Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 32 of 322
Found at i:9590046 original size:52 final size:54
Alignment explanation
Indices: 9589946--9590060 Score: 121
Period size: 52 Copynumber: 2.1 Consensus size: 54
9589936 TTTTAAATTT
* * *
9589946 TTTTTACTTTGTATCATATTTATATATAAATTTTCATTCAAGCTCTTTTATA-CA
1 TTTTTA-TTTGTATCATATGTATATATAAATTTTCATTCAAACCCTTTTATATCA
* *
9590000 TTTTTATTT-TATCATATGTATATATATTATTTAT-ATT-AAACCCTTTTTTATCA
1 TTTTTATTTGTATCATATGTATATATA-AATTT-TCATTCAAACCCTTTTATATCA
*
9590053 TTGTTATT
1 TTTTTATT
9590061 ATTCTTATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
52 26 0.50
53 19 0.37
54 7 0.13
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.57
Consensus pattern (54 bp):
TTTTTATTTGTATCATATGTATATATAAATTTTCATTCAAACCCTTTTATATCA
Found at i:9590095 original size:21 final size:21
Alignment explanation
Indices: 9590052--9590096 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9590042 CTTTTTTATC
* * *
9590052 ATTGTTATTATTCTTATTTTT
1 ATTGCTATTATTCTTAATATT
*
9590073 ATTGCTATTATTTTTAATATT
1 ATTGCTATTATTCTTAATATT
9590094 ATT
1 ATT
9590097 ATTGTTATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
ATTGCTATTATTCTTAATATT
Found at i:9590104 original size:21 final size:21
Alignment explanation
Indices: 9590080--9590121 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9590070 TTTATTGCTA
*
9590080 TTATTTTTAATATTATTATTG
1 TTATATTTAATATTATTATTG
*
9590101 TTATATTTAGTATTATTATTG
1 TTATATTTAATATTATTATTG
9590122 CATTCATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
TTATATTTAATATTATTATTG
Found at i:9602685 original size:44 final size:45
Alignment explanation
Indices: 9602599--9602695 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 45
9602589 ATTATCATTT
* *
9602599 TTATTATTATATTTAGGTTTTTATTGATTTTTATTTATATTCTTA
1 TTATTATTATATTTAGGTTTTTATTGATTATTATTTACATTCTTA
* * *
9602644 TTATT-TTATCTTTAGTTGTTTTA-TGATTATTGTTTACATTCTTA
1 TTATTATTATATTTAGGT-TTTTATTGATTATTATTTACATTCTTA
*
9602688 TTTTTATT
1 TTATTATT
9602696 TTTCCGATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 32 0.73
45 12 0.27
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (45 bp):
TTATTATTATATTTAGGTTTTTATTGATTATTATTTACATTCTTA
Found at i:9602734 original size:3 final size:3
Alignment explanation
Indices: 9602726--9602777 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
9602716 TTTTTATTTA
9602726 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
9602774 TCT T
1 TCT T
9602778 ATATATATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:9602784 original size:2 final size:2
Alignment explanation
Indices: 9602777--9602801 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9602767 TTCTTCTTCT
9602777 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9602802 TTATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9609572 original size:47 final size:47
Alignment explanation
Indices: 9609503--9609593 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
9609493 GATATACAAC
* *
9609503 TGTCCAAACTTGGAGGGTTTCATAAGCAGATATACAAGGGAAGGCAT
1 TGTCCAAACATGGAGGGCTTCATAAGCAGATATACAAGGGAAGGCAT
* * *
9609550 TGTCCAAACATGGAGGGCTTCATATGTAGATATGCAAGGGAAGG
1 TGTCCAAACATGGAGGGCTTCATAAGCAGATATACAAGGGAAGG
9609594 GAACCAACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (47 bp):
TGTCCAAACATGGAGGGCTTCATAAGCAGATATACAAGGGAAGGCAT
Found at i:9620402 original size:53 final size:53
Alignment explanation
Indices: 9620335--9620492 Score: 194
Period size: 53 Copynumber: 3.0 Consensus size: 53
9620325 AAAAAAGAAA
* * *
9620335 TTTTTTTTAATACTA-AGTCTGGTGCCGGCCATTGACAAGCCAGCTCTAAATT
1 TTTTTTTTAATACTAGACTCTGGTGCCGGCCATTGACAAGCCAGCACAAAATT
*
9620387 TTTTTTTTAAATACTAGTACTCTGGTGCCGGCCATTGACAAGTCAGCACAAAATT
1 TTTTTTTT-AATACTAG-ACTCTGGTGCCGGCCATTGACAAGCCAGCACAAAATT
* * ** *
9620442 TTTTTTTGAA-ACTCGTACTCTGGTGCTAGCCATTGACAGGCCAGCACAAAA
1 TTTTTTTTAATACTAG-ACTCTGGTGCCGGCCATTGACAAGCCAGCACAAAA
9620493 AATTTTAATT
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
52 8 0.09
53 43 0.46
54 2 0.02
55 40 0.43
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (53 bp):
TTTTTTTTAATACTAGACTCTGGTGCCGGCCATTGACAAGCCAGCACAAAATT
Found at i:9620415 original size:55 final size:53
Alignment explanation
Indices: 9620335--9620661 Score: 203
Period size: 55 Copynumber: 6.2 Consensus size: 53
9620325 AAAAAAGAAA
* * *
9620335 TTTTTTTTAATACTA--AGTCTGGTGCCGGCCATTGACAAGCCAGCTCTAAATT
1 TTTTTTTTAATACTAGTACTCTGGTGCCGGCCATTGACAAGCCAGCAC-AAAAT
*
9620387 TTTTTTTTAAATACTAGTACTCTGGTGCCGGCCATTGACAAGTCAGCACAAAAT
1 TTTTTTTT-AATACTAGTACTCTGGTGCCGGCCATTGACAAGCCAGCACAAAAT
* ** *
9620441 TTTTTTTTGAA-ACTCGTACTCTGGTGCTAGCCATTGACAGGCCAGCACAAAA-
1 TTTTTTTT-AATACTAGTACTCTGGTGCCGGCCATTGACAAGCCAGCACAAAAT
** ** ** * * *
9620493 --AATTTTAATTTTTTTACT-TGGTACCGGCCATTGATAGGCCAGCACCAAAAAAT
1 TTTTTTTTAATACTAGTACTCTGGTGCCGGCCATTGACAAGCCAGCA-C--AAAAT
* * * *
9620546 TTTGATTTTT--T-TTTGTACT-TGGTGCCGGCCATTGACAGGCCAGCACCAAAT
1 TTT--TTTTTAATACTAGTACTCTGGTGCCGGCCATTGACAAGCCAGCACAAAAT
* * * * * * *
9620597 TTTTTTTAAAAAAACTCA-TACCCTGGTGCCGGTCATTGGC-AGACCAGAACCAAAT
1 TTTTTTT--TAATACT-AGTACTCTGGTGCCGGCCATTGACAAG-CCAGCACAAAAT
9620652 TTTTTTTTAA
1 TTTTTTTTAA
9620662 AATACTGGTA
Statistics
Matches: 219, Mismatches: 36, Indels: 39
0.74 0.12 0.13
Matches are distributed among these distances:
49 28 0.13
50 10 0.05
51 7 0.03
52 12 0.05
53 46 0.21
54 50 0.23
55 62 0.28
57 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (53 bp):
TTTTTTTTAATACTAGTACTCTGGTGCCGGCCATTGACAAGCCAGCACAAAAT
Found at i:9620577 original size:54 final size:51
Alignment explanation
Indices: 9620456--9620595 Score: 185
Period size: 54 Copynumber: 2.7 Consensus size: 51
9620446 TTTGAAACTC
**
9620456 GTACTCTGGTGCTAGCCATTGACAGGCCAGCA-CAAAAAATTTTAATTTTTT
1 GTACT-TGGTGCCGGCCATTGACAGGCCAGCACCAAAAAATTTTAATTTTTT
* * *
9620507 -TACTTGGTACCGGCCATTGATAGGCCAGCACCAAAAAATTTTGATTTTTTTTT
1 GTACTTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAATTTT-A--ATTTTTT
9620560 GTACTTGGTGCCGGCCATTGACAGGCCAGCACCAAA
1 GTACTTGGTGCCGGCCATTGACAGGCCAGCACCAAA
9620596 TTTTTTTTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
49 22 0.29
50 15 0.19
51 1 0.01
53 6 0.08
54 33 0.43
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (51 bp):
GTACTTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAATTTTAATTTTTT
Found at i:9622767 original size:12 final size:12
Alignment explanation
Indices: 9622750--9622777 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9622740 AGCAAAACAG
9622750 GTTTTTAGCGGC
1 GTTTTTAGCGGC
9622762 GTTTTTAGCGGC
1 GTTTTTAGCGGC
9622774 GTTT
1 GTTT
9622778 GAATGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.32, T:0.46
Consensus pattern (12 bp):
GTTTTTAGCGGC
Found at i:9623222 original size:13 final size:13
Alignment explanation
Indices: 9623204--9623230 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9623194 TAAAAGAGAT
9623204 AGTATTAATTTTA
1 AGTATTAATTTTA
9623217 AGTATTAATTTTA
1 AGTATTAATTTTA
9623230 A
1 A
9623231 AATATTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
AGTATTAATTTTA
Found at i:9623324 original size:15 final size:15
Alignment explanation
Indices: 9623304--9623351 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
9623294 ACTATTGTAA
9623304 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
9623319 GGTTTAAGGATTAT-
1 GGTTTATGGATTATG
* *
9623333 GGTTAATGGTTTATG
1 GGTTTATGGATTATG
9623348 GGTT
1 GGTT
9623352 AAGGGTTAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:9623326 original size:22 final size:22
Alignment explanation
Indices: 9623255--9623456 Score: 125
Period size: 22 Copynumber: 9.4 Consensus size: 22
9623245 TATCATTATA
* *
9623255 GTTTAGGGTTTAT-GGTTAAGG
1 GTTTAAGGTTTATGGGTTATGG
* *
9623276 GTTTAATGTTTATGAGTTACT--
1 GTTTAAGGTTTATGGGTTA-TGG
* *
9623297 ATTGTAAGGTTTATGGATTATGG
1 GTT-TAAGGTTTATGGGTTATGG
*
9623320 GTTTAAGGATTAT-GGTTAAT-G
1 GTTTAAGGTTTATGGGTT-ATGG
* * *
9623341 GTTTATGGGTTAAGGGTTA-GG
1 GTTTAAGGTTTATGGGTTATGG
* * *
9623362 GTTTAAGTTTTAGGGGGTT-GGG
1 GTTTAAGGTTTA-TGGGTTATGG
* *
9623384 GTTTAAGGTTTAGGGGTTAAGG
1 GTTTAAGGTTTATGGGTTATGG
**
9623406 G-TTAAGGGTTTATGTTTTAT-G
1 GTTTAA-GGTTTATGGGTTATGG
*
9623427 GTTTAAGGTTTAGGGGTTATGG
1 GTTTAAGGTTTATGGGTTATGG
*
9623449 GGTTAAGG
1 GTTTAAGG
9623457 GTTAGGGATT
Statistics
Matches: 139, Mismatches: 28, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
21 62 0.45
22 75 0.54
23 2 0.01
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (22 bp):
GTTTAAGGTTTATGGGTTATGG
Found at i:9623336 original size:29 final size:28
Alignment explanation
Indices: 9623304--9623475 Score: 86
Period size: 29 Copynumber: 6.2 Consensus size: 28
9623294 ACTATTGTAA
*
9623304 GGTTTATGGATTATGGGTTTAAGGATTAT
1 GGTTTATGGATTATGGG-TTAAGGATTAG
* * *
9623333 GGTTAATGGTTTATGGGTTAAGGGTTAG
1 GGTTTATGGATTATGGGTTAAGGATTAG
* ** *
9623361 GGTTTAAGTTTTA-GGG----GG-TTGG
1 GGTTTATGGATTATGGGTTAAGGATTAG
* * * *
9623383 GGTTTAAGGTTTAGGGGTTAAGGGTTAAG
1 GGTTTATGGATTATGGGTTAAGGATT-AG
** * *
9623412 GGTTTATGTTTTATGGTTTAAGGTTTAG
1 GGTTTATGGATTATGGGTTAAGGATTAG
* * * *
9623440 GGGTTATGGGGTTAAGGGTTAGGGATTTAG
1 GGTTTAT-GGATTATGGGTTAAGGA-TTAG
9623470 GGTTTA
1 GGTTTA
9623476 GATTAATTAG
Statistics
Matches: 111, Mismatches: 23, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
22 15 0.14
23 5 0.05
27 5 0.05
28 29 0.26
29 48 0.43
30 9 0.08
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.41
Consensus pattern (28 bp):
GGTTTATGGATTATGGGTTAAGGATTAG
Found at i:9623346 original size:14 final size:15
Alignment explanation
Indices: 9623314--9623459 Score: 58
Period size: 14 Copynumber: 10.1 Consensus size: 15
9623304 GGTTTATGGA
*
9623314 TTATGGGTTTAA-GGA
1 TTATGGG-TTAAGGGT
*
9623329 TTAT-GGTTAATGGT
1 TTATGGGTTAAGGGT
9623343 TTATGGGTTAAGGG-
1 TTATGGGTTAAGGGT
*
9623357 TTA-GGGTTTAA-GTT
1 TTATGGG-TTAAGGGT
* *
9623371 TTAGGGGGTT-GGGGT
1 TTA-TGGGTTAAGGGT
* * *
9623386 TTA-AGGTTTAGGGG
1 TTATGGGTTAAGGGT
*
9623400 TTAAGGGTTAAGGGT
1 TTATGGGTTAAGGGT
* * *
9623415 TTAT-GTTTTATGGT
1 TTATGGGTTAAGGGT
* * *
9623429 TTA-AGGTTTAGGGG
1 TTATGGGTTAAGGGT
9623443 TTATGGGGTTAAGGGT
1 TTAT-GGGTTAAGGGT
9623459 T
1 T
9623460 AGGGATTTAG
Statistics
Matches: 98, Mismatches: 21, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
13 12 0.12
14 44 0.45
15 30 0.31
16 12 0.12
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (15 bp):
TTATGGGTTAAGGGT
Found at i:9623411 original size:43 final size:42
Alignment explanation
Indices: 9623340--9623475 Score: 112
Period size: 43 Copynumber: 3.1 Consensus size: 42
9623330 TATGGTTAAT
* * * * *
9623340 GGTTTATGGGTTAAGGGTT-AGGGTTTAAGTTTTAGGGGGTTGG
1 GGTTTAAGGTTTAGGGGTTAAGGG-TTAAGGTTTA-GGGGTTAG
* ** *
9623383 GGTTTAAGGTTTAGGGGTTAAGGGTTAAGGGTTTATGTTTTAT
1 GGTTTAAGGTTTAGGGGTTAAGGGTTAA-GGTTTAGGGGTTAG
* * *
9623426 GGTTTAAGGTTTAGGGGTTATGGGGTTAAGGGTTAGGGATTTAG
1 GGTTTAAGGTTTAGGGGTTA-AGGGTTAAGGTTTAGGG-GTTAG
9623470 GGTTTA
1 GGTTTA
9623476 GATTAATTAG
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
43 49 0.65
44 26 0.35
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (42 bp):
GGTTTAAGGTTTAGGGGTTAAGGGTTAAGGTTTAGGGGTTAG
Found at i:9623475 original size:7 final size:7
Alignment explanation
Indices: 9623340--9623476 Score: 80
Period size: 7 Copynumber: 19.0 Consensus size: 7
9623330 TATGGTTAAT
9623340 GGTTTATG
1 GGTTTA-G
*
9623348 GGTTAAG
1 GGTTTAG
9623355 GG-TTAG
1 GGTTTAG
*
9623361 GGTTTAA
1 GGTTTAG
*
9623368 GTTTTAGG
1 GGTTTA-G
* *
9623376 GGGTTGG
1 GGTTTAG
*
9623383 GGTTTAA
1 GGTTTAG
9623390 GGTTTAGG
1 GGTTTA-G
*
9623398 GGTTAAG
1 GGTTTAG
*
9623405 GGTTAAG
1 GGTTTAG
*
9623412 GGTTTAT
1 GGTTTAG
* *
9623419 GTTTTAT
1 GGTTTAG
*
9623426 GGTTTAA
1 GGTTTAG
9623433 GGTTTAGG
1 GGTTTA-G
*
9623441 GGTTATGG
1 GGTT-TAG
*
9623449 GGTTAAG
1 GGTTTAG
9623456 GG-TTAG
1 GGTTTAG
9623462 GGATTTAG
1 GG-TTTAG
9623470 GGTTTAG
1 GGTTTAG
9623477 ATTAATTAGT
Statistics
Matches: 99, Mismatches: 23, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
6 10 0.10
7 60 0.61
8 28 0.28
9 1 0.01
ACGTcount: A:0.19, C:0.00, G:0.41, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:9626743 original size:2 final size:2
Alignment explanation
Indices: 9626736--9626760 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9626726 CGAATTTAAC
9626736 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9626761 CTAAATGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9628633 original size:19 final size:17
Alignment explanation
Indices: 9628611--9628655 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
9628601 AATTTTAATA
*
9628611 TTATTATTTTCATTATTTT
1 TTATTATTTCCA--ATTTT
9628630 TTATTATCTTCCAATTTT
1 TTATTAT-TTCCAATTTT
9628648 TTATTATT
1 TTATTATT
9628656 ATTAGTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 12 0.50
19 7 0.29
20 4 0.17
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTATTTCCAATTTT
Found at i:9628654 original size:3 final size:3
Alignment explanation
Indices: 9628648--9628848 Score: 76
Period size: 3 Copynumber: 68.3 Consensus size: 3
9628638 TTCCAATTTT
* * * * *
9628648 TTA TTA TTA TTA GTG TTA TT- TCA TGA TTA TTA TATA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* * * * * *
9628693 -CA TTCC TTA TT- TTA TT- TT- TTA TT- TTC TTA TTC TTT TTA CTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
9628734 ATA TTA TTA TTA TTA TTA TTA TTC TTA CTA TTA TACA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
** * * * * * * *
9628780 CCA TTA CTA TTT TTA TTA TTC TTT TTC TTAA ATA TTA TTA -TA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
* *
9628825 TTA TTA TT- TTA CTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
9628849 ATACTATAAT
Statistics
Matches: 142, Mismatches: 45, Indels: 22
0.68 0.22 0.11
Matches are distributed among these distances:
2 14 0.10
3 120 0.85
4 8 0.06
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:9628777 original size:25 final size:25
Alignment explanation
Indices: 9628738--9628842 Score: 92
Period size: 25 Copynumber: 4.2 Consensus size: 25
9628728 TTACTAATAT
9628738 TATTAT-TATTATTATTATTCTTAC
1 TATTATATATTATTATTATTCTTAC
* *
9628762 TATTATACATTATTATTA-CCATTAC
1 TATTATATATTATTATTATTC-TTAC
* * * *
9628787 TATT-TTTATTATTCTTTTTCTTAAA
1 TATTATATATTATTATTATTCTT-AC
*
9628812 TATTATTATACTATTATTATT-TTAC
1 TATTA-TATATTATTATTATTCTTAC
9628837 TATTAT
1 TATTAT
9628843 TTTTATATAC
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
24 19 0.31
25 30 0.48
26 2 0.03
27 11 0.18
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTATATATTATTATTATTCTTAC
Found at i:9628831 original size:14 final size:14
Alignment explanation
Indices: 9628812--9628849 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
9628802 TTTTCTTAAA
9628812 TATTATTATACTAT
1 TATTATTATACTAT
*
9628826 TATTATTTTACTAT
1 TATTATTATACTAT
*
9628840 TATTTTTATA
1 TATTATTATA
9628850 TACTATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTATTATACTAT
Found at i:9630293 original size:16 final size:16
Alignment explanation
Indices: 9630272--9630302 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9630262 CTATGCATGC
*
9630272 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
9630288 AAAATACAAAAGACA
1 AAAATACAAAAGACA
9630303 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:9635696 original size:26 final size:26
Alignment explanation
Indices: 9635656--9635740 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
9635646 TCCGCTCATA
* *
9635656 GTCCTCCGACCAACTCAAATTCAAAG
1 GTCCTCCAACCAACTCAAACTCAAAG
*
9635682 GTCCTCCAACTAACTCAAACTC-AAG
1 GTCCTCCAACCAACTCAAACTCAAAG
* * * *
9635707 AGACCTCTAACCCATCTCAAACTCAAGG
1 -GTCCTCCAA-CCAACTCAAACTCAAAG
9635735 GTCCTC
1 GTCCTC
9635741 AGACCCACTC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
25 3 0.06
26 26 0.55
27 16 0.34
28 2 0.04
ACGTcount: A:0.33, C:0.36, G:0.11, T:0.20
Consensus pattern (26 bp):
GTCCTCCAACCAACTCAAACTCAAAG
Found at i:9635740 original size:27 final size:25
Alignment explanation
Indices: 9635668--9635752 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 25
9635658 CCTCCGACCA
* * **
9635668 ACTCAAATTCAAAGGTCCTCCAACTA
1 ACTCAAACTCAAGGGTCCT-CAACCC
* *
9635694 ACTCAAACTCAAGAGACCTCTAACCC
1 ACTCAAACTCAAGGGTCCTC-AACCC
9635720 ATCTCAAACTCAAGGGTCCTCAGACCC
1 A-CTCAAACTCAAGGGTCCTCA-ACCC
9635747 ACTCAA
1 ACTCAA
9635753 TCTTGCTAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.02
26 25 0.52
27 22 0.46
ACGTcount: A:0.36, C:0.35, G:0.09, T:0.19
Consensus pattern (25 bp):
ACTCAAACTCAAGGGTCCTCAACCC
Found at i:9640089 original size:12 final size:11
Alignment explanation
Indices: 9640064--9640110 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
9640054 TTTACAAATA
9640064 AAATATAT-AT
1 AAATATATAAT
9640074 AAATCATATAAT
1 AAAT-ATATAAT
9640086 AAATAATATAA-
1 AAAT-ATATAAT
9640097 AAATATATAAT
1 AAATATATAAT
9640108 AAA
1 AAA
9640111 ATGTATACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
10 10 0.30
11 11 0.33
12 12 0.36
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATATATAAT
Found at i:9640089 original size:22 final size:22
Alignment explanation
Indices: 9640064--9640110 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
9640054 TTTACAAATA
*
9640064 AAAT-ATATATAAATCATATAAT
1 AAATAATATAAAAAT-ATATAAT
9640086 AAATAATATAAAAATATATAAT
1 AAATAATATAAAAATATATAAT
9640108 AAA
1 AAA
9640111 ATGTATACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATAATATAAAAATATATAAT
Found at i:9640111 original size:12 final size:12
Alignment explanation
Indices: 9640060--9640117 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
9640050 ATAATTTACA
9640060 AATAAAATATAT
1 AATAAAATATAT
9640072 -AT-AAATCATAT
1 AATAAAAT-ATAT
9640083 AAT-AAATA-AT
1 AATAAAATATAT
9640093 -ATAAAAATATAT
1 AAT-AAAATATAT
*
9640105 AATAAAATGTAT
1 AATAAAATATAT
9640117 A
1 A
9640118 CAGTATACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 2 0.05
10 6 0.15
11 12 0.31
12 17 0.44
13 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (12 bp):
AATAAAATATAT
Found at i:9640117 original size:22 final size:23
Alignment explanation
Indices: 9640060--9640117 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
9640050 ATAATTTACA
*
9640060 AATAAAATATATATAAATCATAT
1 AATAAAATATATAAAAATCATAT
9640083 AAT-AAATAATATAAAAAT-ATAT
1 AATAAAAT-ATATAAAAATCATAT
*
9640105 AATAAAATGTATA
1 AATAAAATATATA
9640118 CAGTATACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAAAATATATAAAAATCATAT
Found at i:9640535 original size:23 final size:22
Alignment explanation
Indices: 9640486--9640541 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
9640476 TAATTAATAA
9640486 AATATAAATAATATATATACCAT
1 AATA-AAATAATATATATACCAT
9640509 -ATAAAATAATATAATAATA-CAT
1 AATAAAATAATAT-AT-ATACCAT
9640531 AATAAAATAAT
1 AATAAAATAAT
9640542 TTTATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 9 0.30
22 8 0.27
23 13 0.43
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AATAAAATAATATATATACCAT
Found at i:9641447 original size:18 final size:18
Alignment explanation
Indices: 9641424--9641482 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
9641414 TAAACCACTA
9641424 TGTTTTATTATATATGTG
1 TGTTTTATTATATATGTG
* * ** * *
9641442 TGTTTTTTTCTCCA-CTA
1 TGTTTTATTATATATGTG
9641459 TGTTTTATTATATATGTG
1 TGTTTTATTATATATGTG
9641477 TGTTTT
1 TGTTTT
9641483 TTTCTCAAAA
Statistics
Matches: 28, Mismatches: 12, Indels: 2
0.67 0.29 0.05
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.63
Consensus pattern (18 bp):
TGTTTTATTATATATGTG
Found at i:9641457 original size:35 final size:35
Alignment explanation
Indices: 9641418--9641488 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
9641408 CTTTGATAAA
9641418 CCACTATGTTTTATTATATATGTGTGTTTTTTTCT
1 CCACTATGTTTTATTATATATGTGTGTTTTTTTCT
9641453 CCACTATGTTTTATTATATATGTGTGTTTTTTTCT
1 CCACTATGTTTTATTATATATGTGTGTTTTTTTCT
9641488 C
1 C
9641489 AAAAATGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (35 bp):
CCACTATGTTTTATTATATATGTGTGTTTTTTTCT
Found at i:9642942 original size:3 final size:3
Alignment explanation
Indices: 9642934--9642980 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
9642924 GTTTACTACC
9642934 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9642981 CATCATCATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9642985 original size:3 final size:3
Alignment explanation
Indices: 9642979--9643005 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9642969 TATTATTATT
9642979 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
9643006 TTAATATATA
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:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:9652009 original size:7 final size:7
Alignment explanation
Indices: 9651997--9652021 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9651987 TCAAAGTCTG
9651997 TATGGAT
1 TATGGAT
9652004 TATGGAT
1 TATGGAT
9652011 TATGGAT
1 TATGGAT
9652018 TATG
1 TATG
9652022 AGCTCGCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (7 bp):
TATGGAT
Found at i:9654814 original size:18 final size:18
Alignment explanation
Indices: 9654774--9654817 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
9654764 AAATAAAAAT
*
9654774 AATTTTTAAAATTTACAA
1 AATTTATAAAATTTACAA
*
9654792 TATTTATAAAAGTTT-CAA
1 AATTTATAAAA-TTTACAA
9654810 AATTTATA
1 AATTTATA
9654818 TTCTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTTATAAAATTTACAA
Found at i:9658633 original size:6 final size:6
Alignment explanation
Indices: 9658614--9658677 Score: 56
Period size: 6 Copynumber: 10.2 Consensus size: 6
9658604 CAGATGAAGT
* * * * *
9658614 AAAAGA AAAGGA AAAAGA AACAGAAA CAAAAGA AAAGGT AAAAGA AGAAGA
1 AAAAGA AAAAGA AAAAGA AA-A-AGA -AAAAGA AAAAGA AAAAGA AAAAGA
9658665 AAAAGA AAAAGA A
1 AAAAGA AAAAGA A
9658678 GAGATTGCCA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
6 37 0.82
7 3 0.07
8 3 0.07
9 2 0.04
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:9665915 original size:22 final size:22
Alignment explanation
Indices: 9665887--9665930 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
9665877 ATGGGTCGAA
9665887 ACTGAAATAAAGGAACTTTGGC
1 ACTGAAATAAAGGAACTTTGGC
9665909 ACTGAAATAAAGGAACTTTGGC
1 ACTGAAATAAAGGAACTTTGGC
9665931 TAAGAAAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (22 bp):
ACTGAAATAAAGGAACTTTGGC
Found at i:9667912 original size:42 final size:42
Alignment explanation
Indices: 9667857--9667972 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 42
9667847 GCACACAAGT
* * * **
9667857 GCTAAACGAAAACCCGTAAGGGTTGAA-TAGAAGCTCGTAAGA
1 GCTAAACAAAAACCCATAAGGGTTAAACT-GAAGCTCAAAAGA
*
9667899 GCTGAACAAAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
1 GCTAAACAAAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
*
9667941 GCTAAACGAAAACCCA-ATAGGGTTAAACTGAA
1 GCTAAACAAAAACCCATA-AGGGTTAAACTGAA
9667973 AATCATACGA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.02
42 62 0.97
43 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (42 bp):
GCTAAACAAAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
Found at i:9670342 original size:528 final size:528
Alignment explanation
Indices: 9669346--9670405 Score: 2102
Period size: 528 Copynumber: 2.0 Consensus size: 528
9669336 TTGAATCACT
9669346 GTCTTTAACACCACCGGAAATTAGGTTGTTATAAGTACGGATTTCAAAGGCTGATGGGTGAAGCT
1 GTCTTTAACACCACCGGAAATTAGGTTGTTATAAGTACGGATTTCAAAGGCTGATGGGTGAAGCT
9669411 TGAACAATATTTTCATTGCTGAAGGAGTGCTTGATTGTGATAAAGTGTGCACAATGATGTTACAT
66 TGAACAATATTTTCATTGCTGAAGGAGTGCTTGATTGTGATAAAGTGTGCACAATGATGTTACAT
9669476 CTGGAGGGTTGGGCATTCGATTGGCACCATTTCTATGCCTAGAAGCATGGTGGTCTCCATTTGCT
131 CTGGAGGGTTGGGCATTCGATTGGCACCATTTCTATGCCTAGAAGCATGGTGGTCTCCATTTGCT
9669541 ACATTGGACATGTTATGCTTACAGTTTAAGAGGGATTTGAGTTGAGCATCTTCAAGGATCCTAAG
196 ACATTGGACATGTTATGCTTACAGTTTAAGAGGGATTTGAGTTGAGCATCTTCAAGGATCCTAAG
9669606 GTGGAGTTGGTGACACTGAAGCGACAAGAATCTAAGGAGCACTACCATGACCAGTTTGTAAGTCT
261 GTGGAGTTGGTGACACTGAAGCGACAAGAATCTAAGGAGCACTACCATGACCAGTTTGTAAGTCT
9669671 TTTGAAAGCCTGAGTCTTATGCCTTCAATATATTTGTTAGTAATCTGAAATTGGAAATTAGTCAA
326 TTTGAAAGCCTGAGTCTTATGCCTTCAATATATTTGTTAGTAATCTGAAATTGGAAATTAGTCAA
9669736 TATCTTCAACTCTTTAGACCTCAAACGTTGGTAGACAGTTTCCATATTGCCAGGAAAGTCAAAAC
391 TATCTTCAACTCTTTAGACCTCAAACGTTGGTAGACAGTTTCCATATTGCCAGGAAAGTCAAAAC
*
9669801 TATTTTTAAGGACCCTCCTAGGTATAATTCACCTATGCCATTTTCTTCTGTCTCCAATAGACCAA
456 TATTTTTAAGGACCCTCCTAGGTATAATTCACCTATGCCATTTTCTTCTGTCTCCAATAAACCAA
9669866 CTAGTTTC
521 CTAGTTTC
9669874 GTCTTTAACACCACCGGAAATTAGGTTGTTATAAGTACGGATTTCAAAGGCTGATGGGTGAAGCT
1 GTCTTTAACACCACCGGAAATTAGGTTGTTATAAGTACGGATTTCAAAGGCTGATGGGTGAAGCT
9669939 TGAACAATATTTTCATTGCTGAAGGAGTGCTTGATTGTGATAAAGTGTGCACAATGATGTTACAT
66 TGAACAATATTTTCATTGCTGAAGGAGTGCTTGATTGTGATAAAGTGTGCACAATGATGTTACAT
*
9670004 CTGGAGGGTTGGGCATTCGATTGGCACCATTTTTATGCCTAGAAGCATGGTGGTCTCCATTTGCT
131 CTGGAGGGTTGGGCATTCGATTGGCACCATTTCTATGCCTAGAAGCATGGTGGTCTCCATTTGCT
9670069 ACATTGGACATGTTATGCTTACAGTTTAAGAGGGATTTGAGTTGAGCATCTTCAAGGATCCTAAG
196 ACATTGGACATGTTATGCTTACAGTTTAAGAGGGATTTGAGTTGAGCATCTTCAAGGATCCTAAG
9670134 GTGGAGTTGGTGACACTGAAGCGACAAGAATCTAAGGAGCACTACCATGACCAGTTTGTAAGTCT
261 GTGGAGTTGGTGACACTGAAGCGACAAGAATCTAAGGAGCACTACCATGACCAGTTTGTAAGTCT
9670199 TTTGAAAGCCTGAGTCTTATGCCTTCAATATATTTGTTAGTAATCTGAAATTGGAAATTAGTCAA
326 TTTGAAAGCCTGAGTCTTATGCCTTCAATATATTTGTTAGTAATCTGAAATTGGAAATTAGTCAA
9670264 TATCTTCAACTCTTTAGACCTCAAACGTTGGTAGACAGTTTCCATATTGCCAGGAAAGTCAAAAC
391 TATCTTCAACTCTTTAGACCTCAAACGTTGGTAGACAGTTTCCATATTGCCAGGAAAGTCAAAAC
9670329 TATTTTTAAGGACCCTCCTAGGTATAATTCACCTATGCCATTTTCTTCTGTCTCCAATAAACCAA
456 TATTTTTAAGGACCCTCCTAGGTATAATTCACCTATGCCATTTTCTTCTGTCTCCAATAAACCAA
9670394 CTAGTTTC
521 CTAGTTTC
9670402 GTCT
1 GTCT
9670406 AATCTACTTC
Statistics
Matches: 530, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
528 530 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (528 bp):
GTCTTTAACACCACCGGAAATTAGGTTGTTATAAGTACGGATTTCAAAGGCTGATGGGTGAAGCT
TGAACAATATTTTCATTGCTGAAGGAGTGCTTGATTGTGATAAAGTGTGCACAATGATGTTACAT
CTGGAGGGTTGGGCATTCGATTGGCACCATTTCTATGCCTAGAAGCATGGTGGTCTCCATTTGCT
ACATTGGACATGTTATGCTTACAGTTTAAGAGGGATTTGAGTTGAGCATCTTCAAGGATCCTAAG
GTGGAGTTGGTGACACTGAAGCGACAAGAATCTAAGGAGCACTACCATGACCAGTTTGTAAGTCT
TTTGAAAGCCTGAGTCTTATGCCTTCAATATATTTGTTAGTAATCTGAAATTGGAAATTAGTCAA
TATCTTCAACTCTTTAGACCTCAAACGTTGGTAGACAGTTTCCATATTGCCAGGAAAGTCAAAAC
TATTTTTAAGGACCCTCCTAGGTATAATTCACCTATGCCATTTTCTTCTGTCTCCAATAAACCAA
CTAGTTTC
Found at i:9677866 original size:14 final size:14
Alignment explanation
Indices: 9677833--9677868 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
9677823 ATATGGTAAA
*
9677833 ATATAATATAAATT
1 ATATAATATAAATC
*
9677847 AAATAATATAAATC
1 ATATAATATAAATC
9677861 ATATAATA
1 ATATAATA
9677869 AATAATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATAATATAAATC
Found at i:9677871 original size:12 final size:11
Alignment explanation
Indices: 9677832--9677892 Score: 58
Period size: 11 Copynumber: 5.5 Consensus size: 11
9677822 AATATGGTAA
9677832 AATATAATATA-
1 AATA-AATATAT
9677843 AATTAAATA-AT
1 AA-TAAATATAT
9677854 -ATAAATCATAT
1 AATAAAT-ATAT
9677865 AATAAATAATAT
1 AATAAAT-ATAT
9677877 AA-AAATATAT
1 AATAAATATAT
9677887 AATAAA
1 AATAAA
9677893 ATGTATACAG
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
9 5 0.12
10 9 0.21
11 15 0.35
12 14 0.33
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAATATAT
Found at i:9677872 original size:21 final size:21
Alignment explanation
Indices: 9677837--9677892 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
9677827 GGTAAAATAT
9677837 AATATA-AATTAAATAATAT-A
1 AATATATAA-TAAATAATATAA
9677857 AATCATATAATAAATAATATAAA
1 AAT-ATATAATAAATAATAT-AA
9677880 AATATATAATAAA
1 AATATATAATAAA
9677893 ATGTATACAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.09
21 13 0.41
22 12 0.38
23 4 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AATATATAATAAATAATATAA
Found at i:9677885 original size:8 final size:9
Alignment explanation
Indices: 9677832--9677891 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 9
9677822 AATATGGTAA
9677832 AATATAATAT
1 AATATAA-AT
9677842 AA-ATTAAAT
1 AATA-TAAAT
9677851 AATATAAAT
1 AATATAAAT
9677860 CATATAATAAAT
1 -A-AT-ATAAAT
9677872 AATATAAA-
1 AATATAAAT
9677880 AATATATAAT
1 AATATA-AAT
9677890 AA
1 AA
9677892 AATGTATACA
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
8 6 0.14
9 17 0.40
10 11 0.26
11 3 0.07
12 6 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
AATATAAAT
Found at i:9677893 original size:12 final size:12
Alignment explanation
Indices: 9677829--9677899 Score: 51
Period size: 12 Copynumber: 5.9 Consensus size: 12
9677819 GGAAATATGG
9677829 TAAAATATA-ATA
1 TAAAATATATA-A
* *
9677841 TAAATTAAATAA
1 TAAAATATATAA
9677853 TATAAATCATATAA
1 TA-AAAT-ATATAA
9677867 T-AAATA-AT-A
1 TAAAATATATAA
9677876 TAAAAATATATAA
1 T-AAAATATATAA
*
9677889 TAAAATGTATA
1 TAAAATATATA
9677900 CAGTATACAA
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
9 2 0.04
10 2 0.04
11 6 0.13
12 25 0.53
13 6 0.13
14 6 0.13
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (12 bp):
TAAAATATATAA
Found at i:9677899 original size:22 final size:23
Alignment explanation
Indices: 9677846--9677892 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
9677836 TAATATAAAT
9677846 TAAATAATAT--AAATCATATAA
1 TAAATAATATAAAAATCATATAA
9677867 TAAATAATATAAAAAT-ATATAA
1 TAAATAATATAAAAATCATATAA
9677889 TAAA
1 TAAA
9677893 ATGTATACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.42
22 10 0.42
23 4 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAATAATATAAAAATCATATAA
Found at i:9678318 original size:23 final size:22
Alignment explanation
Indices: 9678269--9678324 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
9678259 TAATTAAAAA
9678269 AATATAAATAATATATATACCAT
1 AATA-AAATAATATATATACCAT
9678292 -ATAAAATAATATAATAATA-CAT
1 AATAAAATAATAT-AT-ATACCAT
9678314 AATAAAATAAT
1 AATAAAATAAT
9678325 TTTATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 9 0.30
22 8 0.27
23 13 0.43
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AATAAAATAATATATATACCAT
Found at i:9679100 original size:25 final size:25
Alignment explanation
Indices: 9679072--9679119 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
9679062 TGACATGTAG
9679072 GGCGGTCAGAGTTCGAAACGTCTAC
1 GGCGGTCAGAGTTCGAAACGTCTAC
9679097 GGCGGTCAGAGTTCGAAACGTCT
1 GGCGGTCAGAGTTCGAAACGTCT
9679120 TAACACCGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.21
Consensus pattern (25 bp):
GGCGGTCAGAGTTCGAAACGTCTAC
Found at i:9683729 original size:43 final size:43
Alignment explanation
Indices: 9683630--9683752 Score: 117
Period size: 43 Copynumber: 2.9 Consensus size: 43
9683620 ATTGAGATGT
* * * *
9683630 GATTACATGTAAGACCCTGTGTGGGACAATGGCATTGTATTAC
1 GATTACGTATAAGACCCTGTGTGGGACAATGGCATCGTAATAC
* *
9683673 GATTACGTGTAAGACCATGTGTGGGAC-ATCGGCATCGTTAAT-C
1 GATTACGTATAAGACCCTGTGTGGGACAAT-GGCATCG-TAATAC
** *
9683716 GACTT-CGTATAAGACCCTGTGCAGGACAGTGGCATCG
1 GA-TTACGTATAAGACCCTGTGTGGGACAATGGCATCG
9683753 ATATGTGTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
42 2 0.03
43 59 0.88
44 6 0.09
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (43 bp):
GATTACGTATAAGACCCTGTGTGGGACAATGGCATCGTAATAC
Found at i:9686403 original size:42 final size:42
Alignment explanation
Indices: 9686324--9686462 Score: 147
Period size: 43 Copynumber: 3.3 Consensus size: 42
9686314 TCCCGGACGT
* * * *
9686324 GGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGACAG
1 GGTCTTACACGTAAATCAATA-CGATGCCTATGTCCCAGACAC
* *
9686367 GGTCTTACACG-AAATCAGATACGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAAATCA-ATACGATGCCTATGTCCCAGACAC
* * *
9686409 GGTCTTATACGTAAATCTCAAT-CGAGGCCTGTGTCCCAGACAC
1 GGTCTTACACGTAAA--TCAATACGATGCCTATGTCCCAGACAC
9686452 GGTCTTACACG
1 GGTCTTACACG
9686463 ATGTCTCAGA
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
42 33 0.41
43 43 0.53
44 2 0.02
45 3 0.04
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (42 bp):
GGTCTTACACGTAAATCAATACGATGCCTATGTCCCAGACAC
Found at i:9690177 original size:33 final size:33
Alignment explanation
Indices: 9690130--9690206 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
9690120 TGCATTTCGC
* *
9690130 ACTGAACTGATACTGTATAGGGCTCTGGCCCAG
1 ACTGTACTGATACTGAATAGGGCTCTGGCCCAG
* *
9690163 ACTGTACTGATACTGAATAGGGCTTTTGCCCAG
1 ACTGTACTGATACTGAATAGGGCTCTGGCCCAG
*
9690196 ACTGTAGTGAT
1 ACTGTACTGAT
9690207 GCTATGTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.29
Consensus pattern (33 bp):
ACTGTACTGATACTGAATAGGGCTCTGGCCCAG
Found at i:9690509 original size:17 final size:16
Alignment explanation
Indices: 9690467--9690514 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
9690457 CTAGTCTAGG
9690467 AAAACACGAGTTTTCA
1 AAAACACGAGTTTTCA
9690483 AAATAGCACG-GTTTTCTA
1 AAA-A-CACGAGTTTTC-A
9690501 ACAAACACGAGTTT
1 A-AAACACGAGTTT
9690515 CCAACAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.11
17 11 0.41
18 11 0.41
19 2 0.07
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (16 bp):
AAAACACGAGTTTTCA
Found at i:9698524 original size:13 final size:15
Alignment explanation
Indices: 9698504--9698534 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
9698494 GTTTAATACC
9698504 ATTATTATATCGTTAT
1 ATTATTAT-TCGTTAT
9698520 ATTATTATTCGTTAT
1 ATTATTATTCGTTAT
9698535 CTTAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (15 bp):
ATTATTATTCGTTAT
Found at i:9700075 original size:41 final size:41
Alignment explanation
Indices: 9700018--9700100 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
9700008 CAAGTAATTC
9700018 CTGGCATGTGGTTCTGTATTCCAGAAAAGTTCTGGAAAGAG
1 CTGGCATGTGGTTCTGTATTCCAGAAAAGTTCTGGAAAGAG
*
9700059 CTGGCGTGTGGTTCTGTATTCCAGAAAAGTTCTGGAAAGAG
1 CTGGCATGTGGTTCTGTATTCCAGAAAAGTTCTGGAAAGAG
9700100 C
1 C
9700101 AGCCCCATTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (41 bp):
CTGGCATGTGGTTCTGTATTCCAGAAAAGTTCTGGAAAGAG
Found at i:9702922 original size:22 final size:22
Alignment explanation
Indices: 9702836--9702974 Score: 140
Period size: 22 Copynumber: 6.1 Consensus size: 22
9702826 TACCTATATA
9702836 TCAGCTC-GTAAGAGCTTACTGTT
1 TCAGCTCAGT-AGAGCTTACTG-T
*
9702859 TACAGCTCAATAGAGCTTATCAT-T
1 T-CAGCTCAGTAGAGCTTA-C-TGT
*
9702883 TCATCT-AGTATGAGCTTACTGT
1 TCAGCTCAGTA-GAGCTTACTGT
*
9702905 TCAGCTCAGTAGAACTTACTGT
1 TCAGCTCAGTAGAGCTTACTGT
* *
9702927 TCAGCTCAATAGAGCTTACCGTT
1 TCAGCTCAGTAGAGCTTACTG-T
*
9702950 TCAGTTCAGTAGAGCTTACTGT
1 TCAGCTCAGTAGAGCTTACTGT
9702972 TCA
1 TCA
9702975 TCAGCTCAAG
Statistics
Matches: 97, Mismatches: 11, Indels: 17
0.78 0.09 0.14
Matches are distributed among these distances:
21 1 0.01
22 42 0.43
23 35 0.36
24 16 0.16
25 2 0.02
26 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (22 bp):
TCAGCTCAGTAGAGCTTACTGT
Found at i:9702952 original size:67 final size:69
Alignment explanation
Indices: 9702836--9702974 Score: 189
Period size: 67 Copynumber: 2.0 Consensus size: 69
9702826 TACCTATATA
* *
9702836 TCAGCTCGTAAGAGCTTACTGTTTACAGCTCAATAGAGCTTATCATTTCA--TCTAGTATGAGCT
1 TCAGCTCGTAAGAACTTACTGTTTACAGCTCAATAGAGCTTACCATTTCAGTTC-AGTA-GAGCT
9702899 TACTGT
64 TACTGT
*
9702905 TCAGCTCAGT-AGAACTTACTG-TT-CAGCTCAATAGAGCTTACCGTTTCAGTTCAGTAGAGCTT
1 TCAGCTC-GTAAGAACTTACTGTTTACAGCTCAATAGAGCTTACCATTTCAGTTCAGTAGAGCTT
9702967 ACTGT
65 ACTGT
9702972 TCA
1 TCA
9702975 TCAGCTCAAG
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
67 37 0.58
68 6 0.09
69 19 0.30
70 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (69 bp):
TCAGCTCGTAAGAACTTACTGTTTACAGCTCAATAGAGCTTACCATTTCAGTTCAGTAGAGCTTA
CTGT
Found at i:9702953 original size:45 final size:44
Alignment explanation
Indices: 9702846--9702974 Score: 145
Period size: 45 Copynumber: 2.9 Consensus size: 44
9702836 TCAGCTCGTA
* * *
9702846 AGAGCTTACTGTTTACAGCTCAATAGAGCTTATCAT-TTCATCTAGT
1 AGAGCTTACTGTTT-CAGCTCAGTAGAGCTTA-C-TGTTCAGCTAAT
*
9702892 ATGAGCTTACTG-TTCAGCTCAGTAGAACTTACTGTTCAGCTCAAT
1 A-GAGCTTACTGTTTCAGCTCAGTAGAGCTTACTGTTCAGCT-AAT
* *
9702937 AGAGCTTACCGTTTCAGTTCAGTAGAGCTTACTGTTCA
1 AGAGCTTACTGTTTCAGCTCAGTAGAGCTTACTGTTCA
9702975 TCAGCTCAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
43 1 0.01
44 16 0.22
45 42 0.58
46 3 0.04
47 10 0.14
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (44 bp):
AGAGCTTACTGTTTCAGCTCAGTAGAGCTTACTGTTCAGCTAAT
Found at i:9708579 original size:26 final size:26
Alignment explanation
Indices: 9708543--9708597 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
9708533 TACCTTTGAT
9708543 TCAAAATATCACAGAGTTTCACATCC
1 TCAAAATATCACAGAGTTTCACATCC
9708569 TCAAAATATCACAGAGTTTCACATCC
1 TCAAAATATCACAGAGTTTCACATCC
9708595 TCA
1 TCA
9708598 CTAAAGATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.27
Consensus pattern (26 bp):
TCAAAATATCACAGAGTTTCACATCC
Found at i:9712381 original size:26 final size:26
Alignment explanation
Indices: 9712345--9712399 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
9712335 TACCTTTGAT
9712345 TCAAAATATCACAGAGTTTCACATCC
1 TCAAAATATCACAGAGTTTCACATCC
9712371 TCAAAATATCACAGAGTTTCACATCC
1 TCAAAATATCACAGAGTTTCACATCC
9712397 TCA
1 TCA
9712400 CTAAAGATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.27
Consensus pattern (26 bp):
TCAAAATATCACAGAGTTTCACATCC
Found at i:9715166 original size:51 final size:51
Alignment explanation
Indices: 9715090--9715206 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
9715080 CTGATCACAT
*
9715090 TTATCACTTGTCACTTTTAACTGATCAAATAAGTGTAGC-AGAAGCCACCAC
1 TTATCACTTGTCACTTGTAACTGATCAAATAAGTGTAGCTA-AAGCCACCAC
* * * *
9715141 TTATCACTTATCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACTAC
1 TTATCACTTGTCACTTGTAACTGATCAAATAAGTGTAGCTAAAGCCACCAC
9715192 TTATCACTTGTCACT
1 TTATCACTTGTCACT
9715207 GATCAGAAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 58 0.98
52 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTAACTGATCAAATAAGTGTAGCTAAAGCCACCAC
Found at i:9736279 original size:22 final size:24
Alignment explanation
Indices: 9736251--9736303 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
9736241 TATGCTAAGC
* *
9736251 TACCAAACTTTAAACT-GGC-ACA
1 TACCAAAATATAAACTAGGCAACA
9736273 TACCAAAATATAAACTAGGCTAACA
1 TACCAAAATATAAACTAGGC-AACA
9736298 TACCAA
1 TACCAA
9736304 CATAGCCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 14 0.54
23 3 0.12
25 9 0.35
ACGTcount: A:0.47, C:0.25, G:0.08, T:0.21
Consensus pattern (24 bp):
TACCAAAATATAAACTAGGCAACA
Found at i:9738031 original size:9 final size:9
Alignment explanation
Indices: 9738013--9738054 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
9738003 CGTGTGCCCC
*
9738013 TTTCTCTCT
1 TTTCTTTCT
9738022 TTTCTTTC-
1 TTTCTTTCT
9738030 TTTCTTTACTT
1 TTTCTTT-C-T
9738041 TTTCTTTCT
1 TTTCTTTCT
9738050 TTTCT
1 TTTCT
9738055 AATGTTTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 1 0.03
11 7 0.24
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:9747014 original size:59 final size:59
Alignment explanation
Indices: 9746917--9747127 Score: 298
Period size: 59 Copynumber: 3.6 Consensus size: 59
9746907 GTGAAAGTTG
* *
9746917 AAAAGCCCCAGTTGTGTTATCTTTCAAAATTTTATTAAGTATGAAATAACTCGCAGATT
1 AAAATCCCCAGTTGTGTTATCTTTCAAAATTTTCTTAAGTATGAAATAACTCGCAGATT
* * *
9746976 AAAATCCCCAGTTGTGTTATCTTTCAAATTTTTCTTAAGTACGAAATAGA-TCGTAGATT
1 AAAATCCCCAGTTGTGTTATCTTTCAAAATTTTCTTAAGTATGAAATA-ACTCGCAGATT
* * * * *
9747035 AAAATCCCCAATTGTGTTATCTTTCAAAATTTTCTAAAGTATGAAATAGCTTGCGGATT
1 AAAATCCCCAGTTGTGTTATCTTTCAAAATTTTCTTAAGTATGAAATAACTCGCAGATT
* *
9747094 AACATCCCTAGTTGTGTTATCTTTCAAAATTTTC
1 AAAATCCCCAGTTGTGTTATCTTTCAAAATTTTC
9747128 CTATGCCTCG
Statistics
Matches: 134, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
59 133 0.99
60 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (59 bp):
AAAATCCCCAGTTGTGTTATCTTTCAAAATTTTCTTAAGTATGAAATAACTCGCAGATT
Found at i:9749826 original size:8 final size:8
Alignment explanation
Indices: 9749815--9749844 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9749805 TACCTTTTTT
9749815 TTTTTTAC
1 TTTTTTAC
*
9749823 TTTTTAAC
1 TTTTTTAC
9749831 TTTTTTAC
1 TTTTTTAC
9749839 TTTTTT
1 TTTTTT
9749845 TTGTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTAC
Found at i:9749851 original size:16 final size:15
Alignment explanation
Indices: 9749809--9749852 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
9749799 TGTCAGTACC
9749809 TTTTTTTTTTTTACT
1 TTTTTTTTTTTTACT
**
9749824 TTTTAACTTTTTTACT
1 TTTT-TTTTTTTTACT
9749840 TTTTTTTGTTTTT
1 TTTTTTT-TTTTT
9749853 TTTGTCTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTACT
Found at i:9749866 original size:4 final size:4
Alignment explanation
Indices: 9749859--9749889 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
9749849 TTTTTTTGTC
9749859 TTTA TTTA TTTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TT
9749890 ATTATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:9749870 original size:17 final size:17
Alignment explanation
Indices: 9749859--9749902 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
9749849 TTTTTTTGTC
9749859 TTTATTTATTTTATTTA
1 TTTATTTATTTTATTTA
9749876 TTTATTTA-TTTA-TTA
1 TTTATTTATTTTATTTA
*
9749891 -TTATTAATTTTA
1 TTTATTTATTTTA
9749903 AAAATTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.24
15 7 0.28
16 4 0.16
17 8 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTATTTTATTTA
Found at i:9749883 original size:21 final size:22
Alignment explanation
Indices: 9749859--9749900 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
9749849 TTTTTTTGTC
*
9749859 TTTATTTATT-TTATTTATTTA
1 TTTATTTATTATTATTAATTTA
9749880 TTTATTTATTATTATTAATTT
1 TTTATTTATTATTATTAATTT
9749901 TAAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTATTATTATTAATTTA
Found at i:9749957 original size:24 final size:23
Alignment explanation
Indices: 9749897--9749975 Score: 83
Period size: 22 Copynumber: 3.4 Consensus size: 23
9749887 ATTATTATTA
9749897 ATTTTAAAA-ATTTTGAAATATAT
1 ATTTTAAAATATTTT-AAATATAT
9749920 A-TTTAAAATATTTTATTAATATAT
1 ATTTTAAAATATTTTA--AATATAT
**
9749944 ATTTTTTAAT-TTTTAAATATAT
1 ATTTTAAAATATTTTAAATATAT
*
9749966 ATTTTGAAAT
1 ATTTTAAAAT
9749976 TACTTTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
22 23 0.48
23 6 0.12
24 13 0.27
25 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (23 bp):
ATTTTAAAATATTTTAAATATAT
Found at i:9749960 original size:34 final size:34
Alignment explanation
Indices: 9749921--9750011 Score: 107
Period size: 34 Copynumber: 2.6 Consensus size: 34
9749911 GAAATATATA
*
9749921 TTTAAA-ATATTTTATTAATATATA-TTTTTTAATT
1 TTTAAATATATTTT-TTAATAT-TACTTTTTTAAAT
*
9749955 TTTAAATATATATTTTGAA-ATTACTTTTTTAAAT
1 TTTAAATATAT-TTTTTAATATTACTTTTTTAAAT
9749989 TTTAAATATTATTTTTTAATATT
1 TTTAAATA-TATTTTTTAATATT
9750012 TAAATATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
33 2 0.04
34 31 0.63
35 13 0.27
36 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (34 bp):
TTTAAATATATTTTTTAATATTACTTTTTTAAAT
Found at i:9749990 original size:21 final size:22
Alignment explanation
Indices: 9749964--9750019 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
9749954 TTTTAAATAT
*
9749964 ATATTTTGAA-ATTACTTTTTTA
1 ATATTTTAAATATTA-TTTTTTA
9749986 A-ATTTTAAATATTATTTTTTA
1 ATATTTTAAATATTATTTTTTA
9750007 ATA-TTTAAATATT
1 ATATTTTAAATATT
9750020 TTAAACTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
ATATTTTAAATATTATTTTTTA
Found at i:9750071 original size:19 final size:19
Alignment explanation
Indices: 9750044--9750093 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
9750034 TTTTTATTAG
9750044 TTTTATAATTATTTA-AATA
1 TTTT-TAATTATTTATAATA
*
9750063 TTATTTAATTTTTTATAATA
1 TT-TTTAATTATTTATAATA
*
9750083 TTTTAAATTAT
1 TTTTTAATTAT
9750094 GATTTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAATTATTTATAATA
Found at i:9750385 original size:23 final size:22
Alignment explanation
Indices: 9750359--9750434 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 22
9750349 TTTGTTATTA
*
9750359 ATTTTAAAAATTTTAACATGTAT
1 ATTTTAAAAATTTTAA-ATATAT
* **
9750382 ATTTGAAATGTTTTATAATATAT
1 ATTTTAAAAATTTTA-AATATAT
*
9750405 ATTTTTTAAAATTTTAAATAT-T
1 A-TTTTAAAAATTTTAAATATAT
9750427 ATTTTAAA
1 ATTTTAAA
9750435 TTATTTTTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
21 6 0.14
22 2 0.05
23 23 0.55
24 11 0.26
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTTAAAAATTTTAAATATAT
Found at i:9750448 original size:12 final size:11
Alignment explanation
Indices: 9750403--9750451 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
9750393 TTTATAATAT
9750403 ATATTTTTTAA
1 ATATTTTTTAA
9750414 A-A--TTTTAA
1 ATATTTTTTAA
9750422 ATATTATTTTAA
1 ATATT-TTTTAA
9750434 ATTATTTTTTAA
1 A-TATTTTTTAA
9750446 AT-TTTT
1 ATATTTT
9750452 AATATTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 5 0.15
11 2 0.06
12 14 0.42
13 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTTTTTAA
Found at i:9750460 original size:21 final size:21
Alignment explanation
Indices: 9750427--9750490 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
9750417 TTTAAATATT
9750427 ATTTTAA-ATTATTTTTTAAA
1 ATTTTAATATTATTTTTTAAA
*
9750447 TTTTTAATATTATTTTTTAAA
1 ATTTTAATATTATTTTTTAAA
* * *
9750468 AATTAAATATATATTTTTAAAA
1 ATTTTAATAT-TATTTTTTAAA
9750490 A
1 A
9750491 AAAAATTTAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.16
21 20 0.54
22 11 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTAATATTATTTTTTAAA
Found at i:9750496 original size:21 final size:21
Alignment explanation
Indices: 9750452--9750506 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
9750442 TTAAATTTTT
**
9750452 AATATTATTTTTTAAAAATTA
1 AATATTATTTTTTAAAAAAAA
9750473 AATA-TATATTTTTAAAAAAAA
1 AATATTAT-TTTTTAAAAAAAA
9750494 AAT-TTACTTTTTT
1 AATATTA-TTTTTT
9750507 TTAAACTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 3 0.10
21 25 0.86
22 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTATTTTTTAAAAAAAA
Found at i:9750595 original size:13 final size:14
Alignment explanation
Indices: 9750577--9750605 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9750567 TTTATTTTTA
9750577 TTTTATT-TTAATT
1 TTTTATTATTAATT
9750590 TTTTATTATTAATT
1 TTTTATTATTAATT
9750604 TT
1 TT
9750606 AAAAAACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTATTAATT
Found at i:9750604 original size:20 final size:18
Alignment explanation
Indices: 9750571--9750607 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
9750561 TATTTATTTA
9750571 TTTTTATTTTATTTTAAT
1 TTTTTATTTTATTTTAAT
9750589 TTTTTATTATTAATTTTAA
1 TTTTTATT-TT-ATTTTAA
9750608 AAAACTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTATTTTATTTTAAT
Found at i:9750668 original size:22 final size:23
Alignment explanation
Indices: 9750621--9750680 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
9750611 ACTTGAAATG
9750621 TATATTTTAAATGTTTTATAATATA
1 TATATTTTAAA--TTTTATAATATA
*
9750646 TATTTTTTAAATTTTA-AATATA
1 TATATTTTAAATTTTATAATATA
*
9750668 TATATTTGAAATT
1 TATATTTTAAATT
9750681 ATTTTTCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.53
23 5 0.16
25 10 0.31
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (23 bp):
TATATTTTAAATTTTATAATATA
Found at i:9750742 original size:34 final size:34
Alignment explanation
Indices: 9750658--9750746 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 34
9750648 TTTTTTAAAT
* * * * *
9750658 TTTAAATATATATATTTGAAATTATTTTTCTAAAT
1 TTTAAATAT-TATTTTTTAAATCATTTTTCAAAAA
*
9750693 TTTAAATGTTA-TTTTTAAATCATTGTTT-AAAAA
1 TTTAAATATTATTTTTTAAATCATT-TTTCAAAAA
9750726 TTTAAATATTATTTTTTAAAT
1 TTTAAATATTATTTTTTAAAT
9750747 ATTAAAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
33 23 0.51
34 14 0.31
35 8 0.18
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (34 bp):
TTTAAATATTATTTTTTAAATCATTTTTCAAAAA
Found at i:9750772 original size:20 final size:20
Alignment explanation
Indices: 9750722--9750773 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
9750712 TCATTGTTTA
*
9750722 AAAAT-TTAAATATTATTTTT
1 AAAATATTAAA-AATATTTTT
*
9750742 TAAATATTAAAAATATTTTT
1 AAAATATTAAAAATATTTTT
9750762 AATAATA-TAAAA
1 AA-AATATTAAAA
9750774 CATTTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATATTAAAAATATTTTT
Found at i:9750831 original size:136 final size:137
Alignment explanation
Indices: 9750678--9751027 Score: 382
Period size: 139 Copynumber: 2.6 Consensus size: 137
9750668 TATATTTGAA
* * *
9750678 ATTATTTTTCTAA-ATTTTAAATGTTAT-TTTTAAATCATTGTTTAAAAATTTAAATATTATTTT
1 ATTAGTTTTATAATATTTTAAATGTTATATTTTAAAT--TTGTTTTAAAATTTAAATATTATTTT
* *
9750741 TTAAA-TATTAAA-AAT-ATTTT-TAATAATATAAAACAT-TTAAATATTTTAAAGATATGACCT
64 TTAAATTATTAAATAATGATTTTGAAATAATATAAAACATATT--AT-TTTTAAAGATATGACAT
9750801 TTCAAATTTATT
126 TTCAAATTTATT
* **
9750813 ATTAGTTTTATAATATTTTAAATG-TATATTTT-AATTTGTTTTATAATTT-TTTAATTATGATT
1 ATTAGTTTTATAATATTTTAAATGTTATATTTTAAATTTGTTTTAAAATTTAAAT-ATTAT--TT
* * * *
9750875 TTTAAATTATTTTAAATTATGATTTTGAAATCATTTAAAATATATTATTTTTAAAGATATGACAT
63 TTTAAATTA--TTAAATAATGATTTTGAAATAATATAAAACATATTATTTTTAAAGATATGACAT
9750940 TTCAAATTTATT
126 TTCAAATTTATT
* * *
9750952 ATTTGTTTTATAATATTTTAAAT-TTATATTTTAAATTT-TTTTAAATTTTAAATATAATTTTTA
1 ATTAGTTTTATAATATTTTAAATGTTATATTTTAAATTTGTTTTAAAATTTAAATATTATTTTT-
9751015 TAAATTATTAAAT
65 TAAATTATTAAAT
9751028 TTAAAATTAA
Statistics
Matches: 181, Mismatches: 18, Indels: 31
0.79 0.08 0.13
Matches are distributed among these distances:
132 1 0.01
133 17 0.09
135 25 0.14
136 22 0.12
137 4 0.02
138 12 0.07
139 73 0.40
140 13 0.07
141 12 0.07
142 2 0.01
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (137 bp):
ATTAGTTTTATAATATTTTAAATGTTATATTTTAAATTTGTTTTAAAATTTAAATATTATTTTTT
AAATTATTAAATAATGATTTTGAAATAATATAAAACATATTATTTTTAAAGATATGACATTTCAA
ATTTATT
Found at i:9750878 original size:13 final size:13
Alignment explanation
Indices: 9750860--9750900 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
9750850 GTTTTATAAT
9750860 TTTTTAATTATGA
1 TTTTTAATTATGA
*
9750873 TTTTTAA--ATTA
1 TTTTTAATTATGA
*
9750884 TTTTAAATTATGA
1 TTTTTAATTATGA
9750897 TTTT
1 TTTT
9750901 GAAATCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 9 0.39
13 14 0.61
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (13 bp):
TTTTTAATTATGA
Found at i:9750878 original size:33 final size:33
Alignment explanation
Indices: 9750817--9750892 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
9750807 TTTATTATTA
* *
9750817 GTTTTATAATATTTTAAATGTATATTTTAATTT
1 GTTTTATAATTTTTTAAATGTATATTTTAAATT
9750850 GTTTTATAATTTTTT-AAT-TATGATTTTTAAATT
1 GTTTTATAATTTTTTAAATGTAT-A-TTTTAAATT
*
9750883 ATTTTA-AATT
1 GTTTTATAATT
9750893 ATGATTTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 3 0.08
32 8 0.21
33 27 0.71
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (33 bp):
GTTTTATAATTTTTTAAATGTATATTTTAAATT
Found at i:9750892 original size:24 final size:24
Alignment explanation
Indices: 9750851--9750929 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
9750841 TTTTAATTTG
9750851 TTTTATAATT-TTTT-AATTATGAT
1 TTTTA-AATTATTTTAAATTATGAT
9750874 TTTTAAATTATTTTAAATTATGAT
1 TTTTAAATTATTTTAAATTATGAT
* * * *
9750898 TTTGAAATCATTTAAAATATATTAT
1 TTTTAAATTATTTTAAAT-TATGAT
9750923 TTTTAAA
1 TTTTAAA
9750930 GATATGACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 4 0.08
23 9 0.19
24 24 0.50
25 11 0.23
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTAAATTATTTTAAATTATGAT
Found at i:9750982 original size:13 final size:13
Alignment explanation
Indices: 9750964--9750989 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9750954 TTGTTTTATA
9750964 ATATTTTAAATTT
1 ATATTTTAAATTT
9750977 ATATTTTAAATTT
1 ATATTTTAAATTT
9750990 TTTTAAATTT
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:0.00, T:0.62
Consensus pattern (13 bp):
ATATTTTAAATTT
Found at i:9751010 original size:22 final size:23
Alignment explanation
Indices: 9750985--9751027 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
9750975 TTATATTTTA
*
9750985 AATTTTTTTAAATT-TTAAATAT
1 AATTTTTATAAATTATTAAATAT
9751007 AATTTTTATAAATTATTAAAT
1 AATTTTTATAAATTATTAAAT
9751028 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATTTTTATAAATTATTAAATAT
Found at i:9751014 original size:30 final size:29
Alignment explanation
Indices: 9750957--9751041 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 29
9750947 TTATTATTTG
* *
9750957 TTTTATAATATTTTAAATTTATATTTTA-AA
1 TTTTTTAA-ATTTTAAATTAAT-TTTTATAA
9750987 TTTTTTTAAATTTTAAATATAATTTTTATAA
1 -TTTTTTAAATTTTAAAT-TAATTTTTATAA
* * *
9751018 ATTATTAAATTTAAAATTAATTTT
1 TTTTTTAAATTTTAAATTAATTTT
9751042 AAAGATATTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
29 7 0.15
30 28 0.60
31 12 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTTTAAATTTTAAATTAATTTTTATAA
Found at i:9755213 original size:30 final size:30
Alignment explanation
Indices: 9755144--9755247 Score: 120
Period size: 30 Copynumber: 3.5 Consensus size: 30
9755134 CGGTGGTTGC
* * *
9755144 TCTGGGTGAAATGAACTCGAACCGCCTATG
1 TCTGGGTGATATGAACTTGAACTGCCTATG
9755174 TCTGGGTGATATGAACTTGAACTGCCTATG
1 TCTGGGTGATATGAACTTGAACTGCCTATG
* * * *
9755204 T-TCGGGTGATATGTACTTGAACTGGCAATT
1 TCT-GGGTGATATGAACTTGAACTGCCTATG
*
9755234 TCTGAGTGATATGA
1 TCTGGGTGATATGA
9755248 GCTGCTCTGT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
29 1 0.02
30 61 0.97
31 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (30 bp):
TCTGGGTGATATGAACTTGAACTGCCTATG
Found at i:9757595 original size:40 final size:40
Alignment explanation
Indices: 9757562--9757646 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
9757552 AAAAATATAT
* *
9757562 ATTAAGTACATAAATTTATGAATGTGTACTAAAATTAAAAA
1 ATTAA-TACATAAATTTATAAATGTGTACTAAAAATAAAAA
* * *
9757603 ATTAATATATAAATTTATAAATGTGTACTAAAATTTAAAA
1 ATTAATACATAAATTTATAAATGTGTACTAAAAATAAAAA
9757643 ATTA
1 ATTA
9757647 TAACCAACAC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 36 0.88
41 5 0.12
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.38
Consensus pattern (40 bp):
ATTAATACATAAATTTATAAATGTGTACTAAAAATAAAAA
Found at i:9757596 original size:20 final size:20
Alignment explanation
Indices: 9757573--9757644 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
9757563 TTAAGTACAT
*
9757573 AAATTTATGAATGTGTACTA
1 AAATTTATAAATGTGTACTA
* * *
9757593 AAATTAAAAAAT-TAATA-TA
1 AAATTTATAAATGT-GTACTA
9757612 TAAATTTATAAATGTGTACTA
1 -AAATTTATAAATGTGTACTA
*
9757633 AAATTTAAAAAT
1 AAATTTATAAAT
9757645 TATAACCAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (20 bp):
AAATTTATAAATGTGTACTA
Found at i:9758215 original size:24 final size:23
Alignment explanation
Indices: 9758188--9758266 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 23
9758178 CTTTTTTTAT
*
9758188 TAAATAAAAAACTTTAAAATATAA
1 TAAATAAAAAA-TTTAAAACATAA
9758212 TAAATCAAAAAATTTAAAACATAA
1 TAAAT-AAAAAATTTAAAACATAA
*
9758236 -AAATAAATAA--TAAAACA-AA
1 TAAATAAAAAATTTAAAACATAA
9758255 -AAATAAATAAAT
1 TAAATAAA-AAAT
9758267 AATGGGACTA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
19 9 0.18
20 9 0.18
22 5 0.10
23 4 0.08
24 16 0.33
25 6 0.12
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (23 bp):
TAAATAAAAAATTTAAAACATAA
Found at i:9758268 original size:20 final size:20
Alignment explanation
Indices: 9758226--9758264 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
9758216 TCAAAAAATT
9758226 TAAAACATAAAAATAAATAA
1 TAAAACATAAAAATAAATAA
9758246 TAAAACA-AAAAATAAATAA
1 TAAAACATAAAAATAAATAA
9758265 ATAATGGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAAACATAAAAATAAATAA
Found at i:9758791 original size:19 final size:20
Alignment explanation
Indices: 9758753--9758812 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 20
9758743 ACATGATGTG
9758753 ATTTTATAATATATAATTTTA
1 ATTTT-TAATATATAATTTTA
*
9758774 ATTTTTAATTTA-AATTTTA
1 ATTTTTAATATATAATTTTA
*
9758793 CTTTTTAATATATATATTTT
1 ATTTTTAATATATA-ATTTT
9758813 TAAATAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 17 0.50
20 7 0.21
21 10 0.29
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTAATATATAATTTTA
Found at i:9758818 original size:16 final size:15
Alignment explanation
Indices: 9758794--9758845 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
9758784 TAAATTTTAC
*
9758794 TTTTTAATATATATA
1 TTTTTAATAAATATA
*
9758809 TTTTTAAATAAATTTA
1 TTTTT-AATAAATATA
*
9758825 TTTTTTAACAAATAT-
1 -TTTTTAATAAATATA
9758840 TTTTTA
1 TTTTTA
9758846 TTTTCTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 6 0.19
15 5 0.16
16 15 0.48
17 5 0.16
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTAATAAATATA
Found at i:9759240 original size:31 final size:31
Alignment explanation
Indices: 9759128--9759251 Score: 103
Period size: 31 Copynumber: 3.8 Consensus size: 31
9759118 AAATAATTTT
*
9759128 AAAATCATAATTTAAAATATTATAAAA-TAAA
1 AAAATAAT-ATTTAAAATATTATAAAATTAAA
* *
9759159 TTAAATAATATTTAAATTATTATAAAATTAATA
1 -AAAATAATATTTAAAATATTATAAAATTAA-A
9759192 ACAAATTTGAA-AGTTTAAAATATT-TAAATATTAAA
1 A-AAA--T-AATA-TTTAAAATATTATAAA-ATTAAA
*
9759227 AAAATAATATTTAAAAT-TTAAAAAA
1 AAAATAATATTTAAAATATTATAAAA
9759252 AGTAATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
30 3 0.04
31 30 0.39
32 11 0.14
33 4 0.05
34 3 0.04
35 8 0.11
36 17 0.22
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (31 bp):
AAAATAATATTTAAAATATTATAAAATTAAA
Found at i:9759250 original size:23 final size:23
Alignment explanation
Indices: 9759210--9759267 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
9759200 GAAAGTTTAA
9759210 AATATTT-AAATATTAAAAAAAT
1 AATATTTAAAATATTAAAAAAAT
9759232 AATATTTAAAAT-TTAAAAAAAGT
1 AATATTTAAAATATTAAAAAAA-T
*
9759255 AAT-TTCAAAATAT
1 AATATTTAAAATAT
9759268 ATATTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 23 0.72
23 9 0.28
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AATATTTAAAATATTAAAAAAAT
Found at i:9759329 original size:22 final size:22
Alignment explanation
Indices: 9759262--9759332 Score: 81
Period size: 24 Copynumber: 3.1 Consensus size: 22
9759252 AGTAATTTCA
**
9759262 AAATATATA-TTTAAAATTTAAA
1 AAATATATATTTTAAAATTT-TT
*
9759284 AAATATATATTAATAAAATATTTT
1 AAATATATATT-TTAAAAT-TTTT
9759308 AAATATATATTTTAAAATTTTT
1 AAATATATATTTTAAAATTTTT
9759330 AAA
1 AAA
9759333 ATTAATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
22 16 0.38
23 7 0.17
24 17 0.40
25 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATATATATTTTAAAATTTTT
Found at i:9774331 original size:23 final size:23
Alignment explanation
Indices: 9774278--9774333 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
9774268 CCGTTAAATT
*
9774278 AACTTATAAAAAAAATAATATGAC
1 AACTTTTAAAAAAAATAATA-GAC
9774302 AACTTTTAAAATAAATATAATA-AC
1 AACTTTTAAAA-AAA-ATAATAGAC
9774326 AA-TTTTAA
1 AACTTTTAA
9774334 CCTTCAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.21
24 14 0.48
25 3 0.10
26 6 0.21
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (23 bp):
AACTTTTAAAAAAAATAATAGAC
Found at i:9775750 original size:18 final size:17
Alignment explanation
Indices: 9775719--9775757 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
9775709 AATAATTTTA
*
9775719 TTATTTATTAATTATTT
1 TTATTTATTAATTATTG
*
9775736 TTATTCTATTTATTATTG
1 TTATT-TATTAATTATTG
9775754 TTAT
1 TTAT
9775758 ATTAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TTATTTATTAATTATTG
Found at i:9775844 original size:19 final size:19
Alignment explanation
Indices: 9775820--9775870 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 19
9775810 AGTTATAAAA
9775820 ATATTTTAATTAATTAATT
1 ATATTTTAATTAATTAATT
*
9775839 ATATTTTAATT--TTTATT
1 ATATTTTAATTAATTAATT
9775856 ATATTTTAATATAAT
1 ATATTTTAAT-TAAT
9775871 CATACGTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 15 0.54
18 1 0.04
19 11 0.39
20 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTTAATTAATTAATT
Found at i:9775996 original size:18 final size:18
Alignment explanation
Indices: 9775973--9776010 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
9775963 AATAAGTATA
9775973 ATCCGAATCAATTATTAT
1 ATCCGAATCAATTATTAT
9775991 ATCCGAATCAATTATTAT
1 ATCCGAATCAATTATTAT
9776009 AT
1 AT
9776011 AACTCTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (18 bp):
ATCCGAATCAATTATTAT
Found at i:9776067 original size:22 final size:23
Alignment explanation
Indices: 9776019--9776067 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
9776009 ATAACTCTAT
* * *
9776019 TAAACTTATAACCATAATACATT
1 TAAACTTATAACCAAAATAAATC
*
9776042 TAAACTTA-AACTAAAATAAATC
1 TAAACTTATAACCAAAATAAATC
9776064 TAAA
1 TAAA
9776068 GAAAACCCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAACTTATAACCAAAATAAATC
Found at i:9776711 original size:20 final size:20
Alignment explanation
Indices: 9776686--9776725 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9776676 ATATTATATC
9776686 GATTTAGTTATAATTTTAAA
1 GATTTAGTTATAATTTTAAA
9776706 GATTTAGTTATAATTTTAAA
1 GATTTAGTTATAATTTTAAA
9776726 ATATTAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
GATTTAGTTATAATTTTAAA
Found at i:9777554 original size:27 final size:29
Alignment explanation
Indices: 9777504--9777631 Score: 129
Period size: 28 Copynumber: 4.3 Consensus size: 29
9777494 GGTTTTTATT
9777504 AAAATAAATTAAGGTTTATGGA-TTTTAA
1 AAAATAAATTAAGGTTTATGGATTTTTAA
*
9777532 AAAATAAATTAGGGTTTAT-GATTTTTAAAAA
1 AAAATAAATTAAGGTTTATGGATTTTT---AA
* *
9777563 ATAAATTAAATTAAGGTTTAT-TATTTTTTTA
1 A-AAA-TAAATTAAGGTTTATGGA-TTTTTAA
* *
9777594 AAAATAAACTAAGGTTTAGGGATTTTT-A
1 AAAATAAATTAAGGTTTATGGATTTTTAA
9777622 AAAATAAATT
1 AAAATAAATT
9777632 TGTGTTTAGG
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
27 2 0.02
28 32 0.38
29 18 0.21
30 4 0.05
31 5 0.06
32 3 0.04
33 15 0.18
34 5 0.06
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.41
Consensus pattern (29 bp):
AAAATAAATTAAGGTTTATGGATTTTTAA
Found at i:9777573 original size:33 final size:34
Alignment explanation
Indices: 9777536--9777601 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
9777526 TTTTAAAAAA
*
9777536 TAAATTAGGGTTTATGA-TTTTTAAAAAATAAAT
1 TAAATTAAGGTTTATGATTTTTTAAAAAATAAAT
* *
9777569 TAAATTAAGGTTTATTATTTTTTTAAAAATAAA
1 TAAATTAAGGTTTATGATTTTTTAAAAAATAAA
9777602 CTAAGGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (34 bp):
TAAATTAAGGTTTATGATTTTTTAAAAAATAAAT
Found at i:9777611 original size:62 final size:61
Alignment explanation
Indices: 9777503--9777631 Score: 163
Period size: 62 Copynumber: 2.1 Consensus size: 61
9777493 CGGTTTTTAT
* * * *
9777503 TAAAATAAATTAAGGTTTATGGATTTTAAAAAATAAATTAGGGTTTA-TGATTTTTAAAAAA
1 TAAATTAAATTAAGGTTTATGGATTTTAAAAAATAAACTAAGGTTTAGGGATTTTT-AAAAA
* *
9777564 TAAATTAAATTAAGGTTTAT-TATTTTTTTAAAAATAAACTAAGGTTTAGGGATTTTTAAAAA
1 TAAATTAAATTAAGGTTTATGGA--TTTTAAAAAATAAACTAAGGTTTAGGGATTTTTAAAAA
9777626 TAAATT
1 TAAATT
9777632 TGTGTTTAGG
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 1 0.02
61 19 0.32
62 32 0.54
63 7 0.12
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.42
Consensus pattern (61 bp):
TAAATTAAATTAAGGTTTATGGATTTTAAAAAATAAACTAAGGTTTAGGGATTTTTAAAAA
Found at i:9777638 original size:28 final size:27
Alignment explanation
Indices: 9777588--9777646 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
9777578 GTTTATTATT
9777588 TTTTTAAAAATAAACTAAGGTTTAGGG
1 TTTTTAAAAATAAACTAAGGTTTAGGG
**
9777615 ATTTTTAAAAATAAA-TTTGTGTTTAGGG
1 -TTTTTAAAAATAAACTAAG-GTTTAGGG
9777643 TTTT
1 TTTT
9777647 AGGGTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.46
Consensus pattern (27 bp):
TTTTTAAAAATAAACTAAGGTTTAGGG
Found at i:9777886 original size:126 final size:126
Alignment explanation
Indices: 9777716--9778348 Score: 729
Period size: 126 Copynumber: 5.1 Consensus size: 126
9777706 TTTTTTTTGT
* * * * * *
9777716 TCAGCAAAAGTATTGAAAAAAGTTCTCAG-TTGATGCTATTTTTCTACAGTAGTTTCTGAAAAAA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
* * * *
9777780 TAATTTTGAAAAGAT-AGTTCTAAAAAAATAGGGTCAAAAACGCTTCAAGTAAGATGCACTG
66 TAATTTTGAGAAGATGA-TTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAAGATGCACTG
* * * * * *
9777841 TCAGTAAAACTACTGAAAAAAGCTCCCAGCTAGATGCTATGTTTCTACAGTAGTTTCTG----AA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
* * * * * *
9777902 TAATTTTGAGAAGATGGTTCTGAAAAAATAAGGTAAAAAACACTTCAAGCAGGATGCGCTT
66 TAATTTTGAGAAGATGATTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAAGATGCACTG
* *
9777963 TCAGCAAAAGTACTTAAAAAAGCTCCCAGATGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
* * * * * *
9778028 TAATTTTAAGAAGATGATTCTGAAAAAATAAGGTCAAAAACACTTCAAGTAGGATGCACTG
66 TAATTTTGAGAAGATGATTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAAGATGCACTG
*
9778089 TCAGCAAAAGTACAGAAAAAAGCTCCCA-CATGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCAGC-TGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAA
* * * * *
9778153 ATAATTTTGAGAAGATGATTATTAAAATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTG
65 ATAATTTTGAGAAGATGATTCTGAAAAAATAGGGT-AAAAAACGCTTCAAGCAAGATGCACTG
* *
9778216 TCAACAAAAGTACT----AAA----CCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
1 TCAGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
* * * * *
9778273 TAATTTTGAGAAGATGATTATTAAAATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTG
66 TAATTTTGAGAAGATGATTCTGAAAAAATAGGGT-AAAAAACGCTTCAAGCAAGATGCACTG
*
9778335 TCAACAAAAGTACT
1 TCAGCAAAAGTACT
9778349 AAACCACCTG
Statistics
Matches: 452, Mismatches: 47, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
119 114 0.25
120 1 0.00
122 103 0.23
123 3 0.01
125 24 0.05
126 174 0.38
127 33 0.07
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (126 bp):
TCAGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
TAATTTTGAGAAGATGATTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAAGATGCACTG
Found at i:9778021 original size:248 final size:248
Alignment explanation
Indices: 9777715--9778343 Score: 737
Period size: 248 Copynumber: 2.5 Consensus size: 248
9777705 TTTTTTTTTG
* * * * *
9777715 TTCAGCAAAAGTA-TTGAAAAAAGTTCTCAGTTGATGCTATTTTTCTACAGTAGTTTCTGAAAAA
1 TTCAGCAAAAGTACTT-AAAAAAGCTCCCAGTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAA
9777779 ATAATTTTGAAAAGAT-AGTTCTAAAAAAATAGGGTCAAAAACGCTTCAAGTAAGATGCACTGTC
65 ATAATTTTGAAAAGATGA-TTCTAAAAAAATAGGGTCAAAAACGCTTCAAGTAAGATGCACTGTC
* * *
9777843 AGTAAAACTACTGAAAAAAGCTCCCAGC-TAGATGCTATGTTTCTACAGTAGTTTCTG-AATAAT
129 AGCAAAACTACAGAAAAAAGCTCCCA-CATAGACGCTATGTTTCTACAGTAGTTTCTGAAATAAT
* * * *
9777906 TTTGAGAAGATGGTTCTGAAAAAATAAGGTAAAAAACA-CTTCAAGCAGGATGCGCT
193 TTTGAGAAGATGATTATGAAAAAATAAGGTAAAAAA-AGCTTCAAGCAAGATGCACT
9777962 TTCAGCAAAAGTACTTAAAAAAGCTCCCAGATGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAA
1 TTCAGCAAAAGTACTTAAAAAAGCTCCCAG-TGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAA
* * * *
9778027 ATAATTTT-AAGAAGATGATTCTGAAAAAATAAGGTCAAAAACACTTCAAGTAGGATGCACTGTC
65 ATAATTTTGAA-AAGATGATTCTAAAAAAATAGGGTCAAAAACGCTTCAAGTAAGATGCACTGTC
* * * *
9778091 AGCAAAAGTACAGAAAAAAGCTCCCACATGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATA
129 AGCAAAACTACAGAAAAAAGCTCCCACATAGACGCTATGTTTCTACAGTAGTTTCTG---AAATA
* * * *
9778156 ATTTTGAGAAGATGATTATTAAAATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACT
191 ATTTTGAGAAGATGATTATGAAAAAATAAGGTAAAAAAA-GCTTCAAGCAAGATGCACT
* *
9778215 GTCAACAAAAGTAC-T---AAA-C-CACC--TGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAA
1 TTCAGCAAAAGTACTTAAAAAAGCTC-CCAGTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAA
* * * * * * * *
9778272 ATAATTTTGAGAAGATGATTATTAAAATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTGTC
65 ATAATTTTGAAAAGATGATTCTAAAAAAATAGGGT-CAAAAACGCTTCAAGTAAGATGCACTGTC
*
9778337 AACAAAA
129 AGCAAAA
9778344 GTACTAAACC
Statistics
Matches: 330, Mismatches: 38, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
245 62 0.19
246 30 0.09
247 29 0.09
248 139 0.42
249 4 0.01
251 1 0.00
252 38 0.12
253 27 0.08
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (248 bp):
TTCAGCAAAAGTACTTAAAAAAGCTCCCAGTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
TAATTTTGAAAAGATGATTCTAAAAAAATAGGGTCAAAAACGCTTCAAGTAAGATGCACTGTCAG
CAAAACTACAGAAAAAAGCTCCCACATAGACGCTATGTTTCTACAGTAGTTTCTGAAATAATTTT
GAGAAGATGATTATGAAAAAATAAGGTAAAAAAAGCTTCAAGCAAGATGCACT
Found at i:9778286 original size:119 final size:119
Alignment explanation
Indices: 9778114--9778378 Score: 521
Period size: 119 Copynumber: 2.2 Consensus size: 119
9778104 AAAAAAGCTC
*
9778114 CCACATGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGATGATTATTAAA
1 CCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGATGATTATTAAA
9778179 ATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTGTCAACAAAAGTACTAAA
66 ATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTGTCAACAAAAGTACTAAA
9778233 CCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGATGATTATTAAA
1 CCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGATGATTATTAAA
9778298 ATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTGTCAACAAAAGTACTAAA
66 ATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTGTCAACAAAAGTACTAAA
9778352 CCACCTGGACGCTCTTTTTCTACAGTA
1 CCACCTGGACGCTCTTTTTCTACAGTA
9778379 CATCTTGGTT
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 145 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (119 bp):
CCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGATGATTATTAAA
ATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTGTCAACAAAAGTACTAAA
Found at i:9778502 original size:25 final size:25
Alignment explanation
Indices: 9778446--9778517 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
9778436 TTACAATAAG
* *
9778446 AGAAATTAGAGAAGTTCAGAAAAAT
1 AGAAATTAAAGAAGTTCAGAAGAAT
*
9778471 AGAAATTGAAGAAGTTCAGAAGAAT
1 AGAAATTAAAGAAGTTCAGAAGAAT
** * *
9778496 ATCAATTAAACAAGTTAAGAAG
1 AGAAATTAAAGAAGTTCAGAAG
9778518 GTATAAGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (25 bp):
AGAAATTAAAGAAGTTCAGAAGAAT
Found at i:9781037 original size:23 final size:23
Alignment explanation
Indices: 9780955--9781041 Score: 74
Period size: 21 Copynumber: 4.0 Consensus size: 23
9780945 CTTGATCAGT
*
9780955 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* * *
9780977 A-ACGACACACGAGGTGCTTG--
1 ATACGACACACAAAGTGCCTGAA
* * *
9780997 ATATGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
9781020 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
9781042 TCAGTAAAGC
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.02
21 31 0.61
22 1 0.02
23 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:9787611 original size:20 final size:20
Alignment explanation
Indices: 9787586--9787625 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9787576 ATATTATATC
9787586 GATTTAATTATAATTTTAAA
1 GATTTAATTATAATTTTAAA
*
9787606 GATTTAGTTATAATTTTAAA
1 GATTTAATTATAATTTTAAA
9787626 ATATTAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
GATTTAATTATAATTTTAAA
Found at i:9788457 original size:27 final size:28
Alignment explanation
Indices: 9788405--9788532 Score: 139
Period size: 28 Copynumber: 4.4 Consensus size: 28
9788395 GGTTTTTATT
9788405 AAAATAAATTAAGGTTTATGGATTTTAA
1 AAAATAAATTAAGGTTTATGGATTTTAA
* *
9788433 AAAATAAATTAGGGTTTATGGTTTTTAAAAA
1 AAAATAAATTAAGGTTTATGGATTTT---AA
**
9788464 ATAAATTAAATTAAGGTTTATTGTTTTTTAA
1 A-AAA-TAAATTAAGGTTTA-TGGATTTTAA
* * *
9788495 AAAATAAACTAAGGTTTAGGGATTTTTA
1 AAAATAAATTAAGGTTTATGGATTTTAA
9788523 AAAATAAATT
1 AAAATAAATT
9788533 TGTGTTTAGG
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
28 39 0.46
29 13 0.15
30 3 0.04
31 6 0.07
32 3 0.04
33 13 0.15
34 7 0.08
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (28 bp):
AAAATAAATTAAGGTTTATGGATTTTAA
Found at i:9788512 original size:62 final size:61
Alignment explanation
Indices: 9788404--9788532 Score: 179
Period size: 62 Copynumber: 2.1 Consensus size: 61
9788394 CGGTTTTTAT
* * * *
9788404 TAAAATAAATTAAGGTTTATGGATTTTAAAAAATAAATTAGGGTTTATGG-TTTTTAAAAAA
1 TAAATTAAATTAAGGTTTATGGATTTTAAAAAATAAACTAAGGTTTAGGGATTTTT-AAAAA
**
9788465 TAAATTAAATTAAGGTTTATTGTTTTTTAAAAAATAAACTAAGGTTTAGGGATTTTTAAAAA
1 TAAATTAAATTAAGGTTTA-TGGATTTTAAAAAATAAACTAAGGTTTAGGGATTTTTAAAAA
9788527 TAAATT
1 TAAATT
9788533 TGTGTTTAGG
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
61 18 0.30
62 37 0.62
63 5 0.08
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (61 bp):
TAAATTAAATTAAGGTTTATGGATTTTAAAAAATAAACTAAGGTTTAGGGATTTTTAAAAA
Found at i:9788935 original size:247 final size:248
Alignment explanation
Indices: 9788621--9789371 Score: 797
Period size: 247 Copynumber: 3.1 Consensus size: 248
9788611 TTTTGTCCAG
* * * * * *
9788621 TCAGCAAAAGTACTGAAAAAAGTTCTCAGTTGATGCTATTTTTCTACAGTAGTTTCTGAAAAAAT
1 TCAGCAAAAGTACTTAAAAAAGCTCCCAGTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAAT
*
9788686 AATTTTGAAAAGATGGTTCTAAAAAAATAGGGTCAAAAACGCTTCAAGTAAGATGCACTGTCAAC
66 AATTTTGAAAAGATGATTCTAAAAAAATAGGGTCAAAAACGCTTCAAGTAAGATGCACTGTCAAC
* * * *
9788751 AAAACTATTGAAAAAAGCTCCCAGCTGGATGCTATGTTTCTACAGTAGTTTCTG-AATAATTTTA
131 AAAACTACTGAAAAAAGCTCCCAGATGAACGCTATGTTTCTACAGTAGTTTCTGAAATAATTTTA
* * *
9788815 AGAAGATGGTTCTGAAAAAATAGGGTAAAAAACA-CTTCAAGCAAGATGCACTT
196 AGAAGATGATTATGAAAAAATAGGGTAAAAAA-AGCTTCAAGCAAGATGCACTA
9788868 TCAGCAAAAGTACTTAAAAAAGCTCCCAGATGGACGCTCTTTTTCTACAGTAGTTTCTG-AAAAA
1 TCAGCAAAAGTACTTAAAAAAGCTCCCAG-TGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
* * * *
9788932 TAATTTT-AAGAAGATGATTCTGAAAAAATAAGGTCAAAAACACTTCAAGTAGGATGCACTGTCA
65 TAATTTTGAA-AAGATGATTCTAAAAAAATAGGGTCAAAAACGCTTCAAGTAAGATGCACTGTCA
* * * *
9788996 GCAAAAGTACTGAAAAAAGCTCCCAGATGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAA
129 ACAAAACTACTGAAAAAAGCTCCCAGATGAACGCTATGTTTCTACAGTAGTTTCTG---AAATAA
* * * *
9789061 TTTTGAGAAGATGATTATTAAAATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTA
191 TTTTAAGAAGATGATTATGAAAAAATAGGGTAAAAAAA-GCTTCAAGCAAGATGCACTA
** *
9789120 TCAATAAAAGTAC-T---AAA-C-CACC--TGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
1 TCAGCAAAAGTACTTAAAAAAGCTC-CCAGTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAA
* * * * * * * * *
9789177 TAATTTTGAGAAGATGATTATTAAAATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTATCA
65 TAATTTTGAAAAGATGATTCTAAAAAAATAGGGT-CAAAAACGCTTCAAGTAAGATGCACTGTCA
* * * *
9789242 ATAAAAGTACT----AAA-C-CACC---TGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATA
129 ACAAAACTACTGAAAAAAGCTC-CCAGATGAACGCTATGTTTCTACAGTAGTTTCTG---AAATA
* * * *
9789298 ATTTTGAGAAGATGATTATTAAAATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTA
190 ATTTTAAGAAGATGATTATGAAAAAATAGGGTAAAAAAA-GCTTCAAGCAAGATGCACTA
**
9789358 TCAATAAAAGTACT
1 TCAGCAAAAGTACT
9789372 AAACCACCTG
Statistics
Matches: 447, Mismatches: 43, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
238 110 0.25
240 1 0.00
241 3 0.01
242 3 0.01
244 28 0.06
245 32 0.07
246 36 0.08
247 138 0.31
248 29 0.06
250 1 0.00
251 38 0.09
252 28 0.06
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (248 bp):
TCAGCAAAAGTACTTAAAAAAGCTCCCAGTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAAT
AATTTTGAAAAGATGATTCTAAAAAAATAGGGTCAAAAACGCTTCAAGTAAGATGCACTGTCAAC
AAAACTACTGAAAAAAGCTCCCAGATGAACGCTATGTTTCTACAGTAGTTTCTGAAATAATTTTA
AGAAGATGATTATGAAAAAATAGGGTAAAAAAAGCTTCAAGCAAGATGCACTA
Found at i:9788988 original size:125 final size:124
Alignment explanation
Indices: 9788625--9789371 Score: 759
Period size: 119 Copynumber: 6.1 Consensus size: 124
9788615 GTCCAGTCAG
* * * * *
9788625 CAAAAGTACTGAAAAAAGTTCTCAGTTG-ATGCTATTTTTCTACAGTAGTTTCTGAAAAAATAAT
1 CAAAAGTACTTAAAAAAGCTCCCAG-TGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAAT
* * * * *
9788689 TTTGAA-AAGATGGTTCTAAAAAAATAGGGTCAAAAACGCTTCAAGTAAGATGCACTGTCAA
65 TTT-AAGAAGATGATTCTGAAAAAATAGGGT-AAAAACACTTCAAGCAAGATGCACTATCAA
* * * * *
9788750 CAAAACTA-TTGAAAAAAGCTCCCAGCTGGATGCTATGTTTCTACAGTAGTTTCTG----AATAA
1 CAAAAGTACTT-AAAAAAGCTCCCAG-TGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAA
* * *
9788810 TTTTAAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACACTTCAAGCAAGATGCACTTTCAG
64 TTTTAAGAAGATGATTCTGAAAAAATAGGGT-AAAAACACTTCAAGCAAGATGCACTATCAA
*
9788872 CAAAAGTACTTAAAAAAGCTCCCAGATGGACGCTCTTTTTCTACAGTAGTTTCTG-AAAAATAAT
1 CAAAAGTACTTAAAAAAGCTCCCAG-TGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAAT
* * * * *
9788936 TTTAAGAAGATGATTCTGAAAAAATAAGGTCAAAAACACTTCAAGTAGGATGCACTGTCAG
65 TTTAAGAAGATGATTCTGAAAAAATAGGGT-AAAAACACTTCAAGCAAGATGCACTATCAA
*
9788997 CAAAAGTACTGAAAAAAGCTCCCAGATGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAAT
1 CAAAAGTACTTAAAAAAGCTCCCAG-TGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAAT
* * * * * *
9789062 TTTGAGAAGATGATTATTAAAATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTATCAA
65 TTTAAGAAGATGATTCTGAAAAAATAGGGTAAAAACA--CTTCAAGCAAGATGCACTATCAA
*
9789124 TAAAAGTAC-T---AAA-C-CACC--TGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAAT
1 CAAAAGTACTTAAAAAAGCTC-CCAGTGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAAT
* * * * * *
9789181 TTTGAGAAGATGATTATTAAAATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTATCAA
65 TTTAAGAAGATGATTCTGAAAAAATAGGGTAAAAACA--CTTCAAGCAAGATGCACTATCAA
*
9789243 TAAAAGTAC-T---AAA-C-CACC--TGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAAT
1 CAAAAGTACTTAAAAAAGCTC-CCAGTGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAAT
* * * * * *
9789300 TTTGAGAAGATGATTATTAAAATATAGGGTAAAAAAATGCTTCAAGCAAGATGTACTATCAA
65 TTTAAGAAGATGATTCTGAAAAAATAGGGTAAAAACA--CTTCAAGCAAGATGCACTATCAA
*
9789362 TAAAAGTACT
1 CAAAAGTACT
9789372 AAACCACCTG
Statistics
Matches: 572, Mismatches: 38, Indels: 29
0.90 0.06 0.05
Matches are distributed among these distances:
119 229 0.40
121 3 0.01
122 108 0.19
123 5 0.01
124 1 0.00
125 141 0.25
126 59 0.10
127 26 0.05
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (124 bp):
CAAAAGTACTTAAAAAAGCTCCCAGTGAACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAATT
TTAAGAAGATGATTCTGAAAAAATAGGGTAAAAACACTTCAAGCAAGATGCACTATCAA
Found at i:9789525 original size:25 final size:25
Alignment explanation
Indices: 9789469--9789540 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
9789459 TTACAATAAG
* *
9789469 AGAAATTAGAGAAGTTCAGAAAAAT
1 AGAAATTAAAGAAGTTCAGAAGAAT
*
9789494 AGAAATTGAAGAAGTTCAGAAGAAT
1 AGAAATTAAAGAAGTTCAGAAGAAT
** * *
9789519 ATCAATTAAACAAGTTAAGAAG
1 AGAAATTAAAGAAGTTCAGAAG
9789541 GTATAAGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (25 bp):
AGAAATTAAAGAAGTTCAGAAGAAT
Done.