Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008353.1 Hibiscus syriacus cultivar Beakdansim tig00111088_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: 2583621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 12 of 13
Found at i:2362765 original size:22 final size:22
Alignment explanation
Indices: 2362740--2362781 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2362730 AAAAAATATC
2362740 AAAACGTGCTA-AAAGACATAGA
1 AAAACGTGCTATAAA-ACATAGA
*
2362762 AAAATGTGCTATAAAACATA
1 AAAACGTGCTATAAAACATA
2362782 TAAATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.55, C:0.12, G:0.14, T:0.19
Consensus pattern (22 bp):
AAAACGTGCTATAAAACATAGA
Found at i:2364534 original size:21 final size:21
Alignment explanation
Indices: 2364509--2364553 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2364499 TTGTGCCCAG
2364509 CTGGCAATAAGTGCCTTAGCA
1 CTGGCAATAAGTGCCTTAGCA
2364530 CTGGCAATAAGTGCCTTAGCA
1 CTGGCAATAAGTGCCTTAGCA
2364551 CTG
1 CTG
2364554 ATTGGGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
CTGGCAATAAGTGCCTTAGCA
Found at i:2368674 original size:3 final size:3
Alignment explanation
Indices: 2368666--2368706 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2368656 CCTGGCTTAT
2368666 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2368707 TTTAGTAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2372842 original size:20 final size:20
Alignment explanation
Indices: 2372789--2372842 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2372779 AAAAGCTTGA
*
2372789 GTGCATCGATGCACAGTCTT
1 GTGCATCGATGCATAGTCTT
2372809 GTGCATCGATGCATAGTCTT
1 GTGCATCGATGCATAGTCTT
2372829 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2372843 CAAATGCACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATAGTCTT
Found at i:2372893 original size:45 final size:46
Alignment explanation
Indices: 2372809--2372895 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 46
2372799 GCACAGTCTT
* * *
2372809 GTGCATCGATGCATAGTCTTGTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATAGTCATGTACATCGATGCATAAAATGCACTGA
*
2372855 GTGCATCGATGCATGGT-ATGTACATCGATGCATAAAATGCA
1 GTGCATCGATGCATAGTCATGTACATCGATGCATAAAATGCA
2372896 TTCGATATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 21 0.57
46 16 0.43
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (46 bp):
GTGCATCGATGCATAGTCATGTACATCGATGCATAAAATGCACTGA
Found at i:2372940 original size:20 final size:20
Alignment explanation
Indices: 2372915--2372953 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2372905 CAAGAAATTA
2372915 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
2372935 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2372954 CTCTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:2376068 original size:19 final size:20
Alignment explanation
Indices: 2376044--2376094 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2376034 AATGACCAAT
2376044 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
2376063 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
2376083 AAAATCGCAACG
1 AAAATCGCAACG
2376095 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:2376088 original size:20 final size:20
Alignment explanation
Indices: 2376044--2376321 Score: 103
Period size: 20 Copynumber: 13.6 Consensus size: 20
2376034 AATGACCAAT
* *
2376044 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
2376063 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
2376083 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
2376103 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* * **
2376123 ATAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
2376144 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * * *
2376167 AAAATCGCAATGCGAGTGAT
1 AAAATCGCAACGCGATTTAG
* * *
2376187 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
** * *
2376207 AGGATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * * *
2376227 ATAACCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
2376247 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2376270 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
2376290 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
2376310 AGAATCGCAACG
1 AAAATCGCAACG
2376322 TTGAAAATAA
Statistics
Matches: 196, Mismatches: 51, Indels: 23
0.73 0.19 0.09
Matches are distributed among these distances:
19 17 0.09
20 138 0.70
21 13 0.07
23 28 0.14
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:2376236 original size:40 final size:40
Alignment explanation
Indices: 2376170--2376319 Score: 167
Period size: 40 Copynumber: 3.7 Consensus size: 40
2376160 TTAGAAGAAA
* * * *
2376170 ATCGCAATGCGAGTGATAGAATCGCAATGCGATTTATAGG
1 ATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGG
* *
2376210 ATCGCAATGCGATTTATATAACCGCAATGCGATTGAGA-G
1 ATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGG
* * * *
2376249 AGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGA
1 A-TCGCAATGCGATTTA-TAG--AATCGCAATGCGATTGAGAGG
2376293 ATCGCAATGCGATTTATAGAATCGCAA
1 ATCGCAATGCGATTTATAGAATCGCAA
2376320 CGTTGAAAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.02
40 54 0.59
41 1 0.01
42 2 0.02
43 31 0.34
44 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (40 bp):
ATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGG
Found at i:2376430 original size:5 final size:6
Alignment explanation
Indices: 2376391--2376427 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
2376381 GACACGTATT
2376391 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
2376428 CGAGACGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2377134 original size:6 final size:6
Alignment explanation
Indices: 2377118--2377161 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
2377108 TCTCGTCTCG
2377118 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2377162 AATACGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:2377322 original size:20 final size:20
Alignment explanation
Indices: 2377297--2377350 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2377287 TGGAAGATCG
*
2377297 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
2377317 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
2377337 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
2377351 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:2377360 original size:20 final size:20
Alignment explanation
Indices: 2377339--2377610 Score: 310
Period size: 20 Copynumber: 13.3 Consensus size: 20
2377329 CTTTTTAACG
* *
2377339 TTGCGATTTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCA
*
2377359 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
2377379 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
2377399 TTGTGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
2377419 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
* *
2377439 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
*
2377459 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
* *
2377482 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
2377502 TTGTGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
2377522 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
2377542 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
2377562 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
2377582 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
2377605 TTGCGA
1 TTGCGA
2377611 ACTTGGAAGC
Statistics
Matches: 221, Mismatches: 25, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
20 185 0.84
21 2 0.01
22 6 0.03
23 28 0.13
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTCTAAATCGCA
Found at i:2377503 original size:123 final size:123
Alignment explanation
Indices: 2377347--2377610 Score: 456
Period size: 123 Copynumber: 2.1 Consensus size: 123
2377337 CGTTGCGATT
* *
2377347 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGTGATTCTATA
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATA
* * * * *
2377412 AATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
*
2377470 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGTGATTCTATAAATCGCATTGCGATTCTATA
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATA
2377535 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
66 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
2377593 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
2377611 ACTTGGAAGC
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 133 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (123 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATA
AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
Found at i:2377649 original size:20 final size:20
Alignment explanation
Indices: 2377624--2377677 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2377614 TGGAAGCTCG
*
2377624 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
2377644 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
2377664 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
2377678 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:2377704 original size:19 final size:20
Alignment explanation
Indices: 2377664--2377714 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2377654 TTCTTTTTAA
*
2377664 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
2377684 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
2377703 CGTTGCGATTTT
1 CGTTGCGATTTT
2377715 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:2377900 original size:20 final size:19
Alignment explanation
Indices: 2377853--2377891 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2377843 ATGACTAACA
*
2377853 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
2377872 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
2377891 A
1 A
2377892 GTATCGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:2377957 original size:20 final size:20
Alignment explanation
Indices: 2377934--2378043 Score: 125
Period size: 20 Copynumber: 5.4 Consensus size: 20
2377924 GAATATGTAA
2377934 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
2377954 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
**
2377974 AATCGCAACGCGATAAT-ACAT
1 -ATCGCAACGCGATTCTGAC-T
2377995 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
2378016 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2378036 GTCGCAAC
1 ATCGCAAC
2378044 ACTGAATTTC
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
19 2 0.02
20 42 0.51
21 36 0.44
22 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2377980 original size:21 final size:21
Alignment explanation
Indices: 2377933--2378008 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
2377923 CGAATATGTA
**
2377933 AATCGCAACGCGATTCTGAC-T
1 AATCGCAACGCGATAAT-ACAT
2377954 -ATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
2377974 AATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
2377995 AATCGCAACGCGAT
1 AATCGCAACGCGAT
2378009 TCTGACTATC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.04
20 15 0.29
21 34 0.67
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (21 bp):
AATCGCAACGCGATAATACAT
Found at i:2378896 original size:24 final size:24
Alignment explanation
Indices: 2378864--2378917 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2378854 GTATTCTAAA
2378864 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2378888 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2378912 TTTGAT
1 TTTGAT
2378918 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2379125 original size:12 final size:13
Alignment explanation
Indices: 2379110--2379142 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2379100 AAAAGAAGAA
2379110 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
2379122 GAAGAAAGGTCCCC
1 GAAGAAA-GTCCCC
2379136 GAAGAAA
1 GAAGAAA
2379143 ATGCCACGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.45, C:0.24, G:0.24, T:0.06
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:2381477 original size:140 final size:140
Alignment explanation
Indices: 2381225--2381494 Score: 479
Period size: 140 Copynumber: 1.9 Consensus size: 140
2381215 AAACGTTGTA
* *
2381225 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTCTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGATA
* * *
2381290 TGATCTGTTCAGTTGTTATCATTTATTACATATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
2381355 TATGTGTATT
131 TATGTGTATT
2381365 TTATGTGTAAACTTCTAACATTTTCAGTTATG-CATGTATTAGTAACTTGAGTTTGAACATTGAT
1 TTATGTGTAAACTTCTAACATTTTCAGTTA-GACATGTATTAGTAACTTGAGTTTGAACATTGAT
2381429 ATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTA
65 ATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTA
2381494 T
130 T
2381495 CGCAACGCGA
Statistics
Matches: 124, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
140 123 0.99
141 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTCTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGATA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:2381490 original size:20 final size:20
Alignment explanation
Indices: 2381465--2381741 Score: 225
Period size: 20 Copynumber: 14.8 Consensus size: 20
2381455 TTACACATTC
*
2381465 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
2381485 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
2381505 ATTTGATTATCGTAACTC-A
1 ATTTGACTATCGCAACGCGA
*
2381524 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
2381539 ATATGACTATCGTAATGC-A
1 ATTTGACTATCGCAACGCGA
* *
2381558 A----A-AATCGCATCGCGA
1 ATTTGACTATCGCAACGCGA
2381573 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2381593 ATTTGACTATCGCAACGCGG
1 ATTTGACTATCGCAACGCGA
*
2381613 ATTTGATTATCGCAACG-GA
1 ATTTGACTATCGCAACGCGA
*
2381632 TATTTGACTATCGCAACGAGA
1 -ATTTGACTATCGCAACGCGA
* *
2381653 A----A--ATTGTAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
2381667 ATTTGACTATCGTAATGCGA
1 ATTTGACTATCGCAACGCGA
2381687 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
2381707 ATTTGATTATCGCAACTG-GT
1 ATTTGACTATCGCAAC-GCGA
2381727 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
2381742 TGAGAAAATA
Statistics
Matches: 206, Mismatches: 30, Indels: 42
0.74 0.11 0.15
Matches are distributed among these distances:
14 25 0.12
15 6 0.03
16 1 0.00
18 1 0.00
19 7 0.03
20 163 0.79
21 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2381536 original size:34 final size:34
Alignment explanation
Indices: 2381493--2381584 Score: 141
Period size: 34 Copynumber: 2.7 Consensus size: 34
2381483 GAATTTGACT
*
2381493 ATCGCAACGCGAATTTGATTATCGTAACT-CAAAA
1 ATCGCAACGCGAATTTGACTATCGTAA-TGCAAAA
*
2381527 ATCGCAACGCGAATATGACTATCGTAATGCAAAA
1 ATCGCAACGCGAATTTGACTATCGTAATGCAAAA
*
2381561 ATCGCATCGCGAATTTGACTATCG
1 ATCGCAACGCGAATTTGACTATCG
2381585 CAACGCGAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 1 0.02
34 52 0.98
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGTAATGCAAAA
Found at i:2381674 original size:94 final size:93
Alignment explanation
Indices: 2381476--2381792 Score: 346
Period size: 94 Copynumber: 3.5 Consensus size: 93
2381466 TTTGAATATC
* * * **
2381476 GCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGTAACTC-A----AAAATCGCAACG
1 GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGATTTGATTATCGCAACG
* * *
2381536 CGA-ATATGACTATCGTAATGCA-AAAATC
66 -GATATTTGACTATCGCAATG-AGAAAATA
*
2381564 GCATCGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGGATTTGATTATCGCAAC
1 GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGC-GATTTGATTATCGCAAC
* *
2381629 GGATATTTGACTATCGCAACGAGAAAATT
65 GGATATTTGACTATCGCAATGAGAAAATA
* * *
2381658 GTAACGCGAATTTGACTATCGTAATGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAAC
1 GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCG-ATTTGATTATCGCAAC
2381723 TGG-TATTTGACTATCGCAATGAGAAAATA
65 -GGATATTTGACTATCGCAATGAGAAAATA
* * * * * *
2381752 GCAAAGCGTATTAGACTATCACAACGC-AAATTGACTTTCGC
1 GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
2381793 GTTGCAATTT
Statistics
Matches: 194, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
88 43 0.22
90 1 0.01
93 16 0.08
94 132 0.68
95 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (93 bp):
GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGATTTGATTATCGCAACG
GATATTTGACTATCGCAATGAGAAAATA
Found at i:2381956 original size:14 final size:14
Alignment explanation
Indices: 2381896--2381957 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
2381886 CACAAATAAA
*
2381896 AATTATTTACACATC
1 AATT-TTTACAAATC
**
2381911 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
2381926 AACTTTTACAAATC
1 AATTTTTACAAATC
*
2381940 AATTTTTATAAATC
1 AATTTTTACAAATC
2381954 AATT
1 AATT
2381958 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:2383339 original size:21 final size:21
Alignment explanation
Indices: 2383315--2383417 Score: 111
Period size: 21 Copynumber: 4.9 Consensus size: 21
2383305 GTGGGAGGAA
*
2383315 CCTCTTCAACGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
* **
2383336 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
* *
2383357 ACTCTTGAGA-GATGATAGGGG
1 CCTCTTGA-ACGATGACAGGGG
*
2383378 CCTCTTGAACGAT-AGGAGGGG
1 CCTCTTGAACGATGA-CAGGGG
2383399 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
2383418 TTCTTCTTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.20
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:2383354 original size:42 final size:42
Alignment explanation
Indices: 2383295--2383417 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
2383285 ATGAATCGAG
* * *
2383295 CTCTTGAATGGTGGGAGGAACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
*
2383337 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGA-GATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTGA-ACGATGACAGGGGC
* * *
2383379 CTCTTGAACGATAGGAGGGGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGG
2383418 TTCTTCTTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
41 4 0.06
42 61 0.88
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:2383917 original size:20 final size:20
Alignment explanation
Indices: 2383894--2383942 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2383884 CAAAACTTAA
2383894 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
2383914 ATCGCAACGTGGAAATGTCT
1 ATCGCAACGCGAAAATGACT
*
2383934 ATCGTAACG
1 ATCGCAACG
2383943 GGATAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2383971 original size:19 final size:19
Alignment explanation
Indices: 2383947--2383992 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2383937 GTAACGGGAT
*
2383947 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAACAAA
*
2383966 AATCGCAATGCGAAACCAA
1 AATCGCAATGCGAAACAAA
2383985 AATCGCAA
1 AATCGCAA
2383993 CACGAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.50, C:0.22, G:0.15, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAACAAA
Found at i:2383998 original size:19 final size:19
Alignment explanation
Indices: 2383964--2384000 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2383954 ATGCGAAATA
**
2383964 AAAATCGCAATGCGAAACC
1 AAAATCGCAACACGAAACC
2383983 AAAATCGCAACACGAAAC
1 AAAATCGCAACACGAAAC
2384001 TAAATTCGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.27, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAATCGCAACACGAAACC
Found at i:2384041 original size:14 final size:14
Alignment explanation
Indices: 2384022--2384054 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2384012 TGTGATAGTC
*
2384022 ATTTTCGCATTGCG
1 ATTTTCACATTGCG
2384036 ATTTTCACATTGCG
1 ATTTTCACATTGCG
2384050 ATTTT
1 ATTTT
2384055 TATTTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (14 bp):
ATTTTCACATTGCG
Found at i:2384103 original size:20 final size:20
Alignment explanation
Indices: 2384076--2384143 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
2384066 GCGATTATCC
*
2384076 CGTTGCGATAGTCAACTTCG
1 CGTTGCGATAGTCAATTTCG
* *
2384096 CATTGCGATAGT-TATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
2384116 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
2384136 CGTTGCGA
1 CGTTGCGA
2384144 GTTAAGTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:2384326 original size:18 final size:18
Alignment explanation
Indices: 2384303--2384352 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
2384293 TTTACTAAGC
2384303 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
2384321 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
2384339 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
2384353 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:2386178 original size:20 final size:19
Alignment explanation
Indices: 2386067--2386183 Score: 73
Period size: 20 Copynumber: 6.2 Consensus size: 19
2386057 TGAAACTTAA
*
2386067 ATCGCAACACGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* * *
2386087 ATCGTAAAGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
* *
2386107 ATCGCAA--TGAGAT-A--
1 ATCGCAACGCGAAATGACT
**
2386121 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
*
2386140 ATCGCAACACGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
2386160 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
2386180 ATCG
1 ATCG
2386184 TTGCGATTTT
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
14 7 0.09
16 5 0.07
17 2 0.03
18 2 0.03
19 14 0.19
20 44 0.59
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2386585 original size:22 final size:22
Alignment explanation
Indices: 2386558--2386608 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
2386548 GATGGAGATA
2386558 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
2386580 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
2386602 GACGGAT
1 GACGGAT
2386609 GTCACCGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:2386620 original size:22 final size:22
Alignment explanation
Indices: 2386570--2386620 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2386560 CGGATTTCGT
* **
2386570 CGGAGATGGGGACGGATTTCGT
1 CGGAGATGGGGACGGATGTCAC
2386592 CGGAGATGGGGACGGATGTCAC
1 CGGAGATGGGGACGGATGTCAC
*
2386614 CGTAGAT
1 CGGAGAT
2386621 AGTGAGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
CGGAGATGGGGACGGATGTCAC
Found at i:2386799 original size:20 final size:20
Alignment explanation
Indices: 2386774--2386867 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
2386764 ATTTTGTATT
*
2386774 ATCGCGTTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAGA
** **
2386794 ATCGCGTTGATATTATGT-ATT
1 ATCGCGTTGCGA-TA-GTCAGA
2386815 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
2386835 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
2386855 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
2386868 TTACAAATTC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 46 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:2386813 original size:41 final size:41
Alignment explanation
Indices: 2386750--2386843 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 41
2386740 TGGCACTTTG
* * *
2386750 AAAATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTC
1 AAAATCGCGTTGAGATTATGTATTATCGCGTTGCGATAGTC
*
2386791 AAAATCGCGTTGATATTATGTATTATCGCGTTGCGATAGTC
1 AAAATCGCGTTGAGATTATGTATTATCGCGTTGCGATAGTC
*
2386832 AGAATCGCGTTG
1 AAAATCGCGTTG
2386844 CGATAGTCAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (41 bp):
AAAATCGCGTTGAGATTATGTATTATCGCGTTGCGATAGTC
Found at i:2386879 original size:20 final size:21
Alignment explanation
Indices: 2386854--2386901 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2386844 CGATAGTCAG
*
2386854 AATCGCGTTGCGA-TTTACAA
1 AATCGCATTGCGATTTTACAA
* *
2386874 ATTCGCATTGTGATTTTACAA
1 AATCGCATTGCGATTTTACAA
2386895 AATCGCA
1 AATCGCA
2386902 ACGCGAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (21 bp):
AATCGCATTGCGATTTTACAA
Found at i:2386949 original size:41 final size:41
Alignment explanation
Indices: 2386842--2386957 Score: 99
Period size: 41 Copynumber: 2.8 Consensus size: 41
2386832 AGAATCGCGT
* ** ** *
2386842 TGCGATAGTCAGAATCGCGTTGCG-ATTTACAAATTCGCAT
1 TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAACCGCAA
* ** ***
2386882 TGTGATTTTACAAAATCGCAACGCGAATTTGGAAAACCGCAA
1 TGCGATAGT-CAAAATCGCGTTGCGAATTTGGAAAACCGCAA
*
2386924 TGCGATAGTCAAAATCGCGTTGCGAATCTGGAAA
1 TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAA
2386958 CTGATTTGCG
Statistics
Matches: 55, Mismatches: 19, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
40 6 0.11
41 32 0.58
42 17 0.31
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (41 bp):
TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAACCGCAA
Found at i:2386986 original size:20 final size:19
Alignment explanation
Indices: 2386963--2387008 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2386953 GGAAACTGAT
* *
2386963 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
2386983 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
2387002 TTGCGAT
1 TTGCGAT
2387009 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:2386998 original size:19 final size:19
Alignment explanation
Indices: 2386974--2387010 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2386964 TGCGATACTG
*
2386974 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
2386993 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
2387011 TGTTGGTCAT
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:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:2392168 original size:2 final size:2
Alignment explanation
Indices: 2392161--2392190 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2392151 GATTAATGAA
2392161 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
2392191 GGTTAGGATC
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:2392839 original size:2 final size:2
Alignment explanation
Indices: 2392832--2392921 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
2392822 TAACTTAGAT
2392832 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
2392874 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
2392916 TA TA TA
1 TA TA TA
2392922 AGGTTAGAGT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2394120 original size:11 final size:12
Alignment explanation
Indices: 2394096--2394123 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2394086 CGATTTTTCG
2394096 TTATAAATTTTT
1 TTATAAATTTTT
2394108 TTATAAATTTTT
1 TTATAAATTTTT
2394120 TTAT
1 TTAT
2394124 TATACTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATAAATTTTT
Found at i:2397503 original size:35 final size:34
Alignment explanation
Indices: 2397418--2397504 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2397408 AATATAATTT
*
2397418 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
2397452 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
2397490 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2397505 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:2399777 original size:17 final size:18
Alignment explanation
Indices: 2399757--2399797 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2399747 AAATTATATT
2399757 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
2399774 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
2399792 ATTAAA
1 AGTAAA
2399798 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:2400178 original size:30 final size:29
Alignment explanation
Indices: 2400116--2400178 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
2400106 TACTGCTACG
* * *
2400116 GGTGTTAGATCGGGAAATATAATCTGACC
1 GGTGTTAGATCGAGAAATATAATATCACC
* *
2400145 GGTGTTAGATCGATAAATATACTGATCACC
1 GGTGTTAGATCGAGAAATATAAT-ATCACC
2400175 GGTG
1 GGTG
2400179 ATTTTTCGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGAGAAATATAATATCACC
Found at i:2413885 original size:26 final size:27
Alignment explanation
Indices: 2413856--2413937 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 27
2413846 TTCGGTCAAA
2413856 TTAGAGTTCAA-GGTATTTTGG-CATT
1 TTAGAGTTCAAGGGTATTTTGGTCATT
* *
2413881 CTTAGGGTTCAAGGGAATTTTGGTCATT
1 -TTAGAGTTCAAGGGTATTTTGGTCATT
* * * * *
2413909 TCAAAGTTCAATGGTATTTCGATCATT
1 TTAGAGTTCAAGGGTATTTTGGTCATT
2413936 TT
1 TT
2413938 CTTTGATTTA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
26 10 0.23
27 30 0.68
28 4 0.09
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (27 bp):
TTAGAGTTCAAGGGTATTTTGGTCATT
Found at i:2415876 original size:21 final size:21
Alignment explanation
Indices: 2415850--2416006 Score: 180
Period size: 21 Copynumber: 7.6 Consensus size: 21
2415840 GTTTCCAGAT
* *
2415850 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
2415871 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
2415892 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
2415912 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
2415933 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
2415954 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
2415974 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
2415995 TCGCAATGCGAA
1 TCGCAATGCGAA
2416007 TTTGTAAATC
Statistics
Matches: 115, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
20 33 0.29
21 82 0.71
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:2415897 original size:62 final size:63
Alignment explanation
Indices: 2415850--2416006 Score: 187
Period size: 62 Copynumber: 2.5 Consensus size: 63
2415840 GTTTCCAGAT
* **
2415850 TCGCAACGCGA-ACTTCGACTATCGCAATGCGAACTTGGACTATCGC-AATGCGAATATGTAAA
1 TCGCAACGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAAATGCGAATATCCAAA
* **
2415912 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGC-AATGCGAATATGTAAA
1 TCGCAACGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAAATGCGAATATCCAAA
* * *
2415974 TCGCAATGCGA-ACTTGGACTATCGCAATGCGAA
1 TCGCAACGCGATA-GTCGACTATCGCAATGCGAA
2416007 TTTGTAAATC
Statistics
Matches: 89, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
61 1 0.01
62 87 0.98
63 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (63 bp):
TCGCAACGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAAATGCGAATATCCAAA
Found at i:2415977 original size:41 final size:42
Alignment explanation
Indices: 2415850--2416016 Score: 177
Period size: 41 Copynumber: 4.0 Consensus size: 42
2415840 GTTTCCAGAT
* * * *
2415850 TCGCAACGCGAACTTCGACTATCGCAATGCGAACT-TGGACTA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTACAA
* * *
2415892 TCGCAATGCGAA-TATGTA-AATCGCAATGCG-ATA-GTCGACTA
1 TCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT--ACAA
2415933 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACAA
*
2415974 TCGCAATGCGAACTTGGACTATCGCAATGCGAATTTGTA-AA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACAA
2416015 TC
1 TC
2416017 AATTTTTTAA
Statistics
Matches: 108, Mismatches: 9, Indels: 17
0.81 0.07 0.13
Matches are distributed among these distances:
39 2 0.02
40 1 0.01
41 74 0.69
42 26 0.24
43 3 0.03
44 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (42 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACAA
Found at i:2416074 original size:30 final size:30
Alignment explanation
Indices: 2416031--2416115 Score: 134
Period size: 30 Copynumber: 2.8 Consensus size: 30
2416021 TTTTAATTAC
* * **
2416031 AATTAAATCATTTAATTTATTGATTATAAT
1 AATTAATTAATTTAATTTATCAATTATAAT
2416061 AATTAATTAATTTAATTTATCAATTATAAT
1 AATTAATTAATTTAATTTATCAATTATAAT
2416091 AATTAATTAATTTAATTTATCAATT
1 AATTAATTAATTTAATTTATCAATT
2416116 GTTACTATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.51
Consensus pattern (30 bp):
AATTAATTAATTTAATTTATCAATTATAAT
Found at i:2416102 original size:17 final size:16
Alignment explanation
Indices: 2416043--2416106 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 16
2416033 TTAAATCATT
* *
2416043 TAATTTATTGATTATAA
1 TAATTAATTAATT-TAA
2416060 TAATTAATTAATTTAA
1 TAATTAATTAATTTAA
*
2416076 T--TT-ATCAATTATAA
1 TAATTAATTAATT-TAA
2416090 TAATTAATTAATTTAA
1 TAATTAATTAATTTAA
2416106 T
1 T
2416107 TTATCAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.15
14 6 0.15
16 10 0.26
17 17 0.44
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TAATTAATTAATTTAA
Found at i:2416115 original size:17 final size:17
Alignment explanation
Indices: 2416065--2416115 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
2416055 TATAATAATT
2416065 AATTAATTTAATTTATC
1 AATTAATTTAATTTATC
* *
2416082 AATT-A--TAA-TAATT
1 AATTAATTTAATTTATC
2416095 AATTAATTTAATTTATC
1 AATTAATTTAATTTATC
2416112 AATT
1 AATT
2416116 GTTACTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
16 4 0.15
17 11 0.42
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTAATTTAATTTATC
Found at i:2423829 original size:21 final size:21
Alignment explanation
Indices: 2423785--2423829 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2423775 ATATTTTTTA
*
2423785 AATTATTAAAGTATATAAACT
1 AATTATTAAAGTATAAAAACT
*
2423806 AATTATTAAAAG-ATAAAAATT
1 AATTATT-AAAGTATAAAAACT
2423827 AAT
1 AAT
2423830 CAAATAACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (21 bp):
AATTATTAAAGTATAAAAACT
Found at i:2424246 original size:13 final size:14
Alignment explanation
Indices: 2424218--2424246 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2424208 ATATTTTATA
2424218 ATATTTTTACTATT
1 ATATTTTTACTATT
2424232 ATATTTTTACT-TT
1 ATATTTTTACTATT
2424245 AT
1 AT
2424247 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:2426066 original size:18 final size:18
Alignment explanation
Indices: 2426043--2426081 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2426033 CCAGCAGCCA
2426043 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
2426061 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
2426079 CCG
1 CCG
2426082 TCATCGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.21
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:2429537 original size:47 final size:49
Alignment explanation
Indices: 2429467--2429569 Score: 140
Period size: 47 Copynumber: 2.1 Consensus size: 49
2429457 TATACAAAAT
* * * *
2429467 GCGGTACTTGTCCCGCGCTATATAAAATTA-T-GGAGTAAAGGTAT-GTC
1 GCGGTACATGCCCCGCACGATATAAAATTATTAGGAGTAAAGGTATAG-C
2429514 GCGGTACATGCCCCGCACGATATAAAATTATTAGGAGTAAAGGTATAGC
1 GCGGTACATGCCCCGCACGATATAAAATTATTAGGAGTAAAGGTATAGC
2429563 GCGGTAC
1 GCGGTAC
2429570 TTGATCCGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
47 26 0.53
48 1 0.02
49 21 0.43
50 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
GCGGTACATGCCCCGCACGATATAAAATTATTAGGAGTAAAGGTATAGC
Found at i:2429714 original size:49 final size:48
Alignment explanation
Indices: 2429596--2429716 Score: 134
Period size: 49 Copynumber: 2.5 Consensus size: 48
2429586 CCCTACGTGA
* * **
2429596 CGTATAGCGCGCTGCAGGGGCCGCGCTATATCCACGTGACGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGG--GCGCTATACCCACGTGACGCCAAATCAC
** * * *
2429646 CGTATAGCGCGGTATAGGGGGTGCTATACCCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCTATA-CCCACGTGACGCCAAATCAC
2429695 CGTATAGCGCGGTGCAGGGGGC
1 CGTATAGCGCGGTGCAGGGGGC
2429717 ACTTTACTGC
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
48 7 0.12
49 34 0.59
50 17 0.29
ACGTcount: A:0.19, C:0.30, G:0.34, T:0.17
Consensus pattern (48 bp):
CGTATAGCGCGGTGCAGGGGGCGCTATACCCACGTGACGCCAAATCAC
Found at i:2435543 original size:36 final size:35
Alignment explanation
Indices: 2435498--2435568 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
2435488 AACATCTACC
2435498 AAACTTTACCAAACTTTGAAAAACAATTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACAATTTTCAAAG
*
2435533 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACAATTTTCAAAG
2435569 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.30
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACAATTTTCAAAG
Found at i:2435567 original size:21 final size:21
Alignment explanation
Indices: 2435507--2435567 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
2435497 CAAACTTTAC
*
2435507 CAAACTTTGAAAAACAATTTT
1 CAAACTTTGAAAAACATTTTT
**
2435528 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
2435543 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
2435564 CAAA
1 CAAA
2435568 GTTGGTTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 11 0.38
17 1 0.03
19 1 0.03
21 16 0.55
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:2440041 original size:36 final size:37
Alignment explanation
Indices: 2439983--2440062 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 37
2439973 CTCATTCCTA
2439983 TTTTC-AACAAACATCTACCAAACTTTGAAA-AACAT
1 TTTTCAAACAAACATCTACCAAACTTTGAAACAACAT
* * *
2440018 TTTTCAAAGAAACATTTATCAAACTTTGAAACTAACAT
1 TTTTCAAACAAACATCTACCAAACTTTGAAAC-AACAT
2440056 TTTTCAA
1 TTTTCAA
2440063 GTGAACTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 5 0.13
36 22 0.56
38 12 0.31
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.34
Consensus pattern (37 bp):
TTTTCAAACAAACATCTACCAAACTTTGAAACAACAT
Found at i:2443693 original size:35 final size:35
Alignment explanation
Indices: 2443575--2443714 Score: 163
Period size: 36 Copynumber: 3.9 Consensus size: 35
2443565 TGAATAAGAA
2443575 GAACGAAAGGAAACATCAACACTTTCGATTCAAAGT
1 GAACGAAAGGAAACATCAACACTTTCGATTC-AAGT
* ** * *
2443611 GAACGGAAGGAAACATCGGCACTTTTGATTCAAGAA
1 GAACGAAAGGAAACATCAACACTTTCGATTCAAG-T
* **
2443647 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAACATCAACACTTTCGATTCAAGT
* * *
2443682 GAACGGAAGGAAGCATCAACACTTTCAATTCAA
1 GAACGAAAGGAAACATCAACACTTTCGATTCAA
2443715 TTGTTCATCT
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
35 32 0.36
36 58 0.64
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (35 bp):
GAACGAAAGGAAACATCAACACTTTCGATTCAAGT
Found at i:2445437 original size:12 final size:12
Alignment explanation
Indices: 2445420--2445445 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2445410 TTTACCATAG
2445420 CAATTCTCCTCA
1 CAATTCTCCTCA
2445432 CAATTCTCCTCA
1 CAATTCTCCTCA
2445444 CA
1 CA
2445446 CACCCTTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (12 bp):
CAATTCTCCTCA
Found at i:2458166 original size:12 final size:12
Alignment explanation
Indices: 2458151--2458187 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2458141 AAATTCTGCC
2458151 AAAAAAAAAAG-
1 AAAAAAAAAAGA
2458162 -AAAAAAAAAGA
1 AAAAAAAAAAGA
2458173 AAAAAAAAAAGA
1 AAAAAAAAAAGA
2458185 AAA
1 AAA
2458188 TGTAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:2458187 original size:10 final size:10
Alignment explanation
Indices: 2458152--2458180 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2458142 AATTCTGCCA
2458152 AAAAAAAAAG
1 AAAAAAAAAG
2458162 AAAAAAAAAG
1 AAAAAAAAAG
2458172 AAAAAAAAA
1 AAAAAAAAA
2458181 AAGAAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:2460207 original size:23 final size:23
Alignment explanation
Indices: 2460163--2460235 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
2460153 AGTGTTATAT
*
2460163 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAA
* * *
2460186 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAAAATATTAATTAA
* * * *
2460209 AATATTTTTAGATTATTATATTAA
1 TATATTTTAAAAATATTA-ATTAA
2460233 TAT
1 TAT
2460236 TAAATATATA
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 30 0.81
24 7 0.19
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAA
Found at i:2460423 original size:24 final size:23
Alignment explanation
Indices: 2460396--2460457 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
2460386 TATTAAAAAA
2460396 AATAATTATATTATTAGAA-ATATT
1 AATAATTATATT-TTA-AATATATT
* *
2460420 AATAAATATATTTTAAATATTTT
1 AATAATTATATTTTAAATATATT
2460443 AATAATTAATATTTT
1 AATAATT-ATATTTT
2460458 GATTAAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.06
23 13 0.39
24 18 0.55
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AATAATTATATTTTAAATATATT
Found at i:2467589 original size:23 final size:22
Alignment explanation
Indices: 2467545--2467589 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2467535 TCAGAAGTTA
2467545 CAGGAGTTATCTGATTTAATTT
1 CAGGAGTTATCTGATTTAATTT
2467567 CAGGAGTTATAACTG-TTTAATTT
1 CAGGAGTTAT--CTGATTTAATTT
2467590 TTATGCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 8 0.38
24 3 0.14
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (22 bp):
CAGGAGTTATCTGATTTAATTT
Found at i:2468585 original size:22 final size:22
Alignment explanation
Indices: 2468559--2468612 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
2468549 TTACATTTCC
2468559 ATAATGCATACGTTTTATTATA
1 ATAATGCATACGTTTTATTATA
2468581 ATAATGCATACGTTTTATTATA
1 ATAATGCATACGTTTTATTATA
2468603 ATAATGCATA
1 ATAATGCATA
2468613 ATAATGATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (22 bp):
ATAATGCATACGTTTTATTATA
Found at i:2468796 original size:2 final size:2
Alignment explanation
Indices: 2468789--2468817 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2468779 TTTATGTCTT
2468789 TA TA 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 TA TA T
2468818 TAGATTGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2472429 original size:31 final size:31
Alignment explanation
Indices: 2472391--2472453 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2472381 CCCAAGAGTT
2472391 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
1 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
2472422 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
1 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
2472453 T
1 T
2472454 TCACCAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.27
Consensus pattern (31 bp):
TGGGAGTTCCTAGTGAGAAGGACATATTGAA
Found at i:2475047 original size:14 final size:15
Alignment explanation
Indices: 2475028--2475056 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2475018 AGCTGAATTA
2475028 TTTTTATTTT-TTAT
1 TTTTTATTTTGTTAT
2475042 TTTTTATTTTGTTAT
1 TTTTTATTTTGTTAT
2475057 CTAATTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTATTTTGTTAT
Found at i:2482947 original size:102 final size:98
Alignment explanation
Indices: 2482783--2483006 Score: 270
Period size: 102 Copynumber: 2.2 Consensus size: 98
2482773 GTTTCCCTTG
* * * *
2482783 AAACAAATTACGTCTCACTCGAGACAGTTTCCCTTGAAACACAAACTTTAATATCATTTCACTCA
1 AAACAAATTCCATCTCACTTGAGACAGTTTCCCTTGAAACACAAACTTTAAGATCATTTCACTCA
*
2482848 AAAGAAATCTTATCTCACATGATATTAGTTTTT-TTA
66 AAA-AAA--TTATCTCAC-TGAAATTAGTTTTTCTTA
* * *
2482884 AAACAAAATTCCATCTCACTTGAGACAGTTTCCCTTTAAACACAAATTTTAAGATCGTTTCACTC
1 AAAC-AAATTCCATCTCACTTGAGACAGTTTCCCTTGAAACACAAACTTTAAGATCATTTCACTC
** * **
2482949 AAAAAAATTATCTTGCTTAAATTTTTTTTTCTTA
65 AAAAAAATTATCTCACTGAAATTAGTTTTTCTTA
*
2482983 AAACAAATTTCATCTCACTTGAGA
1 AAACAAATTCCATCTCACTTGAGA
2483007 TTGTTTTACC
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
98 29 0.27
99 14 0.13
101 7 0.07
102 57 0.53
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (98 bp):
AAACAAATTCCATCTCACTTGAGACAGTTTCCCTTGAAACACAAACTTTAAGATCATTTCACTCA
AAAAAATTATCTCACTGAAATTAGTTTTTCTTA
Found at i:2483023 original size:98 final size:101
Alignment explanation
Indices: 2482795--2483031 Score: 261
Period size: 102 Copynumber: 2.4 Consensus size: 101
2482785 ACAAATTACG
* * * *
2482795 TCTCACTCGAGACAGTTTCCCTTGAAACACAAACTTTAATATCATTTCACTCAAAAGAAATCTTA
1 TCTCACTTGAGACAGTTTACCTTGAAACACAAATTTTAAGATCATTTCACTCAAAAGAAA-CTTA
*
2482860 TCTCACATGATATTAGTTTTTTTAAAACAAAATTCCA
65 TCTCACATGAAATTAGTTTTTTTAAAACAAAATTCCA
* * *
2482897 TCTCACTTGAGACAGTTTCCCTTTAAACACAAATTTTAAGATCGTTTCACTCAAAA-AAA-TTAT
1 TCTCACTTGAGACAGTTTACCTTGAAACACAAATTTTAAGATCATTTCACTCAAAAGAAACTTAT
** * ** *
2482960 CTTGC-TTAAATTTTTTTTTCTTAAAAC-AAATTTCA
66 CTCACATGAAATTAGTTTTT-TTAAAACAAAATTCCA
**
2482995 TCTCACTTGAGATTGTTTTACC-TGAAACA-AAATTTTA
1 TCTCACTTGAGACAG-TTTACCTTGAAACACAAATTTTA
2483032 TCTCACTCGA
Statistics
Matches: 117, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
97 8 0.07
98 36 0.31
99 19 0.16
101 3 0.03
102 51 0.44
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.38
Consensus pattern (101 bp):
TCTCACTTGAGACAGTTTACCTTGAAACACAAATTTTAAGATCATTTCACTCAAAAGAAACTTAT
CTCACATGAAATTAGTTTTTTTAAAACAAAATTCCA
Found at i:2483262 original size:101 final size:105
Alignment explanation
Indices: 2482998--2483276 Score: 295
Period size: 107 Copynumber: 2.7 Consensus size: 105
2482988 AATTTCATCT
* * * * * *
2482998 CACTTGAGATTGTTTTACCTGAAACAAAATTTTATCTCACTCGAGAT-AGTTTCCCTCGAAACTC
1 CACTTGAGATTGTTTT-TCTTAAACAAAATTTTATCTCACTTGAGATCAGTTACCCTTGAAACAC
* *
2483062 AAACTTCAAGATCATTTTACTTAAAAAAAGAAAATATTATCA
65 AAACTTTAAGATCATTTCACTT-AAAAAAGAAAATATTATCA
*** * *
2483104 TGTTTGAGATTGTTTTTATTTGAAACAAAATTTCATCTCACTTGAGA-CAGTTACCCTTGAAACA
1 CACTTGAGATTGTTTTT-CTT-AAACAAAATTTTATCTCACTTGAGATCAGTTACCCTTGAAACA
* * *
2483168 CAAACTTTAAGATCATTTCAC-T-CAAAAG-AAATCTTATCC
64 CAAACTTTAAGATCATTTCACTTAAAAAAGAAAATATTATCA
*
2483207 CACTTGAGATTGTTTTTCTTAAA-ATAAATTTTATCTCACTTGAGATCA-TTCCCCTTGAAACA-
1 CACTTGAGATTGTTTTTCTTAAACA-AAATTTTATCTCACTTGAGATCAGTTACCCTTGAAACAC
*
2483269 AAATTTTA
65 AAACTTTA
2483277 TCTAGCTCGA
Statistics
Matches: 145, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
100 8 0.06
101 35 0.24
102 4 0.03
103 23 0.16
104 5 0.03
106 15 0.10
107 55 0.38
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (105 bp):
CACTTGAGATTGTTTTTCTTAAACAAAATTTTATCTCACTTGAGATCAGTTACCCTTGAAACACA
AACTTTAAGATCATTTCACTTAAAAAAGAAAATATTATCA
Found at i:2483320 original size:245 final size:236
Alignment explanation
Indices: 2482795--2483479 Score: 691
Period size: 245 Copynumber: 2.8 Consensus size: 236
2482785 ACAAATTACG
* * * * * * * * **
2482795 TCTCACTCGAGACAGTTTCCCTTGAAACACAAACTTTAATATCATTTCACTCAAAAGAAATCTTA
1 TCTCACTCGAGATAGTTCCCCTCGAAACTCAAACTTCAAGATCATTCCACTTAAAA-AAA-AATA
* * * * * *
2482860 TCTCACATGATATTAGTTTTTTTAAAACAAAATTCCATCTCACTTGAGACAGTTTCCCTTTAAAC
64 TATCACATGAGATT-TTTTTTTTGAAACAAAATTTCATCTCACTTGAGACAGTTTCCCTTGAAAC
* * * * *
2482925 ACAAATTTTAAGATCGTTTCACTCAAAA-AAA-TTATCTTGCTT-AAATTTTTTTTTCTTAAAAC
128 ACAAACTTTAAGATCATTTCACTCAAAAGAAATTTATCTCGCTTGAGA-TTGTTTTTCTTAAAAC
* ** *
2482987 AAATTTCATCTCACTTGAGATTGTTTTACCTGAAACAAAATTTTA
192 AAATTTTATCTCACTTGAGATTCATTCACCTGAAACAAAATTTTA
* **
2483032 TCTCACTCGAGATAGTTTCCCTCGAAACTCAAACTTCAAGATCATTTTACTTAAAAAAAGAAAAT
1 TCTCACTCGAGATAGTTCCCCTCGAAACTCAAACTTCAAGATCATTCCACTT--AAAAA-AAAAT
** *
2483097 ATTATCATGTTTGAGATTGTTTTTATTTGAAACAAAATTTCATCTCACTTGAGACAGTTACCCTT
63 A-TATCA--CATGAGATT-TTTTT-TTTGAAACAAAATTTCATCTCACTTGAGACAGTTTCCCTT
* *
2483162 GAAACACAAACTTTAAGATCATTTCACTCAAAAGAAATCTTATCCCACTTGAGATTGTTTTTCTT
123 GAAACACAAACTTTAAGATCATTTCACTCAAAAGAAAT-TTATCTCGCTTGAGATTGTTTTTCTT
* *
2483227 AAAATAAATTTTATCTCACTTGAGA-TCATTCCCCTTGAAACAAAATTTTA
187 AAAACAAATTTTATCTCACTTGAGATTCATTCACC-TGAAACAAAATTTTA
* *
2483277 TCT-AGCTCGAGATAGTTCCCCTC-AGAACAT-AAACTTTAAGATCATTCCACTTAAAAAAAATT
1 TCTCA-CTCGAGATAGTTCCCCTCGA-AAC-TCAAACTTCAAGATCATTCCACTTAAAAAAAAAT
* * * ** * *
2483339 ATCTCACATGAGATTTTTTCTCTTGAAACAAAATTTTATCTCACTCAAGATAGTTTCCCTAGAAA
63 ATATCACATGAGATTTTTT-TTTTGAAACAAAATTTCATCTCACTTGAGACAGTTTCCCTTGAAA
* * * *
2483404 CATAAACTTCAAGATCATTTCATTCAAAAAAGAAAATTTTATCTCGCTTGAGATTGTTTCTCTTA
127 CACAAACTTTAAGATCATTTCACTC--AAAAG-AAA-TTTATCTCGCTTGAGATTGTTTTTCTTA
2483469 AAACAAATTTT
188 AAACAAATTTT
2483480 TTCCTCATTC
Statistics
Matches: 374, Mismatches: 54, Indels: 36
0.81 0.12 0.08
Matches are distributed among these distances:
237 45 0.12
238 66 0.18
239 18 0.05
240 5 0.01
241 51 0.14
242 73 0.20
243 8 0.02
244 7 0.02
245 98 0.26
246 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (236 bp):
TCTCACTCGAGATAGTTCCCCTCGAAACTCAAACTTCAAGATCATTCCACTTAAAAAAAAATATA
TCACATGAGATTTTTTTTTTGAAACAAAATTTCATCTCACTTGAGACAGTTTCCCTTGAAACACA
AACTTTAAGATCATTTCACTCAAAAGAAATTTATCTCGCTTGAGATTGTTTTTCTTAAAACAAAT
TTTATCTCACTTGAGATTCATTCACCTGAAACAAAATTTTA
Found at i:2483397 original size:138 final size:137
Alignment explanation
Indices: 2483123--2483389 Score: 321
Period size: 138 Copynumber: 1.9 Consensus size: 137
2483113 TTGTTTTTAT
* * *
2483123 TTGAAACAAAATTTCATCTCACTTGAGACAGTTACCCTTGAAACACAAACTTTAAGATCATTTCA
1 TTGAAACAAAATTTCATCTCACTCGAGACAGTTACCCTAGAAACACAAACTTTAAGATCATTCCA
* * **
2483188 CTCAAAAGAAATCTTATCCCACTTGAGATTGTTTTTCTTAAAATAAATTTTATCTCACTTGAGAT
66 CTCAAAAGAAATATTATCCCACATGAGATTGTTTTTCTTAAAATAAATTTTATCTCACTCAAGAT
2483253 CATTCCCC
131 CATT-CCC
* * * *
2483261 TTGAAACAAAATTTTATCT-AGCTCGAGATAGTTCCCCTCAG-AACATAAACTTTAAGATCATTC
1 TTGAAACAAAATTTCATCTCA-CTCGAGACAGTTACCCT-AGAAACACAAACTTTAAGATCATTC
* *
2483324 CACTTAAAA-AAA-ATTATCTCACATGAGATT-TTTTCTCTTGAAACA-AAATTTTATCTCACTC
64 CACTCAAAAGAAATATTATCCCACATGAGATTGTTTT-TCTT-AAA-ATAAATTTTATCTCACTC
2483385 AAGAT
126 AAGAT
2483390 AGTTTCCCTA
Statistics
Matches: 111, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
135 4 0.04
136 19 0.17
137 26 0.23
138 61 0.55
139 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (137 bp):
TTGAAACAAAATTTCATCTCACTCGAGACAGTTACCCTAGAAACACAAACTTTAAGATCATTCCA
CTCAAAAGAAATATTATCCCACATGAGATTGTTTTTCTTAAAATAAATTTTATCTCACTCAAGAT
CATTCCC
Found at i:2483433 original size:100 final size:103
Alignment explanation
Indices: 2483227--2483480 Score: 286
Period size: 100 Copynumber: 2.5 Consensus size: 103
2483217 TGTTTTTCTT
* * * * * *
2483227 AAAATAAATTTTATCTCACTTGAGATCATTCCCCTTGAAACAAAATTTTATCTAGCTCGAGATAG
1 AAAAGAAAATTTATCTCACTTGAGATTATTTCTCTTGAAACAAAATTTTATCTAGCTCAAGATAG
*
2483292 TTCCCCTCAGAACATAAACTTTAAGATCATTCCACTT-
66 TTCCCCTCAGAACATAAACTTCAAGATCATTCCACTTA
* *
2483329 AAAA-AAAA-TTATCTCACATGAGATTTTTTCTCTTGAAACAAAATTTTATCTCA-CTCAAGATA
1 AAAAGAAAATTTATCTCACTTGAGATTATTTCTCTTGAAACAAAATTTTATCT-AGCTCAAGATA
* *
2483391 GTTTCCCT-AGAAACATAAACTTCAAGATCATTTCA-TTCAA
65 GTTCCCCTCAG-AACATAAACTTCAAGATCATTCCACTT--A
* * * *
2483431 AAAAGAAAATTTTATCTCGCTTGAGATTGTTTCTCTTAAAACAAATTTTT
1 AAAAGAAAA-TTTATCTCACTTGAGATTATTTCTCTTGAAACAAAATTTT
2483481 TCCTCATTCA
Statistics
Matches: 129, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
99 4 0.03
100 75 0.58
101 4 0.03
102 8 0.06
103 4 0.03
105 34 0.26
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.35
Consensus pattern (103 bp):
AAAAGAAAATTTATCTCACTTGAGATTATTTCTCTTGAAACAAAATTTTATCTAGCTCAAGATAG
TTCCCCTCAGAACATAAACTTCAAGATCATTCCACTTA
Found at i:2483435 original size:344 final size:342
Alignment explanation
Indices: 2482780--2483462 Score: 811
Period size: 344 Copynumber: 2.0 Consensus size: 342
2482770 ATAGTTTCCC
* * *
2482780 TTGAAACAAATTACGTCTCACTCGAGACAGTTTCCCTTGAAACACAAACTTTAATATCATTTCAC
1 TTGAAACAAATTACATCTCACTCGAGACAGTTACCCTTGAAACACAAACTTTAAGATCATTTCAC
* *
2482845 TCAAAAGAAATCTTATCTCACATGATATTAGTTTTTTTAAAACAAAATTCCATCTCACTTGAGAC
66 TCAAAAGAAATCTTATCCCACATGAGATTAGTTTTTTTAAAACAAAATTCCATCTCACTTGAGAC
* * * * **
2482910 AGTTTCCCTTTAAACACAAATTTTAAGATCGTTTCACTCAAAAAAATTATCTTGCTTAAATTTTT
131 AGTTCCCCTTGAAACACAAATTTTAAGATCGTTTCACTCAAAAAAATAAACTT-CTTAAATTCAT
*** * *
2482975 TTTTCTTAAAACAAATTTCATCTCACTTGAGATTGTTTTACCTGAAACAAAATTTTATCTCACTC
195 TCCACTTAAAACAAAATTCATCTCACATGAGATTGTTTTACCTGAAACAAAATTTTATCTCACTC
* * *
2483040 GAGATAGTTTCCCTCGAAACTCAAACTTCAAGATCATTTTACTTAAAAAAAGAAAATATTATCAT
260 AAGATAGTTTCCCTAGAAACTCAAACTTCAAGATCATTTCACTTAAAAAAAGAAAATATTATC-T
*
2483105 -GTTTGAGATTGTTTTTAT
324 CGCTTGAGATTGTTTTTAT
* *
2483123 TTGAAACAAAATTTCATCTCACTTGAGACAGTTACCCTTGAAACACAAACTTTAAGATCATTTCA
1 TTGAAAC-AAATTACATCTCACTCGAGACAGTTACCCTTGAAACACAAACTTTAAGATCATTTCA
* * **
2483188 CTCAAAAGAAATCTTATCCCACTTGAGATT-GTTTTTCTTAAAA-TAAATTTTATCTCACTTGAG
65 CTCAAAAGAAATCTTATCCCACATGAGATTAGTTTTT-TTAAAACAAAATTCCATCTCACTTGAG
* * * *
2483251 ATCA-TTCCCCTTGAAACA-AAATTTTATCTAGCTCGAGATAGTTCCCCTC-AGAACATAAAC-T
129 A-CAGTTCCCCTTGAAACACAAATTTTA---AGATC--G-T--TT-CACTCAAAAAAATAAACTT
2483312 -TTAAGA-TCATTCCACTTAAAA-AAAATT-ATCTCACATGAGATT-TTTT-CTCTTGAAACAAA
184 CTTAA-ATTCATTCCACTTAAAACAAAATTCATCTCACATGAGATTGTTTTAC-C-TGAAACAAA
*
2483371 ATTTTATCTCACTCAAGATAGTTTCCCTAGAAACAT-AAACTTCAAGATCATTTCA-TTCAAAAA
246 ATTTTATCTCACTCAAGATAGTTTCCCTAGAAAC-TCAAACTTCAAGATCATTTCACTTAAAAAA
*
2483434 AGAAAATTTTATCTCGCTTGAGATTGTTT
310 AGAAAATATTATCTCGCTTGAGATTGTTT
2483463 CTCTTAAAAC
Statistics
Matches: 291, Mismatches: 32, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
342 8 0.03
343 45 0.15
344 124 0.43
345 77 0.26
346 6 0.02
347 15 0.05
348 2 0.01
349 1 0.00
350 9 0.03
351 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (342 bp):
TTGAAACAAATTACATCTCACTCGAGACAGTTACCCTTGAAACACAAACTTTAAGATCATTTCAC
TCAAAAGAAATCTTATCCCACATGAGATTAGTTTTTTTAAAACAAAATTCCATCTCACTTGAGAC
AGTTCCCCTTGAAACACAAATTTTAAGATCGTTTCACTCAAAAAAATAAACTTCTTAAATTCATT
CCACTTAAAACAAAATTCATCTCACATGAGATTGTTTTACCTGAAACAAAATTTTATCTCACTCA
AGATAGTTTCCCTAGAAACTCAAACTTCAAGATCATTTCACTTAAAAAAAGAAAATATTATCTCG
CTTGAGATTGTTTTTAT
Found at i:2489078 original size:18 final size:18
Alignment explanation
Indices: 2489055--2489095 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2489045 TCTTCAACCC
2489055 AACCCCATCTTCTTCCTA
1 AACCCCATCTTCTTCCTA
*
2489073 AACCCCATCTTCTTCCTC
1 AACCCCATCTTCTTCCTA
2489091 AACCC
1 AACCC
2489096 AACCTCGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.22, C:0.49, G:0.00, T:0.29
Consensus pattern (18 bp):
AACCCCATCTTCTTCCTA
Found at i:2489096 original size:41 final size:41
Alignment explanation
Indices: 2489039--2489121 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
2489029 GACCGACTCT
* *
2489039 TCTTCTTCTTCAACCCAACCCCATCTTCTTCCTAAACCCCA
1 TCTTCTTCCTCAACCCAACCCCATCTTCTTCCTAAACACCA
* * *
2489080 TCTTCTTCCTCAACCCAACCTCGTCTTCTTCCTTAACACCA
1 TCTTCTTCCTCAACCCAACCCCATCTTCTTCCTAAACACCA
2489121 T
1 T
2489122 TTTGCGCACA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.20, C:0.45, G:0.01, T:0.34
Consensus pattern (41 bp):
TCTTCTTCCTCAACCCAACCCCATCTTCTTCCTAAACACCA
Found at i:2489111 original size:23 final size:23
Alignment explanation
Indices: 2489039--2489112 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
2489029 GACCGACTCT
*
2489039 TCTTCTTCTTCAACCCAACCCCA
1 TCTTCTTCCTCAACCCAACCCCA
2489062 TCTTCTTCCT--A---AACCCCA
1 TCTTCTTCCTCAACCCAACCCCA
* *
2489080 TCTTCTTCCTCAACCCAACCTCG
1 TCTTCTTCCTCAACCCAACCCCA
2489103 TCTTCTTCCT
1 TCTTCTTCCT
2489113 TAACACCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
18 17 0.40
20 1 0.02
21 1 0.02
23 24 0.56
ACGTcount: A:0.18, C:0.46, G:0.01, T:0.35
Consensus pattern (23 bp):
TCTTCTTCCTCAACCCAACCCCA
Found at i:2490446 original size:23 final size:23
Alignment explanation
Indices: 2490416--2490471 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2490406 GATGGTGTTA
* *
2490416 AGGAAGAAGATGGGGTTGGGTTG
1 AGGAAGAAGATAGGGTTAGGTTG
2490439 AGGAAGAAGATAGGGTTAGGTTG
1 AGGAAGAAGATAGGGTTAGGTTG
*
2490462 AAGAAGAAGA
1 AGGAAGAAGA
2490472 AGAGTCGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.45, T:0.18
Consensus pattern (23 bp):
AGGAAGAAGATAGGGTTAGGTTG
Found at i:2494694 original size:11 final size:12
Alignment explanation
Indices: 2494664--2494717 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
2494654 GTTATTTAAA
2494664 CGGGTATTGGGT
1 CGGGTATTGGGT
2494676 CGGGTATTGGGT
1 CGGGTATTGGGT
*
2494688 C-GGTATTGGGC
1 CGGGTATTGGGT
* * *
2494699 CGGGAATCGGGC
1 CGGGTATTGGGT
2494711 CGGGTAT
1 CGGGTAT
2494718 ATATATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.27
12 27 0.73
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:2494722 original size:2 final size:2
Alignment explanation
Indices: 2494715--2494798 Score: 54
Period size: 2 Copynumber: 45.0 Consensus size: 2
2494705 TCGGGCCGGG
* * * *
2494715 TA TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2494755 TT TA AA T- TA AA TT TA T- TA -A TA T- 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
2494793 TA TA TA
1 TA TA TA
2494799 ATTATTTTTA
Statistics
Matches: 61, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
1 6 0.10
2 55 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2494779 original size:24 final size:24
Alignment explanation
Indices: 2494716--2494805 Score: 94
Period size: 24 Copynumber: 3.7 Consensus size: 24
2494706 CGGGCCGGGT
2494716 ATATATATATATATATTTAAATTAA
1 ATATATATATAT-TATTTAAATTAA
*
2494741 ATATATATATTTTATTTAAATTAA
1 ATATATATATATTATTTAAATTAA
* * * *
2494765 ATTTAT-TAATATTATATATA-TAT
1 ATATATAT-ATATTATTTAAATTAA
2494788 ATATATATATAATTATTT
1 ATATATATAT-ATTATTT
2494806 TTAATATTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
23 10 0.19
24 33 0.61
25 11 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATATATATATTATTTAAATTAA
Found at i:2497184 original size:31 final size:31
Alignment explanation
Indices: 2497148--2497222 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
2497138 TTAAAACTTA
*
2497148 CAATATAGTCCTCC-AACATTTAGTT-TATTTG
1 CAATATGGTCC-CCTAACATTTA-TTCTATTTG
*
2497179 TAATATGGTCCCCTAACATTTATTCTATTTG
1 CAATATGGTCCCCTAACATTTATTCTATTTG
2497210 CAATATGGTCCCC
1 CAATATGGTCCCC
2497223 GGTTGTTTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 4 0.10
31 35 0.90
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.40
Consensus pattern (31 bp):
CAATATGGTCCCCTAACATTTATTCTATTTG
Found at i:2499088 original size:30 final size:31
Alignment explanation
Indices: 2499047--2499113 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
2499037 TCAAACAATC
*
2499047 GAGGACTATATTACAAACAGACTAAATGTTG
1 GAGGACCATATTACAAACAGACTAAATGTTG
**
2499078 G-GGACCATATTACAAATGGACTAAATGTTG
1 GAGGACCATATTACAAACAGACTAAATGTTG
2499108 GAGGAC
1 GAGGAC
2499114 TGTATTGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (31 bp):
GAGGACCATATTACAAACAGACTAAATGTTG
Found at i:2506029 original size:2 final size:2
Alignment explanation
Indices: 2506022--2506048 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2506012 AATTAATCAT
2506022 TA 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 TA T
2506049 CGATAGAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2507851 original size:2 final size:2
Alignment explanation
Indices: 2507844--2507868 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2507834 ATTACTTTAT
2507844 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
2507869 GCTGATAGTT
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
Found at i:2515049 original size:19 final size:19
Alignment explanation
Indices: 2515027--2515109 Score: 157
Period size: 19 Copynumber: 4.4 Consensus size: 19
2515017 GATGTTGATA
2515027 GAATCAATTCCCGAAGCCG
1 GAATCAATTCCCGAAGCCG
2515046 GAATCAATTCCCGAAGCCG
1 GAATCAATTCCCGAAGCCG
2515065 GAATCAATTCCCGAAGCCG
1 GAATCAATTCCCGAAGCCG
*
2515084 GAATCAATTCCCGAAGCCA
1 GAATCAATTCCCGAAGCCG
2515103 GAATCAA
1 GAATCAA
2515110 AGATTGCATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 63 1.00
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (19 bp):
GAATCAATTCCCGAAGCCG
Found at i:2515314 original size:18 final size:19
Alignment explanation
Indices: 2515283--2515326 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
2515273 TATTCTCTTA
* *
2515283 TTTTTTTTACTTTAATTGC
1 TTTTATTTACTTTAATCGC
*
2515302 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGC
2515320 TTTTATT
1 TTTTATT
2515327 ACTACTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGC
Found at i:2523889 original size:18 final size:19
Alignment explanation
Indices: 2523859--2523901 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
2523849 TATTTTCTTA
*
2523859 TTTT-TTTACTTTAATTGC
1 TTTTATTTACTTTAATCGC
*
2523877 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGC
2523895 TTTTATT
1 TTTTATT
2523902 ACTACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGC
Found at i:2530341 original size:18 final size:18
Alignment explanation
Indices: 2530318--2530353 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2530308 CGTACAATCG
2530318 GACTCTATGGCAGACTAA
1 GACTCTATGGCAGACTAA
*
2530336 GACTCTATGGCTGACTAA
1 GACTCTATGGCAGACTAA
2530354 ACGGATGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (18 bp):
GACTCTATGGCAGACTAA
Found at i:2532327 original size:24 final size:24
Alignment explanation
Indices: 2532295--2532387 Score: 177
Period size: 24 Copynumber: 3.9 Consensus size: 24
2532285 TCATATAATT
2532295 TGCACCGAAGTGCCACGTAGAATA
1 TGCACCGAAGTGCCACGTAGAATA
2532319 TGCACCGAAGTGCCACGTAGAATA
1 TGCACCGAAGTGCCACGTAGAATA
*
2532343 TGCACCGAAGTGCCACGTAAAATA
1 TGCACCGAAGTGCCACGTAGAATA
2532367 TGCACCGAAGTGCCACGTAGA
1 TGCACCGAAGTGCCACGTAGA
2532388 TTTGTCCCAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (24 bp):
TGCACCGAAGTGCCACGTAGAATA
Found at i:2532416 original size:24 final size:24
Alignment explanation
Indices: 2532382--2532459 Score: 131
Period size: 24 Copynumber: 3.3 Consensus size: 24
2532372 CGAAGTGCCA
*
2532382 CGTAG-ATTTGTCCCAAAGGACCG
1 CGTAGAATTTGTCCCGAAGGACCG
*
2532405 CGTAGAATTTGTCCCGAAGGACCA
1 CGTAGAATTTGTCCCGAAGGACCG
2532429 CGTAGAATTTGTCCCGAAGGACCG
1 CGTAGAATTTGTCCCGAAGGACCG
2532453 CGTAGAA
1 CGTAGAA
2532460 CCCTCGTCTC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 5 0.10
24 46 0.90
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (24 bp):
CGTAGAATTTGTCCCGAAGGACCG
Found at i:2533316 original size:21 final size:20
Alignment explanation
Indices: 2533275--2533323 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
2533265 TTACTATTGG
2533275 TATCGATACCTCCACATCAA
1 TATCGATACCTCCACATCAA
2533295 TATCGATACTACTCCA-ATCAA
1 TATCGATAC--CTCCACATCAA
2533316 TATCGATA
1 TATCGATA
2533324 TTGTTCATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.33
21 13 0.48
22 5 0.19
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.29
Consensus pattern (20 bp):
TATCGATACCTCCACATCAA
Found at i:2533747 original size:15 final size:15
Alignment explanation
Indices: 2533722--2533793 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
2533712 TGGTTTTTCA
2533722 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
2533737 GAATTTGAATTACTG
1 GAAAATGAATTACTG
2533752 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
2533767 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
2533781 GAAAATGAATTAC
1 GAAAATGAATTAC
2533794 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.25
15 36 0.75
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:2533791 original size:29 final size:30
Alignment explanation
Indices: 2533722--2533793 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
2533712 TGGTTTTTCA
2533722 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
2533752 GAAAATGAATTACTGGAATTTGAATT-CTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
2533781 GAAAATGAATTAC
1 GAAAATGAATTAC
2533794 ATTTCTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (30 bp):
GAAAATGAATTACTGGAATTTGAATTACTG
Found at i:2533799 original size:20 final size:20
Alignment explanation
Indices: 2533776--2533845 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
2533766 GGAATTTGAA
2533776 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
2533796 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
2533816 TTCTAGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2533836 TTCTGGAAAA
1 TTCTGGAAAA
2533846 CATCTGGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:2534053 original size:28 final size:27
Alignment explanation
Indices: 2534012--2534076 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
2534002 TTTACTAAAA
* *
2534012 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAAAATTAT
2534040 TCATTATTAAATATATAAAAAAAATTAT
1 T-ATTATTAAATATATAAAAAAAATTAT
2534068 TATATATTA
1 TAT-TATTA
2534077 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 25 0.76
29 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAAAATTAT
Found at i:2534077 original size:31 final size:30
Alignment explanation
Indices: 2534011--2534115 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 30
2534001 CTTTACTAAA
2534011 ATATTATTGAAATATAT--AAATAATATTAT
1 ATATTATT-AAATATATAAAAATAATATTAT
*
2534040 -TCATTATTAAATATATAAAAAAAATTATTAT
1 AT-ATTATTAAATATATAAAAATAA-TATTAT
2534071 ATATTATTAAA-ATA-AAAATATAATATCT-T
1 ATATTATTAAATATATAAAA-ATAATAT-TAT
2534100 ATATTATTATAATATA
1 ATATTATTA-AATATA
2534116 ATTGATTATT
Statistics
Matches: 65, Mismatches: 2, Indels: 16
0.78 0.02 0.19
Matches are distributed among these distances:
28 9 0.14
29 23 0.35
30 14 0.22
31 18 0.28
32 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (30 bp):
ATATTATTAAATATATAAAAATAATATTAT
Found at i:2534087 original size:24 final size:23
Alignment explanation
Indices: 2534042--2534101 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 23
2534032 AATATTATTC
*
2534042 ATTATTAAATA-TA-TAAAAAAA
1 ATTATTATATATTATTAAAAAAA
2534063 ATTATTATATATTATTAAAATAAA
1 ATTATTATATATTATTAAAA-AAA
* * *
2534087 AATATAATATCTTAT
1 ATTATTATATATTAT
2534102 ATTATTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.31
22 2 0.06
23 5 0.16
24 15 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTATTATATATTATTAAAAAAA
Found at i:2534177 original size:22 final size:22
Alignment explanation
Indices: 2534134--2534204 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
2534124 TTTTATATAA
* *
2534134 TATTAAAAATATT-ATATTATAT
1 TATTATAAATATTAATA-AATAT
2534156 TATTATAAATATTAATAAATA-
1 TATTATAAATATTAATAAATAT
* *
2534177 TATTTTAAATATTTTAATAATTAT
1 TATTATAAATA--TTAATAAATAT
2534201 TATT
1 TATT
2534205 TTGATGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 10 0.24
22 15 0.37
23 12 0.29
24 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTATAAATATTAATAAATAT
Found at i:2534188 original size:52 final size:51
Alignment explanation
Indices: 2534069--2534189 Score: 124
Period size: 52 Copynumber: 2.3 Consensus size: 51
2534059 AAAAATTATT
* **
2534069 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATAT-ATATATTATATTATTATAATATAATAA
2534120 AT-TATTTTATATAATATTAAAAATAT-TATATTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATATATATTATATTATTAT-AATA-TAATAA
2534174 ATATATTTTAAATATT
1 ATATATTTTAAATATT
2534190 TTAATAATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 23 0.39
53 7 0.12
54 18 0.31
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATATATATTATATTATTATAATATAATAA
Found at i:2534201 original size:21 final size:21
Alignment explanation
Indices: 2534122--2534203 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
2534112 TATAATTGAT
*
2534122 TATTTTATATAA-TATTAAAAA
1 TATTTTA-ATAATTATTATAAA
* *
2534143 TATTATATTATATTATTATAAA
1 TATTTTAATA-ATTATTATAAA
*
2534165 TA--TTAATAAATATATTTTAAA
1 TATTTTAAT-AAT-TATTATAAA
2534186 TATTTTAATAATTATTAT
1 TATTTTAATAATTATTAT
2534204 TTTGATGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
20 7 0.15
21 23 0.48
22 13 0.27
23 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTTAATAATTATTATAAA
Found at i:2534437 original size:42 final size:42
Alignment explanation
Indices: 2534378--2534497 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
2534368 ATGAATTACA
* *
2534378 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
2534420 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
2534462 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
2534498 TTCGGGAAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:2535351 original size:17 final size:17
Alignment explanation
Indices: 2535306--2535344 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2535296 AACGGTCATG
2535306 GGGTTAATTAGTAAGTT
1 GGGTTAATTAGTAAGTT
2535323 GGGTTAATTAGTAAGTT
1 GGGTTAATTAGTAAGTT
2535340 GGGTT
1 GGGTT
2535345 TGTTAGTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.33, T:0.41
Consensus pattern (17 bp):
GGGTTAATTAGTAAGTT
Found at i:2537674 original size:23 final size:23
Alignment explanation
Indices: 2537644--2537689 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2537634 GGTGAAAATA
2537644 AATATATTAAATTAAAATAAAGT
1 AATATATTAAATTAAAATAAAGT
2537667 AATATATTAAATTAAAATAAAGT
1 AATATATTAAATTAAAATAAAGT
2537690 TAACCCTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
AATATATTAAATTAAAATAAAGT
Found at i:2542463 original size:11 final size:11
Alignment explanation
Indices: 2542439--2542472 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2542429 AATTTTCATC
2542439 CATATATAATAT
1 CATATAT-ATAT
2542451 CATATATATAT
1 CATATATATAT
*
2542462 CACATATATAT
1 CATATATATAT
2542473 ATTACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
CATATATATAT
Found at i:2543664 original size:42 final size:42
Alignment explanation
Indices: 2543566--2543648 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
2543556 GGCTTGGGGC
2543566 TACTGCTCGCGTGGAAGGGAGCTTCTGGGGCTTGTTGGTAGA
1 TACTGCTCGCGTGGAAGGGAGCTTCTGGGGCTTGTTGGTAGA
2543608 TACTGCTCGCGTGGAAGGGAGCTTCTGGGGCTTGTTGGTAG
1 TACTGCTCGCGTGGAAGGGAGCTTCTGGGGCTTGTTGGTAG
2543649 CAGCTGCTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.13, C:0.17, G:0.41, T:0.29
Consensus pattern (42 bp):
TACTGCTCGCGTGGAAGGGAGCTTCTGGGGCTTGTTGGTAGA
Found at i:2548149 original size:212 final size:212
Alignment explanation
Indices: 2547782--2549016 Score: 2033
Period size: 212 Copynumber: 5.9 Consensus size: 212
2547772 CAAGAAAAGT
* **
2547782 TGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGA
1 TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
* *
2547847 CTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTTTCA
*
2547912 ATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
131 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
2547977 CACGACGAAGGGACCGC
196 CACGACGAAGGGACCGC
2547994 TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
1 TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
*
2548059 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTTCA
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTTTCA
*
2548124 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACCT
131 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
*
2548189 CACGACGAAGGGACCGT
196 CACGACGAAGGGACCGC
*
2548206 TGGTTGTCAACAAACAACTTC-CTAATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
1 TGGTTGTCAACAAACAACTTCTC-AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2548270 ACTCCAGACAGCGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-A-TTTCT
65 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTT-T
* * *
2548333 CAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCAAGACAACGCAAGTTCAAC
129 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
2548398 TTCACGACGAAGGGACCGC
194 TTCACGACGAAGGGACCGC
* * *
2548417 TGGTTGTCAACAAA-TATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
1 TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
*
2548481 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-TGGTTGTCAACAAAC-ATTTTTCA
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTTTCA
*
2548544 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTT
131 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
2548609 CACGACGAAGGGACCGC
196 CACGACGAAGGGACCGC
* *
2548626 TGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
1 TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
* * **
2548690 CTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAAC-AACAACTTCCCA
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTTTCA
* *
2548754 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTT
131 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
2548819 CACGACGAAGGGACCGC
196 CACGACGAAGGGACCGC
* *
2548836 TGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC-AAGGATATTGGA
1 TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
* * * *
2548900 CTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAA-TTTCC
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTT-T
* * *
2548963 CAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAAC
129 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
2549017 ATAACTTTCA
Statistics
Matches: 969, Mismatches: 43, Indels: 23
0.94 0.04 0.02
Matches are distributed among these distances:
209 202 0.21
210 259 0.27
211 189 0.20
212 319 0.33
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (212 bp):
TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTTTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGC
Found at i:2548390 original size:105 final size:106
Alignment explanation
Indices: 2547782--2549016 Score: 2049
Period size: 105 Copynumber: 11.7 Consensus size: 106
2547772 CAAGAAAAGT
* * **
2547782 TGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGA
1 TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
*
2547847 CTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGC
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
2547888 TGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
1 TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
2547953 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
2547994 TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
1 TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
2548059 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
2548100 TGGTTGTCAATAAACAACTTT-TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1 TGGTTGTCAACAAACAA-TTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2548164 ACTCCAGACAACGCAAGTTCAACCTCACGACGAAGGGACCGT
65 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
2548206 TGGTTGTCAACAAACAACTTC-CTAATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
1 TGGTTGTCAACAAACAATTTCTC-AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2548270 ACTCCAGACAGCGCAAGTTCAACTTCACGACGAAGGGACCGC
65 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
2548312 TGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGA
1 TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
*
2548376 CTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
2548417 TGGTTGTCAACAAA-TATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
1 TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
2548481 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
2548521 TGGTTGTCAACAAAC-ATTTTTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
1 TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
*
2548585 CTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGC
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
2548626 TGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
1 TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
* *
2548690 CTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCAC
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* * *
2548731 TGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
1 TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
*
2548795 CTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
2548836 TGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC-AAGGATATTGGA
1 TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
* * *
2548900 CTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGAC
66 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-C
* * *
2548941 TGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGA
1 TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
*
2549006 CTCGAGACAAC
66 CTCCAGACAAC
2549017 ATAACTTTCA
Statistics
Matches: 1076, Mismatches: 42, Indels: 22
0.94 0.04 0.02
Matches are distributed among these distances:
104 105 0.10
105 492 0.46
106 477 0.44
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
Found at i:2549614 original size:11 final size:11
Alignment explanation
Indices: 2549590--2549623 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2549580 AATTTTCATC
2549590 CATATATAATAT
1 CATATAT-ATAT
2549602 CATATATATAT
1 CATATATATAT
*
2549613 CACATATATAT
1 CATATATATAT
2549624 ATTACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
CATATATATAT
Found at i:2550815 original size:42 final size:42
Alignment explanation
Indices: 2550717--2550799 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
2550707 GGCTTGGGGC
2550717 TACTGCTCGCGTGGAAGGGAGCTTCTGGGGCTTGTTGGTAGA
1 TACTGCTCGCGTGGAAGGGAGCTTCTGGGGCTTGTTGGTAGA
2550759 TACTGCTCGCGTGGAAGGGAGCTTCTGGGGCTTGTTGGTAG
1 TACTGCTCGCGTGGAAGGGAGCTTCTGGGGCTTGTTGGTAG
2550800 CAGCTGCTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.13, C:0.17, G:0.41, T:0.29
Consensus pattern (42 bp):
TACTGCTCGCGTGGAAGGGAGCTTCTGGGGCTTGTTGGTAGA
Found at i:2552591 original size:32 final size:32
Alignment explanation
Indices: 2552555--2552618 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2552545 GAGAAATGAT
*
2552555 GAATGATGGGGCATCTTTGGAGATTCAACATC
1 GAATGATGGGGCATCTTGGGAGATTCAACATC
*
2552587 GAATGTTGGGGCATCTTGGGAGATTCAACATC
1 GAATGATGGGGCATCTTGGGAGATTCAACATC
2552619 CTGAATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (32 bp):
GAATGATGGGGCATCTTGGGAGATTCAACATC
Found at i:2552770 original size:36 final size:35
Alignment explanation
Indices: 2552721--2552854 Score: 121
Period size: 37 Copynumber: 3.8 Consensus size: 35
2552711 CAAAGCGTCA
2552721 TCTCGCTTGAGACAATTTTCTTAAAAAAGAATTTTG
1 TCTCGCTTGAGACAATTTTCTTAAAAAA-AATTTTG
* * *
2552757 TCTCTCTTAAGACAGA-TTTCTCTAAAAACAAATTTTA
1 TCTCGCTTGAGACA-ATTTTCT-TAAAAA-AAATTTTG
* * ** *
2552794 TCTCACTTGAGATAATTTCTCTCCAAATAAA--TTG
1 TCTCGCTTGAGACAATTT-TCTTAAAAAAAATTTTG
*
2552828 TCTCGCTTGAGACAATTTTCTTTAAAA
1 TCTCGCTTGAGACAATTTTCTTAAAAA
2552855 CACAAATTCT
Statistics
Matches: 78, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
33 6 0.08
34 18 0.23
36 21 0.27
37 29 0.37
38 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (35 bp):
TCTCGCTTGAGACAATTTTCTTAAAAAAAATTTTG
Done.