Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 87 of 310
Found at i:28005460 original size:27 final size:27
Alignment explanation
Indices: 28005428--28005490 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28005418 AANGATTTAC
**
28005428 AAAATTATTGAAATACCCCTGTAGGGT
1 AAAATTACCGAAATACCCCTGTAGGGT
* * * *
28005455 AGAATTACCGAGATACCCTTGTGGGGT
1 AAAATTACCGAAATACCCCTGTAGGGT
28005482 AAAATTACC
1 AAAATTACC
28005491 ATTTTGCCCG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (27 bp):
AAAATTACCGAAATACCCCTGTAGGGT
Found at i:28005729 original size:25 final size:25
Alignment explanation
Indices: 28005695--28005764 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
28005685 AGGAAGTGCT
**
28005695 AAAAGGGCTTTGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAATTTACAA
* *
28005720 AAAAGGGCTTTGCTCCAGTTTACAA
1 AAAAGGGCTTTGCCCCAATTTACAA
28005745 AAAAGGGCTTTGCCCCAATT
1 AAAAGGGCTTTGCCCCAATT
28005765 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAATTTACAA
Found at i:28005786 original size:50 final size:50
Alignment explanation
Indices: 28005695--28005789 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
28005685 AGGAAGTGCT
**
28005695 AAAAGGGCTTTGCCCCAATTTACCGAAAAGGGCTTTGCTCCAGTTTACAA
1 AAAAGGGCTTTGCCCCAATTTACCGAAAAGGGCTAGGCTCCAGTTTACAA
**
28005745 AAAAGGGCTTTGCCCCAA-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTTTGCCCCAATTTACCGAAAAG-GGCTAGG-CTCCAGTT
28005790 ATATGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 5 0.13
49 8 0.21
50 26 0.67
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (50 bp):
AAAAGGGCTTTGCCCCAATTTACCGAAAAGGGCTAGGCTCCAGTTTACAA
Found at i:28012749 original size:27 final size:27
Alignment explanation
Indices: 28012719--28013252 Score: 701
Period size: 27 Copynumber: 19.8 Consensus size: 27
28012709 TTACCAAAGC
* *
28012719 ACCCTCGATTTACAAAATTACCGTTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
*
28012746 ACCCTCGATTTATAGAATTACCATTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
*
28012773 ACCCTCGATTTATAGAATTACCATTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* *
28012800 ACCCTCAATTTATAGAATTACCATTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
*
28012827 ACCCTCGATTTATAGAATTACCATTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
28012854 ACCCTCGATTTATAGAATTACCGTTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* *
28012881 ACCCTCAATTTATAGAATTATCGTTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* *
28012908 ACCCTCGATTTACAGAATTATCGTTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
*
28012935 A-CCTCGATTTATAGAATTATCGTTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* *
28012961 ACCCTCGATTTATAAAATTACAGTTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* * *
28012988 ACCCTCGATTTACAGAACTACCATTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* * * *
28013015 ACCCTCAATTTACAAAATTACCATTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
*
28013042 ACCCTCGATTTATAGAATTACCATTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* *
28013069 ACCCTCGATTGATAGAATTACTGTTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
*
28013096 ACCCTCGATTTACAGAATTACCGTTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* *
28013123 ACCCGCGATTTATAGAATTACCATTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* *
28013150 ACCCTCGACTTACAGAATTACCGTTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* * *
28013177 ACCCTCAATTTACAGAATTACTGTTTT
1 ACCCTCGATTTATAGAATTACCGTTTT
* * *****
28013204 ACCCTCGATTTACAAAATTACTAAAAT
1 ACCCTCGATTTATAGAATTACCGTTTT
*
28013231 ACCCTCGATTTATAAAATTACC
1 ACCCTCGATTTATAGAATTACC
28013253 AAAATGCCCT
Statistics
Matches: 457, Mismatches: 49, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
26 25 0.05
27 432 0.95
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (27 bp):
ACCCTCGATTTATAGAATTACCGTTTT
Found at i:28013302 original size:81 final size:78
Alignment explanation
Indices: 28013217--28013477 Score: 274
Period size: 81 Copynumber: 3.2 Consensus size: 78
28013207 CTCGATTTAC
* * * * *
28013217 AAAATTACTAAAATACCCTCGATTTATAAAATTACCAAAATGCCCTCGATCAGTAAAATTACCAA
1 AAAATTACTAAAATACCCTCGGTTTATAAAATTACCAAAATACCCTGGTTTA-TAAAATTACCAA
28013282 AATATCCCTAGTTTGT
65 AATA-CCCT-GTTTGT
** **
28013298 AAAATTACTAAAATACCC-CTGGTTCGTAAAATTAATAAAATACCCTTGGTTTATAAAATTACCA
1 AAAATTACTAAAATACCCTC-GGTTTATAAAATTACCAAAATACCC-TGGTTTATAAAATTACCA
*
28013362 AAATACCCTTGGTCTGT
64 AAATACCC-T-GTTTGT
* * * *
28013379 AAAATT-CCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAA
1 AAAATTACTAAAATACCCTCGGTTTATAAAATTACCAAAATA-CCCTGGTTTATAAAATTACCAA
28013443 AATACCCCTGATTTGT
65 AATA-CCCTG-TTTGT
* *
28013459 GAAATTACTGAAATACCCT
1 AAAATTACTAAAATACCCT
28013478 TGTAGGGTAG
Statistics
Matches: 149, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
79 1 0.01
80 63 0.42
81 81 0.54
82 4 0.03
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (78 bp):
AAAATTACTAAAATACCCTCGGTTTATAAAATTACCAAAATACCCTGGTTTATAAAATTACCAAA
ATACCCTGTTTGT
Found at i:28013450 original size:27 final size:27
Alignment explanation
Indices: 28013212--28013476 Score: 248
Period size: 27 Copynumber: 9.9 Consensus size: 27
28013202 TTACCCTCGA
* * *
28013212 TTTACAAAATTACTAAAATA-CCCTCGA
1 TTTATAAAATTACCAAAATACCCCT-GG
* *
28013239 TTTATAAAATTACCAAAAT-GCCCTCG
1 TTTATAAAATTACCAAAATACCCCTGG
* * * *
28013265 ATCAGTAAAATTACCAAAATATCCCTAG
1 TTTA-TAAAATTACCAAAATACCCCTGG
* *
28013293 TTTGTAAAATTACTAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCCTGG
** ** *
28013320 TTCGTAAAATTAATAAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCCTGG
*
28013347 TTTATAAAATTACCAAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCCTGG
* * *
28013374 TCTGTAAAATT-CCAAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCCTGG
*
28013400 TTTACAAAATTACCAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCCTGG
* *
28013427 TTTACAAAATTACCAAAATACCCCTGA
1 TTTATAAAATTACCAAAATACCCCTGG
* * **
28013454 TTTGTGAAATTACTGAAATACCC
1 TTTATAAAATTACCAAAATACCC
28013477 TTGTAGGGTA
Statistics
Matches: 201, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
26 25 0.12
27 170 0.85
28 6 0.03
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
TTTATAAAATTACCAAAATACCCCTGG
Found at i:28013498 original size:27 final size:27
Alignment explanation
Indices: 28013459--28013521 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
28013449 CCTGATTTGT
*
28013459 GAAATTACTGAAATACCCTTGTAGGGTA
1 GAAA-TACCGAAATACCCTTGTAGGGTA
28013487 GAAATACCGAAATACCCTTGTAGGGTA
1 GAAATACCGAAATACCCTTGTAGGGTA
*
28013514 GAATTACC
1 GAAATACC
28013522 ATTTTGCCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (27 bp):
GAAATACCGAAATACCCTTGTAGGGTA
Found at i:28019158 original size:27 final size:27
Alignment explanation
Indices: 28019120--28019554 Score: 584
Period size: 27 Copynumber: 16.1 Consensus size: 27
28019110 GGCTGTTACA
*
28019120 TACCGTTTTACCCTCAATTTACAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
*
28019147 TACCGTTTTACCCTTGATTTACAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
28019174 TACCGTTTTACCCTCGATTTACAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
* *
28019201 TATCGTTTTACCCTCGATTTATAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
* *
28019228 TATCGTTTTACCCTCGATTTATAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
* * *
28019255 TACCATTTTACCCTCAATTTATAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
* *
28019282 TACCATTTTACCCTCGATTTATAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
28019309 TACCGTTTTACCCTCGATTTACAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
* * *
28019336 TACTGTTTTACCCTCGATTGACAAAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
* *
28019363 TACCATTTTACCCTCGATTTATAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
* * *
28019390 AACCATTTTACCCTCGATTTATAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
*** * *
28019417 TATTATTTTACCTTCGATTTATAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
**
28019444 TATAGTTTTACCCTCGATTTATC-GAAT
1 TACCGTTTTACCCTCGATTTA-CAGAAT
28019471 TACCGTTTTACCCTCGATTTACAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
*
28019498 TACCGTTTTACCCTCAATTTACAGAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
* * *
28019525 TACCGTTTTATCCTCGATTTAAAAAAT
1 TACCGTTTTACCCTCGATTTACAGAAT
28019552 TAC
1 TAC
28019555 TAAAATGCCC
Statistics
Matches: 371, Mismatches: 35, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
26 1 0.00
27 370 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCGTTTTACCCTCGATTTACAGAAT
Found at i:28019594 original size:54 final size:53
Alignment explanation
Indices: 28019547--28019833 Score: 331
Period size: 54 Copynumber: 5.3 Consensus size: 53
28019537 CTCGATTTAA
* * * *
28019547 AAAATTACTAAAATGCCCTTGATTTACAAAATTACCAAAATACCCTCGATTAGT
1 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCC-CGATTTGT
* ** * *
28019601 AAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCC-GATTTGT
** * * * *
28019655 AAAATTAGTAGAATACCCTTGGTTTATACAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCGA-TTTGT
* * *
28019709 AAAATTACCAAAATACCCTTGGTTTAAAAAATTACCAAATTACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCGA-TTTGT
*
28019763 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCC-GATTTGT
* **
28019817 GAAATTACTGAAATACC
1 AAAATTACCAAAATACC
28019834 GATGTAGGGT
Statistics
Matches: 200, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
53 1 0.00
54 198 0.99
55 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (53 bp):
AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCGATTTGT
Found at i:28019821 original size:27 final size:27
Alignment explanation
Indices: 28019547--28019833 Score: 297
Period size: 27 Copynumber: 10.6 Consensus size: 27
28019537 CTCGATTTAA
* * * * **
28019547 AAAATTACTAAAATGCCCTTGATTTAC
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
28019574 AAAATTACCAAAATA-CCCTCGATTAGT
1 AAAATTACCAAAATACCCCT-GGTTTGT
28019601 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
28019628 AAAATTACTAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
** * * *
28019655 AAAATTAGTAGAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
28019682 ACAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* **
28019709 AAAATTACCAAAATACCCTTGGTTTAA
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
28019736 AAAATTACCAAATTACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* **
28019763 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCTGGTTTGT
**
28019790 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* **
28019817 GAAATTACTGAAATACC
1 AAAATTACCAAAATACC
28019834 GATGTAGGGT
Statistics
Matches: 215, Mismatches: 43, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
26 3 0.01
27 208 0.97
28 4 0.02
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGT
Found at i:28019856 original size:27 final size:27
Alignment explanation
Indices: 28019817--28019879 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28019807 CCTAATTTGT
* *
28019817 GAAATTACTGAAATACCGATGTAGGGTA
1 GAAA-TACCGAAATACCCATGTAGGGTA
*
28019845 GAAATACCGAAATACCCCTGTAGGGTA
1 GAAATACCGAAATACCCATGTAGGGTA
*
28019872 GAATTACC
1 GAAATACC
28019880 ATTTTGCCCG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (27 bp):
GAAATACCGAAATACCCATGTAGGGTA
Found at i:28020120 original size:25 final size:25
Alignment explanation
Indices: 28020084--28020153 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
28020074 AGAAAGTGCT
* * *
28020084 AAAAGGGTTTTGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
28020109 AAAAGGGCTTTGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
28020134 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
28020154 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:28020166 original size:24 final size:24
Alignment explanation
Indices: 28020109--28020180 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
28020099 TAGTTTACCG
*
28020109 AAAAG-GGCTTTGCCCCAGTTTACC
1 AAAAGAGGCTTTGCCCCAG-TTATC
*
28020133 AAAA-AGGGCTTTGCCCCAGTTATT
1 AAAAGA-GGCTTTGCCCCAGTTATC
**
28020157 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGAGGCTTTGCC-CCAGTTAT
28020181 ATGATAAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 18 0.45
25 22 0.55
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (24 bp):
AAAAGAGGCTTTGCCCCAGTTATC
Found at i:28021900 original size:42 final size:42
Alignment explanation
Indices: 28021798--28021904 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 42
28021788 TACAATACCA
* *
28021798 ATGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCC
1 ATGTCCCAGACATGGTCTTACATGAAATCAAATATCGATGCC
* * * *
28021840 ACTGTCCCAAATAGGGTCTTACATGAAATCAAATA-CGATGCTG
1 A-TGTCCCAGACATGGTCTTACATGAAATCAAATATCGATGC-C
*
28021883 ATGTCCGAGACATGGTCTTACA
1 ATGTCCCAGACATGGTCTTACA
28021905 CGTAAATTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 24 0.45
43 29 0.55
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (42 bp):
ATGTCCCAGACATGGTCTTACATGAAATCAAATATCGATGCC
Found at i:28023380 original size:95 final size:95
Alignment explanation
Indices: 28023216--28023387 Score: 208
Period size: 95 Copynumber: 1.8 Consensus size: 95
28023206 TTTCTCAAAT
* * *
28023216 ACAAATTCCTAATTTGGTATCAATATTAAATAGAATATCGATATAATATATATACCAAGAAACTT
1 ACAAATTCATAATTTGGTATCAATATTAAATAGAATATCAATAGAATATATATACCAAGAAACTT
28023281 AATATCGATACCCTTGTTTTTGCACAACAA
66 AATATCGATACCCTTGTTTTTGCACAACAA
* * * *
28023311 ACAAATTCATGATTTGGTAAT-GATATTAAATA-AGATATCAATAGAGTATCA-ATACCAAGCAA
1 ACAAATTCATAATTTGGT-ATCAATATTAAATAGA-ATATCAATAGAATAT-ATATACCAAGAAA
*
28023373 -TTAAATATTGATACC
63 CTT-AATATCGATACC
28023388 AACTTTATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
94 3 0.05
95 59 0.91
96 3 0.05
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.33
Consensus pattern (95 bp):
ACAAATTCATAATTTGGTATCAATATTAAATAGAATATCAATAGAATATATATACCAAGAAACTT
AATATCGATACCCTTGTTTTTGCACAACAA
Found at i:28035385 original size:21 final size:21
Alignment explanation
Indices: 28035340--28035402 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
28035330 TTTGAACCAT
* *
28035340 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
28035362 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
28035383 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
28035403 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:28037452 original size:40 final size:40
Alignment explanation
Indices: 28037378--28037639 Score: 456
Period size: 40 Copynumber: 6.6 Consensus size: 40
28037368 AACCCAAGTA
* *
28037378 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
*
28037417 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
28037457 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
28037497 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28037537 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28037577 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
28037617 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28037640 CATTCGAATA
Statistics
Matches: 215, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
39 12 0.06
40 200 0.93
41 3 0.01
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:28042840 original size:40 final size:40
Alignment explanation
Indices: 28042751--28042879 Score: 161
Period size: 40 Copynumber: 3.2 Consensus size: 40
28042741 TGATGTGTAT
* * *
28042751 CCGGGCTTAAAGACCTGCAGGCTATATGCAGGAATTATAT
1 CCGGACTTAAAGACCTGCAGGCTATATGCTGGAATTATAA
* * * *
28042791 TCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTATAC
1 CCGGACTTAAAGACCTGCAGGCTATATGCTGGAATTATAA
** *
28042831 CCGGACTT-AAGGTCTGCAGGCTATGTGCTGGAATTATAA
1 CCGGACTTAAAGACCTGCAGGCTATATGCTGGAATTATAA
28042870 CCGGACTTAA
1 CCGGACTTAA
28042880 GGTCCGCAGG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 34 0.44
40 43 0.56
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGACTTAAAGACCTGCAGGCTATATGCTGGAATTATAA
Found at i:28042860 original size:39 final size:39
Alignment explanation
Indices: 28042767--28042889 Score: 156
Period size: 39 Copynumber: 3.1 Consensus size: 39
28042757 TTAAAGACCT
* ** * **
28042767 GCAGGCTATATGCAGGAATTATATTCGGGCTTAAAGACCC
1 GCAGGCTATATGCTGGAATTATAACCGGACTT-AAGGTCC
* *
28042807 GCAGGCTATATGCTGGAATTATACCCGGACTTAAGGTCT
1 GCAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCC
*
28042846 GCAGGCTATGTGCTGGAATTATAACCGGACTTAAGGTCC
1 GCAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCC
28042885 GCAGG
1 GCAGG
28042890 NNNNNNNNNN
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 45 0.62
40 28 0.38
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (39 bp):
GCAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCC
Found at i:28049434 original size:39 final size:39
Alignment explanation
Indices: 28049324--28049449 Score: 162
Period size: 39 Copynumber: 3.2 Consensus size: 39
28049314 TGAAAGACCT
* * **
28049324 GCAGGCTATATGCTGGAATTATATCCGGGCTTAAAGACCC
1 GCAGGCTATATGCTGGAATTATAACCGGACTT-AAGGTCC
* * *
28049364 GCAGCCTATATGCTGGAATTATACCCAGACTTAAGGTCC
1 GCAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCC
* *
28049403 ACAGGCTATGTGCTGGAATTATAACCGGACTTAAGGTCC
1 GCAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCC
28049442 GCAGGCTA
1 GCAGGCTA
28049450 CGTGTTGGAA
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 46 0.62
40 28 0.38
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (39 bp):
GCAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCC
Found at i:28049459 original size:39 final size:39
Alignment explanation
Indices: 28049374--28049459 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
28049364 GCAGCCTATA
* *
28049374 TGCTGGAATTATACCCAGACTTAAGGTCCACAGGCTATG
1 TGCTGGAATTATAACCAGACTTAAGGTCCACAGGCTACG
* *
28049413 TGCTGGAATTATAACCGGACTTAAGGTCCGCAGGCTACG
1 TGCTGGAATTATAACCAGACTTAAGGTCCACAGGCTACG
*
28049452 TGTTGGAA
1 TGCTGGAA
28049460 ATATGTCCGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
TGCTGGAATTATAACCAGACTTAAGGTCCACAGGCTACG
Found at i:28055680 original size:25 final size:25
Alignment explanation
Indices: 28055652--28055738 Score: 122
Period size: 26 Copynumber: 3.4 Consensus size: 25
28055642 CTGTAGGCCT
*
28055652 AGCCTCTTTTAAT-AACTGGGGCATA
1 AGCC-CTTTTGATAAACTGGGGCATA
*
28055677 AGCCCTTTTCGATAAACTAGGGCATA
1 AGCCCTTTT-GATAAACTGGGGCATA
28055703 AGCCCTTTCTGATAAACTGGGGCATA
1 AGCCCTTT-TGATAAACTGGGGCATA
28055729 AGCCCTTTTG
1 AGCCCTTTTG
28055739 CACTTCCTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
24 5 0.09
25 8 0.14
26 42 0.75
27 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCATA
Found at i:28055699 original size:26 final size:27
Alignment explanation
Indices: 28055665--28055737 Score: 123
Period size: 26 Copynumber: 2.8 Consensus size: 27
28055655 CTCTTTTAAT
28055665 AACTGGGGCATAAGCCCTTTTC-GATA
1 AACTGGGGCATAAGCCCTTTTCTGATA
*
28055691 AACTAGGGCATAAGCCC-TTTCTGATA
1 AACTGGGGCATAAGCCCTTTTCTGATA
28055717 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
28055738 GCACTTCCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 4 0.09
26 36 0.84
27 3 0.07
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (27 bp):
AACTGGGGCATAAGCCCTTTTCTGATA
Found at i:28057109 original size:447 final size:447
Alignment explanation
Indices: 28056275--28057168 Score: 1788
Period size: 447 Copynumber: 2.0 Consensus size: 447
28056265 ATTCCCGATC
28056275 ATCAACTTAGAGAATCTAACTAACCAATGAGCGTTCTCTTGCTCACAAGTCCTCAAAATGCCAAA
1 ATCAACTTAGAGAATCTAACTAACCAATGAGCGTTCTCTTGCTCACAAGTCCTCAAAATGCCAAA
28056340 ATTTCGGCATTTCGGCATTTCGACATTTATCGATTTAAGCTACGAAAGAAGGTTCGTTACACACC
66 ATTTCGGCATTTCGGCATTTCGACATTTATCGATTTAAGCTACGAAAGAAGGTTCGTTACACACC
28056405 TGATTTGCGATATTCCTCGACGAGATCTCCTACATGATTTCTCCTATAACCAACCGCTTATAGAT
131 TGATTTGCGATATTCCTCGACGAGATCTCCTACATGATTTCTCCTATAACCAACCGCTTATAGAT
28056470 CAGTTTATAATAATTAAACCAAAATGAGAACCATCTATTATCAACACTTACACATTCGGCCACCA
196 CAGTTTATAATAATTAAACCAAAATGAGAACCATCTATTATCAACACTTACACATTCGGCCACCA
28056535 TCCATAATGGCTTTAGAATCCATACCTTTGCCGAAGTTGATGACTAGATCTAGCCACTTCGATGT
261 TCCATAATGGCTTTAGAATCCATACCTTTGCCGAAGTTGATGACTAGATCTAGCCACTTCGATGT
28056600 TCCAAGCTAATCCAAGTCGACCCTACGCCTTGCTGCTCCCCCACTATACAAACCATAAAAAGACG
326 TCCAAGCTAATCCAAGTCGACCCTACGCCTTGCTGCTCCCCCACTATACAAACCATAAAAAGACG
28056665 TAAGGGAAAACCCAATAAGGCCTCTATCCATATTCGGCCACCTCCCTAAACTATAGG
391 TAAGGGAAAACCCAATAAGGCCTCTATCCATATTCGGCCACCTCCCTAAACTATAGG
28056722 ATCAACTTAGAGAATCTAACTAACCAATGAGCGTTCTCTTGCTCACAAGTCCTCAAAATGCCAAA
1 ATCAACTTAGAGAATCTAACTAACCAATGAGCGTTCTCTTGCTCACAAGTCCTCAAAATGCCAAA
28056787 ATTTCGGCATTTCGGCATTTCGACATTTATCGATTTAAGCTACGAAAGAAGGTTCGTTACACACC
66 ATTTCGGCATTTCGGCATTTCGACATTTATCGATTTAAGCTACGAAAGAAGGTTCGTTACACACC
28056852 TGATTTGCGATATTCCTCGACGAGATCTCCTACATGATTTCTCCTATAACCAACCGCTTATAGAT
131 TGATTTGCGATATTCCTCGACGAGATCTCCTACATGATTTCTCCTATAACCAACCGCTTATAGAT
28056917 CAGTTTATAATAATTAAACCAAAATGAGAACCATCTATTATCAACACTTACACATTCGGCCACCA
196 CAGTTTATAATAATTAAACCAAAATGAGAACCATCTATTATCAACACTTACACATTCGGCCACCA
28056982 TCCATAATGGCTTTAGAATCCATACCTTTGCCGAAGTTGATGACTAGATCTAGCCACTTCGATGT
261 TCCATAATGGCTTTAGAATCCATACCTTTGCCGAAGTTGATGACTAGATCTAGCCACTTCGATGT
28057047 TCCAAGCTAATCCAAGTCGACCCTACGCCTTGCTGCTCCCCCACTATACAAACCATAAAAAGACG
326 TCCAAGCTAATCCAAGTCGACCCTACGCCTTGCTGCTCCCCCACTATACAAACCATAAAAAGACG
28057112 TAAGGGAAAACCCAATAAGGCCTCTATCCATATTCGGCCACCTCCCTAAACTATAGG
391 TAAGGGAAAACCCAATAAGGCCTCTATCCATATTCGGCCACCTCCCTAAACTATAGG
28057169 GGTTTCGGCT
Statistics
Matches: 447, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
447 447 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (447 bp):
ATCAACTTAGAGAATCTAACTAACCAATGAGCGTTCTCTTGCTCACAAGTCCTCAAAATGCCAAA
ATTTCGGCATTTCGGCATTTCGACATTTATCGATTTAAGCTACGAAAGAAGGTTCGTTACACACC
TGATTTGCGATATTCCTCGACGAGATCTCCTACATGATTTCTCCTATAACCAACCGCTTATAGAT
CAGTTTATAATAATTAAACCAAAATGAGAACCATCTATTATCAACACTTACACATTCGGCCACCA
TCCATAATGGCTTTAGAATCCATACCTTTGCCGAAGTTGATGACTAGATCTAGCCACTTCGATGT
TCCAAGCTAATCCAAGTCGACCCTACGCCTTGCTGCTCCCCCACTATACAAACCATAAAAAGACG
TAAGGGAAAACCCAATAAGGCCTCTATCCATATTCGGCCACCTCCCTAAACTATAGG
Found at i:28070229 original size:7 final size:7
Alignment explanation
Indices: 28070217--28070245 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28070207 GATAGATCAC
28070217 AAGGTAT
1 AAGGTAT
28070224 AAGGTAT
1 AAGGTAT
28070231 AAGGTAT
1 AAGGTAT
28070238 AAGGTAT
1 AAGGTAT
28070245 A
1 A
28070246 CAGTGTAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (7 bp):
AAGGTAT
Found at i:28072914 original size:19 final size:18
Alignment explanation
Indices: 28072890--28072932 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
28072880 GGGACAAAAT
*
28072890 TGAAAAGATGTAAAATTTA
1 TGAAAAAAT-TAAAATTTA
*
28072909 TGAAAAAAATTAAATTTTA
1 TG-AAAAAATTAAAATTTA
28072928 TGAAA
1 TGAAA
28072933 TACATGGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 12 0.57
20 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (18 bp):
TGAAAAAATTAAAATTTA
Found at i:28073653 original size:26 final size:26
Alignment explanation
Indices: 28073581--28073655 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
28073571 AAAGCTCTTA
*
28073581 TGAGCATCCCG-ATATATGGCTCTTTG
1 TGAGCTTCCCGAATA-ATGGCTCTTTG
*
28073607 TGAGCTTCCCGAATAAAGGCTCTTTG
1 TGAGCTTCCCGAATAATGGCTCTTTG
** *
28073633 TGAGCTTCTTGATTAATGGCTCT
1 TGAGCTTCCCGAATAATGGCTCT
28073656 CCAGAGCTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 39 0.93
27 3 0.07
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (26 bp):
TGAGCTTCCCGAATAATGGCTCTTTG
Found at i:28073735 original size:25 final size:25
Alignment explanation
Indices: 28073706--28073787 Score: 64
Period size: 24 Copynumber: 3.4 Consensus size: 25
28073696 ATCGTTTCCG
*
28073706 GAGCTTCCTAATTAATGGCTCTTCA-
1 GAGCTTCCTAATTAATGGCTC-GCAT
* * *
28073731 GAGCTACC-CATTATTGGCTCGCAT
1 GAGCTTCCTAATTAATGGCTCGCAT
*
28073755 GAGCTTCCTGATT-ATGGCTC-CTAT
1 GAGCTTCCTAATTAATGGCTCGC-AT
*
28073779 GAGATTCCT
1 GAGCTTCCT
28073788 GTTATATAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
23 3 0.07
24 33 0.72
25 10 0.22
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.34
Consensus pattern (25 bp):
GAGCTTCCTAATTAATGGCTCGCAT
Found at i:28081216 original size:26 final size:26
Alignment explanation
Indices: 28081179--28081328 Score: 107
Period size: 26 Copynumber: 6.0 Consensus size: 26
28081169 ACAGCTCTTA
*
28081179 TGAGCATCCTGA-TATATGGCTCTTCG
1 TGAGCTTCCTGATTA-ATGGCTCTTCG
* * *
28081205 TGAGCTTTCTGATTAAAGGCTCTTTG
1 TGAGCTTCCTGATTAATGGCTCTTCG
*
28081231 TGAGCTTCCTGATTAATGGCTC-TCC
1 TGAGCTTCCTGATTAATGGCTCTTCG
* * *
28081256 AGAGCTTCCCGA-T-ATGGCTCTT-T
1 TGAGCTTCCTGATTAATGGCTCTTCG
* * * *
28081279 TAAACTTCCTGA-TATATGGCT-ATCC
1 TGAGCTTCCTGATTA-ATGGCTCTTCG
* *
28081304 TAAGCTTCTTGATTAATGGCTCTTC
1 TGAGCTTCCTGATTAATGGCTCTTC
28081329 AAAGCTACCC
Statistics
Matches: 97, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
23 16 0.16
24 3 0.03
25 33 0.34
26 43 0.44
27 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (26 bp):
TGAGCTTCCTGATTAATGGCTCTTCG
Found at i:28081241 original size:52 final size:48
Alignment explanation
Indices: 28081172--28081299 Score: 123
Period size: 52 Copynumber: 2.6 Consensus size: 48
28081162 ACACACCACA
* * ** * *
28081172 GCTCTTATGAGCATCCTGATATATGGCTCTTCGTGAGCTTTCTGATTAAAG
1 GCTCTTTTGAGCTTCCTGATATATGGCTC-TCCAGAGCTTCCCGA-T-AAG
*
28081223 GCTCTTTGTGAGCTTCCTGAT-TAATGGCTCTCCAGAGCTTCCCGATATG
1 GCTCTTT-TGAGCTTCCTGATAT-ATGGCTCTCCAGAGCTTCCCGATAAG
* *
28081272 GCTCTTTTAAACTTCCTGATATATGGCT
1 GCTCTTTTGAGCTTCCTGATATATGGCT
28081300 ATCCTAAGCT
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
48 17 0.26
49 10 0.15
50 1 0.02
51 18 0.28
52 19 0.29
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (48 bp):
GCTCTTTTGAGCTTCCTGATATATGGCTCTCCAGAGCTTCCCGATAAG
Found at i:28081311 original size:25 final size:25
Alignment explanation
Indices: 28081233--28081326 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 25
28081223 GCTCTTTGTG
28081233 AGCTTCCTGATTAATGGCTCTCC-A
1 AGCTTCCTGATTAATGGCTCTCCTA
* **
28081257 GAGCTTCCCGA-T-ATGGCTCTTTTA
1 -AGCTTCCTGATTAATGGCTCTCCTA
* *
28081281 AACTTCCTGA-TATATGGCTATCCTA
1 AGCTTCCTGATTA-ATGGCTCTCCTA
*
28081306 AGCTTCTTGATTAATGGCTCT
1 AGCTTCCTGATTAATGGCTCT
28081327 TCAAAGCTAC
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
23 17 0.31
24 2 0.04
25 33 0.61
26 2 0.04
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.37
Consensus pattern (25 bp):
AGCTTCCTGATTAATGGCTCTCCTA
Found at i:28088420 original size:26 final size:26
Alignment explanation
Indices: 28088391--28088463 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
28088381 CCTGCTATAT
28088391 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
* * *
28088417 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTCGTGAGCTTCCCGATTAAA
**
28088443 GGCTC-TCCAGAGCTTCCCGAT
1 GGCTCTTCGTGAGCTTCCCGAT
28088464 ATGGCTCGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 12 0.30
26 28 0.70
ACGTcount: A:0.16, C:0.27, G:0.23, T:0.33
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATTAAA
Found at i:28088504 original size:48 final size:51
Alignment explanation
Indices: 28088380--28088513 Score: 132
Period size: 48 Copynumber: 2.7 Consensus size: 51
28088370 ATTATGAGCA
* ** * *
28088380 TCCTGCTATATGGCTCTTCGTGAGCTTCCCGATTAAAGGCTCTTTGTGAGCT
1 TCCTGATATATGGCTCTTCG-GAGCTTCCCGATTAAAGGCTCGCTGTAAACT
* * *
28088432 TCCTGAT-TAATGGCTCTCCAGAGCTTCCCGA-T-ATGGCTCGCT-TAAACT
1 TCCTGATAT-ATGGCTCTTCGGAGCTTCCCGATTAAAGGCTCGCTGTAAACT
* *
28088480 TCCTGATATATGGCTATTCGGAGCTTCCTGATTA
1 TCCTGATATATGGCTCTTCGGAGCTTCCCGATTA
28088514 CTGGCTCTTC
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
48 29 0.44
49 9 0.14
50 1 0.02
51 12 0.18
52 15 0.23
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (51 bp):
TCCTGATATATGGCTCTTCGGAGCTTCCCGATTAAAGGCTCGCTGTAAACT
Found at i:28088577 original size:73 final size:72
Alignment explanation
Indices: 28088400--28088580 Score: 182
Period size: 73 Copynumber: 2.5 Consensus size: 72
28088390 TGGCTCTTCG
* * * *
28088400 TGAGCTTCCCGATTAAAGGCTCTTTGTGAGCTTCCTGATTAATGGCTCTCCAGAGCTTCCCGATA
1 TGAGCTTCCTGATTATA-GCTCTTT-TGAGCTTCCTGATTAATGGCTCTCCAGAACTACCCGATA
* *
28088465 TGGCTCGCT
64 TGGCTAGCA
* * * * ** * * *
28088474 TAAACTTCCTGATATATGGCTATTCGGAGCTTCCTGATTACTGGCTCTTCAGAACTACCCGTTAT
1 TGAGCTTCCTGAT-TATAGCTCTTTTGAGCTTCCTGATTAATGGCTCTCCAGAACTACCCGATA-
*
28088539 TGGTTAGCA
64 TGGCTAGCA
28088548 TGAGCTTCCTGATTATAGCTCTTTTGAGCTTCC
1 TGAGCTTCCTGATTATAGCTCTTTTGAGCTTCC
28088581 CATTATATAG
Statistics
Matches: 83, Mismatches: 22, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
73 49 0.59
74 32 0.39
75 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.35
Consensus pattern (72 bp):
TGAGCTTCCTGATTATAGCTCTTTTGAGCTTCCTGATTAATGGCTCTCCAGAACTACCCGATATG
GCTAGCA
Found at i:28088862 original size:32 final size:32
Alignment explanation
Indices: 28088826--28088929 Score: 190
Period size: 32 Copynumber: 3.2 Consensus size: 32
28088816 GTATTTTTGA
28088826 AATACATGGAAATGTTTTGTACATGTTATATG
1 AATACATGGAAATGTTTTGTACATGTTATATG
28088858 AATACATGGAAATGTTTTGTACATGTTATATG
1 AATACATGGAAATGTTTTGTACATGTTATATG
*
28088890 AATACATGGAAATGTTTTGCACATGTTATATG
1 AATACATGGAAATGTTTTGTACATGTTATATG
*
28088922 AATCCATG
1 AATACATG
28088930 ATATAGAAAG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (32 bp):
AATACATGGAAATGTTTTGTACATGTTATATG
Found at i:28089648 original size:27 final size:28
Alignment explanation
Indices: 28089618--28089674 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
28089608 TTTTTTGATG
28089618 AAATGAGCTATTTG-GG-CTAATTTGTGA
1 AAATGAGCT-TTTGAGGACTAATTTGTGA
*
28089645 AAATGAGGTTTTGAAGGACTAATTTGTGA
1 AAATGAGCTTTTG-AGGACTAATTTGTGA
28089674 A
1 A
28089675 TTTAACATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
27 8 0.31
28 2 0.08
29 12 0.46
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
AAATGAGCTTTTGAGGACTAATTTGTGA
Found at i:28090240 original size:43 final size:42
Alignment explanation
Indices: 28090136--28090240 Score: 97
Period size: 42 Copynumber: 2.5 Consensus size: 42
28090126 GAAATTTAAG
* ** * * *
28090136 TGTAAGACCATGTCTGGGACATCGGCATCGTATCTGTTTTCG
1 TGTAAGACCACGTCTGGGACAGAGGCATCGTATCTGATTACA
* *
28090178 TATAAGACC-CTGTATGGGACAGAGGCATCG-ATACTGAATTACA
1 TGTAAGACCAC-GTCTGGGACAGAGGCATCGTAT-CTG-ATTACA
28090221 TGTAAGACCACGTCTGGGAC
1 TGTAAGACCACGTCTGGGAC
28090241 GTCAGCATTG
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
41 2 0.04
42 27 0.55
43 19 0.39
44 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACAGAGGCATCGTATCTGATTACA
Found at i:28091168 original size:22 final size:22
Alignment explanation
Indices: 28091143--28091191 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
28091133 GCTCTGTCTG
*
28091143 TCCGGTGACTCCTCTTTCTTAT
1 TCCGGTGACTCCCCTTTCTTAT
28091165 TCCGGTGACTCCCCTTTCTTAT
1 TCCGGTGACTCCCCTTTCTTAT
28091187 TCCGG
1 TCCGG
28091192 CGACGGTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.08, C:0.35, G:0.16, T:0.41
Consensus pattern (22 bp):
TCCGGTGACTCCCCTTTCTTAT
Found at i:28098634 original size:13 final size:13
Alignment explanation
Indices: 28098616--28098640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28098606 TATGAGATAT
28098616 GTGTGAAAATTTC
1 GTGTGAAAATTTC
28098629 GTGTGAAAATTT
1 GTGTGAAAATTT
28098641 TATCGTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:28105459 original size:48 final size:48
Alignment explanation
Indices: 28105392--28105532 Score: 171
Period size: 48 Copynumber: 2.9 Consensus size: 48
28105382 CGGATACTCA
* * *
28105392 GAAGTCTCGCACACTAAGTGCCAATATCATGGCTCGAAGCCAACTCAATAT
1 GAAG-CTCGCACCCGAAGTGCCAATATCATGGCTCGAAGCCAAATC--TAT
* * *
28105443 -AA-CTCGCACCCGAAGTGCTAATATCATGGCTCGAAGCTAAATCTGT
1 GAAGCTCGCACCCGAAGTGCCAATATCATGGCTCGAAGCCAAATCTAT
28105489 GAAGCTCGCACCCGAAGTGCCAATATCATGGC-CTGAAGCCAAAT
1 GAAGCTCGCACCCGAAGTGCCAATATCATGGCTC-GAAGCCAAAT
28105533 AAATGTATCC
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
46 2 0.03
47 3 0.04
48 72 0.91
50 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (48 bp):
GAAGCTCGCACCCGAAGTGCCAATATCATGGCTCGAAGCCAAATCTAT
Found at i:28110289 original size:33 final size:33
Alignment explanation
Indices: 28110247--28110312 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
28110237 CAGTTTTAAA
28110247 ACGAAACTGACAACTAATCCTTCACTTAGCTTT
1 ACGAAACTGACAACTAATCCTTCACTTAGCTTT
28110280 ACGAAACTGACAACTAATCCTTCACTTAGCTTT
1 ACGAAACTGACAACTAATCCTTCACTTAGCTTT
28110313 TCCTCGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.30
Consensus pattern (33 bp):
ACGAAACTGACAACTAATCCTTCACTTAGCTTT
Found at i:28112686 original size:23 final size:23
Alignment explanation
Indices: 28112634--28112737 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 23
28112624 TAGTTCATAT
* * *
28112634 GAGCTTACCATTTTAGCTCTTCAG
1 GAGCTTACCGTTTCAGCTCTAC-G
28112658 GA-CTTACCGTTTCAGCTCTACG
1 GAGCTTACCGTTTCAGCTCTACG
***
28112680 GAGCTTACCG-TTCAGCTCTTTA
1 GAGCTTACCGTTTCAGCTCTACG
* *
28112702 GAGCTTACCGTTTATCAGCTCAGAAG
1 GAGCTTACCG-TT-TCAGCTC-TACG
28112728 GAGCTTACCG
1 GAGCTTACCG
28112738 ATCATGACTC
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
22 22 0.34
23 23 0.35
24 3 0.05
25 7 0.11
26 10 0.15
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCTACG
Found at i:28112696 original size:22 final size:22
Alignment explanation
Indices: 28112634--28112713 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
28112624 TAGTTCATAT
* *
28112634 GAGCTTACCATTTTAGCTCTTCAG
1 GAGCTTACC-GTTCAGCTCTTC-G
*
28112658 GA-CTTACCGTTTCAGCTCTACG
1 GAGCTTACCG-TTCAGCTCTTCG
**
28112680 GAGCTTACCGTTCAGCTCTTTA
1 GAGCTTACCGTTCAGCTCTTCG
28112702 GAGCTTACCGTT
1 GAGCTTACCGTT
28112714 TATCAGCTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
22 24 0.50
23 22 0.46
24 2 0.04
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (22 bp):
GAGCTTACCGTTCAGCTCTTCG
Found at i:28112709 original size:45 final size:48
Alignment explanation
Indices: 28112634--28112737 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 48
28112624 TAGTTCATAT
* * * *
28112634 GAGCTTACCATTTTAGCTCTTCAGGACTTACCG-TT-TCAGCTC-TACG
1 GAGCTTACC-GTTCAGCTCTTCAGGACTTACCGTTTATCAGCTCAGAAG
*
28112680 GAGCTTACCGTTCAGCTCTTTA-GAGCTTACCGTTTATCAGCTCAGAAG
1 GAGCTTACCGTTCAGCTCTTCAGGA-CTTACCGTTTATCAGCTCAGAAG
28112728 GAGCTTACCG
1 GAGCTTACCG
28112738 ATCATGACTC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
44 2 0.04
45 17 0.35
46 11 0.22
47 7 0.14
48 12 0.24
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (48 bp):
GAGCTTACCGTTCAGCTCTTCAGGACTTACCGTTTATCAGCTCAGAAG
Found at i:28112923 original size:25 final size:27
Alignment explanation
Indices: 28112895--28112945 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
28112885 GGCTATATGT
28112895 TTTACATGAA-T-TATGAGTTACATGA
1 TTTACATGAATTATATGAGTTACATGA
28112920 TTTACATGAATTATATGAGTTACATG
1 TTTACATGAATTATATGAGTTACATG
28112946 GATAATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 10 0.42
26 1 0.04
27 13 0.54
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (27 bp):
TTTACATGAATTATATGAGTTACATGA
Found at i:28112924 original size:9 final size:9
Alignment explanation
Indices: 28112896--28112945 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
28112886 GCTATATGTT
28112896 TTACATGAA
1 TTACATGAA
*
28112905 TT--ATGAG
1 TTACATGAA
*
28112912 TTACATGAT
1 TTACATGAA
28112921 TTACATGAA
1 TTACATGAA
* *
28112930 TTATATGAG
1 TTACATGAA
28112939 TTACATG
1 TTACATG
28112946 GATAATATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.18
9 27 0.82
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (9 bp):
TTACATGAA
Found at i:28112937 original size:18 final size:18
Alignment explanation
Indices: 28112916--28112956 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
28112906 TATGAGTTAC
*
28112916 ATGATTTACATGAATTAT
1 ATGATTTACATGAATAAT
* *
28112934 ATGAGTTACATGGATAAT
1 ATGATTTACATGAATAAT
28112952 ATGAT
1 ATGAT
28112957 ACATGAGATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (18 bp):
ATGATTTACATGAATAAT
Found at i:28120723 original size:27 final size:27
Alignment explanation
Indices: 28120693--28120781 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
28120683 TTTAGTTTAC
28120693 TAAAATTACTGAAATACGCTTAG-TTTG
1 TAAAATTACTGAAATAC-CTTAGATTTG
* * * *
28120720 TAAAAATACT-AAAAACCCTCGATTTG
1 TAAAATTACTGAAATACCTTAGATTTG
* *
28120746 TAAAATTACTGAAATACCTTCGACTTG
1 TAAAATTACTGAAATACCTTAGATTTG
28120773 TAAAATTAC
1 TAAAATTAC
28120782 CAAAGTACCC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
25 3 0.06
26 18 0.35
27 31 0.60
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.33
Consensus pattern (27 bp):
TAAAATTACTGAAATACCTTAGATTTG
Found at i:28120806 original size:27 final size:27
Alignment explanation
Indices: 28120776--28120837 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
28120766 CGACTTGTAA
* *
28120776 AATTACCAAAGTACCCCTGATTTATAG
1 AATTACCAAAGTACCCCGGATTTACAG
*** *
28120803 AATTACCATTTTACCCCGGATTTACAT
1 AATTACCAAAGTACCCCGGATTTACAG
28120830 AATTACCA
1 AATTACCA
28120838 TTTTACCCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (27 bp):
AATTACCAAAGTACCCCGGATTTACAG
Found at i:28120838 original size:27 final size:27
Alignment explanation
Indices: 28120787--28120854 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
28120777 ATTACCAAAG
*
28120787 TACCCCTGATTTATAGAATTACCATTT
1 TACCCCTGATTTACAGAATTACCATTT
* *
28120814 TACCCCGGATTTACATAATTACCATTT
1 TACCCCTGATTTACAGAATTACCATTT
*
28120841 TACCCTTGATTTAC
1 TACCCCTGATTTAC
28120855 CCTCGACTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (27 bp):
TACCCCTGATTTACAGAATTACCATTT
Found at i:28120880 original size:27 final size:27
Alignment explanation
Indices: 28120850--28120901 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
28120840 TTACCCTTGA
28120850 TTTACCCTCGACTTACAGAATTACCGT
1 TTTACCCTCGACTTACAGAATTACCGT
* * *
28120877 TTTACCCTCGATTTATAGATTTACC
1 TTTACCCTCGACTTACAGAATTACC
28120902 CTCAACTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (27 bp):
TTTACCCTCGACTTACAGAATTACCGT
Found at i:28120898 original size:46 final size:46
Alignment explanation
Indices: 28120848--28120937 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
28120838 TTTTACCCTT
* *
28120848 GATTTACCCTCGACTTACAGAATTACCGTTTTACCCTCGATTTATA
1 GATTTACCCTCAACTTACAGAATTACCATTTTACCCTCGATTTATA
* *
28120894 GATTTACCCTCAACTTACAGAATTACTATTTTACCCTTGATTTA
1 GATTTACCCTCAACTTACAGAATTACCATTTTACCCTCGATTTA
28120938 CAAAATTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (46 bp):
GATTTACCCTCAACTTACAGAATTACCATTTTACCCTCGATTTATA
Found at i:28120926 original size:27 final size:27
Alignment explanation
Indices: 28120896--28120948 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
28120886 GATTTATAGA
*
28120896 TTTACCCTCAACTTACAGAATTACTAT
1 TTTACCCTCAACTTACAAAATTACTAT
** *
28120923 TTTACCCTTGATTTACAAAATTACTA
1 TTTACCCTCAACTTACAAAATTACTA
28120949 AAATACCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.40
Consensus pattern (27 bp):
TTTACCCTCAACTTACAAAATTACTAT
Found at i:28120955 original size:27 final size:27
Alignment explanation
Indices: 28120925--28121177 Score: 161
Period size: 27 Copynumber: 9.3 Consensus size: 27
28120915 ATTACTATTT
*
28120925 TACCCTTGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* * **
28120952 TACCTTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* *
28120979 TACCCCT-AGTTTATAAAATTACCAAAA
1 TACCCTTGA-TTTACAAAATTACCAAAA
* *** *
28121006 TACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTTGATTTACAAAATTACCAAAA
** **
28121033 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* *
28121060 TACCCCTGATTTACAAAGTTA-CAGAAA
1 TACCCTTGATTTACAAAATTACCA-AAA
***
28121087 TACCCTTGACTTT-CTAAAAATTATGGAAA
1 TACCCTTGA-TTTAC--AAAATTACCAAAA
* * **
28121116 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* ** * *
28121143 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
*
28121170 CACCCTTG
1 TACCCTTG
28121178 TAGGATGAAA
Statistics
Matches: 177, Mismatches: 41, Indels: 16
0.76 0.18 0.07
Matches are distributed among these distances:
26 2 0.01
27 152 0.86
28 6 0.03
29 17 0.10
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACCAAAA
Found at i:28121012 original size:81 final size:79
Alignment explanation
Indices: 28120925--28121177 Score: 213
Period size: 81 Copynumber: 3.1 Consensus size: 79
28120915 ATTACTATTT
* *
28120925 TACCCTTGATTTACAAAATTACTAAAATACCTTTGGTTTGTAAAATTACCAAAATACCCCTAGTT
1 TACCCTTGATTT-CAAAATTACTGAAATACCATTGGTTTGTAAAATTACCAAAATACCCCT-GTT
28120990 TATAAAATTACCAAAA
64 TATAAAATTACCAAAA
* ** * * ***
28121006 TACCCTTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATT
1 TACCCTTGATTT-CAAAATTACTGAAATACCATTGGTTTGTAAAATTACCAAAATACCCCTG-TT
* *
28121071 TACAAAGTTA-CAGAAA
64 TATAAAATTACCA-AAA
** ** *
28121087 TACCCTTGACTTTCTAAAAATTA-TGGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTG
1 TACCCTTGA-TTTC--AAAATTACT-GAAATACCATTGGTTTGTAAAATTACCAAAATACCCCT-
* * *
28121151 GTTTGTAGATTTACCAAAA
61 GTTTATAAAATTACCAAAA
*
28121170 CACCCTTG
1 TACCCTTG
28121178 TAGGATGAAA
Statistics
Matches: 134, Mismatches: 30, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
80 3 0.02
81 72 0.54
82 3 0.02
83 53 0.40
84 3 0.02
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (79 bp):
TACCCTTGATTTCAAAATTACTGAAATACCATTGGTTTGTAAAATTACCAAAATACCCCTGTTTA
TAAAATTACCAAAA
Found at i:28121237 original size:27 final size:27
Alignment explanation
Indices: 28121195--28121273 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
28121185 AAATGACTAA
* * *
28121195 AATACCCCTATTAGGGTAAAGTGACTGT
1 AATACCCCT-GTAGGGTAAAATGACCGT
*
28121223 AA-AGCCCTTGTAGGGTAAAATGACCGT
1 AATA-CCCCTGTAGGGTAAAATGACCGT
*
28121250 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTAGGGTAAAATGAC
28121274 GAATATGCCC
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 36 0.84
28 7 0.16
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAATGACCGT
Found at i:28122547 original size:20 final size:20
Alignment explanation
Indices: 28122524--28122562 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
28122514 TAAACATGGT
28122524 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
28122544 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
28122563 TGTAATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:28122644 original size:23 final size:23
Alignment explanation
Indices: 28122614--28122658 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
28122604 AGGAAGTGAA
28122614 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
28122637 AAAGGGCTTATGCCCCAGTTAT
1 AAAGGGCTTATGCCCCAGTTAT
28122659 NNNNNNNNNN
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:28124226 original size:22 final size:22
Alignment explanation
Indices: 28124170--28124232 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
28124160 CCGTTTTAGG
*
28124170 TCTTCGGGGCTTATCGTTTCAAA
1 TCTTCGGGGCTTACCG-TTCAAA
* * **
28124193 TCTACGGAGCTTACCGTTCAGC
1 TCTTCGGGGCTTACCGTTCAAA
28124215 TCTTCGGGGCTTACCGTT
1 TCTTCGGGGCTTACCGTT
28124233 TATCAGCTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.14, C:0.27, G:0.24, T:0.35
Consensus pattern (22 bp):
TCTTCGGGGCTTACCGTTCAAA
Found at i:28136336 original size:45 final size:44
Alignment explanation
Indices: 28136286--28136373 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 44
28136276 CCAAAACATG
28136286 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTC-ATGAGTTCAGA
*
28136331 TGTCACATATATCATGAACTCAGACCACAACTCATGAGTTCAG
1 TGTCACATACATCATGAACTCAGACCACAACTCATGAGTTCAG
28136374 TCACATATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 10 0.24
45 32 0.76
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (44 bp):
TGTCACATACATCATGAACTCAGACCACAACTCATGAGTTCAGA
Found at i:28137549 original size:13 final size:13
Alignment explanation
Indices: 28137531--28137556 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28137521 GCCCAAACGT
28137531 CAAAATTTTCAAA
1 CAAAATTTTCAAA
28137544 CAAAATTTTCAAA
1 CAAAATTTTCAAA
28137557 AAATCATTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
CAAAATTTTCAAA
Found at i:28139079 original size:47 final size:47
Alignment explanation
Indices: 28138980--28139170 Score: 337
Period size: 47 Copynumber: 4.0 Consensus size: 47
28138970 ACAATCAAAT
* *
28138980 TATATACACTTTCACATTTATCACATCGGCCATTAAGCCTTATCACA
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
28139027 TATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
1 TATAT--ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
*
28139076 TATATACACTTTCACATTCATCACATCGGCCATTAGACCTTATCACA
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
28139123 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
28139170 T
1 T
28139171 CCGACTTTGT
Statistics
Matches: 138, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
47 93 0.67
49 45 0.33
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.32
Consensus pattern (47 bp):
TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
Found at i:28139153 original size:94 final size:95
Alignment explanation
Indices: 28138980--28139170 Score: 341
Period size: 96 Copynumber: 2.0 Consensus size: 95
28138970 ACAATCAAAT
*
28138980 TATATACACTTTCACATTTATCACATCGGCCATTAAGCCTTATCACATATATACACACTTTCACA
1 TATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATA-ACACTTTCACA
28139045 TTCATCACATCGGCCATTAGGCCTTATCACA
65 TTCATCACATCGGCCATTAGGCCTTATCACA
28139076 TATATACACTTTCACATTCATCACATCGGCCATT-AGACCTTATCACATATAT-ACACTTTCACA
1 TATATACACTTTCACATTCATCACATCGGCCATTAAG-CCTTATCACATATATAACACTTTCACA
28139139 TTCATCACATCGGCCATTAGGCCTTATCACA
65 TTCATCACATCGGCCATTAGGCCTTATCACA
28139170 T
1 T
28139171 CCGACTTTGT
Statistics
Matches: 93, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
94 43 0.46
95 2 0.02
96 48 0.52
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.32
Consensus pattern (95 bp):
TATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATAACACTTTCACAT
TCATCACATCGGCCATTAGGCCTTATCACA
Found at i:28140765 original size:41 final size:41
Alignment explanation
Indices: 28140679--28140765 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
28140669 GAAATTGGGT
* *
28140679 AAAAACAAAGTATCGAGACCTCGATCTCATAAAACTGAGTT
1 AAAAACAAAGTATCGAGACCTCGATCTCATAAAACTGAATC
28140720 AAAAACAAAGTATCGAGACCTCGATCTCATAAAA-TCGAATC
1 AAAAACAAAGTATCGAGACCTCGATCTCATAAAACT-GAATC
28140761 AAAAA
1 AAAAA
28140766 TATTTTTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 1 0.02
41 42 0.98
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.20
Consensus pattern (41 bp):
AAAAACAAAGTATCGAGACCTCGATCTCATAAAACTGAATC
Found at i:28140831 original size:28 final size:28
Alignment explanation
Indices: 28140797--28140852 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
28140787 GAAGTTAGTG
28140797 ATGTGGTATTAAAATTTTGTTAGGAAAT
1 ATGTGGTATTAAAATTTTGTTAGGAAAT
28140825 ATGTGGTATTAAAATTTTGTTAGGAAAT
1 ATGTGGTATTAAAATTTTGTTAGGAAAT
28140853 TTTAATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (28 bp):
ATGTGGTATTAAAATTTTGTTAGGAAAT
Found at i:28146403 original size:30 final size:30
Alignment explanation
Indices: 28146358--28146427 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
28146348 ACGATTACTA
*
28146358 GGCCGAAGCCTTTTCATAAATCATATCACTG
1 GGCCAAAG-CTTTTCATAAATCATATCACTG
*
28146389 GGCCAAAGCTTTTCATAAATCATTTCACTG
1 GGCCAAAGCTTTTCATAAATCATATCACTG
28146419 GGCCAAAGC
1 GGCCAAAGC
28146428 CTTTACTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
30 30 0.81
31 7 0.19
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (30 bp):
GGCCAAAGCTTTTCATAAATCATATCACTG
Found at i:28146505 original size:42 final size:42
Alignment explanation
Indices: 28146455--28146546 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
28146445 TGGCCCATAG
* * * ** *
28146455 GCCCATTTCAATATTATATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
*
28146497 GCTCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
28146539 GCCCATTT
1 GCCCATTT
28146547 GGGGAGACTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:28146735 original size:26 final size:26
Alignment explanation
Indices: 28146691--28146814 Score: 187
Period size: 26 Copynumber: 4.8 Consensus size: 26
28146681 CCTCTTTAAT
**
28146691 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
28146716 AACTGAGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
* *
28146742 AACTAGGGCATAAGCCCTTTTCAGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
28146768 AATTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
28146794 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
28146815 TATGCCCTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
25 9 0.10
26 79 0.90
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:28146833 original size:37 final size:37
Alignment explanation
Indices: 28146781--28146851 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
28146771 TGGGGCATAA
28146781 GCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTTAT
1 GCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTTAT
**
28146818 GCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTT
1 GCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
28146852 GCACTTCCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (37 bp):
GCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTTAT
Found at i:28166553 original size:23 final size:22
Alignment explanation
Indices: 28166527--28166570 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
28166517 GTGATGAGGT
28166527 TATCTT-ATAAATATGTATGAATC
1 TATCTTGA-AAATATGT-TGAATC
28166550 TATCTTGAAAATATGTTGAAT
1 TATCTTGAAAATATGTTGAAT
28166571 TGGATTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 14 0.70
24 1 0.05
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (22 bp):
TATCTTGAAAATATGTTGAATC
Found at i:28166775 original size:29 final size:29
Alignment explanation
Indices: 28166740--28166901 Score: 200
Period size: 29 Copynumber: 5.5 Consensus size: 29
28166730 CAAGCTATGT
* *
28166740 AATATGAAAAGGGATAGCTTAGGCTATCA
1 AATATGAAAAGGGATAGCTTCGGCTATCG
28166769 AATATGAAAAGGGATAGCTTCGAG-TATCG
1 AATATGAAAAGGGATAGCTTCG-GCTATCG
28166798 AATATGAAAAGGGGATAGCTTCGGCTATCG
1 AATATGAAAA-GGGATAGCTTCGGCTATCG
* * *
28166828 AATATGGAAAGGGGATAGCTTCGACTGTCG
1 AATAT-GAAAAGGGATAGCTTCGGCTATCG
* **
28166858 ATTATGAAAAGGGATAGCTTCAACTATCG
1 AATATGAAAAGGGATAGCTTCGGCTATCG
* *
28166887 ATTATGAAAATGGAT
1 AATATGAAAAGGGAT
28166902 GGTGATGACT
Statistics
Matches: 119, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
29 71 0.60
30 44 0.37
31 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (29 bp):
AATATGAAAAGGGATAGCTTCGGCTATCG
Found at i:28166832 original size:59 final size:58
Alignment explanation
Indices: 28166740--28166901 Score: 216
Period size: 59 Copynumber: 2.8 Consensus size: 58
28166730 CAAGCTATGT
* * *
28166740 AATATGAAAAGGGATAGCTTAGGCTATCAAATATGAAAAGGGATAGCTTCGAGTATCG
1 AATATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCGACTATCG
* *
28166798 AATATGAAAAGGGGATAGCTTCGGCTATCGAATATGGAAAGGGGATAGCTTCGACTGTCG
1 AATATGAAAA-GGGATAGCTTCGGCTATCGAATAT-GAAAAGGGATAGCTTCGACTATCG
* ** * *
28166858 ATTATGAAAAGGGATAGCTTCAACTATCGATTATGAAAATGGAT
1 AATATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGAT
28166902 GGTGATGACT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
58 18 0.20
59 43 0.47
60 30 0.33
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (58 bp):
AATATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCGACTATCG
Found at i:28167563 original size:18 final size:17
Alignment explanation
Indices: 28167534--28167587 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 17
28167524 CATGAAACAG
28167534 GGTCACAC-GCCCGTGT
1 GGTCACACAGCCCGTGT
28167550 GGTCACACATGCCCGTGT
1 GGTCACACA-GCCCGTGT
28167568 GGTCACACACGCCCGTGT
1 GGTCACACA-GCCCGTGT
28167586 GG
1 GG
28167588 CTTGGGACAC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
16 8 0.23
18 27 0.77
ACGTcount: A:0.15, C:0.35, G:0.31, T:0.19
Consensus pattern (17 bp):
GGTCACACAGCCCGTGT
Found at i:28168979 original size:48 final size:46
Alignment explanation
Indices: 28168912--28169094 Score: 162
Period size: 48 Copynumber: 4.0 Consensus size: 46
28168902 CACATAGTAG
* *
28168912 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCGTAGGTC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCGTA--TC
**
28168960 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACA-C
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCGTATC
* * * **
28169005 -AT--CGATTCCGATAG-CCTAG-CTATGGTCTTACATGATATTACGTATC
1 GATGCCAATGCC-AT-GTCCCAGAC-ATGGTCTTACATGGGA-T-CGTATC
* *
28169051 GATCCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCGTA
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCGTA
28169095 CATAACCCTA
Statistics
Matches: 107, Mismatches: 17, Indels: 24
0.72 0.11 0.16
Matches are distributed among these distances:
42 6 0.06
43 20 0.19
44 4 0.04
45 3 0.03
46 5 0.05
47 4 0.04
48 60 0.56
49 5 0.05
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (46 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCGTATC
Found at i:28172309 original size:16 final size:16
Alignment explanation
Indices: 28172279--28172320 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
28172269 TTATTTATTA
28172279 AATTAA-TTT-TAATT
1 AATTAATTTTCTAATT
28172293 AATTAATTTTCTAATT
1 AATTAATTTTCTAATT
*
28172309 AAATAATTTTCT
1 AATTAATTTTCT
28172321 CAACCCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 3 0.12
16 16 0.64
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTAATTTTCTAATT
Found at i:28178219 original size:12 final size:12
Alignment explanation
Indices: 28178202--28178243 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
28178192 GGACACACGA
*
28178202 CCGTGTCTTAGC
1 CCGTGTCTCAGC
28178214 CCGTGTCTCAGC
1 CCGTGTCTCAGC
*
28178226 CCATGTCCTCA-C
1 CCGTGT-CTCAGC
28178238 CCGTGT
1 CCGTGT
28178244 AACTCACCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.10, C:0.40, G:0.21, T:0.29
Consensus pattern (12 bp):
CCGTGTCTCAGC
Found at i:28187013 original size:76 final size:75
Alignment explanation
Indices: 28186887--28187033 Score: 285
Period size: 76 Copynumber: 1.9 Consensus size: 75
28186877 CTGGTACGCA
28186887 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACACATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACACATAGTAGCCTGCACT
28186952 TAGTACNGATG
66 TAGTAC-GATG
28186963 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACACATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACACATAGTAGCCTGCACT
28187028 TAGTAC
66 TAGTAC
28187034 TACACATGCG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (75 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACACATAGTAGCCTGCACT
TAGTACGATG
Found at i:28187018 original size:37 final size:37
Alignment explanation
Indices: 28186901--28187018 Score: 91
Period size: 37 Copynumber: 3.1 Consensus size: 37
28186891 AGCCTGCACT
28186901 TAGTACTACACACGTGATCGAAGTTATCGGGTACACA
1 TAGTACTACACACGTGATCGAAGTTATCGGGTACACA
* * * ** * *
28186938 TAGTAGCCTGCACTTA-GT-A-CNGATG-TAGTAGCCTGCACT
1 TAGTA--CTACAC--ACGTGATC-GAAGTTA-TCGGGTACACA
28186977 TAGTACTACACACGTGATCGAAGTTATCGGGTACACA
1 TAGTACTACACACGTGATCGAAGTTATCGGGTACACA
28187014 TAGTA
1 TAGTA
28187019 GCCTGCACTT
Statistics
Matches: 57, Mismatches: 14, Indels: 20
0.63 0.15 0.22
Matches are distributed among these distances:
35 1 0.02
36 2 0.04
37 25 0.44
38 6 0.11
39 20 0.35
40 2 0.04
41 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (37 bp):
TAGTACTACACACGTGATCGAAGTTATCGGGTACACA
Found at i:28187070 original size:31 final size:31
Alignment explanation
Indices: 28187032--28187093 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
28187022 TGCACTTAGT
*
28187032 ACTACACATGCGACCTCACAATAGATCATTC
1 ACTACACACGCGACCTCACAATAGATCATTC
*
28187063 ACTACACACGTGACCTCACAATAGATCATTC
1 ACTACACACGCGACCTCACAATAGATCATTC
28187094 GTATCGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (31 bp):
ACTACACACGCGACCTCACAATAGATCATTC
Found at i:28192824 original size:17 final size:19
Alignment explanation
Indices: 28192802--28192839 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
28192792 AAAATACCTC
28192802 TAAAACAAGA-TTA-ACAA
1 TAAAACAAGAGTTATACAA
28192819 TAAAACAAGAGTTATACAA
1 TAAAACAAGAGTTATACAA
28192838 TA
1 TA
28192840 TCCAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.21
Consensus pattern (19 bp):
TAAAACAAGAGTTATACAA
Found at i:28192918 original size:29 final size:31
Alignment explanation
Indices: 28192879--28192941 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
28192869 CATAATTGTG
* *
28192879 AAATAGTAAC-AAATAGTAAAAAAACA-AAA
1 AAATAGCAACAAAATAATAAAAAAACAGAAA
*
28192908 AAATAGCAACAAAATAATAAAAAAATAGAAA
1 AAATAGCAACAAAATAATAAAAAAACAGAAA
28192939 AAA
1 AAA
28192942 GTTCTAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 9 0.31
30 14 0.48
31 6 0.21
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.13
Consensus pattern (31 bp):
AAATAGCAACAAAATAATAAAAAAACAGAAA
Found at i:28195884 original size:30 final size:30
Alignment explanation
Indices: 28195850--28195911 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
28195840 ACTTATTTTA
*
28195850 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTCTAAAGGCAT
28195880 TTGTTAATTTTGTTATTATTCTAAAGGCAT
1 TTGTTAATTTTGTTATTATTCTAAAGGCAT
28195910 TT
1 TT
28195912 TCTTGTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTCTAAAGGCAT
Found at i:28201556 original size:13 final size:13
Alignment explanation
Indices: 28201538--28201562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28201528 CCACTACCTG
28201538 GCTACCAAGTGAC
1 GCTACCAAGTGAC
28201551 GCTACCAAGTGA
1 GCTACCAAGTGA
28201563 TGCTTAGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (13 bp):
GCTACCAAGTGAC
Found at i:28205851 original size:40 final size:39
Alignment explanation
Indices: 28205820--28206029 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
28205810 GGACTAAGAT
* *
28205820 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
28205860 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
28205900 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
28205940 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
28205980 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
28206019 CCGAAGGCATT
1 CCGAAGGCATT
28206030 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:28205983 original size:120 final size:120
Alignment explanation
Indices: 28205767--28206029 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
28205757 TTGAATGCTG
* *
28205767 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
28205831 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
28205887 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
28205950 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
28206006 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28206030 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:28206049 original size:79 final size:80
Alignment explanation
Indices: 28205768--28206064 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
28205758 TGAATGCTGT
* ** * * * **
28205768 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
28205831 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
28205848 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
28205912 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
28205928 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
28205992 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
28206007 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
28206065 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:28214459 original size:40 final size:40
Alignment explanation
Indices: 28214404--28214792 Score: 760
Period size: 40 Copynumber: 9.7 Consensus size: 40
28214394 TGAGCATTGG
28214404 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
28214444 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
28214484 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
28214524 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
28214564 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
28214604 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
28214644 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
28214684 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGAT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
28214724 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
28214764 GATATGTCCGGGCTAAGACCCGAAGGCAA
1 GATATATCCGGGCTAAGACCCGAAGGCAA
28214793 ATGTGTTTGC
Statistics
Matches: 346, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 346 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (40 bp):
GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
Found at i:28217374 original size:47 final size:47
Alignment explanation
Indices: 28217307--28217482 Score: 196
Period size: 46 Copynumber: 3.7 Consensus size: 47
28217297 GGTAAGGTGT
* *
28217307 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTC-AAGT
1 CGATGCCATGTCCTAGACAT-GTCTTACACTGGCTCATATCTCGAAGC
* * * ** *
28217354 CGATGCCATGTCCTAGACATGTCTTACCCTTGCTTACGTCTCGAGGC
1 CGATGCCATGTCCTAGACATGTCTTACACTGGCTCATATCTCGAAGC
* * * *
28217401 CGATG-CATATCCTAGACATGTCTTACACTAGCAC-TCATCTCGATGC
1 CGATGCCATGTCCTAGACATGTCTTACACTGGCTCAT-ATCTCGAAGC
28217447 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTC
1 CGATGCCATGTCCTAGACAT-GTCTTACACTGGCTC
28217483 TCATAATGTG
Statistics
Matches: 106, Mismatches: 19, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
46 54 0.51
47 39 0.37
48 13 0.12
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCTAGACATGTCTTACACTGGCTCATATCTCGAAGC
Found at i:28217415 original size:46 final size:47
Alignment explanation
Indices: 28217307--28217526 Score: 193
Period size: 46 Copynumber: 4.7 Consensus size: 47
28217297 GGTAAGGTGT
* * * * *
28217307 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTC-AAGT
1 CGATGCCATGTCCTAGACAT-GTCTTACACTAGCAC-TCATCTCGAGGC
* * * *
28217354 CGATGCCATGTCCTAGACATGTCTTACCCTTGC-TTACGTCTCGAGGC
1 CGATGCCATGTCCTAGACATGTCTTACACTAGCACT-CATCTCGAGGC
* *
28217401 CGATG-CATATCCTAGACATGTCTTACACTAGCACTCATCTCGATGC
1 CGATGCCATGTCCTAGACATGTCTTACACTAGCACTCATCTCGAGGC
* * * *
28217447 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAAT-GTGGC
1 CGATGCCATGTCCTAGACAT-GTCTTACACTAGCACTCAT-CTCGAGGC
*
28217495 CGATG-TATGTGCC-AGACATGTCTTACACTAGC
1 CGATGCCATGT-CCTAGACATGTCTTACACTAGC
28217527 TCACAATAAC
Statistics
Matches: 144, Mismatches: 21, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
44 1 0.01
46 65 0.45
47 50 0.35
48 27 0.19
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (47 bp):
CGATGCCATGTCCTAGACATGTCTTACACTAGCACTCATCTCGAGGC
Found at i:28217513 original size:94 final size:91
Alignment explanation
Indices: 28217307--28217526 Score: 230
Period size: 94 Copynumber: 2.3 Consensus size: 91
28217297 GGTAAGGTGT
* * *
28217307 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCTAGAC
1 CGATG-CATGT-CCAGACAT-GTCTTACACTAGCACATATCTCAAGCCGATGCCATGTCCTAGAC
* * * *
28217372 ATGTCTTACCCTTGCTTACGTCTCGAGGC
63 ATGTCTTACACTGGCTTACATATCGAGGC
* *
28217401 CGATGCATATCCTAGACATGTCTTACACTAGCAC-TCATCTCGATGCCGATGCCATGTCCTAGAC
1 CGATGCATGTCC-AGACATGTCTTACACTAGCACAT-ATCTC-AAGCCGATGCCATGTCCTAGAC
*
28217465 ATGGTCTTACACTGGCTCT-CATAAT-GTGGC
63 AT-GTCTTACACTGGCT-TACAT-ATCGAGGC
*
28217495 CGATGTATGTGCCAGACATGTCTTACACTAGC
1 CGATGCATGT-CCAGACATGTCTTACACTAGC
28217527 TCACAATAAC
Statistics
Matches: 107, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
91 1 0.01
92 20 0.19
93 32 0.30
94 50 0.47
95 4 0.04
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (91 bp):
CGATGCATGTCCAGACATGTCTTACACTAGCACATATCTCAAGCCGATGCCATGTCCTAGACATG
TCTTACACTGGCTTACATATCGAGGC
Found at i:28223241 original size:14 final size:15
Alignment explanation
Indices: 28223218--28223252 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
28223208 TTTGGTGTTG
28223218 TTTTTATTGCTATT-
1 TTTTTATTGCTATTA
*
28223232 TTTTTTTTGCTATTA
1 TTTTTATTGCTATTA
28223247 TTTTTA
1 TTTTTA
28223253 CTGTTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTTATTGCTATTA
Found at i:28223467 original size:9 final size:9
Alignment explanation
Indices: 28223438--28223474 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28223428 TAAGTTTTTA
28223438 AATTCGAAT
1 AATTCGAAT
*
28223447 AACTCGAAT
1 AATTCGAAT
28223456 AATTCGAAT
1 AATTCGAAT
*
28223465 AATTTGAAT
1 AATTCGAAT
28223474 A
1 A
28223475 TCAAACAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28224604 original size:69 final size:69
Alignment explanation
Indices: 28224509--28224683 Score: 314
Period size: 69 Copynumber: 2.5 Consensus size: 69
28224499 TAACTTAATT
28224509 AGTAAACATTTATCAAAACAACATAGTTTTACCTTTTAACTTAAAGGTTTTGACTTTTAACTTTA
1 AGTAAACATTTATCAAAACAACATAGTTTTACCTTTTAACTTAAAGGTTTTGACTTTTAACTTTA
28224574 GAAA
66 GAAA
28224578 AGTAAACATTTATCAAAACAACATAGTTTTACCTTTTAACTTAAAGGTTTTGACTTTTAACTTTA
1 AGTAAACATTTATCAAAACAACATAGTTTTACCTTTTAACTTAAAGGTTTTGACTTTTAACTTTA
28224643 GAAA
66 GAAA
** * *
28224647 AGTAAACATTTATCAAAATGACGTAGTTTTGCCTTTT
1 AGTAAACATTTATCAAAACAACATAGTTTTACCTTTT
28224684 CTTATTTGGA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 102 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (69 bp):
AGTAAACATTTATCAAAACAACATAGTTTTACCTTTTAACTTAAAGGTTTTGACTTTTAACTTTA
GAAA
Found at i:28227851 original size:31 final size:31
Alignment explanation
Indices: 28227808--28227872 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
28227798 ATTGAAAGTT
28227808 ACATTATCGGTGACAACTTGATTAGTAAATG
1 ACATTATCGGTGACAACTTGATTAGTAAATG
*
28227839 ACATTATTGGTGACAACTTGATTAGTAAATG
1 ACATTATCGGTGACAACTTGATTAGTAAATG
28227870 ACA
1 ACA
28227873 AATGTGTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (31 bp):
ACATTATCGGTGACAACTTGATTAGTAAATG
Found at i:28227873 original size:19 final size:19
Alignment explanation
Indices: 28227818--28227873 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
28227808 ACATTATCGG
28227818 TGACAACTTGATTAGTAAA
1 TGACAACTTGATTAGTAAA
*
28227837 TGAC-A-TT-ATT-G---G
1 TGACAACTTGATTAGTAAA
28227849 TGACAACTTGATTAGTAAA
1 TGACAACTTGATTAGTAAA
28227868 TGACAA
1 TGACAA
28227874 ATGTGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
12 4 0.14
13 1 0.04
14 2 0.07
15 4 0.14
16 4 0.14
17 2 0.07
18 1 0.04
19 10 0.36
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (19 bp):
TGACAACTTGATTAGTAAA
Found at i:28228120 original size:14 final size:14
Alignment explanation
Indices: 28228101--28228131 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28228091 TACTACAGTT
28228101 TTACTATTATATTG
1 TTACTATTATATTG
*
28228115 TTACTATTTTATTG
1 TTACTATTATATTG
28228129 TTA
1 TTA
28228132 TTGTTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (14 bp):
TTACTATTATATTG
Found at i:28230309 original size:88 final size:88
Alignment explanation
Indices: 28230200--28230379 Score: 342
Period size: 88 Copynumber: 2.0 Consensus size: 88
28230190 TTTACTTAAG
*
28230200 AATTATTAATGGTGCAGTTATAAGGAATTTGTTTATAAATCTATTAAGGTAGTGTTTTGAAAGCC
1 AATTATTAATGGTGCAGTTATAAGGAATTTGTTTATAAATCCATTAAGGTAGTGTTTTGAAAGCC
28230265 ACCTAATAATTCGATTTGGGTGT
66 ACCTAATAATTCGATTTGGGTGT
*
28230288 AATTATTAATGGTGCAGTTATAAGGAATTTGTTTATAAATCCATTAAGTTAGTGTTTTGAAAGCC
1 AATTATTAATGGTGCAGTTATAAGGAATTTGTTTATAAATCCATTAAGGTAGTGTTTTGAAAGCC
28230353 ACCTAATAATTCGATTTGGGTGT
66 ACCTAATAATTCGATTTGGGTGT
28230376 AATT
1 AATT
28230380 GCTTATAATT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (88 bp):
AATTATTAATGGTGCAGTTATAAGGAATTTGTTTATAAATCCATTAAGGTAGTGTTTTGAAAGCC
ACCTAATAATTCGATTTGGGTGT
Found at i:28231642 original size:23 final size:20
Alignment explanation
Indices: 28231581--28231648 Score: 75
Period size: 19 Copynumber: 3.3 Consensus size: 20
28231571 TAGATGAATG
* * *
28231581 TTTCAAGCAAGGATAGAC-G
1 TTTCAAGCATGGATGGACAA
28231600 TTTCAAGCATGGATGGACAA
1 TTTCAAGCATGGATGGACAA
28231620 TTTCAAGCATGGGACATGGACAA
1 TTTCAAGCAT-GG--ATGGACAA
28231643 TTTCAA
1 TTTCAA
28231649 TGCACAAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 16 0.38
20 10 0.24
21 2 0.05
23 14 0.33
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (20 bp):
TTTCAAGCATGGATGGACAA
Found at i:28231751 original size:50 final size:48
Alignment explanation
Indices: 28231632--28231764 Score: 140
Period size: 50 Copynumber: 2.7 Consensus size: 48
28231622 TCAAGCATGG
* * *
28231632 GACATGGACAATTTCAATGCACAAAGACGTTTTGTAATTCAAATACAT
1 GACATGGACGATTTCAATGCATAAAGACGTTTTCTAATTCAAATACAT
* * * * *
28231680 GATCATGGATGGTTTTCAATGCATAGAGACGTTTATCTCATTTAAATACAT
1 GA-CATGGA-CGATTTCAATGCATAAAGACGTTT-TCTAATTCAAATACAT
* *
28231731 GACATGGACGATTTCAAATGCATGAAGACATTTT
1 GACATGGACGATTTC-AATGCATAAAGACGTTTT
28231765 TCCTCAACCA
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
48 2 0.03
49 12 0.18
50 39 0.57
51 15 0.22
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (48 bp):
GACATGGACGATTTCAATGCATAAAGACGTTTTCTAATTCAAATACAT
Found at i:28231778 original size:51 final size:49
Alignment explanation
Indices: 28231723--28231830 Score: 114
Period size: 51 Copynumber: 2.2 Consensus size: 49
28231713 TATCTCATTT
* *
28231723 AAATACATGA-CATGGAC-GATTTCAAATG-CATGAAGACATTTTTCCTCAACC
1 AAATACATGAGCATAGACAG-TTTC-AATGAAATG-AGACA-TTTTCCT-AACC
* *
28231774 AAATACATTAGCATAGACAGTTTCAATGAAATGAGACATTTTCCTATCC
1 AAATACATGAGCATAGACAGTTTCAATGAAATGAGACATTTTCCTAACC
28231823 AAATACAT
1 AAATACAT
28231831 TTGCATGGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
49 11 0.22
50 7 0.14
51 18 0.36
52 13 0.26
53 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (49 bp):
AAATACATGAGCATAGACAGTTTCAATGAAATGAGACATTTTCCTAACC
Found at i:28242346 original size:26 final size:26
Alignment explanation
Indices: 28242310--28242363 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
28242300 GTAGGGGCTT
* *
28242310 TGGACGCGTGATTGTTTTTCGGTTTA
1 TGGACACGTGATTGTTTTTCAGTTTA
28242336 TGGACACGTGATTGTTTTTCAGTTTA
1 TGGACACGTGATTGTTTTTCAGTTTA
28242362 TG
1 TG
28242364 TTTATGCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.11, G:0.28, T:0.46
Consensus pattern (26 bp):
TGGACACGTGATTGTTTTTCAGTTTA
Found at i:28243171 original size:21 final size:22
Alignment explanation
Indices: 28243147--28243197 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
28243137 TATTAACAAA
28243147 TTAAATATTT-TTTT-TATAATT
1 TTAAATATTTATTTTCTA-AATT
28243168 TTAACA-ATTTATTTTCTAAATT
1 TTAA-ATATTTATTTTCTAAATT
28243190 TTAAATAT
1 TTAAATAT
28243198 AAATTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 9 0.35
22 15 0.58
23 2 0.08
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAAATATTTATTTTCTAAATT
Found at i:28245402 original size:18 final size:18
Alignment explanation
Indices: 28245379--28245435 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
28245369 TACGACCGTT
28245379 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
28245397 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
28245415 TACGGTACTGTTCACGTA
1 TACGGCACTATTCACGTA
28245433 TAC
1 TAC
28245436 AGTAGTTGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:28258154 original size:41 final size:41
Alignment explanation
Indices: 28258072--28258215 Score: 236
Period size: 41 Copynumber: 3.5 Consensus size: 41
28258062 AATAGAGGTG
* * *
28258072 TTTTGTTAAAACGCCGCTAAAA-CTAGAGCATTAGCGACGC
1 TTTTGGTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGC
28258112 TTTTGGTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGC
* *
28258153 TTTTGGTAAAACGCCTCTAAAAGGCAGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGC
28258194 TTTTGGTAAAACGCCGCTAAAA
1 TTTTGGTAAAACGCCGCTAAAA
28258216 ATCATATAAC
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 21 0.22
41 76 0.78
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (41 bp):
TTTTGGTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGC
Found at i:28258312 original size:54 final size:53
Alignment explanation
Indices: 28258231--28258347 Score: 137
Period size: 54 Copynumber: 2.2 Consensus size: 53
28258221 ATAACCCCTA
* ** * *
28258231 AAACCTTAAACCCCAAAAAATCATAAACACTAATCTAT-ACTCCTTAAAACACT
1 AAACCCTAAACCTTAAAAAATCATAAACACTAAACTATAAC-CCCTAAAACACT
* * *
28258284 AAACTCCTAAACCTTAAAAAATCTTAAACCCTAAACTATAACCCCTAAAATACT
1 AAAC-CCTAAACCTTAAAAAATCATAAACACTAAACTATAACCCCTAAAACACT
28258338 AAACCCTAAA
1 AAACCCTAAA
28258348 AAACATCACA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 10 0.19
54 42 0.78
55 2 0.04
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (53 bp):
AAACCCTAAACCTTAAAAAATCATAAACACTAAACTATAACCCCTAAAACACT
Found at i:28258331 original size:14 final size:15
Alignment explanation
Indices: 28258308--28258348 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
28258298 TAAAAAATCT
*
28258308 TAAACCCTAAACTA-
1 TAAACCCTAAAATAC
*
28258322 TAACCCCTAAAATAC
1 TAAACCCTAAAATAC
28258337 TAAACCCTAAAA
1 TAAACCCTAAAA
28258349 AACATCACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACCCTAAAATAC
Found at i:28258549 original size:14 final size:15
Alignment explanation
Indices: 28258517--28258552 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
28258507 TATTTTAAGT
*
28258517 TTTATGGATTATAGG
1 TTTAGGGATTATAGG
28258532 TTTAGGGATTAT-GG
1 TTTAGGGATTATAGG
28258546 TTTAGGG
1 TTTAGGG
28258553 GTTAGGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (15 bp):
TTTAGGGATTATAGG
Found at i:28258822 original size:22 final size:22
Alignment explanation
Indices: 28258769--28258819 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
28258759 ATGATTAAGG
28258769 GTTTAAGGTTTATGAGTTACTA
1 GTTTAAGGTTTATGAGTTACTA
*
28258791 TTTTAAGGTTTATGTA-TTA-TA
1 GTTTAAGGTTTATG-AGTTACTA
28258812 GTTTAAGG
1 GTTTAAGG
28258820 GTTAGGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 9 0.35
22 16 0.62
23 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (22 bp):
GTTTAAGGTTTATGAGTTACTA
Found at i:28259217 original size:13 final size:12
Alignment explanation
Indices: 28259197--28259237 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 12
28259187 CATTGATAAT
28259197 AAAT-AAAAATA
1 AAATAAAAAATA
28259208 AAATACAAAAATA
1 AAATA-AAAAATA
*
28259221 AAATAAAATATA
1 AAATAAAAAATA
28259233 AAATA
1 AAATA
28259238 GAGATTAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 4 0.15
12 11 0.41
13 12 0.44
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:28259225 original size:18 final size:19
Alignment explanation
Indices: 28259197--28259235 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28259187 CATTGATAAT
28259197 AAATAAAAATAAAATACAA
1 AAATAAAAATAAAATACAA
*
28259216 AAAT-AAAATAAAATATAA
1 AAATAAAAATAAAATACAA
28259234 AA
1 AA
28259236 TAGAGATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (19 bp):
AAATAAAAATAAAATACAA
Found at i:28263122 original size:44 final size:42
Alignment explanation
Indices: 28263042--28263185 Score: 180
Period size: 43 Copynumber: 3.3 Consensus size: 42
28263032 TTTCATGACT
* *
28263042 TTTAGCGGCGTTTTTGAGAAAAGTGCCGCTAAAGGTCGTGATC
1 TTTAGCGGCGTTTTGGA-AAAAGCGCCGCTAAAGGTCGTGATC
28263085 TTTAGCGGCGTTTATAGGAAAAAGCGCCGCTAAAGGTCGTGATC
1 TTTAGCGGCGTTT-T-GGAAAAAGCGCCGCTAAAGGTCGTGATC
* * * * *
28263129 TTTAGCAGCGTTTGTGGAAAAAACGTCGCTAAATGTCATGATC
1 TTTAGCGGCGTTT-TGGAAAAAGCGCCGCTAAAGGTCGTGATC
*
28263172 TTTAGCGGTGTTTT
1 TTTAGCGGCGTTTT
28263186 TTAAATAAAC
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
42 1 0.01
43 48 0.54
44 38 0.43
45 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTTGGAAAAAGCGCCGCTAAAGGTCGTGATC
Found at i:28264127 original size:23 final size:23
Alignment explanation
Indices: 28264100--28264151 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
28264090 ATGGCTATAT
28264100 ATATA-ACCAAAACAACATAAGAC
1 ATATAGACC-AAACAACATAAGAC
*
28264123 ATATAGGCCAAACAACATAAGAC
1 ATATAGACCAAACAACATAAGAC
28264146 ATATAG
1 ATATAG
28264152 GCCACATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.56, C:0.19, G:0.10, T:0.15
Consensus pattern (23 bp):
ATATAGACCAAACAACATAAGAC
Found at i:28264152 original size:23 final size:23
Alignment explanation
Indices: 28264109--28264155 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28264099 TATATAACCA
28264109 AAACAACATAAGACATATAGGCC
1 AAACAACATAAGACATATAGGCC
28264132 AAACAACATAAGACATATAGGCC
1 AAACAACATAAGACATATAGGCC
28264155 A
1 A
28264156 CATTAGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (23 bp):
AAACAACATAAGACATATAGGCC
Found at i:28271780 original size:19 final size:19
Alignment explanation
Indices: 28271753--28271793 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
28271743 ACAAGAAAAG
*
28271753 TTCATCAACTGAAGTGTGT
1 TTCACCAACTGAAGTGTGT
28271772 TTCACCAACTGAAGTGTGT
1 TTCACCAACTGAAGTGTGT
28271791 TTC
1 TTC
28271794 TCATAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (19 bp):
TTCACCAACTGAAGTGTGT
Found at i:28272232 original size:54 final size:55
Alignment explanation
Indices: 28272142--28272287 Score: 149
Period size: 54 Copynumber: 2.7 Consensus size: 55
28272132 TTTTTAGTTT
* * *
28272142 AATTTAATAAATTAAATA-CAAATTAGAATCTAAATATTAATTTA-ATAAAAATAA
1 AATTTAATAAATTTAATATCTAAGTAGAATCTAAATATTAA-TTAGATAAAAATAA
* * *
28272196 AATTTAATAAATTTAATATCTAAGTATAA-CTGAATATTAATTAGGTAAAAATAA
1 AATTTAATAAATTTAATATCTAAGTAGAATCTAAATATTAATTAGATAAAAATAA
* * * *
28272250 AATTAAAT-AATTATAATATCTTA-TACAAACTAAATATT
1 AATTTAATAAATT-TAATATCTAAGTAGAATCTAAATATT
28272288 TAACTTATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
53 11 0.14
54 60 0.77
55 7 0.09
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (55 bp):
AATTTAATAAATTTAATATCTAAGTAGAATCTAAATATTAATTAGATAAAAATAA
Found at i:28276087 original size:25 final size:24
Alignment explanation
Indices: 28276050--28276101 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
28276040 AAATTCAAGC
28276050 GAGCCATATCAGGAAGCTCAAAAA
1 GAGCCATATCAGGAAGCTCAAAAA
* *
28276074 GAGCCTATATCAGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCAAAAA
28276099 GAG
1 GAG
28276102 TTGTGTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.15
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCAAAAA
Found at i:28278835 original size:53 final size:53
Alignment explanation
Indices: 28278776--28278907 Score: 165
Period size: 53 Copynumber: 2.5 Consensus size: 53
28278766 AGATCGTAAT
* * *
28278776 TGGTGGGTTATGACATCATATGGGAAGAAGATCATATCATGTAAAATTATAAC
1 TGGTGGGTTATGACATCATATGGAAAGAAGACCATATCATGTAAAACTATAAC
* ** ** * * *
28278829 TGGTGGGGTATGGTATCATATAAAAAGAAGACCATATCGTGTAAGACTGTAAC
1 TGGTGGGTTATGACATCATATGGAAAGAAGACCATATCATGTAAAACTATAAC
28278882 TGGTGGGTTATGACATCATATGGAAA
1 TGGTGGGTTATGACATCATATGGAAA
28278908 TATTTAAGGA
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
53 63 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (53 bp):
TGGTGGGTTATGACATCATATGGAAAGAAGACCATATCATGTAAAACTATAAC
Found at i:28279134 original size:28 final size:28
Alignment explanation
Indices: 28279024--28279289 Score: 210
Period size: 28 Copynumber: 9.5 Consensus size: 28
28279014 CCAAGAAAAG
* * *
28279024 GGAAGCCTTTGTGGTAATATTTGTTAAA
1 GGAAGCCTTTGTGGTGATCTCTGTTAAA
* *
28279052 GGAATCTTTTGTGGTGATCTCTGTTAAA
1 GGAAGCCTTTGTGGTGATCTCTGTTAAA
* * * * * ** *
28279080 GGAATCTTTTGTAGCGACCTCCATTAAT
1 GGAAGCCTTTGTGGTGATCTCTGTTAAA
28279108 GGAAGCCTTTGTGGTGATCTCTGTTAAA
1 GGAAGCCTTTGTGGTGATCTCTGTTAAA
* * *
28279136 GAAAGCCTTTGTGATGATCGCTGTTAAA
1 GGAAGCCTTTGTGGTGATCTCTGTTAAA
* * * * *
28279164 AGAAGCCTTTGTAGCGAGCTTTGTTAAA
1 GGAAGCCTTTGTGGTGATCTCTGTTAAA
** *
28279192 GGATTCCTTT-TCGGTGATCTCTATTAAA
1 GGAAGCCTTTGT-GGTGATCTCTGTTAAA
* * * *
28279220 GGAAGCATTCGTGGCGTTCTCTGTTAAA
1 GGAAGCCTTTGTGGTGATCTCTGTTAAA
* * * * *
28279248 GGAAGCCTTTGTTGCGATATTTGTAAAA
1 GGAAGCCTTTGTGGTGATCTCTGTTAAA
*
28279276 TGAAGCCTTTGTGG
1 GGAAGCCTTTGTGG
28279290 CTATCTTTGA
Statistics
Matches: 182, Mismatches: 54, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
27 1 0.01
28 180 0.99
29 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.36
Consensus pattern (28 bp):
GGAAGCCTTTGTGGTGATCTCTGTTAAA
Found at i:28279201 original size:84 final size:84
Alignment explanation
Indices: 28279024--28279264 Score: 250
Period size: 84 Copynumber: 2.9 Consensus size: 84
28279014 CCAAGAAAAG
* * * * * * *
28279024 GGAAGCCTTTGTGGTAATATTTGTTAAAGGAATCTTTTGTGGTGATCTCTGTTAAAGGAATCTTT
1 GGAAGCCTTTGTGGTGATCTCTGTTAAAGGAAGCATTTGTGGTGATCTCTGTTAAAGGAAGCCTT
*
28279089 TGTAGCGACCTCCATTAAT
66 TGTAGCGACCTCCATTAAA
* * * * *
28279108 GGAAGCCTTTGTGGTGATCTCTGTTAAAGAAAGCCTTTGTGATGATCGCTGTTAAAAGAAGCCTT
1 GGAAGCCTTTGTGGTGATCTCTGTTAAAGGAAGCATTTGTGGTGATCTCTGTTAAAGGAAGCCTT
* ***
28279173 TGTAGCGAGCTTTGTTAAA
66 TGTAGCGACCTCCATTAAA
** * * * *
28279192 GGATTCCTTT-TCGGTGATCTCTATTAAAGGAAGCATTCGTGGCGTTCTCTGTTAAAGGAAGCCT
1 GGAAGCCTTTGT-GGTGATCTCTGTTAAAGGAAGCATTTGTGGTGATCTCTGTTAAAGGAAGCCT
*
28279256 TTGTTGCGA
65 TTGTAGCGA
28279265 TATTTGTAAA
Statistics
Matches: 128, Mismatches: 28, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
83 1 0.01
84 127 0.99
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (84 bp):
GGAAGCCTTTGTGGTGATCTCTGTTAAAGGAAGCATTTGTGGTGATCTCTGTTAAAGGAAGCCTT
TGTAGCGACCTCCATTAAA
Found at i:28281162 original size:40 final size:40
Alignment explanation
Indices: 28281116--28281215 Score: 200
Period size: 40 Copynumber: 2.5 Consensus size: 40
28281106 AATCACAGGC
28281116 CTACTCACACAAGCTGACAGTCAGGACATAACTACTCGGG
1 CTACTCACACAAGCTGACAGTCAGGACATAACTACTCGGG
28281156 CTACTCACACAAGCTGACAGTCAGGACATAACTACTCGGG
1 CTACTCACACAAGCTGACAGTCAGGACATAACTACTCGGG
28281196 CTACTCACACAAGCTGACAG
1 CTACTCACACAAGCTGACAG
28281216 GTACCCACAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (40 bp):
CTACTCACACAAGCTGACAGTCAGGACATAACTACTCGGG
Done.