Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 181 of 199
Found at i:52585317 original size:21 final size:22
Alignment explanation
Indices: 52585266--52585326 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 22
52585256 TAAAAATAAA
* *
52585266 AAATATTTTTAAA-ATAA-TAC
1 AAATATGTTAAAATATAATTAC
* * *
52585286 AAATGTGTTAATATTTAATTAC
1 AAATATGTTAAAATATAATTAC
52585308 AAATAT-TTAAAATATAATT
1 AAATATGTTAAAATATAATT
52585327 TATATATTCT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 9 0.29
21 14 0.45
22 8 0.26
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (22 bp):
AAATATGTTAAAATATAATTAC
Found at i:52596075 original size:43 final size:43
Alignment explanation
Indices: 52596014--52596099 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
52596004 AGCAAAGAGA
52596014 TATAAAAATTTCCAGTTCTAAAAGGTATACTTTTACATCGTAT
1 TATAAAAATTTCCAGTTCTAAAAGGTATACTTTTACATCGTAT
52596057 TATAAAAATTTCCAGTTCTAAAAGGTATACTTTTACATCGTAT
1 TATAAAAATTTCCAGTTCTAAAAGGTATACTTTTACATCGTAT
52596100 ACATATAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (43 bp):
TATAAAAATTTCCAGTTCTAAAAGGTATACTTTTACATCGTAT
Found at i:52597276 original size:30 final size:28
Alignment explanation
Indices: 52597228--52597291 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 28
52597218 TTGCATAACC
*
52597228 TTTTTATTTTCTTATATCATT-TATTTAT
1 TTTTTATTTTCTAATATCATTAT-TTTAT
52597256 TTATTTATTATTCTAATATCATTATTTTAT
1 TT-TTTATT-TTCTAATATCATTATTTTAT
52597286 TTTTTA
1 TTTTTA
52597292 CCCTCTACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 2 0.06
29 10 0.31
30 19 0.59
31 1 0.03
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTTATTTTCTAATATCATTATTTTAT
Found at i:52611082 original size:50 final size:50
Alignment explanation
Indices: 52611028--52611150 Score: 131
Period size: 50 Copynumber: 2.5 Consensus size: 50
52611018 TATACCTCTG
* *
52611028 AAGTTCCAATGGGTCAGATTGAAGTC-ACCATAGCGAATCTTATTTCCCTA
1 AAGTTCCAATGGATCAGATTGAA-TCTACCATAGCGAATCTTATCTCCCTA
* * * * *
52611078 AAGTTGCAGTGGATCAGATTGAATCTACCATAGTGGATCTTATCTCCCTG
1 AAGTTCCAATGGATCAGATTGAATCTACCATAGCGAATCTTATCTCCCTA
* * * *
52611128 AAGTTGCAGTGAAGCAGATTGAA
1 AAGTTCCAATGGATCAGATTGAA
52611151 GTAGCAAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 2 0.03
50 61 0.97
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (50 bp):
AAGTTCCAATGGATCAGATTGAATCTACCATAGCGAATCTTATCTCCCTA
Found at i:52614534 original size:25 final size:27
Alignment explanation
Indices: 52614496--52614545 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
52614486 AAAGGAATAA
*
52614496 ATATATCAATTTATTTTTATAGTAGAT
1 ATATATCAATTTATTTATATAGTAGAT
*
52614523 ATATAT-AA-TTATTTATATTGTAG
1 ATATATCAATTTATTTATATAGTAG
52614546 TCAGCAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 2 0.10
27 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (27 bp):
ATATATCAATTTATTTATATAGTAGAT
Found at i:52615491 original size:19 final size:19
Alignment explanation
Indices: 52615467--52615504 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
52615457 GTAGGTAAGC
* *
52615467 GTTTAAAATCTGAAAATAA
1 GTTTAAAAACTAAAAATAA
52615486 GTTTAAAAACTAAAAATAA
1 GTTTAAAAACTAAAAATAA
52615505 AAGTTCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (19 bp):
GTTTAAAAACTAAAAATAA
Found at i:52632113 original size:20 final size:22
Alignment explanation
Indices: 52632088--52632137 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
52632078 AAATCGAGTG
52632088 AAATTATTCAT-T-AAATTAAA
1 AAATTATTCATGTCAAATTAAA
**
52632108 AAATTAAACATGTCAAATTAAA
1 AAATTATTCATGTCAAATTAAA
*
52632130 ATATTATT
1 AAATTATT
52632138 ATAATATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 9 0.39
21 1 0.04
22 13 0.57
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATTATTCATGTCAAATTAAA
Found at i:52632606 original size:10 final size:10
Alignment explanation
Indices: 52632565--52632611 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
52632555 TATTTAAATA
52632565 TTTAAATTTC
1 TTTAAATTTC
*
52632575 TTTATATGTTC
1 TTTAAAT-TTC
*
52632586 TTTAGAATTTT
1 TTTA-AATTTC
52632597 TTTAAATTT-
1 TTTAAATTTC
52632606 TTTAAA
1 TTTAAA
52632612 AATATAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 6 0.19
10 11 0.34
11 13 0.41
12 2 0.06
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (10 bp):
TTTAAATTTC
Found at i:52633084 original size:28 final size:27
Alignment explanation
Indices: 52633021--52633089 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 27
52633011 TAATAACTTA
*
52633021 TCAATTTAATTAAT-AATCAATTCTTT
1 TCAATTTAATTACTAAATCAATTCTTT
*
52633047 TCAA-TTAATTACTAAAT-AATTTTATT
1 TCAATTTAATTACTAAATCAATTCT-TT
52633073 TCTAATTTAATTACTAA
1 TC-AATTTAATTACTAA
52633090 TATTTCAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 13 0.35
26 11 0.30
27 2 0.05
28 11 0.30
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
TCAATTTAATTACTAAATCAATTCTTT
Found at i:52633102 original size:28 final size:28
Alignment explanation
Indices: 52633023--52633107 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
52633013 ATAACTTATC
*
52633023 AATTTAATTAATAATCAA-TTC-TTTTC-
1 AATTTAATTACTAAT-AATTTCATTTTCT
*
52633049 AA-TTAATTACTAAATAATTTTA-TTTCT
1 AATTTAATTACT-AATAATTTCATTTTCT
52633076 AATTTAATTACTAAT-ATTTCAATTTTCT
1 AATTTAATTACTAATAATTTC-ATTTTCT
52633104 AATT
1 AATT
52633108 CTTTACTCGC
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
25 10 0.20
26 15 0.31
27 6 0.12
28 18 0.37
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTTAATTACTAATAATTTCATTTTCT
Found at i:52634363 original size:21 final size:21
Alignment explanation
Indices: 52634333--52634372 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52634323 ACATTTTAAC
* *
52634333 ATTTTAAAAATTCAAAAAATT
1 ATTTTAAAAAATAAAAAAATT
*
52634354 ATTTTTAAAAATAAAAAAA
1 ATTTTAAAAAATAAAAAAA
52634373 ATCATCACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTTTAAAAAATAAAAAAATT
Found at i:52635936 original size:21 final size:21
Alignment explanation
Indices: 52635880--52635936 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
52635870 TTTCTCACAT
* *
52635880 CAATTTAATATTAAAGAATAA
1 CAATTTAATATAAAACAATAA
* **
52635901 -TATTTTCTATCAAAACAATAA
1 CAATTTAATAT-AAAACAATAA
52635922 CAATTTAATATAAAA
1 CAATTTAATATAAAA
52635937 TATCTCTAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
20 7 0.27
21 12 0.46
22 7 0.27
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (21 bp):
CAATTTAATATAAAACAATAA
Found at i:52640639 original size:15 final size:15
Alignment explanation
Indices: 52640619--52640655 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
52640609 TTCGTGATAA
52640619 AGAAATTGTTTGTTG
1 AGAAATTGTTTGTTG
52640634 AGAAATTGTTTGTTG
1 AGAAATTGTTTGTTG
52640649 AGAAATT
1 AGAAATT
52640656 ATTTACCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.43
Consensus pattern (15 bp):
AGAAATTGTTTGTTG
Found at i:52641383 original size:28 final size:28
Alignment explanation
Indices: 52641343--52641399 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
52641333 TTTAGAAAGA
*
52641343 AGTTGTAGTTGATTGTGAAAAGCTTGGC
1 AGTTGTAGTTGATTGTGAAAAGCCTGGC
52641371 AGTTGTAGTTGATTGTGAAAAGCCTGGC
1 AGTTGTAGTTGATTGTGAAAAGCCTGGC
52641399 A
1 A
52641400 TACTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.09, G:0.32, T:0.33
Consensus pattern (28 bp):
AGTTGTAGTTGATTGTGAAAAGCCTGGC
Found at i:52646123 original size:21 final size:22
Alignment explanation
Indices: 52646086--52646129 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
52646076 CAATAATTTA
52646086 TTTAATTAAATAATTATT-ATT
1 TTTAATTAAATAATTATTGATT
*
52646107 TTTAATTAAA-ATTTTATTGATT
1 TTTAATTAAATA-ATTATTGATT
52646129 T
1 T
52646130 AAGTAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 15 0.75
22 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTAATTAAATAATTATTGATT
Found at i:52656001 original size:15 final size:14
Alignment explanation
Indices: 52655981--52656019 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
52655971 GGAGAAAGAT
52655981 GTTAATTAAGGTTTA
1 GTTAATTAA-GTTTA
52655996 GTTAATTGAAGTTTA
1 GTTAATT-AAGTTTA
*
52656011 ATTAATTAA
1 GTTAATTAA
52656020 TTTTGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (14 bp):
GTTAATTAAGTTTA
Found at i:52657116 original size:70 final size:70
Alignment explanation
Indices: 52656996--52657156 Score: 277
Period size: 70 Copynumber: 2.3 Consensus size: 70
52656986 CATGTGACAT
*
52656996 AGGTTTAGCCTAGACTGGTAATCTTACATGTATATTTTTAACTTAGCCAAGCAATTGAATGTGTC
1 AGGTTTAGCCTGGACTGGTAATCTTACATGTATATTTTTAACTTAGCCAAGCAATTGAATGTGTC
52657061 ATTAA
66 ATTAA
* * *
52657066 AGGTTTAGCCTGGACTAGTAATCTTACATGTATATTTTTATCTTATCCAAGCAATTGAATGTGTC
1 AGGTTTAGCCTGGACTGGTAATCTTACATGTATATTTTTAACTTAGCCAAGCAATTGAATGTGTC
52657131 ATTAA
66 ATTAA
*
52657136 ATGTTTAGCCTGGACTGGTAA
1 AGGTTTAGCCTGGACTGGTAA
52657157 CCTAACAAGA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 85 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (70 bp):
AGGTTTAGCCTGGACTGGTAATCTTACATGTATATTTTTAACTTAGCCAAGCAATTGAATGTGTC
ATTAA
Found at i:52662336 original size:93 final size:94
Alignment explanation
Indices: 52662191--52662395 Score: 211
Period size: 93 Copynumber: 2.2 Consensus size: 94
52662181 TTTAATAAAC
* * * ***
52662191 ATTTGGTAC-TTGAACTTGAGATATTTTTCTAATTTGGTATTTAATTTTTTTTA-ATCCAATTTA
1 ATTTGGTACATAG-ACTTGACATATTTTTCTAATTTGGTACTTAATCACTTTTAGATCCAATTT-
**
52662254 GCATTTGAACTTGACACT-TTTTTTTCT-TA
64 GCACCTGAACTTGACACTCTTTTTTTCTCTA
* * *
52662283 ATTTGGTACATAGACTTGACATTTTTTTCTTAATTTGGTACTTAATCACTTTTAGGTCTAATTTG
1 ATTTGGTACATAGACTTGACATATTTTTC-TAATTTGGTACTTAATCACTTTTAGATCCAATTTG
* * *
52662348 TACCTGAACTTGACTCTCTTTTTTTGTCTA
65 CACCTGAACTTGACACTCTTTTTTTCTCTA
* *
52662378 ATTTGATACATAAACTTG
1 ATTTGGTACATAGACTTG
52662396 CCAAACGTTA
Statistics
Matches: 92, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
92 23 0.25
93 36 0.39
94 15 0.16
95 18 0.20
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (94 bp):
ATTTGGTACATAGACTTGACATATTTTTCTAATTTGGTACTTAATCACTTTTAGATCCAATTTGC
ACCTGAACTTGACACTCTTTTTTTCTCTA
Found at i:52662648 original size:60 final size:60
Alignment explanation
Indices: 52662555--52662670 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
52662545 CTTATTCAAT
* * *
52662555 ATTAATTCGTTAAGTATAACTCAATGCATAACTTGTTAACATGAATTTTCTCTAATTCTG
1 ATTAATTCGTTAAGTAGAACTCAATGCATAACTTGTTAACATGAACTTTATCTAATTCTG
* *
52662615 ATTAATTCGTTAAGTAGAGCTCAATGCATAACTTTTTAACATGAACTTTATCTAAT
1 ATTAATTCGTTAAGTAGAACTCAATGCATAACTTGTTAACATGAACTTTATCTAAT
52662671 ACTAAAGATG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (60 bp):
ATTAATTCGTTAAGTAGAACTCAATGCATAACTTGTTAACATGAACTTTATCTAATTCTG
Found at i:52668275 original size:24 final size:24
Alignment explanation
Indices: 52668248--52668296 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
52668238 GTTGCCTATA
52668248 CCATGGACTAACTTTGATACATTC
1 CCATGGACTAACTTTGATACATTC
52668272 CCATGGACTAACTTTGATACATTC
1 CCATGGACTAACTTTGATACATTC
52668296 C
1 C
52668297 TTTATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (24 bp):
CCATGGACTAACTTTGATACATTC
Found at i:52682470 original size:18 final size:21
Alignment explanation
Indices: 52682438--52682481 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
52682428 TCAAATTTTG
*
52682438 AAAATAATTT-TTAAAATTC-
1 AAAATAATTTATAAAAATTCT
52682457 AAAAT-ATTTATAAAAATTCT
1 AAAATAATTTATAAAAATTCT
52682477 AAAAT
1 AAAAT
52682482 TTGTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 13 0.59
20 5 0.23
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATAATTTATAAAAATTCT
Found at i:52689372 original size:22 final size:22
Alignment explanation
Indices: 52689325--52689374 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
52689315 AATAACACAG
* * *
52689325 TTTTAATAAATGCAGGAAAATC
1 TTTTAATAAATGAAAGAAAATA
52689347 TTTTAATAAATGGAAAGAAAA-A
1 TTTTAATAAAT-GAAAGAAAATA
52689369 TTTTAA
1 TTTTAA
52689375 ACTGTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.34
Consensus pattern (22 bp):
TTTTAATAAATGAAAGAAAATA
Found at i:52706863 original size:14 final size:14
Alignment explanation
Indices: 52706844--52706871 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52706834 CATTCCGAAG
52706844 TATATATATACATA
1 TATATATATACATA
52706858 TATATATATACATA
1 TATATATATACATA
52706872 AGTATGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TATATATATACATA
Found at i:52707384 original size:27 final size:27
Alignment explanation
Indices: 52707354--52707476 Score: 156
Period size: 27 Copynumber: 4.5 Consensus size: 27
52707344 AAATTGTACA
*
52707354 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGAATTGACTATGTT
* * *
52707381 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAATTGACTATGTT
* **
52707408 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTT
* *
52707435 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGA-ATTGACTATGTT
52707463 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
52707477 GACTCAATAT
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 60 0.73
28 22 0.27
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTT
Found at i:52708889 original size:32 final size:32
Alignment explanation
Indices: 52708852--52708932 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
52708842 TTACAATTAG
*
52708852 TTTGTTGGATTTTGAAAATATTATGTTTTAAA
1 TTTGTTGGATATTGAAAATATTATGTTTTAAA
** **
52708884 TTTGTTGGATATTGAATTTATTATGTTTTACG
1 TTTGTTGGATATTGAAAATATTATGTTTTAAA
*
52708916 CTTGTTGGATATTGAAA
1 TTTGTTGGATATTGAAA
52708933 TGATTAGCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.52
Consensus pattern (32 bp):
TTTGTTGGATATTGAAAATATTATGTTTTAAA
Found at i:52712497 original size:16 final size:16
Alignment explanation
Indices: 52712478--52712508 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52712468 TATTTTAGAG
52712478 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
52712494 CATATATATTTGAAA
1 CATATAAATTTGAAA
52712509 ACTTTCTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:52712713 original size:18 final size:18
Alignment explanation
Indices: 52712678--52712739 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
52712668 TTTTTAAGAA
52712678 TTATAAAT-TTTGGAATTT
1 TTATAAATATTTGG-ATTT
52712696 TTATAAATATTTGGATTT
1 TTATAAATATTTGGATTT
* * *
52712714 GTAAAAATTATTTTGATTT
1 TTATAAA-TATTTGGATTT
52712733 TT-TAAAT
1 TTATAAAT
52712740 TTTTAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.03
18 20 0.54
19 16 0.43
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (18 bp):
TTATAAATATTTGGATTT
Found at i:52713681 original size:6 final size:6
Alignment explanation
Indices: 52713670--52713696 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52713660 ATCCCATTTT
52713670 TCTCCC TCTCCC TCTCCC TCTCCC TCT
1 TCTCCC TCTCCC TCTCCC TCTCCC TCT
52713697 TACTCAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
TCTCCC
Found at i:52713745 original size:4 final size:4
Alignment explanation
Indices: 52713738--52713766 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
52713728 TCTCTCTCTC
52713738 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
52713767 TGATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:52720190 original size:11 final size:11
Alignment explanation
Indices: 52720147--52720242 Score: 59
Period size: 11 Copynumber: 9.3 Consensus size: 11
52720137 TTTCCTTCAA
52720147 AAATT-CTCTC
1 AAATTCCTCTC
52720157 -AATTCCGT-TC
1 AAATTCC-TCTC
52720167 AAAATT-CTCTC
1 -AAATTCCTCTC
*
52720178 AAATTCCTTTC
1 AAATTCCTCTC
52720189 AAAATT-CTCTC
1 -AAATTCCTCTC
52720200 AAA---CTCTC
1 AAATTCCTCTC
52720208 AAATTCCT-TCC
1 AAATTCCTCT-C
*
52720219 AAAATCCTCTC
1 AAATTCCTCTC
*
52720230 AATTTCCT-TC
1 AAATTCCTCTC
52720240 AAA
1 AAA
52720243 AATCTCCAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 24
0.69 0.06 0.24
Matches are distributed among these distances:
8 8 0.12
9 4 0.06
10 17 0.25
11 29 0.43
12 10 0.15
ACGTcount: A:0.32, C:0.30, G:0.01, T:0.36
Consensus pattern (11 bp):
AAATTCCTCTC
Found at i:52720202 original size:22 final size:21
Alignment explanation
Indices: 52720133--52720202 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 21
52720123 AAATTCAATA
*
52720133 TCAATTTCCTTCAAAAATTCTC
1 TCAAATTCCTTC-AAAATTCTC
52720155 TC-AATTCCGTTCAAAATTCTC
1 TCAAATTCC-TTCAAAATTCTC
52720176 TCAAATTCCTTTCAAAATTCTC
1 TCAAATTCC-TTCAAAATTCTC
52720198 TCAAA
1 TCAAA
52720203 CTCTCAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.36
22 28 0.64
ACGTcount: A:0.33, C:0.27, G:0.01, T:0.39
Consensus pattern (21 bp):
TCAAATTCCTTCAAAATTCTC
Found at i:52720209 original size:30 final size:30
Alignment explanation
Indices: 52720173--52720231 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
52720163 GTTCAAAATT
* *
52720173 CTCTCAAATTCCTTTCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
52720203 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
52720232 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:52720223 original size:52 final size:49
Alignment explanation
Indices: 52720152--52720252 Score: 132
Period size: 52 Copynumber: 2.0 Consensus size: 49
52720142 TTCAAAAATT
* *
52720152 CTCTCAATTCCGTTCAAAATTCTCTCAAATTCCTTTCAAAATTCTCTCAAA
1 CTCTCAATTCCGTTCAAAATCCTCTCAAATTCC-TTCAAAAATCTC-CAAA
*
52720203 CTCTCAAATTCC-TTCCAAAATCCTCTCAATTTCCTTCAAAAATCTCCAAA
1 CTCTC-AATTCCGTT-CAAAATCCTCTCAAATTCCTTCAAAAATCTCCAAA
52720253 TCCATATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
50 4 0.09
51 18 0.40
52 23 0.51
ACGTcount: A:0.33, C:0.32, G:0.01, T:0.35
Consensus pattern (49 bp):
CTCTCAATTCCGTTCAAAATCCTCTCAAATTCCTTCAAAAATCTCCAAA
Found at i:52720242 original size:21 final size:22
Alignment explanation
Indices: 52720203--52720253 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
52720193 TTCTCTCAAA
52720203 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
52720225 CTCTCAATTTCCTTCAAAAAT-
1 CTCTCAAATTCCTTCCAAAATC
52720246 CTC-CAAAT
1 CTCTCAAAT
52720254 CCATATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 4 0.15
21 3 0.12
22 19 0.73
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:52720350 original size:29 final size:29
Alignment explanation
Indices: 52720287--52720350 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
52720277 TAAATTTCAT
* * *
52720287 TATTTTAAGAAAATTTTAAATTTTTTTAT
1 TATTTTAAAAAAATTTTAAATATTTTTAA
*
52720316 TTTTTTAAAAATAATTTTAAA-ATTTTTAA
1 TATTTTAAAAA-AATTTTAAATATTTTTAA
52720345 TATTTT
1 TATTTT
52720351 CAACAATGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TATTTTAAAAAAATTTTAAATATTTTTAA
Found at i:52723303 original size:45 final size:45
Alignment explanation
Indices: 52723211--52723359 Score: 208
Period size: 45 Copynumber: 3.2 Consensus size: 45
52723201 AATCTCTAAC
52723211 CCTAACCTAATTTAATTAAAAACCCTAACCTTAGCCTAATTTAATTAAAAA
1 CCTAACCTAATTTAATTAAAAACCCTAA-C--A---TAATTTAATTAAAAA
*
52723262 CCTAACCTAATTTAATTAAAAACCCTAACATAATTTAATTAAAAC
1 CCTAACCTAATTTAATTAAAAACCCTAACATAATTTAATTAAAAA
* *
52723307 CCTAACCTAATTTAATTAAAAACCATAACCTAATTTAATTAAAAA
1 CCTAACCTAATTTAATTAAAAACCCTAACATAATTTAATTAAAAA
52723352 CCCTAACC
1 -CCTAACC
52723360 CTAAAATAAT
Statistics
Matches: 93, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
45 56 0.60
46 7 0.08
48 1 0.01
50 1 0.01
51 28 0.30
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.30
Consensus pattern (45 bp):
CCTAACCTAATTTAATTAAAAACCCTAACATAATTTAATTAAAAA
Found at i:52723396 original size:28 final size:27
Alignment explanation
Indices: 52722620--52723377 Score: 721
Period size: 23 Copynumber: 29.4 Consensus size: 27
52722610 TTTTGACATT
*
52722620 ATTTGATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAA-TTA
* * *
52722648 ATATAATTAAAAACCCTTACCCTAACCTA
1 ATTTAATTAAAAACCC-TAACCTAA-TTA
52722677 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAA-TTA
52722705 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAA-TTA
52722733 ATTTAATT-AAAACCCTAACC----TA
1 ATTTAATTAAAAACCCTAACCTAATTA
52722755 ATTTAATT-AAAACCCTAACCTAATTA
1 ATTTAATTAAAAACCCTAACCTAATTA
52722781 ATTTAATT-AAAACCCTAACC----TA
1 ATTTAATTAAAAACCCTAACCTAATTA
* * *
52722803 ATTTAGTTAAAATCCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAA-TTA
52722832 ATTTAATTAAAAACCCTAACC----TA
1 ATTTAATTAAAAACCCTAACCTAATTA
52722855 ATTTAATTAAAAACCCTAACC----TA
1 ATTTAATTAAAAACCCTAACCTAATTA
52722878 ATTTAATTAAAAACCCTAA--T--TTA
1 ATTTAATTAAAAACCCTAACCTAATTA
52722901 ATTTAATTAAAAACCCTAA-C--A-TA
1 ATTTAATTAAAAACCCTAACCTAATTA
* * *
52722924 ATTTAGTTAAAATCCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAA-TTA
*
52722953 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAA-TTA
52722982 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAA-TTA
52723010 ATTTAATTAAAAACCCTAA-C--A-TA
1 ATTTAATTAAAAACCCTAACCTAATTA
52723033 ATTTAATTAAAAACCCTAA-C---TTA
1 ATTTAATTAAAAACCCTAACCTAATTA
*
52723056 ACTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAA-TTA
*
52723084 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAA-TTA
52723112 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAA-TTA
52723140 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAA-TTA
*
52723168 ATTTAATTAAAAACCATAA-C--A-TA
1 ATTTAATTAAAAACCCTAACCTAATTA
* * * *
52723191 ATTTAGTTAAAATCTCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAA-TTA
**
52723220 ATTTAATTAAAAACCCTAACCTTAGCCTA
1 ATTTAATTAAAAACCCTAACC-TA-ATTA
52723249 ATTTAATTAAAAA-CCTAACC----TA
1 ATTTAATTAAAAACCCTAACCTAATTA
52723271 ATTTAATTAAAAACCCTAA-C--A-TA
1 ATTTAATTAAAAACCCTAACCTAATTA
52723294 ATTTAATT-AAAACCCTAACC----TA
1 ATTTAATTAAAAACCCTAACCTAATTA
*
52723316 ATTTAATTAAAAACCATAACC----TA
1 ATTTAATTAAAAACCCTAACCTAATTA
*
52723339 ATTTAATTAAAAACCCTAACCCTAAAATA
1 ATTTAATTAAAAACCCTAA-CCT-AATTA
52723368 ATTTAATTAA
1 ATTTAATTAA
52723378 TGTAAAAACC
Statistics
Matches: 649, Mismatches: 35, Indels: 91
0.84 0.05 0.12
Matches are distributed among these distances:
22 67 0.10
23 199 0.31
24 5 0.01
25 4 0.01
26 22 0.03
27 16 0.02
28 196 0.30
29 140 0.22
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (27 bp):
ATTTAATTAAAAACCCTAACCTAATTA
Found at i:52727846 original size:19 final size:19
Alignment explanation
Indices: 52727798--52727883 Score: 79
Period size: 19 Copynumber: 4.4 Consensus size: 19
52727788 TTTATGAAAA
52727798 TTATA-TTTCTTTAC-ATTT
1 TTATATTTTC-TTACAATTT
52727816 TGTATAATTTTCTTACAATTT
1 T-TAT-ATTTTCTTACAATTT
*
52727837 TTATATTTTCTTACTATTT
1 TTATATTTTCTTACAATTT
* *
52727856 TTCTATTTT-TTTCTAATTT
1 TTATATTTTCTTAC-AATTT
52727875 TTAATATTT
1 TT-ATATTT
52727884 GAATTTTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.07
19 31 0.54
20 13 0.23
21 9 0.16
ACGTcount: A:0.23, C:0.09, G:0.01, T:0.66
Consensus pattern (19 bp):
TTATATTTTCTTACAATTT
Found at i:52731779 original size:26 final size:26
Alignment explanation
Indices: 52731743--52731803 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
52731733 ATAAAAAATA
52731743 ACTAAAATATTATAATTTTTTTATTT
1 ACTAAAATATTATAATTTTTTTATTT
52731769 ACTAAAATATTATAATTTTTTTATTT
1 ACTAAAATATTATAATTTTTTTATTT
*
52731795 ACCAAAATA
1 ACTAAAATA
52731804 AAAAAAACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.51
Consensus pattern (26 bp):
ACTAAAATATTATAATTTTTTTATTT
Found at i:52731979 original size:37 final size:37
Alignment explanation
Indices: 52731938--52732008 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
52731928 CCTGATATGT
52731938 AAATTTACTATTTTGAATTTTGAAAGTGAATTGCTGC
1 AAATTTACTATTTTGAATTTTGAAAGTGAATTGCTGC
52731975 AAATTTACTATTTTGAATTTTGAAAGTGAATTGC
1 AAATTTACTATTTTGAATTTTGAAAGTGAATTGC
52732009 GCACTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (37 bp):
AAATTTACTATTTTGAATTTTGAAAGTGAATTGCTGC
Found at i:52732503 original size:19 final size:19
Alignment explanation
Indices: 52732479--52732574 Score: 115
Period size: 19 Copynumber: 5.2 Consensus size: 19
52732469 TCTAATTAAG
52732479 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
52732498 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
52732516 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
52732535 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
*
52732553 TAATAACTTTATTTTAATT
1 TAATAACTCTATTTTAATT
52732572 TAA
1 TAA
52732575 AAAAATTAAG
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
18 30 0.48
19 32 0.52
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:52732508 original size:18 final size:18
Alignment explanation
Indices: 52732487--52732574 Score: 97
Period size: 18 Copynumber: 4.8 Consensus size: 18
52732477 AGTAATAACT
52732487 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
* * *
52732505 CTATTCTCATTTAATAACT
1 CTATTTTAATTTAATAA-A
52732524 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
* *
52732542 CTATTCTCATTTAAT-AA
1 CTATTTTAATTTAATAAA
52732559 CTTTATTTTAATTTAA
1 C--TATTTTAATTTAA
52732575 AAAAATTAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
17 3 0.05
18 28 0.49
19 26 0.46
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:52732520 original size:37 final size:37
Alignment explanation
Indices: 52732479--52732574 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
52732469 TCTAATTAAG
52732479 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
52732516 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
*
52732553 TAATAACTTTATTTTAATTTAA
1 TAATAACTCTATTTTAATTTAA
52732575 AAAAATTAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (37 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
Found at i:52732647 original size:36 final size:36
Alignment explanation
Indices: 52732600--52732703 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
52732590 TATTTTAATT
52732600 TAATTTTTTTAAAATTAAAATAGAGTTATTAAATGA
1 TAATTTTTTTAAAATTAAAATAGAGTTATTAAATGA
52732636 TAATTTTTTTAAAATTAAAATAGAGTTATTAAATGA
1 TAATTTTTTTAAAATTAAAATAGAGTTATTAAATGA
* *
52732672 GAATAGTTTATT-AAATTAAAATAGAGTTATTA
1 TAAT--TTTTTTAAAATTAAAATAGAGTTATTA
52732704 CTTAATTAGA
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
36 39 0.61
37 20 0.31
38 5 0.08
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (36 bp):
TAATTTTTTTAAAATTAAAATAGAGTTATTAAATGA
Found at i:52732708 original size:18 final size:19
Alignment explanation
Indices: 52732611--52732703 Score: 86
Period size: 19 Copynumber: 5.1 Consensus size: 19
52732601 AATTTTTTTA
52732611 AAATTAAAATAGAGTTATT
1 AAATTAAAATAGAGTTATT
* * * *
52732630 AAATGATAAT---TTTTTT
1 AAATTAAAATAGAGTTATT
52732646 AAAATTAAAATAGAGTTATT
1 -AAATTAAAATAGAGTTATT
* * *
52732666 AAATGAGAATAG-TTTATT
1 AAATTAAAATAGAGTTATT
52732684 AAATTAAAATAGAGTTATT
1 AAATTAAAATAGAGTTATT
52732703 A
1 A
52732704 CTTAATTAGA
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
16 4 0.07
17 8 0.15
18 15 0.27
19 24 0.44
20 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (19 bp):
AAATTAAAATAGAGTTATT
Found at i:52733286 original size:27 final size:27
Alignment explanation
Indices: 52733245--52733296 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
52733235 CATTTTAGTC
52733245 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
52733272 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
52733297 GTGATTGGCC
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:0.13, C:0.33, G:0.23, T:0.31
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:52733304 original size:27 final size:27
Alignment explanation
Indices: 52733247--52733305 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
52733237 TTTTAGTCCT
*
52733247 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * *
52733274 TTGGCACCTTTGGTGCCGCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
52733301 TTGGC
1 TTGGC
52733306 CTAATCAGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.27, T:0.31
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:52733380 original size:27 final size:27
Alignment explanation
Indices: 52733357--52733421 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
52733347 TTTTTTTGGT
*
52733357 ATATTTTGGTAAATAGAAAATTTTTATA
1 ATATTTTGGTAAATA-AAAAATTTTATA
*
52733385 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAATTTTATA
52733412 ATATTTTGGT
1 ATATTTTGGT
52733422 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 20 0.57
28 15 0.43
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAATTTTATA
Found at i:52733380 original size:28 final size:28
Alignment explanation
Indices: 52733357--52733421 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
52733347 TTTTTTTGGT
*
52733357 ATATTTTGGTAAATAGAAAATTTTTATA
1 ATATTTTGGTAAATAAAAAATTTTTATA
*
52733385 ATATTTTGGTAAATAAAAAA-ATTTATA
1 ATATTTTGGTAAATAAAAAATTTTTATA
52733412 ATATTTTGGT
1 ATATTTTGGT
52733422 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAATTTTTATA
Found at i:52733712 original size:20 final size:20
Alignment explanation
Indices: 52733662--52733712 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
52733652 ATTTAATATA
*
52733662 AATATAA-ATATATATAATT
1 AATATAATATTTATATAATT
* *
52733681 ATTAT-TTAATTTATATAATT
1 AATATAAT-ATTTATATAATT
52733701 AATATAATATTT
1 AATATAATATTT
52733713 TTTATAACAT
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
19 4 0.17
20 19 0.79
21 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATAATATTTATATAATT
Found at i:52748068 original size:40 final size:40
Alignment explanation
Indices: 52747970--52748232 Score: 307
Period size: 40 Copynumber: 6.6 Consensus size: 40
52747960 TCCTCGTTCA
* * * * * *
52747970 AATGCCTTTGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
52748009 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52748049 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
52748089 AATTCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
52748129 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
52748169 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
52748209 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
52748233 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 36 0.18
40 153 0.78
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:52755383 original size:40 final size:40
Alignment explanation
Indices: 52755285--52755587 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
52755275 TCCTCGTTCA
* * * * * *
52755285 AATGCCTTTGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
52755324 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52755364 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52755404 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52755444 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
52755484 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
52755524 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
52755564 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
52755588 CAGCATTCAA
Statistics
Matches: 239, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
39 36 0.15
40 195 0.82
41 8 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:52760409 original size:3 final size:3
Alignment explanation
Indices: 52760401--52760425 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52760391 ATAAATTTCA
52760401 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
52760426 GCTTTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:52760774 original size:21 final size:18
Alignment explanation
Indices: 52760743--52760782 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
52760733 TCGTTTTTGT
52760743 TCATTTTTTATTCACATTA
1 TCATTTTTTATTC-CATTA
52760762 TCATGTTTATTATTCCATTA
1 TCAT-TTT-TTATTCCATTA
52760782 T
1 T
52760783 GCATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57
Consensus pattern (18 bp):
TCATTTTTTATTCCATTA
Found at i:52761029 original size:110 final size:109
Alignment explanation
Indices: 52760830--52761110 Score: 411
Period size: 110 Copynumber: 2.6 Consensus size: 109
52760820 TTTCTAATTG
* * * *
52760830 AGGCAATATTTAGCGTTTGGGAAATTCGAGAAAATAATGCCCTAAGGTGCTAGGTGTCGATTTTT
1 AGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAA-CATGCCCTAAGGTGCTGGGTGTCGATTTTT
* * *
52760895 CTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAAATTTTAAAATA
64 CTCATTCAACCAAATGGCTAAATATCCTTTT-AAAAATTTCAAAATA
*
52760942 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
52761007 CATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTCAAAATA
66 CATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTCAAAATA
* * * * *
52761051 AGGCAATGTTTTGCGTTTGGAAATTTGAG-GAACGTTCCCTAAGGTGCTGGGTTTCGATTT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTT
52761111 CTTGTTTAAC
Statistics
Matches: 155, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
108 26 0.17
109 42 0.27
110 56 0.36
111 15 0.10
112 16 0.10
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTCAAAATA
Found at i:52762806 original size:50 final size:51
Alignment explanation
Indices: 52762731--52762865 Score: 227
Period size: 51 Copynumber: 2.7 Consensus size: 51
52762721 CTTACGAATG
* * *
52762731 ATCACTTATCACTTGTCCCTGATCAGATAATTGTAGCTAAA-CTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
52762781 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
52762832 ATCACTTGTCACTTGTCACTGATCAGATAAGTGT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGT
52762866 TGTCACTTGT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 37 0.47
51 42 0.53
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:52762877 original size:28 final size:28
Alignment explanation
Indices: 52762837--52762893 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
52762827 CACTTATCAC
52762837 TTGTCACTTGTCACTGATCAGATAAGTG
1 TTGTCACTTGTCACTGATCAGATAAGTG
52762865 TTGTCACTTGTCACTGATCAGATAAGTG
1 TTGTCACTTGTCACTGATCAGATAAGTG
52762893 T
1 T
52762894 AGCTAAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (28 bp):
TTGTCACTTGTCACTGATCAGATAAGTG
Found at i:52762921 original size:79 final size:79
Alignment explanation
Indices: 52762790--52762944 Score: 292
Period size: 79 Copynumber: 2.0 Consensus size: 79
52762780 TATCACTTGC
52762790 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACTGAT
1 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACTGAT
52762855 CAGATAAGTGTTGT
66 CAGATAAGTGTTGT
* *
52762869 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTTTCATTGAT
1 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACTGAT
52762934 CAGATAAGTGT
66 CAGATAAGTGT
52762945 AGCTGAAGCT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (79 bp):
CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACTGAT
CAGATAAGTGTTGT
Found at i:52762938 original size:130 final size:129
Alignment explanation
Indices: 52762739--52762995 Score: 433
Period size: 130 Copynumber: 2.0 Consensus size: 129
52762729 TGATCACTTA
* *
52762739 TCACTTGTCCCTGATCAGATAATTGTAGCTAAACTACCACTTATCACTTGCCACTTGTCACTGAT
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTGCCACTTGTCACTGAT
*
52762804 CAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTTG
66 CAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTGTCACTGATCAGATAAGTGTTG
* * *
52762868 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTTTCATTGA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAA-CTACCACTTATCACTTGCCACTTGTCACTGA
* *
52762933 TCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTGTCACTGATCAGATAAGTGT
65 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTGTCACTGATCAGATAAGTGT
52762996 AGCTGAAGCT
Statistics
Matches: 119, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
129 31 0.26
130 88 0.74
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (129 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTGCCACTTGTCACTGAT
CAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGCCACTTGTCACTGATCAGATAAGTGTTG
Found at i:52762941 original size:51 final size:51
Alignment explanation
Indices: 52762865--52763025 Score: 268
Period size: 51 Copynumber: 3.2 Consensus size: 51
52762855 CAGATAAGTG
*
52762865 TTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCAC
* * *
52762916 TTGTCACTTTTCATTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCAC
1 TTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCAC
* *
52762967 TTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTTATCAC
1 TTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCAC
52763018 TTGTCACT
1 TTGTCACT
52763026 GATCAGAAGT
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 100 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (51 bp):
TTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCAC
Found at i:52773481 original size:73 final size:71
Alignment explanation
Indices: 52773392--52773529 Score: 222
Period size: 73 Copynumber: 1.9 Consensus size: 71
52773382 AAAAAAGGGA
* * *
52773392 TTTAACTAATAAAAATAATGGTTTGCAGCTTTAAGAACCAAATTAAACTAAAAAAATCCTTCTAA
1 TTTAACTAATAAAAATAATGATTTGCAACTTTAAAAACCAAATTAAACT-AAAAAATCCTTC-AA
52773457 ATATGGGG
64 ATATGGGG
*
52773465 TTTAACTAATAGAAATAATGATTTGCAACTTTAAAAACCAAATTAAACTAAAAAATCCTTCAAAT
1 TTTAACTAATAAAAATAATGATTTGCAACTTTAAAAACCAAATTAAACTAAAAAATCCTTCAAAT
52773530 TTCAATATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 4 0.07
72 12 0.20
73 45 0.74
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (71 bp):
TTTAACTAATAAAAATAATGATTTGCAACTTTAAAAACCAAATTAAACTAAAAAATCCTTCAAAT
ATGGGG
Found at i:52774658 original size:18 final size:17
Alignment explanation
Indices: 52774635--52774696 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
52774625 TACTGTGTTT
52774635 TTTTTAAATTTTATGAAC
1 TTTTTAAATTTTAT-AAC
* *
52774653 TTTTTATATTTTCTAAC
1 TTTTTAAATTTTATAAC
*
52774670 -TTTTAACTTTTTTATAA-
1 TTTTTAA--ATTTTATAAC
52774687 TTTTTAAATT
1 TTTTTAAATT
52774697 ATTTATTGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
16 7 0.20
17 3 0.09
18 25 0.71
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTTAAATTTTATAAC
Found at i:52787349 original size:22 final size:22
Alignment explanation
Indices: 52787321--52787442 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
52787311 TTCCACATCC
52787321 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
52787343 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
52787367 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
52787390 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
52787414 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
52787437 ATCACA
1 ATCACA
52787443 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:52787356 original size:47 final size:47
Alignment explanation
Indices: 52787293--52787889 Score: 873
Period size: 47 Copynumber: 12.6 Consensus size: 47
52787283 CCCTTCGGGA
* * *
52787293 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
52787340 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52787387 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
52787434 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
52787481 CTTAT--CATACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAC-T-TTCACATTCATCACATTGGCCATTCGGC
* *
52787528 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
52787575 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
52787622 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52787671 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52787718 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52787767 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
52787814 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
52787863 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
52787890 TATTCAAATA
Statistics
Matches: 515, Mismatches: 23, Indels: 24
0.92 0.04 0.04
Matches are distributed among these distances:
45 7 0.01
46 1 0.00
47 362 0.70
49 144 0.28
50 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:52787457 original size:94 final size:95
Alignment explanation
Indices: 52787293--52787889 Score: 879
Period size: 96 Copynumber: 6.3 Consensus size: 95
52787283 CCCTTCGGGA
* * *
52787293 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAATATATACA
52787357 CTTTCACATTCATCACATTGGCCATTCGGC
66 CTTTCACATTCATCACATTGGCCATTCGGC
* * * *
52787387 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC-ACATACAC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACAATATATAC
52787450 A-TGTTCACATTCATCACATTGGCCATTCGGC
65 ACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
52787481 CTTAT--CATACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTC-ATATATG
1 CTTATCACATATATACAC-T-TTCACATTCATCACATTGGCCATTCGGCCTTATCACAATATATA
52787543 CA-TGTTCACATTCATCACATTGGCCATTCGGC
64 CACT-TTCACATTCATCACATTGGCCATTCGGC
* *
52787575 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATA
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACA-ATATATA
52787639 CACTTTCACATTCATCACATTGGCCATTCGGC
64 CACTTTCACATTCATCACATTGGCCATTCGGC
* *
52787671 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACA-ATATATAC
* *
52787736 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATTGGCCATTCGGC
* *
52787767 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACA-ATATATAC
*
52787832 ACTTTCACATTCATCACATTGGCCATTAGGC
65 ACTTTCACATTCATCACATTGGCCATTCGGC
52787863 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
52787890 TATTCAAATA
Statistics
Matches: 468, Mismatches: 25, Indels: 18
0.92 0.05 0.04
Matches are distributed among these distances:
92 8 0.02
93 2 0.00
94 203 0.43
96 253 0.54
97 2 0.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (95 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAATATATACA
CTTTCACATTCATCACATTGGCCATTCGGC
Found at i:52789405 original size:56 final size:56
Alignment explanation
Indices: 52789338--52789457 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
52789328 TATTAGTTTA
52789338 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
* *
52789394 TTGCCCATGCTTCTTATTTTATTTTTCTATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
52789450 TTGCCCAT
1 TTGCCCAT
52789458 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:52790769 original size:40 final size:40
Alignment explanation
Indices: 52790724--52790998 Score: 406
Period size: 40 Copynumber: 6.9 Consensus size: 40
52790714 CGAATACACG
* * * *
52790724 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * ** * *
52790764 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
52790804 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
52790844 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
52790884 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCAGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
52790924 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
52790964 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG
52790999 TTATAGTAAC
Statistics
Matches: 213, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 213 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:52790874 original size:80 final size:80
Alignment explanation
Indices: 52790724--52791040 Score: 420
Period size: 80 Copynumber: 4.0 Consensus size: 80
52790714 CGAATACACG
* * * * * * *
52790724 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
* * *
52790789 TTTAGCACGGATATA
66 CTTAGCCCGGATACA
* * *
52790804 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
52790869 CTTAGCCCGGATACA
66 CTTAGCCCGGATACA
* *
52790884 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCAGATACATCACTAGCACGAATGCTCTTCGGAA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
52790949 CTTAGCCCGGATACA
66 CTTAGCCCGGATACA
* * * * * *
52790964 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGC-CTTCAGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAATGCTCTTCGGG
*
52791028 ACTTAACCCGGAT
65 ACTTAGCCCGGAT
52791041 TTAGTAACTC
Statistics
Matches: 209, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
80 196 0.94
81 13 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGA
CTTAGCCCGGATACA
Found at i:52791065 original size:120 final size:119
Alignment explanation
Indices: 52790724--52791078 Score: 439
Period size: 120 Copynumber: 3.0 Consensus size: 119
52790714 CGAATACACG
* * * *
52790724 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGG-ATATAACACCAGCACGAATGCTCTTCGGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTATATAAC-TC-GCACGAATGCTCTTCGGG
** *
52790788 GTTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
64 ACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
* * * *
52790844 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG-TATATAACTCGCACGAATGCTCTTCGGGA
* *
52790909 CTTAGCCCAGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
65 CTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
* *
52790964 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGC-CTTCAGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG-TATA-TAACTCGCACGAATGCTCTTCGGG
* * * * * *
52791028 ACTTAACCCGGATTTAGTAACTCGCACCAATGC-CTTCGG-GCTTAGCCCGGA
64 ACTTAGCCCGGATATA-TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGA
52791079 ATTAGTAACT
Statistics
Matches: 203, Mismatches: 28, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
119 11 0.05
120 162 0.80
121 25 0.12
122 5 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (119 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTATATAACTCGCACGAATGCTCTTCGGGAC
TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:52791158 original size:40 final size:40
Alignment explanation
Indices: 52790737--52791164 Score: 373
Period size: 40 Copynumber: 10.7 Consensus size: 40
52790727 CCAGCATGAT
* * *
52790737 TGCTCTTCGGGACCTAGCCCGGATAT-AACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATCATCACTAGCAC-AA
** *
52790777 TGCTCTTCGGGGTTTAGCACGGATAT-ATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATCATCACTAGCAC-AA
* *
52790817 TGCTCTTCGGAACTTAGCCCGGATA-CATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATCATCACTAGCA-CAA
*
52790857 TGCTCTTCGGGACTTAGCCCGGATA-CATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATCATCACTAGCA-CAA
*
52790897 TGCTCTTCGGGACTTAGCCCAGATA-CATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATCATCACTAGCAC-AA
* *
52790937 TGCTCTTCGGAACTTAGCCCGGATA-CATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATCATCACTAGCA-CAA
* * *
52790977 TGCTCTTCGGGACTTAGCCCGGTTAT-AGTAACTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATATCA-TCACTAGCAC-AA
* * * * *
52791018 TGC-CTTCAGGACTTAACCCGGAT-TTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATCA-TCACTAGCA-CAA
* * *
52791058 TGC-CTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATATCA-TCACTAGCAC-AA
* **
52791097 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAA
1 TGCTCTTCGGGA-CTTAGCCCGGATATCATCAC-TAGCACAA
* *
52791137 AGC-CTTCGGGACTTAGCCCGGACATCAT
1 TGCTCTTCGGGACTTAGCCCGGATATCAT
52791165 TCGAATAACC
Statistics
Matches: 335, Mismatches: 37, Indels: 32
0.83 0.09 0.08
Matches are distributed among these distances:
38 3 0.01
39 33 0.10
40 276 0.82
41 23 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATCATCACTAGCACAA
Found at i:52793496 original size:22 final size:22
Alignment explanation
Indices: 52793468--52793589 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
52793458 TTCCACATCC
52793468 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
52793490 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
52793514 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
52793537 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
52793561 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
52793584 ATCACA
1 ATCACA
52793590 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:52793503 original size:47 final size:47
Alignment explanation
Indices: 52793440--52793989 Score: 802
Period size: 47 Copynumber: 11.6 Consensus size: 47
52793430 CCCTTCGGGA
* * *
52793440 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
52793487 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52793534 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
52793581 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
52793628 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
52793675 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
52793722 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52793769 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52793818 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52793865 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
52793914 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
52793963 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
52793990 TATTCAAATA
Statistics
Matches: 475, Mismatches: 22, Indels: 12
0.93 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 331 0.70
48 1 0.00
49 142 0.30
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:52795504 original size:56 final size:56
Alignment explanation
Indices: 52795437--52795556 Score: 204
Period size: 56 Copynumber: 2.1 Consensus size: 56
52795427 TATTAGTTTA
** *
52795437 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACATGATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACACGTTTCATGACATGTT
*
52795493 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACACGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACACGTTTCATGACATGTT
52795549 TTGCCCAT
1 TTGCCCAT
52795557 CATCCCTTGT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACACGTTTCATGACATGTT
Found at i:52805566 original size:23 final size:25
Alignment explanation
Indices: 52805540--52805602 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 25
52805530 TTTCTTGGTG
52805540 TTTTGATGTTGTTTTTCTA-T-T-AT
1 TTTTGATGTTGTTTTT-TACTGTCAT
* *
52805563 TTTTGCTGGTGTTGTTTTACTGTCAT
1 TTTTGATGTTGTT-TTTTACTGTCAT
*
52805589 TTTTAATGTTGTTT
1 TTTTGATGTTGTTT
52805603 CGTTATCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 13 0.42
24 4 0.13
25 2 0.06
26 12 0.39
ACGTcount: A:0.11, C:0.06, G:0.17, T:0.65
Consensus pattern (25 bp):
TTTTGATGTTGTTTTTTACTGTCAT
Found at i:52806672 original size:16 final size:16
Alignment explanation
Indices: 52806651--52806681 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
52806641 AAACTTATTA
52806651 TACATTTATTTTTCAT
1 TACATTTATTTTTCAT
52806667 TACATTTATTTTTCA
1 TACATTTATTTTTCA
52806682 CACATCTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (16 bp):
TACATTTATTTTTCAT
Found at i:52806686 original size:15 final size:16
Alignment explanation
Indices: 52806652--52806686 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52806642 AACTTATTAT
*
52806652 ACATTTATTTTTCATT
1 ACATTTATTTTTCATC
52806668 ACATTTATTTTTCA-C
1 ACATTTATTTTTCATC
52806683 ACAT
1 ACAT
52806687 CTTAAGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (16 bp):
ACATTTATTTTTCATC
Found at i:52808314 original size:19 final size:19
Alignment explanation
Indices: 52808277--52808366 Score: 65
Period size: 19 Copynumber: 4.6 Consensus size: 19
52808267 ATATGGAAAT
** *
52808277 AAATATATAAAAAATAAAA
1 AAATATATAAATTACAAAA
* *
52808296 AAATATATAATTTAGAAAA
1 AAATATATAAATTACAAAA
*
52808315 AAA-ATCTAAATTACAAAA
1 AAATATATAAATTACAAAA
* * *
52808333 AATTATAAAAATTAAAATTAA
1 AAATATATAAATTACAA--AA
52808354 AAATATGATAAAT
1 AAATAT-ATAAAT
52808367 CAAAAGAAAT
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
18 14 0.26
19 28 0.52
21 7 0.13
22 5 0.09
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
AAATATATAAATTACAAAA
Found at i:52808316 original size:18 final size:18
Alignment explanation
Indices: 52808293--52808341 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
52808283 ATAAAAAATA
* *
52808293 AAAAAATATATAATTTAG
1 AAAAAATATATAAATTAC
* *
52808311 AAAAAAAATCTAAATTAC
1 AAAAAATATATAAATTAC
52808329 AAAAAAT-TATAAA
1 AAAAAATATATAAA
52808342 AATTAAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAAATATATAAATTAC
Found at i:52808350 original size:25 final size:24
Alignment explanation
Indices: 52808314--52808365 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
52808304 AATTTAGAAA
*
52808314 AAAAATCTAAATTACAAAAAATTAT
1 AAAAATCTAAATTA-AAAAAATGAT
*
52808339 AAAAAT-TAAAATTAAAAATATGAT
1 AAAAATCT-AAATTAAAAAAATGAT
52808363 AAA
1 AAA
52808366 TCAAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAAATCTAAATTAAAAAAATGAT
Found at i:52809087 original size:11 final size:11
Alignment explanation
Indices: 52809071--52809099 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
52809061 GATATTTTTC
52809071 ACATTTTCTAA
1 ACATTTTCTAA
52809082 ACATTTTCTAA
1 ACATTTTCTAA
52809093 ACATTTT
1 ACATTTT
52809100 TTTGACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (11 bp):
ACATTTTCTAA
Found at i:52809176 original size:37 final size:37
Alignment explanation
Indices: 52809095--52809184 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 37
52809085 TTTTCTAAAC
*
52809095 ATTTTTTTGACAA-TTTTTAATATTTTTAAAAAATTA
1 ATTTTTTTCACAATTTTTTAATATTTTTAAAAAATTA
** ** *
52809131 ATGATTTTCACAATTTTTTAATA-TTTTAAATAGTTTT
1 ATTTTTTTCACAATTTTTTAATATTTTTAAA-AAATTA
52809168 ATTTTTTTCA-AATTTTT
1 ATTTTTTTCACAATTTTT
52809185 ATAAGTTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
36 24 0.55
37 20 0.45
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.59
Consensus pattern (37 bp):
ATTTTTTTCACAATTTTTTAATATTTTTAAAAAATTA
Found at i:52809197 original size:22 final size:23
Alignment explanation
Indices: 52809169--52809211 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
52809159 AATAGTTTTA
52809169 TTTTTTTCA-AATTTTTATAAGT
1 TTTTTTTCACAATTTTTATAAGT
* *
52809191 TTTTTTTTACATTTTTTATAA
1 TTTTTTTCACAATTTTTATAA
52809212 TGATATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTTTCACAATTTTTATAAGT
Found at i:52809311 original size:19 final size:19
Alignment explanation
Indices: 52809231--52809344 Score: 63
Period size: 19 Copynumber: 5.8 Consensus size: 19
52809221 TAATTTCAAC
* *
52809231 TATTTTTA-CATTTATCT-
1 TATTTTTATAATTTATATA
* *
52809248 TATTTTTTTAATTTGTATA
1 TATTTTTATAATTTATATA
*
52809267 TATATTTTATAATTTATATG
1 TAT-TTTTATAATTTATATA
* *
52809287 TTTTTTTCTAGA-TTATATA
1 TATTTTTATA-ATTTATATA
* * *
52809306 TATTTTCACGAATTTTTTATA
1 TATTTTTA-TAA-TTTATATA
52809327 TATTTTTTATATATTTAT
1 TA-TTTTTATA-ATTTAT
52809345 TTTTAATGTT
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
17 7 0.10
18 6 0.09
19 21 0.30
20 17 0.24
21 13 0.19
22 6 0.09
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (19 bp):
TATTTTTATAATTTATATA
Found at i:52809347 original size:13 final size:11
Alignment explanation
Indices: 52809317--52809342 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52809307 ATTTTCACGA
52809317 ATTTTTTATAT
1 ATTTTTTATAT
52809328 ATTTTTTATAT
1 ATTTTTTATAT
52809339 ATTT
1 ATTT
52809343 ATTTTTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTTTATAT
Found at i:52827908 original size:50 final size:52
Alignment explanation
Indices: 52827782--52827913 Score: 146
Period size: 50 Copynumber: 2.6 Consensus size: 52
52827772 ATGAACAAAT
* *
52827782 GAGTTACTTAATGCA-AGACTTAATTTAATGATGCAGACTTAAACTAACATGA
1 GAGTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGA
** * * *
52827834 GAGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATG-
1 GAGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGA
*
52827883 GAAGTTACATAATGCATAACTTTATTAAATG
1 G-AGTTACATAATGCATAACTTTATTTAATG
52827914 CAGAACACAC
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
49 1 0.02
50 30 0.45
51 15 0.23
52 20 0.30
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (52 bp):
GAGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGA
Found at i:52827993 original size:20 final size:19
Alignment explanation
Indices: 52827952--52827993 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
52827942 AAAAATATGC
*
52827952 AAACTTATTAATTTAAATA
1 AAACTTATTAATTTAAAAA
52827971 AAACTATATTGAA-TTAAAAA
1 AAACT-TATT-AATTTAAAAA
52827991 AAA
1 AAA
52827994 AGTCTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 13 0.65
21 2 0.10
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (19 bp):
AAACTTATTAATTTAAAAA
Found at i:52827994 original size:21 final size:19
Alignment explanation
Indices: 52827952--52827994 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
52827942 AAAAATATGC
* *
52827952 AAACTTATTAATTTAAATA
1 AAACTTATTAATTAAAAAA
52827971 AAACTATATTGAATTAAAAAA
1 AAACT-TATT-AATTAAAAAA
52827992 AAA
1 AAA
52827995 GTCTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (19 bp):
AAACTTATTAATTAAAAAA
Found at i:52833473 original size:26 final size:26
Alignment explanation
Indices: 52833450--52833505 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
52833440 CAGATTAACT
*
52833450 ATTTCAAAAATAATTTTAATTTAATA
1 ATTTCAAAAATAAATTTAATTTAATA
* * *
52833476 ATTTTAATATTAAATTTAATTTAATA
1 ATTTCAAAAATAAATTTAATTTAATA
52833502 ATTT
1 ATTT
52833506 TCTTAATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTCAAAAATAAATTTAATTTAATA
Found at i:52833477 original size:14 final size:14
Alignment explanation
Indices: 52833458--52833506 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
52833448 CTATTTCAAA
52833458 AATAATTTTAATTT
1 AATAATTTTAATTT
52833472 AATAATTTTAATATT
1 AATAATTTTAAT-TT
52833487 -A-AA-TTTAATTT
1 AATAATTTTAATTT
52833498 AATAATTTT
1 AATAATTTT
52833507 CTTAATAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.06
12 7 0.23
13 4 0.13
14 16 0.52
15 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATAATTTTAATTT
Found at i:52834327 original size:22 final size:22
Alignment explanation
Indices: 52834299--52834341 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52834289 TTATGTTGTT
52834299 TTGCTACCATTTCATCATTATA
1 TTGCTACCATTTCATCATTATA
* * *
52834321 TTGCTACTATTTTATTATTAT
1 TTGCTACCATTTCATCATTAT
52834342 TGTATGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (22 bp):
TTGCTACCATTTCATCATTATA
Found at i:52837837 original size:12 final size:12
Alignment explanation
Indices: 52837820--52837844 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52837810 CTGAGGATCT
52837820 AGCAATCAGTAA
1 AGCAATCAGTAA
52837832 AGCAATCAGTAA
1 AGCAATCAGTAA
52837844 A
1 A
52837845 CTCTAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (12 bp):
AGCAATCAGTAA
Found at i:52843004 original size:18 final size:17
Alignment explanation
Indices: 52842990--52843025 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
52842980 ACATTTTTGC
*
52842990 ATTTTTTATTTTTTTATA
1 ATTTTTTATTCTTTT-TA
52843008 ATTTTTTATTCTTTTTA
1 ATTTTTTATTCTTTTTA
52843025 A
1 A
52843026 AATAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTTATTCTTTTTA
Found at i:52848962 original size:45 final size:45
Alignment explanation
Indices: 52848868--52848990 Score: 147
Period size: 45 Copynumber: 2.7 Consensus size: 45
52848858 AGGAAATGAT
* * * * *
52848868 TAAGACCATAGTTGAAAGACACTATGACACTATACCGGAAATAAA
1 TAAGACCATAGTTGAAAGACATTATGGCACCATACCAGAAACAAA
* *
52848913 TAAGACCATAGTTGAAAGACATTATGGCACCATACCAGAAACGAG
1 TAAGACCATAGTTGAAAGACATTATGGCACCATACCAGAAACAAA
* * * *
52848958 TAAGACTATAGCTAAAAGACGTTATGGCACCAT
1 TAAGACCATAGTTGAAAGACATTATGGCACCAT
52848991 GATTCTATTG
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACATTATGGCACCATACCAGAAACAAA
Found at i:52849079 original size:45 final size:45
Alignment explanation
Indices: 52848954--52849066 Score: 181
Period size: 45 Copynumber: 2.5 Consensus size: 45
52848944 ATACCAGAAA
* * * *
52848954 CGAGTAAGACTATAGCTAAAAGACGTTATGGCACCATGATTCTAT
1 CGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTAT
*
52848999 TGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTAT
1 CGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTAT
52849044 CGAGTAAGACCATAGCTGAAAGA
1 CGAGTAAGACCATAGCTGAAAGA
52849067 TGCTGTGGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (45 bp):
CGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTAT
Found at i:52849097 original size:45 final size:45
Alignment explanation
Indices: 52848911--52849121 Score: 131
Period size: 45 Copynumber: 4.7 Consensus size: 45
52848901 ACCGGAAATA
* **
52848911 AATAAGACCATAGTTGAAAGACATTATGGCA-C-C-ATACCAGAAACG
1 AATAAGACCATAGCTGAAAGACGCTATGGCATCACGA-ACC--AAACG
* * * * * * ** * **
52848956 AGTAAGACTATAGCTAAAAGACGTTATGGCACCATGATTCTATTG
1 AATAAGACCATAGCTGAAAGACGCTATGGCATCACGAACCAAACG
* * ** * *
52849001 AGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTATCG
1 AATAAGACCATAGCTGAAAGACGCTATGGCATCACGAACCAAACG
* * * *
52849046 AGTAAGACCATAGCTGAAAGATGCTGTGGCATCATGAACCAAACG
1 AATAAGACCATAGCTGAAAGACGCTATGGCATCACGAACCAAACG
* * *
52849091 AATAAGACTATAGTTGAAAGACACTATGGCA
1 AATAAGACCATAGCTGAAAGACGCTATGGCA
52849122 ACAAAAGAAA
Statistics
Matches: 133, Mismatches: 30, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
45 130 0.98
46 1 0.01
47 1 0.01
48 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (45 bp):
AATAAGACCATAGCTGAAAGACGCTATGGCATCACGAACCAAACG
Found at i:52849156 original size:46 final size:45
Alignment explanation
Indices: 52849090--52849212 Score: 131
Period size: 45 Copynumber: 2.7 Consensus size: 45
52849080 TGAACCAAAC
* *
52849090 GAATAAGACTATAGTTGAAAGACACTATGGCAACAAAAG-AAAAAAT
1 GAATAAGACCATGGTTGAAAGACACTATGGCAAC--AAGTAAAAAAT
* * * ** *
52849136 GAATAAGACCATGGTGGAAAGACACTATGTCATCAAGTCGAGAAT
1 GAATAAGACCATGGTTGAAAGACACTATGGCAACAAGTAAAAAAT
* *
52849181 AAATAAGACCATGGTTGAAAGACACCATGGCA
1 GAATAAGACCATGGTTGAAAGACACTATGGCA
52849213 CCCTTCGATC
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 3 0.05
45 32 0.50
46 29 0.45
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (45 bp):
GAATAAGACCATGGTTGAAAGACACTATGGCAACAAGTAAAAAAT
Found at i:52853665 original size:19 final size:19
Alignment explanation
Indices: 52853641--52853677 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52853631 TGAGTTGTGA
* *
52853641 GTCTGAAGGTGATGTATGG
1 GTCTGAAGATGATCTATGG
52853660 GTCTGAAGATGATCTATG
1 GTCTGAAGATGATCTATG
52853678 TCAAGACTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.35, T:0.32
Consensus pattern (19 bp):
GTCTGAAGATGATCTATGG
Found at i:52863343 original size:60 final size:60
Alignment explanation
Indices: 52863222--52863344 Score: 140
Period size: 60 Copynumber: 2.0 Consensus size: 60
52863212 TTATTTTAAC
* * * *
52863222 ATAAATTTTAATGATTATTATTTAAAATAAATATGTTTTCTTAAATATAAATATTAGTTA
1 ATAAATTTTAATGACTATTATTTAAAATAAATATATTTTCATAAATATAAATATTACTTA
* * * * * *
52863282 ATAAGTTTTAATGGCTATTATTTAACATAAATATAATTTTGATATATATATATA-TACTTA
1 ATAAATTTTAATGACTATTATTTAAAATAAATAT-ATTTTCATAAATATAAATATTACTTA
52863342 ATA
1 ATA
52863345 TTTATTTAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 38 0.73
61 14 0.27
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (60 bp):
ATAAATTTTAATGACTATTATTTAAAATAAATATATTTTCATAAATATAAATATTACTTA
Found at i:52865110 original size:29 final size:29
Alignment explanation
Indices: 52865076--52865143 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 29
52865066 TTAACCATTC
52865076 TTATAATTTAAAAAATAAAGGGATTGAAA
1 TTATAATTTAAAAAATAAAGGGATTGAAA
*
52865105 TTATAATCTAAAAAATAAAGGGATTGAAA
1 TTATAATTTAAAAAATAAAGGGATTGAAA
52865134 TTGA-AATTTA
1 TT-ATAATTTA
52865144 GTGAAGGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.13, T:0.32
Consensus pattern (29 bp):
TTATAATTTAAAAAATAAAGGGATTGAAA
Found at i:52865711 original size:14 final size:14
Alignment explanation
Indices: 52865692--52865731 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
52865682 TTGTTTGGCA
52865692 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
52865706 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
52865720 GGAAAATGTTTT
1 GTAAAATGTTTT
52865732 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:52865740 original size:20 final size:20
Alignment explanation
Indices: 52865715--52865754 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52865705 CGTAAAATGA
*
52865715 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
52865735 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
52865755 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:52865744 original size:34 final size:35
Alignment explanation
Indices: 52865700--52865766 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
52865690 CAGTAAAATG
*
52865700 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
52865734 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
52865767 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:52865770 original size:14 final size:15
Alignment explanation
Indices: 52865694--52865770 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
52865684 GTTTGGCAGT
* *
52865694 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
52865708 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
52865722 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
52865742 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
52865757 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
52865771 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:52865872 original size:14 final size:14
Alignment explanation
Indices: 52865853--52865880 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52865843 TTTTTACATA
52865853 TATTAATATATATT
1 TATTAATATATATT
52865867 TATTAATATATATT
1 TATTAATATATATT
52865881 AATAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:52866130 original size:60 final size:63
Alignment explanation
Indices: 52866064--52866206 Score: 166
Period size: 71 Copynumber: 2.2 Consensus size: 63
52866054 ACTAGAAATA
*
52866064 ATAATATTAT-T-CAAATACATAATTAATGGTACACCACATAGTAACAACATTGT-CTAGTGC
1 ATAATATTATATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGC
*
52866124 ATAATATTACTCCACATATATCCAAATACATAATTAATGGTACACCACATAGTAAGAACATTGTC
1 AT-A-A-TA-T-----TATATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTC
52866189 CAAGTGC
57 CAAGTGC
52866196 ATAATATTATA
1 ATAATATTATA
52866207 CCACATAAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 21
0.75 0.02 0.23
Matches are distributed among these distances:
60 2 0.03
61 1 0.01
62 1 0.01
63 6 0.09
64 1 0.01
68 1 0.01
69 5 0.07
70 2 0.03
71 42 0.61
72 8 0.12
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (63 bp):
ATAATATTATATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGC
Found at i:52867202 original size:35 final size:36
Alignment explanation
Indices: 52867156--52867224 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
52867146 ATTCAACCAT
52867156 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
*
52867191 TTCAATATCCAACAAGCTTAAAATATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
52867225 TCTAACAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:52868774 original size:15 final size:16
Alignment explanation
Indices: 52868754--52868786 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
52868744 AGTACCACTT
52868754 AAAATGAAAGCA-TGA
1 AAAATGAAAGCATTGA
52868769 AAAATGAAAGCATTGA
1 AAAATGAAAGCATTGA
52868785 AA
1 AA
52868787 GTTCAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAATGAAAGCATTGA
Found at i:52871226 original size:25 final size:25
Alignment explanation
Indices: 52871187--52871238 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
52871177 AAAATGTCTG
52871187 CTGCTTAGAAGAGAACAGAAAATGT
1 CTGCTTAGAAGAGAACAGAAAATGT
**
52871212 CTGCTTAG-AGAAGAATGGAAAATGT
1 CTGCTTAGAAG-AGAACAGAAAATGT
52871237 CT
1 CT
52871239 TACCAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (25 bp):
CTGCTTAGAAGAGAACAGAAAATGT
Found at i:52880520 original size:46 final size:44
Alignment explanation
Indices: 52880416--52880523 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
52880406 TGTCTTTGAC
** * * *
52880416 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
52880460 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
52880506 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
52880524 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:52880945 original size:9 final size:9
Alignment explanation
Indices: 52880931--52880964 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
52880921 TTCTATTCTG
52880931 TTTCTTTTC
1 TTTCTTTTC
52880940 TTTCTTTT-
1 TTTCTTTTC
*
52880948 TTTCTATTC
1 TTTCTTTTC
52880957 TTTCTTTT
1 TTTCTTTT
52880965 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:52880957 original size:17 final size:17
Alignment explanation
Indices: 52880931--52880964 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52880921 TTCTATTCTG
*
52880931 TTTCTTTTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
52880948 TTTCTATTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
52880965 GTTTTATGTA
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:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTATTCTTTCTTTT
Found at i:52880986 original size:5 final size:5
Alignment explanation
Indices: 52880973--52881044 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
52880963 TTGTTTTATG
52880973 TATATA TATAA TATAA TATAA TAT-A T-TAA TGATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
52881021 CATAA TCATTAC TATAA TATAA TA
1 TATAA T-A-TAA TATAA TATAA TA
52881045 ATATTTTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 34 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:52880998 original size:19 final size:19
Alignment explanation
Indices: 52880974--52881016 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
52880964 TGTTTTATGT
52880974 ATATATATAAT-ATAATATA
1 ATATAT-TAATGATAATATA
52880993 ATATATTAATGATAATATA
1 ATATATTAATGATAATATA
52881012 ATATA
1 ATATA
52881017 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATATTAATGATAATATA
Found at i:52881026 original size:24 final size:24
Alignment explanation
Indices: 52880980--52881045 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
52880970 ATGTATATAT
* * *
52880980 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
52881004 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
52881028 ATTACTATAATATAATAA
1 A-TAATATAATATAATAA
52881046 TATTTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 19 0.54
25 12 0.34
26 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:52883966 original size:23 final size:22
Alignment explanation
Indices: 52883923--52883966 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
52883913 TTCTAAGTCG
52883923 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
52883946 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
52883967 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:52884091 original size:45 final size:45
Alignment explanation
Indices: 52884011--52884104 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
52884001 AACAGATACT
* * * * *
52884011 CGGTGGATTCAGCACATAGCAACTATCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGTC
*
52884056 CGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGTC
52884101 CGGT
1 CGGT
52884105 TCACACAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGTC
Found at i:52884181 original size:51 final size:50
Alignment explanation
Indices: 52884101--52884296 Score: 189
Period size: 51 Copynumber: 3.9 Consensus size: 50
52884091 CAATGATGTT
* * *
52884101 CGGTTCACACAGTAGCCTGCACGTAGTACTACACATGTGACCATTACCATC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATC
* * * * * * *
52884152 CGATACACATAGTAGCTTGCACATGGTACTACACACGTGATCGAAACTATC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATC
* * ** *
52884203 CGGTA-AGTATAGTAGCCTGTACATAGTACTACACATGCAACC-TATCATTC
1 CGGTACA-CATAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TC
* *
52884253 CGGTACACGTAGTAGCTTGCACATAGTACTACACATGTGACCAT
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
52884297 CACTTTCATT
Statistics
Matches: 112, Mismatches: 28, Indels: 10
0.75 0.19 0.07
Matches are distributed among these distances:
49 2 0.02
50 38 0.34
51 70 0.62
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATACCATC
Found at i:52887963 original size:18 final size:19
Alignment explanation
Indices: 52887935--52887972 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
52887925 ATTTATTATT
52887935 TTTTCATCAGTTTTTTTTG
1 TTTTCATCAGTTTTTTTTG
52887954 TTTT-ATCAGTTTTTTTTG
1 TTTTCATCAGTTTTTTTTG
52887972 T
1 T
52887973 GTCAGATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.11, C:0.08, G:0.11, T:0.71
Consensus pattern (19 bp):
TTTTCATCAGTTTTTTTTG
Found at i:52888322 original size:26 final size:27
Alignment explanation
Indices: 52888276--52888332 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
52888266 AGTTTTGACA
*
52888276 AAAAAAAACAAAACTGTTTAAAAAAAT
1 AAAAAAAACAAAACTGTTTAAAAAAAC
*
52888303 AAAAAAAATAAAACTG-TTAAAAAAAC
1 AAAAAAAACAAAACTGTTTAAAAAAAC
52888329 AAAA
1 AAAA
52888333 TTGATGGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.16
Consensus pattern (27 bp):
AAAAAAAACAAAACTGTTTAAAAAAAC
Found at i:52891474 original size:48 final size:48
Alignment explanation
Indices: 52891414--52891506 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
52891404 CCAATGTACC
* * *
52891414 TAATTTATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATT
1 TAATTTATATTACAAAATTTGTTCCAAGTTGTAATATTGTAATGTATT
*
52891462 TAATTTATATTACAAAATTTGTTCCAAGTTGTAATGTTGTAATGT
1 TAATTTATATTACAAAATTTGTTCCAAGTTGTAATATTGTAATGT
52891507 TGCAATTAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.49
Consensus pattern (48 bp):
TAATTTATATTACAAAATTTGTTCCAAGTTGTAATATTGTAATGTATT
Done.