Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008212.1 Hibiscus syriacus cultivar Beakdansim tig00110834_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: 343056
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:222322 original size:24 final size:24
Alignment explanation
Indices: 222295--222346 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
222285 AACGGATATA
*
222295 TCAAAAATCAAAACATAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
** * *
222319 TCAAGTATCAGATCAAAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
222343 TCAA
1 TCAA
222347 GTATTCGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAATCCAGG
Found at i:222346 original size:12 final size:13
Alignment explanation
Indices: 222311--222393 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 13
222301 ATCAAAACAT
222311 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
222324 TAT-CAGATCAA-
1 AATCCAGGTCAAG
222335 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
222348 TATTC-GATC-AG
1 AATCCAGGTCAAG
222359 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
222372 TATCC-GAT-TAG
1 AATCCAGGTCAAG
222383 AATCCAGGTCA
1 AATCCAGGTCA
222394 TGTATTATAA
Statistics
Matches: 48, Mismatches: 16, Indels: 12
0.63 0.21 0.16
Matches are distributed among these distances:
11 13 0.27
12 24 0.50
13 11 0.23
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:222347 original size:24 final size:23
Alignment explanation
Indices: 222311--222398 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 23
222301 ATCAAAACAT
*
222311 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATC-GATCAG
222335 AATCCAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTA-TCGATCAG
*
222359 AATCCAGGTCAAGTATCCGATTAG
1 AATCCAGGTCAAGTAT-CGATCAG
*
222383 AATCCAGGTCATGTAT
1 AATCCAGGTCAAGTAT
222399 TATAATAGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
23 1 0.02
24 56 0.95
25 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (23 bp):
AATCCAGGTCAAGTATCGATCAG
Found at i:222407 original size:24 final size:23
Alignment explanation
Indices: 222311--222408 Score: 90
Period size: 24 Copynumber: 4.1 Consensus size: 23
222301 ATCAAAACAT
*
222311 AATCCAGGTCAAGTA-TCAGATCAA
1 AATCCAGGTCAAGTATTCA-AT-AG
*
222335 AATCCAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTATTCAAT-AG
* *
222359 AATCCAGGTCAAGTATCCGATTAG
1 AATCCAGGTCAAGTATTC-AATAG
* *
222383 AATCCAGGTCATGTATTATAATAG
1 AATCCAGGTCAAGTATT-CAATAG
222407 AA
1 AA
222409 ATCAAATCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
24 59 0.95
25 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (23 bp):
AATCCAGGTCAAGTATTCAATAG
Found at i:225761 original size:24 final size:23
Alignment explanation
Indices: 225727--225821 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 23
225717 ATTGGGGTGT
225727 TACATATATATATATAGTTTATA
1 TACATATATATATATAGTTTATA
* *
225750 TAGCATATATATACTACAATTTATA
1 TA-CATATATATA-TATAGTTTATA
*
225775 TTA-ATAAAT-TATATAGTTTATA
1 -TACATATATATATATAGTTTATA
* *
225797 TATATATAGTTTATATAGTTTATA
1 TACATATA-TATATATAGTTTATA
225821 T
1 T
225822 TAATAAACTA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.03
22 13 0.22
23 5 0.08
24 29 0.48
25 9 0.15
26 2 0.03
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (23 bp):
TACATATATATATATAGTTTATA
Found at i:225797 original size:9 final size:9
Alignment explanation
Indices: 225783--225821 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
225773 TATTAATAAA
225783 TTATATAGT
1 TTATATAGT
225792 TTATATA--
1 TTATATAGT
225799 -TATATAGT
1 TTATATAGT
225807 TTATATAGT
1 TTATATAGT
225816 TTATAT
1 TTATAT
225822 TAATAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.22
9 21 0.78
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (9 bp):
TTATATAGT
Found at i:225797 original size:22 final size:22
Alignment explanation
Indices: 225769--225833 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 22
225759 TATACTACAA
225769 TTTATATTAATAAATTATATAG
1 TTTATATTAATAAATTATATAG
**
225791 TTTATATATATATAGTTTATATAG
1 TTTATAT-TA-ATAAATTATATAG
*
225815 TTTATATTAATAAACTATA
1 TTTATATTAATAAATTATA
225834 GAAACTATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 14 0.39
23 4 0.11
24 18 0.50
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTATATTAATAAATTATATAG
Found at i:225800 original size:13 final size:15
Alignment explanation
Indices: 225784--225813 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
225774 ATTAATAAAT
225784 TATATAGTTTATATA
1 TATATAGTTTATATA
225799 TATATAGTTTATATA
1 TATATAGTTTATATA
225814 GTTTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:225917 original size:20 final size:20
Alignment explanation
Indices: 225894--225988 Score: 59
Period size: 20 Copynumber: 4.7 Consensus size: 20
225884 ATATATATGC
225894 TATATAGTTCATATATAGTT
1 TATATAGTTCATATATAGTT
* ** *
225914 TATATTAATAAACTATATAATT
1 TATA-TAGTTCA-TATATAGTT
* **
225936 TATACA-TAAAT-TATAGTTT
1 TATATAGTTCATATATAG-TT
**
225955 ATATATAGTTCATATATACAT
1 -TATATAGTTCATATATAGTT
225976 TATATAGTTCATA
1 TATATAGTTCATA
225989 CATACATATA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
18 4 0.07
19 3 0.05
20 26 0.45
21 9 0.16
22 16 0.28
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (20 bp):
TATATAGTTCATATATAGTT
Found at i:225993 original size:20 final size:21
Alignment explanation
Indices: 225954--226002 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
225944 AATTATAGTT
*
225954 TATATATAGTTCATATATACA
1 TATATATAGTTCATACATACA
225975 T-TATATAGTTCATACATACA
1 TATATATAGTTCATACATACA
225995 TATATATA
1 TATATATA
226003 TATAAACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (21 bp):
TATATATAGTTCATACATACA
Found at i:226065 original size:11 final size:11
Alignment explanation
Indices: 226030--226137 Score: 84
Period size: 11 Copynumber: 10.4 Consensus size: 11
226020 CTATATATAG
*
226030 TATATATACTT
1 TATATATAATT
*
226041 TATATATAGTT
1 TATATATAATT
*
226052 TATATATAA-A
1 TATATATAATT
226062 T-TATATAATT
1 TATATATAATT
* *
226072 TTTACATAA--
1 TATATATAATT
226081 TATATATAATT
1 TATATATAATT
**
226092 TATGCATAA--
1 TATATATAATT
226101 TATATATAATT
1 TATATATAATT
* *
226112 CATATATAGTT
1 TATATATAATT
*
226123 TATATATAATA
1 TATATATAATT
226134 TATA
1 TATA
226138 AATACAAATT
Statistics
Matches: 75, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
9 21 0.28
10 2 0.03
11 52 0.69
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (11 bp):
TATATATAATT
Found at i:226066 original size:20 final size:19
Alignment explanation
Indices: 226043--226190 Score: 69
Period size: 20 Copynumber: 8.6 Consensus size: 19
226033 ATATACTTTA
226043 TATATAGTTTATATATAAAT
1 TATATAGTTTATATAT-AAT
* * *
226063 TATATAATTTTTACATAAT
1 TATATAGTTTATATATAAT
* **
226082 ATATATAATTTATGCATAA-
1 -TATATAGTTTATATATAAT
*
226101 TATATA---TA-AT-TCA-
1 TATATAGTTTATATATAAT
226114 TATATAGTTTATATATAA-
1 TATATAGTTTATATATAAT
* *
226132 TATATA---AATACA-AAT
1 TATATAGTTTATATATAAT
*
226147 TACATAG-TT-TATAT-AT
1 TATATAGTTTATATATAAT
226163 TATATAGTTT-T-TATAAT
1 TATATAGTTTATATATAAT
226180 TATATAGTTTA
1 TATATAGTTTA
226191 CATACTATAT
Statistics
Matches: 100, Mismatches: 15, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
13 8 0.08
14 2 0.02
15 11 0.11
16 16 0.16
17 17 0.17
18 14 0.14
19 3 0.03
20 29 0.29
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (19 bp):
TATATAGTTTATATATAAT
Found at i:226084 original size:18 final size:20
Alignment explanation
Indices: 226041--226111 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
226031 ATATATACTT
* *
226041 TATATATAGTTTATATATAA
1 TATATATAATTTATACATAA
*
226061 -ATTATATAATTTTTACATAA
1 TA-TATATAATTTATACATAA
*
226081 TATATATAATTTATGCATAA
1 TATATATAATTTATACATAA
226101 TATATATAATT
1 TATATATAATT
226112 CATATATAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATATAATTTATACATAA
Found at i:226134 original size:16 final size:16
Alignment explanation
Indices: 226115--226217 Score: 59
Period size: 16 Copynumber: 6.3 Consensus size: 16
226105 TATAATTCAT
226115 ATATAGTTTATATATA
1 ATATAGTTTATATATA
** *
226131 ATATA-TAAATACA-A
1 ATATAGTTTATATATA
*
226145 ATTACATAGTTTATATATT
1 A-T--ATAGTTTATATATA
* *
226164 ATATAGTTTTTATAATT
1 ATATAGTTTATAT-ATA
*
226181 ATATAGTTTACATACT-
1 ATATAGTTTATATA-TA
*
226197 ATATAGTTTAGATATA
1 ATATAGTTTATATATA
*
226213 GTATA
1 ATATA
226218 TAAATATAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
14 2 0.03
15 7 0.10
16 33 0.49
17 18 0.27
18 6 0.09
19 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (16 bp):
ATATAGTTTATATATA
Found at i:226183 original size:17 final size:17
Alignment explanation
Indices: 226114--226206 Score: 77
Period size: 16 Copynumber: 5.6 Consensus size: 17
226104 ATATAATTCA
226114 TATATAGTTTATAT-AT
1 TATATAGTTTATATAAT
* ** *
226130 AATATA-TAAATACAAAT
1 TATATAGTTTATA-TAAT
*
226147 TACATAGTTTATAT-AT
1 TATATAGTTTATATAAT
*
226163 TATATAGTTTTTATAAT
1 TATATAGTTTATATAAT
* *
226180 TATATAGTTTACAT-AC
1 TATATAGTTTATATAAT
226196 TATATAGTTTA
1 TATATAGTTTA
226207 GATATAGTAT
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
15 4 0.07
16 31 0.53
17 20 0.34
18 4 0.07
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (17 bp):
TATATAGTTTATATAAT
Found at i:233167 original size:16 final size:16
Alignment explanation
Indices: 233148--233180 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
233138 ATACTGAATA
233148 ATATTTATTTAAAGGT
1 ATATTTATTTAAAGGT
233164 ATATTTATTTAAAGGT
1 ATATTTATTTAAAGGT
233180 A
1 A
233181 GTGCAAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (16 bp):
ATATTTATTTAAAGGT
Found at i:236464 original size:23 final size:23
Alignment explanation
Indices: 236438--236483 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
236428 ATGTTTTAAT
236438 TGACGTGGCGTGGTGCATGTCCA
1 TGACGTGGCGTGGTGCATGTCCA
236461 TGACGTGGCGTGGTGCATGTCCA
1 TGACGTGGCGTGGTGCATGTCCA
236484 ACCTAGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.39, T:0.26
Consensus pattern (23 bp):
TGACGTGGCGTGGTGCATGTCCA
Found at i:240185 original size:182 final size:182
Alignment explanation
Indices: 239599--240453 Score: 1100
Period size: 182 Copynumber: 4.7 Consensus size: 182
239589 TGTCGGTTTA
* * * * * *
239599 TGTCGATACTTTATAA-AACTGTATTGATCCACATCAATATAATAGGTAAAAATATGATAAAACC
1 TGTCGATACTTTATAACAA-TGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACC
* * * * * * * *
239663 GGTCTCGAAAAGATAAAACCGGTA-A-AACGGTACTTG-ATATATTGAAAGTGTCGATACTTTAT
65 GGTCTCTAAAGGACAAAATCGATATAGAGC-G-AC-CGAATATATTGAAAGTGTCGATACTTTAA
* *
239725 TATAAGTATCGACACTTTGTGAATTTAAAAGATAAGCAGTTTTAGA-GTCTATAAAG
127 TATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTA-ACGCCTATAAAG
*
239781 TGTCGATACTTTATAACAATGTATCGATCCACAATGATATAA-AAGGTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAA-GTAAAAATATGACAAAACC
* * * *
239845 GGTATCTAAAGGACAAAATTGGTATAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAAT-T
65 GGTCTCTAAAGGACAAAATCGATATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATAT
*
239909 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
130 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAG
* *
239962 TGTCGATACTTTACAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACTG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
*
240027 GTCTCTAAAGGATAAAATCGATATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCTAAAGGACAAAATCGATATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATA
** *
240092 AAAATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCCATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAG
* * *
240144 TGTCGATACTTTATAACAATGTATCGATCTAAAATGATATAAC-AGTTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAG-TAAAAATATGACAAAACC
* * * * *
240208 GGTCTCTAAAGGACAAAA-CCAGTACAGAGTGACCGAATATATTTAAAGTGTCAATACTTTAATA
65 GGTCTCTAAAGGACAAAATCGA-TATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATA
* * *
240272 TAAGTATCAAAACTTTGTGAATTTAAAAGAGAATCAGTTTTAACGCCTATAAAG
129 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAG
* * * *
240326 TGTCGATACCTGATAACAATGTATC-AGTTCACAACGATATAACATGTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAATGTATCGA-TCCACAACGATATAACAAGTAAAAATATGACAAAACC
* * * * * * * *
240390 GGTCTCGAAATGACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
65 GGTCTCTAAAGGACAAAATCGATATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATA
240454 ACTACGCGTA
Statistics
Matches: 594, Mismatches: 66, Indels: 26
0.87 0.10 0.04
Matches are distributed among these distances:
181 172 0.29
182 414 0.70
183 6 0.01
184 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
GTCTCTAAAGGACAAAATCGATATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAG
Found at i:240267 original size:363 final size:362
Alignment explanation
Indices: 239599--240453 Score: 1182
Period size: 363 Copynumber: 2.3 Consensus size: 362
239589 TGTCGGTTTA
* * * * * *
239599 TGTCGATACTTTATAA-AACTGTATTGATCCACATCAATATAATAGGTAAAAATATGATAAAACC
1 TGTCGATACTTTATAACAA-TGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACC
* * *
239663 GGTCTCGAAAAGATAAAACCGGTAA-AACGGTACTTGATATATTGAAAGTGTCGATACTTTATTA
65 GGTCTCGAAAAGATAAAACCGGTAAGAGC-G-AC-CGATATATTGAAAGTGTCGATACTTTAATA
** * * *
239727 TAAGTATCGACACTTTGTGAATTTAAAAGATAAGCAGTTTTAGAGTCTATAAAGTGTCGATACTT
127 TAAAAATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGAGCCCATAAAGTGTCGATACTT
*
239792 TATAACAATGTATCGATCCACAATGATATAAAAGGTAAAAATATGACAAAACCGGTATCTAAAGG
192 TATAACAATGTATCGATCCAAAATGATATAAAAGGTAAAAATATGACAAAACCGGTATCTAAAGG
*** * * * *
239857 ACAAAATTGGTATAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAAT-TAAGTATCGACAC
257 ACAAAACCAGTACAGAGCGACCAAATATATTGAAAGTGTCAATACTTTAATATAAGTATCAAAAC
*
239921 TTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
322 TTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAG
* *
239962 TGTCGATACTTTACAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACTG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * * *
240027 GTCTCTAAAGGATAAAATCGATATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCGAAAAGATAAAACCGGTA-AGAGCGACCG-ATATATTGAAAGTGTCGATACTTTAATATA
240092 AAAATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTA-ACGCCCATAAAGTGTCGATACTTT
129 AAAATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGA-GCCCATAAAGTGTCGATACTTT
* * * *
240156 ATAACAATGTATCGATCTAAAATGATATAACAGTTAAAAATATGACAAAACCGGTCTCTAAAGGA
193 ATAACAATGTATCGATCCAAAATGATATAAAAGGTAAAAATATGACAAAACCGGTATCTAAAGGA
* * *
240221 CAAAACCAGTACAGAGTGACCGAATATATTTAAAGTGTCAATACTTTAATATAAGTATCAAAACT
258 CAAAACCAGTACAGAGCGACCAAATATATTGAAAGTGTCAATACTTTAATATAAGTATCAAAACT
*
240286 TTGTGAATTTAAAAGAGAATCAGTTTTAACGCCTATAAAG
323 TTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAG
* * * *
240326 TGTCGATACCTGATAACAATGTATC-AGTTCACAACGATATAACATGTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAATGTATCGA-TCCACAACGATATAACAAGTAAAAATATGACAAAACC
* *
240390 GGTCTCGAAATGACAAAACCGGTAA-AGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
65 GGTCTCGAAAAGATAAAACCGGTAAGAGCG--ACC-GATATATTGAAAGTGTCGATACTTTAATA
240454 ACTACGCGTA
Statistics
Matches: 434, Mismatches: 48, Indels: 19
0.87 0.10 0.04
Matches are distributed among these distances:
362 6 0.01
363 265 0.61
364 160 0.37
365 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (362 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
GTCTCGAAAAGATAAAACCGGTAAGAGCGACCGATATATTGAAAGTGTCGATACTTTAATATAAA
AATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGAGCCCATAAAGTGTCGATACTTTATA
ACAATGTATCGATCCAAAATGATATAAAAGGTAAAAATATGACAAAACCGGTATCTAAAGGACAA
AACCAGTACAGAGCGACCAAATATATTGAAAGTGTCAATACTTTAATATAAGTATCAAAACTTTG
TGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAG
Found at i:242873 original size:21 final size:21
Alignment explanation
Indices: 242849--242889 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
242839 AAGATAATCA
242849 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
242870 AGAGTCGAAGAGACACTTGA
1 AGAGTCGAAGAGAAACTTGA
242890 AAGGCATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.32, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:242965 original size:33 final size:33
Alignment explanation
Indices: 242926--243025 Score: 182
Period size: 33 Copynumber: 3.0 Consensus size: 33
242916 AAATAAATGG
*
242926 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
*
242959 ATTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
242992 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
243025 A
1 A
243026 CTTAAGATGG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.29, C:0.00, G:0.46, T:0.25
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
Found at i:244842 original size:18 final size:19
Alignment explanation
Indices: 244804--244851 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
244794 AATGTAGGGT
*
244804 TAATTTTGGATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
244823 TAATTTTGTATATG-TTTA
1 TAATTTTGTATAAGATTTA
244841 TAATTTTGTAT
1 TAATTTTGTAT
244852 GTGAATGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:245182 original size:15 final size:15
Alignment explanation
Indices: 245162--245194 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
245152 GTCCAGTATG
*
245162 GTTCCCAAATGTAAA
1 GTTCCCAAACGTAAA
245177 GTTCCCAAACGTAAA
1 GTTCCCAAACGTAAA
245192 GTT
1 GTT
245195 TCCATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (15 bp):
GTTCCCAAACGTAAA
Found at i:245616 original size:199 final size:199
Alignment explanation
Indices: 245217--246372 Score: 1376
Period size: 199 Copynumber: 5.8 Consensus size: 199
245207 GTAAGAAGAT
* *
245217 GTGTCGATACATTTATAAAAGGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
245282 GGTAATTTTGTAATATAACTGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTATATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * * *
245347 ATTGACACTTTTGAAATTAGTGTTGATACTTTTTTTCCAGAATGAAT-CCCAAAATGGTGAACGC
131 ATCGACAC-TTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGCACGC
245411 ATAAA
195 ATAAA
245416 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
245481 GGTAATTTT-TCAATGTAACCGTTATAACTATACC-TTTTTATGAGAGAATAGATCTGCATAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
* * * * * *
245544 TATCGACACTTATGGAATTTGTGTCGATACTGTTTGTCCAGAAGGAATGTCCAAAAGGGTGCACA
130 TATCGACACTT-TGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGCACG
*
245609 AATAAA
194 CATAAA
* * * * * * *
245615 GTATCGATACATTTTTTAAAAGTGTCAATCCCAGAGATATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* *
245680 GGTAATTTTGTAATGTAACCGGTATAAATATACTGGTTTTAT-ATGAGAATAGGTATACATAATG
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGA-GAGAATAGGTCTACATAATG
* * * * *
245744 TATCGACACATTTAAAATTGGTGTCGATACTTTTTATCCAGAATGAATGCCCAAAATGGTGAATG
130 TATCGACAC-TTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGCACG
245809 CATAAA
194 CATAAA
* * * * *
245815 GTGTCGATACATTTGTAAAAAATGTCGATCCCAGAGACATCG-AACCCATAATTATAATTTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * *
245879 TGTAATTTTGTAATGTAACTGGTATAAATGTACCGGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* ** * * *
245944 ATTGACACTTTTTAATTATGCGTCGATACATTTTGTCCAGAATGAATTCCCAAAAAATGGTGCAC
131 ATCGACACTTTGAAATT-TGTGTCGATACTTTTTGTCCAGAATGAATGCCC--AAAATGGTGCAC
246009 GCATAAA
193 GCATAAA
* * *
246016 GTGTCGATACATTTATAAAAAGTATCGATCCTAGAAACATCGAAACCCATGATTATAATGCAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * * * *
246081 GATAATTTT-TCAATGTAACCGATATAAATATACCGGTTTCATGCG-GAATAGGTCTAGAAAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
* * * *
246144 TATCGACACTTATGAAATTTATGTCGATACTTTTTGTCCAGAAGGAATG-CCAAAAGGGTGCACC
130 TATCGACACTT-TGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGCACG
*
246208 CATTAA
194 CATAAA
* * * * **
246214 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCAAAACCGGTAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* ** ** * * * *
246279 GGTAAATTTCCAATGTAACCAATATAAATATACCGATTTTATGAGAAAATAGATC-ATCATAAAG
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CATAATG
* * *
246343 TATCAACAATTGTTAAATTTGTGTCGATAC
130 TATCGACACTT-TGAAATTTGTGTCGATAC
246373 CATTTTAAAA
Statistics
Matches: 814, Mismatches: 126, Indels: 34
0.84 0.13 0.03
Matches are distributed among these distances:
197 2 0.00
198 180 0.22
199 346 0.43
200 118 0.14
201 108 0.13
202 60 0.07
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (199 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGCACGCA
TAAA
Found at i:248777 original size:21 final size:21
Alignment explanation
Indices: 248751--248795 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
248741 GATTTCTGGG
* *
248751 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
248772 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
248793 CAA
1 CAA
248796 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:250448 original size:149 final size:149
Alignment explanation
Indices: 250261--250575 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
250251 GAGTCGAGGG
* * *
250261 TCTACGCGGTCTTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
250326 ACTTGATCCCCAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCCAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
250391 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
250410 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
250475 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCCAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
250540 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
250559 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
250576 TGCAATTATA
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCCAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:250576 original size:23 final size:23
Alignment explanation
Indices: 250543--250587 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
250533 ATTATTATAT
*
250543 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
250566 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
250588 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:253900 original size:21 final size:21
Alignment explanation
Indices: 253863--253907 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
253853 GATTTCTGGG
*
253863 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
253884 CAAGGGGAA-CTGATACCCCTT
1 CAAGGGGAATC-GATACCCATT
253905 CAA
1 CAA
253908 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:255685 original size:149 final size:149
Alignment explanation
Indices: 255372--255678 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
255362 GAGTCGAGGG
* * *
255372 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
255437 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
255502 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
255521 TCTACGCGGTCCTTCGAGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
255586 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
255651 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
255670 TCTACGCGG
1 TCTACGCGG
255679 CACTTCGGTG
Statistics
Matches: 153, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:255687 original size:23 final size:23
Alignment explanation
Indices: 255654--255698 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
255644 ATTATTATAT
*
255654 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
255677 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
255699 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:257538 original size:24 final size:24
Alignment explanation
Indices: 257492--257539 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
257482 TTTAACACTG
* *
257492 GAGTTTGAATTTAAATTTCAATTT
1 GAGTTTGAATTTAAATATAAATTT
* *
257516 GAGTTTGAGTTTTAATATAAATTT
1 GAGTTTGAATTTAAATATAAATTT
257540 CGGATCGACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (24 bp):
GAGTTTGAATTTAAATATAAATTT
Found at i:259235 original size:200 final size:198
Alignment explanation
Indices: 258877--260043 Score: 1432
Period size: 200 Copynumber: 5.8 Consensus size: 198
258867 TAAAGTTTCC
* * * *
258877 CATAAAGTGTCGATACATGTTTAAAAAGTATCGATCCCAAAAACATCAAAATCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * * * *
258942 GTAATAGGTAAATTTACAATGTAACCAGTATAACTATACCAGTTTTTTGAAAAAATA-GAT-ATA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATATG-TCA-A
* *
259005 CATAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGTG
129 CATAATGTATCGACACTT-T-TAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTG
259070 GTGCACG
192 GTGCACG
* * * *
259077 CATACAGTGTCGATACATTTTTAAAAAGTATCAATCCTAAAAACATCGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * * * *
259142 GTAATAGGTAATTTTATAATATAACCGGTATAAATATACCGGTTTTGTGTGAGAATATGTCTACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATATGTCAACA
* * *
259207 TAATGTGTCGACACTTTTGAATTTTGTGTCGATACTTTTTATCCAGAATGAATGCCCAAA-ATGG
131 TAATGTATCGACACTTTT-AA-TTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACGTGG
*
259271 TGAACG
193 TGCACG
* * * * *
259277 CATAAAGTATCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTACAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * *
259342 GTAATAGGTAAATTTACAATGTAACTGGTATAACTATACCGGTTTTATGAGAGAATATGTCTACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATATGTCAACA
* * * *
259407 TAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCTAAAATGAATGCCAAAAG-GGT
131 TAATGTATCGACACTT-T-TAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGG-
259471 TGCACG
193 TGCACG
* * *
259477 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAATATCGAAACTGATCATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * * * * * *
259542 GTAATAGATAAATTTACAATGTAACCGGTACAAATTTACCAGTTTTATAAGAAAATAGGTGAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATATGTCAACA
* * *
259607 TAATGTATCGACACATTTTAGATTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAACGTTGC
131 TAATGTATCGACAC-TTTTA-ATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGGT
*
259672 GCAGG
194 GCACG
* * * **
259677 CAAAAAATGTCGATACA-TTTGAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * * *
259741 GTAATAGGTAAATTTACAATGTAACCGGAACAAATTTACCGATTTTAT-A-AGAATATAAGTGAA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAT--GTCAA
* *
259804 CATAATGTATCGACACATTTTAGATTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAACGTT
129 CATAATGTATCGACAC-TTTTA-ATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTG
*
259869 GTGCAGG
192 GTGCACG
* * * * ** * *
259876 CAAAAAGTGTTGATGCA-TTTGAAATTGTATCGATCCCAAAAACATCGAAACTGATAATTATAAC
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* *
259940 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATATGTCAACA
*
260005 TAATGTATCGACACTTTTAAATTTGTGTTGATACTTTTT
131 TAATGTATCGACACTTTT-AATTTGTGTCGATACTTTTT
260044 AAATAACGCG
Statistics
Matches: 850, Mismatches: 100, Indels: 36
0.86 0.10 0.04
Matches are distributed among these distances:
197 5 0.01
198 22 0.03
199 297 0.35
200 508 0.60
201 18 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATATGTCAACA
TAATGTATCGACACTTTTAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGGTGC
ACG
Found at i:261511 original size:19 final size:20
Alignment explanation
Indices: 261487--261535 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
261477 AATATAAGGT
261487 TAATTTTGTATAA-GATTTA
1 TAATTTTGTATAACGATTTA
**
261506 TAATTTTACA-AACGATTTA
1 TAATTTTGTATAACGATTTA
261525 TAATTTTGTAT
1 TAATTTTGTAT
261536 GTGAATGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (20 bp):
TAATTTTGTATAACGATTTA
Found at i:264476 original size:197 final size:199
Alignment explanation
Indices: 263972--264657 Score: 779
Period size: 197 Copynumber: 3.5 Consensus size: 199
263962 ATATGTGTTA
* * **
263972 ATACATTT-TCTAAAACTATCGA-CCCAAAAAACATCGAAACCAATAATTATAATGTAATAGGTA
1 ATACATTTAT-TAAAAGTATCGATCCC--AAAACATCAAAACTGATAATTATAATGTAATAGGTA
* * * * * * *
264035 AATTAACAATGTAATCGGTATAAATATATCGG-TTAATTATAAAACAGGTCAACATAATGTATCG
63 AATTTACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTCAGCATAATGTATCG
* *
264099 ACACTTGTGT-AATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACACAT
128 ACACTTGT-TAAATTTGTGTCGATA-TTTTTGTCCATAATGAATGCCCAAACGAGGTGCACACAT
*
264163 CAAGTGTCG
191 AAAGTGTCG
* * * * * ** * * *
264172 ATACATTTATTAAAAATATCAATCCCAATAAAATCGATACTTTTAAATT-TGTATATAATATGTA
1 ATACATTTATTAAAAGTATCGATCCCAA-AACATCAAAACTGAT-AATTAT-AATGTAATAGGTA
*
264236 AATTTACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTCAGCATAAAGTATCG
63 AATTTACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTCAGCATAATGTATCG
* **
264301 ACACTTGTTAAATTTATGTCGATATATTTTGTCCATAATGAATG-CCAAACG-GGTGCATGCATA
128 ACACTTGTTAAATTTGTGTCGATAT-TTTTGTCCATAATGAATGCCCAAACGAGGTGCACACATA
264364 AAGTGTCG
192 AAGTGTCG
* * *
264372 ATACATTTATTAAAAGTATCGATCCCAAAACATCAAAAC-GATCATTACAATGTGATAGGTAAAT
1 ATACATTTATTAAAAGTATCGATCCCAAAACATCAAAACTGATAATTATAATGTAATAGGTAAAT
* * * * *
264436 TTACAATGTACCCGATAGAAATATATCGGTTTTATGAGAAAATAGGTCTGAATAATGTATCGACA
66 TTACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTCAGCATAATGTATCGACA
* * *
264501 CTTTTTAAGTTTGTGTCGATACTTTT-TCCATAATGAATGCCCAAA-GAGGTGCACACATAAAGT
131 CTTGTTAAATTTGTGTCGATATTTTTGTCCATAATGAATGCCCAAACGAGGTGCACACATAAAGT
264564 GTCG
196 GTCG
* *
264568 ATACA---ATTCAAATTGTATTGATCCACAAAACATCAAAACTGATAATTATAATGTAATAGGTA
1 ATACATTTATT-AAA-AGTATCGATCC-CAAAACATCAAAACTGATAATTATAATGTAATAGGTA
*
264630 AATTTGCAATGCT-ACCGGTATAAATATA
63 AATTTACAATG-TAACCGGTATAAATATA
264658 CCGATTTACT
Statistics
Matches: 412, Mismatches: 58, Indels: 35
0.82 0.11 0.07
Matches are distributed among these distances:
193 3 0.01
194 3 0.01
195 23 0.06
196 46 0.11
197 133 0.32
198 2 0.00
199 10 0.02
200 72 0.17
201 57 0.14
202 63 0.15
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (199 bp):
ATACATTTATTAAAAGTATCGATCCCAAAACATCAAAACTGATAATTATAATGTAATAGGTAAAT
TTACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTCAGCATAATGTATCGACA
CTTGTTAAATTTGTGTCGATATTTTTGTCCATAATGAATGCCCAAACGAGGTGCACACATAAAGT
GTCG
Found at i:264729 original size:23 final size:23
Alignment explanation
Indices: 264682--264730 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
264672 AAATAGGTCA
* *
264682 ATATAAACGCTACCTATTATATT
1 ATATAAACGCTACCAAATATATT
* *
264705 ATATAAGCGCTACCAAATATGTT
1 ATATAAACGCTACCAAATATATT
264728 ATA
1 ATA
264731 ATACTTGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCAAATATATT
Found at i:264816 original size:23 final size:23
Alignment explanation
Indices: 264766--264810 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
264756 TGCCTATTTT
* *
264766 ATTATATAAGTGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
264789 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
264811 TGTTATTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:267758 original size:15 final size:15
Alignment explanation
Indices: 267738--267771 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
267728 TATTTTATTA
267738 AAAATTGTGATTAAT
1 AAAATTGTGATTAAT
267753 AAAATTGTGATTAAT
1 AAAATTGTGATTAAT
267768 AAAA
1 AAAA
267772 AGTAAAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (15 bp):
AAAATTGTGATTAAT
Found at i:269798 original size:224 final size:227
Alignment explanation
Indices: 269379--269828 Score: 604
Period size: 224 Copynumber: 2.0 Consensus size: 227
269369 CAGCTCAGTT
* * * *
269379 AAACTGATAATTCCTTATATAGGTTCAAATCGATTGAGGTGGTAATTCTTTACGGACCTAAGGTG
1 AAACCGATAATTCCTTATATAGGTTCAAATCGATCGAGCTGGTAATTCCTTACGGACCTAAGGTG
* * *
269444 ACCCTTGGGTAGGCTCTAAGGCCCCGAGAAACTTTCTTGGGTAGGCTCTCAGACCTAGGGCACTC
66 ACCATTGGGTA----CTAAGGCCCCGAGAAACTTTCTTGGGTAGGCTCTCAGACCCAAGGCACTC
* * * *
269509 CCTTAGGGTGGCTCCTTTGCTGTGTGCTTAGGGTAAGTCCTTATGGATGCAATGATGGGAAAACT
127 CCTTAGGGTGACTCATTTACTGTGTGCTTAGGGTAAGTCCTTATGAATGCAATGATGGGAAAACT
* *
269574 GCATAAAGGTGTTCGGTTGGAGGGTTTTACTCGGTC
192 GCATAAAGGTGTTCGATTAGAGGGTTTTACTCGGTC
* *
269610 AAACCGATAATTCCTTATATAGGTTTAAATCGATCGAGCTGGTAATTCCTTATGGACCTAAGGTG
1 AAACCGATAATTCCTTATATAGGTTCAAATCGATCGAGCTGGTAATTCCTTACGGACCTAAGGTG
* * * *
269675 ACCATT-GG-A-T-AGGCCTCGAGAAATTTTCTTGGGTTA-GCTCTCAGGCCCCAAGGCACTCCT
66 ACCATTGGGTACTAAGGCCCCGAGAAACTTTCTTGGG-TAGGCTCTCA-GACCCAAGGCACTCCC
* * **
269735 TTAGGGTGACTCATTTATTGTGTGCTTAGGGTAAGTCCTTATGAATGCAGTTCTGGGAAAACTGC
129 TTAGGGTGACTCATTTACTGTGTGCTTAGGGTAAGTCCTTATGAATGCAATGATGGGAAAACTGC
269800 ATAAAGGTGTTCGATTAGAGGGTTTTACT
194 ATAAAGGTGTTCGATTAGAGGGTTTTACT
269829 ATGGTTTTAA
Statistics
Matches: 194, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
223 28 0.14
224 99 0.51
229 1 0.01
230 2 0.01
231 64 0.33
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (227 bp):
AAACCGATAATTCCTTATATAGGTTCAAATCGATCGAGCTGGTAATTCCTTACGGACCTAAGGTG
ACCATTGGGTACTAAGGCCCCGAGAAACTTTCTTGGGTAGGCTCTCAGACCCAAGGCACTCCCTT
AGGGTGACTCATTTACTGTGTGCTTAGGGTAAGTCCTTATGAATGCAATGATGGGAAAACTGCAT
AAAGGTGTTCGATTAGAGGGTTTTACTCGGTC
Found at i:270896 original size:18 final size:20
Alignment explanation
Indices: 270873--270910 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
270863 TTAAAATTTA
270873 ATTTCG-ATT-AATTAACCG
1 ATTTCGAATTGAATTAACCG
270891 ATTTCGAATTGAATTAACCG
1 ATTTCGAATTGAATTAACCG
270911 TTAACCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (20 bp):
ATTTCGAATTGAATTAACCG
Found at i:279494 original size:43 final size:43
Alignment explanation
Indices: 279447--279537 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
279437 ATGGTCTCGA
* *
279447 TTAGAGAAAATGAACATAGACACAAATATATGAAGAGTCTTGG
1 TTAGAGAAAATGAACAGAGACACAAATAGATGAAGAGTCTTGG
* * * * **
279490 TTAGATAAGATGAACAGAGACAGAAGTAGATGCCGAGTCTTGG
1 TTAGAGAAAATGAACAGAGACACAAATAGATGAAGAGTCTTGG
279533 TTAGA
1 TTAGA
279538 TATAGGGTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (43 bp):
TTAGAGAAAATGAACAGAGACACAAATAGATGAAGAGTCTTGG
Found at i:282869 original size:14 final size:14
Alignment explanation
Indices: 282850--282885 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
282840 AAGTCAACAT
282850 GTTGACTCGAACGA
1 GTTGACTCGAACGA
*
282864 GTTGACTCGAATGA
1 GTTGACTCGAACGA
282878 GTTGACTC
1 GTTGACTC
282886 AGTCCAGGTT
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:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (14 bp):
GTTGACTCGAACGA
Found at i:282898 original size:15 final size:15
Alignment explanation
Indices: 282878--282931 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
282868 ACTCGAATGA
282878 GTTGACTCAGTCCAG
1 GTTGACTCAGTCCAG
*
282893 GTTGACTCAGGT-GA-
1 GTTGACTCA-GTCCAG
282907 GTTGACTCAGTCCAG
1 GTTGACTCAGTCCAG
*
282922 ATTGACTCAG
1 GTTGACTCAG
282932 GTGAGTTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.06
14 10 0.30
15 19 0.58
16 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (15 bp):
GTTGACTCAGTCCAG
Found at i:282900 original size:29 final size:29
Alignment explanation
Indices: 282875--282947 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
282865 TTGACTCGAA
282875 TGAGTTGACTCAGTCCAGGTTGACTCAGG
1 TGAGTTGACTCAGTCCAGGTTGACTCAGG
*
282904 TGAGTTGACTCAGTCCAGATTGACTCAGG
1 TGAGTTGACTCAGTCCAGGTTGACTCAGG
282933 TGAGTTGACTCAGTC
1 TGAGTTGACTCAGTC
282948 GAGTGAACTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (29 bp):
TGAGTTGACTCAGTCCAGGTTGACTCAGG
Found at i:282951 original size:14 final size:14
Alignment explanation
Indices: 282861--282960 Score: 91
Period size: 14 Copynumber: 7.0 Consensus size: 14
282851 TTGACTCGAA
*
282861 CGAGTTGACTCGAAT
1 CGAGTTGACTC-AGT
282876 -GAGTTGACTCAGT
1 CGAGTTGACTCAGT
*
282889 CCAGGTTGACTCAGGT
1 CGA-GTTGACTCA-GT
282905 -GAGTTGACTCAGT
1 CGAGTTGACTCAGT
*
282918 CCAGATTGACTCAGGT
1 CGAG-TTGACTCA-GT
282934 -GAGTTGACTCAGT
1 CGAGTTGACTCAGT
282947 CGAG-TGAACTCAGT
1 CGAGTTG-ACTCAGT
282961 TCATACCGGT
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
13 8 0.11
14 40 0.56
15 20 0.28
16 4 0.06
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (14 bp):
CGAGTTGACTCAGT
Found at i:284384 original size:114 final size:105
Alignment explanation
Indices: 284157--284384 Score: 233
Period size: 114 Copynumber: 2.1 Consensus size: 105
284147 AGGGTTTAGG
* *
284157 GATGAACACAGATGAACAAGGTTTGAATTTGGGGTGTTTGATCGAAAAACATGATAGGTTTTGGG
1 GATGAACACAGATGAACAAGGGTTGAATTTGGGGTGTTTGATCAAAAAACATGATAGGTTTTGGG
* * *
284222 TTTTTTGTAAAGATCAAAGGAGGAGTTTGGGGATGAACAC
66 TGTTTTGTAAAGATCAAAGGAGGAGTTTGGAGATGAACAA
* * * * *
284262 GAACGAACACAGATGAACAAGGGTTGATTTTTTTGGGTGTTTGATCAAAAAATAGGATATGATTT
1 G-ATGAACACAGATGAACAAGGGTTGA--ATTTGGGGTGTTTGATC--AAAA-A--ACATGA-TA
* * *
284327 GGTTTTTGGTGTTTTGTAAAGATCAAATGAGG-GTTTTTGAGATGAACATA
57 GGTTTTGGGTGTTTTGTAAAGATCAAAGGAGGAG-TTTGGAGATGAACA-A
284377 GATGAACA
1 GATGAACA
284385 AGGGTTGAAT
Statistics
Matches: 98, Mismatches: 14, Indels: 13
0.78 0.11 0.10
Matches are distributed among these distances:
105 1 0.01
106 23 0.23
108 15 0.15
110 3 0.03
111 1 0.01
113 6 0.06
114 48 0.49
115 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.32
Consensus pattern (105 bp):
GATGAACACAGATGAACAAGGGTTGAATTTGGGGTGTTTGATCAAAAAACATGATAGGTTTTGGG
TGTTTTGTAAAGATCAAAGGAGGAGTTTGGAGATGAACAA
Found at i:284853 original size:17 final size:17
Alignment explanation
Indices: 284717--284865 Score: 64
Period size: 19 Copynumber: 8.6 Consensus size: 17
284707 TATAATATTA
*
284717 ATAAACTATA-TTTAAT
1 ATAAACTATAGTTTTAT
284733 ATTAAACTATA-TAATTTAT
1 A-TAAACTATAGT--TTTAT
284752 AT--A-TATAG-TTTAT
1 ATAAACTATAGTTTTAT
*
284765 ATAAAATATAGTTTTTTAT
1 ATAAACTATAG--TTTTAT
* *
284784 ATAAATTATAG-TAT-T
1 ATAAACTATAGTTTTAT
284799 ATAAACTATA-TTTTAT
1 ATAAACTATAGTTTTAT
* * *
284815 AATATTTTATTAATAATTTTAT
1 -ATA---AACT-ATAGTTTTAT
284837 ATAAACTATAGTTTTATT
1 ATAAACTATAGTTTTA-T
284855 AATAAACTATA
1 -ATAAACTATA
284866 TAATTTACAA
Statistics
Matches: 103, Mismatches: 10, Indels: 37
0.69 0.07 0.25
Matches are distributed among these distances:
13 7 0.07
15 17 0.17
16 10 0.10
17 21 0.20
18 4 0.04
19 30 0.29
20 2 0.02
21 6 0.06
22 6 0.06
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
ATAAACTATAGTTTTAT
Found at i:284894 original size:17 final size:17
Alignment explanation
Indices: 284827--284911 Score: 56
Period size: 17 Copynumber: 5.2 Consensus size: 17
284817 TATTTTATTA
284827 ATAATTTTATATAAACT
1 ATAATTTTATATAAACT
*
284844 ATAGTTTTAT-T-AA-T
1 ATAATTTTATATAAACT
* **
284858 A-AA--CTATATAATTT
1 ATAATTTTATATAAACT
*
284872 ACAATTTTATATAAACT
1 ATAATTTTATATAAACT
284889 ATAATTTATATTAATAAACT
1 ATAATTT-TA-T-ATAAACT
284909 ATA
1 ATA
284912 TAATTTATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
11 3 0.06
12 1 0.02
13 2 0.04
14 4 0.08
15 4 0.08
16 1 0.02
17 23 0.45
18 2 0.04
19 1 0.02
20 10 0.20
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (17 bp):
ATAATTTTATATAAACT
Found at i:284914 original size:46 final size:46
Alignment explanation
Indices: 284829--284948 Score: 188
Period size: 46 Copynumber: 2.6 Consensus size: 46
284819 TTTTATTAAT
*
284829 AATTTTATATAAACTATAGTTT-TATTAATAAACTATATAATTTAC
1 AATTTTATATAAACTATAATTTATATTAATAAACTATATAATTTAC
*
284874 AATTTTATATAAACTATAATTTATATTAATAAACTATATAATTTAT
1 AATTTTATATAAACTATAATTTATATTAATAAACTATATAATTTAC
284920 AATTTTTATTAATAAACTATAATTTATAT
1 AA-TTTTA-T-ATAAACTATAATTTATAT
284949 ATTCACTATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
45 21 0.30
46 24 0.35
47 5 0.07
48 1 0.01
49 18 0.26
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (46 bp):
AATTTTATATAAACTATAATTTATATTAATAAACTATATAATTTAC
Found at i:284949 original size:29 final size:29
Alignment explanation
Indices: 284879--284947 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
284869 TTTACAATTT
**
284879 TATATAAACTATAATTTATATTAATAAAC
1 TATATAATTTATAATTTATATTAATAAAC
*
284908 TATATAATTTATAATTTTTATTAATAAAC
1 TATATAATTTATAATTTATATTAATAAAC
284937 --TATAATTTATA
1 TATATAATTTATA
284948 TATTCACTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 11 0.30
29 26 0.70
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (29 bp):
TATATAATTTATAATTTATATTAATAAAC
Found at i:289287 original size:11 final size:11
Alignment explanation
Indices: 289271--289295 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
289261 TCTAGTTGAC
289271 TCTTTAGATTT
1 TCTTTAGATTT
289282 TCTTTAGATTT
1 TCTTTAGATTT
289293 TCT
1 TCT
289296 ATCGACATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (11 bp):
TCTTTAGATTT
Found at i:292984 original size:12 final size:12
Alignment explanation
Indices: 292967--292994 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
292957 TGTTTTGAAC
292967 GGCGTGATTGGT
1 GGCGTGATTGGT
292979 GGCGTGATTGGT
1 GGCGTGATTGGT
292991 GGCG
1 GGCG
292995 ACTGAAGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.11, G:0.54, T:0.29
Consensus pattern (12 bp):
GGCGTGATTGGT
Found at i:294093 original size:18 final size:17
Alignment explanation
Indices: 294051--294093 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
294041 CAAATAAGGG
*
294051 TTTAAAATTTCTAGGGT
1 TTTAAAATTTCTAGCGT
294068 TTTCAAAATTTCTAGCGT
1 TTT-AAAATTTCTAGCGT
294086 TTGTAAAA
1 TT-TAAAA
294094 AAAACGCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 19 0.83
19 1 0.04
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (17 bp):
TTTAAAATTTCTAGCGT
Found at i:294299 original size:83 final size:82
Alignment explanation
Indices: 294184--294401 Score: 213
Period size: 83 Copynumber: 2.6 Consensus size: 82
294174 AAGCGCCACT
* *
294184 AAAGTACTACTCTATTCCGTCATTTTTCTGAAAAACGCCACAATAGATGAAACCTATGGAGGCAT
1 AAAGTACTACTCTATTCGGTCATTTGT-TGAAAAACGCCACAATAGATGAAACCTATGGAGGCAT
294249 TTGTATAAAAACACCGCA
65 TTGTATAAAAACACCGCA
** * * * * * * * *
294267 AAAGTACTACTCTATTGCGGTTGTTTGTTGAAAAATGCCACCATAAATGAATCTTATTGTGGCGT
1 AAAGTACTACTCTATT-CGGTCATTTGTTGAAAAACGCCACAATAGATGAAACCTATGGAGGCAT
* *
294332 TTGTATAAAAACGCCGCT
65 TTGTATAAAAACACCGCA
* * * *
294350 CAAGTATTACTTTATTACGG-CATTTGTTGAAAAAAAACGCCACTATAGATGA
1 AAAGTACTACTCTATT-CGGTCATTTGTTG---AAAAACGCCACAATAGATGA
294402 CCCTATTGCA
Statistics
Matches: 108, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
82 7 0.06
83 77 0.71
84 7 0.06
85 17 0.16
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (82 bp):
AAAGTACTACTCTATTCGGTCATTTGTTGAAAAACGCCACAATAGATGAAACCTATGGAGGCATT
TGTATAAAAACACCGCA
Found at i:294590 original size:2 final size:2
Alignment explanation
Indices: 294580--294721 Score: 57
Period size: 2 Copynumber: 72.0 Consensus size: 2
294570 ATATAGATTT
* * *
294580 TA TA GTA TA TA TA TA TA TA TA TA TA TA AA TA GTT TA TA TA -A TT
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * *
294623 TA TG T- TG GA TA TA -A TA TA TA GTT TA TA TA TA GTA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* * * *
294665 TA -A TT TA TA TA -A GTA AA T- TA CA TA GTT TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
294705 TA TA TA -A TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
294722 GTTCTGAACT
Statistics
Matches: 102, Mismatches: 24, Indels: 28
0.66 0.16 0.18
Matches are distributed among these distances:
1 8 0.08
2 86 0.84
3 8 0.08
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:294661 original size:20 final size:19
Alignment explanation
Indices: 294547--295282 Score: 205
Period size: 20 Copynumber: 38.3 Consensus size: 19
294537 ATAATATTAG
*
294547 TATATAGTTTATATAGATAAA
1 TATATAGTTTATAT--ATATA
294568 CTATATAGATTT-TATAGTATA
1 -TATATAG-TTTATATA-TATA
294589 TATATA---TATATATATA
1 TATATAGTTTATATATATA
*
294605 TAAATAGTTTATATA-AT-
1 TATATAGTTTATATATATA
**
294622 T-TAT-G-TTGGATATA-A
1 TATATAGTTTATATATATA
294637 TATATAGTTTATATATAGTATA
1 TATATAG-TT-TATATA-TATA
* *
294659 TATAAATAATTTATATAAGTAAA
1 TAT--ATAGTTTATAT-A-TATA
*
294682 TTACATAGTTTATATATATAATA
1 -TATATAG-TT-TATATAT-ATA
* *
294705 TATATAATTTATATATAGTTC
1 TATATAGTTTATATATA--TA
* *
294726 TGAACTATATTTTATATGATTTA
1 T--A-TATAGTTTATAT-ATATA
* *
294749 AATATAGTTCAT-TA-ATTAA
1 TATATAGTTTATATATA-T-A
294768 TTATATAGTTTATATATATA
1 -TATATAGTTTATATATATA
294788 TATATA-TATATATATATATA
1 TATATAGT-T-TATATATATA
*
294808 TATATA-TATATATATATA
1 TATATAGTTTATATATATA
294826 TATATAGTTTATATATATA
1 TATATAGTTTATATATATA
* * *
294845 TATATA---CAAATA-ATT
1 TATATAGTTTATATATATA
* *
294860 TACATAG-TTATATTATTAAA
1 TATATAGTTTATA-TA-TATA
294880 CTATATAGTTTATATATAGTA
1 -TATATAGTTTATATATA-TA
*
294901 TATATA--CTATATAGT-TCA
1 TATATAGTTTATATA-TAT-A
294919 TATATAGTTTATATTATTAATAAA
1 TATATAGTTTATA-TA-T-AT--A
* *
294943 CTATATAGTTTATGTATAAA
1 -TATATAGTTTATATATATA
294963 T-TATAGTTTATATAGT-TCA
1 TATATAGTTTATATA-TAT-A
** * *
294982 TATATACATTATAGAGTTTA
1 TATATAGTTTATATA-TATA
295002 TATATAG--TATATA-A-A
1 TATATAGTTTATATATATA
* * * * *
295017 TATAAACTATATAGTGTCTA
1 TATATAGTTTATA-TATATA
* *
295037 TATATAGTATATATACTTTA
1 TATATAGTTTATATA-TATA
*
295057 TATATAGTTTATATAAAT-
1 TATATAGTTTATATATATA
* *
295075 TATATAATTT-TACATAATA
1 TATATAGTTTATATAT-ATA
* *
295094 TATATAATTT-TACATAATA
1 TATATAGTTTATATAT-ATA
* * *
295113 TATATAATTCATATACAATTTA
1 TATATAGTT--TATA-TATATA
* * *
295135 TATATAATATATAAATATAAA
1 TATATAGT-T-TATATATATA
* *
295156 TTACATAGTTTATGTAT-TA
1 -TATATAGTTTATATATATA
*
295175 TATAGA-TTT-TATA-ATA
1 TATATAGTTTATATATATA
* *
295191 TATATAGTTTACATA-CTA
1 TATATAGTTTATATATATA
*
295209 TATAT--TTTAGATATAGTA
1 TATATAGTTTATATATA-TA
295227 TATA-A----ATATA-A-A
1 TATATAGTTTATATATATA
295239 CTATATAGTTTATATATATA
1 -TATATAGTTTATATATATA
*
295259 TATATA-TATATATATATA
1 TATATAGTTTATATATATA
295277 TATATA
1 TATATA
295283 TATATAATTT
Statistics
Matches: 544, Mismatches: 85, Indels: 174
0.68 0.11 0.22
Matches are distributed among these distances:
12 1 0.00
13 4 0.01
14 7 0.01
15 20 0.04
16 36 0.07
17 22 0.04
18 107 0.20
19 77 0.14
20 122 0.22
21 31 0.06
22 57 0.10
23 22 0.04
24 24 0.04
25 14 0.03
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (19 bp):
TATATAGTTTATATATATA
Found at i:294720 original size:22 final size:22
Alignment explanation
Indices: 294547--294850 Score: 133
Period size: 22 Copynumber: 13.2 Consensus size: 22
294537 ATAATATTAG
* *
294547 TATATAGTTTATATAGATAA-A
1 TATATAATTTATATATATAATA
294568 CTATATAGATTT-TATAGTAT-ATA
1 -TATATA-ATTTATATA-TATAATA
* * * *
294591 TATATATATATATATAAATAGTT
1 TATATA-ATTTATATATATAATA
*
294614 TATATAATTTATGT-TGGAT-ATAA
1 TATATAATTTATATAT--ATAAT-A
*
294637 TATATAGTTTATATATAGTATATA
1 TATATAATTTATATATA-TA-ATA
*
294661 TAAATAATTTATATA-AGTAA-A
1 TATATAATTTATATATA-TAATA
* *
294682 TTACATAGTTTATATATATAATA
1 -TATATAATTTATATATATAATA
**
294705 TATATAATTTATATATAGTTCTGA
1 TATATAATTTATATATA-TAAT-A
* *
294729 -ACTATATTTTATATGATTTAAATA
1 TA-TATAATTTATAT-ATAT-AATA
* * *
294753 TAGTTCATTAATTAAT-TATATAGTT
1 TA--T-A-TAATTTATATATATAATA
*
294778 TATATATATATATATATATATATA
1 TATATA-ATTTATATATATA-ATA
*
294802 TATATATATATATATATATATATA
1 TATATA-ATTTATATATATA-ATA
*
294826 TATATAGTTTATATATAT-ATA
1 TATATAATTTATATATATAATA
294847 TATA
1 TATA
294851 CAAATAATTT
Statistics
Matches: 217, Mismatches: 38, Indels: 55
0.70 0.12 0.18
Matches are distributed among these distances:
21 10 0.05
22 67 0.31
23 58 0.27
24 60 0.28
25 10 0.05
26 4 0.02
27 2 0.01
28 6 0.03
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (22 bp):
TATATAATTTATATATATAATA
Found at i:294783 original size:2 final size:2
Alignment explanation
Indices: 294778--295288 Score: 194
Period size: 2 Copynumber: 255.0 Consensus size: 2
294768 TTATATAGTT
294778 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
294820 TA TA TA TA TA TA GTT TA TA TA TA TA TA TA TA CA AA TA -A TT TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
294862 CA TA GT- TA TA T- TA T- TA AA CTA TA TA GTT TA TA TA TA GTA TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA
* *
294903 TA TA CTA TA TA GT- TCA TA TA TA GTT TA TA T- TA T- TA -A TA AA
1 TA TA -TA TA TA -TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
294943 CTA TA TA GTT TA TG TA TA AA T- TA TA GTT TA TA TA GT- TCA TA TA
1 -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA T-A TA TA
* * * * *
294986 TA CA T- TA TA GA GTT TA TA TA TA GTA TA TA AA TA TA AA CTA TA
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * *
295028 TA GTG TC TA TA TA TA GTA TA TA TA CTT TA TA TA TA GTT TA TA TA
1 TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA TA
* * * * *
295072 AA T- TA TA TA -A T- TT TA CA TA -A TA TA TA TA -A T- TT TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
295108 TA -A TA TA TA TA -A T- TCA TA TA CA -A TT TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
295146 TA AA TA TA AA T- TA CA TA GTT TA TG TA T- TA TA TA GA T- TT TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
295186 TA -A TA TA TA TA GTT TA CA TA CTA TA TA T- TT TA GA TA TA GTA
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * *
295227 TA TA AA TA TA AA CTA TA TA GTT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
295271 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
295289 ATTTTTTTAA
Statistics
Matches: 375, Mismatches: 79, Indels: 110
0.66 0.14 0.20
Matches are distributed among these distances:
1 27 0.07
2 315 0.84
3 33 0.09
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:294785 original size:11 final size:11
Alignment explanation
Indices: 294636--295071 Score: 112
Period size: 11 Copynumber: 40.5 Consensus size: 11
294626 GTTGGATATA
294636 ATATATAGTTT
1 ATATATAGTTT
294647 ATATATAGTATAT
1 ATATATAGT-T-T
* *
294660 ATAAATAATTT
1 ATATATAGTTT
**
294671 ATATA-AGTAA
1 ATATATAGTTT
*
294681 ATTACATAGTTT
1 A-TATATAGTTT
*
294693 ATATATA-TAAT
1 ATATATAGT-TT
*
294704 ATATATAATTT
1 ATATATAGTTT
294715 ATATATAGTTCT
1 ATATATAGTT-T
294727 GA-ACTATA-TTT
1 -ATA-TATAGTTT
294738 -TATAT-GATTT
1 ATATATAG-TTT
* *
294748 AAATATAGTTC
1 ATATATAGTTT
*
294759 AT-TA-A-TTA
1 ATATATAGTTT
294767 ATTATATAGTTT
1 A-TATATAGTTT
294779 ATATATA---T
1 ATATATAGTTT
294787 ATATATA---T
1 ATATATAGTTT
*
294795 ATATATA-TAT
1 ATATATAGTTT
*
294805 ATATATA-TAT
1 ATATATAGTTT
*
294815 ATATATA-TAT
1 ATATATAGTTT
294825 ATATATAGTTT
1 ATATATAGTTT
*
294836 ATATATA-TAT
1 ATATATAGTTT
* *
294846 ATATACAAATAATT
1 ATATA-TAGT--TT
*
294860 -TACATAG-TT
1 ATATATAGTTT
*
294869 ATAT-TA-TTAA
1 ATATATAGTT-T
294879 ACTATATAGTTT
1 A-TATATAGTTT
294891 ATATATAGTATATAT
1 ATATATAG--T-T-T
*
294906 ACTATATAGTTC
1 A-TATATAGTTT
294918 ATATATAGTTT
1 ATATATAGTTT
* **
294929 ATATTATTAATAA
1 ATA-TA-TAGTTT
294942 ACTATATAGTTT
1 A-TATATAGTTT
* *
294954 ATGTATA---A
1 ATATATAGTTT
294962 AT-TATAG-TT
1 ATATATAGTTT
*
294971 -TATATAGTTC
1 ATATATAGTTT
**
294981 ATATATA-CAT
1 ATATATAGTTT
*
294991 -TATAGAGTTT
1 ATATATAGTTT
*
295001 ATATATAGTAT
1 ATATATAGTTT
* **
295012 ATAAATA-TAA
1 ATATATAGTTT
295022 ACTATATAGTGTCT
1 A-TATATAGT-T-T
295036 ATATATAG--T
1 ATATATAGTTT
*
295045 ATATATACTTT
1 ATATATAGTTT
295056 ATATATAGTTT
1 ATATATAGTTT
295067 ATATA
1 ATATA
295072 AATTATATAA
Statistics
Matches: 318, Mismatches: 55, Indels: 104
0.67 0.12 0.22
Matches are distributed among these distances:
7 4 0.01
8 22 0.07
9 28 0.09
10 55 0.17
11 133 0.42
12 28 0.09
13 33 0.10
14 6 0.02
15 2 0.01
16 7 0.02
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (11 bp):
ATATATAGTTT
Found at i:294943 original size:63 final size:61
Alignment explanation
Indices: 294759--294987 Score: 214
Period size: 57 Copynumber: 3.9 Consensus size: 61
294749 AATATAGTTC
* * *
294759 ATTAATTAATTATATAGTTTATATATATATATATA-TATATA--TATATATA-TATATA-T
1 ATTAATAAACTATATAGTTTATATATATATATATACTATATAGTTATATATAGTTTATATT
* * * *
294815 ATATATATATA-TATATAGTTTATATATATATATATAC-AAATAATT-TACATAG-TTATATT
1 AT-TA-ATAAACTATATAGTTTATATATATATATATACTATATAGTTATATATAGTTTATATT
294874 A-T--TAAACTATATAGTTTATATATAGTATATATACTATATAGTTCATATATAGTTTATATT
1 ATTAATAAACTATATAGTTTATATATA-TATATATACTATATAGTT-ATATATAGTTTATATT
* * *
294934 ATTAATAAACTATATAGTTTATGTATAAAT-TATAGTTTATATAGTTCATATATA
1 ATTAATAAACTATATAGTTTATATATATATATATA--CTATATAGTT-ATATATA
294988 CATTATAGAG
Statistics
Matches: 143, Mismatches: 12, Indels: 29
0.78 0.07 0.16
Matches are distributed among these distances:
54 3 0.02
55 17 0.12
56 11 0.08
57 38 0.27
58 12 0.08
59 9 0.06
60 8 0.06
61 5 0.03
62 2 0.01
63 38 0.27
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (61 bp):
ATTAATAAACTATATAGTTTATATATATATATATACTATATAGTTATATATAGTTTATATT
Found at i:294994 original size:63 final size:63
Alignment explanation
Indices: 294870--294994 Score: 164
Period size: 63 Copynumber: 2.0 Consensus size: 63
294860 TACATAGTTA
* * **
294870 TATTATTAAACTATATAGTTTATATATAGTATATATACTATATAGTTCATATATAGTTTATAT
1 TATTAATAAACTATATAGTTTATATATAATATATATACTATATAGTTCATATATACATTATAT
* *
294933 TATTAATAAACTATATAGTTTATGTATAA-AT-TATAGTTTATATAGTTCATATATACATTATA
1 TATTAATAAACTATATAGTTTATATATAATATATATA--CTATATAGTTCATATATACATTATA
294995 GAGTTTATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
61 4 0.07
62 2 0.04
63 48 0.89
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (63 bp):
TATTAATAAACTATATAGTTTATATATAATATATATACTATATAGTTCATATATACATTATAT
Found at i:295077 original size:9 final size:10
Alignment explanation
Indices: 295035--295147 Score: 76
Period size: 9 Copynumber: 11.6 Consensus size: 10
295025 ATATAGTGTC
*
295035 TATATAT-AG
1 TATATATAAT
*
295044 TATATATACTT
1 TATATATA-AT
*
295055 TATATATAGT
1 TATATATAAT
*
295065 T-TATATAAA
1 TATATATAAT
295074 T-TATATAAT
1 TATATATAAT
* *
295083 TTTACATAA-
1 TATATATAAT
295092 TATATATAAT
1 TATATATAAT
* *
295102 TTTACATAA-
1 TATATATAAT
295111 TATATATAAT
1 TATATATAAT
*
295121 TCATATACAATT
1 T-ATATATAA-T
295133 TATATATAA-
1 TATATATAAT
295142 TATATA
1 TATATA
295148 AATATAAATT
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
9 42 0.51
10 16 0.20
11 22 0.27
12 2 0.02
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (10 bp):
TATATATAAT
Found at i:296323 original size:4 final size:4
Alignment explanation
Indices: 296314--296786 Score: 946
Period size: 4 Copynumber: 118.2 Consensus size: 4
296304 TATTACATAC
296314 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
296362 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
296410 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
296458 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
296506 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
296554 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
296602 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
296650 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
296698 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
296746 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
296787 ATTAATATAC
Statistics
Matches: 469, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 469 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:298568 original size:55 final size:55
Alignment explanation
Indices: 298485--298659 Score: 224
Period size: 55 Copynumber: 3.2 Consensus size: 55
298475 TATAGTCTCA
* * *
298485 GTTAGAGAAGATGAACAGAGACACAAGTAGATGAAGAGTCTCGGTTAGATATAGG
1 GTTAGAGAACATGAACAGAGACAAAAGTAGATGAAGAGTCTTGGTTAGATATAGG
* *
298540 GTTAGAGAATATGAACAGAGACAAAAGTAGATGAAGAGTCTTAGTTAGATATAGG
1 GTTAGAGAACATGAACAGAGACAAAAGTAGATGAAGAGTCTTGGTTAGATATAGG
* * * * ** * *
298595 GTTAGAGAACATGAACAAAGATATAAGAAGAAAAAGAGTCTTGGTTAGGGTTTAGG
1 GTTAGAGAACATGAACAGAGACAAAAGTAGATGAAGAGTCTTGGTTA-GATATAGG
298651 GTTAGAGAA
1 GTTAGAGAA
298660 GATAAATAGG
Statistics
Matches: 105, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
55 90 0.86
56 15 0.14
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.22
Consensus pattern (55 bp):
GTTAGAGAACATGAACAGAGACAAAAGTAGATGAAGAGTCTTGGTTAGATATAGG
Found at i:298690 original size:47 final size:47
Alignment explanation
Indices: 298639--298754 Score: 153
Period size: 47 Copynumber: 2.5 Consensus size: 47
298629 AGAGTCTTGG
*
298639 TTAGGGTTTAGGGTTAGAGAAGATAAATAGGAGAAGAAGAGGCTCAA
1 TTAGGGTTTAGGGTTAGAGAAGATAAATAGAAGAAGAAGAGGCTCAA
* * * ***
298686 TTAGGGTTTAGGATTAGAGAAAATGAATAGAAGAAGAAGAGGCTTGG
1 TTAGGGTTTAGGGTTAGAGAAGATAAATAGAAGAAGAAGAGGCTCAA
*
298733 TTA-GATTTAGGGTTAGAGAAGA
1 TTAGGGTTTAGGGTTAGAGAAGA
298755 AGAAGTTAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
46 16 0.27
47 43 0.73
ACGTcount: A:0.40, C:0.03, G:0.34, T:0.24
Consensus pattern (47 bp):
TTAGGGTTTAGGGTTAGAGAAGATAAATAGAAGAAGAAGAGGCTCAA
Found at i:299102 original size:113 final size:114
Alignment explanation
Indices: 298968--299173 Score: 256
Period size: 113 Copynumber: 1.8 Consensus size: 114
298958 AAGGATTGAA
* *
298968 TTTGGAGTGTTTGACCGAAAAAAACATGAT-AGGTTTTGGGTTTAGATG-TTTGTAAAGATCAAA
1 TTTGGAGTGTTTGACCG-AAAAAACAGGATAAGG-TATGGGTTTAGATGTTTTGTAAAGATCAAA
299031 GGAGGGTTTGGGGATGAACACCAATGAACATGCATGTATAAGGTTGAATTT
64 GGAGGGTTTGGGGATGAACACCAATGAACATGCATGTATAAGGTTGAATTT
* ** * * * *
299082 TTTGG-GTGTTTGATCGAAAAATTAGGATAAGGTATGGTTTTCGGTGTTTTGTAAAGATCAAATG
1 TTTGGAGTGTTTGACCGAAAAAACAGGATAAGGTATGGGTTTAGATGTTTTGTAAAGATCAAAGG
** **
299146 AGGGTTTTTGGATGAACACGGATGAACA
66 AGGGTTTGGGGATGAACACCAATGAACA
299174 AGATTTGAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
112 19 0.25
113 53 0.69
114 5 0.06
ACGTcount: A:0.31, C:0.07, G:0.29, T:0.33
Consensus pattern (114 bp):
TTTGGAGTGTTTGACCGAAAAAACAGGATAAGGTATGGGTTTAGATGTTTTGTAAAGATCAAAGG
AGGGTTTGGGGATGAACACCAATGAACATGCATGTATAAGGTTGAATTT
Found at i:299598 original size:42 final size:42
Alignment explanation
Indices: 299551--299726 Score: 141
Period size: 42 Copynumber: 4.1 Consensus size: 42
299541 TAATAAACTA
* *
299551 TATAATTTATAATATTA-T-ATATAGTTTATATAAATTATAGTT
1 TATAATTT-TAATATAACTAATA-AGTTTATATAAACTATAGTT
*
299593 TATAATTTTAATATAACTAATAATTTTATATAAACTATAGTT
1 TATAATTTTAATATAACTAATAAGTTTATATAAACTATAGTT
*
299635 TAT-ATTAATATATATATAAAC-AAT-AGTTTATATTAATAAAATATAGTT
1 TATAATT--T-TA-ATAT-AACTAATAAG-TT-TA-T-ATAAACTATAGTT
* *
299683 TATAATTTT-ATATAATTAATAA-TTCTATATAAACTATTGTT
1 TATAATTTTAATATAACTAATAAGTT-TATATAAACTATAGTT
299724 TAT
1 TAT
299727 GTTAATAAAC
Statistics
Matches: 111, Mismatches: 9, Indels: 29
0.74 0.06 0.19
Matches are distributed among these distances:
41 24 0.22
42 31 0.28
43 10 0.09
44 10 0.09
45 10 0.09
46 6 0.05
47 2 0.02
48 15 0.14
49 3 0.03
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (42 bp):
TATAATTTTAATATAACTAATAAGTTTATATAAACTATAGTT
Found at i:299638 original size:16 final size:16
Alignment explanation
Indices: 299617--299667 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
299607 AACTAATAAT
299617 TTTATATAAACTATAG
1 TTTATATAAACTATAG
*
299633 TTTATATTAA-TATA-
1 TTTATATAAACTATAG
*
299647 --TATATAAACAATAG
1 TTTATATAAACTATAG
299661 TTTATAT
1 TTTATAT
299668 TAATAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
15 4 0.14
16 14 0.50
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
TTTATATAAACTATAG
Found at i:299650 original size:28 final size:28
Alignment explanation
Indices: 299619--299672 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
299609 CTAATAATTT
*
299619 TATATAAACTATAGTTTATATTAATATA
1 TATATAAACAATAGTTTATATTAATATA
299647 TATATAAACAATAGTTTATATTAATA
1 TATATAAACAATAGTTTATATTAATA
299673 AAATATAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (28 bp):
TATATAAACAATAGTTTATATTAATATA
Found at i:299760 original size:23 final size:22
Alignment explanation
Indices: 299711--299791 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 22
299701 ATAATTCTAT
* *
299711 ATAAACTATTG-TT-TATGTTA
1 ATAAACTATAGTTTATATATTA
299731 ATAAACTATAGTTTATATATTA
1 ATAAACTATAGTTTATATATTA
* *
299753 TGTAAACTATA---T-GATATTA
1 -ATAAACTATAGTTTATATATTA
299772 ATAAACTATAGTTTATATAT
1 ATAAACTATAGTTTATATAT
299792 ATATATACTT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
18 9 0.19
19 6 0.12
20 11 0.23
21 3 0.06
22 10 0.21
23 9 0.19
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (22 bp):
ATAAACTATAGTTTATATATTA
Found at i:299776 original size:61 final size:61
Alignment explanation
Indices: 299647--299789 Score: 166
Period size: 61 Copynumber: 2.3 Consensus size: 61
299637 TATTAATATA
* * *
299647 TATATAAACAATAGTTTATATTAATAAAATATAGTTTATAATTTTATATAATTAATAATTC
1 TATATAAACTATAGTTTATATTAATAAAATATAGTTTATAATTATATATAACTAATAATTC
* * * * *
299708 TATATAAACTATTGTTTATGTTAATAAACTATAGTTTATATATTATGTA-AACTATATGATAT-
1 TATATAAACTATAGTTTATATTAATAAAATATAGTTTATA-ATTATATATAACTA-ATAAT-TC
299770 TA-ATAAACTATAGTTTATAT
1 TATATAAACTATAGTTTATAT
299790 ATATATATAC
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
61 56 0.81
62 12 0.17
63 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (61 bp):
TATATAAACTATAGTTTATATTAATAAAATATAGTTTATAATTATATATAACTAATAATTC
Found at i:301386 original size:158 final size:158
Alignment explanation
Indices: 301182--301490 Score: 440
Period size: 158 Copynumber: 2.0 Consensus size: 158
301172 GGGGGAGAAT
* *
301182 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATATGGAGATTTAAACGTTTTTCAAAACATGT
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAGATTTAAACGTTTTTCAAAACATGC
* * * * *
301247 CTCATTTTCATTAAATATTTTATTACGGGGGAGTTTTGCCAAATATAGA-TTTTTCAAATGTTTT
66 CTCATTTTCATTAAATATTTTATTAAGGGAGAGCTTTGCCAAAAACA-ATTTTTTCAAATGTTTT
* *
301311 GTTATATGATAAAGGGAGAGATAAATAAG
130 GTTATATCAAAAAGGGAGAGATAAATAAG
* * * * * * * *
301340 TATGGTTTGCAAAATTTAATTTTTCAATGAACAATGGGGAGCTTTAAATGTTTTTCAAAATATGC
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAGATTTAAACGTTTTTCAAAACATGC
*
301405 CTCCTTTTCATTAAATATTTTATTAAGGGAGAGCTTTGCCAAAAACAATTTTTTCAAATGTTTTG
66 CTCATTTTCATTAAATATTTTATTAAGGGAGAGCTTTGCCAAAAACAATTTTTTCAAATGTTTTG
301470 TTATATCAAAAAGGGAGAGAT
131 TTATATCAAAAAGGGAGAGAT
301491 TGTTGAACCA
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
157 1 0.01
158 131 0.99
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (158 bp):
TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAGATTTAAACGTTTTTCAAAACATGC
CTCATTTTCATTAAATATTTTATTAAGGGAGAGCTTTGCCAAAAACAATTTTTTCAAATGTTTTG
TTATATCAAAAAGGGAGAGATAAATAAG
Found at i:303993 original size:158 final size:158
Alignment explanation
Indices: 303813--304121 Score: 476
Period size: 158 Copynumber: 2.0 Consensus size: 158
303803 GGGGGAGAAT
* * *
303813 TATGGTTTGAAAAATTCAATTTCTTAATGAAAAATATGGAAATTTAAATGTTTTTCAAAATATAC
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATAC
* * *
303878 CTAATTTTCATTAAATGTTTTATTAAGGGGGAGTTTTGCCAAAAGCATA-TTTTTCAAATGTTTT
66 CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAA-AATATTTTTTCAAATGTTTT
*
303942 GTTATATGAAAAAGGGGGAGATAAATAAG
130 GTTATATCAAAAAGGGGGAGATAAATAAG
* * * **
303971 TATGGTTTGAAAAATTTAATTTCTCAATGAAAAATGGGGAACTTTAAATGTTTTCCAAAATATGT
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATAC
*
304036 CTCATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
66 CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
*
304101 TTATATCAAAAGGGGGGAGAT
131 TTATATCAAAAAGGGGGAGAT
304122 TGTTTAACCA
Statistics
Matches: 136, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
157 3 0.02
158 133 0.98
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (158 bp):
TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATAC
CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
TTATATCAAAAAGGGGGAGATAAATAAG
Found at i:305928 original size:3 final size:3
Alignment explanation
Indices: 305920--305945 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
305910 TGAAGAGGTC
305920 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
305946 AGAGATGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:306603 original size:158 final size:156
Alignment explanation
Indices: 306423--306729 Score: 472
Period size: 158 Copynumber: 2.0 Consensus size: 156
306413 GGGGGAGAAT
* * *
306423 TATGGTTTGAAAAATTCAATTTCTTAATGAAAAATATGGAAATTTAAATGTTTTTCAAAATATGC
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATGC
* * *
306488 CTAATTTTCATTAAATGTTTTATTAAGGGGGAGTTTTGCCAAAAGCATA-TTTTTCAAATGTTTT
66 CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAA-AATATTTTTTCAAATGTTTT
306552 GTTATATGAAAAAGGGGGAGATAAATAAG
130 GTTATAT-AAAAA-GGGGAGATAAATAAG
* * * *
306581 TATGGTTTGAAAAATTTAATTTCTCAATGAAAAATGGGGAACTTTAAATGTTTTCCAAAATATGT
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATGC
*
306646 CTCATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
66 CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
*
306711 TTATATCAAAAGGGGAGAT
131 TTATATAAAAAGGGGAGAT
306730 TGTTTAACCA
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
156 8 0.06
157 7 0.05
158 121 0.89
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (156 bp):
TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATGC
CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
TTATATAAAAAGGGGAGATAAATAAG
Found at i:308537 original size:3 final size:3
Alignment explanation
Indices: 308529--308554 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
308519 TGAAGAGGTC
308529 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
308555 AGAGATGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:309212 original size:158 final size:158
Alignment explanation
Indices: 309032--309340 Score: 467
Period size: 158 Copynumber: 2.0 Consensus size: 158
309022 GGGGGAGAAT
* * *
309032 TATGGTTTGAAAAATTCAATTTCTTAATGAAAAATATGGAAATTTAAATGTTTTTCAAAATATGC
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATGC
* * *
309097 CTAATTTTCATTAAATGTTTTATTAAGGGGGAGTTTTGCCAAAAGCATA-TTTTTCAAATGTTTT
66 CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAA-AATATTTTTTCAAATGTTTT
*
309161 GTTATATGAAAAAGGGGGAGATAAATAAG
130 GTTATATCAAAAAGGGGGAGATAAATAAG
* * ** *
309190 TATGGTTTGAAAAATTTAATTTCTCAATGAAAAATGGGGAGCTTTAAATGTTTTCCAAAATATGT
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATGC
* *
309255 CTCATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATTTTTTG
66 CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
*
309320 TTATATCAAAAGGGGGGAGAT
131 TTATATCAAAAAGGGGGAGAT
309341 TGTTGAATCA
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
157 3 0.02
158 132 0.98
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (158 bp):
TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATGC
CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
TTATATCAAAAAGGGGGAGATAAATAAG
Found at i:311804 original size:158 final size:158
Alignment explanation
Indices: 311617--311925 Score: 458
Period size: 158 Copynumber: 2.0 Consensus size: 158
311607 GGGGGAGAAT
* * *
311617 TATGGTTTGAAAAATTCAATTTCTTAATGAAAAATATGGAAATTTAAATGTTTTTCAAAATATGC
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATGC
* * *
311682 CTAATTTTCATTAAATGTTTTATTAAGGGGGAGTTTTGCCAAAAGCATA-TTTTTCAAATGTTTT
66 CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAA-AATATTTTTTCAAATGTTTT
*
311746 GTTATATGAAAAAGGGGGAGATAAATAAG
130 GTTATATCAAAAAGGGGGAGATAAATAAG
* * * ** *
311775 TATGGTTTGAAAATTTTAATTTCTCAATGAAAAATGGGGAGCTTTAAATGTTTTCCAAAATATGT
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATGC
**
311840 CTCCTTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
66 CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
*
311905 TTATATCAAAAGGGGGGAGAT
131 TTATATCAAAAAGGGGGAGAT
311926 TATTGAACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
157 3 0.02
158 131 0.98
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.39
Consensus pattern (158 bp):
TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATAGGGAAATTTAAATGTTTTCCAAAATATGC
CTAATTTTCATTAAATGTTTTATTAAGGGAGAGTTTAGCCAAAAAATATTTTTTCAAATGTTTTG
TTATATCAAAAAGGGGGAGATAAATAAG
Found at i:322439 original size:17 final size:19
Alignment explanation
Indices: 322409--322446 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
322399 TCCAAAGTTT
322409 AACAATCCACAAATA-TCA
1 AACAATCCACAAATATTCA
*
322427 AACATTCCA-AAATATTCA
1 AACAATCCACAAATATTCA
322445 AA
1 AA
322447 ATGTTGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (19 bp):
AACAATCCACAAATATTCA
Found at i:324361 original size:20 final size:20
Alignment explanation
Indices: 324332--324391 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
324322 AAATCCAAAA
324332 CCCC-AGGGGGGTATCGATT
1 CCCCTAGGGGGGTATCGATT
* *
324351 CCCCTAGGGGGGAATCGGTT
1 CCCCTAGGGGGGTATCGATT
*
324371 -CCCTCATGGGGGTATCGATT
1 CCCCT-AGGGGGGTATCGATT
324391 C
1 C
324392 TCTCTACACC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 8 0.24
20 25 0.76
ACGTcount: A:0.15, C:0.27, G:0.35, T:0.23
Consensus pattern (20 bp):
CCCCTAGGGGGGTATCGATT
Found at i:330829 original size:26 final size:26
Alignment explanation
Indices: 330800--330849 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
330790 TTTCAAAAAT
330800 TGGTATTGCATAAAGTATATAAGACC
1 TGGTATTGCATAAAGTATATAAGACC
330826 TGGTATTGCATAAAGTATATAAGA
1 TGGTATTGCATAAAGTATATAAGA
330850 GTTGGATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (26 bp):
TGGTATTGCATAAAGTATATAAGACC
Found at i:331258 original size:154 final size:155
Alignment explanation
Indices: 331080--331381 Score: 441
Period size: 154 Copynumber: 2.0 Consensus size: 155
331070 GGGGGAGAAT
* * *
331080 TATGGTTTGAAAAATTCTATTTCTCAATGAAAAATGTGGAGCTTCAAATGTTTTTCAAAATATGT
1 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATGGGGAGCTTCAAATGCTTTTCAAAATATGT
** * *
331145 CTCATTTTCATAAAATGTTTTATTAAGGGGGT-TTTGCC-AAAACAGATTTTTTAAATGTTTTGT
66 CTCATTTTCATAAAATGTTTTATTAAGGAAGTGTTTACCAAAAACA-A-TTTTCAAATGTTTTGT
*
331208 TATATGAAAAA-GGGGAGATAAATAAG
129 TATATCAAAAAGGGGGAGATAAATAAG
*
331234 TATGGTTTGAAAAAATT-AATTTCTCAATGAAAAATGGGGAGCTTTAAATGCTTTTCAAAATATG
1 TATGGTTTG-AAAAATTCAATTTCTCAATGAAAAATGGGGAGCTTCAAATGCTTTTCAAAATATG
* * *
331298 TTTCCTTTTCATTAAATGTTTTATTAAGGAAGTGTTTACCAAAAACAATTTTCAAATGTTTTGTT
65 TCTCATTTTCATAAAATGTTTTATTAAGGAAGTGTTTACCAAAAACAATTTTCAAATGTTTTGTT
331363 ATATCAAAAAGGGGGAGAT
130 ATATCAAAAAGGGGGAGAT
331382 TGTTGAACCA
Statistics
Matches: 132, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
154 105 0.80
155 21 0.16
156 6 0.05
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (155 bp):
TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATGGGGAGCTTCAAATGCTTTTCAAAATATGT
CTCATTTTCATAAAATGTTTTATTAAGGAAGTGTTTACCAAAAACAATTTTCAAATGTTTTGTTA
TATCAAAAAGGGGGAGATAAATAAG
Found at i:332605 original size:662 final size:657
Alignment explanation
Indices: 330939--332916 Score: 3082
Period size: 662 Copynumber: 3.0 Consensus size: 657
330929 TTAAAGTCAA
* * **
330939 ATATTTGTTTGGGATGCTTTTATTAAGGGGGAGCTTTTGATTTGTCATTTGATTTTATGATAAAA
1 ATATTTGTTTGGAATGCTTTTATTAA-GGGGAGCTTTTGATTTTTCAACTGATTTTATGATAAAA
* *
331004 TTTACTACTTACTCTCCATTGTTATTTTTGAACTTTAAAGTTGAATTACTTTTATTATAACAAAA
65 TTTACCACTTACTCTCCATTGTTATTTTTTAACTTTAAAGTTGAATTACTTTT-TTATAACAAAA
* * *
331069 AGGGGGAGAATTATGGTTTGAAAAATTCTATTTCTCAATGAAAAATGTGGAGCTTCAAATGTTTT
129 AGGGGGAGAATTATGGTTTGAAAAATTCAATTTCTCAATGAAAAATATGGAGCTTTAAATGTTTT
* * *
331134 TCAAAATATGTCTCATTTTCATAAAATGTTTTATTAAGGGG-GTTTTGCCAAAACAGATTTTTTA
194 TCAAAATATGTCTCATTTTCATTAAATGTTTTATTAAGGGGAGTTTT-CCAAAACAAATTTTTCA
* **
331198 AATGTTTTGTTATATGAAAAA-GGGGAGATAAATAAGTATGGTTTGAAAAAATTAATTTCTCAAT
258 AATGTTTTGTTATATCAAAAAGGGGGAGATAAATAAGTATGGTTTGAAAATTTTAATTTCTCAAT
* *
331262 GAAAAATGGGGAGCTTTAAATGCTTTTCAAAATATGTTTCCTTTTCATTAAATGTTTTATTAA-G
323 GAAAAATGGGGAGCTTTAAATGTTTTTCAAAATATGTCTCCTTTTCATTAAATGTTTTATTAAGG
*
331326 GA-AGTGTTTACCAAAAACAA--TTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGA
388 GAGAGT-TTTGCCAAAAACAATTTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGA
* *
331388 ACCATGATTTATAATATTTTGATAT--AAATTAAGGCAAAATGTTTTTCGACTTGAATTGAATTT
452 ACCATGTTTTATAATATTTTGATATAAAAATTAAGGCAAAATGTTTTTAGACTTGAATTGAATTT
* * *
331451 ATTCAATGTTTTCAAAAATAATTCAAACTCCATTAAAACTGAATTTAAGCACAAAACTGATTTTC
517 ATTCAAAGTTTTCAAAAATAATTCAAAGTCAATTAAAACTGAATTTAAGCACAAAACTGATTTTC
* * *
331516 AACGTACGTAGTGCCGATACTGTTCTTACTATATCAATACTATATGAACAGTACCAATATTATTC
582 AACGTACGTAGTACCGATACTGTTCTTACAATATCAATACTATATGAACAGTACCGATATTATTC
*
331581 GTGTGGAACCG
647 GTGTGGTACCG
* * * * * *
331592 ATATTTATTTTTTGAATTCTTTTATTATGGGGTGCTTTTTGATTTTTCCACTGATTTTATGATAA
1 ATA-TT-TGTTTGGAATGCTTTTATTAAGGGGAGC-TTTTGATTTTTCAACTGATTTTATGATAA
* *
331657 AATTTACCACTTACTCTCCATTTTTATTTTTTTATCTTTAAAGTTGAATTACTTTTTTATAACAA
63 AATTTACCACTTACTCTCCATTGTTA-TTTTTTAACTTTAAAGTTGAATTACTTTTTTATAACAA
331722 AAAGGGGGAGAATTATGGTTTGAAAAATTCAATTTCTCAATG---AATATGGAGCTTTAAATGTT
127 AAAGGGGGAGAATTATGGTTTGAAAAATTCAATTTCTCAATGAAAAATATGGAGCTTTAAATGTT
* *
331784 TTTCAAAATATGTCTCATTTTCATTAAATGTTTTATTAAGGGGGAGTTTTGCAAAAAAAAGTTTT
192 TTTCAAAATATGTCTCATTTTCATTAAATGTTTTATTAA-GGGGAGTTTTCCAAAACAAA-TTTT
* *
331849 TCAAATGTTTTGGTATATCAAAAAGGGAGAGATAAATAAGTATGGTTTGAAAATTTTAATTTCTC
255 TCAAATGTTTTGTTATATCAAAAAGGGGGAGATAAATAAGTATGGTTTGAAAATTTTAATTTCTC
* * *
331914 AATGAAAAATGGGGAGCTTAAAATGTTTTTCAAAATATGTCTCATTTTTATTAAATGTTTTATTA
320 AATGAAAAATGGGGAGCTTTAAATGTTTTTCAAAATATGTCTCCTTTTCATTAAATGTTTTATTA
* *
331979 AGGGAGAGTTTTGCCATAAACAATTTTTTCAAATGATTTGTTATATCAAAAAGGGGGAGATTGTT
385 AGGGAGAGTTTTGCCAAAAACAATTTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTT
* *
332044 GAACCATGTTTTATAATATTTTGATATAAAAAATTAAAGCAAAATGTTTTTGGACTTGAATTGAA
450 GAACCATGTTTTATAATATTTTGATAT-AAAAATTAAGGCAAAATGTTTTTAGACTTGAATTGAA
332109 TTTATTCAAAGTTTTCAAAAATAATTCAAAGTCAATTAAAACTGAATTTAAGCACAAAACTGA-T
514 TTTATTCAAAGTTTTCAAAAATAATTCAAAGTCAATTAAAACTGAATTTAAGCACAAAACTGATT
* * * *
332173 TTCAACGTACGTAGTACCGATATTGTTCTTAAAATATCAATACTATAAGAACAATACCGATATTA
579 TTCAACGTACGTAGTACCGATACTGTTCTTACAATATCAATACTATATGAACAGTACCGATATTA
*
332238 TTCGTGTGGTACTG
644 TTCGTGTGGTACCG
*
332252 ATATTTGTTTGGAATGCTTTTATTAAGGGGAAGCTTTTGCTTTTTCAACTGATTTTATGATAAAA
1 ATATTTGTTTGGAATGCTTTTATTAAGGGG-AGCTTTTGATTTTTCAACTGATTTTATGATAAAA
332317 TTTACCACTTACTCTCCATTGTTATTTTTTAACTTTAAAGTTGAATTACTTTTTTATAACAAAAA
65 TTTACCACTTACTCTCCATTGTTATTTTTTAACTTTAAAGTTGAATTACTTTTTTATAACAAAAA
332382 GGGGGAGAATTATGGTTTGAAAAATTCAATTTCTCAATGAAAAATATGGAGCTTTAAATGTTTTT
130 GGGGGAGAATTATGGTTTGAAAAATTCAATTTCTCAATGAAAAATATGGAGCTTTAAATG--TTT
* *
332447 TTCAAAATATGTCTCATTTTCATTAAATGTTTTATTACGGGAGAGTTTTACCAAAACATATTTTT
193 TTCAAAATATGTCTCATTTTCATTAAATGTTTTATTAAGGG-GAGTTTT-CCAAAACAAATTTTT
* *
332512 CAAATGTTTTGTTATATCAAAAAGGGGGAGAAAAATAAGTATGGTTTGAAAATTTTATTTTCTCA
256 CAAATGTTTTGTTATATCAAAAAGGGGGAGATAAATAAGTATGGTTTGAAAATTTTAATTTCTCA
* * *
332577 ACGAAAAATGGGGAGCTTTAAATGTTTTTCAAAATACGTCTCCTTTTCATTAAATGTTTTGTTAA
321 ATGAAAAATGGGGAGCTTTAAATGTTTTTCAAAATATGTCTCCTTTTCATTAAATGTTTTATTAA
* * *
332642 GGGAGAGCTTAGCCAAAAATAATTTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTG
386 GGGAGAGTTTTGCCAAAAACAATTTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTG
* * *
332707 AACAATGTTTTATAGTATTTTGATATAACAAATTAAGGAAAAATGTTTTTAGACTTGAATTGAAT
451 AACCATGTTTTATAATATTTTGATATAA-AAATTAAGGCAAAATGTTTTTAGACTTGAATTGAAT
332772 TTA-TCAAAGTTTTCAAAAATAATTCAAAGTCAATTAAAACTGAATTTAAGCACAAAACTGATTT
515 TTATTCAAAGTTTTCAAAAATAATTCAAAGTCAATTAAAACTGAATTTAAGCACAAAACTGATTT
* * * *
332836 TCAACGTACGTAGTACCGATACTGTTCTCACAATATCAATATTATATGAATAGTACCGATATTGT
580 TCAACGTACGTAGTACCGATACTGTTCTTACAATATCAATACTATATGAACAGTACCGATATTAT
*
332901 TCATGTGGTACCG
645 TCGTGTGGTACCG
332914 ATA
1 ATA
332917 CCTTAGGTAA
Statistics
Matches: 1207, Mismatches: 93, Indels: 41
0.90 0.07 0.03
Matches are distributed among these distances:
652 56 0.05
653 14 0.01
654 38 0.03
655 213 0.18
656 42 0.03
657 82 0.07
658 138 0.11
659 4 0.00
660 92 0.08
661 156 0.13
662 365 0.30
663 7 0.01
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (657 bp):
ATATTTGTTTGGAATGCTTTTATTAAGGGGAGCTTTTGATTTTTCAACTGATTTTATGATAAAAT
TTACCACTTACTCTCCATTGTTATTTTTTAACTTTAAAGTTGAATTACTTTTTTATAACAAAAAG
GGGGAGAATTATGGTTTGAAAAATTCAATTTCTCAATGAAAAATATGGAGCTTTAAATGTTTTTC
AAAATATGTCTCATTTTCATTAAATGTTTTATTAAGGGGAGTTTTCCAAAACAAATTTTTCAAAT
GTTTTGTTATATCAAAAAGGGGGAGATAAATAAGTATGGTTTGAAAATTTTAATTTCTCAATGAA
AAATGGGGAGCTTTAAATGTTTTTCAAAATATGTCTCCTTTTCATTAAATGTTTTATTAAGGGAG
AGTTTTGCCAAAAACAATTTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGAACCA
TGTTTTATAATATTTTGATATAAAAATTAAGGCAAAATGTTTTTAGACTTGAATTGAATTTATTC
AAAGTTTTCAAAAATAATTCAAAGTCAATTAAAACTGAATTTAAGCACAAAACTGATTTTCAACG
TACGTAGTACCGATACTGTTCTTACAATATCAATACTATATGAACAGTACCGATATTATTCGTGT
GGTACCG
Found at i:332658 original size:157 final size:159
Alignment explanation
Indices: 332392--332700 Score: 464
Period size: 157 Copynumber: 1.9 Consensus size: 159
332382 GGGGGAGAAT
* * *
332392 TATGGTTTGAAAAATTCAATTTCTCAATGAAAAATATGGAGCTTTAAATGTTTTTTTCAAAATAT
1 TATGGTTTGAAAAATTCAATTTCTCAACGAAAAATAGGGAGCTTTAAATG-TTTTTTCAAAATAC
* *
332457 GTCTCATTTTCATTAAATGTTTTATTACGGGAGAGTTTTACCAAAACAT-A-TTTTTCAAATGTT
65 GTCTCATTTTCATTAAATGTTTTATTAAGGGAGAGTCTTACCAAAA-ATAATTTTTTCAAATGTT
332520 TTGTTATATCAAAAAGGGGGAGAAAAATAAG
129 TTGTTATATCAAAAAGGGGGAGAAAAATAAG
* * * *
332551 TATGGTTTGAAAATTTTATTTTCTCAACGAAAAATGGGGAGCTTTAAATG-TTTTTCAAAATACG
1 TATGGTTTGAAAAATTCAATTTCTCAACGAAAAATAGGGAGCTTTAAATGTTTTTTCAAAATACG
* *
332615 TCTCCTTTTCATTAAATGTTTTGTTAAGGGAGAG-CTTAGCCAAAAATAATTTTTTCAAATGTTT
66 TCTCATTTTCATTAAATGTTTTATTAAGGGAGAGTCTTA-CCAAAAATAATTTTTTCAAATGTTT
332679 TGTTATATCAAAAAGGGGGAGA
130 TGTTATATCAAAAAGGGGGAGA
332701 TTGTTGAACA
Statistics
Matches: 136, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
156 5 0.04
157 51 0.38
158 36 0.26
159 44 0.32
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (159 bp):
TATGGTTTGAAAAATTCAATTTCTCAACGAAAAATAGGGAGCTTTAAATGTTTTTTCAAAATACG
TCTCATTTTCATTAAATGTTTTATTAAGGGAGAGTCTTACCAAAAATAATTTTTTCAAATGTTTT
GTTATATCAAAAAGGGGGAGAAAAATAAG
Found at i:333832 original size:16 final size:16
Alignment explanation
Indices: 333808--333878 Score: 79
Period size: 16 Copynumber: 4.4 Consensus size: 16
333798 AATATATAAA
* *
333808 TATAAATTACATAGTT
1 TATATATTATATAGTT
333824 TATATATTATATAGTT
1 TATATATTATATAGTT
* *
333840 TTTATAATATATAGTT
1 TATATATTATATAGTT
* *
333856 TACATACTATATAGTT
1 TATATATTATATAGTT
*
333872 TAGATAT
1 TATATAT
333879 AGTTTTATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (16 bp):
TATATATTATATAGTT
Found at i:333859 original size:41 final size:42
Alignment explanation
Indices: 333800--333895 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 42
333790 TTGTATATAA
** * *
333800 TATATAAATATAAATTACATAGTTTATA-TATT-ATATAGTTT
1 TATATAAATATAGTTTACATACTATATAGT-TTAATATAGTTT
333841 T-TATAATATATAGTTTACATACTATATAGTTTAGATATAGTTT
1 TATATAA-ATATAGTTTACATACTATATAGTTTA-ATATAGTTT
333884 TATATAAATATA
1 TATATAAATATA
333896 AATTGATCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
40 5 0.11
41 20 0.43
42 1 0.02
43 15 0.33
44 5 0.11
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (42 bp):
TATATAAATATAGTTTACATACTATATAGTTTAATATAGTTT
Found at i:342231 original size:33 final size:34
Alignment explanation
Indices: 342167--342234 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 34
342157 TAAGTTAATA
342167 TGCTTGAATTTCGAAAATTCTGTAAATCGTTGTAT
1 TGCTTGAATTTCGAAAATTC-GTAAATCGTTGTAT
342202 TGCTTGAATTTCGAAAATTC-TAAATCGTTGTAT
1 TGCTTGAATTTCGAAAATTCGTAAATCGTTGTAT
342235 ACCTTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 13 0.39
35 20 0.61
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (34 bp):
TGCTTGAATTTCGAAAATTCGTAAATCGTTGTAT
Done.