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 134 of 310
Found at i:43416346 original size:6 final size:6
Alignment explanation
Indices: 43416284--43416347 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
43416274 TAGATATAAT
* * * **
43416284 TTTAGA TTCAGA TTCAGA TTCAGA TCCAGA TTTAGA TTTAGA TTTAGA
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA
**
43416332 TCCAGA TTTAGA TTTA
1 TTTAGA TTTAGA TTTA
43416348 CATAAATCCT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (6 bp):
TTTAGA
Found at i:43416346 original size:24 final size:24
Alignment explanation
Indices: 43416287--43416347 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
43416277 ATATAATTTT
* *
43416287 AGATTCAGATTCAGATTCAGATCC
1 AGATTTAGATTTAGATTCAGATCC
*
43416311 AGATTTAGATTTAGATTTAGATCC
1 AGATTTAGATTTAGATTCAGATCC
43416335 AGATTTAGATTTA
1 AGATTTAGATTTA
43416348 CATAAATCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (24 bp):
AGATTTAGATTTAGATTCAGATCC
Found at i:43416347 original size:18 final size:18
Alignment explanation
Indices: 43416284--43416345 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
43416274 TAGATATAAT
43416284 TTTAGATTCAGATTCAGA
1 TTTAGATTCAGATTCAGA
* * *
43416302 TTCAGATCCAGATTTAGA
1 TTTAGATTCAGATTCAGA
* *
43416320 TTTAGATTTAGATCCAGA
1 TTTAGATTCAGATTCAGA
43416338 TTTAGATT
1 TTTAGATT
43416346 TACATAAATC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (18 bp):
TTTAGATTCAGATTCAGA
Found at i:43418525 original size:19 final size:19
Alignment explanation
Indices: 43418468--43418526 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
43418458 TCATAGATGC
43418468 GTAACAGAGGCACCAAAGT
1 GTAACAGAGGCACCAAAGT
* * * *
43418487 GCAAATAGAGACACCGAAGT
1 G-TAACAGAGGCACCAAAGT
*
43418507 GTAACAGAGGCACTAAAGT
1 GTAACAGAGGCACCAAAGT
43418526 G
1 G
43418527 AAATCTCGTA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.42, C:0.19, G:0.27, T:0.12
Consensus pattern (19 bp):
GTAACAGAGGCACCAAAGT
Found at i:43419519 original size:14 final size:14
Alignment explanation
Indices: 43419502--43419531 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43419492 TTACTTGTTT
43419502 TTATGTTTTAATTA
1 TTATGTTTTAATTA
*
43419516 TTATTTTTTAATTA
1 TTATGTTTTAATTA
43419530 TT
1 TT
43419532 TTACTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TTATGTTTTAATTA
Found at i:43421833 original size:40 final size:40
Alignment explanation
Indices: 43421717--43421838 Score: 158
Period size: 40 Copynumber: 3.0 Consensus size: 40
43421707 GATGATAACG
**
43421717 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGGAAGTGACTATA-TCC
*
43421757 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTG-GAAGTGACTATATCC
* * *
43421797 GGGCTAAGTCCCGAAGGCATTTGAGGGAGTGGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGGAAGTGACTATATCC
43421837 GG
1 GG
43421839 TTAAAGCCGA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
39 3 0.04
40 66 0.92
41 3 0.04
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGGAAGTGACTATATCC
Found at i:43437529 original size:40 final size:40
Alignment explanation
Indices: 43437474--43437590 Score: 173
Period size: 40 Copynumber: 2.9 Consensus size: 40
43437464 NNNNNNNNNN
*
43437474 ACTAATTCCGGGCTAAGTCCCGAAGGCATTTTTGCGAATT
1 ACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATT
* * *
43437514 ACTAATTTCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTT
1 ACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATT
*
43437554 ACT-ATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGA
1 ACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA
43437591 GTGGCTATAT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 2 0.03
40 67 0.97
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (40 bp):
ACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATT
Found at i:43437599 original size:40 final size:40
Alignment explanation
Indices: 43437480--43437604 Score: 171
Period size: 40 Copynumber: 3.1 Consensus size: 40
43437470 NNNNACTAAT
* *
43437480 TCCGGGCTAAGTCCCGAAGGCATTTTTGCGAATTACTA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* *
43437519 TTTCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* **
43437560 TCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
43437600 TCCGG
1 TCCGG
43437605 TTAAAGCCGA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
40 74 0.99
41 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:43439020 original size:18 final size:18
Alignment explanation
Indices: 43438997--43439031 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43438987 TATTATACAC
*
43438997 ATATACATATACATATAG
1 ATATACAAATACATATAG
*
43439015 ATATACAAATATATATA
1 ATATACAAATACATATA
43439032 TAACTATGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (18 bp):
ATATACAAATACATATAG
Found at i:43442643 original size:14 final size:14
Alignment explanation
Indices: 43442624--43442651 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43442614 TAACATGATG
43442624 TTTAACATTTTCAA
1 TTTAACATTTTCAA
43442638 TTTAACATTTTCAA
1 TTTAACATTTTCAA
43442652 ACAATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAACATTTTCAA
Found at i:43444175 original size:27 final size:27
Alignment explanation
Indices: 43444156--43444314 Score: 219
Period size: 27 Copynumber: 5.8 Consensus size: 27
43444146 ATTACCAAAG
43444156 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
43444183 TACCCTCGATTTATATAGAATTACCGTTT
1 TACCCTCGA-TT-TACAGAATTACCATTT
* *
43444212 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
43444239 TACCCTCAATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
43444266 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
43444293 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
43444315 TAAAATACCC
Statistics
Matches: 120, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
27 94 0.78
28 4 0.03
29 22 0.18
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:43444323 original size:27 final size:27
Alignment explanation
Indices: 43444111--43444460 Score: 161
Period size: 27 Copynumber: 12.9 Consensus size: 27
43444101 AATACTTTAG
* * ** *
43444111 TTTACCAAATTACTAAAATGTCCTCAA
1 TTTACAAAATTACCAAAATACCCTCGA
** *
43444138 TTTGTAAAATTACCAAAGTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* ***
43444165 TTTACAGAATTACCATTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* **** *
43444192 TTTATATAGAATTACCGTTTTACCCTTGA
1 TTTACA-A-AATTACCAAAATACCCTCGA
* * *** *
43444221 TTTATAGAATTACCATTTTACCCTCAA
1 TTTACAAAATTACCAAAATACCCTCGA
* * ****
43444248 TTTATAGAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* ****
43444275 TTTACAGAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* * *
43444302 TTTACAAAATTACTAAAATACCCTTGG
1 TTTACAAAATTACCAAAATACCCTCGA
* *
43444329 TTTACAAAATTACCAAAATATCCCTAGC
1 TTTACAAAATTACCAAAATA-CCCTCGA
*
43444357 TTGT--AAAATTACCAAAATACCACT-GG
1 TT-TACAAAATTACCAAAATACC-CTCGA
*** * *
43444383 TTTGTGAAATTACCGAAATACCCTCAA
1 TTTACAAAATTACCAAAATACCCTCGA
**
43444410 TTTGTAAAATTACCAAAATACCC-CTGA
1 TTTACAAAATTACCAAAATACCCTC-GA
*
43444437 TTTAGAAAATTA-CAGAAATACCCT
1 TTTACAAAATTACCA-AAATACCCT
43444461 TGACTTTCTA
Statistics
Matches: 266, Mismatches: 46, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.00
26 10 0.04
27 223 0.84
28 7 0.03
29 25 0.09
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTCGA
Found at i:43444324 original size:54 final size:54
Alignment explanation
Indices: 43444132--43444343 Score: 226
Period size: 54 Copynumber: 3.9 Consensus size: 54
43444122 ACTAAAATGT
* * *
43444132 CCTCAATTTGTAAAATTACCAAAGTACCCTCGATTTACAGAATTACCATTTTAC
1 CCTCGATTTATAAAATTACCAAATTACCCTCGATTTACAGAATTACCATTTTAC
*** * *
43444186 CCTCGATTTATATAGAATTACCGTTTTACCCTTGATTTATAGAATTACCATTTTAC
1 CCTCGATTTATA-A-AATTACCAAATTACCCTCGATTTACAGAATTACCATTTTAC
* * *** *
43444242 CCTCAATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTAC
1 CCTCGATTTATAAAATTACCAAATTACCCTCGATTTACAGAATTACCATTTTAC
* * * * * *
43444296 CCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCA
1 CCTCGATTTATAAAATTACCAAATTACCCTCGATTTACAGAATTACCA
43444344 AAATATCCCT
Statistics
Matches: 131, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
54 84 0.64
55 1 0.01
56 46 0.35
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.37
Consensus pattern (54 bp):
CCTCGATTTATAAAATTACCAAATTACCCTCGATTTACAGAATTACCATTTTAC
Found at i:43444365 original size:54 final size:53
Alignment explanation
Indices: 43444307--43444545 Score: 187
Period size: 54 Copynumber: 4.4 Consensus size: 53
43444297 CTCGATTTAC
*
43444307 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATATCCCTAGCTTGT
1 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATA-CCCTAGCTTGT
*** * **
43444361 AAAATTACCAAAATACCAC-TGGTTTGTGAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACC-CTTGGTTTACAAAATTACCAAAATACCCT-AGCTTGT
* * * * *
43444415 AAAATTACCAAAATACCCCTGATTTAGAAAATTA-CAGAAATACCCTTGACTTTCT
1 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCA-AAATACCCTAG-C-TTGT
* * ** * *
43444470 AAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTTGT
1 -AAAATTACCA-AAATACCCTTGGTTTACAAAATTACCAAAATACCC-TAGCTTGT
* * *
43444525 AGATTTACCAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
43444546 TAGGATGAAA
Statistics
Matches: 143, Mismatches: 31, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
53 6 0.04
54 91 0.64
55 9 0.06
56 35 0.24
57 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (53 bp):
AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTAGCTTGT
Found at i:43444510 original size:27 final size:27
Alignment explanation
Indices: 43444293--43444545 Score: 149
Period size: 27 Copynumber: 9.3 Consensus size: 27
43444283 ATTACCGTTT
* * *
43444293 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
43444320 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* *
43444347 TATCCCTAGCTTGT--AAAATTACCAAAA
1 TA-CCCTTGGTT-TACAAAATTACCAAAA
*** *
43444374 TACCAC-TGGTTTGTGAAATTACCGAAA
1 TACC-CTTGGTTTACAAAATTACCAAAA
*** **
43444401 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* * *
43444428 TACCCCTGATTTAGAAAATTA-CAGAAA
1 TACCCTTGGTTTACAAAATTACCA-AAA
* *
43444455 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTG-GTTTAC--AAAATTACCA-AAA
* **
43444484 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
** * *
43444511 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
*
43444538 CACCCTTG
1 TACCCTTG
43444546 TAGGATGAAA
Statistics
Matches: 180, Mismatches: 34, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
25 1 0.01
26 8 0.04
27 136 0.76
28 14 0.08
29 21 0.12
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTACCAAAA
Found at i:43444525 original size:110 final size:108
Alignment explanation
Indices: 43444275--43444516 Score: 247
Period size: 108 Copynumber: 2.2 Consensus size: 108
43444265 TTACCCTCGA
* *** * ** * * *
43444275 TTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATT
1 TTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATT
*
43444340 ACCAAAATATCCCTAGCTTGTAAAATTACCAAAATACCACTGG
66 ACCAAAATATCCCTAGCTTCTAAAATTACCAAAATACCACTGG
*** *
43444383 TTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTAGAAAATT
1 TTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATT
* * *
43444448 A-CAGAAATA-CCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGG
66 ACCA-AAATATCCCTAG-C-TTCT-AAAATTACCA-AAATACCACTGG
*
43444493 TTTACAAAATTACTGAAATACCCT
1 TTTACAAAATTACCGAAATACCCT
43444517 TGGTTTGTAG
Statistics
Matches: 107, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
107 7 0.07
108 58 0.54
109 4 0.04
110 38 0.36
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (108 bp):
TTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATT
ACCAAAATATCCCTAGCTTCTAAAATTACCAAAATACCACTGG
Found at i:43445483 original size:25 final size:25
Alignment explanation
Indices: 43445445--43445514 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
43445435 AGGAAGTGCT
* *
43445445 AAAAGGGCTATGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCTAGTTTACCA
* *
43445470 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCTAGTTTACCA
43445495 AAAAGGGCTTTGCCCTAGTT
1 AAAAGGGCTTTGCCCTAGTT
43445515 ATTAAAGGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCTAGTTTACCA
Found at i:43445785 original size:31 final size:30
Alignment explanation
Indices: 43445734--43445816 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 30
43445724 TGCTTACAGT
43445734 AAAGGCTTCGGCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCAGTGATATGATTTATGA
*
43445764 AAAGGCTTTGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCC-AGTGATATGATTTATGA
43445795 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGG-CCAGTGATATG
43445817 TCGAGACTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
30 17 0.35
31 30 0.61
32 2 0.04
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (30 bp):
AAAGGCTTCGGCCAGTGATATGATTTATGA
Found at i:43449536 original size:17 final size:17
Alignment explanation
Indices: 43449516--43449552 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
43449506 TTATCGTTTG
43449516 TTTATTTTTCTTATTTA
1 TTTATTTTTCTTATTTA
*
43449533 TTTATTTTTGTTATTTA
1 TTTATTTTTCTTATTTA
43449550 TTT
1 TTT
43449553 GTATCTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTATTTTTCTTATTTA
Found at i:43451722 original size:22 final size:22
Alignment explanation
Indices: 43451694--43451738 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
43451684 ATCAAAATTA
*
43451694 TAACATAAACAGTGTGTGTGGC
1 TAACATAAACAGTATGTGTGGC
43451716 TAACATAAACAGTATGTGTGGC
1 TAACATAAACAGTATGTGTGGC
43451738 T
1 T
43451739 TTCTCTGAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (22 bp):
TAACATAAACAGTATGTGTGGC
Found at i:43452123 original size:27 final size:26
Alignment explanation
Indices: 43452075--43452134 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
43452065 ACGAGGCTAC
*
43452075 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
43452102 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
43452128 CATATAT
1 CAGATAT
43452135 ATATATATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:43452223 original size:27 final size:26
Alignment explanation
Indices: 43452175--43452226 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
43452165 GCGAGGCTGC
*
43452175 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
43452201 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
43452227 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:43452826 original size:26 final size:27
Alignment explanation
Indices: 43452797--43452850 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
43452787 TCACACAAGT
*
43452797 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
43452823 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
43452850 T
1 T
43452851 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:43452881 original size:27 final size:26
Alignment explanation
Indices: 43452851--43452965 Score: 99
Period size: 27 Copynumber: 4.3 Consensus size: 26
43452841 GGGGCAAAAT
*
43452851 GGTAATTTTACTCCACAAGGGTATCTC
1 GGTAATTTTAC-CCACAAGGGTATTTC
* * *
43452878 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTTTACC-CACAAGGGTATTTC
43452905 GGT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCC-ACAAGGGTATTTC
* * *
43452932 GATAATTCTACCTTAC-AGAGGTATTTC
1 GGTAATTTTACC-CACAAG-GGTATTTC
43452959 GGTAATT
1 GGTAATT
43452966 CTACAACTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
26 6 0.08
27 62 0.87
28 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (26 bp):
GGTAATTTTACCCACAAGGGTATTTC
Found at i:43452938 original size:54 final size:54
Alignment explanation
Indices: 43452851--43452969 Score: 177
Period size: 54 Copynumber: 2.2 Consensus size: 54
43452841 GGGGCAAAAT
* * *
43452851 GGTAATTTTACTCC-ACAAGGGTATCTCGGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTAC-CCTACAAGGGTATCTCGATAATTCTACCTTACAGAGGTATTTC
* *
43452905 GGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCTTACAGAGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATCTCGATAATTCTACCTTACAGAGGTATTTC
43452959 GGTAATTCTAC
1 GGTAATTCTAC
43452970 AACTTATCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 2 0.03
54 56 0.97
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATCTCGATAATTCTACCTTACAGAGGTATTTC
Found at i:43452966 original size:27 final size:27
Alignment explanation
Indices: 43452870--43452969 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
43452860 ACTCCACAAG
* *
43452870 GGTATCTCGGTAATTCTACCTTACAGG
1 GGTATTTCGGTAATTCTACCTTACAGA
* *
43452897 GGTATTTCGGTATTTCTACCCTACA-A
1 GGTATTTCGGTAATTCTACCTTACAGA
*
43452923 GGGTATTTCGATAATTCTACCTTACAGA
1 -GGTATTTCGGTAATTCTACCTTACAGA
43452951 GGTATTTCGGTAATTCTAC
1 GGTATTTCGGTAATTCTAC
43452970 AACTTATCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
27 62 0.98
28 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCTTACAGA
Found at i:43453166 original size:27 final size:27
Alignment explanation
Indices: 43453127--43453367 Score: 367
Period size: 27 Copynumber: 8.9 Consensus size: 27
43453117 AGCTGACGCC
*
43453127 ACCCTACAGGGGTATTTCAGTATTTCT
1 ACCCTACAGGGGTATTTCAGTAATTCT
* *
43453154 ACCCTACAAGGGTATTTCGGTAATTCT
1 ACCCTACAGGGGTATTTCAGTAATTCT
43453181 ACCCTACAGGGGTATTTCAGTAATTCT
1 ACCCTACAGGGGTATTTCAGTAATTCT
43453208 ACCCTACAGGGGTATTTC-GATAATTCT
1 ACCCTACAGGGGTATTTCAG-TAATTCT
*
43453235 ACCTTACAGGGGTATTTCAGTAATTCT
1 ACCCTACAGGGGTATTTCAGTAATTCT
43453262 ACCCTACAGGGGTATTTCAGTAATTCT
1 ACCCTACAGGGGTATTTCAGTAATTCT
* * *
43453289 ACCTTATAGGGGTATTCCAGTAATTCT
1 ACCCTACAGGGGTATTTCAGTAATTCT
*
43453316 ACCCTACAGGGGTATTTCGGTAATTCT
1 ACCCTACAGGGGTATTTCAGTAATTCT
* * *
43453343 ACCTTACAAGGGTATTTCGGTAATT
1 ACCCTACAGGGGTATTTCAGTAATT
43453368 GTACAAATCA
Statistics
Matches: 196, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
26 1 0.01
27 194 0.99
28 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
ACCCTACAGGGGTATTTCAGTAATTCT
Found at i:43453209 original size:54 final size:54
Alignment explanation
Indices: 43453131--43453394 Score: 395
Period size: 54 Copynumber: 4.9 Consensus size: 54
43453121 GACGCCACCC
* * *
43453131 TACAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCC
1 TACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCT
*
43453185 TACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCT
1 TACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCT
*
43453239 TACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCT
1 TACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCT
* *
43453293 TATAGGGGTATTCCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCT
1 TACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCT
* * * ** *
43453347 TACAAGGGTATTTCGGTAATTGTA-CAAATCAGGGGTATTTTGGTAATT
1 TACAGGGGTATTTCAGTAATTCTACCCTA-CAGGGGTATTTCGGTAATT
43453395 TTACAAACTA
Statistics
Matches: 192, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
53 2 0.01
54 190 0.99
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (54 bp):
TACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCT
Found at i:43453382 original size:27 final size:27
Alignment explanation
Indices: 43453131--43453421 Score: 325
Period size: 27 Copynumber: 10.8 Consensus size: 27
43453121 GACGCCACCC
* * *
43453131 TACAGGGGTATTTCAGTATTTCTACCC
1 TACAGGGGTATTTCGGTAATTCTACCA
* *
43453158 TACAAGGGTATTTCGGTAATTCTACCC
1 TACAGGGGTATTTCGGTAATTCTACCA
* *
43453185 TACAGGGGTATTTCAGTAATTCTACCC
1 TACAGGGGTATTTCGGTAATTCTACCA
* *
43453212 TACAGGGGTATTTCGATAATTCTACCT
1 TACAGGGGTATTTCGGTAATTCTACCA
* *
43453239 TACAGGGGTATTTCAGTAATTCTACCC
1 TACAGGGGTATTTCGGTAATTCTACCA
* *
43453266 TACAGGGGTATTTCAGTAATTCTACCT
1 TACAGGGGTATTTCGGTAATTCTACCA
* * * *
43453293 TATAGGGGTATTCCAGTAATTCTACCC
1 TACAGGGGTATTTCGGTAATTCTACCA
*
43453320 TACAGGGGTATTTCGGTAATTCTACCT
1 TACAGGGGTATTTCGGTAATTCTACCA
* *
43453347 TACAAGGGTATTTCGGTAATTGTA-CA
1 TACAGGGGTATTTCGGTAATTCTACCA
* * *
43453373 AATCAGGGGTATTTTGGTAATTTTA-CA
1 TA-CAGGGGTATTTCGGTAATTCTACCA
* *
43453400 AACTAGGGGTATTTTGGTAATT
1 TAC-AGGGGTATTTCGGTAATT
43453422 TTGCTAATCG
Statistics
Matches: 236, Mismatches: 26, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
26 3 0.01
27 233 0.99
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (27 bp):
TACAGGGGTATTTCGGTAATTCTACCA
Found at i:43453422 original size:27 final size:27
Alignment explanation
Indices: 43453351--43453476 Score: 148
Period size: 27 Copynumber: 4.7 Consensus size: 27
43453341 CTACCTTACA
* *
43453351 AGGGTATTTCGGTAATTGTACAAATCAG
1 AGGGTATTTTGGTAATTTTACAAAT-AG
43453379 -GGGTATTTTGGTAATTTTACAAACTAG
1 AGGGTATTTTGGTAATTTTACAAA-TAG
* * *
43453406 -GGGTATTTTGGTAATTTTGCTAATCG
1 AGGGTATTTTGGTAATTTTACAAATAG
* * *
43453432 AGGGTATTTTGGTAATTTTGCTAATTG
1 AGGGTATTTTGGTAATTTTACAAATAG
43453459 AGGGTATTTTGGTAATTT
1 AGGGTATTTTGGTAATTT
43453477 GGTAAACTAA
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
26 2 0.02
27 87 0.97
28 1 0.01
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.43
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTACAAATAG
Found at i:43453464 original size:54 final size:53
Alignment explanation
Indices: 43453322--43453476 Score: 159
Period size: 54 Copynumber: 2.9 Consensus size: 53
43453312 TTCTACCCTA
* * ** * * *
43453322 CAGGGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCGGTAATTGTACAAAT
1 CAGGGGTATTTTGGTAATTTTA-CAAACTAGGGTATTTTGGTAATTTTACAAAT
* *
43453376 CAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTGCTAAT
1 CAGGGGTATTTTGGTAATTTTACAAACTA-GGGTATTTTGGTAATTTTACAAAT
* * *
43453430 C-GAGGGTATTTTGGTAATTTTGCTAATTGAGGGTATTTTGGTAATTT
1 CAG-GGGTATTTTGGTAATTTTACAAACT-AGGGTATTTTGGTAATTT
43453477 GGTAAACTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
53 5 0.06
54 80 0.93
55 1 0.01
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (53 bp):
CAGGGGTATTTTGGTAATTTTACAAACTAGGGTATTTTGGTAATTTTACAAAT
Found at i:43457370 original size:13 final size:13
Alignment explanation
Indices: 43457334--43457370 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
43457324 GAAAAATGAA
*
43457334 TATATGAAAAGGT
1 TATATGAAATGGT
*
43457347 TATATGGAATGGT
1 TATATGAAATGGT
43457360 TATATGAAATG
1 TATATGAAATG
43457371 AATATTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (13 bp):
TATATGAAATGGT
Found at i:43459699 original size:3 final size:3
Alignment explanation
Indices: 43459691--43459717 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43459681 GGCTGGAGAA
43459691 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
43459718 TTGGTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43460357 original size:20 final size:19
Alignment explanation
Indices: 43460321--43460371 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
43460311 ACGGGCTATT
*
43460321 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
43460340 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
43460360 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
43460372 GTTACTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:43465447 original size:62 final size:62
Alignment explanation
Indices: 43465350--43465472 Score: 237
Period size: 62 Copynumber: 2.0 Consensus size: 62
43465340 TATTTCAGCT
*
43465350 TTTACCGATTCAGTCTAAGGGAGGGTGTCGTTTACACACCTGGTTGATGACGATTGATGACA
1 TTTACCGATTCAGTCTAAGGGAGGGTGTCGTTTACACACCTGGTTGATAACGATTGATGACA
43465412 TTTACCGATTCAGTCTAAGGGAGGGTGTCGTTTACACACCTGGTTGATAACGATTGATGAC
1 TTTACCGATTCAGTCTAAGGGAGGGTGTCGTTTACACACCTGGTTGATAACGATTGATGAC
43465473 GATATCTCCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (62 bp):
TTTACCGATTCAGTCTAAGGGAGGGTGTCGTTTACACACCTGGTTGATAACGATTGATGACA
Found at i:43465681 original size:54 final size:54
Alignment explanation
Indices: 43465623--43465725 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
43465613 TTAACACCCT
43465623 AGGGGCAAAATGGTAATTT-TACCCCACAAGGGTATCTCGATAATTCTACCCTAC
1 AGGGGCAAAATGGT-ATTTCTACCCCACAAGGGTATCTCGATAATTCTACCCTAC
* *** * * *
43465677 AGGGGTATTTTGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTAC
1 AGGGGCAAAATGGTATTTCTACCCCACAAGGGTATCTCGATAATTCTAC
43465726 AACTTGGGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 4 0.10
54 37 0.90
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (54 bp):
AGGGGCAAAATGGTATTTCTACCCCACAAGGGTATCTCGATAATTCTACCCTAC
Found at i:43465723 original size:27 final size:27
Alignment explanation
Indices: 43465634--43465725 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
43465624 GGGGCAAAAT
* * *
43465634 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
43465661 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
43465688 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
43465715 GGTAATTCTAC
1 GGTAATTCTAC
43465726 AACTTGGGCC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:43471718 original size:40 final size:40
Alignment explanation
Indices: 43471691--43471833 Score: 202
Period size: 40 Copynumber: 3.6 Consensus size: 40
43471681 CACTGGCTCG
*
43471691 AATGCCTTCGGGACTTAGCCCGG-ATATAGT-AGTTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTCA-CTCGCACA
*
43471731 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA-A
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTCACTCGCACA
* *
43471770 CAATGCCTTCGGGACTTAGCCCGGAATTTGTCACTAGCACA
1 -AATGCCTTCGGGACTTAGCCCGGAATTAGTCACTCGCACA
43471811 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
43471834 TTATCATCCG
Statistics
Matches: 95, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
39 1 0.01
40 90 0.95
41 4 0.04
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTCACTCGCACA
Found at i:43482315 original size:25 final size:25
Alignment explanation
Indices: 43482271--43482321 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
43482261 CCCTTATAAT
*
43482271 GTGAAAATGACCTTTTTACCCCTAG
1 GTGAAAATGACCTTTATACCCCTAG
*
43482296 GTGAAAATGA-CTATTATACCCTTAG
1 GTGAAAATGACCT-TTATACCCCTAG
43482321 G
1 G
43482322 GTTATGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (25 bp):
GTGAAAATGACCTTTATACCCCTAG
Found at i:43482380 original size:10 final size:10
Alignment explanation
Indices: 43482365--43482399 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
43482355 TTTGTACATA
43482365 ATATGCCATG
1 ATATGCCATG
43482375 ATATGCACATG
1 ATATGC-CATG
43482386 ATATGCCATG
1 ATATGCCATG
43482396 ATAT
1 ATAT
43482400 ATACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (10 bp):
ATATGCCATG
Found at i:43482384 original size:21 final size:21
Alignment explanation
Indices: 43482360--43482399 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43482350 ACTGATTTGT
43482360 ACATAATATGCCATGATATGC
1 ACATAATATGCCATGATATGC
*
43482381 ACATGATATGCCATGATAT
1 ACATAATATGCCATGATAT
43482400 ATACATATAT
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:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
ACATAATATGCCATGATATGC
Found at i:43482405 original size:21 final size:20
Alignment explanation
Indices: 43482359--43482411 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
43482349 TACTGATTTG
*
43482359 TACATAATATGCCATGATATG
1 TACAT-ATATGCCATGATATA
*
43482380 CACATGATATGCCATGATATA
1 TACAT-ATATGCCATGATATA
43482401 TACATATATGC
1 TACATATATGC
43482412 ACGGGTTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (20 bp):
TACATATATGCCATGATATA
Found at i:43485486 original size:56 final size:56
Alignment explanation
Indices: 43485400--43485575 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
43485390 ACAAGGGATG
43485400 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
43485456 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
43485512 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
43485568 ATGGGCAA
1 ATGGGCAA
43485576 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:43485610 original size:112 final size:111
Alignment explanation
Indices: 43485400--43485615 Score: 260
Period size: 112 Copynumber: 1.9 Consensus size: 111
43485390 ACAAGGGATG
43485400 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAA
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAA
* * * ** ** ***
43485465 ACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
66 ACATCTAATGAAAAATGAAGTGAGAAAACAAAAA-AAAATAAGAAGC
*
43485512 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAAT
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAA-
43485577 AA-A-CTAAT-AAGAAATGGAAG-GAAGAAAACAAAAAAAAAT
65 AACATCTAATGAA-AAAT-GAAGTG-AGAAAACAAAAAAAAAT
43485616 GTGTGTGAGT
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
110 2 0.02
111 12 0.13
112 73 0.82
113 2 0.02
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (111 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAA
ACATCTAATGAAAAATGAAGTGAGAAAACAAAAAAAAATAAGAAGC
Found at i:43487225 original size:47 final size:47
Alignment explanation
Indices: 43486713--43487211 Score: 815
Period size: 47 Copynumber: 10.6 Consensus size: 47
43486703 AGTGTATATA
* * * *
43486713 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-A-GTGTATA
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
*
43486758 TAAGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 T--GTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
** *
43486807 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCATATA
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
* *
43486854 TGAGGTAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
*
43486901 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
43486948 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
43486995 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
43487042 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
43487089 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
* * *
43487136 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATATA
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACA-TGTGTATG
*
43487183 TGTGGTAAGGCCGAATGGCCAATGTGATG
1 TGTGATAAGGCCGAATGGCCAATGTGATG
43487212 GATGTGGAAG
Statistics
Matches: 429, Mismatches: 20, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
45 1 0.00
46 1 0.00
47 419 0.98
48 1 0.00
49 7 0.02
ACGTcount: A:0.31, C:0.12, G:0.32, T:0.26
Consensus pattern (47 bp):
TGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGTGTATG
Found at i:43489800 original size:40 final size:40
Alignment explanation
Indices: 43489520--43489822 Score: 337
Period size: 40 Copynumber: 7.6 Consensus size: 40
43489510 TCGAATGATG
* **
43489520 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TGTA
* * * *
43489560 TCCGGACTAAGAT-CCGAAG-GCATTTGTG-TGAGTTACTATA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCGTGCT-AGTGA-TGTA
* *
43489600 ACCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
*
43489640 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
*
43489680 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* *
43489720 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* ** * * *
43489760 TCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
* *
43489800 TCCGGGCTAGGTCTCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCA
43489823 ATCATGCTGG
Statistics
Matches: 229, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.00
40 209 0.91
41 18 0.08
42 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
Found at i:43490182 original size:43 final size:43
Alignment explanation
Indices: 43490121--43490226 Score: 187
Period size: 43 Copynumber: 2.5 Consensus size: 43
43490111 GTGGAATTCA
*
43490121 TGTAAGACTTCGTCTGGGACGAAGGCATTGATTTGAGATAGTG
1 TGTAAGACCTCGTCTGGGACGAAGGCATTGATTTGAGATAGTG
43490164 TGTAAGACCTCGTCTGGGACGAAGGCATTGATTTGAGATAGTG
1 TGTAAGACCTCGTCTGGGACGAAGGCATTGATTTGAGATAGTG
43490207 TGTAAGACCAT-GTCTGGGAC
1 TGTAAGACC-TCGTCTGGGAC
43490227 ATGGCATCGG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
43 60 0.98
44 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.28
Consensus pattern (43 bp):
TGTAAGACCTCGTCTGGGACGAAGGCATTGATTTGAGATAGTG
Found at i:43496780 original size:47 final size:47
Alignment explanation
Indices: 43496555--43497092 Score: 717
Period size: 47 Copynumber: 11.3 Consensus size: 47
43496545 NNNNNNNNNN
* *
43496555 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* *
43496602 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 --TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* *
43496651 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 --TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
43496700 TATATATATGTGATAAGGCCTG-ATGGCCGATGTGATGAATGTGAAAGTG
1 --TATATATGTGATAAGGCC-GAATGGCCAATGTGATGAATGTGAAAGTG
* *
43496749 TATATATGTGATAAGGCCGAATGACCAATGTGCTGAATGTGAACA-TG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
* * *
43496796 TGTATGTGTGATAAGGCCGAATGGCCAATGTGAAGAATGTGAACA-TG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
* *
43496843 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
43496890 TATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
* *
43496937 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
* * *
43496984 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* * *
43497031 TATATATGTGGTAAGGCCGAATGGCCAATGTGATGGATGTGGAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* *
43497078 TATAAATATGATAAG
1 TATATATGTGATAAG
43497093 TCCCGAAGGG
Statistics
Matches: 457, Mismatches: 26, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
46 2 0.00
47 310 0.68
48 2 0.00
49 143 0.31
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (47 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
Found at i:43498052 original size:84 final size:84
Alignment explanation
Indices: 43497911--43498077 Score: 307
Period size: 84 Copynumber: 2.0 Consensus size: 84
43497901 TACTCCGTTA
* *
43497911 TTTGAATCTCTGTTTTATAGATTTTGGTTCGTCAGCTATCGGACTCGGGATTTTTGGAAGTCGAA
1 TTTGAATCTCTATTTTATAGATTTTGGTTCGTCAGCTATCGGACTCAGGATTTTTGGAAGTCGAA
43497976 GTCTCCCACACTATCAAAC
66 GTCTCCCACACTATCAAAC
43497995 TTTGAATCTCTATTTTATAGATTTTGGTTCGTCAGCTATCGGACTCAGGATTTTTGGAAGTCGAA
1 TTTGAATCTCTATTTTATAGATTTTGGTTCGTCAGCTATCGGACTCAGGATTTTTGGAAGTCGAA
*
43498060 GTCTCCCGCACTATCAAA
66 GTCTCCCACACTATCAAA
43498078 GCCCCCTTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (84 bp):
TTTGAATCTCTATTTTATAGATTTTGGTTCGTCAGCTATCGGACTCAGGATTTTTGGAAGTCGAA
GTCTCCCACACTATCAAAC
Found at i:43502733 original size:40 final size:40
Alignment explanation
Indices: 43502689--43502840 Score: 225
Period size: 40 Copynumber: 3.8 Consensus size: 40
43502679 GGATATAGCT
* * * * *
43502689 ACTCGCTCGAATGCCTTCGGGGCATAGCCCAG-TTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
43502729 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
43502769 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
43502809 GCTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
43502841 TTATCATCCG
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 101 0.98
41 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:43505371 original size:93 final size:93
Alignment explanation
Indices: 43505259--43505429 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
43505249 GCCCATAAGC
*
43505259 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
43505323 ACGAGTTCGGATGCCTAGTTACATCTCAT
65 ACGAGTTCGGATGCCTAGTTACATCTCAT
*
43505352 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43505417 CGAGTTCGGATGC
66 CGAGTTCGGATGC
43505430 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAT
Found at i:43505424 original size:46 final size:46
Alignment explanation
Indices: 43505251--43505426 Score: 218
Period size: 46 Copynumber: 3.8 Consensus size: 46
43505241 TGTAACCCGC
* * *
43505251 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
*
43505297 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
43505347 -C-TCA-TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
43505390 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
43505427 TGCTCAACCA
Statistics
Matches: 113, Mismatches: 7, Indels: 20
0.81 0.05 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 62 0.55
47 30 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:43515792 original size:25 final size:25
Alignment explanation
Indices: 43515746--43515796 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
43515736 TCCTTATAAT
* *
43515746 GTGAAAATGACCTTTTTGCCCCTAG
1 GTGAAAATGACCTTTATACCCCTAG
43515771 GTGAAAATGA-CTATTATACCCCTAG
1 GTGAAAATGACCT-TTATACCCCTAG
43515796 G
1 G
43515797 GTTATGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
GTGAAAATGACCTTTATACCCCTAG
Found at i:43515855 original size:10 final size:10
Alignment explanation
Indices: 43515840--43515874 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
43515830 TTTGTACATA
43515840 ATATGCCATG
1 ATATGCCATG
43515850 ATATGCACATG
1 ATATGC-CATG
43515861 ATATGCCATG
1 ATATGCCATG
43515871 ATAT
1 ATAT
43515875 ATACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (10 bp):
ATATGCCATG
Found at i:43515859 original size:21 final size:21
Alignment explanation
Indices: 43515835--43515874 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43515825 ACTGATTTGT
43515835 ACATAATATGCCATGATATGC
1 ACATAATATGCCATGATATGC
*
43515856 ACATGATATGCCATGATAT
1 ACATAATATGCCATGATAT
43515875 ATACATATAT
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:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
ACATAATATGCCATGATATGC
Found at i:43515880 original size:21 final size:20
Alignment explanation
Indices: 43515834--43515886 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
43515824 TACTGATTTG
*
43515834 TACATAATATGCCATGATATG
1 TACAT-ATATGCCATGATATA
*
43515855 CACATGATATGCCATGATATA
1 TACAT-ATATGCCATGATATA
43515876 TACATATATGC
1 TACATATATGC
43515887 ACGGGTTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (20 bp):
TACATATATGCCATGATATA
Found at i:43523713 original size:10 final size:10
Alignment explanation
Indices: 43523692--43523725 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
43523682 TTTGTACATA
43523692 ATATGCCATG
1 ATATGCCATG
43523702 ATA-GCACATG
1 ATATGC-CATG
43523712 ATATGCCATG
1 ATATGCCATG
43523722 ATAT
1 ATAT
43523726 ATACATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (10 bp):
ATATGCCATG
Found at i:43523715 original size:20 final size:20
Alignment explanation
Indices: 43523687--43523724 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43523677 ACTGATTTGT
43523687 ACATAATATGCCATGATAGC
1 ACATAATATGCCATGATAGC
*
43523707 ACATGATATGCCATGATA
1 ACATAATATGCCATGATA
43523725 TATACATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (20 bp):
ACATAATATGCCATGATAGC
Found at i:43523735 original size:20 final size:20
Alignment explanation
Indices: 43523686--43523737 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
43523676 TACTGATTTG
*
43523686 TACATAATATGCCATGATAG
1 TACATAATATGCCATGATAA
* *
43523706 CACATGATATGCCATGATATA
1 TACATAATATGCCATGATA-A
43523727 TACAT-ATATGC
1 TACATAATATGC
43523738 ACGGGTTGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (20 bp):
TACATAATATGCCATGATAA
Found at i:43527391 original size:25 final size:25
Alignment explanation
Indices: 43527345--43527395 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
43527335 CCCTTATAAT
* *
43527345 GTGAAAATGACCTTTTTGCCCCTAG
1 GTGAAAATGACCTTTATACCCCTAG
43527370 GTGAAAATGA-CTATTATACCCCTAG
1 GTGAAAATGACCT-TTATACCCCTAG
43527395 G
1 G
43527396 GTTATGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
GTGAAAATGACCTTTATACCCCTAG
Found at i:43527454 original size:10 final size:10
Alignment explanation
Indices: 43527439--43527473 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
43527429 TTTGTACATA
43527439 ATATGCCATG
1 ATATGCCATG
43527449 ATATGCACATG
1 ATATGC-CATG
*
43527460 ATATGCCATT
1 ATATGCCATG
43527470 ATAT
1 ATAT
43527474 ATTAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (10 bp):
ATATGCCATG
Found at i:43527458 original size:21 final size:21
Alignment explanation
Indices: 43527434--43527473 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43527424 ACTGATTTGT
43527434 ACATAATATGCCATGATATGC
1 ACATAATATGCCATGATATGC
* *
43527455 ACATGATATGCCATTATAT
1 ACATAATATGCCATGATAT
43527474 ATTAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (21 bp):
ACATAATATGCCATGATATGC
Found at i:43532808 original size:27 final size:27
Alignment explanation
Indices: 43532778--43532884 Score: 119
Period size: 27 Copynumber: 3.9 Consensus size: 27
43532768 GGCTGCTAGA
* * *
43532778 ACAGATAATGTGACAGAGTCACCAAAT
1 ACAGATAATGTGGCAGAGCCACCAGAT
*
43532805 ACAGATAATCCTGGCAGAGCCACCAGA-
1 ACAGATAAT-GTGGCAGAGCCACCAGAT
*
43532832 ACAGATATATGTGGCAAAGCCACCAGAT
1 ACAGATA-ATGTGGCAGAGCCACCAGAT
*
43532860 -CAGATAATTGTGGCATAGCCACCAG
1 ACAGATAA-TGTGGCAGAGCCACCAG
43532885 GACTCTTCCT
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.01
27 53 0.77
28 15 0.22
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (27 bp):
ACAGATAATGTGGCAGAGCCACCAGAT
Found at i:43532864 original size:54 final size:54
Alignment explanation
Indices: 43532775--43532884 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 54
43532765 CATGGCTGCT
* *
43532775 AGAACAGATAATGTGACAGAGTCACCAAATACAGATAATCCTGGCAGAGCCACC
1 AGAACAGATAATGTGACAAAGCCACCAAATACAGATAATCCTGGCAGAGCCACC
* * ** *
43532829 AGAACAGATATATGTGGCAAAGCCACCAGAT-CAGATAATTGTGGCATAGCCACC
1 AGAACAGATA-ATGTGACAAAGCCACCAAATACAGATAATCCTGGCAGAGCCACC
43532883 AG
1 AG
43532885 GACTCTTCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 32 0.67
55 16 0.33
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (54 bp):
AGAACAGATAATGTGACAAAGCCACCAAATACAGATAATCCTGGCAGAGCCACC
Found at i:43533321 original size:16 final size:15
Alignment explanation
Indices: 43533300--43533333 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
43533290 TCTCAAAATA
43533300 TTGGCTTTTCGGCATT
1 TTGGCTTTTCGGC-TT
43533316 TTGGCTTTTCGGCTT
1 TTGGCTTTTCGGCTT
43533331 TTG
1 TTG
43533334 CCGATCTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.03, C:0.18, G:0.26, T:0.53
Consensus pattern (15 bp):
TTGGCTTTTCGGCTT
Found at i:43538856 original size:24 final size:25
Alignment explanation
Indices: 43538803--43538876 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 25
43538793 TCCGGGCTAT
*
43538803 ATAATCG-GAAGCTCA-TAAGAGCC
1 ATAATCGAGAAGCTCACAAAGAGCC
* * *
43538826 ATAATCGGGAAGTTCACAAAGAACC
1 ATAATCGAGAAGCTCACAAAGAGCC
43538851 AT-ATCGAGAAGCTCACAAAGAGCC
1 ATAATCGAGAAGCTCACAAAGAGCC
43538875 AT
1 AT
43538877 GTAATAGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
23 7 0.16
24 28 0.65
25 8 0.19
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (25 bp):
ATAATCGAGAAGCTCACAAAGAGCC
Found at i:43553309 original size:20 final size:20
Alignment explanation
Indices: 43553276--43553341 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
43553266 TCCTTCGGCA
*
43553276 CCTCTAATTGCATTTTGATG
1 CCTCTGATTGCATTTTGATG
* *
43553296 CCTCTGATTTCATTTTGGTG
1 CCTCTGATTGCATTTTGATG
** *
43553316 CCTCTGATTGCGCTTTGGTG
1 CCTCTGATTGCATTTTGATG
43553336 CCTCTG
1 CCTCTG
43553342 TTTGTACTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (20 bp):
CCTCTGATTGCATTTTGATG
Found at i:43553355 original size:20 final size:20
Alignment explanation
Indices: 43553294--43553356 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
43553284 TGCATTTTGA
* * *
43553294 TGCCTCTGATTTCATTTTGG
1 TGCCTCTGATTGCACTTCGG
* *
43553314 TGCCTCTGATTGCGCTTTGG
1 TGCCTCTGATTGCACTTCGG
* *
43553334 TGCCTCTGTTTGTACTTCGG
1 TGCCTCTGATTGCACTTCGG
43553354 TGC
1 TGC
43553357 TTTTGTTAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.06, C:0.24, G:0.25, T:0.44
Consensus pattern (20 bp):
TGCCTCTGATTGCACTTCGG
Found at i:43561690 original size:21 final size:23
Alignment explanation
Indices: 43561661--43561703 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
43561651 TTAATGCACA
*
43561661 CACCTATACAA-CATA-ACATAG
1 CACCAATACAAGCATATACATAG
43561682 CACCAATACAAGCATATACATA
1 CACCAATACAAGCATATACATA
43561704 CAACTAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 4 0.21
23 5 0.26
ACGTcount: A:0.49, C:0.28, G:0.05, T:0.19
Consensus pattern (23 bp):
CACCAATACAAGCATATACATAG
Found at i:43574296 original size:18 final size:18
Alignment explanation
Indices: 43574262--43574311 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
43574252 ACAAAAAGAA
*
43574262 TCAAAATAATTTTTAAAAT
1 TCAAAAT-ATTTATAAAAT
43574281 TCAAAATATTTATAAAAT
1 TCAAAATATTTATAAAAT
*
43574299 TCCAAAT-TTTATA
1 TCAAAATATTTATA
43574312 TTTTTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.21
18 16 0.55
19 7 0.24
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (18 bp):
TCAAAATATTTATAAAAT
Found at i:43574885 original size:44 final size:46
Alignment explanation
Indices: 43574799--43574885 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
43574789 AGAAGTGTAA
*
43574799 ATTAAATTATAATATTTTTAAACATGTACTAATTATCACAACTCTG
1 ATTAAATTATAATATTTTTAAACATATACTAATTATCACAACTCTG
*
43574845 ATTAAATTATAATTATTTTT-AA-ATATA-TAATTATCTCAACT
1 ATTAAATTATAA-TATTTTTAAACATATACTAATTATCACAACT
43574886 TCTATTTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 13 0.34
45 4 0.11
46 14 0.37
47 7 0.18
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (46 bp):
ATTAAATTATAATATTTTTAAACATATACTAATTATCACAACTCTG
Found at i:43575187 original size:13 final size:13
Alignment explanation
Indices: 43575171--43575196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43575161 AGAATAATTT
43575171 TTTGAAAATTTAG
1 TTTGAAAATTTAG
43575184 TTTGAAAATTTAG
1 TTTGAAAATTTAG
43575197 ACGTTTGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTGAAAATTTAG
Found at i:43576326 original size:42 final size:42
Alignment explanation
Indices: 43576280--43576407 Score: 143
Period size: 42 Copynumber: 3.0 Consensus size: 42
43576270 ATTGCATTAT
* * *
43576280 TATGATATTTCGTATAAGATCATATCTAGGATATGGCATCGA
1 TATGAGATTTCGTGTAAGACCATATCTAGGATATGGCATCGA
* *
43576322 TATGAGA-ATCGTGTAAGACCATAGT-TAGGTTATTGGCATCGA
1 TATGAGATTTCGTGTAAGACCATA-TCTAGGATA-TGGCATCGA
* * * *
43576364 TATGAGATTTCATGTAAGACCATATCTGGGATATGACATTGA
1 TATGAGATTTCGTGTAAGACCATATCTAGGATATGGCATCGA
43576406 TA
1 TA
43576408 CGGTACTATG
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
41 19 0.27
42 33 0.46
43 19 0.27
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.34
Consensus pattern (42 bp):
TATGAGATTTCGTGTAAGACCATATCTAGGATATGGCATCGA
Found at i:43580309 original size:15 final size:15
Alignment explanation
Indices: 43580291--43580322 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
43580281 AATTTTGCTA
43580291 TTATATCTTTTATAT
1 TTATATCTTTTATAT
43580306 TTATATCTTTTATAT
1 TTATATCTTTTATAT
43580321 TT
1 TT
43580323 TGCATGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATATCTTTTATAT
Found at i:43582206 original size:38 final size:38
Alignment explanation
Indices: 43582147--43582268 Score: 208
Period size: 38 Copynumber: 3.2 Consensus size: 38
43582137 ATACATATGT
* * *
43582147 CATGACATAGGATTCCGATATATGTGTACGAGTAAGAC
1 CATGGCATAGGATTCCAATATATGTGTGCGAGTAAGAC
43582185 CATGGCATAGGATTCCAATATATGTGTGCGAGTAAGAC
1 CATGGCATAGGATTCCAATATATGTGTGCGAGTAAGAC
*
43582223 CATGGCATAGGATTCTAATATATGTGTGCGAGTAAGAC
1 CATGGCATAGGATTCCAATATATGTGTGCGAGTAAGAC
43582261 CATGGCAT
1 CATGGCAT
43582269 CGATATGTGA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 80 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (38 bp):
CATGGCATAGGATTCCAATATATGTGTGCGAGTAAGAC
Found at i:43590629 original size:58 final size:58
Alignment explanation
Indices: 43590550--43590665 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
43590540 CATAGTAAGT
43590550 TATTCCAAGCCCCATTTTTAATGTTCTTTACGTTTTTGGAATCTCGGAAGCTCGATTA
1 TATTCCAAGCCCCATTTTTAATGTTCTTTACGTTTTTGGAATCTCGGAAGCTCGATTA
*
43590608 TATTCCAAGCCCCGTTTTTAATGTTCTTTACGTTTTTGGAATCTCGGAAGCTCGATTA
1 TATTCCAAGCCCCATTTTTAATGTTCTTTACGTTTTTGGAATCTCGGAAGCTCGATTA
43590666 AGCTTATGCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (58 bp):
TATTCCAAGCCCCATTTTTAATGTTCTTTACGTTTTTGGAATCTCGGAAGCTCGATTA
Found at i:43599088 original size:19 final size:20
Alignment explanation
Indices: 43599051--43599088 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
43599041 ATAAGGTGGT
43599051 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
43599071 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
43599089 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:43605509 original size:34 final size:34
Alignment explanation
Indices: 43605471--43605535 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
43605461 TGATTAAAGA
43605471 ATTTTCTAGAAAAATTAATTTGGA-AAATTAAGTG
1 ATTTT-TAGAAAAATTAATTTGGATAAATTAAGTG
* * *
43605505 ATTTTTGGAAAAATTGATTTTGATAAATTAA
1 ATTTTTAGAAAAATTAATTTGGATAAATTAA
43605536 AATTAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 15 0.56
34 12 0.44
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.42
Consensus pattern (34 bp):
ATTTTTAGAAAAATTAATTTGGATAAATTAAGTG
Found at i:43607967 original size:62 final size:59
Alignment explanation
Indices: 43607892--43608008 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 59
43607882 AGTGATTATC
* * * *
43607892 TTAATATTTAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTAATAAGAT
1 TTAATATTTAATTTAATCTAATATTTATC-T-TA-ATAAACATTATATTAATTTAATAAGAT
*
43607954 TTAAT-TTTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
1 TTAATATTT-AATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATA
43608009 TTAAAGTGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 20 0.41
60 2 0.04
61 4 0.08
62 23 0.47
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (59 bp):
TTAATATTTAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATAAGAT
Found at i:43610908 original size:27 final size:27
Alignment explanation
Indices: 43610877--43611054 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43610867 TAAATTGTAC
43610877 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43610904 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43610930 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43610958 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
43610986 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43611013 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43611040 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43611055 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:43610991 original size:82 final size:81
Alignment explanation
Indices: 43610878--43611033 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43610868 AAATTGTACA
* *
43610878 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
43610942 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
43610959 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
43611024 TGCGAGTTGA
65 TGCGAATTGA
43611034 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43611045 original size:82 final size:81
Alignment explanation
Indices: 43610874--43611054 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
43610864 GATTAAATTG
* *
43610874 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
43610939 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
43610955 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
43611019 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43611037 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43611055 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:43618971 original size:27 final size:27
Alignment explanation
Indices: 43618940--43619117 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43618930 TAAATTGTAC
43618940 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43618967 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43618993 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43619021 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
43619049 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43619076 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43619103 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43619118 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:43619054 original size:82 final size:81
Alignment explanation
Indices: 43618941--43619096 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43618931 AAATTGTACA
* *
43618941 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
43619005 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
43619022 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
43619087 TGCGAGTTGA
65 TGCGAATTGA
43619097 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43619108 original size:82 final size:81
Alignment explanation
Indices: 43618937--43619117 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
43618927 GATTAAATTG
* *
43618937 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
43619002 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
43619018 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
43619082 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43619100 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43619118 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:43623687 original size:43 final size:43
Alignment explanation
Indices: 43623626--43623780 Score: 267
Period size: 43 Copynumber: 3.6 Consensus size: 43
43623616 CCGGCATTAT
43623626 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGGCACGAA
* *
43623669 GCCTGCTAGGCACGAAGGCCCGAATACACATCA-TCAGCATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACT-GGCACGAA
*
43623712 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGGCACGAA
43623755 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
43623781 TAATACCAGC
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
42 1 0.01
43 104 0.99
ACGTcount: A:0.30, C:0.32, G:0.26, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGGCACGAA
Found at i:43623826 original size:38 final size:38
Alignment explanation
Indices: 43623773--43624068 Score: 375
Period size: 38 Copynumber: 7.8 Consensus size: 38
43623763 GGCACGAAGG
* * * *
43623773 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
43623811 CCAGGATATATTACCAGCACGAAGCCTACGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * *
43623849 CCCAGATATATTA-CAACACGAAGCCTGTGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * * *
43623886 CCGGGATATATTACTAGTACGAAGCCTACGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
43623924 CCCGGATATATTACCAGCATGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
43623962 CCCGGACATATTA-CAGCACGAAGCCTACGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
43623999 CCTGGATATGTTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
43624037 CCCGGATATAATT-CCAGCA-TATAGCCTGCGGG
1 CCCGGATAT-ATTACCAGCACGA-AGCCTGCGGG
43624069 CCTTTAGGCC
Statistics
Matches: 221, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
37 65 0.29
38 154 0.70
39 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (38 bp):
CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
Found at i:43623882 original size:75 final size:76
Alignment explanation
Indices: 43623773--43624055 Score: 401
Period size: 75 Copynumber: 3.8 Consensus size: 76
43623763 GGCACGAAGG
* * * * *
43623773 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAACCAGGATATATTACCAGCACGAAGCCT
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCACGAAGCCT
43623838 ACGGGATTTAA
66 ACGGGATTTAA
* * * * * *
43623849 CCCAGATATATTA-CAACACGAAGCCTGTGGGATTTAACCGGGATATATTACTAGTACGAAGCCT
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCACGAAGCCT
43623913 ACGGGATTTAA
66 ACGGGATTTAA
* *
43623924 CCCGGATATATTACCAGCATGAAGCCTGCGGGATTTAACCCGGACATATTA-CAGCACGAAGCCT
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCACGAAGCCT
43623988 ACGGGATTTAA
66 ACGGGATTTAA
* *
43623999 CCTGGATATGTTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATT-CCAGCA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATAT-ATTACCAGCA
43624056 TATAGCCTGC
Statistics
Matches: 182, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
75 132 0.73
76 50 0.27
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (76 bp):
CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCACGAAGCCT
ACGGGATTTAA
Found at i:43623976 original size:113 final size:113
Alignment explanation
Indices: 43623778--43624068 Score: 406
Period size: 113 Copynumber: 2.6 Consensus size: 113
43623768 GAAGGCCCGA
* * * * * *
43623778 ATATAATACCAGCACTAGGCCTGCGGGATTTAACCAGGATATATTACCAGCACGAAGCCTACGGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCATGAAGCCTGCGGG
* **
43623843 ATTTAACCCAGATATATTACAACACGAAGCCTGTGGGATTTAACCGGG
66 ATTTAACCCAGACATATTACAACACGAAGCCTACGGGATTTAACCGGG
* * *
43623891 ATATATTACTAGTACGAAGCCTACGGGATTTAACCCGGATATATTACCAGCATGAAGCCTGCGGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCATGAAGCCTGCGGG
* * *
43623956 ATTTAACCCGGACATATTACAGCACGAAGCCTACGGGATTTAACCTGG
66 ATTTAACCCAGACATATTACAACACGAAGCCTACGGGATTTAACCGGG
*
43624004 ATATGTTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATT-CCAGCAT-ATAGCCTGCG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATAT-ATTACCAGCATGA-AGCCTGCG
43624067 GG
64 GG
43624069 CCTTTAGGCC
Statistics
Matches: 157, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
112 1 0.01
113 153 0.97
114 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (113 bp):
ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCATGAAGCCTGCGGG
ATTTAACCCAGACATATTACAACACGAAGCCTACGGGATTTAACCGGG
Found at i:43626834 original size:17 final size:17
Alignment explanation
Indices: 43626812--43626844 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43626802 GAATACAAAT
*
43626812 AAATAACTAAAGAAAAG
1 AAATAAATAAAGAAAAG
43626829 AAATAAATAAAGAAAA
1 AAATAAATAAAGAAAA
43626845 ATAAACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (17 bp):
AAATAAATAAAGAAAAG
Found at i:43634638 original size:22 final size:22
Alignment explanation
Indices: 43634610--43634653 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43634600 GCTTAGTAAG
43634610 CTCGTATGAAAGAAATAAACTA
1 CTCGTATGAAAGAAATAAACTA
*
43634632 CTCGTATTAAAGAAATAAACTA
1 CTCGTATGAAAGAAATAAACTA
43634654 ACCTTACCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (22 bp):
CTCGTATGAAAGAAATAAACTA
Found at i:43635805 original size:27 final size:27
Alignment explanation
Indices: 43635730--43635855 Score: 106
Period size: 27 Copynumber: 4.9 Consensus size: 27
43635720 AACAGACATC
* * *
43635730 ACATAGGGGTAAAACAGTCATCTTACC
1 ACATAAGGGTAAAACAGTCATTTTACT
* * *
43635757 ATAAAAGGGCAAAACAGTCATTTTACT
1 ACATAAGGGTAAAACAGTCATTTTACT
43635784 ACATAAGGGTAAAACAGTCA--TT--T
1 ACATAAGGGTAAAACAGTCATTTTACT
* *
43635807 ---TAAGGGTAAAATAGTTATTTTACCT
1 ACATAAGGGTAAAACAGTCATTTTA-CT
*
43635832 -CATAAGGGCAAAACAGTCATTTTA
1 ACATAAGGGTAAAACAGTCATTTTA
43635856 TTAACTTAGG
Statistics
Matches: 78, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
20 15 0.19
22 2 0.03
23 1 0.01
25 3 0.04
27 57 0.73
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (27 bp):
ACATAAGGGTAAAACAGTCATTTTACT
Found at i:43635812 original size:20 final size:20
Alignment explanation
Indices: 43635787--43635828 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
43635777 TTTTACTACA
43635787 TAAGGGTAAAACAGTCATTT
1 TAAGGGTAAAACAGTCATTT
* *
43635807 TAAGGGTAAAATAGTTATTT
1 TAAGGGTAAAACAGTCATTT
43635827 TA
1 TA
43635829 CCTCATAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (20 bp):
TAAGGGTAAAACAGTCATTT
Found at i:43635836 original size:47 final size:47
Alignment explanation
Indices: 43635761--43635855 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 47
43635751 CTTACCATAA
*
43635761 AAGGGCAAAACAGTCATTTTACTACATAAGGGTAAAACAGTCATTTT
1 AAGGGCAAAACAGTCATTTTACTACATAAGGGCAAAACAGTCATTTT
* * *
43635808 AAGGGTAAAATAGTTATTTTACCT-CATAAGGGCAAAACAGTCATTTT
1 AAGGGCAAAACAGTCATTTTA-CTACATAAGGGCAAAACAGTCATTTT
43635855 A
1 A
43635856 TTAACTTAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 41 0.95
48 2 0.05
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (47 bp):
AAGGGCAAAACAGTCATTTTACTACATAAGGGCAAAACAGTCATTTT
Found at i:43637295 original size:12 final size:12
Alignment explanation
Indices: 43637278--43637302 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43637268 TCGCCTAAAA
43637278 CCCTCCTCAAAT
1 CCCTCCTCAAAT
43637290 CCCTCCTCAAAT
1 CCCTCCTCAAAT
43637302 C
1 C
43637303 TCTCAACTGA
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:0.24, C:0.52, G:0.00, T:0.24
Consensus pattern (12 bp):
CCCTCCTCAAAT
Found at i:43647635 original size:46 final size:46
Alignment explanation
Indices: 43647585--43647757 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
43647575 TGGTTGAGCA
43647585 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
43647631 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
43647676 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
43647724 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
43647758 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:43647741 original size:93 final size:93
Alignment explanation
Indices: 43647582--43647752 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
43647572 GGATGGTTGA
* *
43647582 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
43647647 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
43647675 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
43647740 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
43647753 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:43650261 original size:27 final size:28
Alignment explanation
Indices: 43650230--43650295 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
43650220 TGGCATATTT
43650230 GTCATTTTACCATAC-AGGGGTATTACG
1 GTCATTTTACCATACAAGGGGTATTACG
*
43650257 GTCATTTTACCCTACAAGGGGTATTACG
1 GTCATTTTACCATACAAGGGGTATTACG
*
43650285 ATCATTTTACC
1 GTCATTTTACC
43650296 TATTTTGGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (28 bp):
GTCATTTTACCATACAAGGGGTATTACG
Found at i:43655777 original size:56 final size:56
Alignment explanation
Indices: 43655686--43655793 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 56
43655676 TCTTACATGT
* **
43655686 AATCACATATTGATGCCACTGTCCTAGACAGGGTCTTACTCGCACACATATAGCAG
1 AATCACATATTGATGCCAATGTAATAGACAGGGTCTTACTCGCACACATATAGCAG
43655742 AATCACATATTGATGCCAATGTAATA-A-ATGCGGTCTTACTCGCACACATATA
1 AATCACATATTGATGCCAATGTAATAGACA-G-GGTCTTACTCGCACACATATA
43655794 TCGATGCCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
54 1 0.02
55 2 0.04
56 44 0.94
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (56 bp):
AATCACATATTGATGCCAATGTAATAGACAGGGTCTTACTCGCACACATATAGCAG
Found at i:43657985 original size:27 final size:27
Alignment explanation
Indices: 43657927--43657987 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
43657917 CATACATCTC
* *
43657927 ATAGGGGCATATCAGTCATTTTACCAT
1 ATAGGGGCATATCAGTCATTTCACAAT
*
43657954 ATAGGGGCATTTCAGTCATTTCATCAAT
1 ATAGGGGCATATCAGTCATTTCA-CAAT
43657982 -TAGGGG
1 ATAGGGG
43657988 GTCTAGATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (27 bp):
ATAGGGGCATATCAGTCATTTCACAAT
Found at i:43662307 original size:46 final size:46
Alignment explanation
Indices: 43662148--43662307 Score: 141
Period size: 46 Copynumber: 3.5 Consensus size: 46
43662138 GCGAACTAAA
* * * * *
43662148 ACTCAACTCAACAAGCTCGGGCGTTCGCATCTATAAGTGAACTCAG
1 ACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGG
* * * *
43662194 ACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATCTCA-CA---AACTTGG
1 ACTCAACTCAACGAGCTCGGA---C-A-TTCGCATC-CATAAGTGAACTCGG
43662241 ACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGG
1 ACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGG
*
43662287 ACTCAACTCAACGAGTTCGGA
1 ACTCAACTCAACGAGCTCGGA
43662308 TGCCCAAATA
Statistics
Matches: 89, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
42 4 0.04
43 6 0.07
44 1 0.01
46 44 0.49
47 25 0.28
49 1 0.01
50 5 0.06
51 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
ACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGG
Found at i:43677540 original size:23 final size:21
Alignment explanation
Indices: 43677507--43677552 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
43677497 TCATGCTTAT
*
43677507 AATCATATCAAAATCATGCCA
1 AATCATATCAAAATCATACCA
*
43677528 AATCATAATTCAAAGTCATACCA
1 AATCAT-A-TCAAAATCATACCA
43677551 AA
1 AA
43677553 ACGTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (21 bp):
AATCATATCAAAATCATACCA
Found at i:43678337 original size:43 final size:42
Alignment explanation
Indices: 43678268--43678403 Score: 105
Period size: 43 Copynumber: 3.2 Consensus size: 42
43678258 AAGCTCGTCA
* * *
43678268 ATGCCAATGTCCCAGACGTGGCCTTACATGTAATTAAATATCG
1 ATGCCAATGTCCCAGACGTGGCCTTACACGAAATCAAATA-CG
* * *
43678311 ATGCCACTGTCTCAGACAG-GGTCTTACACGAAATCAAATACG
1 ATGCCAATGTCCCAGAC-GTGGCCTTACACGAAATCAAATACG
*** * * *
43678353 ATGTTGATGTCCCATACATGGTCTTACACGTAAATCAGAAGT-CG
1 ATGCCAATGTCCCAGACGTGGCCTTACACG-AAATCA-AA-TACG
43678397 ATGCCAA
1 ATGCCAA
43678404 CATCCCAAAT
Statistics
Matches: 72, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
42 24 0.33
43 38 0.53
44 9 0.12
45 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGCCTTACACGAAATCAAATACG
Found at i:43685102 original size:68 final size:67
Alignment explanation
Indices: 43685030--43685179 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
43685020 CATCATGTGT
* * * *
43685030 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
43685092 ATGTAG
62 ATGTAG
** * *
43685098 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
43685163 AG
66 AG
43685165 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
43685180 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:43685135 original size:64 final size:64
Alignment explanation
Indices: 43685054--43685237 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
43685044 AGACATTATG
* *
43685054 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
43685118 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
43685183 AA
63 AA
* * * *
43685185 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
43685238 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:43688740 original size:23 final size:21
Alignment explanation
Indices: 43688707--43688752 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
43688697 TCATGCTTAT
*
43688707 AATCATATCAAAATCATGCCA
1 AATCATATCAAAATCATACCA
*
43688728 AATCATAATTCAAAGTCATACCA
1 AATCAT-A-TCAAAATCATACCA
43688751 AA
1 AA
43688753 ACTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (21 bp):
AATCATATCAAAATCATACCA
Found at i:43690445 original size:19 final size:19
Alignment explanation
Indices: 43690421--43690460 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
43690411 TGTAAAGAAA
*
43690421 TATATATGTGACTATGGTT
1 TATATATGTGACTATAGTT
43690440 TATATATGTGACTATAGTT
1 TATATATGTGACTATAGTT
43690459 TA
1 TA
43690461 AGTACAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.47
Consensus pattern (19 bp):
TATATATGTGACTATAGTT
Found at i:43690553 original size:40 final size:41
Alignment explanation
Indices: 43690509--43690597 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 41
43690499 GCATTTCAAA
* *
43690509 ATAGCTTCAGCTATAAAT-A-GCACTAAGTGTGTGA-ATTGAG
1 ATAGCTTCAGCTAT--ATGAGGCACTAAGTGTGCGATACTGAG
*
43690549 ATAGCTTCGGCTATATGAGGCACTAAGTGTGCGATACTGAG
1 ATAGCTTCAGCTATATGAGGCACTAAGTGTGCGATACTGAG
43690590 ATAGCTTC
1 ATAGCTTC
43690598 GGTTTATTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 2 0.05
39 1 0.02
40 27 0.63
41 13 0.30
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (41 bp):
ATAGCTTCAGCTATATGAGGCACTAAGTGTGCGATACTGAG
Found at i:43690624 original size:44 final size:40
Alignment explanation
Indices: 43690528--43690626 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 40
43690518 GCTATAAATA
* *
43690528 GCACTAAGTGTGTGAATTGAGATAGCTTCGGCTATATGAG
1 GCACTAAGTGTGCGAACTGAGATAGCTTCGGCTATATGAG
*
43690568 GCACTAAGTGTGCGATACTGAGATAGCTTCGG-TTTATTGAGATG
1 GCACTAAGTGTGCGA-ACTGAGATAGCTTCGGCTATA-T--GA-G
43690612 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
43690627 GATCGATTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 17 0.33
41 16 0.31
43 2 0.04
44 16 0.31
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.29
Consensus pattern (40 bp):
GCACTAAGTGTGCGAACTGAGATAGCTTCGGCTATATGAG
Found at i:43698047 original size:39 final size:39
Alignment explanation
Indices: 43697993--43698070 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
43697983 TACCTCGATA
43697993 CAAAATAGTAGGAAATGGACCTAATCGTCAATAACCTTG
1 CAAAATAGTAGGAAATGGACCTAATCGTCAATAACCTTG
43698032 CAAAATAGTAGGAAATGGACCTAATCGTCAATAACCTTG
1 CAAAATAGTAGGAAATGGACCTAATCGTCAATAACCTTG
43698071 TTTTTCCCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (39 bp):
CAAAATAGTAGGAAATGGACCTAATCGTCAATAACCTTG
Found at i:43723204 original size:40 final size:40
Alignment explanation
Indices: 43723160--43723275 Score: 171
Period size: 40 Copynumber: 2.9 Consensus size: 40
43723150 GGATATAGCT
* *
43723160 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* * *
43723200 ACTCGCACCAATGCCTTCGGGACTTAGCCTGGATT-TGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
43723240 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
43723276 CATCCGAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.03
40 63 0.94
41 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:43731401 original size:27 final size:27
Alignment explanation
Indices: 43731296--43731403 Score: 121
Period size: 27 Copynumber: 4.0 Consensus size: 27
43731286 AGCATGACTG
* * * *
43731296 CCAGAATAGATAA-CGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
43731322 CCAGAACAGATAATTGTGGCAGAACCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
43731349 CCAGAACAGAT-ATATGGGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
43731376 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
43731403 C
1 C
43731404 AGGACGCTTC
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
26 14 0.20
27 53 0.77
28 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:43732850 original size:24 final size:24
Alignment explanation
Indices: 43732812--43732912 Score: 123
Period size: 24 Copynumber: 4.2 Consensus size: 24
43732802 CCAACACTGT
* *
43732812 TCTCCCTAATTAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
43732836 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
* * * *
43732860 TATCCCTTATCAACTCATAAGTCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
43732884 TATCCCTTATC-GACTCCTAAATCC
1 TCTCCCTTATCAG-CTCCTAAATCC
43732908 TCTCC
1 TCTCC
43732913 TGACAGACTT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.24, C:0.39, G:0.04, T:0.34
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:43735552 original size:5 final size:5
Alignment explanation
Indices: 43735544--43735580 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
43735534 CATAAAGTAA
*
43735544 ATTAT ATTAT ATTAT ATTAT A-TA- ATTAT AATAT ATTA
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
43735581 ATAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
3 1 0.04
4 4 0.14
5 23 0.82
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
ATTAT
Found at i:43735572 original size:18 final size:17
Alignment explanation
Indices: 43735549--43735584 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
43735539 AGTAAATTAT
*
43735549 ATTATATTATATTATATA
1 ATTATAATATATTA-ATA
43735567 ATTATAATATATTAATA
1 ATTATAATATATTAATA
43735584 A
1 A
43735585 AATAAAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATAATATATTAATA
Found at i:43743346 original size:17 final size:18
Alignment explanation
Indices: 43743305--43743347 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
43743295 TGTATTTACT
43743305 TATTATATAAGTAAATAA
1 TATTATATAAGTAAATAA
* *
43743323 TAATATA-AAGTAAATTA
1 TATTATATAAGTAAATAA
43743340 TATTATAT
1 TATTATAT
43743348 TATATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TATTATATAAGTAAATAA
Found at i:43743358 original size:18 final size:17
Alignment explanation
Indices: 43743335--43743371 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
43743325 ATATAAAGTA
*
43743335 AATTATATTATATTATAT
1 AATTATAATATATTA-AT
43743353 AATTATAATATATTAAT
1 AATTATAATATATTAAT
43743370 AA
1 AA
43743372 AATAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTATAATATATTAAT
Found at i:43751726 original size:42 final size:39
Alignment explanation
Indices: 43751660--43751803 Score: 153
Period size: 40 Copynumber: 3.6 Consensus size: 39
43751650 CGACAAATCA
* ** * *
43751660 GCTATATGTGGCACTTAAAGTGCGATTCGACATAGCTTCA
1 GCTATATATGGCACTTAGTGTGCGATT-GAGATAGCTTCG
*
43751700 GCTATACATATGGCACTTAGTGTGCGACTTGAGATAGCTTTG
1 GCTAT--ATATGGCACTTAGTGTGCGA-TTGAGATAGCTTCG
*
43751742 GCTATATATGGCACTTAGTGTGCAATTTGAGATAGCTTCG
1 GCTATATATGGCACTTAGTGTGCGA-TTGAGATAGCTTCG
* * *
43751782 GCTATGTACGACACTTAGTGTG
1 GCTATATATGGCACTTAGTGTG
43751804 TGAGATATTG
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 56 0.63
42 31 0.35
43 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (39 bp):
GCTATATATGGCACTTAGTGTGCGATTGAGATAGCTTCG
Found at i:43775800 original size:15 final size:15
Alignment explanation
Indices: 43775782--43775814 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43775772 GAAGCCCAGA
43775782 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
43775797 ATAAAGAAATCCATG
1 ATAAAGAAATCCAAG
43775812 ATA
1 ATA
43775815 CGAGAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:43778964 original size:100 final size:100
Alignment explanation
Indices: 43778792--43779676 Score: 1718
Period size: 100 Copynumber: 8.9 Consensus size: 100
43778782 AGGCTATCTA
* *
43778792 GTACGCATAGTAGCCTGCACTTACTACTACACATG-AACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
43778856 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
66 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
43778891 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
43778956 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
66 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
43778991 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
43779056 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
66 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
43779091 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
43779156 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
66 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
43779191 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
43779256 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
66 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
43779291 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
43779356 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
66 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
43779391 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
43779456 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
66 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
43779491 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
43779556 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
66 GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
**
43779591 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGTTT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
*
43779656 GCACTTAGTACTACACACGTG
66 GCACTTAGTACTACACGCGTG
43779677 GCCTCACAAT
Statistics
Matches: 780, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
99 34 0.04
100 746 0.96
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (100 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
GCACTTAGTACTACACGCGTGATAGAAGTTATCGG
Done.