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 102 of 202
Found at i:31119197 original size:26 final size:26
Alignment explanation
Indices: 31119132--31119197 Score: 100
Period size: 25 Copynumber: 2.6 Consensus size: 26
31119122 TCTTTTTTTA
*
31119132 TTGTATTTT-TAACAATAAGTTGGGTT
1 TTGT-TTTTGTAATAATAAGTTGGGTT
31119158 TTG-TTTTGTAATAATAAGTTGGGTT
1 TTGTTTTTGTAATAATAAGTTGGGTT
31119183 TTGTTTTTGTAATAA
1 TTGTTTTTGTAATAA
31119198 GGCCTTTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
24 4 0.11
25 19 0.51
26 14 0.38
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.53
Consensus pattern (26 bp):
TTGTTTTTGTAATAATAAGTTGGGTT
Found at i:31122071 original size:50 final size:50
Alignment explanation
Indices: 31121946--31122140 Score: 178
Period size: 50 Copynumber: 3.9 Consensus size: 50
31121936 GATAATAACA
* * ** * * *
31121946 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAACGCCATGTCCCAAACATGGCCTTACATGGGACCTCTCATAT-CGG
* * * * **
31121995 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAAACATGGCCTTACATGGGACCTCTCATATCGG
* * ** *
31122045 TGCCCACGCCATGTCTCAAACATGGCCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAAACATGGCCTTACATGGGACCTCTCATATCGG
* * *
31122095 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATA
1 TGCCAACGCCATGTCCCAAACATGGCCTTACATGGGACCTCTCATA
31122141 ATCTCAATGA
Statistics
Matches: 115, Mismatches: 29, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
48 1 0.01
49 37 0.32
50 77 0.67
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAAACATGGCCTTACATGGGACCTCTCATATCGG
Found at i:31123969 original size:29 final size:29
Alignment explanation
Indices: 31123936--31123993 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
31123926 TATGCATACT
31123936 AAGTAAGAACAATCCATATCTTTAACTAA
1 AAGTAAGAACAATCCATATCTTTAACTAA
31123965 AAGTAAGAACAATCCATATCTTTAACTAA
1 AAGTAAGAACAATCCATATCTTTAACTAA
31123994 TTATCAAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (29 bp):
AAGTAAGAACAATCCATATCTTTAACTAA
Found at i:31124285 original size:22 final size:22
Alignment explanation
Indices: 31124248--31124647 Score: 408
Period size: 22 Copynumber: 18.2 Consensus size: 22
31124238 AGCAATTATC
**
31124248 CAACATTCAGACAACATTTAAT
1 CAACATTTGGACAACATTTAAT
* *
31124270 TAACATTTGGATAACATTTAAT
1 CAACATTTGGACAACATTTAAT
* * * *
31124292 CAACAATTGGACAGCAATCAAT
1 CAACATTTGGACAACATTTAAT
* * *
31124314 CAAAATTTTGA-AAGAATTTAAT
1 CAACATTTGGACAA-CATTTAAT
* * *
31124336 CAAGAATTGGACAACATTAAAT
1 CAACATTTGGACAACATTTAAT
31124358 CAACATTTGGACAACATTTAAT
1 CAACATTTGGACAACATTTAAT
* * *
31124380 CAACAATTAGACAACATTCAAT
1 CAACATTTGGACAACATTTAAT
* *
31124402 CAATATTTGGACAGCATTTAAT
1 CAACATTTGGACAACATTTAAT
* * *
31124424 CAATAATTGGACAACATTAAAT
1 CAACATTTGGACAACATTTAAT
*
31124446 CAACATTTGGACAGCATTTAAT
1 CAACATTTGGACAACATTTAAT
* *
31124468 CAACAATTGGACAACATTAAAT
1 CAACATTTGGACAACATTTAAT
*
31124490 CAACATTTGGACAGCATTT-AT
1 CAACATTTGGACAACATTTAAT
* * *
31124511 CAACAATTGGGCAACATTCAAT
1 CAACATTTGGACAACATTTAAT
* **
31124533 CAATATTTGGATGACATTTAAT
1 CAACATTTGGACAACATTTAAT
* *
31124555 CAACAGTTGGACAACATTAAAT
1 CAACATTTGGACAACATTTAAT
* *
31124577 CAACATTTGGAGAGCATTTAAT
1 CAACATTTGGACAACATTTAAT
* *
31124599 CAACAATTGGACAACATTCAAT
1 CAACATTTGGACAACATTTAAT
* * *
31124621 CAATATTTGGATAGCATTTAAT
1 CAACATTTGGACAACATTTAAT
31124643 CAACA
1 CAACA
31124648 AATTTTTACT
Statistics
Matches: 300, Mismatches: 75, Indels: 6
0.79 0.20 0.02
Matches are distributed among these distances:
21 18 0.06
22 280 0.93
23 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (22 bp):
CAACATTTGGACAACATTTAAT
Found at i:31124296 original size:44 final size:44
Alignment explanation
Indices: 31124257--31124648 Score: 527
Period size: 44 Copynumber: 8.9 Consensus size: 44
31124247 CCAACATTCA
* * * *
31124257 GACAACATTTAATTAACATTTGGATAACATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* * * * * * * *
31124301 GACAGCAATCAATCAAAATTTTGAAAGAATTTAATCAAGAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* *
31124345 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTA
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* * *
31124389 GACAACATTCAATCAATATTTGGACAGCATTTAATCAATAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
31124433 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
31124477 GACAACATTAAATCAACATTTGGACAGCATTT-ATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* * * * *
31124520 GGCAACATTCAATCAATATTTGGA-TGACATTTAATCAACAGTTG
1 GACAACATTAAATCAACATTTGGACAG-CATTTAATCAACAATTG
*
31124564 GACAACATTAAATCAACATTTGGAGAGCATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* * *
31124608 GACAACATTCAATCAATATTTGGATAGCATTTAATCAACAA
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAA
31124649 ATTTTTACTT
Statistics
Matches: 304, Mismatches: 41, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
42 1 0.00
43 37 0.12
44 265 0.87
45 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.29
Consensus pattern (44 bp):
GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
Found at i:31125559 original size:43 final size:43
Alignment explanation
Indices: 31125474--31125590 Score: 182
Period size: 43 Copynumber: 2.7 Consensus size: 43
31125464 AAAACGATGT
*
31125474 CAATGTCTCAGACAGGGTCTTACACGT-AATCATATACGACGC
1 CAATGTCTCAGACATGGTCTTACACGTAAATCATATACGACGC
* * *
31125516 CAATGTCCCAAACATGGTCTTACATGTAAATCATATACGACGC
1 CAATGTCTCAGACATGGTCTTACACGTAAATCATATACGACGC
*
31125559 CAATATCTCAGACATGGTCTTACACGTAAATC
1 CAATGTCTCAGACATGGTCTTACACGTAAATC
31125591 TCAAATCGGG
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 23 0.35
43 43 0.65
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (43 bp):
CAATGTCTCAGACATGGTCTTACACGTAAATCATATACGACGC
Found at i:31127561 original size:42 final size:42
Alignment explanation
Indices: 31127513--31127598 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
31127503 TGTTATCCTA
* * *
31127513 GAAAAAATAATTTAAAAGGAGAAGAAGATAATCTTGGGTTGTT
1 GAAAAAATAATTTAAAA-AAGAAGAAGATAAACTTGCGTTGTT
* *
31127556 GAAAAAATAATTTAAAAAAGGAGAAGCTAAACTTGCGTTGTT
1 GAAAAAATAATTTAAAAAAGAAGAAGATAAACTTGCGTTGTT
31127598 G
1 G
31127599 GATTTACCCT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 21 0.55
43 17 0.45
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.27
Consensus pattern (42 bp):
GAAAAAATAATTTAAAAAAGAAGAAGATAAACTTGCGTTGTT
Found at i:31128804 original size:15 final size:15
Alignment explanation
Indices: 31128780--31128811 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31128770 CTTAATTTCA
*
31128780 TTAGTTTAATTTAAC
1 TTAGTCTAATTTAAC
31128795 TTAGTCTAATTTAAC
1 TTAGTCTAATTTAAC
31128810 TT
1 TT
31128812 CTACAAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (15 bp):
TTAGTCTAATTTAAC
Found at i:31130573 original size:29 final size:30
Alignment explanation
Indices: 31130526--31130592 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
31130516 AAGCCATTCT
31130526 TTTTCATAGTTAGATGGTCGTCAACATCCC
1 TTTTCATAGTTAGATGGTCGTCAACATCCC
* * *
31130556 TTTTCATTGTT-GATGGTCGTCACCATCTC
1 TTTTCATAGTTAGATGGTCGTCAACATCCC
31130585 TTTTCATA
1 TTTTCATA
31130593 ATCAATAGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 23 0.70
30 10 0.30
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.43
Consensus pattern (30 bp):
TTTTCATAGTTAGATGGTCGTCAACATCCC
Found at i:31130616 original size:29 final size:29
Alignment explanation
Indices: 31130584--31130649 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
31130574 GTCACCATCT
31130584 CTTTTCATAATCAATAGCCGAACCTATCC
1 CTTTTCATAATCAATAGCCGAACCTATCC
** * * **
31130613 CTTTTCGCATTCGATAGCCGAGGCTATCC
1 CTTTTCATAATCAATAGCCGAACCTATCC
31130642 CTTTTCAT
1 CTTTTCAT
31130650 TCATCGATGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (29 bp):
CTTTTCATAATCAATAGCCGAACCTATCC
Found at i:31138334 original size:32 final size:32
Alignment explanation
Indices: 31138298--31138362 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
31138288 CTATGTCACT
*
31138298 TGGCCATGTGTCACAGAC-GATTGAGACATACG
1 TGGCCATGTGTCACAGACAG-TTGAGACACACG
*
31138330 TGGCCGTGTGTCACAGACAGTTGAGACACACG
1 TGGCCATGTGTCACAGACAGTTGAGACACACG
31138362 T
1 T
31138363 CCATGTCTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (32 bp):
TGGCCATGTGTCACAGACAGTTGAGACACACG
Found at i:31139406 original size:30 final size:29
Alignment explanation
Indices: 31139372--31139619 Score: 143
Period size: 30 Copynumber: 8.4 Consensus size: 29
31139362 TAACCAAAGT
*
31139372 TATCCCTTTTCATAGTTTGACAGTCGAAGC
1 TATCCCTTTTCATAGTTTGATAGTCGAA-C
* * * *
31139402 TATCCCTTTTAATAATTTGATGGTCGTTAC
1 TATCCCTTTTCATAGTTTGATAGTCG-AAC
* * * *
31139432 CAT-CCTTTTCCATTGTTTGA-AGGCCGTCAC
1 TATCCCTTTT-CATAGTTTGATA-GTCG-AAC
* *
31139462 CATCCCTTTTCATAGTTTGATGGTC-ATTAC
1 TATCCCTTTTCATAGTTTGATAGTCGA--AC
* *
31139492 CATCCCTTTTCATAGTTTGATGGTC-ATTAC
1 TATCCCTTTTCATAGTTTGATAGTCGA--AC
* * * * *
31139522 CATCCCTTTTCATA-ATCGATAGCCAAAGC
1 TATCCCTTTTCATAGTTTGATAGTCGAA-C
31139551 TATCCCTTTTCATA-TTTGATAG-CTGAAGC
1 TATCCCTTTTCATAGTTTGATAGTC-GAA-C
*
31139580 TATCCCTTTTCATA-TTTGATAGTTGAAGC
1 TATCCCTTTTCATAGTTTGATAGTCGAA-C
*
31139609 TATCCTTTTTC
1 TATCCCTTTTC
31139620 GTATTCAATA
Statistics
Matches: 181, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 73 0.40
30 99 0.55
31 7 0.04
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (29 bp):
TATCCCTTTTCATAGTTTGATAGTCGAAC
Found at i:31139450 original size:60 final size:60
Alignment explanation
Indices: 31139373--31139537 Score: 174
Period size: 60 Copynumber: 2.8 Consensus size: 60
31139363 AACCAAAGTT
* * *
31139373 ATCCCTTTTCATAGTTTGACA-GTCG-AAGCTATCCCTTTTAATAATTTGATGGTCGTTACC
1 ATCCCTTTTCATAGTTTGA-AGGCCGTAA-CCATCCCTTTTAATAATTTGATGGTCATTACC
* * * *
31139433 AT-CCTTTTCCATTGTTTGAAGGCCGTCACCATCCCTTTTCATAGTTTGATGGTCATTACC
1 ATCCCTTTT-CATAGTTTGAAGGCCGTAACCATCCCTTTTAATAATTTGATGGTCATTACC
* * * * *
31139493 ATCCCTTTTCATAGTTTGATGGTCATTACCATCCCTTTTCATAAT
1 ATCCCTTTTCATAGTTTGAAGGCCGTAACCATCCCTTTTAATAAT
31139538 CGATAGCCAA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
59 7 0.08
60 74 0.84
61 7 0.08
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (60 bp):
ATCCCTTTTCATAGTTTGAAGGCCGTAACCATCCCTTTTAATAATTTGATGGTCATTACC
Found at i:31139571 original size:29 final size:29
Alignment explanation
Indices: 31139523--31139650 Score: 148
Period size: 29 Copynumber: 4.4 Consensus size: 29
31139513 GGTCATTACC
*
31139523 ATCCCTTTTCATAATCGATAGCCAAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
* **
31139552 ATCCCTTTTCATATTTGATAGCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
* ***
31139581 ATCCCTTTTCATATTTGATAGTTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
* * * *
31139610 ATCCTTTTTCGTATTCAATAACCAAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
31139639 ATCCCTTTTCAT
1 ATCCCTTTTCAT
31139651 TCATCGATGA
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (29 bp):
ATCCCTTTTCATATTCGATAGCCAAAGCT
Found at i:31143042 original size:86 final size:87
Alignment explanation
Indices: 31142836--31143081 Score: 352
Period size: 86 Copynumber: 2.8 Consensus size: 87
31142826 CCCTCAGATA
* *
31142836 ATGAAAAGGGATAGCTTC-AGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAGTTTGAAA
1 ATGAAAAGGGATAGCTTCGA-CTATCGATTATGAAAAGGGATGGTGACGACCATCGACTATGAAA
* ** * *
31142900 AGGTATAGCTTCGGCTATCAAAT
65 AGGGATAGCGACGACCATCAAAT
* * *
31142923 ATGAAAAGGGATAGCTTCGACTATTGATTATGAAAATGGATGGTGACGACCATCAACTATGAAAA
1 ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATGGTGACGACCATCGACTATGAAAA
* *
31142988 GGGAT-GGGACGACCATCAACT
66 GGGATAGCGACGACCATCAAAT
*
31143009 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACCATCGACTATGAAAA
1 ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATGGTGACGACCATCGACTATGAAAA
31143074 GGGATAGC
66 GGGATAGC
31143082 TTCGACTATC
Statistics
Matches: 140, Mismatches: 17, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
86 76 0.54
87 63 0.45
88 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (87 bp):
ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATGGTGACGACCATCGACTATGAAAA
GGGATAGCGACGACCATCAAAT
Found at i:31143110 original size:58 final size:58
Alignment explanation
Indices: 31142836--31143102 Score: 317
Period size: 58 Copynumber: 4.6 Consensus size: 58
31142826 CCCTCAGATA
* *
31142836 ATGAAAAGGGATAGCTTC-AGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAGT
1 ATGAAAAGGGATAGCTTCGA-CTATCGACTATGAAAAGGGATGGTGACGACCATCGACT
* * * * * * * * * *
31142894 TTGAAAAGGTATAGCTTCGGCTATCAAATATGAAAAGGGATAGCT-TCGACTATTGATT
1 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGAT-GGTGACGACCATCGACT
* * * * * *
31142952 ATGAAAATGGAT-GGTGACGACCATCAACTATGAAAAGGGATGG-GACGACCATCAACT
1 ATGAAAAGGGATAGCT-TCGACTATCGACTATGAAAAGGGATGGTGACGACCATCGACT
31143009 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACCATCGACT
1 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACCATCGACT
31143067 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAA
1 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAA
31143103 AAGATGGTTT
Statistics
Matches: 173, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
57 46 0.27
58 125 0.72
59 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (58 bp):
ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACCATCGACT
Found at i:31143117 original size:29 final size:29
Alignment explanation
Indices: 31142836--31143117 Score: 208
Period size: 29 Copynumber: 9.8 Consensus size: 29
31142826 CCCTCAGATA
* * *
31142836 ATGAAAAGGGATAGCTTC-AGCTATCGATT
1 ATGAAAAGGGATGGTTTCGA-CTATCGACT
** * *
31142865 ATGAAAAGGGATGGTGACGACCATCGAGT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
* * * * * * *
31142894 TTGAAAAGGTATAGCTTCGGCTATCAAAT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
* * * *
31142923 ATGAAAAGGGATAGCTTCGACTATTGATT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
* ** * *
31142952 ATGAAAATGGATGGTGACGACCATCAACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
** * *
31142981 ATGAAAAGGGATGG-GACGACCATCAACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
* *
31143009 ATGAAAAGGGATAGCTTCGACTATCGACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
** *
31143038 ATGAAAAGGGATGGTGACGACCATCGACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
* *
31143067 ATGAAAAGGGATAGCTTCGACTATCGACT
1 ATGAAAAGGGATGGTTTCGACTATCGACT
** *
31143096 ATGAAAAAAGATGGTTTTGACT
1 ATGAAAAGGGATGGTTTCGACT
31143118 GTCAATTAAA
Statistics
Matches: 199, Mismatches: 52, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
28 27 0.14
29 171 0.86
30 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATGGTTTCGACTATCGACT
Found at i:31147247 original size:25 final size:25
Alignment explanation
Indices: 31147212--31147338 Score: 91
Period size: 25 Copynumber: 5.1 Consensus size: 25
31147202 TGACCCACAA
*
31147212 CTCATGTGAGCATACCAATTTACAG
1 CTCATGAGAGCATACCAATTTACAG
* * *
31147237 CTCATGAGAGCATACCGATCTATAG
1 CTCATGAGAGCATACCAATTTACAG
* * *
31147262 CTCGTGTGAGCATA--AATATTATAG
1 CTCATGAGAGCATACCAAT-TTACAG
* * * *
31147286 GTCGTGAGAGCATACCGATCTACAG
1 CTCATGAGAGCATACCAATTTACAG
*
31147311 CTCGAGTGAG-G-ATACCAATTCACAG
1 CTC-A-TGAGAGCATACCAATTTACAG
31147336 CTC
1 CTC
31147339 GTATGAGCAT
Statistics
Matches: 79, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
23 2 0.03
24 17 0.22
25 53 0.67
26 3 0.04
27 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (25 bp):
CTCATGAGAGCATACCAATTTACAG
Found at i:31157483 original size:25 final size:25
Alignment explanation
Indices: 31157449--31157543 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
31157439 GCAGACACAC
*
31157449 TACAGCTCGT-ATGAGCTTACCAATT
1 TACAGCTCGTGA-GAGCATACCAATT
*
31157474 TACAGCTCGTGAGAGCATACCGATT
1 TACAGCTCGTGAGAGCATACCAATT
** *
31157499 TACAGCTCAAGAGAGCATACCGATT
1 TACAGCTCGTGAGAGCATACCAATT
* * *
31157524 CACAGCTTGTGTGAGCATAC
1 TACAGCTCGTGAGAGCATAC
31157544 ATGTACTAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
25 59 0.98
26 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (25 bp):
TACAGCTCGTGAGAGCATACCAATT
Found at i:31163004 original size:50 final size:50
Alignment explanation
Indices: 31162913--31163048 Score: 159
Period size: 50 Copynumber: 2.7 Consensus size: 50
31162903 TAAAGTTATA
*
31162913 AGAGG-CCCCACGTAAGACCATG-CTAGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCC-CGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATG
* *
31162962 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACTGATATG
1 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATG
** *** * *
31163012 AGAACTCCAATGTAAGACCATATCTAGGATATGGCAT
1 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCAT
31163049 TGACAGTACA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
49 17 0.23
50 58 0.77
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATG
Found at i:31163924 original size:67 final size:67
Alignment explanation
Indices: 31163841--31163974 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
31163831 AAAAATTATC
*
31163841 GAGTTTGTTTTCACATGAAAGAAACAATGTAGGCAAAGGAATTATATATTATGAGATATTTGAAT
1 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGCAAAGGAATTATATATTATGAGATATTTGAAT
31163906 TT
66 TT
*
31163908 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGCAAATGAATTATATATTATGAGATATTTGAAT
1 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGCAAAGGAATTATATATTATGAGATATTTGAAT
31163973 TT
66 TT
31163975 TAGTGAGATA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (67 bp):
GAGTCTGTTTTCACATGAAAGAAACAATGTAGGCAAAGGAATTATATATTATGAGATATTTGAAT
TT
Found at i:31173821 original size:14 final size:14
Alignment explanation
Indices: 31173802--31173829 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31173792 CCAATTTATT
31173802 AATGAATTATTAAA
1 AATGAATTATTAAA
31173816 AATGAATTATTAAA
1 AATGAATTATTAAA
31173830 TATAACTTTA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:31197075 original size:225 final size:222
Alignment explanation
Indices: 31196657--31197080 Score: 580
Period size: 223 Copynumber: 1.9 Consensus size: 222
31196647 GGGTTTTTGG
* * * * * *
31196657 CACAATATTTATTATTTTAAGATTACAGTTTTGTGTTCTGGGCTTAGAGTTTAGGTTTAGGGGTT
1 CACAATATTTATTATTTTAAGATTACAATTTTGCGTACTGGACTTAGAGTTTAGGTTTAGGGCTC
* * ** * *
31196722 GGAGATTGGGGTTTAAGGTTTAGAGTTAACATTTCAGTGTTATTATTGGGTTAGTGTTTATGGCT
66 GGAGATTGGGGTTCAAGGTTTAGAGTTAACATTTCAGTGTTAATATCAGGTTAGGGTTTACGGCT
* * *
31196787 TATAAGAAAATGAAATTTATTGTGTTAGGGATTGACGTTTATGTTTTACGGTTTAGCGTTAATGT
131 TATAAGAAAATGAAATTTACTGTGTTAGGGATTGACGTTTATGGTTTACGGTTTAGCGTTAATGA
31196852 TTTACAATTTGGGGTTAGGGTTCGTTA
196 TTTACAATTTGGGGTTAGGGTTCGTTA
* * *
31196879 CACAATGTTTATTATTTTAGGATTACAATTTTGACG-ACATGGATTTAGAGTTTAGGTTTAGGGC
1 CACAATATTTATTATTTTAAGATTACAATTTTG-CGTAC-TGGACTTAGAGTTTAGGTTTAGGGC
* * *
31196943 TCGGGGATTGGGGTTCAAGGTTTAGAGTTTACATTTTAGTGTTAATATCAGGTTAGGGAATTTAC
64 TCGGAGATTGGGGTTCAAGGTTTAGAGTTAACATTTCAGTGTTAATATCAGGTTAGGG--TTTAC
* * * *
31197008 GGCTTATAAGATAATGAAATTTACTGTTTTAGGGCTTGATGTTTATGGTTTACGGTTTAGCGTTA
127 GGCTTATAAGAAAATGAAATTTACTGTGTTAGGGATTGACGTTTATGGTTTACGGTTTAGCGTTA
31197073 ATGATTTA
192 ATGATTTA
31197081 AGGGTTACGA
Statistics
Matches: 173, Mismatches: 25, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
222 31 0.18
223 72 0.42
225 70 0.40
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (222 bp):
CACAATATTTATTATTTTAAGATTACAATTTTGCGTACTGGACTTAGAGTTTAGGTTTAGGGCTC
GGAGATTGGGGTTCAAGGTTTAGAGTTAACATTTCAGTGTTAATATCAGGTTAGGGTTTACGGCT
TATAAGAAAATGAAATTTACTGTGTTAGGGATTGACGTTTATGGTTTACGGTTTAGCGTTAATGA
TTTACAATTTGGGGTTAGGGTTCGTTA
Found at i:31197914 original size:15 final size:16
Alignment explanation
Indices: 31197888--31197922 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
31197878 ATTTATAAAT
31197888 TTTAATATTGATAATA
1 TTTAATATTGATAATA
*
31197904 TTTAA-ATTGATATTA
1 TTTAATATTGATAATA
31197919 TTTA
1 TTTA
31197923 TAAATTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTAATATTGATAATA
Found at i:31198815 original size:14 final size:15
Alignment explanation
Indices: 31198785--31198818 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
31198775 CTGTTTACGG
*
31198785 TTTCATTTCTATCCA
1 TTTCATTGCTATCCA
31198800 TTTCATTGCT-TCCA
1 TTTCATTGCTATCCA
31198814 TTTCA
1 TTTCA
31198819 CTTTTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.18, C:0.26, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTCATTGCTATCCA
Found at i:31200554 original size:17 final size:17
Alignment explanation
Indices: 31200534--31200626 Score: 83
Period size: 17 Copynumber: 5.9 Consensus size: 17
31200524 TTATTTTCTA
31200534 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
31200551 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
*
31200565 -ATAATTTTTCTAAATT
1 TATAAGTTTTCTAAATT
* * *
31200581 TATTAGTATT-AAAATT
1 TATAAGTTTTCTAAATT
* *
31200597 TATCAG-TAT-TAAATT
1 TATAAGTTTTCTAAATT
31200612 TATAAGTTTTCTAAA
1 TATAAGTTTTCTAAA
31200627 AAAGTGTTCT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
13 10 0.17
14 2 0.03
15 11 0.19
16 14 0.24
17 22 0.37
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:31200562 original size:30 final size:30
Alignment explanation
Indices: 31200527--31200644 Score: 107
Period size: 30 Copynumber: 3.9 Consensus size: 30
31200517 TATTGTTTTA
*
31200527 TTTTCTATATAAGTTTTCTAAATTTATAAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
* *
31200557 TTTTCTAAATAATTTTTCTAAATTTATTAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
* * *
31200587 TATT-AAAATTTATCAG-TAT-TAAATTTATAAG
1 TTTTCTAAA--TA--AGTTTTCTAAATTTATAAG
* *
31200618 TTTTCTAAAAAAGTGTTCTAAATTTAT
1 TTTTCTAAATAAGTTTTCTAAATTTAT
31200645 TATTAATAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
28 2 0.03
29 4 0.06
30 40 0.59
31 16 0.24
32 5 0.07
33 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (30 bp):
TTTTCTAAATAAGTTTTCTAAATTTATAAG
Found at i:31200577 original size:13 final size:13
Alignment explanation
Indices: 31200527--31200579 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
31200517 TATTGTTTTA
*
31200527 TTTTCTATATAAG
1 TTTTCTAAATAAG
31200540 TTTTCTAAATTTATAAG
1 TTTTCT-AA---ATAAG
*
31200557 TTTTCTAAATAAT
1 TTTTCTAAATAAG
31200570 TTTTCTAAAT
1 TTTTCTAAAT
31200580 TTATTAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 20 0.59
14 1 0.03
16 2 0.06
17 11 0.32
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.55
Consensus pattern (13 bp):
TTTTCTAAATAAG
Found at i:31200610 original size:15 final size:15
Alignment explanation
Indices: 31200575--31200614 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
31200565 ATAATTTTTC
*
31200575 TAAATTTATTAGTAT
1 TAAATTTATCAGTAT
31200590 TAAAATTTATCAGTAT
1 T-AAATTTATCAGTAT
31200606 TAAATTTAT
1 TAAATTTAT
31200615 AAGTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (15 bp):
TAAATTTATCAGTAT
Found at i:31200617 original size:61 final size:61
Alignment explanation
Indices: 31200545--31200692 Score: 215
Period size: 61 Copynumber: 2.4 Consensus size: 61
31200535 ATAAGTTTTC
* * *
31200545 TAAATTTATAAGTTTTCTAAATAATTTTTCTAAATTTATTAGTATTAAAATTTATCAGTAT
1 TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
* * *
31200606 TAAATTTATAAGTTTTCTAAAAAAGTGTTCTAAATTTATTATTAATAAAATTTATAAGTAT
1 TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
* * *
31200667 CAATTTTATAATTTTTCTAAATAATT
1 TAAATTTATAAGTTTTCTAAATAATT
31200693 ATATATTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 76 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
Found at i:31200887 original size:21 final size:21
Alignment explanation
Indices: 31200861--31200937 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
31200851 TAACATAATA
* *
31200861 CATAACTTATAT-ATAAGCTTG
1 CATAACTTACATAATAA-CTTC
31200882 CATAACTTACATAATAACTTC
1 CATAACTTACATAATAACTTC
** *
31200903 CATAACTTA-ATACACCACTTA
1 CATAACTTACATA-ATAACTTC
*
31200924 AATAACTTACATAA
1 CATAACTTACATAA
31200938 CTTACATAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.06
21 37 0.79
22 7 0.15
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (21 bp):
CATAACTTACATAATAACTTC
Found at i:31200937 original size:9 final size:9
Alignment explanation
Indices: 31200919--31201379 Score: 182
Period size: 9 Copynumber: 53.7 Consensus size: 9
31200909 TTAATACACC
*
31200919 ACTTAAATA
1 ACTTACATA
31200928 ACTTACATA
1 ACTTACATA
31200937 ACTTACATA
1 ACTTACATA
*
31200946 GCTTACATA
1 ACTTACATA
*
31200955 AC-T-CATT
1 ACTTACATA
31200962 ACTTACATA
1 ACTTACATA
*
31200971 ACATACATA
1 ACTTACATA
31200980 A--TACATA
1 ACTTACATA
31200987 ACTTACATA
1 ACTTACATA
**
31200996 AAATAC--A
1 ACTTACATA
31201003 ACTTACATA
1 ACTTACATA
*
31201012 TCTTACATA
1 ACTTACATA
31201021 A--TACATA
1 ACTTACATA
*
31201028 ACTTATATA
1 ACTTACATA
31201037 A--TACA-A
1 ACTTACATA
*
31201043 CACTTACAAA
1 -ACTTACATA
* *
31201053 AATTAAATA
1 ACTTACATA
* *
31201062 ACCTGCATA
1 ACTTACATA
*
31201071 A--AACATA
1 ACTTACATA
* *
31201078 GCCTACATA
1 ACTTACATA
*
31201087 ACTTATATA
1 ACTTACATA
*
31201096 ACTTTCATA
1 ACTTACATA
**
31201105 AAGTAC--A
1 ACTTACATA
31201112 ACTTACATA
1 ACTTACATA
**
31201121 TTTTACATAAA
1 ACTTACAT--A
31201132 ACTTACATA
1 ACTTACATA
31201141 A--TACATA
1 ACTTACATA
*
31201148 ACTTAC-TT
1 ACTTACATA
**
31201156 ACATAATACAGC
1 AC-T--TACATA
*
31201168 ACTTACACA
1 ACTTACATA
*
31201177 ACTTAAATA
1 ACTTACATA
31201186 ACTTACATA
1 ACTTACATA
31201195 A--TACATA
1 ACTTACATA
31201202 GAC-TACATA
1 -ACTTACATA
*
31201211 ACTTA-ATTTG
1 ACTTACA--TA
*
31201221 CCTTACATA
1 ACTTACATA
31201230 A--TACA-A
1 ACTTACATA
*
31201236 CACTTACACA
1 -ACTTACATA
*
31201246 ACTTAAATA
1 ACTTACATA
*
31201255 ACTTGCATA
1 ACTTACATA
31201264 A--TACATA
1 ACTTACATA
*
31201271 GGC-TACATA
1 -ACTTACATA
*
31201280 ACTTA-ATTTT
1 ACTTACA--TA
*
31201290 CCTTACATA
1 ACTTACATA
**
31201299 A--TACAGC
1 ACTTACATA
31201306 ACTTACATA
1 ACTTACATA
31201315 ACTTACATA
1 ACTTACATA
**
31201324 GGTTACATA
1 ACTTACATA
31201333 A--TACATA
1 ACTTACATA
*
31201340 ACTTAAATA
1 ACTTACATA
*
31201349 ACTTATATA
1 ACTTACATA
31201358 A--TACATA
1 ACTTACATA
31201365 ACTTACATA
1 ACTTACATA
*
31201374 ATTTAC
1 ACTTAC
31201380 TTAATACATA
Statistics
Matches: 333, Mismatches: 73, Indels: 92
0.67 0.15 0.18
Matches are distributed among these distances:
6 2 0.01
7 78 0.23
8 11 0.03
9 215 0.65
10 12 0.04
11 13 0.04
12 2 0.01
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.32
Consensus pattern (9 bp):
ACTTACATA
Found at i:31200968 original size:16 final size:17
Alignment explanation
Indices: 31200928--31201373 Score: 86
Period size: 16 Copynumber: 26.1 Consensus size: 17
31200918 CACTTAAATA
31200928 ACTTACATAACTTACAT
1 ACTTACATAACTTACAT
31200945 AGCTTACATAAC-T-CATT
1 A-CTTACATAACTTACA-T
*
31200962 ACTTACATAACATACAT
1 ACTTACATAACTTACAT
*
31200979 A-ATACATAACTTACAT
1 ACTTACATAACTTACAT
**
31200995 AAAATAC--AACTTACAT
1 -ACTTACATAACTTACAT
31201011 ATCTTACATAA--TACAT
1 A-CTTACATAACTTACAT
* *
31201027 AACTTATATAA--TACAAC
1 -ACTTACATAACTTAC-AT
* * *
31201044 ACTTACAAAAATTAAAT
1 ACTTACATAACTTACAT
* * *
31201061 AACCTGCATAA--AACAT
1 -ACTTACATAACTTACAT
* *
31201077 AGCCTACATAACTTATAT
1 A-CTTACATAACTTACAT
* **
31201095 AACTTTCATAAAGTACA-
1 -ACTTACATAACTTACAT
**
31201112 ACTTACATATTTTACAT
1 ACTTACATAACTTACAT
* *
31201129 AAAACTTACATAATACATAACTT
1 ---ACTTACAT-A-AC-TTACAT
*
31201152 ACTTACATAA--TACAGC
1 ACTTACATAACTTACA-T
* *
31201168 ACTTACACAACTTAAAT
1 ACTTACATAACTTACAT
31201185 AACTTACATAA--TACAT
1 -ACTTACATAACTTACAT
31201201 AGAC-TACATAACTTA-ATTT
1 --ACTTACATAACTTACA--T
* *
31201220 GCCTTACATAA--TACAAC
1 -ACTTACATAACTTAC-AT
* *
31201237 ACTTACACAACTTAAAT
1 ACTTACATAACTTACAT
*
31201254 AACTTGCATAA--TACAT
1 -ACTTACATAACTTACAT
31201270 AGGC-TACATAACTTA-ATTTT
1 A--CTTACATAACTTACA---T
* *
31201290 CCTTACATAA--TACAGC
1 ACTTACATAACTTACA-T
31201306 ACTTACATAACTTACAT
1 ACTTACATAACTTACAT
*
31201323 AGGTTACATAA--TACAT
1 A-CTTACATAACTTACAT
* *
31201339 AACTTAAATAACTTATAT
1 -ACTTACATAACTTACAT
*
31201357 A-ATACATAACTTACAT
1 ACTTACATAACTTACAT
31201373 A
1 A
31201374 ATTTACTTAA
Statistics
Matches: 312, Mismatches: 62, Indels: 111
0.64 0.13 0.23
Matches are distributed among these distances:
15 5 0.02
16 156 0.50
17 24 0.08
18 87 0.28
19 18 0.06
20 17 0.05
21 1 0.00
23 4 0.01
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.32
Consensus pattern (17 bp):
ACTTACATAACTTACAT
Found at i:31201030 original size:25 final size:26
Alignment explanation
Indices: 31200925--31201037 Score: 105
Period size: 25 Copynumber: 4.5 Consensus size: 26
31200915 CACCACTTAA
*
31200925 ATAACTTACATAACTTACATAGCTTAC
1 ATAACTTACATAACTTACATA-CATAC
*
31200952 ATAAC-T-CATTACTTACATAACATAC
1 ATAACTTACATAACTTACAT-ACATAC
*
31200977 ATAA--TACATAACTTACATAAAATAC
1 ATAACTTACATAACTTACAT-ACATAC
*
31201002 --AACTTACATATCTTACATA-ATAC
1 ATAACTTACATAACTTACATACATAC
*
31201025 ATAACTTATATAA
1 ATAACTTACATAA
31201038 TACAACACTT
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
23 6 0.08
24 2 0.03
25 58 0.79
26 2 0.03
27 5 0.07
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (26 bp):
ATAACTTACATAACTTACATACATAC
Found at i:31201171 original size:20 final size:20
Alignment explanation
Indices: 31201132--31201173 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
31201122 TTTACATAAA
*
31201132 ACTTACATAATACATAACTT
1 ACTTACATAATACAGAACTT
*
31201152 ACTTACATAATACAGCACTT
1 ACTTACATAATACAGAACTT
31201172 AC
1 AC
31201174 ACAACTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (20 bp):
ACTTACATAATACAGAACTT
Found at i:31201194 original size:34 final size:34
Alignment explanation
Indices: 31201152--31201365 Score: 170
Period size: 34 Copynumber: 6.3 Consensus size: 34
31201142 TACATAACTT
*
31201152 ACTTACATAATACAGCACTTACACAACTTAAATA
1 ACTTACATAATACAGCACTTACATAACTTAAATA
* *
31201186 ACTTACATAATACATAG-AC-TACATAACTTAATTTG
1 ACTTACATAATAC--AGCACTTACATAACTTAA-ATA
* * *
31201221 CCTTACATAATACAACACTTACACAACTTAAATA
1 ACTTACATAATACAGCACTTACATAACTTAAATA
* * * *
31201255 ACTTGCATAATACATAG-GC-TACATAACTTAATTTT
1 ACTTACATAATAC--AGCACTTACATAACTTAA-ATA
* *
31201290 CCTTACATAATACAGCACTTACATAACTTACATA
1 ACTTACATAATACAGCACTTACATAACTTAAATA
** ** * *
31201324 GGTTACATAATACATAACTTAAATAACTTATATA
1 ACTTACATAATACAGCACTTACATAACTTAAATA
31201358 A--TACATAA
1 ACTTACATAA
31201366 CTTACATAAT
Statistics
Matches: 142, Mismatches: 28, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
32 7 0.05
33 3 0.02
34 79 0.56
35 50 0.35
36 3 0.02
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.31
Consensus pattern (34 bp):
ACTTACATAATACAGCACTTACATAACTTAAATA
Found at i:31201240 original size:69 final size:69
Alignment explanation
Indices: 31201153--31201353 Score: 305
Period size: 69 Copynumber: 2.9 Consensus size: 69
31201143 ACATAACTTA
31201153 CTTACATAATACAGCACTTACACAACTTAAATAACTTACATAATACATAGACTACATAACTTAAT
1 CTTACATAATACAGCACTTACACAACTTAAATAACTTACATAATACATAGACTACATAACTTAAT
31201218 TTGC
66 TTGC
* * *
31201222 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGGCTACATAACTTAAT
1 CTTACATAATACAGCACTTACACAACTTAAATAACTTACATAATACATAGACTACATAACTTAAT
*
31201287 TTTC
66 TTGC
* * ** *
31201291 CTTACATAATACAGCACTTACATAACTTACATAGGTTACATAATACATA-ACTTAAATAACTTA
1 CTTACATAATACAGCACTTACACAACTTAAATAACTTACATAATACATAGAC-TACATAACTTA
31201354 TATAATACAT
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 1 0.01
69 118 0.99
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.31
Consensus pattern (69 bp):
CTTACATAATACAGCACTTACACAACTTAAATAACTTACATAATACATAGACTACATAACTTAAT
TTGC
Found at i:31201337 original size:25 final size:25
Alignment explanation
Indices: 31201309--31201390 Score: 110
Period size: 25 Copynumber: 3.3 Consensus size: 25
31201299 ATACAGCACT
**
31201309 TACATAACTTACATAGGTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
31201334 TACATAACTTAAATAACTTATATAA
1 TACATAACTTACATAACTTACATAA
* *
31201359 TACATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACATAA
31201384 TACATAA
1 TACATAA
31201391 ATATATATCA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:31206974 original size:66 final size:66
Alignment explanation
Indices: 31206868--31207037 Score: 207
Period size: 66 Copynumber: 2.6 Consensus size: 66
31206858 AGCAAATTAC
* * * * * *
31206868 ACAACTTAAAACGGAGGCAGCATCGAGTGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAT
1 ACAACTTAAAGCAGACGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAG
31206932 CT
65 CT
* * *
31206934 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTTCAGC
1 ACAACTTAAAGCAGACGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGC
31206999 T
66 T
* * * *
31207000 GCAGCTTAAAGCAGACGCGGCAGCGAGAGAAGCAGAGG
1 ACAACTTAAAGCAGACGCAGCAGCGAGAGAAGCTGAGG
31207038 CTACAGTGAG
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
66 86 0.96
67 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.15
Consensus pattern (66 bp):
ACAACTTAAAGCAGACGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGC
T
Found at i:31207033 original size:21 final size:21
Alignment explanation
Indices: 31207008--31207078 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
31206998 CTGCAGCTTA
* * *
31207008 AAGCAGACGCGGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
* *
31207029 AAGCAGAGGCTACAGTGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
31207050 AAGTAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
31207071 AAGCAGAG
1 AAGCAGAG
31207079 CAGCGTAGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.34, C:0.17, G:0.44, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:31207473 original size:43 final size:42
Alignment explanation
Indices: 31207416--31207668 Score: 229
Period size: 43 Copynumber: 5.9 Consensus size: 42
31207406 CGTTTTTAAA
* *
31207416 AAAAACGCCACTAAAGGTCATGGTCATTT-GCGGCGTTTGTAG
1 AAAAGCGCCGCTAAAGGTCATGGTC-TTTAGCGGCGTTTGTAG
* * * * *
31207458 AAAAAGCGTCGCTAAAGATCAGGGTCTTTAGTGGCGTTTGTTTG
1 -AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTG-TAG
* * ** *
31207502 GAAAGCGCCGCTAAAGGTCATTGTCTTTAATGGCGTTTTTCAG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT-AG
* * * *
31207545 ATAAGCGCTGCTAAAAGTCATGGTCTTTAGCGGCGTTTGTCGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT-AG
** *** *
31207588 AAAAGCGCCGCTAAAGACCATAACCTTTAGCGGCGTTTGTGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTAG
* *
31207630 TGAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 -AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
31207669 ATTTCTAAAA
Statistics
Matches: 167, Mismatches: 39, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
42 6 0.04
43 159 0.95
44 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTAG
Found at i:31207635 original size:129 final size:129
Alignment explanation
Indices: 31207426--31207668 Score: 321
Period size: 129 Copynumber: 1.9 Consensus size: 129
31207416 AAAAACGCCA
* * * *** *
31207426 CTAAAGGTCATGGTCATTTGCGGCGTTTGTAGAAAAAGCGTCGCTAAAGATCAGGGTCTTTAGTG
1 CTAAAAGTCATGGTCATTTGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGACCAGAACCTTTAGCG
* *
31207491 GCGTTTGTTTGGAAAGCGCCGCTAAAGGTCATT-GTCTTTAATGGCGTTTTTCAGATAAGCGCTG
66 GCGTTTGTGTGGAAAGCGCCGCTAAAGGTC-TTGGTCTTTAACGGCGTTTTTCAGATAAGCGCTG
* * *
31207555 CTAAAAGTCATGGTC-TTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGACCATAACCTTTAGC
1 CTAAAAGTCATGGTCATTT-GCGGCGTTTGTAGAAAAAGCGCCGCTAAAGACCAGAACCTTTAGC
*
31207619 GGCGTTTGTG-GTGAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
65 GGCGTTTGTGTG-GAAAGCGCCGCTAAAGGTCTTGGTCTTTAACGGCGTTT
31207669 ATTTCTAAAA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
128 6 0.06
129 92 0.94
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.30
Consensus pattern (129 bp):
CTAAAAGTCATGGTCATTTGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGACCAGAACCTTTAGCG
GCGTTTGTGTGGAAAGCGCCGCTAAAGGTCTTGGTCTTTAACGGCGTTTTTCAGATAAGCGCTG
Found at i:31214868 original size:34 final size:35
Alignment explanation
Indices: 31214814--31214880 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
31214804 CAAACACCAG
*
31214814 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
31214849 AAAACATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
31214881 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:31221072 original size:16 final size:18
Alignment explanation
Indices: 31221034--31221075 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
31221024 GTTTACAAAT
*
31221034 AAGAAAGAAAATGAGAGCA
1 AAGAAAAAAAATGAGAG-A
31221053 AAGAAAAAAAAT-AGAG-
1 AAGAAAAAAAATGAGAGA
31221069 AAGAAAA
1 AAGAAAA
31221076 GTGAAAAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
18 4 0.18
19 11 0.50
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.05
Consensus pattern (18 bp):
AAGAAAAAAAATGAGAGA
Found at i:31223651 original size:15 final size:15
Alignment explanation
Indices: 31223631--31223666 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
31223621 TCGTTAAATC
31223631 AATCCAATATTGAAG
1 AATCCAATATTGAAG
31223646 AATCCAATATTGAAG
1 AATCCAATATTGAAG
31223661 AATCCA
1 AATCCA
31223667 CTTTATGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.25
Consensus pattern (15 bp):
AATCCAATATTGAAG
Found at i:31249776 original size:22 final size:22
Alignment explanation
Indices: 31249733--31249776 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31249723 GAAAATGATC
**
31249733 AAAATTAATCAAAATTTGACAT
1 AAAATTAATCAAAATTAAACAT
*
31249755 AAAATTAATTAAAATTAAACAT
1 AAAATTAATCAAAATTAAACAT
31249777 TTTCATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATTAATCAAAATTAAACAT
Found at i:31253159 original size:16 final size:16
Alignment explanation
Indices: 31253126--31253155 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31253116 TTTTCTATTA
31253126 ATTTATTAAAATAAAT
1 ATTTATTAAAATAAAT
31253142 ATTTATT-AAATAAA
1 ATTTATTAAAATAAA
31253156 ATATGATCAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTATTAAAATAAAT
Found at i:31253235 original size:22 final size:19
Alignment explanation
Indices: 31253198--31253239 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
31253188 TGTAAAGTTG
31253198 ATAATGATTAATATATATT
1 ATAATGATTAATATATATT
31253217 ATAATAGATATAATTATATATT
1 ATAAT-GAT-TAA-TATATATT
31253239 A
1 A
31253240 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 3 0.15
22 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATAATGATTAATATATATT
Found at i:31260201 original size:27 final size:27
Alignment explanation
Indices: 31260133--31260202 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
31260123 CACACGTGAA
* *
31260133 CACCAACTCGCCGAGCCTACTGGAGAT
1 CACCAACTCGCCAAGCCTACTGGAGAC
**
31260160 CACCAACTCATCAAGCCTACT-GACGAC
1 CACCAACTCGCCAAGCCTACTGGA-GAC
*
31260187 CACCAACTTGCCAAGC
1 CACCAACTCGCCAAGC
31260203 GCCAAACTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.30, C:0.40, G:0.16, T:0.14
Consensus pattern (27 bp):
CACCAACTCGCCAAGCCTACTGGAGAC
Found at i:31260827 original size:12 final size:12
Alignment explanation
Indices: 31260799--31260831 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
31260789 CTTAGTTATT
31260799 TTTATG-TTTTC
1 TTTATGTTTTTC
31260810 -TTATGTTTTTC
1 TTTATGTTTTTC
31260821 TTTATGTTTTT
1 TTTATGTTTTT
31260832 ATTTGCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 5 0.25
12 10 0.50
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTATGTTTTTC
Found at i:31267065 original size:16 final size:16
Alignment explanation
Indices: 31267044--31267075 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31267034 GTTTCGTTGC
*
31267044 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
31267060 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
31267076 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:31267327 original size:12 final size:12
Alignment explanation
Indices: 31267299--31267341 Score: 68
Period size: 12 Copynumber: 3.4 Consensus size: 12
31267289 GATACCGGTT
31267299 CACATAGTAGCCTA
1 CACATAGTA--CTA
31267313 CACATAGTACTA
1 CACATAGTACTA
31267325 CACATAGTACTA
1 CACATAGTACTA
31267337 CACAT
1 CACAT
31267342 GTGACCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 20 0.69
14 9 0.31
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (12 bp):
CACATAGTACTA
Found at i:31267387 original size:51 final size:51
Alignment explanation
Indices: 31267325--31267501 Score: 193
Period size: 51 Copynumber: 3.5 Consensus size: 51
31267315 CATAGTACTA
* * * *
31267325 CACATAGTACTACACATGTGACCATCAATAACCGATACACGTAGTATCCTG
1 CACATAGTACTACACACGTGACCATCAATATCCGGTACACGTAGTAGCCTG
* * *
31267376 CACATAATACTACACACGTG---ATCGAAGCTATCCGGTACGCATAGTAGCCTG
1 CACATAGTACTACACACGTGACCATC-AA--TATCCGGTACACGTAGTAGCCTG
* * *
31267427 CACATAGTACTACAAACGCGACCTATC-AT-TCTGGTACACGTAGTAGCCTG
1 CACATAGTACTACACACGTGACC-ATCAATATCCGGTACACGTAGTAGCCTG
31267477 CACATAGTACTACACACGTGACCAT
1 CACATAGTACTACACACGTGACCAT
31267502 TGCTTTCACT
Statistics
Matches: 104, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
48 3 0.03
49 4 0.04
50 39 0.38
51 54 0.52
53 1 0.01
55 3 0.03
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (51 bp):
CACATAGTACTACACACGTGACCATCAATATCCGGTACACGTAGTAGCCTG
Found at i:31270377 original size:27 final size:27
Alignment explanation
Indices: 31270325--31270393 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
31270315 GTTTTCACAA
31270325 ATTTAAAATTTAATCGATTTATTTTTT
1 ATTTAAAATTTAATCGATTTATTTTTT
* *
31270352 ATTTAAATATTTAATC-CTGTTATTTTTAA
1 ATTTAAA-ATTTAATCGAT-TTATTTTT-T
*
31270381 ATTTTAAATTTAA
1 ATTTAAAATTTAA
31270394 ATTTAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.22
28 22 0.61
29 6 0.17
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (27 bp):
ATTTAAAATTTAATCGATTTATTTTTT
Found at i:31275471 original size:31 final size:30
Alignment explanation
Indices: 31275433--31275497 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
31275423 AATACAAAGA
* *
31275433 ATTCTTTCATTACTCAATACATTTTCATTC
1 ATTCTTTCAATACTCAATACAGTTTCATTC
* *
31275463 TATTCTTTCAATACTTAGTACAGTTTCATTC
1 -ATTCTTTCAATACTCAATACAGTTTCATTC
31275494 ATTC
1 ATTC
31275498 AATACACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.26, C:0.22, G:0.03, T:0.49
Consensus pattern (30 bp):
ATTCTTTCAATACTCAATACAGTTTCATTC
Found at i:31278399 original size:16 final size:16
Alignment explanation
Indices: 31278372--31278442 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
31278362 GTTTGGTTCA
31278372 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
* *
31278388 CTATAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
31278404 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
31278420 TTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
31278436 CTGTAAT
1 CTGTAAT
31278443 CAGTAATTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:31278757 original size:22 final size:24
Alignment explanation
Indices: 31278718--31278771 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
31278708 TAAATATTAT
* *
31278718 TTATTT-ATTTTATCAATACAT-A
1 TTATTTAATTTAATCAATAAATAA
31278740 TTATTTAATTTAAT-AATAAATAA
1 TTATTTAATTTAATCAATAAATAA
*
31278763 TAATTTAAT
1 TTATTTAAT
31278772 CATATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
TTATTTAATTTAATCAATAAATAA
Found at i:31281584 original size:13 final size:13
Alignment explanation
Indices: 31281563--31281594 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
31281553 ATCAAAAGGC
31281563 CTCTATATTTTCT
1 CTCTATATTTTCT
*
31281576 CTCTCTATTTTCT
1 CTCTATATTTTCT
31281589 CTCTAT
1 CTCTAT
31281595 TTTGTCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.59
Consensus pattern (13 bp):
CTCTATATTTTCT
Found at i:31286173 original size:23 final size:23
Alignment explanation
Indices: 31286143--31286264 Score: 190
Period size: 23 Copynumber: 5.3 Consensus size: 23
31286133 AGTGTTATTG
*
31286143 ATCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
31286166 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
31286189 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
31286212 TTCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
31286235 TTCTGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
31286258 ATCAGTG
1 ATCAGTG
31286265 TGGCACTTAT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 91 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:31295333 original size:30 final size:30
Alignment explanation
Indices: 31295276--31295334 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
31295266 TGCCTTTGAA
*
31295276 AATATTTACAAAAAGAGACAGCCAATTTTT
1 AATATTTACAAAAAGAGACAGCAAATTTTT
31295306 AATATTTACAAAAAGAG-CAAGCAAATTTT
1 AATATTTACAAAAAGAGAC-AGCAAATTTT
31295335 GAAAATAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAGCAAATTTTT
Found at i:31306116 original size:43 final size:43
Alignment explanation
Indices: 31306032--31306130 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
31306022 TTCTGTTTTT
* ** * *
31306032 CGATGATGCACTATGCGTGCCAGTATATTTTGATGGGTTTATC
1 CGATGATGCACTACGCGTGCCAGTATATTTCCATCGATTTATC
* *
31306075 CGATGATGCACTACGTGTGCCAGTATATTTCCTTCGATTTATC
1 CGATGATGCACTACGCGTGCCAGTATATTTCCATCGATTTATC
**
31306118 TAATGATGCACTA
1 CGATGATGCACTA
31306131 TAGTGCTAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (43 bp):
CGATGATGCACTACGCGTGCCAGTATATTTCCATCGATTTATC
Found at i:31324600 original size:36 final size:36
Alignment explanation
Indices: 31324553--31324662 Score: 193
Period size: 36 Copynumber: 3.1 Consensus size: 36
31324543 AACATTCATT
*
31324553 TATTAAAACATACTTATGAAATAAATGATTAAAACA
1 TATTAAAACATACTTATGAAAGAAATGATTAAAACA
*
31324589 TATTAAAACATACTTATGAAAGAAATGGTTAAAACA
1 TATTAAAACATACTTATGAAAGAAATGATTAAAACA
*
31324625 TATCAAAACATACTTATGAAAGAAATGATTAAAACA
1 TATTAAAACATACTTATGAAAGAAATGATTAAAACA
31324661 TA
1 TA
31324663 CTTGAAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (36 bp):
TATTAAAACATACTTATGAAAGAAATGATTAAAACA
Found at i:31325827 original size:8 final size:8
Alignment explanation
Indices: 31325814--31325839 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31325804 TTTTAAATGA
31325814 TATTTTAT
1 TATTTTAT
31325822 TATTTTAT
1 TATTTTAT
31325830 TATTTTAT
1 TATTTTAT
31325838 TA
1 TA
31325840 GTATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TATTTTAT
Found at i:31337845 original size:2 final size:2
Alignment explanation
Indices: 31337838--31337864 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31337828 ACTATTTAGT
31337838 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 T
31337865 GTTTTTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31338367 original size:25 final size:25
Alignment explanation
Indices: 31338333--31338390 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
31338323 AAATTATTAT
31338333 TTAGTTTTCATATTTGATTTCGCTC
1 TTAGTTTTCATATTTGATTTCGCTC
31338358 TTAGTTTTCATATTTGATTTCGCTC
1 TTAGTTTTCATATTTGATTTCGCTC
31338383 TTAGTTTT
1 TTAGTTTT
31338391 TTACCTAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.59
Consensus pattern (25 bp):
TTAGTTTTCATATTTGATTTCGCTC
Found at i:31340790 original size:47 final size:47
Alignment explanation
Indices: 31340721--31340815 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
31340711 TGTGTGATTG
*
31340721 TTTTATGCTTTTCTAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
1 TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
31340768 TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
1 TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
31340815 T
1 T
31340816 ATGACGCTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.40
Consensus pattern (47 bp):
TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
Found at i:31340825 original size:47 final size:47
Alignment explanation
Indices: 31340727--31340825 Score: 162
Period size: 47 Copynumber: 2.1 Consensus size: 47
31340717 ATTGTTTTAT
* * * *
31340727 GCTTTTCTAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATTTTAT
1 GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
31340774 GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
1 GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
31340821 GCTTT
1 GCTTT
31340826 ACTTGTTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.37
Consensus pattern (47 bp):
GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
Found at i:31341195 original size:23 final size:23
Alignment explanation
Indices: 31341165--31341208 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
31341155 GAATGTGGTG
31341165 GTTGTGGATAATTAGGATTGTTA
1 GTTGTGGATAATTAGGATTGTTA
*
31341188 GTTGTGGATATTTAGGATTGT
1 GTTGTGGATAATTAGGATTGT
31341209 ATGTGTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (23 bp):
GTTGTGGATAATTAGGATTGTTA
Found at i:31341979 original size:58 final size:60
Alignment explanation
Indices: 31341898--31342013 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 60
31341888 ATCACTTTAA
* * * *
31341898 TATTTAATTAATATAATAATTA-T-CAAGGTAAATATTAGATTTAATTTAATATTAAATC
1 TATTAAATTAATAGAATAATTACTACAAGATAAATATTAAATTTAATTTAATATTAAATC
*
31341956 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTTAATTTAATATTAA
1 TATTAAATTAATAGAATAATTA-CTACAAGATAAATATTAAATTTAATTTAATATTAA
31342014 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 19 0.38
60 1 0.02
61 30 0.60
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.44
Consensus pattern (60 bp):
TATTAAATTAATAGAATAATTACTACAAGATAAATATTAAATTTAATTTAATATTAAATC
Found at i:31346085 original size:10 final size:10
Alignment explanation
Indices: 31346060--31346088 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
31346050 CATTTCCCTT
31346060 TTTCTATTCA
1 TTTCTATTCA
31346070 -TTCTATTCA
1 TTTCTATTCA
31346079 TTTCTATTCA
1 TTTCTATTCA
31346089 AACACGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:31348294 original size:29 final size:29
Alignment explanation
Indices: 31348256--31348465 Score: 251
Period size: 29 Copynumber: 7.2 Consensus size: 29
31348246 ATATCGACGC
31348256 CCATCGAATATGAAAAGGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * **
31348285 CCATCAAATATGAAAAGGGATGCTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * *
31348314 CCATCAAATATGAAAAGGGGTAGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
*
31348343 CCATC-AAGTATGAAAAGGGATGGTTTCTA
1 CCATCGAA-TATGAAAAGGGATGGTTTCGA
* * **
31348372 CCATCGAATATTAAAAAGGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
31348401 CCATCGAATATGAAAAGGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * * *
31348430 CCATTGATTAAAGAAAATGGATGGTTTCGA
1 CCATCGAAT-ATGAAAAGGGATGGTTTCGA
31348460 CCATCG
1 CCATCG
31348466 TTTAGCACAC
Statistics
Matches: 152, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
28 2 0.01
29 125 0.82
30 25 0.16
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.24
Consensus pattern (29 bp):
CCATCGAATATGAAAAGGGATGGTTTCGA
Found at i:31353325 original size:39 final size:39
Alignment explanation
Indices: 31353271--31353387 Score: 128
Period size: 39 Copynumber: 3.0 Consensus size: 39
31353261 TAATTTGGTT
* *
31353271 TGAATATTCAATTATGTCATAATTTGAACATCATTAATA
1 TGAATTTTTAATTATGTCATAATTTGAACATCATTAATA
* *
31353310 TGAATTTTTAATTATGTCATAATCTGAACAACATTAATA
1 TGAATTTTTAATTATGTCATAATTTGAACATCATTAATA
* ** * * *
31353349 AG-GGTTTTAATTATGTCATAGTTTAGGACATCTTTAATA
1 TGAATTTTTAATTATGTCATAATTT-GAACATCATTAATA
31353388 CATGTTTTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 18 0.28
39 47 0.72
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (39 bp):
TGAATTTTTAATTATGTCATAATTTGAACATCATTAATA
Found at i:31356218 original size:14 final size:14
Alignment explanation
Indices: 31356199--31356247 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
31356189 TAGACACAAA
*
31356199 TTTAACAAATAAAT
1 TTTAACAATTAAAT
31356213 TTTAACAATGTTAAAT
1 TTTAACAA--TTAAAT
*
31356229 ATTAACAATTAAAT
1 TTTAACAATTAAAT
31356243 TTTAA
1 TTTAA
31356248 TTTTTAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 18 0.60
16 12 0.40
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (14 bp):
TTTAACAATTAAAT
Found at i:31356781 original size:26 final size:27
Alignment explanation
Indices: 31356745--31356796 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
31356735 ATTACATATT
*
31356745 AAATATATATTTT-TATATTTTTAATC
1 AAATATATATTTTATATATATTTAATC
31356771 AAATATATATTTTATATATATTTAAT
1 AAATATATATTTTATATATATTTAAT
31356797 ATATATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATATATATTTTATATATATTTAATC
Found at i:31356789 original size:11 final size:11
Alignment explanation
Indices: 31356772--31356809 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
31356762 TTTTTAATCA
31356772 AATATATATTT
1 AATATATATTT
*
31356783 TATATATATTT
1 AATATATATTT
31356794 AATATATATTT
1 AATATATATTT
31356805 AATAT
1 AATAT
31356810 GGGCCGGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AATATATATTT
Found at i:31357459 original size:2 final size:2
Alignment explanation
Indices: 31357454--31357483 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
31357444 AGCGCGCGCT
*
31357454 AG AG AG CG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31357484 GACCTTTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31358645 original size:17 final size:16
Alignment explanation
Indices: 31358623--31358654 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
31358613 GAGAAGTAAT
31358623 AGAAAGAAAAAGAAAAA
1 AGAAAG-AAAAGAAAAA
31358640 AGAAAGAAAAGAAAA
1 AGAAAGAAAAGAAAA
31358655 GGATAACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAGAAAAA
Found at i:31359874 original size:22 final size:23
Alignment explanation
Indices: 31359836--31359898 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
31359826 TAATAAAAAA
* *
31359836 ATATATATATGAAAAAAAAATGCAC
1 ATATAT-TAT-AAAAATATATGCAC
* *
31359861 ATGTATTTATAAAAATATATGCAT
1 ATATA-TTATAAAAATATATGCAC
31359885 ATATATTATAAAAA
1 ATATATTATAAAAA
31359899 GAAATACGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 9 0.28
24 15 0.47
25 7 0.22
26 1 0.03
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (23 bp):
ATATATTATAAAAATATATGCAC
Found at i:31359893 original size:23 final size:23
Alignment explanation
Indices: 31359836--31359903 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
31359826 TAATAAAAAA
31359836 ATATATA-TATGAAAAAAAAATGC
1 ATATATATTAT-AAAAAAAAATGC
* * * *
31359859 ACATGTATTTATAAAAATATATGC
1 ATATATA-TTATAAAAAAAAATGC
*
31359883 ATATATATTATAAAAAGAAAT
1 ATATATATTATAAAAAAAAAT
31359904 ACGTATGTAC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
23 17 0.49
24 15 0.43
25 3 0.09
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.32
Consensus pattern (23 bp):
ATATATATTATAAAAAAAAATGC
Found at i:31361529 original size:44 final size:44
Alignment explanation
Indices: 31361368--31361530 Score: 151
Period size: 44 Copynumber: 3.8 Consensus size: 44
31361358 AGGATTCATC
*
31361368 ATTTTAATCTGCTCCACTGCAACTTCAGAGAGATAGGAT-TA-G
1 ATTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATATATG
* ** *
31361410 TTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTATATG
1 ATT-TT-AATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TATATG
* * *
31361457 ----TGATCTGCT-CTCTACAACTTCAGAGAGATAAGATATATG
1 ATTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATATATG
* * *
31361496 ATTTTAATCCGCTCCACTGCAAATTCAGGGAGATA
1 ATTTTAATCTGCTCCACTGCAACTTCAGAGAGATA
31361531 GGATTTTTCA
Statistics
Matches: 95, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
39 6 0.06
40 21 0.22
41 6 0.06
42 3 0.03
43 9 0.09
44 46 0.48
45 1 0.01
46 2 0.02
47 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
ATTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATATATG
Found at i:31361995 original size:88 final size:88
Alignment explanation
Indices: 31361846--31362369 Score: 806
Period size: 88 Copynumber: 6.0 Consensus size: 88
31361836 AAGACTGATG
* *
31361846 TCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTG-TCATTTTC-GACCTACTCCACT
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCT-ATTTTCAG-CCTACTCCACT
* *
31361909 GCTGTCCAGGGAGACAAGGCTGGTA
64 ACTGCCCAGGGAGACAAGGCTGGTA
* * * *
31361934 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGAAAAATCTGTTATCTTCAGCCTACTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGCCTACTCCACTAC
31361999 TGCCCAGGGAGACAAGGCTGGTA
66 TGCCCAGGGAGACAAGGCTGGTA
* *
31362022 TCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCA-CCTGCTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGCCTACTCCACTAC
31362086 TGCCCAGGGAGACAAGGCTGGTA
66 TGCCCAGGGAGACAAGGCTGGTA
* * *
31362109 TCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGCCTACTCCACTAC
31362174 TGCCCAGGGAGACAAGGCTGGTA
66 TGCCCAGGGAGACAAGGCTGGTA
* * *
31362197 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGACAAGATCTGCTATTTTGAAG-CTGCTCCACTA
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTT-CAGCCTACTCCACTA
*
31362261 CTGCCCAGGGGGACAAGGCTGGTA
65 CTGCCCAGGGAGACAAGGCTGGTA
* *
31362285 TCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTA-
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGCCTACTCCACTAC
31362349 TCGCCCAGGGAGACAAGGCTG
66 T-GCCCAGGGAGACAAGGCTG
31362370 AAATTTTACC
Statistics
Matches: 406, Mismatches: 24, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
87 88 0.22
88 315 0.78
89 3 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (88 bp):
TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGCCTACTCCACTAC
TGCCCAGGGAGACAAGGCTGGTA
Found at i:31362318 original size:263 final size:264
Alignment explanation
Indices: 31361846--31362369 Score: 851
Period size: 263 Copynumber: 2.0 Consensus size: 264
31361836 AAGACTGATG
* *
31361846 TCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGTCATTTTCGACCTACTCCACTGC
1 TCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGTCATTTTCAACCTACTCCACTAC
*
31361911 TGTCCAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGAAAAATCTG
66 TGCCCAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGAAAAATCTG
* *
31361976 TTATCTTCAGCCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATCTTTGATCTGCTTCTCTG
131 CTATCTTAAGCCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATCTTTGATCTGCTTCTCTG
*
31362041 TCAGTACAGGAAGGCAAGATCTGCTATTTTC-ACCTGCTCCACTA-CTGCCCAGGGAGACAAGGC
196 TCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTATC-GCCCAGGGAGACAAGGC
31362104 TGGTA
260 TGGTA
* * * *
31362109 TCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTG-CTATTTTCAACCTGCTCCACTA
1 TCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGTC-ATTTTCAACCTACTCCACTA
*
31362173 CTGCCCAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAA-GACAAGATC
65 CTGCCCAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGA-AAAATC
* * *
31362237 TGCTATTTTGAAG-CTGCTCCACTACTGCCCAGGGGGACAAGGCTGGTATCTTTGATCTGCTTCT
129 TGCTATCTT-AAGCCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATCTTTGATCTGCTTCT
31362301 CTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTATCGCCCAGGGAGACAAG
193 CTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTATCGCCCAGGGAGACAAG
31362366 GCTG
258 GCTG
31362370 AAATTTTACC
Statistics
Matches: 242, Mismatches: 14, Indels: 9
0.91 0.05 0.03
Matches are distributed among these distances:
262 3 0.01
263 205 0.85
264 33 0.14
265 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (264 bp):
TCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGTCATTTTCAACCTACTCCACTAC
TGCCCAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGAAAAATCTG
CTATCTTAAGCCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATCTTTGATCTGCTTCTCTG
TCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTATCGCCCAGGGAGACAAGGCT
GGTA
Found at i:31362329 original size:176 final size:175
Alignment explanation
Indices: 31361846--31362369 Score: 845
Period size: 175 Copynumber: 3.0 Consensus size: 175
31361836 AAGACTGATG
* * * *
31361846 TCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTG-TCATTTTCGACCTACTCCACTG
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCT-ATTTT-GACCTGCTCCACTA
* * * *
31361910 CTGTCCAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGAAAAATCT
64 CTGCCCAGGGAGACAAGGCTGGTATCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCT
* * *
31361975 GTTATCTTCAGCCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTA
129 GCTATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTA
* *
31362022 TCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCACCTGCTCCACTACT
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTGACCTGCTCCACTACT
31362087 GCCCAGGGAGACAAGGCTGGTATCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGC
66 GCCCAGGGAGACAAGGCTGGTATCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGC
*
31362152 TATTTTCAACCTGCTCCACTACTGCCCAGGGAGACAAGGCTGGTA
131 TATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTA
* *
31362197 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGACAAGATCTGCTATTTTGAAGCTGCTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTG-ACCTGCTCCACTAC
*
31362262 TGCCCAGGGGGACAAGGCTGGTATCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTG
65 TGCCCAGGGAGACAAGGCTGGTATCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTG
31362327 CTATTTTCAACCTACTCCACTA-TCGCCCAGGGAGACAAGGCTG
130 CTATTTTCAACCTACTCCACTACT-GCCCAGGGAGACAAGGCTG
31362370 AAATTTTACC
Statistics
Matches: 325, Mismatches: 20, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
175 163 0.50
176 161 0.50
177 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (175 bp):
TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTGACCTGCTCCACTACT
GCCCAGGGAGACAAGGCTGGTATCTTTGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGC
TATTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTA
Found at i:31363628 original size:22 final size:20
Alignment explanation
Indices: 31363603--31363650 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 20
31363593 TAGCCTCTCC
31363603 ATTTTTACTTTTTCCATTTTTT
1 ATTTTTA-TTTTTCCA-TTTTT
31363625 ATTTTTTATTTTTCCATTTTT
1 A-TTTTTATTTTTCCATTTTT
31363646 ATTTT
1 ATTTT
31363651 CACACATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.16
21 6 0.24
22 9 0.36
23 6 0.24
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (20 bp):
ATTTTTATTTTTCCATTTTT
Found at i:31364185 original size:22 final size:22
Alignment explanation
Indices: 31364160--31364208 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
31364150 TTTTTGTTTC
* *
31364160 TTTTTGTTTTTATTT-TTTCCTT
1 TTTTTCTTTTT-TTTCTTGCCTT
31364182 TTTTTCTTTTTTTTCTTGCCTT
1 TTTTTCTTTTTTTTCTTGCCTT
31364204 TTTTT
1 TTTTT
31364209 TTGAATCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (22 bp):
TTTTTCTTTTTTTTCTTGCCTT
Found at i:31364197 original size:9 final size:9
Alignment explanation
Indices: 31364150--31364198 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
31364140 GGTAGAGGTT
31364150 TTTTTGTTTC
1 TTTTT-TTTC
31364160 TTTTTGTTT-
1 TTTTT-TTTC
31364169 TTATTTTTTC
1 TT-TTTTTTC
*
31364179 CTTTTTTTC
1 TTTTTTTTC
31364188 TTTTTTTTC
1 TTTTTTTTC
31364197 TT
1 TT
31364199 GCCTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 22 0.63
10 13 0.37
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.84
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:31367589 original size:39 final size:40
Alignment explanation
Indices: 31367519--31367595 Score: 95
Period size: 39 Copynumber: 1.9 Consensus size: 40
31367509 AATAAGGAAA
* * *
31367519 ATGTATATGAATTATAAAATATAAATGTATAT-AAAAACC
1 ATGTAAATGAATAATAAAATATAAATATATATGAAAAACC
*
31367558 ATGTAAATAGAATAATAAAA-ATATATATATATGAAAAA
1 ATGTAAAT-GAATAATAAAATATAAATATATATGAAAAA
31367596 AAAATGCACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 17 0.53
40 15 0.47
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (40 bp):
ATGTAAATGAATAATAAAATATAAATATATATGAAAAACC
Found at i:31367618 original size:22 final size:23
Alignment explanation
Indices: 31367580--31367642 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
31367570 TAATAAAAAT
* *
31367580 ATATATATATGAAAAAAAAATGCAC
1 ATATAT-TAT-AAAAATATATGCAC
* *
31367605 ATGTATTTATAAAAATATATGCAT
1 ATATA-TTATAAAAATATATGCAC
31367629 ATATATTATAAAAA
1 ATATATTATAAAAA
31367643 GAAATACGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 9 0.28
24 15 0.47
25 7 0.22
26 1 0.03
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (23 bp):
ATATATTATAAAAATATATGCAC
Found at i:31369422 original size:9 final size:9
Alignment explanation
Indices: 31369372--31369429 Score: 73
Period size: 9 Copynumber: 6.4 Consensus size: 9
31369362 TTTTGTTAAA
31369372 AATTAACCG
1 AATTAACCG
*
31369381 GATT-ACCTG
1 AATTAACC-G
*
31369390 AATTAATCG
1 AATTAACCG
*
31369399 AATTACCCG
1 AATTAACCG
31369408 AATTAACCG
1 AATTAACCG
31369417 AATTAACCG
1 AATTAACCG
31369426 AATT
1 AATT
31369430 GAATCACTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 3 0.07
9 36 0.88
10 2 0.05
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:31369571 original size:18 final size:18
Alignment explanation
Indices: 31369531--31369574 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31369521 TAATTTTATG
**
31369531 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
31369549 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
31369567 CTTGGGTT
1 ATTGGGTT
31369575 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:31370162 original size:24 final size:24
Alignment explanation
Indices: 31370129--31370176 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
31370119 AATCTAACAT
*
31370129 CATATAAACATTATCATATATCTA
1 CATATAAACATTACCATATATCTA
*
31370153 CATATGAACATTACCATATATCTA
1 CATATAAACATTACCATATATCTA
31370177 TGCCTTGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (24 bp):
CATATAAACATTACCATATATCTA
Found at i:31373972 original size:17 final size:17
Alignment explanation
Indices: 31373952--31374002 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
31373942 TGGTTTAATG
* *
31373952 ATTTTTATTGTTTGTTT
1 ATTTTTATTATTTATTT
*
31373969 ATTTTTCTTATTTATTT
1 ATTTTTATTATTTATTT
**
31373986 ATTTTCGTTATTTATTT
1 ATTTTTATTATTTATTT
31374003 TTATCTCAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.75
Consensus pattern (17 bp):
ATTTTTATTATTTATTT
Found at i:31376632 original size:50 final size:50
Alignment explanation
Indices: 31376566--31376754 Score: 256
Period size: 50 Copynumber: 3.8 Consensus size: 50
31376556 TCTTGTACTA
* * **
31376566 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATACT-GGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTCGGTG
* **
31376616 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
31376666 CCAATGCCATGTCCCAGACATGGTCATACATGGGACCTCTTATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
31376716 CCAACT-CCATGTCCTAGACATGGTCTTACATGGGACCTC
1 CCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTC
31376755 ATTCCCTTAA
Statistics
Matches: 123, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 2 0.02
50 120 0.98
51 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:31384055 original size:4 final size:4
Alignment explanation
Indices: 31384046--31384076 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
31384036 GTTGTAAAGT
31384046 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
31384077 TACTTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:31392088 original size:50 final size:50
Alignment explanation
Indices: 31392012--31392202 Score: 231
Period size: 50 Copynumber: 3.8 Consensus size: 50
31392002 TTTCTTGTAC
* * **
31392012 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATACT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTCGG
* * **
31392062 TGCCCATGCCATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * * * *
31392112 TGCTAACGCCATGTCCCAAACATGATCATACATGGGACCTCTTATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
31392162 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC
31392203 ATTCCCTTAA
Statistics
Matches: 116, Mismatches: 24, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
49 2 0.02
50 114 0.98
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31396880 original size:6 final size:6
Alignment explanation
Indices: 31396869--31396895 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31396859 AACAATTTTG
31396869 TTTAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTT
31396896 TTCTTTTAAT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:31403139 original size:25 final size:25
Alignment explanation
Indices: 31403103--31403169 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
31403093 TCTCGAGCCA
*
31403103 TATAAC-AGGAAGCTCATCTGAA-CTG
1 TATAACGA-GAAGCTCAT-TCAAGCTG
*
31403128 TATAACGAGAAGCTTATTCAAGCTG
1 TATAACGAGAAGCTCATTCAAGCTG
* *
31403153 TATACCGGGAAGCTCAT
1 TATAACGAGAAGCTCAT
31403170 GCGAGCCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 3 0.09
25 31 0.89
26 1 0.03
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (25 bp):
TATAACGAGAAGCTCATTCAAGCTG
Found at i:31404091 original size:35 final size:35
Alignment explanation
Indices: 31404046--31404123 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
31404036 TTTTCTACCA
31404046 TAAAA-CTTCATAATTTAACTATATTCATCCATGG
1 TAAAACCTTCATAATTTAACTATATTCATCCATGG
31404080 TAAAACCTTCATAATTTAACTATATTCATCCATGG
1 TAAAACCTTCATAATTTAACTATATTCATCCATGG
31404115 TAAAACCTT
1 TAAAACCTT
31404124 AGTACTTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 5 0.12
35 38 0.88
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (35 bp):
TAAAACCTTCATAATTTAACTATATTCATCCATGG
Found at i:31416353 original size:18 final size:17
Alignment explanation
Indices: 31416330--31416363 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31416320 TTAATAATAA
31416330 TAATTAAAATTTTTATTC
1 TAATT-AAATTTTTATTC
*
31416348 TAATTAGATTTTTATT
1 TAATTAAATTTTTATT
31416364 GTTTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
TAATTAAATTTTTATTC
Found at i:31416398 original size:13 final size:13
Alignment explanation
Indices: 31416380--31416405 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31416370 AATTAAAAAT
31416380 TATTGAAGATAAA
1 TATTGAAGATAAA
31416393 TATTGAAGATAAA
1 TATTGAAGATAAA
31416406 AAAAATAGAA
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:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
TATTGAAGATAAA
Found at i:31425776 original size:23 final size:23
Alignment explanation
Indices: 31425750--31425871 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
31425740 ATAAGTGCCA
31425750 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
31425773 CACTGATACGTAGTCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
31425796 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
31425819 CACTGATATGTAGCC-ATAGCTAC
1 CACTGATATGTAGCCGA-AGCTAC
* *
31425842 CATTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
31425865 CACTGAT
1 CACTGAT
31425872 CAATAACACT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
22 1 0.01
23 83 0.98
24 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:31425817 original size:46 final size:46
Alignment explanation
Indices: 31425750--31425871 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
31425740 ATAAGTGCCA
* * *
31425750 CACTGATATGTAGCCGAAGCTACCACTGATACGTAGTCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
*
31425796 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
*
31425842 CATTGAAATGTAGCCGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
31425872 CAATAACACT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
Found at i:31440059 original size:19 final size:19
Alignment explanation
Indices: 31440035--31440082 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
31440025 TAAGTTACTG
31440035 AACCATTCAAAGGAATTCA
1 AACCATTCAAAGGAATTCA
31440054 AACCATTCAAAGGAATTCA
1 AACCATTCAAAGGAATTCA
31440073 AACCATTCAA
1 AACCATTCAA
31440083 TTTGTCTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.48, C:0.23, G:0.08, T:0.21
Consensus pattern (19 bp):
AACCATTCAAAGGAATTCA
Found at i:31441361 original size:108 final size:108
Alignment explanation
Indices: 31441197--31441415 Score: 393
Period size: 108 Copynumber: 2.0 Consensus size: 108
31441187 ATACAACATA
* *
31441197 CTTGTAAAATAAAATATGTTATGTTTTATTCTTTAGTCGATTGTTAAAAAATGAACCTTGTCGCA
1 CTTGTAAAATAAAATATGTTATGTTTTATTCTTTAGTCGATTGTTAAAAAACGAACCTTGTCACA
31441262 TAAGTAAAATTTCAAATAAGATTACTGGAACAACTATTGTTCC
66 TAAGTAAAATTTCAAATAAGATTACTGGAACAACTATTGTTCC
*
31441305 CTTGTACAATAAAATATGTTATGTTTTATTCTTTAGTCGATTGTTAAAAAACGAACCTTGTCACA
1 CTTGTAAAATAAAATATGTTATGTTTTATTCTTTAGTCGATTGTTAAAAAACGAACCTTGTCACA
* *
31441370 TAAGTAAAATTTCAAATAGGATTACTGGAGCAACTATTGTTCC
66 TAAGTAAAATTTCAAATAAGATTACTGGAACAACTATTGTTCC
31441413 CTT
1 CTT
31441416 TCAGAAATTC
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (108 bp):
CTTGTAAAATAAAATATGTTATGTTTTATTCTTTAGTCGATTGTTAAAAAACGAACCTTGTCACA
TAAGTAAAATTTCAAATAAGATTACTGGAACAACTATTGTTCC
Found at i:31443277 original size:28 final size:28
Alignment explanation
Indices: 31443235--31443290 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
31443225 GTATACTCTG
31443235 ACAATATTTACATATAAATTCATGAGTA
1 ACAATATTTACATATAAATTCATGAGTA
*
31443263 ACAATATTTATATATAAATTCATGAGTA
1 ACAATATTTACATATAAATTCATGAGTA
31443291 TGAGGAAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (28 bp):
ACAATATTTACATATAAATTCATGAGTA
Found at i:31443982 original size:20 final size:19
Alignment explanation
Indices: 31443940--31443976 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
31443930 TAAAAATTCT
31443940 ATTTAAAACACTAGAAAAA
1 ATTTAAAACACTAGAAAAA
*
31443959 ATTTAAAA-ATTAGAAAAA
1 ATTTAAAACACTAGAAAAA
31443977 CAATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (19 bp):
ATTTAAAACACTAGAAAAA
Found at i:31449868 original size:23 final size:22
Alignment explanation
Indices: 31449838--31449886 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
31449828 ATTTTTAGCA
31449838 TCTGAAGAAGAACCACTTGTAGG
1 TCTGAAGAAGAACCACTTGTA-G
*
31449861 TCTGAAGAAGAACCTCTTGTAG
1 TCTGAAGAAGAACCACTTGTAG
31449883 TCTG
1 TCTG
31449887 TGTTATACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (22 bp):
TCTGAAGAAGAACCACTTGTAG
Found at i:31450677 original size:19 final size:17
Alignment explanation
Indices: 31450652--31450696 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
31450642 TGGTGAGAAG
31450652 TAAAAGTTTGGGGGGAAA
1 TAAAAGTTTGGGGGG-AA
*
31450670 TAAAAAGTTT-TGGGGAA
1 T-AAAAGTTTGGGGGGAA
31450687 TAAAAGTTTG
1 TAAAAGTTTG
31450697 AGGGAAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 5 0.21
19 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (17 bp):
TAAAAGTTTGGGGGGAA
Found at i:31451075 original size:9 final size:9
Alignment explanation
Indices: 31451061--31451097 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31451051 TATAGTTTGA
31451061 TATTCGAAT
1 TATTCGAAT
31451070 TATTCGAAT
1 TATTCGAAT
*
31451079 TATTCGAGT
1 TATTCGAAT
31451088 TATTCGAAT
1 TATTCGAAT
31451097 T
1 T
31451098 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:31455228 original size:4 final size:4
Alignment explanation
Indices: 31455219--31455243 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31455209 CAATTCTGTC
31455219 CAAA CAAA CAAA CAAA CAAA CAAA C
1 CAAA CAAA CAAA CAAA CAAA CAAA C
31455244 GATTCTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:31459014 original size:60 final size:60
Alignment explanation
Indices: 31458913--31459033 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
31458903 CTGGAAACAA
* * * *
31458913 AGAAGCAAATTGGGCCTAATAAATAAACAAAATAAAGTAAAATAAAACTTGTGCTTATCC
1 AGAAACAAATTGGGCCTAATAAATAAACAAAACAAAATAAAATAAAACTCGTGCTTATCC
31458973 AGAAACAAATTGGGCCTAATAAATAAACAAAACAAAATAAAATAAAACTCGTGCTTATCC
1 AGAAACAAATTGGGCCTAATAAATAAACAAAACAAAATAAAATAAAACTCGTGCTTATCC
31459033 A
1 A
31459034 AACCCAGTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (60 bp):
AGAAACAAATTGGGCCTAATAAATAAACAAAACAAAATAAAATAAAACTCGTGCTTATCC
Found at i:31467981 original size:43 final size:42
Alignment explanation
Indices: 31467812--31467981 Score: 164
Period size: 43 Copynumber: 4.0 Consensus size: 42
31467802 CATAATAGCT
* * * * *
31467812 CATACAATGCC-ATATCCCAGATATGGTTTTACATGTTATCA
1 CATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
* * * * *
31467853 CATATCGATGCCACTG-CCCAGACAGGGTCTTATACGAAATCA
1 CATA-CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
* *
31467895 TATGACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
1 CAT-ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
* * *
31467938 CAATACAATACCAATGTCCCAGACATGGTCTTACATGTTATCA
1 C-ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
31467981 C
1 C
31467982 CTCTCAGTAA
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
41 4 0.04
42 37 0.36
43 61 0.59
44 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (42 bp):
CATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
Found at i:31471783 original size:13 final size:13
Alignment explanation
Indices: 31471765--31471789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31471755 TTTTTTTATT
31471765 TTTCATTTATTTA
1 TTTCATTTATTTA
31471778 TTTCATTTATTT
1 TTTCATTTATTT
31471790 CTTTATTATT
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:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCATTTATTTA
Found at i:31471868 original size:24 final size:23
Alignment explanation
Indices: 31471802--31471883 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
31471792 TTATTATTGG
* *
31471802 TTTTATAAAATTTTAAATGTATA
1 TTTTTTAAAATTTTAAATATATA
*
31471825 --TTTTAAATGTTTTATAATAT-TA
1 TTTTTTAAA-ATTTTA-AATATATA
31471847 TTTTTTAAAATTTTAAATATATA
1 TTTTTTAAAATTTTAAATATATA
*
31471870 TATTTTAAAATTTT
1 TTTTTTAAAATTTT
31471884 TATTTTTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
21 6 0.12
22 12 0.24
23 24 0.49
24 7 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTTTAAAATTTTAAATATATA
Found at i:31471930 original size:21 final size:22
Alignment explanation
Indices: 31471886--31471929 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
31471876 AAAATTTTTA
*
31471886 TTTTTTAAATTCTAAATATTAT
1 TTTTTTAAATTATAAATATTAT
31471908 TTTTTTAATATTATAAAATATT
1 TTTTTTAA-ATTAT-AAATATT
31471930 TAAATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTTTAAATTATAAATATTAT
Found at i:31472048 original size:20 final size:21
Alignment explanation
Indices: 31472006--31472050 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
31471996 ATATTTTAAA
31472006 AATTTTAAATATATATATTTT
1 AATTTTAAATATATATATTTT
*
31472027 AATTTTAAATATA-ATTTTTT
1 AATTTTAAATATATATATTTT
31472047 AATT
1 AATT
31472051 ATTTTTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTTTAAATATATATATTTT
Found at i:31472188 original size:13 final size:13
Alignment explanation
Indices: 31472172--31472224 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 13
31472162 TAAAAAAGAG
*
31472172 ATTAAAAATACAT
1 ATTAAAAATATAT
31472185 ATTAGAAAAGTTATATAT
1 ATTA-AAAA--TA--TAT
31472203 ATTAAAAATATAT
1 ATTAAAAATATAT
31472216 ATTAAAAAT
1 ATTAAAAAT
31472225 TAAAAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 16 0.47
14 4 0.12
15 2 0.06
16 2 0.06
17 4 0.12
18 6 0.18
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (13 bp):
ATTAAAAATATAT
Found at i:31472235 original size:31 final size:31
Alignment explanation
Indices: 31472172--31472233 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
31472162 TAAAAAAGAG
*
31472172 ATTAAAAATACATATTAGAAAAGTTATATAT
1 ATTAAAAATACATATTAGAAAAGTTAAATAT
* *
31472203 ATTAAAAATATATATTA-AAAA-TTAAAAAT
1 ATTAAAAATACATATTAGAAAAGTTAAATAT
31472232 AT
1 AT
31472234 ATATTATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.29
30 4 0.14
31 16 0.57
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (31 bp):
ATTAAAAATACATATTAGAAAAGTTAAATAT
Found at i:31472239 original size:13 final size:13
Alignment explanation
Indices: 31472197--31472224 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31472187 TAGAAAAGTT
31472197 ATATATATTAAAA
1 ATATATATTAAAA
31472210 ATATATATTAAAA
1 ATATATATTAAAA
31472223 AT
1 AT
31472225 TAAAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATATATTAAAA
Found at i:31476551 original size:30 final size:29
Alignment explanation
Indices: 31476515--31476615 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 29
31476505 CGTAGAGCAA
*
31476515 TTCATATCATCCGGATATGGGCGGTTCGAG
1 TTCATATCA-CCGGACATGGGCGGTTCGAG
* *
31476545 TTCATATCACCCGAACATGGGTGGTTCGAG
1 TTCATATCA-CCGGACATGGGCGGTTCGAG
*
31476575 TTCATATCACCTGGACATGGGCAGCTT-GAG
1 TTCATATCACC-GGACATGGGC-GGTTCGAG
31476605 TTCATATCACC
1 TTCATATCACC
31476616 CAGAGCAACC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
29 2 0.03
30 57 0.92
31 3 0.05
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.29
Consensus pattern (29 bp):
TTCATATCACCGGACATGGGCGGTTCGAG
Done.