCGAAACTCCTTGTATCACCAGTAGTATATAGCAAATAGCCTCCTTACAAATGTCTTGAA
* ** *
327391 AATTATTTGCCATTTTGT
66 AATTATTAGCCAGCTTAT
* * * *
327409 ATTTCTCAAAATTCTTTGTATCAGCAGTAGTATATAGCAAAT
1 ATTTCTCGAAACTCCTTGTATCACCAGTAGTATATAGCAAAT
327451 TTGTTTGTTC
Statistics
Matches: 106, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
83 106 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (83 bp):
ATTTCTCGAAACTCCTTGTATCACCAGTAGTATATAGCAAATAGCCTCCTTACAAATGTCTTGAA
AATTATTAGCCAGCTTAT
Found at i:328333 original size:184 final size:184
Alignment explanation
Indices: 328025--328421 Score: 624
Period size: 184 Copynumber: 2.2 Consensus size: 184
328015 TTTTTTAATT
* * * *
328025 TATATAA-AAATTAAATGTTTTTAAATTTAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTAAATTTAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
328089 TATAAAATAAAAATTTCAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAATTTCAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
*
328154 AGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGAGG-TGAGCCCATATGTTA
131 AGATCTTAAATTATTAATTGAGTTTTAAATAGTTTG-GGCTGAGCCCATATGTTA
*
328208 TATATAATATATTTAATATTTTTTAA-TTAAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTAAATTTAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* * *
328272 TTATAAAATAAAAATTTTATAT-AAATTTTTAAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 TTATAAAATAAAAATTTCAGATAAAATTTTT-AATTAATTAATATTGATTTAAGTTTAAAAGTTA
*
328336 TTAGATCTTAAATTGTTAATTGAGTTTTAAATAGTTTGGGCTGAGCCCATATGTTA
129 TTAGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTGAGCCCATATGTTA
* *
328392 TATATAATATATTTAA-AATTTAAAATTTAA
1 TATATAATATATTTAATATTTTTAAATTTAA
328422 TTTCGATTAA
Statistics
Matches: 196, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
183 31 0.16
184 165 0.84
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTAAATTTAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTCAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
AGATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTGAGCCCATATGTTA
Found at i:332710 original size:21 final size:21
Alignment explanation
Indices: 332681--332722 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
332671 GGAATTATTA
*
332681 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
332702 TAATTTTTTATAATAAATAAT
1 TAATATTTTAAAATAAATAAT
332723 ATTAATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:332779 original size:25 final size:25
Alignment explanation
Indices: 332730--332788 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
332720 AATATTAATT
* *
332730 ATTATATTAAATAAATATCATAAAATA
1 ATTAT-TTAAATAAAAATCA-AAAAAA
*
332757 ATT-TTTAAATAAAAATTAAAAAAA
1 ATTATTTAAATAAAAATCAAAAAAA
332781 ATTATTTA
1 ATTATTTA
332789 GGATAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 8 0.29
25 16 0.57
26 1 0.04
27 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
ATTATTTAAATAAAAATCAAAAAAA
Found at i:334906 original size:21 final size:21
Alignment explanation
Indices: 334789--334923 Score: 71
Period size: 21 Copynumber: 6.6 Consensus size: 21
334779 ACGCGAAATA
**
334789 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
334809 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
334829 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
334850 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
334871 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
334892 AGAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
334912 AAAATCGCAACG
1 AAAATCGCAACG
334924 TGAACACATA
Statistics
Matches: 84, Mismatches: 27, Indels: 8
0.71 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 35 0.42
21 46 0.55
22 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:334919 original size:20 final size:21
Alignment explanation
Indices: 334894--334985 Score: 120
Period size: 20 Copynumber: 4.6 Consensus size: 21
334884 GATTTTCCAG
*
334894 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACATGATA
* *
334914 AATCGCAACGTGAACA-CATA
1 AATCGCAACGCGAACATGATA
*
334934 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACATGATA
334954 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAACATGATA
334974 AATCGCAACGCG
1 AATCGCAACGCG
334986 TATCCGTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 2 0.03
20 59 0.95
21 1 0.02
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.14
Consensus pattern (21 bp):
AATCGCAACGCGAACATGATA
Found at i:334995 original size:20 final size:20
Alignment explanation
Indices: 334932--335162 Score: 216
Period size: 20 Copynumber: 11.6 Consensus size: 20
334922 CGTGAACACA
* **
334932 TAAATCGCAACGCGAATATG
1 TAAATCGCAACGCGTATCCG
* * **
334952 AAAATCGCAACGCG-AACATA
1 TAAATCGCAACGCGTATC-CG
334972 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
334992 TAAACCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
335012 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
335032 TAAACCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
335052 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
335072 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
335092 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
335112 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
335132 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
335152 TAAATCACAAC
1 TAAATCGCAAC
335163 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 31, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:335124 original size:40 final size:39
Alignment explanation
Indices: 334894--335162 Score: 231
Period size: 40 Copynumber: 6.7 Consensus size: 39
334884 GATTTTCCAG
* * *
334894 AATCGCAACGCGAATATGAAAATCGCAACGTGAA-CACATA
1 AATCGCAACGCGAATCTGTAAATCGCAACGT-AATC-CGTA
* * * **
334934 AATCGCAACGCGAATATGAAAATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATCTGTAAATCGCAACG-TAATC-CGTA
* * *
334974 AATCGCAACGCGTATCCGTAAACCGCAATGCGT-ATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAA--CGTAATCCGTA
* * * *
335014 TATCGCAACGCGTATCCGTAAACCGCAATGCGT-ATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAA--CGTAATCCGTA
* * *
335054 TATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACG-TAATCCGTA
*
335094 AATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACG-TAATCCGTA
* *
335134 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGAATCTGTAAATCGCAAC
335163 ACTGAAATTT
Statistics
Matches: 206, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 1 0.00
40 200 0.97
41 1 0.00
42 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGAATCTGTAAATCGCAACGTAATCCGTA
Found at i:335891 original size:24 final size:24
Alignment explanation
Indices: 335852--335898 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
335842 AAATTTGGTC
335852 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
335876 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
335899 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:336089 original size:12 final size:12
Alignment explanation
Indices: 336072--336096 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
336062 ATATAATCCT
336072 GAAGAAGAAAAA
1 GAAGAAGAAAAA
336084 GAAGAAGAAAAA
1 GAAGAAGAAAAA
336096 G
1 G
336097 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:338301 original size:54 final size:54
Alignment explanation
Indices: 338238--338404 Score: 316
Period size: 54 Copynumber: 3.1 Consensus size: 54
338228 TATTATGTGG
*
338238 ATTTTATGTGTGAACTTTTAACATTTTCAGTTGAATTAATGACTCATGCCAACC
1 ATTTTATGTGTGAACTTTTAACATTTTCAGTTGAATTAATGACTCAGGCCAACC
338292 ATTTTATGTGTGAACTTTTAACATTTTCAGTTGAATTAATGACTCAGGCCAACC
1 ATTTTATGTGTGAACTTTTAACATTTTCAGTTGAATTAATGACTCAGGCCAACC
*
338346 ATTTTAGGTGTGAACTTTTAACATTTTCAGTTGAATTAATGACTCAGGCCAACC
1 ATTTTATGTGTGAACTTTTAACATTTTCAGTTGAATTAATGACTCAGGCCAACC
338400 ATTTT
1 ATTTT
338405 GACTTAACCA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 111 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.40
Consensus pattern (54 bp):
ATTTTATGTGTGAACTTTTAACATTTTCAGTTGAATTAATGACTCAGGCCAACC
Found at i:338532 original size:33 final size:33
Alignment explanation
Indices: 338480--338690 Score: 206
Period size: 33 Copynumber: 6.2 Consensus size: 33
338470 CGGAAATTAC
338480 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGA-AATCGCAATGCGAAATGAA
* *
338513 AATCCCAAC-ATGAACATCGCAATGCGGAATGAA
1 AATCGCAACGATGAA-ATCGCAATGCGAAATGAA
*
338546 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--ATG-AAATCGCAATGCGAAATGAA
338579 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGC-A-ACG--ATG-AAATCGCAATGCGAAATGAA
338617 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGA-AATCGCAATGCGAAATGAA
338650 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGA-AATCGCAATGCGAAATGAA
338683 AATCGCAA
1 AATCGCAA
338691 TGCGAAATTA
Statistics
Matches: 157, Mismatches: 5, Indels: 32
0.81 0.03 0.16
Matches are distributed among these distances:
32 3 0.02
33 120 0.76
34 3 0.02
35 4 0.03
36 5 0.03
37 2 0.01
38 18 0.11
39 2 0.01
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGATGAAATCGCAATGCGAAATGAA
Found at i:338635 original size:85 final size:89
Alignment explanation
Indices: 338480--338708 Score: 341
Period size: 85 Copynumber: 2.7 Consensus size: 89
338470 CGGAAATTAC
* *
338480 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAACATCGCAATGCGG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGG
338540 AATGAAAATCGCAATGCGAAATGAA
65 AATGAAAATCGCAATGCGAAATGAA
*
338565 AATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G-
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGGA
*
338627 A-GAGAATCGCAATGCGAAATGAA
66 ATGAAAATCGCAATGCGAAATGAA
*
338650 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
338709 TTGCGATTCT
Statistics
Matches: 133, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
85 117 0.88
86 1 0.01
87 2 0.02
88 1 0.01
90 12 0.09
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (89 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGGA
ATGAAAATCGCAATGCGAAATGAA
Found at i:338636 original size:14 final size:14
Alignment explanation
Indices: 338617--338671 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
338607 GCGAAATGAA
338617 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
338631 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
338650 AATCGCAACGAGAG
1 AATCGCAACGAGAG
338664 AATCGCAA
1 AATCGCAA
338672 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:338687 original size:52 final size:52
Alignment explanation
Indices: 338494--338714 Score: 272
Period size: 52 Copynumber: 4.2 Consensus size: 52
338484 GCAACGAGAG
* *
338494 AATCGCAATGCGAAATGAAAATCCCAAC-ATGA-ACATCGCAATGCGGAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGA-ATCGCAATGCGAAATGAA
*
338546 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
338598 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* * * * * *
338650 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATTAA
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
*
338702 AATCGCATTGCGA
1 AATCGCAATGCGA
338715 TTCTCTCGTT
Statistics
Matches: 151, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
52 135 0.89
53 9 0.06
54 7 0.05
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:338714 original size:19 final size:19
Alignment explanation
Indices: 338494--338714 Score: 221
Period size: 19 Copynumber: 12.7 Consensus size: 19
338484 GCAACGAGAG
338494 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
338513 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
* *
338527 CATCGCAATGCGGAATGAA
1 AATCGCAATGCGAAATGAA
338546 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
338565 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
338579 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
338598 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
338617 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
338631 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
338650 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
338664 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
338683 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
338702 AATCGCATTGCGA
1 AATCGCAATGCGA
338715 TTCTCTCGTT
Statistics
Matches: 168, Mismatches: 14, Indels: 40
0.76 0.06 0.18
Matches are distributed among these distances:
14 41 0.24
15 3 0.02
16 7 0.04
17 7 0.04
18 3 0.02
19 107 0.64
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:338741 original size:52 final size:52
Alignment explanation
Indices: 338685--338799 Score: 176
Period size: 52 Copynumber: 2.2 Consensus size: 52
338675 GAAATGAAAA
*
338685 TCGCAATGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** * **
338737 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
338789 TCGCATTGCGA
1 TCGCATTGCGA
338800 TAGTCATTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:338807 original size:52 final size:52
Alignment explanation
Indices: 338704--338808 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
338694 GAAATTAAAA
**
338704 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATT
338756 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATT
338808 T
1 T
338809 TTGCCTTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTCATT
Found at i:338808 original size:19 final size:19
Alignment explanation
Indices: 338723--338800 Score: 112
Period size: 19 Copynumber: 4.4 Consensus size: 19
338713 GATTCTCTCG
338723 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
338742 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
338761 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
338775 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
338794 TTGCGAT
1 TTGCGAT
338801 AGTCATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 32 0.62
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:338926 original size:14 final size:14
Alignment explanation
Indices: 338907--338943 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
338897 CATCAATTAC
338907 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
338921 ACAAATCATCTTTT
1 ACAAATCAACTTTT
338935 ACAAATCAA
1 ACAAATCAA
338944 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:340907 original size:19 final size:19
Alignment explanation
Indices: 340881--341037 Score: 154
Period size: 19 Copynumber: 8.8 Consensus size: 19
340871 CATGAAACTT
340881 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
* * **
340900 ATAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATG
* **
340919 AAAATCGCAATGCGAAACC
1 AAAATCGCAACGCGAAATG
340938 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
340957 AAAATCGCAA--CGACA-G
1 AAAATCGCAACGCGAAATG
*
340973 --AATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
340990 AAAATCGCAA--CGAAA-G
1 AAAATCGCAACGCGAAATG
341006 --AATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
341023 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
341038 TTTTGGTTTC
Statistics
Matches: 115, Mismatches: 13, Indels: 20
0.78 0.09 0.14
Matches are distributed among these distances:
14 16 0.14
16 11 0.10
17 11 0.10
19 77 0.67
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:340978 original size:14 final size:14
Alignment explanation
Indices: 340959--341015 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
340949 GCGAAATGAA
*
340959 AATCGCAACGACAG
1 AATCGCAACGAAAG
340973 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
340990 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
341006 AATCGCAACG
1 AATCGCAACG
341016 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:340986 original size:33 final size:33
Alignment explanation
Indices: 340940--341032 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
340930 GCGAAACCAA
*
340940 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
340973 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
341006 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
341033 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:341029 original size:52 final size:54
Alignment explanation
Indices: 340881--341037 Score: 166
Period size: 52 Copynumber: 2.9 Consensus size: 54
340871 CATGAAACTT
* *
340881 AAAATCGCAACGCGAAATGATAATCGCAACGAGAAACCAAAATCGCAATGCGAAACC
1 AAAATCGCAAC-CGAAATGA-AATCGCAACGCGAAA-GAAAATCGCAATGCGAAACC
* **
340938 AAAATCGCAACGCGAAATGAAAATCGCAA--CGACAG--AATCGCAATGCGAAATG
1 AAAATCGCAAC-CGAAATG-AAATCGCAACGCGAAAGAAAATCGCAATGCGAAACC
340990 AAAATCGCAA-CGAAA-G-AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AAAATCGCAACCGAAATGAAATCGCAACGCGAAA-GAAAATCGCAATGCGA
341038 TTTTGGTTTC
Statistics
Matches: 88, Mismatches: 6, Indels: 17
0.79 0.05 0.15
Matches are distributed among these distances:
47 8 0.09
49 5 0.06
50 6 0.07
52 38 0.43
55 3 0.03
57 27 0.31
58 1 0.01
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (54 bp):
AAAATCGCAACCGAAATGAAATCGCAACGCGAAAGAAAATCGCAATGCGAAACC
Found at i:341049 original size:19 final size:19
Alignment explanation
Indices: 341033--341147 Score: 141
Period size: 19 Copynumber: 6.3 Consensus size: 19
341023 AAAATCGCAA
341033 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
341052 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
341071 TGCGATTCT--TTT---GT
1 TGCGATTTTGGTTTCGCGT
**
341085 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
341104 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
341123 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
341143 TGCGA
1 TGCGA
341148 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 55 0.65
20 13 0.15
ACGTcount: A:0.09, C:0.15, G:0.28, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:341380 original size:93 final size:93
Alignment explanation
Indices: 341192--341473 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
341182 ATGGATTGCA
341192 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-AAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
341255 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
341283 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
341348 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
341376 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
341441 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
341469 TTACT
1 TTACT
341474 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
91 4 0.02
92 45 0.24
93 139 0.74
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:343204 original size:20 final size:20
Alignment explanation
Indices: 343173--343269 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
343163 TTTTGGTTGA
343173 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
343193 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
343213 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
343232 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
343247 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
343267 AAT
1 AAT
343270 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:343225 original size:21 final size:21
Alignment explanation
Indices: 343171--343235 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
343161 TCTTTTGGTT
343171 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
343192 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
343212 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
343233 GAA
1 GAA
343236 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:343239 original size:14 final size:14
Alignment explanation
Indices: 343220--343276 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
343210 GAGAAATGAA
343220 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
343234 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
343253 AATCGCAACGAGAG
1 AATCGCAACGAGAG
343267 AATCGCAACG
1 AATCGCAACG
343277 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:343252 original size:33 final size:33
Alignment explanation
Indices: 343171--343293 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
343161 TCTTTTGGTT
*
343171 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
343212 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
343245 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
343278 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
343294 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:343327 original size:19 final size:19
Alignment explanation
Indices: 343294--343412 Score: 95
Period size: 21 Copynumber: 6.3 Consensus size: 19
343284 AAAATCGCAA
** *
343294 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCTCGT
*
343313 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCTCGT
343332 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCTCGT
343346 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCTCGT
***
343367 TGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATT-TCTCGT
343387 TGCGATTTTCATTTATCTCGT
1 TGCGATTTTCA-TT-TCTCGT
343408 TGCGA
1 TGCGA
343413 CTCTTCTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 22 0.27
20 17 0.21
21 27 0.33
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCTCGT
Found at i:343393 original size:41 final size:41
Alignment explanation
Indices: 343336--343413 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
343326 TCGCGTTGCG
*
343336 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
343377 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
343414 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:343398 original size:20 final size:21
Alignment explanation
Indices: 343337--343412 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
343327 CGCGTTGCGA
343337 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
343358 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
343378 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
343399 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
343413 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:343534 original size:33 final size:33
Alignment explanation
Indices: 343492--343562 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
343482 AATACTAACT
343492 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
343525 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
343558 TGAAA
1 TGAAA
343563 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:343967 original size:20 final size:20
Alignment explanation
Indices: 343942--344134 Score: 158
Period size: 20 Copynumber: 9.6 Consensus size: 20
343932 CTTTAAATAT
343942 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
343962 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
343984 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
344003 CGCATTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
344023 CGCATTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
344043 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
344063 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
* *
344083 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
344103 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
344123 CGCGTTGCGATT
1 CGCGTTGCGATT
344135 CTGGAAAATC
Statistics
Matches: 140, Mismatches: 26, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.01
20 121 0.86
21 15 0.11
22 2 0.01
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:344071 original size:40 final size:40
Alignment explanation
Indices: 343941--344134 Score: 210
Period size: 40 Copynumber: 4.8 Consensus size: 40
343931 GCTTTAAATA
*
343941 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * * *
343982 TATCGTTGCGATTTACGGATACGCATTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* * *
344022 ACGCATTGCGGTTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
344062 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
344102 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATT
344135 CTGGAAAATC
Statistics
Matches: 130, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
40 101 0.78
41 29 0.22
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:349256 original size:12 final size:11
Alignment explanation
Indices: 349239--349284 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
349229 GATAACTACG
349239 TAAATGAGTCTA
1 TAAATGAGT-TA
349251 TAAATGAGATTA
1 TAAATGAG-TTA
349263 TAAATGAGTTAA
1 TAAATGAGTT-A
*
349275 TAAACGAGTT
1 TAAATGAGTT
349285 TGTTCATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 2 0.06
12 28 0.90
13 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (11 bp):
TAAATGAGTTA
Found at i:352240 original size:123 final size:122
Alignment explanation
Indices: 352031--352298 Score: 367
Period size: 123 Copynumber: 2.2 Consensus size: 122
352021 TTTTGCGGTA
* * * * *
352031 TTTTTAAAATAAACGCAGCAATAAATCATTGCATTAGTGGCTTTTTTAAATACAAACGCCACGAA
1 TTTTT-AAACAAACGCAGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAAAGCCACAAA
* ** * *
352096 ATGGTAACATTAGCGGTGTTTTCCCAGAAACGTCGA-TATTGACTTGTCTTTTGTGGCTT
65 ATGATAACATTAGCGACGTTTTCCCAGAAAC-ACGACTATTGACTTGTCTTTTGTGGC-G
* *
352155 TTTTTAGACAAACGCTGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAAAGCCACAAAA
1 TTTTTAAACAAACGCAGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAAAGCCACAAAA
* *
352220 TGATAACATTAGCGACGTTTTCCCAGAAACACTACTATTTACTTGTCTTTTGTGGCG
66 TGATAACATTAGCGACGTTTTCCCAGAAACACGACTATTGACTTGTCTTTTGTGGCG
*
352277 TTTTTAAACAAACGCCGCAATA
1 TTTTTAAACAAACGCAGCAATA
352299 GGTTAGTGAA
Statistics
Matches: 127, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
122 22 0.17
123 100 0.79
124 5 0.04
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (122 bp):
TTTTTAAACAAACGCAGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAAAGCCACAAAA
TGATAACATTAGCGACGTTTTCCCAGAAACACGACTATTGACTTGTCTTTTGTGGCG
Found at i:353137 original size:21 final size:21
Alignment explanation
Indices: 353113--353176 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
353103 AACTTTGAAA
353113 AAATGTTTTTCAAAGTTTGGT
1 AAATGTTTTTCAAAGTTTGGT
*
353134 AAATG--TTTC----TTT-GA
1 AAATGTTTTTCAAAGTTTGGT
*
353148 AAATGGTTTTCAAAGTTTGGT
1 AAATGTTTTTCAAAGTTTGGT
353169 AAATGTTT
1 AAATGTTT
353177 CTTTGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 14
0.66 0.06 0.28
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
19 4 0.12
20 3 0.09
21 13 0.39
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.47
Consensus pattern (21 bp):
AAATGTTTTTCAAAGTTTGGT
Found at i:353151 original size:35 final size:36
Alignment explanation
Indices: 353105--353213 Score: 175
Period size: 35 Copynumber: 3.0 Consensus size: 36
353095 TGGTAACCAA
353105 CTTTGAAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
353142 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
353177 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
353214 GTTAAAAAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 34 0.51
36 5 0.07
37 28 0.42
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.46
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:353655 original size:16 final size:16
Alignment explanation
Indices: 353634--353666 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
353624 TACTATTCAT
*
353634 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
353650 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
353666 G
1 G
353667 GTCGACGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:357758 original size:35 final size:35
Alignment explanation
Indices: 357700--357792 Score: 170
Period size: 35 Copynumber: 2.7 Consensus size: 35
357690 TGAAAGTATT
*
357700 AAAATGGTTTTC-AAGTTTGGTAACCAACTTTGAA
1 AAAATGTTTTTCAAAGTTTGGTAACCAACTTTGAA
357734 AAAATGTTTTTCAAAGTTTGGTAACCAACTTTGAA
1 AAAATGTTTTTCAAAGTTTGGTAACCAACTTTGAA
357769 AAAATGTTTTTCAAAGTTTGGTAA
1 AAAATGTTTTTCAAAGTTTGGTAA
357793 ATGTTTCTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
34 11 0.19
35 46 0.81
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (35 bp):
AAAATGTTTTTCAAAGTTTGGTAACCAACTTTGAA
Found at i:357794 original size:21 final size:21
Alignment explanation
Indices: 357770--357833 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
357760 AACTTTGAAA
357770 AAATGTTTTTCAAAGTTTGGT
1 AAATGTTTTTCAAAGTTTGGT
*
357791 AAATG--TTTC----TTT-GA
1 AAATGTTTTTCAAAGTTTGGT
*
357805 AAATGGTTTTCAAAGTTTGGT
1 AAATGTTTTTCAAAGTTTGGT
357826 AAATGTTT
1 AAATGTTT
357834 CTTTGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 14
0.66 0.06 0.28
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
19 4 0.12
20 3 0.09
21 13 0.39
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.47
Consensus pattern (21 bp):
AAATGTTTTTCAAAGTTTGGT
Found at i:357844 original size:36 final size:36
Alignment explanation
Indices: 357727--357881 Score: 192
Period size: 35 Copynumber: 4.3 Consensus size: 36
357717 TGGTAACCAA
****
357727 CTTTGAAAAAATGTTTTTCAAAGTTTGGT-AA-CCAA
1 CTTTG-AAAAATGTTTTTCAAAGTTTGGTAAATGTTT
357762 CTTTGAAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
357799 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
357834 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
*
357871 -GTTGAAAAATG
1 CTTTGAAAAATG
357882 ATAATGGGAT
Statistics
Matches: 108, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
35 64 0.59
36 16 0.15
37 28 0.26
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:360118 original size:30 final size:30
Alignment explanation
Indices: 360082--360145 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
360072 AAGGAACATA
** *
360082 TGGATAGTTGTCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* *
360112 TGGATAGTTACCGGGGTTCTTTATAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
360142 TGGA
1 TGGA
360146 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:363507 original size:64 final size:65
Alignment explanation
Indices: 363422--363582 Score: 184
Period size: 65 Copynumber: 2.5 Consensus size: 65
363412 TTGTTTAAGG
* * ** * *
363422 TGCATCGATGCACATGCAGTGCATCGATGCAT-GATTTTAA-ATAGAAAACATCGAGTAGGA-TT
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAATA-AGAAAACATCGAAT-GCATTT
363484 TA
64 TA
* * * *
363486 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAATAAGGAAACATCGAATGCATTTTA
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAATAAGAAAACATCGAATGCATTTTA
*
363551 TGCATCGATGCACAAGTAGTGCATCGATGCAT
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT
363583 ACCTTCATTA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 31 0.38
65 50 0.61
66 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAATAAGAAAACATCGAATGCATTTTA
Found at i:367359 original size:43 final size:43
Alignment explanation
Indices: 367312--367402 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
367302 TTACAAATGC
*
367312 CACTAAAAACAATAGAATTAGCGGCGTTTGTGGACAAAAACGA
1 CACTAAAAACAAGAGAATTAGCGGCGTTTGTGGACAAAAACGA
* * * ** *
367355 CACTAAAGACAAGAGAATTGGTGTTGTTTGTGGACAAAAACGC
1 CACTAAAAACAAGAGAATTAGCGGCGTTTGTGGACAAAAACGA
367398 CACTA
1 CACTA
367403 TAAATCATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (43 bp):
CACTAAAAACAAGAGAATTAGCGGCGTTTGTGGACAAAAACGA
Found at i:368586 original size:2 final size:2
Alignment explanation
Indices: 368579--368634 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
368569 ATCCTCACTC
368579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
368621 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
368635 TGAAGGGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 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:372952 original size:42 final size:41
Alignment explanation
Indices: 372900--373020 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 41
372890 TGTTTGTTTA
* * * * *
372900 AAAAATGCCGCTATAGAGTAGTACTTTAGTGGCGTTTTAAGT
1 AAAAACGCCGCTA-AAACTAGTACTTTAGTGGCATTTTAAGC
* * *
372942 ACAAACGCCGCTAAAACTCGTACTTTCGTGGCATTTTAAGC
1 AAAAACGCCGCTAAAACTAGTACTTTAGTGGCATTTTAAGC
* * **
372983 AAAAAGGCCGCTAAATACTCGTACTTTAAAGGCATTTT
1 AAAAACGCCGCTAAA-ACTAGTACTTTAGTGGCATTTT
373021 TCTACAAACG
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 35 0.54
42 30 0.46
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (41 bp):
AAAAACGCCGCTAAAACTAGTACTTTAGTGGCATTTTAAGC
Found at i:372973 original size:41 final size:42
Alignment explanation
Indices: 372920--373079 Score: 140
Period size: 41 Copynumber: 4.0 Consensus size: 42
372910 CTATAGAGTA
* * *
372920 GTACTTTAGTGGCGTTTTAAGTACAAACGCCGCTAAA-ACTC
1 GTACTTTAGTGGCATTTTAAGCAAAAACGCCGCTAAATACTC
* *
372961 GTACTTTCGTGGCATTTTAAGCAAAAAGGCCGCTAAATACTC
1 GTACTTTAGTGGCATTTTAAGCAAAAACGCCGCTAAATACTC
** * *
373003 GTACTTTAAAGGCATTTT--TCTACAAACGCCGCTAAATACTC
1 GTACTTTAGTGGCATTTTAAGC-AAAAACGCCGCTAAATACTC
* *
373044 --A---T-GTGGCATTTTAAGCACAAACGCCACTAAAATACT
1 GTACTTTAGTGGCATTTTAAGCAAAAACGCCGCT-AAATACT
373080 ACTCTATTGC
Statistics
Matches: 99, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
35 8 0.08
36 12 0.12
37 8 0.08
39 1 0.01
40 1 0.01
41 50 0.51
42 19 0.19
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (42 bp):
GTACTTTAGTGGCATTTTAAGCAAAAACGCCGCTAAATACTC
Found at i:377017 original size:43 final size:43
Alignment explanation
Indices: 376938--377083 Score: 186
Period size: 43 Copynumber: 3.4 Consensus size: 43
376928 GTATTAGCGA
* * ** * *
376938 CGTTTGTATTCAAAAACGCCGCTAGATATATGACCTTTTGCGG
1 CGTTTGTGTCCAAAAACGCCGCTATTTATCTAACCTTTTGCGG
* ** *
376981 TGAGTGTGTCCAAAAACGCCGCTATTTATCTAACCTTTTGCGA
1 CGTTTGTGTCCAAAAACGCCGCTATTTATCTAACCTTTTGCGG
*
377024 CGTTTGTGTCCAAAAATGCCGCTATTTATCTAACCTTTTGCGG
1 CGTTTGTGTCCAAAAACGCCGCTATTTATCTAACCTTTTGCGG
377067 CGTTTGT-TCCAAAAACG
1 CGTTTGTGTCCAAAAACG
377084 TCGCAAAAGA
Statistics
Matches: 87, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 9 0.10
43 78 0.90
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (43 bp):
CGTTTGTGTCCAAAAACGCCGCTATTTATCTAACCTTTTGCGG
Found at i:382558 original size:9 final size:8
Alignment explanation
Indices: 382534--382608 Score: 51
Period size: 8 Copynumber: 8.9 Consensus size: 8
382524 ACTGCTACAA
382534 TTTTATTT
1 TTTTATTT
*
382542 TGTTATTT
1 TTTTATTT
*
382550 TTTTAATT
1 TTTTATTT
**
382558 TTTGGTTT
1 TTTTATTT
*
382566 TGTTATTTT
1 TTTTA-TTT
382575 TTTTACTTT
1 TTTTA-TTT
*
382584 CTTTTATTA
1 -TTTTATTT
*
382593 TTTTCTTT
1 TTTTATTT
382601 TTCTTATT
1 TT-TTATT
382609 ATGAATTATA
Statistics
Matches: 49, Mismatches: 15, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
8 28 0.57
9 16 0.33
10 5 0.10
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.77
Consensus pattern (8 bp):
TTTTATTT
Found at i:382659 original size:37 final size:36
Alignment explanation
Indices: 382536--382660 Score: 98
Period size: 37 Copynumber: 3.4 Consensus size: 36
382526 TGCTACAATT
* *
382536 TTATTTTGTTATTTTTTT-AATTTTTGGTTTTGTTA
1 TTATTTTTTTATTTTTTTAAATTTTTGGTTTTCTTA
*
382571 -T-TTTTTTTACTTTCTTTTATTATTTTCT--TTTTCTTA
1 TTATTTTTTTA-TTT-TTTTA-AATTTT-TGGTTTTCTTA
** * *
382607 TTATGAATTATATTTTTTTAAATTTTTGGTTTTTTTA
1 TTAT-TTTTTTATTTTTTTAAATTTTTGGTTTTCTTA
382644 TTATTTTTTTGATTTTT
1 TTATTTTTTT-ATTTTT
382661 GATTTTTGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
33 7 0.10
34 4 0.06
35 5 0.07
36 15 0.22
37 28 0.41
38 5 0.07
39 4 0.06
ACGTcount: A:0.16, C:0.03, G:0.06, T:0.74
Consensus pattern (36 bp):
TTATTTTTTTATTTTTTTAAATTTTTGGTTTTCTTA
Found at i:383928 original size:23 final size:23
Alignment explanation
Indices: 383902--383946 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
383892 ATAAAAAAAT
383902 TCTGTATTTATGACACATTTTTA
1 TCTGTATTTATGACACATTTTTA
* * *
383925 TCTGTCTTTGTGGCACATTTTT
1 TCTGTATTTATGACACATTTTT
383947 CGTCTTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (23 bp):
TCTGTATTTATGACACATTTTTA
Found at i:389344 original size:29 final size:28
Alignment explanation
Indices: 389288--389344 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
389278 ATCTCATATT
* **
389288 GTTGAATGATAAAACCAAATTTTCAGTG
1 GTTGAATGATAAAAACAAATCATCAGTG
*
389316 GTTGAATGATAAAAACAAATACATGAGTG
1 GTTGAATGATAAAAACAAAT-CATCAGTG
389345 ATTAAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (28 bp):
GTTGAATGATAAAAACAAATCATCAGTG
Found at i:389997 original size:46 final size:48
Alignment explanation
Indices: 389889--389998 Score: 118
Period size: 50 Copynumber: 2.3 Consensus size: 48
389879 AAGTTTAACC
* *
389889 AACCAATAAATTAATACCTAGGCCAATTGAAAAGTTTCCTTATAAAACAA
1 AACCATTAAATTAATACATAGGCCAATTGAAAAG-TT-CTTATAAAACAA
** * *
389939 AAGGATAAAATTAATACATAGGCCAATTGAAAAG-T-TTAT-AAACTA
1 AACCATTAAATTAATACATAGGCCAATTGAAAAGTTCTTATAAAACAA
389984 AACCACTTAAATTAA
1 AACCA-TTAAATTAA
389999 ATAATATTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
45 8 0.16
46 12 0.24
48 1 0.02
50 29 0.58
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (48 bp):
AACCATTAAATTAATACATAGGCCAATTGAAAAGTTCTTATAAAACAA
Found at i:396577 original size:35 final size:31
Alignment explanation
Indices: 396514--396606 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 31
396504 AATTTATATA
396514 TTATATAAAAAAATTAGTTAATTAGTTTAAG
1 TTATATAAAAAAATTAGTTAATTAGTTTAAG
*
396545 TTATATAAAAGAATAATTATTTAAATTAGTTT-A-
1 TTATAT-AAA-AA-AATTAGTT-AATTAGTTTAAG
* **
396578 TTGT-TATAAATTATTAGTTAATTAGTTTA
1 TTATATA-AAAAAATTAGTTAATTAGTTTA
396607 TTATTATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
29 9 0.18
30 6 0.12
31 8 0.16
32 6 0.12
33 5 0.10
34 8 0.16
35 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (31 bp):
TTATATAAAAAAATTAGTTAATTAGTTTAAG
Found at i:396589 original size:18 final size:18
Alignment explanation
Indices: 396566--396620 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
396556 AATAATTATT
396566 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
396584 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
396596 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
396613 TAAATTAG
1 TAAATTAG
396621 GTAAAACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:396919 original size:29 final size:29
Alignment explanation
Indices: 396882--396959 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
396872 TAGTAATAAA
396882 TTATAATTAAAAATCA-TTTATTAGTTTAA-G
1 TTAT-ATTAAAAAT-AGTTTATTAG-TTAACG
396912 TTATATTAAAAAATAGTTTATTAGTTAACG
1 TTATATT-AAAAATAGTTTATTAGTTAACG
396942 TTATATTAAAGAATAGTT
1 TTATATTAAA-AATAGTT
396960 AAAGTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (29 bp):
TTATATTAAAAATAGTTTATTAGTTAACG
Found at i:396928 original size:22 final size:22
Alignment explanation
Indices: 396903--396983 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
396893 AATCATTTAT
*
396903 TAGTTTAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAGAA
396925 TAGTTTATTAGTTAACGTTATATTAAAGAA
1 TAGTTTA--AG-T----T-ATATTAAAGAA
*
396955 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
396977 TAGTTTA
1 TAGTTTA
396984 TTAGTTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 24 0.50
23 1 0.02
24 2 0.04
25 1 0.02
27 1 0.02
28 2 0.04
29 1 0.02
30 16 0.33
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:399331 original size:25 final size:25
Alignment explanation
Indices: 399303--399351 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
399293 GTTCAAGTCG
*
399303 TAAATCATTATTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
399328 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
399352 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:399352 original size:14 final size:14
Alignment explanation
Indices: 399304--399352 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
399294 TTCAAGTCGT
*
399304 AAATCATTATTATC
1 AAATCATTAATATC
*
399318 AAATCATT-A-CT-
1 AAATCATTAATATC
399329 AAATCATTAATATC
1 AAATCATTAATATC
399343 AAATCATTAA
1 AAATCATTAA
399353 ATATTAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 1 0.03
14 18 0.62
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATCATTAATATC
Found at i:399426 original size:39 final size:38
Alignment explanation
Indices: 399382--399547 Score: 106
Period size: 39 Copynumber: 4.2 Consensus size: 38
399372 ATTACTAATC
399382 ATTACTATCAAGTCATTAAATATTAATAATAATTTCATT
1 ATTACTATCAA-TCATTAAATATTAATAATAATTTCATT
* *
399421 ATTACTAATC-ATCACTAAATTATTAAT-ATCAA-ATCATT
1 ATTACT-ATCAATCATTAAA-TATTAATAAT-AATTTCATT
* * * * * * * * *
399459 AAATATTAAT-AATAATTTCATTATTACTAATCATTACTAAATC
1 -ATTACT-ATCAATCA-TTAAATATTAATAATAATT--T-CATT
399502 ATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTATC-AATCATTAAATATTAATAATAATTTCATT
399541 ATTACTA
1 ATTACTA
399548 ATCATTACTA
Statistics
Matches: 92, Mismatches: 22, Indels: 26
0.66 0.16 0.19
Matches are distributed among these distances:
38 14 0.15
39 42 0.46
40 8 0.09
41 2 0.02
42 20 0.22
43 6 0.07
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (38 bp):
ATTACTATCAATCATTAAATATTAATAATAATTTCATT
Found at i:399458 original size:60 final size:60
Alignment explanation
Indices: 399372--399625 Score: 456
Period size: 60 Copynumber: 4.2 Consensus size: 60
399362 ATAAATTATT
* *
399372 ATTACT-AATCATTACTATCAAGTCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
399431 ATCACTAAATTATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
399491 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
399551 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
399611 ATTACTAAATCATTA
1 ATTACTAAATCATTA
399626 TTATAATTTC
Statistics
Matches: 186, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
59 5 0.03
60 181 0.97
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:399625 original size:21 final size:21
Alignment explanation
Indices: 399481--399625 Score: 67
Period size: 21 Copynumber: 7.2 Consensus size: 21
399471 TAATTTCATT
399481 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* *
399502 ATTACT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
399523 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
399541 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
399562 ATTAAT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
399583 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
399601 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
399622 ATTA
1 ATTA
399626 TTATAATTTC
Statistics
Matches: 90, Mismatches: 20, Indels: 28
0.65 0.14 0.20
Matches are distributed among these distances:
17 4 0.04
18 24 0.27
20 12 0.13
21 30 0.33
22 20 0.22
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:399711 original size:14 final size:14
Alignment explanation
Indices: 399688--399736 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
399678 GTTCAAGTCG
*
399688 TAAATTATTACTAT
1 TAAATCATTACTAT
399702 TAAATCATTAC---
1 TAAATCATTACTAT
*
399713 TAAATCATTAATAT
1 TAAATCATTACTAT
*
399727 CAAATCATTA
1 TAAATCATTA
399737 AATATTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 10 0.34
14 19 0.66
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATCATTACTAT
Found at i:399722 original size:25 final size:25
Alignment explanation
Indices: 399688--399736 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
399678 GTTCAAGTCG
* * *
399688 TAAATTATTACTATTAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
399713 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
399737 AATATTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:399860 original size:60 final size:60
Alignment explanation
Indices: 399704--400126 Score: 719
Period size: 60 Copynumber: 7.1 Consensus size: 60
399694 ATTACTATTA
* * *
399704 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTAGT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
399763 AATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
*
399822 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* * *
399882 AATCATTACTAATTCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTTCT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
399941 AATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* * * *
400000 ATTCATTACTAAATTATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
400060 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
400120 AATCATT
1 AATCATT
400127 GCTATCAAAT
Statistics
Matches: 341, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
58 74 0.22
59 63 0.18
60 204 0.60
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (60 bp):
AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:399888 original size:178 final size:173
Alignment explanation
Indices: 399704--400632 Score: 941
Period size: 178 Copynumber: 5.5 Consensus size: 173
399694 ATTACTATTA
399704 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTAGTAATCAT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAA--ATTATTA-T-ATCAT
399769 TACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAA
62 TACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT-ATCATTACTAA
399834 ATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
126 ATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* * *
399882 AATCATTACTAATTCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTTCTAATCAT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAA--ATTA-TTAT-ATCAT
399947 TACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTATTCATTACTAA
62 TACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTA-TCATTACTAA
* *
400012 ATTATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
126 ATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
400060 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAAT--AATT-TCAT-T-ATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAAATTATTATATCATTACT
*
400120 AATCATTGCTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
66 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT-ATCATTACTAAATCA
* ** * * * * *
400185 TTATTAT-ACTTTCATTACTAGTTATGTAACGAA-AATATGATTAATTGAACC
130 TTAATATCA-AATCATTA--A-ATAT-TAA-TAATAATTTCATT-ATT--ACT
* * * * * * * * *
400236 AAACATT-GT---TTATT-GT-TCAAGTC-GTAAATCATTACT-ATCAAATCA-T-TA-C--TA-
1 AATCATTACTAAATCATTAATATCAAATCATTAAAT-ATTAATAATAAAATTATTATATCATTAC
*
400287 -AATCATTAATATCAAATCATTAAATATTAATAAT-A----A--ATTA-T-T-ATTACT-AATCA
65 TAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTATCATTACTAAATCA
* *
400340 TTACTATCAAATCATTAAATATTAATAATAATCTCATTATTACT
130 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
400384 AATCATTACTAAATCATTAGTATCAAATCATTAAAAATTAATAAT--AA--ATTAT-T-ATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAAATTATTATATCATTACT
* *
400443 AATCATTACTATTAAATCATTAAATATTAATAAT-A----A--ATTA-T-T-ATTACT-AACCAT
66 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTATCATTACTAAATCAT
* *
400497 TACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
131 TAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
400540 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATGACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA---AATTATTA-T-ATCA
400605 TTACTAAATCATTACTATCAAATCATTA
61 TTACT-AATCATTACTATCAAATCATTA
400633 TTATTAAATC
Statistics
Matches: 649, Mismatches: 55, Indels: 104
0.80 0.07 0.13
Matches are distributed among these distances:
148 8 0.01
149 1 0.00
150 5 0.01
151 11 0.02
152 8 0.01
153 6 0.01
154 13 0.02
155 23 0.04
156 142 0.22
157 1 0.00
159 1 0.00
160 4 0.01
161 1 0.00
162 1 0.00
163 3 0.00
164 1 0.00
166 2 0.00
167 38 0.06
168 22 0.03
169 88 0.14
170 14 0.02
171 5 0.01
172 9 0.01
173 10 0.02
174 8 0.01
175 1 0.00
176 8 0.01
177 1 0.00
178 212 0.33
179 2 0.00
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.41
Consensus pattern (173 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAAATTATTATATCATTACT
AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTATCATTACTAAATCAT
TAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:400038 original size:21 final size:21
Alignment explanation
Indices: 400009--400102 Score: 65
Period size: 21 Copynumber: 4.6 Consensus size: 21
399999 TATTCATTAC
400009 TAAATTATTAATATCAAATCAT
1 TAAA-TATTAATATCAAATCAT
*
400031 TAAATATTAATAAT-AATTTCAT
1 TAAATATTAAT-ATCAA-ATCAT
* * *
400053 T-ATTATT-A-ATC--ATTAC
1 TAAATATTAATATCAAATCAT
*
400069 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTAATATCAAATCAT
400091 TAAATATTAATA
1 TAAATATTAATA
400103 ATAATTTCAT
Statistics
Matches: 53, Mismatches: 10, Indels: 19
0.65 0.12 0.23
Matches are distributed among these distances:
16 3 0.06
17 2 0.04
18 5 0.09
20 4 0.08
21 20 0.38
22 19 0.36
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATATTAATATCAAATCAT
Found at i:400113 original size:156 final size:154
Alignment explanation
Indices: 399953--400594 Score: 458
Period size: 156 Copynumber: 4.0 Consensus size: 154
399943 TCATTACTAA
*
399953 TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTATTCATTACTAAATTATT
1 TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTATT-ATTACT-AATCATT
* *
400018 AATATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTAAATCATTACTAT
64 ACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTAT
400083 CAAATCATTAAATATTAATAATAATT
129 CAAATCATTAAATATTAATAATAATT
*
400109 TCATTATTACTAATCATTGCTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 TC------A-T--T-A---CTATCAAATCATTAAATATTAATAATAATTTCATTATTACT-ATTA
* ** * * * * *
400174 TTACTAAATCATTATTAT-ACTTTCATTACTAGTTATGTAACGAA-AATATGATTAATTGAACCA
52 TTACT-AATCATTACTATCA-AATCATTA--A-ATAT-TAA-TAATAATTTCATT-ATT--ACTA
* * ** ** * * * *
400237 AACATT-GTTTATTGTT-CAAGTCGTAAATCATT-ACTATCAAATCATTACTAA-A
107 ATCATTACTAAATCATTACTA-TC--AAATCATTAAATAT-TAAT-A--A-TAATT
*
400289 TCATTAATATCAAATCATTAAATATTAATAAT-A----A--A-T--TATTATTACTAATCATTAC
1 TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTATTATTACTAATCATTAC
* *
400344 TATCAAATCATTAAATATTAATAATAATCTCATTATTACTAATCATTACTAAATCATTAGTATCA
66 TATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
* *
400409 AATCATTAAAAATTAATAATAAAT
131 AATCATTAAATATTAATAATAATT
* * * * * * * * *
400433 T-ATTATTA-CTAATCATT-ACTATTAAATCATTAAATATTAATAATAAATTATTATTACTAACC
1 TCATTACTATCAAATCATTAAATATT-AAT-AAT-AAT-TTCATTAT-TACTATTATTACTAATC
* *
400495 ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAA
61 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAC
400560 TATCAAATCATTAAATATTAATAATAATT
126 TATCAAATCATTAAATATTAATAATAATT
400589 TCATTA
1 TCATTA
400595 TGACTAATCA
Statistics
Matches: 379, Mismatches: 54, Indels: 105
0.70 0.10 0.20
Matches are distributed among these distances:
141 5 0.01
142 11 0.03
143 11 0.03
144 2 0.01
145 1 0.00
146 1 0.00
147 11 0.03
148 11 0.03
149 7 0.02
150 7 0.02
151 10 0.03
152 4 0.01
153 1 0.00
155 17 0.04
156 114 0.30
157 5 0.01
159 1 0.00
160 1 0.00
162 2 0.01
163 1 0.00
165 1 0.00
166 2 0.01
167 25 0.07
168 1 0.00
169 64 0.17
170 3 0.01
171 2 0.01
172 3 0.01
173 11 0.03
174 8 0.02
175 7 0.02
176 11 0.03
177 11 0.03
178 1 0.00
180 3 0.01
181 3 0.01
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (154 bp):
TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTATTATTACTAATCATTAC
TATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
AATCATTAAATATTAATAATAATT
Found at i:400280 original size:14 final size:14
Alignment explanation
Indices: 400261--400308 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
400251 TTCAAGTCGT
400261 AAATCATTACTATC
1 AAATCATTACTATC
400275 AAATCATTAC--T-
1 AAATCATTACTATC
*
400286 AAATCATTAATATC
1 AAATCATTACTATC
400300 AAATCATTA
1 AAATCATTA
400309 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:400342 original size:48 final size:48
Alignment explanation
Indices: 400280--400550 Score: 353
Period size: 48 Copynumber: 5.4 Consensus size: 48
400270 CTATCAAATC
*
400280 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
400329 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATCTCATTATTACTAAT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAAT-A----A--ATTA-T--T
* *
400387 CATTACTAAATCATTAGTATCAAATCATTAAAAATTAATAATAAATTATT
1 -ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
*
400437 ATTACTAATCATTACTATTAAATCATTAAATATTAATAATAAATTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
* * *
400485 ATTACTAACCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATT
400534 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
400551 AATCATTAAT
Statistics
Matches: 198, Mismatches: 11, Indels: 26
0.84 0.05 0.11
Matches are distributed among these distances:
48 113 0.57
49 32 0.16
50 1 0.01
52 1 0.01
53 5 0.03
55 5 0.03
56 1 0.01
58 1 0.01
59 7 0.04
60 32 0.16
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
Found at i:400408 original size:60 final size:59
Alignment explanation
Indices: 400329--400453 Score: 200
Period size: 60 Copynumber: 2.1 Consensus size: 59
400319 ATAAATTATT
*
400329 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAAT-AATCTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAAAT-T-ATTATTACTAATC
*
400388 ATTACTAAATCATTAGTATCAAATCATTAAAAATTAATAATAAATTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAAATTATTATTACTAATC
400447 ATTACTA
1 ATTACTA
400454 TTAAATCATT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
59 26 0.42
60 33 0.53
61 3 0.05
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (59 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAAATTATTATTACTAATC
Found at i:400472 original size:15 final size:14
Alignment explanation
Indices: 400260--400364 Score: 54
Period size: 14 Copynumber: 7.2 Consensus size: 14
400250 GTTCAAGTCG
*
400260 TAAATCATTACTAT
1 TAAATCATTAATAT
* *
400274 CAAATCA-T--TAC
1 TAAATCATTAATAT
400285 TAAATCATTAATAT
1 TAAATCATTAATAT
*
400299 CAAATCATTAAATAT
1 TAAATCATT-AATAT
* *
400314 TAATAATAAATTATTAT
1 T-A-AAT-CATTAATAT
*
400331 TACTAATCATTACTAT
1 TA--AATCATTAATAT
*
400347 CAAATCATTAAATAT
1 TAAATCATT-AATAT
400362 TAA
1 TAA
400365 TAATAATCTC
Statistics
Matches: 69, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
11 8 0.12
12 1 0.01
13 1 0.01
14 23 0.33
15 11 0.16
16 10 0.14
17 12 0.17
18 3 0.04
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATCATTAATAT
Found at i:400558 original size:21 final size:21
Alignment explanation
Indices: 400534--400621 Score: 51
Period size: 21 Copynumber: 4.3 Consensus size: 21
400524 TAATTTCATT
400534 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
400555 ATTAAT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
400576 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
*
400594 ATGACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
400615 ATTACTA
1 ATTACTA
400622 TCAAATCATT
Statistics
Matches: 48, Mismatches: 12, Indels: 14
0.65 0.16 0.19
Matches are distributed among these distances:
17 2 0.04
18 11 0.23
20 6 0.12
21 19 0.40
22 10 0.21
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.40
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:400564 original size:60 final size:60
Alignment explanation
Indices: 400485--400632 Score: 253
Period size: 60 Copynumber: 2.5 Consensus size: 60
400475 ATAAATTATT
* *
400485 ATTACT-AACCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATGACTAATC
* *
400544 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATGACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATGACTAATC
400604 ATTACTAAATCATTACTATCAAATCATTA
1 ATTACTAAATCATTACTATCAAATCATTA
400633 TTATTAAATC
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 6 0.07
60 77 0.93
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATGACTAATC
Found at i:400647 original size:14 final size:14
Alignment explanation
Indices: 400604--400688 Score: 97
Period size: 14 Copynumber: 6.4 Consensus size: 14
400594 ATGACTAATC
*
400604 ATTACTAAATCATT
1 ATTATTAAATCATT
* *
400618 ACTATCAAATCATT
1 ATTATTAAATCATT
400632 ATTATTAAATCATT
1 ATTATTAAATCATT
*
400646 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
400658 ATTA-T-AATGATT
1 ATTATTAAATCATT
400670 ATTATTAAATCATT
1 ATTATTAAATCATT
400684 ATTAT
1 ATTAT
400689 AATGATTGTA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
12 22 0.35
13 2 0.03
14 38 0.61
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.47
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:400660 original size:12 final size:12
Alignment explanation
Indices: 400632--400695 Score: 85
Period size: 12 Copynumber: 5.2 Consensus size: 12
400622 TCAAATCATT
*
400632 ATTATTA-AATC
1 ATTATTATAATG
400643 ATTATTATAATG
1 ATTATTATAATG
400655 ATTATTATAATG
1 ATTATTATAATG
*
400667 ATTATTATTAAATC
1 ATTATTA-T-AATG
400681 ATTATTATAATG
1 ATTATTATAATG
400693 ATT
1 ATT
400696 GTATTATTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
11 7 0.15
12 28 0.60
13 2 0.04
14 10 0.21
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (12 bp):
ATTATTATAATG
Found at i:400710 original size:26 final size:24
Alignment explanation
Indices: 400629--400710 Score: 87
Period size: 23 Copynumber: 3.4 Consensus size: 24
400619 CTATCAAATC
* *
400629 ATTATTATTA-AATCATTATTATA
1 ATTATTATTATAATGATTATTATT
*
400652 ATGATTATTATAATGATTATTATT
1 ATTATTATTATAATGATTATTATT
* *
400676 AAATCATTATTATAATGATT-GTATT
1 --ATTATTATTATAATGATTATTATT
400701 ATTATTATTA
1 ATTATTATTA
400711 CAAATAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
23 18 0.36
24 11 0.22
25 4 0.08
26 17 0.34
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (24 bp):
ATTATTATTATAATGATTATTATT
Found at i:401404 original size:26 final size:26
Alignment explanation
Indices: 401364--401482 Score: 195
Period size: 26 Copynumber: 4.6 Consensus size: 26
401354 TATTTAAATC
* *
401364 ATTATTAAATTATTATTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
*
401390 ATTA-CTAAATCATTATTATAACGATT
1 ATTATC-AAATCATTATTATAATGATT
401416 ATTATCAAATCATTATTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
401442 ATTATCAAATCATTATTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
401468 ATTATCAAATCATTA
1 ATTATCAAATCATTA
401483 CTAAATCATC
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
26 86 0.99
27 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (26 bp):
ATTATCAAATCATTATTATAATGATT
Found at i:401525 original size:12 final size:12
Alignment explanation
Indices: 401504--401541 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
401494 AATCATTAAA
*
401504 TATTAGATTCAT
1 TATTAAATTCAT
401516 TATTAAATTCAT
1 TATTAAATTCAT
401528 TATTAAA-TCAT
1 TATTAAATTCAT
401539 TAT
1 TAT
401542 AATGATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 7 0.28
12 18 0.72
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:401759 original size:20 final size:20
Alignment explanation
Indices: 401727--401768 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
401717 TTTATCACCA
401727 TATTAGTAATTCATTATTAT
1 TATTAGTAATTCATTATTAT
401747 TATTA-TAATTTCATTATTAT
1 TATTAGTAA-TTCATTATTAT
401767 TA
1 TA
401769 ATAATTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTAGTAATTCATTATTAT
Found at i:404853 original size:26 final size:25
Alignment explanation
Indices: 404795--404853 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
404785 CTAATATTAC
*
404795 TAATAATGATTTAATAATTATTATT
1 TAATAATGATTTAATAATTATGATT
* * *
404820 AAACTAATGATTTGATATTTAATGATT
1 TAA-TAATGATTTAATAATT-ATGATT
404847 TAATAAT
1 TAATAAT
404854 AATATGATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.07
26 18 0.67
27 7 0.26
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (25 bp):
TAATAATGATTTAATAATTATGATT
Found at i:406169 original size:65 final size:65
Alignment explanation
Indices: 406095--406220 Score: 209
Period size: 65 Copynumber: 1.9 Consensus size: 65
406085 TGCAGCTACG
* *
406095 GATGCAGGAATCTCTCAGCTATGGATGCTACGCATGCATGA-GTGATAGGGTTAAAGCTTGGTCG
1 GATGCAGGAATCTCCCAGCTATGGATGCAACGCATGCATGAGGT-ATAGGGTTAAAGCTTGGTCG
406159 C
65 C
*
406160 GATGCAGGAATCTCCCAGCTATGGATGCAACGCATGCATGAGGTATAGGGTTAAAGTTTGG
1 GATGCAGGAATCTCCCAGCTATGGATGCAACGCATGCATGAGGTATAGGGTTAAAGCTTGG
406221 GCGTGGTGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 55 0.96
66 2 0.04
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.25
Consensus pattern (65 bp):
GATGCAGGAATCTCCCAGCTATGGATGCAACGCATGCATGAGGTATAGGGTTAAAGCTTGGTCGC
Found at i:406316 original size:16 final size:16
Alignment explanation
Indices: 406295--406347 Score: 79
Period size: 16 Copynumber: 3.1 Consensus size: 16
406285 GCTCTTTGGT
406295 CACCGATCTCCCCATG
1 CACCGATCTCCCCATG
406311 CACCGATCTCCCCATG
1 CACCGATCTCCCCATG
406327 CATGCACGATCTCCCCATG
1 CA--C-CGATCTCCCCATG
406346 CA
1 CA
406348 TGCACCGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
16 18 0.53
18 1 0.03
19 15 0.44
ACGTcount: A:0.21, C:0.47, G:0.13, T:0.19
Consensus pattern (16 bp):
CACCGATCTCCCCATG
Found at i:406332 original size:20 final size:20
Alignment explanation
Indices: 406307--406362 Score: 105
Period size: 19 Copynumber: 2.9 Consensus size: 20
406297 CCGATCTCCC
406307 CATGCACCGATCTCCCCATG
1 CATGCACCGATCTCCCCATG
406327 CATGCA-CGATCTCCCCATG
1 CATGCACCGATCTCCCCATG
406346 CATGCACCGATCTCCCC
1 CATGCACCGATCTCCCC
406363 CCATGCACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.20, C:0.46, G:0.14, T:0.20
Consensus pattern (20 bp):
CATGCACCGATCTCCCCATG
Found at i:406338 original size:19 final size:19
Alignment explanation
Indices: 406298--406362 Score: 100
Period size: 19 Copynumber: 3.5 Consensus size: 19
406288 CTTTGGTCAC
406298 CGATCTCCCCATGCA--C-
1 CGATCTCCCCATGCATGCA
406314 CGATCTCCCCATGCATGCA
1 CGATCTCCCCATGCATGCA
406333 CGATCTCCCCATGCATGCA
1 CGATCTCCCCATGCATGCA
406352 CCGATCTCCCC
1 -CGATCTCCCC
406363 CCATGCACAC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
16 15 0.33
18 1 0.02
19 19 0.42
20 10 0.22
ACGTcount: A:0.18, C:0.48, G:0.14, T:0.20
Consensus pattern (19 bp):
CGATCTCCCCATGCATGCA
Found at i:406463 original size:28 final size:29
Alignment explanation
Indices: 406401--406481 Score: 137
Period size: 28 Copynumber: 2.8 Consensus size: 29
406391 TGGTCGCCCC
*
406401 GAGTGCATGGCGACCTCCTTGGTCGTTGG
1 GAGTGCATGGCGACCTCTTTGGTCGTTGG
406430 GAGTGCATGGCGA-CTCTTTGGTCGTTGG
1 GAGTGCATGGCGACCTCTTTGGTCGTTGG
*
406458 GCGTGCATGGCGACCTCTTTGGTC
1 GAGTGCATGGCGACCTCTTTGGTC
406482 ACTGTAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 26 0.53
29 23 0.47
ACGTcount: A:0.10, C:0.23, G:0.37, T:0.30
Consensus pattern (29 bp):
GAGTGCATGGCGACCTCTTTGGTCGTTGG
Found at i:408881 original size:20 final size:21
Alignment explanation
Indices: 408856--408948 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
408846 TTTTTCCAAT
*
408856 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
408876 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
408897 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
408917 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
408938 TCGCAATGCGA
1 TCGCAATGCGA
408949 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:408901 original size:41 final size:41
Alignment explanation
Indices: 408856--408948 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
408846 TTTTTCCAAT
408856 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
408897 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
408938 TCGCAATGCGA
1 TCGCAATGCGA
408949 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:408961 original size:41 final size:41
Alignment explanation
Indices: 408875--409009 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
408865 GAATAAGTAA
* *
408875 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
408916 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** *
408957 ATCGCAATGCGATAAT-AAAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
408998 TTCGCAACGCGA
1 ATCGCAACGCGA
409010 TTTACATAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
40 4 0.05
41 76 0.93
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:408962 original size:20 final size:20
Alignment explanation
Indices: 408937--409010 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
408927 AATTGGGAAA
*
408937 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
408957 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
408978 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
408998 TTCGCAACGCGAT
1 ATCGCAACGCGAT
409011 TTACATAGCG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:409574 original size:19 final size:19
Alignment explanation
Indices: 409529--409576 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
409519 TTCGAGAATG
*
409529 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
409548 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
409568 AAAATCGCA
1 AAAATCGCA
409577 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:409599 original size:19 final size:19
Alignment explanation
Indices: 409577--409755 Score: 119
Period size: 19 Copynumber: 9.8 Consensus size: 19
409567 CAAAATCGCA
409577 TTGCGATTTTCATTTTGCG
1 TTGCGATTTTCATTTTGCG
**
409596 TTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTTGCG
* *
409615 TTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTTGC-G
*
409635 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTTGCG
*
409654 TTGCGATTGTC----TG-G
1 TTGCGATTTTCATTTTGCG
* ** *
409668 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTTGCG
*
409687 TTGCGA--TTC--TCT-CG
1 TTGCGATTTTCATTTTGCG
**
409701 TTGCGATAGTCATTTCTGCG
1 TTGCGATTTTCATTT-TGCG
*
409721 TTGCGATTCTCATTATCT-CG
1 TTGCGATTTTCATT-T-TGCG
409741 TTGCGATTTTCATTT
1 TTGCGATTTTCATTT
409756 CAACCAAAAG
Statistics
Matches: 128, Mismatches: 19, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
14 18 0.14
15 2 0.02
16 2 0.02
17 2 0.02
18 2 0.02
19 52 0.41
20 47 0.37
21 3 0.02
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTTGCG
Found at i:409643 original size:39 final size:38
Alignment explanation
Indices: 409577--409757 Score: 139
Period size: 33 Copynumber: 4.9 Consensus size: 38
409567 CAAAATCGCA
*
409577 TTGCGATTTTCATTTTGCGTTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCACG
* *
409615 TTGCGATTTTTATTTCGCGGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGC-GTTGCGATTTTCATTTCACG
* * ** *
409654 TTGCGATTGTC---T-G-GTCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCACG
* ** *
409687 TTGCGA--TTC---TCTCGTTGCGATAGTCATTTCTGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTC-ACG
* *
409721 TTGCGATTCTCATTATCTCGTTGCGATTTTCATTTCA
1 TTGCGATTTTCATT-TCGCGTTGCGATTTTCATTTCA
409758 ACCAAAAGAC
Statistics
Matches: 118, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.03
33 39 0.33
34 9 0.08
35 1 0.01
36 3 0.03
38 16 0.14
39 28 0.24
40 19 0.16
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (38 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCACG
Found at i:409674 original size:33 final size:33
Alignment explanation
Indices: 409644--409731 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
409634 GTTGCGATTT
* *
409644 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
409677 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
409710 TCATTTCTGCGTTGCGATTCTC
1 TCATTTC-GCGTTGCGATTCTC
409732 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 37 0.73
34 14 0.27
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:409724 original size:20 final size:19
Alignment explanation
Indices: 409670--409747 Score: 76
Period size: 20 Copynumber: 4.3 Consensus size: 19
409660 TTGTCTGGTC
*
409670 GCGATAGTCATTTCGCGTT
1 GCGATAGTCATTTCTCGTT
409689 GCGAT--TC---TCTCGTT
1 GCGATAGTCATTTCTCGTT
409703 GCGATAGTCATTTCTGCGTT
1 GCGATAGTCATTTCT-CGTT
**
409723 GCGATTCTCATTATCTCGTT
1 GCGATAGTCATT-TCTCGTT
409743 GCGAT
1 GCGAT
409748 TTTCATTTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
14 11 0.22
16 2 0.04
17 2 0.04
19 8 0.16
20 23 0.47
21 3 0.06
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (19 bp):
GCGATAGTCATTTCTCGTT
Found at i:411832 original size:21 final size:21
Alignment explanation
Indices: 411808--411874 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
411798 TCATTCCTCG
411808 AGAGTCCCTTCCCACCGTTCA
1 AGAGTCCCTTCCCACCGTTCA
* * *
411829 AGAGGCCACTGT--CATCGTTGA
1 AGAGTCC-CT-TCCCACCGTTCA
*
411850 AGAGGTCCC-TCCCACCATTCA
1 AGA-GTCCCTTCCCACCGTTCA
411871 AGAG
1 AGAG
411875 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 7, Indels: 11
0.65 0.13 0.21
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 26 0.76
22 5 0.15
23 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCTTCCCACCGTTCA
Found at i:411832 original size:42 final size:41
Alignment explanation
Indices: 411752--411874 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
411742 GCCCGACTCG
* * * * *
411752 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCC-CTCCCACCGTTCAAGAGGCC
411794 CCTATCATTCCTCGAGAGTCCCTTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCC-TCCCACCGTTCAAGAGGCC
* * * * *
411836 ACTGTCA-TCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCTCCCACCGTTCAAGAG
411875 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 5 0.07
42 58 0.85
43 5 0.07
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (41 bp):
CCTATCATTCCTCGAGAGTCCCTCCCACCGTTCAAGAGGCC
Found at i:413251 original size:14 final size:14
Alignment explanation
Indices: 413232--413267 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
413222 ATTGTTTAAT
413232 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
413246 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
413260 TGATTTGT
1 TGATTTGT
413268 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:413468 original size:19 final size:19
Alignment explanation
Indices: 413446--413596 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
413436 CGAAATTAAA
413446 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
413465 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
413480 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
413498 TTCGCATTGC-A----AAA
1 TTCGCGTTGCGATTTTCAT
*
413512 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
413531 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
413546 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
413564 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
413583 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
413597 GGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 26 0.28
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 43 0.46
20 10 0.11
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:413492 original size:33 final size:32
Alignment explanation
Indices: 413450--413576 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
413440 ATTAAATTCG
413450 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
413483 CGTTGCGATTTTCATTTCGCATTGCAAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGC--GATTCCT
413516 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
413549 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
413577 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:413551 original size:66 final size:66
Alignment explanation
Indices: 413443--413573 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
413433 ACGCGAAATT
*
413443 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
413508 A
66 A
*
413509 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
413574 GATAGTAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
A
Found at i:415884 original size:12 final size:12
Alignment explanation
Indices: 415867--415891 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
415857 TCTTCGGGGA
415867 CTTTTTCTTCTT
1 CTTTTTCTTCTT
415879 CTTTTTCTTCTT
1 CTTTTTCTTCTT
415891 C
1 C
415892 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:416100 original size:24 final size:24
Alignment explanation
Indices: 416066--416119 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
416056 CTGAAACATC
* *
416066 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
416090 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
416114 ATCAAA
1 ATCAAA
416120 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:417235 original size:20 final size:20
Alignment explanation
Indices: 417179--417227 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
417169 ATTCATTTGA
417179 CTATCGCAACACG-AAATGG
1 CTATCGCAACACGAAAATGG
417198 CTATCGCAACACGAAAATGG
1 CTATCGCAACACGAAAATGG
*
417218 TTATCGCAAC
1 CTATCGCAAC
417228 GAGAAAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
CTATCGCAACACGAAAATGG
Found at i:417281 original size:14 final size:16
Alignment explanation
Indices: 417262--417331 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 16
417252 AATCGCATTA
417262 CGATTTTC-TCG-TTG
1 CGATTTTCTTCGATTG
417276 CGATTTTCATTTCGCATTG
1 CGATTTTC--TTCG-ATTG
417295 CGATTTTCATTTCGCATTG
1 CGATTTTC--TTCG-ATTG
417314 CGATTTTC-TCG-TTG
1 CGATTTTCTTCGATTG
417328 CGAT
1 CGAT
417332 AGCCATTTCG
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
14 15 0.29
16 3 0.06
17 3 0.06
19 30 0.59
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (16 bp):
CGATTTTCTTCGATTG
Found at i:417295 original size:19 final size:19
Alignment explanation
Indices: 417273--417321 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
417263 GATTTTCTCG
417273 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
417292 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
417311 TTGCGATTTTC
1 TTGCGATTTTC
417322 TCGTTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:419401 original size:19 final size:19
Alignment explanation
Indices: 419321--419438 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
419311 TAGTTTACTT
* *
419321 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
419341 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
419360 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
419380 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
419399 TCGTAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
419413 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
419431 TCGCAACG
1 TCGCAACG
419439 ACAAAATCGC
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.15
19 24 0.30
20 29 0.37
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Done.