Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 56
Found at i:1524469 original size:23 final size:24
Alignment explanation
Indices: 1524429--1524474 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1524419 TAACAAAATC
1524429 TAGAGGAAGAAAATGGAA-GATTA
1 TAGAGGAAGAAAATGGAATGATTA
*
1524452 TAGAGG-AGGAAATGGGAATGATT
1 TAGAGGAAGAAAAT-GGAATGATT
1524475 TAGGGACGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 10 0.50
24 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.20
Consensus pattern (24 bp):
TAGAGGAAGAAAATGGAATGATTA
Found at i:1525119 original size:33 final size:32
Alignment explanation
Indices: 1525058--1525121 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
1525048 GTCGGGATTT
** *
1525058 TTTTTTTAAATTTGAGTTTGGGTCGGGTCGGG
1 TTTTTTTAAAGGTGAGTTCGGGTCGGGTCGGG
*
1525090 TTTTTTTAAAGGTGATGTTCGGGTTGGGTCGG
1 TTTTTTTAAAGGTGA-GTTCGGGTCGGGTCGG
1525122 ATTCCAGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.12, C:0.06, G:0.36, T:0.45
Consensus pattern (32 bp):
TTTTTTTAAAGGTGAGTTCGGGTCGGGTCGGG
Found at i:1526494 original size:23 final size:24
Alignment explanation
Indices: 1526468--1526519 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
1526458 AATCATAATC
1526468 AAAGTTTAAAAATTT-ACTTTTAA
1 AAAGTTTAAAAATTTGACTTTTAA
*
1526491 AAAGTTTAAAATTTTGACTTTTAA
1 AAAGTTTAAAAATTTGACTTTTAA
1526515 AAAGT
1 AAAGT
1526520 CAATAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (24 bp):
AAAGTTTAAAAATTTGACTTTTAA
Found at i:1530828 original size:847 final size:837
Alignment explanation
Indices: 1529205--1530875 Score: 3144
Period size: 847 Copynumber: 2.0 Consensus size: 837
1529195 CCAACGGTTG
1529205 TAGTATGGGGGATCGAACGTTCATTGTCAAATGATTGAGAGTATTTAGAACATATACTACTTTGT
1 TAGTATGGGGGATCGAACGTTCATTGTCAAATGATTGAGAGTATTTAGAACATATACTACTTTGT
*
1529270 AATCACCATAGCTTAATAAAATTTGTTTTATATATAAACACATGAAAATATATACATATAAATAA
66 AATCACCATAGCTTAATAAAATTTGTTTTATATATAAACACATGAAAATATATACATACAAATAA
1529335 ATATAAATATCTTAAAATCTATTTATTATATTTTTAACACTTATAAAATAAAAATGTTAAAAACT
131 ATATAAATATCTTAAAATCTATTTATTATATTTTTAACACTTATAAAATAAAAATGTTAAAAACT
1529400 CATTAAACAATGATAAAAGTGAATATTGTTCTCTTTAAATAATTTGATTTAAGGCATGGATCAAG
196 CATTAAACAATGATAAAAGTGAATATTGTTCTCTTTAAATAATTTGATTTAAGGCATGGATCAAG
1529465 TGACTTCAATGGTTAAGAGACTTGTTGTTATACCTTGATGGGTTTCAGCAATATCATGGTTATGA
261 TGACTTCAATGGTTAAGAGACTTGTTGTTATACCTTGATGGGTTTCAGCAATATCATGGTTATGA
*
1529530 GTATTTACTATCAAATGATTACGAGTAGATAATAGATACTACCTTGTGTTCACCCTTTATTTATT
326 GTATTTACTATCAAATGATTACGAGTAGATAATAGATACTACCTTGTGTTCACCCTGTATTTATT
* * *
1529595 GAAAATTTAAATTCAAACAGTCGTATCTGCAGGGATTGTACATGTGACTAAATATGATCAAATTT
391 GAAAATTTAAATTCAAACAGTCGCACCTGCAGGGAGTGTACATGTGACTAAATATGATCAAATTT
1529660 ATTGAGTTAAAATTTTAATTAATATTAACTTTTTATTTCAATTTCAAACAATTTGCTTCTTTTAT
456 ATTGAGTTAAAATTTTAATTAATATTAACTTTTTATTTCAATTTCAAACAATTTGCTTCTTTTAT
*
1529725 AAAGCATTAAAAATTATATTTATAAAGTTCAAGAGATAAACTAATAAAAATAATTAAATATGAAA
521 AAAGCATTAAAAATTATATTTATAAAGTTCAAGAGATAAACTAATAAAAATAATTAAATATCAAA
1529790 CTACAATTTTTTTACTTAGTACAAGATTCATTTTAGATATCAAACCTTTTGTATGTTTTAAGACT
586 CTACAATTTTTTTACTTAGTACAAGATTCATTTTAGATATCAAACCTTTTGTATGTTTTAAGACT
1529855 AACTTAAAATTATTTTCTTATTACCCAATCTCGACTAATTTTGGATGTACAAGTCACATCTTACC
651 AACTTAAAATTATTTTCTTATTACCCAATCTCGACTAATTTTGGATGTACAAGTCACATCTTACC
1529920 CAACTTGCTTAGAAATTTTTATTATGCATTTCTAATTTATTTTAAGGGTATATTTGTTTCTCTGT
716 CAACTTGCTTAGAAATTTTTATTATGCATTTCTAATTTATTTTAAGGGTATATTTGTTTCTCTGT
1529985 AATTAGTTTTTCGGAAAATGTTTTATTCATTTTCTAATGTTTAGAACATATACTAAT
781 AATTAGTTTTTCGGAAAATGTTTTATTCATTTTCTAATGTTTAGAACATATACTAAT
* *
1530042 TAGTATGGGTGATTGAACGTTCATTGTCAAATGATTGAGAGTATTTAGAACATATACTACTTTGT
1 TAGTATGGGGGATCGAACGTTCATTGTCAAATGATTGAGAGTATTTAGAACATATACTACTTTGT
1530107 AATCACCATAGCTTAATAAAATTTGTTTTATATATAAACACATGAAAATATATACATACAAATAA
66 AATCACCATAGCTTAATAAAATTTGTTTTATATATAAACACATGAAAATATATACATACAAATAA
1530172 TTATATAAATATCTTAAAATCTATTTATTAATATTTTTAACACTTATATAAATTTAAAAATGTTA
131 --ATATAAATATCTTAAAATCTATTTATT-ATATTTTTAACACTTATA-AAA--TAAAAATGTTA
1530237 AAAACTCATTAAACAATGATAAAAGTGAATATTGTTCTCTTTAAATAATTTGATTTAAGGCATGG
190 AAAACTCATTAAACAATGATAAAAGTGAATATTGTTCTCTTTAAATAATTTGATTTAAGGCATGG
1530302 ATCAAGTGACTTCAATGGTTAAGAGACTTGTTGTTATACCTTGATGGGTTTCAGCAATATCATGG
255 ATCAAGTGACTTCAATGGTTAAGAGACTTGTTGTTATACCTTGATGGGTTTCAGCAATATCATGG
1530367 TTATGAGTATTTACTATCAAATGATTACGAGTAGATAATAGATACTACCTTGTGTTCACCCTGTA
320 TTATGAGTATTTACTATCAAATGATTACGAGTAGATAATAGATACTACCTTGTGTTCACCCTGTA
*
1530432 TTTATTGAAAATTTAAATTCAAACAGTCGCGCCTGCAGGGAGTGTACATGTCAGTGACTAAATAT
385 TTTATTGAAAATTTAAATTCAAACAGTCGCACCTGCAGGGAGTGTACA--T--GTGACTAAATAT
* *
1530497 GATCAAATTTATTGAGTTAAAATTTTAATTAATATTAACTTTTTATTTCAGTTTCAAACAATTTT
446 GATCAAATTTATTGAGTTAAAATTTTAATTAATATTAACTTTTTATTTCAATTTCAAACAATTTG
*
1530562 CTTCTTTTATAAAGCATTAAAAATTATATTTATAAAGTTCAAGGGATAAACTAATAAAAATAATT
511 CTTCTTTTATAAAGCATTAAAAATTATATTTATAAAGTTCAAGAGATAAACTAATAAAAATAATT
1530627 AAATATCAAACTACAATTTTTTTACTTAGTACAAGATTCATTTTAGATATCAAACCTTTTGTATG
576 AAATATCAAACTACAATTTTTTTACTTAGTACAAGATTCATTTTAGATATCAAACCTTTTGTATG
1530692 TTTTAAGACTAACTTAAAATTATTTTCTTATTACCCAATCTCGACTAATTTTGGATGTACAAGTC
641 TTTTAAGACTAACTTAAAATTATTTTCTTATTACCCAATCTCGACTAATTTTGGATGTACAAGTC
1530757 ACATCTTACCCAACTTGCTTAGAAATTTTTATTATGCATTTCTAATTTATTTTAAGGGTATATTT
706 ACATCTTACCCAACTTGCTTAGAAATTTTTATTATGCATTTCTAATTTATTTTAAGGGTATATTT
1530822 GTTTCTCTGTAATTAGTTTTTCGGAAAATGTTTTATTCATTTTCTAATGTTTAG
771 GTTTCTCTGTAATTAGTTTTTCGGAAAATGTTTTATTCATTTTCTAATGTTTAG
1530876 TTCGCGGAAA
Statistics
Matches: 812, Mismatches: 12, Indels: 10
0.97 0.01 0.01
Matches are distributed among these distances:
837 127 0.16
839 27 0.03
840 18 0.02
841 3 0.00
843 249 0.31
845 1 0.00
847 387 0.48
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (837 bp):
TAGTATGGGGGATCGAACGTTCATTGTCAAATGATTGAGAGTATTTAGAACATATACTACTTTGT
AATCACCATAGCTTAATAAAATTTGTTTTATATATAAACACATGAAAATATATACATACAAATAA
ATATAAATATCTTAAAATCTATTTATTATATTTTTAACACTTATAAAATAAAAATGTTAAAAACT
CATTAAACAATGATAAAAGTGAATATTGTTCTCTTTAAATAATTTGATTTAAGGCATGGATCAAG
TGACTTCAATGGTTAAGAGACTTGTTGTTATACCTTGATGGGTTTCAGCAATATCATGGTTATGA
GTATTTACTATCAAATGATTACGAGTAGATAATAGATACTACCTTGTGTTCACCCTGTATTTATT
GAAAATTTAAATTCAAACAGTCGCACCTGCAGGGAGTGTACATGTGACTAAATATGATCAAATTT
ATTGAGTTAAAATTTTAATTAATATTAACTTTTTATTTCAATTTCAAACAATTTGCTTCTTTTAT
AAAGCATTAAAAATTATATTTATAAAGTTCAAGAGATAAACTAATAAAAATAATTAAATATCAAA
CTACAATTTTTTTACTTAGTACAAGATTCATTTTAGATATCAAACCTTTTGTATGTTTTAAGACT
AACTTAAAATTATTTTCTTATTACCCAATCTCGACTAATTTTGGATGTACAAGTCACATCTTACC
CAACTTGCTTAGAAATTTTTATTATGCATTTCTAATTTATTTTAAGGGTATATTTGTTTCTCTGT
AATTAGTTTTTCGGAAAATGTTTTATTCATTTTCTAATGTTTAGAACATATACTAAT
Found at i:1531154 original size:31 final size:29
Alignment explanation
Indices: 1531110--1531167 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
1531100 TATTGTTATA
1531110 ATTATATTATAATTATATATATATATATATT
1 ATTATATTATAATTATA-ATA-ATATATATT
*
1531141 ATTATACTT-TAATTTTAATAATATATA
1 ATTATA-TTATAATTATAATAATATATA
1531168 ATAAAGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
30 3 0.12
31 13 0.52
32 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTATATTATAATTATAATAATATATATT
Found at i:1531165 original size:37 final size:38
Alignment explanation
Indices: 1531073--1531167 Score: 95
Period size: 37 Copynumber: 2.5 Consensus size: 38
1531063 TATTTATTGA
* * *
1531073 TAATTTTAATAATATAATATAATTTTTTATTGTTATAAT
1 TAATTTTAATAATAT-ATATAATTATATATTATTATAAT
* * *
1531112 TATATTATAATTATATATAT-A-TATATATTATTATACTT
1 TA-ATTTTAATAATATATATAATTATATATTATTATA-AT
1531150 TAATTTTAATAATATATA
1 TAATTTTAATAATATATA
1531168 ATAAAGTAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
37 25 0.54
38 4 0.09
39 6 0.13
40 11 0.24
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (38 bp):
TAATTTTAATAATATATATAATTATATATTATTATAAT
Found at i:1531295 original size:15 final size:15
Alignment explanation
Indices: 1531264--1531304 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1531254 AAATATAATA
*
1531264 TAATATTATTA-TTT
1 TAATATTATAATTTT
1531278 TAATATTATAATTTT
1 TAATATTATAATTTT
*
1531293 TAATATTTTAAT
1 TAATATTATAAT
1531305 AATATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATATTATAATTTT
Found at i:1531398 original size:37 final size:37
Alignment explanation
Indices: 1531301--1531401 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 37
1531291 TTTAATATTT
* * *
1531301 TAATAATATTATTATTAGTAAATAATTAATATAATTAA
1 TAATAATTTTATT-TTAATAAATAATTAACATAATTAA
* *
1531339 TAATATATTATTCTCATTTTAATAAATAATTAACATAGTTTA
1 TAATA-A-T-TT-T-ATTTTAATAAATAATTAACATAATTAA
1531381 TAATAATTTTATTTTAATAAA
1 TAATAATTTTATTTTAATAAA
1531402 ATATAATAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
37 11 0.21
38 6 0.11
39 3 0.06
40 2 0.04
41 2 0.04
42 26 0.49
43 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (37 bp):
TAATAATTTTATTTTAATAAATAATTAACATAATTAA
Found at i:1531545 original size:23 final size:23
Alignment explanation
Indices: 1531496--1531545 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1531486 ATTATTCTAA
1531496 TATT-TTAAAAATAATATTATCT
1 TATTGTTAAAAATAATATTATCT
1531518 T-TTGTTAATAAATAATATTAT-T
1 TATTGTTAA-AAATAATATTATCT
1531540 TATTGT
1 TATTGT
1531546 ATTTGATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.08
22 7 0.28
23 16 0.64
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
TATTGTTAAAAATAATATTATCT
Found at i:1533184 original size:35 final size:35
Alignment explanation
Indices: 1533138--1533212 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1533128 AAAATACTTT
*
1533138 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTAG
1 AATTTAAGGTTTAGAATGTAATTAAAGTATTTTAG
* * *
1533173 AATTTAAGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAAGGTTTAGAATGTAATTAAAGTATTTTAG
1533208 AATTT
1 AATTT
1533213 TGGACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGTAATTAAAGTATTTTAG
Found at i:1537988 original size:21 final size:21
Alignment explanation
Indices: 1537940--1537989 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1537930 CTACGATTAT
* *
1537940 GACGACGACGATTGTGATCTA
1 GACGACGACGATTATGATCGA
*
1537961 GATGACGACGATTATGAT-GA
1 GACGACGACGATTATGATCGA
1537981 CGACGACGA
1 -GACGACGA
1537990 TGAGTTGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (21 bp):
GACGACGACGATTATGATCGA
Found at i:1540342 original size:21 final size:21
Alignment explanation
Indices: 1540318--1540358 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1540308 AAATAAATTA
1540318 AAAATATAAAATTATTAAAAT
1 AAAATATAAAATTATTAAAAT
1540339 AAAATATAAAATTATTAAAA
1 AAAATATAAAATTATTAAAA
1540359 ATTACTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATATAAAATTATTAAAAT
Found at i:1541143 original size:70 final size:70
Alignment explanation
Indices: 1541066--1541199 Score: 268
Period size: 70 Copynumber: 1.9 Consensus size: 70
1541056 AGGGACGAAA
1541066 ATAACTTTTTAATAAAAATACATAGATAAATCTAAAAATATATTGTAATTTAAAATTTTTAAGGC
1 ATAACTTTTTAATAAAAATACATAGATAAATCTAAAAATATATTGTAATTTAAAATTTTTAAGGC
1541131 GGTCG
66 GGTCG
1541136 ATAACTTTTTAATAAAAATACATAGATAAATCTAAAAATATATTGTAATTTAAAATTTTTAAGG
1 ATAACTTTTTAATAAAAATACATAGATAAATCTAAAAATATATTGTAATTTAAAATTTTTAAGG
1541200 AGCGACCGCC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (70 bp):
ATAACTTTTTAATAAAAATACATAGATAAATCTAAAAATATATTGTAATTTAAAATTTTTAAGGC
GGTCG
Found at i:1543979 original size:74 final size:72
Alignment explanation
Indices: 1543815--1544122 Score: 228
Period size: 72 Copynumber: 4.2 Consensus size: 72
1543805 TTGAAAGAAA
* * * ** *
1543815 AAAATTGTATCTCACTTAAAATAGTTT-TGCTTGAAATAAAATTGTCTCACTCGAGA-AAGTTTT
1 AAAATTTTATCTCACTTGAGATAGTTTCT-CTCAAAATAAAATTATCTCACTCGAGACAA-TTTT
* *
1543878 TCTCAAAAT
64 CCTCAAAAC
* * * * * *
1543887 AAAATTTTCTCTCCCTTGAAATAGTTTCTCTCAAAATAAAATTTTATCTTACTTGAGGCAATTTT
1 AAAATTTTATCTCACTTGAGATAGTTTCTCTCAAAATAAAA--TTATCTCACTCGAGACAATTTT
* * *
1543952 TCTCGAGAC
64 CCTCAAAAC
* * * *
1543961 AAAATTTTATCTTACTTGAGATAGTTCCTTTCGAAATAAAATTATCTCACTCGAGACAATTTTCC
1 AAAATTTTATCTCACTTGAGATAGTTTCTCTCAAAATAAAATTATCTCACTCGAGACAATTTTCC
*
1544026 TTAAAAC
66 TCAAAAC
* * * * * * *
1544033 ATAAATTTTATATCACTTGAGATAGTTT-TATTTAAAACAAAATTTCATCTCACTCAAGATAGTT
1 A-AAATTTTATCTCACTTGAGATAGTTTCT-CTCAAAATAAAA-TT-ATCTCACTCGAGACAATT
* **
1544097 TTTCTTGAAAC
62 TTCCTCAAAAC
1544108 -AAATTTTATCTCACT
1 AAAATTTTATCTCACT
1544123 CTAAACAATT
Statistics
Matches: 189, Mismatches: 39, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
72 59 0.31
73 47 0.25
74 57 0.30
75 26 0.14
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (72 bp):
AAAATTTTATCTCACTTGAGATAGTTTCTCTCAAAATAAAATTATCTCACTCGAGACAATTTTCC
TCAAAAC
Found at i:1544075 original size:73 final size:73
Alignment explanation
Indices: 1543888--1544122 Score: 179
Period size: 73 Copynumber: 3.2 Consensus size: 73
1543878 TCTCAAAATA
* * * * * * * * ** * *
1543888 AAATTTTCTCTCCCTTGAAATAGTTTCTCTCAAAATAAAATTTTATCTTACTTGAGGCAATTTTT
1 AAATTTTATCTCACTTGAGATAGTTCCTTTCAAAACAAAATTTCATCTCACTCAAGACAATTTTC
** *
1543953 CTCGAGAC
66 CTTAAAAC
* * * *
1543961 AAAATTTTATCTTACTTGAGATAGTTCCTTTCGAAATAAAA-TT-ATCTCACTCGAGACAATTTT
1 -AAATTTTATCTCACTTGAGATAGTTCCTTTCAAAACAAAATTTCATCTCACTCAAGACAATTTT
1544024 CCTTAAAAC
65 CCTTAAAAC
* * * * *
1544033 ATAAATTTTATATCACTTGAGATAGTT-TTATTTAAAACAAAATTTCATCTCACTCAAGATAGTT
1 --AAATTTTATCTCACTTGAGATAGTTCCT-TTCAAAACAAAATTTCATCTCACTCAAGACAATT
* *
1544097 TTTCTTGAAAC
63 TTCCTTAAAAC
1544108 AAATTTTATCTCACT
1 AAATTTTATCTCACT
1544123 CTAAACAATT
Statistics
Matches: 130, Mismatches: 27, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
72 23 0.18
73 48 0.37
74 35 0.27
75 24 0.18
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.40
Consensus pattern (73 bp):
AAATTTTATCTCACTTGAGATAGTTCCTTTCAAAACAAAATTTCATCTCACTCAAGACAATTTTC
CTTAAAAC
Found at i:1544119 original size:36 final size:37
Alignment explanation
Indices: 1543815--1544123 Score: 184
Period size: 37 Copynumber: 8.5 Consensus size: 37
1543805 TTGAAAGAAA
* ** * * * *
1543815 AAAATTGTATCTCACTTAAAATAGTTTTGCTTGAAAT
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAAC
* * * *
1543852 AAAA--TTGTCTCACTCGAGAAAGTTTTTCTCAAAAT
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAAC
* * * * * * *
1543887 AAAATTTTCTCTCCCTTGAAATAGTTTCTCTCAAAAT
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAAC
* * ** * ** *
1543924 AAAATTTTATCTTACTTGAGGCAATTTTTCTCGAGAC
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAAC
* * * *
1543961 AAAATTTTATCTTACTTGAGATAGTTCCTTTC--GAAAT
1 AAAATTTTATCTCACTCGAGATAGTT--TTTCTTAAAAC
* * *
1543998 AAAA--TTATCTCACTCGAGACAATTTTCCTTAAAAC
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAAC
* *
1544033 ATAAATTTTATATCACTTGAGATAGTTTTAT-TTAAAAC
1 A-AAATTTTATCTCACTCGAGATAGTTTT-TCTTAAAAC
* * *
1544071 AAAATTTCATCTCACTCAAGATAGTTTTTCTTGAAAC
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAAC
1544108 -AAATTTTATCTCACTC
1 AAAATTTTATCTCACTC
1544124 TAAACAATTT
Statistics
Matches: 212, Mismatches: 49, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
33 3 0.01
35 46 0.22
36 19 0.09
37 114 0.54
38 26 0.12
39 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (37 bp):
AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAAC
Found at i:1544142 original size:36 final size:37
Alignment explanation
Indices: 1544002--1544138 Score: 109
Period size: 37 Copynumber: 3.7 Consensus size: 37
1543992 CGAAATAAAA
* *
1544002 TTATCTCACTCGAGACAATTTTCCTTAAAACATAAATT
1 TTATCTCACTCTAAACAATTTTCCTTAAAACA-AAATT
* * * * **
1544040 TTATATCACT-TGAGATAGTTTTATTTAAAACAAAATT
1 TTATCTCACTCT-AAACAATTTTCCTTAAAACAAAATT
* * * * *
1544077 TCATCTCACTC-AAGATAGTTTTTCTTGAAAC-AAATT
1 TTATCTCACTCTAA-ACAATTTTCCTTAAAACAAAATT
1544113 TTATCTCACTCTAAACAATTTTCCTT
1 TTATCTCACTCTAAACAATTTTCCTT
1544139 GAAATTCCAA
Statistics
Matches: 79, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
36 25 0.32
37 29 0.37
38 25 0.32
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (37 bp):
TTATCTCACTCTAAACAATTTTCCTTAAAACAAAATT
Found at i:1550710 original size:22 final size:22
Alignment explanation
Indices: 1550658--1550713 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1550648 AATACTAAAG
1550658 TGATACAAAAGTGCATTCGCAC
1 TGATACAAAAGTGCATTCGCAC
* * * *
1550680 T-AAATCAAAATTGCATTTGCAT
1 TGATA-CAAAAGTGCATTCGCAC
1550702 TGATACAAAAGT
1 TGATACAAAAGT
1550714 CTAAGGAAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (22 bp):
TGATACAAAAGTGCATTCGCAC
Found at i:1553922 original size:20 final size:20
Alignment explanation
Indices: 1553874--1553925 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1553864 AAAATGCAAT
1553874 AATTAAAATAACAGTAGCTA
1 AATTAAAATAACAGTAGCTA
* *
1553894 AATTTAAAATAATAGT-GACTG
1 AA-TTAAAATAACAGTAG-CTA
1553915 AATTAAAATAA
1 AATTAAAATAA
1553926 AACAAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.29
Consensus pattern (20 bp):
AATTAAAATAACAGTAGCTA
Found at i:1554494 original size:24 final size:24
Alignment explanation
Indices: 1554449--1554494 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1554439 GAAACTCAGT
* * *
1554449 AATATGGTATCGATTCTTCTTCTC
1 AATATGATATCGATACTACTTCTC
1554473 AATATGATATCGATACTACTTC
1 AATATGATATCGATACTACTTC
1554495 GAGAATCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (24 bp):
AATATGATATCGATACTACTTCTC
Found at i:1557119 original size:4 final size:4
Alignment explanation
Indices: 1557110--1557318 Score: 55
Period size: 4 Copynumber: 52.2 Consensus size: 4
1557100 AAAAGGTAAG
* *
1557110 AAAT AAAT AAAT AAAT AAAATT AAAAT GAAG AAA- AAAT AAATT AAAT
1 AAAT AAAT AAAT AAAT -AAA-T -AAAT AAAT AAAT AAAT AAA-T AAAT
* * * *
1557157 AAA- AGAT AAGAT AAAG AAA- ACAA- AGAT AAA- ATAAT AAGT AAAAT
1 AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT AAAT A-AAT AAAT -AAAT
* * * * * * *
1557201 AAAT --AT AAAA AAAT AAAAA AAAT AAAG AAAA AGAAG AAAA AAAT ATAT
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
* * *
1557249 AAAT AAAAC AAAT AAAT AAA- ATAA- AAAT AAA- AAGT AAA- AAAT ATAT
1 AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
1557295 ATAT ATA- AAAT AAAT AAAA AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
1557319 GTATATATAT
Statistics
Matches: 155, Mismatches: 29, Indels: 42
0.69 0.13 0.19
Matches are distributed among these distances:
2 2 0.01
3 18 0.12
4 105 0.68
5 25 0.16
6 5 0.03
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:1557167 original size:26 final size:26
Alignment explanation
Indices: 1557118--1557231 Score: 71
Period size: 26 Copynumber: 4.5 Consensus size: 26
1557108 AGAAATAAAT
*
1557118 AAATAAATAAAATTAAAATGAAGAAA
1 AAATAAATAAAATAAAAATGAAGAAA
*
1557144 AAATAAATTAAATAAAAGAT-AAGATAA
1 AAATAAATAAAATAAAA-ATGAAGA-AA
* * *
1557171 AGA-AAACAAAGATAAAATAAT-AAG-TA
1 AAATAAATAAA-AT-AAA-AATGAAGAAA
*
1557197 AAATAAATATAA-AAAAAT-AA-AAA
1 AAATAAATAAAATAAAAATGAAGAAA
*
1557220 AAATAAAGAAAA
1 AAATAAATAAAA
1557232 AGAAGAAAAA
Statistics
Matches: 69, Mismatches: 12, Indels: 17
0.70 0.12 0.17
Matches are distributed among these distances:
23 16 0.23
24 3 0.04
26 28 0.41
27 13 0.19
28 8 0.12
29 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.18
Consensus pattern (26 bp):
AAATAAATAAAATAAAAATGAAGAAA
Found at i:1557189 original size:32 final size:30
Alignment explanation
Indices: 1557142--1557242 Score: 82
Period size: 32 Copynumber: 3.3 Consensus size: 30
1557132 AAAATGAAGA
*
1557142 AAAAATAAATTAAATAAAAGATAAGATAAAG
1 AAAAA-AAATAAAATAAAAGATAAGATAAAG
* *
1557173 AAAACAAAGATAAAATAATAAG-TAAAATAAAT
1 AAAA-AAA-ATAAAATAA-AAGATAAGATAAAG
* *
1557205 ATAAAAAAATAAAA-AAAATA-AAGAAAAAG
1 A-AAAAAAATAAAATAAAAGATAAGATAAAG
1557234 AAGAAAAAA
1 AA-AAAAAA
1557243 ATATATAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
28 1 0.02
29 15 0.26
30 2 0.04
31 12 0.21
32 21 0.37
33 6 0.11
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.15
Consensus pattern (30 bp):
AAAAAAAATAAAATAAAAGATAAGATAAAG
Found at i:1557219 original size:9 final size:9
Alignment explanation
Indices: 1557195--1557316 Score: 68
Period size: 9 Copynumber: 12.9 Consensus size: 9
1557185 AAATAATAAG
*
1557195 TAAAATAAA
1 TAAAAAAAA
1557204 TATAAAAAAA
1 TA-AAAAAAA
1557214 TAAAAAAAA
1 TAAAAAAAA
1557223 TAAAGAAAAA
1 TAAA-AAAAA
*
1557233 GAAGAAAAAA
1 TAA-AAAAAA
* *
1557243 -ATATATAAA
1 TA-AAAAAAA
*
1557252 TAAAACAAA
1 TAAAAAAAA
*
1557261 TAAATAAAA
1 TAAAAAAAA
1557270 TAAAAATAAA
1 TAAAAA-AAA
1557280 -AAGTAAAAAA
1 TAA--AAAAAA
* * *
1557290 TATATATATA
1 TA-AAAAAAA
*
1557300 TAAAATAAA
1 TAAAAAAAA
1557309 TAAAAAAA
1 TAAAAAAA
1557317 TAGTATATAT
Statistics
Matches: 88, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
9 49 0.56
10 33 0.38
11 5 0.06
12 1 0.01
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1557251 original size:48 final size:47
Alignment explanation
Indices: 1557199--1557316 Score: 159
Period size: 47 Copynumber: 2.5 Consensus size: 47
1557189 AATAAGTAAA
1557199 ATAAATATAAAAAAATAAAAAAAATAAAGAA-AAAGAAGAAAAAAATAT
1 ATAAATATAAAAAAATAAAAAAAATAAA-AATAAA-AAGAAAAAAATAT
* * *
1557247 ATAAATA-AAACAAATAAATAAAATAAAAATAAAAAGTAAAAAATAT
1 ATAAATATAAAAAAATAAAAAAAATAAAAATAAAAAGAAAAAAATAT
*
1557293 ATATATATAAAATAAATAAAAAAA
1 ATAAATATAAAA-AAATAAAAAAA
1557317 TAGTATATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
46 20 0.33
47 24 0.39
48 17 0.28
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (47 bp):
ATAAATATAAAAAAATAAAAAAAATAAAAATAAAAAGAAAAAAATAT
Found at i:1557281 original size:38 final size:38
Alignment explanation
Indices: 1557196--1557289 Score: 102
Period size: 38 Copynumber: 2.4 Consensus size: 38
1557186 AATAATAAGT
*
1557196 AAAATAAATATAAAAAAATAAAAAAAATAAAGAAAAAG
1 AAAATAAAAATAAAAAAATAAAAAAAATAAAGAAAAAG
* * * *
1557234 AAGAA-AAAAATATATAAATAAAACAAATAAATAAAATA-
1 AA-AATAAAAATAAAAAAATAAAAAAAATAAAGAAAA-AG
1557272 AAAATAAAAAGTAAAAAA
1 AAAATAAAAA-TAAAAAA
1557290 TATATATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
37 2 0.04
38 35 0.78
39 8 0.18
ACGTcount: A:0.80, C:0.01, G:0.04, T:0.15
Consensus pattern (38 bp):
AAAATAAAAATAAAAAAATAAAAAAAATAAAGAAAAAG
Found at i:1558488 original size:84 final size:85
Alignment explanation
Indices: 1558381--1558538 Score: 246
Period size: 84 Copynumber: 1.9 Consensus size: 85
1558371 ATAATTTTAT
* * *
1558381 TGACAGGTAACCCTTCTTGCCTTGAGTTATGCTGTAAATGATGTGCCATAG-AGCTGAGCATAGT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCATAGAAGCTGAGCATAAT
1558445 CAAACTCGAAGGTCTTTTGG
66 CAAACTCGAAGGTCTTTTGG
* * **
1558465 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCATAGAAGCTGAGCATAAT
1558530 CAAACTCGA
66 CAAACTCGA
1558539 GGGTTTGGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
84 47 0.71
85 19 0.29
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (85 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCATAGAAGCTGAGCATAAT
CAAACTCGAAGGTCTTTTGG
Found at i:1558591 original size:38 final size:36
Alignment explanation
Indices: 1558549--1558635 Score: 104
Period size: 38 Copynumber: 2.4 Consensus size: 36
1558539 GGGTTTGGTT
* *
1558549 TTTCAAAAGAAACATTTTC-AAAGGTTTTTGTGTGTGTG
1 TTTCAAGAGAAACAATTTCGAAAGGTTTTT-T-T-TGTG
**
1558587 TTTCAAGAGAAACAATTTCGAGGGGTTTTTTTTGTG
1 TTTCAAGAGAAACAATTTCGAAAGGTTTTTTTTGTG
1558623 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
1558636 TGTCTCAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 17 0.39
37 1 0.02
38 18 0.41
39 8 0.18
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (36 bp):
TTTCAAGAGAAACAATTTCGAAAGGTTTTTTTTGTG
Found at i:1558661 original size:36 final size:36
Alignment explanation
Indices: 1558621--1558854 Score: 229
Period size: 36 Copynumber: 6.6 Consensus size: 36
1558611 GTTTTTTTTG
*
1558621 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1558657 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
1558694 AG-TTCTAAAAGAAACTATCTCAAGGGAGACAAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1558730 TGTTTCAAG-G-AACAGATATTC-A-A-AG----ATTT
1 TGTTTCAAGAGAAACTG-T-CTCAAGAGAGACAAAATT
1558759 TGTTTCAA-AGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATT
* *
1558795 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
*
1558832 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
1558855 AACTCGTTTT
Statistics
Matches: 164, Mismatches: 17, Indels: 33
0.77 0.08 0.15
Matches are distributed among these distances:
29 13 0.08
30 3 0.02
31 5 0.03
32 2 0.01
33 2 0.01
34 3 0.02
35 3 0.02
36 75 0.46
37 58 0.35
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1558782 original size:102 final size:102
Alignment explanation
Indices: 1558655--1558841 Score: 279
Period size: 102 Copynumber: 1.8 Consensus size: 102
1558645 AGGGACAAAA
*
1558655 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAG-TTCTAAAAGAAACTATCTCAAGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTTC-AAAAGAAACTATCTCAAGA
1558719 GAGACAA-AATTTGTTTCAAGGAACAGATATTCAAAGAT
64 GAGACAAGAATTTGTTTCAAGGAACAGATATTCAAAGAT
* * ** *
1558757 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAAAGAAACTATCTCAAGAGA
*
1558822 GACAAGATTTTGTTTCAAGG
66 GACAAGAATTTGTTTCAAGG
1558842 GAAACTGTCT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
101 25 0.33
102 51 0.67
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAAAGAAACTATCTCAAGAGA
GACAAGAATTTGTTTCAAGGAACAGATATTCAAAGAT
Found at i:1558970 original size:37 final size:37
Alignment explanation
Indices: 1558919--1559107 Score: 132
Period size: 37 Copynumber: 5.4 Consensus size: 37
1558909 TCAAGGTTTA
* *
1558919 TGTTTCAAGAGAAACTATCTTAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
*
1558956 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
** * * * *
1558992 AATTTCAAAGGAAA-TGTTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGGGAGACAAAATTT
* *
1559020 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
* * * *
1559058 TGTTTCAAGGGAAACTACCCCAAGTGAGATAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
*
1559094 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
1559108 TGTTTTCAAT
Statistics
Matches: 116, Mismatches: 23, Indels: 27
0.70 0.14 0.16
Matches are distributed among these distances:
28 2 0.02
29 15 0.13
30 1 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 33 0.28
37 59 0.51
38 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
Found at i:1559020 original size:102 final size:102
Alignment explanation
Indices: 1558899--1559131 Score: 376
Period size: 102 Copynumber: 2.3 Consensus size: 102
1558889 GTGTTTTAAG
* * *
1558899 GGAAACGTTTTCAAGGTTTATGTTTCAAGAGAAACTATCTTAAGGGAGACAAAATTTTGTTTCAA
1 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAA
* *
1558964 GGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAA
66 GGGAAACTACCCCAAGAGAGACAAAATTAATTTCAAA
*
1559001 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA
1 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAA
* * * *
1559066 GGGAAACTACCCCAAGTGAGATAAAATTTATTTCAAG
66 GGGAAACTACCCCAAGAGAGACAAAATTAATTTCAAA
1559103 GGAAATGTTTTCAATGTTTATGTTTCAAG
1 GGAAATGTTTTCAATGTTTATGTTTCAAG
1559132 GGAGACAAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 121 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (102 bp):
GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAA
GGGAAACTACCCCAAGAGAGACAAAATTAATTTCAAA
Found at i:1559131 original size:87 final size:87
Alignment explanation
Indices: 1559040--1559218 Score: 288
Period size: 87 Copynumber: 2.1 Consensus size: 87
1559030 AGAAACTGTC
**
1559040 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGT-GAGATAAAATTTATTTCAAGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAA-TCGAGATAAAATCCATTTCAAGG
*
1559104 GAAATGTTTTCAATGTTTATGTT
65 GAAACGTTTTCAATGTTTATGTT
* * *
1559127 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATCCATTTTAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAATCGAGATAAAATCCATTTCAAGGG
1559192 AAACGTTTTCAATGTTTATGTT
66 AAACGTTTTCAATGTTTATGTT
1559214 TCAAG
1 TCAAG
1559219 AGAAACTATC
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
86 1 0.01
87 84 0.99
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAATCGAGATAAAATCCATTTCAAGGG
AAACGTTTTCAATGTTTATGTT
Found at i:1559318 original size:189 final size:189
Alignment explanation
Indices: 1558940--1559323 Score: 504
Period size: 189 Copynumber: 2.0 Consensus size: 189
1558930 AAACTATCTT
*
1558940 AAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGGAA
1 AAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCAATTTCAAAGGAA
* * * * **
1559005 ATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGA
66 ACGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCCAAAAGA
* * * * * *
1559070 AACTACCCCAAGTGAGATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATGTTTC
131 AAATACCCCAAGGGAGATAAAATTTATTTCAAGGAAAAAGTATTCAATATTTATGTTTC
** * * * *
1559129 AAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATCCATTTTAAGGGAA
1 AAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCAATTTCAAAGGAA
1559194 ACGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCCAAAAGA
66 ACGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCCAAAAGA
** * * *
1559259 AAATGTCTCAAGGGAGATGAAA-TTAGTTTCAATGAAAACAG-ATTCAAATATTT-TGTTTC
131 AAATACCCCAAGGGAGATAAAATTTA-TTTCAAGGAAAA-AGTATTC-AATATTTATGTTTC
1559318 AAGGGA
1 AAGGGA
1559324 AACTTGGAAA
Statistics
Matches: 168, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
188 3 0.02
189 158 0.94
190 7 0.04
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (189 bp):
AAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCAATTTCAAAGGAA
ACGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCCAAAAGA
AAATACCCCAAGGGAGATAAAATTTATTTCAAGGAAAAAGTATTCAATATTTATGTTTC
Found at i:1559661 original size:106 final size:106
Alignment explanation
Indices: 1559496--1559688 Score: 278
Period size: 106 Copynumber: 1.8 Consensus size: 106
1559486 ATCCTCCGCC
* * * *
1559496 GTGAAGTTAAAATTGGCTATGGAACTAAGAAATTGTTTGTTAACAGCCAGTCGTCCCTTCGTTGC
1 GTGAAGTTAAAATTGGCTATGAAACTAAGAAATTATTTGTTAACAACCAGCCGTCCCTTCGTTGC
1559561 GAAGTTGAACTTGTGTTGTCTCGAGTCCAATAATCTTTGTT
66 GAAGTTGAACTTGTGTTGTCTCGAGTCCAATAATCTTTGTT
* * * ** * *
1559602 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGT
1 GTGAAGTTAAAATTGGCTATGAAACTAAGAAATTATTTGTTAACAACCAGCCGTCCCTTCGTTGC
*
1559667 GGAGTTGAACTTGTGTTGTCTC
66 GAAGTTGAACTTGTGTTGTCTC
1559689 AAGTGGCACG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 75 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (106 bp):
GTGAAGTTAAAATTGGCTATGAAACTAAGAAATTATTTGTTAACAACCAGCCGTCCCTTCGTTGC
GAAGTTGAACTTGTGTTGTCTCGAGTCCAATAATCTTTGTT
Found at i:1560339 original size:33 final size:33
Alignment explanation
Indices: 1560270--1560351 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
1560260 TTTGCATCAG
** * *
1560270 GATGTTGAAT-TCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCTCAAAAAAATGCCCCAACATTC
*
1560302 GATGTTGAATCTCAAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAAATGCCCCAACATTC
*
1560335 GATGTTAAATCTTCAAA
1 GATGTTGAATC-TCAAA
1560352 GATGCCCTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 10 0.24
33 27 0.64
34 5 0.12
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (33 bp):
GATGTTGAATCTCAAAAAAATGCCCCAACATTC
Found at i:1561350 original size:69 final size:69
Alignment explanation
Indices: 1561267--1561404 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
1561257 TGTCTCTCTC
* *
1561267 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAATAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAATAATTCAGAAATGATTGTGCTTGATCAATA
1561332 TCAT
66 TCAT
* * * * * *
1561336 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTTCTTGATCAATA
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAATAATTCAGAAATGATTGTGCTTGATCAATA
1561401 TCAT
66 TCAT
1561405 AGTTTGAATC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAATAATTCAGAAATGATTGTGCTTGATCAATA
TCAT
Found at i:1561519 original size:14 final size:13
Alignment explanation
Indices: 1561477--1561525 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
1561467 TTTTCTTCAA
1561477 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
1561489 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
1561501 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
1561516 TTTTCTCTTT
1 TTTTCTCTTT
1561526 TTGCTTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
14 10 0.30
15 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:1561523 original size:27 final size:25
Alignment explanation
Indices: 1561476--1561527 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
1561466 TTTTTCTTCA
1561476 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
1561501 ATTTTCTCTTTGCTTTTTTCTCTTTTT
1 ATTTTC-CTTTG-TTTTTTCTCTTTTT
1561528 GCTTTGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:1564742 original size:28 final size:26
Alignment explanation
Indices: 1564684--1564817 Score: 91
Period size: 27 Copynumber: 5.2 Consensus size: 26
1564674 AAATAAATAT
1564684 AAAAAATATA-AAATAAAGAAAA-AGAA
1 AAAAAATATATAAATAAA-AAAATA-AA
1564710 GAAAAAATATATAAATAAAACAAAT-AA
1 -AAAAAATATATAAATAAAA-AAATAAA
* *
1564737 ATAAAATA-AT-AATAAAAAAGT-AA
1 AAAAAATATATAAATAAAAAAATAAA
* *
1564760 AAATAATATATATATAAAATAAATAAA
1 AAAAAATATATAAATAAAA-AAATAAA
* * * * *
1564787 AAAATAGTATATATATATATAAATAAT
1 AAAA-AATATATAAATAAAAAAATAAA
1564814 AAAA
1 AAAA
1564818 CTGATAATAT
Statistics
Matches: 88, Mismatches: 11, Indels: 16
0.77 0.10 0.14
Matches are distributed among these distances:
23 11 0.12
24 9 0.10
25 8 0.09
26 10 0.11
27 28 0.32
28 22 0.25
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (26 bp):
AAAAAATATATAAATAAAAAAATAAA
Found at i:1564743 original size:53 final size:52
Alignment explanation
Indices: 1564620--1564792 Score: 144
Period size: 49 Copynumber: 3.3 Consensus size: 52
1564610 AAATGAAGAA
* * * * * *
1564620 AAAACAAATTAAATAAAAGATAAGATAAAGAAAGCA-AAGATAAAATA-GTAAGT
1 AAAACAAA-TAAA-AAAATATAAAATAAAGAAA-AAGAAGAAAAAATATATAAAT
*
1564673 AAAATAAATATAAAAAATATAAAATAAAGAAAAAGAAGAAAAAATATATAAAT
1 AAAACAAATA-AAAAAATATAAAATAAAGAAAAAGAAGAAAAAATATATAAAT
* * *
1564726 AAAACAAATAAATAAA-AT--AATAATA-AAAAAGTAA-AAATAATATATATAT
1 AAAACAAATAAAAAAATATAAAATAA-AGAAAAAG-AAGAAAAAATATATAAAT
*
1564775 AAAATAAATAAAAAAATA
1 AAAACAAATAAAAAAATA
1564793 GTATATATAT
Statistics
Matches: 101, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
49 38 0.38
50 4 0.04
51 3 0.03
52 34 0.34
53 22 0.22
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (52 bp):
AAAACAAATAAAAAAATATAAAATAAAGAAAAAGAAGAAAAAATATATAAAT
Found at i:1564787 original size:9 final size:9
Alignment explanation
Indices: 1564672--1564792 Score: 58
Period size: 9 Copynumber: 13.2 Consensus size: 9
1564662 AAATAGTAAG
1564672 TAAAATAAA
1 TAAAATAAA
*
1564681 TATAAAAAATA
1 TA-AAATAA-A
1564692 TAAAATAAA
1 TAAAATAAA
*
1564701 GAAAA-AGAA
1 TAAAATA-AA
*
1564710 GAAAA-AATA
1 TAAAATAA-A
1564719 TATAAATAAA
1 TA-AAATAAA
1564729 -ACAAATAAA
1 TA-AAATAAA
1564738 TAAAATAATAA
1 TAAAAT-A-AA
*
1564749 TAAAA-AAG
1 TAAAATAAA
1564757 TAAAA-ATAA
1 TAAAATA-AA
* *
1564766 T-ATATATA
1 TAAAATAAA
1564774 TAAAATAAA
1 TAAAATAAA
1564783 TAAAA-AAA
1 TAAAATAAA
1564791 TA
1 TA
1564793 GTATATATAT
Statistics
Matches: 89, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
8 18 0.20
9 43 0.48
10 16 0.18
11 12 0.13
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.21
Consensus pattern (9 bp):
TAAAATAAA
Found at i:1564790 original size:36 final size:36
Alignment explanation
Indices: 1564733--1564812 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
1564723 AATAAAACAA
1564733 ATAAATAAAATAATAATAAAAA-AGTAAAAATAATAT
1 ATAAATAAAATAATAATAAAAATAGTAAAAAT-ATAT
* * *
1564769 ATATATAAAATAAATAA-AAAAATAGTATATATATAT
1 ATAAATAAAAT-AATAATAAAAATAGTAAAAATATAT
1564805 ATAAATAA
1 ATAAATAA
1564813 TAAAACTGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 26 0.68
37 12 0.32
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (36 bp):
ATAAATAAAATAATAATAAAAATAGTAAAAATATAT
Found at i:1564799 original size:2 final size:2
Alignment explanation
Indices: 1564794--1564892 Score: 141
Period size: 2 Copynumber: 50.0 Consensus size: 2
1564784 AAAAAAATAG
* *
1564794 TA TA TA TA TA TA TA AA TA -A TA -A AA CTGA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA TA TA TA TA TA
1564835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1564877 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1564893 ATCTAAAAAA
Statistics
Matches: 89, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
1 3 0.03
2 84 0.94
3 1 0.01
4 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1567502 original size:60 final size:59
Alignment explanation
Indices: 1567437--1567548 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
1567427 TATAGGGTGT
* * * * *
1567437 TACTTTGTTGAGTCCTCTGACTACTAAAAGTTATAAAATGGTC-CCCTGACTATAAGTCCC
1 TACTTTGTTGAGACC-CCGACTAATAAAAGCTATAAAATGATCACCC-GACTATAAGTCCC
*
1567497 TACTTTGTTGAGACCCCGACTAATAAAAGCTATTAAATGATCACCCGACTAT
1 TACTTTGTTGAGACCCCGACTAATAAAAGCTATAAAATGATCACCCGACTAT
1567549 TCATATATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
59 28 0.62
60 17 0.38
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (59 bp):
TACTTTGTTGAGACCCCGACTAATAAAAGCTATAAAATGATCACCCGACTATAAGTCCC
Found at i:1568736 original size:22 final size:22
Alignment explanation
Indices: 1568711--1568758 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1568701 ATCAATTTGA
*
1568711 AAAAAAATAAAAGTTTGA-AATT
1 AAAAAAATAAAA-TTTAAGAATT
*
1568733 AAAAAGATAAAATTTAAGAATT
1 AAAAAAATAAAATTTAAGAATT
1568755 AAAA
1 AAAA
1568759 TAACCAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (22 bp):
AAAAAAATAAAATTTAAGAATT
Found at i:1577331 original size:21 final size:23
Alignment explanation
Indices: 1577305--1577355 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1577295 AGGGAATCAA
1577305 TCCCCCCTTG-A-GGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
*
1577326 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
1577349 TCCCCCC
1 TCCCCCC
1577356 ACAGGGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 1 0.04
23 16 0.62
ACGTcount: A:0.18, C:0.41, G:0.22, T:0.20
Consensus pattern (23 bp):
TCCCCCCTTGAAGGGGAACCGAT
Found at i:1577376 original size:20 final size:21
Alignment explanation
Indices: 1577337--1577376 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1577327 CCCCCTTTGA
*
1577337 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
1577358 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
1577377 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:1578616 original size:19 final size:19
Alignment explanation
Indices: 1578592--1578631 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1578582 GTGTTTTAAG
1578592 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
1578611 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
1578630 TG
1 TG
1578632 GGAGAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (19 bp):
TGTGTTTTAAAATGATAAA
Found at i:1586247 original size:140 final size:141
Alignment explanation
Indices: 1586063--1586413 Score: 367
Period size: 140 Copynumber: 2.5 Consensus size: 141
1586053 TTTGGAGGAT
* * * *
1586063 ATTTTAATTTCGTCCTCGCTTTT-T-CTCGAGCTTTCAAATTAATTATTTGATTCAATAAATTGT
1 ATTTTAATTTGGTCATCGCTTTTATGCTCGAGGTTTCATATTAATTATTTGATTCAATAAATTGT
** * *
1586126 TAAAATTGGTTGGGTT-TAAAT-TATAGAGCATTCACCTTAGGTTTAATTTCA-CTTTAGTCCTT
66 TAAAATTGGTTGAATTCTAAGTAT-TAGAGCATTCACCTTA-GATTAATTTCATCTTTAGTCCTT
* * *
1586188 TAATTTAGGTAAA
129 TAACTCACGTAAA
*
1586201 TTTTTAATTTGGTCATCGCTTTTATGCAT-GAGGTTTCATATTAATTATTTGA-TCAAATAAATT
1 ATTTTAATTTGGTCATCGCTTTTATGC-TCGAGGTTTCATATTAATTATTTGATTC-AATAAATT
* * * ** * *
1586264 GTTAAAA-TGGTTTAATTCTTAGTATTAGAGCCTTCATTTTAGATTAATTTTATCTTTGGTCCTT
64 GTTAAAATTGGTTGAATTCTAAGTATTAGAGCATTCACCTTAGATTAATTTCATCTTTAGTCCTT
1586328 TAACTCACGTAAA
129 TAACTCACGTAAA
** * * ** * *
1586341 ATTTTAATTTGGTCATATCCTTTATGCTCGAGGTTTCATTTTAATTATTCAATTAAATAAATTGC
1 ATTTTAATTTGGTCATCGCTTTTATGCTCGAGGTTTCATATTAATTATTTGATTCAATAAATTGT
1586406 TAAAATTG
66 TAAAATTG
1586414 ATTAAGTTAA
Statistics
Matches: 175, Mismatches: 28, Indels: 17
0.80 0.13 0.08
Matches are distributed among these distances:
138 20 0.11
139 20 0.11
140 130 0.74
141 5 0.03
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (141 bp):
ATTTTAATTTGGTCATCGCTTTTATGCTCGAGGTTTCATATTAATTATTTGATTCAATAAATTGT
TAAAATTGGTTGAATTCTAAGTATTAGAGCATTCACCTTAGATTAATTTCATCTTTAGTCCTTTA
ACTCACGTAAA
Found at i:1589187 original size:16 final size:16
Alignment explanation
Indices: 1589168--1589198 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1589158 GTATAACCCG
1589168 ACCTGTTATCAACCTT
1 ACCTGTTATCAACCTT
*
1589184 ACCTGTTATGAACCT
1 ACCTGTTATCAACCT
1589199 GATCTGTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.10, T:0.35
Consensus pattern (16 bp):
ACCTGTTATCAACCTT
Found at i:1589205 original size:16 final size:16
Alignment explanation
Indices: 1589162--1589205 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1589152 TAATTGGTAT
*
1589162 AACCCGACCTGTTATC
1 AACCTGACCTGTTATC
* *
1589178 AACCTTACCTGTTATG
1 AACCTGACCTGTTATC
*
1589194 AACCTGATCTGT
1 AACCTGACCTGT
1589206 AATTGACTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.32
Consensus pattern (16 bp):
AACCTGACCTGTTATC
Found at i:1589433 original size:21 final size:21
Alignment explanation
Indices: 1589408--1589461 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1589398 TTAACTTTCT
*
1589408 ATATAAATTATAATTCTAAT-
1 ATATAAATTATAATTATAATC
* *
1589428 AGTATAAATAATTATTATAATC
1 A-TATAAATTATAATTATAATC
1589450 ATAT-AATTATAA
1 ATATAAATTATAA
1589462 ATAATTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 7 0.26
21 19 0.70
22 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATAAATTATAATTATAATC
Found at i:1589573 original size:23 final size:24
Alignment explanation
Indices: 1589543--1589592 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1589533 ATTTTATGTA
*
1589543 ATAATTAA-TTAATAATTT-AAAT
1 ATAATTAACTTAACAATTTAAAAT
*
1589565 ATAACTTAACTTAACATTTTAAAAT
1 ATAA-TTAACTTAACAATTTAAAAT
1589590 ATA
1 ATA
1589593 TATAAAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 4 0.17
24 8 0.35
25 7 0.30
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (24 bp):
ATAATTAACTTAACAATTTAAAAT
Found at i:1589991 original size:23 final size:23
Alignment explanation
Indices: 1589959--1590026 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
1589949 AGGCAGTAGT
*
1589959 AAGCAACATTGCATCAATTCAAC
1 AAGCATCATTGCATCAATTCAAC
*
1589982 AAGCATCATTGCATCAACTCAAC
1 AAGCATCATTGCATCAATTCAAC
1590005 AAGCATCATTGCATCAATTCAA
1 AAGCATCATTGCATCAATTCAA
1590027 TATTATGCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (23 bp):
AAGCATCATTGCATCAATTCAAC
Found at i:1590035 original size:18 final size:18
Alignment explanation
Indices: 1590014--1590073 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
1590004 CAAGCATCAT
1590014 TGCATCAATTCAATATTA
1 TGCATCAATTCAATATTA
* *
1590032 TGCATTCAA--CAAGCATCA
1 TGCA-TCAATTCAA-TATTA
*
1590050 TTGCATCAATTCATTATTA
1 -TGCATCAATTCAATATTA
1590069 TGCAT
1 TGCAT
1590074 TCAACAAGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
17 3 0.09
18 16 0.50
19 11 0.34
20 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (18 bp):
TGCATCAATTCAATATTA
Found at i:1590042 original size:37 final size:37
Alignment explanation
Indices: 1590000--1590085 Score: 163
Period size: 37 Copynumber: 2.3 Consensus size: 37
1589990 TTGCATCAAC
1590000 TCAACAAGCATCATTGCATCAATTCAATATTATGCAT
1 TCAACAAGCATCATTGCATCAATTCAATATTATGCAT
*
1590037 TCAACAAGCATCATTGCATCAATTCATTATTATGCAT
1 TCAACAAGCATCATTGCATCAATTCAATATTATGCAT
1590074 TCAACAAGCATC
1 TCAACAAGCATC
1590086 CAATCAGTGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.31
Consensus pattern (37 bp):
TCAACAAGCATCATTGCATCAATTCAATATTATGCAT
Found at i:1590903 original size:23 final size:22
Alignment explanation
Indices: 1590854--1590906 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1590844 AAATTCTGAA
* *
1590854 AAAATAAAGAAAAAAAAAGAAT
1 AAAATTAAGAAAAAAAAAAAAT
1590876 AAAATTAAGAAAAAAGAATAAAAT
1 AAAATTAAGAAAAAA-AA-AAAAT
1590900 -AAATTAA
1 AAAATTAA
1590907 AATAAGTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 14 0.52
23 9 0.33
24 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (22 bp):
AAAATTAAGAAAAAAAAAAAAT
Found at i:1590908 original size:19 final size:19
Alignment explanation
Indices: 1590866--1590902 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1590856 AATAAAGAAA
*
1590866 AAAAAAGAATAAAATTAAG
1 AAAAAAGAATAAAATAAAG
1590885 AAAAAAGAATAAAATAAA
1 AAAAAAGAATAAAATAAA
1590903 TTAAAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (19 bp):
AAAAAAGAATAAAATAAAG
Found at i:1593774 original size:7 final size:7
Alignment explanation
Indices: 1593741--1593783 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1593731 ACTATACACA
1593741 CATACA-
1 CATACAT
1593747 CATACAT
1 CATACAT
*
1593754 GCATATATT
1 -CATACA-T
1593763 CATACAT
1 CATACAT
1593770 CATACAT
1 CATACAT
1593777 CATACAT
1 CATACAT
1593784 ATTAACATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 6 0.19
7 15 0.47
8 10 0.31
9 1 0.03
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (7 bp):
CATACAT
Found at i:1593824 original size:2 final size:2
Alignment explanation
Indices: 1593810--1593862 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
1593800 GATTAATTAC
1593810 AT AT AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1593852 AT AT AT AT AT A
1 AT AT AT AT AT A
1593863 CTTAAGTCTC
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 47 0.96
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1594839 original size:111 final size:111
Alignment explanation
Indices: 1594637--1594857 Score: 397
Period size: 111 Copynumber: 2.0 Consensus size: 111
1594627 TCAGAGTATT
1594637 CTTATGGAATAATGCAATACATAACCTTGAGCATATTTGAGATATTTCAATTCTCTCACAATCAC
1 CTTATGGAATAATGCAATACATAACCTTGAGCATATTTGAGATATTTCAATTCTCTCACAATCAC
*
1594702 TTTTTAGAATTTTAGCCATGAGTTGCTTGTGAACTTGCTTAAATTA
66 TTTTTAGAATTTTAGCCATGAATTGCTTGTGAACTTGCTTAAATTA
* *
1594748 CTTATGGAATAATGCAATATATAACCTTGAGCATATTTGATATATTTCAATTCTCTCACAATCAC
1 CTTATGGAATAATGCAATACATAACCTTGAGCATATTTGAGATATTTCAATTCTCTCACAATCAC
* *
1594813 TTTTTAGAATTTTAGCCCTGAATTGCTTGTGAACTTTCTTAAATT
66 TTTTTAGAATTTTAGCCATGAATTGCTTGTGAACTTGCTTAAATT
1594858 GCTCACAATG
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (111 bp):
CTTATGGAATAATGCAATACATAACCTTGAGCATATTTGAGATATTTCAATTCTCTCACAATCAC
TTTTTAGAATTTTAGCCATGAATTGCTTGTGAACTTGCTTAAATTA
Found at i:1595356 original size:2 final size:2
Alignment explanation
Indices: 1595351--1595403 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1595341 TATATATATA
1595351 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1595393 TG TG TG TG TG T
1 TG TG TG TG TG T
1595404 ATTTCAAAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1602995 original size:65 final size:64
Alignment explanation
Indices: 1602920--1603076 Score: 167
Period size: 65 Copynumber: 2.4 Consensus size: 64
1602910 TACACTAGGG
** * *
1602920 TGTGCATCGGTGCACAAATTTGCTTCGATGTTTCAA-AAATAGT-CGGGGGGCATCGATGCATGG
1 TGTGCATCGGTGCACAAATTTAATTCGATGTTTCAATAAA-A-TCCAGAGGGCATCGATGCATGG
1602983 CT
64 -T
* * * *
1602985 TGTGCATCGGTGCACAAAATTAATTCGATGTTTTAATAAAATCCAGAGTGCATTGATGCATGGT
1 TGTGCATCGGTGCACAAATTTAATTCGATGTTTCAATAAAATCCAGAGGGCATCGATGCATGGT
* *
1603049 TGTGCATCAGTGCATAAATTGT-ATTCGA
1 TGTGCATCGGTGCACAAATT-TAATTCGA
1603077 AATGGGTGTG
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
64 25 0.32
65 50 0.64
66 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (64 bp):
TGTGCATCGGTGCACAAATTTAATTCGATGTTTCAATAAAATCCAGAGGGCATCGATGCATGGT
Found at i:1605625 original size:23 final size:23
Alignment explanation
Indices: 1605590--1605670 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
1605580 GCATAACAGA
1605590 GTGCATCGATGCACATTCAAGGG
1 GTGCATCGATGCACATTCAAGGG
* *
1605613 GTGCATC-AGTGCACCTTC-A-TG
1 GTGCATCGA-TGCACATTCAAGGG
*
1605634 GTGAATCGATGCACATTCAAGGG
1 GTGCATCGATGCACATTCAAGGG
*
1605657 ATGCATCGATGCAC
1 GTGCATCGATGCAC
1605671 TAGGTAGTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
21 15 0.32
22 4 0.09
23 28 0.60
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGG
Found at i:1608384 original size:46 final size:46
Alignment explanation
Indices: 1608302--1608413 Score: 172
Period size: 46 Copynumber: 2.4 Consensus size: 46
1608292 GTCGAGGGTC
* * *
1608302 TATGCGGTCCTTCGGGACATAGTGGTCCTTTGGGACATATGTGTTA
1 TATGTGGTCCTTCGGGACATAGTAGTCCTTCGGGACATATGTGTTA
*
1608348 TATGTGG-CCATTCGAGACATAGTAGTCCTTCGGGACATATGTGTTA
1 TATGTGGTCC-TTCGGGACATAGTAGTCCTTCGGGACATATGTGTTA
1608394 TATGTGGTCCTTCGGGACAT
1 TATGTGGTCCTTCGGGACAT
1608414 CTACATGGTC
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
45 2 0.03
46 55 0.93
47 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.34
Consensus pattern (46 bp):
TATGTGGTCCTTCGGGACATAGTAGTCCTTCGGGACATATGTGTTA
Found at i:1609343 original size:64 final size:65
Alignment explanation
Indices: 1609233--1609390 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 65
1609223 TTCAGTGTGT
* * * * * *
1609233 ATCGATGCACATGAAGTGAATCGATGCA-CCCATTAAAAAAGGAAACATCGAATG-CAATTAGTG
1 ATCGATGCATAAGGAGTGCATCGATGCACCCCATTAAAAAAGAAAACATCGAAGGTC-ATTAGTG
1609296 C
65 C
* * *
1609297 ATCGATGCATAAGGAGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTCATTAGTGT
1 ATCGATGCATAAGGAGTGCATCGATGCACCCCATTAAAAAAGAAAACATCGAAGGTCATTAGTGC
* *
1609361 ATCGTTGCAT-GGGTAGTGCATCGATGCACC
1 ATCGATGCATAAGG-AGTGCATCGATGCACC
1609391 TGTTAAAGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
63 2 0.03
64 72 0.90
65 6 0.08
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (65 bp):
ATCGATGCATAAGGAGTGCATCGATGCACCCCATTAAAAAAGAAAACATCGAAGGTCATTAGTGC
Found at i:1609422 original size:20 final size:22
Alignment explanation
Indices: 1609377--1609434 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1609367 GCATGGGTAG
1609377 TGCATCGATGCACCTGTTAAAGAA
1 TGCATCGATGCA-CTGTT-AAGAA
1609401 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1609421 TGCATCGATGCACT
1 TGCATCGATGCACT
1609435 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 3 0.09
24 12 0.35
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1609940 original size:13 final size:14
Alignment explanation
Indices: 1609911--1609941 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1609901 AACAATGCAA
1609911 GTGATATGAATTAT
1 GTGATATGAATTAT
1609925 GTGATATGAA-TAT
1 GTGATATGAATTAT
1609938 GTGA
1 GTGA
1609942 AATATGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (14 bp):
GTGATATGAATTAT
Found at i:1613770 original size:21 final size:22
Alignment explanation
Indices: 1613744--1613786 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1613734 GAGATTATTT
1613744 TCATTTTTCA-ATTTT-GAAATA
1 TCATTTTT-ATATTTTAGAAATA
1613765 TCATTTTTATATTTTAGAAATA
1 TCATTTTTATATTTTAGAAATA
1613787 ATTTCTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.65
22 6 0.30
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (22 bp):
TCATTTTTATATTTTAGAAATA
Found at i:1620156 original size:24 final size:24
Alignment explanation
Indices: 1620129--1620244 Score: 205
Period size: 24 Copynumber: 4.8 Consensus size: 24
1620119 TACTCATTCT
* * *
1620129 CATAGAAGTATTGATACTACTTTA
1 CATAGTAGTATTCATACCACTTTA
1620153 CATAGTAGTATTCATACCACTTTA
1 CATAGTAGTATTCATACCACTTTA
1620177 CATAGTAGTATTCATACCACTTTA
1 CATAGTAGTATTCATACCACTTTA
1620201 CATAGTAGTATTCATACCACTTTA
1 CATAGTAGTATTCATACCACTTTA
1620225 CATAGTAGTATTCATACCAC
1 CATAGTAGTATTCATACCAC
1620245 AAACCCTGTT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 89 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (24 bp):
CATAGTAGTATTCATACCACTTTA
Found at i:1621116 original size:112 final size:111
Alignment explanation
Indices: 1620982--1621184 Score: 282
Period size: 110 Copynumber: 1.8 Consensus size: 111
1620972 TTCATGATTC
* * * * * * *
1620982 TTAAGAAAATAAATTCAACTATTTATTTCCTTTCACAATCCACAATCATATTAGATTCTTTGG-A
1 TTAAAAAAATAAATTAAACTATTTATTT--TTTCACAAACCAAAATCATATAAGATTCATAGGAA
*
1621046 AAATAAATTCAACGATTTATTTCTTTTTTCAAAATAAAATCTTTAAGA
64 AAATAAATTCAACGATTTATTTCCTTTTTCAAAATAAAATCTTTAAGA
*
1621094 TTAAAAAAATAAATTAAACTATTTATTTTTTTACAAACCAAAATCATATAAGATTCATAGGAAAA
1 TTAAAAAAATAAATTAAACTATTTATTTTTTCACAAACCAAAATCATATAAGATTCATAGGAAAA
* *
1621159 ATGAATTCAATGATTTATTTCCTTTT
66 ATAAATTCAACGATTTATTTCCTTTT
1621185 ACAGGATAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
110 27 0.34
111 26 0.33
112 26 0.33
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (111 bp):
TTAAAAAAATAAATTAAACTATTTATTTTTTCACAAACCAAAATCATATAAGATTCATAGGAAAA
ATAAATTCAACGATTTATTTCCTTTTTCAAAATAAAATCTTTAAGA
Found at i:1621175 original size:57 final size:58
Alignment explanation
Indices: 1620987--1621187 Score: 193
Period size: 58 Copynumber: 3.5 Consensus size: 58
1620977 GATTCTTAAG
* * * * * *
1620987 AAAATAAATTCAACTATTTATTTCCTTTCACAATCCACAATCATATTAGATTCTTTGG-
1 AAAATAAATTCAACTATTTATTT-CTTTTACAAACCAAAATCATATAAGATTCATAGGA
* * ** *
1621045 AAAATAAATTCAACGATTTATTTCTTTTTTCAAAATAAAATC-TTTAAGATT-A-A--A
1 AAAATAAATTCAACTATTTATTTC-TTTTACAAACCAAAATCATATAAGATTCATAGGA
*
1621099 AAAATAAATTAAACTATTTATTT-TTTTACAAACCAAAATCATATAAGATTCATAGGA
1 AAAATAAATTCAACTATTTATTTCTTTTACAAACCAAAATCATATAAGATTCATAGGA
*
1621156 AAAATGAATTCAA-TGATTTATTTCCTTTTACA
1 AAAATAAATTCAACT-ATTTATTT-CTTTTACA
1621188 GGATAGAATC
Statistics
Matches: 114, Mismatches: 19, Indels: 19
0.75 0.12 0.12
Matches are distributed among these distances:
52 14 0.12
53 8 0.07
54 22 0.19
55 1 0.01
56 1 0.01
57 28 0.25
58 33 0.29
59 7 0.06
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.39
Consensus pattern (58 bp):
AAAATAAATTCAACTATTTATTTCTTTTACAAACCAAAATCATATAAGATTCATAGGA
Found at i:1621551 original size:58 final size:57
Alignment explanation
Indices: 1621430--1621566 Score: 168
Period size: 58 Copynumber: 2.4 Consensus size: 57
1621420 TCATATATAA
* * * * *
1621430 TTTCCTTATAAAGTTAGAATCATTTAAGACTCTCAAAAAATAAATTCAACAATTTAT
1 TTTCCTTACAAAGTTAGAATCATTTAACACTATCAAAAAATAAATTAAACAACTTAT
* * **
1621487 TTTCCTTACAAAGTTAGAATC-TTTCAACATTATCAATGAAATAAATTAAAGGACTTAT
1 TTTCCTTACAAAGTTAGAATCATTT-AACACTATCAA-AAAATAAATTAAACAACTTAT
1621545 TTTCCTTACAAAGTTAGAATCA
1 TTTCCTTACAAAGTTAGAATCA
1621567 ACAAAAGATT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
56 3 0.04
57 28 0.41
58 37 0.54
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (57 bp):
TTTCCTTACAAAGTTAGAATCATTTAACACTATCAAAAAATAAATTAAACAACTTAT
Found at i:1624408 original size:35 final size:35
Alignment explanation
Indices: 1624362--1624434 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
1624352 AGTTTTTAAT
1624362 GGTGGGTACTAGAATGAAACAAAAAATAAATGTTA
1 GGTGGGTACTAGAATGAAACAAAAAATAAATGTTA
1624397 GGTGGGTACTAGAATGAAACAAAAAATAAATGTTA
1 GGTGGGTACTAGAATGAAACAAAAAATAAATGTTA
1624432 GGT
1 GGT
1624435 ATGATTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.47, C:0.05, G:0.25, T:0.23
Consensus pattern (35 bp):
GGTGGGTACTAGAATGAAACAAAAAATAAATGTTA
Found at i:1625200 original size:4 final size:4
Alignment explanation
Indices: 1625191--1625274 Score: 69
Period size: 4 Copynumber: 19.5 Consensus size: 4
1625181 GAAAAAATAT
* * * *
1625191 AAGA AAGA AAGG AAGA AAGA AAGG AAGA AAGG AAGTA GAAGA AAGA AAGG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG-A -AAGA AAGA AAGA
*
1625241 AAGTA GAAGA AAGA AAGG AAGCA GAAGA AAGA AA
1 AAG-A -AAGA AAGA AAGA AAG-A -AAGA AAGA AA
1625275 TTATCAGGAA
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
4 52 0.81
5 3 0.05
6 9 0.14
ACGTcount: A:0.64, C:0.01, G:0.32, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:1625238 original size:18 final size:18
Alignment explanation
Indices: 1625191--1625274 Score: 123
Period size: 18 Copynumber: 4.6 Consensus size: 18
1625181 GAAAAAATAT
*
1625191 AAGAAAGAAAGGAAGAAAG
1 AAGAAAGAAAGGAAG-TAG
*
1625210 AAAGGAAGAAAGGAAGTAG
1 -AAGAAAGAAAGGAAGTAG
1625229 AAGAAAGAAAGGAAGTAG
1 AAGAAAGAAAGGAAGTAG
*
1625247 AAGAAAGAAAGGAAGCAG
1 AAGAAAGAAAGGAAGTAG
1625265 AAGAAAGAAA
1 AAGAAAGAAA
1625275 TTATCAGGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
18 44 0.73
19 2 0.03
20 14 0.23
ACGTcount: A:0.64, C:0.01, G:0.32, T:0.02
Consensus pattern (18 bp):
AAGAAAGAAAGGAAGTAG
Found at i:1626801 original size:30 final size:31
Alignment explanation
Indices: 1626736--1626804 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
1626726 ACATGCACTA
*
1626736 TTCACATATTCAAATCATATAATTTGTACTT
1 TTCACATATTCAAATCATATAATCTGTACTT
* * *
1626767 TTCACATATTCCAATTATATAATCT-TATTT
1 TTCACATATTCAAATCATATAATCTGTACTT
1626797 TTCACATA
1 TTCACATA
1626805 AGTATAATCC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.35, C:0.17, G:0.01, T:0.46
Consensus pattern (31 bp):
TTCACATATTCAAATCATATAATCTGTACTT
Found at i:1628028 original size:44 final size:44
Alignment explanation
Indices: 1627949--1628735 Score: 734
Period size: 44 Copynumber: 17.9 Consensus size: 44
1627939 GAGATAATGA
* * * * * *
1627949 TGATCCAACTCCCTATGCGATGCAATTGAGCGAAATGATGACGT
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * * **
1627993 TGATACAACTCCTTATGCGATGGAATCGAGTGAAATGTTGATAC
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * * *
1628037 TAATCCAACTGCTTATGTGATTGAATCGAGGGAAATGTTGATGT
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * * *
1628081 TGATCTAACTCCTTATGTGATGAAATCAAGCGAAATGTTAATGT
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * ** *
1628125 TGATCCAACTTCTTATGTGATGGAATCGAGCAAAATGAAGATGC
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* ** * ** * * * * *
1628169 TAATTTAGCTCCTTATGCAATGGAATCAAGCAAAATGGTCATGC
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* *
1628213 TAATCCAACTCCTTATGTGATGGAATCGAGCGAAAGGTTGATGT
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * * * **
1628257 TGATCCAACTTCTTATTTGATGGAATCTAGCAAAACATTGATGT
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * * * *
1628301 TGATCCAACTTCTTATATGATGGAATCAAGCAAAATGATGATGT
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * * ** * * *
1628345 TAATCTATCTCCTTATGCAATAGAATCGAGCGAAATGGTGATGC
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * * *
1628389 TAATCCAACTCCTTATGTGATGGAATCGAGTGAAAGGTTGATGC
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* **
1628433 TGATCCAACTCCTTATGTGATGGAATTGAGCG-AATGGTTGATAC
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAAT-GTTGATGT
* * **
1628477 TGATCCAAATCCTTATGTGATGGAATCGAGCGAAATATTGATAC
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * ** * * *
1628521 TGATCCAATTTCTTATGTGATACAATTGAGAGAATTGTTGATGT
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * *
1628565 TGAT-CAACTCCTTATGTGATGGAATCGAGCAAAAGGTTGATGA
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* *
1628608 TGAT-CAACTCTTTATGTGATGGAATCGAGCAAAATGTTGATGT
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
* * * * * *
1628651 TGATCAAACTCTTTATGTGATAGAATCAAGCAAAATGTTAATGT
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
** ** *
1628695 TGATCCAACTTTTTATGTGATTAAATCGAGAGAAATGTTGA
1 TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGA
1628736 ACGAGTTATT
Statistics
Matches: 609, Mismatches: 131, Indels: 6
0.82 0.18 0.01
Matches are distributed among these distances:
43 75 0.12
44 531 0.87
45 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (44 bp):
TGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGT
Found at i:1628868 original size:81 final size:81
Alignment explanation
Indices: 1628744--1628910 Score: 289
Period size: 81 Copynumber: 2.1 Consensus size: 81
1628734 GAACGAGTTA
* *
1628744 TTCTCATTAGGAACTTCTTCTTCTTCATTTTAGAAAATATTCTCATTAGGAACCCCTTCATTGGA
1 TTCTCATTAGAAACTTCTTCTCCTTCATTTTAGAAAATATTCTCATTAGGAACCCCTTCATTGGA
1628809 AATGTCTCGGTCTATC
66 AATGTCTCGGTCTATC
* * *
1628825 TTCTCATTAGAAACTTCTTCTCCTTCATTTTAGGAATTCTTCTCATTAGGAACCCCTTCATTGGA
1 TTCTCATTAGAAACTTCTTCTCCTTCATTTTAGAAAATATTCTCATTAGGAACCCCTTCATTGGA
1628890 AATGTCTCGGTCTATC
66 AATGTCTCGGTCTATC
1628906 TTCTC
1 TTCTC
1628911 CTTAAAAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (81 bp):
TTCTCATTAGAAACTTCTTCTCCTTCATTTTAGAAAATATTCTCATTAGGAACCCCTTCATTGGA
AATGTCTCGGTCTATC
Found at i:1629591 original size:82 final size:82
Alignment explanation
Indices: 1629378--1629612 Score: 239
Period size: 81 Copynumber: 2.9 Consensus size: 82
1629368 AAGGAATTAT
* * * * *
1629378 CACTCTGCTCAAAATACTTACAGAGGACAT-GAAGGATTTGATCATAATGCTCAAAAAAATTACT
1 CACTCT-CTC-AAAGACTTACAGAGGA-ATCGAAGGATTTAATCATCATGCTCGAAAAACTTACT
* *
1629442 GATGG-CCTAGAGGACTTAC
63 GATGGCCCCAGAGGACTAAC
* * * * *
1629461 CACTGCTC-CAAAGACTTACAGA-GAACCCGGATGATTTAATCACCATGCTCGAAAAACTAACTG
1 CACT-CTCTCAAAGACTTACAGAGGAA-TCGAAGGATTTAATCATCATGCTCGAAAAACTTACTG
1629524 ATGGCCCCA-AGGACTAAC
64 ATGGCCCCAGAGGACTAAC
* *
1629542 CACTCTACTCTAAA-ACTTACAGAGGAATCGAAGGATTTAAACATCATGCTCGAAAGACTTACTG
1 CACTCT-CTC-AAAGACTTACAGAGGAATCGAAGGATTTAATCATCATGCTCGAAAAACTTACTG
1629606 ATGGCCC
64 ATGGCCC
1629613 AAATGACTTA
Statistics
Matches: 125, Mismatches: 19, Indels: 17
0.78 0.12 0.11
Matches are distributed among these distances:
79 1 0.01
80 4 0.03
81 56 0.45
82 51 0.41
83 11 0.09
84 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (82 bp):
CACTCTCTCAAAGACTTACAGAGGAATCGAAGGATTTAATCATCATGCTCGAAAAACTTACTGAT
GGCCCCAGAGGACTAAC
Found at i:1632597 original size:21 final size:21
Alignment explanation
Indices: 1632555--1632597 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1632545 TTTCTGGGTT
* * *
1632555 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1632576 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1632597 A
1 A
1632598 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1632658 original size:67 final size:67
Alignment explanation
Indices: 1632577--1632727 Score: 250
Period size: 67 Copynumber: 2.3 Consensus size: 67
1632567 ACCCATTCAA
1632577 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAAAACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAA-TTCCAGAAAACTAGAGGGGAATCGATACCCCCA
1632642 -GG
65 GGG
** *
1632644 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGTGGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAAAACTAGAGGGGAATCGATACCCCCAG
1632709 GG
66 GG
*
1632711 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1632728 ATGAGAAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
66 30 0.38
67 49 0.62
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAAAACTAGAGGGGAATCGATACCCCCAG
GG
Found at i:1633399 original size:149 final size:149
Alignment explanation
Indices: 1633208--1633511 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
1633198 GGGTAGAGGG
1633208 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
1633273 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1633338 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1633357 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1633422 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1633487 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1633506 TCTACG
1 TCTACG
1633512 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1633534 original size:23 final size:23
Alignment explanation
Indices: 1633490--1633534 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1633480 ATCATTATAT
*
1633490 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1633513 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1633535 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1634400 original size:2 final size:2
Alignment explanation
Indices: 1634393--1634422 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1634383 AAAACAAGGG
1634393 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
1634423 TGTGAAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1636708 original size:19 final size:20
Alignment explanation
Indices: 1636677--1636718 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1636667 TGAAAATGTA
**
1636677 AAATGCAAAAATGTGAATGC
1 AAATGCAAAAATGCAAATGC
1636697 AAATGC-AAAATGCAAATGC
1 AAATGCAAAAATGCAAATGC
1636716 AAA
1 AAA
1636719 AAAGGTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.17
Consensus pattern (20 bp):
AAATGCAAAAATGCAAATGC
Found at i:1636710 original size:13 final size:13
Alignment explanation
Indices: 1636692--1636719 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1636682 CAAAAATGTG
1636692 AATGCAAATGCAA
1 AATGCAAATGCAA
1636705 AATGCAAATGCAA
1 AATGCAAATGCAA
1636718 AA
1 AA
1636720 AAGGTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (13 bp):
AATGCAAATGCAA
Found at i:1637494 original size:23 final size:23
Alignment explanation
Indices: 1637450--1637494 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1637440 CTAAGGTTAA
**
1637450 TAAAGACTTCGATTGTGATCCAT
1 TAAAGACTTCGATTCAGATCCAT
1637473 TAAAGACTTCGAATTCAG-TCCA
1 TAAAGACTTCG-ATTCAGATCCA
1637495 GGGATCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (23 bp):
TAAAGACTTCGATTCAGATCCAT
Found at i:1639147 original size:28 final size:27
Alignment explanation
Indices: 1639107--1639173 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
1639097 CATTTAAAAG
*
1639107 AATAGAATAAATAAATTAAGA-AAATAAA
1 AATA-AATAAATAAA-TAAAACAAATAAA
*
1639135 AATCAAATAAATAAATAAAACAAATAAG
1 AAT-AAATAAATAAATAAAACAAATAAA
1639163 AATAAATAAAT
1 AATAAATAAAT
1639174 TTAACGTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 12 0.34
28 22 0.63
29 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (27 bp):
AATAAATAAATAAATAAAACAAATAAA
Found at i:1639150 original size:19 final size:20
Alignment explanation
Indices: 1639128--1639172 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1639118 TAAATTAAGA
1639128 AAATAAAAATCAAAT-A-AAT
1 AAATAAAAA-CAAATAAGAAT
1639147 AAAT-AAAACAAATAAGAAT
1 AAATAAAAACAAATAAGAAT
1639166 AAATAAA
1 AAATAAA
1639173 TTTAACGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 5 0.22
19 11 0.48
20 2 0.09
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (20 bp):
AAATAAAAACAAATAAGAAT
Found at i:1646916 original size:31 final size:31
Alignment explanation
Indices: 1646855--1646940 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
1646845 AAATTAATTC
* * *
1646855 AGAGATTAAATTGATAATTCATCTATAGTTTA
1 AGAG-TTAAATTAATATTTTATCTATAGTTTA
1646887 AGAGTTAAATTAATATTTTATCTGA-AGTTTA
1 AGAGTTAAATTAATATTTTATCT-ATAGTTTA
* * *
1646918 GGA-TCAAATTAATATTTTGTCTA
1 AGAGTTAAATTAATATTTTATCTA
1646941 CAATTTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
29 1 0.02
30 17 0.36
31 24 0.51
32 5 0.11
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (31 bp):
AGAGTTAAATTAATATTTTATCTATAGTTTA
Found at i:1649700 original size:2 final size:2
Alignment explanation
Indices: 1649693--1649718 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1649683 TACCATCCTC
1649693 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
1649719 AAGAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1650798 original size:2 final size:2
Alignment explanation
Indices: 1650786--1650833 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
1650776 TTTAAAAATA
* * *
1650786 AT AT AT A- AT AT AT AT GT AC AC AT A- 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
1650826 AT AT AT AT
1 AT AT AT AT
1650834 TAAATTGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1651611 original size:22 final size:22
Alignment explanation
Indices: 1651584--1651626 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1651574 CCACAAGAGC
1651584 ATAGAAA-ACACGTGCCATAATA
1 ATAGAAAGA-ACGTGCCATAATA
*
1651606 ATAGAAAGAACGTGCTATAAT
1 ATAGAAAGAACGTGCCATAAT
1651627 GACAAAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (22 bp):
ATAGAAAGAACGTGCCATAATA
Found at i:1651663 original size:18 final size:20
Alignment explanation
Indices: 1651640--1651677 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1651630 AAAGATTCTT
*
1651640 ATTCAA-AATTAAAA-AAAA
1 ATTCAAGAAGTAAAAGAAAA
1651658 ATTCAAGAAGTAAAAGAAAA
1 ATTCAAGAAGTAAAAGAAAA
1651678 CAAAGGGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.18
Consensus pattern (20 bp):
ATTCAAGAAGTAAAAGAAAA
Found at i:1652533 original size:19 final size:20
Alignment explanation
Indices: 1652499--1652539 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1652489 AGATAAACAA
*
1652499 AAACAACGGAAAAAAATTGT
1 AAACAACGGAAAAAAATCGT
*
1652519 AAACAAC-GTAAAAAATCGT
1 AAACAACGGAAAAAAATCGT
1652538 AA
1 AA
1652540 GCTACAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.15
Consensus pattern (20 bp):
AAACAACGGAAAAAAATCGT
Found at i:1652606 original size:21 final size:21
Alignment explanation
Indices: 1652555--1652608 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
1652545 AAAAAGACAG
**
1652555 AGAAAAACATGTCACAAAGGA
1 AGAAAAATGTGTCACAAAGGA
* *
1652576 AGAGATAAATGTGTCATAAAGGT
1 AGA-A-AAATGTGTCACAAAGGA
1652599 AGAAAAATGT
1 AGAAAAATGT
1652609 CACAAGGACA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 9 0.33
22 2 0.07
23 16 0.59
ACGTcount: A:0.52, C:0.07, G:0.22, T:0.19
Consensus pattern (21 bp):
AGAAAAATGTGTCACAAAGGA
Found at i:1669224 original size:2 final size:2
Alignment explanation
Indices: 1669167--1669212 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1669157 TTAAATTATC
1669167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1669209 AT AT
1 AT AT
1669213 TTACTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1670468 original size:37 final size:37
Alignment explanation
Indices: 1670418--1670492 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
1670408 ACCAGTATCG
1670418 ATACTCATACCCCAATCATCACTCATTTTCTCTTTGA
1 ATACTCATACCCCAATCATCACTCATTTTCTCTTTGA
1670455 ATACTCATACCCCAATCATCACTCATTTTCTCTTTGA
1 ATACTCATACCCCAATCATCACTCATTTTCTCTTTGA
1670492 A
1 A
1670493 GTATCGGTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.32, G:0.03, T:0.37
Consensus pattern (37 bp):
ATACTCATACCCCAATCATCACTCATTTTCTCTTTGA
Found at i:1678857 original size:30 final size:30
Alignment explanation
Indices: 1678821--1678882 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1678811 AAACATTACA
1678821 AAGCATTAAATTAGTACTATCAAGTTTGTT
1 AAGCATTAAATTAGTACTATCAAGTTTGTT
1678851 AAGCATTAAATTAGTACTATCAAGTTTGTT
1 AAGCATTAAATTAGTACTATCAAGTTTGTT
1678881 AA
1 AA
1678883 TATTAGTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (30 bp):
AAGCATTAAATTAGTACTATCAAGTTTGTT
Found at i:1685288 original size:20 final size:20
Alignment explanation
Indices: 1685263--1685310 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1685253 GTTGCCTTAA
1685263 GCACTAATCATATTTATCAT
1 GCACTAATCATATTTATCAT
*
1685283 GCACTAATCCTATTTATCAT
1 GCACTAATCATATTTATCAT
1685303 GCAC-AATC
1 GCACTAATC
1685311 CAAACATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.35
Consensus pattern (20 bp):
GCACTAATCATATTTATCAT
Found at i:1688516 original size:12 final size:12
Alignment explanation
Indices: 1688499--1688527 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1688489 TACTGGACTA
1688499 ATGCAACTACAT
1 ATGCAACTACAT
1688511 ATGCAACTACAT
1 ATGCAACTACAT
1688523 ATGCA
1 ATGCA
1688528 TATCTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (12 bp):
ATGCAACTACAT
Found at i:1696068 original size:17 final size:17
Alignment explanation
Indices: 1696046--1696080 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1696036 ATCCCCTATC
*
1696046 TTATTTACTTTATCTTT
1 TTATTTACTTTAACTTT
*
1696063 TTATTTTCTTTAACTTT
1 TTATTTACTTTAACTTT
1696080 T
1 T
1696081 CTCTCAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTACTTTAACTTT
Found at i:1702208 original size:20 final size:20
Alignment explanation
Indices: 1702179--1702239 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1702169 ATATAAATTA
*
1702179 TGAAACATAAAATAATTATT
1 TGAAAAATAAAATAATTATT
1702199 TGAAAAATAAAATAATT-TT
1 TGAAAAATAAAATAATTATT
*
1702218 T--AAAATTAAAT-ATTATT
1 TGAAAAATAAAATAATTATT
*
1702235 CGAAA
1 TGAAA
1702240 TATTATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 3 0.09
17 11 0.31
19 5 0.14
20 16 0.46
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (20 bp):
TGAAAAATAAAATAATTATT
Found at i:1702912 original size:2 final size:2
Alignment explanation
Indices: 1702907--1702932 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1702897 TATCTCTCTC
1702907 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
1702933 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1703181 original size:2 final size:2
Alignment explanation
Indices: 1703174--1703204 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1703164 ATCATAATTC
1703174 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 A
1703205 CAGGGAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1704568 original size:12 final size:12
Alignment explanation
Indices: 1704551--1704577 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1704541 TAGGATAGTG
1704551 TTTTATTATTAT
1 TTTTATTATTAT
1704563 TTTTATTATTAT
1 TTTTATTATTAT
1704575 TTT
1 TTT
1704578 ATCCATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:1705614 original size:8 final size:8
Alignment explanation
Indices: 1705589--1705632 Score: 65
Period size: 8 Copynumber: 5.6 Consensus size: 8
1705579 CATCAAATGG
1705589 AAAAA-CA
1 AAAAATCA
1705596 AAAAAGT-A
1 AAAAA-TCA
1705604 AAAAATCA
1 AAAAATCA
1705612 AAAAATCA
1 AAAAATCA
1705620 AAAAATCA
1 AAAAATCA
1705628 AAAAA
1 AAAAA
1705633 AAAAAAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 6 0.18
8 28 0.82
ACGTcount: A:0.80, C:0.09, G:0.02, T:0.09
Consensus pattern (8 bp):
AAAAATCA
Found at i:1705638 original size:16 final size:15
Alignment explanation
Indices: 1705589--1705644 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
1705579 CATCAAATGG
*
1705589 AAAAACAAAAAAGTAA
1 AAAAACAAAAAA-AAA
* *
1705605 AAAATCAAAAAATCAA
1 AAAAACAAAAAA-AAA
*
1705621 AAAATCAAAAAAAAA
1 AAAAACAAAAAAAAA
1705636 AAAAACAAA
1 AAAAACAAA
1705645 CGAAGAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
15 10 0.29
16 25 0.71
ACGTcount: A:0.82, C:0.09, G:0.02, T:0.07
Consensus pattern (15 bp):
AAAAACAAAAAAAAA
Found at i:1707229 original size:21 final size:21
Alignment explanation
Indices: 1707203--1707264 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1707193 ATTTCCGAGA
1707203 CACTTACCATAG-TACTTCATC
1 CACTTACCA-AGCTACTTCATC
1707224 CACTTACCAAGCTACTTCATC
1 CACTTACCAAGCTACTTCATC
* *
1707245 CACTTACCAAGGTACCTCAT
1 CACTTACCAAGCTACTTCAT
1707265 ATACTTCCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 2 0.05
21 36 0.95
ACGTcount: A:0.29, C:0.35, G:0.06, T:0.29
Consensus pattern (21 bp):
CACTTACCAAGCTACTTCATC
Found at i:1707270 original size:21 final size:21
Alignment explanation
Indices: 1707202--1707270 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
1707192 CATTTCCGAG
*
1707202 ACACTTACCATAG-TACTTCAT
1 ACACTTACCA-AGCTACCTCAT
* *
1707223 CCACTTACCAAGCTACTTCAT
1 ACACTTACCAAGCTACCTCAT
* *
1707244 CCACTTACCAAGGTACCTCAT
1 ACACTTACCAAGCTACCTCAT
*
1707265 ATACTT
1 ACACTT
1707271 CCACTTCATC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 2 0.05
21 40 0.95
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.30
Consensus pattern (21 bp):
ACACTTACCAAGCTACCTCAT
Found at i:1710019 original size:6 final size:6
Alignment explanation
Indices: 1710006--1710043 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
1709996 ATTAGGATAG
*
1710006 TATT-T TATTAT TATTGT TATTGT TATTGT TATT-T TATT
1 TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATT
1710044 CAAAATTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (6 bp):
TATTGT
Found at i:1717248 original size:20 final size:20
Alignment explanation
Indices: 1717223--1717262 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1717213 GAATGTATTG
*
1717223 ATGACAAATTTATGAGAAAT
1 ATGACAAATTTATGACAAAT
**
1717243 ATGACATGTTTATGACAAAT
1 ATGACAAATTTATGACAAAT
1717263 TGATATATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGACAAATTTATGACAAAT
Found at i:1718042 original size:2 final size:2
Alignment explanation
Indices: 1718035--1718072 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1718025 CCTACCATCA
1718035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1718073 GTTAGGATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1718673 original size:24 final size:23
Alignment explanation
Indices: 1718646--1718697 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1718636 TGTTTCTGAG
1718646 GGAATTAGAATATGTGAAGGAATT
1 GGAATTAGAATATGT-AAGGAATT
* * *
1718670 GGAATTGGAATCTGTCAGGAATT
1 GGAATTAGAATATGTAAGGAATT
*
1718693 AGAAT
1 GGAAT
1718698 CTGAATCTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.38, C:0.04, G:0.29, T:0.29
Consensus pattern (23 bp):
GGAATTAGAATATGTAAGGAATT
Found at i:1718697 original size:23 final size:23
Alignment explanation
Indices: 1718663--1718706 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1718653 GAATATGTGA
*
1718663 AGGAATTGGAAT-TGGAATCTGTC
1 AGGAATTAGAATCT-GAATCTGTC
1718686 AGGAATTAGAATCTGAATCTG
1 AGGAATTAGAATCTGAATCTG
1718707 AAACCTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (23 bp):
AGGAATTAGAATCTGAATCTGTC
Found at i:1719313 original size:39 final size:39
Alignment explanation
Indices: 1719252--1719357 Score: 90
Period size: 39 Copynumber: 2.6 Consensus size: 39
1719242 AGCATGTTAG
* * *
1719252 AAAAAAAAGGCAATGAAGATAAAT-AAATTAAA-GAAAAAT
1 AAAAAAAAGGAAATAAAAATAAATGAAA--AAAGGAAAAAT
*
1719291 AAAATAAAGGAAATAAAAATAAATGAAAAAAGGAAAAAT
1 AAAAAAAAGGAAATAAAAATAAATGAAAAAAGGAAAAAT
* *
1719330 AGATAAAGAAAAGACATAAAAAATAAAT
1 A-A-AAA-AAAGGAAAT-AAAAATAAAT
1719358 AAGATAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
38 3 0.06
39 28 0.52
40 4 0.07
41 2 0.04
42 7 0.13
43 10 0.19
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (39 bp):
AAAAAAAAGGAAATAAAAATAAATGAAAAAAGGAAAAAT
Found at i:1719366 original size:16 final size:15
Alignment explanation
Indices: 1719345--1719422 Score: 67
Period size: 14 Copynumber: 5.4 Consensus size: 15
1719335 AAGAAAAGAC
1719345 ATAAAAAATAAATAA
1 ATAAAAAATAAATAA
1719360 GATAAAAAATAAATAA
1 -ATAAAAAATAAATAA
1719376 A-AAAAACATAAA-AA
1 ATAAAAA-ATAAATAA
* *
1719390 A-AGAAATTAAA-AA
1 ATAAAAAATAAATAA
* *
1719403 ATGAAGAA-AAATAA
1 ATAAAAAATAAATAA
1719417 ATAAAA
1 ATAAAA
1719423 TAATCAAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
13 10 0.20
14 20 0.39
15 6 0.12
16 15 0.29
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.15
Consensus pattern (15 bp):
ATAAAAAATAAATAA
Found at i:1719391 original size:23 final size:22
Alignment explanation
Indices: 1719363--1719440 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
1719353 TAAATAAGAT
1719363 AAAAAATAAATAAAAAAAACATA
1 AAAAAATAAATAAAAAAAACA-A
* * **
1719386 AAAAAAGAAATTAAAAAATGAA
1 AAAAAATAAATAAAAAAAACAA
* * *
1719408 GAAAAATAAATAAAATAATCAA
1 AAAAAATAAATAAAAAAAACAA
1719430 AATAAAGATAA
1 AA-AAA-ATAA
1719441 CGAGCTAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 19 0.44
23 20 0.47
24 4 0.09
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (22 bp):
AAAAAATAAATAAAAAAAACAA
Done.