Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 60 of 226
Found at i:19475402 original size:16 final size:16
Alignment explanation
Indices: 19475378--19475411 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19475368 CATTTCACTA
*
19475378 TTATATCTTTTGTATT
1 TTATATCTTTTATATT
*
19475394 TTATGTCTTTTATATT
1 TTATATCTTTTATATT
19475410 TT
1 TT
19475412 GCATGCATAG
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:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (16 bp):
TTATATCTTTTATATT
Found at i:19480382 original size:23 final size:24
Alignment explanation
Indices: 19480330--19480380 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
19480320 AAAGAACAAG
*
19480330 AAAATAGCAACAAAACAATAAAAA
1 AAAACAGCAACAAAACAATAAAAA
* *
19480354 AAAACAGCAACAAAATAGTAAAAA
1 AAAACAGCAACAAAACAATAAAAA
19480378 AAA
1 AAA
19480381 CATTCGGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.75, C:0.12, G:0.06, T:0.08
Consensus pattern (24 bp):
AAAACAGCAACAAAACAATAAAAA
Found at i:19481564 original size:11 final size:12
Alignment explanation
Indices: 19481537--19481565 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
19481527 TAATTTTAAT
19481537 TTTTTAAAATAC
1 TTTTTAAAATAC
19481549 TTTTTAAAATAC
1 TTTTTAAAATAC
19481561 TTTTT
1 TTTTT
19481566 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTAAAATAC
Found at i:19481584 original size:20 final size:19
Alignment explanation
Indices: 19481549--19481586 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19481539 TTTAAAATAC
*
19481549 TTTTTAAAATACTTTTTTA
1 TTTTTAAAATAATTTTTTA
*
19481568 TTTTTAAAATAAATTTTTA
1 TTTTTAAAATAATTTTTTA
19481587 GTGTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATAATTTTTTA
Found at i:19511789 original size:16 final size:16
Alignment explanation
Indices: 19511768--19511801 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
19511758 TTTAAATAAA
19511768 ATTAAAACTAATTGTT
1 ATTAAAACTAATTGTT
*
19511784 ATTAAAATTAATTGTT
1 ATTAAAACTAATTGTT
19511800 AT
1 AT
19511802 ACATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTAAAACTAATTGTT
Found at i:19515735 original size:773 final size:772
Alignment explanation
Indices: 19513461--19516556 Score: 4903
Period size: 773 Copynumber: 4.0 Consensus size: 772
19513451 TACCAACTAC
* * * * *
19513461 AATTGGGAAGAAGAATTTTCCACCGAATGTCTTGGACATTAGATCTATGCATATGGGTCTTTCCC
1 AATTGGGAAGAAGAATTTTCCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTATTTCCC
*
19513526 TACTGCAAGCCGCTTGTACAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* * *
19513591 TATTGTGGTTGCACAAGACTGGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTGGAGTTGG
131 TATTGTGGTTGCACAAGACTGGAACCAGAACTTGCTACTGATAGTGTTTGCCATTGTAGAGTTAG
* *
19513656 AGAACATGAAATCGCCAGAATTCTTCTTGACGAACTTGAGGACGTATGTTGTTAAAGAAGACAAT
196 AGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGA-AAT
* * * *
19513721 ATTTGTATCATATTTGATAGGTAGAAGACTAATTGCCGCGATTAGGCGCTCCGGTGTTCCATGAA
260 ATTTGCATCATATTCGATAGGTAGAAGACTAATTGCCGCGATTAGGAGTTCCGGTGTTCCATGAA
* * *
19513786 AATCTGTTTACTGTATCCATCATATTGCCACCTACTTCTACTGAGACTACATGAATGCAGACTAG
325 AATCTGTTTACTGTATCCACCATATTGCCACCAACTTCTACTGAGACTACAAGAATGCAGACTAG
*
19513851 CGCAAACAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATACTT
390 CGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATACTT
* *
19513916 CCATAAATTAATTCGAAAACGTAGCATGTCTTTTCGAAATATATACGCAGTGTACGAGCTGGAAC
455 CCATAAATTAATTCGAAAACGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGGAAC
19513981 AACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACTCTT
520 AACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACTCTT
*
19514046 TTTTTAGAGTGGTTGGGTACCATAGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCTCG
585 TTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCTCG
*
19514111 ATATGGTCATATGACCACCAACCTAACAAGTGTTATTAACTTTGTCTTGAAGCAAACACGACATT
650 ATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGACATT
* * *
19514176 TTCCAATTTTATTTATTTTTTCAACTATATTTTACAGACTGACAACATTTATGCCAAG
715 TTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACCGACAACATTTATGCCAAG
** *
19514234 AATTGGGAAGAAGAATTTTCCATAAAATGTCCTGGACATTCGATCTATGCATGTTGGTATTTCCC
1 AATTGGGAAGAAGAATTTTCCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTATTTCCC
* * *
19514299 TACTGCAAGCTGCTTGTGCAAGTTGATGACACCTGGTTATATGAAAAATATACGCAGATCCTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* *
19514364 TATTGTGGTTGCACAATA-TGGGAACCAGAACTTGCTACGGATAGTGTTTGCCATTGTAGAGTTA
131 TATTGTGGTTGCACAAGACT-GGAACCAGAACTTGCTACTGATAGTGTTTGCCATTGTAGAGTTA
* * *
19514428 AAGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGCGGATGTATGTTGTTAGAGAAGACAA
195 GAGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGA-AA
* * *
19514493 TATTTGCATCATATTCGATAGGTAGAAGAGACTAATTGCTGTGATTAGGAGTTTCGGTGTTCCAT
259 TATTTGCATCATATTCGATAGGTAG-A-AGACTAATTGCCGCGATTAGGAGTTCCGGTGTTCCAT
* * * **
19514558 GAAAATCTCTTTACAGTATCCGCCATATCACCACCAACTTCTACTGAGACTACAAGAATGCAGAC
322 GAAAATCTGTTTACTGTATCCACCATATTGCCACCAACTTCTACTGAGACTACAAGAATGCAGAC
19514623 TAGCGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATA-TCTTAATA
387 TAGCGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATA
* *
19514687 CTTCCATAAATTAATTCGAAAATGTAGCTTGTCTTTTCGAAATACATACGCAGCGTACGAGCTGG
452 CTTCCATAAATTAATTCGAAAACGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGG
* *
19514752 AACAACACTGTTTCAAGCAAAGGCTGACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACA
517 AACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACT
*
19514817 CTTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAACTCAAAGTTTTGATGACGGATC
582 CTTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATC
* *
19514882 TCGATATGGTCATATGACCACCAACCTGACAAATGTTATTAACTTTTTCTTGAAGCAAACACGAC
647 TCGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGAC
* *
19514947 ATTTTTTAATTTTATTTATTTTCTCAACTATATTTTACAGGCCG-CAAACATTTATGCCAAG
712 ATTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACCGAC-AACATTTATGCCAAG
* * * *
19515008 AATTGGAAAGAAGAATTTTTCACCAAATGTCCTGGATATTCGATCTATGCATGTGGGTCTTTCCC
1 AATTGGGAAGAAGAATTTTCCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTATTTCCC
* *
19515073 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGATTATACGAAAAATATACGCAGATACTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* * * *
19515138 TATTATAGTTGCACAAGA-TGAATACCAGAACTTGCTACTGATAGTGTTTGCCATTGTAGAGTTG
131 TATTGTGGTTGCACAAGACTGGA-ACCAGAACTTGCTACTGATAGTGTTTGCCATTGTAGAGTTA
* *
19515202 GAGAACATGAAATCGCCAGAATTCTTCTTGACGAACTTGAGGACGTATGTTGTTAGAGAAG-ATT
195 GAGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGAAAT
* * * *
19515266 ATTTGCATCATATTCGATAAGTAGAAGAGACTAATTGCCGCGATTAGGAGATCCGATGTTTCATG
260 ATTTGCATCATATTCGATAGGTAG-A-AGACTAATTGCCGCGATTAGGAGTTCCGGTGTTCCATG
* * * *
19515331 AAAATCTGTTTACTGTATCCGCCATATTGCCGCCAACTTCCACTGAGACTACAAGAATGCAGAAT
323 AAAATCTGTTTACTGTATCCACCATATTGCCACCAACTTCTACTGAGACTACAAGAATGCAGACT
*
19515396 AGCGCAAA-ATAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTATTAATA
388 AGCGCAAATA-AGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATA
*
19515460 CTTCCATAAATTAATTCGAAAACGTAGCATGTCTTTTTGAAATACATACGCAGCGTACGAGCTGG
452 CTTCCATAAATTAATTCGAAAACGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGG
*
19515525 AACAACACTGTTTCAAGCAAAGGCTGACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACT
517 AACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACT
* *
19515590 CTTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTTATGACAGATC
582 CTTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATC
19515655 TCGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGAC
647 TCGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGAC
**
19515720 ATTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACTAACAACATTTATGCCAAG
712 ATTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACCGACAACATTTATGCCAAG
* * * *
19515781 AATTGGGAAGAAGAATTTTTCACCAAATGTCCTGGATATTCGATTTATGCATGTAGGTATTTCCC
1 AATTGGGAAGAAGAATTTTCCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTATTTCCC
* *
19515846 TACTGCATGCCGCTTGTGCAGGTTGATGACACCTGGTTATACAAAAAATATACGCAGATCCTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* * * * * * *
19515911 TATTGTGGTCGCACAATACGGGAACCATAACTTACTA-TCAATAGTGTTTGCCATTGTGGAGTTA
131 TATTGTGGTTGCACAAGACTGGAACCAGAACTTGCTACT-GATAGTGTTTGCCATTGTAGAGTTA
* *
19515975 GAGAATATGAAATCGCCAGAATTCTTCCTGACGAACTTGCAGG-CATATGTTGTTAGAGAAGACA
195 GAGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTG-AGGACGTATGTTGTTAGAGAAGA-A
* * * *
19516039 ATATTTGCATCATATTTGATAGGTAGAAGACTAATTGTCGCGATTAGGTGTTCTGGTGTTCCATG
258 ATATTTGCATCATATTCGATAGGTAGAAGACTAATTGCCGCGATTAGGAGTTCCGGTGTTCCATG
* * * * * *
19516104 AAAATCTATTTACTGTATCCACCACACTGCTACCAACTTCTACCGAGACTACATGAATGCAGACT
323 AAAATCTGTTTACTGTATCCACCATATTGCCACCAACTTCTACTGAGACTACAAGAATGCAGACT
*
19516169 AGGGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATAC
388 AGCGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATAC
* * * ** *
19516234 TTCCATAATTTAATTCGAAAAGGTAGCTTGTCTTTTCGAAATACATACATAGCGTACGAACTGGA
453 TTCCATAAATTAATTCGAAAACGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGGA
* *
19516299 ACAACACTGTTTCAAACAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTAAAACGAATACTC
518 ACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACTC
*
19516364 TTTTTTTTGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCT
583 TTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCT
* * *
19516429 CGATATGGTCATATGACCACTAACCTGACAAATGTTATTAACTTTGTCTTGAAGCAAACACAACA
648 CGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGACA
* ** **
19516494 TTTTCTAATTTTATTTATTTTTTCAACTATATTTTACAGATTGGTAACATTTATGCCAAG
713 TTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACCGACAACATTTATGCCAAG
19516554 AAT
1 AAT
19516557 GAGGCTAAAA
Statistics
Matches: 2141, Mismatches: 168, Indels: 28
0.92 0.07 0.01
Matches are distributed among these distances:
771 1 0.00
772 173 0.08
773 1249 0.58
774 550 0.26
775 168 0.08
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (772 bp):
AATTGGGAAGAAGAATTTTCCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTATTTCCC
TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
TATTGTGGTTGCACAAGACTGGAACCAGAACTTGCTACTGATAGTGTTTGCCATTGTAGAGTTAG
AGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGAAATA
TTTGCATCATATTCGATAGGTAGAAGACTAATTGCCGCGATTAGGAGTTCCGGTGTTCCATGAAA
ATCTGTTTACTGTATCCACCATATTGCCACCAACTTCTACTGAGACTACAAGAATGCAGACTAGC
GCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATACTTC
CATAAATTAATTCGAAAACGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGGAACA
ACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACTCTTT
TTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCTCGA
TATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGACATTT
TCTAATTTTATTTATTTTCTCAACTATATTTTACAGACCGACAACATTTATGCCAAG
Found at i:19519855 original size:43 final size:43
Alignment explanation
Indices: 19519808--19520031 Score: 274
Period size: 43 Copynumber: 5.2 Consensus size: 43
19519798 TATAGACCAT
* * *
19519808 GACCTTTAGTGGCGCTTTTCCCACAAACGCCGCTATAAATCAG
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAAATCAA
* * * *
19519851 GACCTTTAGCGGTGATTTTTCCACAAACACCGCTATAGATCAA
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAAATCAA
* **
19519894 GACCTTTAGCGGCGCTTTTTTCACAAACGCCGCTATAGCTCAA
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAAATCAA
* *
19519937 GACCTTTAGTGGCGCTTTTTCCATAAACGCCGCTA-AAGATCAA
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAA-ATCAA
* **
19519980 GACCTTTAGCAGCGCTTTCCCCACAAACGCCGCTATAGAA-CAA
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATA-AATCAA
19520023 -ACCTTTAGC
1 GACCTTTAGC
19520032 AACGCTTCTC
Statistics
Matches: 156, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
42 10 0.06
43 143 0.92
44 2 0.01
45 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.26
Consensus pattern (43 bp):
GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAAATCAA
Found at i:19520050 original size:42 final size:42
Alignment explanation
Indices: 19519789--19520052 Score: 251
Period size: 43 Copynumber: 6.2 Consensus size: 42
19519779 TTTTAGAAAT
* * * * **
19519789 AAACGCTGTTATAGACCATGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCAGCGCTTTT-CCAC
* * * * *
19519832 AAACGCCGCTATAAATCAGGACCTTTAGCGGTGATTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCAGCG-CTTTTCCAC
* * *
19519875 AAACACCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTTCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCAGCGC-TTTTCCAC
* ** *
19519918 AAACGCCGCTATAGCTCAAGACCTTTAGTGGCGCTTTTTCCAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCAGCGC-TTTTCCAC
* *
19519961 AAACGCCGCTAAAGATCAAGACCTTTAGCAGCGCTTTCCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCAGCGCTTT-TCCAC
* * * *
19520004 AAACGCCGCTATAGAACAA-ACCTTTAGCAACGCTTCTCGCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCAGCGCTTTTC-CAC
19520046 AAACGCC
1 AAACGCC
19520053 ACTAAAAACA
Statistics
Matches: 186, Mismatches: 31, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 27 0.15
43 154 0.83
44 4 0.02
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCAGCGCTTTTCCAC
Found at i:19524224 original size:14 final size:15
Alignment explanation
Indices: 19524205--19524236 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
19524195 CTTAAACCAG
19524205 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
19524219 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
19524234 AAT
1 AAT
19524237 TTATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:19524305 original size:14 final size:14
Alignment explanation
Indices: 19524286--19524322 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
19524276 ATCCTAAATT
19524286 AACCATATACCCTA
1 AACCATATACCCTA
*
19524300 AACCATATACCTTA
1 AACCATATACCCTA
*
19524314 AATCATATA
1 AACCATATA
19524323 TATTAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
AACCATATACCCTA
Found at i:19524682 original size:41 final size:41
Alignment explanation
Indices: 19524637--19524715 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
19524627 ATAAAATGTT
* **
19524637 TTTGCGGCGCATT-TTCAAAAATATTGCTAAAGCCCCGAGCA
1 TTTGCGGCGC-TTCTTCAAAAACACCGCTAAAGCCCCGAGCA
**
19524678 TTTGCGGTTCTTCTTCAAAAACACCGCTAAAGCCCCGA
1 TTTGCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGA
19524716 AAGGTCAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 2 0.06
41 30 0.94
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (41 bp):
TTTGCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAGCA
Found at i:19537658 original size:23 final size:24
Alignment explanation
Indices: 19537594--19537658 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
19537584 ATGTATGCAT
*
19537594 ATAA-AAAATATTTATAAATATTAA
1 ATAATAAAATA-TAATAAATATTAA
19537618 ATAATAAAAT-TAAGTAAAT-TTAA
1 ATAATAAAATATAA-TAAATATTAA
19537641 AT-ATAAAATATACATAAA
1 ATAATAAAATATA-ATAAA
19537659 AATAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 7 0.19
23 14 0.39
24 10 0.28
25 5 0.14
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
ATAATAAAATATAATAAATATTAA
Found at i:19538847 original size:13 final size:13
Alignment explanation
Indices: 19538829--19538853 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19538819 GTATAGTAAA
19538829 ATATTTAAAAAAT
1 ATATTTAAAAAAT
19538842 ATATTTAAAAAA
1 ATATTTAAAAAA
19538854 AAAGAGATAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATTTAAAAAAT
Found at i:19539200 original size:28 final size:28
Alignment explanation
Indices: 19539168--19539251 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 28
19539158 AATCTACATG
19539168 AGGAAATAAATTTCTCATATTTTATTAT
1 AGGAAATAAATTTCTCATATTTTATTAT
* * *
19539196 AGG-AATCACATTGC-C--A-TGT-TTAT
1 AGGAAAT-AAATTTCTCATATTTTATTAT
19539219 AGGAAATAAATTTCTCATATTTTATTAT
1 AGGAAATAAATTTCTCATATTTTATTAT
19539247 AGGAA
1 AGGAA
19539252 TCACATTGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
23 12 0.28
24 6 0.14
25 1 0.02
26 1 0.02
27 6 0.14
28 17 0.40
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (28 bp):
AGGAAATAAATTTCTCATATTTTATTAT
Found at i:19539221 original size:23 final size:23
Alignment explanation
Indices: 19539192--19539270 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 23
19539182 TCATATTTTA
19539192 TTATAGGAATCACATTGCCATGT
1 TTATAGGAATCACATTGCCATGT
* * *
19539215 TTATAGGAAAT-AAATTTCTCATATTTT
1 TTATAGG-AATCACATTGC-C--A-TGT
19539242 ATTATAGGAATCACATTGCCATGT
1 -TTATAGGAATCACATTGCCATGT
19539266 TTATA
1 TTATA
19539271 AGAAAGTAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
23 17 0.40
24 6 0.14
25 1 0.02
26 1 0.02
27 6 0.14
28 12 0.28
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (23 bp):
TTATAGGAATCACATTGCCATGT
Found at i:19539224 original size:51 final size:51
Alignment explanation
Indices: 19539168--19539275 Score: 207
Period size: 51 Copynumber: 2.1 Consensus size: 51
19539158 AATCTACATG
19539168 AGGAAATAAATTTCTCATATTTTATTATAGGAATCACATTGCCATGTTTAT
1 AGGAAATAAATTTCTCATATTTTATTATAGGAATCACATTGCCATGTTTAT
19539219 AGGAAATAAATTTCTCATATTTTATTATAGGAATCACATTGCCATGTTTAT
1 AGGAAATAAATTTCTCATATTTTATTATAGGAATCACATTGCCATGTTTAT
*
19539270 AAGAAA
1 AGGAAA
19539276 GTAACTCCCA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (51 bp):
AGGAAATAAATTTCTCATATTTTATTATAGGAATCACATTGCCATGTTTAT
Found at i:19541142 original size:29 final size:27
Alignment explanation
Indices: 19541092--19541155 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
19541082 TGTAATTTTT
* *
19541092 AAAAATTATAAAAAATGCAAAAATATG
1 AAAAATTATAAAAAATACAAAAATATA
*
19541119 AAAAATTATATAAAAATTATAAAAATATA
1 AAAAATTATA-AAAAA-TACAAAAATATA
19541148 ACAAAATT
1 A-AAAATT
19541156 TTTTTTATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.32
28 5 0.16
29 10 0.32
30 6 0.19
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (27 bp):
AAAAATTATAAAAAATACAAAAATATA
Found at i:19542146 original size:24 final size:23
Alignment explanation
Indices: 19542118--19542163 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
19542108 TTTGGAGAAT
19542118 TTTGTATTT-ACGTTTTGAGGGTTC
1 TTTGT-TTTCACGTTTTG-GGGTTC
*
19542142 TTTGTTTTCAGGTTTTGGGGTT
1 TTTGTTTTCACGTTTTGGGGTT
19542164 TAGTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.09, C:0.07, G:0.28, T:0.57
Consensus pattern (23 bp):
TTTGTTTTCACGTTTTGGGGTTC
Found at i:19542611 original size:17 final size:17
Alignment explanation
Indices: 19542589--19542622 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19542579 ATCAAATACG
19542589 AACATTTCATATCATTT
1 AACATTTCATATCATTT
19542606 AACATTTCATATCATTT
1 AACATTTCATATCATTT
19542623 CCAGATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (17 bp):
AACATTTCATATCATTT
Found at i:19543589 original size:21 final size:21
Alignment explanation
Indices: 19543519--19543590 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
19543509 TCATGAGAGC
*
19543519 TAAACAAAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
* * * * *
19543540 TGAACGGAAGCTCGTAAGAGG-
1 TAAACAGAAACCCATAAG-GGT
* *
19543561 TGAGCAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
19543582 TAAACAGAA
1 TAAACAGAA
19543591 GCTTAAAAGA
Statistics
Matches: 36, Mismatches: 13, Indels: 4
0.68 0.25 0.08
Matches are distributed among these distances:
20 2 0.06
21 32 0.89
22 2 0.06
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.14
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGGGT
Found at i:19543613 original size:42 final size:42
Alignment explanation
Indices: 19543500--19543632 Score: 113
Period size: 42 Copynumber: 3.2 Consensus size: 42
19543490 CCGAAAGCTG
* ** * * *
19543500 AACAAAAGCTCATGAGAGCTAAACAAAAACCCATAAGGGTTG
1 AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
* ** * *
19543542 AACGGAAGCTCGTAAGAGGTGAGCAGAAACCCATAAGGGTTA
1 AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
* * ** * *
19543584 AACAGAAGCTTAAAAGAGCTGAACGGAAACTAATATGAGTTA
1 AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
19543626 AACAGAA
1 AACAGAA
19543633 ACTCGTGAGA
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:19547076 original size:20 final size:21
Alignment explanation
Indices: 19547038--19547076 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
19547028 TTGTTTTCAT
**
19547038 AATTTTATATAATTTTTTTGC
1 AATTTTATATAATAATTTTGC
19547059 AATTTT-TATAATAATTTT
1 AATTTTATATAATAATTTT
19547077 AATAGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
AATTTTATATAATAATTTTGC
Found at i:19547103 original size:9 final size:9
Alignment explanation
Indices: 19547062--19547141 Score: 56
Period size: 9 Copynumber: 8.6 Consensus size: 9
19547052 TTTTTGCAAT
19547062 TTTTATAATA
1 TTTT-TAATA
*
19547072 ATTTTAATA
1 TTTTTAATA
19547081 GTTTTT-ATA
1 -TTTTTAATA
19547090 TTTTTAATA
1 TTTTTAATA
19547099 TTTTTTGCAAT-
1 -TTTTT--AATA
* *
19547110 TTTATATTA
1 TTTTTAATA
19547119 TTTTTAATA
1 TTTTTAATA
* *
19547128 TATTTAATG
1 TTTTTAATA
19547137 TTTTT
1 TTTTT
19547142 TATAACTTGT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
8 7 0.13
9 29 0.53
10 16 0.29
12 3 0.05
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTTAATA
Found at i:19547104 original size:18 final size:18
Alignment explanation
Indices: 19547073--19547145 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
19547063 TTTATAATAA
*
19547073 TTTTAATAGTTTTTATAT
1 TTTTAATATTTTTTATAT
19547091 TTTTAATATTTTTTGCA-AT
1 TTTTAATATTTTTT--ATAT
* *
19547110 TTTATATTATTTTTAATAT
1 TTT-TAATATTTTTTATAT
* *
19547129 ATTTAATGTTTTTTATA
1 TTTTAATATTTTTTATA
19547146 ACTTGTCATT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
18 25 0.57
19 9 0.20
20 10 0.23
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTTAATATTTTTTATAT
Found at i:19547141 original size:47 final size:47
Alignment explanation
Indices: 19547047--19547141 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 47
19547037 TAATTTTATA
*
19547047 TAATTTTTTTGCAATTTTTATAATAATTTTAATAGTTTTTATATTTT
1 TAATTTTTTTGCAATTTTTATAATAATTTTAATAGTTTTAATATTTT
* * *
19547094 TAATATTTTTTGCAA-TTTTATATTATTTTTAATA-TATTTAATGTTTT
1 TAAT-TTTTTTGCAATTTTTATAATAATTTTAATAGT-TTTAATATTTT
19547141 T
1 T
19547142 TATAACTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 1 0.02
47 31 0.74
48 10 0.24
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (47 bp):
TAATTTTTTTGCAATTTTTATAATAATTTTAATAGTTTTAATATTTT
Found at i:19547220 original size:19 final size:21
Alignment explanation
Indices: 19547196--19547241 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
19547186 AAAGTTTAAG
*
19547196 TATTTTAAAT-ATTTTTTAT-
1 TATTTTAAATAAATTTTTATA
*
19547215 TATTTTTAATAAATTTTTATA
1 TATTTTAAATAAATTTTTATA
19547236 TATTTT
1 TATTTT
19547242 CAAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 8 0.35
21 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTAAATAAATTTTTATA
Found at i:19548612 original size:14 final size:14
Alignment explanation
Indices: 19548593--19548619 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19548583 TTCTATATTC
19548593 TCAATCCTCAATTT
1 TCAATCCTCAATTT
19548607 TCAATCCTCAATT
1 TCAATCCTCAATT
19548620 ATATTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (14 bp):
TCAATCCTCAATTT
Found at i:19549702 original size:63 final size:63
Alignment explanation
Indices: 19549626--19549759 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 63
19549616 TATTCCCCGT
* * * * * * * * *
19549626 ATCAAAACCTTCAACTCTAGTTTATTTTACCCAAGCACCATAGCATGCACAATCATTTCTTAC
1 ATCAACACATTCAACACTAGTTTATTTTACACAAGCACCACAACACGCACAATCATTCCCTAC
*
19549689 ATCAACACATTCAACACTAGTTTATTTTACACAAGCACCACAACACGCGCAATCATTCCCTAC
1 ATCAACACATTCAACACTAGTTTATTTTACACAAGCACCACAACACGCACAATCATTCCCTAC
19549752 ATCAACAC
1 ATCAACAC
19549760 CTTTAGGGAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.36, C:0.31, G:0.06, T:0.27
Consensus pattern (63 bp):
ATCAACACATTCAACACTAGTTTATTTTACACAAGCACCACAACACGCACAATCATTCCCTAC
Found at i:19552594 original size:104 final size:104
Alignment explanation
Indices: 19552477--19552672 Score: 313
Period size: 104 Copynumber: 1.9 Consensus size: 104
19552467 GGCCAAAAAG
* *
19552477 GTATCAATATTTTTTGAATTATCGATACCCCCTCTTAAAAGCGATACCAAAA-ATGCATTTTATT
1 GTATCAATATTTTTTGAATTATCGATACCCCATCTTAAAAGCAATACCAAAATA-GCATTTTATT
*
19552541 TTTCACAAACCCTACTAAGTATCGATACCTTTTTGGTCAA
65 TTTCACAAACCCTACGAAGTATCGATACCTTTTTGGTCAA
* * *
19552581 GTATCGATATTTTTTGAATTATCGATACCCTATCTTAAAAGCAATACCAAAATAGCATTTTGTTT
1 GTATCAATATTTTTTGAATTATCGATACCCCATCTTAAAAGCAATACCAAAATAGCATTTTATTT
*
19552646 TTCTCAAACCCTACGAAGTATCGATAC
66 TTCACAAACCCTACGAAGTATCGATAC
19552673 GGTATCGATA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
104 83 0.99
105 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.36
Consensus pattern (104 bp):
GTATCAATATTTTTTGAATTATCGATACCCCATCTTAAAAGCAATACCAAAATAGCATTTTATTT
TTCACAAACCCTACGAAGTATCGATACCTTTTTGGTCAA
Found at i:19555619 original size:18 final size:18
Alignment explanation
Indices: 19555559--19555620 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
19555549 ATAATGTAGA
*
19555559 TGAAAAAATAATGATATT
1 TGAAATAATAATGATATT
* *
19555577 TGAAAT-ATTAT-ACATAT
1 TGAAATAATAATGATAT-T
**
19555594 AAAAATAATAATGATATT
1 TGAAATAATAATGATATT
19555612 TGAAATAAT
1 TGAAATAAT
19555621 TATTTAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
16 3 0.09
17 9 0.28
18 17 0.53
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (18 bp):
TGAAATAATAATGATATT
Found at i:19556357 original size:20 final size:20
Alignment explanation
Indices: 19556324--19556362 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19556314 TATATAAAAA
19556324 TATTTTTAGAAAAACAAAATT
1 TATTTTTAGAAAAA-AAAATT
*
19556345 TATTTTT-GTAAAAAAAAT
1 TATTTTTAGAAAAAAAAAT
19556363 ATAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TATTTTTAGAAAAAAAAATT
Found at i:19559938 original size:43 final size:43
Alignment explanation
Indices: 19559872--19559957 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
19559862 ATTTGCCTGT
*
19559872 GTCAGATAGATGATATTCTTCTTTTACCAGTTGAAGTTTTACA
1 GTCAAATAGATGATATTCTTCTTTTACCAGTTGAAGTTTTACA
*
19559915 GTCAAATAGATGATATTCTTCTTTTACCAGTTTAAGTTTTACA
1 GTCAAATAGATGATATTCTTCTTTTACCAGTTGAAGTTTTACA
19559958 CTTTTTTGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (43 bp):
GTCAAATAGATGATATTCTTCTTTTACCAGTTGAAGTTTTACA
Found at i:19563098 original size:28 final size:26
Alignment explanation
Indices: 19563042--19563100 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
19563032 ATATTTTGGT
*
19563042 AAAATATTATTTTTAAAATTATAAAA
1 AAAATATTATTTTTAAAATAATAAAA
*
19563068 AAAATATT-TTTTGTACAAATAAATAATA
1 AAAATATTATTTT-TA-AAAT-AATAAAA
19563096 AAAAT
1 AAAAT
19563101 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 4 0.14
26 10 0.36
27 4 0.14
28 10 0.36
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAATATTATTTTTAAAATAATAAAA
Found at i:19566856 original size:21 final size:22
Alignment explanation
Indices: 19566824--19566867 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
19566814 ATGGTATATG
19566824 TTATAAATTATTTA-TATTAAA
1 TTATAAATTATTTATTATTAAA
19566845 TTATATAA-TATTTATTATTAAA
1 TTATA-AATTATTTATTATTAAA
19566867 T
1 T
19566868 ATTTATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATAAATTATTTATTATTAAA
Found at i:19569618 original size:14 final size:15
Alignment explanation
Indices: 19569588--19569618 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19569578 TACTTCTACA
19569588 TTTTGATGCCACTTT
1 TTTTGATGCCACTTT
*
19569603 TTTTTATGCCACTTT
1 TTTTGATGCCACTTT
19569618 T
1 T
19569619 GATTTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.19, G:0.10, T:0.58
Consensus pattern (15 bp):
TTTTGATGCCACTTT
Found at i:19569626 original size:61 final size:60
Alignment explanation
Indices: 19569492--19569609 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 60
19569482 AGTAGTTCTA
*
19569492 CATCTGCATTATTGAACAAAATCGATACTTCTACATTTTAATGCCACTTTTGATTTATTTG
1 CATCTGCATTATTGAACAAAATCGATACTTCTACATTTTAATGCCACTTTT-ATTTATATG
* *
19569553 CATCTGCATTATTGAACAAAATCGATACTTCTACATTTTGATGCCACTTTTTTTTAT
1 CATCTGCATTATTGAACAAAATCGATACTTCTACATTTTAATGCCACTTTTATTTAT
19569610 GCCACTTTTG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 5 0.09
61 50 0.91
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (60 bp):
CATCTGCATTATTGAACAAAATCGATACTTCTACATTTTAATGCCACTTTTATTTATATG
Found at i:19569658 original size:76 final size:76
Alignment explanation
Indices: 19569527--19569671 Score: 281
Period size: 76 Copynumber: 1.9 Consensus size: 76
19569517 TACTTCTACA
19569527 TTTTAATGCCACTTTTGATTTATTTGCATCTGCATTATTGAACAAAATCGATACTTCTACATTTT
1 TTTTAATGCCACTTTTGATTTATTTGCATCTGCATTATTGAACAAAATCGATACTTCTACATTTT
19569592 GATGCCACTTT
66 GATGCCACTTT
*
19569603 TTTTTATGCCACTTTTGATTTATTTGCATCTGCATTATTGAACAAAATCGATACTTCTACATTTT
1 TTTTAATGCCACTTTTGATTTATTTGCATCTGCATTATTGAACAAAATCGATACTTCTACATTTT
19569668 GATG
66 GATG
19569672 TTCTTTCAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (76 bp):
TTTTAATGCCACTTTTGATTTATTTGCATCTGCATTATTGAACAAAATCGATACTTCTACATTTT
GATGCCACTTT
Found at i:19570698 original size:44 final size:44
Alignment explanation
Indices: 19570636--19570719 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
19570626 TGATGGATTG
19570636 TTGTATTAACCAAATCATTTTCATATGCTTATCAAATATAAGTA
1 TTGTATTAACCAAATCATTTTCATATGCTTATCAAATATAAGTA
19570680 TTGTATTAACCAAATCATTTTCATATGCTTATCAAATATA
1 TTGTATTAACCAAATCATTTTCATATGCTTATCAAATATA
19570720 GCATCTAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (44 bp):
TTGTATTAACCAAATCATTTTCATATGCTTATCAAATATAAGTA
Found at i:19570715 original size:22 final size:22
Alignment explanation
Indices: 19570646--19570716 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
19570636 TTGTATTAAC
19570646 CAAATCATTTTCATATGCTTAT
1 CAAATCATTTTCATATGCTTAT
** * *
19570668 CAAAT-ATAAGT-AT-TGTATTAAC
1 CAAATCAT-TTTCATATG-CTT-AT
19570690 CAAATCATTTTCATATGCTTAT
1 CAAATCATTTTCATATGCTTAT
19570712 CAAAT
1 CAAAT
19570717 ATAGCATCTA
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 2 0.06
21 6 0.17
22 19 0.54
23 6 0.17
24 2 0.06
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (22 bp):
CAAATCATTTTCATATGCTTAT
Found at i:19576613 original size:21 final size:21
Alignment explanation
Indices: 19576587--19576629 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19576577 CTTTTCCTAA
*
19576587 AATATGAATTGGATTGAATTG
1 AATATGAATTGGATTAAATTG
*
19576608 AATATGAATTGTATTAAATTG
1 AATATGAATTGGATTAAATTG
19576629 A
1 A
19576630 GTTAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (21 bp):
AATATGAATTGGATTAAATTG
Found at i:19577049 original size:24 final size:23
Alignment explanation
Indices: 19576949--19577045 Score: 77
Period size: 24 Copynumber: 4.0 Consensus size: 23
19576939 CAGCTCGAAA
* * *
19576949 GAGCATCCCGTTATTAGCCCTCTC
1 GAGCTTCCCGTTAATAGCTCT-TC
* * *
19576973 GAGCTTTCCGTTATATTGTTCTTAC
1 GAGCTTCCCGTTA-ATAGCTCTT-C
* * *
19576998 GAGTTTCCCATTAATAGCTCTTGT
1 GAGCTTCCCGTTAATAGCTCTT-C
19577022 GAGCTTCCCGTTAATAGCTCTTC
1 GAGCTTCCCGTTAATAGCTCTTC
19577045 G
1 G
19577046 GAGCATCCTG
Statistics
Matches: 55, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
23 1 0.02
24 39 0.71
25 15 0.27
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (23 bp):
GAGCTTCCCGTTAATAGCTCTTC
Found at i:19577228 original size:24 final size:24
Alignment explanation
Indices: 19577209--19577268 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
19577199 GGAGCTTCTT
19577209 GTTAATGGCTCTTCGAAGCTACCC
1 GTTAATGGCTCTTCGAAGCTACCC
*
19577233 GTTATTGGCTCTTCGAAGCTACCC
1 GTTAATGGCTCTTCGAAGCTACCC
*
19577257 GTTATTGGCTCT
1 GTTAATGGCTCT
19577269 CATGAGCTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.35
Consensus pattern (24 bp):
GTTAATGGCTCTTCGAAGCTACCC
Found at i:19577276 original size:24 final size:23
Alignment explanation
Indices: 19577225--19577309 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 23
19577215 GGCTCTTCGA
19577225 AGCTACCCGTTATTGGCTCT-TCG
1 AGCTACCCGTTATTGGCTCTAT-G
19577248 AAGCTACCCGTTATTGGCTCTCATG
1 -AGCTACCCGTTATTGGCTCT-ATG
*
19577273 AGCTTCCCGATTA-TGGCTCTTATG
1 AGCTACCCG-TTATTGGCTC-TATG
*
19577297 AGCTTCCCGTTAT
1 AGCTACCCGTTAT
19577310 ACAGCCCTGA
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
23 3 0.05
24 46 0.84
25 5 0.09
26 1 0.02
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.35
Consensus pattern (23 bp):
AGCTACCCGTTATTGGCTCTATG
Found at i:19577364 original size:25 final size:25
Alignment explanation
Indices: 19577249--19577366 Score: 82
Period size: 25 Copynumber: 4.8 Consensus size: 25
19577239 GGCTCTTCGA
* *
19577249 AGCTACCCGTTAT-TGGCTC-TCATG
1 AGCTTCCCGTTATATAGCTCAT-ATG
* * *
19577273 AGCTTCCCGAT-TATGGCTCTTATG
1 AGCTTCCCGTTATATAGCTCATATG
* * *
19577297 AGCTTCCCGTTATACAGC-CCTGATA
1 AGCTTCCCGTTATATAGCTCAT-ATG
* *
19577322 AGCTTCTCGTTACATAGCTCATATG
1 AGCTTCCCGTTATATAGCTCATATG
* *
19577347 AGCTTCTCGTTATGTAGCTC
1 AGCTTCCCGTTATATAGCTC
19577367 GAGAGAGTGC
Statistics
Matches: 75, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
23 1 0.01
24 30 0.40
25 42 0.56
26 2 0.03
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (25 bp):
AGCTTCCCGTTATATAGCTCATATG
Found at i:19607037 original size:31 final size:31
Alignment explanation
Indices: 19606971--19607039 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
19606961 TCAAACAATT
* * *
19606971 CAATGACTTAAATCAAAATTTTTGAATAGTT
1 CAATAACTTAAATCAAAATTTTTAAATAGTC
* *
19607002 CAATAACTTAAATGAATATTTTTAAAT-GATC
1 CAATAACTTAAATCAAAATTTTTAAATAG-TC
19607033 CAATAAC
1 CAATAAC
19607040 CATCTTGAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (31 bp):
CAATAACTTAAATCAAAATTTTTAAATAGTC
Found at i:19607381 original size:86 final size:85
Alignment explanation
Indices: 19607280--19607437 Score: 230
Period size: 87 Copynumber: 1.8 Consensus size: 85
19607270 TTTTCTTCTG
* * *
19607280 CACTCAATTGAGTACTT-AACATTCAAAATGCATCAAAAAGGCCCTCAAACT-TCTTCAAAAAAA
1 CACTCAATTGAGTACTTGAACATTCAAAATGCATCAAAAAGACCCTAAAAATGT-TT--AAAAAA
19607343 GCAATTAAGCTCATACTTTTTTT
63 GCAATTAAGCTCATACTTTTTTT
* *
19607366 CACTCGATTGGGTACTTGAACATTCAAAATGCATCAAAAAGACCCTAAAAATGTTTAAAAAAGCA
1 CACTCAATTGAGTACTTGAACATTCAAAATGCATCAAAAAGACCCTAAAAATGTTTAAAAAAGCA
19607431 ATTAAGC
66 ATTAAGC
19607438 CCCTGCTATT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
85 16 0.25
86 15 0.23
87 33 0.51
88 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (85 bp):
CACTCAATTGAGTACTTGAACATTCAAAATGCATCAAAAAGACCCTAAAAATGTTTAAAAAAGCA
ATTAAGCTCATACTTTTTTT
Found at i:19607512 original size:19 final size:19
Alignment explanation
Indices: 19607470--19607506 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
19607460 GAAAAGATAA
19607470 AAAAATTTATTAATTTTAG
1 AAAAATTTATTAATTTTAG
19607489 AAAAA-TTATTGAATTTTA
1 AAAAATTTATT-AATTTTA
19607507 ATAAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
AAAAATTTATTAATTTTAG
Found at i:19607526 original size:20 final size:21
Alignment explanation
Indices: 19607489--19607533 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
19607479 TTAATTTTAG
* *
19607489 AAAAATTATTGAATTTTAATA
1 AAAAATTATTAAAGTTTAATA
*
19607510 AAAAATT-TTAAAGTTTATTA
1 AAAAATTATTAAAGTTTAATA
19607530 AAAA
1 AAAA
19607534 TTAGAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
AAAAATTATTAAAGTTTAATA
Found at i:19607795 original size:19 final size:18
Alignment explanation
Indices: 19607726--19607815 Score: 60
Period size: 19 Copynumber: 4.7 Consensus size: 18
19607716 TTATACCAAA
19607726 TTTATATTTATTTAC-ATT
1 TTTATATTT-TTTACAATT
*
19607744 TTGTATAATTTTCTTACAA-C
1 TT-TAT-ATTTT-TTACAATT
**
19607764 TTTATAAAATTTTACAATT
1 TTTAT-ATTTTTTACAATT
19607783 TTTATACTTTTTT-CTAATT
1 TTTATA-TTTTTTAC-AATT
19607802 TTTAATATTTTTTA
1 TTT-ATATTTTTTA
19607816 TTAAAATTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
18 10 0.18
19 33 0.58
20 13 0.23
21 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.01, T:0.61
Consensus pattern (18 bp):
TTTATATTTTTTACAATT
Found at i:19607852 original size:49 final size:46
Alignment explanation
Indices: 19607764--19607864 Score: 107
Period size: 49 Copynumber: 2.2 Consensus size: 46
19607754 TTCTTACAAC
* * *
19607764 TTTATAAAATTTTACAATTTTTATACTTTTTTCTAATTTTTAATATTT
1 TTTATAAAATTTAACAATATTTATACTTTTATCTAA-TTTTAAT-TTT
* *
19607812 TTTATTAAAATTTAATAATATTTATAGCTTTTAT-TGATTTTAA-TTT
1 TTTA-TAAAATTTAACAATATTTATA-CTTTTATCTAATTTTAATTTT
19607858 TTTATAA
1 TTTATAA
19607865 TTTTTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
45 3 0.07
46 7 0.15
48 10 0.22
49 20 0.43
50 6 0.13
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (46 bp):
TTTATAAAATTTAACAATATTTATACTTTTATCTAATTTTAATTTT
Found at i:19613842 original size:38 final size:38
Alignment explanation
Indices: 19613721--19613868 Score: 136
Period size: 38 Copynumber: 3.8 Consensus size: 38
19613711 TAAAGACATG
* * * ***
19613721 TATTAAAGATG-TCTAAACTAGGACATATTTAAAATATA
1 TATTAAAGATGTTC-AAATTATGACATAATTAAAACCCA
* * * *
19613759 TATTTAAGATGTCCTAAACTATGACATAATTAAAAACCCT
1 TATTAAAGATGTTC-AAATTATGACATAATT-AAAACCCA
* *
19613799 TATTAAAGATGTTCAGATTATGACATAATTAAAACTCA
1 TATTAAAGATGTTCAAATTATGACATAATTAAAACCCA
* *
19613837 TATTAATGATGTTTAAATTATGACATAATTAA
1 TATTAAAGATGTTCAAATTATGACATAATTAA
19613869 GTACTTAAAC
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 45 0.49
39 30 0.33
40 16 0.18
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (38 bp):
TATTAAAGATGTTCAAATTATGACATAATTAAAACCCA
Found at i:19616642 original size:19 final size:19
Alignment explanation
Indices: 19616618--19616654 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
19616608 TCAACTACTT
19616618 GCCTTTGAAGTTTCTTAGA
1 GCCTTTGAAGTTTCTTAGA
19616637 GCCTTTGAAGTTTCTTAG
1 GCCTTTGAAGTTTCTTAG
19616655 TTTCTTCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (19 bp):
GCCTTTGAAGTTTCTTAGA
Found at i:19617688 original size:39 final size:38
Alignment explanation
Indices: 19617645--19617772 Score: 129
Period size: 39 Copynumber: 3.3 Consensus size: 38
19617635 TCTAAACTAG
* *
19617645 GACATATTTAAAATATATATTTAAGATGTCCTAAATTAT
1 GACATAATTAAAATATATATTTAAGATGTTC-AAATTAT
* **
19617684 GACATAATTAAAA-ACCCT-TATTAAAGATGTTCAGGTTAT
1 GACATAATTAAAATA---TATATTTAAGATGTTCAAATTAT
19617723 GACATAATTAAAACT-TATA-TTAATGATGTTCAAATTAT
1 GACATAATTAAAA-TATATATTTAA-GATGTTCAAATTAT
19617761 GACATAATTAAA
1 GACATAATTAAA
19617773 GACTTAAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
37 4 0.05
38 27 0.36
39 30 0.41
40 12 0.16
41 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (38 bp):
GACATAATTAAAATATATATTTAAGATGTTCAAATTAT
Found at i:19617745 original size:38 final size:38
Alignment explanation
Indices: 19617628--19617784 Score: 149
Period size: 38 Copynumber: 4.1 Consensus size: 38
19617618 GACATGTGTC
* * *
19617628 AAAGATG-TCTAAACTAGGACATATTTAAAA-TATATATT
1 AAAGATGTTC-AAATTATGACATAATTAAAACT-TATATT
* * *
19617666 TAAGATGTCCTAAATTATGACATAATTAAAAACCCT-TATT
1 AAAGATGTTC-AAATTATGACATAATT-AAAA-CTTATATT
**
19617706 AAAGATGTTCAGGTTATGACATAATTAAAACTTATATT
1 AAAGATGTTCAAATTATGACATAATTAAAACTTATATT
* *
19617744 AATGATGTTCAAATTATGACATAATTAAAGACTTAAATT
1 AAAGATGTTCAAATTATGACATAATTAAA-ACTTATATT
19617783 AA
1 AA
19617785 TTTAACTAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
37 2 0.02
38 40 0.41
39 39 0.40
40 16 0.16
41 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (38 bp):
AAAGATGTTCAAATTATGACATAATTAAAACTTATATT
Found at i:19620311 original size:9 final size:9
Alignment explanation
Indices: 19620282--19620352 Score: 54
Period size: 10 Copynumber: 7.4 Consensus size: 9
19620272 TTTTATCTTT
19620282 TTTTTATAAA
1 TTTTTAT-AA
*
19620292 TTTCCTATAA
1 TTT-TTATAA
19620302 TTTTTATAA
1 TTTTTATAA
19620311 TATTTTATATA
1 T-TTTTATA-A
* *
19620322 TTGTTATAT
1 TTTTTATAA
19620331 TTATTTATAA
1 TT-TTTATAA
*
19620341 TTTCTAT-A
1 TTTTTATAA
19620349 TTTT
1 TTTT
19620353 ATGTATTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 4 0.08
9 12 0.24
10 28 0.57
11 5 0.10
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:19620330 original size:10 final size:9
Alignment explanation
Indices: 19620303--19620361 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
19620293 TTCCTATAAT
19620303 TTTTATAATA
1 TTTTAT-ATA
19620313 TTTTATATA
1 TTTTATATA
19620322 TTGTTATAT-
1 TT-TTATATA
19620331 TTATT-TATA
1 TT-TTATATA
* *
19620340 ATTTCTATA
1 TTTTATATA
*
19620349 TTTTATGTA
1 TTTTATATA
19620358 TTTT
1 TTTT
19620362 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
8 5 0.12
9 24 0.59
10 12 0.29
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTATATA
Found at i:19644851 original size:3 final size:3
Alignment explanation
Indices: 19644831--19644882 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
19644821 ATTCACCAAG
* *
19644831 ATA ATA ACA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATCA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
19644880 ATA
1 ATA
19644883 TATCATATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:19645070 original size:17 final size:17
Alignment explanation
Indices: 19645022--19645071 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
19645012 TTAACATAGG
*
19645022 TAATACATATAAAATAA
1 TAATACATATATAATAA
*
19645039 -AA-ACATA-ATAGTAA
1 TAATACATATATAATAA
*
19645053 TAATACATATATACTAA
1 TAATACATATATAATAA
19645070 TA
1 TA
19645072 TATATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.19
15 7 0.26
16 7 0.26
17 8 0.30
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (17 bp):
TAATACATATATAATAA
Found at i:19645534 original size:45 final size:45
Alignment explanation
Indices: 19645464--19645600 Score: 147
Period size: 45 Copynumber: 3.0 Consensus size: 45
19645454 TAAATAGTAC
* * *
19645464 ATAATGAATTTAAAATATTGATATATGTTAAAT-TTAAATAATATTA
1 ATAATAAATTTAAAATAATG-TATA-GTTAAATATTAAATAATACTA
19645510 ATAAT-AATTTAAAATAATAGTATA-TTAAATATTAAAATAATACTA
1 ATAATAAATTTAAAATAAT-GTATAGTTAAATATT-AAATAATACTA
* *
19645555 ATGATAAATTTAAAACAATGT-TAAGCTTAAATATTAAATAATACTA
1 ATAATAAATTTAAAATAATGTAT-AG-TTAAATATTAAATAATACTA
19645601 TTTGTCAAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
43 6 0.08
44 3 0.04
45 33 0.41
46 29 0.36
47 9 0.11
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (45 bp):
ATAATAAATTTAAAATAATGTATAGTTAAATATTAAATAATACTA
Found at i:19645567 original size:23 final size:22
Alignment explanation
Indices: 19645470--19645569 Score: 82
Period size: 23 Copynumber: 4.4 Consensus size: 22
19645460 GTACATAATG
* *
19645470 AATTTAAAATATTGATATATGTTA
1 AATTTAAAATAAT-ATA-ATGATA
*
19645494 AATTT-AAATAATATTAATAAT-
1 AATTTAAAATAATA-TAATGATA
19645515 AATTTAAAATAATAGT-AT-ATTA
1 AATTTAAAATAATA-TAATGA-TA
19645537 AATATTAAAATAATACTAATGATA
1 AAT-TTAAAATAATA-TAATGATA
19645561 AATTTAAAA
1 AATTTAAAA
19645570 CAATGTTAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.02
21 8 0.12
22 16 0.25
23 26 0.41
24 12 0.19
25 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTTAAAATAATATAATGATA
Found at i:19645594 original size:46 final size:44
Alignment explanation
Indices: 19645491--19645600 Score: 127
Period size: 46 Copynumber: 2.5 Consensus size: 44
19645481 TTGATATATG
* *
19645491 TTAAAT-TTAAATAATATTAATAATAATTTAAAATAATAGTATA
1 TTAAATATTAAATAATACTAATAATAATTTAAAACAATAGTATA
*
19645534 TTAAATATTAAAATAATACTAATGATAAATTTAAAACAAT-GT-TAA
1 TTAAATATT-AAATAATACTAATAAT-AATTTAAAACAATAGTAT-A
19645579 GCTTAAATATTAAATAATACTA
1 --TTAAATATTAAATAATACTA
19645601 TTTGTCAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
43 6 0.10
44 3 0.05
45 17 0.29
46 23 0.40
47 9 0.16
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (44 bp):
TTAAATATTAAATAATACTAATAATAATTTAAAACAATAGTATA
Found at i:19648428 original size:18 final size:19
Alignment explanation
Indices: 19648384--19648434 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
19648374 ATGTAAAAAT
19648384 TAAATTAA-AAAAATATAA
1 TAAATTAATAAAAATATAA
* * *
19648402 AAAAATAATAAAAAT-TAC
1 TAAATTAATAAAAATATAA
19648420 TAAATTAATAGAAAA
1 TAAATTAATA-AAAA
19648435 AAATTTTCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
TAAATTAATAAAAATATAA
Found at i:19656920 original size:61 final size:63
Alignment explanation
Indices: 19656849--19656983 Score: 175
Period size: 61 Copynumber: 2.2 Consensus size: 63
19656839 TCTCGATTAG
* * * * * *
19656849 TTGGGCGACCAAATTAAAAAAATTGATAGTTAGATG-CCAAAAAAG-AAAAAAGGGGCAATAA
1 TTGGGTGACCAAAATAAAAAAAATAATAATTAGATGACCAAAAAAGAAAAAAAAGGGCAATAA
* * *
19656910 TTGGGTGACCAAAATAAAAAAAATAATAATTGGGTGACCAAAAAAGAAAAAAAAGGGCAATAG
1 TTGGGTGACCAAAATAAAAAAAATAATAATTAGATGACCAAAAAAGAAAAAAAAGGGCAATAA
19656973 TTGGGTGACCA
1 TTGGGTGACCA
19656984 GTGGTGTAGT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 29 0.46
62 9 0.14
63 25 0.40
ACGTcount: A:0.50, C:0.10, G:0.22, T:0.18
Consensus pattern (63 bp):
TTGGGTGACCAAAATAAAAAAAATAATAATTAGATGACCAAAAAAGAAAAAAAAGGGCAATAA
Found at i:19656938 original size:29 final size:30
Alignment explanation
Indices: 19656905--19656962 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
19656895 AAAAAGGGGC
*
19656905 AATAATTGGGTGACCAAAATA-AAAAAAAT
1 AATAATTGGGTGACCAAAAAAGAAAAAAAT
19656934 AATAATTGGGTGACCAAAAAAGAAAAAAA
1 AATAATTGGGTGACCAAAAAAGAAAAAAA
19656963 AGGGCAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.60, C:0.07, G:0.16, T:0.17
Consensus pattern (30 bp):
AATAATTGGGTGACCAAAAAAGAAAAAAAT
Found at i:19658906 original size:23 final size:23
Alignment explanation
Indices: 19658878--19658925 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
19658868 CTTTTATTCA
19658878 AGTTTTAGTTTGCAACTTTATTT
1 AGTTTTAGTTTGCAACTTTATTT
* * *
19658901 AGTTTTAGTTTTCAATTTTCTTT
1 AGTTTTAGTTTGCAACTTTATTT
19658924 AG
1 AG
19658926 GTTATTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.08, G:0.12, T:0.58
Consensus pattern (23 bp):
AGTTTTAGTTTGCAACTTTATTT
Found at i:19659967 original size:187 final size:187
Alignment explanation
Indices: 19659650--19660022 Score: 710
Period size: 187 Copynumber: 2.0 Consensus size: 187
19659640 CCATTGGGCA
19659650 CGATTCTCAGATTACTTCCATACTTCATTGTATAAACTATATTACAACTTGACCCGTATACTTGC
1 CGATTCTCAGATTACTTCCATACTTCATTGTATAAACTATATTACAACTTGACCCGTATACTTGC
* *
19659715 GAAAACTGCCTAACAATATTTGGTTGCAATATTCACACTCTAGACATTAGTATGTCAAGAGGCGG
66 GAAAACTGCCTAACAATATTTGGTTGCAATATTCACACTCTAGACATTAGTACGTCAAAAGGCGG
*
19659780 TCACTTACTGGATTCTTTACTTTCCAGACTTGAGTATTACATTTACCTCCTTATGCT
131 TCACTTACTGGATTCTTTACTGTCCAGACTTGAGTATTACATTTACCTCCTTATGCT
19659837 CGATTCTCAGATTACTTCCATACTTCATTGTATAAACTATATTACAACTTGACCCGTATACTTGC
1 CGATTCTCAGATTACTTCCATACTTCATTGTATAAACTATATTACAACTTGACCCGTATACTTGC
19659902 GAAAACTGCCTAACAATATTTGGTTGCAATATTCACACTCTAGACATTAGTACGTCAAAAGGCGG
66 GAAAACTGCCTAACAATATTTGGTTGCAATATTCACACTCTAGACATTAGTACGTCAAAAGGCGG
*
19659967 TCACTTACTGGATTCTTTACTGTCCAGACTTGAGTCTTACATTTACCTCCTTATGC
131 TCACTTACTGGATTCTTTACTGTCCAGACTTGAGTATTACATTTACCTCCTTATGC
19660023 AAAGTGTAAC
Statistics
Matches: 182, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
187 182 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (187 bp):
CGATTCTCAGATTACTTCCATACTTCATTGTATAAACTATATTACAACTTGACCCGTATACTTGC
GAAAACTGCCTAACAATATTTGGTTGCAATATTCACACTCTAGACATTAGTACGTCAAAAGGCGG
TCACTTACTGGATTCTTTACTGTCCAGACTTGAGTATTACATTTACCTCCTTATGCT
Found at i:19661462 original size:13 final size:13
Alignment explanation
Indices: 19661444--19661469 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19661434 AGAACATTGC
19661444 TCGTTGAATCTTT
1 TCGTTGAATCTTT
19661457 TCGTTGAATCTTT
1 TCGTTGAATCTTT
19661470 CATAATATCG
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:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
TCGTTGAATCTTT
Found at i:19661615 original size:25 final size:24
Alignment explanation
Indices: 19661587--19661643 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
19661577 CATAAATGGA
**
19661587 AAGCTCATGTGAGCCATGTAACGGG
1 AAGCTCATGAAAGCCAT-TAACGGG
** *
19661612 AAGCTTTTGAAAGCCATTAATGGG
1 AAGCTCATGAAAGCCATTAACGGG
19661636 AAGCTCAT
1 AAGCTCAT
19661644 ACGAGCCAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (24 bp):
AAGCTCATGAAAGCCATTAACGGG
Found at i:19661660 original size:24 final size:24
Alignment explanation
Indices: 19661633--19661687 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
19661623 AGCCATTAAT
19661633 GGGAAGCTCATA-CGAGCCAATATC
1 GGGAAGCTCA-AGCGAGCCAATATC
*
19661657 GGGAAGGTTCAAGCGAGCCAATATC
1 GGGAA-GCTCAAGCGAGCCAATATC
19661682 GGGAAG
1 GGGAAG
19661688 TTTCGGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.15
Consensus pattern (24 bp):
GGGAAGCTCAAGCGAGCCAATATC
Found at i:19661840 original size:24 final size:25
Alignment explanation
Indices: 19661808--19661865 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
19661798 ACAACCAATT
* * *
19661808 GGGATGCTCCGAAGAGCTAT-TAAC
1 GGGAAGCTCAGAAGAACTATATAAC
*
19661832 GGGAAGCTCATAAGAACTATATAAC
1 GGGAAGCTCAGAAGAACTATATAAC
*
19661857 GGAAAGCTC
1 GGGAAGCTC
19661866 GTGAGAGCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (25 bp):
GGGAAGCTCAGAAGAACTATATAAC
Found at i:19661863 original size:25 final size:24
Alignment explanation
Indices: 19661819--19661865 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
19661809 GGATGCTCCG
* *
19661819 AAGAGCTATTAACGGGAAGCTCAT
1 AAGAACTATTAACGGAAAGCTCAT
19661843 AAGAACTATATAACGGAAAGCTC
1 AAGAACTAT-TAACGGAAAGCTC
19661866 GTGAGAGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (24 bp):
AAGAACTATTAACGGAAAGCTCAT
Found at i:19661907 original size:25 final size:24
Alignment explanation
Indices: 19661862--19661912 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
19661852 ATAACGGAAA
* *
19661862 GCTCGTGAGAGCCATATATTGGGAT
1 GCTCATGAGAGCAATATATT-GGAT
19661887 GCTCATGAGAGCTAATA-ATTGGAT
1 GCTCATGAGAGC-AATATATTGGAT
19661911 GC
1 GC
19661913 CCTTTCGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 6 0.26
25 14 0.61
26 3 0.13
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (24 bp):
GCTCATGAGAGCAATATATTGGAT
Found at i:19668707 original size:262 final size:262
Alignment explanation
Indices: 19668242--19668768 Score: 1018
Period size: 262 Copynumber: 2.0 Consensus size: 262
19668232 AAGCTTCTCC
19668242 ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
1 ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
*
19668307 CTCAGTTATGTTAAGAAAGTTATAAATGCAGAAAAAACAATAACAGTTGTGTTGTAATGTTCTTT
66 CTCAGTTATGGTAAGAAAGTTATAAATGCAGAAAAAACAATAACAGTTGTGTTGTAATGTTCTTT
19668372 ATGTTGCCACCGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
131 ATGTTGCCACCGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
19668437 AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAATGAAAAACTGATAAAGTAATCT
196 AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAATGAAAAACTGATAAAGTAATCT
19668502 GA
261 GA
19668504 ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
1 ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
*
19668569 CTCAGTTATGGTAAGAAAGTTATAAATGCAGAAAAAACAATATCAGTTGTGTTGTAATGTTCTTT
66 CTCAGTTATGGTAAGAAAGTTATAAATGCAGAAAAAACAATAACAGTTGTGTTGTAATGTTCTTT
*
19668634 ATGTTGCCACTGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
131 ATGTTGCCACCGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
*
19668699 AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAGTGAAAAACTGATAAAGTAATCT
196 AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAATGAAAAACTGATAAAGTAATCT
19668764 GA
261 GA
19668766 ATA
1 ATA
19668769 GAACATACTC
Statistics
Matches: 261, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
262 261 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (262 bp):
ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
CTCAGTTATGGTAAGAAAGTTATAAATGCAGAAAAAACAATAACAGTTGTGTTGTAATGTTCTTT
ATGTTGCCACCGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAATGAAAAACTGATAAAGTAATCT
GA
Found at i:19672690 original size:20 final size:20
Alignment explanation
Indices: 19672665--19672710 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
19672655 AACAAATAAG
*
19672665 GGCACCGAAGTGCAATTAGA
1 GGCACCGAAGTGCAATCAGA
* *
19672685 GGCACCGGAGTGCAATCAGT
1 GGCACCGAAGTGCAATCAGA
19672705 GGCACC
1 GGCACC
19672711 TTTCTTAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.33, T:0.13
Consensus pattern (20 bp):
GGCACCGAAGTGCAATCAGA
Found at i:19675843 original size:45 final size:44
Alignment explanation
Indices: 19675765--19675869 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 44
19675755 TATTTCTCAT
** * *
19675765 TTTCA-TT-TCCATTTCGAGAAAACCACATTCATTTCCACATGA
1 TTTCATTTCTCCATTTCGAGAAAACCACAACCATTTACAAATGA
* * *
19675807 TTTCATTTCTCCATTTCGGAGAAAACCATAACCATTTATAAATGT
1 TTTCATTTCTCCATTTC-GAGAAAACCACAACCATTTACAAATGA
19675852 TTTCTATTTCTCCATTTC
1 TTTC-ATTTCTCCATTTC
19675870 CATTCATTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 5 0.10
43 2 0.04
44 8 0.15
45 24 0.46
46 13 0.25
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.41
Consensus pattern (44 bp):
TTTCATTTCTCCATTTCGAGAAAACCACAACCATTTACAAATGA
Found at i:19680436 original size:25 final size:24
Alignment explanation
Indices: 19680399--19680445 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
19680389 ATTTATCATT
*
19680399 AAAAACTTCAAACATTATCAATGA
1 AAAAACTTCAAACATTAACAATGA
* *
19680423 AAAAATTTCAAAACTTTAACAAT
1 AAAAACTTC-AAACATTAACAAT
19680446 TTCGTGAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAAACTTCAAACATTAACAATGA
Found at i:19680652 original size:5 final size:5
Alignment explanation
Indices: 19680642--19680667 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19680632 CCTTAACCTA
19680642 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
19680668 AAACATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:19695395 original size:23 final size:23
Alignment explanation
Indices: 19695363--19695440 Score: 95
Period size: 23 Copynumber: 3.2 Consensus size: 23
19695353 CCCGGATCGT
19695363 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAATTATA
19695387 TTTTTATTAAAATTAAAATTA-A
1 TTTTTATTAAAATTAAAATTATA
*
19695409 TTGTTATTAAAATTGTATCAAATTATA
1 TTTTTATTAAAA-T-TA--AAATTATA
19695436 TTTTT
1 TTTTT
19695441 TTGTACTAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.26
23 17 0.36
24 7 0.15
26 6 0.13
27 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (23 bp):
TTTTTATTAAAATTAAAATTATA
Found at i:19695577 original size:93 final size:93
Alignment explanation
Indices: 19695467--19695650 Score: 350
Period size: 93 Copynumber: 2.0 Consensus size: 93
19695457 TTTGTAAAAT
19695467 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
19695532 ATATCAAATTATTAATTATTAATTGTTA
66 ATATCAAATTATTAATTATTAATTGTTA
*
19695560 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
*
19695625 ATATCAAATTATTAATTGTTAATTGT
66 ATATCAAATTATTAATTATTAATTGT
19695651 ATTAGTTGTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (93 bp):
CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
ATATCAAATTATTAATTATTAATTGTTA
Found at i:19696637 original size:26 final size:25
Alignment explanation
Indices: 19696608--19696656 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
19696598 TTTATTGTAA
* *
19696608 AAATATTGTATTTTTTAAAATTATTT
1 AAATATGGTAGTTTTT-AAATTATTT
*
19696634 AAATATGGTGGTTTTTAAATTAT
1 AAATATGGTAGTTTTTAAATTAT
19696657 CTATGTCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (25 bp):
AAATATGGTAGTTTTTAAATTATTT
Found at i:19703605 original size:36 final size:37
Alignment explanation
Indices: 19703541--19703610 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
19703531 GAATTCAGGG
*
19703541 ATTTCTTCGACTTTGAGTCGATGAGACACTGGGTGTA
1 ATTTCTTCGACTTTGAGCCGATGAGACACTGGGTGTA
*
19703578 ATTTACTTCGA-TTT-AGCCGATTAGACACTGGGT
1 ATTT-CTTCGACTTTGAGCCGATGAGACACTGGGT
19703611 ATCAAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 17 0.57
37 7 0.23
38 6 0.20
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (37 bp):
ATTTCTTCGACTTTGAGCCGATGAGACACTGGGTGTA
Found at i:19706582 original size:25 final size:25
Alignment explanation
Indices: 19706548--19706620 Score: 128
Period size: 25 Copynumber: 2.9 Consensus size: 25
19706538 TTTCTCACCC
19706548 CAATTTTACCCCAGTAAAATTTTGA
1 CAATTTTACCCCAGTAAAATTTTGA
19706573 CAATTTTACCCCAGTAAAATTTTGA
1 CAATTTTACCCCAGTAAAATTTTGA
*
19706598 CAATTTTACCCTCGGTAAAATTT
1 CAATTTTACCC-CAGTAAAATTT
19706621 CATGAAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 36 0.78
26 10 0.22
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (25 bp):
CAATTTTACCCCAGTAAAATTTTGA
Found at i:19708388 original size:75 final size:75
Alignment explanation
Indices: 19708211--19708391 Score: 201
Period size: 75 Copynumber: 2.4 Consensus size: 75
19708201 ATTTTGCATC
* ** * *
19708211 AATA-ATACTTATTTACAATCTACAAAAAAAATTTAAAAATTGTTTGTATTGTATTATATTTATT
1 AATATATACTTATTTACAATCTACAAAAAAAATTAAAAAAAGGCTTGTATTGTATTATATGTATT
19708275 TTATATCAAT
66 TTATATCAAT
* * *
19708285 AATATATACTTATTTACAATCTATAAAAAAAGTTAAAAAAAGGCTTGTATTGTATTCTATCGTAT
1 AATATATACTTATTTACAATCTACAAAAAAAATTAAAAAAAGGCTTGTATTGTATTATAT-GTAT
*
19708350 GTCTTCT-T-AAT
65 -T-TTATATCAAT
*
19708361 -A-ATATACTTATTTACAACCTACGAAAAAAAA
1 AATATATACTTATTTACAATCTAC-AAAAAAAA
19708392 ATTGTTTATA
Statistics
Matches: 90, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
74 23 0.26
75 56 0.62
76 6 0.07
77 2 0.02
78 3 0.03
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (75 bp):
AATATATACTTATTTACAATCTACAAAAAAAATTAAAAAAAGGCTTGTATTGTATTATATGTATT
TTATATCAAT
Found at i:19709707 original size:28 final size:29
Alignment explanation
Indices: 19709675--19709729 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
19709665 CCCTTATTCA
19709675 TTGAATGGTAA-AC-CATTCTTTTGTTTGG
1 TTGAA-GGTAATACTCATTCTTTTGTTTGG
*
19709703 TTGAAGGTAATACTTATTCTTTTGTTT
1 TTGAAGGTAATACTCATTCTTTTGTTT
19709730 CATTTGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 7 0.29
29 12 0.50
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.51
Consensus pattern (29 bp):
TTGAAGGTAATACTCATTCTTTTGTTTGG
Found at i:19709875 original size:17 final size:17
Alignment explanation
Indices: 19709855--19709908 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
19709845 GAAATATTTT
19709855 AATATAATTTAATAT-A
1 AATATAATTTAATATAA
*
19709871 AA-AT-ATTTAATTTTAA
1 AATATAATTTAA-TATAA
* *
19709887 AATATAATTCAAAATAA
1 AATATAATTTAATATAA
19709904 AATAT
1 AATAT
19709909 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
14 6 0.20
15 4 0.13
16 5 0.17
17 10 0.33
18 5 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATAATTTAATATAA
Found at i:19709875 original size:25 final size:25
Alignment explanation
Indices: 19709846--19709930 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 25
19709836 AAAATATTTG
19709846 AAATATTTTAATATAATTTAATATAA
1 AAATATTTTAATATAATTTAATAT-A
* *
19709872 AATATTTAATTTTAAAATATAATTCAAAATA
1 AA-A--T-ATTTT--AATATAATTTAATATA
* *
19709903 AAATATTTTAAAATAATTTGATATA
1 AAATATTTTAATATAATTTAATATA
19709928 AAA
1 AAA
19709931 CTAAAAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
25 15 0.32
26 2 0.04
27 6 0.13
28 1 0.02
29 1 0.02
30 6 0.13
31 3 0.06
32 13 0.28
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (25 bp):
AAATATTTTAATATAATTTAATATA
Found at i:19709889 original size:15 final size:15
Alignment explanation
Indices: 19709850--19709891 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
19709840 TATTTGAAAT
*
19709850 ATTTTAATATAATTTA
1 ATTTTAAAAT-ATTTA
*
19709866 A-TATAAAATATTTA
1 ATTTTAAAATATTTA
19709880 ATTTTAAAATAT
1 ATTTTAAAATAT
19709892 AATTCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.27
15 15 0.68
16 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTAAAATATTTA
Found at i:19709904 original size:32 final size:33
Alignment explanation
Indices: 19709831--19709910 Score: 101
Period size: 32 Copynumber: 2.4 Consensus size: 33
19709821 AGAAAATATA
* *
19709831 AAAATAAAATATTTGAAATATTTTAATATAATTT
1 AAAATAAAATATTT-AAATATTTAAATATAATTC
*
19709865 AATATAAAATATTT-AAT-TTTAAAATATAATTC
1 AAAATAAAATATTTAAATATTT-AAATATAATTC
19709897 AAAATAAAATATTT
1 AAAATAAAATATTT
19709911 TAAAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.07
32 25 0.61
34 13 0.32
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (33 bp):
AAAATAAAATATTTAAATATTTAAATATAATTC
Found at i:19710012 original size:42 final size:44
Alignment explanation
Indices: 19709966--19710057 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 44
19709956 ATATAACAAT
*
19709966 AATTATATTAAAA-ATGTTATTAAATTA-TTA-TTAT-TTTTATTA
1 AATTATATTAAAATATG-T-TTAAAGTATTTATTTATATTTTATTA
*
19710008 AATTATATTAAAATATGTTTAAAGTATTTATTTTTATTTTATTA
1 AATTATATTAAAATATGTTTAAAGTATTTATTTATATTTTATTA
19710052 AATTAT
1 AATTAT
19710058 TTTTAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
41 7 0.16
42 17 0.39
43 6 0.14
44 14 0.32
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (44 bp):
AATTATATTAAAATATGTTTAAAGTATTTATTTATATTTTATTA
Found at i:19710757 original size:6 final size:6
Alignment explanation
Indices: 19710716--19710742 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19710706 TATTGATATC
19710716 TAAATA TAAATA TAAATA TAAATA TAA
1 TAAATA TAAATA TAAATA TAAATA TAA
19710743 TTCAATTTAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATA
Found at i:19711189 original size:40 final size:39
Alignment explanation
Indices: 19711140--19711228 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 39
19711130 TCCATGTCAG
* *
19711140 CGCGCTTTGCTG-ACGTGCACAGAAATCGCGCTGACGTGGA
1 CGCGATTTGCTGAACGTCCACA-AAAT-GCGCTGACGTGGA
* * *
19711180 CGCGATTTGCTGACACGTCCCCAAAGTGCGCTGACGTGTA
1 CGCGATTTGCTGA-ACGTCCACAAAATGCGCTGACGTGGA
19711220 CGCGATTTG
1 CGCGATTTG
19711229 TTGCCACGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 32 0.76
41 3 0.07
42 7 0.17
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.22
Consensus pattern (39 bp):
CGCGATTTGCTGAACGTCCACAAAATGCGCTGACGTGGA
Found at i:19711692 original size:249 final size:251
Alignment explanation
Indices: 19711251--19711799 Score: 904
Period size: 249 Copynumber: 2.2 Consensus size: 251
19711241 GCGCCCCTGG
* * * *
19711251 GGATGCTTTATGAGAGGAATTTGTGAAATCTCGCCCTTGTGGACGCGCTTTTGCTACAGTAGGTC
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCATTTGCTACAGTAGGTC
* *
19711316 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCACATAGTATAAAAAAACGCTTCAAGCAGGA
66 CTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTAT-AAAAAACGCTTCAAGCAGGA
* * *
19711381 TGCTTTATGATAAGCATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTG
130 TGCTTTATGAGAAGAATTTATGAAATCGCACCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTG
19711446 GAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
195 GAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
*
19711503 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCTCATTTGCTACAGTAGGT-
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCATTTGCTACAGTAGGTC
*
19711567 CTTGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTAT-AAAAACGCTTCAAGCAGGAT
66 CTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGAT
* *
19711631 GCTTTATGAGAAGAATTTATGAAATCGCGCCTTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGG
131 GCTTTATGAGAAGAATTTATGAAATCGCACCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGG
19711696 AAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
196 AAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
* * * * * *
19711752 TGATACTTTATCAAAAGAATTTGTGAAATCGCGCCCACGTCGACGCGC
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGC
19711800 TTTTTTTATA
Statistics
Matches: 277, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
249 177 0.64
251 41 0.15
252 59 0.21
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (251 bp):
GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCATTTGCTACAGTAGGTC
CTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGAT
GCTTTATGAGAAGAATTTATGAAATCGCACCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGG
AAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
Found at i:19711810 original size:125 final size:125
Alignment explanation
Indices: 19711251--19711813 Score: 894
Period size: 125 Copynumber: 4.5 Consensus size: 125
19711241 GCGCCCCTGG
* * * *
19711251 GGATGCTTTATGAGAGGAATTTGTGAAATCTCGCCCTTGTGGACGCGCTTTTGCTACAGTAGGTC
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
*
19711316 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCACATAGTATAAAAAAACGCTTCAAGCA
66 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT--AAAAACGCTTCAAGCA
* * *
19711378 GGATGCTTTATGATAAGCATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
19711443 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
66 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
* * *
19711503 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCTCATTTGCTACAGTAGGT-
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
* *
19711567 CTTGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
66 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
* *
19711627 GGATGCTTTATGAGAAGAATTTATGAAATCGCGCCTTCGTGGACGCGCTTTTGCTATAGTAGGTC
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
19711692 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
66 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
* * * * * * **
19711752 TGATACTTTATCAAAAGAATTTGTGAAATCGCGCCCACGTCGACGCGCTTTTTTTATAGTAG
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAG
19711814 CATGTTTGGG
Statistics
Matches: 402, Mismatches: 33, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
124 117 0.29
125 184 0.46
127 101 0.25
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (125 bp):
GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
Found at i:19714937 original size:21 final size:21
Alignment explanation
Indices: 19714912--19715050 Score: 69
Period size: 22 Copynumber: 6.5 Consensus size: 21
19714902 CAAGGGTTAG
19714912 GGTTAGGGTTTTTAAGTTAAT
1 GGTTAGGGTTTTTAAGTTAAT
* *
19714933 GGTTAGGG--TTTAGGGTTTA-
1 GGTTAGGGTTTTTA-AGTTAAT
* *
19714952 GTGTTAGGGGTTTTAGGTT-AT
1 G-GTTAGGGTTTTTAAGTTAAT
19714973 -G---GGGTTTTTAAGTTAAGTT
1 GGTTAGGGTTTTTAAGTTAA--T
*
19714992 AAAGGTTTAGGGTTTTTAAGTTAAG
1 ---GG-TTAGGGTTTTTAAGTTAAT
* *
19715017 GGTTTAGGGGTTTTAAGTTAAG
1 GG-TTAGGGTTTTTAAGTTAAT
19715039 GGTTTAGGGTTT
1 GG-TTAGGGTTT
19715051 GTCAATTAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 31
0.71 0.05 0.23
Matches are distributed among these distances:
16 11 0.12
17 1 0.01
19 7 0.07
20 12 0.13
21 12 0.13
22 36 0.38
23 1 0.01
27 15 0.16
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.45
Consensus pattern (21 bp):
GGTTAGGGTTTTTAAGTTAAT
Found at i:19714976 original size:15 final size:15
Alignment explanation
Indices: 19714948--19714980 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
19714938 GGGTTTAGGG
19714948 TTTAGTGTTAGGGGT
1 TTTAGTGTTAGGGGT
19714963 TTTAG-GTTATGGGGT
1 TTTAGTGTTA-GGGGT
19714978 TTT
1 TTT
19714981 TAAGTTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.12, C:0.00, G:0.36, T:0.52
Consensus pattern (15 bp):
TTTAGTGTTAGGGGT
Found at i:19715011 original size:22 final size:22
Alignment explanation
Indices: 19714985--19715050 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
19714975 GGTTTTTAAG
*
19714985 TTAAGTTAAAGGTTTAGGGTTT
1 TTAAGTTAAGGGTTTAGGGTTT
*
19715007 TTAAGTTAAGGGTTTAGGGGTT
1 TTAAGTTAAGGGTTTAGGGTTT
19715029 TTAAGTTAAGGGTTTAGGGTTT
1 TTAAGTTAAGGGTTTAGGGTTT
19715051 GTCAATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (22 bp):
TTAAGTTAAGGGTTTAGGGTTT
Found at i:19716284 original size:7 final size:7
Alignment explanation
Indices: 19716274--19716299 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19716264 TTATATACAT
19716274 AATACTA
1 AATACTA
19716281 AATACTA
1 AATACTA
19716288 AATACTA
1 AATACTA
19716295 AATAC
1 AATAC
19716300 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:19716505 original size:20 final size:20
Alignment explanation
Indices: 19716468--19716505 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19716458 ATTATTTTTA
*
19716468 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
19716488 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
19716506 TACCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:19717502 original size:11 final size:11
Alignment explanation
Indices: 19717488--19717553 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
19717478 TTAAATATAG
19717488 ATTTGAGAGAA
1 ATTTGAGAGAA
*
19717499 ATTTG-GAAGGA
1 ATTTGAG-AGAA
19717510 ATTTGAGAGCAA
1 ATTTGAGAG-AA
19717522 A-TTGAGAGGAA
1 ATTTGAGA-GAA
19717533 A-TTGAGA-AA
1 ATTTGAGAGAA
19717542 ATAGTTGAGAGA
1 AT--TTGAGAGA
19717554 GGATTAGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
9 3 0.07
10 1 0.02
11 30 0.67
12 10 0.22
13 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:19717537 original size:22 final size:22
Alignment explanation
Indices: 19717490--19717543 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
19717480 AAATATAGAT
*
19717490 TTGAGAGAAATTTGGAAGGAAT
1 TTGAGAGAAATTTGGAAGGAAA
19717512 TTGAGAGCAAA-TT-GAGAGGAAA
1 TTGAGAG-AAATTTGGA-AGGAAA
19717534 TTGAGA-AAAT
1 TTGAGAGAAAT
19717544 AGTTGAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 3 0.11
21 2 0.07
22 20 0.71
23 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (22 bp):
TTGAGAGAAATTTGGAAGGAAA
Found at i:19719202 original size:23 final size:23
Alignment explanation
Indices: 19719173--19719222 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
19719163 CTTGATTCTT
*
19719173 AAAAATTCAAAA-AATAAATATTA
1 AAAAATT-AAAATAAAAAATATTA
*
19719196 AAAAATTAAAATAAAAAATATTT
1 AAAAATTAAAATAAAAAATATTA
19719219 AAAA
1 AAAA
19719223 GTTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAAATTAAAATAAAAAATATTA
Found at i:19720684 original size:48 final size:48
Alignment explanation
Indices: 19720600--19720693 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
19720590 TTTCTTGGCT
* * *
19720600 TAAAAACGCCTAAGTCAGTCTAACTTGCACCGATAAAGGATTCAACCG
1 TAAAAACGCCTAAGTCAGTCTAACTCGCAACAATAAAGGATTCAACCG
19720648 TAAAAACGCCTAAGTCAG-CTCAACTCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGTCT-AACTCGCAACAATAAAGGATTCAAC
19720694 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
47 2 0.05
48 40 0.95
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGTCTAACTCGCAACAATAAAGGATTCAACCG
Found at i:19721341 original size:18 final size:17
Alignment explanation
Indices: 19721318--19721359 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
19721308 ATTTTTTTTC
*
19721318 AAAAAAAAATTAAA-TA
1 AAAAAAAAAATAAATTA
19721334 AAACAAAAAAATAAATTA
1 AAA-AAAAAAATAAATTA
19721352 AAAAAAAA
1 AAAAAAAA
19721360 CTAAACGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 15 0.65
18 5 0.22
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAAAAAAATAAATTA
Found at i:19721343 original size:17 final size:16
Alignment explanation
Indices: 19721318--19721364 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
19721308 ATTTTTTTTC
*
19721318 AAAAAAAAATTAAATA
1 AAAAAAAAAATAAATA
*
19721334 AAACAAAAAAATAAATT
1 AAA-AAAAAAATAAATA
*
19721351 AAAAAAAAACTAAA
1 AAAAAAAAAATAAA
19721365 CGTATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAAAAAATAAATA
Found at i:19721349 original size:22 final size:21
Alignment explanation
Indices: 19721318--19721358 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
19721308 ATTTTTTTTC
*
19721318 AAAAAAAAATTAAATAAAACA
1 AAAAAAAAATTAAAAAAAACA
19721339 AAAAAATAAATTAAAAAAAA
1 AAAAAA-AAATTAAAAAAAA
19721359 ACTAAACGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAAAAAAATTAAAAAAAACA
Found at i:19727058 original size:19 final size:19
Alignment explanation
Indices: 19727036--19727097 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
19727026 AATAATTATA
19727036 AAAAAAGAATGATGAGATT
1 AAAAAAGAATGATGAGATT
** * *
19727055 AAAAATA-AAT-AACATTATA
1 AAAAA-AGAATGATGA-GATT
19727074 AAAAAAGAATGATGAGATT
1 AAAAAAGAATGATGAGATT
19727093 AAAAA
1 AAAAA
19727098 TAAATAATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
18 3 0.10
19 25 0.81
20 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.13, T:0.21
Consensus pattern (19 bp):
AAAAAAGAATGATGAGATT
Found at i:19727081 original size:38 final size:38
Alignment explanation
Indices: 19727030--19727104 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
19727020 AAAGAAAATA
19727030 ATTATAAAAAAAGAATGATGAGATTAAAAATAAATAAC
1 ATTATAAAAAAAGAATGATGAGATTAAAAATAAATAAC
19727068 ATTATAAAAAAAGAATGATGAGATTAAAAATAAATAA
1 ATTATAAAAAAAGAATGATGAGATTAAAAATAAATAA
19727105 TATAAAATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.64, C:0.01, G:0.11, T:0.24
Consensus pattern (38 bp):
ATTATAAAAAAAGAATGATGAGATTAAAAATAAATAAC
Found at i:19727420 original size:9 final size:9
Alignment explanation
Indices: 19727394--19727430 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
19727384 GATAAAAAAA
19727394 TTAAAATTT
1 TTAAAATTT
* *
19727403 TGAAGATTT
1 TTAAAATTT
19727412 TTAAAATTT
1 TTAAAATTT
19727421 TTAAAATTT
1 TTAAAATTT
19727430 T
1 T
19727431 AAGTTCCTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (9 bp):
TTAAAATTT
Found at i:19731916 original size:23 final size:23
Alignment explanation
Indices: 19731890--19731948 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
19731880 CAGCTCGTAT
* *
19731890 GAGCTTACCGTTTCAGCTCTACG
1 GAGCTTACCGTTTCAGCTCAACA
*
19731913 GAGCTTACCGTTTCAGCTCAATA
1 GAGCTTACCGTTTCAGCTCAACA
19731936 GAGCTTACCGTTT
1 GAGCTTACCGTTT
19731949 ATCAGCTCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.32
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCAACA
Found at i:19738701 original size:26 final size:27
Alignment explanation
Indices: 19738670--19738739 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 27
19738660 GTTTTTGAAG
19738670 TTTTAGAATTTGTTAGAAGTTAATATATTTA
1 TTTTAGAATTTGTTAGAAGTT-A-ATA--TA
*
19738701 GTTTTTGAATTTGTTAGAAGTTAATATA
1 -TTTTAGAATTTGTTAGAAGTTAATATA
19738729 TTTTA-AATTTG
1 TTTTAGAATTTG
19738740 GTTTAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 6 0.17
27 4 0.11
28 2 0.06
30 3 0.08
31 1 0.03
32 20 0.56
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
TTTTAGAATTTGTTAGAAGTTAATATA
Found at i:19738711 original size:32 final size:32
Alignment explanation
Indices: 19738668--19738731 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
19738658 ATGTTTTTGA
19738668 AGTTTTAGAATTTGTTAGAAGTTAATATATTT
1 AGTTTTAGAATTTGTTAGAAGTTAATATATTT
*
19738700 AGTTTTTGAATTTGTTAGAAGTTAATATATTT
1 AGTTTTAGAATTTGTTAGAAGTTAATATATTT
19738732 TAAATTTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.52
Consensus pattern (32 bp):
AGTTTTAGAATTTGTTAGAAGTTAATATATTT
Found at i:19739056 original size:21 final size:19
Alignment explanation
Indices: 19739031--19739105 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
19739021 TATTTTTCAA
19739031 AAAAAATAAAAATAGAATTTC
1 AAAAAATAAAAA-A-AATTTC
**
19739052 TAAAAGTTATAAAAAAATTTAC
1 -AAAAAATA-AAAAAAATTT-C
* *
19739074 AAAAAATATAAAAAATTTA
1 AAAAAATAAAAAAAATTTC
19739093 AAAAAATAAAAAA
1 AAAAAATAAAAAA
19739106 TAGAATTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.27
20 9 0.20
21 11 0.25
22 8 0.18
23 4 0.09
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAAAATAAAAAAAATTTC
Found at i:19739086 original size:9 final size:9
Alignment explanation
Indices: 19739074--19739107 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
19739064 AAAAATTTAC
19739074 AAAAAATAT
1 AAAAAATAT
*
19739083 AAAAAATTT
1 AAAAAATAT
19739092 AAAAAA-AT
1 AAAAAATAT
19739100 AAAAAATA
1 AAAAAATA
19739108 GAATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAAATAT
Found at i:19739088 original size:20 final size:18
Alignment explanation
Indices: 19739060--19739105 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 18
19739050 TCTAAAAGTT
19739060 ATAAAAAAATTTACAAAAA
1 ATAAAAAAATTTA-AAAAA
19739079 ATATAAAAAATTTAAAAAA
1 ATA-AAAAAATTTAAAAAA
19739098 ATAAAAAA
1 ATAAAAAA
19739106 TAGAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.19
19 11 0.42
20 10 0.38
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (18 bp):
ATAAAAAAATTTAAAAAA
Found at i:19739118 original size:32 final size:32
Alignment explanation
Indices: 19739030--19739126 Score: 96
Period size: 32 Copynumber: 3.1 Consensus size: 32
19739020 ATATTTTTCA
*
19739030 AAAAAAATAAAAATAGAATTTCT-AAAAGTTAT
1 AAAAAAATAAAAATAGAATTT-TAAAAAATTAT
* *
19739062 AAAAAAATTTACAAA-A-AA-TATAAAAAATT-T
1 AAAAAAA--TAAAAATAGAATTTTAAAAAATTAT
19739092 AAAAAAATAAAAAATAGAATTTTAAAAAATTAT
1 AAAAAAAT-AAAAATAGAATTTTAAAAAATTAT
19739125 AA
1 AA
19739127 TAATTAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
28 1 0.02
29 4 0.08
30 10 0.19
31 9 0.17
32 19 0.37
33 4 0.08
34 5 0.10
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (32 bp):
AAAAAAATAAAAATAGAATTTTAAAAAATTAT
Found at i:19739128 original size:21 final size:21
Alignment explanation
Indices: 19739031--19739129 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
19739021 TATTTTTCAA
* * *
19739031 AAAAAATAAAAATAGAATTTCT
1 AAAAAATTATAATAAAATTT-T
* *
19739053 -AAAAGTTATAA-AAAAATTT
1 AAAAAATTATAATAAAATTTT
* *
19739072 ACAAAAAATATAA-AAAATTTA
1 A-AAAAATTATAATAAAATTTT
* * *
19739093 AAAAAATAAAAAATAGAATTTT
1 AAAAAAT-TATAATAAAATTTT
19739115 AAAAAATTATAATAA
1 AAAAAATTATAATAA
19739130 TTAAAAATAT
Statistics
Matches: 56, Mismatches: 17, Indels: 9
0.68 0.21 0.11
Matches are distributed among these distances:
19 1 0.02
20 10 0.18
21 32 0.57
22 13 0.23
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (21 bp):
AAAAAATTATAATAAAATTTT
Found at i:19739445 original size:26 final size:25
Alignment explanation
Indices: 19739399--19739461 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
19739389 ATATATAATT
* *
19739399 ATTAAAATAAATTAGAATTTTGGAAA
1 ATTAAAATAAATGAGAATTTT-AAAA
*
19739425 ATTAAAATAAA-GAGATTTTTTAAAA
1 ATTAAAATAAATGAGA-ATTTTAAAA
19739450 ATTATAAA-AAAT
1 ATTA-AAATAAAT
19739462 ATAAACATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (25 bp):
ATTAAAATAAATGAGAATTTTAAAA
Found at i:19739450 original size:25 final size:26
Alignment explanation
Indices: 19739399--19739461 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
19739389 ATATATAATT
* *
19739399 ATTAAAATAAATTAGAATTTTGGAAA
1 ATTAAAATAAATGAGAATTTTGAAAA
* *
19739425 ATTAAAATAAA-GAGATTTTTTAAAA
1 ATTAAAATAAATGAGAATTTTGAAAA
19739450 ATTATAAA-AAAT
1 ATTA-AAATAAAT
19739462 ATAAACATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (26 bp):
ATTAAAATAAATGAGAATTTTGAAAA
Found at i:19739544 original size:19 final size:20
Alignment explanation
Indices: 19739510--19739547 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19739500 GAATTTTAAA
19739510 AAATTATAAAAAATTATATG
1 AAATTATAAAAAATTATATG
*
19739530 AAATT-TAACAAATTATAT
1 AAATTATAAAAAATTATAT
19739548 TTTTTTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (20 bp):
AAATTATAAAAAATTATATG
Found at i:19739749 original size:20 final size:20
Alignment explanation
Indices: 19739726--19739800 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
19739716 TTTTTAATAA
*
19739726 TTTTATAATTTTTATATTTT
1 TTTTACAATTTTTATATTTT
*
19739746 TTTTACAATTTATA-ATTTTT
1 TTTTACAATTTTTATA-TTTT
** *
19739766 TTTTGTAA--TTTATAATTT
1 TTTTACAATTTTTATATTTT
19739784 TTTT-CAATTTTTATATT
1 TTTTACAATTTTTATATT
19739801 GAAAAAGTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
17 2 0.05
18 10 0.23
19 9 0.21
20 22 0.51
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (20 bp):
TTTTACAATTTTTATATTTT
Done.