Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 133 of 202
Found at i:41229198 original size:14 final size:14
Alignment explanation
Indices: 41229179--41229208 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
41229169 AGATGAGAGG
41229179 GATGAGGGATGATT
1 GATGAGGGATGATT
41229193 GATGAGGGATGATT
1 GATGAGGGATGATT
41229207 GA
1 GA
41229209 AAAAATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.43, T:0.27
Consensus pattern (14 bp):
GATGAGGGATGATT
Found at i:41240829 original size:16 final size:17
Alignment explanation
Indices: 41240802--41240836 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
41240792 AGAGAGTTGA
41240802 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
41240819 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
41240835 GA
1 GA
41240837 TTGAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:41251626 original size:24 final size:24
Alignment explanation
Indices: 41251611--41251662 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41251601 AATCAAAGTC
41251611 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
41251635 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
41251659 AAAT
1 AAAT
41251663 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:41256035 original size:24 final size:24
Alignment explanation
Indices: 41256020--41256071 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41256010 AATCAAAGTC
41256020 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
41256044 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
41256068 AAAT
1 AAAT
41256072 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:41263682 original size:28 final size:28
Alignment explanation
Indices: 41263651--41263707 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41263641 ACCATTAAAG
41263651 AAAATAAAGGTTTCATCAAGTAATCCCA
1 AAAATAAAGGTTTCATCAAGTAATCCCA
41263679 AAAATAAAGGTTTCATCAAGTAATCCCA
1 AAAATAAAGGTTTCATCAAGTAATCCCA
41263707 A
1 A
41263708 CTCTATGAGA
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:0.47, C:0.18, G:0.11, T:0.25
Consensus pattern (28 bp):
AAAATAAAGGTTTCATCAAGTAATCCCA
Found at i:41264098 original size:42 final size:42
Alignment explanation
Indices: 41264013--41264096 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
41264003 GTAGGGTAAA
* * * *
41264013 TCCAACAACCCAAGTTTTTCTTCTCCTTTTTTAAATTCTTTT
1 TCCAACAACCCAAGATTATCTTCTCCTTCTTCAAATTCTTTT
*
41264055 TCCAACAACCCAAGATTATCTTCTCC-TCTTCAAATTTTTTT
1 TCCAACAACCCAAGATTATCTTCTCCTTCTTCAAATTCTTTT
41264096 T
1 T
41264097 TCTAGGATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 13 0.35
42 24 0.65
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.46
Consensus pattern (42 bp):
TCCAACAACCCAAGATTATCTTCTCCTTCTTCAAATTCTTTT
Found at i:41264797 original size:22 final size:22
Alignment explanation
Indices: 41264733--41264799 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
41264723 CTTGTTCCGC
**
41264733 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGTT
41264755 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGTT
*
41264777 TCACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGTT
41264799 T
1 T
41264800 GAACAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGTT
Found at i:41265638 original size:20 final size:19
Alignment explanation
Indices: 41265594--41265638 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
41265584 AAACTGTGAA
*
41265594 AAATTCAAAATTAAGGGGT
1 AAATTCAAAATTAAGGGCT
*
41265613 AGAATTGAAAATTAAGGAGCT
1 A-AATTCAAAATTAAGG-GCT
41265634 AAATT
1 AAATT
41265639 TGGCCTAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27
Consensus pattern (19 bp):
AAATTCAAAATTAAGGGCT
Found at i:41268350 original size:17 final size:19
Alignment explanation
Indices: 41268319--41268357 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
41268309 GAAATATTTA
*
41268319 TTTTGATGTTTTTAT-TAT
1 TTTTGATGTTATTATATAT
41268337 TTTTGATG-TATTATATAT
1 TTTTGATGTTATTATATAT
41268355 TTT
1 TTT
41268358 CAAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (19 bp):
TTTTGATGTTATTATATAT
Found at i:41277439 original size:21 final size:21
Alignment explanation
Indices: 41277415--41277454 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41277405 TTGTGCCTGC
41277415 ATCTGA-TTCTGGTGTGGATTT
1 ATCTGACTT-TGGTGTGGATTT
*
41277436 ATCTGACTTTGTTGTGGAT
1 ATCTGACTTTGGTGTGGAT
41277455 GTATTTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.15, C:0.10, G:0.28, T:0.47
Consensus pattern (21 bp):
ATCTGACTTTGGTGTGGATTT
Found at i:41278826 original size:17 final size:16
Alignment explanation
Indices: 41278795--41278828 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
41278785 AAATATTCTG
41278795 AAATAAAAACAAACAA
1 AAATAAAAACAAACAA
*
41278811 AAATAAACATCAAACAA
1 AAATAAA-AACAAACAA
41278828 A
1 A
41278829 CGCCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAACAA
Found at i:41283701 original size:205 final size:205
Alignment explanation
Indices: 41283332--41283701 Score: 498
Period size: 205 Copynumber: 1.8 Consensus size: 205
41283322 GCGTAACCGG
* * *
41283332 AAAACGCCAGAACTTTTGAAATCGAAACGCAACGTTTCGTCTTGAGCTATAGCACCTTTAGCAGC
1 AAAACGCCAAAAATTTTGAAACCGAAACGCAACGTTTCGTCTTGAGCTATAGCACCTTTAGCAGC
** * * * * *
41283397 GCTTAGCTGAAAATGCCGCTATATATAAGCTTTTTGTGGCGCTATCCCTGAATCGCCGCAAATAT
66 GCTTAGCCCAAAACGCCGCTATATATAAGCTTTTAGTGGCGCTATCCCTGAAGCGCCGCAAAAAA
* *
41283462 TTTGAACAAAACGCATCGTTCGGGTTTGACGTATAAAGGCATTAGTGGTGCTTACCTGAAAACGC
131 TTTGAACAAAACGCATCGTTCGGGCTTCACGTATAAAGGCATTAGTGGTGCTTACCTGAAAACGC
41283527 CGCTAACTAA
196 CGCTAACTAA
**
41283537 AAAACGCCGAAAAATTTT-AAACCGAAACGCAACGTTTCGTCTTGAGCTATAGCACCTTTAGTGG
1 AAAACGCC-AAAAATTTTGAAACCGAAACGCAACGTTTCGTCTTGAGCTATAGCACCTTTAGCAG
* * *
41283601 CGCTTA-CCCATAAACGCCGCTATATATCAA-CTTTTAGTGGCG-TTTCTGCTTAAGCGCCGCAA
65 CGCTTAGCCCA-AAACGCCGCTATATAT-AAGCTTTTAGTGGCGCTATC-CCTGAAGCGCCGCAA
*
41283663 AAAATTTGACCAAAACGCATCGTTTC-GGCTTCACGTATA
127 AAAATTTGAACAAAACGCATCG-TTCGGGCTTCACGTATA
41283702 GATTCATTAG
Statistics
Matches: 142, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
204 5 0.04
205 125 0.88
206 12 0.08
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (205 bp):
AAAACGCCAAAAATTTTGAAACCGAAACGCAACGTTTCGTCTTGAGCTATAGCACCTTTAGCAGC
GCTTAGCCCAAAACGCCGCTATATATAAGCTTTTAGTGGCGCTATCCCTGAAGCGCCGCAAAAAA
TTTGAACAAAACGCATCGTTCGGGCTTCACGTATAAAGGCATTAGTGGTGCTTACCTGAAAACGC
CGCTAACTAA
Found at i:41284083 original size:13 final size:14
Alignment explanation
Indices: 41284065--41284105 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
41284055 TTTCCAAAGA
41284065 TATGGTTTAGGA-T
1 TATGGTTTAGGACT
*
41284078 TATGGTTTATGACT
1 TATGGTTTAGGACT
*
41284092 TACGGTTTA-GACT
1 TATGGTTTAGGACT
41284105 T
1 T
41284106 TAGGGGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (14 bp):
TATGGTTTAGGACT
Found at i:41284201 original size:25 final size:26
Alignment explanation
Indices: 41284164--41284215 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
41284154 TTATTTGTGG
*
41284164 TTTATGGGTTTAATG-TTTATGGTTAA
1 TTTATGGGTTTAA-GATTTACGGTTAA
41284190 TTTA-GGGTTTAAGATTTACGGTTAA
1 TTTATGGGTTTAAGATTTACGGTTAA
41284215 T
1 T
41284216 GTCTACGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 1 0.04
25 19 0.79
26 4 0.17
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.50
Consensus pattern (26 bp):
TTTATGGGTTTAAGATTTACGGTTAA
Found at i:41284292 original size:7 final size:7
Alignment explanation
Indices: 41284280--41284356 Score: 73
Period size: 7 Copynumber: 11.0 Consensus size: 7
41284270 GTTAATTGAC
41284280 GGGTTTA
1 GGGTTTA
41284287 GGGTTTA
1 GGGTTTA
* *
41284294 AGTTTTA
1 GGGTTTA
*
41284301 TGGTTTA
1 GGGTTTA
*
41284308 GGGTTTG
1 GGGTTTA
41284315 GGGTTTA
1 GGGTTTA
*
41284322 GGGTTAA
1 GGGTTTA
41284329 GGGTTTA
1 GGGTTTA
** *
41284336 TAGTTTG
1 GGGTTTA
41284343 GGGTTTA
1 GGGTTTA
*
41284350 GGATTTA
1 GGGTTTA
41284357 CAATTAATTA
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (7 bp):
GGGTTTA
Found at i:41284514 original size:15 final size:16
Alignment explanation
Indices: 41284482--41284520 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
41284472 GATATTCTAG
41284482 ATTAATATAAATGAAA
1 ATTAATATAAATGAAA
41284498 A-TAATATAAAT-ATAA
1 ATTAATATAAATGA-AA
41284513 ATTAATAT
1 ATTAATAT
41284521 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 13 0.62
16 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTAATATAAATGAAA
Found at i:41285540 original size:16 final size:16
Alignment explanation
Indices: 41285514--41285574 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
41285504 TTGATAAACT
41285514 TTAATTAAAAGATACAA
1 TTAA-TAAAAGATACAA
41285531 TTAATAAAAGATACAA
1 TTAATAAAAGATACAA
* *
41285547 TTAAGAAATAAATA-AA
1 TTAATAAA-AGATACAA
*
41285563 TAAATAAAAGAT
1 TTAATAAAAGAT
41285575 GTGAGATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
15 3 0.08
16 27 0.71
17 8 0.21
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (16 bp):
TTAATAAAAGATACAA
Found at i:41285838 original size:24 final size:24
Alignment explanation
Indices: 41285810--41285871 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
41285800 CACTTAGCCG
41285810 AAATTCCCCCCAAATTTCT-CCCCA
1 AAATTCCCCCC-AATTTCTCCCCCA
* *
41285834 AAATTGCCCCCAATTTTTCCCCCA
1 AAATTCCCCCCAATTTCTCCCCCA
*
41285858 AAAAT-CCCCCAATT
1 AAATTCCCCCCAATT
41285872 CTAGAACCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.31, C:0.42, G:0.02, T:0.26
Consensus pattern (24 bp):
AAATTCCCCCCAATTTCTCCCCCA
Found at i:41290482 original size:21 final size:21
Alignment explanation
Indices: 41290456--41290566 Score: 177
Period size: 21 Copynumber: 5.3 Consensus size: 21
41290446 CAACAACTTA
*
41290456 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGGG
* *
41290477 AAGCAGACGCTGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGGG
41290498 AAGCAGAGGCCGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGGG
41290519 AAGCAGAGGCCGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGGG
* *
41290540 AAGCAGAGGCCGCAACGAGAG
1 AAGCAGAGGCCGCAGCGAGGG
41290561 AAGCAG
1 AAGCAG
41290567 CGAGAGAAGC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 84 1.00
ACGTcount: A:0.32, C:0.23, G:0.45, T:0.01
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGGG
Found at i:41291054 original size:43 final size:43
Alignment explanation
Indices: 41291007--41291088 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
41290997 CATAGTGGCG
*
41291007 TTTGTGAAAT-AAGCGCCGCTAAAGAACACTACTTTTAGCAGCA
1 TTTGT-AAATGAAGCACCGCTAAAGAACACTACTTTTAGCAGCA
* *
41291050 TTTGTAGATGAAGCACCGCTAAAGAACATTACTTTTAGC
1 TTTGTAAATGAAGCACCGCTAAAGAACACTACTTTTAGC
41291089 GGCGTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 3 0.09
43 32 0.91
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (43 bp):
TTTGTAAATGAAGCACCGCTAAAGAACACTACTTTTAGCAGCA
Found at i:41291163 original size:43 final size:42
Alignment explanation
Indices: 41291060--41291240 Score: 172
Period size: 43 Copynumber: 4.2 Consensus size: 42
41291050 TTTGTAGATG
* *
41291060 AAGCACCGCTAAAGAACATTA-CTTTTAGCGGCGTTTTTTACC-
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTT-CCT
* *
41291102 AAGCGCCGCTATAGAACAT-TTCTTTTAGCGGCGTTTTCTTCCT
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTCCT
* * * *
41291145 AAGCGCTGCTAAAGAACATGATCTTTAGCAGCATTTTTTTCGGT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGC-GTTTTTTC-CT
* *
41291189 -AGCGCCGCTAAAGAACATGAGCTTTAGCGGCGTTTTTTTCTGT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTC-CT
41291232 AAGCGCCGC
1 AAGCGCCGC
41291241 AAAAAGTTAG
Statistics
Matches: 117, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
42 35 0.30
43 67 0.57
44 15 0.13
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCT
Found at i:41292873 original size:15 final size:15
Alignment explanation
Indices: 41292840--41292872 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
41292830 CTATAAAGAT
41292840 AAAATAAAATATTTA
1 AAAATAAAATATTTA
41292855 AAAAT-AAATATTTA
1 AAAATAAAATATTTA
41292869 AAAA
1 AAAA
41292873 AATATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAAATATTTA
Found at i:41292879 original size:14 final size:13
Alignment explanation
Indices: 41292839--41292880 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 13
41292829 TCTATAAAGA
41292839 TAAAATAAAATATT
1 TAAAA-AAAATATT
41292853 TAAAAATAAATATT
1 TAAAAA-AAATATT
41292867 TAAAAAAATATATT
1 TAAAAAAA-ATATT
41292881 ATAATTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.12
14 23 0.88
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAAAAATATT
Found at i:41297482 original size:2 final size:2
Alignment explanation
Indices: 41297475--41297517 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
41297465 ATCCCATCCT
41297475 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
41297517 T
1 T
41297518 ATGTATGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:41299158 original size:13 final size:13
Alignment explanation
Indices: 41299140--41299164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41299130 TTCACAATAA
41299140 TTTAATTTTTTAT
1 TTTAATTTTTTAT
41299153 TTTAATTTTTTA
1 TTTAATTTTTTA
41299165 AATTTTAGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTAATTTTTTAT
Found at i:41304432 original size:16 final size:15
Alignment explanation
Indices: 41304411--41304455 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
41304401 AATTGAGTTC
41304411 AAAATATAAATATATA
1 AAAATA-AAATATATA
*
41304427 AAAATAAAAATGAAATA
1 AAAAT-AAAAT-ATATA
41304444 AAAATAAAATAT
1 AAAATAAAATAT
41304456 GATTCGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 1 0.04
16 14 0.56
17 10 0.40
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAATAAAATATATA
Found at i:41304446 original size:17 final size:17
Alignment explanation
Indices: 41304411--41304457 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
41304401 AATTGAGTTC
* *
41304411 AAAATATAAAT-ATATA
1 AAAATAAAAATGAAATA
41304427 AAAATAAAAATGAAATA
1 AAAATAAAAATGAAATA
41304444 AAAATAAAATATGA
1 AAAATAAAA-ATGA
41304458 TTCGAATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 10 0.37
17 13 0.48
18 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAATAAAAATGAAATA
Found at i:41305377 original size:16 final size:16
Alignment explanation
Indices: 41305356--41305400 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
41305346 TGACAAACTA
*
41305356 AAAAAATTAAGTGTTG
1 AAAAAATTAAGTGCTG
*
41305372 AAAAAA-TAAGTACTG
1 AAAAAATTAAGTGCTG
41305387 -AAAAATTAAGTGCT
1 AAAAAATTAAGTGCT
41305401 AGATTTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 5 0.20
15 14 0.56
16 6 0.24
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.27
Consensus pattern (16 bp):
AAAAAATTAAGTGCTG
Found at i:41316378 original size:14 final size:15
Alignment explanation
Indices: 41316359--41316388 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41316349 AGCATAATCC
41316359 ATTCAATC-ATATGA
1 ATTCAATCAATATGA
41316373 ATTCAATCAATATGA
1 ATTCAATCAATATGA
41316388 A
1 A
41316389 GCCACGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
ATTCAATCAATATGA
Found at i:41317653 original size:14 final size:16
Alignment explanation
Indices: 41317621--41317659 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
41317611 TAATTAATTA
41317621 TATTATTTATCATATAT
1 TATTATTTA-CATATAT
41317638 TATTATTTA-ATA-AT
1 TATTATTTACATATAT
41317652 TATTATTT
1 TATTATTT
41317660 TGGTTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 3 0.14
17 9 0.41
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATTTACATATAT
Found at i:41318083 original size:35 final size:36
Alignment explanation
Indices: 41318044--41318119 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 36
41318034 ATATTTTATG
*
41318044 ATTTTTATAAAAAATT-CTAATTTTTAATTTT-TAAT
1 ATTTTTATAAAAAATTAATAATTTTT-ATTTTATAAT
* *
41318079 ATTTTTATTAAAATTTAATAATTTTTATTTTATAAT
1 ATTTTTATAAAAAATTAATAATTTTTATTTTATAAT
41318115 -TTTTT
1 ATTTTT
41318120 CTAATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 24 0.67
36 12 0.33
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (36 bp):
ATTTTTATAAAAAATTAATAATTTTTATTTTATAAT
Found at i:41318132 original size:34 final size:36
Alignment explanation
Indices: 41318044--41318133 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 36
41318034 ATATTTTATG
* **
41318044 ATTTTTA-TAAAAAATTCTAATTTTTAATTTTTAAT
1 ATTTTTACTAAAATATAATAATTTTTAATTTTTAAT
* *
41318079 ATTTTTATTAAAATTTAATAATTTTT-ATTTTATAAT
1 ATTTTTACTAAAATATAATAATTTTTAATTTT-TAAT
*
41318115 -TTTTT-CTAATATATAATAA
1 ATTTTTACTAAAATATAATAA
41318134 GAGCAGGGGC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
34 11 0.24
35 17 0.37
36 18 0.39
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (36 bp):
ATTTTTACTAAAATATAATAATTTTTAATTTTTAAT
Found at i:41321208 original size:296 final size:295
Alignment explanation
Indices: 41320675--41321270 Score: 967
Period size: 296 Copynumber: 2.0 Consensus size: 295
41320665 AAAAGGCATT
*
41320675 GTGACGGTACGAGTTAAGGTGGATATTTGTGGAGTATGCATTGCATTTTGGTCAAATAAAGGAAC
1 GTGACGGTACGAGTTAAGGTGGATATTTGTGGAGTATGCATTGCATTTCGGTCAAATAAAGGAAC
* *
41320740 AAATAGAGAGTGATGTCGACACGAGAAACATGCGATGTCGCAATGACGCAATGATAAAAACATGG
66 AAATAGAGAGTGATGTCGACACGAGAAACATGCAATGTCGCAATGACACAATGATAAAAACATGG
* * *
41320805 GAGAAGTAGAAACGACGTCGCAATGACACGACAGGGAACGTCGTAACGTGGTGATGTGTCATGCA
131 GAGAAGTAGAAACGACGTCGCAATGACACGACAGGGAACGTCGCAACATGGCGATGTGTCATGCA
* * * *
41320870 ATTTTCTATATTTTCTTCTACTAGTTACACTCTGAGTATTTTTTTCAGTCGTTGAAACGACAAAA
196 ATTTTCTAGATTTTCTTCTACTAGTTACACACTGAATATTTTTTTCAGTCGTTGAAACGAAAAAA
*
41320935 ATGTGCAAGTGTACACAATCGTAAAAAATAATAAA
261 ATGTGCAAGTGTACACAATCGCAAAAAATAATAAA
* * * *
41320970 GTGACGGTATGAGTTATGGTGGATATTTGTGGAGTATGCATTGCATTTCGGTCAAATCAAGGCAC
1 GTGACGGTACGAGTTAAGGTGGATATTTGTGGAGTATGCATTGCATTTCGGTCAAATAAAGGAAC
* * * *
41321035 AAATAGAGAGTGTTGTCGACACGAGAAGCCATGCAATGTCGCAATGACACGATGATGAAAACATG
66 AAATAGAGAGTGATGTCGACACGAGAA-ACATGCAATGTCGCAATGACACAATGATAAAAACATG
* *
41321100 GGAGAAGTAGAAATGACGTCGCAATGACACGACAGGGAATGTCGCAACATGGCGATGTGTCATGC
130 GGAGAAGTAGAAACGACGTCGCAATGACACGACAGGGAACGTCGCAACATGGCGATGTGTCATGC
* *
41321165 AATTTTCTAGATTTTCTTCTCCTAGTTACACACTGAATATTTTTTTCAGTCGTTGAAATGAAAAA
195 AATTTTCTAGATTTTCTTCTACTAGTTACACACTGAATATTTTTTTCAGTCGTTGAAACGAAAAA
*
41321230 AATGTGCAAGTGTACACAATCGCAAAAAGTAATAAA
260 AATGTGCAAGTGTACACAATCGCAAAAAATAATAAA
41321266 GTGAC
1 GTGAC
41321271 AAGTAAATGT
Statistics
Matches: 276, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
295 86 0.31
296 190 0.69
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (295 bp):
GTGACGGTACGAGTTAAGGTGGATATTTGTGGAGTATGCATTGCATTTCGGTCAAATAAAGGAAC
AAATAGAGAGTGATGTCGACACGAGAAACATGCAATGTCGCAATGACACAATGATAAAAACATGG
GAGAAGTAGAAACGACGTCGCAATGACACGACAGGGAACGTCGCAACATGGCGATGTGTCATGCA
ATTTTCTAGATTTTCTTCTACTAGTTACACACTGAATATTTTTTTCAGTCGTTGAAACGAAAAAA
ATGTGCAAGTGTACACAATCGCAAAAAATAATAAA
Found at i:41322848 original size:101 final size:101
Alignment explanation
Indices: 41322673--41322874 Score: 359
Period size: 101 Copynumber: 2.0 Consensus size: 101
41322663 CAACGAGTAA
* * *
41322673 TCTGATCTACTATCGAGCCAAGCTGCAATCTTTGATGACTCCGACCTTTACGTATTACACCCAGT
1 TCTGATCTACTATCGAGCCAAGCTACAATCTTTGATGACTCCGACCTCTACGTAATACACCCAGT
*
41322738 TGACTATGAATGGAAGGAATCCCCAAATAGTTTTGG
66 TGACTATGAATGGAAGGAATCCCCAAACAGTTTTGG
*
41322774 TCTGATCTACTATCGAGCCAAGCTACAATCTTTGATGACTCCGACCTCTACGTAATCCACCCAGT
1 TCTGATCTACTATCGAGCCAAGCTACAATCTTTGATGACTCCGACCTCTACGTAATACACCCAGT
41322839 TGACTATGAATGGAAGGAATCCCCAAACAGTTTTGG
66 TGACTATGAATGGAAGGAATCCCCAAACAGTTTTGG
41322875 AGAAGACTTT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (101 bp):
TCTGATCTACTATCGAGCCAAGCTACAATCTTTGATGACTCCGACCTCTACGTAATACACCCAGT
TGACTATGAATGGAAGGAATCCCCAAACAGTTTTGG
Found at i:41328065 original size:12 final size:13
Alignment explanation
Indices: 41328041--41328069 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
41328031 AGGCTATAAC
41328041 TATTGCATTTATT
1 TATTGCATTTATT
41328054 TATTGC-TTTATT
1 TATTGCATTTATT
41328066 TATT
1 TATT
41328070 CTTGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:41334865 original size:13 final size:13
Alignment explanation
Indices: 41334847--41334872 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41334837 AGCTTGGTAG
41334847 ATTGGCTAGGCAA
1 ATTGGCTAGGCAA
41334860 ATTGGCTAGGCAA
1 ATTGGCTAGGCAA
41334873 TCATCATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (13 bp):
ATTGGCTAGGCAA
Found at i:41339245 original size:19 final size:19
Alignment explanation
Indices: 41339216--41339252 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
41339206 ACCTAACACG
41339216 AATTAAATTTAAACCATATT
1 AATTAAATTTAAA-CATATT
41339236 AATT-AATTTAAACATAT
1 AATTAAATTTAAACATAT
41339253 CAACATCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTAAATTTAAACATATT
Found at i:41340789 original size:18 final size:18
Alignment explanation
Indices: 41340714--41340795 Score: 62
Period size: 18 Copynumber: 4.4 Consensus size: 18
41340704 TGTTAAAACA
41340714 AAATATTAATCATTTTAC
1 AAATATTAATCATTTTAC
* *
41340732 AAATGTTAGTGATCAATTGTA-
1 AAATATTA---ATC-ATTTTAC
* *
41340753 AAATTTTCAA--ATATTAC
1 AAATATT-AATCATTTTAC
41340770 AAATATTAATCATTTTAC
1 AAATATTAATCATTTTAC
41340788 AAATATTA
1 AAATATTA
41340796 GTGATCAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
16 6 0.12
17 6 0.12
18 21 0.43
19 1 0.02
21 9 0.18
22 6 0.12
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (18 bp):
AAATATTAATCATTTTAC
Found at i:41340899 original size:18 final size:18
Alignment explanation
Indices: 41340865--41340899 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41340855 AATGTGCAAT
*
41340865 TCATTTTTTTTCGAAAAA
1 TCATTTTTTTTCAAAAAA
*
41340883 TCATTTTTTTTTAAAAA
1 TCATTTTTTTTCAAAAA
41340900 GGTTGCAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (18 bp):
TCATTTTTTTTCAAAAAA
Found at i:41352922 original size:2 final size:2
Alignment explanation
Indices: 41352915--41352945 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41352905 AAAATTTCCA
41352915 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41352946 ACTATCCTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41355554 original size:2 final size:2
Alignment explanation
Indices: 41355547--41355575 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41355537 TTATGAAAAT
41355547 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41355576 CCTCAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41357205 original size:3 final size:3
Alignment explanation
Indices: 41357197--41357297 Score: 139
Period size: 3 Copynumber: 33.7 Consensus size: 3
41357187 TTATATTGTA
*
41357197 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* ** **
41357245 ATC ATT GCT ATT ATT ATT ATT ATT ATT ATT ATT AGC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
41357293 TTT AT
1 ATT AT
41357298 ATATCAATTT
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:41359117 original size:16 final size:16
Alignment explanation
Indices: 41359092--41359125 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41359082 TGTGTTTTGC
* *
41359092 TTTGATTGCATGGCAT
1 TTTGACTGCATAGCAT
41359108 TTTGACTGCATAGCAT
1 TTTGACTGCATAGCAT
41359124 TT
1 TT
41359126 CATCCTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (16 bp):
TTTGACTGCATAGCAT
Found at i:41369807 original size:14 final size:14
Alignment explanation
Indices: 41369790--41369820 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41369780 ATCCAAACAA
41369790 TAATAACAAAATAG
1 TAATAACAAAATAG
*
41369804 TAATAACATAATAG
1 TAATAACAAAATAG
41369818 TAA
1 TAA
41369821 GATGGTAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (14 bp):
TAATAACAAAATAG
Found at i:41370222 original size:28 final size:27
Alignment explanation
Indices: 41370187--41370248 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
41370177 ATTTTTTTTG
* * *
41370187 AATT-TTTTACTTTTTAAAATTTTTTAA
1 AATTCTTTTACATTATAAAATTTTAT-A
*
41370214 AATTCTTTTACATTATAAGATTTTATA
1 AATTCTTTTACATTATAAAATTTTATA
41370241 AATTCTTT
1 AATTCTTT
41370249 ATAATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (27 bp):
AATTCTTTTACATTATAAAATTTTATA
Found at i:41377764 original size:19 final size:21
Alignment explanation
Indices: 41377726--41377765 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
41377716 CCGGCCCGAT
41377726 TTTTAATAAACACAAAAAATA
1 TTTTAATAAACACAAAAAATA
*
41377747 TTTTAA-AAA-ACTAAAAATA
1 TTTTAATAAACACAAAAAATA
41377766 AAAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
TTTTAATAAACACAAAAAATA
Found at i:41384543 original size:28 final size:28
Alignment explanation
Indices: 41384511--41384566 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
41384501 ATGAAAAGTT
41384511 AGCAAAAGATATGTTAACATAATCATCA
1 AGCAAAAGATATGTTAACATAATCATCA
41384539 AGCAAAAGATATGTTAACATAATCATCA
1 AGCAAAAGATATGTTAACATAATCATCA
41384567 CCCCTCGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (28 bp):
AGCAAAAGATATGTTAACATAATCATCA
Found at i:41385291 original size:3 final size:3
Alignment explanation
Indices: 41385283--41385333 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
41385273 AGTAGACATT
41385283 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
41385331 TTC
1 TTC
41385334 ATGCATCAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:41386727 original size:58 final size:60
Alignment explanation
Indices: 41386646--41386761 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 60
41386636 ATCACTTTAA
*** * *
41386646 TATTAAATTAATTTAATACTTA-T-CATGATAAGTATTAGATTAAATTTAATATTAACTC
1 TATTAAATTAAAAAAATACTTACTACATGATAAATATTAAATTAAATTTAATATTAACTC
*
41386704 TATTAAATTAAAAAAATATTTATCTACATGATAAATATTAAATTAAATTTAATATTAA
1 TATTAAATTAAAAAAATACTTA-CTACATGATAAATATTAAATTAAATTTAATATTAA
41386762 ATTTATTACA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
58 18 0.37
60 1 0.02
61 30 0.61
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (60 bp):
TATTAAATTAAAAAAATACTTACTACATGATAAATATTAAATTAAATTTAATATTAACTC
Found at i:41388474 original size:14 final size:14
Alignment explanation
Indices: 41388455--41388482 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41388445 CCCAATAGGG
41388455 CACATTTGTATTTT
1 CACATTTGTATTTT
41388469 CACATTTGTATTTT
1 CACATTTGTATTTT
41388483 GGTTATACTG
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:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
CACATTTGTATTTT
Found at i:41390292 original size:8 final size:9
Alignment explanation
Indices: 41390279--41390328 Score: 50
Period size: 8 Copynumber: 5.3 Consensus size: 9
41390269 GTAGTTAAAG
41390279 TAAGTTAA-
1 TAAGTTAAT
41390287 TAAGTTAAT
1 TAAGTTAAT
41390296 TAAGTATTAAAT
1 TAAG--TT-AAT
41390308 TAA-TTAAT
1 TAAGTTAAT
41390316 TAATGTTAAT
1 TAA-GTTAAT
41390326 TAA
1 TAA
41390329 ACTTAAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 14 0.39
9 6 0.17
10 8 0.22
11 2 0.06
12 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (9 bp):
TAAGTTAAT
Found at i:41393550 original size:20 final size:18
Alignment explanation
Indices: 41393511--41393551 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
41393501 AGTTCGGGAC
*
41393511 TGAAACTTCTAAAATTTT
1 TGAAACTTCTAAAATATT
41393529 TGAAACTTCTGATAAATATT
1 TGAAACTTCT-A-AAATATT
41393549 TGA
1 TGA
41393552 GGCATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 1 0.05
20 9 0.45
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (18 bp):
TGAAACTTCTAAAATATT
Found at i:41403641 original size:16 final size:16
Alignment explanation
Indices: 41403601--41403635 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
41403591 ACAAACGGTC
*
41403601 ATAATTATTCAAGTTG
1 ATAATTATTCAAGTAG
41403617 ATAATTATTCAAGTAG
1 ATAATTATTCAAGTAG
41403633 ATA
1 ATA
41403636 TCTATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (16 bp):
ATAATTATTCAAGTAG
Found at i:41404917 original size:21 final size:22
Alignment explanation
Indices: 41404869--41404921 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
41404859 CTTTCTTTTT
*
41404869 TATGATATATATTTACTTTGAGA
1 TATGATAT-TATTTACTTTGAAA
41404892 TATGATATTATTTA-TTT-AAA
1 TATGATATTATTTACTTTGAAA
41404912 TCATGATATT
1 T-ATGATATT
41404922 TGTAATCAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 11 0.39
22 6 0.21
23 8 0.29
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (22 bp):
TATGATATTATTTACTTTGAAA
Found at i:41412033 original size:25 final size:25
Alignment explanation
Indices: 41411997--41412065 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
41411987 GCCCATTTTC
* * *
41411997 ACAGCTTATGTGAACATACCGATTT
1 ACAGCTCATGTGAGCATACCAATTT
* *
41412022 ATAGCTCGTGTGAGCATACCAATTT
1 ACAGCTCATGTGAGCATACCAATTT
41412047 ACAGCTCATGTGAGCATAC
1 ACAGCTCATGTGAGCATAC
41412066 ATGTACAGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (25 bp):
ACAGCTCATGTGAGCATACCAATTT
Found at i:41413307 original size:12 final size:12
Alignment explanation
Indices: 41413273--41413308 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
41413263 GTTAGACTGT
*
41413273 TACACGGCCTAG
1 TACACGGCCTGG
*
41413285 TACACGACCTGG
1 TACACGGCCTGG
41413297 TACACGGCCTGG
1 TACACGGCCTGG
41413309 CAACCGGGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (12 bp):
TACACGGCCTGG
Found at i:41414424 original size:30 final size:30
Alignment explanation
Indices: 41414385--41414445 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
41414375 TCCTTACAAG
*
41414385 TAAGCCCTTTAACTTGAAAATCATTTTTAT
1 TAAGCCCTTTAACTTAAAAATCATTTTTAT
* *
41414415 TAAGTCCTTTAACTTAAAAATCCTTTTTAT
1 TAAGCCCTTTAACTTAAAAATCATTTTTAT
41414445 T
1 T
41414446 TCATCATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.46
Consensus pattern (30 bp):
TAAGCCCTTTAACTTAAAAATCATTTTTAT
Found at i:41415018 original size:36 final size:36
Alignment explanation
Indices: 41414934--41415044 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 36
41414924 CATCATCAGC
* * *
41414934 CCAACCATAACACATCAAATGCTCACACGAGCCAAT
1 CCAACCATAACACATCAAATGCTCACAAGAGCTAGT
** * *
41414970 CCTTCCAAAACACATCAAATGCTCACAAGAGCTGGT
1 CCAACCATAACACATCAAATGCTCACAAGAGCTAGT
* * *
41415006 CCAACCGTAACACA-CCAATGCTCATAAGAGCTAGT
1 CCAACCATAACACATCAAATGCTCACAAGAGCTAGT
41415041 CCAA
1 CCAA
41415045 GTGAAACACG
Statistics
Matches: 61, Mismatches: 14, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
35 22 0.36
36 39 0.64
ACGTcount: A:0.39, C:0.33, G:0.12, T:0.16
Consensus pattern (36 bp):
CCAACCATAACACATCAAATGCTCACAAGAGCTAGT
Found at i:41415035 original size:35 final size:35
Alignment explanation
Indices: 41414977--41415093 Score: 144
Period size: 35 Copynumber: 3.3 Consensus size: 35
41414967 AATCCTTCCA
* * *
41414977 AAACACATCAAATGCTCACAAGAGCTGGTCCAACCG
1 AAACACA-CCAATGCTCATAAGAGCTAGTCCAACCG
* **
41415013 TAACACACCAATGCTCATAAGAGCTAGTCCAAGTG
1 AAACACACCAATGCTCATAAGAGCTAGTCCAACCG
* *
41415048 AAACACGCCAATGCTCATAAAAGCTAGTCCAACCG
1 AAACACACCAATGCTCATAAGAGCTAGTCCAACCG
*
41415083 AAACATACCAA
1 AAACACACCAA
41415094 ACAGAGAGTA
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 62 0.91
36 6 0.09
ACGTcount: A:0.41, C:0.29, G:0.15, T:0.15
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAGTCCAACCG
Found at i:41420196 original size:23 final size:21
Alignment explanation
Indices: 41420169--41420214 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
41420159 AGAGAGAAAC
41420169 AAAAGAGAACGAAAAAAAAAATT
1 AAAA-AGAAC-AAAAAAAAAATT
*
41420192 -AAAAGAACATAAAAAAAATT
1 AAAAAGAACAAAAAAAAAATT
41420212 AAA
1 AAA
41420215 TTACTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 11 0.52
21 7 0.33
22 3 0.14
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAAAGAACAAAAAAAAAATT
Found at i:41422966 original size:62 final size:63
Alignment explanation
Indices: 41422843--41422967 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 63
41422833 TCAGGTGTCT
41422843 CAACTCCAGTGGGGGTACTGAAGTCAAAAAGGAAAAAATTAGTCATCAATAAAATAGTTAATA
1 CAACTCCAGTGGGGGTACTGAAGTCAAAAAGGAAAAAATTAGTCATCAATAAAATAGTTAATA
*
41422906 CAACTCCAGTGGGGGTACTGAAGTC-AAAAGGGAAAAATTAGTCATCAATAAAATAGTTAATA
1 CAACTCCAGTGGGGGTACTGAAGTCAAAAAGGAAAAAATTAGTCATCAATAAAATAGTTAATA
41422968 ATCCACTAAC
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 36 0.59
63 25 0.41
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (63 bp):
CAACTCCAGTGGGGGTACTGAAGTCAAAAAGGAAAAAATTAGTCATCAATAAAATAGTTAATA
Found at i:41423164 original size:6 final size:6
Alignment explanation
Indices: 41423153--41423191 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
41423143 CTTCAATCTG
* * *
41423153 CTCTTC CTCTTC CTCTTC TTCTTC TTCTTC CTCCTC CTC
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTC
41423192 CTCTTCCTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
CTCTTC
Found at i:41423168 original size:27 final size:24
Alignment explanation
Indices: 41423135--41423197 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
41423125 CATCCTCCAA
41423135 CTCCTCTTCTTCAATCTGCTCTTCCTC
1 CTCCTCTTCTTC-ATCT--TCTTCCTC
* *
41423162 TTCCTCTTCTTCTTCTTCTTCCTC
1 CTCCTCTTCTTCATCTTCTTCCTC
*
41423186 CTCCTCCTCTTC
1 CTCCTCTTCTTC
41423198 CTCCAAATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 18 0.56
26 3 0.09
27 11 0.34
ACGTcount: A:0.03, C:0.46, G:0.02, T:0.49
Consensus pattern (24 bp):
CTCCTCTTCTTCATCTTCTTCCTC
Found at i:41429468 original size:17 final size:17
Alignment explanation
Indices: 41429448--41429491 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41429438 TAATTTTATC
*
41429448 ATAATATTAAATTAAAA
1 ATAATAATAAATTAAAA
* *
41429465 ATAATTAATAATTTAAAT
1 ATAA-TAATAAATTAAAA
41429483 ATAATAATA
1 ATAATAATA
41429492 TCTAACAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATAATAAATTAAAA
Found at i:41432577 original size:18 final size:18
Alignment explanation
Indices: 41432556--41432618 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
41432546 GGTTGATAAC
41432556 GAAGAGGAAGTTGAGAAT
1 GAAGAGGAAGTTGAGAAT
** *
41432574 GAAGAGAGAA-AAGAGAAC
1 GAAGAG-GAAGTTGAGAAT
* *
41432592 AAAGAGGGAGTTGAGAAT
1 GAAGAGGAAGTTGAGAAT
41432610 GAAGAGGAA
1 GAAGAGGAA
41432619 TCTGAAACTG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
17 2 0.06
18 28 0.85
19 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.38, T:0.10
Consensus pattern (18 bp):
GAAGAGGAAGTTGAGAAT
Found at i:41433122 original size:25 final size:25
Alignment explanation
Indices: 41433088--41433136 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
41433078 ATAACGCTCC
41433088 ACATACTTGTGTTGTTACAAGAATT
1 ACATACTTGTGTTGTTACAAGAATT
41433113 ACATACTTGTGTTGTTACAAGAAT
1 ACATACTTGTGTTGTTACAAGAAT
41433137 GATGGCGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (25 bp):
ACATACTTGTGTTGTTACAAGAATT
Found at i:41434861 original size:33 final size:33
Alignment explanation
Indices: 41434824--41434895 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
41434814 TGAGAAAAAG
* * * *
41434824 TGAGAACAAAATAGTTGAGAGAATATGATTGAA
1 TGAGAACAAAAGAATTGACAGAATAGGATTGAA
** *
41434857 TGAGATTAAGAGAATTGACAGAATAGGATTGAA
1 TGAGAACAAAAGAATTGACAGAATAGGATTGAA
41434890 TGAGAA
1 TGAGAA
41434896 AAATGAAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.47, C:0.03, G:0.26, T:0.24
Consensus pattern (33 bp):
TGAGAACAAAAGAATTGACAGAATAGGATTGAA
Found at i:41436871 original size:6 final size:6
Alignment explanation
Indices: 41436853--41436885 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
41436843 ATGGAATTAT
41436853 GGAAAG TGGAAAG GGAAAG GGAAAG GGAAAG GG
1 GGAAAG -GGAAAG GGAAAG GGAAAG GGAAAG GG
41436886 TCTTGGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.03
Consensus pattern (6 bp):
GGAAAG
Found at i:41437104 original size:13 final size:13
Alignment explanation
Indices: 41437086--41437141 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
41437076 TAGATTTTTC
41437086 CTAAATATTATCA
1 CTAAATATTATCA
*
41437099 CTAAATA--AT-T
1 CTAAATATTATCA
41437109 CTAAATATTATCA
1 CTAAATATTATCA
41437122 CTAAATATTATCA
1 CTAAATATTATCA
41437135 CTAAATA
1 CTAAATA
41437142 ATTCAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 7 0.18
11 2 0.05
12 2 0.05
13 27 0.71
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:41439059 original size:17 final size:17
Alignment explanation
Indices: 41439024--41439061 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
41439014 GTCAAAATGC
41439024 AAAAGTGGTATCGATATA
1 AAAAGTGGTATCGA-ATA
41439042 AAAAGATGGTATCG-ATA
1 AAAAG-TGGTATCGAATA
41439059 AAA
1 AAA
41439062 TTCAATAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 5 0.26
19 8 0.42
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (17 bp):
AAAAGTGGTATCGAATA
Found at i:41440635 original size:9 final size:9
Alignment explanation
Indices: 41440621--41440657 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41440611 TATAGTTTGA
41440621 TATTCGAAT
1 TATTCGAAT
41440630 TATTCGAAT
1 TATTCGAAT
*
41440639 TATTCGAGT
1 TATTCGAAT
41440648 TATTCGAAT
1 TATTCGAAT
41440657 T
1 T
41440658 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41445821 original size:3 final size:3
Alignment explanation
Indices: 41445801--41445838 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
41445791 AATAAGGAGG
* *
41445801 AGA AGA GGA AGA ACA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
41445839 GATTTTAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.63, C:0.03, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41446162 original size:23 final size:24
Alignment explanation
Indices: 41446135--41446180 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
41446125 TTTCAATTTC
41446135 AAAATTGACAA-AA-TTAATTTTTT
1 AAAATTGA-AATAATTTAATTTTTT
41446158 AAAATTGAAATAATTTAATTTTT
1 AAAATTGAAATAATTTAATTTTT
41446181 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.10
23 10 0.48
24 9 0.43
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AAAATTGAAATAATTTAATTTTTT
Found at i:41446265 original size:15 final size:16
Alignment explanation
Indices: 41446237--41446266 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41446227 ATATCTTTCA
41446237 TCAATTGTATATAATT
1 TCAATTGTATATAATT
41446253 TCAATTG-ATATAAT
1 TCAATTGTATATAAT
41446267 AACAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
TCAATTGTATATAATT
Found at i:41446798 original size:10 final size:10
Alignment explanation
Indices: 41446757--41446870 Score: 51
Period size: 10 Copynumber: 11.4 Consensus size: 10
41446747 AAAAATTCAT
41446757 AAAATTATTTA
1 AAAATTA-TTA
*
41446768 AAAATT-TAA
1 AAAATTATTA
*
41446777 AATAAATATTA
1 AA-AATTATTA
41446788 AAAATTATTA
1 AAAATTATTA
41446798 AAAACTTA-TA
1 AAAA-TTATTA
**
41446808 AATGTTA-TA
1 AAAATTATTA
*
41446817 AAAACGTA-TA
1 AAAA-TTATTA
* *
41446827 AAATTTCTTA
1 AAAATTATTA
*
41446837 TAAATT-TTA
1 AAAATTATTA
41446846 ATAAATTA-TA
1 A-AAATTATTA
*
41446856 AAAAATATTA
1 AAAATTATTA
41446866 TAAAA
1 -AAAA
41446871 ATAAGGCTTA
Statistics
Matches: 78, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
9 20 0.26
10 41 0.53
11 17 0.22
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (10 bp):
AAAATTATTA
Found at i:41447045 original size:86 final size:89
Alignment explanation
Indices: 41446906--41447074 Score: 256
Period size: 86 Copynumber: 1.9 Consensus size: 89
41446896 TTCAAACTTA
*
41446906 AAAAAAAAGCAATTAAGCCCTTCCTTTTTTTTGCACTTAATTGAGCACTTGAACTTTCAAAATGC
1 AAAAAAAAGCAATTAAGCCC-TCCTTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGC
*
41446971 ATCAAAAAGTCCCTCAAACCTCTTC
65 ATCAAAAAGACCCTCAAACCTCTTC
* *
41446996 AAAAAAAA-CAATTAAG-CC-CCTATTTTTTT-CACTCAATTGGGTACTTGAACTTTCAAAATGC
1 AAAAAAAAGCAATTAAGCCCTCCT-TTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGC
41447057 ATCAAAAAGACCCTCAAA
65 ATCAAAAAGACCCTCAAA
41447075 AGTGACATTT
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
86 49 0.66
87 7 0.09
88 2 0.03
89 8 0.11
90 8 0.11
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (89 bp):
AAAAAAAAGCAATTAAGCCCTCCTTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGCA
TCAAAAAGACCCTCAAACCTCTTC
Found at i:41451374 original size:21 final size:21
Alignment explanation
Indices: 41451348--41451397 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
41451338 GGCTAGAGAA
* *
41451348 TTCTACTGGTAGAATTGGGAG
1 TTCTACCGGTAGAACTGGGAG
41451369 TTCTACCGGTAGAACTGGGAG
1 TTCTACCGGTAGAACTGGGAG
41451390 TTCTACCG
1 TTCTACCG
41451398 ATACAACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (21 bp):
TTCTACCGGTAGAACTGGGAG
Found at i:41451405 original size:21 final size:21
Alignment explanation
Indices: 41451363--41451436 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
41451353 CTGGTAGAAT
* *
41451363 TGGGAGTTCTACCGGTAGAAC
1 TGGGAGTTCTACCGATACAAC
41451384 TGGGAGTTCTACCGATACAAC
1 TGGGAGTTCTACCGATACAAC
* *
41451405 TCTGG-GTTCTACTGATACAAC
1 T-GGGAGTTCTACCGATACAAC
* *
41451426 TTGGACTTCTA
1 TGGGAGTTCTA
41451437 TTGGTAGAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 3 0.07
21 41 0.89
22 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (21 bp):
TGGGAGTTCTACCGATACAAC
Found at i:41459697 original size:41 final size:41
Alignment explanation
Indices: 41459588--41459704 Score: 164
Period size: 41 Copynumber: 2.9 Consensus size: 41
41459578 TAGACTTATC
* *
41459588 GTCCGAATTATTTCACCGGCACAAAGCCTGCTAGACATAAA
1 GTCCGAATAACTTCACCGGCACAAAGCCTGCTAGACATAAA
* *
41459629 GTCCGAATTATTTCACCGGCACAAAGCCTGCTAGACATAAA
1 GTCCGAATAACTTCACCGGCACAAAGCCTGCTAGACATAAA
* *
41459670 GTCCGAATAACTTCATCGGC-CTTAAGCCTGCTAGA
1 GTCCGAATAACTTCACCGGCAC-AAAGCCTGCTAGA
41459705 TTTTAAACCT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.01
41 70 0.99
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (41 bp):
GTCCGAATAACTTCACCGGCACAAAGCCTGCTAGACATAAA
Found at i:41465466 original size:25 final size:25
Alignment explanation
Indices: 41465438--41465606 Score: 132
Period size: 25 Copynumber: 6.8 Consensus size: 25
41465428 TCCTGATATA
*
41465438 TGGCTCTCTTGAGCTTCCCATTATT
1 TGGCTCTCATGAGCTTCCCATTATT
*
41465463 TGGCTCTCACGAGCTT-CC-TTATAAT
1 TGGCTCTCATGAGCTTCCCATTAT--T
41465488 TGGCTCTCATGAGCTTCCCATTATT
1 TGGCTCTCATGAGCTTCCCATTATT
** ** *
41465513 TGGCTCTCACAAGCTTCTTGA-TAAT
1 TGGCTCTCATGAGCTTC-CCATTATT
* *
41465538 TGGCTCTCATAAGCTTCCCTATTA-A
1 TGGCTCTCATGAGCTTCCC-ATTATT
* * * *
41465563 TGGATTTTC-GGAGCTTCCCAATATT
1 TGG-CTCTCATGAGCTTCCCATTATT
*
41465588 TGGCTCTCTTGAGCTTCCC
1 TGGCTCTCATGAGCTTCCC
41465607 GTTTACGTCT
Statistics
Matches: 113, Mismatches: 21, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
23 4 0.04
24 8 0.07
25 89 0.79
26 8 0.07
27 4 0.04
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (25 bp):
TGGCTCTCATGAGCTTCCCATTATT
Found at i:41465501 original size:50 final size:50
Alignment explanation
Indices: 41465438--41465561 Score: 196
Period size: 50 Copynumber: 2.5 Consensus size: 50
41465428 TCCTGATATA
* *
41465438 TGGCTCTCTTGAGCTTCCCATTATTTGGCTCTCACGAGCTTCCTT-ATAAT
1 TGGCTCTCATGAGCTTCCCATTATTTGGCTCTCACAAGCTT-CTTGATAAT
41465488 TGGCTCTCATGAGCTTCCCATTATTTGGCTCTCACAAGCTTCTTGATAAT
1 TGGCTCTCATGAGCTTCCCATTATTTGGCTCTCACAAGCTTCTTGATAAT
*
41465538 TGGCTCTCATAAGCTTCCCTATTA
1 TGGCTCTCATGAGCTTCCC-ATTA
41465562 ATGGATTTTC
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
49 3 0.04
50 62 0.90
51 4 0.06
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.39
Consensus pattern (50 bp):
TGGCTCTCATGAGCTTCCCATTATTTGGCTCTCACAAGCTTCTTGATAAT
Found at i:41468073 original size:20 final size:20
Alignment explanation
Indices: 41468048--41468090 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41468038 GGGAGCAGTT
* *
41468048 TTTCAATCGATTTAAAAATG
1 TTTCAATCGAGTTAAAAAAG
*
41468068 TTTCAATTGAGTTAAAAAAG
1 TTTCAATCGAGTTAAAAAAG
41468088 TTT
1 TTT
41468091 AAACTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (20 bp):
TTTCAATCGAGTTAAAAAAG
Found at i:41475842 original size:13 final size:13
Alignment explanation
Indices: 41475820--41475851 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41475810 GTGAACTTCA
*
41475820 TGTAGTAATATCC
1 TGTAGCAATATCC
41475833 TGTAGCAATATCC
1 TGTAGCAATATCC
41475846 TGTAGC
1 TGTAGC
41475852 TTAGGTCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (13 bp):
TGTAGCAATATCC
Found at i:41477132 original size:29 final size:31
Alignment explanation
Indices: 41477067--41477146 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
41477057 ATCTCAAAAC
* *
41477067 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTTTGATTTAATGTGCAATTG
* *
41477098 TATACATGAACTTTGATTTTA-G-GCAATTT
1 TATACATGAACTTTGATTTAATGTGCAATTG
*
41477127 TATACATGAAAATTTGATTT
1 TATACATG-AACTTTGATTT
41477147 GATCCAATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.33
30 11 0.26
31 18 0.42
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (31 bp):
TATACATGAACTTTGATTTAATGTGCAATTG
Found at i:41477155 original size:30 final size:29
Alignment explanation
Indices: 41477092--41477155 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
41477082 GTTTAATGTG
* * *
41477092 CAATTGTATACATGAACTTTGATTTTAGG
1 CAATTGTATACATGAAATTTGATTTGAGC
* *
41477121 CAATTTTATACATGAAAATTTGATTTGATC
1 CAATTGTATACATG-AAATTTGATTTGAGC
41477151 CAATT
1 CAATT
41477156 CTTGTAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (29 bp):
CAATTGTATACATGAAATTTGATTTGAGC
Found at i:41477364 original size:29 final size:30
Alignment explanation
Indices: 41477292--41477377 Score: 93
Period size: 31 Copynumber: 2.9 Consensus size: 30
41477282 TAAGTAAAAT
* * * *
41477292 TTAAAGTTTCAAGTATACATTTGAACCTCAA
1 TTAAAGTTTCATGTATACAATTGCACC-GAA
* * *
41477323 TTAGAGTTTCATGTGTATAATTGCACCGAA
1 TTAAAGTTTCATGTATACAATTGCACCGAA
41477353 TTAAAG-TTCATGTATACAATTGCAC
1 TTAAAGTTTCATGTATACAATTGCAC
41477378 AATAAATCAA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
29 17 0.38
30 7 0.16
31 21 0.47
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (30 bp):
TTAAAGTTTCATGTATACAATTGCACCGAA
Found at i:41478944 original size:7 final size:7
Alignment explanation
Indices: 41478934--41478994 Score: 54
Period size: 7 Copynumber: 8.6 Consensus size: 7
41478924 AATCTGCATT
41478934 ATTTTAA
1 ATTTTAA
41478941 ATTTTAA
1 ATTTTAA
*
41478948 A-TTTAT
1 ATTTTAA
41478954 ATTATT-A
1 ATT-TTAA
* *
41478961 ATCTATATT
1 AT-TTTA-A
41478970 ATTTTAA
1 ATTTTAA
41478977 ATTTTAA
1 ATTTTAA
41478984 ATTTTAA
1 ATTTTAA
41478991 ATTT
1 ATTT
41478995 ATGTTATACC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
6 5 0.12
7 30 0.70
8 6 0.14
9 2 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTTAA
Found at i:41479112 original size:17 final size:18
Alignment explanation
Indices: 41479090--41479126 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
41479080 TTTCCTCAAA
*
41479090 TCAAACCCTC-CATCCAT
1 TCAAACCCTCAAATCCAT
41479107 TCAAACCCTCAAATCCAT
1 TCAAACCCTCAAATCCAT
41479125 TC
1 TC
41479127 TTCTTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.24
Consensus pattern (18 bp):
TCAAACCCTCAAATCCAT
Found at i:41479170 original size:37 final size:37
Alignment explanation
Indices: 41479120--41479205 Score: 156
Period size: 37 Copynumber: 2.3 Consensus size: 37
41479110 AACCCTCAAA
41479120 TCCATTCTTCTTCTTCAAAAA-TCTCTAAATTAAACCC
1 TCCATTCTTCTTCTTCAAAAATTC-CTAAATTAAACCC
41479157 TCCATTCTTCTTCTTCAAAAATTCCTAAATTAAACCC
1 TCCATTCTTCTTCTTCAAAAATTCCTAAATTAAACCC
41479194 TCCATTCTTCTT
1 TCCATTCTTCTT
41479206 TTTGTTCATT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
37 46 0.96
38 2 0.04
ACGTcount: A:0.29, C:0.30, G:0.00, T:0.41
Consensus pattern (37 bp):
TCCATTCTTCTTCTTCAAAAATTCCTAAATTAAACCC
Found at i:41480322 original size:29 final size:28
Alignment explanation
Indices: 41480270--41480324 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
41480260 AAAAATTCAG
*
41480270 AAAAACTATAAAAAAATTTGAAATATGT
1 AAAAACTATAAAAAAATTTAAAATATGT
* *
41480298 AAAAAGTATACAAAAATTTCAAAATAT
1 AAAAACTATAAAAAAATTT-AAAATAT
41480325 ATTAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (28 bp):
AAAAACTATAAAAAAATTTAAAATATGT
Found at i:41481940 original size:27 final size:28
Alignment explanation
Indices: 41481905--41481964 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
41481895 GAAGGTTCTA
*
41481905 GTTTAGCCTT-AAAAACTACGAGGAAAT
1 GTTTCGCCTTAAAAAACTACGAGGAAAT
*
41481932 GTTTCGCCTTAAAAAACTATGAGGAAAT
1 GTTTCGCCTTAAAAAACTACGAGGAAAT
41481960 GTTTC
1 GTTTC
41481965 ATCTAAGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (28 bp):
GTTTCGCCTTAAAAAACTACGAGGAAAT
Found at i:41482262 original size:3 final size:3
Alignment explanation
Indices: 41482254--41482285 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41482244 AGTTATATGA
41482254 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
41482286 CTGTTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:41501339 original size:44 final size:44
Alignment explanation
Indices: 41501218--41501575 Score: 164
Period size: 44 Copynumber: 8.0 Consensus size: 44
41501208 TAAATCTACC
*
41501218 ATAGCAAGTCTTATTTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
1 ATAGCAAGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTGAAG
** * *
41501263 ATAGCAAACCTTATCTTCCTGAAGTTGCAGTGGAGCA-AGTTTAAG
1 ATAGCAAGTCTTATC-TCCTGAAGTTGCAGTGGAGCAGA-CTGAAG
* * * *
41501308 ATA-CAAGTCTTATCTCCTTGAAGTTGTAGTGGAACAGATTAAAG
1 ATAGCAAGTCTTATCTCC-TGAAGTTGCAGTGGAGCAGACTGAAG
* * * * *
41501352 CTATAAATACCAGATCTTATCTCTCTGAAGTTGTAGTAGAGCAGA-T---C
1 --AT--A-GCAAG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTGAAG
* * * * *
41501399 ATATCAA-ACTTTATCTTCTTGAAGTTGCAGTGGAGCAGAATGAGG
1 ATAGCAAGTC-TTATC-TCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * * * *
41501444 CTA-CAAATCTTATCTCCCTGAAGTGGTAGTGGAGCAAATTGAAG
1 ATAGCAAGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * *
41501488 ACA-CTAA-TCTTATCTCCCTGAAGATGCGGTGGAGCAGATTGAAG
1 ATAGC-AAGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * * *
41501532 ATA-CTAA-TCTTATCTCCCTAAAATTACAGTGGAGTAGATTGAAG
1 ATAGC-AAGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTGAAG
41501576 CGACAAATTC
Statistics
Matches: 249, Mismatches: 43, Indels: 43
0.74 0.13 0.13
Matches are distributed among these distances:
40 1 0.00
41 23 0.09
42 5 0.02
43 5 0.02
44 132 0.53
45 47 0.19
46 3 0.01
48 1 0.00
50 4 0.02
51 27 0.11
52 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (44 bp):
ATAGCAAGTCTTATCTCCTGAAGTTGCAGTGGAGCAGACTGAAG
Found at i:41501563 original size:88 final size:88
Alignment explanation
Indices: 41501409--41501575 Score: 199
Period size: 88 Copynumber: 1.9 Consensus size: 88
41501399 ATATCAAACT
* * * * * * * **
41501409 TTATCTTCTTGAAGTTGCAGTGGAGCAGAATGAGGCTACAAATCTTATCTCCCTGAAGTGGTAGT
1 TTATCTCCCTGAAGATGCAGTGGAGCAGAATGAAGATACAAATCTTATCTCCCTAAAATGACAGT
41501474 GGAGCAAATTGAAGACACTAATC
66 GGAGCAAATTGAAGACACTAATC
* * * *
41501497 TTATCTCCCTGAAGATGCGGTGGAGCAGATTGAAGATACTAATCTTATCTCCCTAAAATTACAGT
1 TTATCTCCCTGAAGATGCAGTGGAGCAGAATGAAGATACAAATCTTATCTCCCTAAAATGACAGT
* *
41501562 GGAGTAGATTGAAG
66 GGAGCAAATTGAAG
41501576 CGACAAATTC
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
88 64 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (88 bp):
TTATCTCCCTGAAGATGCAGTGGAGCAGAATGAAGATACAAATCTTATCTCCCTAAAATGACAGT
GGAGCAAATTGAAGACACTAATC
Found at i:41504763 original size:31 final size:31
Alignment explanation
Indices: 41504723--41504937 Score: 199
Period size: 31 Copynumber: 7.0 Consensus size: 31
41504713 CTCTATAATA
* *
41504723 TATATTCATATACAAATCAATTTCAATAATG
1 TATAATCATATACAAATCAATTTCAACAATG
* *
41504754 TATAATCATATACAAATTAATTTCAGCAATG
1 TATAATCATATACAAATCAATTTCAACAATG
* * *
41504785 AATAATCATATACGAATCAA-TTCAACAGCT-
1 TATAATCATATACAAATCAATTTCAACA-ATG
* *
41504815 TAT-ATCCTTATACAAATCAATTTCAATAATG
1 TATAAT-CATATACAAATCAATTTCAACAATG
*
41504846 TATAATCATATACAAATTAATTTCAACAATG
1 TATAATCATATACAAATCAATTTCAACAATG
* * * *
41504877 AATAATCATATACGAATGAA-TTCAACAGCT-
1 TATAATCATATACAAATCAATTTCAACA-ATG
* * *
41504907 TAT-ATCCTTATACAAATCAAATTCAATAATG
1 TATAAT-CATATACAAATCAATTTCAACAATG
41504938 AGTAACTATA
Statistics
Matches: 148, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
29 4 0.03
30 42 0.28
31 100 0.68
32 2 0.01
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (31 bp):
TATAATCATATACAAATCAATTTCAACAATG
Found at i:41504991 original size:92 final size:92
Alignment explanation
Indices: 41504731--41504981 Score: 409
Period size: 92 Copynumber: 2.7 Consensus size: 92
41504721 TATATATTCA
41504731 TATACAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATAT
1 TATACAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATAT
41504796 ACGAATCAATTCAACAGCTTATATCCT
66 ACGAATCAATTCAACAGCTTATATCCT
*
41504823 TATACAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAACAATGAATAATCATAT
1 TATACAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATAT
*
41504888 ACGAATGAATTCAACAGCTTATATCCT
66 ACGAATCAATTCAACAGCTTATATCCT
* * *
41504915 TATACAAATCAAATTCAATAATG-AGTAA-CTATAAATAAATTAATTTCAGCAATGAAT-ATCGA
1 TATACAAATCAATTTCAATAATGTA-TAATC-ATATACAAATTAATTTCAGCAATGAATAATC-A
41504977 TATAC
63 TATAC
41504982 CCAACAATTC
Statistics
Matches: 150, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
91 5 0.03
92 145 0.97
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (92 bp):
TATACAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATAT
ACGAATCAATTCAACAGCTTATATCCT
Found at i:41511595 original size:46 final size:45
Alignment explanation
Indices: 41511545--41511703 Score: 131
Period size: 46 Copynumber: 3.4 Consensus size: 45
41511535 TATTAAAAAA
* *
41511545 ATTTTAAAAATATCTCAAGGCATATTTGAAAGCATCTTTGAGAGAG
1 ATTTTAAAAACATCTCAAGG-ATATTTGAAAGCATCCTTGAGAGAG
* * * * *
41511591 ATTTTGAAAATATTTCAAGGGAGATATGAAAGTC-TCCTTGAGAGAG
1 ATTTTAAAAACATCTCAA-GGATATTTGAAAG-CATCCTTGAGAGAG
* * * ** *
41511637 GTTTTGAGAACATCTCAAGGATGATTTGGGAGCACCCTTGAGAGAGG
1 ATTTTAAAAACATCTCAAGGAT-ATTTGAAAGCATCCTTGAGAGA-G
* *
41511684 GTTTTAAAAACATTTCAAGG
1 ATTTTAAAAACATCTCAAGG
41511704 TAGATCTGAT
Statistics
Matches: 91, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
45 4 0.04
46 66 0.73
47 21 0.23
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (45 bp):
ATTTTAAAAACATCTCAAGGATATTTGAAAGCATCCTTGAGAGAG
Found at i:41514034 original size:5 final size:5
Alignment explanation
Indices: 41514024--41514057 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
41514014 AATTGATTGT
41514024 ATATC ATATC ATATC ATATC ATATC ATATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATAT
41514058 GTATGTCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:41514904 original size:65 final size:65
Alignment explanation
Indices: 41514835--41514964 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
41514825 TTAAATTAAA
41514835 AAAAATATTTCTTTTGTTTATTTAATATGAATTCGGGCTGAGTCAAAGTGTAAAAGATATTTTTG
1 AAAAATATTTCTTTTGTTTATTTAATATGAATTCGGGCTGAGTCAAAGTGTAAAAGATATTTTTG
41514900 AAAAATATTTCTTTTGTTTATTTAATATGAATTCGGGCTGAGTCAAAGTGTAAAAGATATTTTTG
1 AAAAATATTTCTTTTGTTTATTTAATATGAATTCGGGCTGAGTCAAAGTGTAAAAGATATTTTTG
41514965 TTATACAGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (65 bp):
AAAAATATTTCTTTTGTTTATTTAATATGAATTCGGGCTGAGTCAAAGTGTAAAAGATATTTTTG
Found at i:41521658 original size:28 final size:26
Alignment explanation
Indices: 41521612--41521663 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
41521602 ATTATAATGA
* *
41521612 AAAATTGACATGTAGTAAAGTATATT
1 AAAAGTGACATGTAGTAAAATATATT
41521638 AAAAGTGACATGTCATGTAAAATATA
1 AAAAGTGACATGT-A-GTAAAATATA
41521664 AAATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 1 0.05
28 9 0.41
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (26 bp):
AAAAGTGACATGTAGTAAAATATATT
Found at i:41528788 original size:24 final size:24
Alignment explanation
Indices: 41528761--41528819 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
41528751 CCCTAAACAC
* **
41528761 AAAAATCCTAAAATTAAAAATATT
1 AAAAACCCTAAAACAAAAAATATT
*
41528785 -AAAACCCTTAAACCAAAAAATATT
1 AAAAACCC-TAAAACAAAAAATATT
41528809 AAAAACCCTAA
1 AAAAACCCTAA
41528820 CCCTGGGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.21
24 16 0.55
25 7 0.24
ACGTcount: A:0.61, C:0.17, G:0.00, T:0.22
Consensus pattern (24 bp):
AAAAACCCTAAAACAAAAAATATT
Found at i:41530903 original size:48 final size:48
Alignment explanation
Indices: 41530849--41530941 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
41530839 GCAGGGTCAC
* * * * *
41530849 TTATTACCTCCCGTAAGTCTCTCTCATGCATCTAGGAGTAGGGAAACT
1 TTATTACCTACCGTAAGCCTCCCCCATGCATCAAGGAGTAGGGAAACT
* *
41530897 TTATTACTTACTGTAAGCCTCCCCCATGCATCAAGGAGTAGGGAA
1 TTATTACCTACCGTAAGCCTCCCCCATGCATCAAGGAGTAGGGAA
41530942 TCCAAGCCCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (48 bp):
TTATTACCTACCGTAAGCCTCCCCCATGCATCAAGGAGTAGGGAAACT
Found at i:41531069 original size:58 final size:59
Alignment explanation
Indices: 41530946--41531069 Score: 137
Period size: 58 Copynumber: 2.1 Consensus size: 59
41530936 AGGGAATCCA
* ** * *
41530946 AGCCCCTCTGTGAATTCTTTGGACTTTCGGCAGAGGTGAGGCATATCTTTGACATTTAG
1 AGCCCCTCTATGAACCCTTTGGACTTTCGGCAAAGGTGAGGCATATCTTTCACATTTAG
* * * *
41531005 -GACCCTCTATGAACCCTTTGGGCTTTCGGCAAAGTTGAGGCATATC-TTCA-ATATTCG
1 AGCCCCTCTATGAACCCTTTGGACTTTCGGCAAAGGTGAGGCATATCTTTCACAT-TTAG
41531062 AGCCCCTC
1 AGCCCCTC
41531070 CGTGAAACCT
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
56 2 0.04
57 6 0.11
58 45 0.85
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (59 bp):
AGCCCCTCTATGAACCCTTTGGACTTTCGGCAAAGGTGAGGCATATCTTTCACATTTAG
Found at i:41534220 original size:10 final size:10
Alignment explanation
Indices: 41534205--41534233 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41534195 GAAATGTTTG
41534205 ATGATATAAT
1 ATGATATAAT
41534215 ATGATATAAT
1 ATGATATAAT
41534225 A-GATATAAT
1 ATGATATAAT
41534234 TTTTTATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (10 bp):
ATGATATAAT
Found at i:41534500 original size:37 final size:37
Alignment explanation
Indices: 41534454--41534568 Score: 153
Period size: 37 Copynumber: 3.1 Consensus size: 37
41534444 TGTTTTTGGT
41534454 TGGACTAGCTTTTCGAAGCAATTGGCGTGTTATCGGG
1 TGGACTAGCTTTTCGAAGCAATTGGCGTGTTATCGGG
* * * * *
41534491 TGGATTAGCTCTTAT-G-AGCATTTGGTGTGTTTTCGGT
1 TGGACTAGCT-TT-TCGAAGCAATTGGCGTGTTATCGGG
41534528 TGGACTAGCTTTTCGAAGCAATTGGCGTGTTATCGGG
1 TGGACTAGCTTTTCGAAGCAATTGGCGTGTTATCGGG
41534565 TGGA
1 TGGA
41534569 TGAGCTCTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
35 1 0.02
36 3 0.05
37 56 0.88
38 3 0.05
39 1 0.02
ACGTcount: A:0.17, C:0.14, G:0.32, T:0.37
Consensus pattern (37 bp):
TGGACTAGCTTTTCGAAGCAATTGGCGTGTTATCGGG
Found at i:41534564 original size:74 final size:74
Alignment explanation
Indices: 41534443--41534599 Score: 287
Period size: 74 Copynumber: 2.1 Consensus size: 74
41534433 CTGTTTTGAC
* *
41534443 GTGTTTTTGGTTGGACTAGCTTTTCGAAGCAATTGGCGTGTTATCGGGTGGATTAGCTCTTATGA
1 GTGTTTTCGGTTGGACTAGCTTTTCGAAGCAATTGGCGTGTTATCGGGTGGATGAGCTCTTATGA
41534508 GCATTTGGT
66 GCATTTGGT
41534517 GTGTTTTCGGTTGGACTAGCTTTTCGAAGCAATTGGCGTGTTATCGGGTGGATGAGCTCTTATGA
1 GTGTTTTCGGTTGGACTAGCTTTTCGAAGCAATTGGCGTGTTATCGGGTGGATGAGCTCTTATGA
*
41534582 GCATTTTGT
66 GCATTTGGT
41534591 GTGTTTTCG
1 GTGTTTTCG
41534600 AATGGATTAC
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 80 1.00
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.41
Consensus pattern (74 bp):
GTGTTTTCGGTTGGACTAGCTTTTCGAAGCAATTGGCGTGTTATCGGGTGGATGAGCTCTTATGA
GCATTTGGT
Found at i:41534606 original size:37 final size:36
Alignment explanation
Indices: 41534470--41534606 Score: 116
Period size: 37 Copynumber: 3.7 Consensus size: 36
41534460 AGCTTTTCGA
* * * *
41534470 AGCAATTGGCGTGTTATCGGGTGGATTAGCTCTTATG
1 AGCATTTGGTGTGTTTTCGGATGGA-TAGCTCTTATG
*
41534507 AGCATTTGGTGTGTTTTCGGTTGGACTAGCT-TT-TCG
1 AGCATTTGGTGTGTTTTCGGATGGA-TAGCTCTTAT-G
* * * *
41534543 AAGCAATTGGCGTGTTATCGGGTGGATGAGCTCTTATG
1 -AGCATTTGGTGTGTTTTCGGATGGAT-AGCTCTTATG
* *
41534581 AGCATTTTGTGTGTTTTCGAATGGAT
1 AGCATTTGGTGTGTTTTCGGATGGAT
41534607 TACTGTACTC
Statistics
Matches: 80, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
35 1 0.01
36 4 0.05
37 71 0.89
38 3 0.04
39 1 0.01
ACGTcount: A:0.18, C:0.12, G:0.31, T:0.39
Consensus pattern (36 bp):
AGCATTTGGTGTGTTTTCGGATGGATAGCTCTTATG
Found at i:41535817 original size:21 final size:20
Alignment explanation
Indices: 41535777--41535818 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
41535767 GTCTCGAATT
*
41535777 GCCTCAAAGCTATTTTTAGG
1 GCCTCAAAGCTATATTTAGG
*
41535797 GCCTCAAAGGCTCTATTTAGG
1 GCCTCAAA-GCTATATTTAGG
41535818 G
1 G
41535819 ACGATATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (20 bp):
GCCTCAAAGCTATATTTAGG
Found at i:41538452 original size:13 final size:13
Alignment explanation
Indices: 41538434--41538468 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
41538424 CGTGGCAAAT
*
41538434 TTGGAGGATTTGC
1 TTGGAGGACTTGC
41538447 TTGGAGGACTTGC
1 TTGGAGGACTTGC
*
41538460 TCGGAGGAC
1 TTGGAGGAC
41538469 ATGTCACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.40, T:0.29
Consensus pattern (13 bp):
TTGGAGGACTTGC
Found at i:41542763 original size:186 final size:185
Alignment explanation
Indices: 41542441--41543046 Score: 875
Period size: 186 Copynumber: 3.3 Consensus size: 185
41542431 TTTACCAAAA
* * **
41542441 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTT-TTCTTCAAAATACATGGCCGGCTCA
1 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTCA
*
41542505 TTTCATCTACAATAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTCTGTAAATCC
66 TTTCATCTACAATAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTTTGTAAA-CC
* *
41542570 GCACCACACTTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTGTCGGTTGCCAT
130 ACACCACACTTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTGTCGGCTGCCAT
* * *
41542626 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTTAAAACATATGTTTGGCTCA
1 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTCA
*
41542691 TTTCATCTACAAGAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTTTGTAAACGC
66 TTTCATCTACAATAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTTTGTAAAC-C
* *
41542756 ACACCACACCTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTATCGGCTGCCAT
130 ACACCACACTTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTGTCGGCTGCCAT
* * *
41542812 TTTTTCTCTTTTATTTTCTCTCTTGCCAAACACC-TTTTTCTTCTTCAAAACACATGGTTGGCGC
1 TTTTT-TCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTC
** * * *
41542876 ATTTCATCTACAATAATTTCCACCAACATGATTATAATCATGCTTTTATGCAATTTTTGTAAACC
65 ATTTCATCTACAATAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTTTGTAAA-C
* * * * *
41542941 CACACCACACTTTCAACTTAAAACCA---TTTTTTCCCCT-CGCTGTCAGCTGCCA-
129 CACACCACACTTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTGTCGGCTGCCAT
* *
41542993 TTTTTTCTCTCATTTTCTCTCTTTCCAAACACTATTTTTCTTCTTCAAAACACA
1 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACA
41543047 ACATCTAGTT
Statistics
Matches: 380, Mismatches: 36, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
180 24 0.06
181 25 0.07
182 12 0.03
183 10 0.03
185 39 0.10
186 243 0.64
187 27 0.07
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (185 bp):
TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTCA
TTTCATCTACAATAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTTTGTAAACCA
CACCACACTTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTGTCGGCTGCCAT
Found at i:41542864 original size:20 final size:22
Alignment explanation
Indices: 41542825--41542864 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
41542815 TTCTCTTTTA
*
41542825 TTTTCTCTCTTGCCAAACACCT
1 TTTTCTCTCTTGCAAAACACCT
41542847 TTTTCT-TCTT-CAAAACAC
1 TTTTCTCTCTTGCAAAACAC
41542865 ATGGTTGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.23, C:0.33, G:0.03, T:0.42
Consensus pattern (22 bp):
TTTTCTCTCTTGCAAAACACCT
Found at i:41543389 original size:14 final size:15
Alignment explanation
Indices: 41543362--41543390 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41543352 ACAGTTAGAG
41543362 GGGAAGAGAGAAAGA
1 GGGAAGAGAGAAAGA
41543377 GGGAAGA-AGAAAGA
1 GGGAAGAGAGAAAGA
41543391 AAATGGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (15 bp):
GGGAAGAGAGAAAGA
Found at i:41549755 original size:53 final size:51
Alignment explanation
Indices: 41549688--41549837 Score: 162
Period size: 50 Copynumber: 2.9 Consensus size: 51
41549678 TGCACTAAAG
* *
41549688 GACCATATCATGTAAGATCGTAACTGGGGGGTTATGACATTATATGGAAAGAA
1 GACCATATCATGTAAGATCGTAACTGGTGGGTTAT-ACATCATATGGAAA-AA
* *
41549741 GACCATATTC-TGTAAGACCATAACTGGTGGGTTATATCATCATAT--AAAAA
1 GACCATA-TCATGTAAGATCGTAACTGGTGGGTTATA-CATCATATGGAAAAA
* * * *
41549791 AACCATATCGTGTAAGATTGTAACTGGTGGGTTTTAACATCATATGG
1 GACCATATCATGTAAGATCGTAACTGGTGGGTTAT-ACATCATATGG
41549838 GGAAGTTTGA
Statistics
Matches: 82, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
49 2 0.02
50 37 0.45
51 4 0.05
52 1 0.01
53 36 0.44
54 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (51 bp):
GACCATATCATGTAAGATCGTAACTGGTGGGTTATACATCATATGGAAAAA
Found at i:41550056 original size:60 final size:60
Alignment explanation
Indices: 41549963--41550299 Score: 354
Period size: 60 Copynumber: 5.6 Consensus size: 60
41549953 AAAGGACAGT
* * *
41549963 CTTTGTGGCAAAACTCTGGACA-AGAAAGCCTTTGTGGAAAGTATTGAATGTAAAGGATGC
1 CTTTGTGGCAAAACTCTAGACAGA-AAAGCCTTTGTGGCAAGTACTGAATGTAAAGGATGC
* * * * **
41550023 ATTTGTGGCAAAACTCTACATAGAAAAGTCTTTGTGGTGAGTGA-TGAATGTAAAGGATGC
1 CTTTGTGGCAAAACTCTAGACAGAAAAGCCTTTGTGGCAAGT-ACTGAATGTAAAGGATGC
* * * * * *
41550083 CTTTGTGGAAAAAATCTTGATAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAATGATGC
1 CTTTGTGGCAAAACTCTAGACAGAAAAGCCTTTGTGGCAAGTACTGAATGTAAAGGATGC
* * ** *
41550143 CTTCGTGGCAAAACTCTGGACAGAAAAGCCTTTGTGGCAAGTGTTGAATGTAAATGATGC
1 CTTTGTGGCAAAACTCTAGACAGAAAAGCCTTTGTGGCAAGTACTGAATGTAAAGGATGC
* * * ** * *
41550203 CTTTGTAGCCAAACTCTAGACAGAAAAGCCTTTTTGGTGAGTACTAAATGTAAAAGATGC
1 CTTTGTGGCAAAACTCTAGACAGAAAAGCCTTTGTGGCAAGTACTGAATGTAAAGGATGC
* * * **
41550263 TTTTGTGGCAAACCTCTAGAAAGTTAAGCCTTTGTGG
1 CTTTGTGGCAAAACTCTAGACAGAAAAGCCTTTGTGG
41550300 AAACCTTTGT
Statistics
Matches: 230, Mismatches: 44, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
59 1 0.00
60 227 0.99
61 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (60 bp):
CTTTGTGGCAAAACTCTAGACAGAAAAGCCTTTGTGGCAAGTACTGAATGTAAAGGATGC
Found at i:41550207 original size:31 final size:31
Alignment explanation
Indices: 41550110--41550208 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
41550100 TGATAGGAAA
*
41550110 GCCTTTGTGGCAAGTACTGAATGTAAATGAT
1 GCCTTTGTGGCAAGTATTGAATGTAAATGAT
* *
41550141 GCCTTCGTGGCAA-AACTCTGGACA-G-AAA--A-
1 GCCTTTGTGGCAAGTA-T-T-GA-ATGTAAATGAT
*
41550170 GCCTTTGTGGCAAGTGTTGAATGTAAATGAT
1 GCCTTTGTGGCAAGTATTGAATGTAAATGAT
41550201 GCCTTTGT
1 GCCTTTGT
41550209 AGCCAAACTC
Statistics
Matches: 52, Mismatches: 6, Indels: 20
0.67 0.08 0.26
Matches are distributed among these distances:
26 1 0.02
27 3 0.06
28 4 0.08
29 13 0.25
30 3 0.06
31 20 0.38
32 4 0.08
33 3 0.06
34 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (31 bp):
GCCTTTGTGGCAAGTATTGAATGTAAATGAT
Found at i:41550294 original size:180 final size:180
Alignment explanation
Indices: 41549967--41550299 Score: 454
Period size: 180 Copynumber: 1.9 Consensus size: 180
41549957 GACAGTCTTT
*
41549967 GTGGCAAAACTCTGGACAAGAAAGCCTTTGTGGAAAGTATTGAATGTAAAGGATGCATTTGTGGC
1 GTGGCAAAACTCTGGACAAGAAAGCCTTTGTGGAAAGTATTGAATGTAAAGGATGCATTTGTAGC
* * * *
41550032 AAAACTCTACATAGAAAAGTCTTTGTGGTGAGTGATGAATGTAAAGGATGCCTTTGTGGAAAAAA
66 AAAACTCTACACAGAAAAGCCTTTGTGGTGAGTGATAAATGTAAAAGATGCCTTTGTGGAAAAAA
* *
41550097 TCTTGATAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAATGATGCCTTC
131 TCTAGAAAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAATGATGCCTTC
* * * *
41550147 GTGGCAAAACTCTGGAC-AGAAAAGCCTTTGTGGCAAGTGTTGAATGTAAATGATGCCTTTGTAG
1 GTGGCAAAACTCTGGACAAG-AAAGCCTTTGTGGAAAGTATTGAATGTAAAGGATGCATTTGTAG
* * * * *
41550211 CCAAACTCTAGACAGAAAAGCCTTTTTGGTGAGT-ACTAAATGTAAAAGATGCTTTTGTGGCAAA
65 CAAAACTCTACACAGAAAAGCCTTTGTGGTGAGTGA-TAAATGTAAAAGATGCCTTTGTGGAAAA
** **
41550275 CCTCTAGAAAGTTAAGCCTTTGTGG
129 AATCTAGAAAGGAAAGCCTTTGTGG
41550300 AAACCTTTGT
Statistics
Matches: 131, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
179 3 0.02
180 128 0.98
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (180 bp):
GTGGCAAAACTCTGGACAAGAAAGCCTTTGTGGAAAGTATTGAATGTAAAGGATGCATTTGTAGC
AAAACTCTACACAGAAAAGCCTTTGTGGTGAGTGATAAATGTAAAAGATGCCTTTGTGGAAAAAA
TCTAGAAAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAATGATGCCTTC
Found at i:41552340 original size:147 final size:146
Alignment explanation
Indices: 41552011--41552399 Score: 399
Period size: 146 Copynumber: 2.7 Consensus size: 146
41552001 ATGAAATTTT
* * * * * * * * * *
41552011 CATT-AGATTCCACAATCCGGTATTGCTAGGTGCAGACCATGATGTGCGAAGCTCCGGGCCTTAG
1 CATTAAGATACCACCATACGGTATTGCTGGGTACAAACCATAATATGTGAAGCTCTGGGCCTTAG
* * ** * ** * *
41552075 GAGGGGTCATTGCGGTGTTTGAGCATCAATATTAGAAATGACGAATGGAGGTATGGGCAGATGAA
66 GAGGGGACATTGCGGTGTTCGAGCATCAAGGTTAGAAATGACAAACAGAGGTATGAGCAAATGAA
*
41552140 TAGGGACATGAAATTC
131 TAGGGACATGAAATGC
*
41552156 CATTAAGATACCACCATACGGTATTGCTGGGTGCAAACCATAATATGTGAAGCTCTGGGCCTTAG
1 CATTAAGATACCACCATACGGTATTGCTGGGTACAAACCATAATATGTGAAGCTCTGGGCCTTAG
* * * *
41552221 GGGGGGACATTGCGATGTTCGAGTATCAAGGTTAGAAATGGCAAAACAGAGGTATGAGCAAATGA
66 GAGGGGACATTGCGGTGTTCGAGCATCAAGGTTAGAAATGAC-AAACAGAGGTATGAGCAAATGA
*
41552286 ATAGGGACATGGAATGC
130 ATAGGGACATGAAATGC
** * * ** * * *
41552303 CATTAAGATACTGCCATACGGTATTGTTTGGTACAAACTGTGATGTGTGAAGCT-TCGGGCATT-
1 CATTAAGATACCACCATACGGTATTGCTGGGTACAAACCATAATATGTGAAGCTCT-GGGCCTTA
* *
41552366 -GTGGGGACATTACGGTGTTCGAGCATCAAGGTTA
65 GGAGGGGACATTGCGGTGTTCGAGCATCAAGGTTA
41552400 AATGTGAAAT
Statistics
Matches: 203, Mismatches: 38, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
145 34 0.17
146 86 0.42
147 83 0.41
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (146 bp):
CATTAAGATACCACCATACGGTATTGCTGGGTACAAACCATAATATGTGAAGCTCTGGGCCTTAG
GAGGGGACATTGCGGTGTTCGAGCATCAAGGTTAGAAATGACAAACAGAGGTATGAGCAAATGAA
TAGGGACATGAAATGC
Found at i:41552632 original size:27 final size:28
Alignment explanation
Indices: 41552593--41552670 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 28
41552583 AAACTAATAG
**
41552593 AGTCCACTGGGACAGTAAACATGGGG-T
1 AGTCCACCAGGACAGTAAACATGGGGAT
41552620 AGTCCACCAGGACA-TAAA-ATGTGGGAT
1 AGTCCACCAGGACAGTAAACATG-GGGAT
** * *
41552647 AGTCTTCCAGGATAGTGAACATGG
1 AGTCCACCAGGACAGTAAACATGG
41552671 AGAATAATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
25 3 0.07
26 7 0.17
27 24 0.59
28 4 0.10
29 3 0.07
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (28 bp):
AGTCCACCAGGACAGTAAACATGGGGAT
Found at i:41556607 original size:3 final size:3
Alignment explanation
Indices: 41556599--41556650 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
41556589 TAAACTATTC
41556599 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41556647 TAT T
1 TAT T
41556651 TACATAGTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41557228 original size:2 final size:2
Alignment explanation
Indices: 41557223--41557251 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41557213 AAGAAAAAAC
41557223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41557252 CAGAAATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.