Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold81
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: 1151237
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 79344 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:221222 original size:52 final size:51
Alignment explanation
Indices: 221154--221282 Score: 150
Period size: 52 Copynumber: 2.5 Consensus size: 51
221144 AATAACGAGG
* ** * *
221154 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAA
1 TTGGAGTATCCCCGATTGTGAAAAATTGACA-TTTTGAAAATAAAACCGGAA
** * **
221206 TTGGAGTATCCCCGATTAAAGGAAAATTGACATTTTGAAAATAAAACCGGGG
1 TTGGAGTATCCCCGATT-GTGAAAAATTGACATTTTGAAAATAAAACCGGAA
221258 TTGGAGTATCCCCGATTGTGAAAAA
1 TTGGAGTATCCCCGATTGTGAAAAA
221283 ATTAGAGTTT
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
51 5 0.08
52 49 0.78
53 9 0.14
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTGTGAAAAATTGACATTTTGAAAATAAAACCGGAA
Found at i:221349 original size:28 final size:27
Alignment explanation
Indices: 221328--221379 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
221318 TCCCCTCGGA
*
221328 AATAACGGGGTTGGAGTATCCCCGATG
1 AATAACGGGGTTGGAGTATCCCCGAGG
*
221355 ATTAACGGGGTTGGAGTATCCCCGA
1 AATAACGGGGTTGGAGTATCCCCGA
221380 TTGTGAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (27 bp):
AATAACGGGGTTGGAGTATCCCCGAGG
Found at i:221450 original size:52 final size:51
Alignment explanation
Indices: 221368--221481 Score: 140
Period size: 50 Copynumber: 2.2 Consensus size: 51
221358 AACGGGGTTG
* * * *
221368 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCAATTAT-AAGAAATTAGTG--TTTTGAAAATAAAATCGGAGTTA
*
221422 GAGTATCCCCAATTAT-AGAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCAATTATAAGAAATTAGTGTTTTGAAAATAAAATCGGAGTTA
*
221472 GAATATCCCC
1 GAGTATCCCC
221482 GATTGTGGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
50 30 0.56
52 10 0.19
54 14 0.26
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (51 bp):
GAGTATCCCCAATTATAAGAAATTAGTGTTTTGAAAATAAAATCGGAGTTA
Found at i:221461 original size:211 final size:212
Alignment explanation
Indices: 221086--221488 Score: 598
Period size: 211 Copynumber: 1.9 Consensus size: 212
221076 TATTTTGGGA
* * * *
221086 ATAAAGCCGAGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGAGGTTAGAGCATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
221151 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATC
66 AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTAGAGTATC
* * *
221216 CCCGATTAAAGGAAAATTGACATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAA
131 CCCAATTAAAGGAAAATTGACATTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGAAA
221281 AAATTAGAGTTTTAGCG
196 AAATTAGAGTTTTAGCG
*
221298 ATAAAACCGAGGTTAGAGCATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGAGGTTAGAGCATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* * *
221362 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAATTAGAGTA
* ** *
221427 TCCCCAATTATA-G-AAATT-AGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTG
129 TCCCCAATTAAAGGAAAATTGA-CATTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTG
221489 GAGAATTGAG
Statistics
Matches: 171, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
210 1 0.01
211 71 0.42
212 62 0.36
213 37 0.22
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (212 bp):
ATAAAACCGAGGTTAGAGCATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTAGAGTATC
CCCAATTAAAGGAAAATTGACATTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGAAA
AAATTAGAGTTTTAGCG
Found at i:223907 original size:13 final size:13
Alignment explanation
Indices: 223889--223913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223879 ACAATACTTA
223889 TGTATCGATACAT
1 TGTATCGATACAT
223902 TGTATCGATACA
1 TGTATCGATACA
223914 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:223912 original size:32 final size:32
Alignment explanation
Indices: 223870--223932 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
223860 TAGCTAATTA
* *
223870 TGTATTGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
223902 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
223933 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:223926 original size:19 final size:19
Alignment explanation
Indices: 223867--223934 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
223857 CAGTAGCTAA
* *
223867 TTATGTATTGATACAATAC
1 TTATGTATCGATACAAAAC
223886 TTATGTATCGATAC---A-
1 TTATGTATCGATACAAAAC
223901 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
223918 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
223935 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 1 0.02
19 27 0.64
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:224431 original size:28 final size:28
Alignment explanation
Indices: 224378--224431 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
224368 GCTTTGGAAA
* * *
224378 GGGCGCTGCCAACTTGTGCGGGCTTTTT
1 GGGCGCTGACAACTTGTGCAGACTTTTT
224406 GGGCGCTGACAACTTGTGCAGACTTT
1 GGGCGCTGACAACTTGTGCAGACTTT
224432 AGGAGGGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.13, C:0.24, G:0.33, T:0.30
Consensus pattern (28 bp):
GGGCGCTGACAACTTGTGCAGACTTTTT
Found at i:224753 original size:55 final size:54
Alignment explanation
Indices: 224657--225323 Score: 797
Period size: 55 Copynumber: 12.0 Consensus size: 54
224647 ATAAAGTGTA
* * ** *
224657 TCCTGCTCATTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAGGCGG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG-TG
* * *
224713 T-CTGGTCTTAGAGGACTGAAAGGTGCCACTAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
224767 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
224822 TCCTGCTCTTTG-GAGACTGAAAGGTGCTACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAG-GACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
224877 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGGGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
224932 TCCTGCTCTTTGGGGACTGAAATGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
224987 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
225042 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACATGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
225097 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
*
225156 TCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG-G
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * * *
225214 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT---GAAAGGTG
* * ** *
225271 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTCATGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG
225324 AAAAGGCATC
Statistics
Matches: 554, Mismatches: 35, Indels: 45
0.87 0.06 0.07
Matches are distributed among these distances:
54 45 0.08
55 330 0.60
56 25 0.05
57 22 0.04
58 71 0.13
59 61 0.11
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:225064 original size:27 final size:27
Alignment explanation
Indices: 224982--225064 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
224972 GGGCTTTAAG
224982 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
* ** * * * *
225009 A-ATG-CCACCAACTTGTGTGGGCTTTGAA
1 AGGTGTCCTGC-TCTT-TGAGGAC-TGGAA
225037 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
225064 A
1 A
225065 ATGCCACCAA
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 11 0.30
28 10 0.27
29 5 0.14
30 3 0.08
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (27 bp):
AGGTGTCCTGCTCTTTGAGGACTGGAA
Found at i:226341 original size:8 final size:8
Alignment explanation
Indices: 226319--226376 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
226309 AAGTAGGTTC
226319 TTTTTC-T
1 TTTTTCTT
*
226326 TTTCTCTT
1 TTTTTCTT
226334 TTTTTCTT
1 TTTTTCTT
*
226342 TGTTTTGTT
1 T-TTTTCTT
*
226351 TTTTTGTT
1 TTTTTCTT
226359 TTTTT-TT
1 TTTTTCTT
226366 GTTTTT-TT
1 -TTTTTCTT
226374 TTT
1 TTT
226377 GAAGAGAATG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
7 10 0.22
8 28 0.62
9 7 0.16
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:226355 original size:18 final size:17
Alignment explanation
Indices: 226332--226376 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
226322 TTCTTTTCTC
*
226332 TTTTTTTCTTTGTTTTG
1 TTTTTTTTTTTGTTTTG
*
226349 TTTTTTTGTTTTTTTTTG
1 TTTTTTT-TTTTGTTTTG
226367 TTTTTTTTTT
1 TTTTTTTTTT
226377 GAAGAGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (17 bp):
TTTTTTTTTTTGTTTTG
Found at i:226358 original size:13 final size:12
Alignment explanation
Indices: 226332--226376 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
226322 TTCTTTTCTC
*
226332 TTTTTTTCTTTG
1 TTTTTTTTTTTG
226344 TTTTGTTTTTTTG
1 TTTT-TTTTTTTG
226357 --TTTTTTTTTG
1 TTTTTTTTTTTG
226367 TTTTTTTTTT
1 TTTTTTTTTT
226377 GAAGAGAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 8 0.28
11 2 0.07
12 12 0.41
13 7 0.24
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:226366 original size:23 final size:23
Alignment explanation
Indices: 226333--226376 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
226323 TCTTTTCTCT
226333 TTTTTTCTTTGTTTTGTTTTTTTG
1 TTTTTTCTTTGTTTT-TTTTTTTG
226357 TTTTTT-TTTGTTTTTTTTTT
1 TTTTTTCTTTGTTTTTTTTTT
226377 GAAGAGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (23 bp):
TTTTTTCTTTGTTTTTTTTTTTG
Found at i:226372 original size:10 final size:10
Alignment explanation
Indices: 226349--226375 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
226339 CTTTGTTTTG
226349 TTTTTTTGTT
1 TTTTTTTGTT
226359 TTTTTTTGTT
1 TTTTTTTGTT
226369 TTTTTTT
1 TTTTTTT
226376 TGAAGAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:244121 original size:28 final size:27
Alignment explanation
Indices: 244089--244157 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 27
244079 ATAAAGCCGG
244089 GGTTGGAGTATCCCC-TCGAAAGTAACGA
1 GGTTGGAGTATCCCCAT-GAAA-TAACGA
244117 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCC-ATGAAATAACGA
244145 GGTTGGAGTATCC
1 GGTTGGAGTATCC
244158 TCTATTGTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (27 bp):
GGTTGGAGTATCCCCATGAAATAACGA
Found at i:244277 original size:52 final size:52
Alignment explanation
Indices: 244145--244313 Score: 155
Period size: 52 Copynumber: 3.2 Consensus size: 52
244135 GAAATAACGA
* * * * *
244145 GGTTGGAGTATCCTCTATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCTCGATTGTGGAAAAATTGG-AGTTTTGAAAATAAAACCGG
* * ** *
244197 AGTTGGAGTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCTCGATT-GTGGAAAAATTGGAGTTTTGAAAATAAAACCGG
* * * **
244249 GGTTAGAGTATCCTCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGG
1 GGTTGGAGTATCCTCGATTGTGGAAAAATTGGAGTTTTGA-AAATAAAACCGG
244301 GGTTGGAGTATCC
1 GGTTGGAGTATCC
244314 CCTCGAAAAT
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
51 3 0.03
52 81 0.87
53 8 0.09
54 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (52 bp):
GGTTGGAGTATCCTCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCGG
Found at i:244361 original size:27 final size:27
Alignment explanation
Indices: 244289--244373 Score: 111
Period size: 27 Copynumber: 3.1 Consensus size: 27
244279 AGTGTTTTAG
*
244289 CGATAAA-ACCGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTAT-CCC
244316 TCGA-AAATAACGGGGTTGGAGTATCCC
1 -CGATAAATAACGGGGTTGGAGTATCCC
* *
244343 CGATGATTAACGGGGTTGGAGTATCCC
1 CGATAAATAACGGGGTTGGAGTATCCC
244370 CGAT
1 CGAT
244374 TGTAAAGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
26 3 0.06
27 31 0.60
28 18 0.35
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (27 bp):
CGATAAATAACGGGGTTGGAGTATCCC
Found at i:244438 original size:212 final size:212
Alignment explanation
Indices: 244079--244484 Score: 602
Period size: 212 Copynumber: 1.9 Consensus size: 212
244069 TATTTTGGGA
* *
244079 ATAAAGCCGGGGTTGGAGTATCCCCTCGAAAGTAACGAGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATGAAATAACG
* * * *
244144 AGGTTGGAGTATCCTCTATTGTGAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTGGAGTATC
66 AGGTTGGAGTATCCCCGATTGTAAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTAGAGTATC
* * * *
244209 CCCGATTAAAGGAAAATTGGCGTTTTGAAAA-TAAAACCGGGGTTAGAGTATCCTCGATTGTGGA
131 CCCGATTAAAGGAAAATTAGCGTTTT-AAAACTAAAACCGGAGTTAGAATATCCCCGATTGTGGA
244273 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
* *
244291 ATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATGAAATAACG
* * *
244355 GGGTTGGAGTATCCCCGATTGTAAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGATTGTAAA-AAATTGGT-ATTTTTGGAAATAAAATCAGAGTTAGAGTA
* * *
244420 TCCCCGATTATA-GAAAATTAGTGTTTTAAAACTAAAATCGGAGTTAGAATATCCCCGATTGTGG
129 TCCCCGATTAAAGGAAAATTAGCGTTTTAAAACTAAAACCGGAGTTAGAATATCCCCGATTGTGG
244484 A
194 A
244485 GAATTGAGAA
Statistics
Matches: 173, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
211 31 0.18
212 104 0.60
213 38 0.22
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCCCGATTGTAAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTAGAGTATC
CCCGATTAAAGGAAAATTAGCGTTTTAAAACTAAAACCGGAGTTAGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:244465 original size:51 final size:53
Alignment explanation
Indices: 244361--244479 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
244351 AACGGGGTTG
* * *
244361 GAGTATCCCCGATTGTAAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATAAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
244415 GAGTATCCCCGATTATAGA-AAATTAGTG-TTTT-AAAACTAAAATCGGAGTTA
1 GAGTATCCCCGATTATAAAGAAATTAGTGTTTTTGAAAA-TAAAATCGGAGTTA
*
244466 GAATATCCCCGATT
1 GAGTATCCCCGATT
244480 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
50 3 0.05
51 31 0.53
53 8 0.14
54 17 0.29
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATAAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:246867 original size:33 final size:33
Alignment explanation
Indices: 246829--246895 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
246819 AAAATTTCCA
* ***
246829 AATGTATTGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
246862 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
246895 A
1 A
246896 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:246868 original size:13 final size:13
Alignment explanation
Indices: 246850--246875 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
246840 ACAAAGATCC
246850 ATGTATCGATACA
1 ATGTATCGATACA
246863 ATGTATCGATACA
1 ATGTATCGATACA
246876 CAGAAAAATG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:246939 original size:19 final size:18
Alignment explanation
Indices: 246915--246982 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
246905 CAGTAGCTAA
246915 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
246934 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
246949 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
246966 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
246983 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:246955 original size:13 final size:13
Alignment explanation
Indices: 246937--246961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
246927 ACAATACTTA
246937 TGTATCGATACAT
1 TGTATCGATACAT
246950 TGTATCGATACA
1 TGTATCGATACA
246962 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:246959 original size:32 final size:32
Alignment explanation
Indices: 246918--246980 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
246908 TAGCTAATTA
*
246918 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
246950 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
246981 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:248502 original size:21 final size:21
Alignment explanation
Indices: 248469--248510 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
248459 ATTTAATTAT
*
248469 AAATATTTATAAATATTAAAA
1 AAATATTTATAAATAGTAAAA
248490 AAATAATTT-TAAATAGTAAAA
1 AAAT-ATTTATAAATAGTAAAA
248511 TAAGAGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATATTTATAAATAGTAAAA
Found at i:249302 original size:2 final size:2
Alignment explanation
Indices: 249295--249328 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
249285 TACCTCTCCT
249295 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
249329 CAACAAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:250208 original size:2 final size:2
Alignment explanation
Indices: 250201--250241 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
250191 AGTAAGAGCC
250201 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
250242 GTATGTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:253085 original size:27 final size:27
Alignment explanation
Indices: 253039--253094 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
253029 GTATAAAATC
253039 TTGATCTTTTAAAAAAAATTTGTT-ATT
1 TTGATCTTTTAAAAAAAATTT-TTAATT
* **
253066 TTGATTTTTTAAAATCAATTTTTAATT
1 TTGATCTTTTAAAAAAAATTTTTAATT
253093 TT
1 TT
253095 TTGTCTCAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (27 bp):
TTGATCTTTTAAAAAAAATTTTTAATT
Found at i:255587 original size:52 final size:51
Alignment explanation
Indices: 255502--255625 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
255492 ATATGAAAAG
* *
255502 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
255553 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
255605 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
255626 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:255638 original size:51 final size:51
Alignment explanation
Indices: 255502--255645 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
255492 ATATGAAAAG
*
255502 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
255554 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
255605 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
255646 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:255652 original size:13 final size:13
Alignment explanation
Indices: 255634--255658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
255624 CAAAGATCAG
255634 TGTATCGATACAA
1 TGTATCGATACAA
255647 TGTATCGATACA
1 TGTATCGATACA
255659 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:255736 original size:33 final size:33
Alignment explanation
Indices: 255699--255765 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
255689 AGTAGCTTAA
255699 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
255732 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
255765 A
1 A
255766 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:255739 original size:13 final size:13
Alignment explanation
Indices: 255721--255745 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
255711 CAAAAAAATA
255721 TGTATCGATACAT
1 TGTATCGATACAT
255734 TGTATCGATACA
1 TGTATCGATACA
255746 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:257962 original size:160 final size:160
Alignment explanation
Indices: 257778--258103 Score: 616
Period size: 160 Copynumber: 2.0 Consensus size: 160
257768 CATCATAATG
257778 TCAACACCTTATCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACCTCACCTTTCACCCCAAA
1 TCAACACCTTATCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACCTCACCTTTCACCCCAAA
* *
257843 ATTTTGGCTATAAATAGACTAATGCAATCATAGCAAAAGATCCCTTTTTCAACCACATTTTCTAG
66 ATTTTGGCTATAAATAGACCAATGCAATCATAGCAAAAGATCCCTTCTTCAACCACATTTTCTAG
257908 CCTCATTACCATCCATATCTTAGCAAAACA
131 CCTCATTACCATCCATATCTTAGCAAAACA
257938 TCAACACCTTATCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACCTCACCTTTCACCCCAAA
1 TCAACACCTTATCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACCTCACCTTTCACCCCAAA
*
258003 ATTTTGGCTATAAATAGACCAATGCAATCCTAGCAAAAGATCCCTTCTTCAACCACATTTTCTAG
66 ATTTTGGCTATAAATAGACCAATGCAATCATAGCAAAAGATCCCTTCTTCAACCACATTTTCTAG
*
258068 CCTCATTACCATCCATATCTTAGCGAAACA
131 CCTCATTACCATCCATATCTTAGCAAAACA
258098 TCAACA
1 TCAACA
258104 TAAAAACTCA
Statistics
Matches: 162, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.27
Consensus pattern (160 bp):
TCAACACCTTATCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACCTCACCTTTCACCCCAAA
ATTTTGGCTATAAATAGACCAATGCAATCATAGCAAAAGATCCCTTCTTCAACCACATTTTCTAG
CCTCATTACCATCCATATCTTAGCAAAACA
Found at i:263448 original size:20 final size:19
Alignment explanation
Indices: 263425--263499 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
263415 AAAAAGATAG
263425 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
263444 GAATGTATCGATATATTCATA
1 -AATGTATCGATACATTGA-A
* *
263465 CATGTATCGATACATTGTCA
1 AATGTATCGATACATTG-AA
263485 AATGTATCGATACAT
1 AATGTATCGATACAT
263500 CTGGATAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 45 0.98
21 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:263749 original size:13 final size:13
Alignment explanation
Indices: 263731--263757 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
263721 TTTGTAGTTT
263731 GTTATTGCAACAA
1 GTTATTGCAACAA
263744 GTTATTGCAACAA
1 GTTATTGCAACAA
263757 G
1 G
263758 GGATGGGTGC
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:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (13 bp):
GTTATTGCAACAA
Found at i:266941 original size:2 final size:2
Alignment explanation
Indices: 266936--266963 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
266926 AAAAAAGACC
266936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
266964 GAGTTTCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:268535 original size:37 final size:37
Alignment explanation
Indices: 268494--268591 Score: 108
Period size: 37 Copynumber: 2.6 Consensus size: 37
268484 TGACAAGTAA
* * *
268494 TATTTGGGTGGC-TTGGTCAATCCACTATGATTGTTAG
1 TATTTGGGTGGCAGT-GCCAATCCACTATAATTGTTAG
*
268531 TATTTGGGTGGCAGTGCCAATTCACTATAATTGTTAG
1 TATTTGGGTGGCAGTGCCAATCCACTATAATTGTTAG
* * **
268568 AATTTAGGTGGCAGCACCAATCCA
1 TATTTGGGTGGCAGTGCCAATCCA
268592 AAAAAAATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 50 0.98
38 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (37 bp):
TATTTGGGTGGCAGTGCCAATCCACTATAATTGTTAG
Found at i:273291 original size:37 final size:36
Alignment explanation
Indices: 273235--273332 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 36
273225 CAACAAGTAA
*
273235 TATTTGGGTGGCTTGGCCAATCCACTATGATTGTTAG
1 TATTTGGGTGG-TAGGCCAATCCACTATGATTGTTAG
273272 TATTTGGGTGGTAGTGCCAATCCACTATGATTGTTAG
1 TATTTGGGTGGTAG-GCCAATCCACTATGATTGTTAG
* * *
273309 AATTTAGGTGGCAGCGCCAATCCA
1 TATTTGGGTGGTAG-GCCAATCCA
273333 AAAAAAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 2 0.04
37 53 0.96
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (36 bp):
TATTTGGGTGGTAGGCCAATCCACTATGATTGTTAG
Found at i:277758 original size:20 final size:20
Alignment explanation
Indices: 277721--277758 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
277711 CAACACTTAC
* *
277721 AATTCATACTTAGGAATTCA
1 AATTCATACTCAGAAATTCA
277741 AATTCATACTCAGAAATT
1 AATTCATACTCAGAAATT
277759 TAAGTAACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (20 bp):
AATTCATACTCAGAAATTCA
Found at i:278345 original size:18 final size:17
Alignment explanation
Indices: 278322--278373 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
278312 AATTATTATT
278322 ATATAATAATTAATATAA
1 ATATAATAA-TAATATAA
*
278340 ATAT-A-AACAATATTAA
1 ATATAATAATAATA-TAA
*
278356 ATATAATTATAATATAA
1 ATATAATAATAATATAA
278373 A
1 A
278374 ATACACAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 4 0.14
16 9 0.32
17 6 0.21
18 9 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATAATAATAATATAA
Found at i:278352 original size:27 final size:27
Alignment explanation
Indices: 278322--278373 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
278312 AATTATTATT
278322 ATATAATAAT-TAA-TATAAATATAAACA
1 ATATAA-AATATAATTAT-AATATAAACA
*
278349 ATATTAAATATAATTATAATATAAA
1 ATATAAAATATAATTATAATATAAA
278374 ATACACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 3 0.14
27 16 0.73
28 3 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATAAAATATAATTATAATATAAACA
Found at i:279389 original size:94 final size:93
Alignment explanation
Indices: 279270--279462 Score: 332
Period size: 94 Copynumber: 2.1 Consensus size: 93
279260 AAGTTAAAAG
*
279270 CAACATGTCTTTGGACTATTAATAGTAAACCTTCCCTCGTATTTATGTTATAATTATTTTTTTCT
1 CAACATGTCTTCGGACTATTAATAGTAAACCTTCCCTCGTATTTATGTTATAATTATTTTTTTCT
*
279335 AAAGTACTTAATCTCCAACATCTATATT
66 AAAATACTTAATCTCCAACATCTATATT
*
279363 CAACATGTCCTTCGGACTATTAATAGTAAACCTTTCCTCGTATTTATGTTATAATTATTTTTTTC
1 CAACATGT-CTTCGGACTATTAATAGTAAACCTTCCCTCGTATTTATGTTATAATTATTTTTTTC
* *
279428 TAAAATACTTAATCTTCAACATTTATATT
65 TAAAATACTTAATCTCCAACATCTATATT
279457 CAACAT
1 CAACAT
279463 ATACCGACTT
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 8 0.09
94 86 0.91
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (93 bp):
CAACATGTCTTCGGACTATTAATAGTAAACCTTCCCTCGTATTTATGTTATAATTATTTTTTTCT
AAAATACTTAATCTCCAACATCTATATT
Found at i:279714 original size:11 final size:11
Alignment explanation
Indices: 279684--279717 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
279674 TTAAATAAGT
279684 TATAATATAAA
1 TATAATATAAA
*
279695 AAT-ATATAAA
1 TATAATATAAA
279705 TATAATATAAA
1 TATAATATAAA
279716 TA
1 TA
279718 CTCGGATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAATATAAA
Found at i:281261 original size:2 final size:2
Alignment explanation
Indices: 281222--281249 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
281212 TAAGTCTTGA
281222 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
281250 CATTCGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:281761 original size:3 final size:3
Alignment explanation
Indices: 281746--281803 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
281736 AAACATTTAC
* *
281746 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -TT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
281793 AAT ATT AAT AA
1 AAT AAT AAT AA
281804 AAGACCATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 1 0.02
3 47 0.98
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:284941 original size:20 final size:20
Alignment explanation
Indices: 284918--284958 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
284908 ATTTAATTAT
*
284918 AAAT-ATTTATAAATATTAAA
1 AAATAATTT-TAAATAGTAAA
284938 AAATAATTTTAAATAGTAAA
1 AAATAATTTTAAATAGTAAA
284958 A
1 A
284959 TAAAAGTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATAATTTTAAATAGTAAA
Found at i:286406 original size:22 final size:22
Alignment explanation
Indices: 286380--286438 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
286370 CCTATATATA
*
286380 TATGTATGTATGTATATGTGCG
1 TATGTATGTATGTATATGTACG
* *
286402 TATGTATATA-GATATATGTATG
1 TATGTATGTATG-TATATGTACG
286424 TATGTATGTATGTAT
1 TATGTATGTATGTAT
286439 GTATGTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (22 bp):
TATGTATGTATGTATATGTACG
Found at i:286408 original size:4 final size:4
Alignment explanation
Indices: 286380--286446 Score: 70
Period size: 4 Copynumber: 17.8 Consensus size: 4
286370 CCTATATATA
** * *
286380 TATG TATG TATG TA-- TATG TGCG TATG TATA TA-G -ATA TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
286424 TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TAT
286447 ATGTGAAAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 3 0.06
4 48 0.94
ACGTcount: A:0.28, C:0.01, G:0.22, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:287574 original size:2 final size:2
Alignment explanation
Indices: 287569--287597 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
287559 AAGTTTTTTA
287569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
287598 CACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:289122 original size:26 final size:25
Alignment explanation
Indices: 289077--289126 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
289067 GTATAAAATC
289077 TTGATCTTTTAAAAAAAATTATTTAT
1 TTGATCTTTTAAAAAAAATT-TTTAT
* **
289103 TTGATTTTTTAAAATCAATTTTTA
1 TTGATCTTTTAAAAAAAATTTTTA
289127 ATTTTTTGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (25 bp):
TTGATCTTTTAAAAAAAATTTTTAT
Found at i:294106 original size:14 final size:15
Alignment explanation
Indices: 294069--294106 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
294059 GATTTAGTTA
294069 ATTTTAATAAAATTG
1 ATTTTAATAAAATTG
* *
294084 AGTTAAATAAAA-TG
1 ATTTTAATAAAATTG
294098 ATTTTAATA
1 ATTTTAATA
294107 GATTTATTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (15 bp):
ATTTTAATAAAATTG
Found at i:294795 original size:31 final size:33
Alignment explanation
Indices: 294742--294803 Score: 110
Period size: 31 Copynumber: 1.9 Consensus size: 33
294732 TCTCCCTCGC
294742 AATAATTAAATATATTAATATTAAATATAAAAA
1 AATAATTAAATATATTAATATTAAATATAAAAA
294775 AATAATTAAA-ATA-TAATATTAAATATAAA
1 AATAATTAAATATATTAATATTAAATATAAA
294804 TATATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 16 0.55
32 3 0.10
33 10 0.34
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
AATAATTAAATATATTAATATTAAATATAAAAA
Found at i:294804 original size:37 final size:36
Alignment explanation
Indices: 294753--294822 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
294743 ATAATTAAAT
294753 ATATTAATATTAAATATAAAAAAATAATTAAAATATA
1 ATATTAATATTAAATATAAAAAAAT-ATTAAAATATA
* *
294790 ATATTAA-ATATAAATATATAAAAATTTTAAAAT
1 ATATTAATAT-TAAATATAAAAAAATATTAAAAT
294823 TTACATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 9 0.30
37 21 0.70
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (36 bp):
ATATTAATATTAAATATAAAAAAATATTAAAATATA
Found at i:294876 original size:16 final size:18
Alignment explanation
Indices: 294851--294908 Score: 75
Period size: 16 Copynumber: 3.3 Consensus size: 18
294841 TTATTAAATT
*
294851 TATATAAATATAATATAA
1 TATATAAATATAATAAAA
*
294869 T-T-TAAATATGATAAAA
1 TATATAAATATAATAAAA
294885 TATATAAATATAATACAAA
1 TATATAAATATAATA-AAA
294904 TATAT
1 TATAT
294909 TATATAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 13 0.38
17 2 0.06
18 11 0.32
19 8 0.24
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
TATATAAATATAATAAAA
Found at i:295068 original size:8 final size:9
Alignment explanation
Indices: 295057--295104 Score: 57
Period size: 8 Copynumber: 5.7 Consensus size: 9
295047 ATTAAATTTG
295057 ATAA-AAAT
1 ATAATAAAT
295065 ATAATAAA-
1 ATAATAAAT
*
295073 ATAATATAT
1 ATAATAAAT
*
295082 TTAATAAAT
1 ATAATAAAT
295091 ATAA-AAAT
1 ATAATAAAT
295099 ATAATA
1 ATAATA
295105 TAATTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
8 19 0.58
9 14 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAATAAAT
Found at i:295102 original size:26 final size:26
Alignment explanation
Indices: 295061--295111 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
295051 AATTTGATAA
*
295061 AAATATAATAAAATAATATATTTAAT
1 AAATATAATAAAATAATATAATTAAT
295087 AAATATAA-AAATATAATATAATTAA
1 AAATATAATAAA-ATAATATAATTAA
295112 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATATAATAAAATAATATAATTAAT
Found at i:295120 original size:24 final size:21
Alignment explanation
Indices: 295062--295121 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
295052 ATTTGATAAA
* *
295062 AATATAATAAAATAATATATTT
1 AATA-AATAAAAAAATATATAT
*
295084 AATAAATATAAAAATATAATAT
1 AATAAATAAAAAAATAT-ATAT
295106 AATTAAATTAAAAAAA
1 AA-TAAA-TAAAAAAA
295122 ATTTAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 11 0.35
22 9 0.29
23 4 0.13
24 7 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAATAAAAAAATATATAT
Found at i:300217 original size:2 final size:2
Alignment explanation
Indices: 300210--300243 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
300200 TACAGCAAGT
300210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
300244 CAAGTACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:301487 original size:76 final size:75
Alignment explanation
Indices: 301252--301641 Score: 465
Period size: 76 Copynumber: 5.1 Consensus size: 75
301242 TCTTTGACTC
* * * *
301252 AATGTAGTCTTCAGGTTAGGTTATGTTCCGGTAATCAAACGTTTGAACTTCTTCGAGTCCATTGA
1 AATGTAGTCTTCTGGTTAGGCTATGTTCCGGTAATCAAACGTTTGAACTTTTTCGAGTCCATGGA
301317 AGCCATGGTT
66 AGCCATGGTT
* * * * * * * *
301327 AATGTAGGCTTCTGGCTAAGCTATGTTCTGATAATCAAACCTTTAAAACTTTTTTGAAGTCCATG
1 AATGTAGTCTTCTGGTTAGGCTATGTTCCGGTAATCAAACGTTT-GAACTTTTTCG-AGTCCATG
301392 GAAGCCATGGTT
64 GAAGCCATGGTT
* * *
301404 AATGTAGTCTTCTGGTAAGGCTATGTTCCAGTAATCAAACGTTCGAACTTTTTTCGAGTCCATGG
1 AATGTAGTCTTCTGGTTAGGCTATGTTCCGGTAATCAAACGTTTGAAC-TTTTTCGAGTCCATGG
301469 AAGCCATGGTT
65 AAGCCATGGTT
* * ** *
301480 GATGTAGTATTCTGGTTAGGCTATGTTCCGGTAATCAAACAATTGAACTTTTTCGAGTCTATGGA
1 AATGTAGTCTTCTGGTTAGGCTATGTTCCGGTAATCAAACGTTTGAACTTTTTCGAGTCCATGGA
301545 AGCCATGGTTAATTGTT
66 AGCCAT-G------GTT
* * *
301562 AATGTAGTCTTCGGGTTAGGCTATGTTCCGGTAATCAACACGTTTGAACTTTTTCGGGTCCATAG
1 AATGTAGTCTTCTGGTTAGGCTATGTTCCGGTAATCAA-ACGTTTGAACTTTTTCGAGTCCATGG
*
301627 ATGCCATGGTT
65 AAGCCATGGTT
301638 AATG
1 AATG
301642 GTTAATGTAA
Statistics
Matches: 264, Mismatches: 40, Indels: 21
0.81 0.12 0.06
Matches are distributed among these distances:
75 58 0.22
76 80 0.30
77 60 0.23
82 39 0.15
83 27 0.10
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (75 bp):
AATGTAGTCTTCTGGTTAGGCTATGTTCCGGTAATCAAACGTTTGAACTTTTTCGAGTCCATGGA
AGCCATGGTT
Found at i:301586 original size:82 final size:83
Alignment explanation
Indices: 301474--301668 Score: 284
Period size: 83 Copynumber: 2.4 Consensus size: 83
301464 CATGGAAGCC
* *
301474 ATGGTTGATGTAGTATTCTGGTTAGGCTATGTTCCGGTAATCAA-ACAATTGAACTTTTTCGAGT
1 ATGGTTAATGTAGTCTTCTGGTTAGGCTATGTTCCGGTAATCAACACAATTGAACTTTTTCGAGT
* *
301538 CTATGGAAGCCATGGTTA
66 CCATAGAAGCCATGGTTA
* * ** *
301556 ATTGTTAATGTAGTCTTCGGGTTAGGCTATGTTCCGGTAATCAACACGTTTGAACTTTTTCGGGT
1 ATGGTTAATGTAGTCTTCTGGTTAGGCTATGTTCCGGTAATCAACACAATTGAACTTTTTCGAGT
*
301621 CCATAGATGCCATGGTTA
66 CCATAGAAGCCATGGTTA
*
301639 ATGGTTAATGTAATCTTCTGGTTAGGCTAT
1 ATGGTTAATGTAGTCTTCTGGTTAGGCTAT
301669 AATATGGTAA
Statistics
Matches: 99, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
82 40 0.40
83 59 0.60
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (83 bp):
ATGGTTAATGTAGTCTTCTGGTTAGGCTATGTTCCGGTAATCAACACAATTGAACTTTTTCGAGT
CCATAGAAGCCATGGTTA
Found at i:301623 original size:158 final size:152
Alignment explanation
Indices: 301252--301641 Score: 478
Period size: 158 Copynumber: 2.5 Consensus size: 152
301242 TCTTTGACTC
* * *
301252 AATGTAGTCTTCAGGTTAGGTTATGTTCCGGTAATCAAACGTTTGAACTTCTTCGAGTCCATTGA
1 AATGTAGTCTTCAGGTTAGGCTATGTTCCGGTAATCAAACGTTTGAACTTTTTCGAGTCCATAGA
* * ** *
301317 AGCCATGGTTAATGTAGGCTTCTGGCTAAGCTATGTTCTGATAATCAAACCTTTAAAACTTTTTT
66 AGCCATGGTTAATGTAGGATTCTGGCTAAGCTATGTTCCGATAATCAAACAATTAAAACTTTTTC
301382 GAAGTCCATGGAAGCCATGGTT
131 GAAGTCCATGGAAGCCATGGTT
* * * * *
301404 AATGTAGTCTTCTGGTAAGGCTATGTTCCAGTAATCAAACGTTCGAACTTTTTTCGAGTCCATGG
1 AATGTAGTCTTCAGGTTAGGCTATGTTCCGGTAATCAAACGTTTGAAC-TTTTTCGAGTCCATAG
* * * * * *
301469 AAGCCATGGTTGATGTAGTATTCTGGTTAGGCTATGTTCCGGTAATCAAACAATT-GAACTTTTT
65 AAGCCATGGTTAATGTAGGATTCTGGCTAAGCTATGTTCCGATAATCAAACAATTAAAACTTTTT
*
301533 CG-AGTCTATGGAAGCCATGGTTAATTGTT
130 CGAAGTCCATGGAAGCCAT-G------GTT
* *
301562 AATGTAGTCTTCGGGTTAGGCTATGTTCCGGTAATCAACACGTTTGAACTTTTTCGGGTCCATAG
1 AATGTAGTCTTCAGGTTAGGCTATGTTCCGGTAATCAA-ACGTTTGAACTTTTTCGAGTCCATAG
*
301627 ATGCCATGGTTAATG
65 AAGCCATGGTTAATG
301642 GTTAATGTAA
Statistics
Matches: 202, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
151 15 0.07
152 53 0.26
153 60 0.30
158 65 0.32
159 9 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (152 bp):
AATGTAGTCTTCAGGTTAGGCTATGTTCCGGTAATCAAACGTTTGAACTTTTTCGAGTCCATAGA
AGCCATGGTTAATGTAGGATTCTGGCTAAGCTATGTTCCGATAATCAAACAATTAAAACTTTTTC
GAAGTCCATGGAAGCCATGGTT
Found at i:303047 original size:23 final size:23
Alignment explanation
Indices: 302989--303065 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
302979 TCAAACCCAA
302989 ATTAATATTTTAATAATAAAAAT-T
1 ATTAATA-TTTAAT-ATAAAAATAT
303013 ATTTAA-ATTTAATTATAAAAATAT
1 A-TTAATATTTAA-TATAAAAATAT
*
303037 ATTAATA-TTAA-A-AATAATAT
1 ATTAATATTTAATATAAAAATAT
*
303057 TTTAATATT
1 ATTAATATT
303066 AACTTACATA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
20 13 0.28
21 2 0.04
23 21 0.46
24 6 0.13
25 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTAATATTTAATATAAAAATAT
Found at i:303048 original size:17 final size:19
Alignment explanation
Indices: 303019--303067 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 19
303009 AATTATTTAA
303019 ATTTAAT-TATAAAAAT-AT
1 ATTTAATAT-TAAAAATAAT
303037 A-TTAATATTAAAAATAAT
1 ATTTAATATTAAAAATAAT
303055 ATTTTAATATTAA
1 A-TTTAATATTAA
303068 CTTACATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 12 0.44
18 5 0.19
20 10 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAATATTAAAAATAAT
Found at i:303560 original size:11 final size:12
Alignment explanation
Indices: 303538--303570 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
303528 TCAAAATAAA
303538 ATTTATATTTTT
1 ATTTATATTTTT
303550 ATTTA-ATTTTT
1 ATTTATATTTTT
*
303561 ATTTTTATTT
1 ATTTATATTT
303571 AAAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTATATTTTT
Found at i:303576 original size:19 final size:19
Alignment explanation
Indices: 303534--303597 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 19
303524 TCTTTCAAAA
*
303534 TAAAATTTATATTTTTATT
1 TAAAATTTTTATTTTTATT
303553 T--AATTTTTATTTTTATT
1 TAAAATTTTTATTTTTATT
*
303570 TAAAA-TTTAATTTTATATAT
1 TAAAATTTTTATTTT-TAT-T
303590 TAAAATTT
1 TAAAATTT
303598 ATAAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 16 0.42
18 8 0.21
19 6 0.16
20 6 0.16
21 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAAAATTTTTATTTTTATT
Found at i:304433 original size:15 final size:15
Alignment explanation
Indices: 304413--304444 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
304403 AAATTGAAGG
304413 ATTAAAATTCTTCAA
1 ATTAAAATTCTTCAA
304428 ATTAAAATTCTTCAA
1 ATTAAAATTCTTCAA
304443 AT
1 AT
304445 AATAAATGAC
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:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAAATTCTTCAA
Found at i:304971 original size:23 final size:25
Alignment explanation
Indices: 304936--304981 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
304926 TTAAGTTTTC
304936 AAATTTTGAAAAA-TAT-ATAAATT
1 AAATTTTGAAAAATTATCATAAATT
**
304959 AAATTTTTTAAAATTATCATAAA
1 AAATTTTGAAAAATTATCATAAA
304982 GAGATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 3 0.16
25 5 0.26
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
AAATTTTGAAAAATTATCATAAATT
Found at i:305123 original size:10 final size:9
Alignment explanation
Indices: 305098--305179 Score: 70
Period size: 8 Copynumber: 9.4 Consensus size: 9
305088 TACTCATATA
305098 ATATT-AAT
1 ATATTAAAT
305106 ATA-TAAAT
1 ATATTAAAT
305114 ATATTAAA-
1 ATATTAAAT
305122 ATA-TATAAT
1 ATATTA-AAT
*
305131 ATTTTAAAT
1 ATATTAAAT
305140 ATAATT-AAT
1 AT-ATTAAAT
305149 ATA-TAAAT
1 ATATTAAAT
305157 ATATATAAAT
1 ATAT-TAAAT
305167 ATAATTAAA-
1 AT-ATTAAAT
305176 ATAT
1 ATAT
305180 ACTTATTATT
Statistics
Matches: 62, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
7 4 0.06
8 23 0.37
9 18 0.29
10 15 0.24
11 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATTAAAT
Found at i:305165 original size:27 final size:28
Alignment explanation
Indices: 305104--305180 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
305094 TATAATATTA
305104 ATATATAAATAT-ATTAAAATATATAAT
1 ATATATAAATATAATTAAAATATATAAT
* *
305131 AT-TTTAAATATAATTAATATATA-AAT
1 ATATATAAATATAATTAAAATATATAAT
305157 ATATATAAATATAATTAAAATATA
1 ATATATAAATATAATTAAAATATA
305181 CTTATTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.30
27 31 0.70
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATATAAATATAATTAAAATATATAAT
Found at i:305192 original size:27 final size:26
Alignment explanation
Indices: 305098--305193 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 26
305088 TACTCATATA
*
305098 ATATTAATATATAAATAT-ATTAAAAT
1 ATATTATTAT-TAAATATAATTAAAAT
*
305124 ATATAATATT-TTAAATATAATTAATAT
1 ATAT--TATTATTAAATATAATTAAAAT
*
305151 ATA-AATATATATAAATATAATTAAAAT
1 ATATTAT-TAT-TAAATATAATTAAAAT
305178 ATACTTATTATTAAAT
1 ATA-TTATTATTAAAT
305194 CTATTATTAG
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
24 2 0.04
25 1 0.02
26 12 0.21
27 34 0.60
28 6 0.11
29 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
ATATTATTATTAAATATAATTAAAAT
Found at i:305516 original size:18 final size:18
Alignment explanation
Indices: 305474--305518 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
305464 TTTTATGTAA
305474 AAATAAAATTATTAAATT
1 AAATAAAATTATTAAATT
* *
305492 TATTAAAATT-TTAAATAT
1 AAATAAAATTATTAAAT-T
305510 AAATAAAAT
1 AAATAAAAT
305519 ACATATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATAAAATTATTAAATT
Found at i:306820 original size:17 final size:17
Alignment explanation
Indices: 306737--306820 Score: 62
Period size: 17 Copynumber: 4.7 Consensus size: 17
306727 AGTGTACTAG
*
306737 ATTTTTATAATTGAT-AT
1 ATTTATATAATT-ATAAT
306754 ATTTATATTAAATTTATATAT
1 ATTTATA-T-AA-TTATA-AT
* * *
306775 TTTTATATTATTATTAT
1 ATTTATATAATTATAAT
* *
306792 ATTTAAAAAATTATAAT
1 ATTTATATAATTATAAT
306809 ATTTATATAATT
1 ATTTATATAATT
306821 TTTTTAAGTT
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
17 30 0.59
18 5 0.10
19 5 0.10
20 3 0.06
21 8 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
ATTTATATAATTATAAT
Found at i:306913 original size:16 final size:16
Alignment explanation
Indices: 306875--306920 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
306865 ATATTAAGTA
306875 TTGTATTTATATTATTT
1 TTGTATTT-TATTATTT
306892 TT-TATTTTA-TATTT
1 TTGTATTTTATTATTT
*
306906 TTAGTATTTTTTTAT
1 TT-GTATTTTATTAT
306921 GTCGTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 7 0.28
15 2 0.08
16 11 0.44
17 5 0.20
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (16 bp):
TTGTATTTTATTATTT
Found at i:308232 original size:23 final size:22
Alignment explanation
Indices: 308191--308242 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
308181 TAATTAAGTT
308191 ATTATTT-ATAATAATAAT-AA
1 ATTATTTAATAATAATAATAAA
*
308211 ATTATTTAATTAATTATAAATAAA
1 ATTATTTAA-TAATAAT-AATAAA
308235 ATT-TTTAA
1 ATTATTTAA
308243 ATTTTACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 7 0.26
21 1 0.04
22 6 0.22
23 8 0.30
24 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTATTTAATAATAATAATAAA
Found at i:310299 original size:11 final size:11
Alignment explanation
Indices: 310283--310325 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
310273 GTGTGCATGA
310283 TTAAATTAAAT
1 TTAAATTAAAT
*
310294 TTAAATAAAAT
1 TTAAATTAAAT
* *
310305 TTAAAATAATT
1 TTAAATTAAAT
310316 TTAAATTAAA
1 TTAAATTAAA
310326 AATTAAAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:310308 original size:22 final size:23
Alignment explanation
Indices: 310282--310333 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
310272 TGTGTGCATG
*
310282 ATTAAATTAAATTTAAA-TAAAA
1 ATTAAAATAAATTTAAATTAAAA
* *
310304 TTTAAAATAATTTTAAATTAAAA
1 ATTAAAATAAATTTAAATTAAAA
310327 ATTAAAA
1 ATTAAAA
310334 AATTAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTAAAATAAATTTAAATTAAAA
Found at i:310462 original size:40 final size:40
Alignment explanation
Indices: 310396--310527 Score: 101
Period size: 40 Copynumber: 3.2 Consensus size: 40
310386 CCTATTATAA
* *
310396 TTATA-TAATTTTATAAATTTTAATATATTAATAAT-TTATT
1 TTATATTAATTTTA-ATATATT-ATATATTAATAATATTATT
* *
310436 TTATATTAATTTTAATATGTATATATAATTATAATAAATAATATT
1 TTATATTAATTTTAATATAT-TATAT-A-T-TAAT-AATATTATT
* *
310481 TTA-ATTATTTTTTATATATTATAT-TTATATAATATTATT
1 TTATATTAATTTTAATATATTATATATTA-ATAATATTATT
*
310520 TAATATTA
1 TTATATTA
310528 TCAATTTTAT
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
39 12 0.16
40 20 0.27
41 10 0.13
42 1 0.01
43 9 0.12
44 16 0.21
45 7 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (40 bp):
TTATATTAATTTTAATATATTATATATTAATAATATTATT
Found at i:310509 original size:13 final size:13
Alignment explanation
Indices: 310491--310528 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
310481 TTAATTATTT
310491 TTTATATATTATA
1 TTTATATATTATA
*
310504 TTTATATAATATTA
1 TTTATATATTA-TA
310518 TTTA-ATATTAT
1 TTTATATATTAT
310529 CAATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 1 0.05
13 15 0.68
14 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTATATATTATA
Found at i:310528 original size:40 final size:42
Alignment explanation
Indices: 310418--310528 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 42
310408 ATAAATTTTA
*
310418 ATATA-TTA-ATAAT-TTATTTTATATTAATTTTAATATGTAT
1 ATATATTTATATAATATTATTTTATATT-ATTTTAATATATAT
* * *
310458 ATATAATTATAATAAATAATATTTTA-ATTATTTT-TTATATAT
1 ATATATTTAT-AT-AATATTATTTTATATTATTTTAATATATAT
*
310500 -TATATTTATATAATATTATTTAATATTAT
1 ATATATTTATATAATATTATTTTATATTAT
310529 CAATTTTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
39 10 0.17
40 12 0.20
41 11 0.19
42 6 0.10
43 7 0.12
44 6 0.10
45 7 0.12
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (42 bp):
ATATATTTATATAATATTATTTTATATTATTTTAATATATAT
Found at i:310594 original size:15 final size:15
Alignment explanation
Indices: 310568--310626 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 15
310558 ATATTTATTT
310568 TATAAAT-A-TTAAA
1 TATAAATAATTTAAA
310581 TATAAATAATTTAAAAA
1 TATAAATAATTT--AAA
*
310598 TATAAA-AAATTAAA
1 TATAAATAATTTAAA
310612 -ATAATATAATTTAAA
1 TATAA-ATAATTTAAA
310627 AAAAAGATCC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 11 0.29
14 5 0.13
15 9 0.24
16 4 0.11
17 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATAATTTAAA
Found at i:310598 original size:17 final size:17
Alignment explanation
Indices: 310578--310628 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 17
310568 TATAAATATT
310578 AAATATAAATAATTTAA
1 AAATATAAATAATTTAA
*
310595 AAATATAAA-AAATT-A
1 AAATATAAATAATTTAA
*
310610 AAATA-ATATAATTTAA
1 AAATATAAATAATTTAA
310626 AAA
1 AAA
310629 AAAGATCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 2 0.07
15 10 0.34
16 8 0.28
17 9 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATAAATAATTTAA
Found at i:312863 original size:19 final size:21
Alignment explanation
Indices: 312814--312865 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
312804 ATTTTAGACA
**
312814 AAAT-ATAATTACGAAAAAGT
1 AAATAATAATTAAAAAAAAGT
312834 AAATAATAATTAAAAAAAAGT
1 AAATAATAATTAAAAAAAAGT
312855 AAA-AA-AATTAA
1 AAATAATAATTAA
312866 GTAATTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 17 0.59
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATAATAATTAAAAAAAAGT
Found at i:313574 original size:23 final size:24
Alignment explanation
Indices: 313529--313574 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
313519 ATTTTATATT
313529 TATTAAATTTGTAGTATTAACAAA
1 TATTAAATTTGTAGTATTAACAAA
*
313553 TATTAAATTTGTA-TATTTACAA
1 TATTAAATTTGTAGTATTAACAA
313575 TTTTAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (24 bp):
TATTAAATTTGTAGTATTAACAAA
Found at i:314502 original size:17 final size:17
Alignment explanation
Indices: 314480--314513 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
314470 AATATATTTA
314480 ATAAATACAAATAATAT
1 ATAAATACAAATAATAT
*
314497 ATAAATACAATTAATAT
1 ATAAATACAAATAATAT
314514 GACACATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAATACAAATAATAT
Found at i:315477 original size:28 final size:28
Alignment explanation
Indices: 315401--315477 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 28
315391 AAATCAGTTT
*
315401 TATTAATTAAAATAATATTTTTATT-TAAA
1 TATTAATT-AAA-AATAATTTTATTATAAA
*
315430 T-TTAATTATAAA-AA---TA-TATAAA
1 TATTAATTAAAAATAATTTTATTATAAA
315452 TATTAATTAAAAATAATTTTATTATA
1 TATTAATTAAAAATAATTTTATTATA
315478 TTTTAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 15
0.68 0.05 0.27
Matches are distributed among these distances:
21 1 0.03
22 7 0.18
23 10 0.26
24 2 0.05
25 1 0.03
26 2 0.05
27 4 0.11
28 10 0.26
29 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TATTAATTAAAAATAATTTTATTATAAA
Found at i:315521 original size:6 final size:6
Alignment explanation
Indices: 315511--315541 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
315501 TAAACCCAAA
*
315511 TAAATA TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT T
315542 TTTTTCTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:315729 original size:11 final size:11
Alignment explanation
Indices: 315713--315786 Score: 52
Period size: 10 Copynumber: 7.1 Consensus size: 11
315703 TCATAATTTA
315713 ATTTATTATAT
1 ATTTATTATAT
315724 ATTTA-TATA-
1 ATTTATTATAT
315733 ATTT-TTAATAT
1 ATTTATT-ATAT
* *
315744 ATTTATAATTT
1 ATTTATTATAT
*
315755 ATATTA-TATAA
1 AT-TTATTATAT
*
315766 ATTT-TAATAT
1 ATTTATTATAT
315776 ATTTATT-TAT
1 ATTTATTATAT
315786 A
1 A
315787 ATATATTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
9 5 0.10
10 20 0.42
11 19 0.40
12 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTATTATAT
Found at i:315734 original size:20 final size:20
Alignment explanation
Indices: 315711--315764 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
315701 ATTCATAATT
315711 TAATTTATTATATATTTATA
1 TAATTTATTATATATTTATA
315731 TAATTT-TTAATATATTTATA
1 TAATTTATT-ATATATTTATA
*
315751 -ATTTATATTATATA
1 TAATT-TATTATATA
315765 AATTTTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.17
20 23 0.77
21 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATTTATTATATATTTATA
Found at i:315781 original size:20 final size:19
Alignment explanation
Indices: 315720--315778 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
315710 TTAATTTATT
*
315720 ATATATTTATATAATTTTTA
1 ATATA-TTATATAAATTTTA
315740 ATATATT-TAT-AA--TT-
1 ATATATTATATAAATTTTA
315754 -TATATTATATAAATTTTA
1 ATATATTATATAAATTTTA
315772 ATATATT
1 ATATATT
315779 TATTTATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
13 6 0.19
14 3 0.09
15 4 0.12
17 3 0.09
18 3 0.09
19 8 0.25
20 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATATTATATAAATTTTA
Found at i:315793 original size:15 final size:15
Alignment explanation
Indices: 315751--315794 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
315741 TATATTTATA
* **
315751 ATTTATATTATATAA
1 ATTTATAATATATTT
315766 ATTT-TAATATATTT
1 ATTTATAATATATTT
315780 ATTTATAATATATTT
1 ATTTATAATATATTT
315795 TAATTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTATAATATATTT
Found at i:315809 original size:32 final size:33
Alignment explanation
Indices: 315708--315810 Score: 104
Period size: 36 Copynumber: 3.1 Consensus size: 33
315698 TATATTCATA
*
315708 ATTTAATTTATTATATA-TTTATATAATTTTTA-
1 ATTT-ATTTATAATATATTTTATATAATTTTTAT
* * *
315740 ATATATTTATAATTTATATTATATAAATTTTAATAT
1 ATTTATTTATAATATATTTTATAT-AATTTT--TAT
*
315776 ATTTATTTATAATATATTTTA-ATTATTTTTAT
1 ATTTATTTATAATATATTTTATATAATTTTTAT
315808 ATT
1 ATT
315811 ATATAATCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
31 10 0.17
32 15 0.26
33 6 0.10
34 5 0.09
35 4 0.07
36 18 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
ATTTATTTATAATATATTTTATATAATTTTTAT
Found at i:315811 original size:11 final size:12
Alignment explanation
Indices: 315716--315814 Score: 54
Period size: 11 Copynumber: 8.7 Consensus size: 12
315706 TAATTTAATT
315716 TATTATATATTTA
1 TATTATAT-TTTA
315729 TA-TA-ATTTT-
1 TATTATATTTTA
*
315738 TAATATA-TTTA
1 TATTATATTTTA
*
315749 TAATT-TATATTA
1 T-ATTATATTTTA
*
315761 TA-TAAATTTTA
1 TATTATATTTTA
*
315772 -ATATATTTATTTA
1 TAT-TATAT-TTTA
*
315785 TAATATATTTTA
1 TATTATATTTTA
315797 -ATTAT-TTTTA
1 TATTATATTTTA
315807 TATTATAT
1 TATTATAT
315815 AATCATATCA
Statistics
Matches: 65, Mismatches: 9, Indels: 25
0.66 0.09 0.25
Matches are distributed among these distances:
9 2 0.03
10 15 0.23
11 21 0.32
12 16 0.25
13 10 0.15
14 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:315814 original size:24 final size:25
Alignment explanation
Indices: 315752--315815 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 25
315742 ATATTTATAA
315752 TTTATATTATATAAATTTTAATATATT
1 TTTATATTATAT--ATTTTAATATATT
*
315779 TATT-TATAATATATTTTAAT-TATT
1 T-TTATATTATATATTTTAATATATT
315803 TTTATATTATATA
1 TTTATATTATATA
315816 ATCATATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 2 0.06
24 13 0.39
25 8 0.24
27 8 0.24
28 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTATATTATATATTTTAATATATT
Found at i:317230 original size:14 final size:16
Alignment explanation
Indices: 317198--317231 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
317188 TGATTATTCT
317198 TATATTCATAATTTAA
1 TATATTCATAATTTAA
317214 TATATT-ATAATTT-A
1 TATATTCATAATTTAA
317228 TATA
1 TATA
317232 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 7 0.39
16 6 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTCATAATTTAA
Found at i:317232 original size:24 final size:26
Alignment explanation
Indices: 317205--317254 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
317195 TCTTATATTC
317205 ATAA-TTTAATATATT-ATAATTTAT
1 ATAATTTTAATATATTAATAATTTAT
317229 ATAATTTTTAATATATTAATAATTTA
1 ATAA-TTTTAATATATTAATAATTTA
317255 CATCACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.17
26 11 0.48
27 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATAATTTTAATATATTAATAATTTAT
Found at i:317254 original size:16 final size:16
Alignment explanation
Indices: 317198--317254 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
317188 TGATTATTCT
*
317198 TATATTCATAATTTAA
1 TATATTAATAATTTAA
317214 TATATT-ATAA-TT--
1 TATATTAATAATTTAA
*
317226 TATA-TAAT-TTTTAA
1 TATATTAATAATTTAA
317240 TATATTAATAATTTA
1 TATATTAATAATTTA
317255 CATCACATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
11 1 0.03
12 8 0.24
14 6 0.18
15 8 0.24
16 10 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTAATAATTTAA
Found at i:317299 original size:16 final size:16
Alignment explanation
Indices: 317272--317326 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
317262 TAAATTTTCA
317272 TATATT-TA-TTTATT
1 TATATTATATTTTATT
*
317286 TATATTATATTTTAAT
1 TATATTATATTTTATT
* * *
317302 TATTTTTTATTTTATA
1 TATATTATATTTTATT
317318 TA-ATTATAT
1 TATATTATAT
317327 CATATTTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
16 19 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTATATTTTATT
Found at i:317602 original size:13 final size:13
Alignment explanation
Indices: 317584--317624 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
317574 AACAAAATTC
317584 TTATTTAAATAAT
1 TTATTTAAATAAT
* *
317597 TTATTTTAATATT
1 TTATTTAAATAAT
*
317610 TTATTAAAATAAT
1 TTATTTAAATAAT
317623 TT
1 TT
317625 TAGGACACAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATTTAAATAAT
Found at i:317699 original size:18 final size:18
Alignment explanation
Indices: 317676--317717 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
317666 GGATCAGTTC
*
317676 AATTTTTATGTT-AATATG
1 AATTTTTACGTTGAATA-G
317694 AA-TTTTACGTTGAATAG
1 AATTTTTACGTTGAATAG
317711 AATTTTT
1 AATTTTT
317718 CATATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (18 bp):
AATTTTTACGTTGAATAG
Found at i:320996 original size:2 final size:2
Alignment explanation
Indices: 320989--321013 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
320979 AATCTAAATT
320989 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
321014 TCTTTCAAGG
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:321452 original size:2 final size:2
Alignment explanation
Indices: 321445--321474 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
321435 ATTTCATTAG
321445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
321475 CCATTATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322590 original size:2 final size:2
Alignment explanation
Indices: 322578--322623 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
322568 CTTAAATACA
*
322578 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
322620 AT AT
1 AT AT
322624 CTTTTGTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:323508 original size:17 final size:18
Alignment explanation
Indices: 323478--323511 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
323468 TTTCATTCTA
323478 AAAAATTAAATATATAAT
1 AAAAATTAAATATATAAT
*
323496 AAAAA-TAATTATATAA
1 AAAAATTAAATATATAA
323512 ATTAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATTAAATATATAAT
Found at i:323970 original size:22 final size:22
Alignment explanation
Indices: 323928--323971 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
323918 AAATTAATTT
*
323928 AAATATAATAATTATTTAATAA
1 AAATATAATAATTATTAAATAA
*
323950 AAATATAA-AGTTAATTAAATAA
1 AAATATAATAATT-ATTAAATAA
323972 TATGATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATATAATAATTATTAAATAA
Found at i:324708 original size:30 final size:30
Alignment explanation
Indices: 324674--324734 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
324664 GATTTAGTTC
324674 ACTGACTTGATTTAAGACAATTCGATGATG
1 ACTGACTTGATTTAAGACAATTCGATGATG
324704 ACTGACTTGATTTAAGACAATTCGATGATG
1 ACTGACTTGATTTAAGACAATTCGATGATG
324734 A
1 A
324735 GAACCATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (30 bp):
ACTGACTTGATTTAAGACAATTCGATGATG
Found at i:324897 original size:13 final size:13
Alignment explanation
Indices: 324876--324905 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
324866 GTCTAGATAT
*
324876 ATATTAAATATAA
1 ATATCAAATATAA
324889 ATATCAAATATAA
1 ATATCAAATATAA
324902 ATAT
1 ATAT
324906 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATCAAATATAA
Found at i:328584 original size:34 final size:34
Alignment explanation
Indices: 328511--328726 Score: 258
Period size: 34 Copynumber: 6.2 Consensus size: 34
328501 ATTCTTTAAG
* *
328511 GTTTAAAAGGACAACCTTGAAAACCCATCAAAGCTA
1 GTTTCAAA-GACAACCTTGAAAAACCATC-AAGCTA
**
328547 GTTTCAAAGACAATTTTGAAAAACCATCAAGCTA
1 GTTTCAAAGACAACCTTGAAAAACCATCAAGCTA
*
328581 GTTTCAAAGACAACCTTAAAAAAACCCATCAAGCTA
1 GTTTCAAAGACAACCTT-GAAAAA-CCATCAAGCTA
**
328617 GTTTC-AAGACAACCTTGAGAACCCCATCAAGCTA
1 GTTTCAAAGACAACCTTGA-AAAACCATCAAGCTA
*
328651 GTTTCAAA-ACAACCTTAAAAAACCCATCAAGCTA
1 GTTTCAAAGACAACCTTGAAAAA-CCATCAAGCTA
**
328685 GTTTC-AAGACAACCTTGAGAACCCCATCAAGCTA
1 GTTTCAAAGACAACCTTGA-AAAACCATCAAGCTA
328719 GTTTCAAA
1 GTTTCAAA
328727 CTAAGTTTTA
Statistics
Matches: 156, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
33 4 0.03
34 88 0.56
35 41 0.26
36 23 0.15
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.22
Consensus pattern (34 bp):
GTTTCAAAGACAACCTTGAAAAACCATCAAGCTA
Found at i:328678 original size:104 final size:102
Alignment explanation
Indices: 328520--328725 Score: 299
Period size: 104 Copynumber: 2.0 Consensus size: 102
328510 GGTTTAAAAG
** *
328520 GACAACCTTGAAAACCCATCAAAGCTAGTTTCAAAGACAATTTTGAAAAACCATCAAGCTAGTTT
1 GACAACCTTGAAAACCCATCAAAGCTAGTTTCAAAGACAACCTTAAAAAACCATCAAGCTAGTTT
328585 CAAAGACAACCTTAAAAAAACCCATCAAGCTAGTTTCAA
66 C-AAGACAACCTT-AAAAAACCCATCAAGCTAGTTTCAA
*
328624 GACAACCTTGAGAACCCCATC-AAGCTAGTTTCAAA-ACAACCTTAAAAAACCCATCAAGCTAGT
1 GACAACCTTGA-AAACCCATCAAAGCTAGTTTCAAAGACAACCTTAAAAAA-CCATCAAGCTAGT
* * *
328687 TTCAAGACAACCTTGAGAACCCCATCAAGCTAGTTTCAA
64 TTCAAGACAACCTTAAAAAACCCATCAAGCTAGTTTCAA
328726 ACTAAGTTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
102 22 0.24
103 22 0.24
104 41 0.44
105 8 0.09
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (102 bp):
GACAACCTTGAAAACCCATCAAAGCTAGTTTCAAAGACAACCTTAAAAAACCATCAAGCTAGTTT
CAAGACAACCTTAAAAAACCCATCAAGCTAGTTTCAA
Found at i:328693 original size:68 final size:69
Alignment explanation
Indices: 328511--328726 Score: 321
Period size: 68 Copynumber: 3.1 Consensus size: 69
328501 ATTCTTTAAG
* * ** **
328511 GTTTAAAAGGACAACCTT-GAAAACCCATCAAAGCTAGTTTCAAAGACAATTTTGA-AAAACCAT
1 GTTTCAAA-GACAACCTTAAAAAACCCATC-AAGCTAGTTTC-AAGACAACCTTGAGAACCCCAT
328574 CAAGCTA
63 CAAGCTA
328581 GTTTCAAAGACAACCTTAAAAAAACCCATCAAGCTAGTTTCAAGACAACCTTGAGAACCCCATCA
1 GTTTCAAAGACAACCTT-AAAAAACCCATCAAGCTAGTTTCAAGACAACCTTGAGAACCCCATCA
328646 AGCTA
65 AGCTA
328651 GTTTCAAA-ACAACCTTAAAAAACCCATCAAGCTAGTTTCAAGACAACCTTGAGAACCCCATCAA
1 GTTTCAAAGACAACCTTAAAAAACCCATCAAGCTAGTTTCAAGACAACCTTGAGAACCCCATCAA
328715 GCTA
66 GCTA
328719 GTTTCAAA
1 GTTTCAAA
328727 CTAAGTTTTA
Statistics
Matches: 137, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
68 60 0.44
69 28 0.20
70 39 0.28
71 10 0.07
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.22
Consensus pattern (69 bp):
GTTTCAAAGACAACCTTAAAAAACCCATCAAGCTAGTTTCAAGACAACCTTGAGAACCCCATCAA
GCTA
Found at i:329667 original size:15 final size:15
Alignment explanation
Indices: 329647--329676 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
329637 GAAAAACTTT
*
329647 ATTTTTAAATTTAAA
1 ATTTTTAAAATTAAA
329662 ATTTTTAAAATTAAA
1 ATTTTTAAAATTAAA
329677 GATGTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTAAAATTAAA
Found at i:329817 original size:24 final size:24
Alignment explanation
Indices: 329788--329833 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
329778 AAAAATAAAA
329788 TTTAAATATCAAATTATAAATTTT
1 TTTAAATATCAAATTATAAATTTT
*
329812 TTTAAATATTAAATTATAAATT
1 TTTAAATATCAAATTATAAATT
329834 AAATTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAAATATCAAATTATAAATTTT
Found at i:329848 original size:12 final size:13
Alignment explanation
Indices: 329816--329845 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
329806 AATTTTTTTA
329816 AATATTAAATTAT
1 AATATTAAATTAT
329829 AA-ATTAAATTAT
1 AATATTAAATTAT
329841 AATAT
1 AATAT
329846 AAAAATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATATTAAATTAT
Found at i:329848 original size:24 final size:23
Alignment explanation
Indices: 329780--329848 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 23
329770 TGTATAATAA
*
329780 AAATAAAATTTAAATATCAAATTAT
1 AAATTAAA-TTAAATAT-AAATTAT
***
329805 AAATTTTTTTAAATATTAAATTAT
1 AAATTAAATTAAATA-TAAATTAT
329829 AAATTAAATTATAATATAAA
1 AAATTAAATTA-AATATAAA
329849 AATCAAATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTAAATTAAATATAAATTAT
Found at i:336425 original size:51 final size:51
Alignment explanation
Indices: 336364--336468 Score: 185
Period size: 51 Copynumber: 2.1 Consensus size: 51
336354 AAGAGATGTC
336364 GTTGTTGAAAGCAACCTACTTC-GATGCTACTGTTGAAAAAGATGCGACTAA
1 GTTGTTGAAAGCAACCTACTTCAG-TGCTACTGTTGAAAAAGATGCGACTAA
*
336415 GTTGTTGAAAGCTACCTACTTCAGTGCTACTGTTGAAAAAGATGCGACTAA
1 GTTGTTGAAAGCAACCTACTTCAGTGCTACTGTTGAAAAAGATGCGACTAA
336466 GTT
1 GTT
336469 CGATAGGAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
51 51 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (51 bp):
GTTGTTGAAAGCAACCTACTTCAGTGCTACTGTTGAAAAAGATGCGACTAA
Found at i:339944 original size:2 final size:2
Alignment explanation
Indices: 339937--339969 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
339927 GGATTTTCAA
339937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
339970 ACAAGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:340952 original size:52 final size:52
Alignment explanation
Indices: 340893--341132 Score: 221
Period size: 52 Copynumber: 4.6 Consensus size: 52
340883 GGTGCTAATA
* * *
340893 TGCTGATTCAAGGCCAGCGATATCGGGCTTAAAAATAAAAAAAATG-TGAATG
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAATAAAAAAAATGCT-AGTG
* * * * * *** *
340945 TGCTGATTCAGGGCCAGCCACATTGGGCTTAAACATGATAAGGGTGCTAGTT
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAATAAAAAAAATGCTAGTG
* * *
340997 TGCTGATTCAAGGCCAACGACATTGGGCTTAAAAATGAAAAGAATGCTAGTG
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAATAAAAAAAATGCTAGTG
* * * * **
341049 TGCTGATTTAAGGCCTAGCAACATTGAGCTTAACAATAAAAAAGGTGCTAGTG
1 TGCTGATTCAAGGCC-AGCGACATTGGGCTTAAAAATAAAAAAAATGCTAGTG
* * ** *
341102 TGCTGAGTCAAAGTTAGCAACATTGGGCTTA
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTA
341133 GAAGGAAATG
Statistics
Matches: 151, Mismatches: 35, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
52 111 0.74
53 40 0.26
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (52 bp):
TGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAATAAAAAAAATGCTAGTG
Found at i:341125 original size:105 final size:104
Alignment explanation
Indices: 340917--341132 Score: 238
Period size: 105 Copynumber: 2.1 Consensus size: 104
340907 CAGCGATATC
* * * *
340917 GGGCTTAAAAATAAAAAAAATGTGAATGTGCTGATTCAGGGCCAGCCACATTGGGCTTAAACATG
1 GGGCTTAAAAATAAAAAAAATGTGAATGTGCTGATTCAAGGCCAGCAACATTGAGCTTAAACATA
* * * * * *
340982 ATAAGGGTGCTAGTTTGCTGATTCAAGGCCAACGACATT
66 AAAAAGGTGCTAGTGTGCTGAGTCAAAGCCAACAACATT
* * * *
341021 GGGCTTAAAAATGAAAAGAATGCT-AGTGTGCTGATTTAAGGCCTAGCAACATTGAGCTT-AACA
1 GGGCTTAAAAATAAAAAAAATG-TGAATGTGCTGATTCAAGGCC-AGCAACATTGAGCTTAAAC-
** *
341084 ATAAAAAAGGTGCTAGTGTGCTGAGTCAAAGTTAGCAACATT
63 ATAAAAAAGGTGCTAGTGTGCTGAGTCAAAGCCAACAACATT
341126 GGGCTTA
1 GGGCTTA
341133 GAAGGAAATG
Statistics
Matches: 92, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
104 39 0.42
105 53 0.58
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (104 bp):
GGGCTTAAAAATAAAAAAAATGTGAATGTGCTGATTCAAGGCCAGCAACATTGAGCTTAAACATA
AAAAAGGTGCTAGTGTGCTGAGTCAAAGCCAACAACATT
Found at i:341188 original size:33 final size:34
Alignment explanation
Indices: 341151--341232 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 34
341141 TGCCATCAAT
* *
341151 TTGTGTGGACTTT-AGAAGAA-GATTGCCACTAAC
1 TTGTGTGGACTTTGAAAAAAAGGA-TGCCACTAAC
*
341184 TTGTGTGGGCTTTGAAAAAAAGGATGCCACTAAC
1 TTGTGTGGACTTTGAAAAAAAGGATGCCACTAAC
341218 TTGTGTAGG-CTTTGA
1 TTGTGT-GGACTTTGA
341233 CTCAGGTGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 12 0.28
34 27 0.63
35 4 0.09
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (34 bp):
TTGTGTGGACTTTGAAAAAAAGGATGCCACTAAC
Done.