Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008091.1 Hibiscus syriacus cultivar Beakdansim tig00110602_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: 2471235
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:2188792 original size:21 final size:20
Alignment explanation
Indices: 2188746--2188821 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
2188736 CGTAGAGCGA
* *
2188746 CTACCTCATCACGTAAAGTAG
1 CTACCTCATCACGTAAA-CAC
* *
2188767 ATACCTCATCACGTGAAACAT
1 CTACCTCATCACGT-AAACAC
* *
2188788 CTACCTCACCACGTAAAGAC
1 CTACCTCATCACGTAAACAC
2188808 CGTACCTCATCACG
1 C-TACCTCATCACG
2188822 CCATGCACCA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.11
21 37 0.82
22 3 0.07
ACGTcount: A:0.33, C:0.34, G:0.12, T:0.21
Consensus pattern (20 bp):
CTACCTCATCACGTAAACAC
Found at i:2188866 original size:21 final size:21
Alignment explanation
Indices: 2188840--2188887 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2188830 CATTGTCTTC
*
2188840 ACGTAAAGTACCGACCTCATG
1 ACGTAAAGCACCGACCTCATG
*
2188861 ACGTAAAGCACCGACCTCATT
1 ACGTAAAGCACCGACCTCATG
2188882 ACGTAA
1 ACGTAA
2188888 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
ACGTAAAGCACCGACCTCATG
Found at i:2190580 original size:19 final size:19
Alignment explanation
Indices: 2190535--2190582 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
2190525 TTCTAAAATT
*
2190535 TAAATTCGCAACGCGAAAA
1 TAAAATCGCAACGCGAAAA
*
2190554 TAAAAATCGCAACGCGAAAC
1 T-AAAATCGCAACGCGAAAA
2190574 TAAAATCGC
1 TAAAATCGC
2190583 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.15
Consensus pattern (19 bp):
TAAAATCGCAACGCGAAAA
Found at i:2190996 original size:22 final size:22
Alignment explanation
Indices: 2190961--2191015 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
2190951 TCTGAGAGAT
*
2190961 GGAGATA--GACGTATTTTGTC
1 GGAGATAGGGACGTATTTCGTC
2190981 GGAGATAGGGACGTATTTCGTC
1 GGAGATAGGGACGTATTTCGTC
*
2191003 GGAGATGGGGACG
1 GGAGATAGGGACG
2191016 GATGTTGCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 7 0.23
22 24 0.77
ACGTcount: A:0.24, C:0.11, G:0.40, T:0.25
Consensus pattern (22 bp):
GGAGATAGGGACGTATTTCGTC
Found at i:2191219 original size:20 final size:20
Alignment explanation
Indices: 2191177--2191370 Score: 125
Period size: 20 Copynumber: 9.7 Consensus size: 20
2191167 TAAACGCGCT
*
2191177 TTGCGAATTTGACTTTC-ACG
1 TTGCGAATTTGACTATCGA-G
*
2191197 TTGCGGATTTGACTATCGAG
1 TTGCGAATTTGACTATCGAG
* *
2191217 TTGCGAATTTTACTTAT-GTG
1 TTGCGAATTTGAC-TATCGAG
* **
2191237 TTGCG-ATTT-ACAAATTCGCC
1 TTGCGAATTTGAC-TA-TCGAG
* *
2191257 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC-TA-TCGAG
2191277 TTGCGAATTTGACTATCGCA-
1 TTGCGAATTTGACTATCG-AG
*
2191297 TTGCAAATTTGACTATCGCA-
1 TTGCGAATTTGACTATCG-AG
* * *
2191317 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATCGAG
*
2191337 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTATCGAG
*
2191357 TTGGGAATTTGACT
1 TTGCGAATTTGACT
2191371 TTTGTGTTTC
Statistics
Matches: 144, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.02
19 5 0.03
20 125 0.87
21 9 0.06
22 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGAG
Found at i:2191371 original size:40 final size:40
Alignment explanation
Indices: 2191272--2191378 Score: 151
Period size: 40 Copynumber: 2.7 Consensus size: 40
2191262 ATTTACAGAT
* * **
2191272 TCGCGTTGCGAATTTGACTATCGCATTGCAAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTA
* *
2191312 TCGCATTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTA
*
2191352 TCGCGTTGGGAATTTGACTTTTGTGTT
1 TCGCGTTGCGAATTTGACTTTTGTGTT
2191379 TCGATTTACA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTA
Found at i:2191906 original size:3 final size:3
Alignment explanation
Indices: 2191898--2191972 Score: 62
Period size: 3 Copynumber: 25.0 Consensus size: 3
2191888 AATTTTTCGT
** ** * * *
2191898 TTA TTA TTA TTA AAA TTA TTA AAA TTA TTA TAA ATA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2191946 -TA ATA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA
2191973 AATATATATA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:2191981 original size:2 final size:2
Alignment explanation
Indices: 2191974--2192003 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2191964 TTATTATTAA
2191974 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
2192004 TACAAATTAC
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:2193591 original size:126 final size:125
Alignment explanation
Indices: 2193478--2193701 Score: 317
Period size: 126 Copynumber: 1.8 Consensus size: 125
2193468 AAAAATAATC
* *
2193478 ATATTTT-GATATTTATTTATTTTT-AATATCGAAGAAAAGAGCTGTCTTAAGGCACTTAGAAGC
1 ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC
* ** *
2193541 CCTTTTCTGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTATTTTAAGAAA
66 CCTTTTATGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTA-TAGAAAAAA
* * * *
2193602 ATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGTTGTCTTAAGGTACCTAGAAGC
1 ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC
* *
2193667 TCTTTTATGATATTTTTGAATAAATAAATATCTTA
66 CCTTTTATGATATTTTTAAATAAATAAATATCTTA
2193702 CTATATTAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 6 0.07
125 16 0.18
126 67 0.75
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (125 bp):
ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC
CCTTTTATGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTATAGAAAAAA
Found at i:2193731 original size:115 final size:116
Alignment explanation
Indices: 2193599--2193817 Score: 307
Period size: 116 Copynumber: 1.9 Consensus size: 116
2193589 TTATTTTAAG
* * * * *
2193599 AAAATGTTTTGGTTATTTATTTA-TTTTTCAATATCAAAGAAAAGAGTTGTCTTAAGGTACCTAG
1 AAAATGTTTTGGATATTTATTTATTTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACATAG
* * *
2193663 -AAGCTCTTTTATGATATTTTTGAATAAATAAATATCTTACTATATTAAAAT
66 AAATC-CTTTTATGATATTTCTAAATAAATAAATATCTTACTATATTAAAAT
* *
2193714 AAAATGTTTTTGATATTTATTTATTTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACATAG
1 AAAATGTTTTGGATATTTATTTATTTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACATAG
* *
2193779 AAATCCTTTTCTGATATTTCTAAATAAGTAAATATCTTA
66 AAATCCTTTTATGATATTTCTAAATAAATAAATATCTTA
2193818 TTTATGTATA
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
115 21 0.23
116 66 0.73
117 3 0.03
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (116 bp):
AAAATGTTTTGGATATTTATTTATTTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACATAG
AAATCCTTTTATGATATTTCTAAATAAATAAATATCTTACTATATTAAAAT
Found at i:2202153 original size:54 final size:54
Alignment explanation
Indices: 2202070--2202227 Score: 271
Period size: 54 Copynumber: 2.9 Consensus size: 54
2202060 TGATTGAGAA
2202070 ATCTGAGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * *
2202124 GTCTGAGCAGAAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* *
2202178 ATCTGAGCAGAAGCCACAGGAAAGGATGAATGAGTTGTCAAATGTTTTAC
1 ATCTGAGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAC
2202228 AAACCTGCTA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.25
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:2202624 original size:22 final size:22
Alignment explanation
Indices: 2202599--2202675 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
2202589 ATCTACATTC
*
2202599 TTCAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2202621 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
2202643 TTTAAATATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2202665 TTCAAAGATGA
1 TTCAAAGATGA
2202676 AGGCTTTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2203502 original size:165 final size:167
Alignment explanation
Indices: 2203191--2203515 Score: 539
Period size: 165 Copynumber: 2.0 Consensus size: 167
2203181 AAAATGAGCA
2203191 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACG
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACG
* ** *
2203256 ATTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
**
2203321 CTTAGTTTTTTTACTTAGTAAACTATTTCCAATAGCC
131 CTTAGTTTCCTTACTTAGTAAACTATTTCCAATAGCC
** *
2203358 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAAA-ATAATGAGAAAACG
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACG
2203421 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
2203486 CCTTAG-TTCCTTACTTAGTAAACTATTTCC
130 CCTTAGTTTCCTTACTTAGTAAACTATTTCC
2203516 CACATCTGTA
Statistics
Matches: 148, Mismatches: 9, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
165 62 0.42
166 43 0.29
167 43 0.29
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (167 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACG
ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
CTTAGTTTCCTTACTTAGTAAACTATTTCCAATAGCC
Found at i:2203644 original size:76 final size:76
Alignment explanation
Indices: 2203518--2204610 Score: 2001
Period size: 76 Copynumber: 14.4 Consensus size: 76
2203508 CTATTTCCCA
2203518 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2203583 AGCCTTAGGGT
66 AGCCTTAGGGT
2203594 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2203658 AGCCTTAGGGT
66 AGCCTTAGGGT
2203669 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2203734 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2203745 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2203810 AAGCCTTAGGGT
65 AAGCCTTAGGGT
*
2203822 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2203887 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
2203898 CATATGTAAGTCCTGCAGTGCATGATGTTTCCAAAAA-TCTTCGTGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2203962 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2203973 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2204038 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2204049 CATCTGTAAGTGCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2204114 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2204125 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2204190 AGCCTTAGGGT
66 AGCCTTAGGGT
2204201 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2204266 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2204277 CATCTGTAAGTCCTGCAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2204342 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2204353 CATCTGTAAGTCCTACAGTGTATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2204418 AGCCTTAGGGT
66 AGCCTTAGGGT
* * * *
2204429 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGAAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2204494 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2204505 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2204570 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2204581 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
2204611 TTAAGACCTC
Statistics
Matches: 988, Mismatches: 26, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
75 146 0.15
76 767 0.78
77 75 0.08
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:2204763 original size:3 final size:3
Alignment explanation
Indices: 2204755--2204830 Score: 64
Period size: 3 Copynumber: 25.3 Consensus size: 3
2204745 AATTTTTCGT
** * * *
2204755 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
2204803 -TA ATA ATA ATA TTA TTA TTTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA T
2204831 ATATATATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
2 2 0.03
3 56 0.92
4 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:2204775 original size:15 final size:16
Alignment explanation
Indices: 2204755--2204830 Score: 64
Period size: 17 Copynumber: 4.6 Consensus size: 16
2204745 AATTTTTCGT
2204755 TTATTATTATTAA-AA
1 TTATTATTATTAATAA
2204770 TTATTATTATTATTATAA
1 TTATTATTATTA--ATAA
*
2204788 ATATTATTATTAATATA
1 TTATTATTATTAATA-A
* * * * *
2204805 ATAATAATATTATTAT
1 TTATTATTATTAATAA
2204821 TTATTATTAT
1 TTATTATTAT
2204831 ATATATATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
15 12 0.24
16 10 0.20
17 14 0.29
18 13 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATTATTATTAATAA
Found at i:2204778 original size:18 final size:17
Alignment explanation
Indices: 2204755--2204821 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 17
2204745 AATTTTTCGT
2204755 TTATTATTATTAAAATTA
1 TTATTATTATTAAAA-TA
2204773 TTATTATTATTATAAATA
1 TTATTATTATTA-AAATA
2204791 TTATTATTAATATAATAATA
1 TTATTATT-AT-TAA-AATA
*
2204811 ATATTATTATT
1 TTATTATTATT
2204822 TATTATTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
18 23 0.52
19 8 0.18
20 13 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTATTATTAAAATA
Found at i:2204792 original size:27 final size:28
Alignment explanation
Indices: 2204762--2204853 Score: 61
Period size: 24 Copynumber: 3.4 Consensus size: 28
2204752 CGTTTATTAT
2204762 TATTA-AAATTATTATTATTATTATAAA
1 TATTACAAATTATTATTATTATTATAAA
* * *
2204789 TATT----ATTATTAATATAATAAT-AA
1 TATTACAAATTATTATTATTATTATAAA
** * *
2204812 TATTATTATTTATTATTATATATATATATA
1 TATTACAAATTATTATTAT-TAT-TATAAA
2204842 TATTACAAATTA
1 TATTACAAATTA
2204854 CATCAGAAGC
Statistics
Matches: 47, Mismatches: 11, Indels: 11
0.68 0.16 0.16
Matches are distributed among these distances:
23 6 0.13
24 14 0.30
27 13 0.28
28 2 0.04
29 2 0.04
30 10 0.21
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTACAAATTATTATTATTATTATAAA
Found at i:2206430 original size:126 final size:125
Alignment explanation
Indices: 2206317--2206540 Score: 308
Period size: 126 Copynumber: 1.8 Consensus size: 125
2206307 AAAAATAATC
* * * *
2206317 ATATTTT-GATATTTATTTATTTTT-AATATCGATGAAAAGAGCTGTCTTAAGGCACTTAGAAGC
1 ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAAAAGC
** *
2206380 CCTTTTCTGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTATTTTAAGAAA
66 CCTTTTCTGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTA-TAGAAAAAA
* * * *
2206441 ATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGTTGTCTTAAGGTACCTAAAAGC
1 ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAAAAGC
* *
2206506 TCTTTTCTGATATTTTTGAATAAATAAATATCTTA
66 CCTTTTCTGATATTTTTAAATAAATAAATATCTTA
2206541 CTATATTAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
124 6 0.07
125 16 0.18
126 66 0.75
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (125 bp):
ATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAAAAGC
CCTTTTCTGATATTTTTAAATAAATAAATATCTTATTAAAATAAATTTTTATAGAAAAAA
Found at i:2206574 original size:115 final size:115
Alignment explanation
Indices: 2206438--2206655 Score: 314
Period size: 115 Copynumber: 1.9 Consensus size: 115
2206428 TTATTTTAAG
* * *
2206438 AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGTTGTCTTAAGGTACCTA-A
1 AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
* * *
2206502 AAGCTCTTTTCTGATATTTTTGAATAAATAAATATCTTACTATATTAAAAT
66 AA-CCCTTTTCTGATATTTCTAAATAAATAAATATCTTACTATATTAAAAT
* * *
2206553 AAAATGTTTT-TTATATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACTTAG
1 AAAATGTTTTGGT-TATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAG
*
2206617 AAACCCTTTTCTGATATTTCTAAATAAGTAAATATCTTA
65 AAACCCTTTTCTGATATTTCTAAATAAATAAATATCTTA
2206656 TTTATGTATA
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
114 1 0.01
115 87 0.96
116 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (115 bp):
AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
AACCCTTTTCTGATATTTCTAAATAAATAAATATCTTACTATATTAAAAT
Found at i:2212723 original size:47 final size:47
Alignment explanation
Indices: 2212662--2212757 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
2212652 TTTACCTTAT
2212662 ATTCAACTTCATTTATTTTAATTTAAGAGCATTTATCAGCTTATTGA
1 ATTCAACTTCATTTATTTTAATTTAAGAGCATTTATCAGCTTATTGA
2212709 ATTCAACTTCATTTATTTTAATTTAAGAGCATTTATCAGCTTATTGA
1 ATTCAACTTCATTTATTTTAATTTAAGAGCATTTATCAGCTTATTGA
2212756 AT
1 AT
2212758 GATCTCGTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.47
Consensus pattern (47 bp):
ATTCAACTTCATTTATTTTAATTTAAGAGCATTTATCAGCTTATTGA
Found at i:2220373 original size:35 final size:35
Alignment explanation
Indices: 2220327--2220396 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2220317 GAACTACTTA
2220327 GTTAAATTATTGCTCTTGATGGTATATCTTATGTT
1 GTTAAATTATTGCTCTTGATGGTATATCTTATGTT
2220362 GTTAAATTATTGCTCTTGATGGTATATCTTATGTT
1 GTTAAATTATTGCTCTTGATGGTATATCTTATGTT
2220397 AAGCGCATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (35 bp):
GTTAAATTATTGCTCTTGATGGTATATCTTATGTT
Found at i:2220892 original size:10 final size:10
Alignment explanation
Indices: 2220877--2220908 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2220867 TGGATATTTG
2220877 TGTTGATGAA
1 TGTTGATGAA
2220887 TGTTGATGAA
1 TGTTGATGAA
*
2220897 TGTTGTTGAA
1 TGTTGATGAA
2220907 TG
1 TG
2220909 AAATATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (10 bp):
TGTTGATGAA
Found at i:2222781 original size:21 final size:21
Alignment explanation
Indices: 2222756--2222798 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2222746 ATAAATTGTG
*
2222756 TATCGATGCACTATTACAGTA
1 TATCGATGCACTACTACAGTA
*
2222777 TATCGATGCACTGCTACAGTA
1 TATCGATGCACTACTACAGTA
2222798 T
1 T
2222799 TATTACAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (21 bp):
TATCGATGCACTACTACAGTA
Found at i:2223540 original size:31 final size:31
Alignment explanation
Indices: 2223505--2223647 Score: 214
Period size: 31 Copynumber: 4.6 Consensus size: 31
2223495 AGACCATAGA
* *
2223505 TCCCGAAGAATCTAGGTAATCAATCCATATG
1 TCCCGAAGAATATAGGTAAACAATCCATATG
* *
2223536 TCCCGAAAAAAATAGGTAAACAATCCATATG
1 TCCCGAAGAATATAGGTAAACAATCCATATG
* *
2223567 TCTCGAAGAATATAGGTAAACAGTCCATATG
1 TCCCGAAGAATATAGGTAAACAATCCATATG
*
2223598 TCCCGAAGAATATAGGTAAACAGTCCATATG
1 TCCCGAAGAATATAGGTAAACAATCCATATG
*
2223629 TCCCGAAGAACATAGGTAA
1 TCCCGAAGAATATAGGTAA
2223648 CCCTCGACCC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (31 bp):
TCCCGAAGAATATAGGTAAACAATCCATATG
Found at i:2227047 original size:114 final size:114
Alignment explanation
Indices: 2226847--2227077 Score: 453
Period size: 114 Copynumber: 2.0 Consensus size: 114
2226837 TTAACATTTC
2226847 CTTTCATTCAGACAAATTTCAGAACTTTTATATTTCCTTTTCATAACCCAAAGTATATTTAAAAG
1 CTTTCATTCAGACAAATTTCAGAACTTTTATATTTCCTTTTCATAACCCAAAGTATATTTAAAAG
2226912 AATGCAAGGTACGCGAGTCAGACCAGTGTGAGCAATAAGCACGTCAATA
66 AATGCAAGGTACGCGAGTCAGACCAGTGTGAGCAATAAGCACGTCAATA
*
2226961 CTTTCATTCAGACAAATTTCAGTACTTTTATATTTCCTTTTCATAACCCAAAGTATATTTAAAAG
1 CTTTCATTCAGACAAATTTCAGAACTTTTATATTTCCTTTTCATAACCCAAAGTATATTTAAAAG
2227026 AATGCAAGGTACGCGAGTCAGACCAGTGTGAGCAATAAGCACGTCAATA
66 AATGCAAGGTACGCGAGTCAGACCAGTGTGAGCAATAAGCACGTCAATA
2227075 CTT
1 CTT
2227078 ATATCAAAAT
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 116 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (114 bp):
CTTTCATTCAGACAAATTTCAGAACTTTTATATTTCCTTTTCATAACCCAAAGTATATTTAAAAG
AATGCAAGGTACGCGAGTCAGACCAGTGTGAGCAATAAGCACGTCAATA
Found at i:2234997 original size:21 final size:21
Alignment explanation
Indices: 2234972--2235011 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2234962 CTTATTTTAT
*
2234972 TTTATATAAATTTAATTATAA
1 TTTATATAAATATAATTATAA
2234993 TTTATATAAATATAATTAT
1 TTTATATAAATATAATTAT
2235012 CACTATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATATAAATATAATTATAA
Found at i:2237041 original size:3 final size:3
Alignment explanation
Indices: 2237023--2237070 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
2237013 CAAATAGTTG
* *
2237023 TAA TAAA TAT TAA TAA TAA TAA TAA TCA T-A TAA T-A TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2237067 TAA T
1 TAA T
2237071 TATTATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2237045 original size:19 final size:19
Alignment explanation
Indices: 2237023--2237093 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 19
2237013 CAAATAGTTG
2237023 TAATAAATATTAATAATAA
1 TAATAAATATTAATAATAA
*
2237042 TAATAATCATATAATATAATAA
1 TAATAA--ATATTA-ATAATAA
* * *
2237064 TAATAATTATT-ATTATTA
1 TAATAAATATTAATAATAA
2237082 TAATATAATATT
1 TAATA-AATATT
2237094 TATATCCCGG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 10 0.24
19 11 0.26
20 3 0.07
21 5 0.12
22 13 0.31
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATTAATAATAA
Found at i:2237048 original size:22 final size:21
Alignment explanation
Indices: 2237023--2237098 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 21
2237013 CAAATAGTTG
2237023 TAATAAATATTAATAATAATAA
1 TAATAAATATTAAT-ATAATAA
*
2237045 TAAT-CATA-TAATATAATAA
1 TAATAAATATTAATATAATAA
* * *
2237064 TAATAATTATTATTATTATAA
1 TAATAAATATTAATATAATAA
*
2237085 T-AT-AATATTTATAT
1 TAATAAATATTAATAT
2237099 CCCGGACAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
19 19 0.43
20 8 0.18
21 13 0.30
22 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATAAATATTAATATAATAA
Found at i:2237418 original size:52 final size:52
Alignment explanation
Indices: 2237349--2237797 Score: 727
Period size: 52 Copynumber: 8.6 Consensus size: 52
2237339 TCGCTCTCTA
* * *
2237349 TTTCTTCAGGGAGTAGAACTCGAACGATAATCTTTCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
2237401 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
2237453 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
2237505 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * * *
2237557 TTTCTTCAGGGACTAGAACTCAAAAAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * * *
2237609 TTTCTTCAAGGACTAGAACTCGAACAATAATCTTCCTATGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
2237661 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTTCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* *
2237713 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
2237765 TTTCTTCAAGGACTAGAACTCGAACAATAATCT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
2237798 CTAACGATCG
Statistics
Matches: 369, Mismatches: 28, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 369 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (52 bp):
TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
Found at i:2237852 original size:55 final size:55
Alignment explanation
Indices: 2237782--2238072 Score: 469
Period size: 55 Copynumber: 5.3 Consensus size: 55
2237772 AAGGACTAGA
*
2237782 ACTCGAACAATAATCTCTAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAAT-CT-TC-AACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
2237840 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
2237895 ACTCGAACAATCTTCAACGATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
2237950 A-TC-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
2238003 ACTCGAATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
2238058 ACTCGAACAATCTTC
1 ACTCGAACAATCTTC
2238073 TTTTGCTTCA
Statistics
Matches: 216, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
53 47 0.22
54 4 0.02
55 151 0.70
56 2 0.01
57 1 0.00
58 11 0.05
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:2238000 original size:108 final size:110
Alignment explanation
Indices: 2237782--2238072 Score: 487
Period size: 108 Copynumber: 2.6 Consensus size: 110
2237772 AAGGACTAGA
*
2237782 ACTCGAACAATAATCTCTAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA
1 ACTCGAACAAT-CT-TC-AACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA
2237847 CAATCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAG
63 CAATCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAG
* *
2237895 ACTCGAACAATCTTCAACGATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAA
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* *
2237958 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAG
*
2238003 ACTCGAATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
2238068 TCTTC
66 TCTTC
2238073 TTTTGCTTCA
Statistics
Matches: 168, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
108 101 0.60
109 4 0.02
110 49 0.29
111 2 0.01
112 1 0.01
113 11 0.07
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (110 bp):
ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
TCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAG
Found at i:2239368 original size:9 final size:9
Alignment explanation
Indices: 2239351--2239479 Score: 59
Period size: 9 Copynumber: 13.7 Consensus size: 9
2239341 TTGAACCCCC
2239351 TTTTATTTT
1 TTTTATTTT
*
2239360 TTTTGTTTTT
1 TTTT-ATTTT
*
2239370 TTCTTCTTCTT
1 TT-TTATT-TT
*
2239381 TTTTA-ATT
1 TTTTATTTT
2239389 TTTTATTTT
1 TTTTATTTT
**
2239398 TTCCATTTT
1 TTTTATTTT
2239407 TTTCTATTTT
1 TTT-TATTTT
2239417 TATTT-TTCATT
1 T-TTTATT--TT
*
2239428 TATTTCATTTA
1 T-TTT-ATTTT
*
2239439 TTTCATTTT
1 TTTTATTTT
2239448 TTTTCATTTT
1 TTTT-ATTTT
*
2239458 TTTCA--TT
1 TTTTATTTT
*
2239465 TTTCATTTT
1 TTTTATTTT
2239474 TTTTAT
1 TTTTAT
2239480 CTTTAAGCAA
Statistics
Matches: 92, Mismatches: 15, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
7 7 0.08
8 7 0.08
9 32 0.35
10 27 0.29
11 17 0.18
13 2 0.02
ACGTcount: A:0.12, C:0.09, G:0.01, T:0.78
Consensus pattern (9 bp):
TTTTATTTT
Found at i:2239407 original size:10 final size:9
Alignment explanation
Indices: 2239387--2239476 Score: 86
Period size: 9 Copynumber: 10.7 Consensus size: 9
2239377 TCTTTTTTAA
2239387 TTTTTT-AT
1 TTTTTTCAT
*
2239395 TTTTTCCAT
1 TTTTTTCAT
2239404 TTTTTTC-T
1 TTTTTTCAT
*
2239412 ATTTTT-A-
1 TTTTTTCAT
2239419 -TTTTTCAT
1 TTTTTTCAT
*
2239427 TTATTTCAT
1 TTTTTTCAT
*
2239436 TTATTTCATT
1 TTTTTTCA-T
2239446 TTTTTTCAT
1 TTTTTTCAT
2239455 TTTTTTCA-
1 TTTTTTCAT
2239463 -TTTTTCAT
1 TTTTTTCAT
2239471 TTTTTT
1 TTTTTT
2239477 TATCTTTAAG
Statistics
Matches: 69, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
6 5 0.07
7 8 0.12
8 11 0.16
9 37 0.54
10 8 0.12
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:2239422 original size:32 final size:33
Alignment explanation
Indices: 2239376--2239448 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
2239366 TTTTTTCTTC
* *
2239376 TTCT-TTTTTAATTTTTTATTT-TTTCCATTTTT
1 TTCTATTTTTAATTTTTCATTTATTT-CATTTAT
2239408 TTCTATTTTT-ATTTTTCATTTATTTCATTTAT
1 TTCTATTTTTAATTTTTCATTTATTTCATTTAT
2239440 TTC-ATTTTT
1 TTCTATTTTT
2239449 TTTCATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 6 0.16
32 23 0.62
33 8 0.22
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (33 bp):
TTCTATTTTTAATTTTTCATTTATTTCATTTAT
Found at i:2239454 original size:19 final size:19
Alignment explanation
Indices: 2239421--2239467 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
2239411 TATTTTTATT
*
2239421 TTTCA-TTTATTTCATTTA
1 TTTCATTTTTTTTCATTTA
*
2239439 TTTCATTTTTTTTCATTTT
1 TTTCATTTTTTTTCATTTA
2239458 TTTCATTTTT
1 TTTCATTTTT
2239468 CATTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTCATTTTTTTTCATTTA
Found at i:2239456 original size:28 final size:26
Alignment explanation
Indices: 2239419--2239477 Score: 91
Period size: 28 Copynumber: 2.2 Consensus size: 26
2239409 TCTATTTTTA
2239419 TTTTTCATTTATTTCATTTATTTCATTT
1 TTTTTCATTTATTTCA-TT-TTTCATTT
*
2239447 TTTTTCATTTTTTTCATTTTTCATTT
1 TTTTTCATTTATTTCATTTTTCATTT
2239473 TTTTT
1 TTTTT
2239478 ATCTTTAAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 13 0.43
27 2 0.07
28 15 0.50
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTCATTTATTTCATTTTTCATTT
Found at i:2247307 original size:3 final size:3
Alignment explanation
Indices: 2247289--2247376 Score: 92
Period size: 3 Copynumber: 29.7 Consensus size: 3
2247279 CAAATAGTTG
* *
2247289 TAA TAAA TAT TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TCA
1 TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * *
2247336 T-A TAA T-A TAA TAA TAA TAA TAA TTA TTA TTA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2247377 TTTATATCTC
Statistics
Matches: 75, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
2 6 0.08
3 63 0.84
4 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2247311 original size:19 final size:19
Alignment explanation
Indices: 2247289--2247354 Score: 87
Period size: 19 Copynumber: 3.3 Consensus size: 19
2247279 CAAATAGTTG
2247289 TAATAAATATTAATAATAA
1 TAATAAATATTAATAATAA
*
2247308 TAATAAATAATAATAATAA
1 TAATAAATATTAATAATAA
*
2247327 TAATAATCATATAATATAATAA
1 TAATAA--ATATTA-ATAATAA
2247349 TAATAA
1 TAATAA
2247355 TAATTATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 24 0.59
21 4 0.10
22 13 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATAAATATTAATAATAA
Found at i:2249664 original size:16 final size:17
Alignment explanation
Indices: 2249624--2249667 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2249614 CCCTACTTGA
2249624 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** *
2249641 TTTTATATTT-TTAAAT
1 TTAAATATTTAATAAAT
2249657 TTAAATATTTA
1 TTAAATATTTA
2249668 TTTGTACATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:2258473 original size:2 final size:2
Alignment explanation
Indices: 2258466--2258499 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2258456 ATTAATATTA
2258466 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
2258500 TGATAATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2263930 original size:102 final size:93
Alignment explanation
Indices: 2263750--2264057 Score: 375
Period size: 102 Copynumber: 3.2 Consensus size: 93
2263740 ACTTTACTCT
* * * * * *
2263750 ACACACTTGGTCCTACACAGAGACTACAAAACAAAACTAGAACACTTATGGAATTTGATCTTGAA
1 ACACACTTGGTCCTACACAAAAACGAAAAAAC-AAACTAGAACAATTATGGAATTCGATCTTGAA
2263815 TTTTAGCCCCCGAATACTAGCATACCTCA
65 TTTTAGCCCCCGAATACTAGCATACCTCA
*
2263844 ACACACTTGGTCCTACACACACCAAACCGAGGAATAAATCGAAACTAAAACAATTATGGAATTCG
1 ACACACTTGGTCCTACACA-A--AAA-CGA--AA-AAA-C-AAACTAGAACAATTATGGAATTCG
2263909 ATCTTGAATTTTAGCCCCCGAATACTAGCATACCTCA
57 ATCTTGAATTTTAGCCCCCGAATACTAGCATACCTCA
* * * * * *
2263946 ACACACTTGGTCCTACACAAAGACTACAAAACAATACTAGAAC-ACTATAGAATTCGATCTTAAA
1 ACACACTTGGTCCTACACAAAAACGAAAAAACAA-ACTAGAACAATTATGGAATTCGATCTTGAA
* *
2264010 TTTTAACCCCCGAATACTAGCAGACCTCA
65 TTTTAGCCCCCGAATACTAGCATACCTCA
2264039 ACACACTTGGTCCTACACA
1 ACACACTTGGTCCTACACA
2264058 GAGACTACAA
Statistics
Matches: 188, Mismatches: 17, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
93 66 0.35
94 27 0.14
95 3 0.02
96 1 0.01
97 2 0.01
98 4 0.02
99 2 0.01
100 1 0.01
101 4 0.02
102 78 0.41
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (93 bp):
ACACACTTGGTCCTACACAAAAACGAAAAAACAAACTAGAACAATTATGGAATTCGATCTTGAAT
TTTAGCCCCCGAATACTAGCATACCTCA
Found at i:2264063 original size:93 final size:93
Alignment explanation
Indices: 2263750--2264070 Score: 383
Period size: 93 Copynumber: 3.3 Consensus size: 93
2263740 ACTTTACTCT
* * * * *
2263750 ACACACTTGGTCCTACACAGAGACTACAAAACAAAACTAGAACACTTATGGAATTTGATCTTGAA
1 ACACACTTGGTCCTACACAAAGACTACAAAACAATACTAGAACAC-TATAGAATTCGATCTTAAA
* *
2263815 TTTTAGCCCCCGAATACTAGCATACCTCA
65 TTTTAACCCCCGAATACTAGCAGACCTCA
* * * * * *
2263844 ACACACTTGGTCCTACACACACCAAACCGAGGAATAAATCGAA-ACTAAAACAATTATGGAATTC
1 ACACACTTGGTCCTACACA-A--AGA-CTA--CA-AAA-C-AATACTAGAAC-ACTATAGAATTC
* * *
2263908 GATCTTGAATTTTAGCCCCCGAATACTAGCATACCTCA
56 GATCTTAAATTTTAACCCCCGAATACTAGCAGACCTCA
2263946 ACACACTTGGTCCTACACAAAGACTACAAAACAATACTAGAACACTATAGAATTCGATCTTAAAT
1 ACACACTTGGTCCTACACAAAGACTACAAAACAATACTAGAACACTATAGAATTCGATCTTAAAT
2264011 TTTAACCCCCGAATACTAGCAGACCTCA
66 TTTAACCCCCGAATACTAGCAGACCTCA
*
2264039 ACACACTTGGTCCTACACAGAGACTACAAAAC
1 ACACACTTGGTCCTACACAAAGACTACAAAAC
2264071 TCCATCACCT
Statistics
Matches: 199, Mismatches: 17, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
93 78 0.39
94 27 0.14
95 3 0.02
96 1 0.01
97 2 0.01
98 4 0.02
99 2 0.01
100 1 0.01
101 4 0.02
102 74 0.37
103 3 0.02
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (93 bp):
ACACACTTGGTCCTACACAAAGACTACAAAACAATACTAGAACACTATAGAATTCGATCTTAAAT
TTTAACCCCCGAATACTAGCAGACCTCA
Found at i:2265004 original size:24 final size:20
Alignment explanation
Indices: 2264963--2265020 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2264953 ATGTGAAATT
2264963 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
*
2264983 TGTCCCGAAGGACCTCTGTA
1 TGTCCCGAAGGACCTATGTA
*
2265003 TGTCCCGAATGACCTATG
1 TGTCCCGAAGGACCTATG
2265021 AACCCTCGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATGTA
Found at i:2275043 original size:29 final size:30
Alignment explanation
Indices: 2275010--2275077 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
2275000 TAGTTTAAAT
2275010 TTTAAATTTTACATTAAA-TACCAATTTG-A
1 TTTAAATTTTACA-TAAAGTACCAATTTGAA
* * * *
2275039 TTTAAACTTTAGATAAAGTATCAGTTTGAA
1 TTTAAATTTTACATAAAGTACCAATTTGAA
2275069 TTTAAATTT
1 TTTAAATTT
2275078 AGATAAAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 4 0.12
29 19 0.59
30 9 0.28
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (30 bp):
TTTAAATTTTACATAAAGTACCAATTTGAA
Found at i:2275090 original size:29 final size:29
Alignment explanation
Indices: 2275034--2275090 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2275024 TAAATACCAA
**
2275034 TTTGATTTAAACTTTAGATAAAGTATCAG
1 TTTGATTTAAACTTTAGATAAAACATCAG
2275063 TTTGAATTTAAA-TTTAGATAAAACATCA
1 TTTG-ATTTAAACTTTAGATAAAACATCA
2275091 ATTTAGTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (29 bp):
TTTGATTTAAACTTTAGATAAAACATCAG
Found at i:2276909 original size:20 final size:20
Alignment explanation
Indices: 2276884--2276977 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
2276874 CTATCGCAAA
*
2276884 TTCGCGTTGCGATTTTTCAT
1 TTCGCGTTGCGATTTTCCAT
* ** *
2276904 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
*
2276925 ATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
*
2276945 TTCGCGTTACGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
2276965 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
2276978 AGTCTACAGT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 46 0.75
21 15 0.25
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.41
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:2276994 original size:22 final size:22
Alignment explanation
Indices: 2276969--2277040 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
2276959 TTCCATTTCG
2276969 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
2276991 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
2277010 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
2277032 CGTTGCGAT
1 CGTTGCGAT
2277041 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:2277014 original size:19 final size:19
Alignment explanation
Indices: 2276990--2277055 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
2276980 TCTACAGTTG
2276990 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
2277009 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
2277030 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
2277050 TCGTTG
1 TCGTTG
2277056 TGATAGTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:2277019 original size:41 final size:41
Alignment explanation
Indices: 2276969--2277062 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2276959 TTCCATTTCG
2276969 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
2277010 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
*
2277051 CGTTGTGATAGT
1 CGTTGCGATAGT
2277063 TTAAAAAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:2277139 original size:6 final size:6
Alignment explanation
Indices: 2277128--2277184 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
2277118 GACACGTATT
2277128 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2277176 ACCACG ACC
1 ACCACG ACC
2277185 CGAGACGGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2277816 original size:22 final size:22
Alignment explanation
Indices: 2277788--2277840 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
2277778 AATTTGGAAA
2277788 ATCGCAACGATAACTGTAGACT
1 ATCGCAACGATAACTGTAGACT
*
2277810 ATCGCAACAATAACTGTAGACT
1 ATCGCAACGATAACTGTAGACT
2277832 ATCGCAACG
1 ATCGCAACG
2277841 CGATTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (22 bp):
ATCGCAACGATAACTGTAGACT
Found at i:2278818 original size:23 final size:24
Alignment explanation
Indices: 2278781--2278832 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
2278771 CCACAAGATA
2278781 AGAGAAAAAGCGTGTCACGAGAAC
1 AGAGAAAAAGCGTGTCACGAGAAC
* * *
2278805 AGAGAAAAA-TGTGTCACTAGGAC
1 AGAGAAAAAGCGTGTCACGAGAAC
2278828 AGAGA
1 AGAGA
2278833 TTTTTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.46, C:0.13, G:0.29, T:0.12
Consensus pattern (24 bp):
AGAGAAAAAGCGTGTCACGAGAAC
Found at i:2279142 original size:2 final size:2
Alignment explanation
Indices: 2279137--2279161 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2279127 TTCGTGTGTG
2279137 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
2279162 GAGATATTTA
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:2281048 original size:21 final size:21
Alignment explanation
Indices: 2280996--2281058 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 21
2280986 TATTTCTAAA
*
2280996 TTAAGTTAATAATAAAATATATT
1 TTAAGTTGAT-ATAAAA-ATATT
2281019 TAATAAGTTGATATAAAAATATT
1 T--TAAGTTGATATAAAAATATT
2281042 TTAAGTTGATATAAAAA
1 TTAAGTTGATATAAAAA
2281059 ATTATATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 16 0.43
23 7 0.19
24 6 0.16
25 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (21 bp):
TTAAGTTGATATAAAAATATT
Found at i:2281276 original size:22 final size:22
Alignment explanation
Indices: 2281248--2281299 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
2281238 GGGGACTACA
2281248 CGGGGACGGCTGAGGTACGTAC
1 CGGGGACGGCTGAGGTACGTAC
*
2281270 CGGGGACGGTTGAGGTACGTAC
1 CGGGGACGGCTGAGGTACGTAC
2281292 CGGGGACG
1 CGGGGACG
2281300 TTCCACGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.21, G:0.48, T:0.13
Consensus pattern (22 bp):
CGGGGACGGCTGAGGTACGTAC
Found at i:2282351 original size:75 final size:75
Alignment explanation
Indices: 2282220--2282401 Score: 188
Period size: 75 Copynumber: 2.4 Consensus size: 75
2282210 TGATTTGGGT
* * * * *
2282220 TTAATATTATGGTTTGAGT-TTTAAGATTTAACACTTTAATATTATGATTTTATTATGGATTTCA
1 TTAATATTATAGTTTGAATCTTGAA-ATTTGACACTTTAATATTATGATTGTATTATGGATTTCA
* *
2282284 TTATTCGATAG
65 TTATTCGAAAC
* * *
2282295 TTAATATTATAGTTTGAATCTTGAAATTTGACATTTTAATATTATGGCTTGT-TTATGGATTTTA
1 TTAATATTATAGTTTGAATCTTGAAATTTGACACTTTAATATTAT-GATTGTATTATGGATTTCA
* *
2282359 TTGTTCTAAAC
65 TTATTCGAAAC
* * * *
2282370 TTAATATTGTTGTTTGACTCTTGATATTTGAC
1 TTAATATTATAGTTTGAATCTTGAAATTTGAC
2282402 TTTATTTATA
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
75 81 0.91
76 8 0.09
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.51
Consensus pattern (75 bp):
TTAATATTATAGTTTGAATCTTGAAATTTGACACTTTAATATTATGATTGTATTATGGATTTCAT
TATTCGAAAC
Found at i:2284540 original size:21 final size:20
Alignment explanation
Indices: 2284454--2284611 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
2284444 AAATGACCAA
**
2284454 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2284473 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2284493 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2284513 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
2284534 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2284555 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2284575 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
2284596 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2284612 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2284604 original size:20 final size:20
Alignment explanation
Indices: 2284579--2284889 Score: 79
Period size: 20 Copynumber: 15.5 Consensus size: 20
2284569 GATTTTCAAT
* *
2284579 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2284599 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2284619 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2284639 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
2284659 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
2284679 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2284699 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2284719 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2284740 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2284760 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
2284780 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2284800 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
2284820 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2284840 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
2284860 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2284880 AATCGCAACG
1 AATCGCAACG
2284890 ATAATCCGTA
Statistics
Matches: 244, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.01
20 224 0.92
21 16 0.07
22 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2284624 original size:40 final size:40
Alignment explanation
Indices: 2284579--2284968 Score: 439
Period size: 40 Copynumber: 9.7 Consensus size: 40
2284569 GATTTTCAAT
* ** * * *
2284579 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
2284619 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
2284659 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
2284699 TATCGCAACGCGTATCCGTAAATCGCAACGA-TAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGT-A
* *
2284740 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
2284780 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
2284820 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
2284860 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
2284900 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
2284940 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
2284969 ACTGAAATTT
Statistics
Matches: 312, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.01
40 272 0.87
41 34 0.11
42 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
Found at i:2284896 original size:20 final size:19
Alignment explanation
Indices: 2284617--2284968 Score: 398
Period size: 20 Copynumber: 17.6 Consensus size: 19
2284607 CGCGAACACA
2284617 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
2284637 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
2284657 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
2284677 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
2284697 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
2284717 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
2284737 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
2284758 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
2284778 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
2284798 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
2284818 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
2284838 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
2284858 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
2284878 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
2284898 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
2284918 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
2284938 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
2284958 TAAATCACAAC
1 TAAATCGCAAC
2284969 ACTGAAATTT
Statistics
Matches: 290, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 270 0.93
21 16 0.06
22 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:2285684 original size:24 final size:24
Alignment explanation
Indices: 2285645--2285691 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2285635 AAATTTGGTC
2285645 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2285669 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2285692 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2285883 original size:12 final size:12
Alignment explanation
Indices: 2285866--2285890 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2285856 ATATAATCCT
2285866 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2285878 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2285890 G
1 G
2285891 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2288194 original size:19 final size:19
Alignment explanation
Indices: 2288172--2288445 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
2288162 CGGAAAATAC
*
2288172 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2288191 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
2288205 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
2288225 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2288239 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2288258 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2288277 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2288291 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2288310 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2288329 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
2288348 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2288367 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2288386 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
2288400 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2288419 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2288438 AATCGCAA
1 AATCGCAA
2288446 CAAGATAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 40 0.18
15 2 0.01
16 11 0.05
17 10 0.04
18 3 0.01
19 147 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2288287 original size:52 final size:52
Alignment explanation
Indices: 2288200--2288467 Score: 446
Period size: 52 Copynumber: 5.0 Consensus size: 52
2288190 AAATCCCAAC
2288200 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
2288253 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
2288305 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
2288362 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
2288414 ATGAAAATCGCAATGCGAAATGAAAATCGCAACAAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
2288466 AT
1 AT
2288468 TATAAACGCA
Statistics
Matches: 206, Mismatches: 4, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 133 0.65
53 17 0.08
54 4 0.02
55 5 0.02
56 1 0.00
57 46 0.22
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:2288374 original size:109 final size:104
Alignment explanation
Indices: 2288200--2288467 Score: 439
Period size: 109 Copynumber: 2.5 Consensus size: 104
2288190 AAATCCCAAC
*
2288200 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCA
*
2288265 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
65 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
2288305 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA--G-AATCGCAATGCGAAATGAAAAT
2288370 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
61 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
2288414 ATGAAAATCGCAATGCGAAATGAAAATCGCAAC-AAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAA-AGAATCGCAATGCGAAAT
2288468 TATAAACGCA
Statistics
Matches: 154, Mismatches: 3, Indels: 13
0.91 0.02 0.08
Matches are distributed among these distances:
104 32 0.21
105 16 0.10
106 6 0.04
107 2 0.01
108 1 0.01
109 97 0.63
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:2288564 original size:19 final size:19
Alignment explanation
Indices: 2288474--2288556 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
2288464 AAATTATAAA
2288474 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2288493 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2288513 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
2288529 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2288546 CGCATTGCGAT
1 CGCATTGCGAT
2288557 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:2288682 original size:14 final size:14
Alignment explanation
Indices: 2288663--2288699 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2288653 CATCAATTAC
2288663 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2288677 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2288691 ACAAATCAA
1 ACAAATCAA
2288700 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2290672 original size:14 final size:14
Alignment explanation
Indices: 2290653--2290709 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2290643 GCGAAATGAA
*
2290653 AATCGCAACGACAG
1 AATCGCAACGAAAG
2290667 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2290684 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2290700 AATCGCAACG
1 AATCGCAACG
2290710 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2290680 original size:33 final size:33
Alignment explanation
Indices: 2290634--2290726 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2290624 GCGAAACCAA
*
2290634 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2290667 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2290700 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2290727 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2290691 original size:19 final size:19
Alignment explanation
Indices: 2290597--2290731 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2290587 TAGTTTACTT
* *
2290597 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2290617 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2290636 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2290655 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2290669 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2290688 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2290702 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2290721 TCGCAATGCGA
1 TCGCAACGCGA
2290732 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2290749 original size:19 final size:19
Alignment explanation
Indices: 2290727--2290855 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2290717 AAAATCGCAA
2290727 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2290746 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2290760 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2290779 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2290793 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2290812 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2290831 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2290851 TGCGA
1 TGCGA
2290856 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2290769 original size:33 final size:33
Alignment explanation
Indices: 2290727--2290818 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2290717 AAAATCGCAA
2290727 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2290760 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2290793 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2290819 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2291069 original size:92 final size:93
Alignment explanation
Indices: 2290899--2291277 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
2290889 TTGAATGGAT
2290899 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2290964 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2290992 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2291056 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2291084 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2291148 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2291176 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
2291241 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2291269 AAATTTACT
1 AAATTTACT
2291278 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2291228 original size:185 final size:185
Alignment explanation
Indices: 2290899--2291277 Score: 733
Period size: 185 Copynumber: 2.0 Consensus size: 185
2290889 TTGAATGGAT
2290899 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2290964 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2291029 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
2291084 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2291148 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
2291213 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
2291269 AAATTTACT
1 AAATTTACT
2291278 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 100 0.52
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2293000 original size:14 final size:14
Alignment explanation
Indices: 2292981--2293070 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
2292971 TTGAAATGAA
2292981 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2292995 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
2293012 ACAATCGCAACAAGAG
1 --AATCGCAACGAGAG
*
2293028 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2293047 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2293061 AATCGCAACG
1 AATCGCAACG
2293071 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 7 0.11
17 7 0.11
18 1 0.02
19 18 0.29
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2293018 original size:33 final size:33
Alignment explanation
Indices: 2292973--2293087 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
2292963 TCTTTTGGTT
2292973 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
2293006 GAGATGACAATCGCAACAAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2293039 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2293072 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2293088 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2293019 original size:19 final size:19
Alignment explanation
Indices: 2292995--2293092 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2292985 GCAACGAGAG
* *
2292995 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
*
2293014 AATCGCAA--C--AA-GAG
1 AATCGCAACGCGAAATGAA
2293028 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2293047 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2293061 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2293080 AATCGCAATGCGA
1 AATCGCAACGCGA
2293093 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 3 0.05
19 32 0.51
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2293123 original size:14 final size:14
Alignment explanation
Indices: 2293104--2293158 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2293094 TTTGGTTTCG
2293104 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2293118 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2293137 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2293151 CGTTGCGA
1 CGTTGCGA
2293159 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2293136 original size:33 final size:33
Alignment explanation
Indices: 2293088--2293158 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2293078 AAAATCGCAA
**
2293088 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2293121 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2293154 TGCGA
1 TGCGA
2293159 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2293166 original size:33 final size:33
Alignment explanation
Indices: 2293099--2293180 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
2293089 GCGATTTTGG
***
2293099 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
2293132 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
2293165 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
2293181 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:2293185 original size:20 final size:20
Alignment explanation
Indices: 2293111--2293199 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
2293101 TCGCGTTGCG
2293111 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2293131 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
2293144 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
2293164 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2293184 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
2293200 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2293321 original size:33 final size:33
Alignment explanation
Indices: 2293279--2293349 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2293269 AATACTAACT
*
2293279 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2293312 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2293345 TGAAA
1 TGAAA
2293350 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2293583 original size:22 final size:22
Alignment explanation
Indices: 2293531--2293585 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2293521 TGGTTGTGAG
**
2293531 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2293553 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2293575 GGATTTCTTCG
1 GGATTTCTTCG
2293586 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2293756 original size:20 final size:20
Alignment explanation
Indices: 2293731--2293923 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
2293721 CTTTAAATAT
2293731 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2293751 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2293773 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2293792 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2293812 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2293832 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2293852 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2293872 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2293892 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2293912 CGCGTTGCGATT
1 CGCGTTGCGATT
2293924 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2293918 original size:60 final size:60
Alignment explanation
Indices: 2293731--2293923 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2293721 CTTTAAATAT
**
2293731 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
2293792 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
2293852 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2293912 CGCGTTGCGATT
1 CGCGTTGCGATT
2293924 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2294408 original size:30 final size:28
Alignment explanation
Indices: 2294387--2294441 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
2294377 CGGTGATCGG
2294387 TATATTTACCGATCTAACACCGGTCAGAT
1 TATATTTACCGATCTAACACCGGT-AGAT
* *
2294416 TATATTTCCCGATCTAACACCCGTAG
1 TATATTTACCGATCTAACACCGGTAG
2294442 CAATAAAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (28 bp):
TATATTTACCGATCTAACACCGGTAGAT
Found at i:2298144 original size:35 final size:34
Alignment explanation
Indices: 2298059--2298145 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2298049 ATTTGGTATT
*
2298059 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
2298093 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
2298131 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2298146 ACTGAAATAT
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:2300488 original size:17 final size:18
Alignment explanation
Indices: 2300445--2300485 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2300435 GAATTATATT
2300445 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
2300462 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
2300480 ATTAAA
1 AGTAAA
2300486 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:2300546 original size:10 final size:10
Alignment explanation
Indices: 2300527--2300557 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2300517 CTTAAACAGA
*
2300527 GAGAGTATTT
1 GAGAGAATTT
2300537 GAGAGAATTT
1 GAGAGAATTT
2300547 GAGAGAATTT
1 GAGAGAATTT
2300557 G
1 G
2300558 GTGTGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:2316957 original size:83 final size:83
Alignment explanation
Indices: 2316818--2316984 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
2316808 AGGTAAAAGG
*
2316818 TCTGCAGTCTGCGGTCCACATCTGCAGGCATCTGCAGCAGAAGAGGTGGACCAAAAGTCTGCAGT
1 TCTGCAGTCTGCGGACCACATCTGCAGGCATCTGCAGCAGAAGAGGTGGACCAAAAGTCTGCAGT
2316883 CTGCAAGAAGAAGACTGT
66 CTGCAAGAAGAAGACTGT
2316901 TCTGCAGTCTGCGGACCACATCTGCAGGCATCTGCAGCAGAAGAGGTGGACCAAAAGTCTGCAGT
1 TCTGCAGTCTGCGGACCACATCTGCAGGCATCTGCAGCAGAAGAGGTGGACCAAAAGTCTGCAGT
2316966 CTGCAAGAAGAAGACTGT
66 CTGCAAGAAGAAGACTGT
2316984 T
1 T
2316985 TGTTTTTTAA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.19
Consensus pattern (83 bp):
TCTGCAGTCTGCGGACCACATCTGCAGGCATCTGCAGCAGAAGAGGTGGACCAAAAGTCTGCAGT
CTGCAAGAAGAAGACTGT
Found at i:2317149 original size:21 final size:20
Alignment explanation
Indices: 2317125--2317170 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2317115 CATACAACTA
2317125 AAATAATAAATTATTTAAAAT
1 AAATAATAAA-TATTTAAAAT
**
2317146 AAATTAATCCATATTTAAAAT
1 AAA-TAATAAATATTTAAAAT
2317167 AAAT
1 AAAT
2317171 CAATCCATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAATAAATATTTAAAAT
Found at i:2317175 original size:21 final size:21
Alignment explanation
Indices: 2317136--2317179 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2317126 AATAATAAAT
*
2317136 TATTTAAAATAAATTAATCCA
1 TATTTAAAATAAATCAATCCA
2317157 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
2317178 TA
1 TA
2317180 CTAATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCCA
Found at i:2317314 original size:32 final size:31
Alignment explanation
Indices: 2317236--2317678 Score: 323
Period size: 32 Copynumber: 15.8 Consensus size: 31
2317226 AATCAATCTA
*
2317236 TATTTAAAATAAATCAATCCATACAAATAAAT
1 TATTTAAAATAAATCAATCCATACTAAT-AAT
*
2317268 TATTT-AAATAAATCAATCTATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAAT-AAT
2317299 TATTTAAAATAAATCAAT-C---C--AT-A-
1 TATTTAAAATAAATCAATCCATACTAATAAT
2317322 T-TTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAAT-AAT
2317353 TATTTAAAATAAATCAAT---T-C--AT-A-
1 TATTTAAAATAAATCAATCCATACTAATAAT
2317376 T-TTTAAAATAAATCAATCCATACTAATAAT
1 TATTTAAAATAAATCAATCCATACTAATAAT
*
2317406 TATTTAAAATAAATCAATACATAC-AACTACA-
1 TATTTAAAATAAATCAATCCATACTAA-TA-AT
2317437 -A--T--AATAAATCAATCC--A-T-AT---
1 TATTTAAAATAAATCAATCCATACTAATAAT
* *
2317456 --TTTAAAATAAATCAATTCATACAAATAAAT
1 TATTTAAAATAAATCAATCCATACTAAT-AAT
*
2317486 TATTTAAAATAAATCAATCCATACAAATAAAT
1 TATTTAAAATAAATCAATCCATACTAAT-AAT
*
2317518 TATTTAAAATAAATCAATCGA-ACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAAT-AAT
2317549 TATTTAAAATAAATCAAT-C---C-----A-
1 TATTTAAAATAAATCAATCCATACTAATAAT
2317570 TATTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAAT-AAT
2317602 TATTTAAAATAAATCAAT-C---C-----A-
1 TATTTAAAATAAATCAATCCATACTAATAAT
* *
2317623 TATTTAAATTAAATCAATCTATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAAT-AAT
2317655 TATTTAAAATAAATCAATCCATAC
1 TATTTAAAATAAATCAATCCATAC
2317679 AACTACAACA
Statistics
Matches: 337, Mismatches: 15, Indels: 118
0.72 0.03 0.25
Matches are distributed among these distances:
20 1 0.00
21 35 0.10
22 48 0.14
23 4 0.01
24 4 0.01
25 3 0.01
26 20 0.06
28 9 0.03
29 2 0.01
30 5 0.01
31 83 0.25
32 123 0.36
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (31 bp):
TATTTAAAATAAATCAATCCATACTAATAAT
Found at i:2317327 original size:22 final size:22
Alignment explanation
Indices: 2317301--2317343 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2317291 TAATAAATTA
2317301 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2317323 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2317344 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2317348 original size:54 final size:53
Alignment explanation
Indices: 2317128--2317536 Score: 313
Period size: 54 Copynumber: 7.5 Consensus size: 53
2317118 ACAACTAAAA
*
2317128 TAATAAATTATTTAAAATAAATTAATCCATATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTAAAATAAATCAATCCATAC
* **
2317181 TAATAAATTATTTAAAATAAATCAAT-C-TA--TACAACTACAAT-AATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATATTTA-AAATA-AATCAATCCATAC
** ** * *
2317230 -AATCTA-TATTTAAAATAAATCAATCCATACAAATAAATTATTTAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCAT--ATTTAAA--A--TAAATCAATCCATAC
2317286 TATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TA-A-T---AAATTATTTAAAATAAATCAATCCATA-TTTAAAATAAATCAATCCATAC
*
2317345 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTAAAATAAATCAATCCATAC
* ** *
2317399 TAAT-AATTATTTAAAATAAATCAATACATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---A-TTTAA-AATAAATCAATCCATA--C
* * * * * *
2317458 TAAAATAAATCAATTCATACAAATAAAT---TATTTAAAATAAATCAATCCATAC
1 T--AATAAATTATTTAAAATAAATCAATCCATATTTAAAATAAATCAATCCATAC
*
2317510 AAATAAATTATTTAAAATAAATCAATC
1 TAATAAATTATTTAAAATAAATCAATC
2317537 GAACTAATAA
Statistics
Matches: 288, Mismatches: 36, Indels: 66
0.74 0.09 0.17
Matches are distributed among these distances:
47 18 0.06
48 5 0.02
49 4 0.01
50 28 0.10
51 6 0.02
52 3 0.01
53 51 0.18
54 69 0.24
55 6 0.02
56 14 0.05
57 18 0.06
58 13 0.05
59 6 0.02
60 1 0.00
61 4 0.01
62 20 0.07
63 22 0.08
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (53 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTAAAATAAATCAATCCATAC
Found at i:2317352 original size:22 final size:22
Alignment explanation
Indices: 2317303--2317351 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2317293 ATAAATTATT
**
2317303 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2317325 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2317348 TAAA
1 TAAA
2317352 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2317381 original size:22 final size:22
Alignment explanation
Indices: 2317355--2317397 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2317345 TAATAAATTA
*
2317355 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
2317377 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2317398 CTAATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2317575 original size:21 final size:21
Alignment explanation
Indices: 2317549--2317592 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2317539 ACTAATAAAT
2317549 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
2317570 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
2317591 TA
1 TA
2317593 CTAATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCCA
Found at i:2317613 original size:53 final size:53
Alignment explanation
Indices: 2317518--2317677 Score: 286
Period size: 53 Copynumber: 3.0 Consensus size: 53
2317508 ACAAATAAAT
*
2317518 TATTTAAAATAAATCAATCGA-ACTAATAAATTATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
2317570 TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
* *
2317623 TATTTAAATTAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
2317676 TA
1 TA
2317678 CAACTACAAC
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 20 0.19
53 84 0.81
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.35
Consensus pattern (53 bp):
TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
Found at i:2317628 original size:21 final size:21
Alignment explanation
Indices: 2317602--2317641 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2317592 ACTAATAAAT
2317602 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
*
2317623 TATTTAAATTAAATCAATC
1 TATTTAAAATAAATCAATC
2317642 TATACTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCCA
Found at i:2317755 original size:15 final size:15
Alignment explanation
Indices: 2317726--2317842 Score: 130
Period size: 15 Copynumber: 7.5 Consensus size: 15
2317716 AATTCATACT
2317726 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
2317740 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
2317755 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
2317777 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
2317792 AATAAATTA-TTTAT
1 AATAAATTATTTTAA
2317806 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2317821 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2317836 AATAAAT
1 AATAAAT
2317843 AACTTTTTAA
Statistics
Matches: 88, Mismatches: 6, Indels: 17
0.79 0.05 0.15
Matches are distributed among these distances:
14 22 0.25
15 49 0.56
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:2317759 original size:29 final size:30
Alignment explanation
Indices: 2317726--2317842 Score: 130
Period size: 29 Copynumber: 3.7 Consensus size: 30
2317716 AATTCATACT
2317726 AATAAATTA-TTTAAAATAAATTATTTTAA
1 AATAAATTATTTTAAAATAAATTATTTTAA
* *
2317755 AATAAATCAATCCATATTTTATAATAATTTATTTTAA
1 AAT--A--AAT---TATTTTAAAATAAATTATTTTAA
*
2317792 AATAAATTA-TTTATAATAAATTATTTTAA
1 AATAAATTATTTTAAAATAAATTATTTTAA
2317821 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
2317843 AACTTTTTAA
Statistics
Matches: 75, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
29 31 0.41
30 13 0.17
31 1 0.01
33 6 0.08
35 1 0.01
36 2 0.03
37 21 0.28
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (30 bp):
AATAAATTATTTTAAAATAAATTATTTTAA
Found at i:2317876 original size:81 final size:82
Alignment explanation
Indices: 2317725--2317891 Score: 198
Period size: 81 Copynumber: 2.0 Consensus size: 82
2317715 CAATTCATAC
** * *
2317725 TAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTT
1 TAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAATCCATAAATTATAATAAATTATTTA
2317790 AAAATAA-ATTA-TTTA
66 AAAATAACATTATTTTA
*** *
2317805 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT-AACTTTTTAAATTAT-TTAAATTATT
1 TAATAAATTA-TTTAAAATAAATTATTTTAAAATAAATCAA-TCCATAAATTATAATAAATTATT
*
2317868 TAATAAATAACTTTATTTTA
64 TAA-AAATAACATTATTTTA
2317888 TAAT
1 TAAT
2317892 TGTTCTTGAA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
80 22 0.30
81 40 0.55
82 3 0.04
83 8 0.11
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (82 bp):
TAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAATCCATAAATTATAATAAATTATTTA
AAAATAACATTATTTTA
Found at i:2323626 original size:3 final size:3
Alignment explanation
Indices: 2323618--2323761 Score: 54
Period size: 3 Copynumber: 46.7 Consensus size: 3
2323608 AATATTAATG
* *
2323618 TAA TAA TAA TAA TAA -ATA TAA T-A TAA TATA TAC T-A TAA TATG TACA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TA-A TA-A
* * *
2323664 TAAA TAA T-A TAC T-A TGA TAA T-A TAA TATA TAA TAT TAA T-A TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
2323707 TAA TAA TAA TATA TAC TATA TATA TACA CTAA TTAA T-A TAA T-A TAA
1 TAA TAA TAA TA-A TAA TA-A TA-A TA-A -TAA -TAA TAA TAA TAA TAA
2323753 TATA TAA TA
1 TA-A TAA TA
2323762 TATATATCAT
Statistics
Matches: 109, Mismatches: 14, Indels: 36
0.69 0.09 0.23
Matches are distributed among these distances:
2 15 0.14
3 62 0.57
4 29 0.27
5 3 0.03
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2323628 original size:17 final size:16
Alignment explanation
Indices: 2323593--2323829 Score: 97
Period size: 17 Copynumber: 13.8 Consensus size: 16
2323583 GCTAATCATA
*
2323593 AATATAATTA-AATAT
1 AATATAAATATAATAT
* *
2323608 AATATTAATGTAATAAT
1 AATATAAATATAAT-AT
2323625 AATAATAAATATAATAT
1 AAT-ATAAATATAATAT
*
2323642 AATATATACTATAATAT
1 AATATA-AATATAATAT
* *
2323659 -GTACATAA-ATAATAT
1 AATATA-AATATAATAT
*
2323674 ACTATGATAATATAATATAT
1 AATAT-A-AATAT-A-ATAT
*
2323694 AATATTAATATAATAAT
1 AATATAAATATAAT-AT
* *
2323711 AATA-ATATATACTAT
1 AATATAAATATAATAT
*
2323726 ATATATACACTAATTAATAT
1 A-ATATA-AAT-A-TAATAT
2323746 AATATAATATATAATAT
1 AATATAA-ATATAATAT
*
2323763 ATATATCATATTATTAATAT
1 A-ATAT-A-AATA-TAATAT
* *
2323783 -ATATACTATATAACAT
1 AATATA-AATATAATAT
*
2323799 ACTATATAATAATAATAT
1 AATATA-AAT-ATAATAT
*
2323817 ACTATAACATATA
1 AATATAA-ATATA
2323830 TAATACGTGA
Statistics
Matches: 170, Mismatches: 29, Indels: 44
0.70 0.12 0.18
Matches are distributed among these distances:
15 17 0.10
16 29 0.17
17 51 0.30
18 41 0.24
19 11 0.06
20 21 0.12
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (16 bp):
AATATAAATATAATAT
Found at i:2323640 original size:5 final size:5
Alignment explanation
Indices: 2323593--2323909 Score: 118
Period size: 5 Copynumber: 59.2 Consensus size: 5
2323583 GCTAATCATA
*
2323593 AATAT AAT-T AAATAT AATATT AATGT AATAAT AATAAT AAATAT AATAT
1 AATAT AATAT -AATAT AATA-T AATAT AAT-AT AAT-AT -AATAT AATAT
* *
2323642 AATAT ATACTAT AATAT GTACAT AA-AT AATAT ACTATGAT AATAT AATATAT
1 AATAT A-A-TAT AATAT -AATAT AATAT AATAT A--AT-AT AATAT -A-ATAT
* *
2323694 AATATT AATAT AATAAT AATA- ATATAT ACTAT ATATAT ACA-CT AAT-T
1 AATA-T AATAT AAT-AT AATAT A-ATAT AATAT A-ATAT A-ATAT AATAT
* *
2323741 AATAT AATAT AATATAT AATAT ATATAT CATAT TAT-T AATAT -ATAT
1 AATAT AATAT -A-ATAT AATAT A-ATAT AATAT AATAT AATAT AATAT
* * *
2323787 ACTATAT AACAT ACTATAT AATAAT AATAT ACTAT AACAT -ATAT AATACGT
1 A--ATAT AATAT A--ATAT AAT-AT AATAT AATAT AATAT AATAT AATA--T
* * *
2323838 GATAT AATACT AATAT AGTACAT ATTAT ACATACT -ATAT -ATAT AATAT
1 AATAT AATA-T AATAT A--ATAT AATAT A-ATA-T AATAT AATAT AATAT
* *
2323886 -ATAT AATAT -ATAT CATAT ATTAT A
1 AATAT AATAT AATAT AATAT AATAT A
2323910 TAAACATTGT
Statistics
Matches: 244, Mismatches: 26, Indels: 84
0.69 0.07 0.24
Matches are distributed among these distances:
4 34 0.14
5 115 0.47
6 57 0.23
7 35 0.14
8 3 0.01
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:2323685 original size:13 final size:12
Alignment explanation
Indices: 2323593--2323912 Score: 172
Period size: 12 Copynumber: 26.6 Consensus size: 12
2323583 GCTAATCATA
2323593 AATATAAT-TA-
1 AATATAATATAT
2323603 AATATAATAT-T
1 AATATAATATAT
*
2323614 AATGTAATA-AT
1 AATATAATATAT
2323625 AATAATAA-ATAT
1 AAT-ATAATATAT
2323637 AATATAATATAT
1 AATATAATATAT
* *
2323649 ACTATAATATGT
1 AATATAATATAT
*
2323661 -ACAT-A-A-AT
1 AATATAATATAT
*
2323669 AATATACTATGAT
1 AATATAATAT-AT
2323682 AATATAATATAT
1 AATATAATATAT
2323694 AATATTAATATAAT
1 AATA-TAATAT-AT
2323708 AATAATAATATAT
1 AAT-ATAATATAT
*
2323721 ACTAT-ATATAT
1 AATATAATATAT
*
2323732 ACACTA-ATTAATAT
1 A-A-TATAAT-ATAT
2323746 AATATAATATAT
1 AATATAATATAT
2323758 AATAT-ATATAT
1 AATATAATATAT
* *
2323769 CATATTAT-TAAT
1 AATATAATAT-AT
*
2323781 ATATATACTATAT
1 A-ATATAATATAT
* *
2323794 AACATACTATAT
1 AATATAATATAT
2323806 AATAATAATATACT
1 AAT-ATAATATA-T
2323820 -ATA-ACATATAT
1 AATATA-ATATAT
**
2323831 AATA-CGTGATAT
1 AATATAAT-ATAT
2323843 AATACTAATATAGT
1 AATA-TAATATA-T
* *
2323857 ACATATTATACAT
1 A-ATATAATATAT
*
2323870 ACTAT-ATATAT
1 AATATAATATAT
2323881 AATAT-ATATAAT
1 AATATAATAT-AT
*
2323893 ATATATCATATAT
1 A-ATATAATATAT
*
2323906 TATATAA
1 AATATAA
2323913 ACATTGTAAT
Statistics
Matches: 243, Mismatches: 32, Indels: 68
0.71 0.09 0.20
Matches are distributed among these distances:
8 1 0.00
9 4 0.02
10 9 0.04
11 55 0.23
12 85 0.35
13 55 0.23
14 30 0.12
15 4 0.02
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (12 bp):
AATATAATATAT
Found at i:2323764 original size:9 final size:9
Alignment explanation
Indices: 2323594--2323905 Score: 149
Period size: 9 Copynumber: 34.2 Consensus size: 9
2323584 CTAATCATAA
*
2323594 ATATAATTAA
1 ATATAA-TAT
2323604 ATATAATATT
1 ATATAATA-T
*
2323614 AATGTAATA-
1 -ATATAATAT
*
2323623 ATAATAATAA
1 AT-ATAATAT
2323633 ATATAATAT
1 ATATAATAT
2323642 A-AT-ATAT
1 ATATAATAT
2323649 ACTATAATAT
1 A-TATAATAT
* *
2323659 GTA-CATA-
1 ATATAATAT
2323666 A-ATAATAT
1 ATATAATAT
*
2323674 ACTATGATA-
1 A-TATAATAT
2323683 ATATAATAT
1 ATATAATAT
*
2323692 ATAATATTA-
1 AT-ATAATAT
2323701 ATATAATA-
1 ATATAATAT
2323709 ATAATAATAT
1 AT-ATAATAT
2323719 ATACT-ATAT
1 ATA-TAATAT
2323728 ATATACACTA-
1 ATATA-A-TAT
2323738 AT-TAATAT
1 ATATAATAT
2323746 AATATAATAT
1 -ATATAATAT
2323756 ATA-ATATAT
1 ATATA-ATAT
*
2323765 ATATCATAT
1 ATATAATAT
2323774 -TATTAATAT
1 ATA-TAATAT
*
2323783 ATATACTAT
1 ATATAATAT
2323792 ATA-ACATACT
1 ATATA-ATA-T
2323802 ATAT-A-AT
1 ATATAATAT
2323809 A-ATAATAT
1 ATATAATAT
*
2323817 ACTATAACAT
1 A-TATAATAT
2323827 ATATAATACGT
1 ATATAATA--T
2323838 GATATAATACT
1 -ATATAATA-T
* *
2323849 AATATAGTAC
1 -ATATAATAT
* *
2323859 ATATTATAC
1 ATATAATAT
2323868 ATACT-ATAT
1 ATA-TAATAT
2323877 ATATAATAT
1 ATATAATAT
2323886 ATATAATAT
1 ATATAATAT
*
2323895 ATATCATAT
1 ATATAATAT
2323904 AT
1 AT
2323906 TATATAAACA
Statistics
Matches: 238, Mismatches: 26, Indels: 77
0.70 0.08 0.23
Matches are distributed among these distances:
6 3 0.01
7 13 0.05
8 32 0.13
9 116 0.49
10 48 0.20
11 18 0.08
12 8 0.03
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (9 bp):
ATATAATAT
Found at i:2323764 original size:37 final size:35
Alignment explanation
Indices: 2323603--2323911 Score: 197
Period size: 37 Copynumber: 8.5 Consensus size: 35
2323593 AATATAATTA
* *
2323603 AATATAATAT-TAATGTA-ATAATAATAATAAATAT
1 AATATAATATATAATATATAT-ATAATAATTAATAT
* *
2323637 AATATAATATATACTATA-ATAT-GTACA-TAA-AT
1 AATATAATATATAATATATATATAATA-ATTAATAT
*
2323669 AATATACTATGATAATATAATATATAAT-ATTAATAT
1 AATATAATAT-ATAATAT-ATATATAATAATTAATAT
2323705 AATAATAATAATATATACTATATATATACACTAATTAATAT
1 AAT-ATAAT-ATATA-A-TATATATATA-A-TAATTAATAT
*
2323746 AATATAATATATAATATATATATCATATTATTAATAT
1 AATATAATATATAATATATATAT-A-ATAATTAATAT
* *
2323783 -ATATACTATATAACATACTATATAATAA-TAATAT
1 AATATAATATATAATATA-TATATAATAATTAATAT
* ** * *
2323817 ACTATAACATATATAATACGTGATATAATACTAATATAGT
1 AATAT-A-ATATATAATATAT-ATATAATAATTA-ATA-T
* * *
2323857 ACATATTATACATACTATATATATAATATATATAATAT
1 A-ATATAATATATAATATATATATAATA-AT-TAATAT
* *
2323895 -ATATCATATATTATATA
1 AATATAATATATAATATA
2323912 AACATTGTAA
Statistics
Matches: 216, Mismatches: 32, Indels: 52
0.72 0.11 0.17
Matches are distributed among these distances:
32 11 0.05
33 10 0.05
34 21 0.10
35 20 0.09
36 37 0.17
37 46 0.21
38 23 0.11
39 25 0.12
40 9 0.04
41 14 0.06
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (35 bp):
AATATAATATATAATATATATATAATAATTAATAT
Found at i:2323876 original size:112 final size:112
Alignment explanation
Indices: 2323623--2323898 Score: 270
Period size: 112 Copynumber: 2.5 Consensus size: 112
2323613 TAATGTAATA
* * * * *
2323623 ATAA-TAATAAATATAATATAATATATACTATA-ATAT-GTACATA-AATA-ATATACTATGATA
1 ATAACTAATTAATATAATATAATACATAATATATATATAATATATATAATATATATACTATGATA
* * *
2323683 ATATAATATATAATATTAATATAATAATAATAATATATACTATATAT
66 ACATAATATATAATAATAATATAATAATAACAATATATACTATATAT
* *
2323730 ATACACTAATTAATATAATATAATATATAATATATATATCATAT-TATTAATATATATACTAT-A
1 ATA-ACTAATTAATATAATATAATACATAATATATATATAATATATA-TAATATATATACTATGA
* *
2323793 TAACATACTATATAATAATAATATACT-ATAACATATATAATACGTGATATA-
64 TAACATAATATATAATAATAATATAATAATAACA-ATAT-ATAC-T-ATATAT
* *
2323844 AT-ACTAA-T-ATAGTACATATTATACATACTATATATATAATATATATAATATATAT
1 ATAACTAATTAATA-TA-ATATAATACATAATATATATATAATATATATAATATATAT
2323899 CATATATTAT
Statistics
Matches: 142, Mismatches: 13, Indels: 23
0.80 0.07 0.13
Matches are distributed among these distances:
107 3 0.02
108 1 0.01
109 26 0.18
110 9 0.06
111 10 0.07
112 70 0.49
113 15 0.11
114 3 0.02
115 5 0.04
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (112 bp):
ATAACTAATTAATATAATATAATACATAATATATATATAATATATATAATATATATACTATGATA
ACATAATATATAATAATAATATAATAATAACAATATATACTATATAT
Found at i:2325941 original size:20 final size:21
Alignment explanation
Indices: 2325904--2325945 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
2325894 TTCCCACAAA
2325904 ATTAAAAAAATAACAAAATAAAC
1 ATTAAAAAAAT-A-AAAATAAAC
2325927 ATTAAAAAAAT-AAAATAAA
1 ATTAAAAAAATAAAAATAAA
2325946 AAGAGAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
23 11 0.58
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (21 bp):
ATTAAAAAAATAAAAATAAAC
Found at i:2329810 original size:3 final size:3
Alignment explanation
Indices: 2329802--2329921 Score: 111
Period size: 3 Copynumber: 40.7 Consensus size: 3
2329792 TCATTTAAAT
** *
2329802 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA GTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
2329849 ATA TAA TAA TAA TAA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * *
2329895 ATA TTA ATA TTA ATA -TA TTA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2329922 TTTAATAAAT
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
2 6 0.06
3 90 0.91
4 3 0.03
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:2329926 original size:19 final size:19
Alignment explanation
Indices: 2329871--2329928 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
2329861 TAATTATTAT
2329871 TATTATTATTATTATTT-AT-
1 TATTA-TATTATT-TTTAATA
* *
2329890 TATTAATATTAATATTAATA
1 TATT-ATATTATTTTTAATA
2329910 TATTATATTATTTTTAATA
1 TATTATATTATTTTTAATA
2329929 AATAATTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.06
19 25 0.78
20 5 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATATTATTTTTAATA
Found at i:2335940 original size:40 final size:41
Alignment explanation
Indices: 2335864--2335941 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
2335854 AAGCCACTTT
2335864 GGGGTCAACCTTTTGGGTTGAAGCTTTAGTATTTGAGTCTTG
1 GGGGTCAACCTTTTGGG-TGAAGCTTTAGTATTTGAGTCTTG
* *
2335906 GGGGTCGACCTTTTGGG-GTAGCTTTAGTATTTGAGT
1 GGGGTCAACCTTTTGGGTGAAGCTTTAGTATTTGAGT
2335942 GAGGGAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 18 0.53
42 16 0.47
ACGTcount: A:0.15, C:0.12, G:0.33, T:0.40
Consensus pattern (41 bp):
GGGGTCAACCTTTTGGGTGAAGCTTTAGTATTTGAGTCTTG
Found at i:2337472 original size:19 final size:19
Alignment explanation
Indices: 2337448--2337489 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2337438 ATACACAAAA
2337448 GAAATGCCAAATCAAGAAC
1 GAAATGCCAAATCAAGAAC
*
2337467 GAAATGGCAAATCAAGAAC
1 GAAATGCCAAATCAAGAAC
2337486 GAAA
1 GAAA
2337490 GGGCGTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.55, C:0.17, G:0.19, T:0.10
Consensus pattern (19 bp):
GAAATGCCAAATCAAGAAC
Found at i:2337501 original size:23 final size:19
Alignment explanation
Indices: 2337455--2337493 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2337445 AAAGAAATGC
*
2337455 CAAATCAAGAACGAAATGG
1 CAAATCAAGAACGAAAGGG
2337474 CAAATCAAGAACGAAAGGG
1 CAAATCAAGAACGAAAGGG
2337493 C
1 C
2337494 GTGGAAATAT
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:0.51, C:0.18, G:0.23, T:0.08
Consensus pattern (19 bp):
CAAATCAAGAACGAAAGGG
Found at i:2341014 original size:28 final size:28
Alignment explanation
Indices: 2340970--2341026 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
2340960 CTGTCGTTGC
2340970 TTTCAAGCAATGACTCGATGACG-TAATA
1 TTTCAAGCAATGACTCGATGA-GATAATA
*
2340998 TTTCAAGC-ATTAGCTCGATGAGATAATA
1 TTTCAAGCAATGA-CTCGATGAGATAATA
2341026 T
1 T
2341027 AAATGAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (28 bp):
TTTCAAGCAATGACTCGATGAGATAATA
Found at i:2341377 original size:56 final size:56
Alignment explanation
Indices: 2341315--2341421 Score: 187
Period size: 56 Copynumber: 1.9 Consensus size: 56
2341305 TATCATTGAG
*
2341315 ACTGTATAATAAGTGTTAAAATACGATAATTTAATATATATTTTTATAACACTGCA
1 ACTGTATAATAAGTGTTAAAATACGATAATTTAATATATAATTTTATAACACTGCA
* *
2341371 ACTGTATAATAAGTGTTAAAATATGGTAATTTAATATATAATTTTATAACA
1 ACTGTATAATAAGTGTTAAAATACGATAATTTAATATATAATTTTATAACA
2341422 GTTGGATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (56 bp):
ACTGTATAATAAGTGTTAAAATACGATAATTTAATATATAATTTTATAACACTGCA
Done.