Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 36 of 168
Found at i:9767829 original size:107 final size:107
Alignment explanation
Indices: 9767716--9767944 Score: 404
Period size: 107 Copynumber: 2.1 Consensus size: 107
9767706 ATAAGTTGAT
* * *
9767716 TATTAACCGAAACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAACCAAACTAA
1 TATTAACCGATACAATTCAAATACATCAAAATAGCTGAAACATGCCAAAATTTTAACCAAACTAA
9767781 AACATATACTACTGTGTACTCATTTAAGATTGAAATGATATA
66 AACATATACTACTGTGTACTCATTTAAGATTGAAATGATATA
*
9767823 TATTAACCGATACAATTCAAATACATCAAAATAGCTGAAACATGCCAAAATTTTAATCAAACTAA
1 TATTAACCGATACAATTCAAATACATCAAAATAGCTGAAACATGCCAAAATTTTAACCAAACTAA
* *
9767888 AACATATACTACTTTGTACTCGTTTAAGATTGAAATGATATA
66 AACATATACTACTGTGTACTCATTTAAGATTGAAATGATATA
9767930 TATTAACCGATACAA
1 TATTAACCGATACAA
9767945 CCCATACCTA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 116 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (107 bp):
TATTAACCGATACAATTCAAATACATCAAAATAGCTGAAACATGCCAAAATTTTAACCAAACTAA
AACATATACTACTGTGTACTCATTTAAGATTGAAATGATATA
Found at i:9773740 original size:15 final size:14
Alignment explanation
Indices: 9773716--9773747 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
9773706 TGGTCTCTCA
9773716 TTTTTCTTTTTCTT
1 TTTTTCTTTTTCTT
9773730 TTTTCTCTTTTTCTT
1 TTTT-TCTTTTTCTT
9773745 TTT
1 TTT
9773748 GAAACATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:9777315 original size:44 final size:44
Alignment explanation
Indices: 9777265--9777464 Score: 207
Period size: 44 Copynumber: 4.5 Consensus size: 44
9777255 TTTGAGTACT
9777265 TCTGATCAATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
9777309 TCTGATCAGTGACAAGTGACAAGTGATGAGTGGTAGCTTTATCTACACTTA
1 TCTG---A-T--CAA-TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
9777360 TCTGATCAGTGACAAGTG---A----TAGCTTTAACTACACTTA
1 TCTGATCAATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
9777397 TCTGATCAGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
9777441 TCTGATTAAGGACAAGTGACAAGT
1 TCTGATCAATGACAAGTGATAAGT
9777465 AATAAATGTG
Statistics
Matches: 132, Mismatches: 10, Indels: 28
0.78 0.06 0.16
Matches are distributed among these distances:
37 35 0.27
40 1 0.01
41 1 0.01
44 49 0.37
45 2 0.02
47 2 0.02
48 2 0.02
50 3 0.02
51 37 0.28
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (44 bp):
TCTGATCAATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:9777355 original size:51 final size:51
Alignment explanation
Indices: 9777274--9777378 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
9777264 TTCTGATCAA
9777274 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
1 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
* *
9777325 TGACAAGTGATGAGTGGTAGCTTTATCTACACTTATCTGATCAGTGACAAG
1 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
9777376 TGA
1 TGA
9777379 TAGCTTTAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
Found at i:9777383 original size:37 final size:37
Alignment explanation
Indices: 9777337--9777416 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
9777327 ACAAGTGATG
* *
9777337 AGTGGTAGCTTTATCTACACTTATCTGATCAGTGACA
1 AGTGATAGCTTTAACTACACTTATCTGATCAGTGACA
9777374 AGTGATAGCTTTAACTACACTTATCTGATCAGTGACA
1 AGTGATAGCTTTAACTACACTTATCTGATCAGTGACA
9777411 AGTGAT
1 AGTGAT
9777417 GAGTGGTAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (37 bp):
AGTGATAGCTTTAACTACACTTATCTGATCAGTGACA
Found at i:9780127 original size:24 final size:25
Alignment explanation
Indices: 9780100--9780152 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
9780090 GGTCTTTTCG
*
9780100 TGAAATTTAATGCAAATG-ATGCAA
1 TGAAATGTAATGCAAATGAATGCAA
* *
9780124 TGAAATGTAATGCAGATGAATGGAA
1 TGAAATGTAATGCAAATGAATGCAA
9780149 TGAA
1 TGAA
9780153 TGCAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (25 bp):
TGAAATGTAATGCAAATGAATGCAA
Found at i:9782205 original size:3 final size:3
Alignment explanation
Indices: 9782184--9782287 Score: 68
Period size: 3 Copynumber: 33.7 Consensus size: 3
9782174 CACGAAAAAT
* * ** *
9782184 ATA ATA CTA ATA GTA ATA ATA ACG ATA ATA ATA ATA GTA ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * *
9782230 ATG TTA ATA TTA ATAA ATA ATA A-A CATA ATA ATA A-A GTTA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA -ATA ATA ATA
9782276 ATA ATGA ATA AT
1 ATA AT-A ATA AT
9782288 CGAAATTTGA
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
2 2 0.03
3 63 0.83
4 11 0.14
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9782352 original size:18 final size:19
Alignment explanation
Indices: 9782323--9782366 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
9782313 AATATAAATA
9782323 TGTAAAT-A-AATAAATAA-
1 TGTAAATGACAAT-AATAAG
9782340 TG-AAATGACAATAATAAG
1 TGTAAATGACAATAATAAG
9782358 TGTAAATGA
1 TGTAAATGA
9782367 TAAAATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.17
17 8 0.35
18 5 0.22
19 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (19 bp):
TGTAAATGACAATAATAAG
Found at i:9782545 original size:3 final size:3
Alignment explanation
Indices: 9782530--9782673 Score: 54
Period size: 3 Copynumber: 47.0 Consensus size: 3
9782520 TAAAACAAAT
* * * * * * *
9782530 TAA TAA CAA TAA TAA TAA TAA TAA TAG TAA AAA TAA AAA TAT TAG TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * * * * *
9782578 TTG TAA TAA TGGAA GTAA TAG TAA CAG TAA TAA TAA CAA TAA TAG TAC
1 TAA TAA TAA T--AA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * *
9782626 TAC TAC TAC TAC TAC TAC TAC TAA TAA TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9782674 AAGGACAAAA
Statistics
Matches: 110, Mismatches: 28, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
3 105 0.95
4 2 0.02
5 2 0.02
6 1 0.01
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:9790389 original size:12 final size:12
Alignment explanation
Indices: 9790374--9790407 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
9790364 TTATTTTTCT
9790374 TTACTTTATTTA
1 TTACTTTATTTA
9790386 TTACTTTATTTTA
1 TTACTTTA-TTTA
9790399 TTA-TTTATT
1 TTACTTTATT
9790408 ACTTATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:9790398 original size:17 final size:15
Alignment explanation
Indices: 9790357--9790400 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
9790347 CAACCCAATT
9790357 TTTATTATTATTTTTC
1 TTTATT-TTATTTTTC
*
9790373 TTTACTTTATTTATTAC
1 TTTATTTTATTT-TT-C
9790390 TTTATTTTATT
1 TTTATTTTATT
9790401 ATTTATTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 11 0.46
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTTATTTTTC
Found at i:9793312 original size:13 final size:12
Alignment explanation
Indices: 9793294--9793323 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
9793284 AAGAGTTAAA
9793294 TAAAAATTTAATT
1 TAAAAA-TTAATT
9793307 TAAAAATTAATT
1 TAAAAATTAATT
9793319 TAAAA
1 TAAAA
9793324 TATCAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAAAATTAATT
Found at i:9793584 original size:107 final size:107
Alignment explanation
Indices: 9793374--9793591 Score: 409
Period size: 107 Copynumber: 2.0 Consensus size: 107
9793364 ATTAACTAAA
9793374 ACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAATCAAACTAAAACATATACTA
1 ACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAATCAAACTAAAACATATACTA
* *
9793439 CTTTGTACTCATTTAAGATTGAAATGATATATATTAACCTAT
66 CTTTGTACCCATTTAAGATTGAAATGATATATATTAACCGAT
9793481 ACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAATCAAACTAAAACATATACTA
1 ACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAATCAAACTAAAACATATACTA
*
9793546 CTTTGTACCCGTTTAAGATTGAAATGATATATATTAACCGAT
66 CTTTGTACCCATTTAAGATTGAAATGATATATATTAACCGAT
9793588 ACAA
1 ACAA
9793592 CCCATACCTA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (107 bp):
ACAATTCAAATACATCGAAATAGTTGAAACATGCCAAAATTTTAATCAAACTAAAACATATACTA
CTTTGTACCCATTTAAGATTGAAATGATATATATTAACCGAT
Found at i:9795040 original size:29 final size:29
Alignment explanation
Indices: 9794997--9795136 Score: 149
Period size: 29 Copynumber: 4.8 Consensus size: 29
9794987 ACAAAAAATA
*
9794997 AAAATTTATATTTTGACCCCAAACTTTGCT-
1 AAAA-TTACATTTTGACCCCAAACTTT-CTC
*
9795027 AAAATTACATTTTGGCCCCAAACTTTCTC
1 AAAATTACATTTTGACCCCAAACTTTCTC
* * *
9795056 AAAATTACACTTTGACCCCTAAACTTTTTG
1 AAAATTACATTTTGACCCC-AAACTTTCTC
* * *
9795086 AAAATTACATTTTGGCCCCATATTTTC-C
1 AAAATTACATTTTGACCCCAAACTTTCTC
*
9795114 TAAAATTACATTTTTACCCCAAA
1 -AAAATTACATTTTGACCCCAAA
9795137 TATTTTGCGT
Statistics
Matches: 92, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.02
29 61 0.66
30 29 0.32
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCAAACTTTCTC
Found at i:9795090 original size:59 final size:58
Alignment explanation
Indices: 9795008--9795136 Score: 172
Period size: 59 Copynumber: 2.2 Consensus size: 58
9794998 AAATTTATAT
9795008 TTTGACCCCAAACTTTGCTAAAATTACATTTTGGCCCCAAACTTT-CTCAAAATTACAC
1 TTTGACCCCAAACTTTGCTAAAATTACATTTTGGCCCCAAACTTTCCT-AAAATTACAC
* * * *
9795066 TTTGACCCCTAAACTTT-TTGAAAATTACATTTTGGCCCCATATTTTCCTAAAATTACAT
1 TTTGACCCC-AAACTTTGCT-AAAATTACATTTTGGCCCCAAACTTTCCTAAAATTACAC
*
9795125 TTTTACCCCAAA
1 TTTGACCCCAAA
9795137 TATTTTGCGT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
58 13 0.21
59 48 0.76
60 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (58 bp):
TTTGACCCCAAACTTTGCTAAAATTACATTTTGGCCCCAAACTTTCCTAAAATTACAC
Found at i:9795310 original size:25 final size:24
Alignment explanation
Indices: 9795280--9795326 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
9795270 AGACAAGAAG
9795280 AAAAAGGACAAAAAAT-GAAGAGATT
1 AAAAA-GA-AAAAAATGGAAGAGATT
*
9795305 AAAAAGAAGAAAATGGAAGAGA
1 AAAAAGAAAAAAATGGAAGAGA
9795327 AGAAAGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 9 0.45
25 5 0.25
ACGTcount: A:0.66, C:0.02, G:0.23, T:0.09
Consensus pattern (24 bp):
AAAAAGAAAAAAATGGAAGAGATT
Found at i:9795661 original size:6 final size:6
Alignment explanation
Indices: 9795651--9795744 Score: 100
Period size: 6 Copynumber: 15.3 Consensus size: 6
9795641 GTGCTGCCCG
* * * * *
9795651 AAGAAG AAGAAA AA-AGA AAGAAAA AAGAAG AAGAAA AAGGGAG AAGAAA
1 AAGAAA AAGAAA AAGAAA AAG-AAA AAGAAA AAGAAA AA-GAAA AAGAAA
*
9795700 AAGAAA AAGAAA AAGAGA AAGAAA AAGAAA AAGAAAA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG-AAA AAGAAA AA
9795745 AATTTAAAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
5 4 0.05
6 54 0.74
7 15 0.21
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:9795683 original size:24 final size:24
Alignment explanation
Indices: 9795651--9795746 Score: 126
Period size: 24 Copynumber: 4.0 Consensus size: 24
9795641 GTGCTGCCCG
*
9795651 AAGAAGAAGAAAAA-AGAAAGAAAA
1 AAGAAAAAGAAAAAGAGAAAG-AAA
* *
9795675 AAGAAGAAGAAAAAGGGAGAAGAAA
1 AAGAAAAAGAAAAAGAGA-AAGAAA
9795700 AAGAAAAAGAAAAAGAGAAAGAAA
1 AAGAAAAAGAAAAAGAGAAAGAAA
9795724 AAGAAAAAGAAAAA-AGAAA-AAA
1 AAGAAAAAGAAAAAGAGAAAGAAA
9795746 A
1 A
9795747 TTTAAAAGTC
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.06
23 5 0.07
24 34 0.51
25 21 0.31
26 3 0.04
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (24 bp):
AAGAAAAAGAAAAAGAGAAAGAAA
Found at i:9795713 original size:37 final size:37
Alignment explanation
Indices: 9795651--9795744 Score: 113
Period size: 37 Copynumber: 2.5 Consensus size: 37
9795641 GTGCTGCCCG
*
9795651 AAGAAGAAGAAAAA-AGAAAGAAAAAAGA-AGAAGAAA
1 AAGAAGAAGAAAAAGAAAAAGAAAAAAGAGA-AAGAAA
*
9795687 AAGGGAGAAGAAAAAGAAAAAG-AAAAAGAGAAAGAAA
1 AA-GAAGAAGAAAAAGAAAAAGAAAAAAGAGAAAGAAA
*
9795724 AAGAAAAAGAAAAAAGAAAAA
1 AAGAAGAAG-AAAAAGAAAAA
9795745 AATTTAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
36 7 0.14
37 37 0.74
38 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (37 bp):
AAGAAGAAGAAAAAGAAAAAGAAAAAAGAGAAAGAAA
Found at i:9795721 original size:43 final size:43
Alignment explanation
Indices: 9795650--9795732 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 43
9795640 GGTGCTGCCC
* *
9795650 GAAGAAGAAGAAAAAAGAAAGAAAAAAGAAGAAGAAAAAGGGA
1 GAAGAAAAAGAAAAAAGAAAGAAAAAAGAAAAAGAAAAAGGGA
9795693 GAAGAAAAAG-AAAAAGAAA-AAGAGAAAGAAAAAGAAAAAG
1 GAAGAAAAAGAAAAAAGAAAGAA-A-AAAGAAAAAGAAAAAG
9795733 AAAAAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 2 0.06
42 10 0.28
43 24 0.67
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (43 bp):
GAAGAAAAAGAAAAAAGAAAGAAAAAAGAAAAAGAAAAAGGGA
Found at i:9795741 original size:43 final size:43
Alignment explanation
Indices: 9795651--9795744 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
9795641 GTGCTGCCCG
* * ** *
9795651 AAGAAGAAGAAAAAAGAAAGAAAAAAGAAGAAGAAAAAGGGAG
1 AAGAAAAAGAAAAAAGAAAGAAAAAAGAAAAAGAAAAAGAAAA
9795694 AAGAAAAAG-AAAAAGAAA-AAGAGAAAGAAAAAGAAAAAGAAAA
1 AAGAAAAAGAAAAAAGAAAGAA-A-AAAGAAAAAGAAAAAGAAAA
9795737 AAGAAAAA
1 AAGAAAAA
9795745 AATTTAAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 2 0.05
42 10 0.23
43 32 0.73
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (43 bp):
AAGAAAAAGAAAAAAGAAAGAAAAAAGAAAAAGAAAAAGAAAA
Found at i:9796024 original size:23 final size:23
Alignment explanation
Indices: 9795978--9796021 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9795968 TCCAGTCCAG
9795978 GCCCAACAGCACCTAGCAGGCCA
1 GCCCAACAGCACCTAGCAGGCCA
* *
9796001 GCCCAGCAGCAGC-AGCAGGCC
1 GCCCAACAGCACCTAGCAGGCC
9796022 CAGTACCGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.27, C:0.43, G:0.27, T:0.02
Consensus pattern (23 bp):
GCCCAACAGCACCTAGCAGGCCA
Found at i:9796153 original size:20 final size:20
Alignment explanation
Indices: 9796126--9796166 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
9796116 GCAGGCCCAA
9796126 AAAAAAAAGAAAAAAAAGGAAG
1 AAAAAAAAG--AAAAAAGGAAG
9796148 AAAAAAAAGAAAAAAGGAA
1 AAAAAAAAGAAAAAAGGAA
9796167 AAGGGCCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAGGAAG
Found at i:9796652 original size:17 final size:17
Alignment explanation
Indices: 9796608--9796656 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
9796598 TTAAAAAAAA
*
9796608 TCGTGTTTCACAAATTTT
1 TCGTGTTTCA-AAATTTC
*
9796626 TACGT-CTTCAAAATTTC
1 T-CGTGTTTCAAAATTTC
9796643 TCGTGTTTCAAAAT
1 TCGTGTTTCAAAAT
9796657 AATAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 3 0.12
17 15 0.58
18 5 0.19
19 3 0.12
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (17 bp):
TCGTGTTTCAAAATTTC
Found at i:9796763 original size:17 final size:16
Alignment explanation
Indices: 9796713--9796764 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
9796703 CTTTTCAAAA
9796713 AAAAAATTTCCGTGTTTT
1 AAAAAATTT-CGTG-TTT
* *
9796731 CAAAAATTCTCTTGTTT
1 AAAAAATT-TCGTGTTT
9796748 AAAAAATGTTCGTGTTT
1 AAAAAAT-TTCGTGTTT
9796765 TCGTGTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 16 0.57
18 11 0.39
19 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
AAAAAATTTCGTGTTT
Found at i:9796915 original size:17 final size:17
Alignment explanation
Indices: 9796889--9796961 Score: 55
Period size: 18 Copynumber: 4.3 Consensus size: 17
9796879 CGTGTTTAAA
9796889 AAAAATTTCGCA-TTTC
1 AAAAATTTCGCATTTTC
*
9796905 AAAAATCTTCGTATTTTC
1 AAAAAT-TTCGCATTTTC
9796923 -AAAA-TTC-CAATGTTTC
1 AAAAATTTCGC-AT-TTTC
**
9796939 AAAAATTGTCGTGTTTTC
1 AAAAATT-TCGCATTTTC
9796957 AAAAA
1 AAAAA
9796962 AAAAAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
15 5 0.11
16 10 0.22
17 13 0.29
18 14 0.31
19 3 0.07
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATTTCGCATTTTC
Found at i:9796968 original size:24 final size:24
Alignment explanation
Indices: 9796939--9796984 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
9796929 CCAATGTTTC
9796939 AAAAATTGTCGTGTTTTCAAAAAA
1 AAAAATTGTCGTGTTTTCAAAAAA
* *
9796963 AAAAATTTTCTTGTTTTCAAAA
1 AAAAATTGTCGTGTTTTCAAAA
9796985 GTCCCGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (24 bp):
AAAAATTGTCGTGTTTTCAAAAAA
Found at i:9797044 original size:17 final size:17
Alignment explanation
Indices: 9797016--9797127 Score: 82
Period size: 17 Copynumber: 6.2 Consensus size: 17
9797006 CTTGTCTTCA
*
9797016 AAAAAATTCCGTGTTTC
1 AAAAATTTCCGTGTTTC
*
9797033 ATAAATTTCCGTGTTTTC
1 AAAAATTTCCGTG-TTTC
* *
9797051 AAAAAAAATT-CGTCTTTC
1 --AAAAATTTCCGTGTTTC
*
9797069 AAAAATTTTCGTGTTTTC
1 AAAAATTTCCGTG-TTTC
*
9797087 AAAAAAATTGACCGTGTTTC
1 --AAAAATT-TCCGTGTTTC
* *
9797107 ATAAATTTTCGTGTTTC
1 AAAAATTTCCGTGTTTC
9797124 AAAA
1 AAAA
9797128 GAAAATCCTC
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
16 7 0.09
17 25 0.34
18 18 0.24
19 3 0.04
20 17 0.23
21 4 0.05
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (17 bp):
AAAAATTTCCGTGTTTC
Found at i:9797069 original size:36 final size:37
Alignment explanation
Indices: 9797002--9797144 Score: 168
Period size: 36 Copynumber: 3.9 Consensus size: 37
9796992 ATTTCGAAAG
* *
9797002 TTTTCTTGTCTTC-AAAAAAATTCCGTGTTTCATAAA
1 TTTTCGTGTTTTCAAAAAAAATTCCGTGTTTCATAAA
* * *
9797038 TTTCCGTGTTTTCAAAAAAAATT-CGTCTTTCAAAAA
1 TTTTCGTGTTTTCAAAAAAAATTCCGTGTTTCATAAA
9797074 TTTTCGTGTTTTC-AAAAAAATTGACCGTGTTTCATAAA
1 TTTTCGTGTTTTCAAAAAAAATT--CCGTGTTTCATAAA
*
9797112 TTTTCGTG-TTTCAAAAGAAAATCCTCGTGTTTC
1 TTTTCGTGTTTTCAAAA-AAAATTC-CGTGTTTC
9797145 GTATTTTATC
Statistics
Matches: 91, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
35 9 0.10
36 33 0.36
37 14 0.15
38 30 0.33
39 5 0.05
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (37 bp):
TTTTCGTGTTTTCAAAAAAAATTCCGTGTTTCATAAA
Found at i:9797110 original size:74 final size:72
Alignment explanation
Indices: 9796993--9797133 Score: 203
Period size: 72 Copynumber: 1.9 Consensus size: 72
9796983 AAGTCCCGTA
* * *
9796993 TTTCGAAAGTTTTCTTGTCTTCAAAAAAATTCCGTGTTTCATAAATTTCCGTGTTTTCAAAA-AA
1 TTTCAAAAATTTTCGTGTCTTCAAAAAAATTCCGTGTTTCATAAATTTCCGTG-TTTCAAAAGAA
9797057 AATTCGTC
65 AATTCGTC
* *
9797065 TTTCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTTTCGTGTTTCAAAAGA
1 TTTCAAAAATTTTCGTGTCTTCAAAAAAATT--CCGTGTTTCATAAATTTCCGTGTTTCAAAAGA
9797130 AAAT
64 AAAT
9797134 CCTCGTGTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
72 27 0.44
73 8 0.13
74 26 0.43
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (72 bp):
TTTCAAAAATTTTCGTGTCTTCAAAAAAATTCCGTGTTTCATAAATTTCCGTGTTTCAAAAGAAA
ATTCGTC
Found at i:9797193 original size:16 final size:17
Alignment explanation
Indices: 9797153--9797322 Score: 60
Period size: 18 Copynumber: 9.5 Consensus size: 17
9797143 TCGTATTTTA
*
9797153 TCAAAAATATTATGT-TT
1 TCAAAAA-ATTTTGTGTT
*
9797170 TCAAAAAAAATTTGTGTT
1 TC-AAAAAATTTTGTGTT
*
9797188 TTAAAAAATTTTTGTGTT
1 TCAAAAAA-TTTTGTGTT
* *
9797206 TCAAAAAGAAAATTCGTGTT
1 TC--AAA-AAATTTTGTGTT
* *
9797226 TCCTAAAAAATCTCGTGTT
1 T-C-AAAAAATTTTGTGTT
*
9797245 TC--AAAATTTTCGTTTT
1 TCAAAAAATTTT-GTGTT
* * *
9797261 TTAAAAGAGTTCTGTGTT
1 TCAAAA-AATTTTGTGTT
* * *
9797279 TC-TAAAATGCTTGTATT
1 TCAAAAAAT-TTTGTGTT
*
9797296 TAAATAAAATTTTGTGTTT
1 TCAA-AAAATTTTGTG-TT
9797315 TCAAAAAA
1 TCAAAAAA
9797323 AAAAAGAAAA
Statistics
Matches: 110, Mismatches: 28, Indels: 29
0.66 0.17 0.17
Matches are distributed among these distances:
15 6 0.05
16 7 0.06
17 21 0.19
18 33 0.30
19 25 0.23
20 14 0.13
21 4 0.04
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (17 bp):
TCAAAAAATTTTGTGTT
Found at i:9797193 original size:18 final size:18
Alignment explanation
Indices: 9797155--9797226 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 18
9797145 GTATTTTATC
*
9797155 AAAAATATTATGTTTTCAAA
1 AAAAAT-TTGTGTTTT-AAA
9797175 AAAAATTTGTGTTTTAAA
1 AAAAATTTGTGTTTTAAA
** *
9797193 AAATTTTTGTGTTTCAAAA
1 AAAAATTTGTGTTT-TAAA
*
9797212 AGAAAATTCGTGTTT
1 A-AAAATTTGTGTTT
9797227 CCTAAAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 15 0.35
19 12 0.28
20 16 0.37
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (18 bp):
AAAAATTTGTGTTTTAAA
Found at i:9807687 original size:9 final size:9
Alignment explanation
Indices: 9807674--9807744 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
9807664 AAAACAAACA
9807674 AAAAAAATAG
1 AAAAAAA-AG
*
9807684 AAAAAAAAC
1 AAAAAAAAG
*
9807693 AAAAAACAG
1 AAAAAAAAG
9807702 AAAAAAACAG
1 AAAAAAA-AG
*
9807712 ACAAAACAA-
1 A-AAAAAAAG
*
9807721 AAAACAAA-
1 AAAAAAAAG
*
9807729 AAAAAAGAG
1 AAAAAAAAG
9807738 AAAAAAA
1 AAAAAAA
9807745 TCAAGATGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
8 11 0.23
9 21 0.44
10 11 0.23
11 5 0.10
ACGTcount: A:0.83, C:0.08, G:0.07, T:0.01
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:9807687 original size:10 final size:10
Alignment explanation
Indices: 9807664--9807744 Score: 59
Period size: 10 Copynumber: 8.7 Consensus size: 10
9807654 TGCTTAAAAA
9807664 AAAACAAACA-
1 AAAA-AAACAG
*
9807674 AAAAAAATAG
1 AAAAAAACAG
9807684 AAAAAAA-A-
1 AAAAAAACAG
*
9807692 CAAAAAACAG
1 AAAAAAACAG
9807702 AAAAAAACAG
1 AAAAAAACAG
*
9807712 -ACAAAAC--
1 AAAAAAACAG
*
9807719 -AAAAAACAA
1 AAAAAAACAG
*
9807728 AAAAAAAGAG
1 AAAAAAACAG
9807738 AAAAAAA
1 AAAAAAA
9807745 TCAAGATGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
7 6 0.10
8 6 0.10
9 12 0.21
10 34 0.59
ACGTcount: A:0.83, C:0.10, G:0.06, T:0.01
Consensus pattern (10 bp):
AAAAAAACAG
Found at i:9807705 original size:26 final size:25
Alignment explanation
Indices: 9807660--9807744 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 25
9807650 ATTATGCTTA
* *
9807660 AAAAAAAACAAACAA-AAAAAATAG
1 AAAAAAAACAAAAAACAAAAAAAAG
*
9807684 AAAAAAAACAAAAAACAGAAAAAAAC
1 AAAAAAAACAAAAAACA-AAAAAAAG
* *
9807710 AGACAAAACAAAAAACAAAAAAAAAG
1 AAAAAAAACAAAAAAC-AAAAAAAAG
9807736 AGAAAAAAA
1 A-AAAAAAA
9807745 TCAAGATGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
24 14 0.29
25 1 0.02
26 28 0.57
27 6 0.12
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.01
Consensus pattern (25 bp):
AAAAAAAACAAAAAACAAAAAAAAG
Found at i:9808729 original size:77 final size:78
Alignment explanation
Indices: 9808614--9809846 Score: 1585
Period size: 76 Copynumber: 15.9 Consensus size: 78
9808604 TAAAAAAAAA
*
9808614 TTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
*
9808679 TATTTTTTTTAAT
66 TATTTTTTTAAAT
9808692 TTCTGCTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
9808756 TA--TTTTTAAAT
66 TATTTTTTTAAAT
* *
9808767 TTCTGTTTTTTTTCAAAAAATCAACTCATAATACAGATGTGAGTTGAGCCTCGGGTCACGCTGAG
1 TTCTG-CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAG
9808832 GTA--TTTTTAAAT
65 GTATTTTTTTAAAT
9808844 TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
9808909 TATTTTTTTAAAT
66 TATTTTTTTAAAT
9808922 TTCTGCTTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
1 TTCTGC-TTTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
* *
9808987 GGTATTTTTTTTATT
64 GGTATTTTTTTAAAT
* * *
9809002 TTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGG
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
9809067 TATTTCTTTTAAAT
66 TATTT-TTTTAAAT
* * *
9809081 TT-T-CGTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGG
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
9809143 TATTTCTTTTAAAT
66 TATTT-TTTTAAAT
* ** * *
9809157 TTCTG--TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTAGGACCATGCCGAGG
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
9809219 TATTTCTTTTAAAT
66 TATTT-TTTTAAAT
* * *
9809233 TTATG--TTTTTC-AAAAATCAACTCAT-ATACAGAGGTGAG-TGAGCCTCGGGTCATGCCGAGG
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
9809293 TATTTCTTTTAAAT
66 TATTT-TTTTAAAT
* * ** * * *
9809307 TTCTG--TTTTTC-AAAAATCAACTCATAATATAGAGGTGAGTTGAGCCTAGGACCATGCCGAGA
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
9809369 TATTTCTTTTAAAT
66 TATTT-TTTTAAAT
* * * *
9809383 TTATG--TTTTT-GAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAG
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAG
9809445 GTATTTTTTTTTAAAT
65 GTA--TTTTTTTAAAT
9809461 TTCTGCTTTTTTCAAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
1 TTCTGCTTTTTTC--AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
*
9809526 GGTATTTTTTTTAAT
64 GGTATTTTTTTAAAT
* * * *
9809541 TTCTACTTTTTTCAAAAAATCAACTCATAAGACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGG
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
9809606 TATTTCTTTTAAAT
66 TATTT-TTTTAAAT
* * *
9809620 TT-T-CGTTTTTCAAAAAAATCAACTCATAA-ACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAG
1 TTCTGCTTTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAG
*
9809682 GTATTTCTTTCAAAT
65 GTATTT-TTTTAAAT
* * *
9809697 TTTTG--TTTTTC-AAAAATCAACTCATAATGCGAGAGATG-GTTTGAGCCTCGGGTCACGCTGA
1 TTCTGCTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAG-TTGAGCCTCGGGTCACGCTGA
* *
9809758 -G-A-TATTTTCAAT
64 GGTATTTTTTTAAAT
* * * *
9809770 TTCTGTTTTTTTTCAAAAAAAAAATCAACTCATAATGCTAGAAGTGAGTTGAGCCTCGGGTTACG
1 TTCTG-CTTTTTTC----AAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACG
9809835 CTGAGGTATTTT
60 CTGAGGTATTTT
9809847 CAATATCTAT
Statistics
Matches: 1053, Mismatches: 63, Indels: 72
0.89 0.05 0.06
Matches are distributed among these distances:
73 10 0.01
74 58 0.06
75 55 0.05
76 292 0.28
77 241 0.23
78 168 0.16
79 34 0.03
80 95 0.09
81 44 0.04
82 36 0.03
83 18 0.02
84 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (78 bp):
TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
TATTTTTTTAAAT
Found at i:9810342 original size:29 final size:29
Alignment explanation
Indices: 9810310--9810445 Score: 150
Period size: 30 Copynumber: 4.6 Consensus size: 29
9810300 AATAAAAATT
9810310 TTACATTTTGACCCCAAACTTTGCT-AAAA
1 TTACATTTTGACCCCAAACTTT-CTCAAAA
*
9810339 TTACATTTTGGCCCCCAAACTTTCTCAAAA
1 TTACATTTT-GACCCCAAACTTTCTCAAAA
* * *
9810369 TTACACTTTGACCCCTAAACTTTTTGAAAA
1 TTACATTTTGACCCC-AAACTTTCTCAAAA
* * *
9810399 TTACATTTTGGCCCCATATTTTC-CTAAAA
1 TTACATTTTGACCCCAAACTTTCTC-AAAA
*
9810428 TTACATTTTTACCCCAAA
1 TTACATTTTGACCCCAAA
9810446 TATTTTGCGT
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
29 40 0.45
30 49 0.55
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.37
Consensus pattern (29 bp):
TTACATTTTGACCCCAAACTTTCTCAAAA
Found at i:9810414 original size:59 final size:59
Alignment explanation
Indices: 9810310--9810445 Score: 179
Period size: 59 Copynumber: 2.3 Consensus size: 59
9810300 AATAAAAATT
9810310 TTACATTTTGACCCCAAACTTTGCTAAAATTACATTTTGGCCCCCAAACTTT-CTCAAAA
1 TTACATTTTGACCCCAAACTTTGCTAAAATTACATTTTGGCCCCCAAACTTTCCT-AAAA
* * * *
9810369 TTACACTTTGACCCCTAAACTTT-TTGAAAATTACATTTTGG-CCCCATATTTTCCTAAAA
1 TTACATTTTGACCCC-AAACTTTGCT-AAAATTACATTTTGGCCCCCAAACTTTCCTAAAA
*
9810428 TTACATTTTTACCCCAAA
1 TTACATTTTGACCCCAAA
9810446 TATTTTGCGT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
58 3 0.04
59 41 0.60
60 24 0.35
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.37
Consensus pattern (59 bp):
TTACATTTTGACCCCAAACTTTGCTAAAATTACATTTTGGCCCCCAAACTTTCCTAAAA
Found at i:9810978 original size:13 final size:12
Alignment explanation
Indices: 9810960--9811036 Score: 82
Period size: 13 Copynumber: 6.0 Consensus size: 12
9810950 GGTGCTGCCC
9810960 GAAGAAGAAGAAA
1 GAAGAAGAA-AAA
9810973 GAAGAAAGATAAAA
1 GAAG-AAGA-AAAA
9810987 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
9810999 GGGAGAAGAAAAA
1 -GAAGAAGAAAAA
*
9811012 GAAAAAGAAAAA
1 GAAGAAGAAAAA
*
9811024 GAAAAAAGAAAAA
1 G-AAGAAGAAAAA
9811037 AAATTAAAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
12 15 0.26
13 30 0.53
14 11 0.19
15 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:9811037 original size:7 final size:6
Alignment explanation
Indices: 9810964--9811036 Score: 74
Period size: 6 Copynumber: 11.3 Consensus size: 6
9810954 CTGCCCGAAG
* * *
9810964 AAGAAGA AAGAAGA AAGATAA AAGAAG AAGAAA AAGGGAG AAGAAA AAGAAA
1 AAGAA-A AAGAA-A AAGA-AA AAGAAA AAGAAA AA-GAAA AAGAAA AAGAAA
9811016 AAGAAA AAGAAAA AAGAAA AA
1 AAGAAA AAG-AAA AAGAAA AA
9811037 AAATTAAAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
6 30 0.53
7 26 0.46
8 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.01
Consensus pattern (6 bp):
AAGAAA
Found at i:9811315 original size:23 final size:23
Alignment explanation
Indices: 9811269--9811312 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9811259 TCCAGTCCAG
9811269 GCCCAACAGCACCTAGCAGGCCA
1 GCCCAACAGCACCTAGCAGGCCA
* *
9811292 GCCCAGCAGCAGC-AGCAGGCC
1 GCCCAACAGCACCTAGCAGGCC
9811313 CAGTACCGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.27, C:0.43, G:0.27, T:0.02
Consensus pattern (23 bp):
GCCCAACAGCACCTAGCAGGCCA
Found at i:9811444 original size:20 final size:20
Alignment explanation
Indices: 9811417--9811457 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
9811407 GCAGGCCCAA
9811417 AAAAAAAAGAAAAAAAAGGAAG
1 AAAAAAAAG--AAAAAAGGAAG
9811439 AAAAAAAAGAAAAAAGGAA
1 AAAAAAAAGAAAAAAGGAA
9811458 AAGGGCCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAGGAAG
Found at i:9811944 original size:17 final size:17
Alignment explanation
Indices: 9811900--9811948 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
9811890 TTAAAAAAAA
*
9811900 TCGTGTTTCACAAATTTT
1 TCGTGTTTCA-AAATTTC
*
9811918 TACGT-CTTCAAAATTTC
1 T-CGTGTTTCAAAATTTC
9811935 TCGTGTTTCAAAAT
1 TCGTGTTTCAAAAT
9811949 AATAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 3 0.12
17 15 0.58
18 5 0.19
19 3 0.12
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (17 bp):
TCGTGTTTCAAAATTTC
Found at i:9812018 original size:26 final size:26
Alignment explanation
Indices: 9811971--9812020 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
9811961 ATTTCCCGTG
* * *
9811971 TTTCAAAAATATATATTGGTGTTTCT
1 TTTCAAAAAAAAATATTCGTGTTTCT
*
9811997 TTTCAAAAAAAAATTTTCGTGTTT
1 TTTCAAAAAAAAATATTCGTGTTT
9812021 TCAAAAATTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (26 bp):
TTTCAAAAAAAAATATTCGTGTTTCT
Found at i:9812028 original size:18 final size:18
Alignment explanation
Indices: 9812005--9812057 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
9811995 CTTTTCAAAA
9812005 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
** * *
9812023 AAAAATTCCCTTG-TTTG
1 AAAAATTTTCGTGTTTTC
*
9812040 AAAAATGTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
9812058 GTGTTTTCAA
Statistics
Matches: 25, Mismatches: 9, Indels: 2
0.69 0.25 0.06
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:9812103 original size:24 final size:24
Alignment explanation
Indices: 9812056--9812103 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
9812046 GTTCGTGTTT
*
9812056 TCGTGTTTTCAAAAAAATAATTTC
1 TCGTGTTTTCAAAAAAAAAATTTC
9812080 TCGTG-TTTCAAAAAAAAAACTTTC
1 TCGTGTTTTCAAAAAAAAAA-TTTC
9812104 GCGAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (24 bp):
TCGTGTTTTCAAAAAAAAAATTTC
Found at i:9812208 original size:17 final size:17
Alignment explanation
Indices: 9812182--9812254 Score: 55
Period size: 18 Copynumber: 4.3 Consensus size: 17
9812172 TGTTTAAAAA
9812182 AAAAATTTCGCA-TTTC
1 AAAAATTTCGCATTTTC
*
9812198 AAAAATCTTCGTATTTTC
1 AAAAAT-TTCGCATTTTC
9812216 -AAAA-TTC-CAGTGTTTC
1 AAAAATTTCGCA-T-TTTC
**
9812232 AAAAATTGTCGTGTTTTC
1 AAAAATT-TCGCATTTTC
9812250 AAAAA
1 AAAAA
9812255 AAAAAATTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
14 1 0.02
15 4 0.09
16 10 0.22
17 13 0.29
18 14 0.31
19 3 0.07
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (17 bp):
AAAAATTTCGCATTTTC
Found at i:9812251 original size:18 final size:17
Alignment explanation
Indices: 9812194--9812382 Score: 73
Period size: 17 Copynumber: 10.5 Consensus size: 17
9812184 AAATTTCGCA
*
9812194 TTTCAAAAATCTTCGTAT
1 TTTCAAAAAT-TTCGTGT
*
9812212 TTTC-AAAATTCCAGTG-
1 TTTCAAAAATTTC-GTGT
9812228 TTTCAAAAATTGTCGTGT
1 TTTCAAAAATT-TCGTGT
* *
9812246 TTTCAAAAAAAAAAATTCTTGT
1 TTTC-----AAAAATTTCGTGT
* ** *
9812268 TTTCAAAAGTCCCGT-A
1 TTTCAAAAATTTCGTGT
** *
9812284 TTTCGAAAGTTTTCTTGT
1 TTTC-AAAAATTTCGTGT
* *
9812302 CTTCAAAAAAATTCCGTG-
1 TTTC-A-AAAATTTCGTGT
*
9812320 TTTCATAAATTTCCGTGT
1 TTTCAAAAATTT-CGTGT
*
9812338 TTTCAAAAAAATTTCGT-C
1 TTTC--AAAAATTTCGTGT
9812356 TTTCAAAAATTTTCGTGT
1 TTTCAAAAA-TTTCGTGT
9812374 TTTCAAAAA
1 TTTCAAAAA
9812383 AATTGACCGT
Statistics
Matches: 124, Mismatches: 29, Indels: 36
0.66 0.15 0.19
Matches are distributed among these distances:
16 20 0.16
17 39 0.31
18 33 0.27
19 10 0.08
20 7 0.06
22 9 0.07
23 6 0.05
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (17 bp):
TTTCAAAAATTTCGTGT
Found at i:9812335 original size:17 final size:17
Alignment explanation
Indices: 9812307--9812418 Score: 91
Period size: 17 Copynumber: 6.2 Consensus size: 17
9812297 CTTGTCTTCA
*
9812307 AAAAAATTCCGTGTTTC
1 AAAAATTTCCGTGTTTC
*
9812324 ATAAATTTCCGTGTTTTC
1 AAAAATTTCCGTG-TTTC
*
9812342 AAAAAAATTT-CGTCTTTC
1 --AAAAATTTCCGTGTTTC
*
9812360 AAAAATTTTCGTGTTTTC
1 AAAAATTTCCGTG-TTTC
*
9812378 AAAAAAATTGACCGTGTTTC
1 --AAAAATT-TCCGTGTTTC
* *
9812398 ATAAATTTTCGTGTTTC
1 AAAAATTTCCGTGTTTC
9812415 AAAA
1 AAAA
9812419 GAAAATCCTC
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
16 8 0.11
17 25 0.33
18 18 0.24
19 3 0.04
20 18 0.24
21 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAAATTTCCGTGTTTC
Found at i:9812350 original size:36 final size:36
Alignment explanation
Indices: 9812293--9812418 Score: 173
Period size: 36 Copynumber: 3.5 Consensus size: 36
9812283 ATTTCGAAAG
* *
9812293 TTTTCTTGTCTTCAAAAAAATTCCGTGTTTCATAAA
1 TTTTCGTGTTTTCAAAAAAATTCCGTGTTTCATAAA
* * * *
9812329 TTTCCGTGTTTTCAAAAAAATTTCGTCTTTCAAAAA
1 TTTTCGTGTTTTCAAAAAAATTCCGTGTTTCATAAA
9812365 TTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAA
1 TTTTCGTGTTTTCAAAAAAATT--CCGTGTTTCATAAA
9812403 TTTTCGTG-TTTCAAAA
1 TTTTCGTGTTTTCAAAA
9812419 GAAAATCCTC
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
36 51 0.65
37 8 0.10
38 19 0.24
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (36 bp):
TTTTCGTGTTTTCAAAAAAATTCCGTGTTTCATAAA
Found at i:9812432 original size:38 final size:37
Alignment explanation
Indices: 9812293--9812435 Score: 150
Period size: 36 Copynumber: 3.9 Consensus size: 37
9812283 ATTTCGAAAG
* * *
9812293 TTTTCTTGTCTTCAAAAAAATTC-CGTGTTTCATAAA
1 TTTTCGTGTTTTCAAAAAAAATCTCGTGTTTCATAAA
* * * *
9812329 TTTCCGTGTTTTC-AAAAAAATTTCGTCTTTCAAAAA
1 TTTTCGTGTTTTCAAAAAAAATCTCGTGTTTCATAAA
*
9812365 TTTTCGTGTTTTCAAAAAAATTGAC-CGTGTTTCATAAA
1 TTTTCGTGTTTTCAAAAAAAAT--CTCGTGTTTCATAAA
9812403 TTTTCGTG-TTTCAAAAGAAAATCCTCGTGTTTC
1 TTTTCGTGTTTTCAAAA-AAAAT-CTCGTGTTTC
9812436 GTATTTTATC
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
35 7 0.08
36 33 0.38
37 16 0.18
38 31 0.36
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (37 bp):
TTTTCGTGTTTTCAAAAAAAATCTCGTGTTTCATAAA
Found at i:9812479 original size:20 final size:19
Alignment explanation
Indices: 9812446--9812486 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
9812436 GTATTTTATC
*
9812446 AAAAATATTATGTTTTCAAA
1 AAAAAAATTATGTTTT-AAA
*
9812466 AAAAAAATTGTGTTTTAAA
1 AAAAAAATTATGTTTTAAA
9812485 AA
1 AA
9812487 TTTTTGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (19 bp):
AAAAAAATTATGTTTTAAA
Found at i:9812535 original size:39 final size:36
Alignment explanation
Indices: 9812459--9812541 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 36
9812449 AATATTATGT
* * *
9812459 TTTCAAAAAAAAAATTGTGTTTTAAAAATTTTTGTG
1 TTTCAAAAAAAAAATTGTGTTTTAAAAAATCTCGTG
*
9812495 TTTCAAAAAGAAAATTCGTGTTTCCTAAAAAATCTCGTG
1 TTTCAAAAAAAAAATT-GTGTTT--TAAAAAATCTCGTG
9812534 TTTCAAAA
1 TTTCAAAA
9812542 TTTTCGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 15 0.38
37 6 0.15
39 19 0.47
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTCAAAAAAAAAATTGTGTTTTAAAAAATCTCGTG
Found at i:9812601 original size:18 final size:20
Alignment explanation
Indices: 9812580--9812616 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9812570 TCTAAAATGC
9812580 TTGT-ATTT-AAAAAAAAAT
1 TTGTGATTTCAAAAAAAAAT
*
9812598 TTGTGTTTTCAAAAAAAAA
1 TTGTGATTTCAAAAAAAAA
9812617 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 3 0.19
20 9 0.56
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (20 bp):
TTGTGATTTCAAAAAAAAAT
Found at i:9817619 original size:7 final size:7
Alignment explanation
Indices: 9817603--9817635 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
9817593 TGGCCTCTCA
9817603 TTTTTC-
1 TTTTTCT
9817609 TTTTTCT
1 TTTTTCT
9817616 TTTTTCT
1 TTTTTCT
9817623 TTTTTCT
1 TTTTTCT
9817630 CTTTTT
1 -TTTTT
9817636 TTGAAACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 14 0.56
8 5 0.20
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:9817626 original size:14 final size:14
Alignment explanation
Indices: 9817598--9817635 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
9817588 CACCTTGGCC
9817598 TCTCATTTTTCTTTT
1 TCTC-TTTTTCTTTT
9817613 TCT-TTTTTCTTTTT
1 TCTCTTTTTC-TTTT
9817627 TCTCTTTTT
1 TCTCTTTTT
9817636 TTGAAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 7 0.33
15 8 0.38
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTCTTTTTCTTTT
Found at i:9821173 original size:51 final size:51
Alignment explanation
Indices: 9821092--9821299 Score: 286
Period size: 51 Copynumber: 4.2 Consensus size: 51
9821082 ACTTCTTAAA
* *
9821092 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCGGTGACAAG
1 TGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
* * *
9821143 TGACAAGTGATGAGTGGAAGCTTTATCTACACTTATCTAATCAGTGACAAG
1 TGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
* *
9821194 TG---A--GA--AGTGATAGCTTTAACTACACTTATCTGATCAGTGACAAG
1 TGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
* *
9821238 TGACAAGTGATGAGTAGTAGCTTTAGCTACACTTATCTGATCAGGGACAAG
1 TGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
9821289 TGACAAGTGAT
1 TGACAAGTGAT
9821300 AAATGTGATC
Statistics
Matches: 137, Mismatches: 13, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
44 37 0.27
46 2 0.01
47 1 0.01
48 1 0.01
49 2 0.01
51 94 0.69
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
TGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
Found at i:9821189 original size:44 final size:43
Alignment explanation
Indices: 9821141--9821291 Score: 151
Period size: 44 Copynumber: 3.3 Consensus size: 43
9821131 ATCGGTGACA
*
9821141 AGTGACAAGTGATGAGTGGAAGCTTTATCTACACTTATCTAATC
1 AGTGACAAGTGATGAGT-GAAGCTTTAACTACACTTATCTAATC
9821185 AGTGACAAGTGA-GAAGTGATAGCTTTAACTACACTTATCTGATCAGTGAC
1 AGTGACAAGTGATG-AGTGA-AGCTTTAACTACACTTATCT-A--A-T--C
* * *
9821235 AAGTGACAAGTGATGAGTAGTAGCTTTAGCTACACTTATCTGATC
1 -AGTGACAAGTGATGAGT-GAAGCTTTAACTACACTTATCTAATC
*
9821280 AGGGACAAGTGA
1 AGTGACAAGTGA
9821292 CAAGTGATAA
Statistics
Matches: 91, Mismatches: 5, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
43 3 0.03
44 45 0.49
45 2 0.02
47 2 0.02
48 2 0.02
50 1 0.01
51 34 0.37
52 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (43 bp):
AGTGACAAGTGATGAGTGAAGCTTTAACTACACTTATCTAATC
Found at i:9821260 original size:95 final size:95
Alignment explanation
Indices: 9821092--9821300 Score: 328
Period size: 95 Copynumber: 2.2 Consensus size: 95
9821082 ACTTCTTAAA
* * * *
9821092 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCGGTGACAAGTGACAAGTGATGAG
1 TGACAAGTGACAAGTGATAGCTTTAACTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAG
* *
9821157 TGGAAGCTTTATCTACACTTATCTAATCAG
66 TAGAAGCTTTAGCTACACTTATCTAATCAG
*
9821187 TGACAAGTGAGAAGTGATAGCTTTAACTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAG
1 TGACAAGTGACAAGTGATAGCTTTAACTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAG
* *
9821252 TAGTAGCTTTAGCTACACTTATCTGATCAG
66 TAGAAGCTTTAGCTACACTTATCTAATCAG
*
9821282 GGACAAGTGACAAGTGATA
1 TGACAAGTGACAAGTGATA
9821301 AATGTGATCT
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 104 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (95 bp):
TGACAAGTGACAAGTGATAGCTTTAACTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAG
TAGAAGCTTTAGCTACACTTATCTAATCAG
Found at i:9826035 original size:3 final size:3
Alignment explanation
Indices: 9826014--9826117 Score: 59
Period size: 3 Copynumber: 33.7 Consensus size: 3
9826004 CACGAAAAAT
* * ** *
9826014 ATA ATA CTA ATA GTA ATA ATA ACG ATA ATA ATA ATA GTA ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * * *
9826060 ATG TTA ATA TTA ATAA ATA A-A AAA CATA ATA ATA A-A GTTA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA -ATA ATA ATA
9826106 ATA ATGA ATA AT
1 ATA AT-A ATA AT
9826118 CGAAATTTGA
Statistics
Matches: 75, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
2 3 0.04
3 60 0.80
4 12 0.16
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:9826395 original size:3 final size:3
Alignment explanation
Indices: 9826389--9826553 Score: 100
Period size: 3 Copynumber: 54.7 Consensus size: 3
9826379 CAACAACAAC
*
9826389 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * ** * *
9826437 AGT AA- AAT AA- AAT ATT AGT ATT TGT AAT AAT GGAAGT AAT AGT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT --AA-T AAT AAT AAT
* * * * * * * * * * * *
9826483 AGT AAT AAT AAC AAT AAT AGT AGT AGT ACT ACT ACT ACT ACT ACT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9826531 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
9826554 AAGGACAAAA
Statistics
Matches: 135, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
2 4 0.03
3 126 0.93
4 2 0.01
5 2 0.01
6 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9833788 original size:28 final size:27
Alignment explanation
Indices: 9833736--9833788 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
9833726 TTTGAATACC
*
9833736 CACATGGCCTGAGACACGGGCGTGTCT
1 CACATGGCCTGAGACACAGGCGTGTCT
9833763 CACATGGCCTG-GCCACACAGGCGTGT
1 CACATGGCCTGAG--ACACAGGCGTGT
9833789 GTCCTCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 11 0.48
28 11 0.48
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.17
Consensus pattern (27 bp):
CACATGGCCTGAGACACAGGCGTGTCT
Found at i:9839486 original size:12 final size:12
Alignment explanation
Indices: 9839451--9839493 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
9839441 TTTAAATACA
* *
9839451 TTAAAAGTTAAA
1 TTAAAATTTAAT
*
9839463 TAAAAATTTAAT
1 TTAAAATTTAAT
9839475 TTAAAATTTAAT
1 TTAAAATTTAAT
9839487 TTAAAAT
1 TTAAAAT
9839494 ATAAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
TTAAAATTTAAT
Found at i:9844622 original size:18 final size:21
Alignment explanation
Indices: 9844596--9844633 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
9844586 ACTGATATTA
9844596 TTGGACTTT-TA-ATTTTTAT
1 TTGGACTTTATATATTTTTAT
9844615 TTGG-CTTTATATATTTTTA
1 TTGGACTTTATATATTTTTA
9844634 AATGTTTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (21 bp):
TTGGACTTTATATATTTTTAT
Found at i:9845234 original size:44 final size:43
Alignment explanation
Indices: 9845136--9845626 Score: 260
Period size: 44 Copynumber: 11.5 Consensus size: 43
9845126 ATTTTAATTC
* * * *
9845136 GCTCCACTGTAATCTCAAGGAAATAGGATTACTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCT-GCTTCAATCT
*
9845180 AG-TCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCT
1 -GCTCCACTGTAATCTCAGGGAGATAAGATTTCT-GCTTCAATCT
* * **
9845224 GCTCTACTGTAACCTCA-GGAGATAAGA-TT-T--TTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCTGCTTCAATCT
** *
9845262 ATTCCACTGTAATCTCAGGGAGATAAGA--T-T-CTTCAGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCTGCTTCAATCT
** * * * * *
9845301 ATTCCATTGTAATCTCAGGGAGATAAGA-CT-TGATGCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCTGCTTCAATCT
* * * ** * *
9845342 ACTCTACTGTAAT-TCTAGAGAGATAAGATCCTT-TATTTTAATCC
1 GCTCCACTGTAATCTC-AGGGAGATAAGAT--TTCTGCTTCAATCT
* * *
9845386 GCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCT-GCTTCAATCT
* * * **
9845430 GCTCCACTGTAACCTCAGGGAGATAAGATTTGAAATTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTT---CTGCTTCAATCT
** * * ** * *
9845476 ATTCCACTGTAATATCAGGGAGATAAGA--CCTAATGCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCTGCTTCAATCT
* * * * * ** *
9845517 ACTCTACTGTGATTTCAGAGAGATAAGATCCTT-TATTTTAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT--TTCTGCTTCAATCT
* * *
9845561 GCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTTCT-GCTTCAATCT
*
9845605 GCTCCGCTGTAATCTCAGGGAG
1 GCTCCACTGTAATCTCAGGGAG
9845627 GTAAAATCCG
Statistics
Matches: 343, Mismatches: 82, Indels: 43
0.73 0.18 0.09
Matches are distributed among these distances:
38 21 0.06
39 44 0.13
40 4 0.01
41 57 0.17
42 4 0.01
43 13 0.04
44 165 0.48
45 3 0.01
46 31 0.09
47 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (43 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTTCTGCTTCAATCT
Found at i:9845280 original size:38 final size:39
Alignment explanation
Indices: 9845171--9845328 Score: 165
Period size: 39 Copynumber: 3.9 Consensus size: 39
9845161 GGATTACTGG
* * *
9845171 CTTCAATCTAGTCCGCTGTAATCTCAGGGAGATAAGATTTCT
1 CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGA--T-T
* ** * *
9845213 GGCTTCAATCTGCTCTACTGTAACCTCA-GGAGATAAGATT
1 --CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGATT
* *
9845253 TTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGATT
1 CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGATT
*
9845292 CTTCAGTCTATTCCATTGTAATCTCAGGGAGATAAGA
1 CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGA
9845329 CTTGATGCGA
Statistics
Matches: 98, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
38 19 0.19
39 46 0.47
40 1 0.01
41 1 0.01
43 10 0.10
44 21 0.21
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (39 bp):
CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGATT
Found at i:9845548 original size:175 final size:175
Alignment explanation
Indices: 9845289--9845626 Score: 579
Period size: 175 Copynumber: 1.9 Consensus size: 175
9845279 GGGAGATAAG
* * * *
9845289 ATTCTTCAGTCTATTCCATTGTAATCTCAGGGAGATAAGACTTGATGCGATCTACTCTACTGTAA
1 ATTCTTCAGTCTATTCCACTGTAATATCAGGGAGATAAGACCTAATGCGATCTACTCTACTGTAA
9845354 TTCTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACT
66 TTCTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACT
9845419 GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTTGAA
131 GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTTGAA
* *
9845464 ATTCTTCGGTCTATTCCACTGTAATATCAGGGAGATAAGACCTAATGCGATCTACTCTACTGTGA
1 ATTCTTCAGTCTATTCCACTGTAATATCAGGGAGATAAGACCTAATGCGATCTACTCTACTGTAA
*
9845529 TT-TCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAAATAGGATTAC
66 TTCT-AGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
* *
9845593 TGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
130 TGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
9845627 GTAAAATCCG
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
174 1 0.01
175 152 0.99
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (175 bp):
ATTCTTCAGTCTATTCCACTGTAATATCAGGGAGATAAGACCTAATGCGATCTACTCTACTGTAA
TTCTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACT
GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTTGAA
Found at i:9863319 original size:24 final size:24
Alignment explanation
Indices: 9863272--9863319 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
9863262 ATGGAATAAT
*
9863272 ATTTTATTTAAATAAATATTAATA
1 ATTTTATTTAAATAAATATAAATA
*
9863296 ATTTTGTTTAAATATAAT-TAAATA
1 ATTTTATTTAAATA-AATATAAATA
9863320 TTAAACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTTATTTAAATAAATATAAATA
Found at i:9864701 original size:18 final size:19
Alignment explanation
Indices: 9864680--9864731 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
9864670 TTCCTTTACA
9864680 TTATTTCTCTCTT-TATTT
1 TTATTTCTCTCTTCTATTT
* *
9864698 TTATTTTTGCTTCTTCTTTTT
1 TTATTTCT-C-TCTTCTATTT
9864719 TTATTTCT-TCTTC
1 TTATTTCTCTCTTC
9864732 CTTTATAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 12 0.43
19 1 0.04
20 4 0.14
21 11 0.39
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (19 bp):
TTATTTCTCTCTTCTATTT
Found at i:9864731 original size:21 final size:20
Alignment explanation
Indices: 9864680--9864737 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
9864670 TTCCTTTACA
9864680 TTATTTC-TC-TCTTTATTT
1 TTATTTCTTCTTCTTTATTT
*
9864698 TTATTT-TTGCTTCTTCTTTTT
1 TTATTTCTT-CTTCTT-TATTT
9864719 TTATTTCTTCTTCCTTTAT
1 TTATTTCTTCTT-CTTTAT
9864738 AATGTCAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 7 0.22
19 1 0.03
20 4 0.12
21 15 0.47
22 5 0.16
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (20 bp):
TTATTTCTTCTTCTTTATTT
Found at i:9871080 original size:6 final size:7
Alignment explanation
Indices: 9871064--9871093 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
9871054 TCTCTCTTTG
9871064 TTTTT-A
1 TTTTTCA
9871070 TTTTTCA
1 TTTTTCA
9871077 TTTTTCA
1 TTTTTCA
9871084 TTTTTCA
1 TTTTTCA
9871091 TTT
1 TTT
9871094 CTTCTTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCA
Found at i:9884200 original size:70 final size:66
Alignment explanation
Indices: 9884104--9884243 Score: 158
Period size: 70 Copynumber: 2.1 Consensus size: 66
9884094 ACTTTTAAAC
* * * * *
9884104 TAAAAAATCTGACATTGGTTGCGCCATTATA-TATAGCTCCACCAAATAAAATATTAGTTTTTAA
1 TAAAAAATCTGACACTGGTTGCGCCA-TATAGAATAGCACCACCAAATAAAATATCA-ATTTT-A
9884168 TTTT
63 TTTT
*
9884172 TAAAAATATCATGACACTGG-TGACGCCATATAGAATGGCACCACCAAATAAAATATCAATTTTA
1 TAAAAA-ATC-TGACACTGGTTG-CGCCATATAGAATAGCACCACCAAATAAAATATCAATTTTA
9884236 TTTT
63 TTTT
9884240 TAAA
1 TAAA
9884244 TTAAAAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
68 15 0.24
69 13 0.21
70 34 0.55
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.34
Consensus pattern (66 bp):
TAAAAAATCTGACACTGGTTGCGCCATATAGAATAGCACCACCAAATAAAATATCAATTTTATTT
T
Found at i:9890140 original size:29 final size:29
Alignment explanation
Indices: 9890098--9890154 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
9890088 CATTGGGGCT
*
9890098 TAGCCACTAATTCAGAGCAGAATACTTCC
1 TAGCCACTAATTCAGAGCAAAATACTTCC
9890127 TAGCCACTAATTCAGAGCAAAATACTTC
1 TAGCCACTAATTCAGAGCAAAATACTTC
9890155 ACAATACCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (29 bp):
TAGCCACTAATTCAGAGCAAAATACTTCC
Found at i:9894531 original size:14 final size:14
Alignment explanation
Indices: 9894512--9894551 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
9894502 TTGTTTGGCA
9894512 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
9894526 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
9894540 GGAAAATGTTTT
1 GTAAAATGTTTT
9894552 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:9894560 original size:20 final size:20
Alignment explanation
Indices: 9894535--9894574 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9894525 CGTAAAATGA
*
9894535 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
9894555 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
9894575 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:9894564 original size:34 final size:35
Alignment explanation
Indices: 9894520--9894586 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
9894510 CAGTAAAATG
*
9894520 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
9894554 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
9894587 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:9894590 original size:14 final size:15
Alignment explanation
Indices: 9894514--9894590 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
9894504 GTTTGGCAGT
* *
9894514 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
9894528 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
9894542 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
9894562 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
9894577 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
9894591 TGTTTGGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:9894645 original size:32 final size:31
Alignment explanation
Indices: 9894567--9894651 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
9894557 TCTGTAAAAT
* *
9894567 GATTTACTGGAAAATATTTTCTGGTGTTTGGTA
1 GATTT-CT-GAAAATATTTTCTGCTGTTTGGCA
* * *
9894600 AATCTGTGTAAAATATTTTCTGCTGTTTGGCA
1 GATTTCTG-AAAATATTTTCTGCTGTTTGGCA
9894632 GATTTCCTGAAAATATTTTC
1 GATTT-CTGAAAATATTTTC
9894652 CGGAAAAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
31 1 0.02
32 36 0.86
33 5 0.12
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (31 bp):
GATTTCTGAAAATATTTTCTGCTGTTTGGCA
Found at i:9899598 original size:25 final size:25
Alignment explanation
Indices: 9899562--9899610 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9899552 ATGTCAGCTG
9899562 CTTAGAAGAGAACAGAAAATGTCTA
1 CTTAGAAGAGAACAGAAAATGTCTA
**
9899587 CTTAG-AGAAGAATGGAAAATGTCT
1 CTTAGAAG-AGAACAGAAAATGTCT
9899611 TACCAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.22
Consensus pattern (25 bp):
CTTAGAAGAGAACAGAAAATGTCTA
Found at i:9904329 original size:21 final size:22
Alignment explanation
Indices: 9904285--9904338 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
9904275 GCTTTGCCGA
*
9904285 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTCATGTGTCG-ATT
*
9904308 TCAGGCACTTCGTGTGTC-ATT
1 TCAGGCACTTCATGTGTCGATT
9904329 TCAGGCACTT
1 TCAGGCACTT
9904339 ATATGACGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 13 0.45
23 16 0.55
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (22 bp):
TCAGGCACTTCATGTGTCGATT
Found at i:9905029 original size:12 final size:12
Alignment explanation
Indices: 9904988--9905029 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
9904978 TTAAATAGAA
9904988 ATGAATGAAATT
1 ATGAATGAAATT
*
9905000 ATCAAT-AAATT
1 ATGAATGAAATT
* *
9905011 TTGAATGATATT
1 ATGAATGAAATT
9905023 ATGAATG
1 ATGAATG
9905030 CTTATTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (12 bp):
ATGAATGAAATT
Found at i:9905672 original size:85 final size:85
Alignment explanation
Indices: 9905579--9905738 Score: 232
Period size: 85 Copynumber: 1.9 Consensus size: 85
9905569 GTGGTTTGTT
**
9905579 CACGAACCAAGTGAC-AGTTTGTTTAATCTGCAAATATGTTATGCACCCACAACAAGTGGCAATA
1 CACGAACCAAGTGACGA-TTTCCTTAATCTGCAAATATGTTATGCACCCACAACAAGTGGCAATA
*
9905643 AGTGCAAATATATGGTTCGAC
65 ACTGCAAATATATGGTTCGAC
* * * * *
9905664 CACGAACCAAGTGGCGATTTCCTTAATCTGCAAATTTGTTGTTCACCCACAACAAGTGGTAATAA
1 CACGAACCAAGTGACGATTTCCTTAATCTGCAAATATGTTATGCACCCACAACAAGTGGCAATAA
9905729 CTGCAAATAT
66 CTGCAAATAT
9905739 TGTTTGAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
85 65 0.98
86 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (85 bp):
CACGAACCAAGTGACGATTTCCTTAATCTGCAAATATGTTATGCACCCACAACAAGTGGCAATAA
CTGCAAATATATGGTTCGAC
Found at i:9913092 original size:53 final size:53
Alignment explanation
Indices: 9913014--9913236 Score: 401
Period size: 53 Copynumber: 4.2 Consensus size: 53
9913004 TGTACACTAA
* *
9913014 TAAAGTTTGGAGTCATATGACTAGTAAATGTATATTTTCAATGAAGAAGTGAC
1 TAAAGTTTGGAGTCATATTACTAGTAAATGTATATTTTCAATGAAGAAATGAC
*
9913067 TAAAGTTTGGAGTCATATTACTAGTAAATGTATATTATCAATGAAGAAATGAC
1 TAAAGTTTGGAGTCATATTACTAGTAAATGTATATTTTCAATGAAGAAATGAC
**
9913120 TAAAGTTTGGAGTCATATTACTAGTAAATGTATATTTTCAATGTTGAAATGAC
1 TAAAGTTTGGAGTCATATTACTAGTAAATGTATATTTTCAATGAAGAAATGAC
9913173 TAAAGTTTGGAGTCATATTACTAGTAAATGTATATTTTCAATGAAGAAATGAC
1 TAAAGTTTGGAGTCATATTACTAGTAAATGTATATTTTCAATGAAGAAATGAC
9913226 TAAAGTTTGGA
1 TAAAGTTTGGA
9913237 CATTGTAATT
Statistics
Matches: 162, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 162 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (53 bp):
TAAAGTTTGGAGTCATATTACTAGTAAATGTATATTTTCAATGAAGAAATGAC
Found at i:9917348 original size:14 final size:17
Alignment explanation
Indices: 9917316--9917353 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
9917306 AATTATAAAG
9917316 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
9917333 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
9917347 TATATTA
1 TATATTA
9917354 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:9917603 original size:19 final size:20
Alignment explanation
Indices: 9917555--9917604 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
9917545 GTTGGTAAAT
*
9917555 ACATATGTA-ATAATAATAA
1 ACATATGTATTTAATAATAA
9917574 ACATATGTATTTAATAATAA
1 ACATATGTATTTAATAATAA
9917594 A-ATATGTATTT
1 ACATATGTATTT
9917605 CTTATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (20 bp):
ACATATGTATTTAATAATAA
Found at i:9917731 original size:5 final size:6
Alignment explanation
Indices: 9917714--9917738 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9917704 AGGGAAAAGG
9917714 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
9917739 CTAGAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:9918127 original size:17 final size:18
Alignment explanation
Indices: 9918105--9918141 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
9918095 TAAATGAGTT
9918105 AATTAGGAT-TAAATTGA
1 AATTAGGATATAAATTGA
*
9918122 AATTAGGGTATAAATTGA
1 AATTAGGATATAAATTGA
9918140 AA
1 AA
9918142 AGAAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (18 bp):
AATTAGGATATAAATTGA
Found at i:9918627 original size:23 final size:23
Alignment explanation
Indices: 9918600--9918664 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
9918590 GCTTTGCCGA
9918600 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
9918623 TCAGGCACTTTGTGTGTCG--TT
1 TCAGGCACTTTATGTGTCGTATT
* *
9918644 TCAAGCAC-TAATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
9918665 ACTAATCAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 8 0.22
21 9 0.25
22 1 0.03
23 18 0.50
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:9919043 original size:3 final size:3
Alignment explanation
Indices: 9919035--9919068 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
9919025 AATTATATTC
9919035 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9919069 TGAATTATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9920002 original size:85 final size:85
Alignment explanation
Indices: 9919911--9920070 Score: 241
Period size: 85 Copynumber: 1.9 Consensus size: 85
9919901 ATGGTTTGTT
*
9919911 CACGAACCAAGT-GATAGTTTGTTTAATCTGCAAATATGTTATGCACCCACAACAAGTGGTAGTA
1 CACGAACCAAGTGGATA-TTTGTTTAATCTGCAAATATGTTATGCACCCACAACAAGTGGTAATA
9919975 ACCGCAAATATATGGTTCGAC
65 ACCGCAAATATATGGTTCGAC
* * * * *
9919996 CACGAACCAAGTGGCTATTTGTTTAATCTGCAAATTTTTTGTTCACCCACAACAAGTGGTAATAA
1 CACGAACCAAGTGGATATTTGTTTAATCTGCAAATATGTTATGCACCCACAACAAGTGGTAATAA
*
9920061 CTGCAAATAT
66 CCGCAAATAT
9920071 TGTTTGAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 64 0.96
86 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (85 bp):
CACGAACCAAGTGGATATTTGTTTAATCTGCAAATATGTTATGCACCCACAACAAGTGGTAATAA
CCGCAAATATATGGTTCGAC
Found at i:9920474 original size:23 final size:24
Alignment explanation
Indices: 9920437--9920499 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
9920427 ATGATGTAAA
*
9920437 AAAATGAAAACGAAAAGGGAAA-AATG
1 AAAATG-AAA-GAAAAGAGAAATAA-G
9920463 AAAA-GAAAGAAAAGAGAAATAAG
1 AAAATGAAAGAAAAGAGAAATAAG
*
9920486 AAAATGAAGGAAAA
1 AAAATGAAAGAAAA
9920500 ACAAAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 15 0.45
24 13 0.39
25 1 0.03
26 4 0.12
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.06
Consensus pattern (24 bp):
AAAATGAAAGAAAAGAGAAATAAG
Found at i:9921897 original size:27 final size:26
Alignment explanation
Indices: 9921867--9921942 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 26
9921857 GTAAAACAGC
9921867 CATTTTACCCTATAGGGGTATTTCCGT
1 CATTTTACCCTAT-GGGGTATTTCCGT
*
9921894 CATTTTACCCTATGAGGGTATTTCGGT
1 CATTTTACCCTATG-GGGTATTTCCGT
*
9921921 CATTTTACCCTATGAGGTATTT
1 CATTTTACCCTATGGGGTATTT
9921943 ACCTTATAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 8 0.17
27 38 0.83
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (26 bp):
CATTTTACCCTATGGGGTATTTCCGT
Found at i:9931731 original size:28 final size:29
Alignment explanation
Indices: 9931687--9931742 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
9931677 CTAAAGATCT
9931687 AGCATTAGCGGCA-TTTTTCAAAAAAAAG
1 AGCATTAGCGGCATTTTTTCAAAAAAAAG
* *
9931715 AGCATTAGCGGCGTTTTTTGAAAAAAAA
1 AGCATTAGCGGCATTTTTTCAAAAAAAA
9931743 AGGCAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (29 bp):
AGCATTAGCGGCATTTTTTCAAAAAAAAG
Found at i:9931847 original size:41 final size:41
Alignment explanation
Indices: 9931787--9931985 Score: 265
Period size: 41 Copynumber: 4.9 Consensus size: 41
9931777 TAACAAATTT
*
9931787 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* ** *
9931828 GGTGCTTTAGCGGCGTTTTTGAAAAAGCGCCATTAATGCTG
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* * *
9931869 GGGGCTTTAGCGGCGTTTTAG-AAAAGCGCTGCTAATGCTT
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* **
9931909 GGGGCTCTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTA
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
** *
9931950 GGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCACTAA
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
9931986 AAACATTTTA
Statistics
Matches: 140, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 34 0.24
41 106 0.76
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (41 bp):
GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
Found at i:9931921 original size:81 final size:82
Alignment explanation
Indices: 9931787--9931968 Score: 267
Period size: 81 Copynumber: 2.2 Consensus size: 82
9931777 TAACAAATTT
* * *
9931787 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGTGCTTTAGCGGCGTTTTTGAAA
1 GGGGCTTTAGCGGCGTTTTAGAAAAAGCGCCGCTAATGCTCGGGGCTCTAGCGGCGTTTTTGAAA
* *
9931852 AAGCGCCATTAATGCTG
66 AAGCGCCACTAATGCTA
* * **
9931869 GGGGCTTTAGCGGCGTTTTAG-AAAAGCGCTGCTAATGCTTGGGGCTCTAGCGGCGTTTTTGGGA
1 GGGGCTTTAGCGGCGTTTTAGAAAAAGCGCCGCTAATGCTCGGGGCTCTAGCGGCGTTTTTGAAA
*
9931933 AAGCGCCGCTAATGCTA
66 AAGCGCCACTAATGCTA
9931950 GGGGCTTTAGCGGCGTTTT
1 GGGGCTTTAGCGGCGTTTT
9931969 TGGGAAAGCG
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 70 0.78
82 20 0.22
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (82 bp):
GGGGCTTTAGCGGCGTTTTAGAAAAAGCGCCGCTAATGCTCGGGGCTCTAGCGGCGTTTTTGAAA
AAGCGCCACTAATGCTA
Found at i:9932353 original size:15 final size:15
Alignment explanation
Indices: 9932333--9932379 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
9932323 TATTTTAAGG
*
9932333 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
9932348 TTTAGGGATTAT-GA
1 TTTAGGGATTATGGA
*
9932362 ATTAGGGATTATGG-
1 TTTAGGGATTATGGA
9932376 TTTA
1 TTTA
9932380 AGGGTTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:9932400 original size:21 final size:22
Alignment explanation
Indices: 9932326--9932429 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 22
9932316 GAGTTACTAT
*
9932326 TTTAAGGTTTAGGGAG-TATGGA
1 TTTAAGGTTTAGGG-GTTAGGGA
* * * **
9932348 TTTAGGGATTATGAATTAGGGA
1 TTTAAGGTTTAGGGGTTAGGGA
* *
9932370 -TTATGGTTTAAGGGTT-GGGA
1 TTTAAGGTTTAGGGGTTAGGGA
9932390 TTTAAGGTTTAGGGGTTAGGG-
1 TTTAAGGTTTAGGGGTTAGGGA
*
9932411 TTTAGGGGTTTAGGGGTTA
1 TTTA-AGGTTTAGGGGTTA
9932430 AGAGTTAGAG
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
20 4 0.06
21 29 0.45
22 31 0.48
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (22 bp):
TTTAAGGTTTAGGGGTTAGGGA
Found at i:9932412 original size:14 final size:15
Alignment explanation
Indices: 9932390--9932425 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
9932380 AGGGTTGGGA
*
9932390 TTTAAGGTTTAGGGG
1 TTTAGGGTTTAGGGG
9932405 -TTAGGGTTTAGGGG
1 TTTAGGGTTTAGGGG
9932419 TTTAGGG
1 TTTAGGG
9932426 GTTAAGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.39
Consensus pattern (15 bp):
TTTAGGGTTTAGGGG
Found at i:9932419 original size:8 final size:8
Alignment explanation
Indices: 9932395--9932428 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
9932385 TGGGATTTAA
9932395 GGTTTAGG
1 GGTTTAGG
9932403 GG-TTA-G
1 GGTTTAGG
9932409 GGTTTAGG
1 GGTTTAGG
9932417 GGTTTAGG
1 GGTTTAGG
9932425 GGTT
1 GGTT
9932429 AAGAGTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 6 0.25
8 15 0.62
ACGTcount: A:0.12, C:0.00, G:0.50, T:0.38
Consensus pattern (8 bp):
GGTTTAGG
Found at i:9932437 original size:22 final size:23
Alignment explanation
Indices: 9932390--9932453 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
9932380 AGGGTTGGGA
*
9932390 TTTA-AGGTTTAGGGGTT-AGGG
1 TTTAGAGGTTTAGGGGTTAAGAG
*
9932411 TTTAGGGGTTTAGGGGTTAAGAG
1 TTTAGAGGTTTAGGGGTTAAGAG
* *
9932434 -TTAGAGATTTAGGGTTTAAG
1 TTTAGAGGTTTAGGGGTTAAG
9932454 GATTCATGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.11
22 29 0.81
23 3 0.08
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.38
Consensus pattern (23 bp):
TTTAGAGGTTTAGGGGTTAAGAG
Found at i:9932529 original size:25 final size:24
Alignment explanation
Indices: 9932487--9932543 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 24
9932477 TTGGGTTTAG
*
9932487 ATTAATTATTTTTTTAATTTATAT
1 ATTAAATATTTTTTTAATTTATAT
*
9932511 TTTAAATATGTTTTTTAATTTATAT
1 ATTAAATAT-TTTTTTAATTTATAT
9932536 ATTAAATA
1 ATTAAATA
9932544 ATTTCATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTAAATATTTTTTTAATTTATAT
Found at i:9932728 original size:14 final size:15
Alignment explanation
Indices: 9932698--9932735 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
9932688 GGGGATTATA
*
9932698 TATGGATTTAGGGAT
1 TATGGATTTACGGAT
9932713 TATGGA-TTACGGAT
1 TATGGATTTACGGAT
9932727 TATGG-TTTA
1 TATGGATTTA
9932736 AGGGTTGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (15 bp):
TATGGATTTACGGAT
Found at i:9932764 original size:7 final size:7
Alignment explanation
Indices: 9932754--9932815 Score: 79
Period size: 7 Copynumber: 8.9 Consensus size: 7
9932744 GATTTAAGGT
9932754 TTAGGGG
1 TTAGGGG
*
9932761 TTAGGAG
1 TTAGGGG
*
9932768 TTAGGAG
1 TTAGGGG
9932775 TTAGGGG
1 TTAGGGG
*
9932782 TTAGGAG
1 TTAGGGG
9932789 TTAGGGG
1 TTAGGGG
9932796 TTAGGGG
1 TTAGGGG
* *
9932803 TTAAGAG
1 TTAGGGG
9932810 TTAGGG
1 TTAGGG
9932816 ATTTAAGGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.23, C:0.00, G:0.48, T:0.29
Consensus pattern (7 bp):
TTAGGGG
Found at i:9932815 original size:21 final size:21
Alignment explanation
Indices: 9932754--9932815 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
9932744 GATTTAAGGT
*
9932754 TTAGGGGTTAGGAGTTAGGAG
1 TTAGGGGTTAGGAGTTAGGGG
9932775 TTAGGGGTTAGGAGTTAGGGG
1 TTAGGGGTTAGGAGTTAGGGG
*
9932796 TTAGGGGTTAAGAGTTAGGG
1 TTAGGGGTTAGGAGTTAGGG
9932816 ATTTAAGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.00, G:0.48, T:0.29
Consensus pattern (21 bp):
TTAGGGGTTAGGAGTTAGGGG
Found at i:9933186 original size:19 final size:20
Alignment explanation
Indices: 9933164--9933206 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
9933154 ATTATAAGAA
*
9933164 AAAAATAAAATACAAAAA-T
1 AAAAATAAAATAAAAAAACT
*
9933183 AAAAATGAAATAAAAAAACT
1 AAAAATAAAATAAAAAAACT
9933203 AAAA
1 AAAA
9933207 TTTATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAATAAAATAAAAAAACT
Found at i:9937781 original size:43 final size:43
Alignment explanation
Indices: 9937734--9937828 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 43
9937724 GTGAGAAGCA
* *
9937734 CCGCTAAAGGTATCGAGTTATAGCGGCGTTTGTGGAAAAAGAG
1 CCGCTAAAGGTATCGAGCTATAGCGACGTTTGTGGAAAAAGAG
*
9937777 CCGCTAAAGGTATCGAGCTATAGCGACGTTTGTGGAAAAAGCG
1 CCGCTAAAGGTATCGAGCTATAGCGACGTTTGTGGAAAAAGAG
9937820 CCGCTAAAG
1 CCGCTAAAG
9937829 CTCTTGCGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.21
Consensus pattern (43 bp):
CCGCTAAAGGTATCGAGCTATAGCGACGTTTGTGGAAAAAGAG
Found at i:9937895 original size:43 final size:43
Alignment explanation
Indices: 9937844--9937948 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 43
9937834 GCGTTTCTGA
* * * *
9937844 GAAAAGCGCCACTAAATGTCTTGAGCTATAGTGGCGTTTGTAG
1 GAAAAGCGCCACTAAAGGTCTCGAGATATAGCGGCGTTTGTAG
* *
9937887 GAAAAGCGCCGCTAAAGGTCTCGAGATATAGCGGCGTTTTTAG
1 GAAAAGCGCCACTAAAGGTCTCGAGATATAGCGGCGTTTGTAG
* * *
9937930 G-ATAGCACCGCTAAAGGTC
1 GAAAAGCGCCACTAAAGGTC
9937949 AATGTCTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
42 16 0.30
43 38 0.70
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (43 bp):
GAAAAGCGCCACTAAAGGTCTCGAGATATAGCGGCGTTTGTAG
Found at i:9937991 original size:43 final size:42
Alignment explanation
Indices: 9937915--9938012 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 42
9937905 TCTCGAGATA
9937915 TAGCGGCGTTTTTAGGATAGCACCGCTAAAGGTCAAT-GTCTT
1 TAGCGGCGTTTTTAGGATAGCACCGCTAAAGGTC-ATGGTCTT
* * *
9937957 TAGTGGCGTTTGTTAGAGA-AGCGCCGCTATAGGTCATGGTCTT
1 TAGCGGCGTTT-TTAG-GATAGCACCGCTAAAGGTCATGGTCTT
*
9938000 TAGCGGCGCTTTT
1 TAGCGGCGTTTTT
9938013 CCAAAAACGC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
42 14 0.29
43 32 0.67
44 2 0.04
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (42 bp):
TAGCGGCGTTTTTAGGATAGCACCGCTAAAGGTCATGGTCTT
Found at i:9938093 original size:21 final size:21
Alignment explanation
Indices: 9938067--9938110 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
9938057 TTTTGCGGCG
*
9938067 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
**
9938088 CTAAAAAGTGCCGCTAAAAGC
1 CTAAAAAACGCCGCTAAAAGC
9938109 CT
1 CT
9938111 GTTTTGGTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.14
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:9942647 original size:28 final size:28
Alignment explanation
Indices: 9942595--9942654 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
9942585 AAATAGAAAT
**
9942595 ATAATCAAATATAATAATATCAATAACA
1 ATAATCAAATATAATAATAAAAATAACA
*
9942623 ATAAT-AAATAGTAATAATAAAAATAATA
1 ATAATCAAATA-TAATAATAAAAATAACA
9942651 ATAA
1 ATAA
9942655 ATTAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (28 bp):
ATAATCAAATATAATAATAAAAATAACA
Found at i:9942665 original size:15 final size:13
Alignment explanation
Indices: 9942595--9942656 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 13
9942585 AAATAGAAAT
9942595 ATAATCAAAT-ATA
1 ATAAT-AAATAATA
*
9942608 ATAATATCAATAACA
1 ATAATA--AATAATA
*
9942623 ATAATAAATAGTA
1 ATAATAAATAATA
9942636 ATAATAAA-AATA
1 ATAATAAATAATA
9942648 ATAATAAAT
1 ATAATAAAT
9942657 TAATTAATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 12 0.29
13 18 0.44
14 3 0.07
15 8 0.20
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (13 bp):
ATAATAAATAATA
Found at i:9946488 original size:18 final size:18
Alignment explanation
Indices: 9946465--9946500 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9946455 CAATTAAACC
9946465 ATTTGATTGATATATTTA
1 ATTTGATTGATATATTTA
* *
9946483 ATTTGATTTATTTATTTA
1 ATTTGATTGATATATTTA
9946501 TAAATAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
ATTTGATTGATATATTTA
Found at i:9946719 original size:14 final size:14
Alignment explanation
Indices: 9946700--9946726 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9946690 GAAAAGTAAA
9946700 TCATTTTCCAGAAG
1 TCATTTTCCAGAAG
9946714 TCATTTTCCAGAA
1 TCATTTTCCAGAA
9946727 AACATTTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (14 bp):
TCATTTTCCAGAAG
Found at i:9946732 original size:14 final size:14
Alignment explanation
Indices: 9946701--9946734 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9946691 AAAAGTAAAT
**
9946701 CATTTTCCAGAAGT
1 CATTTTCCAGAAAA
9946715 CATTTTCCAGAAAA
1 CATTTTCCAGAAAA
9946729 CATTTT
1 CATTTT
9946735 ACTGGCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (14 bp):
CATTTTCCAGAAAA
Found at i:9950075 original size:1 final size:1
Alignment explanation
Indices: 9950071--9950100 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
9950061 CCCCCCCCCG
*
9950071 AAAAAAAAAAAAAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9950101 CCACCTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9957822 original size:14 final size:14
Alignment explanation
Indices: 9957780--9957823 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
9957770 AATCAAACAC
*
9957780 CAGAAAATATTTTC
1 CAGAAAATATTTTA
*
9957794 CAGTAAATCATTTTA
1 CAGAAAAT-ATTTTA
*
9957809 CGGAAAATATTTTA
1 CAGAAAATATTTTA
9957823 C
1 C
9957824 TGGCAATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (14 bp):
CAGAAAATATTTTA
Found at i:9963793 original size:13 final size:13
Alignment explanation
Indices: 9963747--9963793 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 13
9963737 AAATAATACA
*
9963747 AACAAAAAGAAGG
1 AACAAAAAGAAAG
*
9963760 AA-AAAAATAAAG
1 AACAAAAAGAAAG
9963772 ACGACAAAAAGAAAG
1 A--ACAAAAAGAAAG
9963787 AACAAAA
1 AACAAAA
9963794 GTAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 9 0.32
13 8 0.29
14 1 0.04
15 10 0.36
ACGTcount: A:0.74, C:0.09, G:0.15, T:0.02
Consensus pattern (13 bp):
AACAAAAAGAAAG
Found at i:9975217 original size:16 final size:16
Alignment explanation
Indices: 9975197--9975233 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
9975187 CAAATTTATT
9975197 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
9975214 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
9975229 TAATA
1 TAATA
9975234 TTCATCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:9978997 original size:8 final size:7
Alignment explanation
Indices: 9978980--9979063 Score: 52
Period size: 7 Copynumber: 11.7 Consensus size: 7
9978970 AAAGTTAAAA
9978980 TATATAT
1 TATATAT
9978987 TATAGTAT
1 TATA-TAT
*
9978995 TATAAAT
1 TATATAT
*
9979002 TATATCT
1 TATATAT
9979009 TA-ATTAT
1 TATA-TAT
9979016 TA-AGTA-
1 TATA-TAT
9979022 TATATAT
1 TATATAT
9979029 TATAT-T
1 TATATAT
9979035 ATATTATAT
1 -TA-TATAT
9979044 TATAT-T
1 TATATAT
9979050 ATATTATAT
1 -TA-TATAT
9979059 TATAT
1 TATAT
9979064 TATATTATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
6 7 0.11
7 36 0.58
8 17 0.27
9 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (7 bp):
TATATAT
Found at i:9979000 original size:22 final size:22
Alignment explanation
Indices: 9978975--9979032 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
9978965 AACTTAAAGT
9978975 TAAAATATATATTATAGTATTA
1 TAAAATATATATTATAGTATTA
* * *
9978997 TAAATTATATCTTA-ATTATTA
1 TAAAATATATATTATAGTATTA
**
9979018 -AGTATATATATTATA
1 TAAAATATATATTATA
9979033 TTATATTATA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 9 0.32
21 7 0.25
22 12 0.43
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (22 bp):
TAAAATATATATTATAGTATTA
Done.