Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008000.1 Hibiscus syriacus cultivar Beakdansim tig00110457_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: 1646480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1262654 original size:3 final size:3
Alignment explanation
Indices: 1262641--1262672 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1262631 GAAGATAACA
*
1262641 ATG ACG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1262673 CCAAACAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:1264650 original size:197 final size:198
Alignment explanation
Indices: 1264187--1264731 Score: 751
Period size: 200 Copynumber: 2.7 Consensus size: 198
1264177 AAAGAGTTGC
* *
1264187 ACGCATAAAGTGTCGATACATTTATTAAAAATATCGATCCCAAAAACATTGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTAT
* * * *
1264252 AATGTAATAGGTAATTTTGTAATATAATTGGTATACATATACCGGTTTTATGAGATAATAGGTCT
66 AATGTAATAGGTAATTTTGTAATATAATCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCT
*
1264317 ATAATATGTATCGAAACTTCTTAATATTGTGTCGATAATTAATGTCCAAAATGGATGCCAAAAAG
131 ATAATATGTA-CGACACTTCTTAATATTGTGTCGATAATT-ATGTCCAAAATGGATGCCAAAAAG
*
1264382 GGTGA
194 GATGA
*
1264387 ACGCATAAAGTGTCGATACATTT-TAAAAAAGTGA-CGATCCCAAAAACATCGAAACCCATAATT
1 ACGCATAAAGTGTCGATACATTTAT-TAAAAGT-ATCGATCCCAAAAACATCGAAACCCATAATT
* ** * *
1264450 ATAATGTAATAGGTAAATTTACAATGTAATCGGTATAAATATACTGGTTTTATGAGAGAATATGT
64 ATAATGTAATAGGTAATTTTGTAATATAATCGGTATAAATATACTGGTTTTATGAGAGAATAGGT
* * * * *
1264515 CTATAATATGTAGCGACACTTGTTAA-ATTTGTGTCGATACTT-T-TTCAGAATGGATGCTAAAA
129 CTATAATATGTA-CGACACTTCTTAATA-TTGTGTCGATAATTATGTCCAAAATGGATGCCAAAA
1264577 AGGATGA
192 AGGATGA
* * *
1264584 ACGCACAAAGTGTCGATACATTTATTAAAAGTATCGATACCTAAAACATCGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTAT
* *
1264649 AATGTAATAGGTAATTTTGTAATATAACCAGTATAAATATA-TCGGTTTTATGAGAGAATAGGTC
66 AATGTAATAGGTAATTTTGTAATATAATCGGTATAAATATACT-GGTTTTATGAGAGAATAGGTC
* *
1264713 TACAACATGTACGACACTT
130 TATAATATGTACGACACTT
1264732 TGTAAATAAA
Statistics
Matches: 306, Mismatches: 33, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
196 10 0.03
197 143 0.47
198 2 0.01
199 2 0.01
200 148 0.48
201 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (198 bp):
ACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTAT
AATGTAATAGGTAATTTTGTAATATAATCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCT
ATAATATGTACGACACTTCTTAATATTGTGTCGATAATTATGTCCAAAATGGATGCCAAAAAGGA
TGA
Found at i:1267685 original size:200 final size:197
Alignment explanation
Indices: 1267262--1267987 Score: 729
Period size: 200 Copynumber: 3.6 Consensus size: 197
1267252 ACCTAAATAT
* * *
1267262 GTGTCGATACATTT-TATACAAGTATCGA-CCCAAAAAATATCAAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTATA-AAAAGTATCGATCCC-AAAAACATCAAAACCGATAATTATAATGTAA
* * * * * * *
1267325 TAGGTAAATTAACAATGTAATCGGTATAAATATACCAG-TTAATTAGAAAACATGTCAACATAAT
64 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATAAT
* * *
1267389 GTATCGACACTTATGTAATTTGTGTCGATACTTATTGTCCAGAATGAAT-GCACAAACGAGGTGC
128 GTATCGACACGT-TGTAATTTGTGTCGATACTT-TTGTCCAGAATGAATATCA-AAAAG-GGTGC
1267453 -ACGCATAAA
189 AAC-CATAAA
* * * * *
1267462 TTGTTGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTATTA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
* *
1267527 GGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGATAAAATAGGTCAGCATCAA-G
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCA-CAT-AATG
1267591 TATCGACAC-TTGCTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATATCAAAAAGGGTGCAA
129 TATCGACACGTTG-T-AATTTGTGTCGATACTTTT-GTCCAGAATGAATATCAAAAAGGGTGCAA
1267655 CCATAAA
191 CCATAAA
* ** *
1267662 GTGTCGATATATTTATAAAAAGTATCGATCCCGGAAACATCAAAACAC-ATAAGTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAAC-CGATAATTATAATGTAAT
* *
1267726 AGGTAAATGTT-CAATGTAACCGGTATAAATATACCGGTTTTATGAGATAATAGGTCTAAATAAT
65 AGGTAAAT-TTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATAAT
* * *
1267790 GTATCGACACGTTGTCAGTTTGTGTCGATACTTTTTTCCAGAATGAAATATGAATGCCCAACCA-
128 GTATCGACACGTTGT-AATTTGTGTCGATACTTTTGTCCAGAATG-AATATCAA-----AA--AG
*
1267854 GGTGCAAGCATAAA
184 GGTGCAACCATAAA
** * * ** * * * *
1267868 GTGTCGATACATTTA-AAATTGTATTGGTCTAAAAAACATTATAACCGATAATAATATTGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
** * **
1267932 GGTAAATTTGTAATGTTACCGGTATAAATATACCGG-TTTACTTCGAAAATAGGTCA
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTA-TGAGAAAATAGGTCA
1267988 ATATAAGCGA
Statistics
Matches: 444, Mismatches: 56, Indels: 48
0.81 0.10 0.09
Matches are distributed among these distances:
199 13 0.03
200 240 0.54
201 73 0.16
202 4 0.01
204 8 0.02
205 78 0.18
206 27 0.06
207 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (197 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCACATAATGTA
TCGACACGTTGTAATTTGTGTCGATACTTTTGTCCAGAATGAATATCAAAAAGGGTGCAACCATA
AA
Found at i:1268090 original size:87 final size:87
Alignment explanation
Indices: 1267988--1268150 Score: 308
Period size: 87 Copynumber: 1.9 Consensus size: 87
1267978 AAATAGGTCA
1267988 ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1268053 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
1268075 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1268140 CCGGTTAAATG
66 CCGGTTAAATG
1268151 ATATAACATT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (87 bp):
ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:1268122 original size:23 final size:23
Alignment explanation
Indices: 1268072--1268116 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1268062 TGCCTATTTT
*
1268072 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
1268095 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1268117 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1268780 original size:62 final size:62
Alignment explanation
Indices: 1268683--1268814 Score: 176
Period size: 62 Copynumber: 2.1 Consensus size: 62
1268673 CTGATGGTTA
* * *
1268683 CAACTGGTCGTACGTTACACTGTCATCGTCATTGAGTTTCTCACCCTGCTATGAAGAAAATT
1 CAACTGGTCGTACGTTACACTGCCACCGTCATTGAGTTTCTCACCCTGCTACGAAGAAAATT
* * * *
1268745 CAACTGGTCGTACGTTACAC-GACCGCCGTCATTGAGTTTCTCACCCTTCTCCGAATAAAATT
1 CAACTGGTCGTACGTTACACTG-CCACCGTCATTGAGTTTCTCACCCTGCTACGAAGAAAATT
*
1268807 CAATTGGT
1 CAACTGGT
1268815 GGTGACCCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
61 1 0.02
62 60 0.98
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (62 bp):
CAACTGGTCGTACGTTACACTGCCACCGTCATTGAGTTTCTCACCCTGCTACGAAGAAAATT
Found at i:1270692 original size:21 final size:21
Alignment explanation
Indices: 1270667--1270710 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1270657 AAGAAAATTA
*
1270667 AATTTAAAATTTATATATATT
1 AATTTAAAAATTATATATATT
* *
1270688 AATTTAAAAATTATTTTTATT
1 AATTTAAAAATTATATATATT
1270709 AA
1 AA
1270711 AAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTAAAAATTATATATATT
Found at i:1271658 original size:15 final size:16
Alignment explanation
Indices: 1271629--1271658 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1271619 ATGTATAATA
1271629 AATTTAAACTAAAATG
1 AATTTAAACTAAAATG
1271645 AATTTAAA-TAAAAT
1 AATTTAAACTAAAAT
1271659 TCAACTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
AATTTAAACTAAAATG
Found at i:1277038 original size:92 final size:91
Alignment explanation
Indices: 1276876--1277058 Score: 233
Period size: 92 Copynumber: 2.0 Consensus size: 91
1276866 AATTACATTG
* * *
1276876 GTGTCTGTTAGAAGAGTTCGTTAATCCGAGAATAATATAAAAAAATAATTATAATAATATCGTTA
1 GTGTCTGTTAGAAGAGTTCGTTAATCCGAGAATAATATAAAAAAATAATGATAATAAAATCATTA
* *
1276941 TAAAAATTAAAGAGAAAAAATGAGTT
66 AAAAAATTAAAGAGAAAAAACGAGTT
* ** ** *
1276967 GTGTGTGTTAGAAAGAGATT-GTTAATTTGAGAATAATATAAAAGTATAATGGTAATAAAATCAT
1 GTGTCTGTTAG-AAGAG-TTCGTTAATCCGAGAATAATATAAAAAAATAATGATAATAAAATCAT
*
1277031 TAAAAAAATTAAAGAGAATAAACGAGTT
64 TAAAAAAATTAAAGAGAAAAAACGAGTT
1277059 TACTATCTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
91 10 0.13
92 66 0.85
93 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.17, T:0.31
Consensus pattern (91 bp):
GTGTCTGTTAGAAGAGTTCGTTAATCCGAGAATAATATAAAAAAATAATGATAATAAAATCATTA
AAAAAATTAAAGAGAAAAAACGAGTT
Found at i:1277948 original size:91 final size:89
Alignment explanation
Indices: 1277770--1277949 Score: 263
Period size: 91 Copynumber: 2.0 Consensus size: 89
1277760 AAGAAATATG
* * * * *
1277770 AAATTAATATAAATATTAAATTCATCAATTTAATTCACCTTTTTTCTAACAATCCACCAGATGAA
1 AAATTAATAAAAATATTAAATCCATCAATTAAATTCACCTTTTTTCCAACAATCCACCACATGAA
1277835 TGAAATTGGTGATTTAAACAAAAA
66 TGAAATTGGTGATTTAAACAAAAA
*
1277859 AAATTAATAAAAATATTAAATCCATCAATTAAATTCAACTCTTTTTTCCAACAGTCC-CTCACAT
1 AAATTAATAAAAATATTAAATCCATCAATTAAATTC-AC-CTTTTTTCCAACAATCCAC-CACAT
*
1277923 GAATGAAATTGGTGATTTAATCAAAAA
63 GAATGAAATTGGTGATTTAAACAAAAA
1277950 CATTTTGGCA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
89 33 0.41
90 3 0.04
91 45 0.56
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (89 bp):
AAATTAATAAAAATATTAAATCCATCAATTAAATTCACCTTTTTTCCAACAATCCACCACATGAA
TGAAATTGGTGATTTAAACAAAAA
Found at i:1284140 original size:13 final size:14
Alignment explanation
Indices: 1284117--1284157 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1284107 AATCATGTGC
*
1284117 ACATGATATTTCAA
1 ACATGATATTTAAA
1284131 ACAT-ATATTTAAA
1 ACATGATATTTAAA
*
1284144 ACATG-TTTTTAAA
1 ACATGATATTTAAA
1284157 A
1 A
1284158 ACAGTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (14 bp):
ACATGATATTTAAA
Found at i:1284616 original size:13 final size:13
Alignment explanation
Indices: 1284598--1284623 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1284588 TTTGACTTTT
1284598 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
1284611 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
1284624 CGAGTTGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
TGGTCAAAGTCAA
Found at i:1284653 original size:18 final size:19
Alignment explanation
Indices: 1284613--1284660 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
1284603 AAAGTCAATG
* *
1284613 GTCAAAGTCAACGAGTTGG
1 GTCAAAGTCAACGAGTCGA
*
1284632 GTC-AAGTCAACGGGTCGA
1 GTCAAAGTCAACGAGTCGA
1284650 GTCAAAGTCAA
1 GTCAAAGTCAA
1284661 TAGGTCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (19 bp):
GTCAAAGTCAACGAGTCGA
Found at i:1287606 original size:15 final size:15
Alignment explanation
Indices: 1287586--1287617 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1287576 AATGGTTAGA
1287586 GGATTAGACTTGAAG
1 GGATTAGACTTGAAG
1287601 GGATTAGACTTGAAG
1 GGATTAGACTTGAAG
1287616 GG
1 GG
1287618 CCCAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.38, T:0.25
Consensus pattern (15 bp):
GGATTAGACTTGAAG
Found at i:1295044 original size:17 final size:18
Alignment explanation
Indices: 1294998--1295045 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1294988 TGTTTATGAG
1294998 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
* *
1295016 GAAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
*
1295033 GGAATTGAAATCT
1 GGAATTGGAATCT
1295046 AATTCCATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:1297603 original size:18 final size:18
Alignment explanation
Indices: 1297532--1297604 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
1297522 TTATAAATTT
1297532 TATTAAAATTTTA-AAAA
1 TATTAAAATTTTATAAAA
*
1297549 TATTGAAATTTTTATAAAA
1 TATT-AAAATTTTATAAAA
***
1297568 -ATTAAAAACCCTATAAAA
1 TATT-AAAATTTTATAAAA
1297586 TATTATAAATTTTA-AAAA
1 TATTA-AAATTTTATAAAA
1297604 T
1 T
1297605 CAAAAGTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.09
18 27 0.63
19 12 0.28
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (18 bp):
TATTAAAATTTTATAAAA
Found at i:1298160 original size:18 final size:18
Alignment explanation
Indices: 1298089--1298161 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
1298079 TTATAAATTT
1298089 TATTAAAATTTTA-AAAA
1 TATTAAAATTTTATAAAA
*
1298106 TATTGAAATTTTTATAAAA
1 TATT-AAAATTTTATAAAA
***
1298125 -ATTAAAAACCCTATAAAA
1 TATT-AAAATTTTATAAAA
1298143 TATTATAAATTTTA-AAAA
1 TATTA-AAATTTTATAAAA
1298161 T
1 T
1298162 CAAAAGTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.09
18 27 0.63
19 12 0.28
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (18 bp):
TATTAAAATTTTATAAAA
Found at i:1298387 original size:556 final size:557
Alignment explanation
Indices: 1297282--1298399 Score: 2220
Period size: 557 Copynumber: 2.0 Consensus size: 557
1297272 TTATATTTTT
1297282 TAATTATATTAGTTTTTTTTAAAACTGATTTAATTGTGTTAAAGTCATCTTTTGATGATCTATCT
1 TAATTATATTAGTTTTTTTTAAAACTGATTTAATTGTGTTAAAGTCATCTTTTGATGATCTATCT
1297347 GTTACGATGTTGACATGCCAATTAACTATGCTAATGCCACAATTCATTCTGATGACATAACAATC
66 GTTACGATGTTGACATGCCAATTAACTATGCTAATGCCACAATTCATTCTGATGACATAACAATC
1297412 CATATGTGAATGATGAAATAACAAAAGAGTTTAATTGATTTTTAGTCGAGTTCAAAAATATAATT
131 CATATGTGAATGATGAAATAACAAAAGAGTTTAATTGATTTTTAGTCGAGTTCAAAAATATAATT
1297477 GATTTTAACTGAAAATACAAAATATTTTTAATATTTAAGGAAAAATTATAAATTTTATTAAAATT
196 GATTTTAACTGAAAATACAAAATATTTTTAATATTTAAGGAAAAATTATAAATTTTATTAAAATT
1297542 TTAAAAATATTGAAATTTTTATAAAAATTAAAAACCCTATAAAATATTATAAATTTTAAAAATCA
261 TTAAAAATATTGAAATTTTTATAAAAATTAAAAACCCTATAAAATATTATAAATTTTAAAAATCA
1297607 AAAGTTATAAAATGATAAGTTATAAATATATAAAAGTAAAATTTAAAAATATTTATAAAGTATTA
326 AAAGTTATAAAATGATAAGTTATAAATATATAAAAGTAAAATTTAAAAATATTTATAAAGTATTA
1297672 AAAAATTTGATATTTCATTGAAAAAGTTTTCAACAATCTCTTATTAGGCTGTGTCTACTCCTCTT
391 AAAAATTTGATATTTCATTGAAAAAGTTTTCAACAATCTCTTATTAGGCTGTGTCTACTCCTCTT
1297737 CTTTCAACATACTTTTAGTAGAATTAATTTTATAATAGGGTAACAATAAAACTCAAATTTCCTTC
456 CTTTCAACATACTTTTAGTAGAATTAATTTTATAATAGGGTAACAATAAAACTCAAATTTCCTTC
1297802 GATTTATTACACCAAATATTAATGAAAATTTGAGAAC
521 GATTTATTACACCAAATATTAATGAAAATTTGAGAAC
1297839 TAATTATATTAGTTTTTTTTAAAACTGATTTAATTGTGTTAAAGTCATCTTTTGATGATCTATCT
1 TAATTATATTAGTTTTTTTTAAAACTGATTTAATTGTGTTAAAGTCATCTTTTGATGATCTATCT
1297904 GTTACGATGTTGACATGCCAATTAACTATGCTAATGCCACAATTCATTCTGATGACATAACAATC
66 GTTACGATGTTGACATGCCAATTAACTATGCTAATGCCACAATTCATTCTGATGACATAACAATC
1297969 CATATGTGAATGATGAAATAACAAAAGAGTTTAATTGATTTTTAGTCGAGTTCAAAAATATAATT
131 CATATGTGAATGATGAAATAACAAAAGAGTTTAATTGATTTTTAGTCGAGTTCAAAAATATAATT
1298034 GATTTTAACTGAAAATACAAAATATTTTTAATATTTAAGGAAAAATTATAAATTTTATTAAAATT
196 GATTTTAACTGAAAATACAAAATATTTTTAATATTTAAGGAAAAATTATAAATTTTATTAAAATT
1298099 TTAAAAATATTGAAATTTTTATAAAAATTAAAAACCCTATAAAATATTATAAATTTTAAAAATCA
261 TTAAAAATATTGAAATTTTTATAAAAATTAAAAACCCTATAAAATATTATAAATTTTAAAAATCA
1298164 AAAGTTATAAAATGATAAGTTATAAATATAT-AAAGTAAAATTTAAAAATATTTATAAAGTATTA
326 AAAGTTATAAAATGATAAGTTATAAATATATAAAAGTAAAATTTAAAAATATTTATAAAGTATTA
1298228 AAAAATTTGATATTTCATTGAAAAAGTTTTCAACAATCTCTTATTAGGCTGTGTCTACTCCTCTT
391 AAAAATTTGATATTTCATTGAAAAAGTTTTCAACAATCTCTTATTAGGCTGTGTCTACTCCTCTT
1298293 CTTTCAACATACTTTTAGTAGAATTAATTTTATAATAGGGTAACAATAAAACTCAAATTTCCTTC
456 CTTTCAACATACTTTTAGTAGAATTAATTTTATAATAGGGTAACAATAAAACTCAAATTTCCTTC
1298358 GATTTATTACACCAAATATTAATGAAAATTTGAGAAC
521 GATTTATTACACCAAATATTAATGAAAATTTGAGAAC
*
1298395 CAATT
1 TAATT
1298400 TAGTGTAACA
Statistics
Matches: 560, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
556 204 0.36
557 356 0.64
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (557 bp):
TAATTATATTAGTTTTTTTTAAAACTGATTTAATTGTGTTAAAGTCATCTTTTGATGATCTATCT
GTTACGATGTTGACATGCCAATTAACTATGCTAATGCCACAATTCATTCTGATGACATAACAATC
CATATGTGAATGATGAAATAACAAAAGAGTTTAATTGATTTTTAGTCGAGTTCAAAAATATAATT
GATTTTAACTGAAAATACAAAATATTTTTAATATTTAAGGAAAAATTATAAATTTTATTAAAATT
TTAAAAATATTGAAATTTTTATAAAAATTAAAAACCCTATAAAATATTATAAATTTTAAAAATCA
AAAGTTATAAAATGATAAGTTATAAATATATAAAAGTAAAATTTAAAAATATTTATAAAGTATTA
AAAAATTTGATATTTCATTGAAAAAGTTTTCAACAATCTCTTATTAGGCTGTGTCTACTCCTCTT
CTTTCAACATACTTTTAGTAGAATTAATTTTATAATAGGGTAACAATAAAACTCAAATTTCCTTC
GATTTATTACACCAAATATTAATGAAAATTTGAGAAC
Found at i:1298908 original size:2 final size:2
Alignment explanation
Indices: 1298896--1298953 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
1298886 GTTTAATTTG
1298896 TA TA T- 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
1298937 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1298954 TAGATTAACT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1309253 original size:16 final size:16
Alignment explanation
Indices: 1309232--1309268 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1309222 GGATATTTGT
1309232 TATTGATGCTTTGGAA
1 TATTGATGCTTTGGAA
1309248 TATTGATGCTTTGGAA
1 TATTGATGCTTTGGAA
1309264 TATTG
1 TATTG
1309269 TATTCTAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.46
Consensus pattern (16 bp):
TATTGATGCTTTGGAA
Found at i:1313407 original size:20 final size:20
Alignment explanation
Indices: 1313384--1313435 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1313374 AACGCGATCC
1313384 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1313404 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1313424 CCAAAATCGCAA
1 CCAGAATCGCAA
1313436 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1313452 original size:21 final size:20
Alignment explanation
Indices: 1313425--1313523 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1313415 AATCAGTTTC
1313425 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1313446 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1313467 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1313487 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1313508 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1313524 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1313552 original size:20 final size:20
Alignment explanation
Indices: 1313490--1313683 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1313480 CGATTTTCCA
* ** *
1313490 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1313510 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1313530 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1313550 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1313570 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1313590 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1313610 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1313630 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1313650 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1313671 AAATCGCAACGCG
1 AAATCGCAACGCG
1313684 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1313574 original size:60 final size:60
Alignment explanation
Indices: 1313490--1313683 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1313480 CGATTTTCCA
* ** * *
1313490 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1313550 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1313610 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1313671 AAATCGCAACGCG
1 AAATCGCAACGCG
1313684 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1314104 original size:33 final size:33
Alignment explanation
Indices: 1314065--1314135 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1314055 TTCACTTAGA
*
1314065 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1314098 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1314131 TTTCA
1 TTTCA
1314136 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1314308 original size:19 final size:19
Alignment explanation
Indices: 1314268--1314312 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1314258 GCAACGAGAG
***
1314268 AATCGCAACGCGAAATGGA
1 AATCGCAACGCGAAACCAA
1314287 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1314306 AATCGCA
1 AATCGCA
1314313 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.44, C:0.27, G:0.20, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1314398 original size:19 final size:18
Alignment explanation
Indices: 1314308--1314419 Score: 86
Period size: 14 Copynumber: 6.8 Consensus size: 18
1314298 GAAACCAAAA
* *
1314308 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
1314327 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
*
1314343 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATC
*
1314359 TCGCGTTACGA-TTC-TC
1 TCGCGTTGCGATTTCATC
1314375 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
1314392 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
1314408 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
1314420 TCATTTCAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
14 23 0.30
15 6 0.08
16 11 0.14
17 11 0.14
18 8 0.10
19 18 0.23
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:1314404 original size:33 final size:33
Alignment explanation
Indices: 1314313--1314426 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
1314303 CAAAATCGCA
1314313 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1314346 TTGCGA-TTTCATTTCGCGTTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1314378 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1314411 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1314427 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
32 31 0.42
33 43 0.58
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1316353 original size:185 final size:186
Alignment explanation
Indices: 1316124--1316596 Score: 939
Period size: 185 Copynumber: 2.5 Consensus size: 186
1316114 TAGATTGCTT
1316124 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1316189 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1316254 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1316309 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1316374 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1316439 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1316495 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1316560 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
1316597 ATCCATTCAA
Statistics
Matches: 287, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
185 155 0.54
186 132 0.46
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1316438 original size:93 final size:93
Alignment explanation
Indices: 1316124--1316596 Score: 939
Period size: 93 Copynumber: 5.1 Consensus size: 93
1316114 TAGATTGCTT
1316124 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1316189 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1316217 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1316281 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1316309 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1316374 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1316402 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1316467 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1316495 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1316560 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1316588 AGTAAATTT
1 AGTAAATTT
1316597 ATCCATTCAA
Statistics
Matches: 379, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.24
93 287 0.76
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1316680 original size:19 final size:19
Alignment explanation
Indices: 1316640--1316768 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1316630 TAGTTTACTT
* *
1316640 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1316660 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1316679 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1316698 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1316712 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1316731 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1316745 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1316764 TCGCA
1 TCGCA
1316769 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1316719 original size:33 final size:32
Alignment explanation
Indices: 1316676--1316768 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1316666 CGCGAAACCA
**
1316676 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1316708 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1316741 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1316769 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1316766 original size:52 final size:52
Alignment explanation
Indices: 1316640--1316768 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1316630 TAGTTTACTT
**
1316640 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1316692 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1316745 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1316769 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1316786 original size:19 final size:19
Alignment explanation
Indices: 1316764--1316898 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1316754 GAAACCAAAA
*
1316764 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1316783 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1316799 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1316816 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1316832 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1316849 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1316868 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1316888 TCGTGTTGCGA
1 TCGCGTTGCGA
1316899 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1316805 original size:14 final size:14
Alignment explanation
Indices: 1316786--1316842 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1316776 TTTCATTTCG
1316786 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1316800 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1316817 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1316833 CGTTGCGATT
1 CGTTGCGATT
1316843 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1316811 original size:33 final size:33
Alignment explanation
Indices: 1316769--1316861 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1316759 CAAAATCGCA
*
1316769 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1316802 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1316835 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1316862 TTGGTTTCGC
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:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1318822 original size:14 final size:14
Alignment explanation
Indices: 1318803--1318838 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1318793 ATTGTTTAAT
1318803 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1318817 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1318831 TGATTTGT
1 TGATTTGT
1318839 GTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1318961 original size:19 final size:19
Alignment explanation
Indices: 1318945--1319046 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1318935 AAAAATGACT
1318945 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1318964 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1318983 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1318997 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1319016 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1319036 ATCGCAATGCG
1 ATCGCAATGCG
1319047 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1319099 original size:19 final size:19
Alignment explanation
Indices: 1319075--1319353 Score: 355
Period size: 19 Copynumber: 15.7 Consensus size: 19
1319065 GATTATCTCG
1319075 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1319094 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1319113 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1319127 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1319146 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1319165 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1319184 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1319203 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
1319218 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1319236 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1319255 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1319269 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1319288 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1319307 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1319321 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1319341 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1319354 GTTGGGATTT
Statistics
Matches: 228, Mismatches: 11, Indels: 41
0.81 0.04 0.15
Matches are distributed among these distances:
14 21 0.09
15 2 0.01
16 29 0.13
17 27 0.12
18 4 0.02
19 132 0.58
20 13 0.06
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1319150 original size:71 final size:71
Alignment explanation
Indices: 1319075--1319314 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
1319065 GATTATCTCG
1319075 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1319140 TTCGCA
66 TTCGCA
* *
1319146 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
* *
1319209 TT-ATGTCG-G
61 TTCATTTCGCA
*
1319218 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1319282 TTCGCA
66 TTCGCA
1319288 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1319315 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 6 0.04
68 6 0.04
69 7 0.05
70 2 0.01
71 107 0.71
72 2 0.01
73 7 0.05
74 7 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:1319234 original size:142 final size:137
Alignment explanation
Indices: 1319043--1319377 Score: 505
Period size: 142 Copynumber: 2.4 Consensus size: 137
1319033 AAAATCGCAA
1319043 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
1319107 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
65 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-
*
1319172 TTTCATTTCGTAT
129 -TTC-TCTCG--T
*
1319185 TGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTATCTC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1319249 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
65 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
1319314 TCTCTCGT
130 TCTCTCGT
* * * *
1319322 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGC
1 TGCGATTTTAATTT-CGCATTGCGATTATC-TCGTTGCGATTTTCATTTCGCATTGC
1319378 AATTGTATTT
Statistics
Matches: 180, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
137 17 0.09
138 31 0.17
139 5 0.03
140 3 0.02
142 118 0.66
143 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (137 bp):
TGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
CTCTCGT
Found at i:1319320 original size:52 final size:52
Alignment explanation
Indices: 1319075--1319353 Score: 354
Period size: 52 Copynumber: 5.2 Consensus size: 52
1319065 GATTATCTCG
*
1319075 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
1319127 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
1319184 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
1319236 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1319288 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
1319341 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1319354 GTTGGGATTT
Statistics
Matches: 212, Mismatches: 7, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
51 3 0.01
52 152 0.72
53 19 0.09
54 6 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:1321700 original size:12 final size:12
Alignment explanation
Indices: 1321683--1321707 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1321673 TCTTCGGGGA
1321683 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1321695 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1321707 C
1 C
1321708 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:1321916 original size:24 final size:24
Alignment explanation
Indices: 1321882--1321928 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1321872 CTGAAACATC
1321882 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1321906 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1321929 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1322630 original size:20 final size:20
Alignment explanation
Indices: 1322602--1322970 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1322592 AAATTTCAGT
* * * *
1322602 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1322622 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1322642 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1322662 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1322682 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1322702 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1322722 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1322742 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1322762 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1322782 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1322802 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1322822 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1322842 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1322862 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1322882 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1322902 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1322922 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1322942 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1322962 GTTGCGATT
1 GTTGCGATT
1322971 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1335043 original size:12 final size:13
Alignment explanation
Indices: 1335026--1335058 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1335016 GAGTGTGAGT
1335026 AGAGAGAAAAA-G
1 AGAGAGAAAAATG
*
1335038 AGAGAGAAAAATT
1 AGAGAGAAAAATG
1335051 AGAGAGAA
1 AGAGAGAA
1335059 TTGTAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (13 bp):
AGAGAGAAAAATG
Found at i:1352840 original size:24 final size:21
Alignment explanation
Indices: 1352820--1352859 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1352810 ATATAGAATT
1352820 TATCCCAAAGGACCACATAGA
1 TATCCCAAAGGACCACATAGA
*
1352841 TGTCCCAAAGGACCACATA
1 TATCCCAAAGGACCACATA
1352860 TAACATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.30, G:0.15, T:0.15
Consensus pattern (21 bp):
TATCCCAAAGGACCACATAGA
Found at i:1355954 original size:24 final size:24
Alignment explanation
Indices: 1355920--1355979 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1355910 TATATATACA
*
1355920 TATCATCATCATCATCACTATCAT
1 TATCATTATCATCATCACTATCAT
*
1355944 TATCATTATCAACATCACTATCAT
1 TATCATTATCATCATCACTATCAT
*
1355968 TATTATTATCAT
1 TATCATTATCAT
1355980 TCATTGTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (24 bp):
TATCATTATCATCATCACTATCAT
Found at i:1355960 original size:18 final size:18
Alignment explanation
Indices: 1355920--1355980 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
1355910 TATATATACA
* *
1355920 TATCATCATCATCATCAC
1 TATCATTATCATTATCAC
1355938 TATCATTATCATTATCAAC
1 TATCATTATCATTATC-AC
* * *
1355957 -ATCACTATCATTATTAT
1 TATCATTATCATTATCAC
1355974 TATCATT
1 TATCATT
1355981 CATTGTTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 1 0.03
18 32 0.91
19 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (18 bp):
TATCATTATCATTATCAC
Found at i:1355977 original size:12 final size:12
Alignment explanation
Indices: 1355920--1355980 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
1355910 TATATATACA
*
1355920 TATCATCATCAT
1 TATCATTATCAT
* *
1355932 CATCACTATCAT
1 TATCATTATCAT
*
1355944 TATCATTATCAA
1 TATCATTATCAT
* *
1355956 CATCACTATCAT
1 TATCATTATCAT
*
1355968 TATTATTATCAT
1 TATCATTATCAT
1355980 T
1 T
1355981 CATTGTTCAT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (12 bp):
TATCATTATCAT
Found at i:1356137 original size:23 final size:23
Alignment explanation
Indices: 1356108--1356208 Score: 69
Period size: 23 Copynumber: 4.4 Consensus size: 23
1356098 ACCGAAGTGT
1356108 CACATAGAAATGTCCCAAAGGAC
1 CACATAGAAATGTCCCAAAGGAC
* * *
1356131 CACATAGTATTGT-CCAGAAAGAC
1 CACATAGAAATGTCCCA-AAGGAC
* * * **
1356154 CGCGTAGAAATGTTCTGAAGGAC
1 CACATAGAAATGTCCCAAAGGAC
* * * *
1356177 CACATAGTATTGTCCCGAATGAC
1 CACATAGAAATGTCCCAAAGGAC
*
1356200 CGCATAGAA
1 CACATAGAA
1356209 CCCTCGACTC
Statistics
Matches: 57, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
22 3 0.05
23 53 0.93
24 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (23 bp):
CACATAGAAATGTCCCAAAGGAC
Found at i:1356164 original size:46 final size:46
Alignment explanation
Indices: 1356110--1356208 Score: 144
Period size: 46 Copynumber: 2.2 Consensus size: 46
1356100 CGAAGTGTCA
1356110 CATAGAAATGTCCCAAAGGACCACATAGTATTGTCCAGAAAGACCG
1 CATAGAAATGTCCCAAAGGACCACATAGTATTGTCCAGAAAGACCG
* * ** * *
1356156 CGTAGAAATGTTCTGAAGGACCACATAGTATTGTCCCGAATGACCG
1 CATAGAAATGTCCCAAAGGACCACATAGTATTGTCCAGAAAGACCG
1356202 CATAGAA
1 CATAGAA
1356209 CCCTCGACTC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (46 bp):
CATAGAAATGTCCCAAAGGACCACATAGTATTGTCCAGAAAGACCG
Found at i:1356385 original size:45 final size:45
Alignment explanation
Indices: 1356331--1356478 Score: 156
Period size: 45 Copynumber: 3.3 Consensus size: 45
1356321 CCATTGCCAA
* * * *
1356331 ATAGCTTATATCACATTTTCAGATT-TTTACATAGTTTAATATCAC
1 ATAGTTTATATCACATGTTCA-ATTGTTCACATAGTTCAATATCAC
* * *
1356376 ATAGTTTATATCACATGTTCACTTGTTCACGTAGTTCGATATCAC
1 ATAGTTTATATCACATGTTCAATTGTTCACATAGTTCAATATCAC
* * **
1356421 ATAGTTTATATCACATGTTTACA-TGTTCACGTAGTTCGGTATCAC
1 ATAGTTTATATCACATGTTCA-ATTGTTCACATAGTTCAATATCAC
*
1356466 ATAGCTTATATCA
1 ATAGTTTATATCA
1356479 TTTTCTTATG
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
44 2 0.02
45 88 0.98
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (45 bp):
ATAGTTTATATCACATGTTCAATTGTTCACATAGTTCAATATCAC
Found at i:1356388 original size:14 final size:14
Alignment explanation
Indices: 1356359--1356441 Score: 71
Period size: 15 Copynumber: 5.7 Consensus size: 14
1356349 TCAGATTTTT
1356359 ACATAGTTTAATATC
1 ACATAGTTT-ATATC
1356374 ACATAGTTTATATC
1 ACATAGTTTATATC
* *
1356388 ACAT-GTTCACTTGTTC
1 ACATAGTTTA--T-ATC
* *
1356404 ACGTAGTTCGATATC
1 ACATAGTT-TATATC
1356419 ACATAGTTTATATC
1 ACATAGTTTATATC
1356433 ACAT-GTTTA
1 ACATAGTTTA
1356442 CATGTTCACG
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
13 9 0.16
14 18 0.32
15 19 0.34
16 6 0.11
17 3 0.05
18 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (14 bp):
ACATAGTTTATATC
Found at i:1361488 original size:21 final size:20
Alignment explanation
Indices: 1361440--1361492 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1361430 CCCTTCAAAG
1361440 AGTATCGATACTCGGGGTCT
1 AGTATCGATACTCGGGGTCT
* *
1361460 AATATCGATACTCTGATGGTC-
1 AGTATCGATACTC-G-GGGTCT
1361481 AGTATCGATACT
1 AGTATCGATACT
1361493 GAGGTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.43
21 12 0.43
22 4 0.14
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (20 bp):
AGTATCGATACTCGGGGTCT
Found at i:1361549 original size:18 final size:20
Alignment explanation
Indices: 1361526--1361575 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
1361516 GTTGATTTTG
*
1361526 GTATCGATACTC-ATGG-GA
1 GTATCGATACTCAAGGGAGA
1361544 GTATCGATAC-CAAGGGTAGA
1 GTATCGATACTCAAGGG-AGA
1361564 GTATCGATACTC
1 GTATCGATACTC
1361576 CCCATAGGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 1 0.04
18 13 0.48
20 12 0.44
21 1 0.04
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (20 bp):
GTATCGATACTCAAGGGAGA
Found at i:1363093 original size:95 final size:95
Alignment explanation
Indices: 1362930--1363119 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
1362920 GTTAATAGCA
1362930 TCCGACGTTGTCGTCAGACATTTGGTATGAGTCGATATGAGACTCACTTATCAGCCTTGGGATCG
1 TCCGACGTTGTCGTCAGACATTTGGTATGAGTCGATATGAGACTCACTTATCAGCCTTGGGATCG
1362995 AGCAGTGGTCACATCAAGGCCAAAAGTACT
66 AGCAGTGGTCACATCAAGGCCAAAAGTACT
1363025 TCCGACGTTGTCGTCAGACATTTGGTATGAGTCGATATGAGACTCACTTATCAGCCTTGGGATCG
1 TCCGACGTTGTCGTCAGACATTTGGTATGAGTCGATATGAGACTCACTTATCAGCCTTGGGATCG
1363090 AGCAGTGGTCACATCAAGGCCAAAAGTACT
66 AGCAGTGGTCACATCAAGGCCAAAAGTACT
1363120 CCAAATTTAT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (95 bp):
TCCGACGTTGTCGTCAGACATTTGGTATGAGTCGATATGAGACTCACTTATCAGCCTTGGGATCG
AGCAGTGGTCACATCAAGGCCAAAAGTACT
Found at i:1364540 original size:24 final size:24
Alignment explanation
Indices: 1364508--1364580 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
1364498 TTATTCTTTC
*
1364508 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAACTCAAATTTTAG
1364532 GCTTCAATTGAACTCAAATTTTAG
1 GCTTCAATTGAACTCAAATTTTAG
*
1364556 GCTTCAATCGAACTTCTAAATTTTA
1 GCTTCAATTGAAC-TC-AAATTTTA
1364581 TTTTGAGTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 35 0.78
25 2 0.04
26 8 0.18
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAACTCAAATTTTAG
Found at i:1366039 original size:14 final size:14
Alignment explanation
Indices: 1366017--1366047 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1366007 AATATTCATT
1366017 TTTACTTTATTTTA
1 TTTACTTTATTTTA
*
1366031 TTTATTTTATTTTA
1 TTTACTTTATTTTA
1366045 TTT
1 TTT
1366048 CATCTAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTACTTTATTTTA
Found at i:1367094 original size:17 final size:17
Alignment explanation
Indices: 1367074--1367106 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1367064 CTCACTAACC
*
1367074 CTTTTATTTTTTGTTCG
1 CTTTTATTTTGTGTTCG
1367091 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
1367107 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.70
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCG
Found at i:1371476 original size:84 final size:84
Alignment explanation
Indices: 1371182--1372255 Score: 1328
Period size: 84 Copynumber: 12.9 Consensus size: 84
1371172 GCTCAAGACA
* * * * **
1371182 AGAAGGGCTATTTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTTAAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
1371247 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCT
* ** * * * * *
1371266 AGAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
** * *
1371327 TCACATCATAACTCAAGTCT
65 TTGCAGCATAACTTAAGTCT
* * * *
1371347 AGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
1371411 TGCAGCACAACTTAAGTCT
66 TGCAGCATAACTTAAGTCT
* *
1371430 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
*
1371494 TTGCAGCATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCT
* * *
1371514 AGAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
1371579 TGCAGTACAACTTAAGTCT
66 TGCAGCATAACTTAAGTCT
* * *
1371598 AGAAGGGTTGTCTGCCAACAAAAGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
1371663 TGCAGCACAACTTAAGTCT
66 TGCAGCATAACTTAAGTCT
* * * *
1371682 AGAAGGGTTGTCTACCAACAAAAGACCTTTGAGTTCTACTACGCTCAGCT-CAACGGCACATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
*
1371746 TTGCAGCATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCT
* *
1371766 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGATCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
1371831 TGCAGTACAACTTAAGTCT
66 TGCAGCATAACTTAAGTCT
* * *
1371850 AGAAGGGTTGTCTGCCAACACAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
1371915 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCT
* * * * * * * *
1371934 AGAATGGCTATCTG-C--C-AAAGACC-CCTGAGTTCGATTACACTCAGCTTCGAGGGCACGTCA
1 AGAAGGGTTATCTGCCAACAAAAGACCTTC-GAGTTCGACTACGCTCAGC-TCCAAGGCACATCA
*
1371994 TTTGCAGCATAACTTAAGTCG
64 TTTGCAGCATAACTTAAGTCT
*
1372015 AGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
1372080 TACATCATAACTTAAGGCT
66 TGCAGCATAACTTAAGTCT
* * *
1372099 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* ** *
1372164 TGCGGCATAACGCAAGGCT
66 TGCAGCATAACTTAAGTCT
* * **
1372183 AGAAGGGTTATCTGCCAAC-AAAGACCTTCAAGTTCGACTACGCTCATCTCTTAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
1372247 TACAGCATA
66 TGCAGCATA
1372256 GCCCAAGGCA
Statistics
Matches: 859, Mismatches: 115, Indels: 33
0.85 0.11 0.03
Matches are distributed among these distances:
79 1 0.00
80 48 0.06
81 83 0.10
82 2 0.00
83 98 0.11
84 596 0.69
85 30 0.03
86 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAACTTAAGTCT
Found at i:1374035 original size:14 final size:14
Alignment explanation
Indices: 1374016--1374042 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1374006 TAATATTCAT
1374016 TTTTATTTTATTTA
1 TTTTATTTTATTTA
1374030 TTTTATTTTATTT
1 TTTTATTTTATTT
1374043 CATCTAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTTATTTA
Found at i:1385509 original size:64 final size:63
Alignment explanation
Indices: 1385376--1385532 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
1385366 TAATGAAGGT
* * * ** *
1385376 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
1385440 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
1385502 G
63 G
*
1385503 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
1385533 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:1392429 original size:64 final size:64
Alignment explanation
Indices: 1392278--1392431 Score: 170
Period size: 64 Copynumber: 2.4 Consensus size: 64
1392268 TAATGAAGGT
* * * * **
1392278 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGAG
1 ATGCATCGATGCATTACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* * *
1392342 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCATTACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
1392404 G
64 G
*
1392405 AGTGCATCGATGCATTACCAATGCATC
1 A-TGCATCGATGCATTACTAATGCATC
1392432 AATACACCTT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 3 0.04
64 66 0.87
65 7 0.09
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCATTACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:1393847 original size:21 final size:20
Alignment explanation
Indices: 1393821--1393869 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1393811 TATCTAATCT
1393821 ATAATATAAATAATAAAAAAA
1 ATAATATAAATAA-AAAAAAA
* *
1393842 ATAATAT-TATAAATAAAAA
1 ATAATATAAATAAAAAAAAA
1393861 ATGAATATA
1 AT-AATATA
1393870 TTTCTTGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 9 0.38
21 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAATATAAATAAAAAAAAA
Found at i:1394509 original size:12 final size:12
Alignment explanation
Indices: 1394488--1394517 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1394478 CCTACCAATA
*
1394488 ATGCATCTTATG
1 ATGCACCTTATG
1394500 ATGCACCTTATG
1 ATGCACCTTATG
1394512 ATGCAC
1 ATGCAC
1394518 ATAATGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (12 bp):
ATGCACCTTATG
Found at i:1394866 original size:19 final size:20
Alignment explanation
Indices: 1394822--1394866 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1394812 ATATTTTTTT
*
1394822 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
1394842 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
1394861 AATAAA
1 AATAAA
1394867 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:1408918 original size:11 final size:13
Alignment explanation
Indices: 1408886--1408915 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1408876 TGGCCAAAGA
1408886 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1408899 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1408911 TGAAA
1 TGAAA
1408916 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1423151 original size:18 final size:19
Alignment explanation
Indices: 1423116--1423152 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1423106 CACGGAATGT
1423116 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1423136 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1423153 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1430045 original size:21 final size:22
Alignment explanation
Indices: 1430019--1430081 Score: 92
Period size: 23 Copynumber: 2.9 Consensus size: 22
1430009 ATATGTGTTA
*
1430019 TATGTGGTCATTCGGGACA-TC
1 TATGTGGTCCTTCGGGACATTC
1430040 TATGTGGTCCTTCGGGACATTTC
1 TATGTGGTCCTTCGGGACA-TTC
*
1430063 TATGTGGTCCTCCGGGACA
1 TATGTGGTCCTTCGGGACA
1430082 AATCCTATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 18 0.47
23 20 0.53
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (22 bp):
TATGTGGTCCTTCGGGACATTC
Found at i:1430276 original size:2 final size:2
Alignment explanation
Indices: 1430264--1430308 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1430254 GTGTTTTATG
*
1430264 AT AT GT 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
1430306 AT A
1 AT A
1430309 AATGATAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1436830 original size:26 final size:26
Alignment explanation
Indices: 1436800--1436861 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
1436790 CAGTGTTGAC
1436800 TGATTCAGCAAAACAGTGGTGCTGAA
1 TGATTCAGCAAAACAGTGGTGCTGAA
1436826 TGATTCAGCAAAACAGTGGTGCTGAA
1 TGATTCAGCAAAACAGTGGTGCTGAA
1436852 TGATTCAGCA
1 TGATTCAGCA
1436862 TTTAAACATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (26 bp):
TGATTCAGCAAAACAGTGGTGCTGAA
Found at i:1441953 original size:19 final size:17
Alignment explanation
Indices: 1441931--1441976 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
1441921 TGAAACAAAT
1441931 ATAAAAAAAATGAAATTGA
1 ATAAAAAAAAT-AAATT-A
1441950 ATAAAATAAAATAAATTA
1 ATAAAA-AAAATAAATTA
*
1441968 AGAAAAAAA
1 ATAAAAAAA
1441977 TATATATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 6 0.24
19 11 0.44
20 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (17 bp):
ATAAAAAAAATAAATTA
Found at i:1442097 original size:28 final size:28
Alignment explanation
Indices: 1442056--1442147 Score: 93
Period size: 27 Copynumber: 3.4 Consensus size: 28
1442046 AAGAAACTAA
* *
1442056 AAATATAATGAAAATAAATAAATAGTAT
1 AAATAAAATAAAAATAAATAAATAGTAT
1442084 AAATAAAATAAAAATAAA-AAATA-TAT
1 AAATAAAATAAAAATAAATAAATAGTAT
* **
1442110 ATAA-AAATATAAAAATATATGTATAGTAT
1 A-AATAAA-ATAAAAATAAATAAATAGTAT
1442139 -AATAAAATA
1 AAATAAAATA
1442148 CTAAATAGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
26 7 0.13
27 22 0.41
28 22 0.41
29 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (28 bp):
AAATAAAATAAAAATAAATAAATAGTAT
Found at i:1442282 original size:13 final size:13
Alignment explanation
Indices: 1442264--1442288 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1442254 TAACGTTAGG
1442264 AAATATAGTAAAA
1 AAATATAGTAAAA
1442277 AAATATAGTAAA
1 AAATATAGTAAA
1442289 TAAGTAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AAATATAGTAAAA
Found at i:1442363 original size:3 final size:3
Alignment explanation
Indices: 1442309--1442352 Score: 52
Period size: 3 Copynumber: 13.3 Consensus size: 3
1442299 TAGATAAAAA
1442309 AAT AAT AAT AAT ATAT ATAT ATAT ATAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT A-AT A-AT A-AT A-AT AAT AAT AAT AAT AAT A
1442353 GGAAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 25 0.62
4 15 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:1442421 original size:9 final size:9
Alignment explanation
Indices: 1442400--1442429 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1442390 AAAAAATTAT
1442400 AATAAAT-A
1 AATAAATAA
1442408 AATAAATAA
1 AATAAATAA
1442417 AATAAATAA
1 AATAAATAA
1442426 AATA
1 AATA
1442430 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AATAAATAA
Found at i:1443883 original size:106 final size:106
Alignment explanation
Indices: 1443699--1444762 Score: 1664
Period size: 106 Copynumber: 10.0 Consensus size: 106
1443689 GCATTGTTCC
* * * * *
1443699 GAGTCCAATATCCTCCGTCT-TGAAGTTAAAATTGGCTCTGGAATCGGGAAATTGTTTCTTGACA
1 GAGTCCAATATCCTTCGT-TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
1443763 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1443805 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1443870 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
1443911 GAGTCCAATATCATTTGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1443976 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1444017 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1444082 CCAGCGGTCTCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1444123 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1444188 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1444229 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGCTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1444294 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * **
1444335 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
1444400 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1444441 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1444506 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1444547 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1444612 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1444653 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
1444718 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1444759 GAGT
1 GAGT
1444763 GGCACGATAT
Statistics
Matches: 892, Mismatches: 64, Indels: 4
0.93 0.07 0.00
Matches are distributed among these distances:
105 2 0.00
106 890 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1445750 original size:22 final size:22
Alignment explanation
Indices: 1445724--1445778 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1445714 TTGTGTTTGG
1445724 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1445746 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1445768 TCAAATGTTTG
1 TCAAAGGTTTG
1445779 ATGGAGTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1446417 original size:14 final size:14
Alignment explanation
Indices: 1446400--1446441 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1446390 TTGATTTTTG
1446400 TTCTTTTTTTGTTC
1 TTCTTTTTTTGTTC
1446414 TTC-TTTTTTGCTTC
1 TTCTTTTTTTG-TTC
*
1446428 TTTTCTTTTTTGTT
1 TTCT-TTTTTTGTT
1446442 TTTGCCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 7 0.29
14 8 0.33
15 2 0.08
16 7 0.29
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
TTCTTTTTTTGTTC
Found at i:1449861 original size:19 final size:20
Alignment explanation
Indices: 1449833--1449870 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1449823 TGCAGATGAT
*
1449833 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
1449852 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
1449871 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:1451050 original size:19 final size:17
Alignment explanation
Indices: 1451028--1451072 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
1451018 TGAAACAAAT
1451028 ATAAAAAAAATGAAATTGA
1 ATAAAAAAAAT-AAA-TGA
1451047 ATAAAATAAAATAAATGA
1 ATAAAA-AAAATAAATGA
*
1451065 AGAAAAAA
1 ATAAAAAA
1451073 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 8 0.33
19 9 0.38
20 5 0.21
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
ATAAAAAAAATAAATGA
Found at i:1451191 original size:18 final size:18
Alignment explanation
Indices: 1451164--1451216 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1451154 AACATAATGA
* *
1451164 AAAT-AAATAAATAGTAT
1 AAATAAAATAAAAAATAT
1451181 AAATAAAATAAAAAATAT
1 AAATAAAATAAAAAATAT
*
1451199 ATATAAAAATATAAAAAT
1 AAAT-AAAATA-AAAAAT
1451217 GTATGTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 4 0.13
18 14 0.47
19 6 0.20
20 6 0.20
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAAATAAAAAATAT
Found at i:1451225 original size:22 final size:22
Alignment explanation
Indices: 1451163--1451236 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
1451153 AAACATAATG
1451163 AAAATAAATAAATA-GTATAAAT
1 AAAATAAA-AAATATGTATAAAT
*
1451185 AAAATAAAAAATATATATAAA-
1 AAAATAAAAAATATGTATAAAT
* *
1451206 AATATAAAAATGTATGTAT-AAT
1 AAAATAAAAA-ATATGTATAAAT
*
1451228 ATAATAAAA
1 AAAATAAAA
1451237 TACTAAATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 16 0.37
22 27 0.63
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (22 bp):
AAAATAAAAAATATGTATAAAT
Found at i:1451383 original size:12 final size:12
Alignment explanation
Indices: 1451366--1451390 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1451356 TAACGTTAGG
1451366 AAAATATAGTAA
1 AAAATATAGTAA
1451378 AAAATATAGTAA
1 AAAATATAGTAA
1451390 A
1 A
1451391 TAAGTAAACA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATATAGTAA
Found at i:1451493 original size:10 final size:9
Alignment explanation
Indices: 1451480--1451517 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
1451470 AAAATGAAAA
1451480 AAATTATAAT
1 AAATTA-AAT
1451490 AAA-TAAAT
1 AAATTAAAT
1451498 AAATTAAAT
1 AAATTAAAT
1451507 ATAATTAAAT
1 A-AATTAAAT
1451517 A
1 A
1451518 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 6 0.23
9 8 0.31
10 12 0.46
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTAAAT
Found at i:1451522 original size:2 final size:2
Alignment explanation
Indices: 1451515--1451547 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1451505 ATATAATTAA
1451515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1451548 ATAATAAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1452990 original size:24 final size:22
Alignment explanation
Indices: 1452963--1453030 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 22
1452953 TAAAATCAAG
1452963 AAAAACACAGAAGAATAAGAACAC
1 AAAAACACAGAA-AATAAGAAC-C
* *
1452987 AAAAAAACCAGAAAATACGAACC
1 AAAAACA-CAGAAAATAAGAACC
** *
1453010 CTAAACCCAGAAAATAAGAAC
1 AAAAACACAGAAAATAAGAAC
1453031 GATAGACGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
22 13 0.36
23 4 0.11
24 14 0.39
25 5 0.14
ACGTcount: A:0.63, C:0.21, G:0.10, T:0.06
Consensus pattern (22 bp):
AAAAACACAGAAAATAAGAACC
Found at i:1453386 original size:31 final size:31
Alignment explanation
Indices: 1453351--1453411 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1453341 AACGAGAAAA
1453351 TATTAAAATAAAACTAAAACT-AAATTTTAAG
1 TATTAAAATAAAAC-AAAACTGAAATTTTAAG
*
1453382 TATTAAAATAAATCAAAACTGAAATTTTAA
1 TATTAAAATAAAACAAAACTGAAATTTTAA
1453412 ACGCATAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (31 bp):
TATTAAAATAAAACAAAACTGAAATTTTAAG
Found at i:1455278 original size:21 final size:20
Alignment explanation
Indices: 1455192--1455349 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1455182 AAATGACCAA
**
1455192 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1455211 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1455231 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1455251 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1455272 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* * *
1455293 CAAATTTGCAATGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1455313 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1455334 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1455350 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1455378 original size:20 final size:20
Alignment explanation
Indices: 1455316--1455509 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1455306 CGATTTTCCA
* ** *
1455316 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1455336 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1455356 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1455376 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1455396 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1455416 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1455436 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1455456 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1455476 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1455497 AAATCGCAACGCG
1 AAATCGCAACGCG
1455510 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1455400 original size:60 final size:60
Alignment explanation
Indices: 1455316--1455509 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1455306 CGATTTTCCA
* ** * *
1455316 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1455376 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1455436 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1455497 AAATCGCAACGCG
1 AAATCGCAACGCG
1455510 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1455931 original size:33 final size:33
Alignment explanation
Indices: 1455892--1455962 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1455882 TTCACTTAGA
*
1455892 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* * *
1455925 TTTCATTTCGTGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1455958 TTTCA
1 TTTCA
1455963 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1456068 original size:21 final size:20
Alignment explanation
Indices: 1456042--1456149 Score: 95
Period size: 21 Copynumber: 5.7 Consensus size: 20
1456032 TGCAGAAGAG
1456042 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
1456063 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
1456083 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
1456104 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
1456118 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
*
1456137 TCGCAACGCGAAA
1 TCGCAACGAGAAA
1456150 CCAAAATCGC
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.15
16 2 0.03
17 2 0.03
19 12 0.17
20 18 0.25
21 26 0.37
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1456086 original size:20 final size:20
Alignment explanation
Indices: 1456042--1456118 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 20
1456032 TGCAGAAGAG
*
1456042 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1456063 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1456083 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1456104 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1456119 CGCAACGCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 20 0.42
21 28 0.58
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1456099 original size:41 final size:41
Alignment explanation
Indices: 1456041--1456118 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1456031 TTGCAGAAGA
*
1456041 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
1456082 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1456119 CGCAACGCGA
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:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:1456140 original size:19 final size:19
Alignment explanation
Indices: 1456054--1456160 Score: 80
Period size: 19 Copynumber: 5.7 Consensus size: 19
1456044 GCAACGAGAT
*
1456054 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*** *
1456073 AGAATGACTGTCGCAACGAGAG
1 A-AATGAAAATCGCAAC--GCG
1456095 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
1456112 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
1456128 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
**
1456147 AAACCAAAATCGCA
1 AAATGAAAATCGCA
1456161 TTGCGATTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 1 0.01
18 1 0.01
19 27 0.39
20 12 0.17
21 11 0.16
22 4 0.06
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:1456178 original size:19 final size:19
Alignment explanation
Indices: 1456156--1456253 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1456146 GAAACCAAAA
*
1456156 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1456175 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1456189 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1456208 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1456222 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
1456241 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1456254 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1456197 original size:14 final size:14
Alignment explanation
Indices: 1456178--1456267 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1456168 TTTCATTTCG
1456178 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1456192 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1456211 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1456225 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
1456244 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1456258 CGTTGCGATT
1 CGTTGCGATT
1456268 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1456203 original size:33 final size:33
Alignment explanation
Indices: 1456161--1456275 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
1456151 CAAAATCGCA
1456161 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1456194 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1456227 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1456260 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1456276 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1458127 original size:93 final size:93
Alignment explanation
Indices: 1457968--1458340 Score: 728
Period size: 93 Copynumber: 4.0 Consensus size: 93
1457958 TAGATTGCTT
*
1457968 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1458033 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1458061 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1458126 TTTGTCTTTGTTTTGTCTTTTAGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1458154 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1458219 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1458247 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1458312 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1458340 A
1 A
1458341 TAGCATTGCG
Statistics
Matches: 277, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 277 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1458370 original size:19 final size:19
Alignment explanation
Indices: 1458346--1458475 Score: 127
Period size: 19 Copynumber: 7.3 Consensus size: 19
1458336 TGAAATAGCA
1458346 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
1458365 TTGCGA--TTC-TTT--CG
1 TTGCGATTTTCATTTCGCG
*
1458379 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
1458398 TTGCGA--TTC-TGT--CG
1 TTGCGATTTTCATTTCGCG
1458412 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
1458431 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
1458450 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
1458470 TTGCGA
1 TTGCGA
1458476 AAGTAAACTA
Statistics
Matches: 91, Mismatches: 9, Indels: 21
0.75 0.07 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 42 0.46
20 12 0.13
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:1458382 original size:14 final size:14
Alignment explanation
Indices: 1458363--1458419 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1458353 TTTCATTTCG
1458363 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1458377 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1458394 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1458410 CGTTGCGATT
1 CGTTGCGATT
1458420 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1458388 original size:33 final size:33
Alignment explanation
Indices: 1458346--1458438 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1458336 TGAAATAGCA
*
1458346 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1458379 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1458412 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1458439 TTGGTTTCGC
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:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1460412 original size:14 final size:14
Alignment explanation
Indices: 1460393--1460428 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1460383 ATTGTTTAAT
1460393 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1460407 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1460421 TGATTTGT
1 TGATTTGT
1460429 GTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1460551 original size:19 final size:19
Alignment explanation
Indices: 1460535--1460612 Score: 112
Period size: 19 Copynumber: 4.4 Consensus size: 19
1460525 AAAAATGACC
1460535 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1460554 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1460573 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1460587 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1460606 ATCGCAA
1 ATCGCAA
1460613 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 36 0.69
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1460591 original size:14 final size:14
Alignment explanation
Indices: 1460572--1460626 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1460562 GCGAAATGAA
1460572 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1460586 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1460605 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1460619 AATCGCAA
1 AATCGCAA
1460627 TGCGTTTATA
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:1460644 original size:33 final size:33
Alignment explanation
Indices: 1460553--1460630 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
1460543 GCGAAATGAA
1460553 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1460586 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1460619 AATCGCAATGCG
1 AATCGCAATGCG
1460631 TTTATAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:1460674 original size:33 final size:33
Alignment explanation
Indices: 1460637--1460789 Score: 150
Period size: 33 Copynumber: 4.5 Consensus size: 33
1460627 TGCGTTTATA
1460637 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
1460670 ATTTCACATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
1460710 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1460741 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1460774 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
1460790 TTCATTTCGC
Statistics
Matches: 95, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 51 0.54
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 8 0.08
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:1460683 original size:19 final size:19
Alignment explanation
Indices: 1460659--1460875 Score: 231
Period size: 19 Copynumber: 12.4 Consensus size: 19
1460649 GATTCTCTCG
*
1460659 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
1460678 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1460697 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1460711 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1460730 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1460749 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1460763 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1460782 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1460801 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1460815 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1460835 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
1460849 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1460868 TTGCGATT
1 TTGCGATT
1460876 CTCTCGTTGC
Statistics
Matches: 166, Mismatches: 11, Indels: 42
0.76 0.05 0.19
Matches are distributed among these distances:
14 28 0.17
16 23 0.14
17 20 0.12
18 3 0.02
19 80 0.48
20 12 0.07
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1460694 original size:52 final size:52
Alignment explanation
Indices: 1460637--1460847 Score: 395
Period size: 52 Copynumber: 4.0 Consensus size: 52
1460627 TGCGTTTATA
*
1460637 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1460689 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1460741 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1460793 ATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1460846 AT
1 AT
1460848 GTTGGGATTT
Statistics
Matches: 156, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 139 0.89
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1460897 original size:33 final size:33
Alignment explanation
Indices: 1460678--1460889 Score: 225
Period size: 33 Copynumber: 6.2 Consensus size: 33
1460668 TCATTTCACA
1460678 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1460711 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1460747 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
*
1460782 TTGCGATTTTCATTTCGCATTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1460815 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1460849 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1460882 TTGCGATT
1 TTGCGATT
1460890 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 18, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
31 8 0.05
32 6 0.04
33 73 0.50
34 28 0.19
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1463188 original size:12 final size:12
Alignment explanation
Indices: 1463171--1463195 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1463161 TCTTCGGGGA
1463171 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1463183 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1463195 C
1 C
1463196 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:1463404 original size:24 final size:24
Alignment explanation
Indices: 1463370--1463416 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1463360 CTGAAACATC
1463370 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1463394 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1463417 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1464127 original size:20 final size:20
Alignment explanation
Indices: 1464099--1464328 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
1464089 AAATTTCAGT
* * *
1464099 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1464119 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1464139 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1464159 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1464179 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1464199 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1464219 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1464239 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1464259 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1464279 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1464299 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1464319 GTTGCGATTT
1 GTTGCGATTT
1464329 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1464345 original size:21 final size:21
Alignment explanation
Indices: 1464315--1464397 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1464305 ATTTTCATAT
*
1464315 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1464336 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1464357 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1464378 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1464398 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1464388 original size:42 final size:43
Alignment explanation
Indices: 1464295--1464393 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1464285 ATTTATGTGT
* *
1464295 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1464336 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1464378 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1464394 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1464805 original size:18 final size:19
Alignment explanation
Indices: 1464771--1464811 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
1464761 AAAAATGAAT
1464771 GAACGTAACAAACACAAAC
1 GAACGTAACAAACACAAAC
*
1464790 GAACG-AACATAA-ACAAGC
1 GAACGTAACA-AACACAAAC
1464808 GAAC
1 GAAC
1464812 ATAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.56, C:0.24, G:0.15, T:0.05
Consensus pattern (19 bp):
GAACGTAACAAACACAAAC
Found at i:1465063 original size:14 final size:14
Alignment explanation
Indices: 1465036--1465077 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1465026 TGAGCATAAT
*
1465036 GAACACAAACGAAC
1 GAACATAAACGAAC
*
1465050 GAACATAAATGAAC
1 GAACATAAACGAAC
*
1465064 GAATATAAACGAAC
1 GAACATAAACGAAC
1465078 AGATTATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.57, C:0.19, G:0.14, T:0.10
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:1468580 original size:2 final size:2
Alignment explanation
Indices: 1468573--1468597 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1468563 ATAGATTAAT
1468573 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1468598 TTGATTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.